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* Context.--Next-generation sequencing (NGS)-based assays are used for diagnosis of diverse inherited disorders. Limited data are available pertaining to interlaboratory analytical performance of these assays. Objective.--To report on the College of American Pathologists (CAP) NGS Germline Program, which is methods based, and explore the evolution in laboratory testing practices. Design.--Results from the NGS Germline Program from 2016-2020 were analyzed for interlaboratory analytical performance. Self-reported laboratory testing practices were also evaluated. Results.--From 2016-2020, a total of 297 laboratories participated in at least 1 program mailing. Of the 289 laboratories that provided information on tests offered, 138 (47.8%) offered only panel testing throughout their enrollment, while 35 (12.1%) offered panels and exome testing, 30 (10.4%) offered only exomes, 9 (3.1%) offered only genomes, and 15 (5.2%) offered panels, exomes, and genomes. The remainder (62 laboratories, 21.4%) changed their test offerings during the 2016-2020 timeframe. Considering each genomic position/interval, the median detection percentage at variant positions across the 2016-2020 mailings ranged from 94.3% to 100%, while at reference positions (no variant detected), the median correct response percentage was 100% across all mailings. When considering performance of individual laboratories, 89.5% (136 of 152) to 98.0% (149 of 152) of laboratories successfully met the detection threshold ([greater than or equal to] 90% of the variants present), while 94.6% (87 of 92) to 100% (163 of 163) of laboratories met the 95% specificity threshold across mailings. Conclusions.--Since the inception of this program, laboratories have consistently performed well. The median sensitivity and specificity of detection of sequence variants included in this program (eg, single nucleotide variants, insertions, and deletions) were 100.0%. doi: 10.5858/arpa.2023-0090-CP), Next-generation sequencing (NGS)-based tests are of higher complexity than most traditional molecular tests owing to the interrogation of many positions simultaneously, as well as requirements for extensive laboratory wet bench [...]

A major goal in human genetics is to use natural variation to understand the phenotypic consequences of altering each protein-coding gene in the genome. Here we used exome sequencing.sup.1 to explore protein-altering variants and their consequences in 454,787 participants in the UK Biobank study.sup.2. We identified 12 million coding variants, including around 1 million loss-of-function and around 1.8 million deleterious missense variants. When these were tested for association with 3,994 health-related traits, we found 564 genes with trait associations at P [less than or equal to] 2.18 × 10.sup.-11. Rare variant associations were enriched in loci from genome-wide association studies (GWAS), but most (91%) were independent of common variant signals. We discovered several risk-increasing associations with traits related to liver disease, eye disease and cancer, among others, as well as risk-lowering associations for hypertension (SLC9A3R2), diabetes (MAP3K15, FAM234A) and asthma (SLC27A3). Six genes were associated with brain imaging phenotypes, including two involved in neural development (GBE1, PLD1). Of the signals available and powered for replication in an independent cohort, 81% were confirmed; furthermore, association signals were generally consistent across individuals of European, Asian and African ancestry. We illustrate the ability of exome sequencing to identify gene-trait associations, elucidate gene function and pinpoint effector genes that underlie GWAS signals at scale. Whole-exome sequencing analysis of 454,787 individuals in the UK Biobank is used to examine the association of protein-coding variants with nearly 4,000 health-related traits, identifying 564 distinct genes with significant trait associations., Author(s): Joshua D. Backman [sup.1] , Alexander H. Li [sup.1] , Anthony Marcketta [sup.1] , Dylan Sun [sup.1] , Joelle Mbatchou [sup.1] , Michael D. Kessler [sup.1] , Christian Benner [...]

Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global concern and affects all classes of antimicrobial drugs used for treatment. Penicillin, ciprofloxacin, and cefixime were the recommended first-line antimicrobial drug [...]

The underrepresentation of non-Europeans in human genetic studies so far has limited the diversity of individuals in genomic datasets and led to reduced medical relevance for a large proportion of the world's population. Population-specific reference genome datasets as well as genome-wide association studies in diverse populations are needed to address this issue. Here we describe the pilot phase of the GenomeAsia 100K Project. This includes a whole-genome sequencing reference dataset from 1,739 individuals of 219 population groups and 64 countries across Asia. We catalogue genetic variation, population structure, disease associations and founder effects. We also explore the use of this dataset in imputation, to facilitate genetic studies in populations across Asia and worldwide. Using whole-genome sequencing data from 1,739 individuals, the GenomeAsia 100K Project catalogues genetic variation, population structure and disease associations to facilitate genetic studies in Asian populations and increase representation in genetics studies worldwide., Author(s): Jeffrey D. Wall [sup.14] [sup.1] , Eric W. Stawiski [sup.2] [sup.3] [sup.44] , Aakrosh Ratan [sup.4] , Hie Lim Kim [sup.5] [sup.6] , Changhoon Kim [sup.7] [sup.8] , Ravi [...]

Belugas, Delphinapterus leucas, are one of only three whale species endemic to Arctic and sub-Arctic seas. They are found in both the Atlantic and Pacific Arctic and sub-Arctic, and are managed at a regional or national level within each of the five Arctic-range countries, along with international fora used to share information and management strategies. Genetic data--primarily mtDNA control region sequences and microsatellites--have played an important role in defining appropriate management units. Here, we review the genetic studies published to date and, for the first time, present a range-wide, circumpolar analysis of levels of mtDNA diversity and differentiation in beluga stocks. Our meta analysis is based on 302 bp of overlapping mtDNA control region sequence and includes 2,933 individuals spanning all 21 recognized beluga stocks. We find that all stocks are significantly differentiated from each other, except in five cases. Belugas in the St. Lawrence Estuary are the most distinct--the stock has the lowest range-wide level of genetic diversity and, with only two haplotypes present not found elsewhere, it is also the most well differentiated. Belugas in the Barents, Kara, and Laptev Seas stock have the highest level of diversity, supporting that this geographically far-ranging stock may harbor several distinct sub-units. Our study showcases insights gained from studying species at a range-wide level, while highlighting the challenges associated with compiling and comparing data from various publications with different study designs., Introduction Belugas (also known as white whales, Delphinapterus leucas) have a discontinuous circumpolar distribution and are one of only two toothed whale species found in the Arctic year round (O'Corry-Crowe, [...]

It has been thought that the Japanese house mouse carries the [A.sup.w] allele at the agouti locus causing light-colored bellies, but they do not always show this coloration. Thus, the presence of the [A.sup.w] allele seems to be doubtful in them. To ascertain whether the [A.sup.w] allele is present, a two-pronged approach was used. First, we compared lengths of DNA fragments obtained from three PCRs conducted on them to the known fragment sizes generated from mouse strains exhibiting homozygosities of either a/a, A/A,or [A.sup.w]/[A.sup.w]. PCR I, PCR II, and PCR III amplify only in the A and [A.sup.w] alleles, the a and [A.sub.w] alleles, and the a allele, respectively, and we detected amplifications in strains with A/A and [A.sup.w]/[A.sup.w] by PCR I, in those with a/a and the Japanese house mouse by PCR II, and in those with a/a by PCR III. Second, we sequenced the exon 1A region of the agouti gene and obtained sequences corresponding to the above strains and the Japanese house mouse, but their sequences were similar to those of the a allele. We concluded that their agouti allele is not identical to the [A.sup.w] allele and seems to be a novel type similar to the a allele. Key words: agouti allele, [A.sup.w], A, a, Japanese house mouse. On croit que les souris communes au Japon portent l'allele [A.sup.w] au locus agouti et que cela expliquerait leur ventre au pelage pale, bien qu'elles ne montrent pas toujours une telle coloration. Ainsi, la presence de l'allele [A.sup.w] peut etre mise en doute. Afin de verifier si l'allele [A.sup.w] est present, une approche double a ete employee. D'abord, les auteurs ont compare la longueur des fragments d'ADN obtenus suite a trois amplifications PCR avec les tailles obtenues chez des souches de souris homozygotes pour les alleles a/a, A/A ou [A.sup.w]/[A.sup.w]. Les PCR I, PCR II et PCR III peuvent uniquement amplifier les alleles suivants, respectivement : A et [A.sup.w], a et [A.sup.w], a seul. Les auteurs ont obtenu des produits d'amplification chez des souches A/A et [A.sup.w]/[A.sup.w] avec la PCR I, avec la PCR II chez les souches a/a et les souris communes du Japon, et finalement avec les souches a/a a l'aide de la PCR III. Ensuite, les auteurs ont sequence l'exon 1A du gene agouti et obtenu les sequences a partir des souches decrites plus haut et des souris japonaises, mais cette fois, la sequence etait semblable a celle de l'allele a. Les auteurs concluent que l'allele agouti n'est pas identique a l'allele [A.sup.w] et semble correspondre a un type nouveau semblable a l'allele a. [Traduit par la Redaction] Mots-cles : allele agouti, [A.sup.w], A, a, souris commune du Japon., Introduction The Japanese house mouse, Mus musculus, is characterized by a smaller body as compared to mice in Eurasia and by an agouti back and a light-colored belly coat (Hamajima [...]

Risk for ischemic stroke has a strong genetic basis, but heritable factors also contribute to the extent of damage after a stroke has occurred. We previously identified a locus on distal mouse chromosome 7 that contributes over 50% of the variation in postischemic cerebral infarct volume observed between inbred strains. Here, we used ancestral haplotype analysis to fine-map this locus to 12 candidate genes. The gene encoding the IL-21 receptor (Il21r) showed a marked difference in strain- specific transcription levels and coding variants in neonatal and adult cortical tissue. Collateral vessel connections were moderately reduced in Il27r-deficient mice, and cerebral infarct volume increased 2.3-fold, suggesting that Il21r modulates both collateral vessel anatomy and innate neuroprotection. In brain slice explants, oxygen deprivation (OD) activated apoptotic pathways and increased neuronal cell death in IL-21 receptor-deficient (IL-21R-deficient) mice compared with control animals. We determined that the neuroprotective effects of IL-21R arose from signaling through JAK/STAT pathways and upregulation of caspase 3. Thus, natural genetic variation in murine Il21r influences neuronal cell viability after ischemia by modulating receptor function and downstream signal transduction. The identification of neuroprotective genes based on naturally occurring allelic variations has the potential to inform the development of drug targets for ischemic stroke treatment., Introduction Stroke is the fourth leading cause of death in the US, with almost 800,000 new cases occurring each year (1). The majority (over 80%) of strokes are of ischemic [...]

The ability of populations to adapt to environmental change and the spatial scale at which this adaptation occurs are fundamentally important issues in evolutionary biology, and ones that may benefit greatly from the study of genetic variability in reaction norms, which represent the plasticity of phenotypic traits across an environmental gradient. Therefore variable reaction norms can reflect genetic differences in the ability of individuals, families, populations, and species to respond to natural and anthropogenic environmental change. Fishes are ideal organisms in which to study plasticity because of their remarkable intraspecific morphological, physiological, behavioural, and life history variation. Here, we review studies demonstrating genetic variability in reaction norms in fishes. Genetic variability in plasticity among full- and half-sib families suggests potential for some populations to develop an adaptive norm of reaction (recalling that plasticity need not be adaptive). Reaction norm variability among populations suggests that adaptive genetic divergence can occur rapidly when selection pressures are strong and that the spatial scale of adaptation is much smaller than previously believed for some species with high dispersal capabilities. These studies demonstrate the potential of using reaction norms to study the evolution of novel phenotypes and the influence of temporal environmental variability and gene flow on the evolution of phenotypic plasticity, which can then be used to predict how populations will respond to directional environmental change. To promote future research into genetic variability in reaction norms, we propose questions that would benefit from such an approach and discuss some important considerations for designing experiments to investigate questions related to genetic variation in plasticity and phenotypic evolution. Key words: phenotypic plasticity, genotype-environment interaction, adaptation, environmental change. La capacite d'adaptation au changement environnemental et l'echelle spatiale a laquelle cette adaptation survient, constituent des defis d'importance fondamentale en biologie evolutive, un sujet qui pourrait beneficier grandement de l'etude de la variabilite des normes de reaction. Les normes de reaction representent la plasticite des traits phenotypiques le long d'un gradient environnemental. Consequemment, des normes de reaction variables peuvent refleter des differences genetiques dans la capacite des individus, des familles, des populations et des especes a reagir au changement environnemental naturel et anthropogene. Les poissons constituent des organismes ideaux pour l'etude de la plasticite compte tenu de la variation intraspecifique remarquable de leur morphologie, de leur physiologie, de leur comportement et de leur cycle de vie. Les auteurs passent en revue les etudes demontrant la variabilite genetique des normes de reaction chez les poissons. La variabilite de la plasticite parmi les familles biparentales ou mono parentales suggere la capacite de certaines populations a developper une norme de reaction adaptative (en se rappelant que la plasticite ne doit pas necessairement etre adaptative). La variabilite des normes de reaction parmi les populations suggere qu'une divergence genetique adaptative peut se manifester rapidement, lorsque les pressions de selection sont fortes et que l'echelle spatiale d'adaptation est beaucoup plus petite qu'on le croyait, chez certaines especes ayant de fortes capacites de dispersion. Ces etudes demontrent que le potentiel de l'utilisation des normes de reaction pour etudier l'evolution de nouveaux phenotypes et l'influence de la variabilite temporelle environnementale ainsi que flux de genes sur l'evolution de la plasticite phenotypique, lesquels peuvent alors etre utilises pour predire comment les populations repondront au changement environnemental directionnel. Pour promouvoir des recherches futures sur la variabilite genetique des normes de reaction, les auteurs proposent quelques questions qui beneficieraient d'une telle approche, et discutent quelques considerations importantes pour concevoir des experiences soulevant des questions reliees a la variation genetique de la plasticite de l'evolution phenotypique. [Traduit par la Redaction] Mots-cles: plasticite phenotypique, interaction genotype environnement, adaptation, changement environnemental., Introduction The ability of individuals or populations to respond to environmental change is integral to species persistence. If a fitness-related trait is optimally expressed in specific environmental conditions, then a [...]

Geographic patterns of genetic variation in wild species reflect the interplay of ecological and evolutionary processes. We assessed genetic variation in three genomes across four North American diploid strawberry taxa, with special emphasis on the gynodioecious Fragaria vesca subsp. bracteata (A.Heller) Staudt. Specifically, we sequenced one chloroplast (rpoC2) and two mitochondrial (atp8 and atp8-orf225) genes along with several nuclear microsatellite markers. In addition, we assessed indicators of breeding system (pollen viability and female frequency) for all taxa. The geographic perspective on the distribution of cytoplasmic and nuclear variation revealed the genetic affiliation of the restricted taxa (Fragaria vesca subsp. californica (Cham. & Schltdl.) Staudt and Fragaria mexicana Schltdl.) with the widespread F. vesca subsp. bracteata and identified a hotspot of hybridization within gynodioecious F. vesca subsp. bracteata. Higher pollen viability of hermaphrodites was found in the three hermaphroditic taxa relative to the gynodioecious one. Although theoretically predicted to be associated, the proportion of females within F. vesca subsp. bracteata populations was not correlated with population-level genetic variation, suggesting that the history of hybridization or population size variation is more influential on the distribution of genetic variation than sex ratio in this gynodioecious species. The documented patterns of genetic variation in this complex serve as an important point of reference for future ecological and evolutionary research in diploid Fragaria. Keywords: chloroplast, hybridization, genetic structure, gynodioecy, mitochondria, pollen viability. Les patrons geographiques de la variation genetique d'especes sauvages refletent l'interrelation entre les processus ecologiques et les evolutifs. Les auteurs ont evalue la variation de trois genomes a travers quatre taxons diploides de fraises en Amerique du Nord, en portant une attention particuliere a Fragaria vesca subsp. bracteata (A.Heller) Staudt gynodio'ique. Specifiquement, ils ont sequence un gene du chloroplaste (rpoC2) et deux genes mitochondriaux (atp8 et atp8-orf225) parallelement a plusieurs marqueurs microsatellites nucleaires. De plus, ils ont evalue des indicateurs du systeme de reproduction (viabilite du pollen et frequence des femelles) chez tous les taxons. La perspective geographique de la distribution de la variation cytoplasmique et nucleaire a revele l'affiliation genetique des taxons restreints (Fragaria vesca subsp. californica (Cham. & Schltdl.) Staudt et Fragaria mexicana Schltdl.) au taxon repandu F. vesca subsp. bracteata, et identifie un point chaud d'hybridation a l'interieur de F. vesca subsp. bracteata gynodio'ique. Une viabilite du pollen des hermaphrodites plus elevee a ete trouvee chez les trois taxons hermaphrodites comparativement au taxon gynodio'ique. Malgre les predictions theoriques d'une association, la proportion de femelles a l'interieur des populations de F. vesca subsp. bracteata n'etait pas correlee a la variation genetique au niveau de la population, suggerant que l'historique d'hybridation ou la variation de la taille de la population exerce une influence plus grande sur la distribution de la variation genetique que le ratio des sexes chez cette espece gynodio'ique. Les patrons documentes de variation genetique dans ce complexe servent de point de reference important pour la recherche future sur l'ecologie et l'evolution de Fragaria diploide. [Traduit par la Redaction] Mots-cles : chloroplaste, hybridation, structure genetique, gynodrecie, mitochondrie, viabilite du pollen., Introduction Patterns of phenotypic and genetic variation of wild species reflect their ecological and evolutionary history. Important questions that have emerged are: How is variation partitioned among and within populations [...]

Typical use of diversity indices in forest stands does not reflect within-stand variation in species and structure. Despite numerous efforts to design stand diversity indices that capture spatial variation in two- or three-dimensional space, the application of these indices is limited due to their complexity or lack of ecological relevance. In this research note, we illustrate the application of diversity indices at the neighbourhood scale using stem mapping data from a boreal mixedwood stand in northeastern Ontario, which was assessed before and after partial harvesting. Among the three diversity indices (Shannon species diversity, Shannon structural diversity by height class distribution, and structural diversity by height variation), neighbourhood structural diversity by height variation was less dependent on neighbourhood size (between 4 and 12 trees) and more sensitive to stand structural change than Shannon structural diversity by height class distribution. Despite general increases in Shannon species diversity and structural diversity by height variation at both stand and neighbourhood scales after the harvest--an indication of higher diversity--within-stand variation (coefficients of variation) in neighbourhood diversity values decreased, suggesting that residual stands were spatially more uniform after the harvest. Therefore, the neighbourhood diversity indices are useful for capturing spatial variation in species and structural diversity, especially in managed stands in which spatial distributions and patterns can be significantly modified by management interventions. Key words: tree neighbours, structural diversity, within-stand variation, spatial scale, forest stand structure. L'utilisation typique des indices de diversite dans les peuplements forestiers ne reflete pas la variation intrapeuplement des especes et de la structure. Malgre de nombreux efforts pour concevoir des indices de diversite de peuplement qui refletent la variation spatiale dans un espace a deux ou trois dimensions, l'application de ces indices est limitee a cause de leur complexite ou de leur manque de pertinence ecologique. Dans cette note de recherche, nous illustrons l'application d'indices de diversite a l'echelle du voisinage a l'aide de donnees d'arbres cartographies avant et apres une coupe partielle dans un peuplement boreal mixte du nord-est de l'Ontario. Entre les trois indices de diversite (la diversite specifique de Shannon, la diversite structurale de Shannon par distribution de classes de hauteur et la diversite structurale par variation de la hauteur), la diversite structurale des arbres voisins par variation de la hauteur etait moins dependante du nombre de voisins (entre 4 et 12 arbres) et plus sensible au changement de structure du peuplement que la diversite structurale de Shannon par distribution de classes de hauteur. Malgre une augmentation generale de la diversite specifique de Shannon et de la diversite structurale par variation de la hauteur aux echelles du peuplement et du voisinage apres la coupe, ce qui temoigne d'une plus grande diversite, la variation intra-peuplement (les coefficients de variation) dans la valeur de ces indices diminuait, ce qui indique que les peuplements residuels etaient spatialement plus uniformes apres la coupe. Les indices de diversite du voisinage sont donc utiles pour refleter la variation spatiale des especes et de la diversite structurale, particulierement dans les peuplements amenages oU la distribution et les patrons spatiaux peuvent etre substantiellement modifies par les interventions d'amenagement. [Traduit par la Redaction] Mots-cles : arbres voisins, diversite structurale, variation intra-peuplement, echelle spatiale, structure des peuplements forestiers., Introduction Stand structure is an important element of stand biodiversity and can strongly influence the diversity of understory plants, insects, birds, wildlife, and soil flora and fauna. Structurally diverse stands [...]

Inherent variability in the spectral properties of boreal forests complicates the retrieval of canopy properties such as canopy leaf area index from satellite images. Understanding the drivers of this variability could help provide better estimates of desired canopy cover properties. Field plot data from the Finnish National Forest Inventory and Landsat thematic mapper (TM) images were used to investigate the variation in canopy and understory reflectance during stand development in coniferous boreal forests. Spectral data for each plot were obtained from the Landsat pixel within which the plot center coordinates fell. Nonlinear unmixing was used to estimate the bidirectional reflectance factors (BRFs) of the 'sunlit understory' and 'canopy and shaded ground' components by site fertility and stand development classes. A forest albedo model was used to estimate the contribution of diffuse radiation reflected downwards from the canopy to the sunlit understory component. The sunlit understory BRF in the near-infrared spectral band decreased as the site fertility decreased and the forest matured, whereas the sunlit understory BRFs in the red and shortwave-infrared spectral bands concurrently increased. The BRFs of the canopy and shaded ground component decreased slightly during stand development, mostly in the near-infrared spectral band. Adding the diffuse contribution to the sunlit understory component changed the estimated component BRFs only a little (0.1%-1.7%) compared with those obtained using a linear mixing assumption. This effect was largest in the near-infrared spectral band and smallest in the red spectral band. For Norway spruce plots, the measured and estimated forest variables were well correlated with the BRFs in all of the studied spectral bands, but for the Scots pine plots, the correlations were notably weaker. Results show a greater importance of the fraction of visible sunlit understory on forest reflectance in Scots pine than in Norway spruce forests. Key words: boreal forest, reflectance, linear and nonlinear umixing, Landsat, understory. La variabilite inherente des proprietes spectrales des forets boreales complique l'extraction des proprietes du couvert forestier telles que l'indice de surface foliaire a partir des images satellites. La comprehension des causes de cette variabilite pourrait aider a obtenir de meilleures estimations des proprietes du couvert forestier qui presentent un interet. Des donnees de placettes-echantillons sur le terrain provenant de l'inventaire forestier national finlandais et des images satellitaires Landsat TM ont ete utilisees pour etudier la variation de la reflectance du couvert forestier et du sous-bois au cours du developpement des peuplements dans les forets boreales resineuses. Les donnees spectrales de chaque placette-echantillon ont ete obtenues a partir du pixel de Landsat correspondant aux coordonnees du centre des placettes-echantillons. La deconvolution non lineaire a ete utilisee pour estimer les facteurs de reflectance bidirectionnelle (FRB) des composantes 'sous-bois ensoleille' et 'couvert forestier et terrain ombrage' par classes de fertilite du sol et de developpement des peuplements. Un modele d'albedo du couvert forestier a ete utilise pour estimer la contribution du rayonnement diffus reflechi vers le bas du couvert forestier, vers la composante sous-bois ensoleille. Le FRB du sous-bois ensoleille dans la bande spectrale proche infrarouge (PIR) diminuait a mesure que la fertilite de la station diminuait et que la foret devenait mature, tandis que simultanement les FRB dans les bandes spectrales rouge et infrarouge ondes courtes augmentaient. Les FRB de la composante couvert forestier et terrain ombrage diminuait legerement durant le developpement des peuplements surtout dans le PIR. L'ajout de la contribution du rayonnement diffus a la composante sous-bois ensoleille modifiait seulement un peu (0,1 % a 1,7 %) les FRB estimes de la composante comparativement a aux valeurs obtenues en utilisant l'hypothese du mixage lineaire. Cet effet etait plus prononce dans le PIR et moins prononce dans la bande spectrale rouge. Dans les placettes-echantillons d'epicea, les variables forestieres estimees et mesurees etaient bien correlees avec les FBR dans toutes les bandes spectrales etudiees mais les correlations etaient manifestement plus faibles dans les placettes-echantillons de pin. Les resultats montrent que la fraction du rayonnement visible du sous-bois ensoleille a plus d'impact sur la reflectance de la foret dans les peuplements de pin que dans les peuplements d'epicea. [Traduit par la Redaction] Mots-cles : foret boreale, reflectance, deconvolution lineaire et non lineaire, Landsat, sous-bois., 1. Introduction The retrieval of forest resource estimates from remote sensing observations in combination with field observations usually targets forest structural variables such as volume of growing stock, biomass, or [...]

Contact zones between divergent lineages of aquatic taxa have been described from the northeastern Pacific Ocean. We surveyed samples of Dolly Varden (Salvelinus malma) from their North American range for variation at 14 microsatellite DNA loci. After accounting for hybridization between Dolly Varden and co-occurring bull trout (Salvelinus confluentus) and Arctic char (Salvelinus alpinus), we found evidence for two genetic lineages of Dolly Varden consistent with the previously recognized subspecies, northern Dolly Varden (S. m. malma) and southern Dolly Varden (S. m. lordii). We documented a contact zone between the two subspecies from the eastern Alaska Peninsula to Cook Inlet, Alaska, where admixture values (i.e., the proportion of the genome estimated to be composed of northern Dolly Varden, [Q.sub.NDV]) ranged between [Q.sub.NDV] = 0.245 and 0.754 across about 700 ocean kilometres. Populations of Dolly Varden showing low admixture (i.e., less than 5%) were located a minimum of 346 km to the west to 1200 km to the southeast, respectively, from the contact zone. The two lineages of Dolly Varden probably stem from isolation and subsequent divergence in, and dispersal from, distinct northern and southern Pleistocene glacial refugia and substantiate the treatment of S. malma as two subspecies and as at least two designatable units under Canada's Species at Risk Act. Des zones de contact entre des lignees divergentes de taxons aquatiques ont ete decrites dans le nord-est de l'ocean Pacifique. Nous avons examine des echantillons d'ombles Dolly Varden (Salvelinus malma) provenant de l'aire de repartition nord-americaine de l'espece pour evaluer les variations dans 14 microsatellites d'ADN. Une fois les effets de l'hybridation entre les Dolly Varden et les ombles a tete plate (Salvelinus confluentus) et ombles chevaliers (Salvelinus alpinus) cooccurrents pris en compte, nous avons trouve des indices de la presence de deux lignees genetiques de Dolly Varden coincidant avec des sousespeces deja reconnues, les ombles Dolly Varden du Nord (S. m. malma) et du Sud (S. m. lordii). Nous avons documente une zone de contact entre les deux sous-especes allant de l'est de la peninsule de l'Alaska jusqu'a Cook Inlet (Alaska), oU les valeurs de melange (c.-a-d. la proportion estimee du genome provenant du Dolly Varden du Nord, [Q.sub.NDV]) allaient de 0,245 a 0,754 sur environ 700 km d'ocean. Les populations de Dolly Varden presentant un faible melange (c.-a-d. moins de 5 %) etaient situees a au moins 346 km a l'ouest a 1200 km au sud-est, respectivement, de la zone de contact. Les deux lignees de Dolly Varden sont probablement issues de l'isolement et de la divergence subsequente dans des refuges glaciaires pleistocenes septentrional et meridional distincts, suivis de leur dispersion a partir de ces refuges. Les resultats soulignent la pertinence de traiter S. malma comme comprenant deux sous-especes et au moins deux unites pouvant etre designees en vertu de la Loi sur les especes en peril du Canada. [Traduit par la Redaction], Introduction Fishes of the Holarctic genus Salvelinus (i.e., chars) have provided many opportunities to study geographic variation in morphology, genetics, and ecology, and their implications for understanding processes of evolutionary [...]

Cancer genome sequencing has revealed considerable variation in somatic mutation rates across the human genome, with mutation rates elevated in heterochromatic late replicating regions and reduced in early replicating euchromatin [...]

The proliferation of genetically modified mouse models has exposed phenotypic variation between investigators and institutions that has been challenging to control (1-5). In many cases, the microbiota is the presumed cause of the variation. Current solutions to account for phenotypic variability include littermate and maternal controls or defined microbial consortia in gnotobiotic mice (6,7). In conventionally raised mice, the microbiome is transmitted from the dam (2,8,9). Here we show that microbially driven dichotomous faecal immunoglobulinA (IgA) levels in wild-type mice within the same facility mimic the effects of chromosomal mutations. We observe in multiple facilities that vertically transmissible bacteria in IgA-low mice dominantly lower faecal IgA levels in IgA-high mice after co-housing or faecal transplantation. In response to injury, IgA-low mice show increased damage that is transferable by faecal transplantation and driven by faecal IgA differences. We find that bacteria from IgA-low mice degrade the secretory component of secretory IgA as well as IgA itself. These data indicate that phenotypic comparisons between mice must take into account the non-chromosomal hereditary variation between different breeders. We propose faecal IgA as one marker of microbial variability and conclude that co-housing and/or faecal transplantation enables analysis of progeny from different dams., We chose to study the role of secretory immunoglobulin A (SIgA), which is a critical intersection between the host immune system and the microbiota (10). While interrogating baseline intestinal IgA [...]

Autism is a multifactorial neurodevelopmental disorder affecting more males than females; consequently, under a multifactorial genetic hypothesis, females are affected only when they cross a higher biological threshold. We hypothesize that deleterious variants at conserved residues are enriched in severely affected patients arising from female-enriched multiplex families with severe disease, enhancing the detection of key autism genes in modest numbers of cases. Here we show the use of this strategy by identifying missense and dosage sequence variants in the gene encoding the adhesive junction-associated δ-catenin protein (CTNND2) in female-enriched multiplex families and demonstrating their loss-of-function effect by functional analyses in zebrafish embryos and cultured hippocampal neurons from wild-type and Ctnnd2 null mouse embryos. Finally, through gene expression and network analyses, we highlight a critical role for CTNND2 in neuronal development and an intimate connection to chromatin biology. Our data contribute to the understanding of the genetic architecture of autism and suggest that genetic analyses of phenotypic extremes, such as female-enriched multiplex families, are of innate value in multifactorial disorders., Autism is a common neurodevelopmental disorder with a profound sex-bias: four times more males than females are affected (1) whereas disease recurrence risk to siblings of autistic females is larger [...]

We aim to improve diversity of domesticated wheat by transferring genetic variation for important target traits from related wild and cultivated grass species. The present study describes the development of [F.sub.1] hybrids between wheat and related species from the genera Aegilops, Secale, Thinopyrum, and Triticum and production of new amphidiploids. Amphidiploid lines were produced from 20 different distant relatives. Both colchicine and caffeine were successfully used to double the chromosome numbers. The genomic constitution of the newly formed amphidiploids derived from seven distant relatives was determined using genomic in situ hybridization (GISH). Altogether, 42 different plants were analysed, 19 using multicolour GISH separating the chromosomes from the A, B, and D genomes of wheat, as well as the distant relative, and 23 using single colour GISH. Restructuring of the allopolyploid genome, both chromosome losses and aneuploidy, was detected in all the genomes contained by the amphidiploids. From the observed chromosome numbers there is an indication that in amphidiploids the B genome of wheat suffers chromosome losses less frequently than the other wheat genomes. Phenotyping to realize the full potential of the wheat--related grass germplasm is underway, linking the analyzed genotypes to agronomically important target traits. Key words: amphidiploid, Triticum aestivum, wheat, Aegilops, Secale, Thinopyrum, Triticum, chromosome doubling, genomic in situ hybridization. Les auteurs visent a augmenter la diversite genetique au sein du ble domestique en introduisant de la variation genetique pour des caracteres d'interet a partir d'especes apparentees de graminees sauvages et cultivees. Le present travail decrit l'obtention d'hybrides [F.sub.1] entre le ble et des especes apparentees appartenant aux genres Aegilops, Secale, Thinopyrum et Triticum ainsi que la production de nouveaux amphidiploides. Les lignees amphidiploides ont ete produites a partir de 20 genotypes distants apparentes. La colchicine et la cafeine ont toutes deux ete employees avec succes pour doubler le nombre de chromosomes. La composition genomique des amphidiploides nouvellement formes et derives de sept genotypes distants apparentes a ete determinee a l'aide de l hybridation genomique in situ (GISH). Au total, 42 plantes differentes ont ete analysees dont 19 au moyen d une analyse GISH multicolore permettant d assigner les chromosomes aux genomes A, B et D du ble de meme qu aux especes apparentees; les 23 autres plantes ayant ete examinees au moyen d'une analyse GISH monochrome. Des remaniements du genome allopolyploide ont ete observes, tant des pertes chromosomiques que de l'aneuploidie, chez tous les genomes presents au sein des amphidiploides. Sur la base du nombre observe de chromosomes, il semblerait que le genome B serait moins souvent sujet a des pertes chromosomiques que les autres genomes du ble chez les amphidiploides. Une analyse phenotypique de ces amphidiploides est en cours afin de tirer le maximum de ce germoplasme ble--graminee apparentee en associant les genotypes analyses a des caracteres agronomiques importants. [Traduit par la Redaction] Mots-cles : amphidiploide, Triticum aestivum, ble, Aegilops, Secale, Thinopyrum, Triticum, doublement chromosomique, hybridation genomique in situ., Introduction Hexaploid bread wheat (Triticum aestivum, 2n = 6x = 42, genomes AABBDD), which evolved between 10 000 and 8500 years ago, is an allohexaploid derived from hybridization events between [...]

Porcine epidemic diarrhea virus (PEDV) (family Coronaviridae, subfamily Coronavirinae, genus Alphacoronavirus) is an enveloped, positive-sense, single-stranded RNA virus. PEDV causes an acute and highly contagious enteric disease characterized by severe [...]

Peste des petits ruminants is a highly contagious and devastating viral disease of small ruminants that is endemic to much of Africa, the Middle East, and Asia (1,2). The causative [...]

In humans, vWF levels predict the risk of myocardial infarction and thrombosis; however, the factors that influence vWF levels are not completely understood. Recent genome-wide association studies (GWAS) have identified syntaxin-binding protein 5 (STXBPS) as a candidate gene linked to changes in vWF plasma levels, though the functional relationship between STXBP5 and vWF is unknown. We hypothesized that STXBP5 inhibits endothelial cell exocytosis. We found that STXBP5 is expressed in human endothelial cells and colocalizes with and interacts with syntaxin 4. In human endothelial cells reduction of STXBP5 increased exocytosis of vWF and P-selectin. Mice lacking StxbpS had higher levels of vWF in the plasma, increased P-selectin translocation, and more platelet-endothelial interactions, which suggests that STXBP5 inhibits endothelial exocytosis. However, StxbpS KO mice also displayed hemostasis defects, including prolonged tail bleeding times and impaired mesenteric arteriole and carotid artery thrombosis. Furthermore, platelets from StxbpS KO mice had defects in platelet secretion and activation; thus, STXBP5 inhibits endothelial exocytosis but promotes platelet secretion. Our study reveals a vascular function for STXBP5, validates the functional relevance of a candidate gene identified by GWAS, and suggests that variation within STXBPS is a genetic risk for venous thromboembolic disease., Introduction Venous thromboembolism is a major cause of morbidity and mortality (1, 2). Venous thrombosis is the second leading cause of death in patients with cancer (3). The pathophysiology of [...]

It has been well documented that free radial damage and the accompanying inflammation created by free radicals is often the root cause of most of the chronic conditions we see [...]

Severe intellectual disability (ID) occurs in 0.5% of newborns and is thought to be largely genetic in origin (1,2). The extensive genetic heterogeneity of this disorder requires a genome-wide detection of all types of genetic variation. Microarray studies and, more recently, exome sequencing have demonstrated the importance of de novo copy number variations (CNVs) and single-nucleotide variations (SNVs) in ID, but the majority of cases remain undiagnosed (3-6). Here we applied whole-genome sequencing to 50 patients with severe ID and their unaffected parents. All patients included had not received a molecular diagnosis after extensive genetic prescreening, including microarray-based CNV studies and exome sequencing. Notwithstanding this prescreening, 84 denovo SNVs affecting the coding region were identified, which showed a statistically significant enrichment of loss-of-function mutations as well as an enrichment for genes previously implicated in ID-related disorders. In addition, we identified eight denovo CNVs, including single-exon and intra-exonic deletions, as well as interchromosomal duplications. These CNVs affected known ID genes more frequently than expected. On the basis of diagnostic interpretation of all de novo variants, a conclusive genetic diagnosis was reached in 20 patients. Together with one compound heterozygous CNV causing disease in a recessive mode, this results in a diagnostic yield of 42% in this extensively studied cohort, and 62% as a cumulative estimate in an unselected cohort. These results suggest that denovo SNVs and CNVs affecting the coding region are a major cause of severe ID. Genome sequencing can be applied as a single genetic test to reliably identify and characterize the comprehensive spectrum of genetic variation, providing a genetic diagnosis in the majority of patients with severe ID., Whole-genome sequencing (WGS) is considered to be the most comprehensive genetic test so far (7), but widespread application to patient diagnostics has been hampered by challenges in data analysis, the [...]

Parkinsonism and attention deficit hyperactivity disorder (ADHD) are widespread brain disorders that involve disturbances of dopaminergic signaling. The sodium-coupled dopamine transporter (DAT) controls dopamine homeostasis, but its contribution to disease remains poorly understood. Here, we analyzed a cohort of patients with atypical movement disorder and identified 2 DAT coding variants, DAT-Ile312Phe and a presumed de novo mutant DAT-Asp421Asn, in an adult male with early-onset parkinsonism and ADHD. According to DAT single-photon emission computed tomography (DAT-SPECT) scans and a fluoro-deoxy-glucose-PET/MRI (FDG-PET/MRI) scan, the patient suffered from progressive dopaminergic neurodegeneration. In heterologous cells, both DAT variants exhibited markedly reduced dopamine uptake capacity but preserved membrane targeting, consistent with impaired catalytic activity. Computational simulations and uptake experiments suggested that the disrupted function of the DAT- Asp421Asn mutant is the result of compromised sodium binding, in agreement with Asp421 coordinating sodium at the second sodium site. For DAT-Asp421Asn, substrate efflux experiments revealed a constitutive, anomalous efflux of dopamine, and electrophysiological analyses identified a large cation leak that might further perturb dopaminergic neurotransmission. Our results link specific DAT missense mutations to neurodegenerative early-onset parkinsonism. Moreover, the neuropsychiatric comorbidity provides additional support for the idea that DAT missense mutations are an ADHD risk factor and suggests that complex DAT genotype and phenotype correlations contribute to different dopaminergic pathologies., Introduction Dopamine is an important neurotransmitter regulating motor activity, cognition, neuroendocrine functions, and reward mechanisms. Moreover, disturbances in dopaminergic signaling are of central importance in several common brain diseases including [...]

Kidney disease is one of the most prevalent chronic conditions and is a frequent complication of diabetes, cardiovascular disease, and obesity. Recent advances in biomedical research and novel technologies have created opportunities to study kidney disease in a variety of platforms, applied to human populations. The Reviews in this series discuss the kidney in hypertension, diabetes, and monogenic forms of kidney disease, as well as the cellular and molecular mediators of acute kidney injury and fibrosis, IgA nephropathy and idiopathic membranous nephropathy, and kidney transplantation. In this introduction, we briefly review new insights into focal segmental glomerulosclerosis and the role of podocytes in health and disease. Additionally, we discuss how new technologies, therapeutics, and the availability of patient data can help shape the study of kidney disease and ultimately inform policies concerning biomedical research and health care., The burden of kidney disease The advent of a uniform definition and staging of kidney disease radically altered our understanding of its impact on human health (1). Prior to this, [...]

A primary goal of the Human Microbiome Project (HMP) was to provide a reference collection of 16S ribosomal RNA gene sequences collected from sites across the human body that would [...]

Genetic variation at the chromosome 9p21 risk locus promotes cardiovascular disease; however, it is unclear how or which proteins encoded at this locus contribute to disease. We have previously demonstrated that loss of one candidate gene at this locus, cyclin-dependent kinase inhibitor 2B (Cdkn2b), in mice promotes vascular SMC apoptosis and aneurysm progression. Here, we investigated the role of Cdnk2b in atherogenesis and found that in a mouse model of atherosclerosis, deletion of Cdnk2b promoted advanced development of atherosclerotic plaques composed of large necrotic cores. Furthermore, human carriers of the 9p21 risk allele had reduced expression of CDKN2B in atherosclerotic plaques, which was associated with impaired expression of calreticulin, a ligand required for activation of engulfment receptors on phagocytic cells. As a result of decreased calreticulin, CDKN2B-deficient apoptotic bodies were resistant to efferocytosis and not efficiently cleared by neighboring macrophages. These uncleared SMCs elicited a series of proatherogenic juxtacrine responses associated with increased foam cell formation and inflammatory cytokine elaboration. The addition of exogenous calreticulin reversed defects associated with loss of Cdkn2b and normalized engulfment of Cdkn2b-deficient cells. Together, these data suggest that loss of CDKN2B promotes atherosclerosis by increasing the size and complexity of the lipid-laden necrotic core through impaired efferocytosis., Introduction Traditional risk factors account for approximately half of an individual's lifetime risk of cardiovascular disease (1), (2). The balance, therefore, is accounted for by a combination of unmeasured environmental [...]

Hematodinium perezi (genotype III) is a parasitic dinoflagellate that infects blue crabs along the eastern seaboard and Gulf of Mexico, USA. In order to examine the intra-specific genetic variation of this parasite, eleven microsatellite markers from H. perezi (III) were amplified from 227 infected blue crabs collected during 2008-2009 from six sites in Virginia. Simultaneous infections with multiple genetic types in a single-host individual were common and observed in 42 % of the samples. The remaining 58 % of samples had a single allele per locus at all eight polymorphic loci suggesting that the life history stages of the parasite in the host hemolymph are likely haploid. The composition and distribution of multi-locus genotypes (MLG) from samples with infections of a single genetic type indicated high genotypic variation along the Delmarva Peninsula, Virginia, with no evidence of population structure. The lack of linkage disequilibrium combined with the large number of unique MLGs (84 %) is strong evidence for recombination in the life cycle, but the sexual stages remain undetermined. This is the first evidence of ploidy level, infections by multiple genetic types in an individual host animal, high levels of genotypic variation, and sexual reproduction for any species of Hematodinium., Introduction Hematodinium perezi is an endoparasitic dinoflagellate that infects the American blue crab, Callinectes sapidus (Messick and Shields 2000; Stentiford and Shields 2005), with infections reported from Delaware to Texas [...]

Author(s): Muin J. Khoury 1,*, W. Gregory Feero 2, David A. Chambers 3, Lawrence E. Brody 4, Nazneen Aziz 5, Robert C. Green 6, A. Cecile J.W. Janssens 7, Michael [...]

Genome-wide association studies (GWAS) have identified several risk variants for late-onset Alzheimer's disease (LOAD) (1,2). These common variants have replicable but small effects on LOAD risk and generally do not have obvious functional effects. Low-frequency coding variants, not detected by GWAS, are predicted to include functional variants with larger effects on risk. To identify low-frequency coding variants with large effects on LOAD risk, we carried out whole-exome sequencing (WES) in 14 large LOAD families and follow-up analyses of the candidate variants in several large LOAD case-control data sets. A rare variant in PLD3 (phospholipase D3; Val232Met) segregated with disease status in two independent families and doubled risk for Alzheimer's disease in seven independent case-control series with a total of more than 11,000 cases and controls of European descent. Gene-based burden analyses in 4,387 cases and controls of European descent and 302 African American cases and controls, with complete sequence data for PLD3, reveal that several variants in this gene increase risk for Alzheimer's disease in both populations. PLD3 is highly expressed in brain regions that are vulnerable to Alzheimer's disease pathology, including hippocampus and cortex, and is expressed at significantly lower levels in neurons from Alzheimer's disease brains compared to control brains. Overexpression of PLD3 leads to a significant decrease in intracellular amyloid-b precursor protein (APP) and extracellular Aβ42 and Aβ42 (the 42and 40-residue isoforms of the amyloid-β peptide), and knockdown of PLD3 leads to a significant increase in extracellular Aβ42 and Aβ42. Together, our genetic and functional data indicate that carriers of PLD3 coding variants have a twofold increased risk for LOAD and that PLD3 influences APP processing. This study provides an example of how densely affected families may help to identify rare variants with large effects on risk for disease or other complex traits. NIA Knight NIA-UK total MAF % p-value OR (95% CI) EVS SIFT Polyphen, The identification of pathogenic mutations in APP, presenilin 1 (PSEN1) and PSEN2, and the association of apolipoprotein E (APOE) genotype with disease risk led to a better understanding of the [...]

To determine the genetic relationship between head circumference (HC) and Autism Spectrum Disorders (ASDs). Twin pairs with at least one twin with an ASD were assessed. HCs in affected and unaffected individuals were compared, as were HC correlations in monozygotic and dizygotic pairs. 404 subjects, ages 4-18, were included. 20 % of males and 27 % of females with an ASD had macrocephaly. Unaffected co-twins showed similar rates (16 % of males and 22 % of females). Statistical analysis revealed no significant difference in HCs between affected and unaffected twins. Twins with ASDs and unaffected co-twins have similar HCs and increased rates of macrocephaly. Correlations demonstrated partial inheritance of HCs. Thus, macrocephaly may represent an endophenotype in ASDs. Keywords Macrocephaly * Head circumference * Twins * Endophenotype * Genetics, Introduction Twin studies suggest that a combination of genetic and environmental factors lead to the development of the Autism Spectrum Disorders (ASDs) (Bailey et al. 1995; Folstein and Rutter 1977; [...]

By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations., Recent efforts to map human genetic variation by sequencing exomes (1) and whole genomes (2-4) have characterized the vast majority of common single nucleotide polymorphisms (SNPs) and many structural variants [...]

Recent advances in whole-genome sequencing have brought the vision of personal genomics and genomic medicine closer to reality. However, current methods lack clinical accuracy and the ability to describe the context (haplotypes) in which genome variants co-occur in a cost-effective manner. Here we describe a low-cost DNA sequencing and haplotyping process, long fragment read (LFR) technology, which is similar to sequencing long single DNA molecules without cloning or separation of metaphase chromosomes. In this study, ten LFR libraries were made using only ~100 picograms of human DNA per sample. Up to 97% of the heterozygous single nucleotide variants were assembled into long haplotype contigs. Removal of false positive single nucleotide variants not phased by multiple LFR haplotypes resulted in a final genome error rate of 1 in 10megabases. Cost-effective and accurate genome sequencing and haplotyping from 10-20 human cells, as demonstrated here, will enable comprehensive genetic studies and diverse clinical applications., The extraordinary advancements made in DNA sequencing technologies over the past few years have led to the elucidation of ~10,000 (refs 1-13) individual human genomes (30 x or greater base [...]

Protein tyrosine phosphatase nonreceptor type 22 (PTPN22) gene polymorphisms are associated with many autoimmune diseases. The major risk allele encodes an R620W amino acid change that alters B cell receptor (BCR) signaling involved in the regulation of central B cell tolerance. To assess whether this PTPN22 risk allele affects the removal of developing autoreactive B cells, we tested by ELISA the reactivity of recombinant antibodies isolated from single B cells from asymptomatic healthy individuals carrying one or two PTPN22 risk allele(s) encoding the PTPN22 R620W variant. We found that new emigrant/transitional and mature naive B cells from carriers of this PTPN22 risk allele contained high frequencies of autoreactive clones compared with those from non-carriers, revealing defective central and peripheral B cell tolerance checkpoints. Hence, a single PTPN22 risk allele has a dominant effect on altering autoreactive B cell counterselection before any onset of autoimmunity. In addition, gene array experiments analyzing mature naive B cells displaying PTPN22 risk allele(s) revealed that the association strength of PTPN22 for autoimmunity may be due not only to the impaired removal of autoreactive B cells but also to the upregulation of genes such as CD40, TRAF1, and IRF5, which encode proteins that promote B cell activation and have been identified as susceptibility genes associated with autoimmune diseases. These data demonstrate that early B cell tolerance defects in autoimmunity can result from specific polymorphisms and precede the onset of disease., Introduction Autoimmune diseases affect about 5% of the population and are often characterized by the production of autoantibodies directed against self-antigens (1). An important role for B cells in autoimmune [...]

Chronic kidney disease (CKD) results from a wide array of processes that impair the kidney's ability to perform its major functions. As many as 20 million Americans suffer from CKD and nearly a half million from end-stage renal disease, but there are also examples of centenarians with adequate renal function. Family-based and genome-wide studies suggest that genetic differences substantially influence an individual's lifetime risk for kidney disease. One emerging theme is that evolution of genes related to host defense against pathogens may limit kidney longevity. The identification of these genetic factors will be critical for expanding our understanding of renal development and function as well as for the design of novel therapeutics for kidney disease., Introduction Natural selection determines which genes are successfully transmitted to future generations, but the dramatic increase in the human lifespan over the past century has presented an unexpected challenge to [...]

Pseudomonas aeruginosa has long been known to produce phenotypic variants during chronic mucosal surface infections. These variants are thought to be generated to ensure bacterial survival against the diverse challenges in the mucosal environment. Studies have begun to elucidate the mechanisms by which these variants emerge in vitro; however, too little information exists on phenotypic variation in vivo to draw any links between variants generated in vitro and in vivo. Consequently, in this study, the P. aeruginosa gacS gene, which has previously been linked to the generation of small colony variants (SCVs) in vitro, was studied in an in vivo mucosal surface infection model. More specifically, the rat prostate served as a model mucosal surface to test for the appearance of SCVs in vivo following infections with P. aeruginosa [gacS.sup.-] strains. As in in vitro studies, deletion of the gacS gene led to SCV production in vivo. The appearance of these in vivo SCVs was important for the sustainability of a chronic infection. In the subset of rats in which P. aeruginosa [gacS.sup.-] did not convert to SCVs, clearance of the bacteria took place and healing of the tissue ensued. When comparing the SCVs that arose at the mucosal surface (MS-SCVs) with in vitro SCVs (IV-SCVs) from the same [gacS.sup.-] parent, some differences between the phenotypic variants were observed. Whereas both MS-SCVs and IV-SCVs formed dense biofilms, MS-SCVs exhibited a less diverse resistance profile to antimicrobial agents than IV-SCVs. Additionally, MS-SCVs were better suited to initiate an infection in the rat model than IV-SCVs. Together, these observations suggest that phenotypic variation in vivo can be important for maintenance of infection, and that in vivo variants may differ from in vitro variants generated from the same genetic parent. DOI 10.1099/mic.0.040824-0

The molecular diversity of a novel Neisseria meningitidis antigen, encoded by the ORF NMB0088 of MC58 (FadL-like protein), was assessed in a panel of 64 diverse meningococcal strains. The panel consisted of strains belonging to different serogroups, serotypes, serosubtypes and MLST sequence types, of different clinical sources, years and countries of isolation. Based on the sequence variability of the protein, the FadL-like protein has been divided into four variant groups in this species. Antigen variants were associated with specific serogroups and MLST clonal complexes. Maximum-likelihood analyses were used to determine the relationships among sequences and to compare the selection pressures acting on the encoded protein. Furthermore, a model of population genetics and molecular evolution was used to detect natural selection in DNA sequences using the non-synonymous : synonymous substitution ([d.sub.N] : [d.sub.S]) ratio. The meningococcal sequences were also compared with those of the related surface protein in non-pathogenic commensal Neisseria species to investigate potential horizontal gene transfer. The N. meningitidis fadL gene was subject to only weak positive selection pressure and was less diverse than meningococcal major outer-membrane proteins. The majority of the variability in fadL was due to recombination among existing alleles from the same or related species that resulted in a discrete mosaic structure in the meningococcal population. In general, the population structuring observed based on the FadL-like membrane protein indicates that it is under intermediate immune selection. However, the emergence of a new subvariant within the hyperinvasive lineages demonstrates the phenotypic adaptability of N. meningitidis, probably in response to selective pressure. DOI 10.1099/mic.0.043182-0