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At least 415 records · Page 23Linked to original sources
PubMed2005

Positive selection of primate TRIM5alpha identifies a critical species-specific retroviral restriction domain.

Primate genomes encode a variety of innate immune strategies to defend themselves against retroviruses. One of these, TRIM5alpha, can restrict diverse retroviruses in a species-specific manner. Thus, whereas rhesus TRIM5alpha can strongly restrict HIV-1, human TRIM5alpha only has weak HIV-1 restriction. The biology of TRIM5alpha restriction suggests that it is locked in an antagonistic conflict with the proteins encoding the viral capsid. Such antagonistic interactions frequently result in rapid amino acid replacements at the protein-protein interface, as each genetic entity vies for evolutionary dominance. By analyzing its evolutionary history, we find strong evidence for ancient positive selection in the primate TRIM5alpha gene. This selection is strikingly variable with some of the strongest selection occurring in the human lineage. This history suggests that TRIM5alpha evolution has been driven by antagonistic interactions with a wide variety of viruses and endogenous retroviruses that predate the origin of primate lentiviruses. A 13-aa "patch" in the SPRY protein domain bears a dense concentration of positively selected residues, potentially implicating it as an antiviral interface. By using functional studies of chimeric TRIM5alpha genes, we show that this patch is generally essential for retroviral restriction and is responsible for most of the species-specific antiretroviral restriction activity. Our study highlights the power of evolutionary analyses, in which positive selection identifies not only the age of genetic conflict but also the interaction interface where this conflict plays out.

Amino Acid Sequence↗
PubMed1992

Species-specific identification of and distinction between Borrelia burgdorferi genomic groups by using 16S rRNA-directed oligonucleotide probes.

Examination of a number of previously published aligned Borrelia 16S rRNA sequences revealed the presence of regions which could serve as oligonucleotide probe targets for both species-specific identification of Borrelia burgdorferi and distinction between genomic groups. Total cellular RNA isolated from Borrelia cultures was used in slot blot analysis. Radiolabeled oligonucleotides designed to hybridize to specific 16S rRNA targets were used as probes. These probes allowed for both species-specific identification and genomic group typing of B. burgdorferi.

Bacterial Typing Techniques↗
PubMed1989

[Characteristics of monoclonal antibodies directed to species specific and group specific antigens of Rickettsia prowazekii].

A number of hybridomas against different determinants of R. prowazekii were obtained by hybridization of splenocytes from BALB/c mice immunized with whole cells or soluble antigens of the organism. Some of the monoclonal antibodies bound to thermolabile species specific protein of R. prowazekii and did not react with R. mooseri antigens (monoclonal antibodies series B4/4 and A3). Monoclonal antibodies C5/2 and A3/2 reacted with group specific thermostabile antigen which is common for both R. prowazekii and R. mooseri. Monoclonal antibodies against species specific antigen were found to be of Ig G2a subclass. The monoclonal antibodies can be used to identify R. prowazekii and R. mooseri and solve the problem of differentiating Rickettsiae of typhus group.

Animals↗
PubMed2005

Efficacy of species-specific recA PCR tests in the identification of Burkholderia cepacia complex environmental isolates.

In this study, we evaluated if recA species-specific PCR assays could be successfully applied to identify environmental isolates of the widespread Burkholderia cepacia complex (Bcc) species. A total of 729 Bcc rhizosphere isolates collected in different samplings were assigned to the species B. cepacia genomovar I (61), B. cenocepacia recA lineage IIIB (514), B. ambifaria (124) and B. pyrrocinia (30), by means of recA (RFLP) analysis, and PCR tests were performed to assess sensitivity and specificity of recA species-specific primers pairs. B. cepacia genomovar I specific primers produced the expected amplicon with all isolates of the corresponding species (sensitivity, 100%), and cross-reacted with all B. pyrrocinia isolates. On the contrary, B. cenocepacia IIIB primers did not give the expected amplicon in 164 B. cenocepacia IIIB isolates (sensitivity, 68.1%), and isolates of distinct populations showed different sensitivity. B. ambifaria primers failed to amplify a recA-specific fragment only in a few isolates of this species (sensitivity, 93.5%). The absence of specific amplification in a high number of B. cenocepacia rhizosphere isolates indicates that recA specific PCR assays can lead to an underestimation of environmental microorganisms belonging to this bacterial species.

Bacterial Proteins↗
PubMed2003

Species specific identification of the Neofabraea pathogen complex associated with pome fruits using PCR and multiplex DNA amplification.

Five species of pathogenic fungi belong to Neofabraea. One of these, N. krawtzewii (syn. N. populi), is responsible for bark lesions on poplar (Populus) trees. The other four species cause post-harvest bull's eye rot of pome fruits, and at least two of these also cause bark cankers on pome fruit trees. Morphological variation among these species is slight, and overlap in geographic range sometimes occurs. As a consequence, identification based on conventional criteria can be tenuous. PCR primers with putative species specificity were developed following genetic analysis of the beta-tubulin gene for isolates of each of the five species of Neofabraea. PCR conditions required to achieve specificity of the primer sets were determined, and a multiplex PCR protocol was developed to optimize their diagnostic utility on apple fruits. A protocol with higher annealing temperatures in the initial PCR cycles followed by lower temperatures in later cycles gave complete species-specificity when the primer sets were used individually and in multiplex, resulting in successful detection of the pathogens from axenic culture and infected apple fruits.

Ascomycota↗
PubMed2005

Potential for using isotopically altered metalloproteins in species-specific isotope dilution analysis of proteins by HPLC coupled to inductively coupled plasma mass spectrometry.

The production and evaluation of an isotopically enriched metalloprotein standard for use as a calibrant in species-specific isotope dilution analysis by HPLC coupled to inductively coupled plasma mass spectrometry is described. Using a model system involving the copper-containing protein rusticyanin (Rc) from the bacterium Acido-thiobacillus ferrooxidans, it was possible to demonstrate the analytical conditions that could be used for the measurement of metalloproteins by on-line IDMS analysis. Rc was chosen because it is a well-characterized protein with an established amino acid sequence and can be produced in suitable quantities using a bacterial recombinant system. Three different forms of the protein were studied by organic and inorganic mass spectrometry: the native form of the protein containing a natural isotopic profile for copper, an isotopically enriched species containing virtually all of its copper as the 65Cu isotope, and the nonmetalated apo form. Incorporation of the copper isotopes into the apo form of the protein was determined using a UV-vis spectrophotometric assay and shown to be complete for each of the copper-containing species. The experimental conditions required to maintain the conformational form of the protein with a nonexchangeable copper center were established using +ve electrospray mass spectrometry. A pH 7.0 buffer was found to afford the most appropriate conditions, and this was then used with HPLC-ICP-MS to verify the stability of the copper center by analysis of mixtures of different isotopic solutions. No exchange of the enriched copper isotope from Rc with an added naturally abundant inorganic copper cation was observed under a neutral pH environment, indicating that species-specific ID-MS analysis of metalloproteins is possible.

Acidithiobacillus thiooxidans↗
PubMed2006

Species-specific fibroblasts required for triggering invasiveness of partially transformed oral keratinocytes.

This study tests the hypothesis that invasion of partially transformed keratinocytes is initiated by diffusible, proinvasive signals provided by species-specific fibroblasts. In vitro organotypic cultures of neoplastic human oral mucosa were constructed by growing a partially transformed, nontumorigenic keratinocytic cell line isolated from a dysplastic human oral lesion (DOK-ECACC94122104) on top of various types of connective tissue equivalents. Cultured tissues were analyzed by histomorphometry (depth and area of invasion: Dinv, Ainv) and immunohistochemistry. Presence of human fibroblasts in the matrix induced a local invasion of DOK (Dinv = 95.6 +/- 7.1 microm, Ainv = 45.8 +/- 3.5%). Minimal invasion (P < 0.05) was observed when DOK grew on simple collagen matrix (Dinv = 14.1 +/- 2.1 microm, Ainv = 3.7 +/- 0.8%) or matrices containing fibroblasts from mouse (Dinv = 11.5 +/- 4.0 microm, Ainv = 4.3 +/- 1.0%) or rat (Dinv = 15.6 +/- 1.2 microm, Ainv = 6.1 +/- 0.5%). In these cultures, local invasion could be induced by the presence of human fibroblasts in a bottom layer of the collagen matrix (P < 0.05) or by conditioned medium from organotypic cultures of DOK on human fibroblast-containing matrix (P < 0.05) but not by conditioned medium from human fibroblast monocultures (P > 0.05). Deposition of human collagen IV was observed at epithelial-matrix interface only when DOK behaved invasively. In conclusion, invasion of partially transformed oral keratinocytes was triggered by keratinocyte-induced fibroblast-derived diffusible factor(s) in a species-specific manner and associated with de novo synthesis of collagen IV.

Animals↗
PubMed1996

[A study on plasma non-species specific antibody in employees working in a automobile engine testing workshop].

To investigate the existence of the non-species specific antibody in plasma of the employees working in an automobile engine testing workshop, and to use it as a scanning marker of various hazards, the heat-stress protein antigen method and western blot technique were used. This study showed that employees working in the automoblile engine testing workshop were affected by various hazards, such as noise, toxic chemicals (carbon monoxide, lead fume, benzene, and so on), and there existed non-species specific antibodies against protein 103,900 and 54,200 of rat liver in their plasma, which were postulated as the specific products produced by exposure to occupational hazards, such as noise, carbon monoxide, et al.

Adult↗
PubMed2004

Is voice processing species-specific in human auditory cortex? An fMRI study.

Recent studies suggested a sensitivity of regions of the human superior temporal sulcus (STS) to the sound of the human voice. However, the question of the species specificity of this response is still open. Healthy adult volunteers were scanned in an event-related fMRI design to compare responses in the STS to human and animal vocalizations, as well as to control nonvocal sounds (e.g., musical instruments). Bilateral activation of anterior STS was observed for human vocalizations, when contrasted with both nonvocal sounds and animal vocalizations. Animal vocalizations, compared to nonvocal sounds, elicited a more restricted left STS activation, although this region responded even more strongly to human vocalizations. This study provides the first evidence suggesting a species specificity in STS responses to vocalizations in humans.

Acoustic Stimulation↗
PubMed1996

Granulocytic protein p25 is a DNA-binding subunit of protein M(r) = 50,000: subcellular localization, cell and species specificity.

We have previously reported the presence and isolation of the novel protein M(r) = 25,000 (p25) from human granulocytes. In this study, the protein p25 was characterized by its: (a) ability to bind DNA, (b) subunit association, (c) partial protein sequencing, (d) subcellular localization, (e) cellular and species specificity and (f) stability in the presence of released granulocytic proteinases. For the detection of p25 in various extracts, fractions and types of human or animal hematopoietic cells, SDS-PAGE/Western blotting and immunohistochemical staining were used. The protein p25 was subjected to N-terminal amino acid sequence analysis. Protein p25-DNA interactions were monitored using Southwestern blotting. Selective inhibition of granulocytic proteinases was performed. Granulocytic protein p25 was found to be a product of oxidative cleavage of disulfide bridges in the p50 dimer. It was shown that neither protein p50 nor the p25 subunit is a degradation product of a protein of higher molecular weight. The N-terminal amino acid sequence of p25 was: RLNYNKPHAA. Binding capacity for double stranded DNA without significant sequence specificity was revealed and nuclear localization of some fraction of p50 dimer was established. The data concerning the cell and species specificity demonstrated that the protein is expressed only in normal human granulocytes. In summary, protein p25 originates from splitting of the p50 dimer. This subunit shows no identity with proteins already sequenced. DNA-binding of p25 is not sequence specific. It is concluded that the protein p50 is localized in the nuclei and cytoplasmic granules of mature human polymorphonuclear leukocytes or granulocytes of species high on the evolutionary tree. The functions of this protein remain to be determined.

Amino Acid Sequence↗
PubMed2004

Cytokine response profiles predict species-specific infection patterns in human GI nematodes.

This study investigated associations between pre-treatment cytokine expression and infection patterns, before and after de-worming, in humans exposed to two gastrointestinal nematode species. Quantitative measures of Ascaris lumbricoides and Trichuris trichiura infection (based on faecal egg counts) were estimated immediately before and 8-9 months after treatment in a Cameroonian population. Whole blood cytokine responses to parasite-derived antigens were assayed immediately pre-treatment. An overall measure of the tendency towards species-specific infection (increasing with A. lumbricoides faecal egg counts and decreasing with T. trichiura faecal egg counts) was significantly positively related to IL-10 levels in older (14-57 year) hosts. There was a significant negative influence of IL-5 on reinfection probability in T. trichiura but not A. lumbricoides. This effect coincided with reduced reinfection success in T. trichiura compared to A. lumbricoides. T(H)2 cytokine expression by younger hosts (4-13 year) was negatively associated with contemporary A. lumbricoides faecal egg counts before treatment. Following treatment, the pre-treatment T(H)2 cytokine expression data for younger hosts (now reflecting responsiveness 8-9 months in the past) were negatively associated with T. trichiura faecal egg counts. Taken together, these observations suggest a successional interaction between T(H)2-driven immune responses and species infection over time. However, any differential effects of the measured immune responses on species-specific recruitment, maturation and mortality were superimposed upon (and outweighed by) the effects of other factors favouring coinfection.

Adolescent↗
PubMed1988

Species-specificity of estradiol regulated growth factors in breast cancer.

Recent evidence indicates that autocrine/paracrine mechanisms may mediate the mitogenic effect of estradiol (E2) both in human and experimental breast cancer. However, the species-specificity of E2-regulated growth factors with regard to their biologic action has not been evaluated. To test this issue, we examined, in the soft agar clonogenic assay, the colony-stimulating activity in human breast cancers of conditioned media obtained from rat mammary carcinomas exposed to E2 (rat E2-CM). Of 22 primary human breast cancers plated in soft agar in the absence of serum, 18 (82%) successfully grew with a mean colony number of 62.4 +/- 9.8 (S.E.M.) (range 14-193). Rat E2-CM significantly stimulated colony formation in 10/18 (56%) human breast cancers to 155 +/- 11% (S.E.M.) of control. E2 administration (10(-9) M) in these tumors had a virtually identical overall effect (154 +/- 13% of control colony number). In the remaining eight tumors (44%), neither rat E2-CM nor E2 had, in general, a significant colony-stimulating effect. The growth-promoting action of rat E2-CM and E2 was not influenced by the hormone receptor status of the tumor. These results suggest that E2-regulated growth factors may not be species-specific, at least with regard to their colony-stimulating effects in soft agar.

Adult↗
PubMed2000

The high resolution crystal structure of green abalone sperm lysin: implications for species-specific binding of the egg receptor.

Abalone sperm lysin is a 16 kDa acrosomal protein used by sperm to create a hole in the egg vitelline envelope. Lysins from seven California abalone exhibit species-specificity in binding to their egg receptor, and range in sequence identity from 63 % to 90 %. The crystal structure of the sperm lysin dimer from Haliotis fulgens (green abalone) has been determined to 1.71 A by multiple isomorphous replacement. Comparisons with the structure of the lysin dimer from Haliotis rufescens (red abalone) reveal a similar overall fold and conservation of features contributing to lysin's amphipathic character. The two structures do, however, exhibit differences in surface residues and electrostatics. A large clustering of non-conserved surface residues around the waist and clefts of the dimer, and differences in charged residues around these regions, indicate areas of the molecule which may be involved in species-specific egg recognition.

Acrosome↗
PubMed2000

Expression of green fluorescent protein in Streptococcus gordonii DL1 and its use as a species-specific marker in coadhesion with Streptococcus oralis 34 in saliva-conditioned biofilms in vitro.

Streptococcus gordonii is one of the predominant streptococci in the biofilm ecology of the oral cavity. It interacts with other bacteria through receptor-adhesin complexes formed between cognate molecules on the surfaces of the partner cells. To study the spatial organization of S. gordonii DL1 in oral biofilms, we used green fluorescent protein (GFP) as a species-specific marker to identify S. gordonii in a two-species in vitro oral biofilm flowcell system. To drive expression of gfp, we isolated and characterized an endogenous S. gordonii promoter, PhppA, which is situated upstream of the chromosomal hppA gene encoding an oligopeptide-binding lipoprotein. A chromosomal chloramphenicol acetyltransferase (cat) gene fusion with PhppA was constructed and used to demonstrate that PhppA was highly active throughout the growth of bacteria in batch culture. A promoterless 0.8-kb gfp ('gfp) cassette was PCR amplified from pBJ169 and subcloned to replace the cat cassette downstream of the S. gordonii-derived PhppA in pMH109-HPP, generating pMA1. Subsequently, the PhppA-'gfp cassette was PCR amplified from pMA1 and subcloned into pDL277 and pVA838 to generate the Escherichia coli-S. gordonii shuttle vectors pMA2 and pMA3, respectively. Each vector was transformed into S. gordonii DL1 aerobically to ensure GFP expression. Flow cytometric analyses of aerobically grown transformant cultures were performed over a 24-h period, and results showed that GFP could be successfully expressed in S. gordonii DL1 from PhppA and that S. gordonii DL1 transformed with the PhppA-'gfp fusion plasmid stably maintained the fluorescent phenotype. Fluorescent S. gordonii DL1 transformants were used to elucidate the spatial arrangement of S. gordonii DL1 alone in biofilms or with the coadhesion partner Streptococcus oralis 34 in two-species biofilms in a saliva-conditioned in vitro flowcell system. These results show for the first time that GFP expression in oral streptococci can be used as a species-specific marker in model oral biofilms.

Amino Acid Sequence↗
PubMed1995

Operational RNA code for amino acids: species-specific aminoacylation of minihelices switched by a single nucleotide.

The genetic code is based on aminoacylation reactions where specific amino acids are attached to tRNAs bearing anticodon trinucleotides. However, the anticodon-independent specific aminoacylation of RNA minihelix substrates by bacterial and yeast tRNA synthetases suggested an operational RNA code for amino acids whereby specific RNA sequences/structures in tRNA acceptor stems correspond to specific amino acids. Because of the possible significance of the operational RNA code for the development of the genetic code, we investigated aminoacylation of synthetic RNA minihelices with a human enzyme to understand the sequences needed for that aminoacylation compared with those needed for a microbial system. We show here that the species-specific aminoacylation of glycine tRNAs is recapitulated by a species-specific aminoacylation of minihelices. Although the mammalian and Escherichia coli minihelices differ at 6 of 12 base pairs, two of the three nucleotides essential for aminoacylation by the E. coli enzyme are conserved in the mammalian minihelix. The two conserved nucleotides were shown to be also important for aminoacylation of the mammalian minihelix by the human enzyme. A simple interchange of the differing nucleotide enabled the human enzyme to now charge the bacterial substrate and not the mammalian minihelix. Conversely, this interchange made the bacterial enzyme specific for the mammalian substrate. Thus, the positional locations (if not the actual nucleotides) for the operational RNA code for glycine appear conserved from bacteria to mammals.

Amino Acyl-tRNA Synthetases↗
PubMed1987

Species-specific antibodies to Leishmania tropica (minor) recognize somatic antigens and exometabolites.

Monoclonal antibodies were raised against membranes of Leishmania tropica (formerly L. tropica minor). These antibodies do not react with membranes or homogenates prepared from any other species of Leishmania examined. The antigens identified by all four monoclonal antibodies reside on the external surface of the promastigote and are released into the culture medium. Immunoprecipitation of metabolically ([3H]glucose, -glucosamine, or [35S]methionine)-labeled, [125I]lactoperoxidase-labeled, or Western blot analysis of the parasites identified species-specific determinants residing on several different molecules with Mr between 12,000 and 140,000. All of the monoclonal antibodies appear to recognize determinants on a common [3H]sugar-labeled glycoconjugate, Mr = 32,000 to 44,000, but also react with additional components of 55,000, 80,000, 92,000, and 130,000 m.w. Antibody binding to the parasites is very sensitive to mild oxidation with periodate, suggesting that the species-specific determinants are carbohydrate in nature.

Animals↗
PubMed1992

Proximal sequence element factor binding and species specificity in vertebrate U6 snRNA promoters.

The Xenopus tropicalis U6 gene is very poorly transcribed both when introduced into human cells by transfection, and in human cell-free extracts. By analysis of hybrid promoters constructed from human and Xenopus sequences in various combinations, we show that species specificity is mediated by the proximal sequence elements (PSEs) of the promoters. We demonstrate the PSE-dependence of U6 transcription in a fractionated extract of HeLa cells. One of the fractions required for transcription contains an activity designated PSE-binding protein (PBP), previously shown to bind to the PSE of the mouse U6 gene. Binding of PBP to various wild-type and hybrid U6 PSE sequences correlates with their activity in transcription in HeLa cell extracts. This provides strong evidence that PBP is the PSE-binding factor involved in U6 transcription. In addition, it suggests that the differential affinities of the promoters for PBP is responsible for the observed species specificity. The divergence between U snRNA promoters in different species contrasts with the relatively strong conservation of other families of RNA polymerase II and III transcribed gene promoters. Possible mechanisms by which this diversity could be generated are discussed.

Animals↗
PubMed2002

Species-specific differences in organization of orthopoxvirus kelch-like proteins.

Organization of orthopoxvirus proteins of the kelch superfamily and their genes were analyzed and compared. Complete genomic sequences of variola (VAR), monkeypox (MPV), vaccinia (VAC), and species-specific regions of cowpox (CPV) viruses were used in the work. Despite the multiplicity of kelch-like proteins in orthopoxviruses, their function is still vague. It has been discovered that the genes of orthopoxvirus kelch-like proteins are localized only to the terminal variable regions of the genome and display species-specific differences in the lengths of the proteins they potentially encode. All the genes belonging to kelch superfamily in the genome of VAR, which has the only host-the man, are mutationally destroyed. However, CPV, displaying the widest host range among orthopoxviruses, encode the most numerous set of kelch-like proteins. Weak homologies between kelch-like proteins of one virus were demonstrated as well as high homologies between isologues of different orthopoxvirus species. The comparison performed suggest that CPV virus is most ancient and may be considered as the ancestor of other orthopoxviruses pathogenic for humans.

Amino Acid Sequence↗