“Polygenic Adaptation”
For just the second time, a patient with AIDS appears to have been cured of the disease after receiving a stem cell transplant from a donor with a genetic mutation that provides resistance to HIV, which causes AIDS. But the mutation is exceedingly rare, raising controversial questions of whether it may be replicated using nascent gene-editing tools like CRISPR/Cas9.
Scientists have revealed how certain wild plants with naturally doubled ‘supergenomes’ can stay ahead of the game when it comes to adapting to climate volatility and hostile environments.
This world-first study, published in Nature Ecology and Evolution,could have significant implications for plant and crop sustainability in the face of climate change.
NEW YORK (GenomeWeb) – Some large structural variants in the human genome exhibit population-specific patterns, according to a new analysis of more than 150 genome maps.
Large structural variants — those that are bigger than 2 kilobases — are difficult to detect, especially as short-read sequencing technologies are the most commonly used tools in genomic analysis.
For their study, Pui-Yan Kwok from the University of California, San Francisco and his colleagues analyzed optical genome maps generated for more than 150 individuals representing more than two dozen populations. A phylogenetic analysis of these maps indicated that some SVs and CNVs show variable population patterns. The researchers were also able to characterize SVs in typically intractable regions of the genome, including spots not covered by the human reference genome. Their results were published yesterday in Nature Communications.
What makes a pathogen successful? What determines a plant’s ability to defend itself against an invader? The outcome of a myriad of encounters between plants and their pathogens have preoccupied humans since the dawn of agriculture. Crop diseases have a devastating economic impact that reaches billions of dollars annually and are a recurring global threat to food production (Horvath 2018). Discovering the key that unlocks the code of plant-pathogen interactions has motivated extensive research on the molecular determinants of pathogen virulence and plant resistance, and on devising strategies to apply this knowledge in modern agricultural practices.
The connection between an influenza virus surface protein and a host cell lipid has been discovered by researchers at the University of Maine and the National Institutes of Health. Confirmation of direct interaction between the protein and lipid could lead to new antiviral therapies.
Despite being globally infrequent, testicular germ cell tumors (TGCTs) represent the most common neoplasms in young adult Caucasian men. They are challenging tumors, hallmarked by striking heterogeneity; however, they show very few mutations and share the same (almost) unifying cytogenetic abnormality, in the form of isochromosome 12p. This leaves room for Epigenetic phenomena to explain such diversity. Epigenetic mechanisms frequently deregulated in various cancer types include DNA methylation, non-coding RNAs, but also the effect on chromatin accessibility subsequent to histone post-translational modifications (PTMs) and to the action of chromatin remodeling complexes (ChRCs). These modifications are introduced by complex families of enzymes (DNA and histone modifying enzymes) which show, naturally, deregulated expression in cancer. However, and despite epigenetic (de)regulation being especially relevant in TGCTs, few studies have addressed the role of these enzymes in this tumor model.
The genome editor CRISPR has transformed many areas of biology, but using this tool to enhance certain varieties of crops such as wheat and corn remains difficult because of the plants’ tough cell walls. Now, a major agricultural company has creatively solved that problem by using pollen from one genetically modified plant to carry CRISPR’s components into another plant’s cells. The solution promises to speed the creation of better and more versatile crops, scientists say.
CRISPR-Cas9 genome editing therapy has been shown by the Salk Institute team to suppress the accelerated aging observed in mice with Hutchinson-Gilford Progeria syndrome; and provided insight into the molecular pathways involved in accelerated aging, and how to reduce toxic proteins via gene therapy.
NEW YORK (GenomeWeb) – In a study published in Science late last week, researchers from the US, China, and Germany reported a new method they've developed to detect off-target mutations created from editing one blastomere of two-cell mouse embryos using either CRISPR-Cas9 or one of two base editing technologies.
This method — named GOTI (Genome-wide Off-target analysis by Two-cell embryo Injection) — found that off-target single nucleotide variants (SNVs) were rare in embryos edited by CRISPR-Cas9 or the adenine base editor 7.10 (ABE7.10), which both caused off-target effects with a frequency close to the spontaneous mutation rate. However, the researchers also found that the cytosine base editor 3 (BE3) induced SNVs with frequencies more than 20-fold higher than the spontaneous mutation rate.
Coordinating the sort of full-spectrum analysis more commonly deployed in cancer research, scientists based at Houston Methodist examined flesh-eating strains of Streptococcus pyogenesboth genomically and transcriptomally. Once the scientists had amassed an unusually large data set, they sifted through it with artificial intelligence tools and discovered a novel virulence mechanism. In addition to explaining how a run-of-the-mill strep infection can turn into a devastating flesh-eating disease, the mechanism may guide efforts to develop vaccines and therapies.
Comprehensive clinical genomic testing of an adolescent patient, including whole genome sequencing, helped researchers identify mutations in a single gene that drive the most common childhood melanoma. The St. Jude Children's Research Hospital study appears as an advance online publication today in the journal Nature Medicine.
It seems that even data scientists are not immune to the corrosive impact of artificial intelligence on the jobs market. Russia's Sberbank claims to have created an algorithm - Auto ML (machine learning) - that "acts like a data scientist", creating its own models that then solve application tasks.
The bank carried out its first pilot in January, using Auto ML algos to create several baseline models to help with the targeting of sales campaigns.
Is there any more daunting animal to study than the great white shark? Just you try attaching a radio transmitter or drawing a tube of blood from a two-ton, razor-toothed, meat-seeking missile. But the scientific understanding of these iconic apex predators has been limited by technical challenges as much as a human bias for studying species that reside on closer branches of the taxonomic tree. Sharks evolved from the rest of the animal kingdom 400 million years ago—before the first adventurous amphibians left the oceans for dry land. What could the great white possibly teach 21st century humans?
A lot actually, according to the scientists who have spent years painfully decoding its DNA. Today, they reported their efforts mapping the first great white shark genome in the latest issue of the Proceedings of the National Academy of Sciences.
China has proposed new rules for gene editing and other “high risk” biomedical technologies. The proposals come three months after a Chinese researcher was widely criticized after claiming he had created the world’s first genetically-edited babies.
A draft of the measures was published this week on the website of China’s National Health Commission. The new rules would cover gene editing, stem cell experiments and biological products created for the human body, the Chinese government-supported Global Times newspaper reported.
CRISPR, the gene editing technique that promises to revolutionize healthcare and medicine, is not perfect. Right from the beginning, there have been concerns that this technique, which makes it easy to select specific areas of the genome and quickly and easily snip out and replace pieces of DNA, may also make unintended cuts in other areas of the genome at the same time. And two new studies, one in mice embryos and the other in rice plants, seem to confirm this.
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