97 research outputs found
FOOD HABITS AND MANAGEMENT OF INTRODUCED RED FOX IN SOUTHERN CALIFORNIA
Introduced red fox in urban Orange County, California ate a wide variety of foods. Mammals and birds were consumed at all times of the year and both taxa appeared in approximately half or more of the fecal samples at all times of the year. Human supplied food remains were also common and supplemental feeding occurred at all study sites. Supplemental feeding has the potential to exacerbate problems for management of introduced red fox and several endangered species
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State of the California Current 2014-15: Impacts of the Warm-Water "Blob"
In 2014, the California Current (~28˚–48˚N) saw average, or below average, coastal upwelling and relatively low productivity in most locations, except from 38˚–43˚N during June and July. Chlorophyll-a levels were low throughout spring and summer at most locations, except in a small region around 39˚N. Catches of juvenile rockfish (an indicator of upwelling-related fish species) remained high throughout the area surveyed (32˚–43˚N). In the fall of 2014, as upwelling ceased, many locations saw an unprecedented increase in sea surface temperatures (anomalies as large as 4˚C), particularly at 45˚N due to the coastal intrusion of an extremely anomalous pool of warm water. This warm surface anomaly had been building offshore in the Gulf of Alaska since the fall of 2013, and has been referred to as the “blob.” Values of the Pacific Decadal Oscillation index (PDO) continued to climb during 2014, indicative of the increase in warm coastal surface waters, whereas the North Pacific Gyre Oscillation index (NPGO) saw a slight rebound to more neutral values (indicative of average productivity levels) during 2014. During spring 2015, the upwelling index was slightly higher than average for locations in the central and northern region, but remained below average at latitudes south of 35˚N. Chlorophyll a levels were slightly higher than average in ~0.5˚ latitude patches north of 35˚N, whereas productivity and phytoplankton biomass were low south of Pt. Conception. Catches of rockfish remained high along most of the coast, however, market squid remained high only within the central coast (36˚–38˚N), and euphausiid abundance decreased everywhere, as compared to the previous year. Sardine and anchovy were nearly absent from the southern portion of the California Current system (CCS), whereas their larvae were found off the coast of Oregon and Washington during winter for the first time in many years. Waters warmed dramatically in the southern California region due to a change in wind patterns similar to that giving rise to the blob in the broader northeast Pacific. For most of the coast, there were intrusions of species never found before or found at much higher abundances than usual, including fish, crustaceans, tunicates and other gelatinous zooplankton, along with other species often indicative of an El Niño. Thus species richness was high in many areas given the close juxtaposition of coastal upwelling-related species with the offshore warm-water intrusive or El Niño-typical taxa. Thus the California Current by 2015 appears to have transitioned to a very different state than previous observations
Genetic mechanisms of critical illness in COVID-19.
Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 × 10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice
Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity
The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management. © 2021, The Author(s)
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State of the California Current 2013-14: El Niño Looming
In 2013, the California current was dominated by
strong coastal upwelling and high productivity. Indices
of total cumulative upwelling for particular coastal
locations reached some of the highest values on record.
Chlorophyll a levels were high throughout spring and
summer. Catches of upwelling-related fish species were
also high. After a moderate drop in upwelling during fall
2013, the California current system underwent a major
change in phase. Three major basin-scale indicators, the
PDO, the NPGO, and the ENSO-MEI, all changed
phase at some point during the winter of 2013/14. The
PDO changed to positive values, indicative of warmer
waters in the North Pacific; the NPGO to negative values,
indicative of lower productivity along the coast; and
the MEI to positive values, indicative of an oncoming
El Niño. Whereas the majority of the California Current
system appears to have transitioned to an El Niño
state by August 2014, based on decreases in upwelling
and chlorophyll a concentration, and increases in SST,
there still remained pockets of moderate upwelling,
cold water, and high chlorophyll a biomass at various central
coast locations, unlike patterns seen during the
more major El Niños (e.g., the 97–98 event). Catches of
rockfish, market squid, euphausiids, and juvenile sanddab
remained high along the central coast, whereas catches
of sardine and anchovy were low throughout the CCS.
2014 appears to be heading towards a moderate El Niño
state, with some remaining patchy regions of upwelling-driven
productivity along the coast. Superimposed on
this pattern, three major regions have experienced possibly
non-El Niño-related warming since winter: the
Bering Sea, the Gulf of Alaska, and offshore of southern
California. It is unclear how this warming may interact
with the predicted El Niño, but the result will likely be
reduced growth or reproduction for many key fisheries
species
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State of the California Current 2012–13: No Such Thing as an "Average" Year
This report reviews the state of the California Current System (CCS) between winter 2012 and spring 2013, and includes observations from Washington State to Baja California. During 2012, large-scale climate modes indicated the CCS remained in a cool, productive phase present since 2007. The upwelling season was delayed north of 42˚N, but regions to the south, especially 33˚ to 36˚N, experienced average to above average upwelling that persisted throughout the summer. Contrary to the indication of high production suggested by the climate indices, chlorophyll observed from surveys
and remote sensing was below average along much of
the coast. As well, some members of the forage assemblages
along the coast experienced low abundances in
2012 surveys. Specifically, the concentrations of all lifestages
observed directly or from egg densities of Pacific
sardine, Sardinops sagax, and northern anchovy, Engraulis
mordax, were less than previous years’ survey estimates.
However, 2013 surveys and observations indicate an
increase in abundance of northern anchovy. During winter
2011/2012, the increased presence of northern copepod
species off northern California was consistent with
stronger southward transport. Krill and small-fraction
zooplankton abundances, where examined, were generally
above average. North of 42˚N, salps returned to
typical abundances in 2012 after greater observed concentrations
in 2010 and 2011. In contrast, salp abundance
off central and southern California increased after a
period of southward transport during winter 2011/2012.
Reproductive success of piscivorous Brandt’s cormorant,
Phalacrocorax penicillatus, was reduced while planktivorous
Cassin’s auklet, Ptychoramphus aleuticus was elevated.
Differences between the productivity of these two seabirds
may be related to the available forage assemblage observed in the surveys. California sea lion pups from
San Miguel Island were undernourished resulting in a
pup mortality event perhaps in response to changes in
forage availability. Limited biological data were available
for spring 2013, but strong winter upwelling coastwide
indicated an early spring transition, with the strong
upwelling persisting into early summer
Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis
Publisher Copyright: © 2022, The Author(s).Background: Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results: To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3–5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions: Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.Peer reviewe