Soil Fertility under Grassland Compared to Other Land Uses in Acid Soil of Himachal Pradesh, India

In the last decades severe changes in land use occurred in tropical countries, due to increasing population and their demand for food resources. Forest land is rapidly converted into agriculture or pastureland which may cause significant changes in soil fertility. Land-use exerts significant effect on nutrient availability and may also influence secondary succession and biomass production (Lu et al., 2002). Nutrient cycling in agroforestry is in between natural forest ecosystems of the tropics and most of the agricultural systems with are ‘‘leaky’’ having higher nutrient losses. Research indicated that decline of soil organic matter may occur due to conversion of forest and grassland into agriculture (Ouattara et al., 2006). Tree growth is highly influenced by base cations (Ca, Mg, K, Na) concentration, cation exchange capacity, and concentrations of Al and Mn. Calcium and N are specifically important, as they are primary constituents of biomass and regulate cell function of many tree species. Base cations also help in alleviating the effects of Al toxicity in acid soil

Isoform-level gene signature improves prognostic stratification and accurately classifies glioblastoma subtypes.

Molecular stratification of tumors is essential for developing personalized therapies. Although patient stratification strategies have been successful; computational methods to accurately translate the gene-signature from high-throughput platform to a clinically adaptable low-dimensional platform are currently lacking. Here, we describe PIGExClass (platform-independent isoform-level gene-expression based classification-system), a novel computational approach to derive and then transfer gene-signatures from one analytical platform to another. We applied PIGExClass to design a reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) based molecular-subtyping assay for glioblastoma multiforme (GBM), the most aggressive primary brain tumors. Unsupervised clustering of TCGA (the Cancer Genome Altas Consortium) GBM samples, based on isoform-level gene-expression profiles, recaptured the four known molecular subgroups but switched the subtype for 19% of the samples, resulting in significant (P = 0.0103) survival differences among the refined subgroups. PIGExClass derived four-class classifier, which requires only 121 transcript-variants, assigns GBM patients' molecular subtype with 92% accuracy. This classifier was translated to an RT-qPCR assay and validated in an independent cohort of 206 GBM samples. Our results demonstrate the efficacy of PIGExClass in the design of clinically adaptable molecular subtyping assay and have implications for developing robust diagnostic assays for cancer patient stratification

IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data

<p>Abstract</p> <p>Background</p> <p>mRNA-Seq technology has revolutionized the field of transcriptomics for identification and quantification of gene transcripts not only at gene level but also at isoform level. Estimating the expression levels of transcript isoforms from mRNA-Seq data is a challenging problem due to the presence of constitutive exons.</p> <p>Results</p> <p>We propose a novel algorithm (IsoformEx) that employs weighted non-negative least squares estimation method to estimate the expression levels of transcript isoforms. Validations based on <it>in silico </it>simulation of mRNA-Seq and qRT-PCR experiments with real mRNA-Seq data showed that IsoformEx could accurately estimate transcript expression levels. In comparisons with published methods, the transcript expression levels estimated by IsoformEx showed higher correlation with known transcript expression levels from simulated mRNA-Seq data, and higher agreement with qRT-PCR measurements of specific transcripts for real mRNA-Seq data.</p> <p>Conclusions</p> <p>IsoformEx is a fast and accurate algorithm to estimate transcript expression levels and gene expression levels, which takes into account short exons and alternative exons with a weighting scheme. The software is available at <url>http://bioinformatics.wistar.upenn.edu/isoformex</url>.</p

Switching of ferroelectric liquid crystal doped with cetyltrimethylammonium bromide-assisted CdS nanostructures

Large scale high yield cadmium sulfide (CdS) nanowires with uniform diameter were synthesized using a rapid and simple solvo-chemical and hydrothermal route assisted by the surfactant cetyltrimethylammonium bromide (CTAB). Unique CdS nanowires of different morphologies could be selectively produced by only varying the concentration of CTAB in the reaction system with cadmium acetate, sulfur powder and ethylenediamine. We obtained CdS nanowires with diameters of 64–65 nm and lengths of up to several micrometers. A comparative study of the optical properties of ferroelectric liquid crystal (FLC) Felix-017/100 doped with 1% of CdS nanowires was performed. Response times of the order of from 160 to 180 μs, rotational viscosities of the order of from 5000 to 3000 mN s m−2 and polarizations of the order of from 10 to 70 nC cm−2 were measured. We also observed an anti-ferroelectric to ferroelectric transition for CdS doped FLC instead of the ferroelectric to paraelectric transition for pure FLC

Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data

BACKGROUND: Use of alternative gene promoters that drive widespread cell-type, tissue-type or developmental gene regulation in mammalian genomes is a common phenomenon. Chromatin immunoprecipitation methods coupled with DNA microarray (ChIP-chip) or massive parallel sequencing (ChIP-seq) are enabling genome-wide identification of active promoters in different cellular conditions using antibodies against Pol-II. However, these methods produce enrichment not only near the gene promoters but also inside the genes and other genomic regions due to the non-specificity of the antibodies used in ChIP. Further, the use of these methods is limited by their high cost and strong dependence on cellular type and context. METHODS: We trained and tested different state-of-art ensemble and meta classification methods for identification of Pol-II enriched promoter and Pol-II enriched non-promoter sequences, each of length 500 bp. The classification models were trained and tested on a bench-mark dataset, using a set of 39 different feature variables that are based on chromatin modification signatures and various DNA sequence features. The best performing model was applied on seven published ChIP-seq Pol-II datasets to provide genome wide annotation of mouse gene promoters. RESULTS: We present a novel algorithm based on supervised learning methods to discriminate promoter associated Pol-II enrichment from enrichment elsewhere in the genome in ChIP-chip/seq profiles. We accumulated a dataset of 11,773 promoter and 46,167 non-promoter sequences, each of length 500 bp, generated from RNA Pol-II ChIP-seq data of five tissues (Brain, Kidney, Liver, Lung and Spleen). We evaluated the classification models in building the best predictor and found that Bagging and Random Forest based approaches give the best accuracy. We implemented the algorithm on seven different published ChIP-seq datasets to provide a comprehensive set of promoter annotations for both protein-coding and non-coding genes in the mouse genome. The resulting annotations contain 13,413 (4,747) protein-coding (non-coding) genes with single promoters and 9,929 (1,858) protein-coding (non-coding) genes with two or more alternative promoters, and a significant number of unassigned novel promoters. CONCLUSION: Our new algorithm can successfully predict the promoters from the genome wide profile of Pol-II bound regions. In addition, our algorithm performs significantly better than existing promoter prediction methods and can be applied for genome-wide predictions of Pol-II promoters

Knowledge, anxiety levels and attitudes of infertile couples towards COVID-19 and its impact on self-funded fertility treatment : a cross-sectional questionnaire survey

Acknowledgement We thank the couples who were willing to participate in the study. Funding This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.Peer reviewedPublisher PD

"The fruits of independence": Satyajit Ray, Indian nationhood and the spectre of empire

Challenging the longstanding consensus that Satyajit Ray's work is largely free of ideological concerns and notable only for its humanistic richness, this article shows with reference to representations of British colonialism and Indian nationhood that Ray's films and stories are marked deeply and consistently by a distinctively Bengali variety of liberalism. Drawn from an ongoing biographical project, it commences with an overview of the nationalist milieu in which Ray grew up and emphasizes the preoccupation with colonialism and nationalism that marked his earliest unfilmed scripts. It then shows with case studies of Kanchanjangha (1962), Charulata (1964), First Class Kamra (First-Class Compartment, 1981), Pratidwandi (The Adversary, 1970), Shatranj ke Khilari (The Chess Players, 1977), Agantuk (The Stranger, 1991) and Robertsoner Ruby (Robertson's Ruby, 1992) how Ray's mature work continued to combine a strongly anti-colonial viewpoint with a shifting perspective on Indian nationhood and an unequivocal commitment to cultural cosmopolitanism. Analysing how Ray articulated his ideological positions through the quintessentially liberal device of complexly staged debates that were apparently free, but in fact closed by the scenarist/director on ideologically specific notes, this article concludes that Ray's reputation as an all-forgiving, ‘everybody-has-his-reasons’ humanist is based on simplistic or even tendentious readings of his work

Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq

Alternative promoters that are differentially used in various cellular contexts and tissue types add to the transcriptional complexity in mammalian genome. Identification of alternative promoters and the annotation of their activity in different tissues is one of the major challenges in understanding the transcriptional regulation of the mammalian genes and their isoforms. To determine the use of alternative promoters in different tissues, we performed ChIP-seq experiments using antibody against RNA Pol-II, in five adult mouse tissues (brain, liver, lung, spleen and kidney). Our analysis identified 38 639 Pol-II promoters, including 12 270 novel promoters, for both protein coding and non-coding mouse genes. Of these, 6384 promoters are tissue specific which are CpG poor and we find that only 34% of the novel promoters are located in CpG-rich regions, suggesting that novel promoters are mostly tissue specific. By identifying the Pol-II bound promoter(s) of each annotated gene in a given tissue, we found that 37% of the protein coding genes use alternative promoters in the five mouse tissues. The promoter annotations and ChIP-seq data presented here will aid ongoing efforts of characterizing gene regulatory regions in mammalian genomes

Not Available

Not AvailableRock phosphate-enriched pressmud compost (RPEPMC) was prepared by composting fresh pressmud and rock phosphate mixture in the ratio of 20:1 (w:w basis) in cylindrical plastic container with a composite microbial culture at 0.1% (w:w) level. A field experiment was conducted during rainy season (kharif) followed by winter (rabi) season of 2006-07 to evaluate the RPEPMC as partial substitute of fertilizer phosphorus (P) in terms of direct and residual P uptake and P use efficiency (PUE) by crops to study the changes in available P at 60 days after sowing (DAS) as well as after harvest of both the crops and various inorganic P fractions in soil after cropping. Results showed that pearl millet responded up to 26.1 kg ha-1 of P application. Application of diammonium phosphate (DAP) proved superior to RPEPMC with respect to grain and stover yield, P derived from P sources, total P uptake and PUE by pearl millet at 34.8 kg P ha-1 level. Among the various ratios of RPEPMC and DAP (3:1, 1:1 and 1:3) tried at 34.8 kg P ha-1 level, the 1:3 ratio showed best performance followed by 1:1 and 3:1 ratios. Phosphorus applied to pearl millet had considerable residual effect on succeeding mustard, the effect being more pronounced at higher levels of P application. The residual effect of P applied at 34.8 kg P ha-1 through RPEPMC and DAP produced 74.3 and 59.6% relative grain yield and 74.6 and 56.2% relative total P uptake, respectively at maturity against fresh application of 34.8 kg P ha-1 through DAP in mustard. The relative total P uptake by mustard at 34.8 kg P ha-1 through the three ratios was in the order of 3:1>1:1>1:3. Residual effect of RPEPMC and DAP in combination applied at 34.8 kg P ha-1 in a 3:1 ratio showed higher available P at 60 DAS as well as after harvest of mustard. Moreover, the application of RPEPMC in soils of medium available P status (Typic Haplustepts) in pearl millet-mustard sequence replaced about half to two-third of P requirement of crops from fertilizer with no appreciable change in soil P fertility.Not Availabl