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  • 1
    Electronic Resource
    Electronic Resource
    A microsatellite marker associated with a QTL for grain protein content on chromosome arm 2DL of bread wheat (1999)
    Springer
    Theoretical and applied genetics 99 (1999), S. 341-345 
    Details
    ISSN: 1432-2242
    Keywords: Key words Bread wheat ; Grain protein content ; Microsatellite ; STMS ; QTL analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  This study was undertaken with a view to tag gene(s) controlling grain protein content (GPC) using molecular markers in bread wheat. For this purpose, the genotype PH132 with high protein content (13.5%) was crossed with genotype WL711 with significantly lower protein content (9.7%), and 100 RILs were derived. These RILs showed normal distribution for protein content. The parental genotypes were analysed with 232 STMS primer pairs for detection of polymorphism. Of these, 167 primer pairs gave scorable amplification products, and 57 detected polymorphism between the parents. Using each of these 57 primer pairs, we carried out bulked segregant analysis on RILs representing the two extremes of the distribution. One primer pair for the locus wmc41 showed association with protein content. This was further confirmed through selective genotyping. The co-segregation data on the molecular marker (wmc41) and protein content on 100 RILs was analysed by means of a single-marker linear regression approach. Significant regression suggested linkage between wmc41 and a QTL (designated as QGpc.ccsu-2D.) for protein content. The results showed that this marker-linked QTL accounted for 18.73% of the variation for protein content between the parents. The marker has been located on chromosome arm 2DL using nulli-tetrasomic lines and two ditelocentric stocks for chromosome 2D.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220051242
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  • 2
    Electronic Resource
    Electronic Resource
    Identification of a microsatellite on chromosomes 6B and a STS on 7D of bread wheat showing an association with preharvest sprouting tolerance (1999)
    Springer
    Theoretical and applied genetics 99 (1999), S. 336-340 
    Details
    ISSN: 1432-2242
    Keywords: Key words Preharvest sprouting ; Microsatellite ; STMS ; STS ; Linkage ; Bread wheat
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220051241
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  • 3
    Electronic Resource
    Electronic Resource
    Intraspecific genetic variability analysis of Neovossia indica causing Karnal bunt of wheat using repetitive elements (2000)
    Springer
    Theoretical and applied genetics 100 (2000), S. 569-575 
    Details
    ISSN: 1432-2242
    Keywords: Key words Karnal bunt ; Repetitive elements ; Genome diversity ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Neovossia indica (Tilletia indica), causing Karnal bunt of wheat, affects major wheat growing regions all over the world. Karnal bunt ranks as one of the major diseases of wheat causing quality losses and monetary losses due to international quarantine regulations. The present work is the first report of a genetic diversity analysis of Indian isolates of N. indica. A library of N. indica isolate Ni7 was constructed in a λZAPII system, and three repetitive elements were identified for molecular analysis. These repetitive elements generated complex hybridization profiles producing fingerprint patterns of all seven isolates. Copy-number estimation of these three elements, pNiR9, pNiR12 and pNiR16, indicated the presence of 32, 61 and 64 copies, respectively. Cluster analysis based on hybridization patterns grouped together moderately virulent isolates Ni1, Ni7 and Ni8, thus suggesting a positive correlation between virulence typing and cluster analysis based on molecular data. Variability analysis of N. indica isolates will aid in checking new resistant sources in host germplasm.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050075
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  • 4
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    ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-20
    Description: : Unlike DNA, RNA abundances can vary over several orders of magnitude. Thus, identification of RNA–protein binding sites from high-throughput sequencing data presents unique challenges. Although peak identification in ChIP-Seq data has been extensively explored, there are few bioinformatics tools tailored for peak calling on analogous datasets for RNA-binding proteins. Here we describe ASPeak (abundance sensitive peak detection algorithm), an implementation of an algorithm that we previously applied to detect peaks in exon junction complex RNA immunoprecipitation in tandem experiments. Our peak detection algorithm yields stringent and robust target sets enabling sensitive motif finding and downstream functional analyses. Availability: ASPeak is implemented in Perl as a complete pipeline that takes bedGraph files as input. ASPeak implementation is freely available at https://sourceforge.net/projects/as-peak under the GNU General Public License. ASPeak can be run on a personal computer, yet is designed to be easily parallelizable. ASPeak can also run on high performance computing clusters providing efficient speedup. The documentation and user manual can be obtained from http://master.dl.sourceforge.net/project/as-peak/manual.pdf . Contact: alper.kucukural@umassmed.edu or ccenik@stanford.edu
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 5
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    The DcpS inhibitor RG3039 improves survival, function and motor unit pathologies in two SMA mouse models (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-25
    Description: Spinal muscular atrophy (SMA) is caused by insufficient levels of the survival motor neuron (SMN) protein due to the functional loss of the SMN1 gene and the inability of its paralog, SMN2 , to fully compensate due to reduced exon 7 splicing efficiency. Since SMA patients have at least one copy of SMN2 , drug discovery campaigns have sought to identify SMN2 inducers. C5-substituted quinazolines increase SMN2 promoter activity in cell-based assays and a derivative, RG3039, has progressed to clinical testing. It is orally bioavailable, brain-penetrant and has been shown to be an inhibitor of the mRNA decapping enzyme, DcpS. Our pharmacological characterization of RG3039, reported here, demonstrates that RG3039 can extend survival and improve function in two SMA mouse models of varying disease severity (Taiwanese 5058 Hemi and 2B/– SMA mice), and positively impacts neuromuscular pathologies. In 2B/– SMA mice, RG3039 provided a 〉600% survival benefit (median 18 days to 〉112 days) when dosing began at P4, highlighting the importance of early intervention. We determined the minimum effective dose and the associated pharmacokinetic (PK) and exposure relationship of RG3039 and DcpS inhibition ex vivo . These data support the long PK half-life with extended pharmacodynamic outcome of RG3039 in 2B/– SMA mice. In motor neurons, RG3039 significantly increased both the average number of cells with gems and average number of gems per cell, which is used as an indirect measure of SMN levels. These studies contribute to dose selection and exposure estimates for the first studies with RG3039 in human subjects.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 6
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    Lithospheric structure of southern Indian shield and adjoining oceans: integrated modelling of topography, gravity, geoid and heat flow data (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-11
    Description: For the present 2-D lithospheric density modelling, we selected three geotransects of more than 1000 km in length each crossing the southern Indian shield, south of 16°N, in N–S and E–W directions. The model is based on the assumption of local isostatic equilibrium and is constrained by the topography, gravity and geoid anomalies, by geothermal data, and where available by seismic data. Our integrated modelling approach reveals a crustal configuration with the Moho depth varying from ~40 km beneath the Dharwar Craton, and ~39 km beneath the Southern Granulite Terrane to about 15–20 km beneath the adjoining oceans. The lithospheric thickness varies significantly along the three profiles from ~70–100 km under the adjoining oceans to ~130–135 km under the southern block of Southern Granulite Terrane including Sri Lanka and increasing gradually to ~165–180 km beneath the northern block of Southern Granulite Terrane and the Dharwar Craton. This step-like lithosphere–asthenosphere boundary (LAB) structure indicates a normal lithospheric thickness beneath the adjoining oceans, the northern block of Southern Granulite Terrane and the Dharwar Craton. The thin lithosphere below the southern block of Southern Granulite Terrane including Sri Lanka is, however, atypical considering its age. Our results suggest that the southern Indian shield as a whole cannot be supported isostatically only by thickened crust; a thin and hot lithosphere beneath the southern block of Southern Granulite Terrane including Sri Lanka is required to explain the high topography, gravity, geoid and crustal temperatures. The widespread thermal perturbation during Pan-African (550 Ma) metamorphism and the breakup of Gondwana during late Cretaceous are proposed as twin cause mechanism for the stretching and/or convective removal of the lower part of lithospheric mantle and its replacement by hotter and lighter asthenosphere in the southern block of Southern Granulite Terrane including Sri Lanka. Unusually thinned LAB beneath the region near Bangalore apparently indicates the preserved tectonocompositional effect of late Proterozoic rifted margin of Dharwar Craton.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 7
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    Prediction of tunnelling impact on flow rates of adjacent extraction water wells (2019)
    Geological Society of London
    Details
    Publication Date: 2019
    Description: 〈span〉〈div〉Abstract〈/div〉The decline or drying up of groundwater sources near a tunnel route is damaging to groundwater users. Therefore, forecasting the impact of a tunnel on nearby groundwater sources is a challenging task in tunnel design. In this study, numerical and analytical approaches were applied to the Qomroud water conveyance tunnel (located in Lorestan province, Iran) to assess the impact of tunnelling on the nearby extraction water wells. Using simulation of groundwater-level fluctuation owing to tunnelling, the drawdown at the well locations was determined. From the drawdowns and using Dupuit's equation, the depletion of well flow rates after tunnelling was estimated. To evaluate the results, observed well flow rates before and after tunnelling were compared with the predicted flow rates. The observed and estimated water well flows (before and after tunnelling) showed a regression factor of 0.64, pointing to satisfactory results〈/span〉
    Print ISSN: 1470-9236
    Electronic ISSN: 2041-4803
    Topics: Geosciences
    Published by Geological Society of London
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  • 8
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    Interaction of survival of motor neuron (SMN) and HuD proteins with mRNA cpg15 rescues motor neuron axonal deficits [Neuroscience] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-06-22
    Description: Spinal muscular atrophy (SMA), caused by the deletion of the SMN1 gene, is the leading genetic cause of infant mortality. SMN protein is present at high levels in both axons and growth cones, and loss of its function disrupts axonal extension and pathfinding. SMN is known to associate with the RNA-binding protein hnRNP-R, and together they are responsible for the transport and/or local translation of β-actin mRNA in the growth cones of motor neurons. However, the full complement of SMN-interacting proteins in neurons remains unknown. Here we used mass spectrometry to identify HuD as a novel neuronal SMN-interacting partner. HuD is a neuron-specific RNA-binding protein that interacts with mRNAs, including candidate plasticity-related gene 15 (cpg15). We show that SMN and HuD form a complex in spinal motor axons, and that both interact with cpg15 mRNA in neurons. CPG15 is highly expressed in the developing ventral spinal cord and can promote motor axon branching and neuromuscular synapse formation, suggesting a crucial role in the development of motor axons and neuromuscular junctions. Cpg15 mRNA previously has been shown to localize into axonal processes. Here we show that SMN deficiency reduces cpg15 mRNA levels in neurons, and, more importantly, cpg15 overexpression partially rescues the SMN-deficiency phenotype in zebrafish. Our results provide insight into the function of SMN protein in axons and also identify potential targets for the study of mechanisms that lead to the SMA pathology and related neuromuscular diseases.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 9
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    Establishing minimum economic field size and analyzing its role in exploration-project risks assessment: A practical approach (2016)
    Society of Exploration Geophysicists (SEG)
    Details
    Publication Date: 2016-02-03
    Description: The upstream E&P industry is one of the riskiest businesses in which to invest and is dominated by different types of uncertainties: political, economic, social, and technical. Many factors can lead to optimistic or pessimistic risk assessment. Overestimation, underestimation, misidentifying critical risks, overselling projects, and underselling projects are some of the problems. For consistent risk analysis of exploration projects, a systematic approach is used that includes geologic risk, minimum economic field size (MEFS), resource-size distribution, development cost, rate streams, commodity price, and discount rate. This approach requires highly skilled geoscientists and reservoir, facility, and drilling engineers to estimate field-development costs, generate the economic indicator, rank the exploratory prospects' potential success, and support the business decisions. The definition of "exploration success" contains two main variables: (1) probability of geologic success (P g ) and (2) probability of economic success (P e ). To remove the risk of subeconomic volumes from the volumetric distribution, the industry uses the estimation of minimum required resources for the full project life cycle, considering the most likely development scenario. An effort is made to describe the appropriate MEFS estimation methodology, which is an essential component for consistent exploratory-project risk analysis. The influence of key parameters on MEFS estimation, including some illustrative examples, also are analyzed to demonstrate the criticality of MEFS estimation and its impact on exploratory-prospect risk assessment and to achieve an overall economic success.
    Print ISSN: 1070-485X
    Electronic ISSN: 1938-3789
    Topics: Geosciences
    Published by Society of Exploration Geophysicists (SEG)
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  • 10
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    Mitochondrial complex II has a key role in mitochondrial-derived reactive oxygen species influence on plant stress gene regulation and defense [Plant Biology] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-06-30
    Description: Mitochondria are both a source of ATP and a site of reactive oxygen species (ROS) production. However, there is little information on the sites of mitochondrial ROS (mROS) production or the biological role of such mROS in plants. We provide genetic proof that mitochondrial complex II (Complex II) of the electron transport chain contributes to localized mROS that regulates plant stress and defense responses. We identify an Arabidopsis mutant in the Complex II subunit, SDH1-1, through a screen for mutants lacking GSTF8 gene expression in response to salicylic acid (SA). GSTF8 is an early stress-responsive gene whose transcription is induced by biotic and abiotic stresses, and its expression is commonly used as a marker of early stress and defense responses. Transcriptional analysis of this mutant, disrupted in stress responses 1 (dsr1), showed that it had altered SA-mediated gene expression for specific downstream stress and defense genes, and it exhibited increased susceptibility to specific fungal and bacterial pathogens. The dsr1 mutant also showed significantly reduced succinate dehydrogenase activity. Using in vivo fluorescence assays, we demonstrated that root cell ROS production occurred primarily from mitochondria and was lower in the mutant in response to SA. In addition, leaf ROS production was lower in the mutant after avirulent bacterial infection. This mutation, in a conserved region of SDH1-1, is a unique plant mitochondrial mutant that exhibits phenotypes associated with lowered mROS production. It provides critical insights into Complex II function with implications for understanding Complex II's role in mitochondrial diseases across eukaryotes.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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