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  • 1
    Publication Date: 2013-12-29
    Description: The U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a national user facility, serves the diverse scientific community by providing integrated high-throughput sequencing and computational analysis to enable system-based scientific approaches in support of DOE missions related to clean energy generation and environmental characterization. The JGI Genome Portal ( http://genome.jgi.doe.gov ) provides unified access to all JGI genomic databases and analytical tools. The JGI maintains extensive data management systems and specialized analytical capabilities to manage and interpret complex genomic data. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. Here we describe major updates of the Genome Portal in the past 2 years with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2014-12-10
    Description: Broadly neutralizing antibodies (bnAbs) targeting the trimer apex of HIV envelope are favored candidates for vaccine design and immunotherapy because of their great neutralization breadth and potency. However, methods of isolating bnAbs against this site have been limited by the quaternary nature of the epitope region. Here we report the...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 3
    Publication Date: 2014-04-11
    Description: Downregulation of FAP suppresses cell proliferation and metastasis through PTEN/PI3K/AKT and Ras-ERK signaling in oral squamous cell carcinoma Cell Death and Disease 5, e1155 (April 2014). doi:10.1038/cddis.2014.122 Authors: H Wang, Q Wu, Z Liu, X Luo, Y Fan, Y Liu, Y Zhang, S Hua, Q Fu, M Zhao, Y Chen, W Fang & X Lv
    Keywords: FAPOSCCcell proliferationmetastasisPTEN/AKT/PI3KRAS/ERK
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 4
    Publication Date: 2009-01-24
    Description: We constructed a large-scale functional network model in Drosophila melanogaster built around two key transcription factors involved in the process of embryonic segmentation. Analysis of the model allowed the identification of a new role for the ubiquitin E3 ligase complex factor SPOP. In Drosophila, the gene encoding SPOP is a target of segmentation transcription factors. Drosophila SPOP mediates degradation of the Jun kinase phosphatase Puckered, thereby inducing tumor necrosis factor (TNF)/Eiger-dependent apoptosis. In humans, we found that SPOP plays a conserved role in TNF-mediated JNK signaling and was highly expressed in 99% of clear cell renal cell carcinomas (RCCs), the most prevalent form of kidney cancer. SPOP expression distinguished histological subtypes of RCC and facilitated identification of clear cell RCC as the primary tumor for metastatic lesions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756524/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756524/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Jiang -- Ghanim, Murad -- Xue, Lei -- Brown, Christopher D -- Iossifov, Ivan -- Angeletti, Cesar -- Hua, Sujun -- Negre, Nicolas -- Ludwig, Michael -- Stricker, Thomas -- Al-Ahmadie, Hikmat A -- Tretiakova, Maria -- Camp, Robert L -- Perera-Alberto, Montse -- Rimm, David L -- Xu, Tian -- Rzhetsky, Andrey -- White, Kevin P -- P50 GM081892/GM/NIGMS NIH HHS/ -- P50 GM081892-01A1/GM/NIGMS NIH HHS/ -- R01 HG003012/HG/NHGRI NIH HHS/ -- R01 HG003012-04/HG/NHGRI NIH HHS/ -- UL1 RR024999/RR/NCRR NIH HHS/ -- UL1 RR024999-02/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2009 Feb 27;323(5918):1218-22. doi: 10.1126/science.1157669. Epub 2009 Jan 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomics and Systems Biology, University of Chicago and Argonne National Laboratory, Chicago, IL 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19164706" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Apoptosis ; Carcinoma, Renal Cell/*genetics/metabolism ; Cell Line ; Compound Eye, Arthropod/embryology/metabolism ; Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/embryology/*genetics/metabolism ; Embryo, Nonmammalian/metabolism ; Fushi Tarazu Transcription Factors/genetics/metabolism ; Gene Expression Profiling ; Gene Regulatory Networks ; Homeodomain Proteins/genetics/metabolism ; Humans ; Janus Kinases/*metabolism ; Kidney/metabolism ; Kidney Neoplasms/*genetics/metabolism ; Molecular Sequence Data ; Nervous System/embryology ; Nuclear Proteins/*genetics/metabolism ; Phosphoprotein Phosphatases/metabolism ; Phosphorylation ; Repressor Proteins/*genetics/metabolism ; *Signal Transduction ; Transcription Factors/genetics/metabolism ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2004-10-23
    Description: We used a maskless photolithography method to produce DNA oligonucleotide microarrays with unique probe sequences tiled throughout the genome of Drosophila melanogaster and across predicted splice junctions. RNA expression of protein coding and nonprotein coding sequences was determined for each major stage of the life cycle, including adult males and females. We detected transcriptional activity for 93% of annotated genes and RNA expression for 41% of the probes in intronic and intergenic sequences. Comparison to genome-wide RNA interference data and to gene annotations revealed distinguishable levels of expression for different classes of genes and higher levels of expression for genes with essential cellular functions. Differential splicing was observed in about 40% of predicted genes, and 5440 previously unknown splice forms were detected. Genes within conserved regions of synteny with D. pseudoobscura had highly correlated expression; these regions ranged in length from 10 to 900 kilobase pairs. The expressed intergenic and intronic sequences are more likely to be evolutionarily conserved than nonexpressed ones, and about 15% of them appear to be developmentally regulated. Our results provide a draft expression map for the entire nonrepetitive genome, which reveals a much more extensive and diverse set of expressed sequences than was previously predicted.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stolc, Viktor -- Gauhar, Zareen -- Mason, Christopher -- Halasz, Gabor -- van Batenburg, Marinus F -- Rifkin, Scott A -- Hua, Sujun -- Herreman, Tine -- Tongprasit, Waraporn -- Barbano, Paolo Emilio -- Bussemaker, Harmen J -- White, Kevin P -- P20LM007276-01/LM/NLM NIH HHS/ -- T32GM008224-17/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Oct 22;306(5696):655-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15499012" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Animals ; Computational Biology ; DNA, Intergenic ; Drosophila/genetics ; Drosophila Proteins/genetics/physiology ; Drosophila melanogaster/*genetics/growth & development ; Evolution, Molecular ; Exons ; Female ; *Gene Expression ; *Gene Expression Profiling ; Genes, Insect ; *Genome ; Introns ; Life Cycle Stages ; Male ; Oligonucleotide Array Sequence Analysis ; Oligonucleotide Probes ; RNA Splicing ; Synteny ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2013-03-29
    Description: Cancer cells have metabolic dependencies that distinguish them from their normal counterparts. Among these dependencies is an increased use of the amino acid glutamine to fuel anabolic processes. Indeed, the spectrum of glutamine-dependent tumours and the mechanisms whereby glutamine supports cancer metabolism remain areas of active investigation. Here we report the identification of a non-canonical pathway of glutamine use in human pancreatic ductal adenocarcinoma (PDAC) cells that is required for tumour growth. Whereas most cells use glutamate dehydrogenase (GLUD1) to convert glutamine-derived glutamate into alpha-ketoglutarate in the mitochondria to fuel the tricarboxylic acid cycle, PDAC relies on a distinct pathway in which glutamine-derived aspartate is transported into the cytoplasm where it can be converted into oxaloacetate by aspartate transaminase (GOT1). Subsequently, this oxaloacetate is converted into malate and then pyruvate, ostensibly increasing the NADPH/NADP(+) ratio which can potentially maintain the cellular redox state. Importantly, PDAC cells are strongly dependent on this series of reactions, as glutamine deprivation or genetic inhibition of any enzyme in this pathway leads to an increase in reactive oxygen species and a reduction in reduced glutathione. Moreover, knockdown of any component enzyme in this series of reactions also results in a pronounced suppression of PDAC growth in vitro and in vivo. Furthermore, we establish that the reprogramming of glutamine metabolism is mediated by oncogenic KRAS, the signature genetic alteration in PDAC, through the transcriptional upregulation and repression of key metabolic enzymes in this pathway. The essentiality of this pathway in PDAC and the fact that it is dispensable in normal cells may provide novel therapeutic approaches to treat these refractory tumours.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656466/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656466/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Son, Jaekyoung -- Lyssiotis, Costas A -- Ying, Haoqiang -- Wang, Xiaoxu -- Hua, Sujun -- Ligorio, Matteo -- Perera, Rushika M -- Ferrone, Cristina R -- Mullarky, Edouard -- Shyh-Chang, Ng -- Kang, Ya'an -- Fleming, Jason B -- Bardeesy, Nabeel -- Asara, John M -- Haigis, Marcia C -- DePinho, Ronald A -- Cantley, Lewis C -- Kimmelman, Alec C -- 5P30CA006516-46/CA/NCI NIH HHS/ -- P01 CA117969/CA/NCI NIH HHS/ -- P01 CA120964/CA/NCI NIH HHS/ -- P01CA120964-05/CA/NCI NIH HHS/ -- P30 CA006516/CA/NCI NIH HHS/ -- R01 CA157490/CA/NCI NIH HHS/ -- R01 GM056203/GM/NIGMS NIH HHS/ -- T32 CA009382-26/CA/NCI NIH HHS/ -- England -- Nature. 2013 Apr 4;496(7443):101-5. doi: 10.1038/nature12040. Epub 2013 Mar 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23535601" target="_blank"〉PubMed〈/a〉
    Keywords: Adenocarcinoma/genetics/metabolism/pathology ; Aspartate Aminotransferases/deficiency/genetics/metabolism ; Cell Line, Tumor ; Cell Proliferation ; Citric Acid Cycle ; Glutamate Dehydrogenase/metabolism ; Glutamine/*metabolism ; Homeostasis ; Humans ; Ketoglutaric Acids/metabolism ; *Metabolic Networks and Pathways ; Oncogene Protein p21(ras)/genetics/*metabolism ; Oncogenes/genetics ; Oxidation-Reduction ; Pancreatic Neoplasms/genetics/*metabolism/*pathology ; Proto-Oncogene Proteins/genetics/*metabolism ; Reactive Oxygen Species/metabolism ; ras Proteins/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2013-05-17
    Description: Loss of connective tissue growth factor as an unfavorable prognosis factor activates miR-18b by PI3K/AKT/C-Jun and C-Myc and promotes cell growth in nasopharyngeal carcinoma Cell Death and Disease 4, e634 (May 2013). doi:10.1038/cddis.2013.153 Authors: X Yu, Y Zhen, H Yang, H Wang, Y Zhou, E Wang, F M Marincola, C Mai, Y Chen, H Wei, Y Song, X Lyu, Y Ye, L Cai, Q Wu, M Zhao, S Hua, Q Fu, Y Zhang, K Yao, Z Liu, X Li & W Fang
    Keywords: CTGFNPCmiR-18bPI3K/AKT
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 8
    Publication Date: 2017-04-22
    Description: UAVs have played important roles in many fields. However, due to the insufficient energy of electric UAVs, the future development has a major obstacle. This problem can be solved by laser power transmission. This paper summarizes the research results at abroad and domestic, introduces the work flow of the whole system, discusses the key technologies and puts forward the prospect.
    Print ISSN: 1755-1307
    Electronic ISSN: 1755-1315
    Topics: Geography , Geosciences , Physics
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  • 9
    Publication Date: 2013-06-14
    Description: Loss of connective tissue growth factor as an unfavorable prognosis factor activates miR-18b by PI3K/AKT/C-Jun and C-Myc and promotes cell growth in nasopharyngeal carcinoma Cell Death and Disease 4, e672 (June 2013). doi:10.1038/cddis.2013.216 Authors: X Yu, Y Zhen, H Yang, H Wang, Y Zhou, E Wang, F M Marincola, C Mai, Y Chen, H Wei, Y Song, X Lyu, Y Ye, L Cai, Q Wu, M Zhao, S Hua, Q Fu, Y Zhang, K Yao, Z Liu, X Li & W Fang
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 10
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Giant magnetoresistance (GMR) of CoNiCu/Cu multilayers grown by electrodeposition was measured as a function of the copper layer thickness and effects of the order of 14% were obtained. The copper layer thickness ranged from 0.7 to 3.5 nm. Two peaks in the magnetoresistance were observed. One was centered at a copper thickness of ∼1.0 nm and the second was centered at ∼2.3 nm. Comparison of the field dependence of the magnetoresistance with the field dependence of the magnetization, as determined by vibrating-sample magnetometer, suggests that the saturation field for GMR and the magnetization are similar for the larger copper thicknesses, but are strikingly different near 1.0 nm copper thickness. This observation suggests that the GMR is affected by different factors depending on the thickness of the copper layer.
    Type of Medium: Electronic Resource
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