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  • 2005  (18)
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  • 2005  (18)
  • 1
    Language: English
    In: Genome biology, 2005, Vol.6(9), pp.R73
    Description: Whole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp. MED4 has the most compact of these genomes and it is enigmatic how the few identified regulatory proteins efficiently sustain the lifestyle of an ecologically successful marine microorganism. Small non-coding RNAs (ncRNAs) control a plethora of processes in eukaryotes as well as in bacteria; however, systematic searches for ncRNAs are still lacking for most eubacterial phyla outside the enterobacteria. Based on a computational prediction we show the presence of several ncRNAs (cyanobacterial functional RNA or Yfr) in several different cyanobacteria of the Prochlorococcus-Synechococcus lineage. Some ncRNA genes are present only in two or three of the four strains investigated, whereas the RNAs Yfr2 through Yfr5 are structurally highly related and are encoded by a rapidly evolving gene family as their genes exist in different copy numbers and at different sites in the four investigated genomes. One ncRNA, Yfr7, is present in at least seven other cyanobacteria. In addition, control elements for several ribosomal operons were predicted as well as riboswitches for thiamine pyrophosphate and cobalamin. This is the first genome-wide and systematic screen for ncRNAs in cyanobacteria. Several ncRNAs were both computationally predicted and their presence was biochemically verified. These RNAs may have regulatory functions and each shows a distinct phylogenetic distribution. Our approach can be applied to any group of microorganisms for which more than one total genome sequence is available for comparative analysis.
    Keywords: Cyanobacteria -- Genetics ; Genome, Bacterial -- Genetics ; RNA, Untranslated -- Genetics
    ISSN: 14656906
    E-ISSN: 1474-760X
    E-ISSN: 14656914
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  • 2
    Language: English
    In: Biological chemistry, December 2005, Vol.386(12), pp.1219-38
    Description: Small non-coding RNAs (sRNAs) have attracted considerable attention as an emerging class of gene expression regulators. In bacteria, a few regulatory RNA molecules have long been known, but the extent of their role in the cell was not fully appreciated until the recent discovery of hundreds of potential sRNA genes in the bacterium Escherichia coli. Orthologs of these E. coli sRNA genes, as well as unrelated sRNAs, were also found in other bacteria. Here we review the disparate experimental approaches used over the years to identify sRNA molecules and their genes in prokaryotes. These include genome-wide searches based on the biocomputational prediction of non-coding RNA genes, global detection of non-coding transcripts using microarrays, and shotgun cloning of small RNAs (RNomics). Other sRNAs were found by either co-purification with RNA-binding proteins, such as Hfq or CsrA/RsmA, or classical cloning of abundant small RNAs after size fractionation in polyacrylamide gels. In addition, bacterial genetics offers powerful tools that aid in the search for sRNAs that may play a critical role in the regulatory circuit of interest, for example, the response to stress or the adaptation to a change in nutrient availability. Many of the techniques discussed here have also been successfully applied to the discovery of eukaryotic and archaeal sRNAs.
    Keywords: Gene Expression Regulation, Bacterial ; RNA, Bacterial ; RNA, Untranslated ; RNA-Binding Proteins
    ISSN: 1431-6730
    E-ISSN: 14374315
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  • 3
    Language: English
    In: Theoretical Computer Science, 2005, Vol.349(3), pp.382-391
    Description: Kemeny proposed a voting scheme which is distinguished by the fact that it is the unique voting scheme that is neutral, consistent, and Condorcet. Bartholdi, Tovey, and Trick showed that determining the winner in Kemeny's system is NP-hard. We provide a stronger lower bound and an upper bound matching the lower bound, namely, we show that determining the winner in Kemeny's system is complete for , the class of sets solvable via parallel access to NP.
    Keywords: Computational Complexity ; Election Systems ; Parallel Access to Np ; Computer Science ; Mathematics
    ISSN: 0304-3975
    E-ISSN: 1879-2294
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  • 4
    Language: English
    In: Genes & Development, 2005, Vol.19(19), pp.2355-2366
    Description: This paper shows that the small RNA MicA (previously SraD) is an antisense regulator of ompA in Escherichia coli. MicA accumulates upon entry into stationary phase and down-regulates the level of ompA mRNA. Regulation of ompA (outer membrane protein A), previously attributed to Hfq/mRNA binding, is lost upon deletion of the micA gene, whereas overexpression of MicA inhibits the synthesis of OmpA. In vitro, MicA binds to the ompA mRNA leader. Enzymatic and chemical probing was used to map the structures of MicA, the ompA mRNA leader, and the complex formed upon binding. MicA binding generates a footprint across the ompA Shine-Dalgarno sequence, consistent with a 12 + 4 base-pair interaction, which is additionally supported by the effect of mutations in vivo and by bioinformatics analysis of enterobacterial micA/ompA homolog sequences. MicA is conserved in many enterobacteria, as is its ompA target site. In vitro toeprinting confirmed that binding of MicA specifically interferes with ribosome binding. We propose that MicA, when present at high levels, blocks ribosome binding at the ompA translation start site, which—in line with previous work—secondarily facilitates RNase E cleavage and subsequent mRNA decay. MicA requires the presence of the Hfq protein, although the mechanistic basis for this remains unclear.
    Keywords: Medical And Health Sciences ; Medicin Och Hälsovetenskap ; Antisense Rna ; Hfq ; Ompa ; Regulatory Rna ; Translational Control
    ISSN: 0890-9369
    E-ISSN: 15495477
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  • 5
    Language: English
    In: Handbook of RNA biochemistry, pp.595-613
    Keywords: Natural Sciences ; Naturvetenskap
    ISBN: 3527308261
    Source: SwePub (National Library of Sweden)
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  • 6
    Language: English
    In: Handbook of RNA Biochemistry, pp.614-642
    Keywords: Natural Sciences ; Naturvetenskap
    ISBN: 978-3-527-30826-2
    Source: SwePub (National Library of Sweden)
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  • 7
    Language: English
    In: urn:ISSN:1474-7596© 2005 Axmann et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Genome Biology, v.6 (2005), 2005, Vol.6(2005)
    Description: BackgroundWhole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp. MED4 has the most compact of these genomes and it is enigmatic how the few identified regulatory proteins efficiently sustain the lifestyle of an ecologically successful marine microorganism. Small non-coding RNAs (ncRNAs) control a plethora of processes in eukaryotes as well as in bacteria; however, systematic searches for ncRNAs are still lacking for most eubacterial phyla outside the enterobacteria.ResultsBased on a computational prediction we show the presence of several ncRNAs (cyanobacterial functional RNA or Yfr) in several different cyanobacteria of the Prochlorococcus-Synechococcus lineage. Some ncRNA genes are present only in two or three of the four strains investigated, whereas the RNAs Yfr2 through Yfr5 are structurally highly related and are encoded by a rapidly evolving gene family as their genes exist in different copy numbers and at different sites in the four investigated genomes. One ncRNA, Yfr7, is present in at least seven other cyanobacteria. In addition, control elements for several ribosomal operons were predicted as well as riboswitches for thiamine pyrophosphate and cobalamin.ConclusionThis is the first genome-wide and systematic screen for ncRNAs in cyanobacteria. Several ncRNAs were both computationally predicted and their presence was biochemically verified. These RNAs may have regulatory functions and each shows a distinct phylogenetic distribution. Our approach can be applied to any group of microorganisms for which more than one total genome sequence is available for comparative analysis.
    Source: AGRIS (Food and Agriculture Organization of the United Nations)
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  • 8
    Language: English
    In: Permafrost and Periglacial Processes, July 2005, Vol.16(3), pp.277-290
    Description: Minkowski densities and density functions are measures for quantifying arbitrary binary patterns. They are employed here to describe permafrost patterns obtained from aerial photographs. We demonstrate that images taken at two neighbouring sites shown distinctly different patterns and quantify the difference. It is found that one of the sites exhibits an essentially single‐scale structure while the other one has a multiscale organization. Minkowski densities and density functions are thus proposed as sensitive and objective measures to quantify the change of permafrost patterns in space or in time. Copyright © 2005 John Wiley & Sons, Ltd.
    Keywords: Permafrost ; Patterned Ground ; Density Functions
    ISSN: 1045-6740
    E-ISSN: 1099-1530
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  • 9
    In: American Journal of Gastroenterology, 2005, Vol.100(1), pp.27-37
    Description: OBJECTIVES: At present, surveillance of premalignant small bowel polyps in hereditary polyposis syndromes has a number of limitations. Capsule endoscopy (CE) is a promising new method to endoscopically assess the entire length of the small bowel. METHODS: We prospectively examined 40 patients with hereditary polyposis syndromes (29 familial adenomatous polyposis (FAP), 11 Peutz-Jeghers syndrome (PJS)). Results were compared with push-enteroscopy (PE) results in FAP and with esophagogastroduodenoscopy, PE, (MR)-enteroclysis, and surgical specimen in PJS patients. RESULTS: A total of 76% of the patients with FAP with duodenal adenomas (n = 21) had additional adenomas in the proximal jejunum that could be detected by CE and PE. Moreover, 24% of these FAP patients had further polyps in the distal jejunum or ileum that could only be detected by CE. In contrast, in FAP patients without duodenal polyps (n = 8), jejunal or ileal polyps occurred rarely (12%). CE detected polyps in 10 of 11 patients with PJS, a rate superior to all other reference procedures employed. Importantly, the findings of CE had immediate impact on further clinical management in all PJS patients. CONCLUSIONS: Our results suggest that CE may be of clinical value in selected patients with FAP, whereas in PJS, CE could be used as first line surveillance procedure.
    Keywords: Capsules ; Endoscopy, Gastrointestinal ; Adenomatous Polyposis Coli -- Complications ; Intestinal Polyps -- Pathology ; Peutz-Jeghers Syndrome -- Complications ; Video Recording -- Instrumentation;
    ISSN: 0002-9270
    E-ISSN: 15720241
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  • 10
    Language: English
    In: Biomaterials, 2005, Vol.26(29), pp.5879-5889
    Description: Bone substitute materials can induce bone formation in combination with mesenchymal stem cells (MSC). The aim of the current study was to examine ectopic in vivo bone formation with and without MSC on a new resorbable ceramic, called calcium deficient hydroxyapatite (CDHA). Ceramic blocks characterized by a large surface (48 m /g) were compared with -tricalcium phosphate ( -TCP), hydroxyapatite (HA) ceramics (both ca. 0.5 m /g surface) and demineralized bone matrix (DBM). Before implantation in the back of SCID mice carriers were freshly loaded with 2×10 expanded human MSC or loaded with cells and kept under osteogenic conditions for two weeks in vitro. Culture conditions were kept free of xenogenic supplements. Deposits of osteoid at the margins of ceramic pores occurred independent of osteogenic pre-induction, contained human cells, and appeared in MSC/CDHA composites compared to MSC/ -TCP composites. ALP activity was significantly higher in samples with MSC versus empty controls ( ). Furthermore, ALP was significantly ( ) higher for all ceramics when compared to the DBM matrix. Compared to previous studies, overall bone formation appeared to be reduced possibly due to the strict human protocol. Ectopic bone formation in the novel biomaterial CDHA varied considerably with the cell pool and was at least equal to -TCP blocks.
    Keywords: Bone Healing ; Biocompatibility ; Bone ; Bone Regeneration ; Bone Tissue Engineering ; Calcium Phosphate ; Ceramic Structure ; Composite ; Hydroxyapatite ; In Situ Hybridization ; In Vivo Test ; Mesenchymal Stem Cell ; Osteoblast ; Osteoconduction ; Osteogenesis ; Platelet ; Progenitor Cell ; Porosity ; Surface Roughness ; Medicine ; Engineering
    ISSN: 0142-9612
    E-ISSN: 1878-5905
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