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  • Oxford University Press  (15)
  • Cambridge University Press  (8)
  • American Geophysical Union  (5)
  • 1
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    Estimation of effective infiltration rates in cracked soils (1982)
    Cambridge University Press
    Details
    Publication Date: 1982-12-01
    Description: Infiltration is the most important aspect in the hydraulics of surface irrigation, since the design of irrigation systems depends to a large extent upon the infiltration characteristics of the soil. Many workers have contributed to the theoretical understanding of the infiltration phenomenon (Kirkham & Powers, 1972). However, very little work is available on the evaluation of infiltration into cracked soils. Measurement of infiltration into these soils poses a special problem. Depending on the degree of cracking, a fraction of the water added on the soil surface flows down through cracks and goes to waste. The water flowing through the cracks does not contribute to the moisture storage of the soil profile which may subsequently be used by the crops. Also, infiltration rates measured using ring infiltrometers are erroneous. In order to have an efficient design for an irrigation system, realistic estimates of infiltration characteristics for this type of soil are essential. In the present paper an attempt has been made to estimate the effective infiltration rate into such cracked soils. The procedvire suggested has been tested under limited conditions and found useful under field conditions. However, extensive field testing under various soil conditions is necessary before it can be recommended for general use.
    Print ISSN: 0021-8596
    Electronic ISSN: 1469-5146
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Cambridge University Press
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  • 2
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    A legion of potential regulatory sRNAs exists beyond the typical microRNAs microcosm (2015)
    Oxford University Press
    Details
    Publication Date: 2015-10-15
    Description: Post ENCODE, regulatory sRNAs (rsRNAs) like miRNAs have established their status as one of the core regulatory elements of cell systems. However, large number of rsRNAs are compromised due to traditional approaches to identify miRNAs, limiting the otherwise vast world of rsRNAs mainly to hair-pin loop bred typical miRNAs. The present study has analyzed for the first time a huge volume of sequencing data from 4997 individuals and 25 cancer types to report 11 234 potentially regulatory small RNAs which appear to have deep reaching impact. The rsRNA-target interactions have been studied and validated extensively using experimental data from AGO-crosslinking, DGCR8 knockdown, CLASH, proteome and expression data. A subset of such interactions was also validated independently in the present study using multiple cell lines, by qPCR. Several of the potential rsRNAs have emerged as a critical cancer biomarker controlling some important spots of cell system. The entire study has been presented into an interactive info-analysis portal handling more than 260 GB of processed data. The possible degree of cell system regulation by sRNAs appears to be much higher than previously assumed.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Transcriptome-wide expansion of non-coding regulatory switches: evidence from co-occurrence of Alu exonization, antisense and editing (2013)
    Oxford University Press
    Details
    Publication Date: 2013-02-20
    Description: Non-coding RNAs from transposable elements of human genome are gaining prominence in modulating transcriptome dynamics. Alu elements, as exonized, edited and antisense components within same transcripts could create novel regulatory switches in response to different transcriptional cues. We provide the first evidence for co-occurrences of these events at transcriptome-wide scale through integrative analysis of data sets across diverse experimental platforms and tissues. This involved the following: (i) positional anchoring of Alu exonization events in the UTRs and CDS of 4663 transcript isoforms from RefSeq mRNAs and (ii) mapping on to them A-〉I editing events inferred from ~7 million ESTs from dbEST and antisense transcripts identified from virtual serial analysis of gene expression tags represented in Cancer Genome Anatomy Project next-generation sequencing data sets across 20 tissues. We observed significant enrichment of these events in the 3'UTR as well as positional preference within the embedded Alus. More than 300 genes had co-occurrence of all these events at the exon level and were significantly enriched in apoptosis and lysosomal processes. Further, we demonstrate functional evidence of such dynamic interactions between Alu-mediated events in a time series data from Integrated Personal Omics Profiling during recovery from a viral infection. Such ‘single transcript—multiple fate’ opportunity facilitated by Alu elements may modulate transcriptional response, especially during stress.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Detecting Selective Sweeps from Pooled Next-Generation Sequencing Samples (2012)
    Oxford University Press
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    Publication Date: 2012-08-23
    Description: Due to its cost effectiveness, next-generation sequencing of pools of individuals (Pool-Seq) is becoming a popular strategy for characterizing variation in population samples. Because Pool-Seq provides genome-wide SNP frequency data, it is possible to use them for demographic inference and/or the identification of selective sweeps. Here, we introduce a statistical method that is designed to detect selective sweeps from pooled data by accounting for statistical challenges associated with Pool-Seq, namely sequencing errors and random sampling among chromosomes. This allows for an efficient use of the information: all base calls are included in the analysis, but the higher credibility of regions with higher coverage and base calls with better quality scores is accounted for. Computer simulations show that our method efficiently detects sweeps even at very low coverage (0.5 x per chromosome). Indeed, the power of detecting sweeps is similar to what we could expect from sequences of individual chromosomes. Since the inference of selective sweeps is based on the allele frequency spectrum (AFS), we also provide a method to accurately estimate the AFS provided that the quality scores for the sequence reads are reliable. Applying our approach to Pool-Seq data from Drosophila melanogaster , we identify several selective sweep signatures on chromosome X that include some previously well-characterized sweeps like the wapl region.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Detecting Evolutionary Strata on the Human X Chromosome in the Absence of Gametologous Y-Linked Sequences (2013)
    Oxford University Press
    Details
    Publication Date: 2013-10-12
    Description: Mammalian sex chromosomes arose from a pair of homologous autosomes that differentiated into the X and Y chromosomes following a series of recombination suppression events between the X and Y. The stepwise recombination suppressions from the distal long arm to the distal short arm of the chromosomes are reflected as regions with distinct X-Y divergence, referred to as evolutionary strata on the X. All current methods for stratum detection depend on X-Y comparisons but are severely limited by the paucity of X-Y gametologs. We have developed an integrative method that combines a top-down, recursive segmentation algorithm with a bottom-up, agglomerative clustering algorithm to decipher compositionally distinct regions on the X, which reflect regions of unique X-Y divergence. In application to human X chromosome, our method correctly classified a concatenated set of 35 previously assayed X-linked gene sequences by evolutionary strata. We then extended our analysis, applying this method to the entire sequence of the human X chromosome, in an effort to define stratum boundaries. The boundaries of more recently formed strata on X-added region, namely the fourth and fifth strata, have been defined by previous studies and are recapitulated with our method. The older strata, from the first up to the third stratum, have remained poorly resolved due to paucity of X-Y gametologs. By analyzing the entire X sequence, our method identified seven evolutionary strata in these ancient regions, where only three could previously be assayed, thus demonstrating the robustness of our method in detecting the evolutionary strata.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Glycoxidation of biological macromolecules: A critical approach to halt the menace of glycation (2014)
    Oxford University Press
    Details
    Publication Date: 2014-10-02
    Description: Glycation is the result of covalent bonding of a free amino group of biological macromolecules with a reducing sugar, which results in the formation of a Schiff base that undergoes rearrangement, dehydration and cyclization to form a more stable Amadori product. The final products of nonenzymatic glycation of biomacromolecules like DNA, proteins and lipids are known as advanced glycation end products (AGEs). AGEs may be generated rapidly or over long times stimulated by distinct triggering mechanisms, thereby accounting for their roles in multiple settings and disease states. Both Schiff base and Amadori glycation products generate free radicals resulting in decline of antioxidant defense mechanisms and can damage cellular organelles and enzymes. This critical review primarily focuses on the mechanistic insight of glycation and the most probable route for the formation of glycation products and their therapeutic interventions. Furthermore, the prevention of glycation reaction using therapeutic drugs such as metformin, pyridoxamine and aminoguanidine (AG) are discussed with special emphasis on the novel concept of the bioconjugation of these drugs like, AG with gold nanoparticles (GNPs). At or above 10 mM concentration, AG is found to be toxic and therefore has serious health concerns, and the study warrants doing this novel bioconjugation of AG with GNPs. This approach might increase the efficacy of the AG at a reduced concentration with low or no toxicity. Using the concept of synthesis of GNPs with abovementioned drugs, it is assumed that toxicity of various drugs which are used at high doses can be minimized more effectively.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 7
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    Influence of indigenous arbuscular mycorrhizal fungus and bacterial bioinoculants on growth and yield of Capsicum chinense cultivated in non-sterilized soil (2019)
    Cambridge University Press
    Details
    Publication Date: 2019
    Description: 〈div data-abstract-type="normal"〉〈p〉Despite the global importance of 〈span〉Capsicum〈/span〉 species, there is limited information on the indigenous endomycorrhizal fungal association in this crop. Therefore, the diversity and colonization patterns of arbuscular mycorrhizal fungi (AMF) in roots of Naga King chilli (〈span〉Capsicum chinense〈/span〉) were assessed during pre-flowering, flowering and fruit ripening growth stages under a sub-tropical shifting cultivation system of North Eastern India. All the roots examined had AMF colonization and the presence of 〈span〉Paris〈/span〉-type arbuscular mycorrhizal morphology is reported for the first time in 〈span〉C. chinense〈/span〉. A total of 11 AMF spore morphotypes were isolated from both field and trap culture soils. Maximum AMF spore density and root colonization were recorded during the pre-flowering and flowering stages, respectively. The influence of 〈span〉Funneliformis geosporum〈/span〉, individually or in combination with 〈span〉Pseudomonas fluorescens〈/span〉 and 〈span〉Azotobacter chroococcum〈/span〉, on growth and yield of 〈span〉C. chinense〈/span〉, was evaluated in a pot experiment using sterilized and non-sterilized soils. The application of AMF and 〈span〉P. fluorescens〈/span〉 to sterilized soil significantly increased the growth, flower and fruit production, and nutrient content of 〈span〉C. chinense〈/span〉. The highest growth rates and yields of 〈span〉C. chinense〈/span〉 in non-sterilized soils were achieved when AMF was combined with both 〈span〉P. fluorescens〈/span〉 and 〈span〉A. chroococcum〈/span〉. The results of the current study indicate the value of applying microorganisms to improve plant growth and performance in chillies. One of the mechanisms for this could be the facilitated assimilation of nutrients promoted by AMF and bacterial bioinoculants.〈/p〉〈/div〉
    Print ISSN: 0021-8596
    Electronic ISSN: 1469-5146
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Cambridge University Press
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  • 8
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    An infrared photometric and spectroscopic study of post-AGB stars (2017)
    Oxford University Press
    Details
    Publication Date: 2017-08-24
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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  • 9
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    Further milliarcsecond resolution results on cool giants and binary stars from lunar occultations at Devashtal (2020)
    Oxford University Press
    Details
    Publication Date: 2020-09-02
    Description: We report on 26 lunar occultation events observed in the context of a programme started at Devasthal in 2017. In addition to the customary observations with the 1.3-m telescope, we report here also the first attempts performed with the TIRCAM2 camera at the 3.6-m Devasthal Optical Telescope in the near-infrared (near-IR). The results consist in the first-time angular diameters for two late-type giants, in a measurement of the well-known asymptotic giant branch pulsating variable SW Vir, and in the measurement of eight small separation binaries one of which is detected for the first time (HR 1860). We also measured the wider binaries SAO 94431 and 55 Tau (twice). The remaining sources were found to be unresolved with upper limits as small as 1 mas. We plan to develop further the high-speed capability of the TIRCAM2 instrument, so as to include in our programme also more near-IR, highly extincted sources.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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  • 10
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    PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq) (2011)
    Oxford University Press
    Details
    Publication Date: 2011-10-23
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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