Counter-Gradient Momentum Transport Through Subtropical Shallow Convection in ICON-LEM Simulations.

It is well known that subtropical shallow convection transports heat and water vapor upwards from the surface. It is less clear if it also transports horizontal momentum upwards to significantly affect the trade winds in which it is embedded. We utilize unique multiday large-eddy simulations run over the tropical Atlantic with ICON-LEM to investigate the character of shallow convective momentum transport (CMT). For a typical trade-wind profile during boreal winter, CMT acts as an apparent friction to decelerate the north-easterly flow. This effect maximizes below the cloud base while in the cloud layer, friction is very small, although present over a relatively deep layer. In the cloud layer, the zonal component of the momentum flux is counter-gradient and penetrates deeper than reported in traditional shallow cumulus LES cases. The transport through conditionally sampled convective updrafts and downdrafts explains a weak friction effect, but not the counter-gradient flux near the cloud tops. The analysis of the momentum flux budget reveals that, in the cloud layer, the counter-gradient flux is driven by convectively triggered nonhydrostatic pressure-gradients and horizontal circulations surrounding the clouds. A model set-up with large domain size and realistic boundary conditions is necessary to resolve these effects.

SAGE: a comprehensive resource of genetic variants integrating South Asian whole genomes and exomes.

South Asia is home to $\sim $20% of the world population and characterized by distinct ethnic, linguistic, cultural and genetic lineages. Only limited representative samples from the region have found its place in large population-scale international genome projects. The recent availability of genome scale data from multiple populations and datasets from South Asian countries in public domain motivated us to integrate the data into a comprehensive resource. In the present study, we have integrated a total of six datasets encompassing 1213 human exomes and genomes to create a compendium of 154 814 557 genetic variants and adding a total of 69 059 255 novel variants. The variants were systematically annotated using public resources and along with the allele frequencies are available as a browsable-online resource South Asian genomes and exomes. As a proof of principle application of the data and resource for genetic epidemiology, we have analyzed the pathogenic genetic variants causing retinitis pigmentosa. Our analysis reveals the genetic landscape of the disease and suggests subset of genetic variants to be highly prevalent in South Asia.

Pharmacogenetic landscape of DPYD variants in south Asian populations by integration of genome-scale data.

AIM: Adverse drug reactions to 5-Fluorouracil(5-FU) is frequent and largely attributable to genetic variations in the DPYD gene, a rate limiting enzyme that clears 5-FU. The study aims at understanding the pharmacogenetic landscape of DPYD variants in south Asian populations. MATERIALS & METHODS: Systematic analysis of population scale genome wide datasets of over 3000 south Asians was performed. Independent evaluation was performed in a small cohort of patients. RESULTS: Our analysis revealed significant differences in the the allelic distribution of variants in different ethnicities. CONCLUSIONS: This is the first and largest genetic map the DPYD variants associated with adverse drug reaction to 5-FU in south Asian population. Our study highlights ethnic differences in allelic frequencies.

Occipital cortex dysgenesis with white matter changes due to mutations in Laminin a2.

Yis U, Dixit V, Isikay S, Karakaya M, Baydan F, Diniz G, Polat I, Hiz-Kurul S, Çirak S. Occipital cortex dysgenesis with white matter changes due to mutations in Laminin a2. Turk J Pediatr 2017; 59: 338-341. Laminin α2 related congenital muscular dystrophy is one of the most common congenital muscular dystrophies of childhood with or without clinical evidence of central nervous system involvement. It may be associated with significant white matter abnormalities resembling leukodystrophies. In this study, we elaborated on two cases with laminin α2 related congenital muscular dystrophy who had occipital cortex dysgenesis in addition to characteristic white matter abnormalities. Although laminin α2 related congenital muscular dystrophy with white matter abnormalities is known, the association with occipital cortex dysplasia has been not well recognized by clinical colleagues.

Case Report: Application of whole exome sequencing for accurate diagnosis of rare syndromes of mineralocorticoid excess.

Syndromes of mineralocorticoid excess (SME) are closely related clinical manifestations occurring within a specific set of diseases. Overlapping clinical manifestations of such syndromes often create a dilemma in accurate diagnosis, which is crucial for disease surveillance and management especially in rare genetic disorders. Here we demonstrate the use of whole exome sequencing (WES) for accurate diagnosis of rare SME and report that p.R337C variation in the HSD11B2 gene causes progressive apparent mineralocorticoid excess (AME) syndrome in a South Indian family of Mappila origin.

Case Report: Whole exome sequencing helps in accurate molecular diagnosis in siblings with a rare co-occurrence of paternally inherited 22q12 duplication and autosomal recessive non-syndromic ichthyosis.

Lamellar ichthyosis (LI), considered an autosomal recessive monogenic genodermatosis, has an incidence of approximately 1 in 250,000. Usually associated with mutations in the transglutaminase gene ( TGM1), mutations in six other genes have, less frequently, been shown to be causative. Two siblings, born in a collodion membrane, presented with fish like scales all over the body. Karyotyping revealed duplication of the chromosome arm on 22q12+ in the father and two siblings. Whole exome sequencing revealed a homozygous p.Gly218Ser variation in TGM1; a variation reported earlier in an isolated Finnish population in association with autosomal recessive non-syndromic ichthyosis. This concurrence of a potentially benign 22q12+ duplication and LI, both rare individually, is reported here likely for the first time.

Draft Genome Sequence of the Extremely Halophilic Bacterium Halomonas salina Strain CIFRI1, Isolated from the East Coast of India.

Halomonas salina strain CIFRI1 is an extremely salt-stress-tolerant bacterium isolated from the salt crystals of the east coast of India. Here we report the annotated 3.45-Mb draft genome sequence of strain CIFRI1 having 86 contigs with 3,139 protein coding loci, including 62 RNA genes.

Identification and characterization of Rhipicephalus (Boophilus) microplus and Haemaphysalis bispinosa ticks (Acari: Ixodidae) of northeast India by ITS2 and 16S rDNA sequences and morphological analysis.

To investigate and identify the ticks prevalent in the North East part of India, scanning electron microscope (SEM) and DNA sequence of nuclear second internal transcribed spacer (ITS2) and mitochondrial 16S ribosomal DNA (rDNA) were used. Based on the morphological and molecular analysis, the ticks infesting cattle of North East India were found to be Rhipicephalus (Boophilus) microplus and Haemaphysalis bispinosa. ITS2 and 16S rDNA sequence from R. (B.) microplus and H. bispinosa were amplified using universal and gene specific primers, sequenced and analysed. The length of the amplified ITS2 sequence of R. (B.) microplus and H. bispinosa, were found to be approximately 1,500 and 1,700 bp, respectively. The length of the 16S rDNA sequences in both the ticks was found to be similar in size, but they differ in their base pair constitutions. This is the first report of the nucleotide sequences of ITS2 and 16S rDNA of H. bispinosa. Phylogenetic analysis revealed that H. bispinosa is a close relative of H. longicornis. A polymerase chain reaction-restriction fragment length polymorphism diagnostic tool was developed based on HindIII digestion of ITS2 in order to facilitate the identification of these two species which cannot be distinguished once it is fully-fed. Present study describes the use of SEM and 16S rDNA/ITS2 based molecular analysis in identification and differentiation of fully fed tick species.