ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
  • 2020-2023  (2)
  • 2010-2014  (114)
Collection
Keywords
Publisher
Language
Years
Year
  • 1
    facet.materialart.
    Unknown
    Phylogenomic Distance Method for Analyzing Transcriptome Evolution Based on RNA-seq Data (2013)
    Oxford University Press
    Details
    Publication Date: 2013-10-01
    Description: Thanks to the microarray technology, our understanding of transcriptome evolution at the genome level has been considerably advanced in the past decade. Yet, further investigation was challenged by several technical limitations of this technology. Recent innovation of next-generation sequencing, particularly the invention of RNA-seq technology, has shed insightful lights on resolving this problem. Though a number of statistical and computational methods have been developed to analyze RNA-seq data, the analytical framework specifically designed for evolutionary genomics remains an open question. In this article we develop a new method for estimating the genome expression distance from the RNA-seq data, which has explicit interpretations under the model of gene expression evolution. Moreover, this distance measure takes the data overdispersion, gene length variation, and sequencing depth variation into account so that it can be applied to multiple genomes from different species. Using mammalian RNA-seq data as example, we demonstrated that this expression distance is useful in phylogenomic analysis.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 2
    facet.materialart.
    Unknown
    CFH, oxidized phospholipids, and AMD [Medical Sciences] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-08-22
    Description: The rs1061170T/C variant encoding the Y402H change in complement factor H (CFH) has been identified by genome-wide association studies as being significantly associated with age-related macular degeneration (AMD). However, the precise mechanism by which this CFH variant impacts the risk of AMD remains largely unknown. Oxidative stress plays an important...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 3
    facet.materialart.
    Unknown
    PlantGSEA: a gene set enrichment analysis toolkit for plant community (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-23
    Description: Gene Set Enrichment Analysis (GSEA) is a powerful method for interpreting biological meaning of a list of genes by computing the overlaps with various previously defined gene sets. As one of the most widely used annotations for defining gene sets, Gene Ontology (GO) system has been used in many enrichment analysis tools. EasyGO and agriGO, two GO enrichment analysis toolkits developed by our laboratory, have gained extensive usage and citations since their releases because of their effective performance and consistent maintenance. Responding to the increasing demands of more comprehensive analysis from the users, we developed a web server as an important component of our bioinformatics analysis toolkit, named PlantGSEA, which is based on GSEA method and mainly focuses on plant organisms. In PlantGSEA, 20 290 defined gene sets deriving from different resources were collected and used for GSEA analysis. The PlantGSEA currently supports gene locus IDs and Affymatrix microarray probe set IDs from four plant model species ( Arabidopsis thaliana , Oryza sativa , Zea mays and Gossypium raimondii ). The PlantGSEA is an efficient and user-friendly web server, and now it is publicly accessible at http://structuralbiology.cau.edu.cn/PlantGSEA .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 4
    facet.materialart.
    Unknown
    Rational reprogramming of nrPKS PT domains [Applied Biological Sciences] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-04-03
    Description: Resorcylic acid lactones and dihydroxyphenylacetic acid lactones represent important pharmacophores with heat shock response and immune system modulatory activities. The biosynthesis of these fungal polyketides involves a pair of collaborating iterative polyketide synthases (iPKSs): a highly reducing iPKS with product that is further elaborated by a nonreducing iPKS (nrPKS) to...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 5
    facet.materialart.
    Unknown
    Observations and simulations of seismoionospheric GPS total electron content anomalies before the 12 January 2010 M7 Haiti earthquake (2011)
    Wiley
    Details
    Publication Date: 2011-04-02
    Description: In this paper, the total electron content (TEC) of the global ionosphere map (GIM) is used to detect seismoionospheric anomalies associated with the 12 January 2010 M7 Haiti earthquake, and an ionospheric model is applied to simulate the detected anomalies. The GIM temporal variation shows that the TEC over the epicenter significantly enhances on 11 January 2010, 1 day before the earthquake. The latitude-time-TEC (LTT) plots reveal three anomalies: (1) the northern crest of equatorial ionization anomaly (EIA) moves poleward, (2) the TECs at the epicenter and its conjugate increase, and (3) the TECs at two dense bands in the midlatitude ionosphere of 35°N and 60°S further enhance. The spatial analysis demonstrates that the TEC enhancement anomaly appears specifically and persistently in a small region of the northern epicenter area. The simulation well reproduces the three GIM TEC anomalies, which indicate that the dynamoelectric field of the ionospheric plasma fountain might have been perturbed by seismoelectric signals generated around the epicenter during the earthquake preparation period.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 6
    facet.materialart.
    Unknown
    Crucial role of copper in detection of metal-coordinating odorants [Chemistry] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-02-29
    Description: Odorant receptors (ORs) in olfactory sensory neurons (OSNs) mediate detection of volatile odorants. Divalent sulfur compounds, such as thiols and thioethers, are extremely potent odorants. We identify a mouse OR, MOR244-3, robustly responding to (methylthio)methanethiol (MeSCH2SH; MTMT) in heterologous cells. Found specifically in male mouse urine, strong-smelling MTMT [human threshold 100 parts per billion (ppb)] is a semiochemical that attracts female mice. Nonadjacent thiol and thioether groups in MTMT suggest involvement of a chelated metal complex in MOR244-3 activation. Metal ion involvement in thiol–OR interactions was previously proposed, but whether these ions change thiol-mediated OR activation remained unknown. We show that copper ion among all metal ions tested is required for robust activation of MOR244-3 toward ppb levels of MTMT, structurally related sulfur compounds, and other metal-coordinating odorants (e.g., strong-smelling trans-cyclooctene) among 〉125 compounds tested. Copper chelator (tetraethylenepentamine, TEPA) addition abolishes the response of MOR244-3 to MTMT. Histidine 105, located in the third transmembrane domain near the extracellular side, is proposed to serve as a copper-coordinating residue mediating interaction with the MTMT–copper complex. Electrophysiological recordings of the OSNs in the septal organ, abundantly expressing MOR244-3, revealed neurons responding to MTMT. Addition of copper ion and chelator TEPA respectively enhanced and reduced the response of some MTMT-responding neurons, demonstrating the physiological relevance of copper ion in olfaction. In a behavioral context, an olfactory discrimination assay showed that mice injected with TEPA failed to discriminate MTMT. This report establishes the role of metal ions in mammalian odor detection by ORs.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 7
    facet.materialart.
    Unknown
    SWI2/SNF2 chromatin remodeling ATPases overcome polycomb repression and control floral organ identity with the LEAFY and SEPALLATA3 transcription factors [Plant Biology] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-02-29
    Description: Patterning of the floral organs is exquisitely controlled and executed by four classes of homeotic regulators. Among these, the class B and class C floral homeotic regulators are of central importance as they specify the male and female reproductive organs. Inappropriate induction of the class B gene APETALA3 (AP3) and the class C gene AGAMOUS (AG) causes reduced reproductive fitness and is prevented by polycomb repression. At the onset of flower patterning, polycomb repression needs to be overcome to allow induction of AP3 and AG and formation of the reproductive organs. We show that the SWI2/SNF2 chromatin-remodeling ATPases SPLAYED (SYD) and BRAHMA (BRM) are redundantly required for flower patterning and for the activation of AP3 and AG. The SWI2/SNF2 ATPases are recruited to the regulatory regions of AP3 and AG during flower development and physically interact with two direct transcriptional activators of class B and class C gene expression, LEAFY (LFY) and SEPALLATA3 (SEP3). SYD and LFY association with the AP3 and AG regulatory loci peaks at the same time during flower patterning, and SYD binding to these loci is compromised in lfy and lfy sep3 mutants. This suggests a mechanism for SWI2/SNF2 ATPase recruitment to these loci at the right stage and in the correct cells. SYD and BRM act as trithorax proteins, and the requirement for SYD and BRM in flower patterning can be overcome by partial loss of polycomb activity in curly leaf (clf) mutants, implicating the SWI2/SNF2 chromatin remodelers in reversal of polycomb repression.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 8
    facet.materialart.
    Unknown
    Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-07
    Description: In silico prediction of genomic long non-coding RNAs (lncRNAs) is prerequisite to the construction and elucidation of non-coding regulatory network. Chromatin modifications marked by chromatin regulators are important epigenetic features, which can be captured by prevailing high-throughput approaches such as ChIP sequencing. We demonstrate that the accuracy of lncRNA predictions can be greatly improved when incorporating high-throughput chromatin modifications over mouse embryonic stem differentiation toward adult Cerebellum by logistic regression with LASSO regularization. The discriminating features include H3K9me3, H3K27ac, H3K4me1, open reading frames and several repeat elements. Importantly, chromatin information is suggested to be complementary to genomic sequence information, highlighting the importance of an integrated model. Applying integrated model, we obtain a list of putative lncRNAs based on uncharacterized fragments from transcriptome assembly. We demonstrate that the putative lncRNAs have regulatory roles in vicinity of known gene loci by expression and Gene Ontology enrichment analysis. We also show that the lncRNA expression specificity can be efficiently modeled by the chromatin data with same developmental stage. The study not only supports the biological hypothesis that chromatin can regulate expression of tissue-specific or developmental stage-specific lncRNAs but also reveals the discriminating features between lncRNA and coding genes, which would guide further lncRNA identifications and characterizations.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 9
    facet.materialart.
    Unknown
    Reprogramming the fate of human glioma cells to impede brain tumor development (2014)
    Springer Nature
    Details
    Publication Date: 2014-10-17
    Description: Reprogramming the fate of human glioma cells to impede brain tumor development Cell Death and Disease 5, e1463 (October 2014). doi:10.1038/cddis.2014.425 Authors: Z Su, T Zang, M-L Liu, L-L Wang, W Niu & C-L Zhang
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 10
    facet.materialart.
    Unknown
    Virtual Satellite Construction and Application for Image Classification (2014)
    Institute of Physics (IOP)
    Details
    Publication Date: 2014-03-19
    Description: Nowadays, most remote sensing image classification uses single satellite remote sensing data, so the number of bands and band spectral width is consistent. In addition, observed phenomenon such as land cover have the same spectral signature, which causes the classification accuracy to decrease as different data have unique characteristic. Therefore, this paper analyzes different optical remote sensing satellites, comparing the spectral differences and proposes the ideas and methods to build a virtual satellite. This article illustrates the research on the TM, HJ-1 and MODIS data. We obtained the virtual band X 0 through these satellites' bands combined it with the 4 bands of a TM image to build a virtual satellite with five bands. Based on this, we used these data for image classification. The experimental results showed that the virtual satellite classification results of building land and water information were superior to the HJ-1 and TM data respectively.
    Print ISSN: 1755-1307
    Electronic ISSN: 1755-1315
    Topics: Geography , Geosciences , Physics
    Published by Institute of Physics (IOP)
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...