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Results for “conservation genetics”

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At least 217 records · Page 12Linked to original sources

PubMed2006

A drug-sensitive genetic network masks fungi from the immune system.

Fungal pathogens can be recognized by the immune system via their beta-glucan, a potent proinflammatory molecule that is present at high levels but is predominantly buried beneath a mannoprotein coat and invisible to the host. To investigate the nature and significance of "masking" this molecule, we characterized the mechanism of masking and consequences of unmasking for immune recognition. We found that the underlying beta-glucan in the cell wall of Candida albicans is unmasked by subinhibitory doses of the antifungal drug caspofungin, causing the exposed fungi to elicit a stronger immune response. Using a library of bakers' yeast (Saccharomyces cerevisiae) mutants, we uncovered a conserved genetic network that is required for concealing beta-glucan from the immune system and limiting the host response. Perturbation of parts of this network in the pathogen C. albicans caused unmasking of its beta-glucan, leading to increased beta-glucan receptor-dependent elicitation of key proinflammatory cytokines from primary mouse macrophages. By creating an anti-inflammatory barrier to mask beta-glucan, opportunistic fungi may promote commensal colonization and have an increased propensity for causing disease. Targeting the widely conserved gene network required for creating and maintaining this barrier may lead to novel broad-spectrum antimycotics.

Animals↗

PubMed1994

Multiple genotypes of mitochondrial DNA within a horse population from a small region in Yunnan Province of China.

mtDNA genotypes of six domestic horses (three adult short horses whose heights are under 1 m and three common domestic horses) from a small region of 15 km2 in Malipo county of Yunnan province of China were investigated by the technique of restriction fragment length polymorphism (RFLP) with 16 restriction endonucleases which recognize 6-bp sequences. An average of 56 fragments for an individual was obtained. Unlike other domestic animals, this population of horses exhibits high mtDNA genetic diversity. Each of the six horses has a specific mtDNA genotype showing a pattern of multiple maternal origins, as suggested by fossil and literature records. We think the population of horses is an amazing seed-resource pool of horses and hence deserves to be paid more attention from the view of conservation genetics. However, it is also remarkable that we did not find any typical mtDNA genetic markers which would discriminate between short horses and common domestic horses.

Animals↗

PubMed2005

Genetic dissection of neurodegeneration and CNS inflammation.

Inflammation and neurodegeneration characterize multiple sclerosis, as well as many other diseases of the central nervous system (CNS). The understanding of the molecular pathways that regulate these processes is of fundamental importance for the development of new therapies. Nerve lesions paradigms in animals can serve as important tools to dissect central features of human CNS disease and by using these models certain key regulators have also been identified. However, our knowledge of how aspects of neurodegeneration and CNS inflammation are regulated on a genomic level is very limited. Such knowledge may help to unravel disease mechanisms. By using a standardized nerve trauma model, ventral root avulsion (VRA), in a series of inbred rat strains we here demonstrate a potent genetic regulation of the degree of neuron death and glial activation. Genome wide mapping of these phenotypes in experimental rat strain crosses identifies several quantitative trait loci (QTLs) controlling nerve lesion-induced nerve cell death, local T cell accumulation and expression of MHC class II on microglia. This approach may lead to the identification of evolutionary conserved genetic polymorphisms in key controlling genes, which can serve as prime candidates for association studies in several human CNS diseases.

Animals↗

PubMed2005

Risk for HIV-1 infection associated with a common CXCL12 (SDF1) polymorphism and CXCR4 variation in an African population.

CXC chemokine ligand 12 (CXCL12), or stromal cell-derived factor 1 (SDF1), is the only known natural ligand for the HIV-1 coreceptor, CXC chemokine receptor 4 (CXCR4). A single nucleotide polymorphism (SNP) in the CXCL12 gene (SDF1-3'A) has been associated with disease progression to AIDS in some studies, but not others. Mutations in the CXCR4 gene are generally rare and have not been implicated in HIV-1/AIDS pathogenesis. This study analyzed the SDF1-3'A SNP and performed mutation screening for polymorphic markers in the CXCR4 gene to determine the presence or absence of significant associations with susceptibility to HIV-1 infection. The study consisted of 257 HIV-1-seropositive patients and 113 HIV-1-seronegative controls representing a sub-Saharan African population belonging to the Xhosa ethnic group of South Africa. The SDF1-3'A SNP was associated with an increased risk for HIV-1 infection (P = 0.0319) whereas no significant association was observed between the occurrence of the SDF1-3'A SNP and increased or decreased plasma levels of CXCL12. Comprehensive mutation analysis of the CXCR4 gene confirmed a high degree of genetic conservation within the coding region of this ancient population.

Black People↗

PubMed2001

Structural comparison of three types of staphylococcal cassette chromosome mec integrated in the chromosome in methicillin-resistant Staphylococcus aureus.

The beta-lactam resistance gene mecA of Staphylococcus aureus is carried by a novel mobile genetic element, designated staphylococcal cassette chromosome mec (SCCmec), identified in the chromosome of a Japanese methicillin-resistant S. aureus (MRSA) strain. We now report identification of two additional types of mecA-carrying genetic elements found in the MRSA strains isolated in other countries of the world. There were substantial differences in the size and nucleotide sequences between the elements and the SCCmec. However, new elements shared the chromosomal integration site with the SCCmec. Structural analysis of the new elements revealed that they possessed all of the salient features of the SCCmec: conserved terminal inverted repeats and direct repeats at the integration junction points, conserved genetic organization around the mecA gene, and the presence of cassette chromosome recombinase (ccr) genes responsible for the movements of SCCmec. The elements, therefore, were considered to comprise the SCCmec family of staphylococcal mobile genetic elements together with the previously identified SCCmec. Among 38 epidemic MRSA strains isolated in 20 countries, 34 were shown to possess one of the three typical SCCmec elements on the chromosome. Our findings indicated that there are at least three distinct MRSA clones in the world with different types of SCCmec in their chromosome.

Amino Acid Sequence↗

PubMed2004

Microsatellite diversity, population subdivision and gene flow in the Lipizzan horse.

Blood samples of 561 Lipizzan horses from subpopulations (studs) of seven European countries representing a large fraction of the breed's population were used to examine the genetic diversity, population subdivision and gene flow in the breed. DNA analysis based on 18 microsatellite loci revealed that genetic diversity (observed heterozygosity = 0.663, gene diversity = 0.675 and the mean number of alleles = 7.056) in the Lipizzan horse is similar to other horse breeds as well as to other domestic animal species. The genetic differentiation between Lipizzan horses from different studs, although moderate, was apparent (pairwise F(ST) coefficients ranged from 0.021 to 0.080). Complementary findings explaining the genetic relationship among studs were revealed by genetic distance and principal component analysis. One genetic cluster consisted of the subpopulations of Austria, Italy and Slovenia, which represent the classical pool of Lipizzan horse breeding. A second cluster was formed by the Croatian, Hungarian and Slovakian subpopulations. The Romanian subpopulation formed a separate unit. The largest genetic differentiation was found between the Romanian and Italian subpopulation. Genetic results are consistent with the known breeding history of the Lipizzan horse. Correct stud assignment was obtained for 80.9% and 92.1% of Lipizzan horses depending on the inclusion or exclusion of migrant horses, respectively. The results of the present study will be useful for the development of breeding strategies, which consider classical horse breeding as well as recent achievements of population and conservation genetics.

Animals↗

PubMed1996

Construction of a chromosome map for the phage group II Staphylococcus aureus Ps55.

The genome size and a partial physical and genetic map have been defined for the phage group II Staphylococcus aureus Ps55. The genome size was estimated to be 2,771 kb by pulsed-field gel electrophoresis (PFGE) using the restriction enzymes SmaI, CspI, and SgrAI. The Ps55 chromosome map was constructed by transduction of auxotrophic and cryptic transposon insertions, with known genetic and physical locations in S. aureus NCTC 8325, into the Ps55 background. PFGE and DNA hybridization analysis were used to detect the location of the transposon in Ps55. Ps55 restriction fragments were then ordered on the basis of genetic conservation between the two strains. Cloned DNA probes containing the lactose operon (lac) and genes encoding staphylococcal protein A (spa), gamma hemolysin (hlg), and coagulase (coa) were also located on the map by PFGE and hybridization analysis. This methodology enabled a direct comparison of chromosomal organization between NCTC 8325 and Ps55 strains. The chromosome size, gene order, and some of the restriction sites are conserved between the two phage group strains.

Bacteriophage Typing↗

PubMed1997

Genetic parameters for egg number, egg weight, and eggshell color in three Catalan poultry breeds.

Heritabilities for egg number, egg weight, and eggshell color (percentage light absorbance) at 39 wk of age, and the genetic correlations between them were estimated by restricted maximum likelihood in three Catalan poultry breeds: Penedesenca Negra (PN), Prat Lleonada (PL), and Empordanesa Roja (ER). Additive genetic differences between these breeds were also estimated. Data were from the IRTA Poultry Genetic Conservation Program and consisted of records from 1,309 PN, 1,466 PL, and 1,440 ER hens, which were obtained from 80 contemporary batches per breed hatched between 1987 and 1992. Estimates of heritability for egg number, egg weight, and eggshell color were, 0.20, 0.59, and 0.49 for PN, 0.31, 0.48, and 0.53 for PL; and 0.33, 0.50, and 0.27 for ER. Estimated genetic correlations between egg number and egg weight, egg number and shell color, and egg weight and shell color were, for PN, -0.22, -0.03, and 0.00; for PL, -0.21, -0.06, and 0.09; and -0.19, -0.29, and 0.30 for ER. Heritability for eggshell color and genetic correlation between eggshell color and other traits showed a different genetic pattern in ER breed. Significant additive genetic differences (P < 0.05) were found between ER and PN base populations for egg number (3.89), egg weight (0.91), and eggshell color (-3.50); and between ER and PL for egg number (6.69) and eggshell color (35.39). The PN and PL breeds differed significantly (P < 0.05) for eggshell color (38.22), which was darker in PN. These results could be taken as the expected genetic differences for these breeds.

Aging↗

PubMed2002

Assessment of population genetic structure in common wild rice Oryza rufipogon Griff. using microsatellite and allozyme markers.

The genetic structure of five natural populations of common wild rice Oryza rufipogon Griff. from China, was investigated with 21 microsatellite loci and compared to estimates of genetic diversity and genetic differentiation detected by 22 allozyme loci. Microsatellite loci, as expected, have much higher levels of genetic diversity (mean values of A = 3.1, P = 73.3%, Ho = 0.358 and He = 0.345) than allozyme loci (mean values of A = 1.2, P = 12.7%, Ho = 0.020 and He = 0.030). Genetic differentiation detected by microsatellite loci ( FST = 0.468, mean I = 0.472) was higher than that for allozyme loci ( FST =0.388, mean I = 0.976). However, microsatellite markers showed less deviation from Hardy-Weinberg expectation (Wright's inbreeding coefficient FIS = -0.069) than do allozymes ( FIS = 0.337). These results suggest that microsatellite markers are powerful high-resolution tools for the accurate assessment of important parameters in population biology and conservation genetics of O. rufipogon, and offer advantages over allozyme markers.

Edible Grain↗

PubMed1993

Molecular characterization of flavanone 3 beta-hydroxylases. Consensus sequence, comparison with related enzymes and the role of conserved histidine residues.

A heterologous cDNA probe from Petunia hybrida was used to isolate flavanone-3 beta-hydroxylase-encoding cDNA clones from carnation (Dianthus caryophyllus), china aster (Callistephus chinensis) and stock (Matthiola incana). The deduced protein sequences together with the known sequences of the enzyme from P. hybrida, barley (Hordeum vulgare) and snapdragon (Antirrhinum majus) enabled the determination of a consensus sequence which revealed an overall 84% similarity (53% identity) of flavanone 3 beta-hydroxylases from the different sources. Alignment with the sequences of other known enzymes of the same class and to related non-heme iron-(II) enzymes demonstrated the strict genetic conservation of 14 amino acids, in particular, of three histidines and an aspartic acid. The conservation of the histidine motifs provides strong support for the possible conservation of structurally similar iron-binding sites in these enzymes. The putative role of histidines as chelators of ferrous ions in the active site of flavanone 3 beta-hydroxylases was corroborated by diethyl-pyrocarbonate modification of the partially purified recombinant Petunia enzyme.

Amino Acid Sequence↗

PubMedDate not supplied

[Genetic control of development of the Malpighian vessels in Drosophila melanogaster].

Malpighian tubules of insects are a functional analog of mammalian kidneys and serve as a classical model for studying the structure and functions of transport epithelium. The review contains the data on structural organization, functioning, and formation of the Malpighian tubules during embryogenesis in Drosophila melanogaster. Various systems of genes are described that control the program of development of the renal (Malpighian) tubules in D. melanogaster. A special attention is paid to the ways of signal transduction and factors involved in cell differentiation, proliferation, and morphological transformation during development of the Malpighian tubules. Evolutionarily conservative genetic systems are considered that are involved in the control of development of both the renal epithelium of Drosophila and mammalian kidneys. A relationship was noted between the disturbed balance of genetic material and congenital defects of the human excretory system.

Animals↗

PubMed1992

Potential contribution of cryopreserved germ plasm to the preservation of genetic diversity and conservation of endangered species in captivity.

Demographic and genetic objectives of captive propagation programs for endangered species focus on establishing demographically secure populations that maintain adequate levels of genetic diversity. Long-term storage and utilization of cryopreserved germ plasm could extend the population's generation length and allow higher levels of genetic variation to be maintained in smaller populations. Since fewer breeding animals would be needed, more species would be "rescued" from extinction using the cage facilities currently available at existing institutions. Doubling generation lengths for callitrichid primates through use of cryopreservation could almost triple the number of species that could be rescued in world zoos. Additionally, long-term cryopreservation would allow for a third population, that of the frozen zoo. Three-way exchange of germ from germ plasm banks to captive and wild populations would increase genetic diversity at reduced risk and expense. Advances in reproductive technology and better understanding of the reproductive physiology of these animal populations are necessary to permit routine application of artificial insemination and embryo transfer using frozen-stored germ plasm.

Animals↗

PubMed1994

DNA sequences encoding enolase are remarkably conserved from yeast to mammals.

Enolase (2-phospho-D-glycerate hydrolase, EC 4.2.1.11), particularly isoform neuron-specific enolase (NSE), is primarily localized in neurons and neuroendocrine cells and is a cancer diagnostic marker for brain tumors. Homology of enolase-coding DNA sequences from human, dog, cow, rat, mouse, rabbit, chicken, and yeast cells was investigated using hybridization techniques, percent sequence divergence, and amino acid analysis. Because enolase is a significant enzyme of the glycolytic pathway, enolase-coding DNA sequences have been found in all organisms tested so far. The human enzyme was found to be more like those of monkey and dog in structure than to those of chicken and yeast. The implications of the existence of the genetic conservation of enolase-coding DNA sequences in understanding concerted evolution as well as post-transcriptional regulation during differentiation are discussed. This is the first report is which sequence divergence in the coding region for enolase has been determined in a variety of organisms.

Amino Acid Sequence↗

PubMed2004

[Analysis of microsatellite loci of the chloroplast genome in the genus Capsicum (Pepper)].

Six plastome microsatellites were examined in 43 accessions of the genus Capsicum. In total, 33 allelic variants were detected. A specific haplotype of chloroplast DNA was identified for each Capsicum species. Species-specific allelic variants were found for most wild Capsicum species. The highest intraspecific variation was observed for the C. baccatum plastome. Low cpDNA polymorphism was characteristic of C. annuum: the cpSSRs were either monomorphic or dimorphic. The vast majority of C. annuum accessions each had alleles of one type. Another allele type was rare and occurred only in wild accessions. The results testified again to genetic conservation of C. annuum and especially its cultivated forms. The phylogenetic relationships established for the Capsicum species on the basis of plastome analysis were similar to those inferred from the morphological traits, isozyme patterns, and molecular analysis of the nuclear genome.

Base Sequence↗

PubMed2003

Mpi recombinase globally modulates the surface architecture of a human commensal bacterium.

The mammalian gut represents a complex and diverse ecosystem, consisting of unique interactions between the host and microbial residents. Bacterial surfaces serve as an interface that promotes and responds to this dynamic exchange, a process essential to the biology of both symbionts. The human intestinal microorganism, Bacteroides fragilis, is able to extensively modulate its surface. Analysis of the B. fragilis genomic sequence, together with genetic conservation analyses, cross-species cloning experiments, and mutational studies, revealed that this organism utilizes an endogenous DNA inversion factor to globally modulate the expression of its surface structures. This DNA invertase is necessary for the inversion of at least 13 regions located throughout the genome, including the promoter regions for seven of the capsular polysaccharide biosynthesis loci, an accessory polysaccharide biosynthesis locus, and five other regions containing consensus promoter sequences. Bacterial DNA invertases of the serine site-specific recombinase family are typically encoded by imported elements such as phage and plasmids, and act locally on a single region of the imported element. In contrast, the conservation and unique global regulatory nature of the process in B. fragilis suggest an evolutionarily ancient mechanism for surface adaptation to the changing intestinal milieu during commensalism.

Bacterial Capsules↗

PubMed1978

RNA tumor virus genes and the transforming genes: genetic transmission, infectious spread, and modes of expression.

The genetic conservation and evolution of virogenes in mammalian species are described in relation to the horizontal, vertical, and congenital transmission of type C RNA oncogenic viruses within members of a given species, or among members of near and/or distantly related species. Examples of oncogenic virus infection between ancestors of the mouse, cat, pig, and primates as well as the integration of the virus into the host's genome are documented. The possible normal functions of the virogenes as a part of the cellular genome of many species are explored. Recent evidence of genetic recombination (genetic mixing) among distinct type C viruses is also reviewed, thus completing an overview of the evolutionary past, present, and complex future relationships of oncogenic RNA viruses and mammalian species.

Animals↗

PubMed2004

Highly polymorphic DNA markers to specify strains of the ectomycorrhizal basidiomycete Tricholoma matsutake based on sigmamarY1, the long terminal repeat of gypsy-type retroelement marY1.

The ectomycorrhizal basidiomycete Tricholoma matsutake produces commercially valuable fruit bodies--matsutake--in Pinus sp. forest. Here we report that PCR with outward facing primers designed based on sequences comprising sigma(marY1), the long terminal repeat of the gypsy-type retroelement marY1, specifies strains of T. matsutake. PCR with a primer based on the 22-bp sequence conserved at the 5'-end of sigma(marY1) conferred 73 reliable bands overall whose profiles depend upon strains of T. matsutake and T. magnivelare, the latter known as 'American matsutake'. This PCR system gave no detectable band in any other species of Tricholoma tested, including T. bakamatsutake and T. fulvocastaneum, symbionts closely related to T. matsutake, as well as a host plant, Pinus densiflora. Similarly, PCR with a set of primers based on 26-bp and 28-bp sequences at bp 48-73 and bp 281-308 of sigma(marY1), internal regions that are mutated in a variant of marY1, conferred 90 reliable bands only in strains of T. matsutake. Theoretically, PCR with the 22-bp primer would allow generation of 2(73), or 9.4x10(21), types of polymorphism, and PCR with a combination of 26- and 28-bp primers, 2(90), or 1.2x10(27) types. The probability of falsely specifying two different isolates as the same strain is <1/10(21). While polymorphisms conferred by the primer based on the 5' end of sigma(marY1) rather exhibit genetic conservation of a group of T. matsutake, those resulting from primers based on the internal sequences more clearly demonstrate intra-specific diversification. Both systems revealed that T. matsutake is divergent within the species. Ectomycorrhizas formed between P. densiflora and T. matsutake were identified by the PCR systems developed in the present study. This method, using sigma(marY1) as a genetic marker, is useful in analyzing the diversity of T. matsutake, monitoring the behavior of individual mycorrhizas, and specifying the ecological background of fruit bodies traded in markets.

Agaricales↗

PubMed1993

Antigenic and genetic analysis of a recently isolated H1N1 swine influenza virus.

Hemagglutinins (HA) of H1N1 swine influenza viruses isolated in the United States have remained antigenically and genetically conserved for many years. In contrast to such conservation, the HA of A/Swine/Nebraska/1/92 (Sw/Neb) could readily be distinguished from those of contemporary porcine viruses. Twenty-eight amino acid mutations differentiated the HA of Sw/Neb and A/Swine/Indiana/1726/88, the most recent H1N1 swine influenza virus for which HA sequence data were available. Among these differences were mutations at potential asparagine-linked glycosylation sites and charge changes at many residues. The Sw/Neb virus also could be differentiated from other swine influenza viruses in hemagglutination-inhibition assays with monoclonal antibodies to recent H1 swine HA. Nonetheless, overall sequence analysis of the HA and the nucleoprotein genes of Sw/Neb indicated that this virus was more closely related genetically to classic H1N1 swine influenza viruses than to H1N1 avian or human viruses. Infection of swine with Sw/Neb under experimental conditions induced clinical signs and lesions typical of swine influenza. However, affected swine in the field had high, persistent fevers, but relatively mild signs of respiratory tract disease. This study indicated that an antigenically and genetically novel variant of swine influenza virus was detected in the United States.

Amino Acid Sequence↗