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At least 451 records · Page 25Linked to original sources
PubMed2001

Relationships within the Proteobacteria of plant pathogenic Acidovorax species and subspecies, Burkholderia species, and Herbaspirillum rubrisubalbicans by sequence analysis of 16S rDNA, numerical analysis and determinative tests.

Sequence data for 16S rDNA of the type strains of Acidovorax avenae subsp. avenae, A. avenae subsp. cattleyae, A. avenae subsp. citrulli, A. konjaci and Herbaspirillum rubrisubalbicans were compared with GenBank library accessions of Burkholderia spp., Comamonas sp., Ralstonia solanacearum and Variovorax sp. Maximum Parsimony analysis produced two clusters: 1. Acidovorax spp., Comamonas sp., and Variovorax sp. (all in the Comamonadaceae), and 2. Burkholderia spp., Ralstonia solanacearum, and Herbaspirillum rubrisubalbicans. Maximum Likelihood analysis produced only one cluster (of the Comamonadaceae). Using nutritional and laboratory tests, all Acidovorax spp., Burkholderia spp., and Herbaspirillum rubrisubalbicans were discriminated in distinct clusters at the species level, and could be identified by selected determinative tests. There were no phenotypic tests constituted as a circumscription of the genera and which permitted the allocation of strains to genera. Strain identification as species allowed allocation to genera only by inference. The nomenclatural implications of these data are discussed.

Base Sequence↗
PubMed1996

Blood radicals: reactive nitrogen species, reactive oxygen species, transition metal ions, and the vascular system.

Free radicals, such as superoxide, hydroxyl and nitric oxide, and other "reactive species", such as hydrogen peroxide, hypochlorous acid and peroxynitrite, are formed in vivo. Some of these molecules, e.g. superoxide and nitric oxide, can be physiologically useful, but they can also cause damage under certain circumstances. Excess production of reactive oxygen or nitrogen species (ROS, RNS), their production in inappropriate relative amounts (especially superoxide and NO) or deficiencies in antioxidant defences may result in pathological stress to cells and tissues. This oxidative stress can have multiple effects. It can induce defence systems, and render tissues more resistant to subsequent insult. If oxidative stress is excessive or if defence and repair responses are inadequate, cell injury can be caused by such mechanisms as oxidative damage to essential proteins, lipid peroxidation, DNA strand breakage and base modification, and rises in the concentration of intracellular "free" Ca(2+). Considerable evidence supports the view that oxidative damage involving both ROS and RNS is an important contributor to the development of atherosclerosis. Peroxynitrite (derived by reaction of superoxide with nitric oxide) and transition metal ions (perhaps released by injury to the vessel wall) may contribute to lipid peroxidation in atherosclerotic lesions.

Animals↗
PubMed1981

Development of species identification in ducklings: VIII. Embryonic versus postnatal critical period for the maintenance of species-typical perception.

It was previously demonstrated that the domestic mallard duck embryo must be exposed to its embryonic contact-contentment call at a repetition rate of four notes per second in order for the neonate to manifest the species-typical preference for the species maternal call at its normal rate (3.7 notes/sec) after hatching. The present study examined whether the exposure to the contact call must occur in the late embryonic period in order to be effective. It was found that exposure for as little as 5 min/hr for 24 hr was sufficient for normal perceptual development and that such stimulation could occur either before or after hatching, provided that a 48-hr "consolidation" period intervened between the end of stimulation and testing.

Age Factors↗
PubMed1995

Immunohistological staining of lymphoid tissue in four Australian marsupial species using species cross-reactive antibodies.

Antibodies raised against evolutionarily conserved intracytoplasmic peptide sequences of human T and B lymphocyte antigens and an antibody raised specifically against koala serum IgG were assessed for their capacity for immunoperoxidase staining of formalin fixed lymphoid tissues of koalas (Phascolarctos cinereus), common brushtail possums (Trichosurus vulpecula), common ringtail possums (Pseudocheirus peregrinus) and tammar wallabies (Macropus eugenii). Utilizing microwave pretreatment and a streptavidin biotin-horseradish peroxidase method for histochemical staining, polyclonal anti-human CD3 (for T cells), monoclonal anti-human CD5 (for T cells), monoclonal anti-human CD79b cy (for B cells) and polyclonal anti-koala IgG (for plasma cells) consistently stained lymphoid elements in a wide range of tissues from all four marsupial species. Monoclonal anti-human CD79a cy (for B cells) stained lymphoid elements in only brushtail possums. This is the first report of immunohistological staining of lymphocytes in Australian marsupials, thereby vastly increasing the scope for immunological studies in these species.

Amino Acid Sequence↗
PubMed1978

Species specificity of cholecystokinin in gut and brain of several mammalian species.

Immunoreactive intact cholecystokinin and its COOH-terminal octapeptide are found in brain as well as in extracts of gut of the monkey, dog, and pig, by using an antiserum with equivalent sensitivities for detecting the octapeptide in free form or incorporated in the intact molecule. The failure to detect intact cholecystokinin in extracts from monkey or dog by using an antiserum developed by immunization with porcine cholecystokinin is presumed to be due to marked species differences in the NH2-terminal portion of the molecule. Tryptic digestion converted the intact cholecystokinin from all species to a peptide resembling the COOH-terminal octapeptide. The amount of cholecystokinin in the brain is comparable to that found in the gastrointestinal tract, the traditional site for this peptide.

Animals↗
PubMed2002

Development of novel fluorescence probes that can reliably detect reactive oxygen species and distinguish specific species.

We designed and synthesized 2-[6-(4'-hydroxy)phenoxy-3H-xanthen-3-on-9-yl]benzoic acid (HPF) and 2- [6-(4'-amino)phenoxy-3H-xanthen-3-on-9-yl]benzoic acid (APF) as novel fluorescence probes to detect selectively highly reactive oxygen species (hROS) such as hydroxyl radical (*OH) and reactive intermediates of peroxidase. Although HPF and APF themselves scarcely fluoresced, APF selectively and dose-dependently afforded a strongly fluorescent compound, fluorescein, upon reaction with hROS and hypochlorite ((-)OCl), but not other reactive oxygen species (ROS). HPF similarly afforded fluorescein upon reaction with hROS only. Therefore, not only can hROS be differentiated from hydrogen peroxide (H(2)O(2)), nitric oxide (NO), and superoxide (O2*-) by using HPF or APF alone, but (-)OCl can also be specifically detected by using HPF and APF together. Furthermore, we applied HPF and APF to living cells and found that HPF and APF were resistant to light-induced autoxidation, unlike 2',7'-dichlorodihydrofluorescein, and for the first time we could visualize (-)OCl generated in stimulated neutrophils. HPF and APF should be useful as tools to study the roles of hROS and (-)OCl in many biological and chemical applications.

Carcinoma, Hepatocellular↗
PubMed1992

Comparative life spans of species: why do species have the life spans they do?

Proximate answers to questions about species longevity are to be found in the physiological processes that regulate duration of life. But what are these processes, and how are they themselves controlled? This leads to ultimate, evolutionary questions about longevity. What are the selection forces that favor one life span instead of another for a given species? To understand the evolution of life span we need also to understand the evolution of aging. A plausible hypothesis is that because of the requirement for reproduction, natural selection favors a strategy that invests fewer resources in maintenance of somatic cells and tissues than are necessary for indefinite survival. This "disposable soma" theory predicts that aging is due to the accumulation of unrepaired somatic defects and the primary genetic control of longevity operates through selection to raise or lower the investment in basic cellular maintenance systems in relation to the level of environmental hazard.

Aging↗
PubMed1998

The regulation of primate immunodeficiency virus infectivity by Vif is cell species restricted: a role for Vif in determining virus host range and cross-species transmission.

The primate immunodeficiency virus Vif proteins are essential for replication in appropriate cultured cell systems and, presumably, for the establishment of productive infections in vivo. We describe experiments that define patterns of complementation between human and simian immunodeficiency virus (HIV and SIV) Vif proteins and address the determinants that underlie functional specificity. Using human cells as virus producers, it was found that the HIV-1 Vif protein could modulate the infectivity of HIV-1 itself, HIV-2 and SIV isolated from African green monkeys (SIVAGM). In contrast, the Vif proteins of SIVAGM and SIV isolated from Sykes' monkeys (SIVSYK) were inactive for all HIV and SIV substrates in human cells even though, at least for the SIVAGM protein, robust activity could be demonstrated in cognate African green monkey cells. These observations suggest that species-specific interactions between Vif and virus-producing cells, as opposed to between Vif and virus components, may govern the functional consequences of Vif expression in terms of inducing virion infectivity. The finding that the replication of murine leukemia virus could also be stimulated by HIV-1 Vif expression in human cells further supported this notion. We speculate that species restrictions to Vif function may have contributed to primate immunodeficiency virus zoonosis.

Animals↗
PubMed1983

The nucleotide sequences of 5S rRNAs from two Annelida species, Perinereis brevicirris and Sabellastarte japonica, and an Echiura species, Urechis unicinctus.

The nucleotide sequences of 5S rRNAs from two Annelida species, Perinereis brevicirris and Sabellastarte japonica, and an Echiura species, Urechis unicinctus have been determined. Their sequences are all 120 nucleotides long. The sequence similarity percents are 88% (Perinereis/Sabellastarte), 90% (Sabellastarte/Urechis) and 92% (Perinereis/Urechis), indicating that the Echiura is indistinguishable from the Annelida by their 5S rRNAs. The 5S rRNA sequences from the Annelida/Echiura are most related to those from the Nemertinea (87%), the Mollusca (87%) and the Rotifera (88%).

Animals↗
PubMed2000

A quantitative genetic model for analyzing species differences in outcrossing species.

A genetic model based on a two-level intra- and interspecific mating design is proposed to estimate the genetic architecture of species differences and heterosis for outcrossing species. The underlying genetic analyses make use of classical quantitative genetic theories and recent results from molecular genetic studies. Gene effects across different quantitative trait loci (QTL) can be approximated by a geometric series. Under natural selection, gene effects are often associated with allele frequencies in a particular way, which can be approximated by the gamma distribution. By incorporating these approximations into family structural analyses in the mating design, we are able to estimate a number of genetic parameters that contribute to quantitative genetic variation based on a nonlinear optimization approach. These parameters include the number of QTL, their gene effects, and their allele frequencies in the parental populations. We perform simulation studies and illustrate an example to demonstrate the statistical property and procedure of the method.

Alleles↗
PubMed1979

Species specific grass pollen sensitivity: diagnosis and treatment with single grass species Allpyral vaccines.

Skin test titrations and nasal provocation tests in sixty patients with hay fever showed specific reactions to extracts of individual grass species. There was, however, no correlation between skin and nasal sensitivity. Repeat testing after treatment with Allpyral vaccines consisting of only the grass species to which the nasal reaction was most severe, or only one of several pollens to which reactions were equally severe, showed marked diminution of skin and nasal sensitivity not only to the single pollen used for immuno-therapy but to all five common pollens used in the Allpyral grass mix. Clinical results seemed much improved as compared with results in the same year for Allpyral five grass mix vaccines, especially in the case of patients treated with Timothy, rye, or cocksfoot. It was concluded that these three grassees were to be preferred for treatment in England, and that these grasses contain common allergens.

Dose-Response Relationship, Immunologic↗
PubMed1978

Alfalfa mosaic virus RNA. Determination of the sequence homology between the four RNA species and a comparison with the four RNA species of cucumber mosaic virus.

The method of Taylor et al. [Taylor, J. M., Illmensee, R & Summers, J. (1976) Biochim. Biophys. Acta, 442, 324--330 and Gould and Symons (1977) Nucleic Acids Res. 4, 3787--3802] has been used to transcribe complementary DNA probes from the four major RNAs of alfalfa mosaic virus (AMV). Analysis of the kinetics of hybridization of these probes in homologous and heterologous complementary DNA . RNA hybridization reactions has shown that the sequence of the smallest RNA (RNA 4), which contains the coat protein gene, is present within RNA 3 and located at the 3' end of this RNA species. RNAs 1 and 2 are unique RNA molecules with little or no sequence homology between them or RNAs 3 and 4. This latter observation contrasts with the situation that occurs in cucumber mosaic virus (CMV) as CMV RNAs 1--4 were shown to have a common nucleotide stretch of 200 bases at their 3' termini; the location of RNA 4 within RNA 3 of CMV was also shown to be at the 3' end of this RNA species.

Avian Myeloblastosis Virus↗
PubMed2005

Species-directed 16S rRNA gene nested PCR detection of Olsenella species in association with endodontic diseases.

AIMS: To investigate the occurrence of Olsenella uli and Olsenella profusa in samples taken from infections of endodontic origin using a devised 16S RNA gene-based nested PCR protocol. METHODS AND RESULTS: DNA extracted from clinical samples was initially amplified using universal 16S rRNA gene primers followed by a second round of amplification using the first PCR products to detect a specific fragment of either O. uli or O. profusa 16S rRNA gene. Olsenella uli was detected in 27% of samples from teeth with asymptomatic periradicular lesions and in 20% of pus samples taken from symptomatic (abscess) lesions. Olsenella profusa was detected in 7% of asymptomatic teeth and in 13% of symptomatic teeth. A new Olsenella phylotype was also detected. CONCLUSIONS: Olsenella species can take part in the microbiota associated with infections of the root canal of human teeth and a role in the pathogenesis of periradicular diseases is suspected. SIGNIFICANCE AND IMPACT OF THE STUDY: The present study demonstrates that molecular genetic methods keep expanding the list of candidate endodontic pathogens to include Olsenella species.

Actinobacteria↗
PubMed2000

Rapid identification of 11 human intestinal Lactobacillus species by multiplex PCR assays using group- and species-specific primers derived from the 16S-23S rRNA intergenic spacer region and its flanking 23S rRNA.

Rapid and reliable two-step multiplex polymerase chain reaction (PCR) assays were established to identify human intestinal lactobacilli; a multiplex PCR was used for grouping of lactobacilli with a mixture of group-specific primers followed by four multiplex PCR assays with four sorts of species-specific primer mixtures for identification at the species level. Primers used were designed from nucleotide sequences of the 16S-23S rRNA intergenic spacer region and its flanking 23S rRNA gene of members of the genus Lactobacillus which are commonly isolated from human stool specimens: Lactobacillus acidophilus, Lactobacillus crispatus, Lactobacillus delbrueckii (ssp. bulgaricus and ssp. lactis), Lactobacillus fermentum, Lactobacillus gasseri, Lactobacillus jensenii, Lactobacillus paracasei (ssp. paracasei and ssp. tolerans), Lactobacillus plantarum, Lactobacillus reuteri, Lactobacillus rhamnosus and Lactobacillus salivarius (ssp. salicinius and ssp. salivarius). The established two-step multiplex PCR assays were applied to the identification of 84 Lactobacillus strains isolated from human stool specimens and the PCR results were consistent with the results from the DNA-DNA hybridization assay. These results suggest that the multiplex PCR system established in this study is a simple, rapid and reliable method for the identification of common Lactobacillus isolates from human stool samples.

Bacterial Typing Techniques↗
PubMed1999

Extensive biliary excretion of the sulfasalazine analogue, susalimod, but different concentrations in the bile duct in various animal species correlating to species-specific hepatobiliary toxicity.

Studies on biliary concentrations of susalimod were conducted in rat, dog and monkey to clarify the interspecies differences observed in toxicology studies with respect to hepatobiliary toxicity after long-term administration of the compound. Dose-related bile duct hyperplasia appeared only in dogs at doses > or =75 mg/kg/day, while in rats and monkeys it did not appear at doses up to 1500 and 2000 mg/kg/day respectively. Biliary excretion was investigated after intraduodenal administration of susalimod in anaesthetised animals. In addition excretion routes were determined by collecting urine and faeces following a radiolabelled intravenous dose. Susalimod was extensively excreted via the bile in all animal species, > or =90%, mainly as non-conjugated parent compound. However, the local concentrations in bile varied between the species. Highest concentrations were obtained in the dog. The bile/plasma concentration ratio was 3400 in the dog, 300 in the monkey and 50 in the rat. In the dog, bile duct concentrations of susalimod about 30,000 micromol/l was obtained at plasma concentrations approximately similar to those at which hepatobiliary toxicity occurred, while in rat and monkey the levels were < or =7000 micromol/l at plasma concentrations similar to those obtained at the highest doses in the toxicology studies. From these results supported by a previous biliary excretion study in conscious dogs with chronic bile fistula receiving repeated administration of susalimod (Påhlman et al. 1999), it is likely that the hepatotoxic findings in dog are induced by the high concentrations of susalimod in the bile duct.

Animals↗
PubMed2006

Genome sequence and global gene expression of Q54, a new phage species linking the 936 and c2 phage species of Lactococcus lactis.

The lytic lactococcal phage Q54 was previously isolated from a failed sour cream production. Its complete genomic sequence (26,537 bp) is reported here, and the analysis indicated that it represents a new Lactococcus lactis phage species. A striking feature of phage Q54 is the low level of similarity of its proteome (47 open reading frames) with proteins in databases. A global gene expression study confirmed the presence of two early gene modules in Q54. The unusual configuration of these modules, combined with results of comparative analysis with other lactococcal phage genomes, suggests that one of these modules was acquired through recombination events between c2- and 936-like phages. Proteolytic cleavage and cross-linking of the major capsid protein were demonstrated through structural protein analyses. A programmed translational frameshift between the major tail protein (MTP) and the receptor-binding protein (RBP) was also discovered. A "shifty stop" signal followed by putative secondary structures is likely involved in frameshifting. To our knowledge, this is only the second report of translational frameshifting (+1) in double-stranded DNA bacteriophages and the first case of translational coupling between an MTP and an RBP. Thus, phage Q54 represents a fascinating member of a new species with unusual characteristics that brings new insights into lactococcal phage evolution.

Amino Acid Sequence↗
PubMed1997

Diversity of the 32-kilodalton protein gene may form a basis for species determination of potentially pathogenic mycobacterial species.

In this study, partial gene sequences of the mycobacterial 32-kDa protein gene were determined by PCR-based sequencing. A total of 50 strains representing 18 potentially pathogenic mycobacterial species were studied. In 10 cases, all three strains of the species studied were identical, and intraspecies variability was found in 6 cases. Thus, the 32-kDa protein gene may be a good target for identification of mycobacteria by PCR-based sequencing.

Amino Acid Sequence↗
PubMed2005

Use of the Diversi Lab System for species and strain differentiation of Fusarium species isolates.

Advances in molecular typing of fusariosis would facilitate the study of its epidemiology. We tested 26 such isolates by the commercially available Diversi Lab System. The system utilizes automated repetitive sequence-based PCR (rep-PCR) and web-based data analyses. rep-PCR dendrogram cluster analysis showed agreement with species sequence identification (elongation factor 1 alpha gene). Additionally, subtype differences within the same species were noted.

Bacterial Typing Techniques↗