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41.
42.
43.
《Systematic and applied microbiology》2020,43(5):126123
The aim of the study was to characterise the diversity and niche-specific colonization of Vibrio spp. in a marine aquaria system by a cultivation-dependent approach. A total of 53 Vibrio spp. isolates were cultured from different ecological niches in a marine aquarium including microplastic (MP) and sandy sediment particles (12 weeks after added sterile to the system), detritus, and the surrounding aquarium water. Based on the 16S rRNA gene sequence phylogeny and multilocus sequence analysis (MLSA) the isolates were assigned to seven different phylotypes. Six phylotypes were identified by high probability to the species level. The highest phylotype diversity was cultured from detritus and water (six out of seven phylotypes), while only two phylotypes were cultured from MP and sediment particles. Genomic fingerprinting indicated an even higher genetic diversity of Vibrio spp. at the strain (genotype) level. Again, the highest diversity of genotypes was recovered from detritus and water while only few partially particle-type specific genotypes were cultured from MP and sediment particles. Phylotype V-2 formed an independent branch in the MLSA tree and could not be assigned to a described Vibrio species. Isolates of this phylotype showed highest 16S rRNA gene sequence similarity to type strains of Vibrio japonicus (98.5%) and Vibrio caribbeanicus (98.4%). A representative isolate, strain THAF100T, was characterised by a polyphasic taxonomic approach and Vibrio aquimaris sp. nov., with strain THAF100T (=DSM 109633T = LMG 31434T = CIP 111709T) as type strain, is proposed as novel species. 相似文献
44.
45.
Thirty-four strains belonging to various species of the genus Thermus (T. aquaticus, "T. thermophilus,"
"T. brockianus,"
T. scotoductus, and genomic species 2) isolated from hot springs of different geographical areas were examined for plasmid content and restriction
fragment length polymorphism (RFLP) of plasmid DNAs. The four strains of the numerical taxonomy cluster E of genomic species
2 did not harbor plasmid DNA. Overall examination of the HindIII-RFLP profiling of plasmid DNA showed considerable variability between and within genomic species, with the exception
of presumed clonal isolates. In spite of this heterogeneity, HindIII plasmid digests within a numerical taxonomic cluster gave a subset of restriction fragments of similar or identical length.
Strains belonging to genomic species 2 or unclassified isolates from S. Pedro do Sul that harbored plasmid DNA (7 of the 14
strains studied) exhibited strong DNA homology between plasmid regions. No homologous sequences to these plasmid regions were
found in chromosomal DNA from strains isolated from S. Pedro do Sul in which no plasmids were detected. The strains belonging
to T. scotoductus formed two plasmid DNA homology groups, as estimated by probing with a plasmid fragment that coincided with the two numerical
taxonomy clusters proposed previously. Among the other species, homology of plasmid regions was also found between some strains.
Strong homology was also found between plasmid regions from some strains of different taxonomic groups, isolated from the
same and from different sources, suggesting that these sequences are highly conserved in plasmids present in Thermus. For plasmid-containing strains, results of plasmid RFLP profiling/DNA homology appear promising for the typing of Thermus at the level of biotypes or of individual strains, namely, for monitoring the diversity and frequency of isolates from a
particular hot spring.
Received: 24 October 1994 / Accepted: 6 March 1995 相似文献
46.
Expression levels of the human DNA repair protein metnase influence lentiviral genomic integration 总被引:2,自引:0,他引:2
Williamson EA Farrington J Martinez L Ness S O'Rourke J Lee SH Nickoloff J Hromas R 《Biochimie》2008,90(9):1422-1426
We recently identified a Transposase domain protein called Metnase, which assists in repairing DNA double-strand breaks (DSB) via non-homologous end-joining (NHEJ), and is important for foreign DNA integration into a host cell genome. Since integration is essential for productive lentiviral infection we examined whether Metnase expression levels could have an influence on lentiviral genomic integration. Using cells stably transduced to either over- or under-express Metnase we determined that the expression level of Metnase did indeed correlate with live lentiviral integration. Changes in Metnase levels were accompanied by changes in the number of copies of integrated lentiviral cDNA. While Metnase levels affected lentiviral integration, it had no effect on the amount of either total cellular viral RNA, cDNA or 2-LTR circles. Therefore, Metnase enhances the integration of lentivirus DNA into the host cell genome. 相似文献
47.
Summary Several genes of the achaete-scute complex (ASC) of Drosophila melanogaster encode a 60 amino acids long conserved domain which shares a significant homology with a region of the vertebrate myc proteins. Based on these results, the existence of a family of Drosophila genes that would share both this conserved domain and the neurogenic function of the AS-C has been postulated. To test this proposal, we have searched a D. melanogaster genomic library with a probe that encodes the conserved domain. Only under very low stringency hybridization conditions, clones not belonging to the AS-C cross-hybridized with the probe. Those that gave the strongest signals were characterized. Sequencing of the cross-hybridizing regions showed that they had no significant homology with the conserved domain, the sequence similarity extending at the most for 37 nucleotides. Although our results do not conclusively disprove the existence of a family of AS-C-like genes, they indicate that the conservation of the domain would be lower than that found for shared motifs in other families of Drosophila developmental genes. 相似文献
48.
Christopher Kasbek Feng Wang Carolyn M. Price 《The Journal of biological chemistry》2013,288(42):30139-30150
TEN1 is a component of the mammalian CTC1-STN1-TEN1 complex. CTC1 and/or STN1 functions in telomere duplex replication, C-strand fill-in, and genome-wide restart of replication following fork stalling. Here we examine the role of human TEN1 and ask whether it also functions as a specialized replication factor. TEN1 depletion causes an increase in multitelomere fluorescent in situ hybridization (FISH) signals similar to that observed after CTC1 or STN1 depletion. However, TEN1 depletion also results in increased telomere loss. This loss is not accompanied by increased telomere deprotection, recombination, or T-circle release. Thus, it appears that both the multiple telomere signals and telomere loss stem from problems in telomere duplex replication. TEN1 depletion can also affect telomere length, but whether telomeres lengthen or shorten is cell line-dependent. Like CTC1 and STN1, TEN1 is needed for G-overhang processing. Depletion of TEN1 does not effect overhang elongation in mid-S phase, but it delays overhang shortening in late S/G2. These results indicate a role for TEN1 in C-strand fill-in but do not support a direct role in telomerase regulation. Finally, TEN1 depletion causes a decrease in genome-wide replication restart following fork stalling similar to that observed after STN1 depletion. However, anaphase bridge formation is more severe than with CTC1 or STN1 depletion. Our findings indicate that TEN1 likely functions in conjunction with CTC1 and STN1 at the telomere and elsewhere in the genome. They also raise the possibility that TEN1 has additional roles and indicate that TEN1/CTC1-STN1-TEN1 helps solve a wide range of challenges to the replication machinery. 相似文献
49.
A Genomic Islands (GI) is a chunk of DNA sequence in a genome whose origin can be traced back to other organisms or viruses.
The detection of GIs plays an indispensable role in biomedical research, due to the fact that GIs are highly related to special
functionalities such as disease-causing GIs - pathogenicity islands. It is also very important to visualize genomic islands, as well as
the supporting features corresponding to the genomic islands in the genome. We have developed a program, Genomic Island
Visualization (GIV), which displays the locations of genomic islands in a genome, as well as the corresponding supportive feature
information for GIs. GIV was implemented in C++, and was compiled and executed on Linux/Unix operating systems.
Availability
GIV is freely available for non-commercial use at http://www5.esu.edu/cpsc/bioinfo/software/GIV 相似文献50.
Laurence Rohmer Michael A Jacobs Mitchell J Brittnacher Christine Fong Hillary S Hayden Didier Hocquet Eli J Weiss Matthew Radey Yves Germani Kaisar Ali Talukder Anthony J Hager John M Kemner Elizabeth H Sims-Day Susana Matamouros Kyle R Hager Samuel I Miller 《BMC genomics》2014,15(1)