The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve the community as it enters its 23rd ...year. This year has seen an emphasis in clinical data, with new tracks and an expanded Recommended Track Sets feature on hg38 as well as the addition of a single cell track group. SARS-CoV-2 continues to remain a focus, with regular annotation updates to the browser and continued curation of our phylogenetic sequence placing tool, hgPhyloPlace, whose tree has now reached over 12M sequences. Our GenArk resource has also grown, offering over 2500 hubs and a system for users to request any absent assemblies. We have expanded our bigBarChart display type and created new ways to visualize data via bigRmsk and dynseq display. Displaying custom annotations is now easier due to our chromAlias system which eliminates the requirement for renaming sequence names to the UCSC standard. Users involved in data generation may also be interested in our new tools and trackDb settings which facilitate the creation and display of their custom annotations.
The UCSC Genome Browser (http://genome.ucsc.edu) is a graphical viewer for genomic data now in its 13th year. Since the early days of the Human Genome Project, it has presented an integrated view of ...genomic data of many kinds. Now home to assemblies for 58 organisms, the Browser presents visualization of annotations mapped to genomic coordinates. The ability to juxtapose annotations of many types facilitates inquiry-driven data mining. Gene predictions, mRNA alignments, epigenomic data from the ENCODE project, conservation scores from vertebrate whole-genome alignments and variation data may be viewed at any scale from a single base to an entire chromosome. The Browser also includes many other widely used tools, including BLAT, which is useful for alignments from high-throughput sequencing experiments. Private data uploaded as Custom Tracks and Data Hubs in many formats may be displayed alongside the rich compendium of precomputed data in the UCSC database. The Table Browser is a full-featured graphical interface, which allows querying, filtering and intersection of data tables. The Saved Session feature allows users to store and share customized views, enhancing the utility of the system for organizing multiple trains of thought. Binary Alignment/Map (BAM), Variant Call Format and the Personal Genome Single Nucleotide Polymorphisms (SNPs) data formats are useful for visualizing a large sequencing experiment (whole-genome or whole-exome), where the differences between the data set and the reference assembly may be displayed graphically. Support for high-throughput sequencing extends to compact, indexed data formats, such as BAM, bigBed and bigWig, allowing rapid visualization of large datasets from RNA-seq and ChIP-seq experiments via local hosting.
High-speed fluorescence image-enabled cell sorting Schraivogel, Daniel; Kuhn, Terra M; Rauscher, Benedikt ...
Science (American Association for the Advancement of Science),
01/2022, Letnik:
375, Številka:
6578
Journal Article
Recenzirano
Odprti dostop
Fast and selective isolation of single cells with unique spatial and morphological traits remains a technical challenge. Here, we address this by establishing high-speed image-enabled cell sorting ...(ICS), which records multicolor fluorescence images and sorts cells based on measurements from image data at speeds up to 15,000 events per second. We show that ICS quantifies cell morphology and localization of labeled proteins and increases the resolution of cell cycle analyses by separating mitotic stages. We combine ICS with CRISPR-pooled screens to identify regulators of the nuclear factor κB (NF-κB) pathway, enabling the completion of genome-wide image-based screens in about 9 hours of run time. By assessing complex cellular phenotypes, ICS substantially expands the phenotypic space accessible to cell-sorting applications and pooled genetic screening.
During early adulthood, a phase in which the central nervous system displays considerable plasticity and in which important cognitive traits are shaped, the effects of exercise on cognition remain ...poorly understood. We performed a cohort study of all Swedish men born in 1950 through 1976 who were enlisted for military service at age 18 (N = 1,221,727). Of these, 268,496 were full-sibling pairs, 3,147 twin pairs, and 1,432 monozygotic twin pairs. Physical fitness and intelligence performance data were collected during conscription examinations and linked with other national databases for information on school achievement, socioeconomic status, and sibship. Relationships between cardiovascular fitness and intelligence at age 18 were evaluated by linear models in the total cohort and in subgroups of full-sibling pairs and twin pairs. Cardiovascular fitness, as measured by ergometer cycling, positively associated with intelligence after adjusting for relevant confounders (regression coefficient b = 0.172; 95% CI, 0.168-0.176). Similar results were obtained within monozygotic twin pairs. In contrast, muscle strength was not associated with cognitive performance. Cross-twin cross-trait analyses showed that the associations were primarily explained by individual specific, non-shared environmental influences (greater-than-or-equal80%), whereas heritability explained <15% of covariation. Cardiovascular fitness changes between age 15 and 18 y predicted cognitive performance at 18 y. Cox proportional-hazards models showed that cardiovascular fitness at age 18 y predicted educational achievements later in life. These data substantiate that physical exercise could be an important instrument for public health initiatives to optimize educational achievements, cognitive performance, as well as disease prevention at the society level.
Background
Trichomoniasis commonly affects women of childbearing age and has been linked to several adverse birth outcomes.
Objective
To elucidate the association between trichomoniasis in pregnant ...women and adverse birth outcomes, including preterm delivery, prelabour rupture of membranes and low birthweight.
Search strategy
MEDLINE, EMBASE and ClinicalTrials.gov were systematically searched in December 2020 without time or language restrictions.
Selection criteria
Original research studies were included if they assessed at least one of the specified adverse birth outcomes in pregnant women with laboratory‐diagnosed trichomoniasis.
Data collection and analysis
Estimates from included articles were either extracted or calculated and then pooled to produce a combined estimate of the association of trichomoniasis with each adverse birth outcome using the random effects model. Heterogeneity was assessed using the I2 statistic and Cochran's Q test.
Main results
Literature search produced 1658 publications after removal of duplicates (n = 770), with five additional publications identified by hand search. After screening titles and s for relevance, full text of 84 studies was reviewed and 19 met inclusion criteria for meta‐analysis. Significant associations were found between trichomoniasis and preterm delivery (OR 1.27; 95% CI 1.08–1.50), prelabour rupture of membranes (OR 1.87; 95% CI 1.53–2.29) and low birthweight (OR 2.12; 95% CI 1.15–3.91).
Conclusions
Trichomoniasis in pregnant women is associated with preterm delivery, prelabour rupture of membranes and low birthweight. Rigorous studies are needed to determine the impact of universal trichomoniasis screening and treatment during pregnancy on reducing perinatal morbidity.
Tweetable
This systematic review and meta‐analysis found that in the setting of pregnancy, trichomoniasis is significantly associated with multiple adverse birth outcomes, including preterm delivery, low birthweight, and prelabour rupture of membranes.
Tweetable
This systematic review and meta‐analysis found that in the setting of pregnancy, trichomoniasis is significantly associated with multiple adverse birth outcomes, including preterm delivery, low birthweight, and prelabour rupture of membranes.
VIRAC: the VVV Infrared Astrometric Catalogue Smith, L. C; Lucas, P. W; Kurtev, R ...
Monthly notices of the Royal Astronomical Society,
02/2018, Letnik:
474, Številka:
2
Journal Article
Recenzirano
Odprti dostop
Abstract
We present VIRAC version 1, a near-infrared proper motion and parallax catalogue of the VISTA Variables in the Via Lactea (VVV) survey for 312 587 642 unique sources averaged across all ...overlapping pawprint and tile images covering 560 deg2 of the bulge of the Milky Way and southern disc. The catalogue includes 119 million high-quality proper motion measurements, of which 47 million have statistical uncertainties below 1 mas yr−1. In the 11 < Ks < 14 magnitude range, the high-quality motions have a median uncertainty of 0.67 mas yr−1. The catalogue also includes 6935 sources with quality-controlled 5σ parallaxes with a median uncertainty of 1.1 mas. The parallaxes show reasonable agreement with the Tycho-Gaia Astrometric Solution, though caution is advised for data with modest significance. The SQL data base housing the data is made available via the web. We give example applications for studies of Galactic structure, nearby objects (low-mass stars and brown dwarfs, subdwarfs, white dwarfs) and kinematic distance measurements of young stellar objects. Nearby objects discovered include LTT 7251 B, an L7 benchmark companion to a G dwarf with over 20 published elemental abundances, a bright L subdwarf, VVV 1256−6202, with extremely blue colours and nine new members of the 25 pc sample. We also demonstrate why this catalogue remains useful in the era of Gaia. Future versions will be based on profile fitting photometry, use the Gaia absolute reference frame and incorporate the longer time baseline of the VVV extended survey.
Diseases that occur during the transition period are exacerbated when cows are unable to cope with an increased pro-oxidant load that results in oxidative stress. Dairy cattle are routinely ...supplemented with the vitamin E analog α-tocopherol to mitigate the severity of oxidative stress. Nonetheless, oxidative stress remains a disease predisposing condition for many dairy cattle. A better method of optimizing the antioxidant functions of vitamin E is needed. α-Tocopherol is only 1 of 8 analogs of vitamin E, all of which have varying antioxidant properties in other mammals, albeit a shorter physiological half-life compared with α-tocopherol. A primary bovine mammary endothelial cell oxidant challenge model was used to determine functions of certain vitamin E analogs. The aim of this study was to determine if other analogs, namely γ-tocopherol or γ-tocotrienol, have antioxidative functions in bovine cells and if these functions may protect cellular viability and endothelial function from oxidant damage. Physiological (10 μM) and supraphysiological (50 μM) concentrations of γ-tocopherol and γ-tocotrienol had a greater capacity to reduce accumulated reactive oxygen species derived from a nitric oxide donating pro-oxidant antagonist, when compared with α-tocopherol, after 30 min to 6 h of treatment. Further, γ-tocotrienol (10 μM) decreased cell cytotoxicity to a greater amount than other analogs at like concentrations, whereas γ-tocopherol (10 μM) reduced lipid peroxidation and apoptosis more effectively than other analogs. Last, α-tocopherol (5 and 10 μM) and γ-tocopherol (5 and 10 μM) significantly slowed pro-oxidant induced loss of endothelial cell barrier integrity over a 48-h period using an electrical cell-substrate impedance sensing system. Concerningly, γ-tocotrienol drastically reduced the endothelial barrier integrity at only 5 μM despite no apparent effect on cellular viability at like concentrations. γ-Tocotrienol, however, was also the only analog to show significant cytotoxicity and reductions in viability at supraphysiological doses (25 and 50 μM). Our results suggest that γ-tocopherol has antioxidant activities that reduces cellular damage and loss of function due to oxidant challenge as effectively as α-tocopherol. These data set the foundation for further investigation into the antioxidant properties of vitamin E analogs in other bovine cells types or whole animal models.
Abstract
The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis-12 ...assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences and an interactive navigator for gene interactions. Other upgrades from the past year include a command-line version of the Variant Annotation Integrator, support for Human Genome Variation Society variant nomenclature input and output, and a revised highlighting tool that now supports multiple simultaneous regions and colors.
ABSTRACT
This work extends previous kinematic studies of young stars in the head of the Orion A cloud (OMC-1/2/3/4/5). It is based on large samples of infrared, optical, and X-ray selected ...pre-main-sequence stars with reliable radial velocities and Gaia-derived parallaxes and proper motions. Stellar kinematic groups are identified assuming they mimic the motion of their parental gas. Several groups are found to have peculiar kinematics: the NGC 1977 cluster and two stellar groups in the extended Orion nebula (EON) cavity are caught in the act of departing their birthplaces. The abnormal motion of NGC 1977 may have been caused by a global hierarchical cloud collapse, feedback by massive Ori OB1ab stars, supersonic turbulence, cloud–cloud collision, and/or slingshot effect; the former two models are favoured by us. EON groups might have inherited anomalous motions of their parental cloudlets due to small-scale ‘rocket effects’ from nearby OB stars. We also identify sparse stellar groups to the east and west of Orion A that are drifting from the central region, possibly a slowly expanding halo of the Orion nebula cluster. We confirm previously reported findings of varying line-of-sight distances to different parts of the cloud’s Head with associated differences in gas velocity. 3D movies of star kinematics show contraction of the groups of stars in OMC-1 and global contraction of OMC-123 stars. Overall, the head of Orion A region exhibits complex motions consistent with theoretical models involving hierarchical gravitational collapse in (possibly turbulent) clouds with OB stellar feedback.
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