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Repetitive-element PCR Genomic Fingerprinting of The Genus Streptomyces
链霉菌的rep-PCR基因指纹分析

ZHANG Jian,Li LIU Zhi-Heng,
张建丽
,刘志恒

微生物学报 , 2004,
Abstract: Repetitive element PCR (rep PCR) genomic fingerprinting with the BOXA1R primer was investigated as a molecular typing tool for strains of Streptomyces. The results indicated that rep PCR DNA fingerprints of Streptomyces strains were relatively unique, simple, stable, and reproducible. To some extent, rep PCR generated genomic fingerprint analyses yield results that are in agreement with 16S rDNA sequences study. This method appears to reflect the genotypic, phylogenetic and taxonomic relationships of the genus Streptomyces in the species strain level. Therefore, it can be used as a rapid and efficient means of determining taxonomic diversity and phylogenetic structure, especially of large collections of strains.
Molecular and phylogenetic characterization of two species of the genus Nostoc (Cyanobacteria) based on the cpcB-IGS-cpcA locus of the phycocyanin operon  [PDF]
IVANKA TENEVA,PLAMEN STOYANOV,RUMEN MLADENOV,BALIK DZHAMBAZOV
Journal of BioScience and Biotechnology , 2012,
Abstract: Traditionally, the taxonomy of the genus Nostoc is based on morphological and physiological characters. The extreme morphological variability of the Nostoc species, due to their life cycle and environmental conditions, hampers the correct identification of the individual species. This is also one of the reasons for the disputed taxonomic positions and relationships between the genera Anabaena–Aphanizomenon as well as between Anabaena–Nostoc. Therefore, it is necessary to use additional markers for development of a polyphasic classification system of order Nostocales. In light of this, we here present the first molecular and phy-logenetic characterization of two species of the genus Nostoc (Nostoc linckia and Nostoc punctiforme) based on the cpcB-IGS-cpcA locus of the phycocyanin oper-on. The phylogenetic position of these two species within order Nostocales as well as within division Cyanobacteria has been determined. Our results indicate that genus Nostoc is heterogeneous. Analysis of the IGS region between cpcB and cpcA showed that Nostoc and Anabaena are distinct genera. Reported molecular and phylogenetic data will be useful to solve other problematic points in the tax-onomy of genera Aphanizomenon, Anabaena and Nostoc.
DNA Fingerprinting Based on Repetitive Sequences of Iranian Indigenous Lactobacilli Species by (GTG)5- REP-PCR  [cached]
Farzaneh Tafvizi,Maryam Tajabadi Ebrahimi
Journal of Fasa University of Medical Sciences , 2012,
Abstract: Background and Objective: The use of lactobacilli as probiotics requires the application of accurate and reliable methods for the detection and identification of bacteria at the strain level. Repetitive sequence-based polymerase chain reaction (rep-PCR), a DNA fingerprinting technique, has been successfully used as a powerful molecular typing method to determine taxonomic and phylogenetic relationships among bacteria. The aim of this study was to evaluate and detect the genetic diversity of lactobacilli species isolated from different sources in Iran. Material and Methods: Twenty strains were isolated from Iranian traditional yoghurt, cheese, and Tarkhineh. PCR-mediated amplification was carried out by degenerate primers. Sequencing was performed after purification of the PCR product. The rep-PCR fingerprinting by (GTG) 5 oligonucleotide primers was conducted for the discrimination and genotypic grouping of isolates. Results: Isolates were deposited as novel stains of lactobacillus casei, brevis, plantarum, and Entrococcus facium in GenBank. Clustering methods were performed on molecular data by NTSYS software, which was also supported by PCO ordination plot. The rep-PCR profiles showed that the 20 isolates produced different banding patterns. In UPGMA dendrogram, three main clusters were formed. Conclusion: According to our findings, rep-PCR appeared to be a very practical method and highly sensitive in the discrimination of the lactobacillus species. The results of sequencing corresponded to the clustering in dendrogram.
Isolation and phylogenetic analysis of one actinomycete strain YIM 90022 exhibiting anticancer activity
具抗肿瘤活性放线菌菌株YIM 90022的分离和系统发育分析

CHEN Yi-guang,LI Wen-jun,CUI Xiao-long,JIANG Cheng-lin,XU Li-hua,
陈义光
,李文均,崔晓龙,姜成林,徐丽华

微生物学报 , 2006,
Abstract: One facultative alkaliphilic actinomycete strain YIM 90022 was isolated from hypersaline alkaline soil in Qinghai province, China. An almost-complete 16S rRNA gene sequence (1500 bp) for strain YIM 90022 was obtained. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 90022 was closely related to four members of the genus Nocardiopsis with 16S rRNA gene sequence similarity values of 98.8% (N. exhalans DSM 44407T), 98.5% (N. prasina DSM 43845T), 98.4% (N. metallicus DSM 44598T) and 97.8% (N. listeri DSM 40297T), but represented a distinct phylogenetic lineage. Repetitive element sequence-based PCR (rep-PCR) genomic fingerprinting was evaluated on strain YIM 90022 and its closest relatives to investigate their genetic relatedness. The analysis of the rep-PCR genomic fingerprints showed that strain YIM 90022 was distinguishable from its closest relatives. The polyphasic taxonomic data presented in this study, including its morphology, physiological and biochemical characteristics, chemotaxonomy, 16S rRNA gene sequence-based phylogenetic analysis and rep-PCR genomic fingerprinting, supported the view that strain YIM 90022 represented a potential new species of the genus Nocardiopsis. The fermentation broth of strain YIM 90022 strongly inhibited growth of cell series of gastric cancer, lung cancer, mammary cancer, melanoma cancer, renal cancer and uterus cancer. Strain YIM 90022 grew well on most tested media, producing exuberant vegetative hyphae and aerial hyphae. The vegetative hyphae are long and fragmented. Light yellow to deep brown diffusible pigments were produced on ISP 2, ISP 3 and ISP 6. Growth of the strain occurred in the pH range 6.0-12.0, with optimal pH8.5. The NaCl tolerate range was 0-15% (W/V). Cell walls contain meso-diaminopimelic acid and have no diagnostic sugars. Polar lipids are phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmethylethanolamine. Major menaquinones are MK-10 (H4, H6). The DNA G + C content is 71.5 mol %.
Anabaena bergii Ostenf. [f. minor (Kisselev) Kossinsk.] (Cyanoprokaryota): The first record in Serbia, its taxonomic status, and that of the genus Anabaena Bory ex Born. & Flah.
Cvijan M.,Krizmani? Jelena
Archives of Biological Sciences , 2009, DOI: 10.2298/abs0904883c
Abstract: Within the framework of a detailed survey of the algal community in salt marshes of the Vojvodina Province (Northern Serbia), we rather unexpectedly found the blue-green alga Anabaena bergii Ostenf. [forma minor (Kisselev) Kossinsk.] in water samples from Slatina Pond near Opovo. Our finding represents its first record in Serbia. The present paper gives general characteristics of this alga and of the habitat in which it was found. Based on analysis of a large number of works dealing with characteristics and the taxonomic status of the genus Anabaena, the species A. bergii, and its forma minor, it is concluded that there are numerous problems in taxonomy of the given genus, with no consensus among researchers. In light of the available data, the authors retain the name of the species A. bergii, but accept forma minor with some reserve.
Identification and phylogenetic analysis of filamentous Cyanobacteria using random amplified polymorphic DNA (RAPD) fingerprinting
GM Perumal, V Ganesan, N Anand
African Journal of Biotechnology , 2009,
Abstract: RAPD techniques were used for the detection of genetic heterogeneticity among the axenic culture of fresh water cyanobacterial isolates. The electrophoretic patterns for 12 cyanobacterial strains belonging to 2 genera (8 Oscillatoria strains and 4 Lyngbya strains) were used for molecular analysis using the RAPD technique. A total of 12 cyanobacterial isolates were selected and mass cultured in BG11 medium. Genomic DNA was extracted from fresh water cyanobacterial isolates and was amplified using primers D7, M13, OPC11, OPC12, OPC13, OPC14 and OPC15 and distinct PCR fingerprint were generated. Unique banding patterns were observed from all tested cyanobacterial species and their molecular weights of each band were used to calculate their genetic distance among them. Random amplification of polymorphic DNA (RAPD) was carried out for the phylogenetic characterization of these strains. RAPD fingerprinting results clearly showed the genetic variation among the cyanobacterial isolates.
Phylogenetic relationships of the genus Hoplia Illiger (Scarabaeidae: Hopliinae)
Carrillo-Ruiz, H;Morón, MA;
Neotropical Entomology , 2011, DOI: 10.1590/S1519-566X2011000200010
Abstract: results of phylogenetic analysis based on 34 morphological characters of 24 species of 11 genera of hopliinae from europe, japan, south africa, madagascar, north and central america, indicates that the genus hoplia is a monophyletic group with species distributed in europe, japan and america. based in this analysis the asiatic genus ectinohoplia is the closest relative of the genus hoplia, and the south american genus barybas (melolonthinae: macrodactylini) is the sister group of hopliinae.
Phylogenetic relationships in the genus Aethomys (Rodentia: Muridae)  [cached]
C.T. Chimimba
African Zoology , 2011,
Abstract: Phylogenetic relationships in the genusAethomys were examined based on qualitative cranial data for all currently recognized species. A cladistic analysis suggested the presence of three clades: 1) A. bocagei, A. thomasi, A. silindensis, A. kaiseri, and A. nyikae; 2) A. chrysophilus, A. ineptus, and A. hindei; 3) A. granti, A. namaquensis, and A. stannarius. These phylogenetic groupings are largely inconsistent with previously postulated supraspecific relationships for the genus. Nonetheless, relationships within each clade broadly correspond with some previously suggested evolutionary hypotheses among some members of the genus, the only notable
Arbitrarily primed PCR fingerprinting of RNA and DNA in Entamoeba histolytica
VALLE, Paulo Renato;SOUZA, Maria Betania G.;PIRES, Edna M.;SILVA, Edward F.;GOMES, Maria A.;
Revista do Instituto de Medicina Tropical de S?o Paulo , 2000, DOI: 10.1590/S0036-46652000000500003
Abstract: differences were detected in the gene expression of strains of e. histolytica using rna (rap-pcr) and dna fingerprinting (rapd). analysis of the electrophoretic profiles of the gels revealed some polymorphic markers that could be used in the individual characterization of the strains. the 260 bands generated by using five different primers for rap-pcr, as well as rapd, were employed in the construction of dendograms. the dendogram obtained based on the rapd products permitted the distinction of symptomatic and asymptomatic isolates, as well the correlation between the polymorphism exhibited and the virulence of the strains. the dendogram obtained for the rap-pcr products did not show a correlation with the virulence of the strains but revealed a high degree of intraspecific transcriptional variability that could be related to other biological features, whether or not these are involved in the pathogenesis of amebiasis.
Arbitrarily primed PCR fingerprinting of RNA and DNA in Entamoeba histolytica  [cached]
VALLE Paulo Renato,SOUZA Maria Betania G.,PIRES Edna M.,SILVA Edward F.
Revista do Instituto de Medicina Tropical de S?o Paulo , 2000,
Abstract: Differences were detected in the gene expression of strains of E. histolytica using RNA (RAP-PCR) and DNA fingerprinting (RAPD). Analysis of the electrophoretic profiles of the gels revealed some polymorphic markers that could be used in the individual characterization of the strains. The 260 bands generated by using five different primers for RAP-PCR, as well as RAPD, were employed in the construction of dendograms. The dendogram obtained based on the RAPD products permitted the distinction of symptomatic and asymptomatic isolates, as well the correlation between the polymorphism exhibited and the virulence of the strains. The dendogram obtained for the RAP-PCR products did not show a correlation with the virulence of the strains but revealed a high degree of intraspecific transcriptional variability that could be related to other biological features, whether or not these are involved in the pathogenesis of amebiasis.
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