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PubMed2006

Assessment of the diversity and species specificity of the mutualistic association between Epicephala moths and Glochidion trees.

The obligate mutualisms between flowering plants and their seed-parasitic pollinators constitute fascinating examples of interspecific mutualisms, which are often characterized by high levels of species diversity and reciprocal species specificity. The diversification in these mutualisms has been thought to occur through simultaneous speciation of the partners, mediated by tight reciprocal adaptation; however, recent studies cast doubt over this general view. In this study, we examine the diversity and species specificity of Epicephala moths (Gracillariidae) that pollinate Glochidion trees (Phyllanthaceae), using analysis of mitochondrial and nuclear gene sequences. Phylogenetic analysis of Epicephala moths associated with five Glochidion species in Japan and Taiwan reveal six genetically isolated species that are also distinguishable by male genital morphology: (i) two species specific to single host species (G. acuminatum and G. zeylanicum, respectively); (ii) two species that coexist on G. lanceolatum; and (iii) two species that share two, closely-related parapatric hosts (G. obovatum and G. rubrum). Statistical analysis shows that the two species associated with G. lanceolatum are not sister species, indicating the colonization of novel Glochidion host in at least one lineage. Behavioural observations suggest that all six species possess the actively-pollinating habit, thus none of the studied species has become a nonmutualistic 'cheater' that exploits the benefit resulting from pollination by other species. Our results parallel recent findings in ecologically similar associations, namely the fig-fig wasp and yucca-yucca moth mutualisms, and contribute to a more general understanding of the factors that determine ecological and evolutionary outcomes in these mutualisms.

Adaptation, Physiological↗
PubMed2003

Development of a species-specific recA-based PCR test for Burkholderia fungorum.

The genus Burkholderia comprises over 28 species and species-specific, recA-based polymerase chain reaction (PCR) tests are available for several species, but not for some soil-inhabiting species including B. fungorum. Previous analysis of several novel rhizospheric, environmental isolates belonging to the B. cepacia complex suggested they may be closely related to B. fungorum. To discover any relationship between these isolates and B. fungorum we set out to clone and sequence a portion of the B. fungorum recA gene in order to design species-specific primer pairs for use in a recA-based PCR assay. Using a similar procedure we extended the recA-based PCR assay to identify B. sacchari and B. caledonica, two additional soil-inhabiting Burkholderia spp.

Burkholderia↗
PubMed2004

A single amino acid of APOBEC3G controls its species-specific interaction with virion infectivity factor (Vif).

The virion infectivity factor (Vif) accessory protein of HIV-1 forms a complex with the cellular cytidine deaminase APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G) to block its antiviral activity. The antiviral property of APOBEC3G is conserved in several mammalian species, but the ability of Vif to block this activity is species-specific. HIV-1 Vif blocks human APOBEC3G but does not block the mouse or African green monkey (AGM) enzyme. Conversely, SIV(AGM) Vif blocks the antiviral activity of AGM but not human APOBEC3G. We demonstrate that the species specificity is caused by a single amino acid difference in APOBEC3G. Replacement of Asp-128 in human APOBEC3G with the Lys-128 of AGM APOBEC3G caused the enzyme to switch its interaction, becoming sensitive to SIV(AGM) Vif and resistant to HIV-1 Vif. Conversely, the reciprocal Lys to Asp switch in AGM APOBEC3G reversed its specificity for Vif. The reversal of biological activity was accompanied by the corresponding switch in the species specificity with which the enzyme physically associated with Vif and was excluded from virions. The charge of the amino acid at position 128 was a critical determinant of species specificity. Based on the crystal structure of the distantly related Escherichia coli cytidine deaminase, we propose that this amino acid is positioned on a solvent-exposed loop of APOBEC3G on the same face of the protein as the catalytic site.

APOBEC-3G Deaminase↗
PubMed2005

Responses to species-specific vocalizations in the auditory cortex of awake and anesthetized guinea pigs.

Species-specific vocalizations represent an important acoustical signal that must be decoded in the auditory system of the listener. We were interested in examining to what extent anesthesia may change the process of signal decoding in neurons of the auditory cortex in the guinea pig. With this aim, the multiple-unit activity, either spontaneous or acoustically evoked, was recorded in the auditory cortex of guinea pigs, at first in the awake state and then after the injection of anesthetics (33 mg/kg ketamine with 6.6 mg/kg xylazine). Acoustical stimuli, presented in free-field conditions, consisted of four typical guinea pig calls (purr, chutter, chirp and whistle), a time-reversed version of the whistle and a broad-band noise burst. The administration of anesthesia typically resulted in a decrease in the level of spontaneous activity and in changes in the strength of the neuronal response to acoustical stimuli. The effect of anesthesia was mostly, but not exclusively, suppressive. Diversity in the effects of anesthesia led in some recordings to an enhanced response to one call accompanied by a suppressed response to another call. The temporal pattern of the response to vocalizations was changed in some cases under anesthesia, which may indicate a change in the synaptic input of the recorded neurons. In summary, our results suggest that anesthesia must be considered as an important factor when investigating the processing of complex sounds such as species-specific vocalizations in the auditory cortex.

Acoustic Stimulation↗
PubMed2000

Detection and identification of mycobacteria by amplification of the internal transcribed spacer regions with genus- and species-specific PCR primers.

We evaluated the usefulness of PCR assays that target the internal transcribed spacer (ITS) region for identifying mycobacteria at the species level. The conservative and species-specific ITS sequences of 33 species of mycobacteria were analyzed in a multialignment analysis. One pair of panmycobacterial primers and seven pairs of mycobacterial species-specific primers were designed. All PCRs were performed under the same conditions. The specificities of the primers were tested with type strains of 20 mycobacterial species from the American Type Culture Collection; 205 clinical isolates of mycobacteria, including 118 Mycobacterium tuberculosis isolates and 87 isolates of nontuberculous mycobacteria from 10 species; and 76 clinical isolates of 28 nonmycobacterial pathogenic bacterial species. PCR with the panmycobacterial primers amplified fragments of approximately 270 to 400 bp in all mycobacteria. PCR with the M. tuberculosis complex-specific primers amplified an approximately 120-bp fragment only for the M. tuberculosis complex. Multiplex PCR with the panmycobacterial primers and the M. tuberculosis complex-specific primers amplified two fragments that were specific for all mycobacteria and the M. tuberculosis complex, respectively. PCR with M. avium complex-, M. fortuitum-, M. chelonae-, M. gordonae-, M. scrofulaceum-, and M. szulgai-specific primers amplified specific fragments only for the respective target organisms. These novel primers can be used to detect and identify mycobacteria simultaneously under the same PCR conditions. Furthermore, this protocol facilitates early and accurate diagnosis of mycobacteriosis.

Base Sequence↗
PubMed2000

The species specificity of growth hormone requires the cooperative interaction of two motifs.

Primate growth hormones (GH) activate both primate and non-primate somatotrophic receptors (GH receptors), but non-primate GHs do not activate primate GH receptors. Previous studies argued the interaction of Asp(171) of human GH and Arg(43) of the receptor produced an attractive ionic interaction. In non-primate GHs, His(170) replaces the homologous Asp(171), producing a repulsive interaction with Arg(43) of the primate receptor which was believed to reduce the attraction of non-primate GH for the human GH receptor, thus providing species specificity. In this report, H170D bovine GH had activity and affinity for human GH receptors approaching those of human GH. In contrast, replacing Asp(171) of human GH with His did not significantly reduce somatotrophic activity, indicating that species specificity is not wholly explained by this residue's interaction with Arg(43) of the receptor. Deletion of either Phe(44) (a residue present only in primate GHs) or residues 32-46 (20-kDa form of human GH) each only marginally reduced somatotrophic activities. But the combination of the D171H mutation with either DeltaPhe(44) or Delta32-46 in human GH reduced binding and activity in a greater than additive fashion, indicated a functional interaction between these distant structural features. In bovine GH addition of phenylalanine at position 44 increased the somatotrophic activity and receptor affinity in cells containing the human GH receptor. The combination of the H170D mutation and the addition of phenylalanine at position 44 created a bovine GH with activity indistinguishable from wild-type human GH. Based on evidence from both bovine and human GHs, the cooperative interaction of these two distant motifs determined the species specificity and indicated that structural plasticity was a critical feature necessary for the species specificity of somatotrophic activity.

Animals↗
PubMed1999

A genus- and species-specific nested polymerase chain reaction malaria detection assay for epidemiologic studies.

A nested polymerase chain reaction (PCR) assay that uses Plasmodium genus-specific primers for the initial PCR (nest 1) amplification and either genus- or species-specific primers for the nest 2 amplifications was tested on laboratory and field samples. With in vitro cultured Plasmodium falciparum-infected blood samples, it was capable of detecting six parasites/microl of blood using DNA prepared from 25-microl blood spots on filter paper. The assay was evaluated on fingerprick blood samples collected on filter paper from 129 individuals living in a malaria-endemic area in Malaysia. Malaria prevalence by genus-specific nested PCR was 35.6% (46 of 129) compared with 28.7% (37 of 129) by microscopy. The nested PCR detected seven more malaria samples than microscopy in the first round of microscopic examination, malaria in three microscopically negative samples, six double infections identified as single infections by microscopy and one triple infection identified as a double infection by microscopy. The nested PCR assay described is a sensitive technique for collecting accurate malaria epidemiologic data. When coupled with simple blood spot sampling, it is particularly useful for screening communities in remote regions of the world.

Animals↗
PubMed2002

[Cloning of a species-specific gene fragment from Cryptosporidium parvum and the development of diagnostic PCR primers].

OBJECTIVE: To develop a pair of diagnostic PCR primers for Cryptosporidium parvum. METHODS: A species-specific gene fragment of C. parvum was obtained through RAPD analysis. After the fragment was isolated, purified, cloned and sequenced, a pair of primers FF was designed and synthesised based on the sequence. With the primers, the anticipated fragment in size of 603 bp was amplified by PCR from 2 American strains and 4 Chinese strains of C. parvum. The samples of 35 rabbits feces and 55 human feces were detected by PCR with primers FF and 021, the latter was a species-specific diagnostic primer reported by Morgan. RESULTS: All six strains amplified by the primers FF showed same detection rate with 021. Sensitivity test indicated that DNA of 1 oocyst per gram of feces could be detected by the PCR. CONCLUSION: The primers FF showed high specificity and sensitivity, and can be used for diagnosing Crytosporidium parvum infection.

Animals↗
PubMed1995

HMG box 4 is the principal determinant of species specificity in the RNA polymerase I transcription factor UBF.

Transcription of ribosomal genes requires, in addition to RNA polymerase I, the trans-acting factors UBF and Rib1 in Xenopus or SL1 in humans. RNA polymerase I transcription is remarkably species specific. Between closely related species SL1 is the sole determinant of this specificity. Between more distantly related species, however, UBF is also a component of this species specificity. Xenopus UBF cannot function in human RNA polymerase I transcription and human UBF cannot function in Xenopus RNA polymerase I transcription. Xenopus and human UBFs are remarkably similar at the amino acid sequence level, both containing multiple HMG box DNA binding motifs. The only major difference between xUBF and hUBF is the lack of a HMG box 4 equivalent in xUBF. Utilizing a series of hybrid UBF molecules we have identified HMG box 4 as the principal determinant of species specificity. Addition of human HMG box 4 to xUBF converts it to a form that functions in human RNA polymerase I transcription. Deletion of HMG box 4 from hUBF converts it to a form that functions in Xenopus RNA polymerase I transcription. Furthermore, mutations within Xenopus UBF demonstrate that UBF requires a precise arrangement and number of HMG boxes to function in RNA polymerase I transcription.

Animals↗
PubMed1985

Species specificity and temperature dependency of temporal processing by the auditory midbrain of two species of treefrogs.

The mating (advertisement) calls of two sibling species of gray treefrogs, Hyla versicolor and Hyla chrysoscelis, are spectrally identical but differ in trill rate; being higher for H. chrysoscelis. Single-unit recordings were made from the torus semicircularis of both species to investigate the neural mechanisms by which this species-specific temporal feature is analyzed. Using sinusoidally amplitude-modulated (AM) white noise as a stimulus, the temporal selectivity of these midbrain auditory neurons could be described by five response categories: 'AM nonselective' (34%); 'AM high-pass' (7%); 'AM low-pass' (6%); 'AM band-suppression' (12%); 'AM tuned' (40%). The distributions of temporal tuning values (i.e., modulation rate at which each AM-tuned unit responds maximally) are broad; in both species, neurons were found which were tuned to modulation rates greater than those found in their advertisement calls. Nevertheless, the temporal tuning values for H. versicolor (median = 25 Hz) were significantly lower than those for H. chrysoscelis (median = 32.5 Hz). The temporal selectivities of AM band-suppression neurons were found to be temperature dependent. The modulation rate at which a response minimum was observed shifted to higher values as the temperature was elevated. These results extend our earlier findings of temperature-dependent temporal selectivity in the gray treefrog. The selectivity of band-suppression and AM-tuned neurons to various rates of amplitude modulation was largely, but not completely, independent of whether sinusoidal or natural forms of AM were used.

Animals↗
PubMed1981

Partial purification and characterization of the major species-specific protein antigens of Rickettsia typhi and Rickettsia prowazekii identified by rocket immunoelectrophoresis.

Species-specific antigens from Rickettsia typhi and Rickettsia prowazekii were readily solubilized by French pressure cell extraction or sonication of Renografin density gradient-purified rickettsiae and were identified by rocket immunoelectrophoresis. As measured by quantitative rocket immunoelectrophoresis, the species-specific typhus rocket antigens (STRAs) appeared to be proteins; they were denatured by heating at 56 degrees C for 30 min but not by 50 degrees C treatment, and they were sensitive to pronase and trypsin but were not affected by periodate oxidation, glycosidases of various specificities, phospholipase A, or lipase. STRAs from both R. typhi and R. prowazekii were separated from common antigens by DE52 column chromatography of 100,000-X-g supernatant fractions of rickettsial extracts. The purified STRAs were characterized by crossed immunoelectrophoresis, by polyacrylamide gel electrophoresis on Davis and sodium dodecyl sulfate gels, and by an enzyme-linked immunosorbent assay. The two purified STRAs were proteins with similar native electrophoretic mobilities in agarose and polyacrylamide gels, and these proteins had similar polypeptide patterns on sodium dodecyl sulfate gels. Most of the STRA activity migrated as a single protein band on sodium dodecyl sulfate-polyacrylamide and Davis polyacrylamide gels, although minor protein bands with STRA activity were also detected. The major STRA proteins constituted 10 to 15% of the total cellular protein of R. typhi and R. prowazekii. According to sensitive enzyme-linked immunosorbent assay titrations, the STRA of R. prowazekii had substantial cross-reactivity with rabbit antiserum prepared against R. typhi, as shown also by rocket immunoelectrophoresis, whereas the STRA of R. typhi reacted only very weakly with antiserum prepared against R. prowazekii according to the enzyme-linked immunosorbent assay and not at all according to rocket immunoelectrophoresis.

Antigens, Bacterial↗
PubMed1997

Species-specific identification of microsporidia in stool and intestinal biopsy specimens by the polymerase chain reaction.

In view of the increasing number of cases of human microsporidiosis, simple and rapid methods for clear identification of microsporidian parasites to the species level are required. In the present study, the polymerase chain reaction (PCR) was used for species-specific detection of Encephalitozoon cuniculi. Encephalitozoon hellem, Encephalitozoon (Septata) intestinalis, and Enterocytozoon bieneusi in both tissue and stool. Using stool specimens and intestinal biopsies of patients infected with Enterocytozoon bieneusi (n = 9), Encephalitozoon spp. (n = 2), and Encephalitozoon intestinalis (n = 1) as well as stool spiked with spores of Encephalitozoon cuniculi and Encephalitozoon hellem and tissue cultures of Encephalitozoon cuniculi and Encephalitozoon hellem, three procedures were developed to produce PCR-ready DNA directly from the samples. Specific detection of microsporidian pathogens was achieved in the first PCR. The subsequent nested PCR permitted species determination and verified the first PCR products. Without exception, the PCR assay confirmed electron microscopic detection of Enterocytozoon bieneusi and Encephalitozoon intestinalis in stool specimens and their corresponding biopsies and in spiked stool samples and tissue cultures infected with Encephalitozoon cuniculi and Encephalitozoon hellem. Moreover, identification of Encephalitozoon spp. could be specified as Encephalitozoon intestinalis. Whereas standard methods such as light and transmission electron microscopy may lack sensitivity or require more time and special equipment, the PCR procedure described facilitates species-specific identification of microsporidian parasites in stool, biopsies, and, probably, other samples in about five hours.

AIDS-Related Opportunistic Infections↗
PubMed1983

The molecular biology of rotaviruses. VI. RNA species-specific terminal conservation in rotaviruses.

The use of T1 RNase fingerprinting of terminally labelled genomic double-stranded RNA species from various rotavirus isolates, to analyse the near terminal G-residue positions, has revealed an RNA species-specific fingerprint pattern covering approximately 40 nucleotides at the termini. These RNA species-specific terminal fingerprint patterns were found to be conserved in both rotavirus RNAs isolated from various animal species, and in isolates from a single animal species where gross divergence of internal RNA sequence for a particular RNA species was evident. This conservation of near terminal G-residue positions suggests that, internal to the short regions of absolute terminal sequence conservation that we have previously shown to be present on all rotavirus RNA species, there is a region of conserved sequence which is specific for a particular RNA species.

Animals↗
PubMed1979

Species-specific sperm adhesion in sea urchins. A quantitative investigation of bindin-mediated egg agglutination.

Bindin, a protein component of the acrosomal vesicle of sea urchin sperm, has been isolated from Arbacia punctulata and strongylocentrous purpuratus. Using this isolated bindin, we have devised a quantitative assay for bindin-mediated egg agglutination and compared the agglutination of bindin eggs from A. puntulata and S. purpuratus. Bindin- mediated agglutination is species -specific in both species, although a measurable degree of heterotypic interaction is observed. Homotypic bindin-egg interactions differ significantly from heterotypic interactions both in the extent of agglutination and the size of the resulting aggregates. We also provide direct evidence that bindin particles agglutinate eggs by adhering to the surfaces of adjacent eggs. Although the A. punctulata bindin preparation displays the same functional properties and consists of one major polypeptide of the same apparent molecular weight as S. purpuratus bindin, its morphology is very different. Unlike the spherical aggregates observed with S. purpuratus bindin, A punctulata bindin exists as lamellar vesicles and binds significant amounts of phospholipids and Triton X-100, suggesting that it may be tightly associated with the acrosomal membrane. Having defined a number of the basic parameters of bindin-mediated agglutination, we examined the effect of a number of saccharides and glycopeptides on bindin-mediated egg agglutination. Carbohydrate-containing components derived from the egg cell surface by proteolysis were found to inhibit bindin-mediated egg agglutination at low concentrations, but this inhibition is not species specific.

Acrosome↗
PubMed2000

Quantification of Methanosaeta Species in Anaerobic Bioreactors Using Genus- and Species-Specific Hybridization Probes.

A BSTRACTTo evaluate the role of Methanosaeta spp. in a variety of anaerobic environments, small-subunit rRNA targeted oligonucleotide hybridization probes were developed and experimentally characterized. The probes were designed to be genus specific for Methanosaeta and species specific for Methanosaeta concilii and Methanosaeta thermophila. The temperature of dissociation was determined for each probe. Probe specificities were determined using a diverse collection of Archaea and through an evaluation of probe nesting using samples from a variety of anaerobic bioreactors. Cell fixation and hybridization conditions for fluorescence in situ hybridizations were also evaluated. Although permeability of methanogens was variable, M. concilii cells could be permeabilized using a range of paraformaldehyde and ethanol based fixation conditions. Using the newly designed probes together with previously designed probes for methanogens, it was determined that Methanosaeta spp. were the dominant aceticlastic methanogens in a variety of anaerobic bioreactors when acetate concentrations were low. Their levels were higher in bioreactors with granular sludge than in those with flocculent sludge. In lab-scale upflow anaerobic sludge blanket reactors, the levels of M. concilii rRNA were as high as 30% of the total rRNA.

Journal Article↗
PubMed1986

Identification of larval and adult Simulium yahense and Simulium sanctipauli based on species-specific enzyme markers and their distribution at different breeding habitats in Central Liberia.

Human-biting adults and late instar larvae of the Simulium damnosum complex from four ecologically different simuliid breeding habitats in the Firestone Rubber Plantation at Harbel, Liberia, were identified morphologically and the monthly species composition of each site was recorded. Samples of the predominant species found at each site were assayed electrophoretically for species-specific variants of phosphoglucomutase (PGM) and trehalase (TRE). Enzyme identifications of flies and larvae were compared with morphological identifications to determine the accuracy of field identifications relying upon morphological characters. Enzyme identifications confirmed the accuracy of over 98% of the adult female identifications. S. yahense was found to be the predominant human-biting species at each site over the 10 months of sampling, with S. sanctipauli comprising a small percentage of the biting fly population. Species-specific larval enzymes confirmed the accuracy of more than 96% of the larval identifications. S. yahense was the predominant larval species found in smaller, more shaded, cooler breeding waters, while S. sanctipauli predominated in the single large watercourse that was sampled. Normally allopatric, mixed populations of these two larval species were found to exist at all sites, but sympatry occurred primarily during the wet season months of May-October. Biting activity of S. sanctipauli was found to be greatest during wet season months, and generally reflected the increase of S. sanctipauli in the larval populations of habitats dominated by S. yahense. The low human-biting activity of S. sanctipauli at all sites and during times which fostered large populations of S. sanctipauli larvae may be an indication of this specie's zoophilic tendency. Circumstantial evidence of hybridization, the expression of PGM and TRE species-specific variants for both species, was found in adults and larvae morphologically identified as S. yahense. The frequency of this "hybrid" condition, based upon PGM and TRE, was calculated to be comparable to the frequency of hybridization as determined by larval chromosome inversions.

Animals↗
PubMed1995

Polymerase chain reaction and a liquid-phase, nonisotopic hybridization for species-specific and sensitive detection of malaria infection.

In the present study, we describe a polymerase chain reaction (PCR)-based enzyme-linked immunosorbent assay for the detection of malaria infection. The target region of the 18S ribosomal DNA is amplified by a PCR using an 18S rRNA, genus-specific, biotinylated (5') and an unlabeled primer (3') pair. The detection probes are digoxigenin-labeled DNA oligonucleotides derived from species-specific rRNA sequences. The amplified fragments are allowed to hybridize with the species-specific, digoxigenin-labeled oligonucleotide probes. The oligo/DNA complex is allowed to bind onto streptavidin-coated microtiter plates, followed by incubation with a peroxidase-streptavidin conjugate and a colorimetric-peroxidase substrate. The resulting test demonstrated specificity for the four human Plasmodium species, and was able to detect a level of parasitemia of at least 0.0001% in a laboratory-induced P. falciparum infection in monkeys. This liquid hybridization assay is sensitive, specific, simple, and reliable, with wide applicability in epidemiologic studies, accurate detection of mixed infections, detection of low-level parasitemia, and evaluation of chemotherapy and vaccine efficacy.

Animals↗
PubMed2000

Species-specific double-strand break repair and genome evolution in plants.

Even closely related eukaryotic species may differ drastically in genome size. While insertion of retroelements represents a major source of genome enlargement, the mechanism mediating species- specific deletions is fairly obscure. We analyzed the formation of deletions during double-strand break (DSB) repair in Arabidopsis thaliana and tobacco, two dicotyledonous plant species differing >20-fold in genome size. DSBs were induced by the rare cutting restriction endonuclease I-SCE:I and deletions were identified by loss of function of a negative selectable marker gene containing an I-SCE:I site. Whereas the partial use of micro-homologies in junction formation was similar in both species, in tobacco 40% of the deletions were accompanied by insertions. No insertions could be detected in Arabidopsis , where larger deletions were more frequent, indicating a putative inverse correlation between genome size and the average length of deletions. Such a correlation has been postulated before by a theoretical study on the evolution of related insect genomes and our study now identifies a possible molecular cause for the phenomenon, indicating that species-specific differences in DSB repair might indeed influence genome evolution.

Arabidopsis↗