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1.
Comparison of 16S rRNA gene sequences of genus <Emphasis Type="Italic">Methanobrevibacter</Emphasis>
Abhijit?S?Dighe Kamlesh?Jangid José?M?González Vyankatesh?J?Pidiyar Milind?S?Patole Dilip?R?Ranade Yogesh?S?Shouche
Background
The phylogeny of the genus Methanobrevibacter was established almost 25 years ago on the basis of the similarities of the 16S rRNA oligonucleotide catalogs. Since then, many 16S rRNA gene sequences of newly isolated strains or clones representing the genus Methanobrevibacter have been deposited. We tried to reorganize the 16S rRNA gene sequences of this genus and revise the taxonomic affiliation of the isolates and clones representing the genus Methanobrevibacter. 相似文献2.
Two repeated DNA sequences isolated from a partial genomic DNA library of Helianthus annuus, p HaS13 and p HaS211, were shown to represent portions of the int gene of a Ty3 /gypsy retroelement and of the RNase-Hgene of a Ty1 /copia retroelement, respectively. Southern blotting patterns obtained by hybridizing the two probes to BglII- or DraI-digested genomic DNA from different Helianthus species showed p HaS13 and p HaS211 were parts of dispersed repeats at least 8 and 7 kb in length, respectively, that were conserved in all species studied. Comparable hybridization patterns were obtained in all species with p HaS13. By contrast, the patterns obtained by hybridizing p HaS211 clearly differentiated annual species from perennials. The frequencies of p HaS13- and p HaS211-related sequences in different species were 4.3x10(4)-1.3x10(5) copies and 9.9x10(2)-8.1x10(3) copies per picogram of DNA, respectively. The frequency of p HaS13-related sequences varied widely within annual species, while no significant difference was observed among perennial species. Conversely, the frequency variation of p HaS211-related sequences was as large within annual species as within perennials. Sequences of both families were found to be dispersed along the length of all chromosomes in all species studied. However, Ty3 /gypsy-like sequences were localized preferentially at the centromeric regions, whereas Ty1/ copia-like sequences were less represented or absent around the centromeres and plentiful at the chromosome ends. These findings suggest that the two sequence families played a role in Helianthusgenome evolution and species divergence, evolved independently in the same genomic backgrounds and in annual or perennial species, and acquired different possible functions in the host genomes. 相似文献
3.
Nouioui I Ghodhbane-Gtari F Beauchemin NJ Tisa LS Gtari M 《Antonie van Leeuwenhoek》2011,100(4):579-587
To construct an evolutionary hypothesis for the genus Frankia, gyrB (encoding gyrase B), nifH (encoding nitrogenase reductase) and glnII (encoding glutamine synthetase II) gene sequences were considered for 38 strains. The overall clustering pattern among
Frankia strains based on the three analyzed sequences varied among themselves and with the previously established 16S rRNA gene phylogeny
and they did not reliably reflect clear evolution of the four discerned Frankia clusters (1, 2, 3 and 4). Based on concatenated gyrB, nifH and glnII, robust phylogenetic trees were observed with the three treeing methods (Maximum Likelihood, Parsimony and Neighbor-Joining)
and supported by strong bootstrap and posterior probability values (>75%) for overall branching. Cluster 4 (non-infective
and/or non-nitrogen-fixing Frankia) was positioned at a deeper branch followed by cluster 3 (Rhamnaceae and Elaeagnaceae infective Frankia), while cluster 2 represents uncultured Frankia microsymbionts of the Coriariaceae, Datiscaceae, Rosaceae and of Ceanothus sp. (Rhamnaceae); Cluster 1 (Betulaceae, Myricaceae and Casuarinaceae infective Frankia) appears to have diverged more recently. The present study demonstrates the utility of phylogenetic analyses based upon concatenated
gyrB, nifH and glnII sequences to help resolve previously unresolved or poorly resolved nodes and will aid in describing species among the genus
Frankia. 相似文献
4.
LV Dos Santos MV de Queiroz MF Santana MA Soares EG de Barros EF de Araújo T Langin 《World journal of microbiology & biotechnology》2012,28(3):1087-1095
A nonautonomous element of 624 bp, called RetroCl1 (Retroelement Colletotrichum lindemuthianum 1), was identified in the plant pathogenic fungus Colletotrichum lindemuthianum. RetroCl1 contains terminal direct repeats (223 bp) that are surrounded by CTAGT sequences. It has a short internal domain of 178 bp
and shows characteristics of terminal-repeat retrotransposon in miniature (TRIM) family. We used RetroCl1 sequence to develop molecular markers for the Colletotrichum genus. IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism)
markers were used to analyze the genetic diversity of C. lindemuthianum. Fifty-four isolates belonging to different races were used. A total of 45 loci were amplified. The Nei index showed significant
differences among the populations divided according to race, indicating that they are structured according to pathotype. No
clear correlation between IRAP and REMAP markers with pathogenic characterization was found. C. lindemuthianum has high genetic diversity, and the analysis of molecular variance showed that 51% of variability is found among the populations
of different races. The markers were also tested in different Colletotrichum species. In every case, multiple bands were amplified, indicating that these markers can be successfully used in different
species belonging to the Colletotrichum genus. 相似文献
5.
Marcelo D Bechara Márcio C Moretzsohn Darío A Palmieri Jomar P Monteiro Maurício BacciJr Joaquim MartinsJr José FM Valls Catalina R Lopes Marcos A Gimenes 《BMC plant biology》2010,10(1):255
Background
The genus Arachis comprises 80 species and it is subdivided into nine taxonomic sections (Arachis, Caulorrhizae, Erectoides, Extranervosae, Heteranthae, Procumbentes, Rhizomatosae, Trierectoides, and Triseminatae). This genus is naturally confined to South America and most of its species are native to Brazil. In order to provide a better understanding of the evolution of the genus, we reconstructed the phylogeny of 45 species using the variation observed on nucleotide sequences in internal transcribed spacer regions (ITS1 and ITS2) and 5.8 S of nuclear ribosomal DNA. 相似文献6.
Thomas P. West 《Antonie van Leeuwenhoek》2010,97(3):307-311
Control of pyrimidine formation was examined in Pseudomonas fulva ATCC 31418. Pyrimidine supplementation lowered pyrimidine biosynthetic pathway enzyme activities in cells grown on glucose
or succinate as a carbon source indicating possible repression of enzyme synthesis. Pyrimidine limitation experiments were
conducted using an orotidine 5′-monophosphate decarboxylase mutant strain isolated in this study. Compared to uracil-supplemented,
glucose-grown mutant cells, pyrimidine limitation of this strain caused aspartate transcarbamoylase, dihydroorotase, dihydroorotate
dehydrogenase and orotate phosphoribosyltransferase activities to increase about 6-, 13-, 3-, 15-fold, respectively, which
confirmed regulation of enzyme synthesis by pyrimidines. At the level of enzyme activity, transcarbamoylase activity in Ps. fulva was strongly inhibited by pyrophosphate, CTP, GTP and GDP under saturating substrate concentrations. 相似文献
7.
8.
Studying Pneumocystis has proven to be a challenge from the perspective of propagating a significant amount of the pathogen in a facile manner.
The study of several fungal pathogens has been aided by the use of invertebrate model hosts. Our efforts to infect the invertebrate
larvae Galleria
mellonella with Pneumocystis proved futile since P. murina neither caused disease nor was able to proliferate within G. mellonella. It did, however, show that the pathogen could be rapidly cleared from the host. 相似文献
9.
Noel H. Holmgren 《Brittonia》2018,70(1):115-139
A revision of Penstemon sect. Saccanthera subsect. Serrulati includes a new species (P. salmonensis), a new variety (P. triphyllus var. infernalis), and the elevation of a subspecies to species (P. curtiflorus), bringing the total number of species to eight, which are keyed and described, complete with nomenclature and type citations. 相似文献
10.
We have developed a protocol for the in vitro propagation of the genus Clivia. Shoots were regenerated when fragments of the peduncle-pedicel junction (PP junction) from young inflorescences were used as explants. The optimal media for PP junction were Murashige and Skoog (MS)-based medium containing 10 M of 6-benzyladenine (BA) and 10 M of 2,4-dichlorophenoxyacetic acid (2,4-D) or MS supplemented with 5 M BA, 10 M -naphthaleneacetic acid (NAA), 250 mg l-1 glutamine and 500 mg l–1 casein hydrolysate and their usage depended on the breeding lines. Multiplication from initiations and in vitro seedlings was the best when the explants were cut longitudinally through the meristem and placed on MS plus 44 M BA. Plantlets were transferred on to hormone -free MS medium with charcoal for rooting. 相似文献
11.
A. V. Beloded D. A. Paramonov M. V. Korovina S. A. Mulyashov N. S. Markvichev 《Applied Biochemistry and Microbiology》2005,41(1):42-46
The nature of phenylalanine auxotrophy in Pseudomonas sp. strain M9 was studied. A metabolic defect was found after the aromatic amino acid pathway branches from chorismate, so that the latter could not be converted to phenylpiruvate. It was shown that enzymatic activity of the strain could convert phenyllactate to phenylalanine. The reaction mechanisms were studied, and approaches to increasing the rate of the process and phenylalanine yield were proposed.Translated from Prikladnaya Biokhimiya i Mikrobiologiya, Vol. 41, No. 1, 2005, pp. 48–52.Original Russian Text Copyright © 2005 by Beloded, Paramonov, Korovina, Mulyashov, Markvichev. 相似文献
12.
Dong Q Zhang L Goh KL Forman D O'Rourke J Harris A Mitchell H 《Antonie van Leeuwenhoek》2007,92(3):301-307
Bacterial ssrA encodes tmRNA that functions both as a tRNA and an mRNA to rescue the stalled ribosome on defective mRNAs. In this study, ssrA was identified in four gastric species of Helicobacters and four enterohepatic species of Helicobacters. The tag peptide of 14 amino acids encoded by ssrA showed a pattern of Val(1)Ala(13) in gastric species, a pattern of Ala(1)Val(13 )in enterohepatic species, in contrast to the pattern of Ala(1)Ala(13) in W. succinogenes and C. jejuni, which are closely related to helicobacters. Phylogenetic analysis and the patterns of the tag peptide suggest that the Helicobacter genus could be separated into two genera. High conservation of ssrA in H. pylori was observed. The annotated ORF HP0784 in H. pylori, which largely overlaps ssrA, is unlikely to be functional. H. pylori ssrA interestingly expressed a large and a small tmRNA molecule. 相似文献
13.
A genetic transformation system has been developed for callus cells of Crataegus
aronia using Agrobacterium
tumefaciens. Callus culture was established from internodal stem segments incubated on Murashige and Skoog (MS) medium supplemented with
5 mg l−1 Indole-3-butyric acid (IBA) and 0.5 mg l−1 6-benzyladenine (BA). In order to optimize the callus culture system with respect to callus growth and coloration, different
types and concentrations of plant growth regulators were tested. Results indicated that the best average fresh weight of red
colored callus was obtained on MS medium supplemented with 2 mg l−1 2,4-dichlorophenoxyacetic acid (2,4-D) and 1.5 mg l−1 kinetin (Kin) (callus maintenance medium). Callus cells were co-cultivated with Agrobacterium harboring the binary plasmid pCAMBIA1302 carrying the mgfp5 and hygromycin phosphotransferase (hptII) genes conferring green fluorescent protein (GFP) activity and hygromycin resistance, respectively. Putative transgenic calli
were obtained 4 weeks after incubation of the co-cultivated explants onto maintenance medium supplemented with 50 mg l−1 hygromycin. Molecular analysis confirmed the integration of the transgenes in transformed callus. To our knowledge, this
is the first time to report an Agrobacterium-mediated transformation system in Crataegus
aronia. 相似文献
14.
Itoh N Kawanami T Nitta C Iwata N Usami S Abe Y Koide Y 《Applied microbiology and biotechnology》2003,61(3):240-246
The complete nucleotide sequence of pNI10 (3.75 kb), from which pNI105 and pNI107 were constructed as medium-host-range vectors for Gram-negative bacteria, was determined. A fragment of about 2.1 kb of pNI10 was essential for replication in Escherichia coli and Pseudomonas fluorescens. This fragment encodes a putative origin of replication ( ori) and one putative replication-controlling protein (Rep). An improved version of the medium-host-range plasmid vector pNUK73 (5.13 kb) was constructed with the basic-replicon of pNI10 and pHSG298 (2.68 kb). We show that expression in pseudomonads of the bromoperoxidase gene ( bpo) of Pseudomonas putida, inserted downstream of the lac promoter in pNUK73, resulted in about 30% (13.6 U/l culture) of the enzyme level obtained in E. coli. 相似文献
15.
Eun-Heui Han Soo Jin Lee Man Bae Kim Yong-Wook Shin Yun-Hee Kim Shin-Woo Lee 《Plant biotechnology reports》2017,11(2):127-133
SNPs can be used to discriminate allele-specific genotypes based on the 3′-terminal nucleotide of a primer corresponding to a specific SNP site. However, reliable discrimination between alleles in closely related species is not sufficient for molecular genetic identification. To overcome this problem, the present study evaluated the amplification refractory mutation system (ARMS)-PCR analysis method to discriminate closely related species, which utilizes specific primers that have a base pair change within three bases closest to the SNP site. The aim of this study was to develop a simple and precise DNA-based method for molecular authentication of C. wilfordii when compared with the highly similar species C. auriculatum. Molecular authentication of C. wilfordii and C. auriculatum was achieved using specific modified primers for DNA sequences of chloroplast TrnL-F and nuclear internal transcribed spacer (ITS) regions. A species-specific SNP was detected for each of the two species, and mismatched ARMS-PCR was conducted to specifically identify the SNP site. Plant samples collected from different locations were used to validate the selectively modified SNP markers, and the established method was determined to be effective. Therefore, this study provides a rapid and reliable method for specific identification of the medicinal plants, C. wilfordii and C. auriculatum. 相似文献
16.
Brian Schrire 《Kew Bulletin》2008,63(3):477-479
Summary Eleven species comprising the Madagascan genus Vaughania are subsumed within the large pantropical genus Indigofera. Six new combinations are made; the remaining species were originally described in Indigofera. 相似文献
17.
Milad Mohkam Navid Nezafat Aydin Berenjian Mohammad Ali Mobasher Younes Ghasemi 《Probiotics and antimicrobial proteins》2016,8(1):8-18
Some Bacillus species, especially Bacillus subtilis and Bacillus pumilus groups, have highly similar 16S rRNA gene sequences, which are hard to identify based on 16S rDNA sequence analysis. To conquer this drawback, rpoB, recA sequence analysis along with randomly amplified polymorphic (RAPD) fingerprinting was examined as an alternative method for differentiating Bacillus species. The 16S rRNA, rpoB and recA genes were amplified via a polymerase chain reaction using their specific primers. The resulted PCR amplicons were sequenced, and phylogenetic analysis was employed by MEGA 6 software. Identification based on 16S rRNA gene sequencing was underpinned by rpoB and recA gene sequencing as well as RAPD-PCR technique. Subsequently, concatenation and phylogenetic analysis showed that extent of diversity and similarity were better obtained by rpoB and recA primers, which are also reinforced by RAPD-PCR methods. However, in one case, these approaches failed to identify one isolate, which in combination with the phenotypical method offsets this issue. Overall, RAPD fingerprinting, rpoB and recA along with concatenated genes sequence analysis discriminated closely related Bacillus species, which highlights the significance of the multigenic method in more precisely distinguishing Bacillus strains. This research emphasizes the benefit of RAPD fingerprinting, rpoB and recA sequence analysis superior to 16S rRNA gene sequence analysis for suitable and effective identification of Bacillus species as recommended for probiotic products. 相似文献
18.
This paper discusses a number of experiments performed, involving the fusion by an electric field of mesophyll protoplasts
from Solanum tuberosum cv. Bintje, S. tuberosum dihaploid clones 243, 299 and the wild tuberous disease-resistant species S. bulbocastanum and S. pinnatisectum. Three fusion experiments (S. bulbocastanum + S. tuberosum dihaploid 243, S. pinnatisectum + S. tuberosum cv. Bintje and S. pinnatisectum + S. tuberosum dihaploid 299) yielded 542 calli, the 52 ones of which produced shoots. Obtained regenerants were estimated by the flow-cytometry (FC)
and RAPD analysis to determine hybrid plants.The utilisation of the FC as a useful method for detecting somatic hybrids is
also discussed in this paper. The combination S. bulbocastanum + S. tuberosum dihaploid 243 led to the creation of eight somatic hybrids, the combination S. pinnatisectum + S. tuberosum cv. Bintje yielded four somatic hybrids and the combination S. pinnatisectum + S. tuberosum dihaploid 299 resulted in no hybrid regenerants. Morphology in vitro, growth vigour and production of tuber-like structures
were evaluated in hybrid plants. Plants were transferred in vivo for further estimation (acclimatization, habitus evaluation
and tuberization ability). 相似文献
19.
We isolated the full-length cDNAs of engrailed and dpp-BMP2/4 orthologues from the pond snail Lymnaea stagnalis and examined their expression patterns during development by the whole mount in situ hybridization. At the gastrula and trochophore
stages, engrailed is expressed in the peripheral ectoderm of the presumptive and invaginating shell gland, corroborating its role in the shell
formation that is widely conserved among molluscs. At the same stages, dpp-BMP2/4 is expressed in the right-hand side ectoderm of the shell gland and in the invaginating stomodaeum. Unlike in the gastropod
Patella vulgata, our results suggested that dpp-BMP2/4 has a role in the shell formation, rather than in the regional specification and that it could be involved in the specification
pathway of the left–right asymmetry of the developing shell in L. stagnalis. 相似文献
20.
Chuan-Gen Lin Yun Chen Eric H. C. McKenzie Darbhe J. Bhat Hiran A. Ariyawansa Kevin D. Hyde Yong Wang 《Mycological Progress》2016,15(12):1313-1326
The genus Fusariella, typified by F. atrovirens, is characterised by semi- to macronematous, mononematous conidiophores, with cylindrical, subulate or lageniform phialidic conidiogenous cells that produce catenate, septate, curved to straight, subhyaline to brown conidia. During a survey of hyaline-spored hyphomycetes from karst areas in Thailand, we collected a new species of Fusariella with curved conidia and introduce it in this paper as Fusariella curvata sp. nov. In addition, all hitherto described species of Fusariella are reviewed. The result of phylogenetic analyses, based on combined SSU, LSU, TEF and RPB2 sequence data, indicates that the genus belongs in the family Bionectriaceae (Hypocreales, Sordariomycetes). 相似文献