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Genes, proteomes, and their interaction

Posted in Alzheimer's Disease, CANCER BIOLOGY & Innovations in Cancer Therapy, Cell Biology, Signaling & Cell Circuits, Cerebrovascular and Neurodegenerative Diseases, Chemical Biology and its relations to Metabolic Disease, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Enzyme Induction, Evolutionary cognition, Gene Regulation, Genome Biology, Genomic Expression, Human Immune System in Health and in Disease, Ionic Transporters Na+, Metabolomics, Placenta, Proteomics, Reproductive Andrology, Embryology, Genomic Endocrinology, Preimplantation Genetic Diagnosis and Reproductive Genomics, Signaling, Technology Advance Assessment of, Transcriptomics, tagged genomics, Na-transporter, PARC, Proteomics, signaling pathways, thyroid hormone, transcrition on July 28, 2014| Leave a Comment »

Larry H. Bernstein, MD, FCAP, Author and Curator

http://pharmaceuticalintelligence.com/7/17/2014/Genes, proteomes, and their interaction

This is the third discussion of a several part series leading from the genome, to protein synthesis (1), posttranslational modification of proteins (2), examples of protein effects on metabolism and signaling pathways (3), and leading to disruption of signaling pathways in disease (4), and effects leading to mutagenesis.

1. A Primer on DNAand DNA Replication

http://pharmaceuticalintelligence.com/2014-28-07/A_Primer_on_DNA_and_DNA_Replication

2. Overview of translational medicine

http://pharmaceuticalintelligence.com/2014-07-28/larryhbern/overview-of-posttranslational-medicine

3. Genes, proteomes, and their interaction

http://pharmaceuticalintelligence.com/7/17/2014/Genes, proteomes, and their interaction

4. Regulation of somatic stem cell Function

http://pharmaceuticalintelligence.com/2013-01-23/larryhbern/Regulation-of-somatic-stem-cell-function/

5. Proteomics – The Pathway to Understanding and Decision-making in Medicine

http://pharmaceuticalintelligence.com/2014/06/24/proteomics-the-pathway-to-understanding-and-decision-making-in-medicine/

6. Genomics, Proteomics and standards

http://pharmaceuticalintelligence.com/2014/07/06/genomics-proteomics-and-standards/

7. Long Non-coding RNAs Can Encode Proteins After All

8. Proteins and cellular adaptation to stress

http://pharmaceuticalintelligence.com/2014/07/08/proteins-and-cellular-adaptation-to-stress/

9. Loss of normal growth regulation

http://pharmaceuticalintelligence.com/2014/07/06/loss-of-normal-growth-regulation/

This discussion is the beginning of a diversion away from the routine discussion of a specific sequence and pairing of nucleotides in the classic model, to explore the interaction between proteins, or folded proteins and RNA or hidtones that reside in the nucleus and contribute to induction or inactivation of gene expression. The basic text document is rigid, inflexible, and resides in all cells. Yet, in bacteria, yeast, and eukaryotic cells, there are models of gene expression, and in eukaryotes, there is the development of expressed organ systems. These systems have similar proteins or enzymes that are functionally identical, but they have isoforms that bind with proteins, membranes, lipopolysaccharides, and lipoproteins – which has an impact on the catabolic and anabolic activity of the cells, and they are affected by oxidative stress, and they are often dependent on the energy of binding with metal ions,i.e., Mn, Cu, Cd, Zn,..,Fe, and in other cases anionic ligands, such as I, and they may transiently act through a nucleotide or influenced by a hormone.

This will be presented as a group of predetermined articles to follow:

1. Scientists discover a broad spectrum of alternatively spliced human protein variants within a well-studied family of genes.

2. Thyroid Hormone Key to Lipid Kinase Regulation

3. Mammalian Target of Rapamycin Complex 1 Orchestrates Invariant NKT Cell Differentiation and Effector Function

4 The E3 ligase PARC mediates the degradation of cytosolic cytochrome c to promote survival in neurons and cancer cells

5. Nf k-beta signaling pathway

6. P181 cAMP-mediated Rac1 activation regulates the re-establishment of endothelial adherens junctions and barrier restoration during inflammation.

7. Structure of the DDB1–CRBN E3 ubiquitin ligase in complex with thalidomide

8. Protein misfolding, congophilia, oligomerization, and defective amyloid processing in preeclampsia

9. Removing parts of shape-shifting protein explains how blood clots

1. Added Layers of Proteome Complexity

Scientists discover a broad spectrum of alternatively spliced human protein variants within a well-studied family of genes.

By Anna Azvolinsky | July 17, 2014

added layers of proteome

There may be more to the human proteome than previously thought. Some genes are known to have several different alternatively spliced protein variants, but the Scripps Research Institute’s Paul Schimmel and his colleagues have now uncovered almost 250 protein splice variants of an essential, evolutionarily conserved family of human genes. The results were published today (July 17) in Science.

Focusing on the 20-gene family of aminoacyl tRNA synthetases (AARSs), the team captured AARS transcripts from human tissues—some fetal, some adult—and showed that many of these messenger RNAs (mRNAs) were translated into proteins. Previous studies have identified several splice variants of these enzymes that have novel functions, but uncovering so many more variants was unexpected, Schimmel said. Most of these new protein products lack the catalytic domain but retain other AARS non-catalytic functional domains.

“The main point is that a vast new area of biology, previously missed, has been uncovered,” said Schimmel.

“This is an incredible study that fundamentally changes how we look at the protein-synthesis machinery,” Michael Ibba, a protein translation researcher at Ohio State University who was not involved in the work, told The Scientist in an e-mail. “The unexpected and potentially vast expanded functional networks that emerge from this study have the potential to influence virtually any aspect of cell growth.”

The team—including researchers at the Hong Kong University of Science and Technology, Stanford University, and aTyr Pharma, a San Diego-based biotech company that Schimmel co-founded—comprehensively captured and sequenced the AARS mRNAs from six human tissue types using high-throughput deep sequencing. While many of the transcripts were expressed in each of the tissues, there was also some tissue specificity.

Next, the team showed that a proportion of these transcripts, including those missing the catalytic domain, indeed resulted in stable protein products: 48 of these splice variants associated with polysomes. In vitro translation assays and the expression of more than 100 of these variants in cells confirmed that many of these variants could be made into stable protein products.

The AARS enzymes—of which there’s one for each of the 20 amino acids—bring together an amino acid with its appropriate transfer RNA (tRNA) molecule. This reaction allows a ribosome to add the amino acid to a growing peptide chain during protein translation. AARS enzymes can be found in all living organisms and are thought to be among the first proteins to have originated on Earth.

To understand whether these non-catalytic proteins had unique biological activities, the researchers expressed and purified recombinant AARS fragments, testing them in cell-based assays for proliferation, cell differentiation, and transcriptional regulation, among other phenotypes. “We screened through dozens of biological assays and found that these variants operate in many signaling pathways,” said Schimmel.

“This is an interesting finding and fits into the existing paradigm that, in many cases, a single gene is processed in various ways [in the cell] to have alternative functions,” said Steven Brenner, a computational genomics researcher at the University of California, Berkeley.

The team is now investigating the potentially unique roles of these protein splice variants in greater detail—in both human tissue as well as in model organisms. For example, it is not yet clear whether any of these variants directly bind tRNAs.

“I do think [these proteins] will play some biological roles,” said Tao Pan, who studies the functional roles of tRNAs at the University of Chicago. “I am very optimistic that interesting biological functions will come out of future studies on these variants.”

Brenner agreed. “There could be very different biological roles [for some of these proteins]. Biology is very creative that way, [it’s] able to generate highly diverse new functions using combinations of existing protein domains.” However, the low abundance of these variants is likely to constrain their potential cellular functions, he noted.

Because AARSs are among the oldest proteins, these ancient enzymes were likely subject to plenty of change over time, said Karin Musier-Forsyth, who studies protein translational at the Ohio State University. According to Musier-Forsyth, synthetases are already known to have non-translational functions and differential localizations. “Like the addition of post-translational modifications, splicing variation has evolved as another way to repurpose protein function,” she said.

One of the protein variants was able to stimulate skeletal muscle fiber formation ex vivo and upregulate genes involved in muscle cell differentiation and metabolism in primary human skeletal myoblasts. “This was really striking,” said Musier-Forsyth. “This suggests that, perhaps, peptides derived from these splice variants could be used as protein-based therapeutics for a variety of diseases.”

W.S. Lo et al., “Human tRNA synthetase catalytic nulls with diverse functions,” Science, http://dx.doi.org:/10.1126/science.1252943, 2014.

Tags tRNA, proteomics, protein synthesis and human proteome project

2. Thyroid Hormone Key to Lipid Kinase Regulation

Published: Jul 16, 2014 | Updated: Jul 17, 2014
By Salynn Boyles, Contributing Writer, MedPage Today
Reviewed by Zalman S. Agus, MD; Emeritus Professor, Perelman School of Medicine at the University of Pennsylvania and
Dorothy Caputo, MA, BSN, RN, Nurse Planner

Action Points

Thyroid hormone is an essential regulator of human growth, brain maturation, and adult cognition and metabolism.
This study provides evidence that cytoplasmic thyroid hormone signaling through phosphatidylinositol 3-kinase appears to be an essential mechanism underlying normal synaptic maturation and plasticity in the postnatal mouse hippocampus

Thyroid hormones are key for brain development and synaptic maturation, and researchers have identified a specific molecular mechanism for rapid lipid kinase activation by the thyroid hormone receptor beta (TR-beta) that involves a cytoplasmic complex of the gene.

Many effects of the thyroid hormone on mammalian cells in vitro have been shown to be mediated by the phosphatidylinositol 3-kinase (PI3K), but the molecular mechanism of PI3K regulation and its relevance to brain development have not been clear, according to David L. Armstrong, PhD, of the National Institute of Environmental Health and Development in Research Triangle, N.C., and colleagues.

They identified a specific molecular mechanism for rapid PI3 kinase activation by TR-beta which involves a cytoplasmic complex of TR-beta, the p85 regulatory subunit of PI3 kinase and the Src family kinase, Lyn, they wrote in Endocrinology.Armstrong’s co-authors are from Duke University and Loyola University in Chicago.

This complex provides a unique mechanism for integrating growth signals through thyroid hormone and receptor tyrosine kinases, they explained.

“Most everyone agrees that thyroid hormones are essential for brain development and synaptic maturation, but we didn’t know how exactly,” Armstrong told MedPage Today. “We show that nongenomic signaling in TR-beta through PI3 kinase is essential for one of its physiological actions.”

The Role of T3 Hormone

The recognition that many hormones regulate gene expression through receptor proteins that bind to DNA is a major biological discovery over the past 50 years, the researchers noted.

“More recently, it has become clear that in many cases the same hormones produce rapid effects on cell physiology though the same receptors signaling in the cytoplasm,” they wrote. “However, testing the relative importance of the genomic and nongenomic mechanisms in vivo has been prevented by the absence of specific molecular mechanisms for the nongenomic effects that could be blocked by mutation of the receptor without disrupting its direct effects on gene expression.”

The thyroid hormone T3 has been shown to be a regulator of many physiological effects, including human growth, brain maturation, and adult cognition and metabolism.

Many of these effects have been found to be mediated through the regulation of gene expression by zinc-finger nuclear receptor proteins that are encoded by the THRA and THRB genes. But many in vitro effects of T3 are too rapid to be explained by transcriptional regulation, Armstrong and colleagues noted.

In earlier work, they identified PI3 kinase as a key player in these rapid effects. Like thyroid hormone, PI3 kinase activity has been identified as essential for growth, metabolism, and brain development.

PI3 kinase is regulated primarily by receptor tyrosine kinases, and an integrin receptor has been identified that mediates some of the PI3 kinase-dependent effects of thyroxine (T4), the widely circulated precursor of T3.

Both TR-alpha and TR-beta have also been reported to associate with PI3 kinase and stimulate its activity in many cell types. In a 2006 study in the Proceedings of the National Academy of Sciences, Armstrong and colleagues demonstrated that TRis required to reconstitute T3 and PI3 kinase-dependent regulation of Kv11.1 channels in cell-free membrane patches from Chinese hamster ovary (CHO) cells.

Based on that research, they concluded that TR-beta signaling through PI3K “provides a molecular explanation for the essential role of thyroid hormone in human brain development and adult lipid metabolism.”

Measuring PIP3 Production

In the newly reported series of experiments, the researchers used fluorescent PIP₃ indicator to directly measure PIP₃ production in response to thyroid hormone on the same time scale as the electrophysiological measurements in the CHO cells expressing recombinant human thyroid hormone receptors.

The research revealed that, in the absence of hormone, the nuclear receptor TR-beta forms a cytoplasmic complex with the p85 subunit of PI3 kinase and the Src family tyrosine kinase, Lyn, which depends on two canonical phosphotyrosine motifs in the second zinc finger of TR that are not conserved in TR-beta

“When hormone is added, [TR-beta] dissociates and moves to the nucleus, and PIP₃production goes up rapidly,” the researchers wrote. “Mutating either tyrosine to a phenylalanine prevents rapid signaling through PI3 kinase but does not prevent hormone-dependent transcription of genes with a thyroid hormone response element.”

“It is only when you have both thyroid hormone and phosphotyrosine signaling that you get maximal stimulation of PI3 kinase,” Armstrong said, adding that the novel methodology of the study, which involved serum from thyroidectomized animals, led to the finding.

These experiments led to in vivo research to test the physiological relevance of thyroid hormone signaling through PI3 kinase for brain development in a novel mouse line created by the researchers.

“We reasoned that blocking binding of TR-beta to p85 by mutating Y171 might eliminate any dominant negative effect of the mutant, in much the same way that receptor knockdown proved much less deleterious to the organism than hormone withdrawal, presumably because many of the effects of the receptor on gene expression are mediated by binding of the unliganded receptor,” they wrote.

They created a novel mouse line with a targeted mutation knocked into the THRB gene to substitute phenylalanine for tyrosine at residue 147 of TR-beta-1, which prevents Lyn binding to the mutant receptor.

They confirmed that the mutation did not alter total circulating levels of thyroxine (T4) or T3 by mass spectrometry of serum samples from 4-month-old mice.

“When the rapid signaling mechanism was blocked chronically throughout development in mice by a targeted point mutation in both alleles of THRB, circulating hormone levels, TR-betaexpression, and direct gene regulation by TR-beta in the brain and liver were all unaffected,” the researchers wrote. “The mutation did significantly impair maturation and plasticity of the Schaffer collateral synapses on CA1 pyramidal neurons in the postnatal hippocampus. Thus, phosphotyrosine-dependent association of TR-betawith PI3K provides a potential mechanism for integrating regulation of development and metabolism by thyroid hormone and receptor tyrosine kinases.”

A Novel Finding

The finding that thyroid hormone signaling through PI3 kinase appears to be an essential mechanism underlying normal synaptic maturation and plasticity in the postnatal mouse hippocampus is novel.

The researchers noted that they could not formally exclude some more subtle effects of the mutation on the regulation of an unknown gene that plays as central a role in synaptic development as PI3K, but the added that “our results do categorically rule out a role for other thyroid hormone receptors in this particular aspect of synaptic maturation in the mouse hippocampus.

“In either case, given the importance of thyroid hormone signaling for human brain development and adult metabolism, future studies will need to investigate whether PI₃ kinase stimulation by thyroid hormone is also susceptible to disruption by environmental toxicants,” they wrote.

Armstrong also pointed out that the tyrosine motifs in TR-beta, which were shown to be essential for signaling through PI3 kinase, are present in all mammals, but not in other species with known genome data, with the exception of the gecko and the axolotl (Mexican salamander).

“Mammals evolved from reptiles, and the thinking is that they survived by adopting a nocturnal niche,” he said. “This is exactly what thyroid hormone does, so it may be that this mutation contributed to the (evolutionary) success of mammals.”

Primary source: Endocrinology
Source reference: Martin NP, et al “A rapid cytoplasmic mechanism for PI3 kinase regulation by the nuclear thyroid hormone receptor, TR beta, and genetic evidence for its role in the maturation of mouse hippocampal synapses in vivo”

Endocrinology 2014; http://dx.doi.org:/10.1210/en.2013-2058.

3. Mammalian Target of Rapamycin Complex 1 Orchestrates Invariant NKT Cell Differentiation and Effector Function.

Lianjun Zhang, Benjamin O Tschumi, Stéphanie Corgnac, Markus A Rüegg,Michael N Hall, Jean-Pierre Mach, Pedro Romero, Alena Donda

Journal of immunology (Baltimore, Md. : 1950) 07/2014; http://dx.doi.org:/10.4049/jimmunol.1400769

Source: PubMed

ABSTRACT Invariant NKT (iNKT) cells play critical roles in bridging innate and adaptive immunity. The Raptor containing mTOR complex 1 (mTORC1) has been well documented to control peripheral CD4 or CD8 T cell effector or memory differentiation. However, the role of mTORC1 in iNKT cell development and function remains largely unknown. By using mice with T cell-restricted deletion of Raptor, we show that mTORC1 is selectively required for iNKT but not for conventional T cell development. Indeed, Raptor-deficient iNKT cells are mostly blocked at thymic stage 1-2, resulting in a dramatic decrease of terminal differentiation into stage 3 and severe reduction of peripheral iNKT cells. Moreover, residual iNKT cells in Raptor knockout mice are impaired in their rapid cytokine production upon αGalcer challenge. Bone marrow chimera studies demonstrate that mTORC1 controls iNKT differentiation in a cell-intrinsic manner. Collectively, our data provide the genetic evidence that iNKT cell development and effector functions are under the control of mTORC1 signaling.

4. PARC

The E3 ligase PARC mediates the degradation of cytosolic cytochrome c to promote survival in neurons and cancer cells

Vivian Gama^1,2, Vijay Swahari^1,2, Johanna Schafer^1*, Adam J. Kole², Allyson Evans², Yolanda Huang², Anna Cliffe^1,2, Brian Golitz^3,4, Noah Sciaky^3,4, Xin-Hai Pei^5,6, Yue Xiong^5,6, and Mohanish Deshmukh^1,2,5

¹ Neuroscience Center, ² Department of Cell Biology and Physiology, ³ UNC RNAi Screening Facility,⁴ Department of Pharmacology, ⁵ Lineberger Comprehensive Cancer Center, ⁶ Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.^* Present address: Vanderbilt University, Nashville, TN 37232, USA. Present address: Cell Press, Cambridge, MA 02139, USA. Present address: Department of Anesthesiology, Columbia University Medical Center, New York, NY 10032, USA.

Abstract: The ability to withstand mitochondrial damage is especially critical for the survival of postmitotic cells, such as neurons. Likewise, cancer cells can also survive mitochondrial stress. We found that cytochrome c (Cyt c), which induces apoptosis upon its release from damaged mitochondria, is targeted for proteasome-mediated degradation in mouse neurons, cardiomyocytes, and myotubes and in human glioma and neuroblastoma cells, but not in proliferating human fibroblasts. In mouse neurons, apoptotic protease-activating factor 1 (Apaf-1) prevented the proteasome-dependent degradation of Cyt c in response to induced mitochondrial stress. An RNA interference screen in U-87 MG glioma cells identified p53-associated Parkin-like cytoplasmic protein (PARC, also known as CUL9) as an E3 ligase that targets Cyt c for degradation. The abundance of PARC positively correlated with differentiation in mouse neurons, and overexpression of PARC reduced the abundance of mitochondrially-released cytosolic Cyt c in various cancer cell lines and in mouse embryonic fibroblasts. Conversely, neurons from Parc-deficient mice had increased sensitivity to mitochondrial damage, and neuroblastoma or glioma cells in which PARC or ubiquitin was knocked down had increased abundance of mitochondrially-released cytosolic Cyt c and decreased viability in response to stress. These findings suggest that PARC-mediated ubiquitination and degradation of Cyt c is a strategy engaged by both neurons and cancer cells to prevent apoptosis during conditions of mitochondrial stress.
Sci. Signal., 15 July 2014 Vol. 7, Issue 334, p. ra67
http://dx.doi.org:/10.1126/scisignal.2005309

Citation: V. Gama, V. Swahari, J. Schafer, A. J. Kole, A. Evans, Y. Huang, A. Cliffe, B. Golitz, N. Sciaky, X.-H. Pei, Y. Xiong, M. Deshmukh, The E3 ligase PARC mediates the degradation of cytosolic cytochrome c to promote survival in neurons and cancer cells. Sci. Signal. 7, ra67 (2014).

Killing the Killer: PARC/CUL9 Promotes Cell Survival by Destroying Cytochrome c

Jonathan Lopez and Stephen W. G. Tait^*Cancer Research UK Beatson Institute, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK.

Abstract: Balanced amounts of apoptotic cell death are essential for health; its deregulation plays key roles in neurodegeneration, autoimmunity, and cancer. Mitochondria orchestrate apoptosis through a process called mitochondrial outer-membrane permeabilization (MOMP). After MOMP, mitochondrial cytochrome c is released into the cytoplasm, where it binds the adaptor molecule APAF1, triggering caspase protease activation and cell death. In this issue of Science Signaling, Deshmukh and colleagues define a new survival mechanism downstream of mitochondrial permeabilization. Specifically, they identify proteasomal degradation of cytochrome c as a major determinant of cell survival. In an unbiased approach, PARC (also known as CUL9) was found to be the ubiquitin ligase responsible for the ubiquitination and proteasomal degradation of cytochrome c. The consequences of this survival process may be double-edged because both cancer cells and postmitotic cells use PARC/CUL9–mediated cytochrome c degradation to ensure cell survival. Ultimately, differential targeting of this process may promote survival of postmitotic tissue or enhance tumor-specific killing.

Citation: J. Lopez, S. W. G. Tait, Killing the Killer: PARC/CUL9 Promotes Cell Survival by Destroying Cytochrome c. Sci. Signal. 7, pe17 (2014).

Sci. Signal., 15 July 2014 Vol. 7, Issue 334, p. pe17
http://dx.doi.org:/10.1126/scisignal.2005619

4. The WNK-SPAK/OSR1 pathway: Master regulator of cation-chloride cotransporters

Dario R. Alessi¹, Jinwei Zhang¹, Arjun Khanna², Thomas Hochdörfer¹, Yuze Shang³, and Kristopher T. Kahle^2,3*¹ MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland.
² Department of Neurosurgery, Massachusetts General Hospital, and Harvard Medical School, ³ Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA 02115, USA.

Abstract: The WNK-SPAK/OSR1 kinase complex is composed of the kinases WNK (with no lysine) and SPAK (SPS1-related proline/alanine-rich kinase) or the SPAK homolog OSR1 (oxidative stress–responsive kinase 1). The WNK family senses changes in intracellular Cl^– concentration, extracellular osmolarity, and cell volume and transduces this information to sodium (Na⁺), potassium (K⁺), and chloride (Cl^–) cotransporters [collectively referred to as CCCs (cation-chloride cotransporters)] and ion channels to maintain cellular and organismal homeostasis and affect cellular morphology and behavior. Several genes encoding proteins in this pathway are mutated in human disease, and the cotransporters are targets of commonly used drugs. WNKs stimulate the kinases SPAK and OSR1, which directly phosphorylate and stimulate Cl^–-importing, Na⁺-driven CCCs or inhibit the Cl^–-extruding, K⁺-driven CCCs. These coordinated and reciprocal actions on the CCCs are triggered by an interaction between RFXV/I motifs within the WNKs and CCCs and a conserved carboxyl-terminal docking domain in SPAK and OSR1. This interaction site represents a potentially druggable node that could be more effective than targeting the cotransporters directly. In the kidney, WNK-SPAK/OSR1 inhibition decreases epithelial NaCl reabsorption and K⁺ secretion to lower blood pressure while maintaining serum K⁺. In neurons, WNK-SPAK/OSR1 inhibition could facilitate Cl^–extrusion and promote -aminobutyric acidergic (GABAergic) inhibition. Such drugs could have efficacy as K⁺-sparing blood pressure–lowering agents in essential hypertension, nonaddictive analgesics in neuropathic pain, and promoters of GABAergic inhibition in diseases associated with neuronal hyperactivity, such as epilepsy, spasticity, neuropathic pain, schizophrenia, and autism.
Citation: D. R. Alessi, J. Zhang, A. Khanna, T. Hochdörfer, Y. Shang, K. T. Kahle, The WNK-SPAK/OSR1 pathway: Master regulator of cation-chloride cotransporters. Sci. Signal. 7, re3 (2014).

Sci. Signal., 15 July 2014 Vol. 7, Issue 334, p. re3
http://dx.doi.org:/10.1126/scisignal.2005365

5. Nf k-beta signaling pathway

Cracking the NF-B Code

Karen E. Tkach, Jennifer E. Oyler, and Grégoire Altan-Bonnet^*ImmunoDynamics Group, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.

Abstract: The discovery of feedback loops between signaling and gene expression is ushering in new quantitative models of cellular regulation. In a recent issue of Science Signaling, Sung et al. showed how positive feedback downstream of nuclear factor B (NF-B) signaling enhances the capacity of macrophages to scale their antimicrobial responses to the dose of pathogen-associated molecular cues. This finding stemmed from analysis of cell-to-cell variability and computational modeling of time integration between signaling and transcriptional responses. Ultimately, such quantitative approaches challenge the oft-assumed time separation of “fast” signal transduction followed by “slow” gene expression, and they provide a better understanding of complex biological regulation over long time scales.

Citation: K. E. Tkach, J. E. Oyler, G. Altan-Bonnet, Cracking the NF-B Code. Sci. Signal. 7, pe5 (2014).

Sci. Signal., 18 February 2014 Vol. 7, Issue 313, p. pe5
http://dx.doi.org:/10.1126/scisignal.2005108

Switching of the Relative Dominance Between Feedback Mechanisms in Lipopolysaccharide-Induced Nfk-B Signaling

Myong-Hee Sung^1*, Ning Li², Qizong Lao¹, Rachel A. Gottschalk², Gordon L. Hager^1*, and Iain D. C. Fraser^2*¹ Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, ² Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Abstract: A fundamental goal in biology is to gain a quantitative understanding of how appropriate cell responses are achieved amid conflicting signals that work in parallel. Through live, single-cell imaging, we monitored both the dynamics of nuclear factor B (NF-B) signaling and inflammatory cytokine transcription in macrophages exposed to the bacterial product lipopolysaccharide (LPS). Our analysis revealed a previously uncharacterized positive feedback loop involving induction of the expression of Rela, which encodes the RelA (p65) NF-B subunit. This positive feedback loop rewired the regulatory network when cells were exposed to LPS above a distinct concentration. Paradoxically, this rewiring of NF-B signaling in macrophages (a myeloid cell type) required the transcription factor Ikaros, which promotes the development of lymphoid cells. Mathematical modeling and experimental validation showed that the RelA positive feedback overcame existing negative feedback loops and enabled cells to discriminate between different concentrations of LPS to mount an effective innate immune response only at higher concentrations. We suggest that this switching in the relative dominance of feedback loops (“feedback dominance switching”) may be a general mechanism in immune cells to integrate opposing feedback on a key transcriptional regulator and to set a response threshold for the host.

Citation: M.-H. Sung, N. Li, Q. Lao, R. A. Gottschalk, G. L. Hager, I. D. C. Fraser, Switching of the Relative Dominance Between Feedback Mechanisms in Lipopolysaccharide-Induced NF-B Signaling. Sci. Signal. 7, ra6 (2014).

Sci. Signal., 14 January 2014 Vol. 7, Issue 308, p. ra6
http://dx.doi.org:/10.1126/scisignal.2004764

Drug development in the Alzheimer’s field has been riddled with failures, and most research efforts have focused on pinpointing genetic and environmental factors responsible for causing or accelerating the progression of the disease.

Now, researchers from Montreal’s Douglas Mental Health Institute and McGill University have identified a relatively frequent genetic variant that may provide protection against the devastating neurodegenerative disease.

“We found that specific genetic variants in a gene called HMG CoA reductase which normally regulates cholesterol production and mobilization in the brain can interfere with, and delay the onset of Alzheimer’s disease by nearly four years. This is an exciting breakthrough in a field where successes have been scarce these past few years,” said Dr. Judes Poirier, whose previous research led to the discovery that a genetic variant was formally associated with the common form of Alzheimer’s disease.

This variant may explain why some people who are carriers of predisposing genetic factors for the common form of Alzheimer’s do not develop the disease, living long lives without memory problems until their nineties.

6. P181 cAMP-mediated Rac1 activation regulates the re-establishment of endothelial adherens junctions and barrier restoration during inflammation.

M Aslam, H Nef, C Troidl, R Schulz, T Noll, C Hamm, D Guenduez

Cardiovascular research 07/2014; 103(suppl 1):S32.
http://dx.doi.org:/10.1093/cvr/cvu082.117
Source: PubMed

ABSTRACT Inflammatory mediators like thrombin and TNFα disrupt endothelial junctions and barrier integrity, leading to edema formation. This increase in endothelial permeability is followed by slow restoration of the endothelial barrier, which is critical for the maintenance of basal endothelial permeability. However, the molecular mechanism of recovery of the endothelial barrier in response to inflammatory mediators has not yet been well delineated. The aim of the present study was to explore the mechanism of this barrier restoration. Specific emphasis was given to the role of Rac1 GTPase activation, which is an important regulator of endothelial adherens junction (AJ) integrity.

7. Thalidomide

Structure of the DDB1–CRBN E3 ubiquitin ligase in complex with thalidomide

Eric S. Fischer, Kerstin Böhm, John R. Lydeard, Haidi Yang, Michael B. Stadler, et al.
Nature (2014) http://dx.doi.org:/10.1038/nature13527

In the 1950s, the drug thalidomide, administered as a sedative to pregnant women, led to the birth of thousands of children with multiple defects. Despite the teratogenicity of thalidomide and its derivatives lenalidomide and pomalidomide, these immunomodulatory drugs (IMiDs) recently emerged as effective treatments for multiple myeloma and 5q-deletion-associated dysplasia. IMiDs target the E3 ubiquitin ligase CUL4–RBX1–DDB1–CRBN (known as CRL4^CRBN) and promote the ubiquitination of the IKAROS family transcription factors IKZF1 and IKZF3 by CRL4^CRBN. Here we present crystal structures of the DDB1–CRBN complex bound to thalidomide, lenalidomide and pomalidomide. The structure establishes that CRBN is a substrate receptor within CRL4^CRBN and enantioselectively binds IMiDs. Using an unbiased screen, we identified the homeobox transcription factor MEIS2 as an endogenous substrate of CRL4^CRBN. Our studies suggest that IMiDs block endogenous substrates (MEIS2) from binding to CRL4^CRBN while the ligase complex is recruiting IKZF1 or IKZF3 for degradation. This dual activity implies that small molecules can modulate an E3 ubiquitin ligase and thereby upregulate or downregulate the ubiquitination of proteins.

Figure 1: The overall structure of the DDB1–CRBN complex.

http://www.nature.com/nature/journal/vaop/ncurrent/carousel/nature13527-f1.jpg

a, Cartoon representation of the structure of the complex of human DDB1, G. gallus CRBN and thalidomide: DDB1, highlighting the domains BPA (red), BPB (magenta), BPC (orange) and DDB1-CTD (grey); G. gallus CRBN, highlighting the domain…

Figure 2: IMiD binding to CRBN.

http://www.nature.com/nature/journal/vaop/ncurrent/carousel/nature13527-f2.jpg

a, Chemical structure of lenalidomide. b, Chemical structure of pomalidomide. c, Sketch of thalidomide and its interactions with G. gallus CRBN. Hydrogen bonds are shown as dashed lines, and hydrophobic interactions are indicated as gr

Figure 3: CRBN is a substrate receptor in the ligase CRL4^CRBN.

http://www.nature.com/nature/journal/vaop/ncurrent/carousel/nature13527-f3.jpg

a, Architecture of the CRL4^DDB2 complex bound to DNA (PDB ID 4A0K). b, Model of CRL4^CRBN bound to thalidomide. c, Firefly luciferase (Fluc) to Renillaluciferase (Rluc) ratios (Fluc:Rluc) of IKZF1-reporter-plasmid-transfected HEK 293T…

Figure 5: Molecular model of IMiD function.

http://www.nature.com/nature/journal/vaop/ncurrent/carousel/nature13527-f5.jpg

a, Thalidomide binds to CRBN at the canonical substrate-binding site. b, The potent anti-myeloma drug thalidomide and its derivatives lenalidomide and pomalidomide occupy the same site but with different solvent-exposed moieties. c, Bi…

8. Preeclampsia of pregnancyand protein misfolding

Protein misfolding, congophilia, oligomerization, and defective amyloid processing in preeclampsia

Irina A. Buhimschi¹^,²^,^*, Unzila A. Nayeri², Guomao Zhao¹, Lydia L. Shook², Anna Pensalfini³, et al.
¹Center for Perinatal Research, The Research Institute at Nationwide Children’s Hospital and Department of Pediatrics, ⁴Depart of ObGyn, The Ohio State University College of Medicine, Columbus, OH
²Depart of ObGyn and Reproductive Sciences, Yale University School of Medicine, New Haven, CT

³Center for Dementia Research, Nathan Kline Institute for Psychiatric Research and Department of Psychiatry, New York University School of Medicine, New York, NY
⁵Depart of ObGyn and Reproductive Sciences, University of Vermont College of Medicine, Burlington, VT .
⁶Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92617, USA.
⁷Department of Biochemistry and Experimental Biochemistry Unit, King Abdulaziz Univ, Jeddah , Saudi Arabia.

Preeclampsia is a pregnancy-specific disorder of unknown etiology and a leading contributor to maternal and perinatal morbidity and mortality worldwide. Because there is no cure other than delivery, preeclampsia is the leading cause of iatrogenic preterm birth. We show that preeclampsia shares pathophysiologic features with recognized protein misfolding disorders. These features include urine congophilia (affinity for the amyloidophilic dye Congo red), affinity for conformational state–dependent antibodies, and dysregulation of prototype proteolytic enzymes involved in amyloid precursor protein (APP) processing. Assessment of global protein misfolding load in pregnancy based on urine congophilia (Congo red dot test) carries diagnostic and prognostic potential for preeclampsia. We used conformational state–dependent antibodies to demonstrate the presence of generic supramolecular assemblies (prefibrillar oligomers and annular protofibrils), which vary in quantitative and qualitative representation with preeclampsia severity. In the first attempt to characterize the preeclampsia misfoldome, we report that the urine congophilic material includes proteoforms of ceruloplasmin, immunoglobulin free light chains, SERPINA1, albumin, interferon-inducible protein 6-16, and Alzheimer’s β-amyloid. The human placenta abundantly expresses APP along with prototype APP-processing enzymes, of which the α-secretase ADAM10, the β-secretases BACE1 and BACE2, and the γ-secretase presenilin-1 were all up-regulated in preeclampsia. The presence of β-amyloid aggregates in placentas of women with preeclampsia and fetal growth restriction further supports the notion that this condition should join the growing list of protein conformational disorders. If these aggregates play a pathophysiologic role, our findings may lead to treatment for preeclampsia.

Citation: I. A. Buhimschi, U. A. Nayeri, G. Zhao, L. L. Shook, A. Pensalfini, E. F. Funai, I. M. Bernstein, C. G. Glabe, C. S. Buhimschi,Protein misfolding, congophilia, oligomerization, and defective amyloid processing in preeclampsia. Sci. Transl. Med. 6, 245ra92 (2014).

9. Blood Clotting

Removing parts of shape-shifting protein explains how blood clots

prothrombin (FII)

Using x-ray crystallography, SLU researchers published the first image of the important blood-clotting protein prothrombin (coagulation factor II). The protein’s flexible structure is key to the development of blood-clotting.In results recently published in Proceedings of the National Academy of Sciences (PNAS), Saint Louis University scientists have discovered that removal of disordered sections of a protein’s structure reveals the molecular mechanism of a key reaction that initiates blood clotting.

Enrico Di Cera, M.D., chair of the Edward A. Doisy department of biochemistry and molecular biology at Saint Louis University, studies thrombin, a key vitamin K-dependent blood-clotting protein, and its inactive precursor prothrombin (or coagulation factor II).

“Prothrombin is essential for life and is the most important clotting factor,” Di Cera said. “We are proud to report that our lab here at SLU has finally succeeded in crystallizing prothrombin for the first time.”

Blood-clotting has long ensured our survival, stopping blood loss after an injury. However, when triggered in the wrong circumstances, clotting can lead to debilitating or fatal conditions such as a heart attack, stroke or deep vein thrombosis.

Before thrombin becomes active, it circulates throughout the blood in the inactive (zymogen) form called prothrombin. When the active enzyme is needed (after a vascular injury, for example), the coagulation cascade is initiated and prothrombin is converted into the active enzyme thrombin that causes blood to clot.

X-ray crystallography is one tool in scientists’ toolbox for understanding processes at the molecular level. It offers a way to obtain a “snap shot” of a protein’s structure.

In this technique, scientists grow crystals of the protein they want to study, shoot x-rays at them and record data about the way the rays are scattered by crystals. Then they use computer programs to create an image of the protein based on that data.

Once scientists can visualize the three dimensional structure of a molecule, they can begin to piece together the way in which the protein functions and interacts with other molecules in the body, or with drugs.

Last year, Di Cera and colleagues published the first structure of prothrombin. This first structure lacked a domain responsible for interaction with membranes and certain other sections were not detected by x-ray analysis. Though the scientists were able to crystallize the protein, there were disordered regions in the structure that they could not see.

Within prothrombin there are two kringle domains (looped sections of a protein named after the Scandinavian pastry) connected by a “linker” region that intrigued the SLU investigators because of its intrinsic disorder.

“We deleted this linker and crystals grew in a few days instead of months, revealing for the first time the full architecture of prothrombin,” Di Cera said.

In addition to this remarkable discovery, Di Cera and colleagues found that the deleted version of prothrombin is activated to thrombin much faster than the intact prothrombin. The structure without the disordered linker is in fact optimized for conversion to thrombin and reveals key information on the mechanism of prothrombin activation.

For over four decades, scientists have tried to crystallize prothrombin but without success.

“It took us almost two years to discover that the disordered linker was the key,” Di Cera said. “Finally, prothrombin revealed its secrets and with that the molecular mechanism of a key reaction of blood clotting finally becomes amenable to rational drug design for therapeutic intervention.”

SLU researchers Nicola Pozzi, Ph.D., Zhiwei Chen, Leslie Pelc and Daniel Shropshire also are authors on the paper.

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Heroes in Medical Research: Green Fluorescent Protein and the Rough Road in Science

Posted in Bio Instrumentation in Experimental Life Sciences Research, Biological Networks, Gene Regulation and Evolution, Cell Biology, Signaling & Cell Circuits, Interviews with Scientific Leaders, Scientist: Career considerations, Ubiquitinylation, tagged Cell Biology, cloning, collaboration, colleagues, DNA, gene expression, Green fluorescent protein, imaging, intracellular localization, medicine, Nobel Prize, Nobel Prize in Chemistry, Proceedings of the National Academy of Sciences of the United States of America, research, scientific discovery, Wood's Hole on July 27, 2014| Leave a Comment »

Heroes in Medical Research: Green Fluorescent Protein and the Rough Road in Science

Curator: Stephen J. Williams, Ph.D.

Article ID #147: Heroes in Medical Research: Green Fluorescent Protein and the Rough Road in Science. Published on 7/27/2014

WordCloud Image Produced by Adam Tubman

In this series, “Heroes in Medical Research”, I like to discuss the people who made some important contributions to science and medicine which underlie the great transformative changes but don’t usually get the notoriety given to Nobel Laureates or who seem to fly under the radar of popular news. Their work may be the development of research tools which allowed a great discovery leading to a line of transformative research, a moment of serendipity leading to discovery of a cure, or just contributions to the development of a new field or the mentoring of a new generation of scientists and clinicians. One such discovery, which has probably been pivotal in many of our research, is the discovery of the green fluorescent protein (GFP), commonly used as an invaluable tool to monitor protein for cellular expression and localization studies. Although the development of research tools, whether imaging tools, vectors, animal models, cell lines, and such are not heralded, they always assist in the pivotal discoveries of our time. The following is a heartwarming story by Discover Magazine’s Yudhijit Bhattacharjee behind Dr. Douglas Prasher’s discovery of the green fluorescent protein, his successful efforts to sequence the gene and subsequent struggles in science and finally scientific recognition for his work. In addition the story describes Dr. Prather’s perseverance, a trait necessary for every scientist.

http://discovermagazine.com/2011/apr/30-how-bad-luck-networking-cost-prasher-nobel

The following is a wonderful entry into Wikipedia about Dr. Prasher at:

http://en.wikipedia.org/wiki/Douglas_Prasher

including a listing of his publications including the seminal Science and PNAS publications^1,2.

(Photo: Dr. Prasher in the lab at UCSD. Photo credit UCSD and John Galstaldo)

In summary, Dr. Prather had been working at Wood’s Hole in Massachusetts trying to discover, isolate, then clone the protein which allowed a species of jellyfish living in the cold waters of the North Pacific, Aequorea victoria, to emit a green glow. Eventually he cloned the GFP gene, but gave up on work to express the gene in mammalian cells. Before leaving Wood’s Hole he gave the gene to Dr. Roger Tsien, who with Dr. Martin Chalfie and Osamu Shimomura showed the utility of GFP as an intracellular tracer to visualize, in real time, the expression and localization of GFP-tagged proteins (all three shared the 2008 Nobel Prize for this work). Dr. Tsien however realized the importance of Douglas’s cloning work as pivotal for their research, contacted Douglas (who now due to the bad economy was working at a Toyota dealership in Alabama) and invited him to the Nobel Prize Award Ceremony in Sweden as his guest. Although Dr. Prasher had “left academic science” he never really stopped his quest for a scientific career, using his spare time to review manuscripts.

Other researchers have invited their colleagues who made important contributions to the ultimate Nobel work. One such guest was one of my colleagues Dr. Leonard Cohen, who worked with Dr. Irwin Rose and Avram Hershko at the Institute for Cancer Research in Philadelphia a cell-free system from clams to discover the mechanism how cyclin B is degraded during the exit from the cell cycle (from A. Hershko’s Nobel speech). Dr. Hershko had acknowledged a slew of colleagues and highlighted their contributions to the ultimate work. It shows how even small discoveries can contribute to the sphere of scientific knowledge and breakthrough.

Luckily, in the end, perseverance has paid off as Dr. Prasher is now using his talents in Roger Tsien‘s group at the University of California in San Diego.

References:

1. Chalfie, M., Tu, Y., Euskirchen, G., Ward, W.W., Prasher, D.C., Green fluorescent protein as a marker for gene expression. Science, 263(5148), 802-805 (1994).

2. Heim, R., Prasher, D.C., Tsien, R.Y., Wavelength mutations and posttranslational autoxidation of green fluorescent protein. Proc. Natl. Acad. Sci. USA, 91(26), 12501-12504 (1994).

More posts on this site on Heroes in Medical Research series include:

Heroes in Medical Research: Developing Models for Cancer Research

Heroes in Medical Research: Dr. Carmine Paul Bianchi Pharmacologist, Leader, and Mentor

Heroes in Medical Research: Dr. Robert Ting, Ph.D. and Retrovirus in AIDS and Cancer

Heroes in Medical Research: Barnett Rosenberg and the Discovery of Cisplatin

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The Experience of a Patient with Thyroid Cancer

Posted in Best evidence, Clinical Diagnostics, Curation, Developmental biology, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Electrophysiology, Endocrine Diseases, Experimental validation, Explanatory, Historical relevance, Immunodiagnostics, Inferential analysis, Innovation in Immunology Diagnostics, Interventional Oncology: Radiofrequency Ablation, Transarterial Chemoembolization, Microwave Ablation and Irreversible Electroporation (IRE), Medical Imaging Technology, Image Processing/Computing, MRI, CT, Nuclear Medicine, Ultra Sound, Nutrition, Patient Experience: Personal Memories of Invasive Medical Intervantion, Personalized and Precision Medicine & Genomic Research, Proteomics, Sensors & Analytics, Signaling, Technology Advance Assessment of, Translational Effectiveness, Translational Science, tagged Graves' disease, thyroid cancer, thyroid eye disease, TSH on July 14, 2014| Leave a Comment »

The Experience of a Patient with Thyroid Cancer

Interviewer and Curator: Larry H Bernstein, MD, FCAP

Thyroid cancer is usually a fairly innocuous disease, but it can present in different ways. There are are perhaps two main types – medullary, and follicular. But an anaplastic type is also a third uncommon type. It is speculative for me to suggest that the anaplastic type is a progression of either of the two main types. A RAS genotype coexists with the aggressive anaplastic carcinoma. Thyroid cancers are BRAF positive in genotype. The histological feature that is used to identify this neoplasm is the presence of “sammoma bodies”. It is more common in women, and less common in the elderly, and the incidence appears to have increased regionally in recent years. A recent paper suggests a common specific feature with breast cancer, which is unconfirmed.

When we consider thyroid disease, we start with euthyroid status, hypothyroid and hyperthyroid, all of which are related to the synthetic activity of the gland, that has a right and left lobe joined by a isthmus. In the midwestern US there is a deficiency of iodine, which leads to nodular thyroid goiter. The Mayo brothers pioneered in thyroid surgery at their clinic in Rochester, MN. This led to the insertion of iodine in table salt (Morton’s salt- “when it rains, it pours). Hyperthyroid status is over production of the hormone by an overactive gland. It is usually primary disease, called Grave’s Disease, after the physician who described it. I am not aware of the occurrence secondary to hyperactivity of the pituitary gland, which would result in both an increased thyroid stimulating hormone (TSH), thyrotropin, and elevated thyroid hormone, except by a primary neoplasm of thyrotropin secreting cells. The two hormones are under feedback control. This feedback is a valuable diagnostic indicator because the TSH is suppressed with Grave’s disease. The TSH assay is very accurate, and as the TSH falls, the TH increases, but the TH assay has never been as accurate as the TSH. The TH is transported in serum by three proteins: thyroxin-binding globulin (TBG), albumin, and trans-thy-retin (TTR), a quadruplex peptide with one subunit binding to retinol-binding protein (RPB), which transports retinol, vitamin A). The importance of TTR is not a subject for discussion here, but it has extremely important ties to metabolic disease that includes hyperhomocysteinemia and Alzheimer’s disease, as this protein is produced by both the liver and the choroid plexus, but the CP production declines in the elderly. The TTR metabolism is closely linked to total body sulfur, measured by K+ isotope measurement of lean body mass (fat free mass), and is a more accurate measure than use of urinary creatinine loss, which only measure the structural body mass, but not the visceral component.

There is another twist to the story in that thyroid hormone may be depressed over time secondary to an autoantibody to thyroid “peroxidase”, leading to destruction of the gland. The thyroid antibody that occurs has been recently reported to be a “peroxidase” antibody in common with the mammary gland. The disorder is denominated – Hashimoto’s thyroiditis. The presence of thyroid antibody may occur with Grave’s disease, with an occular protrusion with inflammation of the adductor muscles of eye movement. This is termed “exophthalmus”. However, thyroid eye disease is known to occur with hypo-, hyper-, and euthyroid status.

I here describe the long and difficult search to identify a confusing case.

Family history: Mother had thyroid cancer, surgically cured at Mayo Clinic. Sister had Hashimoto’s thyroiditis. Father had severe rheumatoid arthritis.

History of Illness. The patient is a male over 65 years age who attended a discussion group for several years and participated in supervised fitness exercises and did daily walks for 2-3 years prior to the discovery of the problem when he recalls, his voice was weak in making presentations to the discussion group (age 86 and over).

At the end of summer, 2013, he experienced shortness of breath and dizziness on walking. His physician had been concerned about the change of voice prior to this. He had a history of sleep apnea, and he was actively trying to lose weight. Cardiac and vascular examination of carotid and of peripheral circulation were unexpectedly excellent. Pulmonary studies were good.

A visit to an ENT physician did not explain the voice impairment. An unexpected low TSH result came back < 0.01, compared to a normal result 9 months earlier. This was the first indication of an active cyst or Grave’s disease. The patient was referred for ultrasound exam, and a thyroid panel was ordered. The result of the ultrasound was an enlarged right lobe with two large degenerate cysts, and a central small calcified cyst. The cyst was biopsied and it was malignant. It was BRAF pos and RAS negative.

He was referred to the nearest world-class academic center for further endocrine evaluation. The endocrinologist palpated a thyroid enlargement, and a biopsy was performed of the lymph nodes under a full scan of the neck. Surgery was scheduled and a surgeon skilled in endocrine surgery and cancer removed the thyroid, and noted that the right lobe compressed the recurrent laryngeal nerve. This was consistent with en ENT examination of the larynx that showed paralysis of the right larynx. The good news was that the prediction was that the nerve innovation was good, and would return.

There were a few involved lymph nodes in the removed specimen. The patient was put on synthroid. The next step was to schedule I131 radioiodine treatment by oral tablets. This required a preparatory diet of no salt or iodine intake prior to treatment. There was also a 5 day isolation for beta ray emission (which kills residual thyroid cells). The neck was scanned with a gamma scanned prior to induction of treatment, which required a dose of synthetic TSH and a low dose of I131. The patiemt is recovered for 14 days post treatment and has regained much energy.

There is a residual burden of the thyroid eye disease that requires special optical care because of loss of distance perception with diplopia. This is stable, but any surgical repair would have to wait for a year.

Notes from PathologyOutlines.com, Nathan Pernick, Editor-in-Chief

Thyroid gland

Reviewer: Zubair W. Baloch, M.D., Shahidul Islam, M.D., Ph.D., Ricardo R. Lastra, M.D., Michelle R. Pramick, M.D., Phillip A. Williams, M.D., MSC (see Reviewers page)

Revised: 11 July 2014, last major update IN PROGRESS
Copyright: (c) 2001-2014, PathologyOutlines.com, Inc.

Endocrine abnormalities and thyroid gland
Hyperthyroidism

Reviewer: Shahidul Islam, M.D., Ph.D.

General
=======================================================

Accelerated thyroid hormone biosynthesis and secretion by thyroid gland
Early symptoms: anxiety, palpitations, rapid pulse, fatigue, muscle weakness, tremor, weight loss, diarrhea, heat intolerance, warm skin, excessive perspiration, menstrual changes, hand tremor
Ocular changes: wide staring gaze and lid lag due to sympathetic overstimulation of levator palpebrae superioris

Thyrotoxicosis: hypermetabolic clinical syndrome due to elevated serum T3 or T4

Types
=======================================================

Primary hyperthyroidism: intrinsic thyroid abnormality
- Low TSH, high free T4, normal TRH stimulation test
Secondary hyperthyroidism: high TSH, abnormal TRH stimulation test
Subclinical hyperthyroidism: low TSH (< 0.1 µIU/ml), normal T3 and T4 (Eur J Endocrinol 2005;152:1), no clinical hyperthyroidism
- May be due to exogenous thyroid hormone (Hormones (Athens) 2006;5:119)
- Patients have increased risk of coronary heart disease (Int J Cardiol 2008;125:41)
T3 hyperthyroidism: 1-4%ofhyperthyroid patients
- Low TSH, high free T3, normal free T4
- Associated with early treatment of hyperthyroidism with antithyroid drugs
T4 hyperthyroidism:highT4, normal T3
- Due to primary hyperthyroidism causes, also iodine, amiodarone (Arch Pathol Lab Med 2003;127:e275), pregnancy (2%)

Graves’ disease (85%)

Micro images
=======================================================

Diffuse hyperplasia of thyroid gland

Additional references
=======================================================

Med J Aust 2004;180:186, eMedicine #1, #2, Wikipedia

Hashimoto’s thyroiditis

General
=======================================================

Autoimmune disease with goiter, elevated circulating anti-thyroid peroxidase and anti-thyroglobulin antibodies
First described by Hakaru Hashimoto in 1912 (World J Surg 2008;32:688)

Epidemiology
=======================================================

90-95% in women, usually 45-65 years old; clusters in families
More common in Whites than Blacks or Japanese (Am J Clin Pathol 1994;101:698)
Most common cause of sporadic goiter in children in iodine sufficient areas (J Pediatr Endocrinol Metab 2007;20:1199)

Clinical features

Clinical features
=======================================================

Adults present with painless, gradual thyroid failure due to autoimmune destruction, may initially have transient hyperthyroidism
Children have variable hypothyroidism and reversion to euthyroidism so must monitor thyroid function (Clin Endocrinol (Oxf) 2009;71:451)

Associated with HLA-DR5 (goitrous form), HLA-DR3 (atrophic form)
May coexist with SLE, rheumatoid arthritis, Sjögren’s syndrome, pernicious anemia, type 2 diabetes, Graves’ disease, chronic active hepatitis, adrenal insufficiency, MALT lymphoma of gastrointestinal tract (80:1 relative risk), other B cell lymphomas
Associated with well differentiated thyroid cancer (J Am Coll Surg 2007;204:764)
May evolve into thyroid lymphoma (J Clin Pathol 2008;61:438)

Laboratory
=======================================================

Autoantibodies include:
- Anti-TSH (specific for Hashimoto’s and Graves’ disease)
- Anti-thyroglobulin (less sensitive but similar specificity as anti-thyroid peroxidase, Clin Chem Lab Med 2006;44:837)
- Anti-thyroid peroxidase (previously called antimicrosomal antibody, sensitive but not specific as 20% of adult women without disease have these antibodies); anti-iodine transporter (rare)
- Note: anti-TSH antibodies block the TSH receptor in Hashimoto’s disease but stimulate the TSH receptor in Graves’ disease

Papillary carcinoma

75-80% of thyroid carcinomas
Occult tumors in 6% at autopsy (1 to 10 mm), 46% multicentric, 14% with nodal metastases (Am J Clin Pathol 1988;90:72)
Occult tumors in up to 24% with other thyroid disease, but with male predominance (Mod Pathol 1996;9:816)

Epidemiology
=======================================================

Usually women (70%) of reproductive age

Clinical features
=======================================================

Usually presents as painless nodule or mass in neck or cervical node; usually cold on scan
Usually diagnosed by FNA
At presentation, 67% in thyroid only, 13% in thyroid and cervical nodes, 20% in nodes only
Parathyroid gland invasion often occurs early (Arch Pathol Lab Med 2002;126:1511)
Nodal involvement is often not clinically apparent due to small size and similar consistency; nodal metastases may undergo cystic change and resemble branchial cleft cysts (The Internet Journal of Nuclear Medicine 2007;4:2)
Proteomic analysis of serum may be useful in future for screening or followup (Arch Otolaryngol Head Neck Surg 2008;134:198)
Lymph nodes:
- Measurement of thyroglobulin in FNA from lymph nodes in patients with history of papillary thyroid carcinoma is useful in detecting recurrent disease, especially if specimen is or likely will be inadequate for evaluation (Cytojournal 2008;5:1)
Risk factors:
- Ionizing radiation before age 20 (for acne – Surgery 1991;110:691, tonsillitis, tinea capitis, enlarged thymus)
- Post-Chernobyl (particularly children, Endocr Pathol 2006;17:307) or after exposure to nuclear explosions at Marshall Islands (J Epidemiol 2003;13:99)
- Hashimoto’s thyroiditis (possibly, Cancer 1995;76:2312)
- Familial adenomatous polyposis (World J Surg 1998;22:738)
- Is familial in 4.5%, similar prognosis as sporadic disease (Surgery 2009;145:100)

Prognostic factors
=======================================================

10 year survival is 98%, similar to general population (versus 92% for follicular carcinoma); 100% if under age 20, even with nodal metastases
Cervical nodal involvement does NOT affect prognosis
5-20% have local recurrences, 10-15% have distant metastases (lung, bones, CNS)
Poorer prognosis:
- Age 40+ or elderly, male (possibly), local invasion (associated with higher incidence of nodal metastases, Arch Pathol Lab Med 1998;122:166), distant metastases (other sites worse than lung, Surgery 2008;143:35), large tumor size, multicentricity, tall cell, columnar or diffuse sclerosing variants
- Poorly differentiated, anaplastic or squamous foci

added July 14, 2014

Summary – Intraoperative laryngeal nerve monitoring
Objectives: The aim of this study was to stimulate the recurrent laryngeal nerve during thyroidectomy or parathyroidectomy and to record the muscle responses in an attempt to predict postoperative vocal fold mobility.
Patients and methods: Intraoperative recurrent laryngeal nerve monitoring during general anaesthesia was performed by using an electrode-bearing endotracheal tube (nerve integrity monitor EMG endotracheal tube [Medtronic Xomed, Jacksonville, Flo, USA]). Two hundred and fifteen recurrent laryngeal nerves from 141 patients undergoing total thyroidectomy (n = 74),
hemithyroidectomy (n = 63), or parathyroidectomy (n = 4) were prospectively monitored. In each case, the muscle potential was recorded after stimulation of the recurrent laryngeal nerve by a monopolar probe.
Results: The nerve stimulation threshold before and after dissection that induced a muscle response of at least 100 V ranged from 0.1 to 0.85 mA (mean 0.4 mA). The supramaximal stimulation intensity was defined as 1 mA. The amplitude of muscle response varied considerably from one patient to another, but the similarity of the muscle response at supramaximal intensity between pre- and postdissection and between postdissection at the proximal and distal exposed
portions of the nerve was correlated with normal postoperative vocal fold function. Inversely, alteration of the muscle response indicated a considerable risk of recurrent laryngeal nerve palsy, but was not predictive of whether or not this lesion would be permanent. http://dx.doi.org:/10.1016/j.anorl.2011.09.003

Summary – Prognostic impact of tumour multifocality in thyroid papillary microcarcinoma
European Annals of Otorhinolaryngology, Head and Neck diseases (2012) 129, 175—178

Objective: The objective of this study was to evaluate the prognostic impact of tumour multifocality in papillary thyroid microcarcinoma (PTMC).
Methods: All patients who underwent total thyroidectomy and central neck dissection for PTMC in our institution between 1990 and 2007 were included in this retrospective study. Statistical correlations between tumour multifocality and various clinical or pathological prognostic parameters were assessed by univariate and multivariate analyses.
Results: A total of 160 patients (133 women and 27 men; mean age: 47.8 ± 13.7 years) were included in this study. Tumour multifocality was demonstrated in 59 (37%) patients. Central neck metastatic lymph node involvement was identified in 46 (28%) patients. No statistical correlation was demonstrated between tumour multifocality and the following factors: age, gender, tumour size, extension beyond the thyroid, metastatic central neck lymph node involvement and risk of recurrence. A tumour diameter greater than 5 mm was associated with a higher risk of recurrence (P = 0.008).
Conclusion: Tumour multifocality does not appear to have a prognostic impact in PTMC. http://dx.doi.org:/10.1016/j.anorl.2011.11.003

Positron emission tomography thyroid carcinoma
European Annals of Otorhinolaryngology, Head and Neck diseases (2012) 129, 251—256

Objectives: Recurrence is observed in 15—20% of patients under surveillance following treatment of differentiated thyroid cancer (DTC). However, due to cell dedifferentiation, the recurrence may be iodine-negative, thereby compromising detection. For this reason, new methods of exploration are indispensable to enable localization of such recurrences. The purpose of this work is to review the contribution of positron emission tomography—computed tomography (PET-CT) in the exploration of iodine-negative recurrent DTC.
Method: A comprehensive review and discussion of the medical literature was carried out.
Results: Depending on the report, the sensitivity of PET-CT ranged from 70% to 85%, with up to 90% specificity. However, the large number of false negatives, which can reach 40%, is the
disadvantage of this examination. PET-CT results lead to change in the therapeutic strategy in approximately 50% of patients with isolated raised serum thyroglobulin levels, and surgical exploration of a precise anatomical area in the neck.
Conclusion: As post-treatment recurrence of a DTC can affect patient survival, a thorough diagnostic work-up is required in these cases. Where thyroglobulin levels are elevated with no uptake on 131-iodine scans, PET-CT can be a useful complementary exploration, especially for localizing the site of recurrence.
http://dx.doi.org:/10.1016/j.anorl.2012.01.003
French ENT Society (SFORL) practice guidelines for lymph-node management in adult differentiated thyroid carcinoma
European Annals of Otorhinolaryngology, Head and Neck diseases (2012) 129, 197—206

Cervical and mediastinal lymph-node management differentiated thyroid carcinoma of the follicular epithelium (DTC) remains controversial. Depending on the situation, pre-operative staging and indications for and extent of lymph-node dissection are still matters of debate, even in case of palpable nodes found on primary surgery. Procedural indications for adenectomy, selective neck dissection, and anatomic regional extension of dissection are not clearly defined.

Questions raised:

• what is lymph-node involvement in DTC?
• what is the prognostic value of lymph-node invasion: for
recurrence, and for survival?

• what baseline assessment is required ahead of treatment
of papillary thyroid carcinoma to assess possible lymphnode
involvement?

• what are the principles of lymph-node surgery?
Central and lateral dissection, and dissection extended to the mediastinum;
• what is the iatrogenesis in cN0 and cN+ neck?
• what is the impact of central and lateral neck dissection on recurrence, survival, secondary treatment and surveillance in cN0 and cN+ ?
• in cN0 patients, when neck dissection is considered, what lymph-node regions should be indicated?
http://www.orlfrance.org/ download.php?id=159.

Molecular Diagnosis for Indeterminate Thyroid Nodules on Fine Needle Aspiration
Expert Rev Mol Diagn. 2013;13(6):613-62

Somatic mutation testing, mRNA gene expression platforms, protein immunocytochemistry and miRNA panels have improved the diagnostic accuracy of indeterminate thyroid nodules, and although no test is perfectly accurate, in the authors’ opinion, these methods will most certainly become an important part of the diagnostic tools for clinicians and cytopathologists in the future.

Several point mutations and gene rearrangements have been identified in thyroid cancer. The most common somatic mutation in differentiated thyroid cancer has been studied as a potential tool to enhance the diagnostic accuracy of indeterminate FNA lesions – BRAF. This mutation occurs in papillary, poorly differentiated and anaplastic thyroid cancer and causes a V600E substitution in the BRAF protein, which results in neoplastic progression by aberrant activation of the MAPK pathway. The BRAF V600E mutation, along with RET/PTC rearrangements, are a hallmark of thyroid cancer and a vast majority of indeterminate thyroid nodules harboring either one of these two mutations are malignant on final pathology.

The RAS proto-oncogene encodes three different membrane associated GTP proteins: HRAS, KRAS and NRAS. Mutation of these domains causes increased signal transduction through both the MAPK and the PI3K/AKT pathways. These mutations are highly prevalent in FTC and in the follicular variant of papillary thyroid cancer (40–50%) and seldom detected in the classic variant papillary thyroid cancer (10%). RAS mutations have also been identified in benign FA; however, it is unclear whether RAS-positive FA have a higher chance of progression to cancer.

Recurrence detection in differentiated thyroid cancer patients..
Clinical endocrinology, Vol. 72, No. 4. (10 September 2009), pp. 558-563, doi:10.1111/j.1365-2265.2009.03693.x

There was a correlation between TgAb level and recurrence (p = 0.032).
). Recurrence was found in 37.5% of 24 TgAb+/Tg- patients who showed a gradually increasing tendency in serial measurements of TgAb. Sixteen cervical foci (21.1%) missed on neck USG and 17 lesions (22.4%) located outside the neck were additionally detected with PET/CT in TgAb+ patients.

Solving the mystery of iodine uptake
Science 20 June 2014: Vol. 344 no. 6190 p. 1355 http://dx.doi.org:/10.1126/science.344.6190.1355-a

The cell membrane protein NIS (sodium/iodine symporter) transports iodine into thyroid cells, but because iodine concentrations outside of the cell are so low, how it does so is a mystery. The key? Moving two sodium ions along with the iodine ion, Nicola et al found. NIS also does not bind sodium very tightly, but the high concentrations of sodium outside the cell allow one sodium ion to bind. This binding increases the affinity of NIS for a second sodium ion and also for iodine. With the three ions bound, NIS changes its conformation so that it opens to the inside of the cell, where the sodium concentration is low enough for NIS to release its sodium ions. When the sodium goes away, so does NIS’s affinity for iodine, leading NIS to release it.

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Research on inflammasomes opens therapeutic ways for treatment of rheumatoid arthritis

Posted in Cell Biology, Signaling & Cell Circuits, Disease Biology, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Human Immune System in Health and in Disease, Infectious Disease & New Antibiotic Targets, Metabolomics, Population Health Management, Genetics & Pharmaceutical, Proteomics, Signaling, Signaling & Cell Circuits, Small Molecules in Development of Therapeutic Drugs, Systemic Inflammatory Response Related Disorders, Translational Research, Translational Science, tagged inflammasomes, RA on July 12, 2014| Leave a Comment »

Research on inflammasomes opens therapeutic ways for treatment of rheumatoid arthritis

Reporter: Larry H. Bernstein, MD, FCAP

One of the processes accounted for by inflammasomes is the production of interleukin-1, a protein with an important role in inflammatory reactions. Stopping the effects of interleukin-1 resulted in a cure for the mice. In this manner, Vande Walle and Lamkanfi demonstrated that the mouse model is perfectly suitable for studying the correlation between inflammasomes and RA.

RA is a syndrome rather than a single disease
Previous research has already demonstrated that other proteins in our immune system – such as TNF and IL-17 – could possibly play a role in RA
We could evolve towards a more personalized approach for RA

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Update on mitochondrial function, respiration, and associated disorders

Posted in Anaerobic Glycolysis, Ca2+ triggered activation, Ca2+ triggered activation, Cell Biology, Signaling & Cell Circuits, Curation, Discovery process, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Experimental validation, Explanatory, Inferential analysis, Metabolomics, Na-K-ATPase, Nephrology, Neurohumoral Transmission, Oxidative phosphorylation, Phosphorylation, Proteomics, Translational Science, tagged 5HT1F, alpha ketoglutarate, ATP synthase, brown adipose tissue (BAT), C. Elegans, ca-uniporter (MCU), Ca2+-regulation, Cancer - General, CLL, coupled respiration, Glut4 transporter, inner membrane, K-depolarization, mitochondria, mTOR, NADPH, neurons, OCR, Oxidative phosphorylation, pyruvate -rate limiting, ROS, Sestrin2, TOR, UCP1 on July 8, 2014| Leave a Comment »

Larry H. Benstein, MD, FCAP, Gurator and writer

http://pharmaceuticalintelligence.com/7/8/2014/Update on mitochondrial function, respiration, and associated disorders

This is a condensed account of very recent published work on respiration and disturbed mitochondrail function. We know that their is an equilibrium between respiration and autophagy in eukaryotic cells. The Krebs Cycle produces 32 ATPs in oxidative phosphorylation, which is far more efficient than glycolysis. There is also a different contribution of mitochondrial metabolism, in the balance, between tissues that are synthetic and those that are catabolic. This is a subject long understood, essential for cellular energetics, and not adequately explored.

Gain-of-Function Mutant p53 Promotes Cell Growth and Cancer Cell Metabolism via Inhibition of AMPK Activation.

Zhou G¹, Wang J², Zhao M², Xie TX², Tanaka N², et al.
Mol Cell. 2014 Jun 19;54(6):960-974. doi: 10.1016/j.molcel.2014.04.024.

Many mutant p53 proteins (mutp53s) exert oncogenic gain-of-function (GOF) properties, but the mechanisms mediating these functions remain poorly defined.

We show here that GOF mutp53s inhibit AMP-activated protein kinase (AMPK) signaling in head and neck cancer cells.

Conversely, downregulation of GOF mutp53s enhances AMPK activation under energy stress, decreasing the activity of the anabolic factors acetyl-CoA carboxylase and ribosomal protein S6 and inhibiting aerobic glycolytic potential and invasive cell growth.

Under conditions of energy stress, GOF mutp53s, but not wild-type p53, preferentially bind to the AMPKα subunit and inhibit AMPK activation.

Given the importance of AMPK as an energy sensor and tumor suppressor that inhibits anabolic metabolism, our findings reveal that direct inhibition of AMPK activation is an important mechanism through which mutp53s can gain oncogenic function. PMID:24857548

Investigating and Targeting Chronic Lymphocytic Leukemia Metabolism with the HIV Protease Inhibitor Ritonavir and Metformin.

Adekola KU, Aydemir SD, Ma S, Zhou Z, Rosen ST, Shanmugam M.
Leuk Lymphoma. 2014 May 14:1-23.

Chronic Lymphocytic Leukemia (CLL) remains fatal due to the development of resistance to existing therapies. Targeting abnormal glucose metabolism sensitizes various cancer cells to chemotherapy and/or elicits toxicity.

Examination of glucose dependency in CLL demonstrated variable sensitivity to glucose deprivation. Further evaluation of metabolic dependencies of CLL cells resistant to glucose deprivation revealed increased engagement of fatty acid oxidation upon glucose withdrawal.

Investigation of glucose transporter expression in CLL reveals up-regulation of glucose transporter GLUT4. Treatment of CLL cells with HIV protease inhibitor ritonavir, that inhibits GLUT4, elicits toxicity similar to that elicited upon glucose-deprivation.

CLL cells resistant to ritonavir are sensitized by co-treatment with metformin, potentially targeting compensatory mitochondrial complex 1 activity. Ritonavir and metformin have been administered in humans for treatment of diabetes in HIV patients, demonstrating the tolerance of this combination in humans. Our studies strongly substantiate further investigation of FDA approved ritonavir and metformin for CLL.

KEYWORDS: Basic Biology; Chemotherapeutic approaches; Lymphoid Leukemia; Signal transduction PMID: 24828872

Utilizing hydrogen sulfide as a novel anti-cancer agent by targeting cancer glycolysis and pH imbalance.

Lee ZW¹, Teo XY, Tay EY, Tan CH, Hagen T, Moore PK, Deng LW.
Br J Pharmacol. 2014 May 15. doi: 10.1111/bph.12773

Many disparate studies have reported the ambiguous role of hydrogen sulfide (H₂ S) in cell survival. The present study investigated the effect of H₂ S on viability of cancer and non-cancer cells.

Cancer and non-cancer cells were exposed to H₂ S (using sodium hydrosulfide, NaHS and GYY4137) and cell viability was examined by crystal violet assay. We then examined cancer cellular glycolysis process by in vitro enzymatic assays and pH regulator activity. Lastly, intracellular pH (pHi) was determined by ratiometric pHi measurement using BCECF staining.

Continuous, but not single, exposure to H₂ S decreased cell survival more effectively in cancer cells, as compared to non-cancer cells. Slow H₂ S-releasing donor, GYY4137, significantly increased glycolysis leading to overproduction of lactate. H₂ S also decreased anion exchanger and sodium/proton exchanger activity. The combination of increased metabolic acid production and defective pH regulation resulted in an uncontrolled intracellular acidification leading to cancer cell death. In contrast, no significant intracellular acidification or cell death was observed in non-cancer cells.

Low and continuous exposure to H₂ S targets metabolic processes and pH homeostasis in cancer cells, potentially serving as a novel and selective anti-cancer strategy.

KEYWORDS: cancer cell death; cancer glucose metabolism; hydrogen sulfide; pH homeostasis PMID: 24827113

Agonism of the 5-Hydroxytryptamine 1F Receptor Promotes Mitochondrial Biogenesis and Recovery from Acute Kidney Injury

Garrett SM, Whitaker RM, Beeson CC, and Schnellmann RG

Center for Cell Death, Injury, and Regeneration, Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, South Carolina (S.M.G., R.M.W., C.C.B., R.G.S.); and Ralph H. Johnson Veterans Affairs Medical Center, Charleston, South Carolina (R.G.S.)
Address correspondence to: Dr. Rick G. Schnellmann, Department of Drug Discovery and Biomedical Sciences, MUSC, Charleston, SC 29425.
E-mail: schnell@musc.edu

Many acute and chronic conditions, such as acute kidney injury, chronic kidney disease, heart failure, and liver disease, involve mitochondrial dysfunction. Although we have provided evidence that drug-induced stimulation of mitochondrial biogenesis (MB) accelerates mitochondrial and cellular repair, leading to recovery of organ function, only a limited number of chemicals have been identified that induce MB.

The goal of this study was to assess the role of the 5-hydroxytryptamine 1F (5-HT_1F) receptor in MB. Immunoblot and quantitative polymerase chain reaction analyses revealed 5-HT_1F receptor expression in renal proximal tubule cells (RPTC). A MB screening assay demonstrated that two selective 5-HT_1F receptor agonists,

LY334370 (4-fluoro-N-[3-(1-methyl-4-piperidinyl)-1H-indol-5-yl]benzamide) and
LY344864 (N-[(3R)-3-(dimethylamino)-2,3,4,9-tetrahydro-1H-carbazol-6-yl]-4-fluorobenzamide; 1–100 nM)

increased carbonylcyanide-p-trifluoromethoxyphenylhydrazone–uncoupled oxygen consumption in RPTC, and

validation studies confirmed both agonists increased mitochondrial proteins in vitro.
[e.g., ATP synthase β, cytochrome c oxidase 1 (Cox1), and NADH dehydrogenase (ubiquinone) 1β subcomplex subunit 8 (NDUFB8)]

Small interfering RNA knockdown of the 5-HT_1F receptor

blocked agonist-induced MB.

Furthermore, LY344864 increased

peroxisome proliferator–activated receptor (PPAR) coactivator 1-α, Cox1, and
NDUFB8 transcript levels and
mitochondrial DNA (mtDNA) copy number

in murine renal cortex, heart, and liver.

Finally, LY344864 accelerated recovery of renal function, as indicated by

decreased blood urea nitrogen and kidney injury molecule 1 and
increased mtDNA copy number

following ischemia/reperfusion-induced acute kidney injury (AKI).

In summary, these studies reveal that

the 5-HT_1F receptor is linked to MB, 5-HT_1F receptor agonism promotes MB in vitro and in vivo, and

5-HT_1F receptor agonism promotes recovery from AKI injury.

Induction of MB through 5-HT_1F receptor agonism represents a new target and approach to treat mitochondrial organ dysfunction.

Footnotes

Portions of this work have been presented previously: Garrett SM, Wills LP, and Schnellmann RG (2012) Serotonin (5-HT) 1F receptor agonism as a potential treatment for acceleration of recovery from acute kidney injury.American Society of Nephrology Annual Meeting; 2012 Nov 1–4; San Diego, CA.
dx.doi.org/10.1124/jpet.114.214700.

Ca2+ regulation of mitochondrial function in neurons.

Rueda CB¹, Llorente-Folch I¹, Amigo I¹, Contreras L¹, González-Sánchez P¹, Martínez-Valero P¹, Juaristi I¹, Pardo B¹, Del Arco A², Satrústegui J³

Biochim Biophys Acta. 2014 May 10. pii: S0005-2728(14)00126-1.
doi: 10.1016/j.bbabio.2014.04.010.

Calcium is thought to regulate respiration but it is unclear whether this is dependent on the increase in ATP demand caused by any Ca²⁺ signal or to Ca²⁺ itself.

[Na⁺]_i, [Ca²⁺]_i and [ATP]_i dynamics in intact neurons exposed to different workloads in the absence and presence of Ca²⁺ clearly showed that

Ca²⁺-stimulation of coupled respiration is required to maintain [ATP]_i levels.

Ca²⁺ may regulate respiration by

activating metabolite transport in mitochondria from outer face of the inner mitochondrial membrane, or
after Ca²⁺ entry in mitochondria through the calcium uniporter (MCU).

Two Ca²⁺-regulated mitochondrial metabolite transporters are expressed in neurons,

the aspartate-glutamate exchanger ARALAR/AGC1/Slc25a12, a component of the malate-aspartate shuttle, with a Kd for Ca²⁺ activation of 300nM, and
the ATP-Mg/Pi exchanger SCaMC-3/Slc25a23, with S_0.5 for Ca²⁺ of 300nM and 3.4μM, respectively.

The lack of SCaMC-3 results in a smaller Ca²⁺-dependent stimulation of respiration only at high workloads, as caused by veratridine, whereas

the lack of ARALAR reduced by 46% basal OCR in intact neurons using glucose as energy source and the Ca²⁺-dependent responses to all workloads (veratridine, K⁺-depolarization, carbachol).

The lack of ARALAR caused a reduction of about 65-70% in the response to the high workload imposed by veratridine, and

completely suppressed the OCR responses to moderate (K⁺-depolarization) and small (carbachol) workloads,
effects reverted by pyruvate supply.

For K⁺-depolarization, this occurs in spite of the presence of large [Ca²⁺]_mit signals and increased reduction of mitochondrial NAD(P)H.

These results show that ARALAR-MAS is a major contributor of Ca²⁺-stimulated respiration in neurons

by providing increased pyruvate supply to mitochondria.

In its absence and under moderate workloads, matrix Ca²⁺ is unable to stimulate pyruvate metabolism and entry in mitochondria suggesting a limited role of MCU in these conditions.

KEYWORDS: ATP-Mg/Pi transporter; Aspartate–glutamate transporter; Calcium; Calcium-regulated transport; Mitochondrion; Neuronal respiration PMID: 24820519

Sestrin2 inhibits uncoupling protein 1 expression through suppressing reactive oxygen species.

Ro SH¹, Nam M², Jang I¹, Park HW¹, Park H¹, Semple IA¹, Kim M¹, et al.
Proc Natl Acad Sci U S A. 2014 May 27;111(21):7849-54.
doi: 10.1073/pnas.1401787111.

Uncoupling protein 1 (Ucp1), which is localized in the mitochondrial inner membrane of mammalian brown adipose tissue (BAT), generates heat by uncoupling oxidative phosphorylation. Upon cold exposure or nutritional abundance, sympathetic neurons stimulate BAT to express Ucp1 to induce energy dissipation and thermogenesis. Accordingly, increased Ucp1 expression reduces obesity in mice and is correlated with leanness in humans.

Despite this significance, there is currently a limited understanding of how Ucp1 expression is physiologically regulated at the molecular level. Here, we describe the involvement of Sestrin2 and reactive oxygen species (ROS) in regulation of Ucp1 expression. Transgenic overexpression of Sestrin2 in adipose tissues inhibited both basal and cold-induced Ucp1 expression in interscapular BAT, culminating in decreased thermogenesis and increased fat accumulation.

Endogenous Sestrin2 is also important for suppressing Ucp1 expression because BAT from Sestrin2(-/-) mice exhibited a highly elevated level of Ucp1 expression. The redox-inactive mutant of Sestrin2 was incapable of regulating Ucp1 expression, suggesting that Sestrin2 inhibits Ucp1 expression primarily through reducing ROS accumulation.

Consistently, ROS-suppressing antioxidant chemicals, such as butylated hydroxyanisole and N-acetylcysteine, inhibited cold- or cAMP-induced Ucp1 expression as well. p38 MAPK, a signaling mediator required for cAMP-induced Ucp1 expression, was inhibited by either Sestrin2 overexpression or antioxidant treatments.

Taken together, these results suggest that Sestrin2 and antioxidants inhibit Ucp1 expression through suppressing ROS-mediated p38 MAPK activation, implying a critical role of ROS in proper BAT metabolism.

KEYWORDS: aging; homeostasis; mouse; β-adrenergic signaling PMID: 24825887 PMCID: PMC4040599

Mitochondrial EF4 links respiratory dysfunction and cytoplasmic translation in Caenorhabditis elegans.

Yang F¹, Gao Y¹, Li Z², Chen L³, Xia Z⁴, Xu T⁵, Qin Y⁶Biochim Biophys Acta. 2014 May 15. pii: S0005-2728(14)00499-X.
doi: 10.1016/j.bbabio.2014.05.353.

How animals coordinate cellular bioenergetics in response to stress conditions is an essential question related to aging, obesity and cancer. Elongation factor 4 (EF4/LEPA) is a highly conserved protein that promotes protein synthesis under stress conditions, whereas its function in metazoans remains unknown.

Here, we show that, in Caenorhabditis elegans, the mitochondria-localized CeEF4 (referred to as mtEF4) affects mitochondrial functions, especially at low temperature (15°C).

At worms’ optimum growing temperature (20°C), mtef4 deletion leads to self-brood size reduction, growth delay and mitochondrial dysfunction.

Transcriptomic analyses show that mtef4 deletion induces retrograde pathways, including mitochondrial biogenesis and cytoplasmic translation reorganization.

At low temperature (15°C), mtef4 deletion reduces mitochondrial translation and disrupts the assembly of respiratory chain supercomplexes containing complex IV.

These observations are indicative of the important roles of mtEF4 in mitochondrial functions and adaptation to stressful conditions.

KEYWORDS: C. elegans; EF4(LepA/GUF1); Mitochondrial dysfunction; Retrograde pathways; Translation PMID: 24837196

The metabolite α-ketoglutarate extends lifespan by inhibiting ATP synthase and TOR.

Chin RM¹, Fu X², Pai MY³, Vergnes L⁴, Hwang H⁵, Deng G⁶, Diep S², et al.
Nature 2014 Jun 19;509(7505):397-401. doi: 10.1038/nature13264.

Metabolism and ageing are intimately linked. Compared with ad libitum feeding, dietary restriction consistently extends lifespan and delays age-related diseases in evolutionarily diverse organisms. Similar conditions of nutrient limitation and genetic or pharmacological perturbations of nutrient or energy metabolism also have longevity benefits.

Recently, several metabolites have been identified that modulate ageing; however, the molecular mechanisms underlying this are largely undefined. Here we show that α-ketoglutarate (α-KG), a tricarboxylic acid cycle intermediate, extends the lifespan of adult Caenorhabditis elegans.

ATP synthase subunit β is identified as a novel binding protein of α-KG using a small-molecule target identification strategy termed drug affinity responsive target stability (DARTS). The ATP synthase, also known as complex V of the mitochondrial electron transport chain, is the main cellular energy-generating machinery and is highly conserved throughout evolution.

Although complete loss of mitochondrial function is detrimental, partial suppression of the electron transport chain has been shown to extend C. elegans lifespan.

We show that α-KG inhibits ATP synthase and, similar to ATP synthase knockdown, inhibition by α-KG leads to reduced ATP content, decreased oxygen consumption, and increased autophagy in both C. elegans and mammalian cells.

We provide evidence that the lifespan increase by α-KG requires ATP synthase subunit β and is dependent on target of rapamycin (TOR) downstream.

Endogenous α-KG levels are increased on starvation and α-KG does not extend the lifespan of dietary-restricted animals, indicating that α-KG is a key metabolite that mediates longevity by dietary restriction.

Our analyses uncover new molecular links between a common metabolite, a universal cellular energy generator and dietary restriction in the regulation of organismal lifespan, thus suggesting new strategies for the prevention and treatment of ageing and age-related diseases.

PMID: 24828042

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Bzzz! Are fruitflies like us?

Posted in Cell Biology, Signaling & Cell Circuits, Curation, Genome Biology, Metabolomics, Molecular Genetics & Pharmaceutical, Nutrigenomics, Proteomics, Regenerative Biology and Medicine, RNA Biology, Cancer and Therapeutics, Signaling, Translational Research, Translational Science, tagged cell regulation, fruit fly, RNA, Transcriptomics on July 7, 2014| Leave a Comment »

Larry H. Bernstein, MD, FCAP, Curator

http://pharmaceuticalintelligence.com/7/7/2014/Bzzz! Are fruitflies like us?

We are following closely the developments in genomics that have had a progression since the Double-Helix dogma served the Nobel Prize to Watson and Crick, and that achievement led to the completion of a provisional Human Genome at the birth of the 21st century. Since then there has been exploration of cellular regulation, signaling pathways, and protein-protein as well as protein membrane interactions in eukaryotes. But we can go further back prior to the double-helix and remind ourselves of the huge contributions that led up to the double helix. This was a time of great research that set the tone for what is now called molecular biology. We associate the work with the genetic studies of Thomas Hunt Morgan on the fruit fly. There may yet be a new chapter that is stradling the gap between DNA, RNA and transcription turning toward a deeper understanding of gene expression and organ specificities. Is it a new beginning? There is certainly going to be a deeper understanding of the several roles of RNA as well as proteins.

The Gateway Opens

THOMAS HUNT MORGAN AT COLUMBIA UNIVERSITY
Genes, Chromosomes, and the Origins of Modern Biology
Eric R. Kandel, MD
2000 recipent of Nobel Prize in Medicine

University Professor & Kavli Professor of Brain Science,
Co-director, Mind Brain Behavior Initiative
Director, The Kavli Institute for Brain Science
Senior Investigator, Howard Hughes Medical Institute
Columnia University

When future historians turn to examine the major intellectual accomplishments of the twentieth century, they will undoubtedly give a special place to the extraordinary achievements in biology, achievements that have revolutionized our understanding of life’s processes and of disease. Important intimations of what was to happen in biology were already apparent in the second half of the nineteenth century. Darwin had delineated the evolution of animal species, Mendel had discovered some basic rules about inheritance, and Weissman, Roux, Driesch, de Vries, and other embryologists were beginning to decipher how an organism develops from a single cell. What was lacking at the end of the nineteenth century, however, was an overarching sense of how these bold advances were related to one another.

The insight that unified these three fields- heredity, evolution, and development- and set biology on the course toward its current success came only at the beginning of the twentieth century. It derived from the discovery that the gene, localized to specific positions on the chromosome, was at once the unit of Mendelian heredity, the driving force for Darwinian evolution, and the control switch for development. This remarkable discovery can be traced directly to one person and to one institution: Thomas Hunt Morgan and Columbia University. Much as Darwin’s insights into the evolution of animal species first gave coherence to nineteenth-century biology as a descriptive science, Morgan’s findings about genes and their location on chromosomes helped transform biology into an experimental science.

“ aware that abstract thinking, remote from, and even antagonistic to the study of nature, leads easily into dogma, taboos and fettering of free thinking because it does not carry its own corrective, the recourse to factual evidence. The scientist, therefore, with all respect for the many facets of the human mind, is more impressed by the revolutions in thinking brought about by great factual discoveries, which by their very nature lead to generalizations which change at once the outlook of many, if not all, lines of thought.”

. . . . the rise and development of genetics to mature age is another instance of an all-comprising and all-affecting generalization based upon an overwhelming body of integrated facts, . . . [and] will rank in the history of science with such other great events ..”

–Richard B. Goldschmidt, The Impact of Genetics Upon Science (1950)

Even more important, Morgan’s discoveries made it possible to address a series of questions regarding the function and structure of genes. What is their chemical nature? How do genes duplicate themselves? What goes wrong when genes mutate? How do genes provide the basis for understanding genetic disease? How do genes determine the properties of cells, the development of organisms, and the course of evolution?

Thomas Hunt Morgan

Morgan

Eric Kandel

New Study of Fruit Fly Genome Reveals Complexity of RNA and Provides a Model for Studying Mechanisms for Hereditary Diseases in Humans

July 7, 2014

This investigation of the fruit fly’s transcriptome—the complete collection of the genome’s RNA—unearthed thousands of new genes, transcripts, and proteins

Scientists have teased another level of information out of the genome. This time, the new insights were developed from studies of the fruit fly’s transcriptome. This knowledge will give pathologists another channel of information that may be useful in developing assays to support more precise diagnosis and therapeutic decisions.

The findings were published in a recent issue of Nature. The study focused on the transcriptome—a complete collection of the genome’s RNA—of the common fruit fly−Drosophila melangogaster.

Why Studies of the Fruit Fly Are Useful

The fruit fly has been used as a genetics model to study human genetics for more than a 100 years. Not only are they easy to care for and work with, but they share 75% of the same genes as humans. Today, the fruit fly genome has emerged as a critical tool tor understanding human biology and disease, by providing an understanding of genes and life processes that are conserved over extensive evolutionary changes.

The research consortium included 41 researchers from 11 universities and institutes that are members of the National Human Genome Research Institute’s Model Organism Encyclopedia of DNA Elements, called modENCODE for short. This project used state-of-the-art gene sequencing to study all of the expressed RNAs produced by a genome in greater detail than ever before accomplished.

RNA Sequenced in Diverse Tissues at Different Stages of Development

RNA was sequenced at different stages of development, in diverse tissues, in cells growing in culture, and in flies stressed by environmental contaminants, stated a IU press release issued by Indiana University Bloomington (IUB).

The modENCODE study revealed that the fruit fly genome is far more complex than previously suspected. These new findings suggest that this also may be true for the genomes of higher animals. Specifically, the researchers found that:

a small set of genes in the nervous system is responsible for much of the complexity;
long regulatory and antisense RNA (asRNA), a single-stranded RNA complementary to a messenger RNA transcribed within a cell, are prominent during gonadal development;
splicing factors, proteins involved in controlling maturation of RNAs, are themselves spliced in complex ways; and,
the fruit fly transcriptome undergoes major changes in response toenvironmental stressors.

How Study of Fruit Fly RNA Benefits Human Genome Research

“The modENCODE work is intended to provide a new baseline for research using Drosophila,” declared Peter Cherbas, Ph.D., an IUB Professor Emeritus of Biology and one of 10 IUB researchers who served as co-authors of the study. “The goal is to provide researchers working on particular processes with much of the detailed background information they would otherwise need to collect for themselves.

Click here for photo
Peter Cherbas, Ph.D. (pictured), Professor Emeritus of Biology at Indiana University Bloomington, says that the modENCORE study of the fruit fly’s complete RNA answered a lot of questions about the genome of organisms, but raised even more questions that science will want to answer. (Photo copyright Indiana University Bloomington.)

“As usual in science, we’ve answered a number of questions and raised even more,” observed Cherbas. “For example, we identified 1,468 new genes, of which 536 were found to reside in previously uncharacterized gene-free zones.”

“We think these results could influence gene regulation research in all animals,” added Thom Kaufman, Ph.D., IUB Distinguished Professor of Biology who also co-authored the study. “This exhaustive study also identified a number of phenomena previously reported only in mammals, and that alone is really telling about the versatility of Drosophila melanogaster as a model organism. The new work provides a number of new potential uses for this powerful model system,” he stressed.

Click here for photo
Thom Kaufman, Ph.D. (pictured), Indiana University Bloomington Distinguished Professor of Biology, says that the modENCORE study provides a powerful model for studying gene regulation in all organisms. (Photo copyright Indiana University Bloomington.)

Impact of Environmental Stressors on Gene Expression

Both Kaufman and Cherbas cited perturbation experiments that identified genes and transcripts. The new genes were identified after subjecting adult fruit flies to heat and cold shock, then exposing them to heavy metals, caffeine and the herbicide paraquat. Fruit fly larvae were treated with heavy metals, caffeine, ethanol, or the insecticide rotenone.

These environmental stressors generated small changes in the expression level of thousands of genes. One treatment experiment resulted in four newly modeled genes being expressed altogether differently, noted the researchers. Perturbation experiments, in fact, revealed a total of 5,249 transcript models for 811 genes.

In fact, the findings from these perturbation experiments mirror similar findings made following the 2010 British Petroleum Deepwater Horizon oil spill in the Gulf of Mexico. Researchers studying the impact on marsh fishes found that, similar to the fruit flies, these fish responded to chronic hydrocarbon exposure with a number of expressions beyond the heat shock pathway. These expressions included the down regulation of genes encoding eggshell and yolk proteins.

The response overlap between species indicates that the modENCODE consortium may have identified a conserved metazoan [animal] stress response that enhances metabolism and suppresses genes involved in reproduction.

What This Means for Pathologists and Laboratory Professionals

This study is significant for pathologists and medical laboratory professionals because it peels away another layer of information encoded in DNA and RNA. The findings of this study also show how genomic knowledge is moving to the next level in the quest to understand the origins of disease.
—by Patricia Kirk

Study of complete RNA collection of fruit fly uncovers unprecedented complexity

IU plays key role in consortium; 1,468 new genes discovered March 17, 2014

BLOOMINGTON, Ind. — Scientists from Indiana University are part of a consortium that has described the transcriptome of the fruit fly Drosophila melanogaster in unprecedented detail, identifying thousands of new genes, transcripts and proteins.

In the new work, published Sunday in the journal Nature, scientists studied the transcriptome — the complete collection of RNAs produced by a genome — at different stages of development, in diverse tissues, in cells growing in culture, and in flies stressed by environmental contaminants. To do so, they used contemporary sequencing technology to sequence all of the expressed RNAs in greater detail than ever before possible.

The paper shows that the Drosophila genome is far more complex than previously suspected and suggests that the same will be true of the genomes of other higher organisms. The paper also reports a number of novel, particular results: that a small set of genes used in the nervous system are responsible for a disproportionate level of complexity; that long regulatory and so-called “antisense” RNAs are especially prominent during gonadal development; that “splicing factors” (proteins that control the maturation of RNAs by splicing) are themselves spliced in complex ways; and that the Drosophila transcriptome undergoes large and interesting changes in response to environmental stresses.

The importance of Drosophila melanogaster as a model system cannot be overstated. Using it, the mechanisms of heredity were worked out about 100 years ago. Today, as biologists have developed increasing appreciation of how well genes and critical life processes are conserved over long evolutionary distances, flies have emerged as critical tools for understanding human biology and disease. Drosophila research is an area that has long had associations with IU, beginning with Nobel Laureate Herman J. Muller.

IU has 10 co-authors on the paper from the IU Bloomington College of Arts and Sciences’ Department of Biology and the university’s Center for Genomics and Bioinformatics. They are included among the 41 co-authors from 11 universities and institutes that are members of the National Human Genome Research Institute’s Model Organism Encyclopedia of DNA Elements project, or modENCODE. Among the IU co-authors are Professor Emeritus of Biology Peter Cherbas, who helped manage the expansive project, and Distinguished Professor of Biology Thom Kaufman, who helped oversee design of the project and the production of biological samples.

“The modENCODE work is intended to provide a new baseline for research using Drosophila,” Cherbas said. “The goal is to provide researchers working on particular processes with much of the detailed background information they would otherwise need to collect for themselves.

“As usual in science, we’ve answered a number of questions and raised even more. For example, we identified 1,468 new genes, of which 536 were found to reside in previously uncharacterized gene-free zones.”

“We think these results could influence gene regulation research in all animals,” Kaufman said. “This exhaustive study also identified a number of phenomena previously reported only in mammals, and that alone is really telling about the versatility of Drosophila melanogaster as a model organism. The new work provides a number of new potential uses for this powerful model system.”

An example they pointed to was the perturbation experiments that identified new genes and transcripts. New genes were identified in experiments where adults were challenged with heat shock, cold shock, exposure to heavy metals, the drug caffeine and the herbicide paraquat, while larvae were treated with heavy metals, caffeine, ethanol or the insecticide rotenone.

Those environmental stresses resulted in small changes in expression level at thousands of genes; and in one treatment, four newly modeled genes were expressed altogether differently. In total, 5,249 transcript models for 811 genes were revealed only under perturbed conditions.

As did the flies in this new research, scientists who studied the Deepwater Horizon incident in the Gulf of Mexico found that marsh fishes responding to chronic hydrocarbon exposure had a number of expressional responses beyond the heat shock pathway, including the down regulation of genes encoding eggshell and yolk proteins as did the flies. To see this response overlap across phyla means the consortium may have identified a conserved metazoan stress response involving enhanced metabolism and the suppression of genes involved in reproduction.

Indiana University co-authors with Cherbas and Kaufman were co-first author Robert Eisman, Justen Andrews, Lucy Cherbas, Brian D. Eads, David Miller, Keithanne Mockaitis, Johnny Roberts and Dayu Zhang. All were associated with the Department of Biology and/or the Center for Genomics and Bioinformatics.

“Diversity and dynamics of the Drosophila transcriptome,” published March 16 in the journal Nature, also included 31 other co-authors whose affiliations were with the University of California, Berkeley; Lawrence Berkeley National Laboratory; University of Connecticut Health Center; Cold Spring Harbor Laboratory; Sloan-Kettering Institute; National Institute of Diabetes and Digestive and Kidney Diseases; RIKEN Yokohama Institute (Japan); Harvard Medical School; and Howard Hughes Medical Institute.

Antisense RNA

From Wikipedia, the free encyclopedia

Antisense RNA (asRNA) is a single-stranded RNA that is complementary to a messenger RNA (mRNA) strand transcribed within a cell. Some authors have used the term micRNA (mRNA-interfering complementary RNA) to refer to these RNAs but it is not widely used.^[1]

Antisense RNA may be introduced into a cell to inhibit translation of a complementary mRNA by base pairing to it and physically obstructing the translation machinery.^[2] ^[3] This effect is therefore stoichiometric. An example of naturally occurring mRNA antisense mechanism is the hok/sok system of the E. coli R1 plasmid. Antisense RNA has long been thought of as a promising technique for disease therapy; the only such case to have reached the market is the drug fomivirsen. One commentator has characterized antisense RNA as one of “dozens of technologies that are gorgeous in concept, but exasperating in [commercialization]”.^[4] Generally, antisense RNA still lack effective design, biological activity, and efficient route of administration.^[5]

Historically, the effects of antisense RNA have often been confused with the effects of RNA interference (RNAi), a related process in which double-stranded RNA fragments called small interfering RNAs trigger catalytically mediated gene silencing, most typically by targeting the RNA-induced silencing complex (RISC) to bind to and degrade the mRNA. Attempts to genetically engineer transgenic plants to express antisense RNA instead activate the RNAi pathway, although the processes result in differing magnitudes of the same downstream effect; gene silencing. Well-known examples include the Flavr Savr tomato and two cultivars of ringspot-resistant papaya.^[6]^[7]

Transcription of longer cis-antisense transcripts is a common phenomenon in the mammalian transcriptome.^[8] Although the function of some cases have been described, such as the Zeb2/Sip1 antisense RNA, no general function has been elucidated. In the case of Zeb2/Sip1,^[9] the antisense noncoding RNA is opposite the 5′ splice site of an intron in the 5’UTR of the Zeb2 mRNA. Expression of the antisense ncRNA prevents splicing of an intron that contains a ribosome entry site necessary for efficient expression of the Zeb2 protein. Transcription of long antisense ncRNAs is often concordant with the associated protein-coding gene,^[10] but more detailed studies have revealed that the relative expression patterns of the mRNA and antisense ncRNA are complex.^[11]^[12]

Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase

Structure of the N-terminal domain of the yeast Hsp90 chaperone

Pincer movement of Hsp90 coupled to the ATPase cycle. NTD = N-terminal domain, MD = middle domain, CTD = C-terminal domain.

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Health benefit of anthocyanins from apples and berries noted for men

Posted in Glycobiology: Biopharmaceutical Production, Pharmacodynamics and Pharmacokinetics, Health Economics and Outcomes Research, Healthcare costs and reimbursement, Indigent Nutrition, Inferential analysis, Innovations in Neurophysiology & Neuropsychology, Metabolomics, Molecular Genetics & Pharmaceutical, Neurodegenerative Diseases, Neurohumoral Transmission, Nutrigenomics, Nutrition, Nutritional Supplements: Atherogenesis, lipid metabolism, Personalized and Precision Medicine & Genomic Research, Population Health Management, Nutrition and Phytochemistry, Signaling, Skilled Nursing Facilities, Systemic Inflammatory Response Related Disorders, Translational Effectiveness, Translational Research, Translational Science, Uninsured and Underinsured, tagged anthocyanins, Bias measurement tools, flavonoids, fruits, Parkinsons disease on July 6, 2014| Leave a Comment »

Larry H Bernstein, MD, FCAP, Curator

http://pharmaceuticalintelligence.com/6/7/2014/Health benefit of anthocyanins from apples and berries noted for men

After significant studies have been completed, particularly on a relationship between anthocyanins consumption and decreasd risk of Parkinson’s Disease in men, it is unclear why a comparable effect is not seen in women. This would lead one to ask questions about predominant time course of development in relationship to androgen activity. Pre- and postmenopausal status would seem to make no difference. It is reported that the anthocyanins cross the blood brain barrier. There are other questions that need to be raised. There is a decline in the production of transthyretin by the choroid plexus in the elderly – not sex related – with an elevation of homocysteine that is reciprocal to decline in transthyretin-RBP complex, that is related to AD. This is mediated by cystathionine-beta synthase, and involves matrix metalloproteinases. A mechanism for Parkinson’s Disease has been postulated to be related to Parkin gene expression, but how does this work, and why do we see the sex assymetry?

Eating flavonoids protects men against Parkinson’s disease

General Diet, Missed – Medical Breakthroughs • Tags: Anthocyanin, Flavonoid, Harvard University,Health, Neurology, Parkinson, Parkinson Disease, University of East Anglia

http://healthresearchreport.me/ 07 Apr 2012

Men who eat flavonoid-rich foods such as berries, tea, apples and red wine significantly reduce their risk of developing Parkinson’s disease, according to new research by Harvard University and the University of East Anglia (UEA).

Published today in the journal Neurology ®, the findings add to the growing body of evidence that regular consumption of some flavonoids can have a marked effect on human health. Recent studies have shown that these compounds can offer protection against a wide range of diseases including heart disease, hypertension, some cancers and dementia.

This latest study is the first study in humans to show that flavonoids can protect neurons against diseases of the brain such as Parkinson’s.

Around 130,000 men and women took part in the research. More than 800 had developed Parkinson’s disease within 20 years of follow-up. After a detailed analysis of their diets and adjusting for age and lifestyle, male participants who ate the most flavonoids were shown to be 40 per cent less likely to develop the disease than those who ate the least. No similar link was found for total flavonoid intake in women.

The research was led by Dr Xiang Gao of Harvard School of Public Health in collaboration with Prof Aedin Cassidy of the Department of Nutrition, Norwich Medical School at UEA.

“These exciting findings provide further confirmation that regular consumption of flavonoids can have potential health benefits,” said Prof Cassidy.

“This is the first study in humans to look at the associations between the range of flavonoids in the diet and the risk of developing Parkinson’s disease and our findings suggest that a sub-class of flavonoids called anthocyanins may have neuroprotective effects.”

Prof Gao said: “Interestingly, anthocyanins and berry fruits, which are rich in anthocyanins, seem to be associated with a lower risk of Parkinson’s disease in pooled analyses. Participants who consumed one or more portions of berry fruits each week were around 25 per cent less likely to develop Parkinson’s disease, relative to those who did not eat berry fruits. Given the other potential health effects of berry fruits, such as lowering risk of hypertension as reported in our previous studies, it is good to regularly add these fruits to your diet.”

Flavonoids are a group of naturally occurring, bioactive compunds found in many plant-based foods and drinks. In this study the main protective effect was from higher intake of anthocyanins, which are present in berries and other fruits and vegetables including aubergines, blackcurrants and blackberries. Those who consumed the most anthocyanins had a 24 per cent reduction in risk of developing Parkinson’s disease and strawberries and blueberries were the top two sources in the US diet.

The findings must now be confirmed by other large epidemiological studies and clinical trials.

Parkinson’s disease is a progresssive neurological condition affecting one in 500 people, which equates to 127,000 people in the UK. There are few effective drug therapies available. Dr Kieran Breen, director of research at Parkinson’s UK said: “This study raises lots of interesting questions about how diet may influence our risk of Parkinson’s… there are still a lot of questions to answer and much more research to do before we really know how important diet might be for people with Parkinson’s.”

Eating berries may lower risk of Parkinson’s

Missed – Medical Breakthroughs • Tags: Berry, Doctor of Philosophy, Flavonoid, Parkinson,Parkinson Disease, Xiang Gao

http://healthresearchreport.me/ Public release date: 13-Feb-2011

ST. PAUL, Minn. –New research shows men and women who regularly eat berries may have a lower risk of developing Parkinson’s disease, while men may also further lower their risk by regularly eating apples, oranges and other sources rich in dietary components called flavonoids. The study was released today and will be presented at the American Academy of Neurology’s 63rd Annual Meeting in Honolulu April 9 to April 16, 2011.

Flavonoids are found in plants and fruits and are also known collectively as vitamin P and citrin. They can also be found in berry fruits, chocolate, and citrus fruits such as grapefruit.

The study involved 49,281 men and 80,336 women. Researchers gave participants questionnaires and used a database to calculate intake amount of flavonoids. They then analyzed the association between flavonoid intakes and risk of developing Parkinson’s disease. They also analyzed consumption of five major sources of foods rich in flavonoids: tea, berries, apples, red wine and oranges or orange juice. The participants were followed for 20 to 22 years.

During that time, 805 people developed Parkinson’s disease. In men, the top 20 percent who consumed the most flavonoids were about 40 percent less likely to develop Parkinson’s disease than the bottom 20 percent of male participants who consumed the least amount of flavonoids. In women, there was no relationship between overall flavonoid consumption and developing Parkinson’s disease. However, when sub-classes of flavonoids were examined, regular consumption of anthocyanins, which are mainly obtained from berries, were found to be associated with a lower risk of Parkinson’s disease in both men and women.

“This is the first study in humans to examine the association between flavonoids and risk of developing Parkinson’s disease,” said study author Xiang Gao, MD, PhD, with the Harvard School of Public Health in Boston. “Our findings suggest that flavonoids, specifically a group called anthocyanins, may have neuroprotective effects. If confirmed, flavonoids may be a natural and healthy way to reduce your risk of developing Parkinson’s disease.”
May 10, 2013

Could eating peppers prevent Parkinson’s?

Missed – Medical Breakthroughs • Tags: American Neurological Association, Annals of Neurology,Group Health Cooperative, Nicotine, Parkinson, Parkinson’s disease, Solanaceae, University of Washington

Contact: Dawn Peters sciencenewsroom@wiley.com 781-388-8408 Wiley

Dietary nicotine may hold protective key

New research reveals that Solanaceae—a flowering plant family with some species producing foods that are edible sources of nicotine—may provide a protective effect against Parkinson’s disease. The study appearing today inAnnals of Neurology, a journal of the American Neurological Association and Child Neurology Society, suggests that eating foods that contain even a small amount of nicotine, such as peppers and tomatoes, may reduce risk of developing Parkinson’s.

Parkinson’s disease is a movement disorder caused by a loss of brain cells that produce dopamine. Symptoms include facial, hand, arm, and leg tremors, stiffness in the limbs, loss of balance, and slower overall movement. Nearly one million Americans have Parkinson’s, with 60,000 new cases diagnosed in the U.S. each year, and up to ten million individuals worldwide live with this disease according to the Parkinson’s Disease Foundation. Currently, there is no cure for Parkinson’s, but symptoms are treated with medications and procedures such as deep brain stimulation.

Previous studies have found that cigarette smoking and other forms of tobacco, also a Solanaceae plant, reduced relative risk of Parkinson’s disease. However, experts have not confirmed if nicotine or other components in tobacco provide a protective effect, or if people who develop Parkinson’s disease are simply less apt to use tobacco because of differences in the brain that occur early in the disease process, long before diagnosis.

For the present population-based study Dr. Susan Searles Nielsen and colleagues from the University of Washington in Seattle recruited 490 patients newly diagnosed with Parkinson’s disease at the university’s Neurology Clinic or a regional health maintenance organization, Group Health Cooperative. Another 644 unrelated individuals without neurological conditions were used as controls. Questionnaires were used to assess participants’ lifetime diets and tobacco use, which researchers defined as ever smoking more than 100 cigarettes or regularly using cigars, pipes or smokeless tobacco.

Vegetable consumption in general did not affect Parkinson’s disease risk, but as consumption of edible Solanaceae increased, Parkinson’s disease risk decreased, with peppers displaying the strongest association. Researchers noted that the apparent protection from Parkinson’s occurred mainly in men and women with little or no prior use of tobacco, which contains much more nicotine than the foods studied.

“Our study is the first to investigate dietary nicotine and risk of developing Parkinson’s disease,” said Dr. Searles Nielsen. “Similar to the many studies that indicate tobacco use might reduce risk of Parkinson’s, our findings also suggest a protective effect from nicotine, or perhaps a similar but less toxic chemical in peppers and tobacco.” The authors recommend further studies to confirm and extend their findings, which could lead to possible interventions that prevent Parkinson’s disease.

###

This study is published in Annals of Neurology. Media wishing to receive a PDF of this article may contact sciencenewsroom@wiley.com.

Full citation: “Nicotine from Edible Solanaceae and Risk of Parkinson Disease.” Susan Searles Nielsen, Gary M. Franklin, W.T. Longstreth Jr, Phillip D. Swanson and Harvey Checkoway. Annals of Neurology; Published May 9, 2013 (DOI:10.1002/ana.23884).

URL Upon Publication: http://doi.wiley.com/10.1002/ana.23884

Author Contact: To arrange an interview with Dr. Susan Searles Nielsen, please contact Leila Gray with the University of Washington Health Sciences News Office at +1 206-685-0381 or at leilag@uw.edu.

About the Journal

Annals of Neurology, the official journal of the American Neurological Association and the Child Neurology Society, publishes articles of broad interest with potential for high impact in understanding the mechanisms and treatment of diseases of the human nervous system. All areas of clinical and basic neuroscience, including new technologies, cellular and molecular neurobiology, population sciences, and studies of behavior, addiction, and psychiatric diseases are of interest to the journal. The journal is published by Wiley on behalf of the
American Neurological Association and Child Neurology Society. For more information, please visit http://onlinelibrary.wiley.com/journal/10.1002/ana.

Flavonoids from berries shown to protect men against Parkinson’s disease

December 19, 2013 · by MrT

by: John Phillip, John is a Certified Nutritional Consultant and Health Researcher

(NaturalNews) Past research bodies have confirmed the health-protective effect of a natural diet rich in flavonoids to protect against a wide range of diseases including heart disease, hypertension, some cancers, and dementia. Researchers from Harvard University and the University of East Anglia have published the result of a study in the journalNeurology that demonstrates how these plant-based phytonutrients can significantly lower the risk of developing Parkinson’s disease, especially in men.

Flavonoids from healthy foods such as berries, tea, apples, and red wine cross the delicate blood-brain barrier to protect neurons against neurologic diseases such as Parkinson’s. This large scale study included more than 130,000 men and women participants that were followed for a period of twenty years. During this time, more than 800 individuals developed Parkinson’s disease.

A diet high in flavonoids from berries lowers Parkinson’s disease risk by forty percent

After a detailed analysis of their diets and adjusting for age and lifestyle, male participants who ate the most flavonoids were shown to be forty percent less likely to develop the disease than those who ate the least. No similar link was found for total flavonoid intake in women.

”This was the first study to examine the connection between flavonoid consumption and the development of Parkinson’s disease. The findings suggest that a sub-class of flavonoids called anthocyanins may exhibit neuroprotective effects. Participants consuming one or more portions of berry fruits each week were around twenty-five percent less likely to develop Parkinson’s disease, relative to those who did not eat berry fruits.

Flavonoids are the bioactive, naturally occurring chemical compounds found in many plant-based foods and drinks.

This study demonstrated the main protective effect was from the consumption of anthocyanins, which are present in berries and other fruits and vegetables including aubergines, blackcurrants, and blackberries. Strawberries and blueberries are the two most common sources of flavonoids in the US diet, contributing to a twenty-four percent lowered risk in this research.

Parkinson’s disease is among a group of chronic diseases presently affecting one in 500 people, with new cases on the rise. Drug therapies are ineffective and bear significant side effects.

Nutrition experts recommend adding a minimum of three to five servings of flavonoids to your diet each week. Include all varieties of berries, apples, and green tea to guard against Parkinson’s disease and other neurodegenerative illnesses.

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The Discovery and Properties of Avemar – Fermented Wheat Germ Extract: Carcinogenesis Suppressor

Posted in Anaerobic Glycolysis, Biomedical Measurement Science, Ca2+ triggered activation, CANCER BIOLOGY & Innovations in Cancer Therapy, Discovery process, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Drug Toxicity, Experimental validation, FDA, CE Mark & Global Regulatory Affairs: process management and strategic planning - GCP, GLP, ISO 14155, Historical relevance, Intellectual Property, Innovations, Commercialization, Investment in technological breakthrough, International Global Work in Pharmaceutical, Interviews with Scientific Leaders, ISO 10993 for Product Registration: FDA & CE Mark for Development of Medical Devices and Diagnostics, Metabolomics, Nutrition, Oxidative phosphorylation, Phosphorylation, Population Health Management, Nutrition and Phytochemistry, Proteomics, Scientific & Biotech Conferences: Press Coverage, Signaling, Translational Science, Ubiquitinylation, tagged alternative medicine, Avemar, Chemotherapy, complementary medicine, Dietary supplement, experimental cancer research, fermented wheat germ extract, functional foods, gene expression, glucose consumption, pancreatic carcinoma, regulation of metabolism, RNA, tyrosine phosphorylation on June 7, 2014| Leave a Comment »

Larry H Bernstein, MD, FCAP, Contributor

Article ID #143: The Discovery and Properties of Avemar – Fermented Wheat Germ Extract: Carcinogenesis Suppressor. Published on 6/7/2014

WordCloud Image Produced by Adam Tubman

http://pharmaceuticalintelligence.com/5-6-2014/larryhbern/ The Discovery_and_Properties_of_Avemar – Fermented_ Wheat_Germ_Extract:_Carcinogenesis_Suppressor

The following discussion will be a review of the current interest in Avemar, a nontoxic, fermentation product of wheat germ extract, garnering interest with respect to alternative and complementary medicinal use.

Extracts from an interview by Sandra Cascio with Mate Hidvegi

Mate’s Transylvania Professor Lajos David was the organizer of the Department of Pharmacy of the University of Szeged in the 1920’s. He was elected as the Dean of the Faculty of Medicine, the first and only pharmacist who reached this high position at the University since. Dr. Hidvegy’s grandfather was a devout Roman catholic, who publicly opposed Nazi persecution of Jews during the Holocaust. One of his colleagues and, perhaps his best friend, was Albert SzentGyorgyi, the Nobel laureate who discovered vitaminC. SzentGyorgyi moved to the United States after World War II, where he turned to studies of muscle biochemistry. In his later years he turned to cancer research. He theorized that a revolutionary anticancer drug could be based upon vitamin C combined with methoxysubstituted benzoquinones, the precursors of which can be found in wheat germ. After completion of the PhD, Dr. Hidvegi spent two years with the Wheat Grain Trust in Winnipeg, Canada, before returning to Hungary in 1990. He decided to followthepathwaythat SzentGyorgyi was now engaged intocompletehisgoals.He contacted anoldfriend,GaborFodor, a brilliantchemist, also a collaborator withSzentGyorgyiincancerresearch.

He wasinvited by Hermann Esterbauer, the head of the Institute of Biochemistry at the University of Graz, to work in his laboratory. Thanks to the generosity of Professor Esterbauer, he accomplished much at Graz together with his student, Dr. Rita Farkas. It was soon after Szent-Gyorgyi’s death when, with the help of Dr. Fodor, they prepared the chemicals to make the drug Szent-Gyorgyi had intended to make, with encouragement from the great quantum biochemist, Janos Ladik. They made wheat germ extracts with the highest free benzoquinone content.This required a fermentation process to liberate the benzoquinone moieties from the chemical bonds which keep them in natural forms: in glycosides. He recalls the purple colored active molecules in the fermentation liquid. Living cells with their exo and endoenzymes are used to split bonds and make new molecules. This is also true for the manufacturing process of Avemar. This extract contains new molecules which cannot be found elsewhere.

“WhenAvemar was voted by the majority of the more than 50,000 professionals for NutrAward, it became obvious that this product is of biological efficacy plus safety, and it is based on good science.” It received the financial support needed. From this, he was able to complete the experiments and get the approval for the registration. The time arrived when he really had to give a name to the product which had only had a code name. One late night it just came: Avemar, from the Latin prayer: Ave Maria.

Avemar with widely used chemotherapeutic drugs completely inhibited the development of metastases. Exploring its whole activity profile might even take a lifetime of research. So far he has supervised Avemar research done in Hungary, Israel, the United States, Austria, Italy, Spain, Slovakia, the Czech Republic, Germany,the United Kingdom, Russia, Australia, Korea, Vietnam. It has been a good experience to see the scientific interest it has generated worldwide. In 2009, Dr. Hidvegy received an invitation from the Nobel laureate, James Watson, codiscoverer of DNA’s double helix. It was a great honor. Avemar, he hopes,will be a significant cancer drug.

Mate Hidvegi was born in Budapest, Hungary, in 1955. He studied, then taught at what is now Budapest University of Technology and Economics. After finishing university, he worked in the cereal industry and was codeveloper of patented feed advisory system based on near infrared ingredient data. In Hungary, Hidvegi was one of the pioneers in the development of technologies for large scale production of instantized extracts for therapeutic use.

Carcinogenesis vol.22 no.10 pp.1649–1652, 2001

Wheat germ extract inhibits experimental colon carcino-genesis in F-344 rats

Attila Zalatnai, Karoly Lapis, Bela Szende, Erzsebet Raso, Andros Telekes, Akos Resetar, and Mate Hidvegi

It has been demonstrated for the ﬁrst time that a wheat germ extract prevents colonic cancer in laboratory animals. Four-week-old inbred male F-344 rats were used in the study. Colon carcinogenesis was induced by azoxy-methane (AOM). Ten rats served as untreated controls (group 1). For the treatment of the animals in group 2, AOM was dissolved in physiologic saline and the animals were given three weekly subcutaneous injections at 15 mg/kg body weight (b/w). In two additional groups Avemar (MSC), a fermented wheat germ extract standardized to 2,6-dimethoxy-p-benzoquinone was administered as a tentative chemo-preventive agent. MSC was dissolved in water and was given by gavage at a dose of 3 g/kg b/w once a day. In group 3, animals started to receive MSC 2 weeks prior to the ﬁrst injection of AOM daily and continuously thereafter until they were killed 32 weeks later. In group 4 only the basal diet and MSC were administered. At the end of the experiment all the rats were exsanguinated under a light ether anesthesia and necropsied. Percentage of animals developing colon tumors and number of tumors per animals: group 1 – 0 and 0; group 2– 83.0 and 2.3; group 3 – 44.8 (P ≤ 0.001) and 1.3 (P ≤ 0.004); group 4 – 0 and 0. All the tumors were histologically neoplastic. The numbers of the aberrant crypt foci (ACF) per area (cm²) in group 2 were 4.85 while in group 3 the ACF numbers were 2.03 only (P ≤ 0.0001).

Table I. Macroscopic ﬁndings in the large intestines of F-344 rats treated with MSC or MSC + AOM

No. of animals w/tumorw

Average
# tumors

Average
diameter

1	Untreated controls (10)	0/10	0/10
2.	AOM (47)	39/47 (83.0%)	2.3 + 0.21 (range 1–8)	2.35 + 0.25
3.	MSC + AOM (29)	13/29 (44.8%)	1.3 + 0.17 (range 1–3)	2.21 + 0.12
4.	MSC (9)	0/9	0/9

Fig. 1. Experimental schedule. Colon carcinogenesis was induced by three consecutive s.c. doses of AOM 1 week apart in F-344 rats. Oral administration of MSC was started 2 weeks before the carcinogen treatments. All the animals were killed at the end of the experiment, e.g. on the 32nd week. (not shown)

Summing up, although the chemoprevention of colon cancers (and their pre-neoplastic lesions) has well and long been established and could be achieved by totally different compounds, the mechanisms have still remained to be clariﬁed. This is also true for MSC.

The exact mechanism by which the fermented wheat germ concentration can prevent colon cancer is still partly unknown. MSC did inhibit the AOM-induced ACF and colon neoplasm formation, the multiplicity of the tumors, apparently acting in the initiation phase. Regarding this, we can hypothesize that MSC acts as an immunomodulator.

Wheat Germ Extract Decreases Glucose Uptake and RNARibose Formation but Increases Fatty Acid Synthesis in MIAPancreatic Adenocarcinoma Cell

LG Boros, K Lapis, B Szende, R Tömösközi-Farkas, Ádám Balogh, …., and M Hidvégi

UCLA School of Medicine, Harbor-UCLA Research and Education Institute, Torrance, Ca.; First Institute of Pathology and Experimental Cancer Research, Semmelweis Medical University, Budapest, Hungary; Central Food Research Institute, Budapest, Hungary; Department of Surgery, Albert Szent-Gyorgyi Medical and Pharmaceutical Center, School of General Medicine, University of Szeged, Szeged, Hungary; Department of Biochemistry and Molecular Biology, Institut d’Investigacions Biomediques August Pi i Sunyer, University of Barcelona, Barcelona, Spain; andDepartment of Biochemistryand Food Technology, Technical University of Budapest and Biromedicina Company, Budapest, Hungary

Pancreas 2001; 23 (2), pp. 141–147

Summary: The fermented wheat germ extract with standardized composition has potent tumor inhibitory properties. The fermented wheat germ extract controls tumor propagation. The authors show that this extract induces profound metabolic changes in cultured MIA pancreatic adenocarcinoma cells when the [1,2- ¹³C₂] glucose isotope is used as the single tracer with biologic gas chromatography–mass spectrometry.

MIA cells treated with 0.1, 1, and 10 mg/mL wheat germ extract showed a dose-dependent decrease in cell glucose consumption, consumption, uptake of isotope into ribosomal RNA (2.4%, 9.4%, and 8.0%), and release of ¹³CO₂ . Conversely, direct glucose oxidation and ribose recycling in the pentose cycle showed a dose-dependent increase of 1.2%, 20.7%, and 93.4%. The newly synthesized fraction of cell palmitate and the ¹³C enrichment of acetyl units were also increased with all doses of wheat germ extract.

The fermented wheat germ extract controls tumor propagation primarily by regulating glucose carbon redistribution between cell proliferation–related and cell differentiation–related macromolecules. Wheat germ extract treatment is likely associated with the phosphor-ylation and transcriptional regulation of metabolic enzymes that are involved in glucose carbon redistribution between cell the direct oxidative degradation of glucose,proliferation–related structural and functional macromolecules(RNA, DNA) and the direct oxidative degradation and survival of pancreatic adenocarcinoma cells in culture.

Key Words: Pentose cycle—Ribose synthesis—Fermented wheat germ extract—Nonoxidative glucose metabolism—Cell proliferation—Avemar.

Fig 1 glu consumption of MIA pancreatic carcinoma cells in response to WGE

Figure 1. Glucose consumption of MIA pancreatic adenocarcinoma cells in response to increasing doses of fermented wheat germ extract (Avemar) treatment after 72 hours of culture. Glucose consumption (measured in milligrams) was estimated by the difference in media glucose content between Avemar-treated and control cultures. MIA cell glucose consumption was significantly inhibited in the presence of either 1 mg/mL (*p < 0.05) or 10 mg/mL (**p < 0.01) Avemar (x + SD; n = 6).

fig-3-rna-syn-of-mia-pancreatic-carcinoma-cells-in-response-to-wge.jpg

Figure 3. Ribosomal RNA synthesis of MIA pancreatic adenocarcinoma cells in response to increasing doses of fermented wheat germ extract (Avemar) treatment after 72 hours of culture. Glucose carbon incorporation into ribose isolated from ribosomal RNA is expressed as molar enrichment. The dose-dependent decrease in of rRNA after Avemar treatment indicates that ribosomal RNA synthesis is the primary site significantly affected by all doses of Avemar treatment with a maximum decrease of 29% after 10 mg/mL treatment (x + SD; n = 9; *p < 0.05, **p < 0.01).

changes in metabolic activity indicate that Avemar treatment affects cell metabolism primarily by decreasing glucose uptake and nucleic acid ribose synthesis while increasing glucose oxidation through the oxidative reactions of the pentose cycle and fatty acid synthesis from glucose carbon. The effect of Avemar treatment on lactate production and TCA cycle anapleurotic flux compared with glucose oxidation is less prominent

Fermented wheat germ extract induces apoptosis and downregulation of major histocompatibility complex class I proteins in tumor T and B cell lines

R FAJKA-BOJA, M HIDVÉGI, Y SHOENFELD, G ION, D DEMYDENKO, R TÖMÖSKÖZI-FARKAS, et al.

INTL J ONCOLOGY 2002; 20: 563-570.

Lymphocyte Signal Transduction Laboratory, Institute of Genetics, and Cytokine Group, Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged; Department of Biochemistry and Food Technology, Budapest University of Technology and Economics, Budapest, Hungary; Department of Medicine ‘B’, Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel; Central Food Research Institute; National Institute of Oncology; Biromedicina Co., Budapest, Hungary
Abstract. The fermented wheat germ extract (code name: on cyto-fluorimeter using a monoclonal antibody to the MSC, trade name: Avemar), with standardized benzoquinone non-polymorphic region of the human MHC class I. MSC content has been shown to inhibit tumor propagation and stimulated tyrosine phosphorylation of intracellular proteins metastases formation in vivo. The aim of this study was to understand the molecular and cellular mechanisms of the anti-tumor effect of MSC. Therefore, we have designed in vitro model experiments using T and B tumor lymphocytic cell lines. As a result of the MSC treatment, cell surface MHC class I proteins was downregulated by 70-85% compared to the non-stimulated control.

Prominent apoptosis of and the influx of extracellular Ca²⁺ resulted in elevation of the amount of the intracellular Ca²⁺ concentration. 20-40% was detected upon 24 h of MSC treatment of the cell lines. Apoptosis was measured with cytofluorimetry by staining the DNA with propidium iodide and detecting the ‘sub-G ’ cell population.

Tyrosine phosphorylation of intra-cellular proteins and elevation of the intracellular Ca²⁺ concentration were examined using immunoblotting with anti-phosphotyrosine antibody and cytofluorimetry by means of Ca²⁺ sensitive fluorescence dyes, Fluo-3AM and FuraRed-AM, respectively. MSC did not induce a similar degree of apoptosis in healthy peripheral blood mononuclear cells.

Inhibition of the cellular tyrosine phosphatase activity or Ca²⁺ influx resulted in the opposite effect – increasing or diminishing the Avemar induced apoptosis as well as the MHC class I downregulation. The level of the cell surface MHC class I molecules was analysed with indirect immunofluorescence. The benzoquinone component (2,6-dimethoxi-p-benzoquinone) in MSC induced similar apoptosis and downregulation of the MHC class I molecules in the tumor T and B cell lines to that of MSC. These results suggest that MSC acts on lymphoid tumor cells by reducing MHC class I expression and selectively promoting apoptosis of tumor cells on a tyrosine phosphorylation and Ca²⁺ influx dependent way. One of the components in MSC, 2,6-dimethoxi-p-benzoquinone was shown to be an important factor in MSC mediated cell response.

Abbreviations:MHC, major histocompatibility complex;NK, natural killer;DMBQ, 2,6-dimethoxi-p-benzoquinone; FCS, fetal calf serum;PBMC, peripheral bloodmononuclear cells; TCR, T cell receptor;BCR, B cell receptor; mAb, monoclonal antibody;PMSF,phenylmethyl-sulfonylfluoride;pNPP, para-nitrophenyl-phosphate; PHA,phytohemagglutinineKey words: fermented wheat germ extract, Avemar, MSC, 2+ benzoquinone, tyrosine phosphorylation, intracellular Ca , CD45, tyrosine phosphatase, MHC class I downregulation, apoptosis

fig-4-apoptosis-of-t-cell-lines-induced-by-avamer.jpg

Figure 4. Apoptosis of tumor T cell lines and healthy lymphocytes upon MSC treatment. Jurkat cells were treated with 1 mg/ml MSC or .3 µg/ml DMBQ and PBMC were treated with 1 mg/ml
MSC for 24 h (A) or Jurkat cells were treated for 12 h (thick line in panel B). Control cells were left unstimulated (black bars in panel A or thin line on panel B). Apoptotic cells were enumerated
with the DNA analysis of the ‘sub-G ’ population (A) or with staining the cells with FITC1 labeled Annexin V
(B). Representative experiments are shown. The difference between the % of apoptosis in the case of treated and non-treated Jurkat cells was significant (MSC, p<0.001, n=14; DMBQ, p<0.05, n=3,
using paired, two-tailed t-test). No difference was found for PBMC (n=2).

MSC treatment causes prominent apoptosis in lymphoid tumor cells but it does not induce apoptosis of healthy resting mononuclear cells. Moreover, although MSC blocks the proliferation of PBM cells stimulated with PHA, it does not induce apoptosis in PHA stimulated cells (data not shown).

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Cancer Labs at School of Medicine @ Technion: Janet and David Polak Cancer and Vascular Biology Research Center

Posted in Academic Publishing, Autologous Cell Therapy, Bio Instrumentation in Experimental Life Sciences Research, BioBanking, Biological Networks, Gene Regulation and Evolution, Biomarkers & Medical Diagnostics, Biomedical Measurement Science, BioSimilars, CANCER BIOLOGY & Innovations in Cancer Therapy, Cardiac muscle regeneration, Cardiovascular Pharmacogenomics, Cell Biology, Signaling & Cell Circuits, Chemical Biology and its relations to Metabolic Disease, Chemical Genetics, Circulating Progenitor Cells, Computational Biology/Systems and Bioinformatics, Cytoskeleton, Diagnostic Immunology, Drug Delivery Platform Technology, Drug Toxicity, Frontiers in Cardiology and Cardiovascular Disorders, Genome Biology, Genomic Testing: Methodology for Diagnosis, Human Immune System in Health and in Disease, Immunodiagnostics, Innovation in Immunology Diagnostics, Intellectual Property, Innovations, Commercialization, Investment in technological breakthrough, Interviews with Scientific Leaders, Personalized and Precision Medicine & Genomic Research, Pharmaceutical Analytics, Pharmaceutical R&D Investment, Pharmacogenomics, Pharmacologic toxicities, Population Health Management, Genetics & Pharmaceutical, Proteomics, Regenerative Biology and Medicine, Regulated Clinical Trials: Design, Methods, Components and IRB related issues, Scientist: Career considerations, Signaling, Stem Cells for Regenerative Medicine, Technology Transfer: Biotech and Pharmaceutical, Translational Science, Ubiquitinylation on May 28, 2014| Leave a Comment »

Cancer Labs at School of Medicine @ Technion

Reporter: Aviva Lev-Ari, PhD, RN

Article ID #139: Cancer Labs at School of Medicine @ Technion: Janet and David Polak Cancer and Vascular Biology Research Center. Published on 5/28/2014

WordCloud Image Produced by Adam Tubman

Janet and David Polak Cancer and Vascular Biology Research Center. The Rappaport Faculty of Medicine Research Institute and Faculty of Medicine, Technion – Israel Institute of Technology, Haifa, Israel

The center was established in 2003 to promote an in-depth interdisciplinary basic and clinical research on the control of cellular and molecular processes that are involved in cancer initiation and progression. We strongly believe that the understanding of basic biological processes that underlie normal development and their deregulation in cancer, is crucial for our ability to identify molecular targets for early detection, intervention, and cure of the disease. We are interested in a broad view of cancer – from the single malignantly transformed cell and its microenvironment, through the entire tumor in the animal. We focus on targeted ubiquitin-mediated degradation of key regulatory proteins that are involved in malignant transformation [Prof. Aaron Ciechanover (Nobel Prize in Chemistry 2004)], angiogenesis and cancer progression (Prof. Gera Neufeld), metastasis and tumor microenvironment (Prof. Israel Vlodavsky), as well as genetic and genomic dissection of embryonic and cancer transcriptional networks (Dr. Amir Orian). Towards these objectives, we combine molecular, biochemical, cell biological with Drosophila genetic and genomics experimental approaches, as well as employing advanced models of angiogenesis and metastasis.

We believe that scientific excellence and collegiality go together. Therefore, the center has an open and friendly atmosphere, creating a highly stimulating environment. The center is located in the 11th Floor of the Rappaport Faculty of Medicine building. It currently trains 45 graduate students, post-doctoral fellows, clinicians and researchers that are at the heart of our research. Formal and informal collaborations between individuals and laboratories are on-going and encouraged. We are running a series of joint seminars to which we invite researchers from Israel and abroad. The Center has advanced state-of-the-art microscopic and image analysis equipment, as well as other shared pieces of infrastructural equipment . The center is an integral part of the Faculty of Medicine and the Rappaport Research Institute which are home for excellent research groups, and enjoys their advanced Interdepartmental Equipment Unit. It is also adjacent to the Rambam Medical Center – the major hospital in the north of Israel – which provides us with access to rich clinical material and collaboration with clinicians. Many of them spend active research periods in our laboratories and bring the bench closer to the patient bed and vice versa. The Center is in an active phase of growth, and offers excellent research opportunities, space and facilities for students, post-doctoral fellows, and physicians.

Research Groups

The Ubiquitin System and Cellular Protein Turnover and Interactions	Immunity and Host Defense
Cardiovascular Biology	The Central Nervous System in Health and Disease
Developmental Biology and Cancer Research	Genetics

SOURCE

http://www.rappaport.org.il/Rappaport/Templates/ShowPage.asp?DBID=1&TMID=842&FID=76

The cancer and vascular biology research center was established in 2003 to promote an in-depth interdisciplinary basic and clinical research on the control of cellular and molecular processes that are involved in cancer development and progression. Our goal is to advance knowledge in fundamental biological questions that are highly relevant for cancer.


	The cancer and vascular biology research center was established in 2003 to promote an in-depth interdisciplinary basic and clinical research on the control of cellular and molecular processes that are involved in cancer development and progression. Our goal is to advance knowledge in fundamental biological questions that are highly relevant for cancer.

SOURCE

http://www.technioncancer.co.il/index.php

Home >> Research Groups

Aaron Ciechanover
Protein Turnover

Intracellular protein degradation and mechanisms of cancer

Israel Vlodavsky
Cancer Biology

Impact of heparanase and the tumor microenvironment on cancer progression: Basic aspects and clinical implications

Gera Neufeld
Tumor Progression & Angiogenesis

Blood vessels and tumor progression: The neuropilin connection

Amir Orian
Genetic Networks

Genetic networks in development and cancer

Home
About the Cancer Centers
Research Groups
Administration / Contact
Join – Us

Seminars and Events
Links
Beyond Science
Friends and supporters

Ms. Sigal Alfasi – Izrael, Center’s coordinator
e-mail: gsigal@tx.technion.ac.il
Tel: +972-4-829-5424
Fax: +972-4-852-3947

SOURCE

http://www.technioncancer.co.il/ResearchGroups.php

Yuval Shaked, PhD

Publications by Yuval Shaked, PhD

Assistant Professor of Molecular Pharmacology
PhD, 2004 – Hebrew University, Israel

Understanding host – tumor interactions during cancer therapy

Personalized medicine holds promise of better cures with fewer side effects for many diseases. Individualized cancer therapy is sometimes utilized after multiple attempts of standard therapies and is based on several considerations, such as tumor type, acquired resistance to a specific therapy, previous treatment protocols, and other tumor-related factors. We have recently demonstrated that many cancer therapies can induce pro-tumorigenic or metastatic effects that derive not only from the tumor cells themselves, but also from host cells within the tumor microenvironment. The focus of research in my laboratory is to identify, characterize, and seek ways to block such pro-tumorigenic host effects observed after anti-cancer therapy, and thus potentially improve the outcome of current cancer therapies. Our findings may foster a paradigm shift in cancer therapy by minimizing the gap between preclinical findings and the clinical setting, laying the foundation for development of entirely new strategies for improving cancer therapy.

SOURCE

http://www.rappaport.org.il/Rappaport/Templates/ShowPage.asp?DBID=1&TMID=610&FID=77&PID=0&IID=1268

Immunity and Host Defense – A Bibliography of Research @Technion

Posted in Biological Networks, Gene Regulation and Evolution, Biomarkers & Medical Diagnostics, Biomedical Measurement Science, CANCER BIOLOGY & Innovations in Cancer Therapy, Cancer Prevention: Research & Programs, Cell Biology, Signaling & Cell Circuits, Chemical Biology and its relations to Metabolic Disease, Chemical Genetics, Diagnostic Immunology, Drug Delivery Platform Technology, Drug Toxicity, FDA Regulatory Affairs, Genome Biology, Genomic Testing: Methodology for Diagnosis, Human Immune System in Health and in Disease, Immunodiagnostics, Innovation in Immunology Diagnostics, Intellectual Property, Innovations, Commercialization, Investment in technological breakthrough, Interviews with Scientific Leaders, Medical and Population Genetics, Molecular Genetics & Pharmaceutical, Personalized and Precision Medicine & Genomic Research, Pharmaceutical Analytics, Pharmaceutical R&D Investment, Pharmacogenomics, Pharmacologic toxicities, Population Health Management, Genetics & Pharmaceutical, Proteomics, Regulated Clinical Trials: Design, Methods, Components and IRB related issues, Scientist: Career considerations, Signaling, Technology Transfer: Biotech and Pharmaceutical, Translational Science on May 27, 2014| Leave a Comment »

Immunity and Host Defense – A Bibliography of Research @Technion

Reporter: Aviva Lev-Ari, PhD, RN

Article ID #138: Immunity and Host Defense – A Bibliography of Research @Technion. Published on 5/27/2014

WordCloud Image Produced by Adam Tubman

Antigen-Dependent Integration of Opposing Proximal TCR-Signaling Cascades Determines the Functional Fate of T Lymphocytes

2014

Shai Shen-Orr, PhD
Authors : Wolchinsky R, Hod-Marco M, Oved K, Shen-Orr SS, Bendall SC, Nolan GP, Reiter Y.

J Immunol. 2014 Mar 1;192(5):2109-19.

Identification of functionally important conserved trans-membrane residues of bacterial P(IB) -type ATPases

2013

Oded Lewinson, PhD
Authors : Zhitnitsky D, Lewinson O.

Mol Microbiol. 2013 Dec 19. doi: 10.1111/mmi.12495. [Epub ahead of print] PubMed PMID: 24350798.

Variability in the immune system: of vaccine responses and immune states

2013

Shai Shen-Orr, PhD
Authors : Shen-Orr SS, Furman D.

Curr Opin Immunol. 2013 Aug;25(4):542-7.

Computational deconvolution: extracting cell type-specific information from heterogeneous samples.

2013

Shai Shen-Orr, PhD
Authors : Shen-Orr SS, Gaujoux R.

Curr Opin Immunol. 2013 Oct 19. [Epub ahead of print] PubMed PMID: 24148234.

Challenges and promise for the development of human immune monitoring.

2013

Shai Shen-Orr, PhD
Authors : Shen-Orr S.

Rambam Maimonides Med J. 2012 Oct 31;3(4):e0023.

Homeostatic regulation of aging and rejuvenation in the B lineage cells

2013

Doron Melamed, PhD
Authors : Melamed D.

Crit Rev Immunol. 2013;33(1):41-56.

Variability in the immune system: of vaccine responses and immune states

2013

Shai Shen-Orr, PhD
Authors : Shen-Orr S, Furman D.

Curr Opin Immunol. 2013 Aug 13. doi:pii: S0952-7915(13)00113-1.

A single intact ATPase site of the ABC transporter BtuCD drives 5% transport activity yet supports full in-vivo vitamin B12 utilization.

2013

Oded Lewinson, PhD
Authors : Tal N, Ovcharenko E, Lewinson O.

Proc Natl Acad Sci U S A. (March 19 Epub ahead of print)

Apoptosis and other immune biomarkers predict influenza vaccine responsiveness.

2013

Shai Shen-Orr, PhD
Authors : Furman D, Jojic V, Kidd B, Shen-Orr S, Price J, Jarrell J, Tse T, Huang H, Lund P, Maecker HT, Utz PJ, Dekker CL, Koller D, Davis MM.

Molecular Systems Biology. 9, 659

The dual roles of inflammatory cytokines and chemokines in the regulation of autoimmune diseases and their clinical implications.

2013

Nathan Karin, PhD
Authors : Shachar, I., and N. Karin.

J Leukoc Biol 93:51-61.

Two molybdate/tungstate ABC transporters that interact very differently with their substrate binding proteins.

2013

Oded Lewinson, PhD
Authors : Vigonsky, Ovcharenko E, Lewinson O.

Proc Natl Acad Sci U S A. (March 19 Epub ahead of print)

Dissecting the Autocrine and Paracrine Roles of the CCR2-CCL2 Axis in Tumor Survival and Angiogenesis.

2012

Nathan Karin, PhD
Authors : Izhak, L., G. Wildbaum, S. Jung, A. Stein, Y. Shaked, and N. Karin.

PloS one 7:e28305

Dose-related effects of hyperoxia on the lung inflammatory response in septic rats

2012

Nitza Lahat, PhD
Authors : Waisman D, Brod V, Rahat MA, Amit-Cohen BC, Lahat N, Rimar D, Menn-Josephy H, David M, Lavon O, Cavari Y, Bitterman H.

Shock. 2012 Jan;37(1):95-102.

Robust and sensitive analysis of xMap bead arrays using SAxCyB.

2012

Shai Shen-Orr, PhD
Authors : Won JH, Goldberger O, Shen-Orr SS, David MM, Olshen RA.

Proc Natl Acad Sci U S A. 109, 2848-53.

The Entamoeba histolytica methylated LINE-binding protein EhMLBP provides protection against heat shock

2012

Serge Ankri, PhD
Authors : Katz S, Kushnir O, Tovy A, Siman Tov R, Ankri S.

Cell Microbiol. 2012 Jan;14(1):58-70

Hypoxia increases membranal and secreted HLA-DR in endothelial cells, rendering them T-cell activators.

2011

Nitza Lahat, PhD
Authors : Lahat N, Bitterman H, Weiss-Cerem L, Rahat MA.

Transpl Int. 2011 Oct;24(10):1018-26.

The Entamoeba histolytica methylated LINE-binding protein EhMLBP provides protection against heat shock.

2011

Serge Ankri, PhD
Authors : Katz S, Kushnir O, Tovy A, Siman Tov R, Ankri S.

Cell Microbiol. 2011 Sep 8. [Epub ahead of print]

Dose-Related Effects of Hyperoxia on the Lung Inflammatory Response in Septic Rats. Shoc

2011

Nitza Lahat, PhD
Authors : Waisman D, Brod V, Rahat MA, Amit-Cohen BC, Lahat N, Rimar D, Menn-Josephy H, David M, Lavon O, Cavari Y, Bitterman H.

2011 Sep 3. [Epub ahead of print]

Glucose starvation boosts Entamoeba histolytica virulence.

2011

Serge Ankri, PhD
Authors : Tovy A, Hertz R, Siman-Tov R, Syan S, Faust D, Guillen N, Ankri S.

PLoS Negl Trop Dis. 2011 Aug;5(8):e1247.

The binding activity of Mel-18 at the Il17a promoter is regulated by the integrated signals of the TCR and polarizing cytokines.

2011

Eur J Immunol. 2011 Aug;41(8):2424-35.

phosphorylation of SLP-76 at tyrosine 173 is required for activation of T and mast cells.

2011

Deborah Yablonski, PhD
Authors : Sela M, Bogin Y, Beach D, Oellerich T, Lehne J, Smith-Garvin JE, Okumura M, Starosvetsky E, Kosoff R, Libman E, Koretzky G, Kambayashi T, Urlaub H, Wienands J, Chernoff J, Yablonski D. Sequential

EMBO J. 2011 Jul 1;30(15):3160-72.

The binding activity of Mel-18 at the Il17a promoter is regulated by the integrated signals of the TCR and polarizing cytokines.

2011

Orly Avni, PhD
Authors : Hod-Dvorai R, Jacob E, Boyko Y, Avni O.

Eur J Immunol. 2011 Jun 15. [Epub ahead of print]

MMP expression in leaking filtering blebs and tears after glaucoma filtering surgery.

2011

Nitza Lahat, PhD
Authors : Mathalone N, Marmor S, Rahat MA, Lahat N, Oron Y, Geyer O.

Graefes Arch Clin Exp Ophthalmol. 2011 Mar 31. [Epub ahead of print]

B cell depletion reactivates B lymphopoiesis in the BM and rejuvenates the B lineage in aging.

2011

Doron Melamed, PhD
Authors : Keren Z, Naor S, Nussbaum S Golan K, Itkin T, Sasaki Y, Schmidt-Supprian M, Lapidot T, Melamed D.

Blood 117, 3104 – 3112.

Chronic B cell deficiency from birth prevents age-related alterations in the B lineage J.

2011

Doron Melamed, PhD
Authors : Keren Z, Averbuch D, Shahaf G, Zisman-Rozen S, Golan K, Itkin T, Lapidot T, Mehr R, Melamed D.

Immunol 187, 2140 – 2147.

Epigenetics in the unicellular parasite Entamoeba histolytica.

2010

Serge Ankri, PhD
Authors : Tovy A, Ankri S.

Future Microbiol. 2010 Dec;5:1875-84.

The MAPK/ERK and PI3K pathways additively coordinate the transcription of recombination-activating genes in B lineage cells

2010

Orly Avni, PhD
Authors : Novak R, Jacob E, Haimovich J, Avni O, Melamed D.

J Immunol. 2010 Sep 15;185(6):3239-47

A fusion protein encoding the second extracellular domain of CCR5 arrests chemokine-induced cosignaling and effectively suppresses ongoing experimental autoimmune encephalomyelitis

2010

Nathan Karin, PhD
Authors : Sapir Y, Vitenshtein A, Barsheshet Y, Zohar Y, Wildbaum G, Karin N.

J Immunol. 2010 Aug 15;185(4):2589-99.

Antigen-specific CD25- Foxp3- IFN-gamma(high) CD4+ T cells restrain the development of experimental allergic encephalomyelitis by suppressing Th17

2010

Nathan Karin, PhD
Authors : Wildbaum G, Zohar Y, Karin N.

Am J Pathol. 2010 Jun; 176(6):2764-75.

Circulating interleukin-10: association with higher mortality in systolic heart failure patients with elevated tumor necrosis factor-alpha

2010

Nitza Lahat, PhD
Authors : Amir O, Rogowski O, David M, Lahat N, Wolff R, Lewis BS.

Isr Med Assoc J. 2010 Mar;12(3):158-62.

In vitro tRNA Methylation Assay with the Entamoeba histolytica DNA and tRNA Methyltransferase Dnmt2 (Ehmeth) Enzyme

2010

Serge Ankri, PhD
Authors : Tovy A, Hofmann B, Helm M, Ankri S.

J Vis Exp. 2010 Oct 19;(44). pii: 2390. doi: 10.3791/2390.

Circulating interleukin-10: association with higher mortality in systolic heart failure patients with elevated tumor necrosis factor-alpha

2010

Nitza Lahat, PhD
Authors : Amir O, Rogowski O, David M, Lahat N, Wolff R, Lewis BS

Isr Med Assoc J. 2010 Mar;12(3):158-62

A distinct mechanism for the ABC transporter BtuCD-BtuF revealed by the dynamics of complex formation.

2010

Oded Lewinson, PhD
Authors : Lewinson O, Lee AT, Locher KP, Rees DC.

Nat Struct Mol Biol. 17, 332-8.

Extracting Cell-Type-Specific Gene Expression Differences from Complex Tissues.

2010

Shai Shen-Orr, PhD
Authors : Shen-Orr SS*, Tibshirani R*, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM*, Butte AJ*.

Nature Methods 7, 287-9.

The MAPK/ERK and PI(3)K Pathways Additively Coordinate the Transcription of Recombination-Activating Genes in B Lineage Cells.

2010

Doron Melamed, PhD
Authors : Novak R, Jacob E, Haimovich J, Avni O, Melamed D.

Immunol 185, 3239 – 3247.

Protein denitrosylation: enzymatic mechanisms and cellular functions

2009

Moran Benhar, PhD
Authors : Benhar, M., Forrester, M.T., Stamler, J.S.

Nat. Rev. Mol. Cell Biol. 10:721-32.

Psoriasis patients generate increased serum levels of autoantibodies to tumor necrosis factor-alpha and interferon-alpha

2009

Nathan Karin, PhD
Authors : Bergman R, Ramon M, Wildbaum G, Avitan-Hersh E, Mayer E, Shemer A, Karin N.

J Dermatol Sci. 2009 Oct 1. Epub

The role of macrophage-derived IL-1 in induction and maintenance of angiogenesis

2009

Nitza Lahat, PhD
Authors : Carmi Y, Voronov E, Dotan S, Lahat N, Rahat MA, Fogel M, Huszar M, White MR, Dinarello CA, Apte RN.

J Immunol. 2009 Oct 1;183(7):4705-14.

Insights into the mechanism of DNA recognition by the methylated LINE binding protein EhMLBP of Entamoeba histolytica

2009

Serge Ankri, PhD
Authors : Lavi T, Siman-Tov R, Ankri S.

Mol Biochem Parasitol. 2009 Aug;166(2):117-25. Epub 2009 Mar 20.

A novel recombinant fusion protein encoding a 20-amino acid residue of the third extracellular (E3) domain of CCR2 neutralizes the biological activity of CCL2

2009

Nathan Karin, PhD
Authors : Izhak L, Wildbaum G, Zohar Y, Anunu R, Klapper L, Elkeles A, Seagal J, Yefenof E, Ayalon-Soffer M, Karin N

J Immunol. 2009 Jul 1;183(1):732-9

Selective autoantibody production against CCL3‭ ‬is associated with human type 1‭ ‬diabetes mellitus and serves as a novel biomarker for its diagnosis

2009

Nathan Karin, PhD
Authors : Shehadeh N‭, ‬Pollack S‭, ‬Wildbaum G‭, ‬Zohar Y‭, ‬Shafat I‭, ‬Makhoul R‭, ‬Daod E‭,‬

J Immunol‭. ‬2009‭ ‬Jun 15‭;‬182‭(‬12‭):‬8104-9

The effect of 100% oxygen on intestinal preservation and recovery following ischemia-reperfusion injury in rats

2009

Nitza Lahat, PhD
Authors : Sukhotnik I, Brod V, Lurie M, Rahat MA, Shnizer S, Lahat N, Mogilner JG, Bitterman H.

Crit Care Med. 2009 Mar;37(3):1054-61.

Transcriptional regulation of GATA3 in T helper cells by the integrated activities of transcription factors downstream of the interleukin-4 receptor and T cell receptor

2009

Orly Avni, PhD
Authors : Scheinman EJ, Avni O.

J Biol Chem. 2009 30;284(5):3037-48.

TOLL-like receptor ligands stimulate aberrant class switch recombination in early B cell precursors

2008

Doron Melamed, PhD
Authors : Edry E, Azulay-Debby H, Melamed D.

Int Immunol. 2008 Dec;20(12):1575-85. Epub 2008 Oct 29.

EhMLBP is an essential constituent of the Entamoeba histolytica epigenetic machinery and a potential drug target

2008

Serge Ankri, PhD
Authors : Lavi T, Siman-Tov R, Ankri S.

Mol Microbiol. 2008 Jul;69(1):55-66. Epub 2008 May 12

Hypoxia enhances lysosomal TNF-α degradation in mouse peritoneal macrophages

2008

Nitza Lahat, PhD
Authors : Lahat, N., Rahat, M. A., Kinarty, A., Weiss-Cerem, L., Pinchevski, S., Bitterman, H.

Am J Physiol Cell Physiol 295, C2-12.

What do unicellular organisms teach us about DNA methylation?

2008

Serge Ankri, PhD
Authors : Harony H

Trends Parasitol. 2008 May;24(5):205-9. Epub 2008 Apr 9. PMID: 18403268 [PubMed – in process]

Regulated protein denitrosylation by cytosolic and mitochondrial thioredoxins

2008

Moran Benhar, PhD
Authors : Benhar, M., Forrester, M.T., Hess, D.T., Stamler, J.S.

Science 320:1050-4

Trichostatin A regulates peroxiredoxin expression and virulence of the parasite Entamoeba histolytica.

2008

Serge Ankri, PhD
Authors : Isakov E, Siman-Tov R, Weber C, Guillen N

Mol Biochem Parasitol. 2008 Mar;158(1):82-94.

Progress and prospects of gene inactivation in Entamoeba histolytica.

2008

Serge Ankri, PhD
Authors : Abed M

Exp Parasitol. 2008 Feb;118(2):151-5

Class switch recombination: a friend and a foe.

2007

Doron Melamed, PhD
Authors : Edry E.

Clin Immunol. 2007 Jun;123(3):244-51.

Native and fragmented fibronectin oppositely modulate monocyte secretion of MMP-9

2007

Nitza Lahat, PhD
Authors : Marom, B., Rahat, M. A., Lahat, N., Weiss-Cerem, L., Kinarty, A., Bitterman, H.

J Leukoc Biol 81, 1466-1476.

SLP-76 mediates and maintains activation of the Tec family kinase ITK via the T cell antigen receptor-induced association between SLP-76 and ITK.

2007

Deborah Yablonski, PhD
Authors : Bogin Y, Ainey C, Beach D

Proc Natl Acad Sci U S A. 2007 Apr 17;104(16):6638-43.

Dual role of SLP-76 in mediating T cell receptor-induced activation of phospholipase C-gamma1.

2007

Deborah Yablonski, PhD
Authors : Beach D, Gonen R, Bogin Y, Reischl IG

J Biol Chem. 2007 Feb 2;282(5):2937-46. Epub 2006 Dec 4.

Read the Article

B cell receptor editing in tolerance and autoimmunity.

2007

Doron Melamed, PhD
Authors : Azulay-Debby H.

Front Biosci. 2007 Jan 1;12:2136-47.

Genome-wide analysis of mRNA polysomal profiles with spotted DNA microarrays.

2007

Doron Melamed, PhD
Authors : Arava Y.

Methods Enzymol. 2007;431:177-201

Coadministration of plasmid DNA constructs encoding an encephalitogenic determinant and IL-10 elicits regulatory T cell-mediated protective immunity in the central nervous system.

2006

Nathan Karin, PhD
Authors : Schif-Zuck S, Wildbaum G, Karin N.

J Immunol. 2006 Dec 1;177(11):8241-7.

Sensing DNA methylation in the protozoan parasite Entamoeba histolytica.

2006

Serge Ankri, PhD
Authors : Lavi T, Isakov E, Harony H, Fisher O, Siman-Tov R.

Mol Microbiol. 2006 Dec;62(5):1373-86.

Read the Article:

Modulation of matrix metalloproteinase-9 (MMP-9) secretion in B lymphopoiesis.

2006

Doron Melamed, PhD
Authors : Melamed D, Messika O, Glass-Marmor L, Miller A.

Int Immunol. 2006 Sep;18(9):1355-62.

A Pak- and Pix-dependent branch of the SDF-1alpha signalling pathway mediates T cell chemotaxis across restrictive barriers.

2006

Deborah Yablonski, PhD
Authors : Volinsky N, Gantman A, Yablonski D.

Biochem J. 2006 Jul 1;397(1):213-22. PMID: 16515536 [PubMed – in process]

DNA methylation and targeting of LINE retrotransposons in Entamoeba histolytica and Entamoeba invadens.

2006

Serge Ankri, PhD
Authors : Harony H, Bernes S, Siman-Tov R, Ankri S.

Mol Biochem Parasitol. 2006 May;147(1):55-63. Epub 2006 Feb 23. PMID: 16530279 [PubMed � in process]

Pleiotropic phenotype in Entamoeba histolytica overexpressing DNA methyltransferase (Ehmeth).

2006

Serge Ankri, PhD
Authors : Fisher O, Siman-Tov R, Ankri S.

Mol Biochem Parasitol. 2006 May;147(1):48-54. Epub 2006 Feb 9. PMID: 16497397 [PubMed � in process]

Hypoxia reduces the output of matrix metalloproteinase-9 (MMP-9) in monocytes by inhibiting its secretion and elevating membranal association

2006

Nitza Lahat, PhD
Authors : Rahat, M. A., Marom, B., Bitterman, H., Weiss-Cerem, L., Kinarty, A., Lahat, N.

J Leukoc Biol 79, 706-718.

Antisense inhibition of Entamoeba histolytica cysteine proteases inhibits colonic mucus degradation

2006

Serge Ankri, PhD
Authors : Moncada D, Keller K, Ankri S, Mirelman D, Chadee K.

Gastroenterology. 2006 Mar;130(3):721-30. PMID: 16530514 [PubMed � indexed for MEDLINE]

Beneficial autoimmunity participates in the regulation of rheumatoid arthritis.

2006

Nathan Karin, PhD
Authors : Zohar Y, Wildbaum G, Karin N.

Front Biosci. 2006 Jan 1;11:368-79. Review. PMID: 16146738 [PubMed – indexed for MEDLINE]

The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs.

2005

Doron Melamed, PhD
Authors : Lotan R, Bar-On VG, Harel-Sharvit L, Duek L, Melamed D, Choder M.

Genes Dev. 2005 Dec 15;19(24):3004-16. PMID: 16357218 [PubMed – indexed for MEDLINE]

Single point mutations in the zinc finger motifs of the human immunodeficiency virus type 1 nucleocapsid alter RNA binding specificities of the gag protein and enhance packaging and infectivity.

2005

Doron Melamed, PhD
Authors : Mark-Danieli M, Laham N, Kenan-Eichler M, Castiel A, Melamed D, Landau M, Bouvier NM, Evans MJ, Bacharach E.

J Virol. 2005 Jun;79(12):7756-67. PMID: 15919928 [PubMed – indexed for MEDLINE]

Molecular characterization of Entamoeba histolytica Rnase III and AGO2, two RNA interference hallmark proteins.

2005

Serge Ankri, PhD
Authors : Abed M, Ankri S.

Exp Parasitol. 2005 Jul;110(3):265-9. Epub 2005 Apr 7. PMID: 15955322 [PubMed � indexed for MEDLINE]

Targeted overexpression of IL-18 binding protein at the central nervous system overrides flexibility in functional polarization of antigen-specific Th2 cells.

2005

Nathan Karin, PhD
Authors : Schif-Zuck S, Westermann J, Netzer N, Zohar Y, Meiron M, Wildbaum G, Karin N.

Immunol. 2005 Apr 1;174(7):4307-15. PMID: 15778395 [PubMed – indexed for MEDLINE]

T cell receptor-induced activation of phospholipase C-gamma1 depends on a sequence-independent function of the P-I region of SLP-76.

2005

Deborah Yablonski, PhD
Authors : Gonen R, Beach D, Ainey C, Yablonski D.

J Biol Chem. 2005 Mar 4;280(9):8364-70. Epub 2004 Dec 28. PMID: 15623534 [PubMed – indexed for MEDLINE]

Naive, effector, and memory T lymphocytes efficiently scan dendritic cells in vivo: contact frequency in T cell zones of secondary lymphoid organs does not depend on LFA-1 expression and facilitates

2005

Nathan Karin, PhD
Authors : Westermann J, Bode U, Sahle A, Speck U, Karin N, Bell EB, Kalies K, Gebert A.

J Immunol. 2005 Mar 1;174(5):2517-24. PMID: 15728457 [PubMed – indexed for MEDLINE]

Antigen receptor signaling competence and the determination of B cell fate in B-lymphopoiesis.

2005

Doron Melamed, PhD
Authors : Keren Z, Melamed D.

Histol Histopathol. 2005 Jan;20(1):187-96. Review. PMID: 15578437 [PubMed – indexed for MEDLINE]

CD19 regulates positive selection and maturation in B lymphopoiesis: lack of CD19 imposes developmental arrest of immature B cells and consequential stimulation of receptor editing.

2005

Doron Melamed, PhD
Authors : Diamant E, Keren Z, Melamed D.

Blood ;105:3247-3254.

Entamoeba histolytica DNA methyltransferase (Ehmeth) is a nuclear matrix protein that binds EhMRS2, a DNA that includes a scaffold/matrix attachment region (S/MAR).

2005

Serge Ankri, PhD
Authors : Banerjee S, Fisher O, Lohia A, Ankri S.

Mol Biochem Parasitol. 2005 Jan;139(1):91-7. PMID: 15610823 [PubMed � indexed for MEDLINE]

Epigenetic and classical activation of Entamoeba histolytica heat shock protein 100 (EHsp100) expression.

2005

Serge Ankri, PhD
Authors : Bernes S, Siman-Tov R, Ankri S.

FEBS Lett;579:6395-6402.

T cell receptor-induced activation of phospholipase C-γ1 depends on a sequence-independent function of the P-I region of SLP-76.

2005

Deborah Yablonski, PhD
Authors : Gonen R, Beach D, Ainey C, Yablonski D.

J Biol Chem ;280:8364-8370.

Characterization of cytosine methylated regions and 5-cytosine DNA methyltransferase (Ehmeth) in the protozoan parasite Entamoeba histolytica.

2004

Serge Ankri, PhD
Authors : Fisher O, Siman-Tov R, Ankri S.

Nucleic Acids Res ;1:287-297.

Modification of ligandindependent B cell receptor tonic signals activates receptor editing in immature B lymphocytes.

2004

Doron Melamed, PhD
Authors : Keren Z, Diamant E, Ostrovsky O, Bengal E, Melamed D.

J Biol Chem ;279:13418-13424.

A failsafe mechanism for negative selection of isotype-switched B cell precursors is regulated by the Fas/FasL pathway

2003

Doron Melamed, PhD
Authors : Seagal J, Edry E, Keren Z, Leider N, Benny O, Machluf M, Melamed D.

J Exp Med ;198:1609-1619.

Beneficial autoimmunity to proinflammatory mediators restrains the consequences of self-destructive immunity.

2003

Nathan Karin, PhD
Authors : Wildbaum G, Nahir MA, Karin N.

Immunity;19:679-688.

T(H) cell differentiation is accompanied by dynamic changes in histone acetylation of cytokine genes.

2002

Orly Avni, PhD
Authors : Avni O, Lee D, Macian F, Szabo SJ, Glimcher LH, Rao A.

Nat Immunol ;3:643-651.

Tr1 cell-dependent active tolerance blunts the pathogenic effects of determinant spreading.

2002

Nathan Karin, PhD
Authors : Wildbaum G, Netzer N, Karin N.

J Clin Invest ;110:701-710.

A PAK1-PIX-PKL complex is activated by the T-cell receptor independent of Nck, Slp-76 and LAT.

2001

Deborah Yablonski, PhD
Authors : Ku GM, Yablonski D, Manser E, Lim L, Weiss A.

EMBO Journal ;20:457-465.

Identification of a phospholipase C-γ1 (PLC- γ1) SH3 domain-binding site in SLP-76 required for T-cell receptor-mediated activation of PLC-γ1 and NFAT

2001

Deborah Yablonski, PhD
Authors : Yablonski D, Kadlecek T, Weiss A.

Mol Cell Biol ;21:4208-4218.

C-C chemokineencoding DNA vaccines enhance breakdown of tolerance to their gene products and treat ongoing adjuvant arthritis.

2000

Nathan Karin, PhD
Authors : Youssef S, Maor G, Wildbaum G, Grabie N, Gour-Lavie A, Karin N.

J Clin Invest ;106:361-371.

Cell-type-restricted binding of the transcription factor NFAT to a distal IL-4 enhancer in vivo.

2000

Orly Avni, PhD
Authors : Agarwal S, Avni O, Rao A.

Immunity ;12:643-652.

T cell differentiation: a mechanistic view.

2000

Orly Avni, PhD
Authors : Avni O, Rao A.

Curr Opin Immunol; 12:654-659.

A systemic cytokine response defect stratifies older adults into distinct immune profiles.

1900

Shai Shen-Orr, PhD
Authors : Shen-Orr SS*, Furman D*, Kidd BA, Morgan A, Lovelace P, Rosenberg-Hasson Y, Maecker H, Mackey S, Dekker C, Butte AJ, Davis MM.

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Archive for the ‘Signaling’ Category

Genes, proteomes, and their interaction

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The Experience of a Patient with Thyroid Cancer

The Experience of a Patient with Thyroid Cancer

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Update on mitochondrial function, respiration, and associated disorders

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Bzzz! Are fruitflies like us?

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The Discovery and Properties of Avemar – Fermented Wheat Germ Extract: Carcinogenesis Suppressor

Extracts from an interview by Sandra Cascio with Mate Hidvegi

Wheat germ extract inhibits experimental colon carcino-genesis in F-344 rats

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Fermented wheat germ extract induces apoptosis and downregulation of major histocompatibility complex class I proteins in tumor T and B cell lines

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Archive for the ‘Signaling’ Category

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Heroes in Medical Research: Green Fluorescent Protein and the Rough Road in Science

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The Experience of a Patient with Thyroid Cancer

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Research on inflammasomes opens therapeutic ways for treatment of rheumatoid arthritis

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Eating flavonoids protects men against Parkinson’s disease

Eating berries may lower risk of Parkinson’s

Could eating peppers prevent Parkinson’s?

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Flavonoids from berries shown to protect men against Parkinson’s disease

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Extracts from an interview by Sandra Cascio with Mate Hidvegi

Wheat germ extract inhibits experimental colon carcino-genesis in F-344 rats

Wheat Germ Extract Decreases Glucose Uptake and RNARibose Formation but Increases Fatty Acid Synthesis in MIAPancreatic Adenocarcinoma Cell

Fermented wheat germ extract induces apoptosis and downregulation of major histocompatibility complex class I proteins in tumor T and B cell lines

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Cancer Labs at School of Medicine @ Technion

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Yuval Shaked, PhD

Assistant Professor of Molecular Pharmacology

Understanding host – tumor interactions during cancer therapy

Other Related articled published on this Open Access Online Scientific Journal included the following:

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Immunity and Host Defense – A Bibliography of Research @Technion

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