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Genetic Methods (genetic + methods)
Kinds of Genetic Methods Selected AbstractsLinkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolutionEVOLUTIONARY APPLICATIONS (ELECTRONIC), Issue 3 2010Robin S. Waples Abstract Genetic methods are routinely used to estimate contemporary effective population size (Ne) in natural populations, but the vast majority of applications have used only the temporal (two-sample) method. We use simulated data to evaluate how highly polymorphic molecular markers affect precision and bias in the single-sample method based on linkage disequilibrium (LD). Results of this study are as follows: (1) Low-frequency alleles upwardly bias , but a simple rule can reduce bias to Genetics of anxiety disorders: the complex road from DSM to DNA,DEPRESSION AND ANXIETY, Issue 11 2009Jordan W. Smoller M.D. Sc.D. Abstract Anxiety disorders are among the most common psychiatric disorders, affecting one in four individuals over a lifetime. Although our understanding of the etiology of these disorders is incomplete, familial and genetic factors are established risk factors. However, identifying the specific casual genes has been difficult. Within the past several years, advances in molecular and statistical genetic methods have made the genetic dissection of complex disorders a feasible project. Here we provide an overview of these developments, with a focus on their implications for genetic studies of anxiety disorders. Although the genetic and phenotypic complexity of the anxiety disorders present formidable challenges, advances in neuroimaging and experimental animal models of anxiety and fear offer important opportunities for discovery. Real progress in identifying the genetic basis of anxiety disorders will require integrative approaches that make use of these biologic tools as well as larger-scale genomic studies. If successful, such efforts may yield novel and more effective approaches for the prevention and treatment of these common and costly disorders. Depression and Anxiety, 2009. © 2009 Wiley-Liss, Inc. [source] BIODIVERSITY RESEARCH: Genetic diversity in two introduced biofouling amphipods (Ampithoe valida & Jassa marmorata) along the Pacific North American coast: investigation into molecular identification and cryptic diversityDIVERSITY AND DISTRIBUTIONS, Issue 5 2010Erik M. Pilgrim Abstract Aim, We investigated patterns of genetic diversity among invasive populations of Ampithoe valida and Jassa marmorata from the Pacific North American coast to assess the accuracy of morphological identification and determine whether or not cryptic diversity and multiple introductions contribute to the contemporary distribution of these species in the region. Location, Native range: Atlantic North American coast; Invaded range: Pacific North American coast. Methods, We assessed indices of genetic diversity based on DNA sequence data from the mitochondrial cytochrome c oxidase subunit I (COI) gene, determined the distribution of COI haplotypes among populations in both the invasive and putative native ranges of A. valida and J. marmorata and reconstructed phylogenetic relationships among COI haplotypes using both maximum parsimony and Bayesian approaches. Results, Phylogenetic inference indicates that inaccurate species-level identifications by morphological criteria are common among Jassa specimens. In addition, our data reveal the presence of three well supported but previously unrecognized clades of A. valida among specimens in the north-eastern Pacific. Different species of Jassa and different genetic lineages of Ampithoe exhibit striking disparity in geographic distribution across the region as well as substantial differences in genetic diversity indices. Main conclusions, Molecular genetic methods greatly improve the accuracy and resolution of identifications for invasive benthic marine amphipods at the species level and below. Our data suggest that multiple cryptic introductions of Ampithoe have occurred in the north-eastern Pacific and highlight uncertainty regarding the origin and invasion histories of both Jassa and Ampithoe species. Additional morphological and genetic analyses are necessary to clarify the taxonomy and native biogeography of both amphipod genera. [source] Pigments and proteins in green bacterial chlorosomes studied by matrix-assisted laser desorption ionization mass spectrometryFEBS JOURNAL, Issue 2 2000Søren Persson We have used matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for mass determination of pigments and proteins in chlorosomes, the light-harvesting organelles from the photosynthetic green sulfur bacterium Chlorobium tepidum. By applying a small volume (1 µL) of a concentrated suspension of isolated chlorosomes directly to the target of the mass spectrometer we have been able to detect bacteriochlorophyll a and all the major homologs of bacteriochlorophyll c. The peak heights of the different bacteriochlorophyll c homologs in the MALDI spectra were proportional to peak areas obtained from HPLC analysis of the same sample. The same result was also obtained when whole cells of Chl. tepidum were applied to the target, indicating that MALDI-MS can provide a rapid method for obtaining a semiquantitative determination or finger-print of the bacteriochlorophyll homologs in a small amount of green bacterial cells. In addition to information on pigments, the MALDI spectra also contained peaks from chlorosome proteins. Thus we have been able with high precision to confirm the molecular masses of the chlorosome proteins CsmA and CsmE which have been previously determined by conventional biochemical and genetic methods, and demonstrate the presence of truncated versions of CsmA and CsmB. [source] Heritability, correlations and in silico mapping of locomotor behavior and neurochemistry in inbred strains of miceGENES, BRAIN AND BEHAVIOR, Issue 4 2005T. R. Mhyre The midbrain dopamine system mediates normal and pathologic behaviors related to motor activity, attention, motivation/reward and cognition. These are complex, quantitative traits whose variation among individuals is modulated by genetic, epigenetic and environmental factors. Conventional genetic methods have identified several genes important to this system, but the majority of factors contributing to the variation remain unknown. To understand these genetic and environmental factors, we initiated a study measuring 21 behavioral and neurochemical traits in 15 common inbred mouse strains. We report trait data, heritabilities and genetic and non-genetic correlations between pheno-types. In general, the behavioral traits were more heritable than neurochemical traits, and both genetic and non-genetic correlations within these trait sets were high. Surprisingly, there were few significant correlations between the behavioral and the individual neurochemical traits. However, striatal serotonin and one measure of dopamine turnover (DOPAC/DA) were highly correlated with most behavioral measures. The variable accounting for the most variation in behavior was mouse strain and not a specific neurochemical measure, suggesting that additional genetic factors remain to be determined to account for these behavioral differences. We also report the prospective use of the in silico method of quantitative trait loci (QTL) analysis and demonstrate difficulties in the use of this method, which failed to detect significant QTLs for the majority of these traits. These data serve as a framework for further studies of correlations between different midbrain dopamine traits and as a guide for experimental cross designs to identify QTLs and genes that contribute to these traits. [source] Using linked markers to infer the age of a mutationHUMAN MUTATION, Issue 2 2001Bruce Rannala Abstract Advances in sequencing and genotyping technologies over the last decade have enabled geneticists to easily characterize genetic variation at the nucleotide level. Hundreds of genes harboring mutations associated with genetic disease have now been identified by positional cloning. Using variation at closely linked genetic markers, it is possible to predict the times in the past at which particular mutations arose. Such studies suggest that many of the rare mutations underlying human genetic disorders are relatively young. Studies of variation at genetic markers linked to particular mutations can provide insights into human geographic history, and historical patterns of natural selection and disease, that are not available from other sources. We review two approaches for estimating allele age using variation at linked genetic markers. A phylogenetic approach aims to reconstruct the gene tree underlying a sample of chromosomes carrying a particular mutation, obtaining a "direct" estimate of allele age from the age of the root of this tree. A population genetic approach relies on models of demography, mutation, and/or recombination to estimate allele age without explicitly reconstructing the gene tree. Phylogenetic methods are best suited for studies of ancient mutations, while population genetic methods are better suited for studies of recent mutations. Methods that rely on recombination to infer the ages of alleles can be fine-tuned by choosing linked markers at optimal map distances to maximize the information available about allele age. A limitation of methods that rely on recombination is the frequent lack of a fine-scale linkage map. Maximum likelihood and Bayesian methods for estimating allele age that rely on intensive numerical computation are described, as well as "composite" likelihood and moment-based methods that lead to simple estimators. The former provide more accurate estimates (particularly for large samples of chromosomes) and should be employed if computationally practical. Hum Mutat 18:87,100, 2001. © 2001 Wiley-Liss, Inc. [source] Heritability of human cranial dimensions: comparing the evolvability of different cranial regionsJOURNAL OF ANATOMY, Issue 1 2009Neus Martínez-Abadías Abstract Quantitative craniometrical traits have been successfully incorporated into population genetic methods to provide insight into human population structure. However, little is known about the degree of genetic and non-genetic influences on the phenotypic expression of functionally based traits. Many studies have assessed the heritability of craniofacial traits, but complex patterns of correlation among traits have been disregarded. This is a pitfall as the human skull is strongly integrated. Here we reconsider the evolutionary potential of craniometric traits by assessing their heritability values as well as their patterns of genetic and phenotypic correlation using a large pedigree-structured skull series from Hallstatt (Austria). The sample includes 355 complete adult skulls that have been analysed using 3D geometric morphometric techniques. Heritability estimates for 58 cranial linear distances were computed using maximum likelihood methods. These distances were assigned to the main functional and developmental regions of the skull. Results showed that the human skull has substantial amounts of genetic variation, and a t -test showed that there are no statistically significant differences among the heritabilities of facial, neurocranial and basal dimensions. However, skull evolvability is limited by complex patterns of genetic correlation. Phenotypic and genetic patterns of correlation are consistent but do not support traditional hypotheses of integration of the human shape, showing that the classification between brachy- and dolicephalic skulls is not grounded on the genetic level. Here we support previous findings in the mouse cranium and provide empirical evidence that covariation between the maximum widths of the main developmental regions of the skull is the dominant factor of integration in the human skull. [source] Population genetics suggests effectiveness of habitat connectivity measures for the European tree frog in SwitzerlandJOURNAL OF APPLIED ECOLOGY, Issue 4 2009Sonia Angelone Summary 1.,Governmental authorities in many countries financially support the implementation of habitat connectivity measures to enhance the exchange of individuals among fragmented populations. The evaluation of the effectiveness of such measures is crucial for future management directions and can be accomplished by using genetic methods. 2.,We retraced the population history of the European tree frog in two Swiss river valleys (Reuss and Thur), performed comprehensive population sampling to infer the genetic structure at 11 microsatellite markers, and used first-generation migrant assignment tests to evaluate the contemporary exchange of individuals. 3.,Compared with the Thur valley, the Reuss valley has lost almost double the number of breeding sites and exhibited a more pronounced genetic grouping. However, similar numbers of contemporary migrants were detected in both valleys. In the Reuss valley, 81% of the migration events occurred within the identified genetic groups, whereas in the Thur valley migration patterns were diffuse. 4.,Our results show that the connectivity measures implemented in the Reuss valley facilitated effective tree frog migration among breeding sites within distances up to 4 km. Nevertheless, the Reuss valley exhibited high genetic differentiation, which reflected the impact of barriers to tree frog movement such as the River Reuss. By contrast in the Thur valley, a larger number of breeding sites have been preserved and high admixture indicated exchange of individuals at distances up to 16 km. 5.,Synthesis and applications. We show that genetic methods can substantiate the effectiveness of connectivity measures taken in conservation management at the landscape scale. We urge responsible authorities from both river valleys to continue implementing connectivity measures and to create a dense network of breeding sites, as spatial gaps of 8 km are rarely traversed by tree frogs. [source] Multiple molecular approaches yield no evidence for sex-determining genes in lake sturgeon (Acipenser fulvescens)JOURNAL OF APPLIED ICHTHYOLOGY, Issue 6 2008C. R. McCormick Summary Common DNA-based sexing assays have been widely used for the conservation and management of mammals and birds. However, many fishes do not have genetic sex determination and in those that do, the plasticity of the genes involved means that species-specific assays are normally required. Such DNA-sexing markers would be especially valuable in lake sturgeon (Acipenser fulvescens) because of their sexual monomorphism, delayed sexual maturity, and conservation status. We tried to identify genetic differences between male and female lake sturgeon using several different molecular genetic methods, including randomly amplified polymorphic DNA, representational difference analyses, subtractive hybridization, and a candidate gene approach. Ultimately, a number of genes were identified but none was sex-specific. Although the ultimate mechanism of sex determination is yet unknown, it is possible that sex determination is environmental in lake sturgeon, especially since recent studies have also failed to identify sex determination genes in other sturgeon species. [source] Long-standing environmental conditions, geographic isolation and host,symbiont specificity influence the relative ecological dominance and genetic diversification of coral endosymbionts in the genus SymbiodiniumJOURNAL OF BIOGEOGRAPHY, Issue 5 2010Todd C. LaJeunesse Abstract Aim, This study examines the importance of geographic proximity, host life history and regional and local differences in environment (temperature and water clarity) in driving the ecological and evolutionary processes underpinning the global patterns of diversity and distribution of symbiotic dinoflagellates. By comparing and contrasting coral,algal symbioses from isolated regions with differing environmental conditions, we may assess the potential of coral communities to respond to significant changes in climate. Location, Indian Ocean. Methods, Community assemblages of obligate symbiotic invertebrates were sampled at numerous sites from two regions, the north-eastern Indian Ocean (Andaman Sea, western Thailand) and the western Indian Ocean (Zanzibar, Tanzania). Molecular genetic methods, including denaturing gradient gel electrophoresis analysis of the ribosomal internal transcribed spacers, DNA sequencing and microsatellite genotyping, were used to characterize the ,species' diversity and evolutionary relationships of symbiotic dinoflagellates (genus Symbiodinium). Host,symbiont specificity, geographic isolation and local and regional environmental factors were evaluated in terms of their importance in governing the distribution and prevalence of certain symbiont taxa. Results, Host-generalist symbionts (C3u and D1-4, formerly D1a now designated Symbiodinium trenchi) frequently occurred alone and sometimes together in hosts with horizontal modes of symbiont acquisition. However, the majority of Symbiodinium diversity consisted of apparently host-specific ,species'. Clade C Symbiodinium were diverse and dominated host assemblages from sites sampled in the western Indian Ocean, a pattern analogous to symbiont communities on the Great Barrier Reef with similar environmental conditions. Clade D Symbiodinium were diverse and occurred frequently in hosts from the north-eastern Indian Ocean, especially at inshore locations, where temperatures are warmer, water turbidity is high and large tidal exchanges commonly expose coral populations to aerial desiccation. Main conclusions, Regional and local differences in cnidarian,algal combinations indicate that these symbioses are ecologically and evolutionarily responsive and can thrive under various environmental conditions. The high temperatures and turbid conditions of the north-eastern Indian Ocean partly explain the ecological success of Clade D Symbiodinium relative to Clade C. Phylogenetic, ecological and population genetic data further indicate that Clade D has undergone an adaptive radiation, especially in regions around Southeast Asia, during the Pleistocene. [source] Distribution of genetic variation in farmed and natural stocks of european eelJOURNAL OF FISH BIOLOGY, Issue 2004J. M. Pujolar European eel (Anguilla anguilla; Teleostei) is a valuable commercial species. However, over the past 25 years, the population of European eel has been declining to such a degree that major concerns have been raised for its long-term conservation. Since little information is available on the life-cycle and genetic structure of European eel, it has been difficult to evaluate the existence of any population substructuring. Molecular genetic methods contribute to a better knowledge of the demography and population structure in marine fish. In addition, management strategies and conservation goals must consider information on genetic substructuring as well as on life history patterns. The aim of the study is to provide more detailed knowledge on the genetic variability, demography and population substructuring of European eel by analysing and comparing natural and farmed individuals. Natural eel samples have been obtained in two geographical sites (Netherlands, France) including temporal samples in a short-scale (within years) and a long-scale (between years). Simultaneously, farmed glass eels have been grown in two separate batches during one year. Batches have been monitored and genetic samples have been obtained during the year. A combination of selection-sensitive (allozymes) and selection-neutral markers (microsatellites) has been used in the study since selection seems to play an important role in the determination of the quality of future eel spawners. Results suggest a positive correlation between growth and genetic variability since individuals attaining a large length and mass present significant higher heterozygosities. [source] Functional Brain Mapping of Extraversion and Neuroticism: Learning From Individual Differences in Emotion ProcessingJOURNAL OF PERSONALITY, Issue 6 2004Turhan Canli Studies using functional magnetic resonance imaging have shown that individual differences in participants' E and N scores are correlated with individual differences in brain activation in specific brain regions that are engaged during cognitive-affective tasks. Imaging studies using genotyped participants have begun to address the molecular mechanisms that may underlie these individual differences. The multidisciplinary integration of brain imaging and molecular genetic methods offers an exciting and novel approach for investigators who seek to uncover the biological mechanisms by which personality and health are interrelated. [source] Bridging the Gap Between Genomics and EducationMIND, BRAIN, AND EDUCATION, Issue 4 2007Stephen A. Petrill ABSTRACT, Despite several decades of research suggesting the importance of both genetic and environmental factors, these findings are not well integrated into the larger educational literature. Following a discussion of quantitative and molecular genetic methods, this article reviews behavioral genetic findings related to cognitive and academic skills. This literature suggests that (a) the relative importance of genes and environments varies developmentally; (b) genetics, and to a lesser extend the environment, account for a substantial portion of the covariance within and across academic domains; and (c) some forms of disability are qualitatively different from the population, whereas others constitute the lower end of a continuum of ability. Following a discussion of the strengths and limitations of current behavioral genetic research and intervention research, we then discuss the ways in which understanding gene,environment interplay can be used to develop better definitions of learning impairment and better explain the substantial variability in response to intervention. [source] Phylogeography of Douglas-fir based on mitochondrial and chloroplast DNA sequences: testing hypotheses from the fossil recordMOLECULAR ECOLOGY, Issue 9 2010PAUL F. GUGGER Abstract The integration of fossil and molecular data can provide a synthetic understanding of the ecological and evolutionary history of an organism. We analysed range-wide maternally inherited mitochondrial DNA and paternally inherited chloroplast DNA sequence data with coalescent simulations and traditional population genetic methods to test hypotheses of population divergence generated from the fossil record of Douglas-fir (Pseudotsuga menziesii), an ecologically and economically important western North American conifer. Specifically, we tested (i) the hypothesis that the Pliocene orogeny of the Cascades and Sierra Nevada caused the divergence of coastal and Rocky Mountain Douglas-fir varieties; and (ii) the hypothesis that multiple glacial refugia existed on the coast and in the Rocky Mountains. We found that Douglas-fir varieties diverged about 2.11 Ma (4.37 Ma,755 ka), which could be consistent with a Pliocene divergence. Rocky Mountain Douglas-fir probably resided in three or more glacial refugia. More variable molecular markers would be required to detect the two coastal refugia suggested in the fossil record. Comparison of mitochondrial DNA and chloroplast DNA variation revealed that gene flow via pollen linked populations isolated from seed exchange. Postglacial colonization of Canada from coastal and Rocky Mountain refugia near the ice margin at the Last Glacial Maximum produced a wide hybrid zone among varieties that formed almost exclusively by pollen exchange and chloroplast DNA introgression, not seed exchange. Postglacial migration rates were 50,165 m/year, insufficient to track projected 21st century warming in some regions. Although fossil and genetic data largely agree, each provides unique insights. [source] Comparison of quantitative and molecular genetic variation of native vs. invasive populations of purple loosestrife (Lythrum salicaria L., Lythraceae)MOLECULAR ECOLOGY, Issue 14 2009YOUNG JIN CHUN Abstract Study of adaptive evolutionary changes in populations of invasive species can be advanced through the joint application of quantitative and population genetic methods. Using purple loosestrife as a model system, we investigated the relative roles of natural selection, genetic drift and gene flow in the invasive process by contrasting phenotypical and neutral genetic differentiation among native European and invasive North American populations (QST , FST analysis). Our results indicate that invasive and native populations harbour comparable levels of amplified fragment length polymorphism variation, a pattern consistent with multiple independent introductions from a diverse European gene pool. However, it was observed that the genetic variation reduced during subsequent invasion, perhaps by founder effects and genetic drift. Comparison of genetically based quantitative trait differentiation (QST) with its expectation under neutrality (FST) revealed no evidence of disruptive selection (QST > FST) or stabilizing selection (QST < FST). One exception was found for only one trait (the number of stems) showing significant sign of stabilizing selection across all populations. This suggests that there are difficulties in distinguishing the effects of nonadaptive population processes and natural selection. Multiple introductions of purple loosestrife may have created a genetic mixture from diverse source populations and increased population genetic diversity, but its link to the adaptive differentiation of invasive North American populations needs further research. [source] Detecting hybridization between wild species and their domesticated relativesMOLECULAR ECOLOGY, Issue 1 2008ETTORE RANDI Abstract The widespread occurrence of free-ranging domestic or feral carnivores (dogs, cats) or ungulates (pigs, goats), and massive releases of captive-reproduced game stocks (galliforms, waterfowl) is raising fear that introgressive hybridization with wild populations might disrupt local adaptations, leading to population decline and loss of biodiversity. Detecting introgression through hybridization is problematic if the parental populations cannot be sampled (unlike in classical stable hybrid zones), or if hybridization is sporadic. However, the use of hypervariable DNA markers (microsatellites) and new statistical methods (Bayesian models), have dramatically improved the assessment of cryptic population structure, admixture analyses and individual assignment testing. In this paper, I summarize results of projects aimed to identify occurrence and extent of introgressive hybridization in European populations of wolves (Canis lupus), wildcats (Felis silvestris), rock partridges and red-legged partridges (Alectoris graeca and Alectoris rufa), using genetic methods. Results indicate that introgressive hybridization can be locally pervasive, and that conservation plans should be implemented to preserve the integrity of the gene pools of wild populations. Population genetic methods can be fruitfully used to identify introgressed individuals and hybridizing populations, providing data which allow evaluating risks of outbreeding depression. The diffusion in the wild of invasive feral animals, and massive restocking with captive-reproduced game species, should be carefully controlled to avoid loss of genetic diversity and disruption of local adaptations. [source] Working at the interface of phylogenetics and population genetics: a biogeographical analysis of Triaenops spp. (Chiroptera: Hipposideridae)MOLECULAR ECOLOGY, Issue 4 2007A. L. RUSSELL Abstract New applications of genetic data to questions of historical biogeography have revolutionized our understanding of how organisms have come to occupy their present distributions. Phylogenetic methods in combination with divergence time estimation can reveal biogeographical centres of origin, differentiate between hypotheses of vicariance and dispersal, and reveal the directionality of dispersal events. Despite their power, however, phylogenetic methods can sometimes yield patterns that are compatible with multiple, equally well-supported biogeographical hypotheses. In such cases, additional approaches must be integrated to differentiate among conflicting dispersal hypotheses. Here, we use a synthetic approach that draws upon the analytical strengths of coalescent and population genetic methods to augment phylogenetic analyses in order to assess the biogeographical history of Madagascar's Triaenops bats (Chiroptera: Hipposideridae). Phylogenetic analyses of mitochondrial DNA sequence data for Malagasy and east African Triaenops reveal a pattern that equally supports two competing hypotheses. While the phylogeny cannot determine whether Africa or Madagascar was the centre of origin for the species investigated, it serves as the essential backbone for the application of coalescent and population genetic methods. From the application of these methods, we conclude that a hypothesis of two independent but unidirectional dispersal events from Africa to Madagascar is best supported by the data. [source] Evolution on oceanic islands: molecular phylogenetic approaches to understanding pattern and processMOLECULAR ECOLOGY, Issue 6 2002B. C. Emerson Abstract By their very nature oceanic island ecosystems offer great opportunities for the study of evolution and have for a long time been recognized as natural laboratories for studying evolution owing to their discrete geographical nature and diversity of species and habitats. The development of molecular genetic methods for phylogenetic reconstruction has been a significant advance for evolutionary biologists, providing a tool for answering questions about the diversity among the flora and fauna on such islands. These questions relate to both the origin and causes of species diversity both within an archipelago and on individual islands. Within a phylogenetic framework one can answer fundamental questions such as whether ecologically and/or morphologically similar species on different islands are the result of island colonization or convergent evolution. Testing hypotheses about ages of the individual species groups or entire community assemblages is also possible within a phylogenetic framework. Evolutionary biologists and ecologists are increasingly turning to molecular phylogenetics for studying oceanic island plant and animal communities and it is important to review what has been attempted and achieved so far, with some cautionary notes about interpreting phylogeographical pattern on oceanic islands. [source] Dissecting the essentiality of the bifunctional trypanothione synthetase-amidase in Trypanosoma brucei using chemical and genetic methodsMOLECULAR MICROBIOLOGY, Issue 3 2009Susan Wyllie Summary The bifunctional trypanothione synthetase-amidase (TRYS) comprises two structurally distinct catalytic domains for synthesis and hydrolysis of trypanothione (N1,N8 - bis(glutathionyl)spermidine). This unique dithiol plays a pivotal role in thiol-redox homeostasis and in defence against chemical and oxidative stress in trypanosomatids. A tetracycline-dependent conditional double knockout of TRYS (cDKO) was generated in bloodstream Trypanosoma brucei. Culture of cDKO parasites without tetracycline induction resulted in loss of trypanothione and accumulation of glutathione, followed by growth inhibition and cell lysis after 6 days. In the absence of inducer, cDKO cells were unable to infect mice, confirming that this enzyme is essential for virulence in vivo as well as in vitro. To establish whether both enzymatic functions were essential, an amidase-dead mutant cDKO line was generated. In the presence of inducer, this line showed decreased growth in vitro and decreased virulence in vivo, indicating that the amidase function is not absolutely required for viability. The druggability of TRYS was assessed using a potent small molecule inhibitor developed in our laboratory. Growth inhibition correlated in rank order cDKO, single KO, wild-type and overexpressing lines and produced the predicted biochemical phenotype. The synthetase function of TRYS is thus unequivocally validated as a drug target by both chemical and genetic methods. [source] Inversion of the Williams syndrome region is a common polymorphism found more frequently in parents of children with Williams syndrome,AMERICAN JOURNAL OF MEDICAL GENETICS, Issue 2 2010Holly H. Hobart Abstract Williams syndrome (WS) is a multisystem disorder caused by deletion of about 1.55,Mb of DNA (including 26 genes) on chromosome 7q11.23, a region predisposed to recombination due to its genomic structure. Deletion of the Williams syndrome chromosome region (WSCR) occurs sporadically. To better define chance for familial recurrence and to investigate the prevalence of genomic rearrangements of the region, 257 children with WS and their parents were studied. We determined deletion size in probands by metaphase FISH, parent-of-origin of the deleted chromosome by molecular genetic methods, and inversion status of the WSCR in both parents by interphase FISH. The frequency of WSCR inversion in the transmitting parent group was 24.9%. In contrast, the rate of inversion in the non-transmitting parent group (a reasonable estimate of the rate in the general population) was 5.8%. There were no significant gender differences with respect to parent-of-origin for the deleted chromosome or the incidence of the inversion polymorphism. There was no difference in the rate of spontaneous abortion for mothers heterozygous for the WSCR inversion relative to mothers without the inversion. We calculate that for a parent heterozygous for a WSCR inversion, the chance to have a child with WS is about 1 in 1,750, in contrast to the 1 in 9,500 chance for a parent without an inversion. © 2010 Wiley-Liss, Inc. [source] Diversity of Veillonella spp. from subgingival plaque by polyphasic approachAPMIS, Issue 3 2010INGA LEUCKFELD Leuckfeld I, Paster BJ, Kristoffersen AK, Olsen I. Diversity of Veillonella spp. from subgingival plaque by polyphasic approach. APMIS 2010; 118: 230,42. In a biofilm such as the subgingival microflora, strain-specific properties or factors induced by the host may impart a survival advantage to some bacterial strains. Periodontal disease has been associated with chronic obstructive pulmonary disease (COPD) and we previously found high amounts of Veillonella in the subgingival microflora of COPD subjects. Differentiation of Veillonella is difficult. The aims of this study were to identify subgingival Veillonella isolates by phenotypic, genetic typing and molecular genetic methods, and further, to assess if Veillonella strain properties or identity correlated with periodontal disease or COPD. From 22 subjects, 26 subgingival Veillonella isolates and one pulmonary isolate were analysed. The majority of the subgingival Veillonella isolates were identified as Veillonella parvula. Genotyping showed heterogeneity within strains of the same species. A subgingival and pulmonary isolate in one COPD subject was found to be genetically identical strains of V. parvula. Scanning electron microscopy of the lung biopsy confirmed single small cocci adhering or coaggregating with larger cocci on the airway epithelium. Apart from a variation in cellular fatty acid composition of six subgingival isolates from periodontitis subjects, no correlation between the subgingival Veillonella strains or genotypes and the presence of either periodontitis or COPD was found. In conclusion, V. parvula was the predominant subgingival Veillonella species with high genetic variability within strains of the same species. Subgingival V. parvula can translocate to the lungs; however, Veillonella identity or genotype did not correlate with periodontal disease or COPD. [source] Application of molecular genetic methods in macrolide, lincosamide and streptogramin resistance diagnostics and in detection of drug-resistant Mycobacterium tuberculosis,APMIS, Issue 11-12 2004JARI JALAVA Antimicrobial susceptibility testing has traditionally been based on measurements of minimal inhibitory concentrations of antimicrobials. Molecular genetic studies on antimicrobial resistance have produced a great deal of genetic information which can be used for diagnosis of antimicrobial resistance determinants. Bacteria can acquire resistance to macrolides, lincosamides and streptogramin antibiotics by modification of the target site of the drugs, by active efflux of the drugs, and by inactivation of the drugs. The genetic backgrounds of these resistance mechanisms are well known and several molecular methods for detection of resistance determinants have been developed. Outbreaks of multidrug-resistant tuberculosis have focused international attention on the emergence of Mycobacterium tuberculosis strains that are resistant to antimycobacterial agents. Knowledge of the antimycobacterial resistance genetics and progress in molecular methods has made it possible to develop rapid molecular methods for susceptibility testing. This review presents the genetic background of drug resistance and introduces some methods for genotypic susceptibility testing. [source] The genetics of panic disorder: state of the artACTA NEUROPSYCHIATRICA, Issue 2 2004Dirk Van West Panic disorder (PD) is a highly prevalent, debilitating disorder. The heritability of the disease has been estimated by twin studies to be between 30 and 60%. The vulnerability for PD overlaps with an increased risk of bipolar disorder in some families. Classical genetic methods such as linkage analysis and association studies have not yet identified genetic risk factors beyond doubt. However, two independent studies confirm linkage of a specific syndrome characterized by PD, bladder problems, severe headaches, mitral valve prolapse and thyroid dysfunction to genetic markers on chromosome 13q. Association studies, although showing divergent results, give some support to a causative role for the genes encoding for monoamine oxidase A (MAO-A), cholecystokinin (CCK) and catechol-O-methyltransferase (COMT). Finally, a somatic duplication of a 19-Mb region on chromosome 15 has been associated with PD, but this intriguing finding awaits confirmation. [source]
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