Low-cost interventions for big impacts in dryland production systems

A study at selected action sites in semi-arid region of Andhra Pradesh, India, showed widespread land degradation due to low levels of soil organic carbon (78% of fields) and deficiencies of available nutrients like phosphorus (34%), sulfur (93%), calcium (33%), zinc (84%), boron (73%), and copper (33%). Soil test-based addition of deficient micro- and macronutrients increased food grain production by 30–40% and straw (which is used as fodder) production by 10–30%. Micro-watershed scale low-cost cement-lined farm-ponds at smallholder farm level proved a scalable technology for drought-proofing of crops resulting into additional crop yield by more than 30% during 2015. Augmentation of water sources also facilitated farmers’ to successfully diversify the production system. Shared machinery resources improved the operational and economic efficiency of farm sowing operations through higher crop yields by around 10%. We conclude that a mix of low-cost critical interventions if out-scaled in a large number of dryland small holdings through policy support may not only improve productivity and livelihoods, but also enhance their abilities to effectively cope with the climatic aberrations

Prospects of new chickpea varieties in Andhra Pradesh

Andhra Pradesh is an important chickpea growing state in southern India, with spectacular increase in chickpea area from 120,000 ha in 1997/98 to 638,000 ha in 2007/08. The chickpea revolution in Andhra Pradesh has improved the prospects of many resource-poor, small land holding and rainfed farmers of Andhra Pradesh. However, the growing season of chickpea in Andhra Pradesh is warm and short (90-110 days), and drought is the foremost factor responsible for significant yield losses. Rainfall in major chickpea-growing regions is quite uncertain and erratic, resulting in poor yields. The Regional Agricultural Research Station of Acharya N G Ranga Agricultural University, Nandyal, Andhra Pradesh, India is the lead centre responsible for location-specific research in chickpea in Andhra Pradesh. With support from ICRISAT and ICAR, the centre has initiated crop improvement programmes during 2004 and has released four promising chickpea varieties for commercial cultivation. Three desi varieties viz., Nandyal Sanaga 1(NBeG 3), Dheera (NBeG 47), and Nandyal Gram 49 (NBeG 49) released for Andhra Pradesh and one large-seeded kabuli Nandyal Gram 119 (NBeG 119) released for the southern zone comprising Andhra Pradesh, Karnataka and Tamil Nadu, are cutting across chickpea growing regions of Andhra Pradesh. Nandyal Sanaga 1, released in 2012, is a bold-seeded desi variety tolerant to drought and heat; Dheera released during 2015 is also a desi variety and the first of its kind in India, suitable for mechanical harvesting. Nandyal Gram 49 released during 2016 is a highyielding desi variety with attractive seeds; whereas Nandyal Gram 119 is early bold-seeded kabuli variety released during 2015. These varieties have clearly demonstrated their advantage (10%-15 % increase over popular varieties of the tract) in farmers’ holdings in large-scale demonstrations and are being preferred by farmers of not only Andhra Pradesh, but also Karnataka, Tamil Nadu, Odisha and Maharastra. Efforts are underway to promote large-scale adoption of these varieties to maximize long term productivity of chickpeas in rainfed vertisols

The balance of expression of PTPN22 splice forms is significantly different in rheumatoid arthritis patients compared with controls

Complex disease is characterized by the interplay of multiple genetic and environmental factors. Rheumatoid arthritis (RA) is a complex autoimmune disease with a pronounced genetic component, mainly due to HLA-DRB1 gene, but also a multitude of loci outside the HLA region. In this work we strive to contribute to the understanding of the functional involvement of these susceptibility loci in the pathogenesis of RA. This study is based on a large material of whole blood samples and peripheral blood mononuclear cells (PBMCs) from RA patients and matched healthy controls from Sweden. The main methods used in this work included probe-based genotyping and gene-expression assays, cell cultures, RNA-sequencing, gene-gene interaction and pathway analysis, as well as a plethora of common molecular genetics and bioinformatics methods. We investigated the role of expression of known genetic risk factors PTPN22 and PTPN2 in RA, with a special attention to the splicing profile of these genes. Our data indicates significant differences in the expression ratio of splice variants for PTPN22 in whole blood samples from RA patients and healthy controls. For PTPN2 we demonstrate a significant difference in the relative mRNA expression of' transcript TC48 in PBMCs of healthy controls and RA patients. Additionally, we identified new susceptibility SNPs in the PTPN2 locus: rs657555 and rs11080606, by addressing the interaction of PTPN2 variants with HLA-DRB1 shared-epitope (SE) alleles in autoantibody positive RA patients in two independent cohorts. In this work, we also address the functional genetic role of the members of the MAP signaling pathway upstream of p38 and JNK – crucial enzymes in RA – with a regard to splicing profile and their connection to HLA-DRB1. We found a significant statistical interaction for rs10468473 from MAP2K4 locus with SE alleles in autoantibody-positive RA. Importantly, individuals heterozygous for rs10468473 demonstrated higher expression of total MAP2K4 mRNA in blood, compared to A-allele homozygous. We also describe a novel, putatively translated RNA splice form of MAP2K4, that is differentially expressed in peripheral blood mononuclear cells from 88 RA cases and controls, and is modulated in response to TNF in Jurkat cell line. Finally, we performed an expression analysis of multiple validated RA risk loci, and pathway analysis to assess functional relationship between RA susceptibility genes and predict new potential study candidates. New candidate molecules suggested by the pathway analysis, genes ERBB2 and HSPB1, as well as HLA-DRB1, were differentially expressed between RA patients and healthy individuals in RNA-seq data. ERBB2 expression profile was similar in whole blood of both treated and untreated patients compared to healthy individuals. A similar expression profile was replicated for ERBB2 in PBMCs in an independent material. In this work, we approached the task of elucidating the functional aspects of genetic susceptibility of RA, by integrating genetic epidemiology, transcriptomics, proteomics, cellmodels, and bioinformatics. We maintain, that such integrative approach provides the rationale to prioritize genes and genetic events for further functional studies. Our findings also outline the need to consider potential clinical significance of alternative splicing in gene expression studies

Dynamic Changes in the MicroRNA Expression Profile Reveal Multiple Regulatory Mechanisms in the Spinal Nerve Ligation Model of Neuropathic Pain

Neuropathic pain resulting from nerve lesions or dysfunction represents one of the most challenging neurological diseases to treat. A better understanding of the molecular mechanisms responsible for causing these maladaptive responses can help develop novel therapeutic strategies and biomarkers for neuropathic pain. We performed a miRNA expression profiling study of dorsal root ganglion (DRG) tissue from rats four weeks post spinal nerve ligation (SNL), a model of neuropathic pain. TaqMan low density arrays identified 63 miRNAs whose level of expression was significantly altered following SNL surgery. Of these, 59 were downregulated and the ipsilateral L4 DRG, not the injured L5 DRG, showed the most significant downregulation suggesting that miRNA changes in the uninjured afferents may underlie the development and maintenance of neuropathic pain. TargetScan was used to predict mRNA targets for these miRNAs and it was found that the transcripts with multiple predicted target sites belong to neurologically important pathways. By employing different bioinformatic approaches we identified neurite remodeling as a significantly regulated biological pathway, and some of these predictions were confirmed by siRNA knockdown for genes that regulate neurite growth in differentiated Neuro2A cells. In vitro validation for predicted target sites in the 3′-UTR of voltage-gated sodium channel Scn11a, alpha 2/delta1 subunit of voltage-dependent Ca-channel, and purinergic receptor P2rx ligand-gated ion channel 4 using luciferase reporter assays showed that identified miRNAs modulated gene expression significantly. Our results suggest the potential for miRNAs to play a direct role in neuropathic pain

Evidence for a pyrimidine-nucleotide-specific initiation site (the / site) on Escherichia coli RNA polymerase

Escherichia coli RNA polymerase has two sites, the i and i+1, for the binding of the first two substrates. The i site is template- and Mg<SUP>2+</SUP>-independent and purine-nucleotide-specific, whereas the i+1 site is template- and Mg<SUP>2+</SUP>-dependent and shows no nucleotide preference. The specificity of the i site for purine nucleotides is well in accord with the fact that most promoters initiate with a purine nucleotide. But there are a few promoters that initiate with a pyrimidine nucleotide. Dinucleotide synthesis at these promoters is completely inhibited by rifampicin. Earlier studies have failed to identify an i site for pyrimidine nucleotides. In this paper, using a fluorescent analog of UTP, namely uridine 5'-[&#947;-(5-sulfonic acid) naphthylamidate]-triphosphate, abbreviated as UTP[AmNS], we are able to show its binding to RNA polymerase, with a K<SUB>d</SUB> of 0.8 &#956; M, in the absence of Mg<SUP>2+</SUP> and template. This suggests the presence of an i pyrimidine nucleotide site. The fact that UTP-[AmNS] is capable of initiating RNA synthesis from the i site is further evidenced by the abortive transcription analyses at the lac promoter. Fluorescence titration studies performed in the presence and absence of purine initiator molecules indicate that this site is different from the i purine site. Scatchard analysis of the above data indicates the presence of a single binding site for UTP[AmNS] in the absence of Mg<SUP>2+</SUP>. Moreover UTP[AmNS] binds to the core enzyme with a K<SUB>d</SUB> of 3.0 &#956; M implying that, unlike the i purine nucleotide site, the s protein confers a tighter binding of UTP-[AmNS] to the low-K<SUB>d</SUB> site. Forster's energy transfer measurements using UTP[AmNS] as the donor and rifampicin as the acceptor have been used for estimation of the distance of the i pyrimidine nucleotide site from the rifampicin site. From these measurements, we infer that there is no direct interference of rifampicin with the first phosphodiester bond between two pyrimidine nucleotides

Evidence for a ppGpp-binding site on Escherichia coli RNA polymerase: proximity relationship with the rifampicin-binding domain

On amino acid starvation, Escherichia coli cells exhibit an adaptive facility termed the stringent response. This is characterized by the production of high levels of a regulatory nucleotide, ppGpp, and concomitant curtailment in rRNA synthesis. Various studies reported earlier indicated that RNA polymerase is the site of action of ppGpp although a direct demonstration of the interaction of ppGpp with E. coli RNA polymerase is still lacking. Here we report the labelling of PpGpp with a fluorescent probe, 1-aminonapthalene-5-sulphonate (AmNS), at the terminal phosphates. AmNS-ppGpp responded much like a ppGpp molecule in an in vitro total transcription assay at selective promoters. Fluorescence titration of the tryptophan emission of RNA polymerase by AmNS-ppGpp indicated a unique binding site in the absence of template DNA. Competition experiments showed that unlabelled ppGpp binds to the enzyme at the same site. Sigma factor seems to have no effect on this binding. The titration profile is also characterized by a single slope in the Scatchard analysis. The presence of GTP or GDP does not influence the binding of AmNS-ppGpp with RNA polymerase. Forster's distance measurement was carried out which placed AmNS-ppGpp 27&#197; away from the rifampicin-binding domain of RNA polymerase

Proximity relationship between the active site of Escherichia coli RNA polymerase and rifampicin binding domain: a resonance energy-transfer study

Escherichia coli RNA polymerase has two subsites, i and i + 1, for the binding of the first two substrates, and the first phosphodiester bond is formed between them during the initiation of transcription. Various studies have shown earlier that the inhibitor rifampicin has little effect, if any, on the formation of this phosphodiester bond. On an earlier occasion, we measured the distance of the i nucleotide from the rifampicin binding site on RNA polymerase using Forster's energy-transfer mechanism. In this paper, the 1-aminonaphthalene-5-sulfonic acid (AmNS) derivative of UTP in the presence of 10 mM MgCl<SUB>2</SUB> was used as an energy donor, and its distance from rifampicin was estimated. The modified nucleotide ( &#947; -AmNS)-UTP binds to RNA polymerase with a K<SUB>d</SUB> of 3&#956;M and has one binding site in the presence of Mg(II) ion. Fluorescence titration studies performed with or without an initiator that ( &#947;-AmNS)-UTP exclusively binds to RNA polymerase at the (i + 1) site in the presence of Mg(II). Rifampicin was found to form a 1:1 complex with RNA polymerase bound to labeled UTP. Rifampicin and ( &#947;-AmNS)-UTP have a substantial spectral overlap with an energy-transfer efficiency close to 50%. Labeled UTP shows a decrease in its excited-state lifetime when bound to the enzyme; the transfer efficiency calculated from lifetime measurements was found to be lower than that estimated from steady-state spectral analysis. Time-resolved emission spectral analysis was carried out to differentiate between the free and bound UTP over the enzyme surface. Bound UTP showed rapid decay in the presence of the acceptor within 5 ns. The rotational correlation time of the bound probe was estimated to be less than the lifetime of its excited state, indicating that substantial rotation of the donor can occur during its decay. The distance between the donor and the acceptor was estimated to be around 20 &#197;, using Forster's theory of dipole-dipole energy transfer. A model has been proposed where the distances of both i and (i + 1) nucleotides from rifampicin have been fixed, considering they are suitably oriented for phosphodiester synthesis. From this model it becomes apparent how rifampicin could block the translocation event during transcription initiation without hindering the first phosphodiester synthesis

Not Available

The present data provides valuable insights about the glycoproteins present in the elongating cotton fiber cells identified using Gossypium species specific protein sequence databases. 127 N-linked glycosylation sites, from 81 unique glycoproteins including 21 N-linked glycosylation sites corresponding to 17 unique glycoproteins are exclusively reported in the current study. Our analyses using five independent protein databases show that Gossypium hirsutum harbors protein sequences from its parental contributors Gossypium arboreum and Gossypium raimondii. The elucidated glycoproteome composition indirectly provides clues about parental genome contribution and unicellular compartmental requirement behind single cell development.The data presented here delineates the glycoproteome component in the elongating cotton fiber cells attained using complementary proteomic approaches followed by protein and N-linked glycosylation site identification (Kumar et al., 2013) [1]. Utilizing species specific protein sequence databases in proteomic approaches often leads to additional information that may not be obtained using cross-species databases. In this context we have reanalyzed our glycoproteome dataset with the Gossypium arboreum, Gossypium raimondii (version 2.0) and Gossypium hirsutum protein databases that has led to the identification of 21 N-linked glycosylation sites and 18 unique glycoproteins that were not reported in our previous study. The 1D PAGE and solution based glycoprotein identification data is publicly available at the ProteomeXchange Consortium via the PRIDE partner repository (Vizcaíno et al., 2013) [2] using the dataset identifier PXD000178 and the 2D PAGE based protein identification and glycopeptide approach based N-linked glycosylation site identification data is available at the ProteomeXchange Consortium via the PRIDE partner repository (Vizcaíno et al., 2013) [2] using the dataset identifier PXD002849.Not Availabl