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  • 1
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    Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean (Phaseolus vulgaris) (2016)
    Genetics Society of America (GSA)
    Details
    Publication Date: 2016-07-08
    Description: Transposons are ubiquitous genomic components that play pivotal roles in plant gene and genome evolution. We analyzed two genome sequences of common bean ( Phaseolus vulgaris ) and identified a new CACTA transposon family named pvCACTA1. The family is extremely abundant, as more than 12,000 pvCACTA1 elements were found. To our knowledge, this is the most abundant CACTA family reported thus far. The computational and fluorescence in situ hybridization (FISH) analyses indicated that the pvCACTA1 elements were concentrated in terminal regions of chromosomes and frequently generated AT-rich 3 bp target site duplications (TSD, WWW, W is A or T). Comparative analysis of the common bean genomes from two domesticated genetic pools revealed that new insertions or excisions of pvCACTA1 elements occurred after the divergence of the two common beans, and some of the polymorphic elements likely resulted in variation in gene sequences. pvCACTA1 elements were detected in related species but not outside the Phaseolus genus. We calculated the molecular evolutionary rate of pvCACTA1 transposons using orthologous elements that indicated that most transposition events likely occurred before the divergence of the two gene pools. These results reveal unique features and evolution of this new transposon family in the common bean genome.
    Electronic ISSN: 2160-1836
    Topics: Biology
    Published by Genetics Society of America (GSA)
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  • 2
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    Completeness of the Mainland China Earthquake Catalog and Implications for the Setup of the China Earthquake Forecast Testing Center (2013)
    Seismological Society of America (SSA)
    Details
    Publication Date: 2013-03-22
    Description: We describe the setup of testing regions for the China Earthquake Forecast Testing Center and provide preliminary forecast results in the scope of the Collaboratory for the Study of Earthquake Predictability (CSEP) project. We investigate the spatiotemporal variations of the completeness magnitude M c by using the frequency-magnitude distribution of the China Earthquake Networks Center (CENC) catalog. We find three periods of significantly different M c histories: (I) 1 January 1970–30 September 2001, (II) 1 October 2001–30 September 2008, and (III) 1 October 2008–31 August 2011. M c mapping provides median values , 2.2, and 1.6 for the three periods of time, respectively, showing the improvement in catalog completeness over time. We recommend using data from periods II and III to define a baseline long enough for retrospective forecast testing. Small magnitude events from period I should be used with caution due to important fluctuations in completeness. For period III, coordinates of all national and regional seismic stations are available, and we therefore apply the Bayesian magnitude of completeness (BMC) technique, mapping M c continuously by using prior information on the relationship between M c and the density of seismic stations. We define four potential testing/collection areas for CSEP-China: (A) All China, (B) North–South Seismic Belt (NSSB), (C) North and West Xinjiang Seismic Region, and (D) North China Seismic Region. In the current phase of CSEP-China, only the NSSB (region B) is considered. To demonstrate the type of earthquake predictability experiment that will be performed in the Chinese Testing Center, we present a series of retrospective forecast experiments with TripleS, a smoothed seismicity model. Online Material: The CENC earthquake catalog (1 January 1970–31 August 2011, restricted to magnitudes M ≥3.0) as well as completeness magnitude M c ( x , y ) spatial grids.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
    Published by Seismological Society of America (SSA)
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  • 3
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    The cryo-EM structure of a rhinovirus C [Biophysics and Computational Biology] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-08-11
    Description: Isolates of rhinovirus C (RV-C), a recently identified Enterovirus (EV) species, are the causative agents of severe respiratory infections among children and are linked to childhood asthma exacerbations. The RV-C have been refractory to structure determination because they are difficult to propagate in vitro. Here, we report the cryo-EM atomic...
    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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    Isolation and characterization of a subgroup IIa WRKY transcription factor PtrWRKY40 from Populus trichocarpa (2015)
    Oxford University Press
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    Publication Date: 2015-10-23
    Description: Salicylic acid (SA) is a defense-related key signaling molecule involved in plant immunity. In this study, a subgroup IIa WRKY gene PtrWRKY40 was isolated from Populus trichocarpa , which displayed amino acid sequence similar to Arabidopsis AtWRKY40 , AtWRKY18 and AtWRKY60. PtrWRKY40 transcripts accumulated significantly in response to SA, methyl jasmonate and hemibiotrophic fungus Dothiorella gregaria Sacc. Overexpression of PtrWRKY40 in transgenic poplar conferred higher susceptibility to D. gregaria infection. This susceptibility was coupled with reduced expression of SA-associated genes ( PR1.1 , PR2.1 , PR5.9 , CPR5 and SID2 ) and jasmonic acid (JA)-related gene JAZ8 . Decreased accumulation of endogenous SA was observed in transgenic lines overexpressing PtrWRKY40 when compared with wild-type plants. However, constitutive expression of PtrWRKY40 in Arabidopsis thaliana displayed resistance to necrotrophic fungus Botrytis cinerea , and the expression of JA-defense-related genes such as PDF1.2 , VSP2 and PR3 was remarkably increased in transgenic plants upon infection with fugal pathogens. Together, our findings indicate that PtrWRKY40 plays a negative role in resistance to hemibiotrophic fungi in poplar but functions as a positive regulator of resistance toward the necrotrophic fungi in Arabidopsis .
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 5
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    Population variation in total genetic risk of Hirschsprung disease from common RET, SEMA3 and NRG1 susceptibility polymorphisms (2015)
    Oxford University Press
    Details
    Publication Date: 2015-04-23
    Description: The risk of Hirschsprung disease (HSCR) is ~15/100 000 live births per newborn but has been reported to show significant inter-individual variation from the effects of seven common susceptibility alleles at the RET , SEMA3 and NRG1 loci. We show, by analyses of these variants in 997 samples from 376 HSCR families of European ancestry, that significant genetic risk can only be detected at RET (rs2435357 and rs2506030) and at SEMA3 (rs11766001), but not at NRG1. RET rs2435357 also showed significant frequency differences by gender, segment length of aganglionosis and familiality. Further, in combination, disease risk varied 〉30-fold between individuals with none and up to 6 susceptibility alleles. Thus, these polymorphisms can be used to stratify the newborn population into distinct phenotypic classes with defined risks to understand HSCR etiology.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 6
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    Epigenetic dysregulation of hairy and enhancer of split 4 (HES4) is associated with striatal degeneration in postmortem Huntington brains (2015)
    Oxford University Press
    Details
    Publication Date: 2015-02-10
    Description: To investigate epigenetic contributions to Huntington's disease (HD) pathogenesis, we carried out genome-wide mapping of the transcriptional mark, trimethyl-histone H3-lysine 4 (H3K4me3) in neuronal nuclei extracted from prefrontal cortex of HD cases and controls using chromatin immunoprecipitation followed by deep-sequencing. Neuron-specific mapping of the genome-wide distribution of H3K4me3 revealed 136 differentially enriched loci associated with genes implicated in neuronal development and neurodegeneration, including GPR3, TMEM106B, PDIA6 and the Notch signaling genes hairy and enhancer of split 4 ( HES4 ) and JAGGED2 , supporting the view that the neuronal epigenome is affected in HD. Importantly, loss of H3K4me3 at CpG-rich sequences on the HES4 promoter was associated with excessive DNA methylation, reduced binding of nuclear proteins to the methylated region and altered expression of HES4 and HES4 targeted genes MASH1 and P21 involved in striatal development. Moreover, hypermethylation of HES4 promoter sequences was strikingly correlated with measures of striatal degeneration and age-of-onset in a cohort of 25 HD brains ( r = 0.56, P = 0.006). Lastly, shRNA knockdown of HES4 in human neuroblastoma cells altered MASH1 and P21 mRNA expression and markedly increased mutated HTT-induced aggregates and cell death. These findings, taken together, suggest that epigenetic dysregulation of HES4 could play a critical role in modifying HD disease pathogenesis and severity.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 7
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    Mitochondrial biogenesis defects in parkin KOs [Neuroscience] (2015)
    National Academy of Sciences
    Details
    Publication Date: 2015-09-16
    Description: Mutations in parkin lead to early-onset autosomal recessive Parkinson’s disease (PD) and inactivation of parkin is thought to contribute to sporadic PD. Adult knockout of parkin in the ventral midbrain of mice leads to an age-dependent loss of dopamine neurons that is dependent on the accumulation of parkin interacting substrate...
    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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  • 8
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    The interstellar oxygen crisis, or where have all the oxygen atoms gone? (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-26
    Description: The interstellar medium (ISM) seems to have a significant surplus of oxygen which was dubbed as the ‘O crisis’: independent of the adopted interstellar reference abundance, the total number of O atoms depleted from the gas phase far exceeds that tied up in solids by as much as ~160 ppm of O/H. Recently, it has been hypothesized that the missing O could be hidden in μm-sized H 2 O ice grains. We examine this hypothesis by comparing the infrared (IR) extinction and far-IR emission arising from these grains with that observed in the Galactic diffuse ISM. We find that it is possible for the diffuse ISM to accommodate ~160 ppm of O/H in μm-sized H 2 O ice grains without violating the observational constraints including the absence of the 3.1 μm O–H absorption feature. More specifically, H 2 O ice grains of radii ~4 μm and O/H = 160 ppm are capable of accounting for the observed flat extinction at ~3–8 μm and produce no excessive emission in the far-IR. These grains could be present in the diffuse ISM through rapid exchange of material between dense molecular clouds where they form and diffuse clouds where they are destroyed by photosputtering.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    Capped RNA recognition by RIG-I [Biochemistry] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-01-21
    Description: RNAs with 5′-triphosphate (ppp) are detected in the cytoplasm principally by the innate immune receptor Retinoic Acid Inducible Gene-I (RIG-I), whose activation triggers a Type I IFN response. It is thought that self RNAs like mRNAs are not recognized by RIG-I because 5′ppp is capped by the addition of a...
    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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  • 10
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    Novel RNA base pair with higher specificity using single selenium atom (2012)
    Oxford University Press
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    Publication Date: 2012-06-06
    Description: Specificity of nucleobase pairing provides essential foundation for genetic information storage, replication, transcription and translation in all living organisms. However, the wobble base pairs, where U in RNA (or T in DNA) pairs with G instead of A, might compromise the high specificity of the base pairing. The U/G wobble pairing is ubiquitous in RNA, especially in non-coding RNA. In order to increase U/A pairing specificity, we have hypothesized to discriminate against U/G wobble pair by tailoring the steric and electronic effects at the 2-exo position of uridine and replacing the 2-exo oxygen with a selenium atom. We report here the first synthesis of the 2-Se-U-RNAs as well as the 2-Se-uridine ( Se U) phosphoramidite. Our biophysical and structural studies of the Se U-RNAs indicate that this single atom replacement can indeed create a novel U/A base pair with higher specificity than the natural one. We reveal that the Se U/A pair maintains a structure virtually identical to the native U/A base pair, while discriminating against U/G wobble pair. This oxygen replacement with selenium offers a unique chemical strategy to enhance the base pairing specificity at the atomic level.
    Keywords: Nucleic acid modification, Nucleic acid structure
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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