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Aquatic Viruses
mol-biol, bioinformatics and biology
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Rescooped by Ed Rybicki from Virology and Bioinformatics from Virology.ca
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Viral quasispecies inference from 454 pyrosequencing - BMC Bioinformatics. 2013

AbstractBACKGROUND:

Many potentially life-threatening infectious viruses are highly mutable in nature. Characterizing the fittest variants within a quasispecies from infected patients is expected to allow unprecedented opportunities to investigate the relationship between quasispecies diversity and disease epidemiology. The advent of next-generation sequencing technologies has allowed the study of virus diversity with high-throughput sequencing, although these methods come with higher rates of errors which can artificially increase diversity.

RESULTS:

Here we introduce a novel computational approach that incorporates base quality scores from next-generation sequencers for reconstructing viral genome sequences that simultaneously infers the number of variants within a quasispecies that are present. Comparisons on simulated and clinical data on dengue virus suggest that the novel approach provides a more accurate inference of the underlying number of variants within the quasispecies, which is vital for clinical efforts in mapping the within-host viral diversity. Sequence alignments generated by our approach are also found to exhibit lower rates of error.

CONCLUSIONS:

The ability to infer the viral quasispecies colony that is present within a human host provides the potential for a more accurate classification of the viral phenotype. Understanding the genomics of viruses will be relevant not just to studying how to control or even eradicate these viral infectious diseases, but also in learning about the innate protection in the human host against the viruses.


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Agalma: an automated phylogenomics workflow

BACKGROUND:

In the past decade, transcriptome data have become an important component of many phylogenetic studies. They are a cost-effective source of protein-coding gene sequences, and have helped projects grow from a few genes to hundreds or thousands of genes. Phylogenetic studies now regularly include genes from newly sequenced transcriptomes, as well as publicly available transcriptomes and genomes. Implementing such a phylogenomic study, however, is computationally intensive, requires the coordinated use of many complex software tools, and includes multiple steps for which no published tools exist. Phylogenomic studies have therefore been manual or semiautomated. In addition to taking considerable user time, this makes phylogenomic analyses difficult to reproduce, compare, and extend. In addition, methodological improvements made in the context of one study often cannot be easily applied and evaluated in the context of other studies.

RESULTS:

We present Agalma, an automated tool that constructs matrices for phylogenomic analyses. The user provides raw Illumina transcriptome data, and Agalma produces annotated assemblies, aligned gene sequence matrices, a preliminary phylogeny, and detailed diagnostics that allow the investigator to make extensive assessments of intermediate analysis steps and the final results. Sequences from other sources, such as externally assembled genomes and transcriptomes, can also be incorporated in the analyses. Agalma is built on the BioLite bioinformatics framework, which tracks provenance, profiles processor and memory use, records diagnostics, manages metadata, installs dependencies, logs version numbers and calls to external programs, and enables rich HTML reports for all stages of the analysis. Agalma includes a small test data set and a built-in test analysis of these data. In addition to describing Agalma, we here present a sample analysis of a larger seven-taxon data set. Agalma is available for download at https://bitbucket.org/caseywdunn/agalma.

CONCLUSIONS:

Agalma allows complex phylogenomic analyses to be implemented and described unambiguously as a series of high-level commands. This will enable phylogenomic studies to be readily reproduced, modified, and extended. Agalma also facilitates methods development by providing a complete modular workflow, bundled with test data, that will allow further optimization of each step in the context of a full phylogenomic analysis.


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Ed Rybicki's insight:

Looks to be good for Marine Viromics?

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Previously unknown and highly divergent ssDNA viruses populate the oceans

Previously unknown and highly divergent ssDNA viruses populate the oceans | Aquatic Viruses | Scoop.it

Single-stranded DNA (ssDNA) viruses are economically important pathogens of plants and animals, and are widespread in oceans; yet, the diversity and evolutionary relationships among marine ssDNA viruses remain largely unknown. Here we present the results from a metagenomic study of composite samples from temperate (Saanich Inlet, 11 samples; Strait of Georgia, 85 samples) and subtropical (46 samples, Gulf of Mexico) seawater. Most sequences (84%) had no evident similarity to sequenced viruses. In total, 608 putative complete genomes of ssDNA viruses were assembled, almost doubling the number of ssDNA viral genomes in databases. These comprised 129 genetically distinct groups, each represented by at least one complete genome that had no recognizable similarity to each other or to other virus sequences. Given that the seven recognized families of ssDNA viruses have considerable sequence homology within them, this suggests that many of these genetic groups may represent new viral families. Moreover, nearly 70% of the sequences were similar to one of these genomes, indicating that most of the sequences could be assigned to a genetically distinct group. Most sequences fell within 11 well-defined gene groups, each sharing a common gene. Some of these encoded putative replication and coat proteins that had similarity to sequences from viruses infecting eukaryotes, suggesting that these were likely from viruses infecting eukaryotic phytoplankton and zooplankton.

 
Ed Rybicki's insight:

Bugger!  We wanted to do this...B-)  I suppose we still can - southern ocean samples!!

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The MaSuRCA genome assembler

The MaSuRCA genome assembler | Aquatic Viruses | Scoop.it

Motivation: Second-generation sequencing technologies produce high coverage of the genome by short reads at a low cost, which has prompted development of new assembly methods. In particular, multiple algorithms based on de Bruijn graphs have been shown to be effective for the assembly problem. In this article, we describe a new hybrid approach that has the computational efficiency of de Bruijn graph methods and the flexibility of overlap-based assembly strategies, and which allows variable read lengths while tolerating a significant level of sequencing error. Our method transforms large numbers of paired-end reads into a much smaller number of longer ‘super-reads’. The use of super-reads allows us to assemble combinations of Illumina reads of differing lengths together with longer reads from 454 and Sanger sequencing technologies, making it one of the few assemblers capable of handling such mixtures. We call our system the Maryland Super-Read Celera Assembler (abbreviated MaSuRCA and pronounced ‘mazurka’).


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PLOS Computational Biology: Ten Simple Rules for Cultivating Open Science and Collaborative R&D

PLOS Computational Biology: Ten Simple Rules for Cultivating Open Science and Collaborative R&D | Aquatic Viruses | Scoop.it

How can we address the complexity and cost of applying science to societal challenges?

Open science and collaborative R&D may help [1]–[3]. Open science has been described as “a research accelerator” [4]. Open science implies open access [5] but goes beyond it: “Imagine a connected online web of scientific knowledge that integrates and connects data, computer code, chains of scientific reasoning, descriptions of open problems, and beyond …. tightly integrated with a scientific social web that directs scientists' attention where it is most valuable, releasing enormous collaborative potential.” [1].

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Deep-ocean carbon sinks: Basic research on dark ocean microorganisms

Deep-ocean carbon sinks: Basic research on dark ocean microorganisms | Aquatic Viruses | Scoop.it

Although microbes that live in the so-called "dark ocean"-- below a depth of some 600 feet where light doesn't penetrate -- may not absorb enough carbon to curtail global warming, they do absorb considerable amounts of carbon and merit further 

study.

That is one of the findings of a paper published in the International Society of Microbial Ecology (ISME) Journal by Tim Mattes, associate professor of civil and environmental engineering in the University of Iowa College of Engineering, and his colleagues.

Mattes says that while many people are familiar with the concept of trees and grass absorbing carbon from the air, bacteria, and ancient single-celled organisms called "archaea" in the dark ocean hold between 300 million and 1.3 billion tons of carbon.

"A significant amount of carbon fixation occurs in the dark ocean," says Mattes. "What might make this surprising is that carbon fixation is typically linked to organisms using sunlight as the energy source."

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Researchers sequence the genome of global deep ocean

Researchers sequence the genome of global deep ocean | Aquatic Viruses | Scoop.it
Biologists have started to sequence the genome of the global deep ocean. They are using more than 2,000 samples of microorganisms collected in the Atlantic, Indian and Pacific Oceans during the Malaspina Expedition.  

This collection of marine microbial genomic, the first in the world on a global scale, will provide new clues about a reservoir of biodiversity yet to explore, considering that it could imply the discovery of tens of millions of new genes in the coming years.

The works of sequencing (framed in the Malaspinomics project) focus on the viruses, bacteria and protists that inhabit the ocean to 4,000 meters deep. Most of the biomass of marine organisms is composed of microorganism. Of these, a 72% inhabit the dark ocean, from 200 meters deep. However, so far, the DNA or RNA sequencing had been almost exclusively limited to the ocean surface waters.

Malaspinomics preliminary results reveal a wealth of unknown species of microorganisms in the deep ocean, characterized by an intense biological activity. Specifically, 60% of the bacterial species of the deep ocean detected by massive sequencing techniques are unknown.

Ed Rybicki's insight:

Viruses: they'll find lots of viruses.  But they may well miss the ssRNA and small ssDNA viruses - and it'll have to be done again....

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Gretel Posadas's curator insight, August 23, 2013 8:19 AM

#Malaspinomics preliminary results reveal a wealth of unknown species of microorganisms in the deep ocean, characterized by an intense #biologicalactivity. Specifically, 60% of the bacterial species of the deep ocean detected by massive sequencing techniques are unknown.

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Sea creatures race toward cooler waters

Sea creatures race toward cooler waters | Aquatic Viruses | Scoop.it
UC SANTA BARBARA (US) — Ocean animals are moving toward the poles and doing so even faster than their counterparts on land, new research shows.
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A Call to Count More HPV Cancers as AIDS-Defining Illnesses

The Western Connecticut Health Network has called for the U.S. Centers for Disease Control and Prevention (CDC) to expand the definition of “AIDS-defining illnesses” to include the full range of human papillomavirus (HPV)–related cancers. At present, the CDC only categorizes cervical cancer as an AIDS-defining illness. Using a recent case report published in Rare Tumors of a 27-year-old HIV-positive woman with advanced vulvar cancer as evidence, the Connecticut group suggests that the CDC should further recognize vulvar, vaginal, penile, anal, lower lid squamous cell carcinoma and some head and neck cancers as AIDS-defining.

Ed Rybicki's insight:

Absolutely!

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Nanosyringe!

The rod-shaped bacterium Yersinia enterocolitica, which is transmitted through contaminated food, causes gastrointestinal diseases. In Germany alone, several thousand cases are reported annually. Yersinia uses a rather sophisticated tool—its injection apparatus—to infect humans. Not only does the apparatus look like a syringe, it actually serves a similar purpose. A molecular “needle”, which sticks out from the bacterium’s surface, extends across the bacterial membranes to the host cell. It is through this needle that the bacterium “injects” substances that facilitate infection of the host. Now, for the first time, an interdisciplinary team of HZI scientists together with their colleagues at the Biozentrum of the University of Basel and at the Ecole Polytechnique Fédérale de Lausanne in Switzerland, has presented the structure ofYersinia enterocolitica‘s injectisome in high-resolution and 3D. They published their results in the digital scientific magazine eLife.

Ed Rybicki's insight:

Really nice pictures in this paper: thanks @MicrobiologyNet!

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World's Slowest-Moving Drop Caught on Camera at Last

World's Slowest-Moving Drop Caught on Camera at Last | Aquatic Viruses | Scoop.it
The once-forgotten "tar pitch" experiment has yielded results after a seven-decade wait
Ed Rybicki's insight:

Sloooooooow science...B-)

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Climate change slowdown is due to warming of de...

Climate change slowdown is due to warming of de... | Aquatic Viruses | Scoop.it
Climate sceptics have seized on a pause in warming over the past five years, but the long-term trend is still upwards (Climate change slowdown is due to warming of deep oceans, say scientists | @scoopit via @PlaneteNAUSICAA
Ed Rybicki's insight:

And viruses: what will that do to the way viruses interact with their hosts?  I note coral herpesviruses are induced by temperature rise - who knows what could come out of the deep ocean??

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Newly Discovered Marine Viruses Offer Glimpse Into Untapped Biodiversity - Science Daily (press release)

Newly Discovered Marine Viruses Offer Glimpse Into Untapped Biodiversity - Science Daily (press release) | Aquatic Viruses | Scoop.it
Newly Discovered Marine Viruses Offer Glimpse Into Untapped Biodiversity Science Daily (press release) Researchers of the University of Arizona's Tucson Marine Phage Lab have discovered a dozen new types of unknown viruses that infect different...
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Decoding viral puzzles

Decoding viral puzzles | Aquatic Viruses | Scoop.it
The genome of viruses is usually enclosed inside a shell called capsid. Capsids have unique mechanic properties: they have to be resistant and at the same time capable of dissolving in order to release the genome into the infected cell.
Ed Rybicki's insight:

Love that structural stuf....

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ComplexInsight's curator insight, December 11, 2013 6:23 AM

interesting paper looking at capsid mechanisms. 

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Metabolic reprogramming by viruses in the sunlit and dark ocean

Metabolic reprogramming by viruses in the sunlit and dark ocean | Aquatic Viruses | Scoop.it
Background

Marine ecosystem function is largely determined by matter and energy transformations mediated by microbial community interaction networks. Viral infection modulates network properties through mortality, gene transfer and metabolic reprogramming.

Results

Here we explore the nature and extent of viral metabolic reprogramming throughout the Pacific Ocean depth continuum. We describe 35 marine viral gene families with potential to reprogram metabolic flux through central metabolic pathways recovered from Pacific Ocean waters. Four of these families have been previously reported but 31 are novel. These known and new carbon pathway auxiliary metabolic genes were recovered from a total of 22 viral metagenomes in which viral auxiliary metabolic genes were differentiated from low-level cellular DNA inputs based on small subunit ribosomal RNA gene content, taxonomy, fragment recruitment and genomic context information. Auxiliary metabolic gene distribution patterns reveal that marine viruses target overlapping, but relatively distinct pathways in sunlit and dark ocean waters to redirect host carbon flux towards energy production and viral genome replication under low nutrient, niche-differentiated conditions throughout the depth continuum.

Conclusions

Given half of ocean microbes are infected by viruses at any given time, these findings of broad viral metabolic reprogramming suggest the need for renewed consideration of viruses in global ocean carbon models.

Ed Rybicki's insight:

Amen!

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Fossil genes and microbes in the oldest ice on Earth

Although the vast majority of ice that formed on the Antarctic continent over the past 34 million years has been lost to the oceans, pockets of ancient ice persist in the Dry Valleys of the Transantarctic Mountains. Here we report on the potential metabolic activity of microbes and the state of community DNA in ice derived from Mullins and upper Beacon Valleys. The minimum age of the former is 100 ka, whereas that of the latter is ≈8 Ma, making it the oldest known ice on Earth. In both samples, radiolabeled substrates were incorporated into macromolecules, and microbes grew in nutrient-enriched meltwaters, but metabolic activity and cell viability were critically compromised with age. Although a 16S rDNA-based community reconstruction suggested relatively low bacterial sequence diversity in both ice samples, metagenomic analyses of community DNA revealed many diverse orthologs to extant metabolic genes. Analyses of five ice samples, spanning the last 8 million years in this region, demonstrated an exponential decline in the average community DNA size with a half-life of ≈1.1 million years, thereby constraining the geological preservation of microbes in icy environments and the possible exchange of genetic material to the oceans.

 


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Visualizing virus assembly intermediates inside marine cyanobacteria

Abstract - "Cyanobacteria are photosynthetic organisms responsible for ~25% of organic carbon fixation on the Earth. These bacteria began to convert solar energy and carbon dioxide into bioenergy and oxygen more than two billion years ago. Cyanophages, which infect these bacteria, have an important role in regulating the marine ecosystem by controlling cyanobacteria community organization and mediating lateral gene transfer. Here we visualize the maturation process of cyanophage Syn5 inside its host cell, Synechococcus, using Zernike phase contrast electron cryo-tomography (cryoET)1, 2. This imaging modality yields dramatic enhancement of image contrast over conventional cryoET and thus facilitates the direct identification of subcellular components, including thylakoid membranes, carboxysomes and polyribosomes, as well as phages, inside the congested cytosol of the infected cell. By correlating the structural features and relative abundance of viral progeny within cells at different stages of infection, we identify distinct Syn5 assembly intermediates. Our results indicate that the procapsid releases scaffolding proteins and expands its volume at an early stage of genome packaging. Later in the assembly process, we detected full particles with a tail either with or without an additional horn. The morphogenetic pathway we describe here is highly conserved and was probably established long before that of double-stranded DNA viruses infecting more complex organisms."
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Cool stuff! We gotta try that - Trevor??
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Viruses associated with coral epidemic of 'white plague'

Viruses associated with coral epidemic of 'white plague' | Aquatic Viruses | Scoop.it

They call it the "white plague," and like its black counterpart from the Middle Ages, it conjures up visions of catastrophic death, with a cause that was at first uncertain even as it led to widespread destruction -- on marine corals in the Caribbean Sea.

Ed Rybicki's insight:

Hah!  ssDNA viruses!!  I must get me to a coral reef with white spots....

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Deep microbes live long and slow

Deep microbes live long and slow | Aquatic Viruses | Scoop.it
A diverse range of life forms exists deep below Earth's surface, but they survive at an incredibly slow pace.  

Long-lived bacteria, reproducing only once every 10,000 years, have been found in rocks 2.5km (1.5 miles) below the ocean floor that are as much as 100 million years old.

Viruses and fungi have also been found.

The discoveries raise questions about how life persists in such extreme conditions.

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New discovery of how carbon is stored in the Southern Ocean

New discovery of how carbon is stored in the Southern Ocean | Aquatic Viruses | Scoop.it
Scientists have discovered an important method of how carbon is drawn down from the surface of the Southern Ocean to the deep waters beneath.
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The Media, Online Debate and Anti-Vaccine Tactics

The Media, Online Debate and Anti-Vaccine Tactics | Aquatic Viruses | Scoop.it
I've been catching up with my reading. I think some of what I've been catching up on is worth sharing. The journal Vaccine had a special edition in 2012 on The Role of Internet Use in Vaccination D...
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Nice analysis

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Pan genome of the phytoplankton Emiliania underpins its global distribution.

Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.

 
Ed Rybicki's insight:

Great achievement - with a LOT of authors.  Including our very own Declan Schroeder: ex-student and collaborator!

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Pandoravirus, bigger and unlike anything seen before

Pandoravirus, bigger and unlike anything seen before | Aquatic Viruses | Scoop.it
Pandoraviruses, which are physically and genetically unlike any previously known viruses, are now the biggest known viruses.
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Nice commentary from Vincent Racaniello.

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Pandoravirus....

Pandoravirus.... | Aquatic Viruses | Scoop.it
Ed Rybicki's insight:

I do so wish that these folk would stop inventing names that have no basis in conventional virus taxonomy: Latinate double-barrelled names have no place in virology, while obviously the viruses do!!

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Marine Microbe Produces Unknown Antibiotic - Yahoo! News

Marine Microbe Produces Unknown Antibiotic
Yahoo! News
Next time you hit the beach, dig your feet into the sand.
Ed Rybicki's insight:

Could be the answers to every antibiotic need we have are already in the waters around us....

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