Towards an efficient computational mining approach to identify EST-SSR markers

Microsatellites are the markers of choice due to their high abundance reproducibility, degree of polymorphism and co-dominant nature. These are mainly used for studying the genetic variability in different species and Marker assisted selection. Expressed Sequence Tags (ESTs) serve as the main resource for Simple Sequence Repeats (SSRs). The computational approach for detecting SSRs and developing SSR markers from EST-SSRs is preferred over the conventional methods as it reduces time and cost to a great extent. The available EST sequence databases, various web interfaces and standalone tools provide the platform for an easy analysis of the EST sequences leading to the development of potential EST-SSR Markers. This paper is an overview of in silico approach to develop SSR Markers from the EST sequence using some of the most efficient tools that are available freely for academic purpose.     

Alternaria-Induced Release of IL-18 from Damaged Airway Epithelial Cells: An NF-κB Dependent Mechanism of Th2 Differentiation?

Background

A series of epidemiologic studies have identified the fungus Alternaria as a major risk factor for asthma. The airway epithelium plays a critical role in the pathogenesis of allergic asthma. These reports suggest that activated airway epithelial cells can produce cytokines such as IL-25, TSLP and IL-33 that induce Th2 phenotype. However the epithelium-derived products that mediate the pro-asthma effects of Alternaria are not well characterized. We hypothesized that exposure of the airway epithelium to Alternaria releasing cytokines that can induce Th2 differentiation.

Methodology/Principal Finding

We used ELISA to measure human and mouse cytokines. Alternaria extract (ALT-E) induced rapid release of IL-18, but not IL-4, IL-9, IL-13, IL-25, IL-33, or TSLP from cultured normal human bronchial epithelial cells; and in the BAL fluids of naïve mice after challenge with ALT-E. Both microscopic and FACS indicated that this release was associated with necrosis of epithelial cells. ALT-E induced much greater IL-18 release compared to 19 major outdoor allergens. Culture of naïve CD4 cells with rmIL-18 induced Th2 differentiation in the absence of IL-4 and STAT6, and this effect was abrogated by disrupting NF- κB p50 or with a NEMO binding peptide inhibitor.

Conclusion/Significance

Rapid and specific release of IL-18 from Alternaria-exposed damaged airway epithelial cells can directly initiate Th2 differentiation of naïve CD4⁺ T-cells via a unique NF-κB dependent pathway.     

Auriculostoma astyanace n. gen., n. sp. (Digenea: Allocreadiidae), from the banded astyanax, Astyanax fasciatus (Characiformes: Characidae), from Nicaragua, with a reevaluation of neotropical Crepidostomum spp

Auriculostoma n. gen. (Trematoda: Allocreadiidae) is proposed for Auriculostoma astyanace n. sp. from the intestine of the characid fish Astyanax fasciatus in the Atlantic coastal drainages of Nicaragua. The new genus differs from all papillose allocreadiid genera, except Bunoderella, in possessing 2 pairs of muscular oral papillae (instead of 1 or 3), of which the ventrolateral pair is moderately developed and the dorsolateral papillae are long and auricular. Auriculostoma differs from Bunoderella Schell, 1964, in having lateral vitelline follicles, completely separated or confluent only in the posttesticular region, a uterus limited to the pretesticular region or with a few eggs at the level of the testes, and a long cirrus sac that overlaps the acetabulum or usually reaches posteriorly to the ovarian level. Three other allocreadiid species, all from South American freshwater fishes and each of which had previously been placed in Crepidostomum, are transferred to Auriculostoma based on the presence of the diagnostic muscular oral papillae. These include Crepidostomum platense Szidat, 1954, C. macrorchis Szidat, 1954, and C. stenopteri Ma?é-Garzón and Gascón, 1973. Diagnostic features for Auriculostoma also include mainly pretesticular uterus, lateral vitellaria with variation in posttesticular confluence, and tandem testes. The genus appears to be typically associated with neotropical siluriforms (catfishes) and characiforms (tetras).     

Effect of superparasitism on the development,sex ratio and progeny ofBracon greeni Ashmead

Résumé Bracon greeni Ashmead est un ectoparasite larvaire de la noctuelleEublemma amabilis Moore, prédatrice sur laquiers en Inde. L'effet de superparasitisme sur le développement, le sex ratio et la descendance du parasite ont été étudiés en détail. Le pourcentage de développement du parasite décro?t quand le nombre de parasites développés par h?te augmente. La période de développement, de l'œuf à l'éclosion de l'adulte, est de 10, 85 jours et ce délai est un peu plus court quand l'h?te est fortement superparasité. La taille de la femelle adulte décro?t avec l'augmentation du nombre de parasites développés par h?te. Il y a prédominance du sexe femelle chez le parasite. Le superparasitisme ne para?t avoir que peu d'action sur le taux sexuel. Quand plus de trois parasites se partagent un seul h?te, la longévité de l'adulte et la fécondité du parasite sont réduits. De tels individus sont mauvais voiliers et inactifs dans leur comportement.      

Length–weight relationships of Barilius bendelisis (Hamilton, 1807), Barilius shacra (Hamilton, 1822) and Barilius barna (Hamilton, 1822) from Manas River in Assam,India

The present study describes the length–weight relationships (LWRs) for three ornamental hill stream fish species from the Manas River in Assam, India, namely, Barilius bendelisis (Hamilton, 1807), Barilius shacra (Hamilton, 1822), and Barilius barna (Hamilton, 1822). Fishes were collected on a monthly basis from March 2015 to February 2016 with cast nets (270 cm, 1.2 cm) and gillnets (7,500 × 130 cm, 5 cm). This is the first information on LWR data for two of the species.     

Isolation of indigenous Staphylococcus sciuri from chromium-contaminated paddy field and its application for reduction of Cr(VI) in rice plants cultivated in pots

Accumulation of Cr(VI) in rice seeds cultivated in Cr-contaminated soil of the Sundarbans (India) is an environmental problem. Cr(VI) concentration in this soil was 6.2 ± 0.3 mg/kg, whereas total chromium was 32.04 ± 1.60 mg/kg. A Cr(VI)-removing bacterium isolated from Cr-contaminated paddy field soil of Sundarbans was identified as Staphylococcus sciuri. Enrichment culture of S. sciuri was applied to pot cultivation of rice in Cr-contaminated soil. After 8 weeks, 71 ± 3% Cr(VI) (final concentration 2.15 ± 0.01 mg/kg) and 65 ± 2% total Cr removal (end concentration 11.3 ± 0.5 mg/kg) were attained in bacterium-treated soils. Growth parameters indicated healthy development of plants cultivated in bacterium-treated soils that was not observed in control plants. Total Cr removal attained in rice seeds of plants cultivated in bacterium-treated soils compared with control rice seeds was 78 ± 4%. Total Cr concentration in test seeds was 0.72 ± 0.05 mg/kg (World Health Organization [WHO] permissible limit: 1.30 mg/kg), whereas the same in control seeds was 3.27 ± 0.16 mg/kg. Cr(VI) reduction achieved in rice seeds cultivated in bacterium-treated soil compared with control rice seeds was 95 ± 5%. Cr(VI) concentration in rice seeds cultivated in treated soil was 0.050 ± 0.003 mg/kg, whereas the same in untreated control was 0.93 ± 0.05 mg/kg. Successful paddy field soil bioremediation by any Staphylococcus species was demonstrated for the first time.     

MicroRNA-21 orchestrates high glucose-induced signals to TOR complex 1, resulting in renal cell pathology in diabetes

Hyperglycemia induces a wide array of signaling pathways in the kidney that lead to hypertrophy and matrix expansion, eventually culminating in progressive kidney failure. High glucose-induced reduction of the tumor suppressor protein phosphatase and tensin homolog deleted in chromosome 10 (PTEN) contributes to renal cell hypertrophy and matrix expansion. We identified microRNA-21 (miR-21) as the molecular link between high glucose and PTEN suppression. Renal cortices from OVE26 type 1 diabetic mice showed significantly elevated levels of miR-21 associated with reduced PTEN and increased fibronectin content. In renal mesangial cells, high glucose increased the expression of miR-21, which targeted the 3'-UTR of PTEN mRNA to inhibit PTEN protein expression. Overexpression of miR-21 mimicked the action of high glucose, which included a reduction in PTEN expression and a concomitant increase in Akt phosphorylation. In contrast, expression of miR-21 Sponge, to inhibit endogenous miR-21, prevented down-regulation of PTEN and phosphorylation of Akt induced by high glucose. Interestingly, high glucose-stimulated miR-21 inactivated PRAS40, a negative regulator of TORC1. Finally, miR-21 enhanced high glucose-induced TORC1 activity, resulting in renal cell hypertrophy and fibronectin expression. Thus, our results identify a previously unrecognized function of miR-21 that is the reciprocal regulation of PTEN levels and Akt/TORC1 activity that mediate critical pathologic features of diabetic kidney disease.     

Comparative Study of Antibiofilm Activity of Copper Oxide and Iron Oxide Nanoparticles Against Multidrug Resistant Biofilm Forming Uropathogens

The effectiveness of the metal oxide nanoparticles viz. CuO and Fe₂O₃ as antibacterial agents against multidrug resistant biofilm forming bacteria was evaluated. CuO nanoparticles were also experimented for antibiofilm and time kill assay. The CuO displayed maximum antibacterial activity with zone of inhibition of (22 ± 1) mm against methicillin resistant Staphylococcus aureus (MRSA) followed by Escherichia coli (18 ± 1) mm. The Fe₂O₃ showed the zone of inhibition against MRSA of (14 ± 1) mm followed by E. coli (12 ± 1) mm. CuO proved to be more toxic than Fe₂O₃ nanoparticles showing significantly high antibacterial activity and found to possess dose dependent antibiofilm properties.     

The 32 kDa subunit of replication protein A (RPA) participates in the DNA replication of Mung bean yellow mosaic India virus (MYMIV) by interacting with the viral Rep protein

Mung bean yellow mosaic India virus (MYMIV) is a member of genus begomoviridae and its genome comprises of bipartite (two components, namely DNA-A and DNA-B), single-stranded, circular DNA of about 2.7 kb. During rolling circle replication (RCR) of the DNA, the stability of the genome and maintenance of the stem–loop structure of the replication origin is crucial. Hence the role of host single-stranded DNA-binding protein, Replication protein A (RPA), in the RCR of MYMIV was examined. Two RPA subunits, namely the RPA70 kDa and RPA32 kDa, were isolated from pea and their roles were validated in a yeast system in which MYMIV DNA replication has been modelled. Here, we present evidences that only the RPA32 kDa subunit directly interacted with the carboxy terminus of MYMIV-Rep both in vitro as well as in yeast two-hybrid system. RPA32 modulated the functions of Rep by enhancing its ATPase and down regulating its nicking and closing activities. The possible role of these modulations in the context of viral DNA replication has been discussed. Finally, we showed the positive involvement of RPA32 in transient replication of the plasmid DNA bearing MYMIV replication origin using an in planta based assay.     

PI 3 kinase-dependent Akt kinase and PKCepsilon independently regulate interferon-gamma-induced STAT1alpha serine phosphorylation to induce monocyte chemotactic protein-1 expression

Monocyte chemotactic protein-1 (MCP-1) recruits activated phagocytes to the site of tissue injury. Interferon-gamma (IFN-gamma) present in the microenvironment of glomerulus acts on mesangial cells to induce local production of MCP-1. The mechanism by which IFN-gamma stimulates expression of MCP-1 is not clear. We therefore examined the role of PI 3 kinase signaling in regulating the IFN-gamma-induced MCP-1 expression in mesangial cells. Blocking PI 3 kinase activity with Ly294002 attenuated IFN-gamma-induced MCP-1 protein and mRNA expression. IFN-gamma increased Akt kinase activity in a PI 3 kinase-dependent manner. Expression of dominant negative Akt kinase inhibited serine phosphorylation of STAT1alpha, without any effect on its tyrosine phosphorylation, and decreased IFN-gamma-induced expression of MCP-1. These data for the first time indicate a role for PI 3 kinase-dependent Akt kinase in MCP-1 expression. We have recently shown that along with Akt, PKCepsilon is a downstream target of PI 3 kinase in IFN-gamma signaling. Similar to dominant negative Akt kinase, dominant negative PKCepsilon also inhibited serine phosphorylation of STAT1alpha without any effect on tyrosine phosphorylation. Dominant negative PKCepsilon also abrogated MAPK activity, resulting in decrease in IFN-gamma-induced MCP-1 expression. Furthermore, Akt and PKCepsilon are present together in a signaling complex. IFN-gamma had no effect on this complex formation, but did increase PKCepsilon-associated Akt kinase activity. PKCepsilon did not regulate IFN-gamma-induced Akt kinase. Finally, expression of dominant negative Akt kinase blocked IFN-gamma-stimulated MAPK activation. These data provide the first evidence that PI 3 kinase-dependent Akt and PKCepsilon activation independently regulate MAPK activity and serine phosphorylation of STAT1alpha to increase expression of MCP-1.