Sustainability through Agroforestry in Himalayas: An overview

This record was migrated from the OpenDepot repository service in June, 2017 before shutting down

Effect of Crop Establishment Methods on Crop Yield, Weed Dynamics, Profitability and Nutrient Uptake Under Rice-Wheat Cropping System of Indo-Gangetic Plains of Eastern India

The rice–wheat cropping system covering 13.5 million ha in the Indo-Gangetic Plains in South-Asia is vital for food security. Water, energy and labour scarcity, increasing cost of production, diminishing farm profit and the changing climate are major challenges faced by the farmers under intensive tillage based conventional practices. In a field study, we evaluated productivity, weed dynamics, nutrient uptake and economical profitability of four wheat establishment methods during two years. The wheat establishment methods included zero-till wheat (ZTW), happy seeder planted wheat (HSW), bed planted wheat (BPW) and conventional till wheat (CTW). The treatments were completely randomized and replicated five times. Wheat grain yield under HSW was 3.4% and 4.1% higher than BPW, 8.3% and 11.0% higher than ZTW and 20.8% and 24.5% higher than CTW in 2012-13 and 2013-14, respectively. Nutrient (N, P and K) uptake in wheat grain was also higher in HSW than in the other treatments. Weed density and biomass was the lowest under HSW followed by BPT, and the highest in CTW. The weed pressure was reduced in the second growing season compared to the first. Net profit and benefit cost ratio was highest under HSW and the lowest under CTW. This record was migrated from the OpenDepot repository service in June, 2017 before shutting down

Integrated farming system for improving agricultural productivity

This record was migrated from the OpenDepot repository service in June, 2017 before shutting down

Performance of lactating crossbred cows fed on forage based total mixed ration

A study was conducted to evaluate the forage based total mixed ration (TMR) in crossbred lactating cows on milk production and nutrient digestibility. TMR was prepared by mixing wheat straw, chapped green forages (sorghum and rice bean in experiment I and oat and berseem in experiment II) and concentrate feed having 17 percent dietary CP. Two feeding experiments for the period of 60 days duration each during rainy (experiment I) and winter seasons (experiment II) were conducted in first lactating crossbred cows. In both the experiment six first lactating cows were taken and divided into 2 groups. Group 1 (T1)was fed TMR and in Group 2 (T2) ingredients were fed separately. The total daily dry matter intake (DMI) in cows fed TMR increased significantly (p˂0.01) by 15.92 percent in experiment I, when multi cut sorghum and rice bean used as green fodder. However, the differences were negligible in experiment II,when oat and berseem used as green fodder. The dry matter (DM) and crude protein (CP) digestibility as well as digestible energy (DE) value of ration were increased significantly (p˂0.01) in cows fed on TMR based on berseem and oat as green fodder in experiment II. However, differences were non-significant in experiment I, when multi cut sorghum and rice bean used as green fodder in TMR. The overall increase in milk production was recorded by 16.96 and 19.49 percent in cows fed TMR during experiment I and II, respectively. Similarly, an increase in milk production in cows fed different feeds separately was also recorded 10.74 and 6.41 percent,respectively during experiment I and II. Thus, it i s concluded that feeding of TMR is beneficial for proportionate intake of all feed ingredients, overall feed intake and better digestibility of nutrients resulting into higher milk production. This record was migrated from the OpenDepot repository service in June, 2017 before shutting down

The timing of umbilical cord clamping at birth: physiological considerations

While it is now recognized that umbilical cord clamping (UCC) at birth is not necessarily an innocuous act, there is still much confusion concerning the potential benefits and harms of this common procedure. It is most commonly assumed that delaying UCC will automatically result in a time-dependent net placental-to-infant blood transfusion, irrespective of the infant’s physiological state. Whether or not this occurs, will likely depend on the infant’s physiological state and not on the amount of time that has elapsed between birth and umbilical cord clamping (UCC). However, we believe that this is an overly simplistic view of what can occur during delayed UCC and ignores the benefits associated with maintaining the infant’s venous return and cardiac output during transition. Recent experimental evidence and observations in humans have provided compelling evidence to demonstrate that time is not a major factor influencing placental-to-infant blood transfusion after birth. Indeed, there are many factors that influence blood flow in the umbilical vessels after birth, which depending on the dominating factors could potentially result in infant-to-placental blood transfusion. The most dominant factors that influence umbilical artery and venous blood flows after birth are lung aeration, spontaneous inspirations, crying and uterine contractions. It is still not entirely clear whether gravity differentially alters umbilical artery and venous flows, although the available data suggests that its influence, if present, is minimal. While there is much support for delaying UCC at birth, much of the debate has focused on a time-based approach, which we believe is misguided. While a time-based approach is much easier and convenient for the caregiver, ignoring the infant’s physiology during delayed UCC can potentially be counter-productive for the infant

Interaction of Chandipura Virus N and P Proteins: Identification of Two Mutually Exclusive Domains of N Involved in Interaction with P

The nucleocapsid protein (N) and the phosphoprotein (P) of nonsegmented negative-strand (NNS) RNA viruses interact with each other to accomplish two crucial events necessary for the viral replication cycle. First, the P protein binds to the aggregation prone nascent N molecules maintaining them in a soluble monomeric (N0) form (N0-P complex). It is this form that is competent for specific encapsidation of the viral genome. Second, the P protein binds to oligomeric N in the nucleoprotein complex (N-RNA-P complex), and thereby facilitates the recruitment of the viral polymerase (L) onto its template. All previous attempts to study these complexes relied on co-expression of the two proteins in diverse systems. In this study, we have characterised these different modes of N-P interaction in detail and for the first time have been able to reconstitute these complexes individually in vitro in the chandipura virus (CHPV), a human pathogenic NNS RNA virus. Using a battery of truncated mutants of the N protein, we have been able to identify two mutually exclusive domains of N involved in differential interaction with the P protein. An unique N-terminal binding site, comprising of amino acids (aa) 1–180 form the N0-P interacting region, whereas, C-terminal residues spanning aa 320–390 is instrumental in N-RNA-P interactions. Significantly, the ex-vivo data also supports these observations. Based on these results, we suggest that the P protein acts as N-specific chaperone and thereby partially masking the N-N self-association region, which leads to the specific recognition of viral genome RNA by N0

Feedback Enhances Feedforward Figure-Ground Segmentation by Changing Firing Mode

In the visual cortex, feedback projections are conjectured to be crucial in figure-ground segregation. However, the precise function of feedback herein is unclear. Here we tested a hypothetical model of reentrant feedback. We used a previous developed 2-layered feedforwardspiking network that is able to segregate figure from ground and included feedback connections. Our computer model data show that without feedback, neurons respond with regular low-frequency (∼9 Hz) bursting to a figure-ground stimulus. After including feedback the firing pattern changed into a regular (tonic) spiking pattern. In this state, we found an extra enhancement of figure responses and a further suppression of background responses resulting in a stronger figure-ground signal. Such push-pull effect was confirmed by comparing the figure-ground responses withthe responses to a homogenous texture. We propose that feedback controlsfigure-ground segregation by influencing the neural firing patterns of feedforward projecting neurons

Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples

<p>Abstract</p> <p>Background</p> <p>Readthrough fusions across adjacent genes in the genome, or transcription-induced chimeras (TICs), have been estimated using expressed sequence tag (EST) libraries to involve 4-6% of all genes. Deep transcriptional sequencing (RNA-Seq) now makes it possible to study the occurrence and expression levels of TICs in individual samples across the genome.</p> <p>Methods</p> <p>We performed single-end RNA-Seq on three human prostate adenocarcinoma samples and their corresponding normal tissues, as well as brain and universal reference samples. We developed two bioinformatics methods to specifically identify TIC events: a targeted alignment method using artificial exon-exon junctions within 200,000 bp from adjacent genes, and genomic alignment allowing splicing within individual reads. We performed further experimental verification and characterization of selected TIC and fusion events using quantitative RT-PCR and comparative genomic hybridization microarrays.</p> <p>Results</p> <p>Targeted alignment against artificial exon-exon junctions yielded 339 distinct TIC events, including 32 gene pairs with multiple isoforms. The false discovery rate was estimated to be 1.5%. Spliced alignment to the genome was less sensitive, finding only 18% of those found by targeted alignment in 33-nt reads and 59% of those in 50-nt reads. However, spliced alignment revealed 30 cases of TICs with intervening exons, in addition to distant inversions, scrambled genes, and translocations. Our findings increase the catalog of observed TIC gene pairs by 66%.</p> <p>We verified 6 of 6 predicted TICs in all prostate samples, and 2 of 5 predicted novel distant gene fusions, both private events among 54 prostate tumor samples tested. Expression of TICs correlates with that of the upstream gene, which can explain the prostate-specific pattern of some TIC events and the restriction of the <it>SLC45A3-ELK4 </it>e4-e2 TIC to <it>ERG</it>-negative prostate samples, as confirmed in 20 matched prostate tumor and normal samples and 9 lung cancer cell lines.</p> <p>Conclusions</p> <p>Deep transcriptional sequencing and analysis with targeted and spliced alignment methods can effectively identify TIC events across the genome in individual tissues. Prostate and reference samples exhibit a wide range of TIC events, involving more genes than estimated previously using ESTs. Tissue specificity of TIC events is correlated with expression patterns of the upstream gene. Some TIC events, such as <it>MSMB-NCOA4</it>, may play functional roles in cancer.</p

Multiple M. tuberculosis Phenotypes in Mouse and Guinea Pig Lung Tissue Revealed by a Dual-Staining Approach

A unique hallmark of tuberculosis is the granulomatous lesions formed in the lung. Granulomas can be heterogeneous in nature and can develop a necrotic, hypoxic core which is surrounded by an acellular, fibrotic rim. Studying bacilli in this in vivo microenvironment is problematic as Mycobacterium tuberculosis can change its phenotype and also become acid-fast negative. Under in vitro models of differing environments, M. tuberculosis alters its metabolism, transcriptional profile and rate of replication. In this study, we investigated whether these phenotypic adaptations of M. tuberculosis are unique for certain environmental conditions and if they could therefore be used as differential markers. Bacilli were studied using fluorescent acid-fast auramine-rhodamine targeting the mycolic acid containing cell wall, and immunofluorescence targeting bacterial proteins using an anti-M. tuberculosis whole cell lysate polyclonal antibody. These techniques were combined and simultaneously applied to M. tuberculosis in vitro culture samples and to lung sections of M. tuberculosis infected mice and guinea pigs. Two phenotypically different subpopulations of M. tuberculosis were found in stationary culture whilst three subpopulations were found in hypoxic culture and in lung sections. Bacilli were either exclusively acid-fast positive, exclusively immunofluorescent positive or acid-fast and immunofluorescent positive. These results suggest that M. tuberculosis exists as multiple populations in most conditions, even within seemingly a single microenvironment. This is relevant information for approaches that study bacillary characteristics in pooled samples (using lipidomics and proteomics) as well as in M. tuberculosis drug development