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First time ever: Researchers rewrite an entire bacterial genome and add a healthy twist

First time ever: Researchers rewrite an entire bacterial genome and add a healthy twist | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Scientists from Yale and Harvard have recoded the entire genome of an organism and improved a bacterium’s ability to resist viruses, a dramatic demonstration of the potential of rewriting an organism’s genetic code.

“This is the first time the genetic code has been fundamentally changed,” said Farren Isaacs, assistant professor of molecular, cellular, and developmental biology at Yale and co-senior author of the research published Oct. 18 in the journal Science. “Creating an organism with a new genetic code has allowed us to expand the scope of biological function in a number of powerful ways.”

 

The creation of a genomically recoded organism raises the possibility that researchers might be able to retool nature and create potent new forms of proteins to accomplish a myriad purposes — from combating disease to generating new classes of materials.

 

The research — headed by Isaacs and co-author George Church of Harvard Medical School — is a product of years of studies in the emerging field of synthetic biology, which seeks to re-design natural biological systems for useful purposes.

 

In this case, the researchers changed fundamental rules of biology.

Proteins, which are encoded by DNA’s instructional manual and are made up of 20 amino acids, carry out many important functional roles in the cell. Amino acids are encoded by the full set of 64 triplet combinations of the four nucleic acids that comprise the backbone of DNA. These triplets (sets of three nucleotides) are called codons and are the genetic alphabet of life.

 

Isaacs, Jesse Rinehart of Yale, and the Harvard researchers explored whether they could expand upon nature’s handywork by substituting different codons or letters throughout the genome and then reintroducing entirely new letters to create amino acids not found in nature. This work marks the first time that the genetic code has been completely changed across an organism’s genome.

 

In the new study, the researchers working with E. coli swapped a codon and eliminated its natural stop sign that terminates protein production. The new genome enabled the bacteria to resist viral infection by limiting production of natural proteins used by viruses to infect cells. Isaacs — working with Marc Lajoie of Harvard, Alexis Rovner of Yale, and colleagues — then converted the “stop” codon into one that encodes new amino acids and inserted it into the genome in a plug-and-play fashion. 

 

The work now sets the stage to convert the recoded bacterium into a living foundry, capable of biomanufacturing new classes of  “exotic” proteins and polymers. These new molecules could lay the foundation for a new generation of materials, nanostructures, therapeutics, and drug delivery vehicles, Isaacs said.

 

“Since the genetic code is universal, it raises the prospect of recoding genomes of other organisms,” Isaacs said. “This has tremendous implications in the biotechnology industry and could open entirely new avenues of research and applications.”


Via Dr. Stefan Gruenwald
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odysseas spyroglou's curator insight, October 19, 2013 8:46 AM

The brave new world starts here. I hope we'll find our way to a less dystopian future.

Dmitry Alexeev's curator insight, October 20, 2013 4:18 AM

thats a new generation biological tool although there has been already attempts to encode non-standard amino acids - but never before on a full genome scale - intrestingle how soon wilkl this be available as a conventional instrument? this is a novel scientific tool - which will among others help us to study life

Leire Tapia's curator insight, October 21, 2013 4:08 PM

He elegido esta noticia porque la relaciono con la libertad de investigación. Es un derecho vinculado al ser humano y es un derecho exigible. Es también importante comunicar los resultados y no caer en el peligro de la censura. No hay que esconder lo que la ciencia descubre pero si es importante establecer límites relacionados con la protección de la salud y con la dignidad humana.

Viruses, Immunology & Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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It's a group effort - the curators:

It's a group effort - the curators: | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

get in touch if you want to help curate this topic

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Bwana Moses's comment, May 25, 2016 6:13 AM
Great work. Keep it going.
Bwana Moses's comment, March 7, 2017 12:46 PM
Thank You.
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50 Adverbs to avoid in academic writing

50 Adverbs to avoid in academic writing | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Here are 50 adverbs that that you can eliminate in your writing, be it academic or professional.
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Direct Imaging of the circular chromosome of a live bacterium

New assays for quantitative imaging and sequencing have yielded great progress towards understanding the organizational principles of chromosomes. Yet, even for the well-studied model bacterium Escherichia coli, many basic questions remain unresolved regarding chromosomal (sub-)structure, its mechanics and dynamics, and the link between structure and function. Here we resolve the spatial organization of the circular chromosome of bacteria by directly imaging the chromosome in live E. coli cells with a broadened cell shape.

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Sequence motif finder using memetic algorithm

Sequence motif finder using memetic algorithm | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
De novo prediction of Transcription Factor Binding Sites (TFBS) using computational methods is a difficult task and it is an important problem in Bioinformatics. The correct recognition of TFBS plays an important role in understanding the mechanisms of gene regulation and helps to develop new drugs. We here present Memetic Framework for Motif Discovery (MFMD), an algorithm that uses semi-greedy constructive heuristics as a local optimizer. In addition, we used a hybridization of the classic genetic algorithm as a global optimizer to refine the solutions initially found. MFMD can find and classify overrepresented patterns in DNA sequences and predict their respective initial positions. MFMD performance was assessed using ChIP-seq data retrieved from the JASPAR site, promoter sequences extracted from the ABS site, and artificially generated synthetic data. The MFMD was evaluated and compared with well-known approaches in the literature, called MEME and Gibbs Motif Sampler, achieving a higher f-score in the most datasets used in this work. We have developed an approach for detecting motifs in biopolymers sequences. MFMD is a freely available software that can be promising as an alternative to the development of new tools for de novo motif discovery. Its open-source software can be downloaded at
https://github.com/jadermcg/mfmd

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Interactions between Enteric Bacteria and Eukaryotic Viruses Impact the Outcome of Infection

Interactions between Enteric Bacteria and Eukaryotic Viruses Impact the Outcome of Infection | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Enteric viruses encounter a multitude of environments as they traverse the gastrointestinal tract. The interaction of enteric eukaryotic viruses with members of the host microbiota impacts the outcome of infection. Infection with several enteric viruses is impaired in the absence of the gut microbiota, specifically bacteria. The effects of bacteria on virus biology are diverse. Poliovirus capsid stability and receptor engagement are positively impacted by bacteria and bacterial lipopolysaccharides. Norovirus utilizes histo-blood group antigens produced by enteric bacteria to attach and productively infect B cells. Lipopolysaccharides on the envelope of mouse mammary tumor virus promote a tolerogenic environment that allows for the establishment of viral persistence. Reovirus binds Gram negative and Gram-positive bacteria through bacterial envelope components to enhance virion thermostability. Through the direct engagement of bacteria and bacterial components, viruses evolved diverse ways to impact the outcome of infection.
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How Do Virus–Mosquito Interactions Lead to Viral Emergence?

'while wrapid progression and frequency of recent arbovirus outbreaks is associated with long-term changes in human behavior (globalization, urbanization, climate change), there are direct mosquito–virus interactions which drive shifts in host range and alter virus transmission'

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Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. - PubMed - NCBI

Nucleic Acids Res. 2015 Feb 18;43(3):e15. doi: 10.1093/nar/gku1196. Epub 2014 Nov 20. Research Support, Non-U.S. Gov't
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A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. - PubMed - NCBI

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. - PubMed - NCBI | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
J Mol Biol. 2017 Dec 16. pii: S0022-2836(17)30587-9. doi: 10.1016/j.jmb.2017.12.007. [Epub ahead of print]
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ReMILO: reference assisted misassembly detection algorithm using short and long reads | Bioinformatics | Oxford Academic

ReMILO: reference assisted misassembly detection algorithm using short and long reads | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractMotivation. Contigs assembled from the second generation sequencing short reads may contain misassemblies, and thus complicate downstream analysis or e
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Drug Company Under Fire After Revealing Dengue Vaccine May Harm Some

Drug Company Under Fire After Revealing Dengue Vaccine May Harm Some | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
A promising vaccine for dengue fever is in limbo after the Philippines suspended its use amid widespread public anger and fears about its safety.
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Transmissible Viral Vaccines

Genetic engineering now enables the design of live viral vaccines that are potentially
transmissible. Some designs merely modify a single viral genome to improve on the
age-old method of attenuation whereas other designs create chimeras of viral genomes.
Transmission has the benefit of increasing herd immunity above that achieved by direct
vaccination alone but also increases the opportunity for vaccine evolution, which
typically undermines vaccine utility. Different designs have different epidemiological
consequences but also experience different evolution.
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The twilight of immunity: emerging concepts in aging of the immune system

The twilight of immunity: emerging concepts in aging of the immune system | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Review Article

Via Gilbert C FAURE
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CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation | Bioinformatics | Oxford Academic

CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractMotivation. Homology-based gene prediction is a powerful concept to annotate newly sequenced genomes. We have previously demonstrated that whole genome
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Highly parallel direct RNA sequencing on an array of nanopores

Highly parallel direct RNA sequencing on an array of nanopores | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Article
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How good bacteria control your genes

How good bacteria control your genes | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Signals produced by bacteria in the gut could help prevent infections and bowel cancer


Via Integrated DNA Technologies, Kenzibit
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Exosomes serve as novel modes of tick-borne flavivirus transmission from arthropod to human cells and facilitates dissemination of viral RNA and proteins to the vertebrate neuronal cells

Exosomes serve as novel modes of tick-borne flavivirus transmission from arthropod to human cells and facilitates dissemination of viral RNA and proteins to the vertebrate neuronal cells | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
results suggest that flaviviruses uses arthropod-derived exosomes as a novel means for viral RNA and protein transmission from the vector, and the vertebrate exosomes for dissemination within the host that may subsequently allow neuroinvasion and neuropathogenesis.
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Transmission of Human Respiratory Syncytial Virus in the Immunocompromised Ferret Model

Transmission of Human Respiratory Syncytial Virus in the Immunocompromised Ferret Model | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Human respiratory syncytial virus (HRSV) causes substantial morbidity and mortality in vulnerable patients, such as the very young, the elderly, and immunocompromised individuals of any age. Nosocomial transmission of HRSV remains a serious challenge in hospital settings, with intervention strategies largely limited to infection control measures, including isolation of cases, high standards of hand hygiene, cohort nursing, and use of personal protective equipment. No vaccines against HRSV are currently available, and treatment options are largely supportive care and expensive monoclonal antibody or antiviral therapy. The limitations of current animal models for HRSV infection impede the development of new preventive and therapeutic agents, and the assessment of their potential for limiting HRSV transmission, in particular in nosocomial settings. Here, we demonstrate the efficient transmission of HRSV from immunocompromised ferrets to both immunocompromised and immunocompetent contact ferrets, with pathological findings reproducing HRSV pathology in humans. The immunocompromised ferret-HRSV model represents a novel tool for the evaluation of intervention strategies against nosocomial transmission of HRSV.
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Case study: China’s Year of the Rooster looking foul

Case study: China’s Year of the Rooster looking foul | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Anhui Provinces have experie

Via Ian M Mackay, PhD
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Phandango: an interactive viewer for bacterial population genomics | Bioinformatics | Oxford Academic

Phandango: an interactive viewer for bacterial population genomics | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractSummary. Fully exploiting the wealth of data in current bacterial population genomics datasets requires synthesizing and integrating different types of
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Endosymbionts Differentially Alter Exploratory Probing Behavior of a Nonpersistent Plant Virus Vector

Endosymbionts Differentially Alter Exploratory Probing Behavior of a Nonpersistent Plant Virus Vector | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Insect endosymbionts (hereafter, symbionts) can modify plant virus epidemiology by changing the physiology or behavior of vectors, but their role in nonpersistent virus pathosystems remains uninvestig
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African swine fever outbreak alarms wildlife biologists and veterinarians

African swine fever outbreak alarms wildlife biologists and veterinarians | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Deadly virus threatens European pigs and boar
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Why the government is creating lethal viruses

Why the government is creating lethal viruses | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The National Institutes of Health lifted a US government ban on making lethal viruses, saying the research is necessary to "develop strategies" against public health threats.
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Viruses can transfer genes across the superkingdoms of life - Scienmag: Latest Science and Health News

Viruses can transfer genes across the superkingdoms of life - Scienmag: Latest Science and Health News | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
New research shows that viruses can transfer genes to organisms that they aren't known to infect - including organisms in different superkingdoms, or domains. The study, published in open-access ..
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Ebola survivors still immune to virus after 40 years

Ebola survivors still immune to virus after 40 years | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

 

 

Survivors of the world’s first known Ebola outbreak have immunity to the virus 40 years after they were infected, scientists have found. These people who beat infection in 1976 can make antibodies against Ebola today.

 

“It’s interesting to see that after such a long time, people still have this kind of reactivity against the virus,” says virologist Stephan Becker of the Philipps University of Marburg in Germany. The findings were published online on 14 December in the Journal of Infectious Diseases1.

 

Becker says that the discovery was “not completely unexpected”, because previous studies had found that survivors had immune responses to Ebola virus as long as 11 years after they were infected2.

 

But until last year, no one had ever studied immunity in the survivors of the first recorded Ebola outbreak, which occurred in 1976 near the town of Yambuku, in what is now the Democratic Republic of the Congo (DRC).

 

“Nobody even knew if these people were still alive,” says Anne Rimoin, an epidemiologist at the University of California, Los Angeles (UCLA), and the lead author of the latest study.


Via Dr. Stefan Gruenwald
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PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context | Bioinformatics | Oxford Academic

PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context
Pieter Libin Ewout Vanden Eynden Francesca Incardona Ann Nowé Antonia Bezenchek EucoHIV Study Group Anders Sönnerborg Anne-Mieke Vandamme Kristof Theys Guy Baele Author Notes
Bioinformatics, Volume 33, Issue 24, 15 December 2017, Pages 3993–3995
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