Group items tagged

In the flagship article, The ENCODE Project Consortium et al.5 provide a bird's-eye view of the updated encyclopedia, which contains newly added data sets from 6,000 experiments, performed on around 1,300 samples. By integrating these data sets, the consortium has created an online registry of candidate CREs. Most are classified as promoters or enhancers - CREs respectively located at or some distance from the genomic site at which transcription of a gene begins. The consortium tracked the activity of each candidate CRE, along with the proteins that bind to it in many different samples from various tissues. They used chromatin-looping data to link enhancers to genes that they might regulate. This online registry marks a true milestone, turning an overwhelming amount of genomic information into a searchable, filterable and retrievable encyclopedia of DNA elements, which is freely accessible at https://screen.encodeproject.org.

Bart Haagmans (Erasmus MC) concludes: "The observations made in this study provide definite proof that SARS-CoV-2 can multiply in cells of the gastrointestinal tract. However, we don't yet know whether SARS-CoV-2, present in the intestines of COVID-19 patients, plays a significant role in transmission. Our findings indicate that we should look into this possibility more closely." The current study is in line with other recent studies that identified gastrointestinal symptoms in a large fraction of COVID-19 patients and virus in the stool of patients free of respiratory symptoms. Special attention may be needed for those patients with gastrointestinal symptoms. More extensive testing using not only nose and throat swabs, but also rectal swabs or stool samples may thus be needed.

A sweeping effort to map a hospital's microorganisms has found that infectious pathogens hide in a place that's all about cleaning: the sink. Niranjan Nagarajan at the Genome Institute of Singapore and his colleagues sampled bacteria from bed rails, sinks and other sites in a Singapore hospital. Microbes that tend to grow in slimy 'biofilms' and cause hospital-acquired infections were prevalent on sink traps and faucet aerators, whereas skin-dwelling bacteria were abundant on objects, such as door knobs and bed rails, that are often touched. Frequently touched sites harboured multidrug-resistant microbes such as methicillin-resistant Staphylococcus aureus, which might persist in the hospital environment for more than eight years, the team suggested.

Scientists say that widespread testing is needed to get outbreaks of the new coronavirus under control. But in many regions, there's a shortage of the chemicals needed to run tests. In several countries, health officials have started using a strategy that was first proposed in the Second World War: group testing. By testing samples from many people at once, this method can save time, chemical reagents and money, say researchers.

When they are strict and prolonged, the public health and social measures to contain Covid-19 have proven difficult to respect. This column gives evidence of the different outcomes, as of 23 May, across a sample of 20 tourist-dependent island states with populations of between 100,000 and 10 million. If tourist-dependent islands have been hit hard by the shock, most have fared well, particularly those - like Mauritius - that acted early and imposed a strict lockdown.

Antigen tests don't amplify their protein signal, so they are inherently less sensitive. To make matters worse, that signal gets diluted when samples are mixed with the liquid needed to enable the material to flow across test strips. As a result, most antigen tests have a sensitivity of anywhere between 50% and 90%-in other words, one in two infected people might incorrectly be told they don't have the virus. Last month, Spanish health authorities returned thousands of SARS-CoV-2 antigen tests to the Chinese firm Shengzhen Bioeasy Biotechnology after finding the tests correctly identified infected people only 30% of the time, according to a report by the Spanish newspaper El Pais.

In December 2019, the Coronavirus disease 2019 (COVID-19), caused by a novel coronavirus SARS-CoV-2, emerged in Wuhan, Hubei province, China1 and soon spread across the world. In this ongoing pandemic, public health concerns and the urgent need for effective therapeutic measures require a deep understanding of its epidemiology, transmissibility and pathogenesis. Here we analyzed the clinical, molecular and immunological data from 326 confirmed cases of COVID-19 in Shanghai. Genomic sequences of SARS-CoV-2 assembled from 112 quality samples together with sequences in the Global Initiative on Sharing All Influenza Data (GISAID) showed a stable evolution and suggested two major lineages with differential exposure history during the early phase of the outbreak in Wuhan. Nevertheless, they exhibited similar virulence and clinical outcomes. Lymphocytopenia, especially the reduced CD4+ and CD8+ T cell counts upon admission, was predictive of disease progression. High levels of IL-6 and IL-8 during treatment were observed in patients with severe or critical disease and correlated with decreased lymphocyte count. The determinants of disease severity seemed to stem mostly from host factors such as age, lymphocytopenia, and its associated cytokine storm, whereas viral genetic variation did not significantly affect the outcomes.

ot long ago, Joe Davis, the "artist-scientist" in George Church's genetics lab at Harvard Medical School, was in Brittany, France. The region is known for thousand-year-old salterns that produce fleur de sel, or flower of salt-salt that forms as seawater evaporates. Davis was there sampling these brightly colored ponds with a microscope, and found in the shallow waters an abundance of diverse halophiles, organisms that can grow in and tolerate saline conditions. "I wondered what happens to these organisms," he said. "The salt is evaporating, the water's gone. The organisms aren't just going to disappear. Where are they?"