Advertisements
Feeds:
Posts
Comments

Posts Tagged ‘bacteria’


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

 

The bacterial makeup of human milk is influenced by the mode of breastfeeding, according to a new study. Although previously considered sterile, breast milk is now known to contain a low abundance of bacteria. While the complexities of how maternal microbiota influence the infant microbiota are still unknown, this complex community of bacteria in breast milk may help to establish the infant gut microbiota. Disruptions in this process could alter the infant microbiota, causing predisposition to chronic diseases such as allergies, asthma, and obesity. While it’s unclear how the breast milk microbiome develops, there are two theories describing its origins. One theory speculates that it originates in the maternal mammary gland, while the other theory suggests that it is due to retrograde inoculation by the infant’s oral microbiome.

 

To address this gap in knowledge scientists carried out bacterial gene sequencing on milk samples from 393 healthy mothers three to four months after giving birth. They used this information to examine how the milk microbiota composition is affected by maternal factors, early life events, breastfeeding practices, and other milk components. Among the many factors analyzed, the mode of breastfeeding (with or without a pump) was the only consistent factor directly associated with the milk microbiota composition. Specifically, indirect breastfeeding was associated with a higher abundance of potential opportunistic pathogens, such as Stenotrophomonas and Pseudomonadaceae. By contrast, direct breastfeeding without a pump was associated with microbes typically found in the mouth, as well as higher overall bacterial richness and diversity. Taken together, the findings suggest that direct breastfeeding facilitates the acquisition of oral microbiota from infants, whereas indirect breastfeeding leads to enrichment with environmental (pump-associated) bacteria.

 

The researchers argued that this study supports the theory that the breast milk microbiome is due to retrograde inoculation. Their findings indicate that the act of pumping and contact with the infant oral microbiome influences the milk microbiome, though they noted more research is needed. In future studies, the researchers will further explore the composition and function of the milk microbiota. In addition to bacteria, they will profile fungi in the milk samples. They also plan to investigate how the milk microbiota influences both the gut microbiota of infants and infant development and health. Specifically, their projects will examine the association of milk microbiota with infant growth, asthma, and allergies. This work could have important implications for microbiota-based strategies for early-life prevention of chronic conditions.

 

References:

 

https://www.genomeweb.com/sequencing/human-breast-milk-microbiome-affected-mode-feeding#.XIOH0igzZPY

 

http://childstudy.ca/2019/02/13/breastmilk-microbiome-linked-to-method-of-feeding/

 

https://gizmodo.com/pumping-breast-milk-changes-its-microbiome-1832568169

 

https://www.sciencedaily.com/releases/2019/02/190213124445.htm

 

https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(19)30049-6

 

https://www.unicef.org.uk/babyfriendly/news-and-research/baby-friendly-research/infant-health-research/epigenetics-microbiome-research/

Advertisements

Read Full Post »


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

 

Clostridium difficile-associated disease, a significant problem in healthcare facilities, causes an estimated 15,000 deaths in the United States each year. Clostridium difficile, commonly referred to as C. diff, is a bacterium that infects the colon and can cause diarrhea, fever, and abdominal pain. Clostridium difficile-associated disease (CDAD) most commonly occurs in hospitalized older adults who have recently taken antibiotics. However, cases of CDAD can occur outside of healthcare settings as well.

 

Although antibiotics often cure the infection, C. diff can cause potentially life-threatening colon inflammation. People with CDAD usually are treated with a course of antibiotics, such as oral vancomycin or fidaxomicin. However, CDAD returns in approximately 20 percent of people who receive such treatment, according to the Centers for Disease Control and Prevention (CDC).

 

Multiple research studies have indicated that fecal microbiota transplantation (FMT) is an effective method for curing patients with repeat C. diff infections. However, the long-term safety of FMT has not been established. Although more research is needed to determine precisely how FMT effectively cures recurrent CDAD, the treatment appears to rapidly restore a healthy and diverse gut microbiome in recipients. Physicians perform FMT using various routes of administration, including oral pills, upper gastrointestinal endoscopy, colonoscopy, and enema.

 

A research consortium recently began enrolling patients in a clinical trial examining whether FMT by enema (putting stool from a healthy donor in the colon of a recipient) is safe and can prevent recurrent CDAD, a potentially life-threatening diarrheal illness. Investigators aim to enroll 162 volunteer participants 18 years or older who have had two or more episodes of CDAD within the previous six months.

 

Trial sites include Emory University in Atlanta, Duke University Medical Center in Durham, North Carolina, and Vanderbilt University Medical Center in Nashville, Tennessee. Each location is a Vaccine and Treatment Evaluation Unit (VTEU), clinical research sites joined in a network funded by the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health. This randomized, controlled trial aims to provide critical data on the efficacy and long-term safety of using FMT by enema to cure C. diff infections.

 

Volunteers will be enrolled in the trial after completing a standard course of antibiotics for a recurrent CDAD episode, presuming their diarrhea symptoms cease on treatment. They will be randomly assigned to one of two groups. The first group (108 people) will take an anti-diarrheal medication and receive a stool transplant (FMT) delivered by retention enema. The second group (54 people) will take an anti-diarrheal medication and receive a placebo solution delivered by retention enema.

 

Participants in either group who have diarrhea with stools that test positive for C. diff shortly after the enema will be given an active stool transplant for a maximum of two FMTs. If participants in either group have another C. diff infection after receiving two FMTs, then they will be referred to other locally available treatment options. Investigators will evaluate the stool specimens for changes in gut microbial diversity and infectious pathogens and will examine the blood samples for metabolic syndrome markers.

 

To learn more about the long-term outcomes of FMT, the researchers will monitor all participants for adverse side effects for three years after completing treatment for recurrent CDAD. Investigators will also collect information on any new onset of CDAD, related chronic medical conditions or any other serious health issues they may have.

 

References:

 

https://www.nih.gov/news-events/news-releases/clinical-trial-testing-fecal-microbiota-transplant-recurrent-diarrheal-disease-begins

 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4749851/

 

https://bmjopengastro.bmj.com/content/3/1/e000087

 

https://jamanetwork.com/journals/jama/fullarticle/2635633

 

https://www.hopkinsmedicine.org/gastroenterology_hepatology/clinical_services/advanced_endoscopy/fecal_transplantation.html

 

https://en.wikipedia.org/wiki/Fecal_microbiota_transplant

 

https://www.openbiome.org/about-fmt/

 

https://taymount.com/faecal-microbiota-transplantation-fmt

 

Read Full Post »


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

 

The trillions of microbes in the human gut are known to aid the body in synthesizing key vitamins and other nutrients. But this new study suggests that things can sometimes be more adversarial.

 

Choline is a key nutrient in a range of metabolic processes, as well as the production of cell membranes. Researchers identified a strain of choline-metabolizing E. coli that, when transplanted into the guts of germ-free mice, consumed enough of the nutrient to create a choline deficiency in them, even when the animals consumed a choline-rich diet.

 

This new study indicate that choline-utilizing bacteria compete with the host for this nutrient, significantly impacting plasma and hepatic levels of methyl-donor metabolites and recapitulating biochemical signatures of choline deficiency. Mice harboring high levels of choline-consuming bacteria showed increased susceptibility to metabolic disease in the context of a high-fat diet.

 

DNA methylation is essential for normal development and has been linked to everything from aging to carcinogenesis. This study showed changes in DNA methylation across multiple tissues, not just in adult mice with a choline-consuming gut microbiota, but also in the pups of those animals while they developed in utero.

 

Bacterially induced reduction of methyl-donor availability influenced global DNA methylation patterns in both adult mice and their offspring and engendered behavioral alterations. This study reveal an underappreciated effect of bacterial choline metabolism on host metabolism, epigenetics, and behavior.

 

The choline-deficient mice with choline-consuming gut microbes also showed much higher rates of infanticide, and exhibited signs of anxiety, with some mice over-grooming themselves and their cage-mates, sometimes to the point of baldness.

 

Tests have also shown as many as 65 percent of healthy individuals carry genes that encode for the enzyme that metabolizes choline in their gut microbiomes. This work suggests that interpersonal differences in microbial metabolism should be considered when determining optimal nutrient intake requirements.

 

References:

 

https://news.harvard.edu/gazette/story/2017/11/harvard-research-suggests-microbial-menace/

 

http://www.cell.com/cell-host-microbe/fulltext/S1931-3128(17)30304-9

 

https://www.ncbi.nlm.nih.gov/pubmed/23151509

 

https://www.ncbi.nlm.nih.gov/pubmed/25677519

 

http://mbio.asm.org/content/6/2/e02481-14

 

Read Full Post »


Bacterial synthetic factories

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Bacteria seeded with synthetic pathways

http://www.rsc.org/chemistryworld/2016/04/bacteria-living-chemical-synthesis

 

Chinese scientists have taken a biosynthetic pathway from plants and introduced it into bacteria to create potentially health-boosting chemicals. Their route provides an alternative to complicated chemical syntheses or farming hectares of crops.

Shared photosynthetic components between plant chloroplasts and cyanobacteria make these microbes ideal hosts for expressing foreign plant enzymes. Ping Xu and colleagues at the Shanghai Jiao Tong University have genetically engineered the cyanobacterium Synechococcus elongatusPC7942 with plant-derived enzymes. In total, the team created 18 bacterial strains expressing different combinations of enzymes. The different strains generate a variety of compounds with a six-carbon, phenyl group and three-carbon propene tail, called phenylpropanoids.

Phenylpropanoids perform diverse functions in plants, ranging from ultraviolet light protection to pathogen defence. One such compound, resveratrol, is made when the bacteria express the plant enzyme stilbene synthase downstream of enzymes tyrosine ammonia lyase and 4-coumarate:coenzyme A-ligase. Found in the skin of grapes and other berries, resveratrol reduces the risk of heart disease and is a valuable pharmaceutical commodity. Different versions of the engineered bacteria can also churn out the phenylpropanoid antioxidants caffeic acid, naringenin and coumaric acid.

The Shanghai Jia Tong University team genetically engineered cyanobacteria to produce compounds like flavonoids, stilbenes and curcuminoids usually only found in plants

http://www.rsc.org/chemistryworld/sites/default/files/upload/Photoautotrophic-platform_c6gc00317f-f1_630m.jpg

What’s more, the team added feedback-inhibition resistant enzymes to the bacteria so that the chemical yields would surpass physiological levels. Photosynthesis within the cyanobacteria generates the chemicals from just water, carbon dioxide and a few mineral nutrients.

The bacterial growth medium houses the products, but isolating them at an industrially relevant yield is currently the biggest challenge. However, by not needing to harvest crops, generating the compounds from bacteria is potentially more sustainable. Xu stresses the potential of this point: ‘For the production of 1 tonne of natural resveratrol, our method may save about 485 hectare of farmland at its current production level.’

‘The approach deftly sidesteps major economic challenges by targeting chemicals with high intrinsic value,’ comments Paul Fowler, executive director of the Wisconsin Institute for Sustainable Technology in the US.  A world-scale production plant under these circumstances is not a pre-requisite for commercialising this research.’

 REFERENCES

This article is free until 06 June 2016

J Ni et al, Green Chem., 2016, DOI: 10.1039/c6gc00317f

A photoautotrophic platform for the sustainable production of valuable plant natural products from CO2

Jun Ni,ab   Fei Tao,ab   Yu Wang,ab   Feng Yaoab and   Ping Xu
Many plant natural products have remarkable pharmacological activities. They are mainly produced directly by extraction from higher plants, which can hardly keep up with the surging global demand. Furthermore, the over-felling of many medicinal plants has undesirable effects on the ecological balance. In this study, we constructed a photoautotrophic platform with the unicellular cyanobacterium Synechococcus elongatus PCC7942 to directly convert the greenhouse gas CO2 into an array of valuable healthcare products, including resveratrol, naringenin, bisdemethoxycurcumin, p-coumaric acid, caffeic acid, and ferulic acid. These six compounds can be further branched to many other precious and useful natural products. Various strategies including introducing a feedback-inhibition-resistant enzyme, creating functional fusion proteins, and increasing malonyl-CoA supply have been systematically investigated to increase the production. The highest titers of these natural products reached 4.1–128.2 mg L−1 from the photoautotrophic system, which are highly comparable with those obtained by many other heterotrophic microorganisms using carbohydrates. Several advantages such as independence from carbohydrate feedstocks, functionally assembling P450s, and availability of plentiful NADPH and ATP support that this photosynthetic platform is uniquely suited for producing plant natural products. This platform also provides a green route for direct conversion of CO2 to many aromatic building blocks, a promising alternative to petrochemical-based production of bulk aromatic compounds.
Graphical abstract: A photoautotrophic platform for the sustainable production of valuable plant natural products from CO2

Read Full Post »


Molecular On/Off Switches in Bacterial Design

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Controlling Synthetic Bacteria

“Kill switches” ensure that genetically engineered bacteria survive only in certain environmental conditions.

By Kate Yandell | Dec 7, 2015   http://www.the-scientist.com//?articles.view/articleNo/44715/title/Controlling-Synthetic-Bacteria/

http://www.the-scientist.com/images/News/December2015/620ecoli.jpg

FLICKR, NIAID

Two synthetic gene circuits allow researchers to keep genetically engineered (GE) microbes alive only under specific conditions, and to kill them when their services are no longer needed. The circuits, described today (December 7) in Nature Chemical Biology,could help pave the path to safe diagnostics, therapies, or environmental remediation strategies that rely on GE bacteria.

“This is yet another step forward towards better biosafety and biocontainment based on certain aspects of existing technology,” said Guy-Bart Stan, a synthetic biologist at Imperial College London who was not involved in the study.

Study coauthor James Collins, a synthetic biologist at MIT, began to design these gene circuits, or “kill switches,” after becoming interested in using GE microbes for diagnostic and therapeutic purposes. “We were motivated to begin working on the topic as synthetic biology has moved increasingly toward real-world applications,” Collins told The Scientist. Other groups are working to engineer microbes for bioremediation and industrial processes, among other things.

But with genetic modification comes the concern that scientists will create new and uncontrollable species that outcompete or share their genes with wild-type organisms, permanently altering the environment or endangering people’s health.

Earlier this year, two research teams led by Yale bioengineer Farren Isaacs and Harvard geneticist George Church showed that they could genetically modify Escherichia coli to incorporate synthetic amino acids into essential proteins. When the bacteria are not fed the amino acids, they cannot produce these essential proteins, and so they die. This strategy yields bacteria that are very unlikely to survive without support from scientists but requires intensive engineering of the bacterial genome. (See “GMO ‘Kill Switches,’” The Scientist, January 2015.)

In contrast, Collins and his colleagues set out to create kill switches that could work in a more diverse range of microbes. “Our circuit-based safeguards can be conveniently transferred to different bacterial strains without modifying the target cell’s genome,” he wrote in an email.

First, Collins and his colleagues generated a kill switch called “Deadman,” named for a locomotive braking system in which the train will only run if the engineer is affirmatively holding down a pedal. In the microbial version of Deadman, a researcher must feed bacteria a substance called anhydrotetracycline at all times, or else the microbes will express a toxin and self-destruct.

The researchers generated a genetic circuit containing genes for the proteins LacI and TetR, a toxin that is only expressed in the absence of LacI, and a protease that degrades LacI. Under normal circumstances, TetR is preferentially expressed over LacI. TetR expression also triggers expression of the protease, which degrades any LacI that has been expressed. Without LacI, cells express the toxin and die. But when the cells are fed anhydrotetracycline, TetR is inhibited and LacI is expressed. LacI represses the toxin and keeps the cells alive.

Other versions of the Deadman circuit can be designed to degrade essential proteins in the absence of anhydrotetracycline, said Collins.

A second kill switch, “Passcode,” similarly requires that researchers maintain a specific environment for cells lest they express a toxin. Passcode requires a combination of input molecules for cells to survive. The system relies on hybrid transcription factors, each with one component that recognizes a specific DNA sequence, and one component that is sensitive to specific small molecules, such as galactose or cellobiose. One hybrid transcription factor, factor C, turns off expression of a toxin. Two other hybrid transcription factors, factors A and B, suppress expression of factor C. But specific small molecules can keep them from interacting with C. Another small molecule could prevent C from repressing the toxin. Therefore, to keep the cells alive, researchers must provide them with two small molecules that keep factors A and B in check, and make sure not to give them a third small molecule that will interfere with C.

Scientists designing Passcode kill-switches could make hybrid transcription factors respond to whatever combination of small molecules they desired, said Collins. “The strength of our kill switches lies in their flexibility and their ability to detect complex environmental signals for biocontainment.” He noted that companies hoping to keep others from using their cells could keep the recipe for their feed a secret.

“The great advantage is that you can effectively scale this and create different combinations of environments that contain different cocktails of these small molecules, thereby allowing you to effectively create a suite of cells that are going to be viable in different environments,” said Isaacs.

But Church warned that Collins’s circuit-based approach might not as effectively contain bacteria as an amino acid-based method, like one his group developed, since the cells are not fundamentally dependent on foreign biology to survive.

“If you need to have the ability to really scale your containment across a number of different species, then I could see the Passcode kill switches would be incredibly valuable,” said Isaacs. “If you are very concerned about escape frequencies and your degree of biocontainment, maybe you’d opt for something where the organism has been recoded and it relies on a synthetic amino acid.”

Still, Stan said the new paper is a demonstration that creating easy-to-insert kill switches based on genetic circuits is feasible. “I think what they wanted to show in the paper is basically that using some existing genetic circuitry . . .  you can obtain biosafety for the here and now.”

 

C.T.Y. Chan et al., “‘Deadman’ and ‘Passcode’ microbial kill switches for bacterial containment,” Nature Chemical Biology, doi:10.1038/nchembio.1979, 2015.  

Tags   synthetic biology, microbes, genetic engineering and biosafety

 

GMO “Kill Switches”

Scientists design bacteria reliant upon synthetic amino acids to contain genetically modified organisms.

By Kerry Grens | Jan 21, 2015   http://www.the-scientist.com/?articles.view/articleNo/41954/title/GMO–Kill-Switches-/

One of the biggest concerns about genetically modified organisms (GMOs) is that they can infiltrate wild populations and spread their altered genes among naturally occurring species. In Nature today (January 21), two groups present a new method of containing GMOs: by making some of their essential proteins reliant upon synthetic amino acids not found outside of the laboratory.

“What really makes this a valuable step change is that kill switches beforehand were very susceptible to mutation or other conditions, such as metabolic cross feeding, from basically inactivating them,” said Tom Ellis, a synthetic biologist at Imperial College London who was not involved in the studies. The new approach circumvents some of those problems by making it extremely unlikely for the genetically modified bacteria to be able to survive outside of the conditions dictated by their custom-designed genomes.

Both research teams—one led by George Church at Harvard Medical School and the other by Farren Isaacsat Yale University—based their work on so-called genetically recoded organisms (GROs), bacterial genomes that have had all instances of a particular codon replaced by another. Church and Isaacs, along with their colleagues, had previously developed this concept in collaboration. Since then, their respective groups designed the replacement codons to incorporate a synthetic amino acid, and engineered proteins essential to the organism to rely upon the artificial amino acid for proper function.

“Here, for the first time, we’re showing that we’re able to engineer a dependency on synthetic biochemical building blocks for these proteins,” Isaacs told reporters during a conference call.

Both teams found that the cells perished in environments lacking the synthetic amino acid. Although the technology is not ready for industrial-scale deployment, the scientists suggested that such an approach could be applied as a safeguard against the escape of GMOs.

…..

 

‘Deadman’ and ‘Passcode’ microbial kill switches for bacterial containment

Clement T Y ChanJeong Wook LeeD Ewen CameronCaleb J Bashor & James J Collins

Nature Chemical Biology(2015)            http://dx.doi.org:/10.1038/nchembio.1979

Figure 2: The fail-safe mechanism for Deadman circuit activation.

The fail-safe mechanism for Deadman circuit activation.

http://www.nature.com/nchembio/journal/vaop/ncurrent/carousel/nchembio.1979-F2.jpg

To demonstrate active control over host cell viability, cells grown under survival conditions (with ATc) were exposed to 1 mM IPTG to directly induce EcoRI and mf-Lon expression. Cell viability was measured by CFU count and is displayed…

 

Biocontainment systems that couple environmental sensing with circuit-based control of cell viability could be used to prevent escape of genetically modified microbes into the environment. Here we present two engineered safeguard systems known as the ‘Deadman’ and ‘Passcode’ kill switches. The Deadman kill switch uses unbalanced reciprocal transcriptional repression to couple a specific input signal with cell survival. The Passcode kill switch uses a similar two-layered transcription design and incorporates hybrid LacI-GalR family transcription factors to provide diverse and complex environmental inputs to control circuit function. These synthetic gene circuits efficiently killEscherichia coli and can be readily reprogrammed to change their environmental inputs, regulatory architecture and killing mechanism.

 

Nontoxic antimicrobials that evade drug resistance

Stephen A DavisBenjamin M VincentMatthew M EndoLuke WhitesellKaren MarchilloDavid R AndesSusan Lindquist & Martin D Burke

Nature Chemical Biology 2015;11:481–487          http://dx.doi.org:/10.1038/nchembio.1821

Drugs that act more promiscuously provide fewer routes for the emergence of resistant mutants. This benefit, however, often comes at the cost of serious off-target and dose-limiting toxicities. The classic example is the antifungal amphotericin B (AmB), which has evaded resistance for more than half a century. We report markedly less toxic amphotericins that nevertheless evade resistance. They are scalably accessed in just three steps from the natural product, and they bind their target (the fungal sterol ergosterol) with far greater selectivity than AmB. Hence, they are less toxic and far more effective in a mouse model of systemic candidiasis. To our surprise, exhaustive efforts to select for mutants resistant to these more selective compounds revealed that they are just as impervious to resistance as AmB. Thus, highly selective cytocidal action and the evasion of resistance are not mutually exclusive, suggesting practical routes to the discovery of less toxic, resistance-evasive therapies.

 

 

Read Full Post »


RNA Virus Genome as Bacterial Chromosome

Reporter: Larry H Bernstein, MD, FCAP

 

Engineering the largest RNA virus genome as an infectious bacterial artificial chromosome
F Almazan, JM Gonzalez, Z Penzes, A Izeta, E Calvo, J Plana-Duran, and L Enjuanes

PNAS  May 9, 2000; 97(10): 5516–5521.

the application of two strategies,

  • cloning of the cDNAs into a bacterial artificial chromosome and
  • nuclear expression of RNAs that are typically produced within the cytoplasm

is useful for the engineering of large RNA molecules.
A cDNA encoding an infectious coronavirus RNA genome

  • has been cloned as a bacterial artificial chromosome.

The rescued coronavirus

  • conserved all of the genetic markers introduced throughout the sequence and
  • showed a standard mRNA pattern and

the antigenic characteristics expected for the synthetic virus.
The cDNA was transcribed

  • within the nucleus, and
  • the RNA translocated to the cytoplasm.
Interestingly, the recovered virus had
  • essentially the same sequence as the original one, and
      • no splicing was observed.

During the engineering of the infectious cDNA,

  • the spike gene of the virus was replaced by
  • the spike gene of an enteric isolate.

The synthetic virus

  • replicated abundantly in the enteric tract and was fully virulent, demonstrating that
  • the tropism and virulence of the recovered coronavirus can be modified.

the application of two strategies,

  • cloning of the cDNAs into a bacterial artificial chromosome and
  • nuclear expression of RNAs that are typically produced within the cytoplasm,
    • is useful for the engineering of large RNA molecules.

A cDNA encoding an infectious coronavirus RNA genome has been cloned as a bacterial artificial chromosome. The rescued coronavirus

  • conserved all of the genetic markers introduced throughout the sequence and
  • showed a standard mRNA pattern and
  • the antigenic characteristics expected for the synthetic virus.
    • The cDNA was transcribed within the nucleus, and
    • the RNA translocated to the cytoplasm.

Interestingly, the recovered virus had essentially the same sequence as the original one, and no splicing was observed. During the engineering of the infectious cDNA, the spike gene of the virus was replaced by the spike gene of an enteric isolate. The synthetic virus

  • replicated abundantly in the enteric tract and
  • was fully virulent,

demonstrating that the tropism and virulence of the recovered coronavirus can be modified.}
http://www.PNAS.org/Engineering_the_largest_RNAvirus_genome_as_an_infectious_bacterial_artificial_chromosome/

Description: The interaction of mRNA in a cell...

Description: The interaction of mRNA in a cell. Source: http://www.genome.gov/Pages/Hyperion/DIR/VIP/Glossary/Illustration/mrna.shtml (file) License: “All of the illustrations in the Talking Glossary of Genetics are freely available and may be used without special permission.” http://www.genome.gov/page.cfm?pageID=10003803 (Photo credit: Wikipedia)

RNA Protein Virus

RNA Protein Virus (Photo credit: Wikipedia)

This image was created as part of the Philip G...

This image was created as part of the Philip Greenspun illustration project. (Photo credit: Wikipedia)

Read Full Post »


Genomics of Bacterial and Archaeal Viruses

 

Reporter: Larry H Bernstein, MD, FCAP
https://pharmaceuticalintelligence.com/?p=10187/Genomics of Bacterial and Archaeal Viruses/

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere
M Krupovic, D Prangishvili, RW Hendrix, and DH Bamford
Over the past few years, the viruses of prokaryotes have been transformed in the view of microbiologists from simply being convenient experimental model systems into being a major component of the biosphere. They are
  • the global champions of diversity,
  • they constitute a majority of organisms on the planet,
  • they have large roles in the planet’s ecosystems,
  • they exert a significant—some would say dominant—force on
  • the evolution of their bacterial and archaeal hosts, and
  • they have been doing this for billions of years,
  • possibly for as long as there have been cells.
This transformation in status  or, rather, our expanded appreciation of the importance of these viruses in the biosphere is due to a few significant developments in both understanding and technology.
(i) It has become clear that the population sizes of these viruses are astoundingly large. This realization grew out of electron microscopic enumerations of tailed phage virions in costal seawater, and numerous measurements in other environments have been made since then. A current estimate based on these measurements is that
  • there are  1031 individual tailed phage virions in the global biosphere—
  • enough to reach for 200 million light years if laid end to end—and measurements of population turnover suggest that
  • it takes roughly 1024 productive infections per second to maintain the global population.
(ii) Advances in DNA sequencing technology have led to dramatic qualitative improvements in how we understand the
  • genetic structure of viral populations,
  • the mechanisms of viral evolution, and
  • the diversity of viral sequences.
The majority of newly determined gene and protein sequences of these viruses has no relatives detectable in the public sequence databases, and
  • analysis of metagenomic data provides strong evidence that
  • there is more genetic diversity in the genes of the viruses of prokaryotes
    • than in any other compartment of the biosphere.
(iii) Facilitated by these conceptual and technical advances, studies of bacterial and archaeal viruses as important components of global biology have flourished. These viruses are revealed as important players in
  • carbon and energy cycling in the oceans and other natural environments and
  • as major agents in the ecology and evolution of their cellular hosts.
(iv) The isolation and characterization of new viruses have accelerated. This has been especially important for the archaeal viruses, where the discovery of new viruses and of new virus types had lagged behind bacteriophage discovery. For the bacteriophages, the isolation of newly discovered viruses has helped improve the still extremely sparse coverage of sequence diversity and the narrow phylogenetic range of hosts represented by current data.
(v) High-resolution structures determined
  • for capsid proteins and other virion proteins,
  • together with information about virion assembly mechanisms,
  • have allowed surprising inferences about ancestral connections among genes whose DNA sequences and encoded protein sequences
    • have diverged to the point that they are no longer detectably related.
English: Schematic diagram of the hexon of a v...

English: Schematic diagram of the hexon of a virus capsid (Photo credit: Wikipedia)

English: Adsorption of virions to cells. Portu...

English: Adsorption of virions to cells. Português do Brasil: Adsorção de vírus a células. (Photo credit: Wikipedia)

Polio virus (picornavirus)

Polio virus (picornavirus) (Photo credit: Sanofi Pasteur)

Read Full Post »

Older Posts »