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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 | Virology and Bioinformatics from Virology.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.

Virology and Bioinformatics from Virology.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: | Virology and Bioinformatics from Virology.ca | Scoop.it

get in touch if you want to help curate this topic

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Detailed characterisation of Hendra virus infection of different cell types

Hendra virus (HeV) is a pleomorphic virus belonging to the Paramyxovirus family. Our long-term aim is to understand the process of assembly of HeV virions. As a first step, we sought to determine the most appropriate cell culture system with which to study this process, and then to use this model to define the morphology of the virus and identify the site of assembly by imaging key virus encoded proteins in infected cells.
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Scientists tallied up all the advice on Dr. Oz's show. Here's what they found.

We now have science to quantify the quackery on TV.
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KmerStream: streaming algorithms for k-mer abundance estimation

KmerStream: streaming algorithms for k-mer abundance estimation | Virology and Bioinformatics from Virology.ca | Scoop.it
RT @assemblathon: KmerStream: streaming algorithms for k-mer abundance estimation: http://t.co/VnfkQGMJPv

Via Mel Melendrez-Vallard, Pedro Fernandes
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Virology Journal | Full text | Plant-based vaccines against viruses

Plant-made or “biofarmed” viral vaccines are some of the earliest products of the technology of plant molecular farming, and remain some of the brightest prospects for the success of this field. Proofs of principle and of efficacy exist for many candidate viral veterinary vaccines; the use of plant-made viral antigens and of monoclonal antibodies for therapy of animal and even human viral disease is also well established. This review explores some of the more prominent recent advances in the biofarming of viral vaccines and therapies, including the recent use of ZMapp for Ebolavirus infection, and explores some possible future applications of the technology.
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Dengue fever vaccine on the cards after novel antibody discovery

Dengue fever vaccine on the cards after novel antibody discovery | Virology and Bioinformatics from Virology.ca | Scoop.it
The antibodies could be used to treat dengue fever or develop a vaccine that works against all four strains of virus
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Genevisible: new Google-like search engine for genes

Genevisible identifies the most significant tissues, cell lines, diseases or perturbations regulating a gene of interest
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An Evolutionary Battle Against Bacteria

An Evolutionary Battle Against Bacteria | Virology and Bioinformatics from Virology.ca | Scoop.it
A recent study illustrates how our ancestors evolved new defenses to starve meningitis-causing bacteria of the iron they need to grow.
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ENHANCING INFECTIOUS DISEASE MAPPING WITH OPEN ACCESS RESOURCES - Eurosurveillance

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ECOD: An Evolutionary Classification of Protein Domains

ECOD: An Evolutionary Classification of Protein Domains | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Computational Biology is an open-access
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Viral suppressors of the RIG-I-mediated interferon response are pre-packaged in influenza virions : Nature Communications : Nature Publishing Group

Viral suppressors of the RIG-I-mediated interferon response are pre-packaged in influenza virions : Nature Communications : Nature Publishing Group | Virology and Bioinformatics from Virology.ca | Scoop.it

The type I interferon (IFN) response represents the first line of defence to invading pathogens. Internalized viral ribonucleoproteins (vRNPs) of negative-strand RNA viruses induce an early IFN response by interacting with retinoic acid inducible gene I (RIG-I) and its recruitment to mitochondria. Here we employ three-dimensional stochastic optical reconstruction microscopy (STORM) to visualize incoming influenza A virus (IAV) vRNPs as helical-like structures associated with mitochondria. Unexpectedly, an early IFN induction in response to vRNPs is not detected. A distinct amino-acid motif in the viral polymerases, PB1/PA, suppresses early IFN induction. Mutation of this motif leads to reduced pathogenicity in vivo, whereas restoration increases it. Evolutionary dynamics in these sequences suggest that completion of the motif, combined with viral reassortment can contribute to pandemic risks. In summary, inhibition of the immediate anti-viral response is ‘pre-packaged’ in IAV in the sequences of vRNP-associated polymerase proteins.

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Human Viruses and Cancer

Human Viruses and Cancer | Virology and Bioinformatics from Virology.ca | Scoop.it
To date, seven viruses have been consistently linked to different types of human cancer, and infections are estimated to account for up to 20% of all cancer cases worldwide.
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Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch

Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch | Virology and Bioinformatics from Virology.ca | Scoop.it

Knowledge of ancient viruses is limited due to their low concentration and poor preservation in ancient specimens. Using a viral particle-associated nucleic acid enrichment approach, we genetically characterized one complete DNA and one partial RNA viral genome from a 700-y-old fecal sample preserved in ice. Using reverse genetics, we reconstituted the DNA virus, which replicated and systemically spread in a model plant species. Under constant freezing conditions, encapsidated viral nucleic acids may therefore be preserved for centuries. Our finding indicates that cryogenically preserved materials can be repositories of ancient viral nucleic acids, which in turn allow molecular genetics to regenerate viruses to study their biology.

 
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MAVS, cGAS, and endogenous retroviruses in T-independent B cell responses

Scattered across our genome are endogenous retroviruses (ERVs), ancient “footprints” of previous viral infections. Scientists do not fully understand their functions, but Zeng et al. now report a role for ERVs in mobilizing a particular type of B cell–driven immune response in mice (T cell–independent, TID), which is usually mounted in response to viral capids or bacterial polysaccharides (see the Perspective by Grasset and Cerutti). Immunizing mice with a model TID antigen elicited an increase in ERV RNA and DNA in the cytoplasm of B cells. Innate immune receptors that recognize cytoplasmic nucleotides then triggered signaling cascades that resulted in the production of immunoglobulin M.

 
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The diversity of HPV infection among HIV-infected women in Yunnan, China

Yunnan has one of the oldest and the most severe human immunodeficiency virus (HIV) epidemics in China. We conducted an observational study to evaluate the human papillomavirus (HPV) genotype distribution in relation to cervical neoplastic disease risk among HIV-infected women in Yunnan.
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GTPB: IB14S Introductory Bioinformatics, Second course - Home

GTPB: IB14S Introductory Bioinformatics, Second course - Home | Virology and Bioinformatics from Virology.ca | Scoop.it

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Pedro Fernandes's curator insight, December 4, 4:47 AM

This is a 4 day course with minimal pre-requisites that aims at equipping the participants with means to deal with biological sequence data at various levels. In the last day we will focus on NGS data analysis at a basic level.

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Antibodies discovery could lead to universal dengue vaccine

Antibodies discovery could lead to universal dengue vaccine | Virology and Bioinformatics from Virology.ca | Scoop.it
A group of international researchers has identified a new class of antibodies that can neutralise all four types of the dengue virus. The discovery could lead to the development of better vaccines and tests that could eventually lead to reductions in the incidence of the virus, which affects over 100 million people each year.
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FDA approves Gardasil 9 for prevention of cancers caused by five additional types of HPV

FDA approves Gardasil 9 for prevention of cancers caused by five additional types of HPV | Virology and Bioinformatics from Virology.ca | Scoop.it
The U.S. Food and Drug Administration today approved Gardasil 9 (Human Papillomavirus 9-valent Vaccine, Recombinant) for the prevention of certain diseases caused by nine types of Human Papillomavirus (HPV). Covering nine HPV types, five more HPV types than Gardasil (previously approved by the FDA), Gardasil 9 has the potential to prevent approximately 90 percent of cervical, vulvar, vaginal and anal cancers.

 

Thanks to Russell Kightley Media for the cervical cancer graphic


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The Problem Of The Parotid Paramyxovirus (aka Mumps)

The Problem Of The Parotid Paramyxovirus (aka Mumps) | Virology and Bioinformatics from Virology.ca | Scoop.it
The recent outbreak of mumps in the NHL reveals how a vaccine-preventable disease can make a comeback.
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Can you spell   V-A-C-C-I-N-E  ?

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Alpharetroviral Vectors: From a Cancer-Causing Agent to a Useful Tool for Human Gene Therapy

Alpharetroviral Vectors: From a Cancer-Causing Agent to a Useful Tool for Human Gene Therapy | Virology and Bioinformatics from Virology.ca | Scoop.it

Gene therapy using integrating retroviral vectors has proven its effectiveness in several clinical trials for the treatment of inherited diseases and cancer. However, vector-mediated adverse events related to insertional mutagenesis were also observed, emphasizing the need for safer therapeutic vectors. Paradoxically, alpharetroviruses, originally discovered as cancer-causing agents, have a more random and potentially safer integration pattern compared to gammaretro- and lentiviruses. In this review, we provide a short overview of the history of alpharetroviruses and explain how they can be converted into state-of-the-art gene delivery tools with improved safety features. We discuss development of alpharetroviral vectors in compliance with regulatory requirements for clinical translation, and provide an outlook on possible future gene therapy applications. Taken together, this review is a broad overview of alpharetroviral vectors spanning the bridge from their parental virus discovery to their potential applicability in clinical settings

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Influenza Virus-Host Interactome Screen as a Platform for Antiviral Drug Development

Influenza Virus-Host Interactome Screen as a Platform for Antiviral Drug Development | Virology and Bioinformatics from Virology.ca | Scoop.it
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Ebola vaccine trial 'interrupted'

Ebola vaccine trial 'interrupted' | Virology and Bioinformatics from Virology.ca | Scoop.it

The clinical trial of an Ebola vaccine in Switzerland has been interrupted after some patients complained of joint pains in their hands and feet.

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The HIV Mutation Browser: A Resource for Human Immunodeficiency Virus Mutagenesis and Polymorphism Data

The HIV Mutation Browser: A Resource for Human Immunodeficiency Virus Mutagenesis and Polymorphism Data | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Computational Biology is an open-access
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Not Just a Theory—The Utility of Mathematical Models in Evolutionary Biology

Not Just a Theory—The Utility of Mathematical Models in Evolutionary Biology | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines.
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Mega2: validated data-reformatting for linkage and association analyses - Source Code for Biology and Medicine

In a typical study of the genetics of a complex human disease, many different analysis programs are used, to test for linkage and association. This requires extensive and careful data reformatting, as many of these analysis programs use differing input formats. Writing scripts to facilitate this can be tedious, time-consuming, and error-prone. To address these issues, the open source Mega2 data reformatting program provides validated and tested data conversions from several commonly-used input formats to many output formats.
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pH-Dependent entry of chikungunya virus fusion into mosquito cells

Millions of human infections caused by arthropod-borne pathogens are initiated by the feeding of an infected mosquito on a vertebrate. However, interactions between the viruses and the mosquito vector, which facilitates successful infection and transmission of virus to a subsequent vertebrate host, are still not fully understood.
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