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PubMed1999

Specific interaction of Tat with the human but not rodent P-TEFb complex mediates the species-specific Tat activation of HIV-1 transcription.

Tat stimulation of HIV-1 transcriptional elongation is species-specific and is believed to require a specific cellular cofactor present in many human and primate cells but not in nonpermissive rodent cells. Human P-TEFb, composed of Cdk9 and cyclin T1, is a general transcription elongation factor that phosphorylates the C-terminal domain of RNA polymerase II. Previous studies have also implicated P-TEFb as a Tat-specific cellular cofactor and, in particular, human cyclin T1 as responsible for the species-specific Tat activation. To obtain functional evidence in support of these hypotheses, we generated and examined the activities of human-rodent "hybrid" P-TEFb complexes. We found that P-TEFb complexes containing human cyclin T1 complexed with either human or rodent Cdk9 supported Tat transactivation and interacted with the Tat activation domain and the HIV-1 TAR RNA element to form TAR loop-dependent ribonucleoprotein complexes. Although a stable complex containing rodent cyclin T1 and human Cdk9 was capable of phosphorylating CTD and mediating basal HIV-1 elongation, it failed to interact with Tat and to mediate Tat transactivation, indicating that the abilities of P-TEFb to support basal elongation and Tat activation can be separated. Together, our data indicated that the specific interaction of human P-TEFb with Tat/TAR, mostly through cyclin T1, is crucial for P-TEFb to mediate a Tat-specific and species-restricted activation of HIV-1 transcription. Amino acid residues unique to human Cdk9 also contributed partially to the formation of the P-TEFb-Tat-TAR complex. Moreover, the cyclin box of cyclin T1 and its immediate flanking region are largely responsible for the specific P-TEFb-Tat interaction.

Animals↗

PubMed2005

Virtual vocalization stimuli for investigating neural representations of species-specific vocalizations.

Most studies investigating neural representations of species-specific vocalizations in non-human primates and other species have involved studying neural responses to vocalization tokens. One limitation of such approaches is the difficulty in determining which acoustical features of vocalizations evoke neural responses. Traditionally used filtering techniques are often inadequate in manipulating features of complex vocalizations. Furthermore, the use of vocalization tokens cannot fully account for intrinsic stochastic variations of vocalizations that are crucial in understanding the neural codes for categorizing and discriminating vocalizations differing along multiple feature dimensions. In this work, we have taken a rigorous and novel approach to the study of species-specific vocalization processing by creating parametric "virtual vocalization" models of major call types produced by the common marmoset (Callithrix jacchus). The main findings are as follows. 1) Acoustical parameters were measured from a database of the four major call types of the common marmoset. This database was obtained from eight different individuals, and for each individual, we typically obtained hundreds of samples of each major call type. 2) These feature measurements were employed to parameterize models defining representative virtual vocalizations of each call type for each of the eight animals as well as an overall species-representative virtual vocalization averaged across individuals for each call type. 3) Using the same feature-measurement that was applied to the vocalization samples, we measured acoustical features of the virtual vocalizations, including features not explicitly modeled and found the virtual vocalizations to be statistically representative of the callers and call types. 4) The accuracy of the virtual vocalizations was further confirmed by comparing neural responses to real and synthetic virtual vocalizations recorded from awake marmoset auditory cortex. We found a strong agreement between the responses to token vocalizations and their synthetic counterparts. 5) We demonstrated how these virtual vocalization stimuli could be employed to precisely and quantitatively define the notion of vocalization "selectivity" by using stimuli with parameter values both within and outside the naturally occurring ranges. We also showed the potential of the virtual vocalization stimuli in studying issues related to vocalization categorizations by morphing between different call types and individual callers.

Acoustic Stimulation↗

PubMed2005

Reciprocal controlled crosses between Pinus sylvestris and P. mugo verified by a species-specific cpDNA marker.

A species-specific marker of cpDNA (paternally inherited in pines) was used to verify the hybrid origin of seedlings from controlled reciprocal crosses between Pinus sylvestris and P. mugo. A very low degree of compatibility between those two species has been revealed. In the three consecutive years of experiments, no filled seeds were obtained in the combination with P. mugo as the seed parent. From P. sylvestris as the seed parent and P. mugo as the pollen donor, we succeeded to obtain four filled seeds (about 1 %), but only in one year. The seedling obtained from the seeds had cpDNA haplotypes specific to P. mugo, which proves their hybrid origin. This method enables verification of the result of controlled crosses. The importance of the results has been discussed in the aspect of postulated natural hybridisation in sympatric populations of the two species.

DNA, Plant↗

PubMed2001

Species-specific PCR for the identification of ovine, porcine and chicken species in meta and bone meal (MBM).

BSE, first identified in the UK in 1986 is thought to have arisen from feeding scrapie infected Meat and Bone Meal (MBM), produced under sub-optimal conditions, to cattle. For quality and safety reasons there is a requirement for a good analytical test for the surveillance of processed MBM. This study describes species-specific PCR assays for the identification of ovine, porcine and poultry species in MBM. A comparison between two distinct DNA extraction methods, i.e. the silicaguanidiumthiocyanate DNA isolation procedure and a commercial DNA extraction kit, is also presented. Application of this technology to species identification in industrial MBM was investigates as part of this study.

Animal Feed↗

PubMed2002

Characterization of Lactobacillus plantarum from wine must by PCR species-specific and RAPD-PCR.

AIMS: Physiological and molecular analysis such as PCR species-specific and randomly amplified polymorphic PCR (RAPD-PCR) have been used for typing of Lactobacillus plantarum strains from typical wine must. METHODS AND RESULTS: Phenotypic tests such as API 50CH and evaluation of D-L-lactate production from glucose were used to perform a preliminary characterization of lactobacilli. Furthermore, 18 strains of lactobacilli were analyzed by PCR species-specific oligonucleotides based on short sequences of the recA gene. CONCLUSIONS: Four strains were identified as belonging to the L. plantarum species and were further analysed by RAPD-PCR. The RAPD-PCR profiles were similar in all strains that had positive results for species-specific PCR, suggesting that the four L. plantarum strains were closely related. SIGNIFICANCE AND IMPACT OF THE STUDY: Using PCR species-specific as a preliminary screening test and then RAPD-PCR can be as considered the most reliable method of performing a rapid and correct typing of L. plantarum from wine must.

Bacteriocins↗

PubMed1984

Syngeneic monoclonal antibodies against melanoma antigens with species specificity and interspecies cross-reactivity.

The species-specific and the interspecies cross-reactive melanoma antigenic determinants are defined by the monoclonal antibodies raised by syngeneic immunizations. The two types of monoclonal antibodies (M562 or M622 and M2590) were obtained by the fusion of P3U1 murine myeloma cell lines and spleen cells of C57BL/6 mice hyperimmunized with MMC-treated syngeneic B16 melanoma cells. The M2590 antibody recognizes the cross-species melanoma determinant commonly shared among at least mouse, hamster, and human, while the M562 or M622 antibody reacts with the mouse (B16) melanoma antigenic determinant. The immunochemical and physiochemical characteristics of the melanoma antigens on SDS-PAGE analyses show that these two characteristic determinants are present on the same molecule (molecular weight of 31,000) of a glycoprotein. Furthermore, the interspecies cross-reactive melanoma antigenic determinants are possibly composed of the sugar moiety, whereas the species-specific determinants seem to be proteinaceous in nature.

Animals↗

PubMed2005

Species-specific effects of the hepatocarcinogens 3'-methyl-4-dimethyl-aminoazobenzene and ortho-aminoazotoluene in mouse and rat liver.

The effects of rat-specific hepatocarcinogen 3'-methyl-4-dimethylaminoazobenzene (3'-MeDAB), mouse-specific hepatocarcinogen ortho-aminoazotoluene (OAT), non-species-specific hepatocarcinogen diethylnitrosamine (DENA), and non-carcinogenic 4'-methyl-4-dimethylaminoazobenzene (4'-MeDAB) on glucocorticoid induction of tyrosine aminotransferase (TAT) and DNA-binding activity of hepatocyte nuclear factor 3 (HNF3) family of transcription factors were investigated with carcinogen-susceptible and -resistant animals. Species-specific hepatocarcinogens 3'-MeDAB and OAT strongly inhibited glucocorticoid induction of TAT in the liver of susceptible but not resistant animals. DENA, which is highly carcinogenic for the liver of both rats and mice inhibited glucocorticoid induction of TAT in both species, while non-carcinogenic 4'-MeDAB was absolutely ineffective both in rats and mice. The inhibition of TAT activity by the carcinogens was due to reduced levels of TAT mRNA, which is most likely to be a result of the reduced rate of transcription initiation of the TAT gene. In all cases, the TAT inhibition was accompanied by significant reduction of DNA-binding activity of the HNF3 transcription factor, which is known to be critical to glucocorticoid regulation of TAT gene. We also demonstrated that the described species-specific effects of OAT and of 3'-MeDAB on HNF3 DNA-binding activity may be initiated not only by administration in vivo, but also by their direct administration to homogenate, intact nuclei or nuclear lysate, but not to nuclear extract fraction, obtained by precipitation with 0.32 g/mL of ammonium sulfate (Fraction I). We showed, that a factor responsible for this effect might be precipitated in 0.32-0.47 g/mL interval of ammonium sulfate concentration. In contrast, non-specific hepatocarcinogen DENA was effective upon being added directly to Fraction I, implying a different mechanism of its action.

Animals↗

PubMed1995

Species specificity in the cell-free conversion of prion protein to protease-resistant forms: a model for the scrapie species barrier.

Scrapie is a transmissible neurodegenerative disease that appears to result from an accumulation in the brain of an abnormal protease-resistant isoform of prion protein (PrP) called PrPsc. Conversion of the normal, protease-sensitive form of PrP (PrPc) to protease-resistant forms like PrPsc has been demonstrated in a cell-free reaction composed largely of hamster PrPc and PrPsc. We now report studies of the species specificity of this cell-free reaction using mouse, hamster, and chimeric PrP molecules. Combinations of hamster PrPc with hamster PrPsc and mouse PrPc with mouse PrPsc resulted in the conversion of PrPc to protease-resistant forms. Protease-resistant PrP species were also generated in the nonhomologous reaction of hamster PrPc with mouse PrPsc, but little conversion was observed in the reciprocal reaction. Glycosylation of the PrPc precursors was not required for species specificity in the conversion reaction. The relative conversion efficiencies correlated with the relative transmissibilities of these strains of scrapie between mice and hamsters. Conversion experiments performed with chimeric mouse/hamster PrPc precursors indicated that differences between PrPc and PrPsc at residues 139, 155, and 170 affected the conversion efficiency and the size of the resultant protease-resistant PrP species. We conclude that there is species specificity in the cell-free interactions that lead to the conversion of PrPc to protease-resistant forms. This specificity may be the molecular basis for the barriers to interspecies transmission of scrapie and other transmissible spongiform encephalopathies in vivo.

Animals↗

PubMed1989

Molecular mechanisms governing species-specific transcription of ribosomal RNA.

An unusual property of ribosomal RNA transcription is the species specificity of promoter recognition. Unexpectedly, the sequence-specific RNA pol I transcription factors hUBF and xUBF, isolated from human and Xenopus cells, respectively, recognize the same DNA sequence elements. Despite this similarity in DNA binding activity, neither factor will functionally substitute for the other in reconstituted transcription assays, suggesting that the specificity of protein-DNA interactions cannot account for the species-specific activation of transcription by hUBF and xUBF. Interestingly, we find that hUBF and xUBF form distinctly different complexes with human SL1 at both the human and Xenopus promoters. Together these results strongly implicate specific protein-protein interactions between transcription factors as an important determinant of promoter selectivity and species specificity.

Animals↗

PubMed1991

Systematic identification of LINE-1 repetitive DNA sequence differences having species specificity between Mus spretus and Mus domesticus.

LINE-1 is a family of repetitive DNA sequences interspersed among mammalian genes. In the mouse haploid genome there are about 100,000 LINE-1 copies. We asked if the subspecies Mus spretus and Mus domesticus have developed species-specific LINE-1 subfamilies. Sequences from 14 M. spretus LINE-1 elements were obtained and compared to M. domesticus LINE-1 sequences. Using a molecular phylogenetic tree we identified several differences shared among a subset of young repeats in one or the other species as candidates for species-specific LINE-1 variants. Species specificity was tested using oligonucleotide probes complementary to each putative species-specific variant. When hybridized to genomic DNAs, single-variant probes detected an expanded number of elements in the expected mouse. In the other species these probes detected a smaller number of matches consistent with the average rate of random divergence among LINE-1 elements. It was further found that the combination of two species-specific sequence differences in the same probe reduced the detection background in the wrong species below our detection limit.

Animals↗

PubMed1994

PCR amplification of species-specific DNA sequences can distinguish among Phytophthora species.

We used PCR to differentiate species in the genus Phytophthora, which contains a group of devastating plant pathogenic fungi. We focused on Phytophthora parasitica, a species that can infect solanaceous plants such as tomato, and on Phytophthora citrophthora, which is primarily a citrus pathogen. Oligonucleotide primers were derived from sequences of a 1,300-bp P. parasitica-specific DNA segment and of an 800-bp P. citrophthora-specific segment. Under optimal conditions, the primers developed for P. parasitica specifically amplified a 1,000-bp sequence of DNA from isolates of P. parasitica. Primers for P. citrophthora similarly and specifically amplified a 650-bp sequence of DNA from isolates of P. citrophthora. Detectable amplification of these specific DNA sequences required picogram quantities of chromosomal DNA. Neither pair of primers amplified these sequences with DNAs from other species of Phytophthora or from the related genus Pythium. DNAs from P. parasitica and P. citrophthora growing in infected tomato stem tissue were amplified as distinctly as DNAs from axenic cultures of each fungal species. This is the first report on PCR-driven amplification with Phytophthora species-specific primers.

Base Sequence↗

PubMed2003

Reverse transcription-polymerase chain reaction assay for species-specific detection of bovine central nervous system tissue in meat and meat products.

This paper reports the development of a reverse transcription-polymerase chain reaction (RT-PCR) assay coupled with restriction fragment length polymorphism (RFLP) analysis to specifically detect the glial fibrillary acidic protein (GFAP) mRNA of bovine central nervous system (CNS) tissue in minced meat and meat products. RNA extracted from bovine brain tissue and brain tissue from other mammals yielded a 168-bp CNS-specific signal after RT-PCR. The species specificity of the assay can be obtained by subsequent RFLP analysis of the amplified RT-PCR product. To determine the tissue specificity of the RT-PCR assay, various bovine tissues were analyzed. Bovine GFAP mRNA was detected in the brain and spinal cord, and these results are consistent with the reported large amounts of detectable protein in these tissues. Additionally, GFAP mRNA was present in skeletal muscle tissue samples and in some heart muscle tissue samples, but heat treatment of samples prior to extraction resulted in the loss of the non-CNS signals. To evaluate the stability and detectability of bovine GFAP mRNA in comminuted meat and in cooked meat products, mixtures containing bovine brain homogenate at concentrations of 0.5 to 5% were prepared and analyzed. The examination of minced meat with added bovine brain homogenate revealedGFAP mRNA RT-PCR signal stability for at least 7 days at a storage temperature of 4 degrees C. In cooked meat products bovine GFAP mRNA signal was detectable for at least 35 days. Bovine brain homogenate at a concentration of 0.5% was successfully detected in all of the experiments conducted, and no false-negative results were obtained. It is concluded that bovine GFAP mRNA can serve as a sensitive and specific marker for bovine CNS tissue in minced meat and in pasteurized meat products.

Animals↗

PubMed1986

Species-specific allergens from the salivary glands of Triatominae (Heteroptera:Reduviidae).

We investigated allergenic cross-reactivity among species of the blood-feeding insects of the subfamily Triatominae. By skin testing, patients allergic to either Triatoma protracta or T. rubida gave positive responses only to the respective salivary antigen. RAST-inhibition experiments demonstrated that binding of IgE antibodies to T. protracta antigen was not inhibited by salivary extracts from T. rubida, T. cavernicola, T. rubrofasciata, or Rhodnius prolixus. The same level of species specificity was found for IgE antibodies to T. rubida. By direct RAST, no T. rubida positive serum bound T. protracta antigen, and 29 of 30 T. protracta positive sera failed to bind T. rubida. One serum from a T. protracta-allergic patient contained IgE antibodies to both T. protracta and T. rubida. RAST-inhibition experiments demonstrated that these antibodies did not cross-react and that this person had separate species-specific antibodies to T. protracta and T. rubida antigens. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of salivary extracts demonstrated that the lower molecular weight bands that contain the antigens responsible for human allergic reactions differed in number and size in all species tested. These studies demonstrate species specificity for the allergic response to Triatoma and stress the importance of accurate insect identification and the need for species-specific antigens for diagnosis and immunotherapy.

Allergens↗

PubMed2000

Quantification of different Eubacterium spp. in human fecal samples with species-specific 16S rRNA-targeted oligonucleotide probes.

Species-specific 16S rRNA-targeted, Cy3 (indocarbocyanine)-labeled oligonucleotide probes were designed and validated to quantify different Eubacterium species in human fecal samples. Probes were directed at Eubacterium barkeri, E. biforme, E. contortum, E. cylindroides (two probes), E. dolichum, E. hadrum, E. lentum, E. limosum, E. moniliforme, and E. ventriosum. The specificity of the probes was tested with the type strains and a range of common intestinal bacteria. With one exception, none of the probes showed cross-hybridization under stringent conditions. The species-specific probes were applied to fecal samples obtained from 12 healthy volunteers. E. biforme, E. cylindroides, E. hadrum, E. lentum, and E. ventriosum could be determined. All other Eubacterium species for which probes had been designed were under the detection limit of 10(7) cells g (dry weight) of feces(-1). The cell counts obtained are essentially in accordance with the literature data, which are based on colony counts. This shows that whole-cell in situ hybridization with species-specific probes is a valuable tool for the enumeration of Eubacterium species in feces.

Colony Count, Microbial↗

PubMed1997

Species-specificity of the cohesin-dockerin interaction between Clostridium thermocellum and Clostridium cellulolyticum: prediction of specificity determinants of the dockerin domain.

The cross-species specificity of the cohesin-dockerin interaction, which defines the incorporation of the enzymatic subunits into the cellulosome complex, has been investigated. Cohesin-containing segments from the cellulosomes of two different species, Clostridium thermocellum and Clostridium cellulolyticum, were allowed to interact with cellulosomal (dockerin-containing) enzymes from each species. In both cases, the cohesin domain of one bacterium interacted with enzymes from its own cellulosome in a calcium-dependent manner, but the same cohesin failed to recognize enzymes from the other species. Thus, in the case of these two bacteria, the cohesin-dockerin interaction seems to be species-specific. Based on intra- and cross-species sequence comparisons among the different dockerins together with their known specificities, we tender a prediction as to the amino-acid residues critical to recognition of the cohesins. The suspected residues were narrowed down to only four, which comprise a repeated pair located within the calcium-binding motif of two duplicated sequences, characteristic of the dockerin domain. According to the proposed model, these four residues do not participate in the binding of calcium per se; instead, they appear to serve as recognition codes in promoting interaction with the cohesin surface.

Amino Acid Sequence↗

PubMed1995

Multiple receptor-dependent steps determine the species specificity of HCV-229E infection.

Human coronavirus (HCV)-229E causes disease only in humans and grows in human cells and in cells of other species that express recombinant human aminopeptidase N (hAPN), the receptor for HCV-229E. We compared the species specificity of HCV-229E infection with the species specificity of virus binding using immunofluorescence, assay of virus yields, fluorescence activated cell sorting and a monoclonal antibody directed against hAPN that blocks infection. We found that HCV-229E binds to intestinal brush border membranes (BBM) and to membranes of cell lines from cats, dogs, pigs, and humans, however the virus only infects two of these species. HCV-229E will not bind to BBM or to membranes from cell lines derived from hamster or mice. Animal coronaviruses related to HCV-229E, including FIPV, CCV, and TGEV bind to cell membranes from cats, dogs, cows, pigs and humans (but not mice), while each virus infects cells from only a subset of these species. Infectious genomic HCV-229E RNA, can infect cells of all of these species. These data suggest that the species-specificity of infection for this serogroup of coronaviruses is determined at the levels of virus binding and penetration. Since binding of viral spike glycoprotein to cellular receptors is not the only limiting factor, we suggest that one or more steps associated with virus penetration may determine the species specificity of infection with the HCV-229E serogroup of coronaviruses.

Animals↗

PubMed1988

Species-specific oligonucleotide probes for rRNA of Clostridium difficile and related species.

The large copy number of rRNA makes it an appealing target for oligonucleotide probes designed to identify microorganisms. Given that nucleotide sequences in rRNA are known to reflect phylogeny, species-specific rRNA probes should be feasible if the sequences found in closely related species are different. We sequenced portions of the 16S rRNA of three closely related clostridia found in the human colonic microflora: Clostridium bifermentans, C. sordellii, and C. difficile. The rRNAs of these three species showed 97 to 98% sequence similarity. Five oligonucleotide probes complementary to unique segments of the sequences were end labeled with 32P and hybridized on a nylon filter to the immobilized rRNA of each clostridium. Each probe efficiently hybridized only to the rRNA of the species to which it was directed. Complementary probes emitted a signal that exceeded by a factor of 100 to 1,000 the signal of probes that mismatched the target rRNA by 2 to 5 bases. Even a 1-base difference in rRNA sequence allowed a clear distinction between species. A systematic approach can efficiently yield taxon-specific oligonucleotide probes directed at rRNA.

Base Sequence↗

PubMed2003

Identification of campylobacteria isolated from Danish broilers by phenotypic tests and species-specific PCR assays.

AIMS: To validate a phenotypic Campylobacter species identification method employed to identify campylobacters in broilers by comparison with campylobacterial species identification using various species-specific PCR analyses. METHODS AND RESULTS: From a collection of 2733 phenotypically identified campylobacterial cultures, 108 Campylobacter jejuni cultures and 351 campylobacterial cultures other than Camp. jejuni were subjected to various species-specific PCR assays. On the basis of the genotypic tests, it was demonstrated that Camp. jejuni and Camp. coli constituted approx. 99% of all cultures, while other species identified were Helicobacter pullorum, Camp. lari and Camp. upsaliensis. However, 29% of the 309 Camp. coli cultures identified by phenotypic tests were hippurate-variable or negative Camp. jejuni cultures, whereas some Camp. lari cultures and unspeciated campylobacter cultures belonged to H. pullorum. It was also notable that 2-6% of the cultures were, in fact, mixed cultures. CONCLUSIONS: The phenotypic identification scheme employed failed to appropriately differentiate Campylobacter species and particularly to identify the closely related species, H. pullorum. SIGNIFICANCE AND IMPACT OF THE STUDY: Future phenotypic test schemes should be designed to allow a more accurate differentiation of Campylobacter and related species. Preferably, the phenotypic tests should be supplemented with a genotypic strategy to disclose the true campylobacterial species diversity in broilers.

Animals↗