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At least 217 records · Page 12Linked to original sources

PubMed2005

Evolutionary regulation of the blind subterranean mole rat, Spalax, revealed by genome-wide gene expression.

We applied genome-wide gene expression analysis to the evolutionary processes of adaptive speciation of the Israeli blind subterranean mole rats of the Spalax ehrenbergi superspecies. The four Israeli allospecies climatically and adaptively radiated into the cooler, mesic northern domain (N) and warmer, xeric southern domain (S). The kidney and brain mRNAs of two N and two S animals were examined through cross-species hybridizations with two types of Affymetrix arrays (mouse and rat) and muscle mRNA of six N and six S animals with spotted cDNA mouse arrays. The initial microarray analysis was hypothesis-free, i.e., conducted without reference to the origin of animals. Principal component analysis revealed that 20-30% of the expression signal variability could be explained by the differentiation of N-S species. Similar N-S effects were obtained for all tissues and types of arrays: two Affymetrix microarrays using probe oligomer signals and the spotted array. Likewise, ANOVA and t test statistics demonstrated significant N-S ecogeographic divergence and region-tissue specificity in gene expression. Analysis of differential gene expression between species corroborates previous results deduced by allozymes and DNA molecular polymorphisms. Functional categories show significant N-S ecologic putative adaptive divergent up-regulation of genes highlighting a higher metabolism in N, and potential adaptive brain activity and kidney urine cycle pathways in S. The present results confirm ecologic-genomic separation of blind mole rats into N and S. Gene expression regulation appears to be central to the evolution of blind mole rats.

Adaptation, Physiological↗

PubMed1996

Molecular mapping of the tubby (tub) mutation on mouse chromosome 7.

Using 180 F2 progeny of a C57BL6/J >< CAST/Ei tub/+F1 intersubspecific intercross, a map of 28 molecular markers (including eight genes) on chromosome 7 surrounding the tub locus was generated. Using 33 obese F2 progeny, tub was localized approximately 50-52 cM distal to the centromere on mouse chromosome 7 in the interval defined proximally by hemoglobin beta (Hbb), D7Mit38, D7Mit2l7, D7Mit37, D7Mit96, and D7Mit33 and distally by D7Mit98. Using 39 obese F2 progeny from a similar intersubspecific intercross, a telomeric boundary of the interval defining tub was defined by D7Mit53; the order centromere-Hbb/tub-D7Mit53/ D7Mit328/D7Mit220-parathyroid hormone (Pth)-calcitonin (Calc)-zona pellucida 2 (2p2) was established. By combining the data from the two crosses, the most likely gene order on mouse chromosome 7 is centromere-Hbb-tub-Pth-Calc, thus making it likely that the human homolog of tub resides on 17p15, where the gene order HBB-PTH-CALC is conserved. Assignment of the human tubby homolog to 17p15 allows selection and development of polymorphic molecular markers that can be used to examine segregation of a human homolog of tubby in pedigrees segregating for obesity. The gene sulfonylurea receptor was eliminated as a candidate gene for tubby on the basis of its map position, approximately 3.1 +/- 3.1 cM centromeric of tyrosinase and approximately 14.9 +/- 4.8 cM centromeric of Hbb.

Adaptor Proteins, Signal Transducing↗

PubMed2002

The period gene and genetic differentiation between three Brazilian populations of Lutzomyia longipalpis.

Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae), the main vector of visceral leishmaniasis in the Americas, is a putative species complex. Molecular polymorphism was characterized in a 266 bp fragment of L. longipalpis homologous to period, a 'speciation gene' from Drosophila. Samples from the Brazilian localities of Jacobina (BA), Lapinha (MG) and Natal (RN) were analysed and the data indicate that the three populations are highly differentiated, with a very low level of gene flow between them. These results are in agreement with published pheromone and copulation song studies that suggest the existence of a sibling species complex in Brazil.

Amino Acid Sequence↗

PubMed2006

Toxin gene profiling of enterotoxic and emetic Bacillus cereus.

Very different toxins are responsible for the two types of gastrointestinal diseases caused by Bacillus cereus: the diarrhoeal syndrome is linked to nonhemolytic enterotoxin NHE, hemolytic enterotoxin HBL, and cytotoxin K, whereas emesis is caused by the action of the depsipeptide toxin cereulide. The recently identified cereulide synthetase genes permitted development of a molecular assay that targets all toxins known to be involved in food poisoning in a single reaction, using only four different sets of primers. The enterotoxin genes of 49 strains, belonging to different phylogenetic branches of the B. cereus group, were partially sequenced to encompass the molecular diversity of these genes. The sequence alignments illustrated the high molecular polymorphism of B. cereus enterotoxin genes, which is necessary to consider when establishing PCR systems. Primers directed towards the enterotoxin complex genes were located in different CDSs of the corresponding operons to target two toxin genes with one single set of primers. The specificity of the assay was assessed using a panel of B. cereus strains with known toxin profiles and was successfully applied to characterize strains from food and clinical diagnostic labs as well as for the toxin gene profiling of B. cereus isolated from silo tank populations.

Bacillus cereus↗

PubMed2006

New evolutionary lineages, unexpected diversity, and host specificity in the parabasalid genus Tetratrichomonas.

We studied morphological and molecular polymorphism of 53 Tetratrichomonas isolates obtained from amphibian, reptilian, mammalian hosts, and from a slug with the aid of protargol staining and analyses of ITS1-5.8S rRNA-ITS2, SSU rRNA, and alpha-tubulin gene sequences. The phylogenetic tree based on the concatenate of all sequences showed the monophyly of the genus Tetratrichomonas with respect to the genus Trichomonas. Our data suggest that two parabasalid genera, Pentatrichomonoides and Trichomonoides, may belong to the genus Tetratrichomonas. Tetratrichomonas isolates were divided into 16 robust host-specific and monophyletic groups that probably represent separate, mostly new, species. As only five Tetratrichomonas species were described from the examined host taxa so far, our study uncovered considerable species diversity within the genus. The wide host range, high level of species-specific host specificity, and newly revealed biodiversity make the genus Tetratrichomonas a valuable model for studying evolution of parasites.

Animals↗

PubMed2004

Selection and dispersal in a multispecies oak hybrid zone.

The four western North American red oak species (Quercus wislizeni, Q. parvula, Q. agrifolia, and Q. kelloggii) are known to produce hybrid products in all interspecific combinations. However, it is unknown whether hybrids are transitory resulting from interspecific gene flow or whether they are maintained through extrinsic selection. Here, we examine cryptic hybrid structure in Q. wislizeni through a broad region including contact and isolation from three other western North American red oaks using amplified fragment length polymorphism molecular markers. All four species were simultaneously detected in the genetic background of individuals morphologically assigned to Q. wislizeni, although the contribution of Q. kelloggii was minor. In some cases, introgression was detected well outside the region of sympatry with one of the parental species. Molecular structure at the individual level indicated this was due to long-distance pollen dispersal and not to local extinction of parental species. Species admixture proportions were correlated with climatic variables and greater proportions of Q. agrifolia and Q. parvula were present in the genetic background of Q. wislizeni in sites with cooler and more humid summers, corresponding with habitat preferences of the parental species. Partial Mantel tests indicated that climate was more important than distance from pollen source in this association. Despite high levels of introgression, species integrity was maintained in some populations in close proximity to the other species, providing further support to environmental selection in determining population genetic structure. Thus, the contribution of species mixtures to population genetic structure varies across the landscape according to availability of pollen, but more importantly to varying environmental selection pressures that produce a complex pattern of hybrid and pure gene pools.

California↗

PubMed1992

Mapping of a B-cell epitope present in the neuraminidase of Trypanosoma cruzi.

We have previously shown that a polyclonal (rabbit anti-TCNA) and a mouse monoclonal antibody (TCN-2) against the neuraminidase of Trypanosoma cruzi (TCNA) inhibit enzyme activity, immunoprecipitate active enzyme, enhance in vitro infection, and identify a subpopulation of extracellular trypomastigotes. We now report on the identification of a synthetic peptide that contains the epitope recognized by these antibodies. The synthetic peptide (TR) is a dodecamer (D-S-S-A-H-G-T-P-S-T-P-A) deduced from the DNA sequence of the long tandem repeat (LTR) domain present in the TCNA carboxyterminus. By ELISA, rabbit anti-TCNA bound to TR coupled to ovalbumin, and the binding was inhibited by soluble TR but not by BR (Y-S-V-D-D-G-E-T-W-E), a peptide derived from the N-terminal domain of the enzyme. TCN-2 recognized TR, and this reaction as well as TCN-2 binding to endogenous TCNA could be inhibited by soluble TR but not by BR. These results indicate that the rabbit anti-TCNA and TCN-2 react with the LTR region of TCNA. Antibodies to TR reacted by immunoblot with the TCNA of the Silvio X-10/4, MV-13 and Y-H6 strains, identifying the same molecular polymorphism previously observed with the rabbit anti-TCNA and TCN-2. Furthermore, anti-TR antibodies immunoprecipitated active enzyme and immunofluorescence analysis revealed that anti-TR and TCN-2 antibodies detected equally well the differential expression of their epitopes in intra- and extracellular trypomastigotes. Moreover, expression of TR and TCN-2 epitopes on the different stages of T. cruzi paralleled the stage-specificity of TCNA activity. TCN-2 prevented desialylation by TCNA of intact cells but not of soluble glycoconjugates, indicating that TCN-2 epitope is probably not associated with the enzyme catalytic site, in agreement with the predicted sequence of the TCNA gene. Finally, analysis of the humoral response of a Chagasic patient to different areas of the TCNA molecule indicated that the antibody response is predominantly against TR suggesting that the tandem repeat is the immunodominant domain of TCNA.

Amino Acid Sequence↗

PubMed1996

Perinatal energy stores and excessive fat deposition in genetically obese (fa/fa) rats.

To find out whether perinatal differences in energy stores are essential for the phenotypic manifestation of the fa/fa genotype in 16-day-old rats, we investigated Zucker rats (13M) x Brown Norway (BN) hybrids. +/fa and fa/fa hybrids were identified by molecular polymorphisms approximately 1 cM from the fa locus. The fat content of all pups increased rapidly after birth, and differences between +/fa and fa/fa hybrid pups were significant in 7- and 16-day-old rats but not at 0, 1, and 4 days of age. For 16-day-old 13MBN hybrids as well as 13M Zucker rats, plots of carcass fat vs. body mass were closely fitted by parallel regression lines, with carcass fat similarily higher in fa/fa than +/fa pups of both strains. Fetal and neonatal plasma insulin concentration and hepatic glycogen in the 13MBN hybrid pups did not differ between +/fa and fa/fa litter-mates, nor did the hepatic and adipose tissue triglycerides in 24-h-old 13MBN hybrid pups. The manifest differences between fatty and lean 16-day-old pups thus do not depend on differences in perinatal energy stores.

Adipose Tissue↗

PubMed1999

Evidence for frequent OspC gene transfer between Borrelia valaisiana sp. nov. and other Lyme disease spirochetes.

Molecular polymorphism of the ospC gene has been reported in Borrelia burgdorferi sensu stricto, Borrelia garinii and Borrelia afzelii, the spirochetes causing human Lyme borreliosis. To assess the genetic relationship between ospC genes from the recently described Borrelia valaisiana sp. nov. and other B. burgdorferi sensu lato species, the ospC genes from eight B. valaisiana isolates were amplified by PCR, cloned and sequenced. The ospC genes of three B. valaisiana isolates were identical, but clearly distinct from ospC genes from other Borrelia species. Four B. valaisiana isolates possessed ospC genes more related to those of B. garinii, and fell into a cluster representing B. garinii species in the phylogenetic tree. One isolate had an ospC gene encoding a protein identical to that of B. afzelii strain. Since five of the eight (62.5%) B. valaisiana isolates contained a gene highly homologous or even identical to ospC genes found among B. garinii and B. afzelii strains, our findings indicate that ospC gene transfer occurs between B. valaisiana and other Lyme disease spirochetes.

Amino Acid Sequence↗

PubMed2005

A general framework for statistical linkage analysis in multivalent tetraploids.

In multivalent polyploids, simultaneous pairings among homologous chromosomes at meiosis result in a unique cytological phenomenon-double reduction. Double reduction casts an impact on chromosome evolution in higher plants, but because of its confounded effect on the pattern of gene cosegregation, it complicates linkage analysis and map construction with polymorphic molecular markers. In this article, we have proposed a general statistical model for simultaneously estimating the frequencies of double reduction, the recombination fraction, and optimal parental linkage phases between any types of markers, both fully and partially informative, or dominant and codominant, for a tetraploid species that undergoes only multivalent pairing. This model provides an in-depth extension of our earlier linkage model that was built upon Fisher's classifications for different gamete formation modes during the polysomic inheritance of a multivalent polyploid. By implementing a two-stage hierarchical EM algorithm, we derived a closed-form solution for estimating the frequencies of double reduction through the estimation of gamete mode frequencies and the recombination fraction. We performed different settings of simulation studies to demonstrate the statistical properties of our model for estimating and testing double reduction and the linkage in multivalent tetraploids. As shown by a comparative analysis, our model provides a general framework that covers existing statistical approaches for linkage mapping in polyploids that are predominantly multivalent. The model will have great implications for understanding the genome structure and organization of polyploid species.

Algorithms↗

PubMed1992

Sequence and length heterogeneity of alpha Fc gamma R transcripts in AKR mice.

The murine low-affinity receptors for IgG, Fc gamma RIII and Fc gamma RII, are encoded by the alpha and the beta Fc gamma R genes, respectively. By contrast to the sequence and the molecular polymorphism of human Fc gamma RIII, no heterogeneity of the murine Fc gamma RIII has been reported and a single alpha Fc gamma R transcript was observed. We describe here a double heterogeneity of alpha Fc gamma R transcripts. First, by S1 mapping of alpha transcripts and by cloning of cDNA coding for Fc gamma RIII, we found a strain-related sequence heterogeneity: four amino acids in the coding region and two stretches of nucleotides in the 3' untranslated sequences differ between alpha transcripts of AKR and BALB/c mice. Second, in AKR mice, we found a cell-dependent length heterogeneity: a short 0.9 kb alpha transcript was present in peritoneal thioglycolate-elicited cells (PEC) from AKR mice. This transcript was present neither in mast cells and NK cells from AKR and BALB/c mice nor in PEC from BALB/c mice. A short cDNA, with a deletion of all the 3' untranslated sequences, has been cloned from AKR PEC, and corresponds to the short alpha transcript. All the differences found in the 3' untranslated sequences of AKR alpha transcripts are located within the fifth exon of the mouse alpha Fc gamma R gene.

Amino Acid Sequence↗

PubMed2006

Major histocompatibility complex class II variation in the giant panda (Ailuropoda melanoleuca).

Habitat destruction and human activity have greatly impacted the natural history of the giant panda (Ailuropoda melanoleuca). Although the genetic diversity of neutral markers has been examined in this endangered species, no previous work has examined adaptive molecular polymorphisms in the giant panda. Here, the major histocompatibility complex (MHC) class II DRB locus was investigated in the giant panda, using single-strand conformation polymorphism (SSCP) and sequence analysis. Comparisons of DNA samples extracted from faecal and blood samples from the same individual revealed that the two materials yielded similar quantities and qualities of DNA, as well as identical SSCP patterns and allelic sequences, demonstrating the reliability of DNA isolation from panda faeces. Analysis of faecal samples from 60 giant pandas revealed relatively low number of alleles: seven alleles. However, the alleles were quite divergent, varying from each other by a range of 7-47 nucleotide substitutions (4-25 amino acid substitutions). Construction of a neighbour-joining tree and comparisons among DRB alleles from other species revealed that both similar and highly divergent alleles survived in the bottlenecked panda populations. Despite species-specific primers used and excellent faecal DNA isolated, a lower level of heterozygosity than expected was still observed due to inbreeding. There were three types of evidence supporting the presence of balancing selection in the giant panda: (i) an obvious excess of nonsynonymous substitutions over synonymous at the antigen-binding positions; (ii) trans-species evolution of two alleles between the giant panda and other felids; and (iii) a more even distribution of alleles than expected from neutrality.

Alleles↗

PubMed1990

Molecular study of parental origin of extra chromosome 21 in regular and de novo translocation trisomies.

The parental origin of the extra chromosome 21 (or extra 21q) was determined in seven informative families with a Down syndrome (DS) child by using molecular polymorphisms. Five DS patients had regular trisomy, one a de novo 14/21 translocation and another a de novo 21/21 translocation or isochromosome 21q. In four families with regular trisomy, the extra chromosome was of maternal origin, and in one family it was paternally derived. In the two families with a de novo aberration, both the 14/21 translocation and 21/21 rearrangement originated during maternal meiosis. For a better evaluation of the stage of meiotic error and the occurrence of crossovers between nondisjoined chromosomes, the regional map position of four of the nine informative DNA markers, used in this study, was refined, leading to useful localizations in both centromeric and distal regions. Recombination events were found in two families with regular trisomy, one occurring between chromosomes 21 that failed to disjoin at maternal meiosis I, the other prior to a paternal meiosis II nondisjunction.

Blotting, Southern↗

PubMed1975

[Seed globulins from legumes. III. Seed globulins from broad bean (Vicia faba L.)].

The seed globulins from Vicia faba predominantly consist of two components, vicilin and legumin, which are exclusively deposited within the protein bodies of the storage cotyledons. The globulin biosynthesis commences with high intensity within a distinct phase during seed development as a consequence of reactivated genetic information. Isolation and purification of vicilin and legumin were achieved by a combination of zone precipitation, ion exchange chromatography, and gel filtration. Purity was controlled by disc electrophoresis on polyacrylamide e gels at pH 4.3 and by two dimensional immunoelectrophoresis, respectively. Vicilin prepared by zone precipitation and ion exchange chromatography consists of several serologically different proteins. One of them occupies the legumin position on polyacrylamide gels, although not identic with legumin, as revealed by tandem immunoelectrophoresis. The serological nonrelationship of vicilin and legumin was confirmed. Vicilin is characterized by micro heterogeneity which seems to indicate a molecular polymorphism.

Globulins↗

PubMed2006

A framework to monitor environment-induced major genes for developmental trajectories: implication for a prenatal cocaine exposure study.

Whether there are specific genes involved in response to different environmental agents and how such genes regulate developmental trajectories during lifetime are of fundamental importance in health, clinical and pharmaceutical research. In this article, we present a novel statistical model for monitoring environment-induced genes of major effects on longitudinal outcomes of a trait. This model is derived within the maximum likelihood framework, incorporated by mathematical aspects of growth and developmental processes. A typical structural model is implemented to approximate time-dependent covariance matrices for the longitudinal trait. This model allows for a number of biologically meaningful hypothesis tests regarding the effects of major genes on overall growth trajectories or particular stages of development. It can be used to test whether and how major genetic effects are expressed differently under altered environmental agents. In a well-designed case-control study, our model has been employed to detect cocaine-dependent genes that affect growth trajectories for head circumference during childhood. The detected gene triggers significant effects on growth curves in both cocaine-exposed (case) and unexposed groups (control), but with different extents. Significant genotype-environment interactions due to this so-called environment-sensitive gene are promising for further studies toward its genomic mapping using polymorphic molecular markers.

Adult↗

PubMed1984

Transferrin subtypes in cystic fibrosis.

The molecular polymorphism and quantitative data of serum transferrin (Tf) were ascertained in a group of fibrocystic patients, their parents and controls. Quantitative rates of pre-albumin, retinol binding globulin (RBG) and alpha-1-glycoprotein were also investigated as a reference for the evaluation of Tf quantitative data. Neither different allele distributions nor abnormal electrophoretic patterns were observed among CF patients. A slight lowering of Tf, pre-albumin and RBG, probably due to malnutritional condition in CF subjects was found.

Adolescent↗

PubMed1985

Vitamin D-binding protein in the perinatal period.

The molecular polymorphism and quantitative levels of serum vitamin D-binding protein (DBP) were ascertained in a group of preterm, full-term and hypocalcaemic full-term newborn infants. The serum concentration of DBP is not influenced by phenotype and increases with fetal age from the 32nd-33rd week of gestation until the 35th week of gestation. Neither different DBP allele distribution nor abnormal quantitative levels found among 29 hypocalcaemic full-term newborn infants.

Alleles↗

PubMed2006

Functional mapping in pea, as an aid to the candidate gene selection and for investigating synteny with the model legume Medicago truncatula.

The identification of the molecular polymorphisms giving rise to phenotypic trait variability-both quantitative and qualitative-is a major goal of the present agronomic research. Various approaches such as positional cloning or transposon tagging, as well as the candidate gene strategy have been used to discover the genes underlying this variation in plants. The construction of functional maps, i.e. composed of genes of known function, is an important component of the candidate gene approach. In the present paper we report the development of 63 single nucleotide polymorphism markers and 15 single-stranded conformation polymorphism markers for genes encoding enzymes mainly involved in primary metabolism, and their genetic mapping on a composite map using two pea recombinant inbred line populations. The complete genetic map covers 1,458 cM and comprises 363 loci, including a total of 111 gene-anchored markers: 77 gene-anchored markers described in this study, 7 microsatellites located in gene sequences, 16 flowering time genes, the Tri gene, 5 morphological markers, and 5 other genes. The mean spacing between adjacent markers is 4 cM and 90% of the markers are closer than 10 cM to their neighbours. We also report the genetic mapping of 21 of these genes in Medicago truncatula and add 41 new links between the pea and M. truncatula maps. We discuss the use of this new composite functional map for future candidate gene approaches in pea.

Chromosome Mapping↗