"Culturable bacterial abundance at 11 different depths of a 50.26 m ice core from the Tallaksenvarden Nunatak, Antarctica, varied from 0.02 to 5.8 × 103 CFU ml−1 of the melt water. A total of 138 bacterial strains were recovered from the 11 different depths of the ice core. Based on 16S rRNA gene sequence analyses, the 138 isolates could be categorized into 25 phylotypes belonging to phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. All isolates had 16S rRNA sequences similar to previously determined sequences (97.2–100%). No correlation was observed in the distribution of the isolates at the various depths either at the phylum, genus or species level. The 25 phylotypes varied in growth temperature range, tolerance to NaCl, growth pH range and ability to produce eight different extracellular enzymes at either 4 or 18 °C. Iso-, anteiso-, unsaturated and saturated fatty acids together constituted a significant proportion of the total fatty acid composition."
The very first building in the world with a shading system consisting of live micro-algae is being built in the suburb of Wilhemsburg in Hamburg. The “algae house” will be complete in 2013 and will comprise approximately 200 square meters of such elements.
Designed for the International Building Exhibition in Hamburg, the zero-energy house will be the first real-life test for the new façade system. Algae in the bio-reactor façades grow faster in bright sunlight to provide more shade. The bio-reactors power the building by capturing solar thermal heat and producing biomass that can be harvested.
19 water samples were collected aboard the Sorcerer II sailing vessel from the southern Indian Ocean in an effort to more thoroughly understand the lifestyle strategies of the microbial inhabitants of this ultra-oligotrophic region
Earlier this year, a 17-year-old French woman arrived at her ophthalmologist with pain and redness in her left eye. She woman had been using tap water to dilute the cleaning solution for her contact lenses, and even though they were meant to be replaced every month, she would wear them for three. As a result, the fluid in her contact lens case had become contaminated with three species of bacteria, an amoeba called Acanthamoeba polyphaga that can caused inflamed eyes.
The mystery of the woman’s inflamed eyes was solved, but Bernard La Scola and Christelle Desnueslooked inside the amoeba, they found more surprises.
It was carrying two species of bacteria, and a giant virus that no one had seen before—they called it Lentille virus. Inside that, they found a virophage—an virus that infects other viruses—which they called Sputnik 2. And in both Lentille virus and Sputnik 2, they found even smaller genetic parasites – tiny chunks of DNA that can hop around the genomes of the virus, and stow away inside the virophage. They called these transpovirons.
So, the poor red eyes of the French patient were carrying an entire world of parasites, nested within one another like Russian Matryoshka nesting dolls. The transpovirons were hidden in the virophage, which infected the giant virus, which infected the amoeba, which infected the woman’s eyes.
Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both as a single linear representation of the population and, as a backbone on which intra-host variants can be accurately mapped. The availability of consensus assemblies and robustly mapped variants are crucial to the genetic study of viral disease progression, transmission dynamics, and viral evolution. Existing de novo assembly techniques fail to robustly assemble ultra-deep sequence data from genetically heterogeneous populations such as viruses into full-length genomes due to the presence of extensive genetic variability, contaminants, and variable sequence coverage.
Results We present VICUNA, a de novo assembly algorithm suitable for generating consensus assemblies from genetically heterogeneous populations. We demonstrate its effectiveness on Dengue, Human Immunodeficiency and West Nile viral populations, representing a range of intra-host diversity. Compared to state-of-the-art assemblers designed for haploid or diploid systems, VICUNA recovers full-length consensus and captures insertion/deletion polymorphisms in diverse samples. Final assemblies maintain a high base calling accuracy. VICUNA program is publicly available at: http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/viral-genomics-analysis-software
Conclusions We developed VICUNA, a publicly available software tool, that enables consensus assembly of ultra-deep sequence derived from diverse viral populations. While VICUNA was developed for the analysis of viral populations, its application to other heterogeneous sequence data sets such as metagenomic or tumor cell population samples may prove beneficial in these fields of research.
The emergence of the H1N1 influenza virus that leapt from pigs to humans in 2009, triggering a global pandemic, reminded us of the need to monitor animals such as pigs that can host the development of dangerous viral strains.
A study published today re-emphasizes that need. Young-Ki Choi at Chungbuk National University in Cheongju, South Korea, and his colleagues have isolated a new strain of H1N2 influenza from Korean pigs that kills infected ferrets — the model animal of choice for influenza work — and can spread through the air.
Plans for giant Antarctic marine sanctuary falterUSA TODAYWELLINGTON, New Zealand (AP) -- Antarctica's Ross Sea is often described as the most isolated and pristine ocean on Earth, a place where seals and penguins still rule the waves and humans...
"States in the European Union (EU) can’t create their own approval process for growing genetically modified organisms (GMOs), the EU Court of Justice ruled last week (September 6).
The judgment concludes a dispute between the Italian Ministry of Agriculture and the Italian arm of biotechnology company Pioneer Hi-Bred, which produces and distributes conventional and genetically modified (GM) seeds. The Ministry refused to allow Pioneer Hi-Bred to cultivate GM maize—despite prior approval by the EU—claiming a lack of “co-existence” measures between modified, organic, and conventional crops."
Yes - which judgement is vindicated by the recent publication of a meta-analysis showing that there are next to no nutitional advantages to eating organic food, and no proof "normal" crops are more contaminated with pesticides - which, seeing as organic is generally more expensive, means it is a waste of farming space.
What is a virus? Are viruses alive? Should they be classified among microorganisms? One would expect these simple questions to have been settled a century after the discovery of the first viral disease. For years, modern virology successfully unravelled the huge diversity of viruses in terms of genetic material, replication mechanism, pathogenicity, host infection, and more recently particle structure, planet-wide distribution and ecological significance. Yet, little progress was made in understanding their evolutionary origin(s), as well as the fundamental nature of their relationship with the cellular world. Thanks to the recent studies on Mimivirus and other large DNA viruses, we are now entering a new era where the most basic concepts about viruses are revisited, including their true nature, how fundamentally different they are from cellular microorganisms, and how essential they might have been in the major innovations that punctuated the evolution of life.
I thank Russell Kightley for the Mimivirus graphic
"Available treatments for many infectious diseases are limited. In particular, diseases caused by viral pathogens have demonstrated the need for new medicines, due to the increasing appearance of resistance to these available treatments. Thousands of novel compounds have been isolated from various marine organisms and tested for pharmacological properties, many of which are commercially available. The screening of natural products derived from marine species for antiviral activity has yielded a considerable number of active crude aqueous and organic solvent extracts. Today, over 40 compounds are commercially available in pharmacological markets, including alternative antiviral medicines or those being tested as potential antiviral drugs. Many more are being tested as potential antiviral drugs at the preclinical and clinical stages. The growing interest in marine-derived antiviral compounds, along with the development of new technology in marine cultures and extraction, will significantly expedite the current exploration of the marine environment for compounds with significant pharmacological applications, which will continue to be a promising strategy and new trend for modern medicine."
And the reason that marine organisms have all these anti-viral compounds is...they have a lot of viruses. Some of which we aim to find!
A compound discovered by a UCT drug discovery programme has been selected by MMV for its potent activity against multiple points in parasite's lifecycle. A recently discovered compound - named MMV390048 - from the aminopyridine class not only has the potential to become part of a single-dose cure for all strains of malaria, but might also be able to block transmission of the parasite from person to person, according to a research collaboration involving the Medicines for Malaria Venture (MMV), based in Switzerland, and the Drug Discovery and Development Centre (H3-D) at UCT. On the basis of initial results it was selected by MMV for further development - making it the first compound researched on African soil to enter preclinical development in partnership with MMV.
During establishment of primary cell culture from the kidney of a dead Pacific white-sided dolphin (Lagenorhynchus obliquidens), a cytopathic effect was observed. Polymerase chain reaction with a set of herpesvirus consensus primers yielded a fragment of the expected size. Nucleotide sequencing of the product indicated that the isolated virus was closely related to an alphaherpesvirus detected in a bottlenose dolphin in the United States, but the sequence identity at the protein level was low (86.6 %). Phylogenetic analysis of the encoded sequence confirmed that the new isolate belonged to the subfamily Alphaherpesvirinae and clustered together with other cetacean alphaherpesviruses. The complete gene encoding glycoprotein B (2,757 bp) was amplified from the novel isolate; the encoded protein was compared with the corresponding protein of other herpesviruses, revealing that this virus belongs to the genus Varicellovirus. Taken together, these results suggest that this virus corresponds to a novel herpesvirus capable of infecting Pacific white-sided dolphins.
A meeting of government officials reveals that medical equipment is becoming riddled with malware.
In a typical example, at Beth Israel Deaconess Medical Center in Boston, 664 pieces of medical equipment are running on older Windows operating systems that manufactures will not modify or allow the hospital to change—even to add antivirus software—because of disagreements over whether modifications could run afoul of U.S. Food and Drug Administration regulatory reviews, Fu says.
As a result, these computers are frequently infected with malware, and one or two have to be taken offline each week for cleaning, says Mark Olson, chief information security officer at Beth Israel.
"I find this mind-boggling," Fu says. "Conventional malware is rampant in hospitals because of medical devices using unpatched operating systems. There's little recourse for hospitals when a manufacturer refuses to allow OS updates or security patches."
The worries over possible consequences for patients were described last Thursday at a meeting of a medical-device panel at the National Institute of Standards and Technology Information Security & Privacy Advisory Board, of which Fu is a member, in Washington, D.C. At the meeting, Olson described how malware at one point slowed down fetal monitors used on women with high-risk pregnancies being treated in intensive-care wards.
"Viruses with genomes greater than 300 kb and up to 1200 kb are being discovered with increasing frequency. These large viruses (often called giruses) can encode up to 900 proteins and also many tRNAs. Consequently, these viruses have more protein-encoding genes than many bacteria, and the concept of small particle/small genome that once defined viruses is no longer valid. Giruses infect bacteria and animals although most of the recently discovered ones infect protists. Thus, genome gigantism is not restricted to a specific host or phylogenetic clade. To date, most of the giruses are associated with aqueous environments. Many of these large viruses (phycodnaviruses and Mimiviruses) probably have a common evolutionary ancestor with the poxviruses, iridoviruses, asfarviruses, ascoviruses, and a recently discovered Marseillevirus. One issue that is perhaps not appreciated by the microbiology community is that large viruses, even ones classified in the same family, can differ significantly in morphology, lifestyle, and genome structure. This review focuses on some of these differences rather than provides extensive details about individual viruses."
Mimivirus image courtesy Russell Kightley Media. Thanks Ken Y A-B!
The Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) constitute an apparently monophyletic group that consists of at least 6 families of viruses infecting a broad variety of eukaryotic hosts.
A detailed study of the evolution of the genomic core of the NCLDV reveals substantial complexity and diversity of evolutionary scenarios that was largely unsuspected previously. The phylogenetic coherence between the core genes is sufficient to validate the hypothesis on the evolution of all NCLDV from a common ancestral virus although the set of ancestral genes might be smaller than previously inferred from patterns of gene presence-absence.
The discovery of Mimivirus, with its very large genome content, made it possible to identify genes common to the three domains of life (Eukarya, Bacteria and Archaea) and to generate controversial phylogenomic trees congruent with that of ribosomal genes, branching Mimivirus at its root. Here we used sequences from metagenomic databases, Marseillevirus and three new viruses extending the Mimiviridae family to generate the phylogenetic trees of eight proteins involved in different steps of DNA processing. Compared to the three ribosomal defined domains, we report a single common origin for Nucleocytoplasmic Large DNA Viruses (NCLDV), DNA processing genes rooted between Archaea and Eukarya, with a topology congruent with that of the ribosomal tree. As for translation, we found in our new viruses, together with Mimivirus, five proteins rooted deeply in the eukaryotic clade. In addition, comparison of informational genes repertoire based on phyletic pattern analysis supports existence of a clade containing NCLDVs clearly distinct from that of Eukarya, Bacteria and Archaea. We hypothesize that the core genome of NCLDV is as ancient as the three currently accepted domains of life.
NGS4MG: Next Generation Sequencing for Marine Genomics Symposium Vigo (Spain), 27 September 2012. The recent advances in sequencing technology have revolutionized genomic research and have represented a big ...
In episode 63 of MicrobeWorld Video, Dr. Stan Maloy talks with Forest Rohwer Ph.D., Professor of Biology, San Diego State University, about his research on the microbes of the ocean, coral reefs and the human lung. This episode was filmed at the American Association for the Advancement of Science Meeting in Vancouver, Canada on February 18th, 2012.
Viruses make up a large portion of the world's oceans, with over ten million per milliliter of seawater. Rohwer's interest in better understanding these viruses led him to becoming an expert in marine virology and a founder of the field of viral metagenomics.
Forest discovered that these viruses are very good at controlling the number and type of bacteria in the ocean and through the process of gene transfer possess the potential to change marine bacteria into human pathogens.
Among Forest's other interests are coral reefs. He has studied the link between humans inhabiting the land around coral reefs and the decaying health of the corresponding coral.
Forest also studies cystic fibrosis, a disease of the human lung, which mimics what he sees going on with the health of coral reefs. Rohwer explains how his work across many different scientific disciplines has helped his research interests broaden while leading to new discoveries unlikely to have been made without the knowledge and tools of other scientific fields.
Dr Willie Wilson is an algal virus ecologist. He has 21 years research experience and is currently a Senior Research Scientist at Bigelow Laboratory for Ocean Sciences and Director of the NCMA. His research focuses on the many roles of marine algal viruses, which he describes as “lubricants of the great engines of planetary control”. Emerging research interests include giant marine viruses and algal biofuels. He is also enthusiastic about scientific outreach and technology transfer. Dr Wilson’s research has contributed to 85 publications in internationally renowned journals and books and, as PI and co-PI he has won over $15-million in grants from federal agencies since 1998.
"Viruses are the most abundant life forms on Earth, with an estimated 1031 total viruses globally. The majority of these viruses infect microbes, whether bacteria, archaea or microeukaryotes. Given the importance of microbes in driving global biogeochemical cycles, it would seem, based on numerical abundances alone, that viruses also play an important role in the global cycling of carbon and nutrients. However, the importance of viruses in controlling host populations and ecosystem functions, such as the regeneration, storage and export of carbon and other nutrients, remains unresolved. Here, we report on advances in the study of ecological effects of viruses of microbes. In doing so, we focus on an area of increasing importance: the role that ocean viruses play in shaping microbial population sizes as well as in regenerating carbon and other nutrients."
Really good review - not the least because it points out that very few planners take viruses into consieration when considering carbon cycling - especially on land.