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

A global catalog of whole-genome diversity from 233 primate species.

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research

The landscape of tolerated genetic variation in humans and primates.

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases

The association of physical activity to oral glucose tolerance test outcomes in multiple autoantibody positive children : The TEDDY Study

Objective: To examine the association of physical activity (PA), measured by accelerometry, to hemoglobin AIC (HbA1c) and oral glucose tolerance test (OGTT) outcomes in children who were multiple persistent confirmed autoantibody positive for type 1 diabetes (T1D). Methods: The Environmental Determinants of Diabetes in the Young (TEDDY) multinational study followed children from birth. Children ≥3 years of age who were multiple persistent confirmed autoantibody positive were monitored by OGTTs every 6 months. TEDDY children's PA was measured by accelerometry beginning at 5 years of age. We examined the relationship between moderate plus vigorous (mod + vig) PA, HbA1c, and OGTT in 209 multiple autoantibody children who had both OGTT and PA measurements. Results: Mod + vig PA was associated with both glucose and C-peptide measures (fasting, 120-min, and AUC); higher mod + vig PA was associated with a better OGTT response primarily in children with longer duration of multiple autoantibody positivity. Mod + vig PA also interacted with child age; lower mod + vig PA was associated with a greater increase in C-peptide response across age. Mod + vig PA was not related to fasting insulin, HOMA-IR or HbA1c. Conclusions: The OGTT is the gold standard for diabetes diagnosis and is used to monitor those at high risk for T1D. We found higher levels of mod + vig PA were associated with better OGTT outcomes in children ≥5 years of age who have been multiple autoantibody positive for longer periods of time. Physical activity should be the focus of future efforts to better understand the determinants of disease progression in high-risk children

Anointing variation across wild capuchin populations: a review of material preferences, bout frequency and anointing sociality in Cebus and Sapajus

The frequency of anointing bouts and the materials used for self- and social anointing vary across capuchin species in captivity, but there is little published data on capuchin anointing in the wild. Here we present previously unpublished data on anointing behaviors from capuchin monkey populations at ten different field sites and incorporate these data into a review of the anointing literature for captive and wild capuchins. Using a comparative phylogenetic framework, we test four hypotheses derived primarily from captive literature for variation in anointing between wild untufted capuchins (Cebus) and tufted capuchins (Sapajus), including that (1) the frequency of anointing is higher in Cebus, (2) Cebus uses a higher proportion of plant species to insect species for anointing compared with Sapajus, (3) anointing material diversity is higher in Cebus, and (4) social indices of anointing are higher in Cebus. We found that wild Cebus anoints more with plant parts, including fruits, whereas wild Sapajus anoints more with ants and other arthropods. Cebus capucinus in particular uses more plant species per site for anointing compared with other capuchins and may specialize in anointing as an activity independent from foraging, whereas most other capuchin species tend to eat the substances they use for anointing. In agreement with captive studies, we found evidence that wild Cebus anoints at a significantly higher frequency than Sapajus. However, contrary to the captive literature, we found no difference in the range of sociality for anointing between Cebus and Sapajus in the wild. We review anointing in the context of other Neotropical primate rubbing behaviors and consider the evidence for anointing as self-medication; as a mechanism for enhanced sociality; and as a behavioral response to chemical stimuli. Am. J. Primatol. 74:299314, 2012. (c) 2011 Wiley Periodicals, Inc.UCLA Center for Society and GeneticsUCLA Center for Society and GeneticsNSF [BCS-0833375, DGE-0549425]NS

The Ultraviolet Spectrograph on NASA’s Juno Mission

The ultraviolet spectrograph instrument on the Juno mission (Juno-UVS) is a long-slit imaging spectrograph designed to observe and characterize Jupiter’s far-ultraviolet (FUV) auroral emissions. These observations will be coordinated and correlated with those from Juno’s other remote sensing instruments and used to place in situ measurements made by Juno’s particles and fields instruments into a global context, relating the local data with events occurring in more distant regions of Jupiter’s magnetosphere. Juno-UVS is based on a series of imaging FUV spectrographs currently in flight—the two Alice instruments on the Rosetta and New Horizons missions, and the Lyman Alpha Mapping Project on the Lunar Reconnaissance Orbiter mission. However, Juno-UVS has several important modifications, including (1) a scan mirror (for targeting specific auroral features), (2) extensive shielding (for mitigation of electronics and data quality degradation by energetic particles), and (3) a cross delay line microchannel plate detector (for both faster photon counting and improved spatial resolution). This paper describes the science objectives, design, and initial performance of the Juno-UVS

A genome-wide association study on medulloblastoma

IntroductionMedulloblastoma is a malignant embryonal tumor of the cerebellum that occurs predominantly in children. To find germline genetic variants associated with medulloblastoma risk, we conducted a genome-wide association study (GWAS) including 244 medulloblastoma cases and 247 control subjects from Sweden and Denmark.MethodsGenotyping was performed using Illumina BeadChips, and untyped variants were imputed using IMPUTE2.ResultsFifty-nine variants in 11 loci were associated with increased medulloblastoma risk (p < 1 × 10-5), but none were statistically significant after adjusting for multiple testing (p < 5 × 10-8). Thirteen of these variants were genotyped, whereas 46 were imputed. Genotyped variants were further investigated in a validation study comprising 249 medulloblastoma cases and 629 control subjects. In the validation study, rs78021424 (18p11.23, PTPRM) was associated with medulloblastoma risk with OR in the same direction as in the discovery cohort (ORT = 1.59, pvalidation = 0.02). We also selected seven medulloblastoma predisposition genes for investigation using a candidate gene approach: APC, BRCA2, PALB2, PTCH1, SUFU, TP53, and GPR161. The strongest evidence for association was found for rs201458864 (PALB2, ORT = 3.76, p = 3.2 × 10-4) and rs79036813 (PTCH1, ORA = 0.42, p = 2.6 × 10-3).ConclusionThe results of this study, including a novel potential medulloblastoma risk loci at 18p11.23, are suggestive but need further validation in independent cohorts