Porcine Single Nucleotide Polymorphism (SNP) Development and Population Structure of Pigs Assessed by Validated SNPs

In this study, we identified porcine single nucleotide polymorphisms (SNPs) by aligning eight sequences generated with two approaches: amplification of 665 intronic regions using one sample from each of eight breeds, including three East Asian pigs, and amplification of 289 3'-UTR regions using two samples from each of four major commercial breeds. The 1,760 and 599 SNPs were validated using two 384-sample DNA panels by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The phylogenetic tree and Structure analyses classified the pigs into two large clusters: Euro-American and East Asian populations. The membership proportions, however, differed between inferred clusters for K = 2 generated by the two approaches. With intronic SNPs, Euro-American breeds constituted about 100% of the Euro-American cluster, but with 3'-UTR SNPs, about 17% of the East Asian cluster comprised five Euro-American breeds. The differences in the SNP discovery panels may affect population structure found in study panels of large samples.     

Temporal Changes in Population Structure of a Marine Planktonic Diatom

A prevailing question in phytoplankton research addresses changes of genetic diversity in the face of huge population sizes and apparently unlimited dispersal capabilities. We investigated population genetic structure of the pennate planktonic marine diatom Pseudo-nitzschia multistriata at the LTER station MareChiara in the Gulf of Naples (Italy) over four consecutive years and explored possible changes over seasons and from year to year. A total of 525 strains were genotyped using seven microsatellite markers, for a genotypic diversity of 75.05%, comparable to that found in other Pseudo-nitzschia species. Evidence from Bayesian clustering analysis (BA) identified two genetically distinct clusters, here interpreted as populations, and several strains that could not be assigned with ≥90% probability to either population, here interpreted as putative hybrids. Principal Component Analysis (PCA) recovered these two clusters in distinct clouds with most of the putative hybrids located in-between. Relative proportions of the two populations and the putative hybrids remained similar within years, but changed radically between 2008 and 2009 and between 2010 and 2011, when the 2008-population apparently became the dominant one again. Strains from the two populations are inter-fertile, and so is their offspring. Inclusion of genotypes of parental strains and their offspring shows that the majority of the latter could not be assigned to any of the two parental populations. Therefore, field strains classified by BA as the putative hybrids could be biological hybrids. We hypothesize that P. multistriata population dynamics in the Gulf of Naples follows a meta-population-like model, including establishment of populations by cell inocula at the beginning of each growth season and remixing and dispersal governed by moving and mildly turbulent water masses.     

Exogamy and Change in the Biosocial Structure of a Modern Urban Population

Change is traced in the biosocial structure of the Japanese American population of Seattle-King County, Washington, from that of a deme to a state approaching panmixis with surrounding American populations. Data from 2,767 marriage license applications of Japanese Americans between 1930 and 1975 were used to calculate rates of racial exogamy. Rates rose from prewar levels of less than 1% to over 50% in 1975. The total Japanese American county population was subdivided into a nuclear group, tracing its origins back to the original founding immigrants, and a nonnuclear group which has migrated into the area since World War II. Until 1965, the nonnuclear group consistently led the nuclear group in exogamous marriages. In both groups, females consistently out-married more frequently than did the males. Further analysis of community exogamy, i.e., nuclear member marriage to a nonnuclear Japanese American, showed that this type of exogamy within the second generation preceded the high rates of racial exogamy characterizing the marriage patterns of the third generation. Familial analysis suggested that the maternal kin ties of nuclear population females continue to influence marriage choice of their offspring. The patterns of increasing racial exogamy for Japanese Americans are examined against their rise in socioeconomic status, [biosocial structure, exogamy, population]     

Structure of S. aureus HPPK and the discovery of a new substrate site inhibitor

The first structural and biophysical data on the folate biosynthesis pathway enzyme and drug target, 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (SaHPPK), from the pathogen Staphylococcus aureus is presented. HPPK is the second essential enzyme in the pathway catalysing the pyrophosphoryl transfer from cofactor (ATP) to the substrate (6-hydroxymethyl-7,8-dihydropterin, HMDP). In-silico screening identified 8-mercaptoguanine which was shown to bind with an equilibrium dissociation constant, K_d, of ∼13 µM as measured by isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR). An IC₅₀ of ∼41 µM was determined by means of a luminescent kinase assay. In contrast to the biological substrate, the inhibitor has no requirement for magnesium or the ATP cofactor for competitive binding to the substrate site. The 1.65 Å resolution crystal structure of the inhibited complex showed that it binds in the pterin site and shares many of the key intermolecular interactions of the substrate. Chemical shift and ¹⁵N heteronuclear NMR measurements reveal that the fast motion of the pterin-binding loop (L2) is partially dampened in the SaHPPK/HMDP/α,β-methylene adenosine 5′-triphosphate (AMPCPP) ternary complex, but the ATP loop (L3) remains mobile on the µs-ms timescale. In contrast, for the SaHPPK/8-mercaptoguanine/AMPCPP ternary complex, the loop L2 becomes rigid on the fast timescale and the L3 loop also becomes more ordered – an observation that correlates with the large entropic penalty associated with inhibitor binding as revealed by ITC. NMR data, including ¹⁵N-¹H residual dipolar coupling measurements, indicate that the sulfur atom in the inhibitor is important for stabilizing and restricting important motions of the L2 and L3 catalytic loops in the inhibited ternary complex. This work describes a comprehensive analysis of a new HPPK inhibitor, and may provide a foundation for the development of novel antimicrobials targeting the folate biosynthetic pathway.     

云龙县灵长类种群时空动态变化

灵长类动物是世界上较濒危的动物类群之一,掌握灵长类的分布及其数量的动态变化,为保护行动的有效开展提供了必要的基础资料。通过改良的社区访问调查,首次对滇西北云龙县境内集中分布的6种灵长类动物(黑白仰鼻猴Rhinopithecus bieti、菲氏叶猴Presbytis phayrei、红面短尾猴Macaca arctoides、普通猕猴M.mulatta、熊猴M.assamensis和藏猕猴M.thibetana)从20世纪50年代至今的分布和数量进行了调查,共访查了11个乡镇240个自然村,获得968条有效信息。结果表明,云龙县灵长类基本呈斑块状、非连续性分布,其生境被澜沧江、沘江等河流和村落、交通网络分割。从20世纪50年代至今,6种灵长类共消失了62个种群约3 720只个体,种群数量下降率为60%~90%。综合分析云龙县各灵长类物种消失的时间、空间格局,发现1980—1990年代是灵长类动物种群消失最多且最快的时期,而各乡镇灵长类物种的消失斑块数与当地人口增长率呈显著正相关,人类大面积砍伐森林和捕猎导致了云龙县灵长类种群的快速消失。生境保护,尤其是对现存成熟森林的保护,将对云龙县现有灵长类动物的保护起到决定性的作用。     

Clock Polymorphisms and Circadian Rhythms Phenotypes in a Sample of the Brazilian Population

A Clock polymorphism T to C situated in the 3′ untranslated region (3′‐UTR) has been associated with human diurnal preference. At first, Clock 3111C had been reported as a marker for evening preference. However these data are controversial, and data both corroborating and denying them have been reported. This study hypothesizes that differences in Clock genotypes could be observed if extreme morning‐type subjects were compared with extreme evening‐type subjects, and the T3111C and T257G polymorphisms were studied. The possible relationship between both polymorphisms and delayed sleep phase syndrome (DSPS) was also investigated. An interesting and almost complete linkage disequilibrium between the polymorphisms T257G in the 5′ UTR region and the T3111C in the 3′ UTR region of the Clock gene is described. Almost always, a G in position 257 corresponds to a C in position 3111, and a T in position 257 corresponds to a T in position 3111. The possibility of an interaction of these two regions in the Clock messenger RNA structure that could affect gene expression was analyzed using computer software. The analyses did not reveal an interaction between those two regions, and it is unlikely that this full allele correspondence affects Clock gene expression. These results show that there is no association between either polymorphism T3111C or T257G in the Clock gene with diurnal preference or delayed sleep phase syndrome (DSPS). These controversial data could result from the possible effects of latitude and clock genes interaction on circadian phenotypes.     

Population Responses to Environmental Change in a Tropical Ant: The Interaction of Spatial and Temporal Dynamics

Spatial structure can have a profound, but often underappreciated, effect on the temporal dynamics of ecosystems. Here we report on a counterintuitive increase in the population of a tree-nesting ant, Azteca sericeasur, in response to a drastic reduction in the number of potential nesting sites. This surprising result is comprehensible when viewed in the context of the self-organized spatial dynamics of the ants and their effect on the ants’ dispersal-limited natural enemies. Approximately 30% of the trees in the study site, a coffee agroecosystem in southern Mexico, were pruned or felled over a two-year period, and yet the abundance of the ant nests more than doubled over the seven-year study. Throughout the transition, the spatial distribution of the ants maintained a power-law distribution – a signal of spatial self organization – but the local clustering of the nests was reduced post-pruning. A cellular automata model incorporating the changed spatial structure of the ants and the resulting partial escape from antagonists reproduced the observed increase in abundance, highlighting how self-organized spatial dynamics can profoundly influence the responses of ecosystems to perturbations.     

Prevalence of Metabolically Discordant Phenotypes in a Mediterranean Population—the Imap Study

ObjectiveTo study the prevalence and correlates of body size phenotypes in an adult Spanish population.MethodsWe undertook a cross-sectional analysis in a random sample of 2,270 individuals. We defined six body size phenotypes based on body mass index category (normal-weight, 18.5 to 24.9 kg/m²; overweight, 25 to 29.9 kg/m²; obese, ≥30.0 kg/m²) and the presence of ≤1 (meta- bolically healthy) or ≥2 (metabolically abnormal) cardio- metabolic abnormalities: metabolically healthy normal- weight (MHNW), metabolically abnormal normal-weight (MANW), metabolically healthy overweight (MHOW), metabolically abnormal overweight (MAOW), metaboli- cally healthy obese (MHO), and metabolically abnormal obese (MAO). We considered four cardiometabolic abnormalities: systolic and/or diastolic blood pressure ≥130/85 mm Hg, triglycerides ≥150 mg/dL, high-density-lipopro- tein cholesterol levels <40/<50 mg/dL in men/women, and elevated glucose (fasting plasma glucose ≥100 mg/dL or previous diabetes).ResultsSubmitted for publication October 30, 2012 Accepted for publication April 1, 2013From the ¹The prevalence of the MHO, MHOW, and MANW phenotypes was 2.2, 13.9, and 7.9%, respectively. Whereas 9.6% of obese and 32.6% of overweight individuals were metabolically healthy, 21.3% of the normal- weight subjects were metabolically abnormal. A multivariate regression model (adjusted for age, sex, and waist circumference) showed that age >40 years, male sex, and higher waist circumference were independently associated with the metabolically abnormal phenotype MANW, whereas younger age, female sex, and lower waist circumference were independently associated with the metabolically healthy phenotypes.ConclusionThe prevalence of MHO in our population is low and is more common in women and younger people. In contrast, a high proportion of normal-weight individuals (mainly over 40 years of age) in our population show cardiometabolic abnormalities. (Endocr Pract. 2013;19:758-768)     

Genetic Diversity and Temporal Variation in the E. COLI Population of a Human Host

Electrophoretic techniques were employed to study variation in chromosomal genes encoding enzymes and in the distribution of cryptic plasmids in the E. coli population of a human host over an 11-month period. Thirteen of the 15 enzymes studied were polymorphic, and mean genetic diversity per locus was 0.39. Among 550 clones isolated from fecal samples, protein electrophoresis revealed 53 distinct electrophoretic types (ETs). Most ETs appeared on only one or a few days and were considered transients, but two (ET-12 and ET-13) were observed many times over extended periods and represented residents. Complete turnover in the transient ETs in the population occurred in periods of from two weeks to a month. ETs appearing in one month showed no particular genetic similarity to those of the previous month. — All but 4 of the 53 ETs carried one or more "cryptic" plasmids with molecular weights ranging from 1 to 80 megadaltons. With few exceptions, the plasmid composition of each ET was unique. In the course of the 11-month sampling period, there were changes in the plasmid profiles of the resident strains ET-12 and ET-13, and also in the profile of a recurrent strain, ET-2, which was isolated on four days. Modification of the plasmid profile of ET-12 involved the sequential addition of relatively high molecular weight bands. For ET-2 and ET-13, the changes in the plasmid profiles were radical, suggesting invasions of new cell types rather than merely the addition and deletion of plasmids. — The results of this study provide three lines of evidence that recombination plays a minor role in the generation of genetic diversity in the E. coli population of a single host. (1) Several pairs of loci were in strong linkage disequilibrium; compared to a randomly generated array of genotypes, the sample of ETs contained an excess of pairs differing at one or two loci and too many pairs with highly distinctive combinations of electromorphs. (2) In most cases where pairs of ETs differed at a single locus and, therefore, could reasonably have been generated by phage- or plasmid-mobilized gene transfer, the plasmid profiles of the pair members were radically different and/or the potentially transmitted alleles were not present in other ETs in the population. (3) Although ET-12 was abundant, being represented by 252 of the 550 clones sampled, the electrophoretic type most similar to ET-12 different from it at six loci, and ET-12 carried two unique alleles. We conclude that most of the genetic diversity observed in this human host is a consequence of successive invasions of E. coli genotypes.     

Contemporary Land Change Alters Fish Communities in a San Francisco Bay Watershed,California, U.S.A.

Urbanization is one of the leading threats to freshwater biodiversity, and urban regions continue to expand globally. Here we examined the relationship between recent urbanization and shifts in stream fish communities. We sampled fishes at 32 sites in the Alameda Creek Watershed, near San Francisco, California, in 1993–1994 and again in 2009, and we quantified univariate and multivariate changes in fish communities between the sampling periods. Sampling sites were classified into those downstream of a rapidly urbanizing area (“urbanized sites”), and those found in less impacted areas (“low-impacted sites”). We calculated the change from non-urban to urban land cover between 1993 and 2009 at two scales for each site (the total watershed and a 3km buffer zone immediately upstream of each site). Neither the mean relative abundance of native fish nor nonnative species richness changed significantly between the survey periods. However, we observed significant changes in fish community composition (as measured by Bray-Curtis dissimilarity) and a decrease in native species richness between the sampling periods at urbanized sites, but not at low-impacted sites. Moreover, the relative abundance of one native cyprinid (Lavinia symmetricus) decreased at the urbanized sites but not at low-impacted sites. Increased urbanization was associated with changes in the fish community, and this relationship was strongest at the smaller (3km buffer) scale. Our results suggest that ongoing land change alters fish communities and that contemporary resurveys are an important tool for examining how freshwater taxa are responding to recent environmental change.     

Temporal Variation in Genetic Diversity and Structure of a Lotic Population of Burkholderia (Pseudomonas) cepacia

The genetic structure and temporal patterns of genetic diversity in a population of Burkholderia (Pseudomonas) cepacia, isolated from a southeastern blackwater stream, were investigated by multilocus enzyme electrophoresis. Allelic variation in seven structural gene loci was monitored at a single stream location at 0, 6, 12, and 24 h and at 2, 4, 8, 16, and 32 days. Over the length of the study, 217 isolates were collected, from which 65 unique electrophoretic types (ETs) were identified. Most of these ETs were present at only one or two time periods and were considered transients; however, one resident ET was particularly abundant (64 of the 217 isolates [29.4%]) and was found at all time points except day 32. The mean genetic diversity of the entire population was 0.520, and the index of association (a measure of multilocus linkage disequilibrium) was 1.33. These results, taken in conjunction with a previous study focusing on spatial patterns of genetic diversity in lotic B. cepacia, show that these bacterial populations exhibit greater variability among sites than within a site over time, suggesting relative stability over short time periods.     

The Population Genetics of Parthenogenetic Strains of DROSOPHILA MERCATORUM. II. the Capacity for Parthenogenesis in a Natural, Bisexual Population

Drosophila mercatorum is a bisexual species, but certain strains are capable of parthenogenetic reproduction in the laboratory. We investigated the parthenogenetic capacity of the virgin daughters of females captured from a natural, bisexual population in Hawaii. An isozyme survey indicated the natural population is polymorphic at about 50% of its loci, and its individuals heterozygous at 18% of their loci. The predominant mode of parthogenesis in D. mercatorum causes homozygosity for all loci in a single generation. Despite this radical change in genetic state, 23% of the virgin female lines produced adult parthenogenetic progeny, and 16% produced parthenogenetic progeny themselves capable of parthenogenetic reproduction. The parthenogenetic rats as measured by the number of parthenogenetic progeny themselves capable of parthenogenesis divided by the number of eggs laid is arougn 10(-5) for the virgin female lines. We argue that one of the major reasons for this low rate is that very few of the impaternate zygotes have a genotype that can survive and reproduce under the genetic conditions imposed by parthenogenetic reproduction. This intense selective bottleneck can be passed in a single generation if enough unfertilized eggs are laid, and once passed is accompanied by a large (perhaps a thousandfold) increase in the rate of parthenogenesis and by modifications in many phenotypic traits such as morphology and behavior.     

Prevalence and Characterization of Staphylococcus aureus in Growing Pigs in the USA

A decade of research of methicillin-resistant S. aureus (MRSA) in pigs shows that the prevalence and predominant genotypes (i.e., ST398, ST9, ST5) of MRSA vary widely geographically, yet knowledge of the epidemiology of S. aureus generally in swine remains rudimentary. To characterize S. aureus, including MRSA, in the US swine industry, we sampled 38 swine herds in 11 states in major swine producing regions. The herds sampled included pigs sourced from 9 different breeding stock companies, and the sample was likely biased towards larger herds that use regular veterinary services. Twenty nasal swabs were collected from 36 groups of growing pigs by 36 swine veterinarians, 2 more herds were sampled opportunistically, and a historically MRSA-positive herd was included as a positive control. S. aureus was detected on 37 of the 38 herds, and in 77% of pigs sampled. Other than the positive control herd, no MRSA were detected in the study sample, yielding a 95% upper confidence limit of 9.3% for MRSA herd prevalence. All but two (ST1-t127; ST2007-t8314) of 1200 isolates belonged to three MLST lineages (ST9, ST398, and ST5) that have been prominent in studies of MRSA in pigs globally. A total of 35 spa types were detected, with the most prevalent being t337 (ST9), t034 (ST398), and t002 (ST5). A purposively diverse subset of 128 isolates was uniformly negative on PCR testing for major enterotoxin genes. The findings support previous studies suggesting a relatively low herd prevalence of MRSA in the US swine industry, but confirm that methicillin susceptible variants of the most common MRSA genotypes found in swine globally are endemic in the US. The absence of enterotoxin genes suggests that the source of toxigenic S. aureus capable of causing foodborne enterotoxicosis from pork products is most likely post-harvest contamination.     

Expression of the S. aureus hysA gene in S. carnosus from a modified E. coli-staphylococcal shuttle vector

We have modified an E. coli-staphylococcal shuttle vector for use in the general cloning and expression of genes from pathogenic staphylococci in Staphylococcus carnosus. As S. carnosus is non-pathogenic, this expression system will facilitate the study of the roles of individual gene products in the disease process. To evaluate the use of this expression system, a DNA fragment containing the Staphylococcus aureus hyaluronate lyase (hysA) gene was cloned into the modified vector, pNW21, and introduced into S. carnosus. Hyaluronate lyase was both produced and secreted by S. carnosus. In addition, the secreted HysA protein was enzymatically active, as determined using a zymographic assay.     

Identification and Characterization of a Novel Recombinant Porcine Astrovirus from Pigs in Anhui,China

Porcine astroviruses (PAstVs) have wide distribution in swine herds worldwide. At present, five porcine astrovirus genotypes have been identified. In this study, using viral metagenomics, a novel PAstV strain (designated as Ahast) was identified in fecal samples from pigs in Anhui of China, and the complete genomic sequence of Ahast was obtained by assembling and PCR amplification. Genomic structural analysis indicated that Ahast had a typical ribosomal frameshifting signal, and some conserve amino acid motifs were also found in virally encoded proteins. Phylogenetic analysis and sequence comparison indicated that this virus belonged to porcine astrovirus genotype 4 (PAstV4), which formed a clade clustered with other PAstV4. Multiple recombinant events were confirmed by recombination analysis and indicated that Ahast was a potential recombinant. Epidemiological investigation indicated that PAstV4 has a 10.7% prevalence in this pig farm. The new recombinant identified in this study will be beneficial to comprehend the origin, genetic diversity, and evolution of porcine astroviruses in Anhui of China.Key words: porcine astroviruses, viral metagenomics, genome recombination     

Application of Real-Time PCR for Quantification of Microcystin Genotypes in a Population of the Toxic Cyanobacterium Microcystis sp.

The cyanobacterium Microcystis sp. frequently develops water blooms consisting of organisms with different genotypes that either produce or lack the hepatotoxin microcystin. In order to monitor the development of microcystin (mcy) genotypes during the seasonal cycle of the total population, mcy genotypes were quantified by means of real-time PCR in Lake Wannsee (Berlin, Germany) from June 1999 to October 2000. Standard curves were established by relating cell concentrations to the threshold cycle (the PCR cycle number at which the fluorescence passes a set threshold level) determined by the Taq nuclease assay (TNA) for two gene regions, the intergenic spacer region within the phycocyanin (PC) operon to quantify the total population and the mcyB gene, which is indicative of microcystin synthesis. In laboratory batch cultures, the cell numbers inferred from the standard curve by TNA correlated significantly with the microscopically determined cell numbers on a logarithmic scale. The TNA analysis of 10 strains revealed identical amplification efficiencies for both genes. In the field, the proportion of mcy genotypes made up the smaller part of the PC genotypes, ranging from 1 to 38%. The number of mcyB genotypes was one-to-one related to the number of PC genotypes, and parallel relationships between cell numbers estimated via the inverted microscope technique and TNA were found for both genes. It is concluded that the mean proportion of microcystin genotypes is stable from winter to summer and that Microcystis cell numbers could be used to infer the mean proportion of mcy genotypes in Lake Wannsee.