Systematic transcriptome wide analysis of lncRNA-miRNA interactions

Long noncoding RNAs (lncRNAs) are a recently discovered class of non-protein coding RNAs which have now increasingly been shown to be involved in a wide variety of biological processes as regulatory molecules. Little is known regarding the regulatory interactions between noncoding RNA classes. Recent reports have suggested that lncRNAs could potentially interact with other noncoding RNAs including miroRNAs (miRNAs) and modulate their regulatory role through interactions. We hypothesized that long noncoding RNAs could participate as a layer of regulatory interactions with miRNAs. The availability of genome-scale datasets for argonaute targets across human transcriptome has prompted us to reconstruct a genome-scale network of interactions between miRNAs and lncRNAs. We used well characterized experimental Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) datasets and the recent genome-wide annotations for lncRNAs in public domain to construct a comprehensive transcriptome-wide map of miRNA regulatory elements. Comparative analysis revealed many of the miRNAs could target long noncoding RNAs, apart from the coding transcripts thus participating in a novel layer of regulatory interactions between noncoding RNA classes. We also find the miRNA regulatory elements have a positional preference, clustering towards the 3' and 5' ends of the long noncoding transcripts. We also further reconstruct a genome-wide map of miRNA interactions with lncRNAs as well as messenger RNAs. This analysis suggests widespread regulatory interactions between noncoding RNAs classes and suggests a novel functional role for lncRNAs. We also present the first transcriptome scale study on lncRNA-miRNA interactions and the first report of a genome-scale reconstruction of a noncoding RNA regulatory interactome involving lncRNAs

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

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

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

Polarization Vectors, Doublet Structure and Wigner's Little Group in Planar Field Theory

We establish the equivalence of the Maxwell-Chern-Simons-Proca model to a doublet of Maxwell-Chern-Simons models at the level of polarization vectors of the basic fields using both Lagrangian and Hamiltonian formalisms. The analysis reveals a U(1) invariance of the polarization vectors in the momentum space. Its implications are discussed. We also study the role of Wigner's little group as a generator of gauge transformations in three space-time dimensions.Comment: LaTex, 30 pages, no figure

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

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

Comparative Genomic Studies of Salmonella Heidelberg Isolated From Chicken- and Turkey-Associated Farm Environmental Samples

Salmonella is one of the leading causes of human foodborne gastroenteritis in the United States. In addition, Salmonella contributes to morbidity and mortality in livestock. The control of Salmonella is an increasing problematic issue in livestock production due to lack of effective control methods and the constant adaptation of Salmonella to new management practices, which is often related to horizontal acquisition of virulence or antibiotic resistance genes. Salmonella enterica serotype Heidelberg is one of the most commonly isolated serotypes in all poultry production systems in North America. Emergence and persistence of multi-drug resistant Salmonella Heidelberg isolates further impact the poultry production and public health. We hypothesized that distinct poultry production environments affect Salmonella genomic content, and by consequence its survival and virulence abilities. This study compared the genomic composition of S. Heidelberg isolated from environmental samples (19 chicken and 12 turkey isolates) of different breeder farms (16 chicken and 8 turkey farms) in the Midwest, United States. Whole genome comparison of 31 genomes using RAST and SEED identified differences in specific sub-systems in isolates between the chicken- and turkey-associated farm environmental samples. Genes associated with the type IV secretion system (n = 12) and conjugative transfer (n = 3) were absent in turkey farm isolates compared to the chicken ones (p-value < 0.01); Further, turkey farm isolates were enriched in prophage proteins (n = 53; p-value < 0.01). Complementary studies using PHASTER showed that prophages were all Caudovirales phages and were more represented in turkey environmental isolates than the chicken isolates. This study corroborates that isolates from distinct farm environment show differences in S. Heidelberg genome content related to horizontal transfer between bacteria or through viral infections. Complementary microbiome studies of these samples would provide critical insights on sources of these variations. Overall, our findings enhance the understanding of Salmonella genome plasticity and may aid in the development of future effective management practices to control Salmonella

Knowledge and attitudes about health research amongst a group of Pakistani medical students

Background Health research training is an important part of medical education. This study was conducted to assess the level of knowledge and attitudes regarding health research in a group of Pakistani medical students at Aga Khan University, Karachi. Methods It was a cross-sectional pilot study conducted among a group of Pakistani medical students. Through stratified random sampling, a pre-tested, structured and validated questionnaire was administered to 220 medical students. Knowledge and attitudes were recorded on a scale (graduated in percentages). Results Mean scores of students were 49.0% on knowledge scale and 53.7% on attitude scale. Both knowledge and attitudes improved significantly with increasing years of study in medical college [Regression coefficient 4.10 (p-value; 0.019) and 6.67 (p-value; \u3c 0.001) for knowledge and attitudes, respectively]. Conclusion Medical students demonstrate moderate level of knowledge and attitude towards health research. Intensive training in this regard is associated with significant improvement in knowledge and attitudes of students towards health research

Optimal design of parallel triplex forming oligonucleotides containing Twisted Intercalating Nucleic Acids—TINA

Twisted intercalating nucleic acid (TINA) is a novel intercalator and stabilizer of Hoogsteen type parallel triplex formations (PT). Specific design rules for position of TINA in triplex forming oligonucleotides (TFOs) have not previously been presented. We describe a complete collection of easy and robust design rules based upon more than 2500 melting points (Tm) determined by FRET. To increase the sensitivity of PT, multiple TINAs should be placed with at least 3 nt in-between or preferable one TINA for each half helixturn and/or whole helixturn. We find that ΔTm of base mismatches on PT is remarkably high (between 7.4 and 15.2°C) compared to antiparallel duplexes (between 3.8 and 9.4°C). The specificity of PT by ΔTm increases when shorter TFOs and higher pH are chosen. To increase ΔTms, base mismatches should be placed in the center of the TFO and when feasible, A, C or T to G base mismatches should be avoided. Base mismatches can be neutralized by intercalation of a TINA on each side of the base mismatch and masked by a TINA intercalating direct 3′ (preferable) or 5′ of it. We predict that TINA stabilized PT will improve the sensitivity and specificity of DNA based clinical diagnostic assays