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Category: biotech/medical – Page 1918

O.o!

The first sequenced genome was that of the 3569-nucleotide single-stranded RNA (ssRNA) bacteriophage MS2. Despite the recent accumulation of vast amounts of DNA and RNA sequence data, only 12 representative ssRNA phage genome sequences are available from the NCBI Genome database (June 2019). The difficulty in detecting RNA phages in metagenomic datasets raises questions as to their abundance, taxonomic structure, and ecological importance. In this study, we iteratively applied profile hidden Markov models to detect conserved ssRNA phage proteins in 82 publicly available metatranscriptomic datasets generated from activated sludge and aquatic environments. We identified 15,611 nonredundant ssRNA phage sequences, including 1015 near-complete genomes. This expansion in the number of known sequences enabled us to complete a phylogenetic assessment of both sequences identified in this study and known ssRNA phage genomes. Our expansion of these viruses from two environments suggests that they have been overlooked within microbiome studies.

Viruses, particularly bacteriophages targeting prokaryotes, are the most diverse biological entities in the biosphere (1, 2). Currently, there are 11,489 genome sequences available in the NCBI (National Center for Biotechnology Information) Viral RefSeq database (version 94). The vast majority of known phage have a double-stranded DNA (dsDNA) genome (3, 4). Recent metagenomic analysis of 145 marine virome sampling sites identified 195,728 DNA viral populations, highlighting that only a fraction of Earth’s viral diversity has been characterized (5). An additional expansion of known phage populations by Roux et al. (6) revealed that not only dsDNA phages but also single-stranded DNA Inoviridae are far more diverse than previously considered. The rapid expansion in viral discovery through metagenomics is enabling a greater understanding of their roles within environments and their evolutionary relationships, which is subsequently causing a revolution in phage taxonomy (7).

Despite the identification of single-stranded RNA (ssRNA) phages over 50 years ago (8), there are few representative sequences available. The International Committee on Taxonomy of Viruses (ICTV) has currently categorized approximately 5500 viruses (9). Yet, their classification only applies to 25 ssRNA phage sequences (complete or partial) across two genera, Levivirus and Allolevivirus, and an additional 32 sequences unclassified below a family taxonomic rank (10). Historically, methods for classifying Leviviridae depended on molecular weight, density, sedimentation, and serological cross-reactivity (11). A subsequent classification method separated the two genera, with the Alloleviviruses containing a fourth unique gene predicted to encode a lysin (12). Recently, an analysis of the evolution origin of all currently known RNA viruses by Wolf et al. (13) suggested that ssRNA phages may actually be two distinct lineages, which they termed Leviviridae and “Levi-like” viruses.

Continue reading “Expansion of known ssRNA phage genomes: From tens to over a thousand” | >

O.o probs alien o.o circa 2013.

Remember when encyclopaedias were books, and not just websites? You’d have a shelf full of information, packaged into entries, and then into separate volumes. Your genome is organised in a similar way. Your DNA is packaged into large volumes called chromosomes. There are 23 pairs of them, each of which contains a long string of genes. And just as encyclopaedia books are bound in sturdy covers to prevent the pages within from fraying, so too are your chromosomes capped by protective structures called telomeres.

That’s basically how it works in any animal or plant or fungus. The number of chromosomes might vary a lot—fruit flies have 8 while dogs have 78—but the basic organisation is the same.

But there’s a pond-dwelling creature called Oxytricha trifallax whose DNA is organised in a very… different… way. A team of US scientists has sequenced its genome for the first time and discovered genetic chaos. It’s like someone has taken the encyclopaedias, ripped out all the individual pages, torn some of them, photocopied everything dozens of times, and stuffed the whole lot in a gigantic messy drawer.

Continue reading “You Have 46 Chromosomes. This Pond Creature Has 15,600” | >

Researchers-genetically-alter-the-immune-system-of-cancer-patients-without-side-effect.

US scientists have succeeded in genetically editing the immune systems of three cancer patients using CRISPR, without creating any side effects, a first for the tool which is revolutionizing biomedical research.

The highly anticipated results from the first phase of a clinical trial were published in the journal Science on Thursday.

They represent a stepping stone that doesn’t yet prove CRISPR can be used to fight cancer. Indeed, one of the patients has since died and the disease has worsened in the other two — but the trial does show that the technique is non-toxic.

Continue reading “US Trial Shows 3 Cancer Patients Had Their Genomes Altered Safely” | >

Sharks are at the top of the marine food chain for a reason. Their massive size along with a dazzling row of extra-sharp teeth make them the fiercest hunters in our oceans. But it turns out that the shark’s aquatic dominance reaches down into its very DNA, and through its mutations, sharks could teach us how to fight our most deadly affliction—cancer.

This isn’t the first evidence that mutations can prove beneficial for disease resistance and long-term survival. High bone density, a hemoglobin that boosts malaria resistance, and a third retinal cone that improves color vision are some human examples. But new gene mapping conducted by scientists at the Save Our Seas Foundation Shark Research Center at Florida’s Nova Southeastern University, the Guy Harvey Research Institute, and the Cornell University College of Veterinary Medicine shows that sharks have developed genomic adaptations that repair damaged DNA, effectively protecting them against cancer and other diseases.

Read more | >
https://www.youtube.com/watch?v=DXo5BVdzZQE&t=1s

If you’re tired of robocalls you might want to consider one of Google’s Pixel phones. On Thursday, Google announced that its Call Screen feature, which automatically blocks known robocallers in Google’s database, is rolling out to all Pixel phones this week. It was previously only available on the newest Pixel 3 and Pixel 4 devices. (The original Pixel phone, which launched in 2016, stopped receiving software updates last year, but Google says it’ll still get Call Screen.)

Robocalls may be driving you nuts. According to the YouMail robocall index, which is compiled from the YouMail app that’s built to also block robocalls, there were 4.7 billion robocalls placed in the U.S. in January 2020, or 1,800 a second and 14.4 calls per person. Some U.S. carriers, like AT&T, Verizon, T-Mobile and Sprint are working in the background to prevent robocalls, too. Though sometimes they still sneak through or only work on certain phones.

And other companies, like Apple, let you automatically send calls that are received from people who aren’t in your address book right to voicemail. But sometimes you miss an important call from someone, like a doctor whose number you might not have saved.

Read more | >

O.o.

If you’ve ever seen any Jaws movies, you know not to mess with the great white shark. New research says there is more reason to be in awe of these predators: their DNA makes them resilient to diseases like cancer.

A collaborative research team from Nova Southeastern University, Florida, California State University, Cornell University College of Veterinary Medicine, University of Porto, Portugal and others published their findings in PNAS.

“Decoding the white shark genome is providing science with a new set of keys to unlock lingering mysteries about these feared and misunderstood predators – why sharks have thrived for some 500 million years, longer than almost any vertebrate on earth” said Dr. Salvador Jorgensen, a Senior Research Scientist at the Monterey Bay Aquarium, who co-authored the study.

Continue reading “Why Great White Sharks are Invincible: It’s in Their Genes” | >