Genetic analysis of adherence by oral streptococci

Streptococci are one of the most successful bacterial colonizers of the human body and are major components of oral biofilms. The bacterial cells express multiple cell-surface adhesins that are responsible for the ability of streptococci to adhere to a wide range of substrates which include salivary and serous proteins, epithelial cells and other bacterial cells. Analysis of adherence-defective mutants has indicated the importance of high molecular mass wall-associated polypeptides and of enzymes catalyzing extracellular glucan polysaccharide synthesis to the adherence and accumulation of oral streptococci. The analysis of isogenic mutants of streptococci, generated through insertional inactivation (or allelic exchange), has confirmed the essential roles of specific surface polypeptides both to adhesive processes and to correct assembly of the cell wall layers.     

Amylase-binding as a discriminition among oral streptococci

The ability of 51 strains, belonging to Streptococcus sanguis, 'S. mitior', S. oralis and related groups, to bind salivary amylase was studied. Most strains were grouped according to their DNA-relatedness and then compared using 14 phenotypic tests. S. mitis, 'S. mitior' and three relatively new groups of strains ('CR', 'MGH' and 'Tufted mitior') bound salivary amylase, while strains of S. sanguis and S. oralis did not. The ability of strains to bind amylase or not was remarkably consistent within groups and the test proved to be reproducible, rapid and easy to perform. Combination of the amylase-binding test with 6 other conventional physiological tests allowed the construction of a dichotomous identification key which correctly identified 95% of strains for which genetic data was available. These findings suggest that the ability of organisms to bind salivary amylase could become a key test in identification schemes for certain oral streptococci.     

Genetic exchange between oral streptococci during mixed growth

To determine whether oral streptococci might exchange genetic information in the oral cavity, paired transformable strains of Streptococcus mutans, Streptococcus sanguis and Streptococcus milleri were growth together. Chromosomal and plasmid-borne antibiotic resistance markers could be readily transferred from S. mutans GS-5 to S. milleri NCTC 10707 or S. sanguis Challis during mixed growth. However, no exchange from the latter two organisms to strain GS-5 could be detected under these conditions. The transfer of genetic information from S. sanguis to S. milleri was also observed.     

Genetic relationships among the annual species of Cicer L.

Summary Genetic relationships between 7 annual species of the genus Cicer, including the cultivated chickpea, have been studied. These species were assigned to 3 crossability groups. In each group interspecific hybrids could be obtained but their fertility differed considerably in the various cross combinations. Crosses between members of different groups yielded no viable seeds. The possibility of gene transfer from the wild species to the cultivated chickpea C. arietinum was also assessed. Only two species could be considered for this purpose, C. reticulatum, which is the wild progenitor of the cultivated species, and C. echinospermum, which is in the secondary gene pool of C. arietinum. A unique postzygotic reproductive barrier mechanism was found between the members of Group II, C. judaicum, C. pinnatifidum and C. bijugum. It is based on a disharmony in the growth rate of the stigma and the anthers at the time of anthesis of the F₁ interspecific hybrid so that selfpollination is avoided. It is proposed that this kind of mechanism has been involved only when an effective spatial isolation between the three species had been obtained.     

Genetic relationships among Turkish sheep

Genetic relationships among Turkish sheep breeds were analysed on the basis of 30 microsatellite markers. Phylogenetic analyses based on the estimation of genetic distances revealed the closest relationships for the Akkaraman, Morkaraman and Tuj breeds, which were clearly differentiated from the others in the dendrogram. Our pattern was completely confirmed by results from the Factorial Correspondence Analysis. All the results described analysing either population parameters or individuals revealed a clear separation between the fat-tailed group and the others. These results, based on nuclear DNA, are discussed along with those already reported for these breeds through the investigation of mitochondrial DNA, which had revealed the invaluable significance of the genetic background of these Turkish sheep.     

Genetic relationships among the apes and humans

Epistemological difficulties and contradictory sets of molecular genetic data show that the question 'What is our closest living relative?' is surprisingly difficult to answer decisively. It is highly likely that we have not a single closest relative but, at the genus level, two equally close ones.     

Genetic diversity among the T-protein genes of group A streptococci

T protein is a trypsin- and pepsin-resistant molecule on the surface of group A streptococci used as a serological tool to differentiate streptococci of this group. The purpose of this study was to determine the relatedness among the T protein genes of the 25 known T serotypes. DNA probes were constructed which represented various regions of the structural gene for the T6 protein, tee6. The probes were assayed for their ability to hybridize HindIII digests of chromosomal DNA from the 25 different T serotypes. Probe pTEE6.3, coding for the entire T6 protein, and pTEE6(1-299), coding for the amino-terminal half of T6, displayed the highest amount of homology, each binding to 10 of 25 T serotypes. Probes coding for sequences in the carboxy-terminal half of T6 showed considerably less homology among T serotypes with one probe hybridizing with only three out of 25. A synthetic oligonucleotide coding for the carboxy-terminal hydrophobic domain of T6, an area conserved to some degree among several bacterial surface proteins, showed homology with only seven out of 25 T serotypes. Hybridization with sequences outside the tee6 coding area provided additional information on the relatedness of certain sets of T serotypes according to restriction-fragment size heterogeneity. Clearly, there is considerable diversity among T-serotype genes. The data suggest that two or more families of structurally variant T proteins exist, which share only the property of proteolytic resistance and/or, perhaps, some biological function.     

Genetic diversity in the orange subfamily Aurantioideae. II. Genetic relationships among genera and species

Genetic relationships were studied by means of ten isoenzymatic systems, at the genus and species level, using two distances and four methods of aggregation in a germplasm collection of 198 cultivars and accessions of 54 species belonging to Citrus and 13 related genera. The most consistent results were obtained by the chord distance and the neighbor-joining clustering method. Citrus species were distributed in two main groups: the orange-mandarin group and the lime lemon-citron-pummelo group. The species C. halimii and C. tachibana are not included in these groups. Mandarin species fall into three main subgroups: one includes C. sinensis; the second, C. aurantium, the third, small-fruit species. The citron, the pummelo and the ancient lemon subgroups form a cluster to which the species belonging to subgenus Papeda and the cultivated limes, lemons and bergamots are related. Microcitrus spp, to which Severinia buxifolia and Atalantia ceylanica seem to be related, cluster with the lime lemon-citron-pummelo group while Fortunella is close to the orange-mandarin group. Poncirus trifoliata, the most important species for citrus rootstock improvement is located far from Citrus but connected to it through Fortunella spp. A broad distribution of species has been found that should be taken into account to sample new genotypes in the search of desired characters in order to fully and efficiently use genetic resources for citrus improvement.     

Genetic relationships among European cattle breeds

Genetic relationships among 37 European cattle breeds were investigated using blood group and serum protein polymorphisms. The 18 859 animals included in the study represented a random sample from pedigree populations in the UK. Within-breed variation was estimated by average heterozygosity and number of alleles observed, and breed relationships were evaluated by genetic distance. Standard errors of the heterozygosity, number of alleles and genetic distance were obtained by bootstrapping. The significance of breed differences was tested using an exact test of differentiation. French, Italian and Channel Island breeds were found to have generally higher heterozygosities and a greater number of alleles than breeds from mainland Britain and North Europe. Genetic distances ranged between 0·011 (±0·005) and 0·309 (±0·071). Two major breed groups were identified; a group of French, Italian and Channel Island breeds together with the Simmental and Gelbvieh, and a second group consisting of the mainland British and North European breeds. The exact test of breed differentiation showed all breeds to be significantly different from one another ( P < 0·0001). Overall relationships among breeds reflected their geographical origin and common ancestry rather than the agricultural use for which the breeds have been selected.     

Host-parasite relationships among group A streptococci. IV. Suppression of antibody response by streptococcal pyrogenic exotoxin

In rabbits, purified streptococcal pyrogenic exotoxin, at 0.002 of the ld(50) dose, suppressed the antibody response to injected sheep erythrocytes. The antibody suppressed was determined by density gradient ultracentrifugal analysis to be of the 19S class. Background serum antibody (50% hemolytic units), as determined photometrically, correlated well with background antibody-forming spleen cells, as determined by the hemolytic-plaque technique. The exotoxin induced neither positive nor negative changes in background antibody levels, but suppressed the early secondary response to injected antigen. A comparison and control experiment showed that purified gram-negative bacterial endotoxin at identical protocol did not induce antibody suppression, but did induce the well-known adjuvant effect. Because streptococcal pyrogenic exotoxin is known to inhibit the phagocytic function of the reticuloendothelial system (RES), these data strongly support the concept that antigen is processed by cells of the RES before it evokes a secondary immune response. The results also demonstrated that streptococcal pyrogenic exotoxin may play a unique role in lowering the acquired defense of the host against infection. If the anamnestic immune response of the host is temporarily suppressed, then the host-parasite balance would be upset in favor of the parasite.     

Genetic relationships among Spanish sheep using microsatellites

Five indigenous Spanish breeds of sheep, Churra, Latxa, Manchega, Rasa–Aragonesa and Merino, with Awassi sheep as a reference breed were genotyped for 19 DNA microsatellites. Allele frequencies and mean heterozygosities revealed the greatest genetic variation in Merino sheep and the lowest in Awassis. Differences in variability were not great in the other breeds studied. The dendrograms obtained based on genetic distances showed a large differentiation between Awassi sheep and the Spanish breeds, as was to be expected from their distinct genetic origin. Merinos appeared separated from the other four breeds, of which, according to a classification based on the fleece characteristics, Churra and Latxa belong to the churro type and Manchega and Rasa–Aragonesa to the so called entrefino type, though no clear separation was evident between the two types. These results suggest that morphological data alone are insufficient for determining relationships between breeds and that studies involving genetic markers may be of great assistance.     

Genetic and evolutionary relationships among Asian Macaques

Published gene frequency data, checked for consistency of allele definitions across laboratories and for comparability of geographically identical samples, were pooled into a data set containing frequencies at nine loci for each of 20 populations that encompassed 10 macaque species. Genetic distances were calculated by the methods of Kidd and Cavalli-Sforza (1974). These distances were used to construct phylogenetic trees and to evaluate the relationships between divergence times and effective population sizes. Inter-and intraspecific genetic distances and the groupings defined by phenetic tree analyses support Fooden’s (1976) classification of the genus Macacainto four species groups. A paleozoogeographical model of Asia including the known times of major sea-level changes allows us to explain Macacainto four species groups. A paleozoogeographical model of Asia including the known times of major sea-level changes allows us to explain qualitatively the inferred evolutionary relationships among macaque species. Many assumptions are required in order to estimate the variables necessary in the quantitative prediction of genetic differences for a comparison between any two populations. Examination of those assumptions demonstrates the need for more accurate genetic as well as paleozoogeographic information. An erratum to this article is available at .     

Genetic relationships among Eurasian Puccinellia distans genotypes

Puccinellia distans (Jacq.) Parl. is a common grass species found throughout the world. It can grow in arid and saline environments as well as under toxic boron concentrations. In this work we performed sequence related amplified polymorphism (SRAP) marker analysis on 20 wild P. distans genotypes to understand the genetic relationships among different genotypes and subspecies. We tested 119 SRAP primer pairs and found that 43 were polymorphic. The molecular data were then analyzed to determine the genetic relationships and population structure of the genotypes. We were able to trace the origin of genotypes that were carried to distant locations or gathered for research purposes. We also found that geographical distance between genotypes was not an important determinant of genetic relationships as even distantly located Puccinellia genotypes were closely related. As P. distans is known to be tolerant to salinity stress and toxic mineral concentrations, the findings of this work can be used as a starting point for selection of genotypes that should be tested under such conditions.     

Genetic relationships among 527 Gram-negative bacterial plasmids

Plasmids are mosaic in composition with a maintenance "backbone" as well as "accessory" genes obtained via horizontal gene transfer. This horizontal gene transfer complicates the study of their genetic relationships. We describe a method for relating a large number of Gram-negative (GN) bacterial plasmids based on their genetic sequences. Complete coding gene sequences of 527 GN bacterial plasmids were obtained from NCBI. Initial classification of their genetic relationships was accomplished using a computational approach analogous to hybridization of "mixed-genome microarrays." Because of this similarity, the phrase "virtual hybridization" is used to describe this approach. Protein sequences generated from the gene sequences were randomly chosen to serve as "probes" for the virtual arrays, and virtual hybridization for each GN plasmid was achieved using BLASTp. Each resulting intensity matrix was used to generate a distance matrix from which an initial tree was constructed. Relationships were refined for several clusters by identifying conserved proteins within a cluster. Multiple-sequence alignment was applied to the concatenated conserved proteins, and maximum likelihood was used to generate relationships from the results of the alignment. While it is not possible to prove that the genetic relationships among the 527 GN bacterial plasmids obtained in this study are correct, replication of identical results produced in a separate study for a small group of IncA/C plasmids provides evidence that the approach used can correctly predict genetic relationships. In addition, results obtained for clusters of Borrelia plasmids are consistent with the expected exclusivity for plasmids from this genus. Finally, the 527-plasmid tree was used to study the distribution of four common antibiotic resistance genes.     

Genetic relationships among the inhabitants of nine Mediterranean countries

Gene frequency data on 16 protein and blood group loci for the inhabitants of 9 Mediterranean countries were collected from the literature. The frequency of most of these genes was associated with longitude. The genetic distances between the same populations were also determined. The smallest genetic distances were found among the north Mediterranean countries, whereas the highest values were observed between the Algerians and the inhabitants of the other countries.     

Genetic relationships among Pistacia species using AFLP markers

This study addresses the phylogenetic relationship between Pistacia species by amplified fragment length polymorphism (AFLP). The plant materials of this study consisted of a total of 44 accessions belonging to P. vera, P. eurycarpa, P. khinjuk, all subspecies of P. atlantica (atlantica, mutica, kurdica and cabulica), three unknown genotypes and three accessions, proposed to be hybrid from P. eurycarpa × P. atlantica. The accessions were from Iran, Turkey, USA and Syria. Six AFLP primer combinations produced a total of 475 fragments, with average of 79.16 fragments per primer pair, of which, 336 bands were polymorphic. Unweighted pair group method based on arithmetic average (UPGMA) analysis was performed on jaccard’s similarity coefficient matrix and also average similarity of each species. According to the results, two main clusters were developed and P. vera, P. eurycarpa, P. atlantica (subsp. atlantica, kurdica, mutica, cabulica) and the hybrid genotypes located in the first main cluster. P. khinjuk accessions from Iran and USA localized in second main cluster. The hybrid accessions located between eurycarpa and atlantica species and their hybrid nature between these two species were confirmed. One of the unknown accessions clustered with the hybrid ones and the two other were grouped closely with P. Khinjuk. According to this study, the closest species to P. vera was Eurycarpa group, followed by P. atlantica. UPGMA analysis separated P. atlantica subsp. mutica and cabulica from P. atlantica and P. eurycarpa. Subspecies mutica and cabulica were two closest genotypes; hence, P. atlantica subsp. mutica could be classified as a distinct species as P. mutica and the cabulica as a subspecies of P. mutica. This study revealed that P. eurycarpa is synonym for P. atlantica subsp. kurdica and should be considered distinct from P. atlantica; however, P. atlantica showed a closer genetic similarity to P. eurycarpa than the other species.     

A gentle method for the lysis of oral streptococci.

Black lipid planar membranes were prepared by incorporating polymers such as polystyrene in a membrane forming solution. The polymerincorporated planar membranes showed greater stability to applied electric fields and have longer lifertimes. Photopotentials were studied under several conditions; with bacteriorhodopsin in the planar membrane; with bacteriorhodopsin in liposomes; with bacteriorhodopsin fragments in suspension; and with bacteriorhodopsin both in the planar membrane and in liposomes. Skulachev's laboratory has reported that bacteriorhodopsin-liposomes develop potentials across a black lipid planar membrane. In our studies, because the polymer incorporated planar membranes are very stable, it was possible to obtain somewhat larger photopotentials in the presence of bacteriorhodopsin ranging between 30–500 mV. The enhancement of bacteriorhodopsin catalyzed photopotentials, found in the presence of Ca⁺⁺ (or other bivalent cations) and/or applied electric fields, appeared to result from an orientation effect of bacteriorhodopsin at the membrane interface.     

Discrimination between oral streptococci by pyrolysis gas-liquid chromatography.

Washed organisms, including strains of Streptococcus mitior, S. mutans, and S. sanguis, were examined by curie-point pyrolysis gas-liquid chromatography. A linear discriminant function based upon three items from the output data was adequate for segregating the strains according to species. Strains with intermediate properties were also encountered. Sources of variability in cultures were evaluated, chromatographic performance was maintained throughout the investigation, and matching performance from a duplicate pair of chromatographic columns was demonstrated.     

Genetic relationships among three chlorophyll-deficient mutants in peanut,Arachis hypogaea L.

Summary The genetic relationships of three chlorophyll-deficient mutant peanuts, lutescens (lu), aureus (au), and virescent (v) were studied under field and greenhouse conditions. The F₁ plants from crosses between these mutants produced phenotypically normal green. In F₂, aureus X virescent segregated 675 normal green : 225 virescent : 45 aureus : 15 virescent aureus : 64 seedling lethal, and lutescens X virescent segregated 45 normal green : 15 virescent : 3 lutescens : 1 seedling lethal. (Lutescens peanuts were seedling lethal in the field.) As previously reported, the F₂ of aureus X lutescens gave 225 normal green : 15 aureus :15 lutescens : 1 seedling lethal. The three chlorophyll-deficient factors (au, lu, and v) show independent inheritance. The recessive combinations from the parental types between aureus and virescent and between aureus and lutescens would produce plants with a combination of their respective parental characteristics, but the recessive combination between lutescens and virescent was nearly albino. The v-au and lu-au seedlings have a longer life span than the v-lu seedling has. The genotypes for the three mutants are tentatively identified as lutescens VV Au ₁ Au ₁ Au ₂ Au ₂ lu ₁ lu ₁ lu ₂ lu ₂ L ₁ L ₁ L ₂ L ₂, aureus VV au₁au₁ au₂au₂ Lu₁Lu₁ Lu₂Lu₂ L₁L₁ l₂l₂, and virescent vv Au₁Au₁ Au₂Au₂ lu₁lu₁ Lu₂Lu₂ l₁l₁ L₂L₂.