Viruses and Bioinformatics from Virology.uvic.ca
91.7K views | +2 today
Follow
 
Scooped by Ed Rybicki
onto Viruses and Bioinformatics from Virology.uvic.ca
Scoop.it!

Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History

"The history of click-speaking Khoe-San, and African populations in general, remains poorly understood. We genotyped ∼2.3 million SNPs in 220 southern Africans and found that the Khoe-San diverged from other populations ≥100,000 years ago, but structure within the Khoe-San dated back to about 35,000 years ago. Genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa; instead, it indicated a history of admixture and stratification. We found evidence of adaptation targeting muscle function and immune response, potential adaptive introgression of UV-light protection, and selection predating modern human diversification involving skeletal and neurological development. These new findings illustrate the importance of African genomic diversity in understanding human evolutionary history."

 

Ex Africa, semper aliquid novi...or old, in this case!

more...
No comment yet.
Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
Your new post is loading...
Your new post is loading...
Scooped by Chris Upton + helpers
Scoop.it!

It's a group effort - the curators:

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

get in touch if you want to help curate this topic

more...
Bwana Moses's comment, May 25, 2016 6:13 AM
Great work. Keep it going.
Bwana Moses's comment, March 7, 12:46 PM
Thank You.
Rescooped by Bwana Moses from TAL effector science
Scoop.it!

A multi-purpose toolkit to enable advanced genome engineering in plants - Plant Cell

A multi-purpose toolkit to enable advanced genome engineering in plants - Plant Cell | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Cermak et al, 2017

We report a comprehensive toolkit that enables targeted, specific modification of monocot and dicot genomes using a variety of genome engineering approaches. Our reagents, based on TALENs and the CRISPR/Cas9 system, are systematized for fast, modular cloning and accommodate diverse regulatory sequences to drive reagent expression. Vectors are optimized to create either single or multiple gene knockouts and large chromosomal deletions. Moreover, integration of geminivirus-based vectors enables precise gene editing through homologous recombination. Regulation of transcription is also possible. A web-based tool greatly streamlines vector selection and construction. One advantage of our platform is the use of the Csy4 ribonuclease and tRNA processing enzymes to simultaneously express multiple guide RNAs (gRNAs). For example, we demonstrate targeted deletions in up to six genes by expressing twelve gRNAs from a single transcript. Csy4 and tRNA expression systems are almost twice as effective in inducing mutations as gRNAs expressed from individual RNA polymerase III (Pol III) promoters. Mutagenesis can be further enhanced 2.5-fold by incorporating the TREX2 exonuclease. Finally, we demonstrate that Cas9 nickases induce gene targeting at frequencies comparable to native Cas9 when they are delivered on geminivirus replicons. The reagents have been successfully validated in tomato, tobacco, Medicago, wheat and barley.


Via dromius
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Editorial overview: Viral immunology: Dealing with bad news

Understanding immunity to viruses therefore encompasses many, if not nearly all aspects of cell biology and immunology. A positive trend of the past twenty years of viral research is that the connection between viruses and innate cellular anti-viral mechanisms has cemented virology as an important sub-discipline of cell biology, and converted many virologists into at least honorary immunologists. The inherent simplicity of viruses and their marked tendency towards robust expression of their proteome and flagrant manipulation of host cells and immunity, make them superb tools to make basic discoveries.

Pragmatically, basic research in viral immunology provides the foundation for improving and developing new anti-viral vaccines and therapies. Recent outbreaks of MERs, Ebola and Zika viruses provide a pointed reminder of the threat that rapidly evolving viruses pose to human health and even existence, and underscore the importance of having a sufficient understanding of virus host interactions to quickly develop vaccines.

This issue of Current Opinion in Virology features eight outstanding reviews that summarize current knowledge of a number of the immune hurdles to viral replication. The immune system can be broadly, if imprecisely divided into innate vs. adaptive elements. Innate immunity is generally immediate and agent non-specific. Adaptive immunity is based on the functions of B and T cells, which due to their high antigen specificity, exist in relatively small numbers at the start of infection of a naïve host, and need nearly a week of exceedingly rapid division to attain fighting strength (four to six doublings per day, for six days geometrically increases their numbers up to 16 million-fold).
more...
No comment yet.
Scooped by Cindy
Scoop.it!

MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud | Bioinformatics | Oxford Academic

Summary: This paper presents MarDRe, a de novo cloud-ready duplicate and near-duplicate removal tool that can process single-end and paired-end reads from FASTQ/FASTA datasets. MarDRe takes advantage of the widely adopted MapReduce programming model to fully exploit Big Data technologies on cloud-based infrastructures. Written in Java to maximize cross-platform compatibility, MarDRe is built upon the open-source Apache Hadoop project, the most popular distributed computing framework for scalable Big Data processing. On a 16-node cluster deployed on the Amazon EC2 cloud platform, MarDRe is up to 8.52 times faster than a representative state-of-the-art tool.
Availability and Implementation: Source code in Java and Hadoop as well as a user’s guide are freely available under the GNU GPLv3 license at http://mardre.des.udc.es.
more...
No comment yet.
Scooped by Bwana Moses
Scoop.it!

Ahead of Print -Novel Retinal Lesion in Ebola Survivors, Sierra Leone,  - CDC

We conducted a case–control study in Freetown, Sierra Leone, to investigate ocular signs in Ebola virus disease (EVD) survivors. A total of 82 EVD survivors with ocular symptoms and 105 controls from asymptomatic civilian and military personnel and symptomatic eye clinic attendees underwent ophthalmic examination, including widefield retinal imaging. Snellen visual acuity was <6/7.5 in 75.6% (97.5% CI 63%–85.7%) of EVD survivors and 75.5% (97.5% CI 59.1%–87.9%) of controls. Unilateral white cataracts were present in 7.4% (97.5% CI 2.4%–16.7%) of EVD survivors and no controls. Aqueous humor from 2 EVD survivors with cataract but no anterior chamber inflammation were PCR-negative for Zaire Ebola virus, permitting cataract surgery. A novel retinal lesion following the anatomic distribution of the optic nerve axons occurred in 14.6% (97.5% CI 7.1%–25.6%) of EVD survivors and no controls, suggesting neuronal transmission as a route of ocular entry.
more...
No comment yet.
Rescooped by Kenzibit from Immunology
Scoop.it!

Treating Flu with Skin of Frog

Treating Flu with Skin of Frog | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Glands in frog skin secrete substances that possess broad antimicrobial function.
Holthausen et al. mined this soup of natural products and discovered a peptide that
destroys diverse human influenza strains (Holthausen et al., 2017). This study points
the way to the discovery of novel anti-influenza molecules targeting conserved elements
on influenza surface proteins.

Via Gilbert C FAURE
more...
Gilbert C FAURE's curator insight, May 15, 11:20 AM
Witches knew it!
Scooped by Bwana Moses
Scoop.it!

Ebola vaccine could get first real-world test in emerging outbreak

Ebola vaccine could get first real-world test in emerging outbreak | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The Democratic Republic of the Congo has reported nine suspected cases of infection in recent weeks.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB’s Education Committee)

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB’s Education Committee) | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

more...
No comment yet.
Scooped by Bwana Moses
Scoop.it!

Cell particles may help spread HIV infection, NIH study suggests

Cell particles may help spread HIV infection, NIH study suggests | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Cell particles may help spread HIV infection, NIH study suggests
more...
No comment yet.
Scooped by Bwana Moses
Scoop.it!

Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data.

Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data. | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
BMC Genomics. 2017 May 4;18(1):350. doi: 10.1186/s12864-017-3744-0.
more...
No comment yet.
Rescooped by Kenzibit from Amazing Science
Scoop.it!

Scientists engineer baker's yeast to produce penicillin molecules

Scientists engineer baker's yeast to produce penicillin molecules | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

The synthetic biologists from Imperial College London have re-engineered yeast cells to manufacture the non-ribosomal peptide antibiotic penicillin. In laboratory experiments, they were able to demonstrate that this yeast had antibacterial properties against streptococcus bacteria.

 

The authors of the study, which is published today in the journal Nature Communications, say their new method demonstrates the effectiveness of using this kind of synthetic biology as a route for discovering new antibiotics. This could open up possibilities for using re-engineered yeast cells to develop new forms of antibiotics and anti-inflammatory drugs from the non-ribosomal peptide family.

 

Non-ribosomal peptides are normally produced by bacteria and fungi, forming the basis of most antibiotics today. Pharma companies have long experimented with non-ribosomal peptides to make conventional antibiotics. The rise of antimicrobial resistance means there is a need to use genetic engineering techniques to find a new range of antibiotics from bacteria and fungi. However, genetically engineering the more exotic fungi and bacteria- the ones likely to have antibacterial properties—is challenging because scientists don't have the right tools and they are difficult to grow in a lab environment, requiring special conditions.

 

Baker's yeast on the other hand is easy to genetically engineer. Scientists can simply insert DNA from bacteria and fungi into yeast to carry out experiments, offering a viable new host for antibiotic production research. The rise of synthetic biology methods for yeast will allow researchers to make and test many new gene combinations that could produce a whole new range of new antibiotics.

 

However, the authors are keen to point out that the research is still in its early stages. While this approach does show promise, they have so far produced non-ribosomal peptide antibiotic penicillin in small quantities. More research needs to be done to see if it can be adapted to finding other compounds and to get production up to commercially viable quantities.

 

Dr Tom Ellis, from the Centre for Synthetic Biology at Imperial College London, explains: "Humans have been experimenting with yeast for thousands of years. From brewing beer to getting our bread to rise, and more recently for making compounds like anti-malarial drugs, yeast is the microscopic workhorse behind many processes.


Via Dr. Stefan Gruenwald
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

The Go-To Gene Sequencing Machine With Very Strange Results

The Go-To Gene Sequencing Machine With Very Strange Results | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
An update to Illumina's gene sequencing technology could have contaminated the results of recent high-sensitivity data produced on the machines.
more...
No comment yet.
Scooped by Rob Gifford
Scoop.it!

A naturalist's book of viruses

A naturalist's book of viruses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
by Jamie Henzy | Who isn't intrigued by viruses? Capable of wiping out entire populations, causing epidemics of biblical proportions, and wrecking crops, viruses entered the consciousness of humans because of their destructive potential. Too tiny to be seen, they were born from Koch's postulates, at first existing only in the imaginations of their early discoverers, such as Beijerinck, Ivanovsky, Twort, and d'Herelle. In the 1940s, electron micrographs revealed the first shadowy images of bacteriophage particles, and the eeriness of their outlines encouraged dread and captured the imagination of those who saw them.
Rob Gifford's insight:
Share your insight
more...
No comment yet.
Scooped by Vern Paetkau
Scoop.it!

Great New Book - Common Science Space

Great New Book - Common Science Space | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
There’s a great new book about vitamin A, the “vision vitamin”. The title is “Brilliance & Confusion: Saving Children’s Vision & Lives With Vitamin A”. Okay, I confess. It’s my own book, which I just completed (it’s available on Amazon; Kindle version coming soon). One relatively new aspect of this vitamin, which was discovered in 1913 but which has... Continue Reading
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Ten simple rules to make the most out of your undergraduate research career

Ten simple rules to make the most out of your undergraduate research career | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Despite the multiple benefits that research offers, undergraduates sometimes struggle and feel overwhelmed with the research process. Some undergraduates may not be familiar with the dynamics of the lab and may be afraid to interact with their lab colleagues and mentors. Other undergraduates may not completely understand the purpose of their work and feel overwhelmed by not knowing the results of their experiments before performing them. These consequences could, in turn, have detrimental effects on the relationship between undergraduates and their lab colleagues and decrease the motivation for undergraduates to pursue research in the future [4–5]. In light of these concerns, we propose ten simple rules constructed from our experiences as a college senior and a professor who has worked with undergraduate researchers that would help undergraduates enjoy and intellectually enrich their research experiences.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

NCBI researchers and collaborators discover novel group of giant viruses

NCBI researchers and collaborators discover novel group of giant viruses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
An international team of researchers, including NCBI’s Eugene Koonin and Natalya Yutin, has discovered a novel group of giant viruses (dubbed “Klosneuviruses”) with a more complete set of translation machinery genes than any virus that has been described to date. “This discovery significantly expands our understanding of viral evolution,” said Koonin. “These are the most ‘cell-like’ viruses ever identified. However, the computational analysis of the virus genomes shows that these viruses have not evolved from cells by reductive evolution but rather have evolved from smaller viruses, gradually acquiring genes from their hosts at different stages of their evolution.”


more...
No comment yet.
Scooped by Cindy
Scoop.it!

QuickBLASTP adds pre-processing to BLAST search

QuickBLASTP adds pre-processing to BLAST search | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
QuickBLASTP, an accelerated version of BLASTP, adds a new pre-processing step to the non-redundant (nr) protein database. In a matter of seconds, QuickBLASTP will find approximately 97% of the database sequences with 70% or more identity to your query and around 98% of the database sequence with 80% or more identity to your query.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Twenty-five lectures in virology for 2017

With the spring semester behind us, this year’s virology lecture series is complete, and videos are available at YouTube.
more...
No comment yet.
Scooped by Bwana Moses
Scoop.it!

Certain Immune Reactions to Viruses Cause Learning Problems

Certain Immune Reactions to Viruses Cause Learning Problems | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Neuroscience News has recent neuroscience research articles, brain research news, neurology studies and neuroscience resources for neuroscientists, students, and science fans and is always free to join. Our neuroscience social network has science groups, discussion forums, free books, resources, science videos and more.
more...
No comment yet.
Scooped by Bwana Moses
Scoop.it!

Real-time PCR assays for hepatitis B virus DNA quantification may require two different targets

Real-time PCR assays for hepatitis B virus DNA quantification may require two different targets | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Quantification Hepatitis B virus (HBV) DNA plays a critical role in the management of chronic HBV infections. However, HBV is a DNA virus with high levels of genetic variation, and drug-resistant mutations have emerged with the use of antiviral drugs. If a mutation caused a sequence mismatched in the primer or probe of a commercial DNA quantification kit, this would lead to an underestimation of the viral load of the sample. The aim of this study was to determine whether commercial kits, which use only one pair of primers and a single probe, accurately quantify the HBV DNA levels and to develop an improved duplex real-time PCR assay. We developed a new duplex real-time PCR assay that used two pairs of primers and two probes based on the conserved S and C regions of the HBV genome. We performed HBV DNA quantitative detection of HBV samples and compared the results of our duplex real-time PCR assays with the COBAS TaqMan HBV Test version 2 and Daan real-time PCR assays. The target region of the discordant sample was amplified, sequenced, and validated using plasmid. The results of the duplex real-time PCR were in good accordance with the commercial COBAS TaqMan HBV Test version 2 and Daan real-time PCR assays. We showed that two samples from Chinese HBV infections underestimated viral loads when quantified by the Roche kit because of a mismatch between the viral sequence and the reverse primer of the Roche kit. The HBV DNA levels of six samples were undervalued by duplex real-time PCR assays of the C region because of mutations in the primer of C region. We developed a new duplex real-time PCR assay, and the results of this assay were similar to the results of commercial kits. The HBV DNA level could be undervalued when using the COBAS TaqMan HBV Test version 2 for Chinese HBV infections owing to a mismatch with the primer/probe. A duplex real-time PCR assay based on the S and C regions could solve this problem to some extent.
more...
No comment yet.
Scooped by Bwana Moses
Scoop.it!

Not Ebola: Mystery Liberian disease identified as virulent meningitis, but no vaccine in sight | Genetic Literacy Project

Not Ebola: Mystery Liberian disease identified as virulent meningitis, but no vaccine in sight | Genetic Literacy Project | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
When several people died suddenly late last month in Liberia after attending a funeral in the southern county of Sinoe, alarm bells sounded: Had Ebola retu
more...
No comment yet.
Scooped by Bwana Moses
Scoop.it!

Transplacental transmission of torque teno virus

Transplacental transmission of torque teno virus | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
TTV has been detected in almost every human tissue type or body fluid reaching near 100% prevalence. Several studies report mother-to-child postnatal transmission of TTV in infancy but the risk of transplacental transmission of TTV is still unclear. The blood and plasma collected postpartum from 100 mother-child pairs were analyzed using TTV-specific qPCR. Samples were collected from the peripheral vein of the mother and the umbilical cord. Eighty four percent of pregnant women were TTV positive (median titers: 8 × 104 copies/mL; range: 103 – 3 × 107). The TTV load in plasma was approximately 100 times lower than in whole blood. TTV was not detected in any of cord blood samples. Our data demonstrate the lack of transplacental transmission of TTV (or effective prenatal inhibition of viral proliferation). The presence of the virus in infants may be associated with mother-to-child transmission through breast feeding or other routes of transmission.
more...
No comment yet.
Scooped by Bwana Moses
Scoop.it!

Interferon Gamma Prevents Infectious Entry of Human Papillomavirus 16 via an L2-Dependent Mechanism

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance | Bioinformatics | Oxford Academic

Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance | Bioinformatics | Oxford Academic | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
more...
No comment yet.
Scooped by Bwana Moses
Scoop.it!

CRISPR Eliminates HIV in Live Animals | GEN Genetic Engineering & Biotechnology News - Biotech from Bench to Business | GEN

CRISPR Eliminates HIV in Live Animals | GEN Genetic Engineering & Biotechnology News - Biotech from Bench to Business | GEN | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
New research reveals that HIV DNA can be excised from the genomes of living animals to eliminate further infection
more...
No comment yet.
Rescooped by Bwana Moses from Immunology
Scoop.it!

A CRISPR toolbox to study virus-host interactions : Nature Reviews Microbiology : Nature Research

A CRISPR toolbox to study virus-host interactions : Nature Reviews Microbiology : Nature Research | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Via Gilbert C FAURE
more...
No comment yet.