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31.
Gene Sequence Phylogenies of the Family <Emphasis Type="Italic">Microbacteriaceae</Emphasis> 总被引:1,自引:0,他引:1
The type strains of 32 species of 13 genera of the family Microbacteriaceae were analysed with respect to gene-coding phylogeny for DNA gyrase subunit B (gyrB), RNA-polymerase subunit B (rpoB), recombinase A (recA), and polyphosphate kinase (ppk). The resulting gene trees were compared with the 16S rRNA gene phylogeny of the same strains. The topology of neighbour-joining
and maximum parsimony phylogenetic trees, based on nucleic-acid sequences and protein sequences of housekeeping genes, differed
from one another, and no gene tree was identical to that of the 16S rRNA gene tree. Most genera analysed containing >1 strain
formed phylogenetically coherent taxa. The three pathovars of Curtobacterium flaccumfaciens clustered together to the exclusion of the type strains of other Curtobacterium species in all DNA - and protein-based analyses. In no tree did the distribution of a major taxonomic marker, i.e., diaminobutyric acid versus lysine and/or ornithine in the peptidoglycan, or acyl type of peptidoglycan, correlate with the
phylogenetic position of the organisms. The changing phylogenetic position of Agrococcus jenensis was unexpected: This strain defined individual lineages in the trees based on 16S rRNA and gyrB and showed identity with Microbacterium saperdae in the other three gene trees. 相似文献
32.
Alice Brambilla Iris Biebach Bruno Bassano Giuseppe Bogliani Achaz von Hardenberg 《Proceedings. Biological sciences / The Royal Society》2015,282(1798)
Heterozygosity–fitness correlations (HFCs) are a useful tool to investigate the effects of inbreeding in wild populations, but are not informative in distinguishing between direct and indirect effects of heterozygosity on fitness-related traits. We tested HFCs in male Alpine ibex (Capra ibex) in a free-ranging population (which suffered a severe bottleneck at the end of the eighteenth century) and used confirmatory path analysis to disentangle the causal relationships between heterozygosity and fitness-related traits. We tested HFCs in 149 male individuals born between 1985 and 2009. We found that standardized multi-locus heterozygosity (MLH), calculated from 37 microsatellite loci, was related to body mass and horn growth, which are known to be important fitness-related traits, and to faecal egg counts (FECs) of nematode eggs, a proxy of parasite resistance. Then, using confirmatory path analysis, we were able to show that the effect of MLH on horn growth was not direct but mediated by body mass and FEC. HFCs do not necessarily imply direct genetic effects on fitness-related traits, which instead can be mediated by other traits in complex and unexpected ways. 相似文献
33.
34.
Priscila Vaz de Arruda Rita de Cássia Lacerda Brambilla Rodrigues Débora Danielle Virgínio da Silva Maria das Graças de Almeida Felipe 《Biodegradation》2011,22(4):815-822
The evaluation of hexose and pentose in pre-cultivation of Candida guilliermondii FTI 20037 yeast on xylose reductase (XR) and xylitol dehydrogenase (XDH) enzymes activities was performed during fermentation in sugarcane bagasse hemicellulosic hydrolysate. The xylitol production was evaluated by using cells previously growth in 30.0 gl?1 xylose, 30.0 gl?1 glucose and in both sugars mixture (30.0 gl?1 xylose and 2.0 gl?1 glucose). The vacuum evaporated hydrolysate (80 gl?1) was detoxificated by ion exchange resin (A-860S; A500PS and C-150-Purolite®). The total phenolic compounds and acetic acid were 93.0 and 64.9%, respectively, removed by the resin hydrolysate treatment. All experiments were carried out in Erlenmeyer flasks at 200 rpm, 30°C. The maximum XR (0.618 Umg Prot ?1 ) and XDH (0.783 Umg Prot ?1 ) enzymes activities was obtained using inoculum previously growth in both sugars mixture. The highest cell concentration (10.6 gl?1) was obtained with inoculum pre-cultivated in the glucose. However, the xylitol yield and xylitol volumetric productivity were favored using the xylose as carbon source. In this case, it was observed maximum xylose (81%) and acetic acid (100%) consumption. It is very important to point out that maximum enzymatic activities were obtained when the mixture of sugars was used as carbon source of inoculum, while the highest fermentative parameters were obtained when xylose was used. 相似文献
35.
Andrea Forchino Angel Borja Fabio Brambilla José Germán Rodríguez Iñigo Muxika Genciana Terova Marco Saroglia 《Ecological Indicators》2011,11(5):1112-1122
The impact of an off-shore fish farm in Alghero Bay (northwest Sardinia, Italy) on the benthic ecosystem was investigated in 2007 and 2008. In addition to studying the chemical and physical characteristics of the area (i.e., currents and sediment analyses), some biological analyses were also performed. The AZTI's Marine Biotic Index (AMBI) and the multivariate AMBI (M-AMBI) were calculated, which are being used in assessing the ecological status of benthic communities within the European Water Framework Directive (WFD). Clear impact gradients were detected according to both methods; they are related to farm production, prevailing currents, and characteristics of the area (i.e., water depth and distance to the cages). The site affected most was detected within 84 m from the cages; the area that no longer showed effects was over 907 m from the cages. The gradient is shown by decreasing AMBI values and percentage of opportunistic species and increasing richness, diversity, and the presence of sensitive species. This study highlights the importance of setting reference conditions for different areas when calculating M-AMBI. These reference conditions correspond to those in undisturbed sites in the opposite direction of the prevailing currents within the area. 相似文献
36.
Pati A Gronow S Zeytun A Lapidus A Nolan M Hammon N Deshpande S Cheng JF Tapia R Han C Goodwin L Pitluck S Liolios K Pagani I Ivanova N Mavromatis K Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Detter JC Brambilla E Rohde M Göker M Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP Lucas S 《Standards in genomic sciences》2011,4(1):45-53
Bacteroides helcogenes Benno et al. 1983 is of interest because of its isolated phylogenetic location and, although it has been found in pig feces and is known to be pathogenic for pigs, occurrence of this bacterium is rare and it does not cause significant damage in intensive animal husbandry. The genome of B. helcogenes P 36-108(T) is already the fifth completed and published type strain genome from the genus Bacteroides in the family Bacteroidaceae. The 3,998,906 bp long genome with its 3,353 protein-coding and 83 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
37.
Pati A Gronow S Lu M Lapidus A Nolan M Lucas S Hammon N Deshpande S Cheng JF Tapia R Han C Goodwin L Pitluck S Liolios K Pagani I Mavromatis K Mikhailova N Huntemann M Chen A Palaniappan K Land M Hauser L Detter JC Brambilla EM Rohde M Göker M Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP Ivanova N 《Standards in genomic sciences》2011,5(1):41-49
Prevotella multisaccharivorax Sakamoto et al. 2005 is a species of the large genus Prevotella, which belongs to the family Prevotellaceae. The species is of medical interest because its members are able to cause diseases in the human oral cavity such as periodontitis, root caries and others. Although 77 Prevotella genomes have already been sequenced or are targeted for sequencing, this is only the second completed genome sequence of a type strain of a species within the genus Prevotella to be published. The 3,388,644 bp long genome is assembled in three non-contiguous contigs, harbors 2,876 protein-coding and 75 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
38.
Huntemann M Lu M Nolan M Lapidus A Lucas S Hammon N Deshpande S Cheng JF Tapia R Han C Goodwin L Pitluck S Liolios K Pagani I Ivanova N Ovchinikova G Pati A Chen A Palaniappan K Land M Hauser L Jeffries CD Detter JC Brambilla EM Rohde M Spring S Göker M Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP Mavromatis K 《Standards in genomic sciences》2011,4(3):303-311
Hippea maritima (Miroshnichenko et al. 1999) is the type species of the genus Hippea, which belongs to the family Desulfurellaceae within the class Deltaproteobacteria. The anaerobic, moderately thermophilic marine sulfur-reducer was first isolated from shallow-water hot vents in Matipur Harbor, Papua New Guinea. H. maritima was of interest for genome sequencing because of its isolated phylogenetic location, as a distant next neighbor of the genus Desulfurella. Strain MH(2) (T) is the first type strain from the order Desulfurellales with a completely sequenced genome. The 1,694,430 bp long linear genome with its 1,723 protein-coding and 57 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
39.
Lang E Teshima H Lucas S Lapidus A Hammon N Deshpande S Nolan M Cheng JF Pitluck S Liolios K Pagani I Mikhailova N Ivanova N Mavromatis K Pati A Tapia R Han C Goodwin L Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Brambilla EM Kopitz M Rohde M Göker M Tindall BJ Detter JC Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Klenk HP Kyrpides NC 《Standards in genomic sciences》2011,4(1):81-90
40.
Pati A Zhang X Lapidus A Nolan M Lucas S Del Rio TG Tice H Cheng JF Tapia R Han C Goodwin L Pitluck S Liolios K Pagani I Ivanova N Mavromatis K Chen A Palaniappan K Hauser L Jeffries CD Brambilla EM Röhl A Mwirichia R Rohde M Tindall BJ Sikorski J Wirth R Göker M Woyke T Detter JC Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP Land M 《Standards in genomic sciences》2011,4(2):210-220
Oceanithermus profundus Miroshnichenko et al. 2003 is the type species of the genus Oceanithermus, which belongs to the family Thermaceae. The genus currently comprises two species whose members are thermophilic and are able to reduce sulfur compounds and nitrite. The organism is adapted to the salinity of sea water, is able to utilize a broad range of carbohydrates, some proteinaceous substrates, organic acids and alcohols. This is the first completed genome sequence of a member of the genus Oceanithermus and the fourth sequence from the family Thermaceae. The 2,439,291 bp long genome with its 2,391 protein-coding and 54 RNA genes consists of one chromosome and a 135,351 bp long plasmid, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献