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1.
F. Bonomi Stefania Iametti Donald M. Kurtz Jr. Kimberly A. Richie E. Ragg 《Journal of biological inorganic chemistry》1998,3(6):595-605
The single Fe(II) in reduced rubredoxin from Clostridium pasteurianum was found to be quantitatively displaced by either Cd2+ or Zn2+ when a modest molar excess of the substituting metal salt was anaerobically incubated with the reduced rubredoxin under mild
conditions, namely, room temperature, pH 5.4–8.4, and no protein denaturants. Under the same conditions, cadmium-for-zinc substitution was also achieved upon aerobic incubation of the zinc-substituted
rubredoxin with a modest molar excess of Cd2+. Displacements of Fe(II) from the reduced rubredoxin were not observed upon anaerobic incubation with Ni2+, Co2+, or VO2+ salts, and no reaction with any of the divalent metal ions was observed for the oxidized [Fe(III)] rubredoxin. Fe(II) could
not be re-inserted into the Zn- or Cd-substituted rubredoxins without resorting to protein denaturation. 1H and 113Cd NMR experiments showed that the cadmium-substituted rubredoxin prepared by the non-denaturing substitution method retained
the pseudotetrahedral M(SCys)4 coordination geometry and secondary structural elements characteristic of the native rubredoxin, and that "unzipping" of
the β-sheet did not occur during metal substitution. Rates of Fe(II) displacement by M2+ (M=Cd or Zn) increased with increasing M2+/rubredoxin ratio, decreasing pH, and lower ionic strength. The substitution rates were faster for M=Cd than for M=Zn. Rates
of Cd2+ substitution into a V8A-mutated rubredoxin were significantly faster than for the wild-type protein. The side-chain of V8
is on the protein surface and close to the metal-ligating Cys42Sγ at the M(SCys)4 site. Therefore, the rate-limiting step in the substitution process is suggested to involve direct attack of the [M(SCys)4]2– site by the incoming M2+, without global unfolding of the protein. Implications of these results for metal ion incorporation into rubredoxins in vivo are discussed.
Received: 29 May 1998 / Accepted: 11 August 1998 相似文献
2.
Staphylococcal Cassette Chromosome mec (SCCmec) is a mobile genetic element that carries the gene mecA mediating the methicillin resistance in staphylococci. It is composed of mec and ccr gene complexes. Six SCCmec types have been defined so far. SCCmec typing of 13 methicillin-resistant Staphylococcus aureus (MRSA) out of 72 (18%) non redundant S. aureus strains recovered in 1998–2007 at the Bone Marrow Transplant Centre of Tunis was carried out. The isolates were identified
by conventional methods. Antibiotic susceptibility was determined by oxacillin and cefoxitin disks and oxacillin MIC by E-test.
Methicillin resistance was detected by mecA PCR. The SCCmec complex types were determined by PCR. The epidemiology of MRSA has been investigated by PFGE. Among 13 mecA positive strains, 12 were resistant to oxacillin (MIC = 3 to >256 μg/μl) and to cefoxitin and one strain was pre-resistant:
susceptible to oxacillin (MIC = 0.19 μg/μl) and to cefoxitin. Hospital-acquired MRSA (HA-MRSA) strains had essentially SCCmec type IV (nine strains) or III (two strains) or I (one strain). One strain shown to carry ccrAB1 and ccrAB2 genes in combination with class B mec. Seven of 13 MRSA strains isolated from 2000 to 2006 were classified with major similarity group A harbored SCCmec type IV. 相似文献
3.
Barbara Biondi Dante Goldin Elisa Giannini Roberta Lattanzi Lucia Negri Pietro Melchiorri Luigi Ciocca Raniero Rocchi 《International journal of peptide research and therapeutics》2006,12(2):139-144
Syntheses are described of the nociceptin (1–13) amide [NC(1–13)-NH2] and of several analogues in which either one or both the phenylalanine residues (positions 1 and 4), the arginine residues (positions 8 and 12) and the alanine residues (positions 7 and 11) have been replaced by N-benzyl-glycine, N-(3-guanidino-propyl)-glycine and β-alanine, respectively. The preparation is also described of NC(1–13)-NH2 analogues in which either galactose or N-acetyl-galactosamine are β-O-glycosidically linked to Thr5 and/or to Ser10. Preliminary pharmacological experiments on mouse vas deferens preparations showed that Phe4, Thr5, Ala7 and Arg8 are crucial residues for OP4 receptor activation. Manipulation of Phe1 yielded peptides endowed with antagonist activity but [Nphe1] NC(1–13)-NH2 acted as an antagonist still possessing weak agonist activity. Introduction of the βAla residue either in position 7 or 11 of the [Nphe1] NC(1–13)-NH2 sequence, abolished any residual agonist activity and [Nphe1, βAla7] NC(1–13)-NH2 and [Nphe1, βAla11] NC(1–13)-NH2 acted as competitive antagonists only. Modification of both Ala7 and Ala11 abolished the antagonist activity of [Nphe1]NC(1–13)-NH2 probably by hindering receptor binding. Changes at positions 10 and 11 gave analogues still possessing agonist activity. [Ser(βGal)10] NC(1–13)-NH2 displayed an activity comparable with that of NC(1–13)-NH2, [Ser(βGalNAc)10] NC(1–13)-NH2 and [βAla11] NC(1–13)-NH2 were five and 10 times less active, respectively.The α-amino acid residues are of the l-configuration. Standard abbreviations for amino acid derivatives and peptides are according to the suggestions of the IUPAC-IUB Commission on Biochemical Nomeclature (1984), Eur. J. Biochem. 138, 9–37. Abbreviations listed in the guide published in (2003), J. Peptide Sci. 9, 1–8 are used without explanation. 相似文献
4.
Some novel members of extremely halophilic archaea, strains AJ11, AJ12 and AJ13, were isolated from the Aularz Lake located
in the Altun Mountain National Nature Reserve of Xinjiang, Uygur Autonomous Region in China. Partial DNA fragments encoding
a bacteriorhodopsin (BR), as well as for 16S rRNA of isolated strains, were amplified by PCR and their DNA sequences were
determined subsequently. On the basis of homology and phylogenetic analysis of the 16S rDNA, we thought that the isolated
strains forming a microbiological population are the members of the genus Natrinema. The results of genetic analysis, such as GC content, transition/transversion (Ti/Tv) rate ratios and synonymous substitution
rates (Ks) indicate that the br fragments, with a high level of genetic divergence, are faced with both purifying selection and bias mutation pressure. The
study provides the basis for use of species and BR proteins resources.
__________
Translated from Hereditas (Beijing), 2007, 29(3): 376–380 [译自: 遗传] 相似文献
5.
M Ozkan SG Desai Y Zhang DM Stevenson J Beane EA White ML Guerinot LR Lynd 《Journal of industrial microbiology & biotechnology》2001,27(5):275-280
Characteristics of 13 newly isolated thermophilic, anaerobic, and cellulolytic strains were compared with previously described
strains of Clostridium thermocellum: ATCC 27405 and JW20 (ATCC 31549). Colony morphology, antibiotic sensitivity, fermentation end-products, and cellulose degradation
were documented. All 13 strains were sensitive to erythromycin (5 μg/ml) and chloramphenicol (25 μg/ml), and all strains but
one were sensitive to kanamycin (20 μg/ml). Polymerase chain reaction (PCR) amplification using primers based on gene sequences
from C. thermocellum ATCC 27405 was successful for all 13 strains in the case of the hydrogenase gene and 11 strains in the case of phosphotransacetylase/acetate
kinase genes. Ten strains amplified a product of the expected size with primers developed to be specific for C. thermocellum 16SrRNA primers. Two of the 13 strains did not amplify any product with the PCR primers designed for the phosphotransacetylase/acetate
kinase and 16SrRNA primers. A MboI-like GATC- recognizing restriction activity was present in all of the five strains examined. The results of this study have
several positive implications with respect to future development of a transformation system for cellulolytic thermophiles.
Journal of Industrial Microbiology & Biotechnology (2001) 27, 275–280.
Received 12 September 2000/ Accepted in revised form 20 November 2000 相似文献
6.
7.
8.
An Assessment of the Phylogenetic Relationship Among Sugarcane and Related Taxa Based on the Nucleotide Sequence of 5S rRNA Intergenic Spacers 总被引:4,自引:0,他引:4
5S rRNA intergenic spacers were amplified from two elite sugarcane (Saccharumhybrids) cultivars and their related taxa by polymerase chain reaction (PCR) with 5S rDNA consensus primers. Resulting PCR
products were uniform in length from each accession but exhibited some degree of length variation among the sugarcane accessions
and related taxa. These PCR products did not always cross hybridize in Southern blot hybridization experiments. These PCR
products were cloned into a commercial plasmid vector PCR™ 2.1 and sequenced. Direct sequencing of cloned PCR products revealed
spacer length of 231–237 bp for S. officinarum, 233–237 for sugarcane cultivars, 228–238 bp for S. spontaneum, 239–252 bp for S. giganteum, 385–410 bp for Erianthusspp., 226–230 bp for Miscanthus sinensisZebra, 206–207 bp for M. sinensisIMP 3057, 207–209 bp for Sorghum bicolor, and 247–249 bp for Zea mays. Nucleotide sequence polymorphism were found at both the segment and single nucleotide level. A consensus sequence for each
taxon was obtained by Align X. Multiple sequences were aligned and phylogenetic trees constructed using Align X, CLUSTAL and
DNAMAN programs. In general, accessions of the following taxa tended to group together to form distinct clusters: S. giganteum, Erianthusspp., M. sinensis, S. bicolor, and Z. mays. However, the two S. officinarumclones and two sugarcane cultivars did not form distinct clusters but interrelated within the S. spontaneumcluster. The disclosure of these 5S rRNA intergenic spacer sequences will facilitate marker-assisted breeding in sugarcane.
This revised version was published online in July 2006 with corrections to the Cover Date. 相似文献
9.
The unloading of sucrose in the apical part of the hypocotyl of Ricinus communis L. seedlings was measured by 13C-nuclear magnetic resonance (NMR) spectroscopy. The cotyledons of the seedling were immersed in 5 mM Mes buffer containing
100 mM 13C-labeled sucrose. At intervals of 70–90 min, 13C-NMR spectra with broadband decoupling and nuclear Overhauser enhancement were acquired in vivo. The spectra showed growing 13C-resonances of the labeled positions in the sucrose molecule reaching steady-state labeling within 7–8 h. The specific 13C labeling of sucrose in the G1-position changed from 0.38 in the supplied sucrose solution to 0.16 in the sucrose extracted from the hypocotyl piece at
the end of the experiment (13 h). Labeling of starch (and other insolubles) in the hypocotyl piece was ca. 0.10. It is proposed
that the decreased specific labeling of unloaded sucrose is mostly due to the separate local pools of sucrose in the cortex
and pith parenchyma, respectively, and less to continuous starch degradation and conversion to sucrose. The report gives an
example of the application of 13C-NMR spectroscopy in assimilate allocation studies.
Received: 10 October 1998 / Accepted: 31 December 1998 相似文献
10.
Biosurfactants containing rhamnose and β-hydroxydecanoic acid and called rhamnolipids are reviewed with respect to microbial
producers, their physiological role, biosynthesis and genetics, and especially their microbial overproduction, physicochemical
properties and potential applications. With Pseudomonas species, more than 100 g l−1 rhamnolipids were produced from 160 g l−1 soybean oil at a volumetric productivity of 0.4 g l−1 h−1. The individual rhamnolipids are able to lower the surface tension of water from 72 mN m−1 to 25–30 mN m−1 at concentrations of 10–200 mg l−1. After initial testing, rhamnolipids seem to have potential applications in combating marine oil pollution, removing oil
from sand and in combating zoosporic phytopathogens. Rhamnolipids are also a source of l-rhamnose, which is already used for the industrial production of high-quality flavor components.
Received: 1 July 1998 / Received revision: 11 September 1998 / Accepted: 13 September 1998 相似文献
11.
Kazuki Aoyama Yingqian Kang Katsukiyo Yazawa Tohru Gonoi Katsuhiko Kamei Yuzuru Mikami 《Mycopathologia》2009,168(4):175-183
During 1998–2008, there were 31 strains of Gordonia species isolated from clinical specimens in our laboratory. Our identification of the 31 strains of Gordonia species showed that major pathogenic Gordonia species in Japan were classifiable, respectively into 14 and 13 strains of Gordonia sputi and Gordonia bronchialis. The four remaining strains were identified as three Gordonia species: G. aichiensis (2 strains), and G. terrae (1 strain), and G. otitidis (1 strain). Results of drug susceptibility tests for these 31 strains of Gordonia isolates are reported herein. 相似文献
12.
Amino acid and protein analyses have allowed the construction of a model for the C4-based Rodgers and Chido blood group antigens.
The single low-frequency allele (WH) in this blood group system, however, has not been characterized at the molecular level. Two WH+ donors were studied by C4 agarose gel electrophoreses, immunoblot studies using monoclonal anti-Rg: 1 or anti-Ch: 1, serological
phenotyping, polymerase chain reaction-restriction fragment length polymorphism of their C4 genes, and DNA sequencing of the WH allele. The first donor had the C4A1, A3 phenotype; the C4A1 carried Ch: 1, 3, 6 (thus exhibiting reversed antigenicity)
and the C4A3 carried the WH antigen. The amino acid sequence of the WH allele was PCPVLD at positions 1101 – 1106, S at position 1157, and VDLL at positions 1188 – 1191. A second donor typed as
C4A2, A4, B1 and was also WH+. Immunoblot analysis showed that a C4B1 protein expressed Rg: 1. Sequence analysis of the C4B genes showed the amino acids LSPVIH at positions 1101 – 1106, S at position 1157, and ADLR at positions 1188 – 1191. Thus,
the WH antigen is a conformational epitope that can arise through different mechanisms on either a C4A or C4B gene.
Received: 22 November 1995 / Revised: 19 February 1996 相似文献
13.
A collection of 32 lactococcal strains isolated from raw milk in the Camembert RDO (registered designation of origin) area
were phenotypically and genotypically characterized. As expected for environmental isolates, all strains had a Lactococcus lactis subsp. lactis phenotype. The strains were then genotypically identified by the randomly amplified polymorphic DNA (RAPD) technique, using
reference strains of lactococci. Two major clusters were identified containing the two subspecies lactis and cremoris. The subspecies lactis cluster could be divided into five subgroups whereas there was a high coefficient of similarity between all strains in the
subspecies cremoris cluster. This RAPD classification was then compared with that of a traditional PCR assay using L.lactis species-specific primers corresponding to part of the histidine biosynthesis operon. The two subspecies were differentiated
by the size of the fragment amplified (about 200 bp longer for subspecies cremoris). Unlike preliminary phenotypic assignments, the results of PCR experiments corroborated the genotypic identification of
the lactococcal strains by RAPD allowing the technique to be reconsidered on the basis of its taxonomic efficiency.
Received: 14 May 1998 / Accepted: 3 September 1998 相似文献
14.
T. Kakitani 《European biophysics journal : EBJ》1979,5(4):293-312
Using the twisted conformations of the chromophores for visual pigments and intermediates which were theoretically determined
in the previous paper, energy surfaces of the pigment at −190‡ C were obtained as functions of the torsional anglesθ
9–10 andθ
11–12 or of the torsional anglesθ
9–10 andθ
13–14. In these calculations, the existence of specific reaction paths between rhodopsin (R) and bathorhodopsin (B), between isorhodopsin
I (I) and bathorhodopsin, and between isorhodopsin II (I′) and bathorhodopsin were assumed. It was shown that the total energy
surfaces of the excited states had minimaC
1 atθ
9–10 ∼ −10‡ andθ
11–12 ∼ −80‡,C
2 atθ
9–10 ∼ −85‡ andθ
11–12 ∼ −5‡, andC
3 atθ
9–10 ∼ 0‡ andθ
13–14 ∼ −90‡. These minima are considered to correspond to the thermally barrierless common states as denoted by Rosenfeld et al.
Using the total energy surfaces in the ground and excited states, the molecular mechanism of the photoisomerization reaction
was suggested. Quantum yields for the photoconversions among R, I, I′ and B were related to the rates of vibrational relaxations,
radiationless transitions and thermal excitations. Some discussion was made of the temperature effect on the quantum yield.
Similar calculations of the energy surfaces were also made at other temperatures where lumirhodopsin or metarhodopsin I is
stable. Relative energy levels of the pigments and the intermediates were discussed. 相似文献
15.
Hector RE Dien BS Cotta MA Qureshi N 《Journal of industrial microbiology & biotechnology》2011,38(9):1193-1202
Saccharomyces’ physiology and fermentation-related properties vary broadly among industrial strains used to ferment glucose. How genetic
background affects xylose metabolism in recombinant Saccharomyces strains has not been adequately explored. In this study, six industrial strains of varied genetic background were engineered
to ferment xylose by stable integration of the xylose reductase, xylitol dehydrogenase, and xylulokinase genes. Aerobic growth
rates on xylose were 0.04–0.17 h−1. Fermentation of xylose and glucose/xylose mixtures also showed a wide range of performance between strains. During xylose
fermentation, xylose consumption rates were 0.17–0.31 g/l/h, with ethanol yields 0.18–0.27 g/g. Yields of ethanol and the
metabolite xylitol were positively correlated, indicating that all of the strains had downstream limitations to xylose metabolism.
The better-performing engineered and parental strains were compared for conversion of alkaline pretreated switchgrass to ethanol.
The engineered strains produced 13–17% more ethanol than the parental control strains because of their ability to ferment
xylose. 相似文献
16.
Naumov GI Naumova ES Aigle M Masneuf I Belarbi A 《Applied microbiology and biotechnology》2001,55(1):108-111
Using genetic hybridization analysis, pulsed-field gel electrophoresis of chromosomal DNA and PCR/RFLP analysis of the MET2 gene, we reidentified 11 Champagne yeast strains. Two of them, SCPP and SC4, were found to belong to Saccharomyces bayanus var. uvarum and the remaining strains to S. cerevisiae. Strain SCPP (CLIB 2025) of S. bayanus var. uvarum is known as a producer of three pectinolytic enzymes.
Received: 28 April 2000 / Received revision: 20 July 2000 / Accepted: 25 July 2000 相似文献
17.
D Montoya C Arévalo S Gonzales F Aristizabal WH Schwarz 《Journal of industrial microbiology & biotechnology》2001,27(5):329-335
Thirteen new Clostridium strains, previously isolated from soil and found to produce high amounts of solvents from glucose, hydrolyzed a great variety
of α- and β-glycans, including raw starch, xylan, pectin, inulin and cellulose. The sequences of the PCR-amplified DNA fragments
containing the variable 3′ part of one of the 16S rRNA genes were 99.5% identical. The macrorestriction pattern of two endonucleolytic
digests of chromosomal DNA in the pulsed-field gel electrophoresis (PFGE) confirmed their high homogeneity on the DNA level.
The complete 16S rRNA gene sequence of three selected strains was 99.8% identical to the 16S rRNA gene sequence from Clostridium butyricum and separates them from C. acetobutylicum. To the closely related four species of solventogenic clostridia a new group of strains has to be added, which has a great
potential for the direct fermentation of biomass.
Journal of Industrial Microbiology & Biotechnology (2001) 27, 329–335.
Received 12 September 2000/ Accepted in revised form 25 July 2001 相似文献
18.
Paavo Ahvenniemi Matthias Wolf Mari J. Lehtonen Paula Wilson Malgorzata German-Kinnari Jari P. T. Valkonen 《Journal of molecular evolution》2009,69(2):150-163
The rRNA cistron (18S–ITS1–5.8S–ITS2–28S) is used widely for phylogenetic analyses. Recent studies show that compensatory
base changes (CBC) in the secondary structure of ITS2 correlate with genetic incompatibility between organisms. Rhizoctonia solani consists of genetically incompatible strain groups (anastomosis groups, AG) distinguished by lack of anastomosis between
hyphae of strains. Phylogenetic analysis of internal transcribed spacer (ITS) sequences shows a strong correlation with AG
determination. In this study, ITS sequences were reannotated according to the flanking 5.8S and 28S regions which interact
during ribogenesis. One or two CBCs were detected between the ITS2 secondary structure of AG-3 potato strains as compared
to AG-3 tobacco strains, and between these two strains and all other AGs. When a binucleate Rhizoctonia species related to Ceratobasidiaceae was compared to the AGs of R. solani, which were multinucleate (3–21 nuclei per cell), 1–3 CBCs were detected. The CBCs in potato strains of AG-3 distinguish
them from AG-3 tobacco strains and other AGs yielding further evidence that the potato strains of AG-3 originally described
as R. solani are a species distinct from other AGs. The ITS1–5.8S–ITS2 sequences were analyzed by direct sequencing of PCR products from
497 strains of AG-3 isolated from potato. The same 10 and 4 positions in ITS1 and ITS2, respectively, contained variability
in 425 strains (86%). Nine different unambiguous ITS sequences (haplotypes) could be detected in a single strain by sequencing
cloned PCR products indicating that concerted evolution had not homogenized the rRNA cistrons in many AG-3 strains. Importantly,
the sequence variability did not affect the secondary structure of ITS2 and CBCs in AG-3.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
19.
Genetic diversity of Cryptomeria japonica using co-dominant DNA markers based on sequenced-tagged sites 总被引:3,自引:0,他引:3
Y. Tsumura N. Tomaru 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,98(3-4):396-404
We have investigated the genetic diversity of 11 natural populations of C. japonica using 13 polymorphic STS markers. The average unbiased heterozygosities (H
e
), the average number of alleles per locus (N
a
) and the proportion of polymorphic loci (Pl) were 0.281, 1.93 and 76.92%, respectively. Coefficients of linkage disequilibrium were calculated, and no significant deviation
was found except in four combinations – which might have occurred by chance alone. The fixation index (F
IS
) for 3 loci showed statistically significant values at the 1% level. The genetic differentiation between populations was
only 0.047, and there were no clear geographical tendencies in the allele frequencies or the heterozygosities among populations.
Consequently, the results from STS-based co-dominant DNA marker analysis were very similar to those from a previous allozyme
study. However, the resolution of the technique is greater than allozyme analysis because many loci with high heterozygosities
can be evaluated, and it is very simple. Therefore, the STS-based marker approach is very useful and convenient for population
genetics and genome mapping of C. japonica.
Received: 18 July 1998 / Accepted: 13 August 1998 相似文献
20.
Greenhouse-grown plants of turnip rape Brassica rapa ssp. oleifera (syn. B. campestris) cv. Valtti and Sisu were transformed by Agrobacterium tumefaciens infection. Of the three A. tumefaciens strains tested (C58C1, EHA105 and LBA4404), LBA4404 gave the best results. Segments excised from one to two upper internodes
of an inflorescence-carrying stem served as explants for the Agrobacterium infection. Cultivation of the explants horizontally during the first 3 days of co-cultivation with A. tumefaciens following immediate selection of transformed tissue of the stem segments placed vertically basal side down were critical.
Use of silver nitrate (5–10 mg/l) in the culture medium and Micropore (3 M) paper tape for sealing plates was also beneficial.
Transgenic shoots were recovered using either hygromycin or kanamycin (20–25 mg/l) selection. Hygromycin was preferable, as
the proportion of `escapes' was 90% under kanamycin and 10% under hygromycin selection. Regeneration was achieved by culturing
the explants for 3–6 days on 0.5 mg/l of 2,4-di-chlorophenoxyacetic acid and 1–2 weeks on 2–3 mg/l of 6-benzyl aminopurine
with/without 0.05 mg/l α-naphthaleneacetic acid. Recovered shoots were then cultured on hormone-free MS medium. This culture program gave 60–80% shoot
regeneration. Regenerants were tested by histological β-glucuronidase staining and Southern blotting. The recovery rate of transgenic shoots was 4–9% of the number of explants used
in the experiments.
Received: 28 November 1997 / Revision received: 25 March 1998 / Accepted: 22 November 1998 相似文献