Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats

BACKGROUND: Quantitative variation in gene expression has been proposed to underlie phenotypic variation among human individuals. A facilitating step towards understanding the basis for gene expression variability is associating genome wide transcription patterns with potential cis modifiers of gene expression. DESCRIPTION: EXPOLDB, a novel Database, is a new effort addressing this need by providing information on gene expression levels variability across individuals, as well as the presence and features of potentially polymorphic (TG/CA)(n )repeats. EXPOLDB thus enables associating transcription levels with the presence and length of (TG/CA)(n )repeats. One of the unique features of this database is the display of expression data for 5 pairs of monozygotic twins, which allows identification of genes whose variability in expression, are influenced by non-genetic factors including environment. In addition to queries by gene name, EXPOLDB allows for queries by a pathway name. Users can also upload their list of HGNC (HUGO (The Human Genome Organisation) Gene Nomenclature Committee) symbols for interrogating expression patterns. The online application 'SimRep' can be used to find simple repeats in a given nucleotide sequence. To help illustrate primary applications, case examples of Housekeeping genes and the RUNX gene family, as well as one example of glycolytic pathway genes are provided. CONCLUSION: The uniqueness of EXPOLDB is in facilitating the association of genome wide transcription variations with the presence and type of polymorphic repeats while offering the feature for identifying genes whose expression variability are influenced by non genetic factors including environment. In addition, the database allows comprehensive querying including functional information on biochemical pathways of the human genes. EXPOLDB can be accessed a

Aqueous areca nut extract induces oxidative stress in human lung epithelial A549 cells: Probable role of p21 in inducing cell death

Areca nut a well-known masticator used across globe. Habitual chewing of areca nut is associated with serious oral health effects. However, the role of areca nut in oxidative stress induction and cell death is less understood. Hence, in the present study we aimed to evaluate the toxic mechanism of areca nut extract on human lung epithelial A549 cells. Cells were treated with or without aqueous areca nut extract and cell viability was measured by MTT assay. Cells treated with areca nut extract show reduced viability in a dose dependent manner with the IC50 of 0.5 concentration. Areca nut extract induced the reactive oxygen species (ROS), lipid peroxidation followed by membrane damage with leakage of lactate dehydrogenase (LDH) enzyme. Cells with continuous exposure of areca nut extract depletes the free radical neutralizing anti-oxidant enzymes like superoxide dismutase (SOD), Glutathione peroxidase (GSH-Px) and Glutathione-S-transferase (GST). Further, the analysis of mRNA expression of apoptotic genes and cell cycle regulators show decreased expression of anti-apoptotic gene (Bcl-2), Cyclin E1, Cyclin D1, CDK4, Rb and p53 whereas induced expression of p21 and marginal increase of pro-apoptotic gene (Bax) confirms the toxic nature of areca nut. Thus, cell death due to areca nut exposure may be through different mechanism rather than the conventional apoptotic pathway, where p21 induction might be independent of p53 action, which possibly suggests that there may be a role of p21 in oxidative stress induced cell death. Further FACS analysis confirms cell death in areca nut treated cells. © 2016 Elsevier Inc

Cadmium induces oxidative stress and apoptosis in lung epithelial cells

Cadmium (Cd) is one of the well-known highly toxic environmental and industrial pollutants. Cd first accumulates in the nucleus and later interacts with zinc finger proteins of antiapoptotic genes and inhibit the binding of transcriptional factors and transcription. However, the role of Cd in oxidative stress and apoptosis is less understood. Hence, the present study was undertaken to unveil the mechanism of action. A549 cells were treated with or without Cd and cell viability was measured by MTT assay. Treatment of cells with Cd shows reduced viability in a dose-dependent manner with IC50 of 45 μM concentration. Cd significantly induces the reactive oxygen species (ROS), lipid peroxidation followed by membrane damage with the leakage of lactate dehydrogenase (LDH). Cells with continuous exposure of Cd deplete the antioxidant super oxide dismutase (SOD) and glutathione peroxidase (GSH-Px) enzymes. Further, analysis of the expression of genes involved in apoptosis show that both the extrinsic and intrinsic apoptotic pathways were involved. Death receptor marker tumor necrosis factor-α (TNF-α), executor caspase-8 and pro-apoptotic gene (Bax) were induced, while antiapoptotic gene (Bcl-2) was decreased in Cd-treated cells. Fluorescence-activated cell sorting (FACS) analysis further confirms the induction of apoptosis in Cd-treated A549 cells

Differential expression of AP-1 transcription factors in human prostate LNCaP and PC-3 cells: role of Fra-1 in transition to CRPC status

Androgen receptor (AR) signaling axis plays a vital role in the development of prostate and critical in the progression of prostate cancer. Androgen withdrawal initially regresses tumors but eventually develops into aggressive castration-resistant prostate cancer (CRPC). Activator Protein-1 (AP-1) transcription factors are most likely to be associated with malignant transformation in prostate cancer. Hence, to determine the implication of AR and AP-1 in promoting the transition of prostate cancer to the androgen-independent state, we used AR-positive LNCaP and AR-negative PC-3 cells as an in vitro model system. The effect of dihydrotestosterone or anti-androgen bicalutamide on the cell proliferation and viability was assessed by MTT assay. Expression studies on AR, marker genes-PSA, TMPRSS2, and different AP-1 factors were analyzed by semi-quantitative RT-PCR and expressions of AR and Fra-1 proteins were analyzed by Western blotting. Dihydrotestosterone induced the cell proliferation in LNCaP with no effect on PC-3 cells. Bicalutamide decreased the viability of both LNCaP and PC-3 cells. Dihydrotestosterone induced the expression of AR, PSA, c-Jun, and Fra-1 in LNCaP cells, and it was c-Jun and c-Fos in case of PC-3 cells, while bicalutamide decreased their expression. In addition, constitutive activation and non-regulation of Fra-1 by bicalutamide in PC-3 cells suggested that Fra-1, probably a key component, involved in transition of aggressive androgen-independent PC-3 cells with poor prognosis. © 2017, Springer Science+Business Media New York

Study of Photoluminescence Behaviour of Porous Silicon Samples Prepared at 20 mA Current Density

The paper presents a study on a series of porous silicon films of various thicknesses, prepared at 20 mA current density using a photoluminescence fitting model to determine the average crystallite size of sphe-rical shaped interconnected silicon quantum dots. Discrepancy in photoluminescence behavior of the samples is well explained with this model. When you are citing the document, use the following link http://essuir.sumdu.edu.ua/handle/123456789/3097

Mechanical characterization of heat treated Al2219 hybrid composites

Aluminium alloy matrix composites with Al2O3 reinforcements exhibit superior mechanical properties and utilize in several demanding fields’ viz., automobile, aerospace, defense, sports equipment, electronics and bio-medical. The present work emphasizes on improvement of microstructure and mechanical properties of age hardened graphite and alumina reinforced Al alloy matrix hybrid composites. Different composites with a constant carbon content of 1 weight % and 0, 2, 4 and 6 weight % Al2O3 as reinforcements are fabricated by using stir casting technic and tested for hardness, tensile and impact strength. Scanning electron microscopy (SEM) is performed to analyse the failure mode under tensile load. All the composites are subjected to age hardening treatment with solutionising temperature of 530oC and aging temperatures of 100 and 200oC. The peak hardness of the composites at two aging temperatures are noted. Tensile and impact tests are conducted for the peak aged specimens. Results show substantial increase in the hardness of the age hardened specimens in the range of 34-44% in comparison with the as cast specimens. Result analysis shows increase in tensile strength (upto 40%) and decrease in impact resistance (upto 33%) with the increase in weight % of reinforcements. As the aging temperature increases a reduction in tensile strength and impact resistance is observed in each composites

Impact of nitrogen management and nano-urea on yield, quality and storage attributes of garlic (Allium sativum)

The present study was carried out during winter (rabi) seasons of 2020–21 and 2021–22 at Sri Karan Narendra College of Agriculture, Jobner, Jaipur, Rajasthan to evaluate the impact of nitrogen management (organic and inorganic sources), biofertilizer and foliar spraying of nano-urea on yield, quality and storage attributes of garlic (Allium sativum L.). The experiment consisted of 3 levels of organic and inorganic fertilization, 2 levels of bio-fertilizers in main plot, and 4 levels of nano-urea arranged in split plot design (SPD) in sub plot. The results showed that yield, quality and storage attributes of garlic, viz. number of cloves/bulb (16.46%), clove length and girth, average weight of clove (1.56 gm), nitrogen, phosphorus and potassium content in bulb (1.10, 0.31 and 0.51%), physiological loss in weight, shelf-life of bulbs and rooting percentage of bulbs were significantly enhanced by 100% recommended dose of nitrogen through inorganic fertilizers and bio-fertilizer in main plot. In sub plot, the foliar spray of nano-urea @75 ml/ha recorded highest number of cloves per bulb (16.26%), clove length and girth (2.86 and 1.07 cm), average weight of clove (1.55 gm), nitrogen, phosphorus and potassium content in bulb (1.09, 0.31 and 0.51%), shelf-life of bulbs and rooting percentage of bulbs. Therefore, this study concluded that the nitrogen management and nano-urea in garlic crop gives better yield, quality and storage attributes, and can be opted in semi-arid climatic conditions

Protein kinases orchestrate cell cycle regulators in differentiating BeWo choriocarcinoma cells

Abstract Choriocarcinoma, a trophoblastic neoplasia, occurs in women as an incidence of abnormal pregnancy. BeWo choriocarcinoma cells derived from the abnormal placentation are a suitable model system to study the factors associated with differentiation, invasion and other cellular events as an alternative to clinical samples. Many protein kinases orchestrate the complex events of cell cycle and in case of malignancy such regulators are found to be mutated. In the present study, BeWo cells treated with forskolin (Fo) and phorbol 12-myristate 13-acetate (PMA) were used to study the role of PKA (protein kinase A) and PKC (protein kinase C), respectively, on the expression pattern of differentiation-related genes, membrane markers, PKC isoforms and cell cycle regulators. The effect of Fo and PMA on the cell proliferation was assessed. Progressive induction of alkaline phosphatase level and formation of multinucleated differentiated cells were observed in the cells treated with Fo. Exposure of cells to Fo and PMA induced the mRNA transcripts of α-hCG, β-hCG and endoglin and down-regulates E-cadherin at mRNA and protein levels. Synergistic levels of both up- and down-regulated genes/proteins were observed when cells were treated with the combination of Fo and PMA. The mRNA levels of cyclin D1, cyclin E1, p21, Rb, p53, caspase-3 and caspase-8 decreased gradually during differentiation. Fo significantly inhibited the protein levels of PCNA, Rb, PKC-α and PMA stimulated mRNA expression of PKC-ε and PKC-δ. Further, failure in the activation of essential components of the cell cycle machinery caused G2/M phase arrest in differentiating BeWo cells

Multiple ocean parameter-based potential fishing zone (PFZ) location generation and validation in the Western Bay of Bengal

A new conceptual framework based on satellite data, including chlorophyll (CHL), sea surface temperature (SST) fronts, relative winds, current vectors, Ekman transport, and eddies, has been developed to identify potential fishing zones (PFZ) in the Bay of Bengal (BoB). The framework aims to provide persistent forecasts, even under cloudy conditions, based on feature propagation. The validation of the PFZ was carried out using fish catch data collected by the Fishery Survey of India (FSI) between 2016 and 2018. Hooking rates (HR) from longlines and catch per unit effort (CPUE) from trawl nets were used to analyse the data points in hook rate categories (1.0–3.0 and > 3.0) and CPUE categories (50–100 kg and > 100 kg) and interpret them with the PFZ maps. The analysis showed that the high fish catch locations were consistent with persisting features in the BoB, such as high chlorophyll patches, SST fronts, and cyclonic eddies. The high fish catch locations based on hook rate and high CPUE were found to be collocated with the high chlorophyll persisting features and thermal gradients in the BoB. The regression analysis shows that availability of the food (CHL) had the strongest correlation with fish catch, followed by the comfort condition (fronts and eddies)