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  • 1
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    DNA sequencing by synthesis on a nanopore array [Applied Biological Sciences] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-05-12
    Description: DNA sequencing by synthesis (SBS) offers a robust platform to decipher nucleic acid sequences. Recently, we reported a single-molecule nanopore-based SBS strategy that accurately distinguishes four bases by electronically detecting and differentiating four different polymer tags attached to the 5′-phosphate of the nucleotides during their incorporation into a growing DNA...
    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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  • 2
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    Mercury resistance transposons in Bacilli strains from different geographical regions (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-20
    Description: A total of 65 spore-forming mercury-resistant bacteria were isolated from natural environments worldwide in order to understand the acquisition of additional genes by and dissemination of mercury resistance transposons across related Bacilli genera by horizontal gene movement. PCR amplification using a single primer complementary to the inverted repeat sequence of Tn MERI1 -like transposons showed that 12 of 65 isolates had a transposon-like structure. There were four types of amplified fragments: Tn 5084 , Tn 5085 , Tn d MER3 (a newly identified deleted transposon-like fragment) and Tn 6294 (a newly identified transposon). Tn d MER3 is a 3.5-kb sequence that carries a merRETPA operon with no merB or transposase genes. It is related to the mer operon of Bacillus licheniformis strain FA6-12 from Russia. DNA homology analysis shows that Tn 6294 is an 8.5-kb sequence that is possibly derived from Tn d MER3 by integration of a Tn MERI1 -type transposase and resolvase genes and in addition the merR2 and merB1 genes. Bacteria harboring Tn 6294 exhibited broad-spectrum mercury resistance to organomercurial compounds, although Tn 6294 had only merB1 and did not have the merB2 and merB3 sequences for organomercurial lyases found in Tn 5084 of B. cereus strain RC607. Strains with Tn 6294 encode mercuric reductase (MerA) of less than 600 amino acids in length with a single N-terminal mercury-binding domain, whereas MerA encoded by strains MB1 and RC607 has two tandem domains. Thus, Tn d MER3 and Tn 6294 are shorter prototypes for Tn MERI1 -like transposons. Identification of Tn 6294 in Bacillus sp. from Taiwan and in Paenibacillus sp. from Antarctica indicates the wide horizontal dissemination of Tn MERI1 -like transposons across bacterial species and geographical barriers.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Design of a nanopore-polymerase for DNA sequencing [Applied Biological Sciences] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-11-02
    Description: Scalable, high-throughput DNA sequencing is a prerequisite for precision medicine and biomedical research. Recently, we presented a nanopore-based sequencing-by-synthesis (Nanopore-SBS) approach, which used a set of nucleotides with polymer tags that allow discrimination of the nucleotides in a biological nanopore. Here, we designed and covalently coupled a DNA polymerase to...
    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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  • 4
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    Climate and height growth of taiwania (Taiwania cryptomerioides) and Taiwan incense-cedar (Calocedrus formosana) in Taiwan (2016)
    Oxford University Press
    In: Forestry
    Details
    Publication Date: 2016-08-27
    Description: Taiwan incense-cedar ( Calocedrus formosana (Florin) Florin) and taiwania ( Taiwania cryptomerioides Hayata) are coniferous species growing in Taiwan, Republic of China. Both species are red listed, and hence, their management and conservation are important. The objective of this research was to determine the effect of climate on the height growth of Taiwan incense-cedar and taiwania. Height growth data for Taiwan incense-cedar came from stem analysis data and the data for taiwania were from three sets of experimental plots. Climate data were obtained from nearby climate stations. Dynamic height growth models having parameters that were functions of climate variables were fit to the height data. A Chapman–Richards function formed the basis for Taiwan incense-cedar model, and a linear model was fit to the taiwania data. Mean summer temperature and precipitation were predictor variables for Taiwan incense-cedar height growth. These variables, along with growing degree-days, were predictor variables for taiwania. Several scenarios were devised to show the effect of climate on height growth. Under the A1B climate change scenario, the height growth of taiwania is expected to increase, but the height growth of Taiwan incense-cedar will decrease slightly. The climate/height growth relationships can assist in the conservation and stewardship of these species.
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 5
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    Failure to regulate TNF-induced NF-kappaB and cell death responses in A20-deficient mice (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-09-29
    Description: A20 is a cytoplasmic zinc finger protein that inhibits nuclear factor kappaB (NF-kappaB) activity and tumor necrosis factor (TNF)-mediated programmed cell death (PCD). TNF dramatically increases A20 messenger RNA expression in all tissues. Mice deficient for A20 develop severe inflammation and cachexia, are hypersensitive to both lipopolysaccharide and TNF, and die prematurely. A20-deficient cells fail to terminate TNF-induced NF-kappaB responses. These cells are also more susceptible than control cells to undergo TNF-mediated PCD. Thus, A20 is critical for limiting inflammation by terminating TNF-induced NF-kappaB responses in vivo.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582399/" 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/PMC3582399/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, E G -- Boone, D L -- Chai, S -- Libby, S L -- Chien, M -- Lodolce, J P -- Ma, A -- 5T32GM07183/GM/NIGMS NIH HHS/ -- R01 DK052751/DK/NIDDK NIH HHS/ -- T32GM07839/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Sep 29;289(5488):2350-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, The University of Chicago, 5841 South Maryland Avenue, MC 6084, Chicago, IL 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11009421" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Apoptosis ; Cachexia/pathology/physiopathology ; Cells, Cultured ; Cysteine Endopeptidases ; DNA/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Fibroblasts/metabolism ; Gene Targeting ; *I-kappa B Proteins ; Inflammation/pathology/*physiopathology ; Interleukin-1/pharmacology ; Intestines/pathology ; Intracellular Signaling Peptides and Proteins ; Kidney/pathology ; Lipopolysaccharides/immunology ; Liver/pathology ; Mice ; NF-kappa B/*metabolism ; Nuclear Proteins ; Phosphorylation ; Proteins/genetics/*physiology ; Skin/pathology ; T-Lymphocytes/cytology/metabolism ; Tumor Necrosis Factor-alpha/*pharmacology ; Zinc Fingers
    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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  • 6
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    Identification of virus-encoded microRNAs (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-01
    Description: RNA silencing processes are guided by small RNAs that are derived from double-stranded RNA. To probe for function of RNA silencing during infection of human cells by a DNA virus, we recorded the small RNA profile of cells infected by Epstein-Barr virus (EBV). We show that EBV expresses several microRNA (miRNA) genes. Given that miRNAs function in RNA silencing pathways either by targeting messenger RNAs for degradation or by repressing translation, we identified viral regulators of host and/or viral gene expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pfeffer, Sebastien -- Zavolan, Mihaela -- Grasser, Friedrich A -- Chien, Minchen -- Russo, James J -- Ju, Jingyue -- John, Bino -- Enright, Anton J -- Marks, Debora -- Sander, Chris -- Tuschl, Thomas -- R01-GM068476-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Apr 30;304(5671):734-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15118162" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Callithrix ; Cell Line ; Cell Line, Tumor ; Cloning, Molecular ; Computational Biology ; DNA-Binding Proteins/genetics/metabolism ; DNA-Directed DNA Polymerase/genetics/metabolism ; Gene Expression ; Herpesvirus 4, Human/*genetics/physiology ; Humans ; MicroRNAs/*genetics/metabolism ; Proteins/genetics/metabolism ; *RNA Interference ; RNA, Double-Stranded/genetics ; RNA, Messenger/genetics/metabolism ; RNA, Viral/*genetics/metabolism ; Untranslated Regions ; Viral Proteins/genetics/metabolism ; Virus Latency
    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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  • 7
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    The genomic sequence of the accidental pathogen Legionella pneumophila (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-09-28
    Description: We present the genomic sequence of Legionella pneumophila, the bacterial agent of Legionnaires' disease, a potentially fatal pneumonia acquired from aerosolized contaminated fresh water. The genome includes a 45-kilobase pair element that can exist in chromosomal and episomal forms, selective expansions of important gene families, genes for unexpected metabolic pathways, and previously unknown candidate virulence determinants. We highlight the genes that may account for Legionella's ability to survive in protozoa, mammalian macrophages, and inhospitable environmental niches and that may define new therapeutic targets.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chien, Minchen -- Morozova, Irina -- Shi, Shundi -- Sheng, Huitao -- Chen, Jing -- Gomez, Shawn M -- Asamani, Gifty -- Hill, Kendra -- Nuara, John -- Feder, Marc -- Rineer, Justin -- Greenberg, Joseph J -- Steshenko, Valeria -- Park, Samantha H -- Zhao, Baohui -- Teplitskaya, Elita -- Edwards, John R -- Pampou, Sergey -- Georghiou, Anthi -- Chou, I-Chun -- Iannuccilli, William -- Ulz, Michael E -- Kim, Dae H -- Geringer-Sameth, Alex -- Goldsberry, Curtis -- Morozov, Pavel -- Fischer, Stuart G -- Segal, Gil -- Qu, Xiaoyan -- Rzhetsky, Andrey -- Zhang, Peisen -- Cayanis, Eftihia -- De Jong, Pieter J -- Ju, Jingyue -- Kalachikov, Sergey -- Shuman, Howard A -- Russo, James J -- AI 23549/AI/NIAID NIH HHS/ -- U01 1 AI 4437/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2004 Sep 24;305(5692):1966-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Columbia Genome Center, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15448271" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Bacterial ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Legionella pneumophila/*genetics/pathogenicity/physiology ; Plasmids
    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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    Epigenome-wide ovarian cancer analysis identifies a methylation profile differentiating clear-cell histology with epigenetic silencing of the HERG K+ channel (2013)
    Oxford University Press
    Details
    Publication Date: 2013-07-03
    Description: Ovarian cancer remains the leading cause of death in women with gynecologic malignancies, despite surgical advances and the development of more effective chemotherapeutics. As increasing evidence indicates that clear-cell ovarian cancer may have unique pathogenesis, further understanding of molecular features may enable us to begin to understand the underlying biology and histology-specific information for improved outcomes. To study epigenetics in clear-cell ovarian cancer, fresh frozen tumor DNA ( n = 485) was assayed on Illumina Infinium HumanMethylation450 BeadChips. We identified a clear-cell ovarian cancer tumor methylation profile ( n = 163) which we validated in two independent replication sets (set 1, n = 163; set 2, n = 159), highlighting 22 CpG loci associated with nine genes ( VWA1 , FOXP1 , FGFRL1 , LINC00340 , KCNH2 , ANK1 , ATXN2 , NDRG21 and SLC16A11 ). Nearly all of the differentially methylated CpGs showed a propensity toward hypermethylation among clear-cell cases. Several loci methylation inversely correlated with tumor gene expression, most notably KCNH2 (HERG, a potassium channel) ( P = 9.5 x 10 –7 ), indicating epigenetic silencing. In addition, a predicted methylation class mainly represented by the clear-cell cases (20 clear cell out of 23 cases) had improved survival time. Although these analyses included only 30 clear-cell carcinomas, results suggest that loss of expression of KCNH2 (HERG) by methylation could be a good prognostic marker, given that overexpression of the potassium (K + ) channel Eag family members promotes increased proliferation and results in poor prognosis. Validation in a bigger cohort of clear-cell tumors of the ovary is warranted.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 9
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    A placental growth factor is silenced in mouse embryos by the zinc finger protein ZFP568 (2017)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2017-05-19
    Description: Insulin-like growth factor 2 (IGF2) is the major fetal growth hormone in mammals. We identify zinc finger protein 568 (ZFP568), a member of the rapidly evolving Kruppel-associated box–zinc finger protein (KRAB-ZFP) family linked primarily to silencing of endogenous retroelements, as a direct repressor of a placental-specific Igf2 transcript (designated Igf2-P0 ) in mice. Loss of Zfp568 , which causes gastrulation failure, or mutation of the ZFP568-binding site at the Igf2-P0 promoter causes inappropriate Igf2-P0 activation. Deletion of Igf2 can completely rescue Zfp568 gastrulation phenotypes through late gestation. Our data highlight the exquisite selectivity with which members of the KRAB-ZFP family repress their targets and identify an additional layer of transcriptional control of a key growth factor regulating fetal and placental development.
    Keywords: Development
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
    Electronic Resource
    Electronic Resource
    A simple high pressure flow cell for on-line absorption, Raman, and time resolved laser induced fluorescence spectroscopy in supercritical fluids (1998)
    [S.l.] : American Institute of Physics (AIP)
    Review of Scientific Instruments 69 (1998), S. 3127-3131 
    Details
    ISSN: 1089-7623
    Source: AIP Digital Archive
    Topics: Physics , Electrical Engineering, Measurement and Control Technology
    Notes: A versatile spectroscopic flow cell for high pressure liquids and supercritical fluid solutions is described. The cell is capable of being coupled to either standard or fiber optic spectrometers. There are two perpendicular optical paths that are adjustable in length and aperture diameter. The cell has shown it can be used for absorption, emission, or scattering spectroscopy. The design is simple, inexpensive, serviceable, uses conventional materials, and is self aligning. With apertures of 5.7 mm the cell has been tested to pressures up to 500 atm and temperatures up to 90 °C. However, the cell would allow usage at higher temperatures and pressures if desired. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1149071
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    Paper (German National Licenses)
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