916 research outputs found
Adipose tissue Angiopoietin-like proteins 4 (ANGPTL4) in diabetes and its remission following bariatric surgery
This is the author accepted manuscript. The final version is available from Wiley via the DOI in this record In: Special Issue - Abstracts of the Diabetes UK Professional Conference 2019, Liverpool, UK, 6–8 March 2019Novo Nordisk (UK Research Foundation
Species-level functional profiling of metagenomes and metatranscriptomes.
Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types
Three-dimensional femtosecond laser nanolithography of crystals
Nanostructuring hard optical crystals has so far been exclusively feasible at
their surface, as stress induced crack formation and propagation has rendered
high precision volume processes ineffective. We show that the inner chemical
etching reactivity of a crystal can be enhanced at the nanoscale by more than
five orders of magnitude by means of direct laser writing. The process allows
to produce cm-scale arbitrary three-dimensional nanostructures with 100 nm
feature sizes inside large crystals in absence of brittle fracture. To showcase
the unique potential of the technique, we fabricate photonic structures such as
sub-wavelength diffraction gratings and nanostructured optical waveguides
capable of sustaining sub-wavelength propagating modes inside yttrium aluminum
garnet crystals. This technique could enable the transfer of concepts from
nanophotonics to the fields of solid state lasers and crystal optics.Comment: Submitted Manuscript and Supplementary Informatio
Persistence of clinically relevant levels of SARS-CoV2 envelope gene subgenomic RNAs in non-immunocompromised individuals
This is the final version. Available on open access from Elsevier via the DOI in this recordOBJECTIVES: This study aimed to evaluate the associations between COVID-19 severity and active viral load, and to characterize the dynamics of active SARS-CoV-2 clearance in a series of archival samples taken from patients in the first wave of COVID-19 infection in the South West of the UK. METHODS: Subgenomic RNA (sgRNA) and E-gene genomic sequences were measured in a retrospective collection of PCR-confirmed SARS-CoV-2-positive samples from 176 individuals, and related to disease severity. Viral clearance dynamics were then assessed in relation to symptom onset and last positive test. RESULTS: Whilst E-gene sgRNAs declined before E-gene genomic sequences, some individuals retained sgRNA positivity for up to 68 days. 13% of sgRNA-positive cases still exhibited clinically relevant levels of virus after 10 days, with no clinical features previously associated with prolonged viral clearance times. CONCLUSIONS: Our results suggest that potentially active virus can sometimes persist beyond a 10-day period, and could pose a potential risk of onward transmission. Where this would pose a serious public health threat, additional mitigation strategies may be necessary to reduce the risk of secondary cases in vulnerable settings.National Institute for Health Research (NIHR
Echinoderms have bilateral tendencies
Echinoderms take many forms of symmetry. Pentameral symmetry is the major
form and the other forms are derived from it. However, the ancestors of
echinoderms, which originated from Cambrian period, were believed to be
bilaterians. Echinoderm larvae are bilateral during their early development.
During embryonic development of starfish and sea urchins, the position and the
developmental sequence of each arm are fixed, implying an auxological
anterior/posterior axis. Starfish also possess the Hox gene cluster, which
controls symmetrical development. Overall, echinoderms are thought to have a
bilateral developmental mechanism and process. In this article, we focused on
adult starfish behaviors to corroborate its bilateral tendency. We weighed
their central disk and each arm to measure the position of the center of
gravity. We then studied their turning-over behavior, crawling behavior and
fleeing behavior statistically to obtain the center of frequency of each
behavior. By joining the center of gravity and each center of frequency, we
obtained three behavioral symmetric planes. These behavioral bilateral
tendencies might be related to the A/P axis during the embryonic development of
the starfish. It is very likely that the adult starfish is, to some extent,
bilaterian because it displays some bilateral propensity and has a definite
behavioral symmetric plane. The remainder of bilateral symmetry may have
benefited echinoderms during their evolution from the Cambrian period to the
present
The NIH-NIAID Filariasis Research Reagent Resource Center
Filarial worms cause a variety of tropical diseases in humans; however, they are difficult to study because they have complex life cycles that require arthropod intermediate hosts and mammalian definitive hosts. Research efforts in industrialized countries are further complicated by the fact that some filarial nematodes that cause disease in humans are restricted in host specificity to humans alone. This potentially makes the commitment to research difficult, expensive, and restrictive. Over 40 years ago, the United States National Institutes of Health–National Institute of Allergy and Infectious Diseases (NIH-NIAID) established a resource from which investigators could obtain various filarial parasite species and life cycle stages without having to expend the effort and funds necessary to maintain the entire life cycles in their own laboratories. This centralized resource (The Filariasis Research Reagent Resource Center, or FR3) translated into cost savings to both NIH-NIAID and to principal investigators by freeing up personnel costs on grants and allowing investigators to divert more funds to targeted research goals. Many investigators, especially those new to the field of tropical medicine, are unaware of the scope of materials and support provided by the FR3. This review is intended to provide a short history of the contract, brief descriptions of the fiilarial species and molecular resources provided, and an estimate of the impact the resource has had on the research community, and describes some new additions and potential benefits the resource center might have for the ever-changing research interests of investigators
PGA: power calculator for case-control genetic association analyses
<p>Abstract</p> <p>Background</p> <p>Statistical power calculations inform the design and interpretation of genetic association studies, but few programs are tailored to case-control studies of single nucleotide polymorphisms (SNPs) in unrelated subjects.</p> <p>Results</p> <p>We have developed the "Power for Genetic Association analyses" (PGA) package which comprises algorithms and graphical user interfaces for sample size and minimum detectable risk calculations using SNP or haplotype effects under different genetic models and study constrains. The software accounts for linkage disequilibrium and statistical multiple comparisons. The results are presented in graphs or tables and can be printed or exported in standard file formats.</p> <p>Conclusion</p> <p>PGA is user friendly software that can facilitate decision making for association studies of candidate genes, fine-mapping studies, and whole-genome scans. Stand-alone executable files and a Matlab toolbox are available for download at: <url>http://dceg.cancer.gov/bb/tools/pga</url></p
Molecular identification of similar species of the genus Biomphalaria (Mollusca: Planorbidae) determined by a polymerase chain reaction-restriction fragment length polymorphism
On the centenary of the birth of Francis H. C. Crick – from physics to genetics and neuroscience
Sec61alpha synthesis is enhanced during translocation of nascent chains of collagen type IV in F9 teratocarcinoma cells after retinoic acid treatment
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