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At least 361 records · Page 20Linked to original sources
PubMed2004

Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator.

Astraptes fulgerator, first described in 1775, is a common and widely distributed neotropical skipper butterfly (Lepidoptera: Hesperiidae). We combine 25 years of natural history observations in northwestern Costa Rica with morphological study and DNA barcoding of museum specimens to show that A. fulgerator is a complex of at least 10 species in this region. Largely sympatric, these taxa have mostly different caterpillar food plants, mostly distinctive caterpillars, and somewhat different ecosystem preferences but only subtly differing adults with no genitalic divergence. Our results add to the evidence that cryptic species are prevalent in tropical regions, a critical issue in efforts to document global species richness. They also illustrate the value of DNA barcoding, especially when coupled with traditional taxonomic tools, in disclosing hidden diversity.

Animal Feed↗
PubMed1999

The identification of vaginal Lactobacillus species and the demographic and microbiologic characteristics of women colonized by these species.

Lactobacillus acidophilus has been reported to be the predominant vaginal species. Vaginal lactobacilli isolated from 215 sexually active women were identified using whole-chromosomal DNA probes to 20 American Type Culture Collection Lactobacillus strains. Most women were colonized by L. crispatus (32%), followed by L. jensenii (23%), a previously undescribed species designated L. 1086V (15%), L. gasseri (5%), L. fermentum (0.3%), L. oris (0.3%), L. reuteri (0.3%), L. ruminis (0.3%), and L. vaginalis (0.3%). H2O2 was produced by 95% of L. crispatus and 94% of L. jensenii isolates, compared with only 9% of L. 1086V. Colonization by L. crispatus or L. jensenii was positively associated with being white (P<.001), age >/=20 years (P=.05), barrier contraceptive usage (P=.008), and lower frequency of bacterial vaginosis (P<.001) and gonorrhea (P=.03). L. crispatus and L. jensenii, not L. acidophilus, are the most common species of vaginal lactobacilli.

Adolescent↗
PubMed2002

Species-specific subcellular localization of RPGR and RPGRIP isoforms: implications for the phenotypic variability of congenital retinopathies among species.

The retinitis pigmentosa GTPase regulator (RPGR) is encoded by the X-linked RP3 locus, which upon genetic lesions leads to neurodegeneration of photoreceptors and blindness. The findings that RPGR specifically and directly interacts in vivo and in vitro with retina-specific RPGR-interacting protein 1 (RPGRIP) and that human mutations in RPGR uncouple its interaction with RPGRIP provided the first clue for the retina-specific pathogenesis of X-linked RP3. Recently, mutations in RPGRIP were found to lead to the retinal dystrophy, Leber congenital amaurosis. However, mouse models null for RPGR had, surprisingly, a very mild phenotype compared with those observed in XlRP3-affected humans and dogs. Moreover, recent reports are seemingly in disagreement on the localization of RPGR and RPGRIP in photoreceptors. These discrepancies were compounded with the finding of RPGR mutations leading exclusively to X-linked cone dystrophy. To resolve these discrepancies and to gain further insight into the pathology associated with RPGR- and RPGRIP-allied retinopathies, we now show, using several isoform-specific antibodies, that RPGR and RPGRIP isoforms are distributed and co-localized at restricted foci throughout the outer segments of human and bovine, but not mice rod photoreceptors. In humans, they also localize in cone outer segments. RPGRIP is also expressed in other neurons such as amacrine cells. Thus, the data lend support to the existence of species-specific subcellular processes governing the function and/or organization of the photoreceptor outer segment as reflected by the species-specific localization of RPGR and RPGRIP protein isoforms in this compartment, and provide a rationale for the disparity of phenotypes among species and in the human.

Amino Acid Sequence↗
PubMed1985

Conservation of nif- and species-specific domains within repeated promoter sequences from fast-growing Rhizobium species.

In the fast-growing Rhizobium species, repeated DNA sequences, which include the promoter region of the nif HDK operon have been described. These repeated sequences are promoters which specifically activate transcription in the endosymbiotic state. Hybridization analysis of these sequences from R. trifolii has revealed that they may be involved in the species-specific activation of the various genes whose transcription they promote. Comparative analysis of various copies of these repeated sequences, from R. trifolii (the clover symbiont) and R. meliloti (the alfalfa symbiont), reveals the presence of domains of intra- and interspecific conservation within the promoter regions. We suggest that these promoter elements represent sites which are involved in the species-specific and general, nif-specific activation of Rhizobium symbiotic genes.

Klebsiella pneumoniae↗
PubMed1986

On the origin of species specificity of fibronectin. Immunological identification of a species-specific domain of human fibronectin.

We have investigated whether species-specific epitopes of human fibronectin are localized at a specific domain of fibronectin using rabbit polyclonal antibodies. Tryptic fragments of human fibronectin were tested for reactivity with anti-human fibronectin antibody, which had been previously absorbed with other animal fibronectin to establish species specificity. Human-specific epitopes were found to be present on 75,000, 65,000, and 42,000 dalton fragments. The 42,000-dalton fragment shares almost all the epitopes with the 75,000 and 65,000 dalton fragments. It does not promote BHK cell spreading, whereas the 75,000 and 65,000 dalton fragments do. The amino acid sequence from the amino terminus of the 42,000-dalton fragment is Asp/Gly-Gln/Val-?-Ile-Val-, which is almost identical to the sequence Asp-Gln-Cys-Ile-Val- located in the carboxyl terminal 1/3 of the collagen-binding domain of human fibronectin (Kornblihtt et al. (1985) EMBO J. 4, 1755-1759). These results suggest that human fibronectin bears human-specific epitopes mainly on the amino-terminal half of domain 4 (Hayashi & Yamada (1983) J. Biol. Chem. 258, 3332-3340) located between the collagen and cell binding domains almost at the center of the fibronectin polypeptide. The domain specific for human fibronectin may be a general species-specific domain of animal fibronectins.

Amino Acid Sequence↗
PubMed1998

Conservation of locus-specific microsatellite variability across species: a comparison of two Drosophila sibling species, D. melanogaster and D. simulans.

Fifteen microsatellite loci were studied in Drosophila melanogaster and Drosophila simulans, two closely related sibling species which split 2-3.5 MYA. Within-species variances in repeat number were found to differ up to 1,000-fold among individual microsatellite loci. A significant correlation of log variances between both species indicated a locus-specific mutation rate of microsatellites. Hence, locus-specific effects are apparently among the major forces influencing microsatellite variation and deserve more consideration in microsatellite analysis.

Africa↗
PubMed2005

Phylogenetic relationships and species differentiation of 39 Legionella species by sequence determination of the RNase P RNA gene rnpB.

The rnpB gene is ubiquitous in Bacteria, Archaea and Eucarya and encodes the RNA component of RNase P, an endoribonuclease P that consists of one RNA and one protein subunit (C5). In this study, partial rnpB genes were sequenced from 39 type strains and 16 additional strains of the genus Legionella. Models of the putative secondary structures of the RNase P RNA in the genus Legionella are proposed and possible interactions between RNase P RNA and C5 are discussed. The phylogenetic relationships within the genus Legionella were examined and rnpB sequences indicated six main clades that together comprised 27 of the 39 species examined. The phylogenetic relationships were further inferred by analysing combined datasets of sequences from the rnpB, mip, 16S rRNA and rpoB genes. It is concluded that rnpB is suitable for use in phylogenetic studies of closely related species and that it exhibits the potential to discriminate between Legionella species.

Bacterial Proteins↗
PubMed2007

Description of Sphingosinicella xenopeptidilytica sp. nov., a beta-peptide-degrading species, and emended descriptions of the genus Sphingosinicella and the species Sphingosinicella microcystinivorans.

A Gram-negative, rod-shaped bacterium, strain 3-2W4(T), was isolated from the aeration tank of a wastewater treatment plant in Zurich and was found to have the exceptional capacity to degrade synthetic beta-peptides. 16S rRNA gene sequence analysis showed that strain 3-2W4(T) is closely related to Sphingosinicella microcystinivorans Y2(T), but DNA-DNA hybridization experiments between these two strains revealed that they belong to two different species. The two strains displayed different fingerprints after PCR analysis using the repetitive primers BOX, ERIC and REP. Strain 3-2W4(T) did not degrade microcystin, which is a characteristic trait of Sphingosinicella microcystinivorans Y2(T). Like Sphingosinicella microcystinivorans Y2(T), strain 3-2W4(T) had the following characteristics: fatty acids comprising mainly C(18 : 1)omega7c, summed feature 3 (C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH) and C(16 : 0), the presence of ubiquinone Q-10 and sym-homospermidine as the predominant polyamine compound. The polar lipid profiles of the two strains were almost identical, consisting of phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and sphingoglycolipid. Strain 3-2W4(T) and Sphingosinicella microcystinivorans Y2(T) utilized the beta-peptides H-betahVal-betahAla-betahLeu-OH and H-betahAla-betahLeu-OH as sole carbon and energy sources and shared beta-peptidyl aminopeptidase activity in common, which distinguishes them from Sphingomonas and Sphingopyxis type strains. On the basis of these results, strain 3-2W4(T) represents a novel species of the genus Sphingosinicella, for which the name Sphingosinicella xenopeptidilytica sp. nov. is proposed. The type strain is 3-2W4(T) (=DSM 17130(T)=CCUG 52537(T)). The descriptions of the genus Sphingosinicella and the species Sphingosinicella microcystinivorans are emended.

Aminopeptidases↗
PubMed2002

Design of species-specific primers to identify 13 species of Clostridium harbored in human intestinal tracts.

The genus Clostridium is dominant in human intestinal tracts and plays an important role in human health. We designed species-specific primers to identify 13 species of Clostridium (C. perfringens, C. paraputrificum, C. bifermentans, C. difficile, C. clostridiiforme, C. nexile, C. sphenoides, C. indolis, C. ramosum, C. cocleatum, C. butyricum, C. sordellii, and C. innocuum) easily and rapidly. The PCR annealing temperature was set at a uniform 60 C for application to all strains at the same time. To confirm the specificities of these primers, 85 intestinal bacteria in total, including type strains, reference strains, and isolates were used. Ten primers (including those for C. perfringens to C. cocleatum) indicated high specificities. Although there were some cross-reactions with the other three primers, the target species were distinguishable from other bacteria by the different sizes of PCR products.

Clostridium↗
PubMed2004

Biofilm growth of Lactobacillus species is promoted by Actinomyces species and Streptococcus mutans.

The ability of oral bacteria to integrate within a biofilm is pivotal to their survival. A dependence on the amount of biofilm growth by noncoaggregating Lactobacillus rhamnosus and Lactobacillus plantarum on coculture with Actinomyces naeslundii, Actinomyces gerencseriae, Streptococcus mutans and Veillonella parvula was investigated using an artificial-mouth culture system. Biofilm formation by the lactobacilli in mono-culture was poor. In coculture with Actinomyces species the amount of L. rhamnosus increased 7-20 times and L. plantarum 4-7 times compared to its mono-culture biofilm. S. mutans also promoted substantial biofilm growth of lactobacilli but V. parvula had no effect. We conclude that these Actinomyces species promoted growth of key Lactobacillus species in a biofilm, as did S. mutans to a smaller extent, and that the ability of individual bacteria to form mono-culture biofilms is not necessarily an indicator of their survival and pathogenic potential in a complex multispecies biofilm community.

Actinomyces↗
PubMed1980

Comparison of the development of the fatty acid content and composition of the brain of a precocial species (guinea pig) and a non-precocial species (rat).

The fatty acid compositions of the brains of a precocial (guinea pig) and a non-precocial (rat) species have been studied as a function of development. In the rat brain the total fatty acid content expressed as mg g wet wt.-1 increased more than fourfold during the period from 5 days after birth to adulthood. However, the percentage composition of this total fatty acid content when expressed per individual fatty acid remained fairly constant, with the exception of nervonic acid (C24:1) which also increased fourfold on a percentage basis. In the guinea pig brain, however, at birth the total fatty acid content, expressed as mg g wet wt-1, is the same as that of the adult, the concentration doubling during the period from 25 days before birth until birth. Again, if the fatty acid content is analysed and expressed on a percentage basis, the relative concentrations of the individual fatty acids remain fairly constant over the period from 25 days before birth until adulthood, with the exception of nervonic (C24:1) acid which increases about fivefold from 25 days before birth to birth and only marginally (20%) from birth to adulthood. These results are discussed in relationship to the onset of neurological competence in the two species. It is concluded that the increase in fatty acid content (both total and individually) of the brains of these species as a function of the foetal and neonatal development follows a pattern which is similar to the pattern of development of certain key enzymes of energy metabolism and of neurological competence.

Aging↗
PubMed1987

Binding of [3H]Ro 5-4864 and [3H]PK 11195 to cerebral cortex and peripheral tissues of various species: species differences and heterogeneity in peripheral benzodiazepine binding sites.

The binding of [3H]PK 11195 and [3H]Ro 5-4864 to membrane preparations from cerebral cortex and peripheral tissues of various species was studied. [3H]PK 11195 (0.05-10 nM) bound with high affinity to rat and calf cerebral cortical and kidney membranes. [3H]Ro 5-4864 (0.05-30 nM) also successfully labeled rat cerebral cortical and kidney membranes, but in calf cerebral cortical and kidney membranes, its binding capacity was only 3 and 4%, respectively, of that of [3H]PK 11195. Displacement studies showed that unlabeled Ro 5-4864, diazepam, and flunitrazepam were much more potent in displacing [3H]PK 11195 from rat cerebral cortex and kidney membranes than from calf tissues. The potency of unlabeled Ro 5-4864 in displacing [3H]PK 11195 from the cerebral cortex of various other species was also tested, and the rank order of potency was rat = guinea pig greater than cat = dog greater than rabbit greater than calf. Analysis of these displacement curves revealed that Ro 5-4864 bound to two populations of binding sites from rat and calf kidney and from rat, guinea pig, rabbit, and calf cerebral cortex but to a single population of binding sites from cat and dog cerebral cortex. Using [3H]PK 11195 as a ligand, the rank order of binding capacity in cerebral cortex of various species was cat greater than calf greater than guinea pig greater than rabbit greater than dog greater than rat, whereas when [3H]Ro 5-4864 was used, the rank order of binding capacity was cat greater than guinea pig greater than rat greater than rabbit greater than calf greater than dog.

Animals↗
PubMed1996

Conservation and diversity of the Helicobacter pylori copper-transporting ATPase gene (copA) sequence among Helicobacter species and Campylobacter species detected by PCR and RFLP.

BACKGROUND: Helicobacter pylori is a causative pathogen of such human stomach diseases as chronic type B gastritis, ulcer, and possibly gastric carcinoma. As a cofactor in various redox enzymes and an essential trace metal required for the synthesis of metalloproteins, copper might play a role in the pathogenesis of H. pylori. A gene, copA, associated with copper transport, has been isolated from H. pylori UA802. In this study, conservation and diversity of this gene were analyzed among some Helicobacter and Campylobacter species. MATERIALS AND METHODS: Twenty-one clinical isolates and strains of helicobacters and campylobacters were used in this study. Methods including polymerase chain reaction (PCR) amplification, restriction fragment-length polymorphisms (RFLPs), and hybridization were employed to carry out this work. RESULTS: The copA gene was highly conserved in all the H. pylori isolates tested (Helicobacter nemestrinae and Helicobacter felis but not in Helicobacter mustelae and the Campylobacter species), whereas the sequence downstream of the copA appears to diverge among H. pylori isolates. In addition, two restriction patterns of the PCR-amplified copA fragments from seven H. pylori isolates and H. nemestrinae were identified, and the RFLP of H. nemestrinae was identical to that of one of the H. pylori isolate group. CONCLUSIONS: The adenosine triposphatase-derived copper-transporting mechanism is employed by various H. pylori strains, H. nemestrinae, H. felis, and perhaps by other Helicobacter species. The nucleotide mutations have risen in the copA gene. It appears that there is a genetic relatedness of the copA gene to H. pylori and H. nemestrinae.

Adenosine Triphosphatases↗
PubMed2006

Differences among species in compact bone tissue microstructure of mammalian skeleton: use of a discriminant function analysis for species identification.

In order to develop an identification key for distinguishing between several mammalian species, bone structure of their compact bone tissue was analyzed using qualitative and quantitative characteristics. Ninety femora of adult male humans, pigs, cows, sheep, rabbits, and rats were studied. The average area, perimeter, minimum, and maximum diameter of 1863 Haversian canals and 1863 secondary osteons were measured using a digital image device. The observed data were first used to evaluate inter- and intraspecies diversity. After that, we applied a discriminant function analysis for differentiation of the species by these variables. Classification functions for investigated species give cross-validated correct classification rates for 76.17% of cases. This percentage value can be increased by integrating conclusions from the qualitative analysis.

Adult↗
PubMed1994

Tracheobronchial washings from seven vertebrate species as growth media for the four species of Bordetella.

The four species of Bordetella differed in their ability to grow at 37 degrees C in membrane-filtered tracheobronchial washings (TBW) from seven vertebrate species, including their natural hosts. From washed inocula of approximately 2 x 10(3) colony-forming units per ml (cfu ml-1), Bordetella bronchiseptica and B. avium grew much better than the other two bordetellae and yielded stationary-phase cultures containing 10(8)-10(9) cfu ml-1 in most of the TBW samples. These counts were only moderately lower than those attained in CL medium which contains about a 450-times higher concentration of amino acids. B. bronchiseptica and B. avium also grew to a limited extent in phosphate-buffered saline without nutrient supplements. B. parapertussis grew in TBW from man, sheep, rabbit, mouse and chicken, but not in TBW from a dog and a horse or in PBS. B. pertussis grew well in CL medium, but not in PBS or in any of 13 samples of TBW from the seven vertebrate species, which included three samples of lung lavage fluid from human patients. Analysis of the TBW samples for known Bordetella nutrients revealed concentrations of amino acids and nicotinic acid averaging 0.35 mM and 0.56 microgram ml-1 respectively.

Amino Acids↗
PubMed1997

Presence of F420-dependent glucose-6-phosphate dehydrogenase in Mycobacterium and Nocardia species, but absence from Streptomyces and Corynebacterium species and methanogenic Archaea.

A range of organisms known to contain F420 or to be relatives of mycobacteria were examined for F420-dependent glucose-6-phosphate dehydrogenase (FGD) and NADP-dependent glucose-6-phosphate dehydrogenase (NADP-G6PD) activities. All free-growing Mycobacterium species examined (including a virulent Mycobacterium tuberculosis strain) had FGD activities of 0.014-0.418 mumol min-1 mg protein-1, and NADP-G6PD activities of 0.013-0.636 mumol min-1 mg-1. Armadillo-grown Mycobacterium leprae had FGD activity of 0.008 mumol min-1 mg-1, but no detectable NADP-G6PD activity. Nocardia species also had FGD activity (0.088-0.154 mumol min-1 mg-1). Streptomyces and Corynebacterium species had no FGD, but had NADP-G6PD. Methanogenic Archaea had neither activity.

Corynebacterium↗
PubMed1997

Monoclonal antibody against species-specific epitope of Pseudomonas aeruginosa Hsp60 protein cross-reacts with Pseudomonas stutzeri and other Pseudomonas species.

In a previous study, we determined the epitope of the Pseudomonas aeruginosa Hsp60 heat shock protein which is recognized by the specific monoclonal antibody (MAb) 2528. Subsequent investigations revealed a weak cross-reactivity of MAb 2528 with P. stutzeri, P. alcaligenes, P. mendocina and P. pseudoalcaligenes. To elucidate the molecular structure for these cross-reactions, we cloned the P. stutzeri hsp60 gene in Escherichia coli and determined the nucleotide sequence of the gene. In addition, the hsp60 gene of further Pseudomonas species was amplified and sequenced and amino acid substitutions within the epitope recognized by MAb 2528 were determined. The decapeptide QADIEARVLQ is unique to the P. aeruginosa Hsp60 protein, and cross-reaction of MAb 2528 reflects the phylogenetic relationship of Pseudomonas species as P. aeruginosa and all four cross-reacting species constitute a DNA homology group within the rRNA group I of the family Pseudomonadaceae, which belong to the gamma-subclass of the Proteobacteria.

Amino Acid Sequence↗
PubMed1990

Problems associated with identification of Legionella species from the environment and isolation of six possible new species.

Following investigation of an outbreak of legionellosis in South Australia, numerous Legionella-like organisms were isolated from water samples. Because of the limited number of commercially available direct fluorescent-antibody reagents and the cross-reactions found with some reagents, non-pneumophila legionellae proved to be difficult to identify and these isolates were stored at -70 degrees C for later study. Latex agglutination reagents for Legionella pneumophila and Legionella anisa developed by the Institute of Medical and Veterinary Science, Adelaide, Australia, were found to be useful as rapid screening aids. Autofluorescence was useful for placing isolates into broad groups. Cellular fatty acid analysis, ubiquinone analysis, and DNA hybridization techniques were necessary to provide definitive identification. The species which were isolated most frequently were L. pneumophila, followed by L. anisa, Legionella jamestowniensis, Legionella quinlivanii, Legionella rubrilucens, Legionella spiritensis, and a single isolate each of Legionella erythra, Legionella jordanis, Legionella birminghamensis, and Legionella cincinnatiensis. In addition, 10 isolates were found by DNA hybridization studies to be unrelated to any of the 26 currently known species, representing what we believe to be 6 possible new species.

Australia↗