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541.
Pallavi Sinha Vikas K. Singh V. Suryanarayana L. Krishnamurthy Rachit K. Saxena Rajeev K. Varshney 《PloS one》2015,10(4)
Gene expression analysis using quantitative real-time PCR (qRT-PCR) is a very sensitive technique and its sensitivity depends on the stable performance of reference gene(s) used in the study. A number of housekeeping genes have been used in various expression studies in many crops however, their expression were found to be inconsistent under different stress conditions. As a result, species specific housekeeping genes have been recommended for different expression studies in several crop species. However, such specific housekeeping genes have not been reported in the case of pigeonpea (Cajanus cajan) despite the fact that genome sequence has become available for the crop. To identify the stable housekeeping genes in pigeonpea for expression analysis under drought stress conditions, the relative expression variations of 10 commonly used housekeeping genes (EF1α, UBQ10, GAPDH, 18SrRNA, 25SrRNA, TUB6, ACT1, IF4α, UBC and HSP90) were studied on root, stem and leaves tissues of Asha (ICPL 87119). Three statistical algorithms geNorm, NormFinder and BestKeeper were used to define the stability of candidate genes. geNorm analysis identified IF4α and TUB6 as the most stable housekeeping genes however, NormFinder analysis determined IF4α and HSP90 as the most stable housekeeping genes under drought stress conditions. Subsequently validation of the identified candidate genes was undertaken in qRT-PCR based gene expression analysis of uspA gene which plays an important role for drought stress conditions in pigeonpea. The relative quantification of the uspA gene varied according to the internal controls (stable and least stable genes), thus highlighting the importance of the choice of as well as validation of internal controls in such experiments. The identified stable and validated housekeeping genes will facilitate gene expression studies in pigeonpea especially under drought stress conditions. 相似文献
542.
Ming Li Wang Pawan Khera Manish K. Pandey Hui Wang Lixian Qiao Suping Feng Brandon Tonnis Noelle A. Barkley David Pinnow Corley C. Holbrook Albert K. Culbreath Rajeev K. Varshney Baozhu Guo 《PloS one》2015,10(4)
Peanut, a high-oil crop with about 50% oil content, is either crushed for oil or used as edible products. Fatty acid composition determines the oil quality which has high relevance to consumer health, flavor, and shelf life of commercial products. In addition to the major fatty acids, oleic acid (C18:1) and linoleic acid (C18:2) accounting for about 80% of peanut oil, the six other fatty acids namely palmitic acid (C16:0), stearic acid (C18:0), arachidic acid (C20:0), gadoleic acid (C20:1), behenic acid (C22:0), and lignoceric acid (C24:0) are accounted for the rest 20%. To determine the genetic basis and to improve further understanding on effect of FAD2 genes on these fatty acids, two recombinant inbred line (RIL) populations namely S-population (high oleic line ‘SunOleic 97R’ × low oleic line ‘NC94022’) and T-population (normal oleic line ‘Tifrunner’ × low oleic line ‘GT-C20’) were developed. Genetic maps with 206 and 378 marker loci for the S- and the T-population, respectively were used for quantitative trait locus (QTL) analysis. As a result, a total of 164 main-effect (M-QTLs) and 27 epistatic (E-QTLs) QTLs associated with the minor fatty acids were identified with 0.16% to 40.56% phenotypic variation explained (PVE). Thirty four major QTLs (>10% of PVE) mapped on five linkage groups and 28 clusters containing more than three QTLs were also identified. These results suggest that the major QTLs with large additive effects would play an important role in controlling composition of these minor fatty acids in addition to the oleic and linoleic acids in peanut oil. The interrelationship among these fatty acids should be considered while breeding for improved peanut genotypes with good oil quality and desired fatty acid composition. 相似文献
543.
Jyoti Kumari Ankita Mathur A. Rajeshwari Arthi Venkatesan Satyavati S Mrudula Pulimi Natarajan Chandrasekaran R. Nagarajan Amitava Mukherjee 《PloS one》2015,10(8)
The impact of pH and ionic strength on the mobility (individual and co-transport) and deposition kinetics of TiO2 and ZnO NPs in porous media was systematically investigated in this study. Packed column experiments were performed over a series of environmentally relevant ionic strengths with both NaCl (0.1−10 mM) and CaCl2 (0.01–0.1mM) solutions and at pH 5, 7, and 9. The transport of TiO2 NPs at pH 5 was not significantly affected by ZnO NPs in solution. At pH 7, a decrease in TiO2 NP transport was noted with co-existence of ZnO NPs, while at pH 9 an increase in the transport was observed. At pH 5 and 7, the transport of ZnO NPs was decreased when TiO2 NPs was present in the solution, and at pH 9, an increase was noted. The breakthrough curves (BTC) were noted to be sensitive to the solution chemistries; the decrease in the breakthrough plateau with increasing ionic strength was observed under all examined pH (5, 7, and 9). The retention profiles were the inverse of the plateaus of BTCs, as expected from mass balance considerations. Overall, the results from this study suggest that solution chemistries (ionic strength and pH) are likely the key factors that govern the individual and co-transport behavior of TiO2 and ZnO NPs in sand. 相似文献
544.
Adam S. Fisch Laura M. Yerges-Armstrong Joshua D. Backman Hong Wang Patrick Donnelly Kathleen A. Ryan Ankita Parihar Mary A. Pavlovich Braxton D. Mitchell Jeffrey R. O’Connell William Herzog Christopher R. Harman Jonathan D. Wren Joshua P. Lewis 《PloS one》2015,10(9)
Platelet Endothelial Aggregation Receptor 1 (PEAR1) is a newly identified membrane protein reported to be involved in multiple vascular and thrombotic processes. While most studies to date have focused on the effects of this receptor in platelets, PEAR1 is located in multiple tissues including the endothelium, where it is most highly expressed. Our first objective was to evaluate the role of PEAR1 in endothelial function by examining flow-mediated dilation of the brachial artery in 641 participants from the Heredity and Phenotype Intervention Heart Study. Our second objective was to further define the impact of PEAR1 on cardiovascular disease computationally through meta-analysis of 75,000 microarrays, yielding insights regarding PEAR1 function, and predictions of phenotypes and diseases affected by PEAR1 dysregulation. Based on the results of this meta-analysis we examined whether genetic variation in PEAR1 influences endothelial function using an ex vivo assay of endothelial cell migration. We observed a significant association between rs12041331 and flow-mediated dilation in participants of the Heredity and Phenotype Intervention Heart Study (P = 0.02). Meta-analysis results revealed that PEAR1 expression is highly correlated with several genes (e.g. ANG2, ACVRL1, ENG) and phenotypes (e.g. endothelial cell migration, angiogenesis) that are integral to endothelial function. Functional validation of these results revealed that PEAR1 rs12041331 is significantly associated with endothelial migration (P = 0.04). Our results suggest for the first time that genetic variation of PEAR1 is a significant determinant of endothelial function through pathways implicated in cardiovascular disease. 相似文献
545.
Ananya Kar Manpreet Kaur Tanushree Ghosh Md. Muntaz Khan Aparna Sharma Ritu Shekhar Akhil Varshney Sandeep Saxena 《Nucleic acids research》2015,43(10):4962-4974
The primary eukaryotic single-stranded DNA-binding protein, Replication protein A (RPA), binds to single-stranded DNA at the sites of DNA damage and recruits the apical checkpoint kinase, ATR via its partner protein, ATRIP. It has been demonstrated that absence of RPA incapacitates the ATR-mediated checkpoint response. We report that in the absence of RPA, human single-stranded DNA-binding protein 1 (hSSB1) and its partner protein INTS3 form sub-nuclear foci, associate with the ATR-ATRIP complex and recruit it to the sites of genomic stress. The ATRIP foci formed after RPA depletion are abrogated in the absence of INTS3, establishing that hSSB-INTS3 complex recruits the ATR-ATRIP checkpoint complex to the sites of genomic stress. Depletion of homologs hSSB1/2 and INTS3 in RPA-deficient cells attenuates Chk1 phosphorylation, indicating that the cells are debilitated in responding to stress. We have identified that TopBP1 and the Rad9-Rad1-Hus1 complex are essential for the alternate mode of ATR activation. In summation, we report that the single-stranded DNA-binding protein complex, hSSB1/2-INTS3 can recruit the checkpoint complex to initiate ATR signaling. 相似文献
546.
547.
Parej Nath Nishant Ranjan Chauhan Kautilya Kumar Jena Ankita Datey Nilima Dinesh Kumar Subhash Mehto Saikat De Tapas Kumar Nayak Swatismita Priyadarsini Kshitish Rout Ramyasingh Bal Krushna C Murmu Manjula Kalia Srinivas Patnaik Punit Prasad Fulvio Reggiori Soma Chattopadhyay Santosh Chauhan 《EMBO reports》2021,22(11)
The type I interferon (IFN) response is the major host arsenal against invading viruses. IRGM is a negative regulator of IFN responses under basal conditions. However, the role of human IRGM during viral infection has remained unclear. In this study, we show that IRGM expression is increased upon viral infection. IFN responses induced by viral PAMPs are negatively regulated by IRGM. Conversely, IRGM depletion results in a robust induction of key viral restriction factors including IFITMs, APOBECs, SAMHD1, tetherin, viperin, and HERC5/6. Additionally, antiviral processes such as MHC‐I antigen presentation and stress granule signaling are enhanced in IRGM‐deficient cells, indicating a robust cell‐intrinsic antiviral immune state. Consistently, IRGM‐depleted cells are resistant to the infection with seven viruses from five different families, including Togaviridae, Herpesviridae, Flaviviverdae, Rhabdoviridae, and Coronaviridae. Moreover, we show that Irgm1 knockout mice are highly resistant to chikungunya virus (CHIKV) infection. Altogether, our work highlights IRGM as a broad therapeutic target to promote defense against a large number of human viruses, including SARS‐CoV‐2, CHIKV, and Zika virus. 相似文献
548.
549.
550.
J. K. Roy M. Prasad R. K. Varshney H. S. Balyan T. K. Blake H. S. Dhaliwal H-Singh K. J. Edwards P. K. Gupta 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,99(1-2):336-340
In bread wheat, the transfer of tolerance to preharvest sprouting (PHS) that is associated with genotypes having red kernel
colour to genotypes with amber kernels is difficult using conventional methods of plant breeding. The study here was undertaken
to identify DNA markers linked with tolerance to PHS as these would allow indirect marker-assisted selection of PHS-tolerant
genotypes with amber kernels. For this purpose, a set of 100 recombinant inbred lines (RILs) was developed using a cross between
a PHS-tolerant genotype, SPR8198, with red kernels and a PHS-susceptible cultivar, ‘HD2329’, with white kernels. The two parents
were analysed with 232 STMS (sequence-tagged microsatellite site) and 138 STS (sequence-tagged site) primer pairs. A total
of 300 (167 STMSs and 133 STSs) primer pairs proved functional by giving scorable PCR products. Of these, 57 (34%) STMS and
30 (23%) STS primer pairs detected reproducible polymorphism between the parent genotypes. Using these primer pairs, we carried
out bulked segregant analysis on two bulked DNAs, one obtained by pooling DNA from 5 PHS-tolerant RILs and the other similarly
derived by pooling DNA from 5 PHS-susceptible RILs. Two molecular markers, 1 STMS primer pair for the locus wmc104 anda STS primer pair for the locus MST101, showed apparent linkage with tolerance to PHS. This was confirmed following selective genotyping of individual RILs included
in the bulks. Chi-square contingency tests for independence were conducted on the cosegregation data collected on 100 RILs
involving each of the two molecular markers (wmc104 and MST101) and PHS. The tests revealed a strong association between each of the markers and tolerance to PHS. Using nullisomic-tetrasomic
lines, we were able to assign wmc104 and MST101 to chromosomes 6B and 7D, respectively. The results also indicated that the tolerance to PHS in SPR8198 is perhaps governed
by two genes (linked with two molecular markers) exhibiting complementary interaction.
Received: 15 October 1998 / Accepted: 19 December 1998 相似文献