Tools and tips for scientific tinkers and tailors
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Rescooped by Mel Melendrez-Vallard from Virology and Bioinformatics from Virology.ca
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Lateral Gene Transfer from the Dead

Lateral Gene Transfer from the Dead | Tools and tips for scientific tinkers and tailors | Scoop.it

In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer, however, this may not be the case, because the species lineage from which a gene was transferred may have gone extinct or not have been sampled. Because it is not feasible to specify or reconstruct the complete phylogeny of all species, we must describe the evolution of genes outside the represented phylogeny by modeling the speciation dynamics that gave rise to the complete phylogeny. We demonstrate that if the number of sampled species is small compared with the total number of existing species, the overwhelming majority of gene transfers involve speciation to and evolution along extinct or unsampled lineages. We show that the evolution of genes along extinct or unsampled lineages can to good approximation be treated as those of independently evolving lineages described by a few global parameters. Using this result, we derive an algorithm to calculate the probability of a gene tree and recover the maximum-likelihood reconciliation given the phylogeny of the sampled species. Examining 473 near-universal gene families from 36 cyanobacteria, we find that nearly a third of transfer events (28%) appear to have topological signatures of evolution along extinct species, but only approximately 6% of transfers trace their ancestry to before the common ancestor of the sampled cyanobacteria. [Gene tree reconciliation; lateral gene transfer; macroevolution; phylogeny.]


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sweet...and morbid...but sweet.

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Tools and tips for scientific tinkers and tailors
Next gen sequencing, bioinformatics, virology, microbiology, genomes, zoonoses, workshops, conferences, all-around science geekery
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Collaboration keeps your research program alive | Small Pond Science

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Rescooped by Mel Melendrez-Vallard from Twisted Microbiology
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Mouse microbes may make scientific studies harder to replicate

Mouse microbes may make scientific studies harder to replicate | Tools and tips for scientific tinkers and tailors | Scoop.it
The zoo of bacteria and viruses within each lab animal may be confounding experiments

Via Cesar Sanchez
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Rescooped by Mel Melendrez-Vallard from Virology and Bioinformatics from Virology.ca
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Exploring the virome of diseased horses

Exploring the virome of diseased horses | Tools and tips for scientific tinkers and tailors | Scoop.it
Metagenomics was used to characterize viral genomes in clinical specimens of horses with various organ-specific diseases of unknown aetiology. A novel parvovirus as well as a previously described hepacivirus closely related to human hepatitis C viru

Via Bradford Condon, Chris Upton + helpers
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Biologists Search for New Model Organisms | Quanta Magazine

Biologists Search for New Model Organisms |  Quanta Magazine | Tools and tips for scientific tinkers and tailors | Scoop.it
The bulk of biological research is centered on a handful of species. Are we missing a huge chunk of interesting biology?
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Dragons and their Microbiomes – really

Dragons and their Microbiomes – really | Tools and tips for scientific tinkers and tailors | Scoop.it
OK so I love Komodo dragons.  I love microbes and microbiomes.  And I am an editor at mSystems.  So yes I am biased in all sorts of ways about this paper.  So with that caveat – I think this …
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Researchers and public health officials use RNA-Seq to track transmission of epidemic viruses | RNA-Seq Blog

(IEEE Spectrum) -Using a genome sequencer smaller than a stapler, geneticists have demonstrated the role they can play in combating outbreaks of infectious

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F1000Research launches rapid, open, publishing channel to help scientists tackle Zika

Following the World Health Organization's announcement that Zika-linked birth defects and neurological problems pose a global public health emergency, open science platform F1000Research has launched the Zika and Arbovirus Outbreaks channel.
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Optimizing Viral Discovery in Bats

Optimizing Viral Discovery in Bats | Tools and tips for scientific tinkers and tailors | Scoop.it

Viral discovery studies in bats have increased dramatically over the past decade, yet a rigorous synthesis of the published data is lacking.

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Read Until: Real time selective sequencing using Oxford Nanopore MinION

Read Until: Real time selective sequencing using Oxford Nanopore MinION | Tools and tips for scientific tinkers and tailors | Scoop.it

AGBT 2016 is happening now and it has been two years since we heard about the first MinION experiment at AGBT 2014.

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Avian Flu Diary: WHO Update : Yellow Fever Outbreak In Angola

Avian Flu Diary: WHO Update : Yellow Fever Outbreak In Angola | Tools and tips for scientific tinkers and tailors | Scoop.it

#11,006Over the past couple of days there have been media reports of another arbovirus outbreak in west central Africa (see Yellow fever outbreak kills 37 in Angola) vectored by the same mosquito as the Zika (and Dengue & CHKV) virus.Yellow...

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Rescooped by Mel Melendrez-Vallard from Emerging Viruses, Virus Discovery and Virus Characterization
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Zika Fears Spur Pharmaceutical Gold Rush Amid Vaccine Vacuum

Before it became known as a deadly virus, Zika was just a lush forest on the north shores of Lake Victoria, a quiet sanctuary across from Tanzania and its gold mines.

Via Ian M Mackay, PhD
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Rescooped by Mel Melendrez-Vallard from Viral Modeling and Simulation
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Single-Molecule FISH Reveals Non-selective Packaging of Rift Valley Fever Virus Genome Segments

Author Summary The bunyavirus family is one of the largest virus families on Earth, of which several members cause severe disease in humans, animals or plants. Little is known about the mechanisms that facilitate the production of infectious bunyavirus virions, which should contain at least one copy of the small (S), medium (M) and large (L) genome segment. In this study, we investigated the genome packaging process of the Rift Valley fever virus (RVFV) by visualizing individual genome segments inside infected cells and virions. Experiments performed with wild-type virus, two- and four-segmented variants, and a variant with a codon-shuffled M segment showed that the production of infectious virions is a non-selective process and is unlikely to involve the formation of a supramolecular viral RNA complex. These observations have broad implications for understanding the bunyavirus replication cycle and may facilitate the development of new vaccines and the identification of novel antiviral targets.

Via burkesquires
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Rescooped by Mel Melendrez-Vallard from Next Generation Sequencing (NGS)
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Fighting Antibiotic Resistance Through Deeper Sequencing

Fighting Antibiotic Resistance Through Deeper Sequencing | Tools and tips for scientific tinkers and tailors | Scoop.it

Researchers developed a new technique to uncover rare mutations in the bacterial genome and used it to determine how certain antibiotics mutate DNA. How will this approach help combat antibiotic resistance?


Via Integrated DNA Technologies
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The Public’s Love-Hate Relationship with Technology « Science-Based Medicine

There are many complex factors driving up the cost of healthcare, but one major factor is increasing medical technology. Often new expensiv
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The Impact of Teaching Assistantships | PLOS Blogs Network

The Impact of Teaching Assistantships | PLOS Blogs Network | Tools and tips for scientific tinkers and tailors | Scoop.it
Source: The Impact of Teaching Assistantships Graduate teaching assistants (GTAs) are graduate students employed by a university or college to undertake certain teaching responsibilities. These responsibilities may include grading assignments, leading discussion or recitation sessions, or teaching laboratory classes for introductory undergraduate courses. Due to this broad range of responsibilities, GTAs hold a unique position that melds student, researcher, and teacher roles. According to the Bureau of Labor Statistics, there are  125,100 GTAs currently employed in the United States, a testimonial to the importance of the GTA workforce in higher education. In 2005, a survey of 65 institutes of higher education in the United States found that 91% of undergraduate biology laboratory sections were taught by GTAs in research institutes. Clearly, undergraduate education is now dependent on GTAs. Considering this, I ask, how do teaching assistantships impact graduate assistants and their
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Avian Flu Diary: CIDRAP's Antimicrobial Sterwardship Project (ASP)

Avian Flu Diary: CIDRAP's Antimicrobial Sterwardship Project (ASP) | Tools and tips for scientific tinkers and tailors | Scoop.it
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Plant adaptation or acclimation to rising CO2? Insight from first multigenerational RNA-Seq transcriptome - Watson-Lazowski - 2016 - Global Change Biology - Wiley Online Library

Plant adaptation or acclimation to rising CO2? Insight from first multigenerational RNA-Seq transcriptome - Watson-Lazowski - 2016 - Global Change Biology - Wiley Online Library | Tools and tips for scientific tinkers and tailors | Scoop.it
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Two Potentially Important Developments on Nanopore « Homolog.us – Bioinformatics

The first paper demonstrates selective sequencing, whereas the second ones improves accuracy by introducing circularization.

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F1000Research Article: Open drug discovery for the Zika virus.

Read the latest article version by Sean Ekins, Daniel Mietchen, Megan Coffee, Thomas P Stratton, Joel S Freundlich, Lucio Freitas-Junior, Eugene Muratov, Jair Siqueira-Neto, Antony J Williams, Carolina Andrade, at F1000Research.
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Micro-scale Spatial Clustering of Cholera Risk Factors in Urban Bangladesh

Micro-scale Spatial Clustering of Cholera Risk Factors in Urban Bangladesh | Tools and tips for scientific tinkers and tailors | Scoop.it

Author Summary While clustering of cholera incidence had been previously described, the relative role of similar risk behaviors versus transmission dynamics is not well understood.

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mBiosphere: Catching Ebola virus in the act of fusion

Since the first outbreak of Ebola virus in 1976, the frequency and scale of the deadly disease’s outbreaks have increased.

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Epidemiology, Impact and Control of Rabies in Nepal: A Systematic Review

Epidemiology, Impact and Control of Rabies in Nepal: A Systematic Review | Tools and tips for scientific tinkers and tailors | Scoop.it

Author Summary Rabies has been known as a deadly disease in Nepal for decades, but information on epidemiology, impact and control remains scattered.

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Rescooped by Mel Melendrez-Vallard from Next Generation Sequencing (NGS)
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Sophia Genetics and Integrated DNA Technologies (IDT) partner to create NGS solutions in routine clinical diagnostics

Sophia Genetics, the global leader in Data-Driven Medicine (DDM), announced today the signing of a new strategic partnership with Integrated DNA Technologies (IDT). Under the terms of the agreement, Sophia Genetics will combine its Sophia DDM™ analytics platform with IDT’s NGS target capture products. The new bundle will create the most advanced NGS data analytics platform in the market.


Via Integrated DNA Technologies
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Avian Flu Diary: EID Journal: MERS-CoV Antibodies In Alpacas - Qatar

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