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  • 1
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    GAM: a web-service for integrated transcriptional and metabolic network analysis (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-06
    Description: Novel techniques for high-throughput steady-state metabolomic profiling yield information about changes of nearly thousands of metabolites. Such metabolomic profiles, when analyzed together with transcriptional profiles, can reveal novel insights about underlying biological processes. While a number of conceptual approaches have been developed for data integration, easily accessible tools for integrated analysis of mammalian steady-state metabolomic and transcriptional data are lacking. Here we present GAM (‘genes and metabolites’): a web-service for integrated network analysis of transcriptional and steady-state metabolomic data focused on identification of the most changing metabolic subnetworks between two conditions of interest. In the web-service, we have pre-assembled metabolic networks for humans, mice, Arabidopsis and yeast and adapted exact solvers for an optimal subgraph search to work in the context of these metabolic networks. The output is the most regulated metabolic subnetwork of size controlled by false discovery rate parameters. The subnetworks are then visualized online and also can be downloaded in Cytoscape format for subsequent processing. The web-service is available at: https://artyomovlab.wustl.edu/shiny/gam/
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Methylation of TSGs in EBV-infected B cells [Medical Sciences] (2015)
    National Academy of Sciences
    Details
    Publication Date: 2015-09-16
    Description: DNA-methylation at CpG islands is one of the prevalent epigenetic alterations regulating gene-expression patterns in mammalian cells. Hypo- or hypermethylation-mediated oncogene activation, or tumor suppressor gene (TSG) silencing mechanisms, widely contribute to the development of multiple human cancers. Furthermore, oncogenic viruses, including Epstein–Barr virus (EBV)-associated human cancers, were also shown...
    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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  • 3
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    Extensive Copy Number Variations in Admixed Indian Population of African Ancestry: Potential Involvement in Adaptation (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-13
    Description: Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Diffuse phase ferroelectric vs. Polomska transition in (1-x) BiFeO3-(x) Ba Zr0.025Ti0.975O3 (0.1 ≤ x ≤ 0.3) solid solutions (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-01-10
    Description: Investigations on the solid solutions (1-x) BiFeO 3 - (x) Ba Zr 0.025 Ti 0.975 O 3 (0.1 ≤ x ≤ 0.3) in the temperature range 300–750 K show colossal permittivity behavior and the occurrence of diffuse phase ferroelectric transition along with frequency dependent anomaly which disappears at temperature ∼450 K. For x = 0.3, these anomalies have been verified through differential scanning calorimetry and dielectric/impedance/conductivity measurements. The occurrence of peak in pyrocurrent (dP s /dT) vs. T plots also supports phase transition. With the increasing x, transition temperature decreases and diffusivity increases. This anomaly is absent at high frequencies (〉100 kHz) in conductivity plots, indicating Polomska like surface phase transition, which is supported by modulus study.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 5
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    Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs (2014)
    Oxford University Press
    Details
    Publication Date: 2014-05-01
    Description: Ribonuclease L (RNase L) is a metal-ion–independent endoribonuclease associated with antiviral and antibacterial defense, cancer and lifespan. Despite the biological significance of RNase L, the RNAs cleaved by this enzyme are poorly defined. In this study, we used deep sequencing methods to reveal the frequency and location of RNase L cleavage sites within host and viral RNAs. To make cDNA libraries, we exploited the 2', 3'-cyclic phosphate at the end of RNA fragments produced by RNase L and other metal-ion–independent endoribonucleases. We optimized and validated 2', 3'-cyclic phosphate cDNA synthesis and Illumina sequencing methods using viral RNAs cleaved with purified RNase L, viral RNAs cleaved with purified RNase A and RNA from uninfected and poliovirus-infected HeLa cells. Using these methods, we identified (i) discrete regions of hepatitis C virus and poliovirus RNA genomes that were profoundly susceptible to RNase L and other single-strand specific endoribonucleases, (ii) RNase L-dependent and RNase L-independent cleavage sites within ribosomal RNAs (rRNAs) and (iii) 2', 3'-cyclic phosphates at the ends of 5S rRNA and U6 snRNA. Monitoring the frequency and location of metal-ion–independent endoribonuclease cleavage sites within host and viral RNAs reveals, in part, how these enzymes contribute to health and disease.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Actions speak louder than words to prevent language extinctions (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-04-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gautam, Yoshina -- Jha, Aashish -- England -- Nature. 2010 Apr 22;464(7292):1125. doi: 10.1038/4641125e.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20414287" target="_blank"〉PubMed〈/a〉
    Keywords: Humans ; *Language ; Linguistics ; Population Groups/*ethnology/*statistics & numerical data
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
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    Bioactive contaminants leach from disposable laboratory plasticware (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-08
    Description: Disposable plasticware such as test tubes, pipette tips, and multiwell assay or culture plates are used routinely in most biological research laboratories. Manufacturing of plastics requires the inclusion of numerous chemicals to enhance stability, durability, and performance. Some lubricating (slip) agents, exemplified by oleamide, also occur endogenously in humans and are biologically active, and cationic biocides are included to prevent bacterial colonization of the plastic surface. We demonstrate that these manufacturing agents leach from laboratory plasticware into a standard aqueous buffer, dimethyl sulfoxide, and methanol and can have profound effects on proteins and thus on results from bioassays of protein function. These findings have far-reaching implications for the use of disposable plasticware in biological research.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McDonald, G Reid -- Hudson, Alan L -- Dunn, Susan M J -- You, Haitao -- Baker, Glen B -- Whittal, Randy M -- Martin, Jonathan W -- Jha, Amitabh -- Edmondson, Dale E -- Holt, Andrew -- New York, N.Y. -- Science. 2008 Nov 7;322(5903):917. doi: 10.1126/science.1162395.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of Alberta, Edmonton, AB T6G 2B7, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18988846" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Dimethyl Sulfoxide ; Disinfectants/*analysis/pharmacology ; *Disposable Equipment ; Humans ; *Laboratories ; Monoamine Oxidase/*metabolism ; Monoamine Oxidase Inhibitors/pharmacology ; Oleic Acids/*analysis/pharmacology ; Plastics/*chemistry ; Quaternary Ammonium Compounds/*analysis/pharmacology ; Rats ; Solvents
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Band-Gap Engineering in ZnO Thin Films: A Combined Experimental and Theoretical Study (2018)
    American Physical Society (APS)
    Details
    Publication Date: 2018-05-03
    Description: Author(s): Vani Pawar, Pardeep K. Jha, S. K. Panda, Priyanka A. Jha, and Prabhakar Singh Tuning the electronic band gaps of semiconductors is at the core of current research on optoelectronic materials and devices. For ZnO, many studies have tried to enhance the band gap by chemical substitution, but lattice mismatch often thwarts that approach. Instead, this study looks to dimensional reduction. Experiments and first-principles calculations reveal that not only the thickness but also the o r i e n t a t i o n of a film can affect quantum confinement, and thus ZnO’s optoelectronic properties. A suitably oriented and thinned film can boost the band gap to the “solar-blind” region above 4.6 eV, opening up a wide range of possibilities for applications. [Phys. Rev. Applied 9, 054001] Published Wed May 02, 2018
    Electronic ISSN: 2331-7019
    Topics: Physics
    Published by American Physical Society (APS)
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  • 9
    Electronic Resource
    Electronic Resource
    Effect of Nutrient Enrichment on Native Tropical Trees Planted on Singrauli Coalfields, India (2000)
    Boston, MA, USA : Blackwell Science Inc
    Restoration ecology 8 (2000), S. 0 
    Details
    ISSN: 1526-100X
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Growth performance of nine native tropical tree species planted on mine spoil under two levels of NPK treatment was studied by measuring height and diameter. Of the nine species, four were leguminous. All the tree species responded positively to NPK fertilization; however, the impact on leguminous species was little compared to non-leguminous species. In general, the height/diameter ratio decreased from control to full-dose NPK treatment, suggesting that nutrient enrichment influenced the resource allocation pattern such that the diameter growth was favored. The log-transformed height-diameter relationships were significant for the three treatments in all the tree species. The slopes (β) obtained were compared with three different models of tree growth (i.e., elastic similarity, geometric similarity, and constant stress). Acacia catechu, Dalbergia sissoo, Gmelina arborea, and Azadirachta indica fitted the elastic similarity model, whereas Pongamia pinnata and Phyllanthus emblica followed the constant stress model. Tectona grandis was the only species that followed the geometric similarity model. In Albizia lebbeck and Terminalia bellirica, the β values were considerably lower (i.e., below 0.5) and these two species did not fit any of the three models of tree growth. In several cases the β values were considerably influenced by nutrient enrichment.Key words: chemical fertilization, coal mine spoil, growth response, tree structure, tree volume, tropical tree species, height/diameter ratio.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1526-100x.2000.80011.x
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  • 10
    Electronic Resource
    Electronic Resource
    Nd3+-doped fluoroaluminate glasses for a 1.3 μm amplifier (2000)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 87 (2000), S. 2098-2104 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A Nd3+-doped 1.3 μm fiber amplifier has the potential to be an efficient, high-gain device. A major problem to overcome is the long wavelength of the gain spectrum. In the majority of Nd3+-doped glasses the gain is shifted out of the second telecom window as a result of long-wavelength emission and signal excited-state absorption (ESA). In this article we present new fluoroaluminate glasses developed as hosts for the 1.3 μm Nd3+-doped fiber amplifier. Nd3+ emission peaks below 1320 nm were demonstrated in bulk glasses. Gain in the 1310–1320 nm region was measured in unclad fibers, with evidence of significantly reduced ESA. Another serious problem in amplifier design lies in overcoming the competing amplified spontaneous emission (ASE) at 1050 nm. We discuss ASE filtering using in-fiber Bragg gratings and present results supporting its feasibility. The article also examines thermal and viscous properties of matched core and cladding glasses in relation to preform and fiber fabrication. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.372145
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