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Posts Tagged ‘food’

Relation of Diet and Cancer

Posted in CANCER BIOLOGY & Innovations in Cancer Therapy, Cancer Prevention: Research & Programs, Metabolomics, Nutrigenomics, Nutrition, Population Health Management, Genetics & Pharmaceutical, Population Health Management, Nutrition and Phytochemistry, tagged , , , , , on June 4, 2013| 1 Comment »

Reporter and Curator: Dr. Sudipta Saha, Ph.D.

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Word Cloud By Danielle Smolyar

Cancer is one of the most devastating and widespread diseases today. The development of cancer is a multi-step process involving genetic or epigenetic changes often occurring over a longer period of time. Moreover, cancer occurs in more or less all organs and tissues and is characterized by extensive heterogeneity both concerning the type and aggressiveness of the disease. Although some substantial progress in some areas has been made, there are still huge unmet needs in treatment methods and the efficacy of currently available drugs. The pharmaceutical industry has struggled with the ever increasing costs in drug development and unfortunately novel drugs have not seldom demonstrated only marginal improvement in efficacy often at the cost of quality of life of the patients. For these reasons, new approaches are focusing on disease prevention instead of only treating the symptoms. Recently, much attention has been paid to prevention of the disease in parallel to continuous drug discovery.

Intervention in food intake has been demonstrated to play an enormous role in both prevention as well as treatment of diseases. Numerous studies indicate a clear link between cancer and diet. The substantial development of sequencing technologies has resulted in access to enormous amounts of genomics information, which resulted in the establishment of nutrigenomics as an emerging approach to link genomics research to studies on nutrition. Increased understanding has demonstrated how nutrition can influence human health both at genetic and epigenetic levels. It investigates the effects of nutrition and bioactive food compounds on gene expression. This approach has allowed the investigation of the effect on nutrition on individuals with specific genetic features. Moreover, it has provided the basis for nutritional intervention in prevention and treatment of disease and the inauguration of personalized nutrition. However, differences in types of cancer, the level of aggressiveness, and their occurrence at different stages of life have seriously complicated the understanding of the effect of nutrition on cancer prevention and treatment. Other individual variations such as the amounts of food consumed, digestion, metabolism and other factors like geographical, ethnic and sociological diversity has hampered the identification of which food components are most important for human health. Dramatic dietary modifications have proven essential in reducing risk and even prevention of cancer. Moreover, intense revision of diet in cancer patients has revealed significant changes in gene expression and also has provided therapeutic efficacy even after short-term application.

Obviously, a multitude of diets have been evaluated, but probably the common factor for achieving both prophylactic and therapeutic responses is to consume predominantly diets rich in fruits, vegetables, fish and fibers and reduced quantities of especially red meat. There are numerous examples of how dietary intake can promote health on both a preventive as well as therapeutic level. Radical change in diet has resulted in dramatic changes in gene expression in prostate cancer patients revealing that many of those genes involved in cancer development were down-regulated. The importance of nutrigenomics as a multi-task approach involving genomics, proteomics, metabolomics, et cetera has further provided novel possibilities to address the effect of nutrition on human health. Despite encouraging findings on how dietary modifications can prevent disease and restore health, there are a number of factors which complicate the outcome. There are variations in response to dietary changes depending on age and gender. However, the vast amount of accumulated nutrigenomics data should not overshadow the needs to take into account other important factors such as lifestyle, social, geographical and economic factors affecting diet and health.

Source References:

http://www.lifescienceglobal.com/home/cart?view=product&id=121

http://www.frontiersin.org/Nutrigenomics/10.3389/fgene.2011.00091/abstract

http://www.sciencedirect.com/science/article/pii/S0002822308021871

http://ajcn.nutrition.org/content/89/5/1553S

http://www.sciencedirect.com/science/article/pii/S030438350800390X

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Metabolomics: its Applications in Food and Nutrition Research

Posted in Biological Networks, Gene Regulation and Evolution, Medical and Population Genetics, Metabolomics, Nutrigenomics, Nutrition, Personalized and Precision Medicine & Genomic Research, Population Health Management, Genetics & Pharmaceutical, Population Health Management, Nutrition and Phytochemistry, tagged , , , , , , , , , , , on May 12, 2013| 1 Comment »

Metabolomics: its Applications in Food and Nutrition Research

Reporter and Curator: Sudipta Saha, Ph.D.

 

Metabolomics is a relatively new field of “omics” research concerned with the high-throughput identification and quantification of small molecule (<1500 Da) metabolites in the metabolome. The metabolome is formally defined as the collection of all small molecule metabolites or chemicals that can be found in a cell, organ or organism. These small molecules can include a range of endogenous and exogenous chemical entities such as peptides, amino acids, nucleic acids, carbohydrates, organic acids, vitamins, polyphenols, alkaloids, minerals and just about any other chemical that can be used, ingested or synthesized by a given cell or organism.

Metabolomics is ideally positioned to be used in many areas of food science and nutrition research including food component analysis, food quality/authenticity assessment, food consumption monitoring and physiological monitoring in food intervention studies. However, the potential impact of metabolomics is still limited by two factors: (1) technology and (2) databases. In terms of instrumentation, it is clear that significant improvements need to be made to make metabolite detection and quantification technology more robust, automated and comprehensive. While promising advances have been made, current techniques are only capable of detecting perhaps 1/10th of the relevant metabolome. This expanded breadth and depth of coverage is particularly important in food and nutrition studies.

Many more reference spectral or chromatographic databases on metabolites, food components and phytochemicals need to be developed and made public. It is only through these databases that nutritionally relevant compounds can be routinely identified or quantified. Indeed a comprehensive effort, similar to that undertaken to annotate the human metabolome, needs to be made to complete and annotate the “food metabolome”. Similar efforts also need to be directed towards creating publicly accessible, comprehensive nutritional phenotype databases that include quantitative metabolomic (and other omic) data collected from diet-challenge or food intervention experiments. While these kinds of endeavours may take years to complete and cost millions of dollars, hopefully the food science community (and its funding agencies) will find a way of coordinating its activities to complete these efforts. Indeed, having public resource like a food metabolome database or a nutritional phenotype database could be as valuable to food scientists as GenBank has been to molecular biologists.

Source References:

http://www.sciencedirect.com/science/article/pii/S0924224408000770

http://www.sciencedirect.com/science/article/pii/B9780123945983000010

http://www.sciencedirect.com/science/article/pii/S092422440900226X

http://www.sciencedirect.com/science/article/pii/S1359644605036093

http://www.sciencedirect.com/science/article/pii/B9780080885049000520

http://www.sciencedirect.com/science/article/pii/B9780123744135000051

Other articles related to this topic were published on this Open Access Online Scientific Journal, including the following:

Ca2+ signaling: transcriptional control

Larry H. Bernstein, MD, FCAP, Reporter, RN 03/06/2013

http://pharmaceuticalintelligence.com/2013/03/06/ca2-signaling-transcriptional-control/

Harnessing Personalized Medicine for Cancer Management, Prospects of Prevention and Cure: Opinions of Cancer Scientific Leaders @ http://pharmaceuticalintelligence.com

Aviva Lev-Ari, PhD, RN 01/12/2013

http://pharmaceuticalintelligence.com/2013/01/12/harnessing-personalized-medicine-for-cancer-management-prospects-of-prevention-and-cure-opinions-of-cancer-scientific-leaders-httppharmaceuticalintelligence-com/

Breakthrough Digestive Disorders Research: Conditions affecting the Gastrointestinal Tract.

Aviva Lev-Ari, PhD, RN 12/12/2012

http://pharmaceuticalintelligence.com/2012/12/12/breakthrough-digestive-disorders-research-conditions-affecting-the-gastrointestinal-tract/

A Second Look at the Transthyretin Nutrition Inflammatory Conundrum

Larry H. Bernstein, MD, FCAP, Reporter, RN 12/03/2012

http://pharmaceuticalintelligence.com/2012/12/03/a-second-look-at-the-transthyretin-nutrition-inflammatory-conundrum/

Metabolic drivers in aggressive brain tumors

Prabodh Kandala, PhD, RN 11/11/2012

http://pharmaceuticalintelligence.com/2012/11/11/metabolic-drivers-in-aggressive-brain-tumors/

Metabolite Identification Combining Genetic and Metabolic Information: Genetic association links unknown metabolites to functionally related genes

Aviva Lev-Ari, PhD, RN 10/22/2012

http://pharmaceuticalintelligence.com/2012/10/22/metabolite-identification-combining-genetic-and-metabolic-information-genetic-association-links-unknown-metabolites-to-functionally-related-genes/

Advances in Separations Technology for the “OMICs” and Clarification of Therapeutic Targets

Larry H. Bernstein, MD, FCAP, Reporter, RN 10/22/2012

http://pharmaceuticalintelligence.com/2012/10/22/advances-in-separations-technology-for-the-omics-and-clarification-of-therapeutic-targets/

Expanding the Genetic Alphabet and linking the genome to the metabolome

Larry H. Bernstein, MD, FCAP, Reporter, RN 09/24/2012

http://pharmaceuticalintelligence.com/2012/09/24/expanding-the-genetic-alphabet-and-linking-the-genome-to-the-metabolome/

Therapeutic Targets for Diabetes and Related Metabolic Disorders

Aviva Lev-Ari, PhD, RN 08/20/2012

http://pharmaceuticalintelligence.com/2012/08/20/therapeutic-targets-for-diabetes-and-related-metabolic-disorders/

The Automated Second Opinion Generator

Larry H. Bernstein, MD, FCAP, Reporter, RN 08/13/2012

http://pharmaceuticalintelligence.com/2012/08/13/the-automated-second-opinion-generator/

 

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Benefits of Functional Foods in Nutrient Imbalance of Vulnerable Populations

Posted in Chemical Biology and its relations to Metabolic Disease, Metabolomics, Nutrigenomics, Nutrition, Nutritional Supplements: Atherogenesis, lipid metabolism, Population Health Management, Nutrition and Phytochemistry, tagged , , , , , , , , , , , , on March 24, 2013| 2 Comments »

Benefits of Functional Foods in Nutrient Imbalance of Vulnerable Populations

Reporter and Curator: Dr. Sudipta Saha, Ph.D.

There are clear distinctions between a food and a drug. Nutraceuticals, however, occupy a place between the two. Nutraceuticals are naturally derived phytochemicals with potential health benefits and without the characteristics of being essential nutrients. Foods that contain these non-essential substances with potential health benefits may qualify as “functional foods.” As defined by the Food and Nutrition Board of the National Academy of Sciences, the term functional food refers to foods that provide health benefits beyond basic nutrition. Examples of these are

  • psyllium seeds (soluble fiber),
  • soy foods (isoflavones),
  • cranberry juice (proanthocyanidins),
  • purple grape juice (resveratrol),
  • tomatoes (lycopene), and
  • green tea (catechins).

The bioactive components of functional foods:

  • flavonols,
  • monomeric and polymeric flavan-3-ols,
  • highly coloured anthocyanins, and
  • phenolic acids

may be increased in or added to traditional foods. An example is a genetically modified tomato high in lycopene, which has potent antioxidant capabilities.

The risk of nutrient imbalance is highest in vulnerable populations unable to access essential or conditionally essential nutrients. To a large extent, the

  • very young and the
  • frail elderly

are the select groups who might benefit most from alleviating this risk. The lack of adequate nutrition may be due to seasonal and unexpected losses of agricultural produce; however, poverty is a factor on a global scale as a result of growing economic disparities. The question then becomes what role functional foods offer to improve recognized population nutritional deficiencies. The range of work being done on functional foods is impressive, from

  • modified oils that contain heart-healthy ω-3 fatty acids to
  • cassava plants developed with an increased protein content to help counter malnutrition in developing nations.

However, the nutraceutical industry has responded to and relies on the untested expectations of the healthiest members of the world’s population rather than its more vulnerable ones. Due largely to economic causes, those in need are less likely to receive the benefits of nutraceuticals from whole foods or from manufactured foods or supplements. This is particularly striking where the source is locally available and extracted for commerce but is unaffordable or unavailable to the native population.

The rapid advances in biotechnology and functional foods confront us with a need to address the benefits of these with regard to improving health and managing or decreasing disease risks. Conventional dietary recommendations have focused on the consumption of fruits, vegetables, legumes, and whole grains, a decreased sugar intake, and an emphasis on plant oils, recommendations that have unproved benefits for the prevention of chronic diseases and that have complexities involving individual, environmental, and genetic influences.

Although the potential benefits of phytochemicals could have an impact on health status for vulnerable populations, the recommendations focused on plant foods do not address the primary concerns of the undernutrition associated with a poor quality of protein intake. Taken individually, plant sources do not provide a balanced amino acid profile necessary for protein synthesis, being deficient in lysine and/or methionine. Animal sources of protein, specifically meat and fish, also provide essential fatty acids not found in plant sources of protein and that may be otherwise limited. In addition, plants may contain antinutritional factors (wheat, cassava roots, cabbages, soy beans), and plant-based diets may be deficient in important essential nutrients.

Programs must focus on the sustainable production and local processing of indigenous products that can be used by needy populations to improve their nutritional intake and enhance economic stability. In addition, dietary recommendations must not exclude important sources of nutrition for more vulnerable populations by focusing primarily on plant-based sources of food, decreasing saturated fat, and de-emphasizing the importance of high-value biologic protein. The global economic crisis has touched the lives of 80% of the population in most developing countries with a threat to the development of a generation of children (approximately 250 million) who are most vulnerable in the first 2 years of life. An investment in nutrition in this circumstance has a high value, and the use of complementary food supplements to increase a meal’s nutrient content is warranted.

A recent proposal has concluded there are health benefits for foods and food constituents put together in a synergic diet pattern, suggesting that the interrelation between constituents within whole foods is significant, and has recommended dietary variety and the selection of nutrient-rich foods. Providing vulnerable populations with an adequate supply of whole foods should take precedence over the recommendation of food products in supplying not only essential macro- and micronutrients and energy but also phytochemicals whose value to the human diet is still to be determined.

Source References:

http://www.sciencedirect.com/science/article/pii/S0899900711003133

 

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Protein-folding Simulation: Stanford’s Framework for Testing and Predicting Evolutionary Outcomes in Living Organisms – Work by Marcus Feldman

Posted in Biological Networks, Gene Regulation and Evolution, Chemical Genetics, Computational Biology/Systems and Bioinformatics, Genome Biology, Interviews with Scientific Leaders, Medical and Population Genetics, Population Health Management, Genetics & Pharmaceutical, Proteomics, Statistical Methods for Research Evaluation, tagged , , , , , , , , , on March 16, 2013| 2 Comments »

Article 2.5:  Protein-folding Simulation: Stanford’s Framework for Testing and Predicting Evolutionary Outcomes in Living Organisms – Work by Marcus Feldman
 

Protein-folding Simulation: Stanford’s Framework for Testing and Predicting Evolutionary Outcomes in Living Organisms – Work by Marcus Feldman

Reporter: Aviva Lev-Ari, PhD, RN

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WordCloud Image Produced by Adam Tubman

UPDATED 9/16/2013

VIDEO CLIPS
Enzymes That Are Not Proteins: The Discovery of Ribozymes
Listen to past HHMI President Dr. Thomas Cech discussing his Nobel Prize-winning discovery of RNA’s catalytic properties.

http://www.hhmi.org/biointeractive/enzymes-are-not-proteins-discovery-ribozymes

Stanford Report, March 15, 2013

Long-term evolution is ‘surprisingly predictable,’ Stanford experiment shows

A protein-folding simulation shows that the debated theory of long-term evolution is not only possible, but that the outcomes are predictable. The Stanford experiment provides a framework for testing evolutionary outcomes in living organisms.

BY BJORN CAREY

L.A. CiceroVisiting scholar Mike Palmer left, and Professor Marcus FeldmanDr. Michael Palmer, left, and Professor Marcus Feldman, with co-author Arnav Moudgil (not pictured), found that the long-term evolutionary dynamics were surprisingly predictable in a model of protein folding and binding.

Two birds are vying for food. One bird’s beak is shaped, by virtue of a random mutation, such that it’s slightly more adept at cracking seeds. This sets the bird on the road toward acquiring more food, a better chance of scoring a mate and, most important, passing on its genetic endowment.

This individual’s success is an example of short-term evolution, the widely accepted Darwinian process of natural selection by which individual organisms that have better adapted to their surroundings prevail.

In recent years, however, some scientists have argued that natural selection occurs not just at the individual organism level, but also between lineages over the course of many generations. In a new study, Stanford biologists have demonstrated that not only is this long-term evolution possible, but that long-term evolutionary outcomes can be surprisingly predictable.

The group set up a computer simulation in which 128 lineages of proteins continuously folded into new shapes, competing to bind with other molecules, called ligands, in each new configuration. The better each protein could attach itself to the ligands, the more ligands it would scoop up, and the higher its fitness – that is, its average number of “offspring” – would be. The simulation was run for 10,000 generations.

Although the chaos of 128 lineages – a total of more than 16,000 individual proteins – mutating over thousands of generations might seem unpredictable, and that it would be nearly impossible for the same thing to happen twice, it’s actually the opposite.

“Even though things look complicated, the possible evolutionary trajectories are quite constrained,” said lead author Michael Palmer, a computational biologist at Stanford. “There are only a few viable mutations at any point, which makes the dynamics predictable and repeatable, even over the long term.”

The study, co-authored by Marcus Feldman, a biology professor at Stanford, and Stanford research biologist Arnav Moudgil, was recently published in the Journal of the Royal Society Interface.

In some experiments, the lineages that consistently came out on top in the long term were not initially the best adapted at binding to ligands. “The immediate fitness is not the only important thing,” Palmer said. “Yes, a lineage does have to survive in the short term. But just as important is how it is able to adapt to new and potentially variable environments over the longer term.”

A good example of this scenario is Darwin’s famous finches. It’s thought that individuals – perhaps just a single pair of birds – from a South American species ended up on the Galápagos Islands about 1 million years ago. Today their descendants have diversified into about 15 modern species. Some eat seeds, some eat insects, or flowers. Some eat ticks, or even drink the blood of other birds.

“If there was some catastrophe that removed one of those food sources, it might wipe out one or more of the 15 species, but the rest of the lineage – the descendants of that initial pair of birds – would persist,” Palmer said. “Now say there was a competing lineage that was great at cracking seeds, but unable to evolve to other diets due to some prior genetic constraint. The same catastrophe could wipe it out.”

The finding, and others like it, could represent a significant shift in viewpoint for biologists. For one thing, it means that in certain situations, scientists should look beyond the details at the level of the individual organism, as the evolutionary dynamics can be accurately understood as lineage selection.

It also has implications on a species’ genomic architecture, or how a genome is organized on the lineage level. While a lineage’s genome might primarily select for a particular set of traits in order for individuals to survive in the short term, in order to out-compete other lineages, it must also be able to adapt to new conditions over the long term.

“An individual can have a lucky mutation that produces an immediate adaptation,” said Palmer. “Or a lineage can have a lucky mutation that happens to position it to adapt to the range of environments it will experience over the next thousand generations. A single mutation can have a distinct short-term and long-term fitness.”

The authors believe that the work can be replicated in microorganisms, and are now hoping that microbiologists will apply the new metrics of selection in vitro.

“There is already some evidence in vitro that there is a lot of constraint on evolutionary trajectories,” Palmer said, “and we think we’ve come up with a good framework to quantify evolutionary predictability and long-term fitness.”

Media Contact

Michael Palmer, Biology: (415) 867-3653, mepalmer@charles.stanford.edu

Bjorn Carey, Stanford News Service: (650) 725-1944, bccarey@stanford.edu

SOURCE:

http://news.stanford.edu/news/2013/march/long-term-evolution-031513.html

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Arsenic levels in rice and rice products

Posted in Biological Networks, Gene Regulation and Evolution, Chemical Biology and its relations to Metabolic Disease, FDA Regulatory Affairs, Infectious Disease & New Antibiotic Targets, tagged , , , , , , , on September 19, 2012| Leave a Comment »

Reporter: Prabodh Kandala, PhD

As part of an ongoing and proactive effort to monitor food safety and address contaminants in food, the U.S. Food and Drug Administration today released preliminary data on arsenic levels in certain rice and rice products. The data are part of a larger FDA data collection and analysis about arsenic levels in rice and is based on the first set of approximately 200 samples of rice and rice products collected in the U.S. marketplace.

The FDA is in the process of collecting and analyzing a total of approximately 1,200 samples to examine the issue thoroughly. This data collection will be completed by the end of 2012. Once the data collection is completed, FDA will analyze these results and determine whether or not to issue additional recommendations.

Based on the currently available data and scientific literature the FDA does not have an adequate scientific basis to recommend changes by consumers regarding their consumption of rice and rice products.

“We understand that consumers are concerned about this matter. That’s why the FDA has prioritized analyzing arsenic levels in rice. The FDA is committed to ensuring that we understand the extent to which substances such as arsenic are present in our foods, what risks they may pose, whether these risks can be minimized, and to sharing what we know,” said FDA Commissioner Margaret A. Hamburg, M.D. “Our advice right now is that consumers should continue to eat a balanced diet that includes a wide variety of grains – not only for good nutrition but also to minimize any potential consequences from consuming any one particular food.”

There are two types of arsenic compounds found in water, food, air, and soil: organic and inorganic. Together, the two types are referred to as total arsenic.

The new data show how much inorganic arsenic the FDA found in its initial samples, which include various brands of rice (non-Basmati), Basmati rice, brown rice, rice cereals (puffed, non-puffed, hot cereal, and infant cereals), rice cakes, and rice milk.

The FDA’s analysis of these initial samples found average levels of inorganic arsenic for the various rice and rice products of 3.5 to 6.7 micrograms of inorganic arsenic per serving. Serving sizes varied depending on the rice product (for example, one serving of non-Basmati rice was equal to one cup cooked). A summary of the initial 200 sample findings can be found at www.fda.gov4.

While the FDA data is consistent with results that Consumer Reports published today, the initial data collection is a first step in the agency’s ongoing more thorough data analysis. There are many different types of rice and rice products that are grown in different areas and under different conditions. Further analysis is needed to assess how these variations may affect the results.

“It is critical to not get ahead of the science,” said FDA Deputy Commissioner for Foods Michael Taylor. “The FDA’s ongoing data collection and other assessments will give us a solid scientific basis for determining what action levels and/or other steps are needed to reduce exposure to arsenic in rice and rice products.”

Ref:

http://www.fda.gov/NewsEvents/Newsroom/PressAnnouncements/ucm319972.htm

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