A survey of red stars in the direction of the large Magellanic Cloud. 2. Some regions around the bar

We have continued the survey for red stars in the direction of the large Magellanic Cloud using the technique of ultra-low dispersion spectroscopy. This paper which is the second one on the series lists 706 stars located around the bar region. Finding charts and coordinates on the Hodge-Wright Atlas charts are provided

dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation

Background: MicroRNAs (miRNAs) regulate several biological processes through post-transcriptional gene silencing. The efficiency of binding of miRNAs to target transcripts depends on the sequence as well as intramolecular structure of the transcript. Single Nucleotide Polymorphisms (SNPs) can contribute to alterations in the structure of regions flanking them, thereby influencing the accessibility for miRNA binding. Description: The entire human genome was analyzed for SNPs in and around predicted miRNA target sites. Polymorphisms within 200 nucleotides that could alter the intramolecular structure at the target site, thereby altering regulation were annotated. Collated information was ported in a MySQL database with a user-friendly interface accessible through the URL: http://miracle.igib.res.in/ dbSMR. Conclusion: The database has a user-friendly interface where the information can be queried using either the gene name, microRNA name, polymorphism ID or transcript ID. Combination queries using 'AND' or 'OR' is also possible along with specifying the degree of change of intramolecular bonding with and without the polymorphism. Such a resource would enable researchers address questions like the role of regulatory SNPs in the 3' UTRs and population specific regulatory modulations in the context of microRNA targets

Mass segregation in globular clusters

Photoelectric aperture-photometry of ω Cen in U, B, V, R and I bands has established that the cluster is bluer between 2 arcmin and 4 arcmin from the centre, than it is elsewhere. The difference in B-I colour between the centre and this blue zone is ⋍ 0.45 mag. The core radius is found to be dependant on the wavelength band chosen for observation, the smallest core radius being for the I band. Equidensitometry of ω Cen in B, V and infrared bands shows a wavelength dependence with the cluster being nearly spherical in the infrared band. It shows a maximum ellipticity around 3 arcmin from the cluster centre. The blue contribution in this zone comes from both a diffuse background of unresolved stars and an increase in the relative abundance of horizontal branch (HB) stars. The similarity between the diffuse background and the HB stars has been demonstrated. A photographic subtraction technique is used to study the distribution of HB stars in the cluster. Results of equidensitometry of the cluster 47 Tuc, obtained in the present study, are compared with the earlier results of photoelectric photometry. Here too an increase in ellipticity is associated with an increase in the blueness of the cluster. All globular clusters studied so far for ellipticity show a similarity in the dependence of the ellipticity on the distance from the centre. The ellipticity has small values near the centre and in the outer regions, with the maximum value in between. We suggest that the red stars in globular clusters have a nearly spherical distribution. The blue stars form a bulge around the core with a more elliptical distribution and a different orientation. A similarity between the ellipticity aspects of both the globular clusters and rotation in the nucleus of M 31 is pointed out; the M 31 nucleus may thus show a bluer colour and smaller UV excess around the region where the rotation curve shows a peak

Host-virus interaction: a new role for microRNAs

MicroRNAs (miRNAs) are a new class of 18–23 nucleotide long non-coding RNAs that play critical roles in a wide spectrum of biological processes. Recent reports also throw light into the role of microRNAs as critical effectors in the intricate host-pathogen interaction networks. Evidence suggests that both virus and hosts encode microRNAs. The exclusive dependence of viruses on the host cellular machinery for their propagation and survival also make them highly susceptible to the vagaries of the cellular environment like small RNA mediated interference. It also gives the virus an opportunity to fight and/or modulate the host to suite its needs. Thus the range of interactions possible through miRNA-mRNA cross-talk at the host-pathogen interface is large. These interactions can be further fine-tuned in the host by changes in gene expression, mutations and polymorphisms. In the pathogen, the high rate of mutations adds to the complexity of the interaction network. Though evidence regarding microRNA mediated cross-talk in viral infections is just emerging, it offers an immense opportunity not only to understand the intricacies of host-pathogen interactions, and possible explanations to viral tropism, latency and oncogenesis, but also to develop novel biomarkers and therapeutics

Upregulation of miR-23a∼27a∼24-2 Cluster Induces Caspase-Dependent and -Independent Apoptosis in Human Embryonic Kidney Cells

miRNAs have emerged as important players in the regulation of gene expression and their deregulation is a common feature in a variety of diseases, especially cancer. Currently, many efforts are focused on studying miRNA expression patterns, as well as miRNA target validation. Here, we show that the over expression of miR-23a∼27a∼24-2 cluster in HEK293T cells induces apoptosis by caspase-dependent as well as caspase-independent pathway as proved by the annexin assay, caspase activation, release of cytochrome-c and AIF (apoptosis inducing factor) from mitochondria. Furthermore, the over expressed cluster modulates the expression of a number of genes involved in apoptosis including FADD (Fas Associated protein with Death Domain). Bioinformatically, FADD is predicted to be the target of hsa-miR-27a and interestingly, FADD protein was found to be up regulated consistent with very less expression of hsa-miR-27a in HEK293T cells. This effect was direct, as hsa-miR-27a negatively regulated the expression of FADD 3′UTR based reporter construct. Moreover, we also showed that over expression of miR-23a∼27a∼24-2 sensitized HEK293T cells to TNF-α cytotoxicity. Taken together, our study demonstrates that enhanced TNF-α induced apoptosis in HEK293T cells by over expression of miR-23a∼27a∼24-2 cluster provides new insights in the development of novel therapeutics for cancer

Human miRNAs: an antiviral defense mechanism

Background miRNAs are short 21-24 nt RNAs that mediate post transcriptional repression of target genes. Various reports have shown that miRNAs are capable of repressing the gene expression levels of different viruses, leading to the suggestion that miRNAs are key mediators of host-virus interaction [1]. HIV-1 is a retrovirus known to cause AIDS, one of the major diseases in humans. The nef gene of the HIV-1 has been shown to be important for virus repression of CD4+ cells and virus progression. It has also been shown earlier that patients infected with nef deleted HIV-1 do not progress from infected to diseased state for longer periods of time, resulting in the Long Term Non-Progressor phenotype [2]. Materials and methods We computationally predicted five endogenously expressed human miRNAs to target the nef gene of HIV-1 retrovirus. On applying other stringency parameters we could focus on two of the five miRNAs viz. hsa-mir-29a and hsa-mir-29b as they were predicted to target the nef gene, at sites highly conserved amongst other clades of HIV-1 [3]. We then created reporter carrying the nef gene inserted downstream of a luciferase reporter. miRNA expression vectors were also made which would express the pri-miRNA when processed and thereby lead to high levels of the miRNA inside the cells. We then identified various cell lines for validating nef as a target for hsa-mir-29a and hsa-mir-29b. Results and discussion Gene reporter assays and ectopic over-expression of miRNAs conclusively showed that human cellular miRNAs hsa-mir-29a and hsa-mir-29b could bring down the nef protein levels and also affect viral replication [4]. These results would provide a better understanding of the mechanisms that could regulate the viral gene expression and human cellular antiviral defense mechanisms whereby miRNAs could serve as potential therapeutics to treat various viral diseases

Sestrin2 is a leucine sensor for the mTORC1 pathway

Leucine is a proteogenic amino acid that also regulates many aspects of mammalian physiology, in large part by activating the mTOR complex 1 (mTORC1) protein kinase, a master growth controller. Amino acids signal to mTORC1 through the Rag guanosine triphosphatases (GTPases). Several factors regulate the Rags, including GATOR1, aGTPase-activating protein; GATOR2, a positive regulator of unknown function; and Sestrin2, a GATOR2-interacting protein that inhibits mTORC1 signaling. We find that leucine, but not arginine, disrupts the Sestrin2-GATOR2 interaction by binding to Sestrin2 with a dissociation constant of 20 micromolar, which is the leucine concentration that half-maximally activates mTORC1. The leucine-binding capacity of Sestrin2 is required for leucine to activate mTORC1 in cells. These results indicate that Sestrin2 is a leucine sensor for the mTORC1 pathway.United States. National Institutes of Health (R01CA103866)United States. National Institutes of Health (AI47389)United States. Department of Defense (W81XWH-07-0448)United States. National Institutes of Health (T32 GM007753)United States. National Institutes of Health (F30 CA189333)United States. National Institutes of Health (F31 CA180271

Human cellular microRNA hsa-miR-29a interferes with viral nef protein expression and HIV-1 replication

protein expression and HIV-1 replicatio

Barcoding of Asian seabass across its geographic range provides evidence for its bifurcation into two distinct species

Asian seabass or barramundi (Lates calcarifer) is an important food fish with commercial value and a wide geographic distribution. Though some reports based on molecular and/or morphological data exist, a comprehensive effort to establish species identity across its range is lacking. In order to address this issue and especially to ascertain whether the wide-spread distribution has resulted in bifurcation of the species, we collected Asian seabass samples from various locations representing the Western and Eastern Coastline of India, Andaman and Nicobar Islands, Bangladesh and Australia. Samples from Malaysia, Indonesia, Thailand and Singapore were collected as part of a previous study. DNA sequence variations, including cytochrome c oxidase subunit 1 (COI), 16S rDNA and the highly variable D-loop (or control region), were examined to establish species delineation. Data from all the sequences analyzed concordantly point to the existence of at least two distinct species—one representing the Indian subcontinent plus Myanmar, and a second, representing Southeast Asia (Singapore, Malaysia, Thailand and Indonesia) plus Northern Australia. These data are useful for conservation ecology, aquaculture management, for establishing the extent of genetic diversity in the Asian seabass and implementing selective breeding programs for members of this species complex

Normative range of blood biochemical parameters in urban Indian school-going adolescents.

Adolescence is the most critical phase of human growth that radically alters physiology of the body and wherein any inconsistency can lead to serious health consequences in adulthood. The timing and pace at which various developmental events occur during adolescence is highly diverse and thus results in a drastic change in blood biochemistry. Monitoring the physiological levels of various biochemical measures in ample number of individuals during adolescence can call up for an early intervention in managing metabolic diseases in adulthood. Today, only a couple of studies in different populations have investigated blood biochemistry in a small number of adolescents however, there is no comprehensive biochemical data available worldwide. In view, we performed a cross-sectional study in a sizeable group of 7,618 Indian adolescents (3,333 boys and 4,285 girls) aged between 11-17 years to inspect the distribution of values of common biochemical parameters that generally prevails during adolescence and we observed that various parameters considerably follow the reported values from different populations being 3.56-6.49mmol/L (fasting glucose), 10.60-199.48pmol/L (insulin), 0.21-3.22nmol/L (C-peptide), 3.85-6.25% (HbA1c), 2.49-5.54mmol/L (total cholesterol), 1.16-3.69mmol/L (LDL), 0.78-1.85mmol/L (HDL), 0.33-2.24mmol/L (triglycerides), 3.56-11.45mmol/L (urea), 130.01-440.15μmol/L (uric acid) and 22.99-74.28μmol/L (creatinine). Barring LDL and triglycerides, all parameters differed significantly between boys and girls (p< 0.001). Highest difference was seen for uric acid (p = 1.3 x10-187) followed by C-peptide (p = 6.6 x10-89). Across all ages during adolescence, glycemic and nitrogen metabolites parameters varied markedly with gender. Amongst lipid parameters, only HDL levels were found to be significantly associated with gender following puberty (p< 0.001). All parameters except urea, differed considerably in obese and lean adolescents (p< 0.0001). The present study asserts that age, sex and BMI are the essential contributors to variability in blood biochemistry during adolescence. Our composite data on common blood biochemical measures will benefit future endeavors to define reference intervals in adolescents especially when the global availability is scarce