ENSO’s far reaching connection to Indian cold waves

During boreal winters, cold waves over India are primarily due to transport of cold air from higher latitudes. However, the processes associated with these cold waves are not yet clearly understood. Here by diagnosing a suite of datasets, we explore the mechanisms leading to the development and maintenance of these cold waves. Two types of cold waves are identified based on observed minimum surface temperature and statistical analysis. The first type (TYPE1), also the dominant one, depicts colder than normal temperatures covering most parts of the country while the second type (TYPE2) is more regional, with significant cold temperatures only noticeable over northwest India. Quite interestingly the first (second) type is associated with La Niña (El Niño) like conditions, suggesting that both phases of ENSO provide a favorable background for the occurrence of cold waves over India. During TYPE1 cold wave events, a low-level cyclonic anomaly generated over the Indian region as an atmospheric response to the equatorial convective anomalies is seen advecting cold temperatures into India and maintaining the cold waves. In TYPE2 cold waves, a cyclonic anomaly generated over west India anomalously brings cold winds to northwest India causing cold waves only in those parts

ALFRED: an allele frequency resource for research and teaching

ALFRED (http://alfred.med.yale.edu) is a free, web accessible, curated compilation of allele frequency data on DNA sequence polymorphisms in anthropologically defined human populations. Currently, ALFRED has allele frequency tables on over 663 400 polymorphic sites; 170 of them have frequency tables for more than 100 different population samples. In ALFRED, a population may have multiple samples with each ‘sample’ consisting of many individuals on which an allele frequency is based. There are 3566 population samples from 710 different populations with allele frequency tables on at least one polymorphism. Fifty of those population samples have allele frequency data for over 650 000 polymorphisms. Records also have active links to relevant resources (dbSNP, PharmGKB, OMIM, Ethnologue, etc.). The flexible search options and data display and download capabilities available through the web interface allow easy access to the large quantity of high-quality data in ALFRED

Genome-Wide Association Studies of Schizophrenia and Bipolar Disorder in a Diverse Cohort of US Veterans

Background: Schizophrenia (SCZ) and bipolar disorder (BIP) are debilitating neuropsychiatric disorders, collectively affecting 2% of the world\u27s population. Recognizing the major impact of these psychiatric disorders on the psychosocial function of more than 200 000 US Veterans, the Department of Veterans Affairs (VA) recently completed genotyping of more than 8000 veterans with SCZ and BIP in the Cooperative Studies Program (CSP) #572. Methods: We performed genome-wide association studies (GWAS) in CSP #572 and benchmarked the predictive value of polygenic risk scores (PRS) constructed from published findings. We combined our results with available summary statistics from several recent GWAS, realizing the largest and most diverse studies of these disorders to date. Results: Our primary GWAS uncovered new associations between CHD7 variants and SCZ, and novel BIP associations with variants in Sortilin Related VPS10 Domain Containing Receptor 3 (SORCS3) and downstream of PCDH11X. Combining our results with published summary statistics for SCZ yielded 39 novel susceptibility loci including CRHR1, and we identified 10 additional findings for BIP (28 326 cases and 90 570 controls). PRS trained on published GWAS were significantly associated with case-control status among European American (P \u3c 10-30) and African American (P \u3c .0005) participants in CSP #572. Conclusions: We have demonstrated that published findings for SCZ and BIP are robustly generalizable to a diverse cohort of US veterans. Leveraging available summary statistics from GWAS of global populations, we report 52 new susceptibility loci and improved fine-mapping resolution for dozens of previously reported associations

Study of atmospheric forcing and responses (SAFAR) campaign: overview

Study of Atmospheric Forcing and Responses (SAFAR) is a five year (2009-2014) research programme specifically to address the responses of the earth's atmosphere to both natural and anthropogenic forcings using a host of collocated instruments operational at the National Atmospheric Research Laboratory, Gadanki (13.5° N, 79.2° E), India from a unified viewpoint of studying the vertical coupling between the forcings and responses from surface layer to the ionosphere. As a prelude to the main program a pilot campaign was conducted at Gadanki during May-November 2008 using collocated observations from the MST radar, Rayleigh lidar, GPS balloonsonde, and instruments measuring aerosol, radiation and precipitation, and supporting satellite data. We show the importance of the large radiative heating caused by absorption of solar radiation by soot particles in the lower atmosphere, the observed high vertical winds in the convective updrafts extending up to tropopause, and the difficulty in simulating the same with existing models, the upward traveling waves in the middle atmosphere coupling the lower atmosphere with the upper atmosphere, their manifestation in the mesospheric temperature structure and inversion layers, the mesopause height extending up to 100 km, and the electro-dynamical coupling between mesosphere and the ionosphere which causes irregularities in the ionospheric F-region. The purpose of this communication is not only to share the knowledge that we gained from the SAFAR pilot campaign, but also to inform the international atmospheric science community about the SAFAR program as well as to extend our invitation to join in our journey

Tick Transmission of \u3ci\u3eBorrelia burgdorferi\u3c/i\u3e to the Murine Host is not Influenced by Environmentally Acquired Midgut Microbiota

Background Ixodes scapularis is the predominant tick vector of Borrelia burgdorferi, the agent of Lyme disease, in the USA. Molecular interactions between the tick and B. burgdorferi orchestrate the migration of spirochetes from the midgut to the salivary glands—critical steps that precede transmission to the vertebrate host. Over the last decade, research efforts have invoked a potential role for the tick microbiome in modulating tick-pathogen interactions. Results Using multiple strategies to perturb the microbiome composition of B. burgdorferi-infected nymphal ticks, we observe that changes in the microbiome composition do not significantly influence B. burgdorferi migration from the midgut, invasion of salivary glands, or transmission to the murine host. We also show that within 24 and 48 h of the onset of tick feeding, B. burgdorferi spirochetes are within the peritrophic matrix and epithelial cells of the midgut in preparation for exit from the midgut. Conclusions This study highlights two aspects of tick-spirochete interactions: (1) environmental bacteria associated with the tick do not influence spirochete transmission to the mammalian host and (2) the spirochete may utilize an intracellular exit route during migration from the midgut to the salivary glands, a strategy that may allow the spirochete to distance itself from microbiota in the midgut lumen effectively. This may explain in part, the inability of environment-acquired midgut microbiota to significantly influence spirochete transmission. Unraveling a molecular understanding of this exit strategy will be critical to gain new insights into the biology of the spirochete and the tick

The role of potential vorticity anomalies in the Somali Jet on Indian summer monsoon intraseasonal variability

The climate of the Indian subcontinent is dominated by rainfall arising from the Indian summer monsoon (ISM) during the summer season (June to September). Intraseasonal variability during the monsoon is characterized by periods of heavy rainfall interspersed by drier periods, known as active and break events respectively. Understanding and predicting such events is of vital importance for forecasting human impacts such as water resources. The Somali Jet is a key regional feature of this circulation. In the present study, we find that the spatial structure of Somali Jet potential vorticity (PV) anomalies varies considerably during active and break periods. Analysis of these anomalies shows a mechanism whereby sea surface temperature (SST) anomalies propagate north/northwestwards through the Arabian Sea, caused by a positive feedback loop joining anomalies in SST, convection, modification of PV by diabatic heating and mixing in the atmospheric boundary layer, wind stress curl, and upwelling processes. The feedback mechanism is consistent with observed coupled ocean-atmosphere system variability timescales of approximately 20 days. This research suggests that better understanding and prediction of monsoon subseasonal variability in the South Asian monsoon may be gained by analysis of the day-to-day dynamical evolution of PV in the Somali Jet

Analysis of differential gene expression in human melanocytic tumour lesions by custom made oligonucleotide arrays

Melanoma is one of the most aggressive types of cancer and resection of the tumour prior to dissemination of tumour cells is still the most effective treatment. Therefore, early diagnosis of melanocytic lesions is important and identification of novel (molecular) markers would be helpful to improve diagnosis. Moreover, better understanding of molecular targets involved in melanocytic tumorigenesis could possibly lead to development of novel interventions. In this study, we used a custom made oligonucleotide array containing 298 genes that were previously found to be differentially expressed in human melanoma cell lines 1F6 (rarely metastasising) and Mel57 (frequently metastasising). We determined differential gene expression in human common nevocellular nevus and melanoma metastasis lesions. By performing nine dye-swap array experiments, using individual as well as pooled melanocytic lesions, a constant differential expression could be detected for 25 genes in eight out of nine or nine out of nine array analyses. For at least nine of these genes, namely THBD, FABP7, H2AFJ, RRAGD, MYADM, HR, CKS2, NCK2 and GDF15, the differential expression found by array analyses could be verified by semiquantitative and/or real-time quantitative RT–PCR. The genes that we identified to be differentially expressed during melanoma progression could be potent targets for diagnostic, prognostic and/or therapeutic interventions

The northern hemisphere circumglobal teleconnection in a seasonal forecast model and its relationship to European summer forecast skill

Forecasting seasonal variations in European summer weather represents a considerable challenge. Here, we assess the performance of a seasonal forecasting model at representing a major mode of northern hemisphere summer climate variability, the circumglobal teleconnection (CGT), and the implications of errors in its representation on seasonal forecasts for the European summer (June, July, August). Using seasonal hindcasts initialised at the start of May, we find that the model skill for forecasting the interannual variability of 500 hPa geopotential height is poor, particularly over Europe and several other “centres of action” of the CGT. The model also has a weaker CGT pattern than is observed, particularly in August, when the observed CGT wavetrain is strongest. We investigate several potential causes of this poor skill. First, model variance in geopotential height in west-central Asia (an important region for the maintenance of the CGT) is lower than observed in July and August, associated with a poor representation of the link between this region and Indian monsoon precipitation. Second, analysis of the Rossby wave source shows that the source associated with monsoon heating is both too strong and displaced to the northeast in the model. This is related to errors in monsoon precipitation over the Bay of Bengal and Arabian Sea, where the model has more precipitation than is observed. Third, the model jet is systematically shifted northwards by several degrees latitude over large parts of the northern hemisphere, which may affect the propagation characteristics of Rossby waves in the model