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Berlin Brandenburg

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  • 2012  (28)
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  • 2012  (28)
  • 1
    Language: English
    In: Journal of Bacteriology, pp. 6618-6619
    Description: Article discussing the draft genome sequence of the cyanide-utilizing bacterium 'Pseudomonas fluorescens' strain NCIMB 11764.
    Keywords: Pseudomanas Fluorescens ; Genetics ; Cyanide
    ISSN: 00219193
    E-ISSN: 10985530
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  • 2
    Language: English
    In: Plant physiology, May 2012, Vol.159(1), pp.299-310
    Description: Symbiotic nitrogen fixation occurs in nodules, specialized organs on the roots of legumes. Within nodules, host plant cells are infected with rhizobia that are encapsulated by a plant-derived membrane forming a novel organelle, the symbiosome. In Medicago truncatula, the symbiosome consists of the symbiosome membrane, a single rhizobium, and the soluble space between them, called the symbiosome space. The symbiosome space is enriched with plant-derived proteins, including the M. truncatula EARLY NODULIN8 (MtENOD8) protein. Here, we present evidence from green fluorescent protein (GFP) fusion experiments that the MtENOD8 protein contains at least three symbiosome targeting domains, including its N-terminal signal peptide (SP). When ectopically expressed in nonnodulated root tissue, the MtENOD8 SP delivers GFP to the vacuole. During the course of nodulation, there is a nodule-specific redirection of MtENOD8-SP-GFP from the vacuole to punctate intermediates and subsequently to symbiosomes, with redirection of MtENOD8-SP-GFP from the vacuole to punctate intermediates preceding intracellular rhizobial infection. Experiments with M. truncatula mutants having defects in rhizobial infection and symbiosome development demonstrated that the MtNIP/LATD gene is required for redirection of the MtENOD8-SP-GFP from the vacuoles to punctate intermediates in nodules. Our evidence shows that MtENOD8 has evolved redundant targeting sequences for symbiosome targeting and that intracellular localization of ectopically expressed MtENOD8-SP-GFP is useful as a marker for monitoring the extent of development in mutant nodules.
    Keywords: Protein Sorting Signals ; Medicago Truncatula -- Chemistry ; Plant Proteins -- Chemistry ; Vacuoles -- Chemistry
    ISSN: 00320889
    E-ISSN: 1532-2548
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  • 3
    Language: English
    In: PLoS ONE, 2012, Vol.7(5), p.e36298
    Description: Lactobacillus- dominated vaginal microbiotas are associated with reproductive health and STI resistance in women, whereas altered microbiotas are associated with bacterial vaginosis (BV), STI risk and poor reproductive outcomes. Putative vaginal taxa have been observed in male first-catch urine, urethral swab and coronal sulcus (CS) specimens but the significance of these observations is unclear. We used 16 S rRNA sequencing to characterize the microbiota of the CS and urine collected from 18 adolescent men over three consecutive months. CS microbiotas of most participants were more stable than their urine microbiotas and the composition of CS microbiotas were strongly influenced by circumcision. BV-associated taxa, including Atopobium , Megasphaera , Mobiluncus , Prevotella and Gemella , were detected in CS specimens from sexually experienced and inexperienced participants. In contrast, urine primarily contained taxa that were not abundant in CS specimens. Lactobacilllus and Streptococcus were major urine taxa but their abundance was inversely correlated. In contrast, Sneathia , Mycoplasma and Ureaplasma were only found in urine from sexually active participants. Thus, the CS and urine support stable and distinct bacterial communities. Finally, our results suggest that the penis and the urethra can be colonized by a variety of BV-associated taxa and that some of these colonizations result from partnered sexual activity.
    Keywords: Research Article ; Biology ; Medicine ; Public Health And Epidemiology ; Infectious Diseases ; Microbiology ; Urology
    E-ISSN: 1932-6203
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  • 4
    Language: English
    In: Metagenomics, Egypt: Ashdin Publishing
    Description: This article uses full-length 16S rRNA gene alignments from the SILVA database to simulate the PCR products of the combined variable regions.
    Keywords: Microbiome ; Taxonomic Classification ; Bioinformatics
    ISSN: 20905181
    E-ISSN: 2090519X
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  • 5
    Conference Proceeding
    Conference Proceeding
    Language: English
    In: Proceedings of the 12th ACM SIGMETRICS/PERFORMANCE joint international conference on measurement and modeling of computer systems, 11 June 2012, pp.379-380
    Description: Regular expression matching as the core packet inspection engine of network systems has long been striving to be both fast in matching speed (like DFA) and scalable in storage space (like NFA). Recently, ternary content addressable memory (TCAM) has been investigated as a promising way out, by implementing DFA using TCAM for regular express matching. In this paper, we present the first method for implementing NFA using TCAM. Through proper TCAM encoding, our method matches each input byte with one single TCAM lookup --- operating at precisely the same speed as DFA, while using a number of TCAM entries that can be close to NFA size. These properties make our method an important step along a new path --- TCAM-based NFA implementation --- towards the long-standing goal of fast and scalable regular expression matching.
    Keywords: Nfa ; Tcam ; Regular Expression Matching ; Engineering
    ISBN: 9781450310970
    ISBN: 1450310974
    ISSN: 01635999
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  • 6
    Language: English
    In: BMC bioinformatics, 02 August 2012, Vol.13, pp.190
    Description: Web-based synteny visualization tools are important for sharing data and revealing patterns of complicated genome conservation and rearrangements. Such tools should allow biologists to upload genomic data for their own analysis. This requirement is critical because individual biologists are generating large amounts of genomic sequences that quickly overwhelm any centralized web resources to collect and display all those data. Recently, we published a web-based synteny viewer, GSV, which was designed to satisfy the above requirement. However, GSV can only compare two genomes at a given time. Extending the functionality of GSV to visualize multiple genomes is important to meet the increasing demand of the research community. We have developed a multi-Genome Synteny Viewer (mGSV). Similar to GSV, mGSV is a web-based tool that allows users to upload their own genomic data files for visualization. Multiple genomes can be presented in a single integrated view with an enhanced user interface. Users can navigate through all the selected genomes in either pairwise or multiple viewing mode to examine conserved genomic regions as well as the accompanying genome annotations. Besides serving users who manually interact with the web server, mGSV also provides Web Services for machine-to-machine communication to accept data sent by other remote resources. The entire mGSV package can also be downloaded for easy local installation. mGSV significantly enhances the original functionalities of GSV. A web server hosting mGSV is provided at http://cas-bioinfo.cas.unt.edu/mgsv.
    Keywords: Internet ; Software ; Synteny ; Genomics -- Methods
    E-ISSN: 1471-2105
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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  • 7
    Language: English
    In: BMC Bioinformatics, 01 August 2012, Vol.13(1), p.190
    Description: Abstract Background Web-based synteny visualization tools are important for sharing data and revealing patterns of complicated genome conservation and rearrangements. Such tools should allow biologists to upload genomic data for their own analysis. This requirement is critical because individual biologists are generating large amounts of genomic sequences that quickly overwhelm any centralized web resources to collect and display all those data. Recently, we published a web-based synteny viewer, GSV, which was designed to satisfy the above requirement. However, GSV can only compare two genomes at a given time. Extending the functionality of GSV to visualize multiple genomes is important to meet the increasing demand of the research community. Results We have developed a multi-Genome Synteny Viewer (mGSV). Similar to GSV, mGSV is a web-based tool that allows users to upload their own genomic data files for visualization. Multiple genomes can be presented in a single integrated view with an enhanced user interface. Users can navigate through all the selected genomes in either pairwise or multiple viewing mode to examine conserved genomic regions as well as the accompanying genome annotations. Besides serving users who manually interact with the web server, mGSV also provides Web Services for machine-to-machine communication to accept data sent by other remote resources. The entire mGSV package can also be downloaded for easy local installation. Conclusions mGSV significantly enhances the original functionalities of GSV. A web server hosting mGSV is provided at http://cas-bioinfo.cas.unt.edu/mgsv.
    Keywords: Biology
    ISSN: 1471-2105
    E-ISSN: 1471-2105
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  • 8
    Language: English
    In: BMC Bioinformatics, London: BioMed Central
    Description: This article discusses a web-based multi-genome synteny viewer for customized data.
    Keywords: Genomes ; Centralized Web Resources ; Multi-Genome Synteny Viewer ; Mgsv
    Source: University of North Texas
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  • 9
    Language: English
    In: Plant Physiology, Rockville: American Society of Plant Biologists
    Description: Article presenting evidence from GFP fusion experiments that the MtENOD8 protein contains at least three symbiosome targeting domains, including its N-terminal signal peptide (SP).
    Keywords: Plant Cells ; Proteins ; Symbiotic Nitrogen Fixation ; Nodules
    Source: University of North Texas
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  • 10
    Description: Directory-based protocols have been the de facto solution for maintaining cache coherence in shared-memory parallel systems comprising multi/many cores, where each store instruction is eagerly made globally visible by invalidating the private cache (PC) backups of other cores. Consequently, the directory not only consumes large chip area, but also incurs considerable energy consumption and performance degradation, due to the large number of Invalidation/Ack messages transferred in the interconnection network and resulting network congestion. In this paper, we reveal the interesting fact that the directory is actually an unnecessary luxury for practical parallel systems. Because of widely deployed software/hardware techniques involving instruction reordering, most (if not all) parallel systems work under the weak consistency model, where a remote store instruction is allowed to be invisible to a core before the next synchronization of the core, instead of being made visible eagerly by invalidating PC backups of other cores. Based on this key observation, we propose a lightweight novel scheme called {\em DLS (DirectoryLess Shared last-level cache)}, which completely removes the directory and Invalidation/Ack messages, and efficiently maintains cache coherence using a novel {\em self-suspicion + speculative execution} mechanism. Experimental results over SPLASH-2 benchmarks show that on a 16-core processor, DLS not only completely removes the chip area cost of the directory, but also improves processor performance by 11.08%, reduces overall network traffic by 28.83%, and reduces energy consumption of the network by 15.65% on average (compared with traditional MESI protocol with full directory). Moreover, DLS does not involve any modification to programming languages and compilers, and hence is seamlessly compatible with legacy codes. Comment: This paper has been withdrawn by the authors due to a major revision
    Keywords: Computer Science - Hardware Architecture
    Source: Cornell University
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