Characterization of polymorphic microsatellite loci for the invasive monk parakeet (Myiopsitta monachus)

Microsatellite loci were characterized for the monk parakeet (Myiopsitta monachus) from a GT_n‐enriched genomic library. Twelve of 14 microsatellite loci were polymorphic, averaging 6.7 alleles per locus across the 20 individuals genotyped. Mean expected heterozygosity was 0.72, with locus‐specific values ranging from 0.53 to 0.90. An equally high multilocus probability of identity (2.48 × 10^?12) was revealed for this set of loci. In addition, all 12 loci were demonstrated to cross‐amplify to varying extents within three additional parrot genera suggesting their potential utility for population‐level studies in a broad range of Neotropical psittacines.     

PERMANENT GENETIC RESOURCES: Eighteen new polymorphic microsatellite markers for the endangered Florida manatee, Trichechus manatus latirostris

Here we describe 18 polymorphic microsatellite loci for Trichechus manatus latirostris (Florida manatee), isolated using a polymerase chain reaction‐based technique. The number of alleles at each locus ranged from two to four (mean = 2.5) in specimens from southwest (n = 58) and northeast (n = 58) Florida. Expected and observed heterozygosities ranged from 0.11 to 0.67 (mean = 0.35) and from 0.02 to 0.78 (mean = 0.34), respectively. Departures from Hardy–Weinberg equilibrium occurred at two loci. There was no evidence of genotypic disequilibrium for any pair of loci. For individual identification, mean random‐mating and θ‐corrected match probabilities were 9.36 × 10^?7 and 1.95 × 10^?6, respectively.     

Characterization of new microsatellite loci in Pieris amamioshimensis (Ericaceae), a species nearly extinct in the wild

A set of 11 polymorphic microsatellite markers has been developed and characterized for the critically endangered species Pieris amamioshimensis. Fifty‐nine individuals of an ex‐situ population were used to identify these markers. The total number of alleles for each locus ranged from 3 to 9, with an average of 5.4. The expected heterozygosities (H_S) and observed heterozygosities (H_O) ranged from 0.47 to 0.77 and 0.22 to 0.88, respectively. In total, four loci exhibited significant deviations from Hardy–Weinberg equilibrium: two loci showed significant heterozygosity excess and the other two loci showed significant heterozygosity deficit. The polymorphism information content (0.43 ≤ PIC ≤ 0.73), the probability of exclusions (PE₁ = 0.9565, PE₂ = 0.9969 and PE₃ = 0.9999) and probabilities for identity (PI = 3.78 × 10^?9 and PI‐Sib = 2.35 × 10^?4) suggest that these markers are useful for estimating not only genetic diversity but also parentage, for the ex‐situ conservation management of populations.     

Catalytic resonance scattering spectral determination of ultratrace horseradish peroxidase using rhodamine S

A highly sensitive and selective resonance scattering spectral assay was proposed for the determination of horseradish peroxidase (HRP), based on its catalytic effect on the H₂O₂ oxidation of KI to form I₃^?. The I₃^? combined respectively with rhodamine (Rh) dye such as rhodamine S (RhS), rhodamine 6G (Rh6G), rhodamine B (RhB) and butyl‐rhodamine B (b‐RhB), to form association particles (Rh‐I₃)_n. The four Rh systems all exhibit a stronger resonance scattering (RS) peak at 424 nm. For the RhS, Rh6G, RhB and b‐RhB systems, HRP concentration in the range of 3.2 × 10^?12 to 4.8 × 10^?9, 2 × 10^?11 to 3.2 × 10^?9, 1.6 × 10^?11 to 3.2 × 10^?9 and 1.6 × 10^?11 to 4 × 10^?9 g/mL was linear to its RS intensity at 424 nm, with a detection limit of 2.2 × 10^?12, 2.5 × 10^?12, 4.4 × 10^?12 and 2.6 × 10^?12 g/mL, respectively. This RhS system was most sensitive and stable, and was applied for the determination of HRP in the hepatitis B surface antibody labeling HRP and water samples, with satisfactory results. Copyright © 2009 John Wiley & Sons, Ltd.     

Genome‐wide association study of osteochondrosis in the tarsocrural joint of Dutch Warmblood horses identifies susceptibility loci on chromosomes 3 and 10

Equine osteochondrosis is a developmental joint disease that is a significant source of morbidity affecting multiple breeds of horse. The genetic variants underlying osteochondrosis susceptibility have not been established. Here, we describe the results of a genome‐wide association study of osteochondrosis using 90 cases and 111 controls from a population of Dutch Warmblood horses. We report putative associations between osteochondrosis and loci on chromosome 3 (BIEC2‐808543; P = 5.03 × 10^?7) and chromosome 10 (BIEC2‐121323; P = 2.62 × 10^?7).     

Thirty polymorphic microsatellite loci from the critically endangered kakapo (Strigops habroptilus)

Thirty polymorphic microsatellite loci were developed from the critically endangered kakapo (Strigops habroptilus), using an enriched genomic library. Characterization of loci using 90 kakapo revealed an average of 3.3 alleles per locus (range: 2–5) and an average expected heterozygosity of 0.47 (range: 0.17–0.70). The probability of identity (7.2 × 10^?15) and probability of exclusion (0.999999) demonstrate that these loci are a highly informative marker set that can aid the genetic management of the kakapo.     

Characterization of 26 new microsatellite loci in the dugong (Dugong dugon)

Twenty‐six microsatellite loci have been isolated from a dugong (Dugong dugon). The average heterozygosity was 0.52 with two to 10 alleles per locus surveyed from 50 individuals. The markers are suitable for genetic mark–recapture (P_ID = 5 × 10^?16) in dugongs and they could also be used to quantify physical tag loss, estimate relatedness, assign paternity, elucidate population structure and identify migrants. The loci also amplified in Florida manatees (22/26) and Asian elephants (6/26).     

Towards a gene expression biomarker set for human biological age

We have previously described a statistical model capable of distinguishing young (age <65 years) from old (age ≥75 years) individuals. Here we studied the performance of a modified model in three populations and determined whether individuals predicted to be biologically younger than their chronological age had biochemical and functional measures consistent with a younger biological age. Those with ‘younger’ gene expression patterns demonstrated higher muscle strength and serum albumin, and lower interleukin‐6 and blood urea concentrations relative to ‘biologically older’ individuals (odds ratios 2.09, 1.64, 0.74, 0.74; P = 2.4 × 10^?2, 3.5 × 10^?4, 1.8 × 10^?2, 1.5 × 10^?2, respectively). We conclude that our expression signature of age is robust across three populations and may have utility for estimation of biological age.     

Development and characterization of microsatellite markers for the tropical tree species Tabebuia aurea (Bignoniaceae)

In this study, we report the development and characterization of 21 polymorphic microsatellite loci for Tabebuia aurea, using genomic library enrichment. Number of alleles per locus and expected heterozygosity ranged from nine to 26 and from 0.808 to 0.955. The high combined probability of genetic identity (1.03 × 10^?37) and probability of paternity exclusion (0.9889) showed that multilocus genotypes are likely to be unique and will allow detailed parentage studies in natural populations of T. aurea. Additionally, a high percentage of transferability was achieved for the four species of the same genus studied.     

Uncoupling associations of risk alleles with endophenotypes and phenotypes: insights from the ApoB locus and heart‐related traits

Traditionally, genomewide association studies (GWAS) have emphasized the benefits of large samples in the analyses of age‐related traits rather than their specific properties. We adopted a realistic concept of genetic susceptibility to inherently heterogeneous, age‐related traits driven by the elusive role of evolution in their properties. We analyzed in detail the associations of rs693 and rs562338 polymorphisms representing the Apolipoprotein B locus with endophenotypes (total cholesterol [TC] and high‐density lipoprotein cholesterol) and phenotypes (myocardial infarction [MI] and survival) in four large‐scale studies, which include 20 748 individuals with 2357 MI events. We showed that a strong, robust predisposition of rs693 and rs562338 to TC (β = 0.72, P = 7.7 × 10^?30 for rs693 and β = ?1.08, P = 9.8 × 10^?42 for rs562338) is not translated into a predisposition to MI and survival. The rs693_A allele influences risks of MI and mortality after MI additively with lipids. This allele shows antagonistic effects—protecting against MI risks (β = ?0.18, P = 1.1 × 10^?5) or increasing MI risks (β = 0.15, P = 2.8 × 10^?3) and mortality after MI, in different populations. Paradoxically, increased TC concentrations can be protective against MI for the rs693_A allele carriers. Our results uncouple the influences of the same alleles on endophenotypes and phenotypes despite potential causal relationships among the latter. Our strategy reveals virtually genomewide significance for the associations of rs693 with MI (P = 5.5 × 10^?8) that is contrasted with a weak estimate following the traditional, sample‐size‐centered GWAS strategy (P = 0.16) in the same sample. These results caution against the use of the traditional GWAS strategy for gaining profound insights into genetic predisposition to healthspan and lifespan.     

Genetic variation in Sri Lankan leopards

Electrophoretic variation of 50 gene-enzyme systems was typed in a population of 33 captive leopards (Panthera pardus) from the island of Sri Lanka. The captive leopard population was composed of several lineages: (1) wild-caught leopards of the island subspecies (P. p. kotiya), (2) captive-born animals of the same subspecies, (3) a melanistic lineage whose founders were obtained from Malaysia (P. p. delacouri), and (4) leopards of known mixed lineage and unknown status. Two loci, APRT and PGD, were polymorphic in all samples, whereas 48 loci were invariant. Percent polymorphism (P) and percent average heterozygosity (H) were calculated as 4% and 1.4%, respectively, for the wild-caught leopards; 4% and 1.2% for the captive-born kotiya leopards; and 4% and 2.0% for the melanistic lineage. The overall results revealed a detectable decrease in genetic variability compared with a previous study of captive leopards from mainland origins. The mainland leopards had three additional polymorphic loci, ADA, ESI, and HBB. Reexamination of the TF locus using a revised protocol resolved a new allele in the sample of mainland leopards but not in the Sri Lankan sample. With this new polymorphism, recalculated P and H values for the mainland sample are 10% and 3.1%, respectively. No significant differences in polymorphic loci were observed between the leopard subspecies examined.     

Effects of human chorionic gonadotropin (hCG) and handling stress on spermiation of silver perch Leiopotherapon plumbeus (Kner, 1864)

This study determined the effect of human chorionic gonadotropin (hCG) and handling stress on the spermiation and milt response of silver perch Leiopotherapon plumbeus based on the measurement of spermatocrit, sperm density, and milt production. Compared to saline‐injected fish, the mean spermatocrit (or packed sperm) of hCG‐treated fish was significantly lower at 18 h (47.9%) and 30 h (40.2%) post‐injection while mean sperm density was significantly lower at 30 h post‐injection (3.6 × 10⁶ cells μl^?1) but not at 18 h. At 18 h (1.8 μl g‐BW^?1) and 30 h (2.5 μl g‐BW^?1) post‐injection, mean milt production of hCG‐treated fish was significantly higher than in the saline group. Milt consistency was also thinner in the hCG‐treated group. Mean sperm density of handled fish (18.0 × 10⁶ cells μl^?1) was significantly lower than control fish (23.4 × 10⁶ cells μl^?1). However, mean sperm density of handled plus saline‐injected (16.2 × 10⁶ cells μl^?1) and handled plus hCG‐treated fish (8.4 × 10⁶ cells μl^?1) was significantly lower than in the control goup. Having thicker milt consistency, mean spermatocrit and milt production of handled (77.5%; 1.1 μl g‐BW^?1, respectively) and handled plus saline‐injected fish (75.4%; 1.1 μl g‐BW^?1, respectively) were not significantly different from the control fish (76.2%; 1.3 μl g‐BW^?1, respectively). Handled plus hCG‐treated fish had the lowest mean sperm density (8.4 × 10⁶ cells μl^?1) and spermatocrit (54.7%), but had the highest mean milt production (5.5 μl g‐BW^?1) among the treatment groups. These results demonstrate that the hCG injection effectively induces spermiation and milt expression and that handling‐related stress negatively affects such responses. The spermatocrit method may be used to assess the spermiation and milt response of silver perch.     

New luminol chemiluminescence reaction using diperiodatoargentate as oxidate for the determination of amikacin sulfate

A new chemiluminescence (CL) reaction between luminol and diperiodatoargentate {K₂ [Ag (H₂IO₆) (OH) ₂]} was observed in alkaline medium. The CL intensity could be greatly enhanced by amikacin sulfate. Therefore a new CL method for the determination of amikacin sulfate was built by combining with flow injection technology. A possible mechanism of the CL reaction was proposed via the investigation of the CL kinetic characteristics, the CL spectrum and the UV absorption spectra of some related substance. The concentration range of linear response was 5.1 × 10^?8 to 5.1 × 10^?6 mol L^?1 with a detection limit of 1.9 × 10^?8 mol L^?1 (3σ). The proposed method had good reproducibility with a relative standard deviation of 2.8% (n = 7) for 5.1 × 10^?7 mol L^?1 of amikacin sulfate. It was successfully applied to determine amikacin sulfate in serum. Copyright © 2009 John Wiley & Sons, Ltd.     

The DYX2 locus and neurochemical signaling genes contribute to speech sound disorder and related neurocognitive domains

A major milestone of child development is the acquisition and use of speech and language. Communication disorders, including speech sound disorder (SSD), can impair a child's academic, social and behavioral development. Speech sound disorder is a complex, polygenic trait with a substantial genetic component. However, specific genes that contribute to SSD remain largely unknown. To identify associated genes, we assessed the association of the DYX2 dyslexia risk locus and markers in neurochemical signaling genes (e.g., nicotinic and dopaminergic) with SSD and related endophenotypes. We first performed separate primary associations in two independent samples – Cleveland SSD (210 affected and 257 unaffected individuals in 127 families) and Denver SSD (113 affected individuals and 106 unaffected individuals in 85 families) – and then combined results by meta‐analysis. DYX2 markers, specifically those in the 3′ untranslated region of DCDC2 (P = 1.43 × 10^?4), showed the strongest associations with phonological awareness. We also observed suggestive associations of dopaminergic‐related genes ANKK1 (P = 1.02 × 10^?2) and DRD2 (P = 9.22 × 10^?3) and nicotinic‐related genes CHRNA3 (P = 2.51 × 10^?3) and BDNF (P = 8.14 × 10^?3) with case–control status and articulation. Our results further implicate variation in putative regulatory regions in the DYX2 locus, particularly in DCDC2, influencing language and cognitive traits. The results also support previous studies implicating variation in dopaminergic and nicotinic neural signaling influencing human communication and cognitive development. Our findings expand the literature showing genetic factors (e.g., DYX2) contributing to multiple related, yet distinct neurocognitive domains (e.g., dyslexia, language impairment, and SSD). How these factors interactively yield different neurocognitive and language‐related outcomes remains to be elucidated.     

Evaluation of the causality of the low‐density lipoprotein receptor gene (LDLR) for serum lipids in pigs

A significant quantitative trait locus (QTL) for low‐density lipoprotein cholesterol (LDL‐C) and total cholesterol (TC) was identified around the LDLR gene on chromosome 2 (SSC2) in a White Duroc × Erhualian F₂ resource population and Sutai pigs in our previous study. However, in previous reports, the causality of LDLR with serum lipids is controversial in pigs. To systematically assess the causality of LDLR with serum lipids, association analyses were successively performed in three populations: Sutai pigs, a White Duroc × Erhualian F₂ resource population and a Duroc × (Landrace × Large White) population. We first performed a haplotype‐based association study with 60K SNP genotyping data and evidenced the significant association with LDL‐C and TC around the LDLR gene region. We also found that there is more than one QTL for LDL‐C and TC on SSC2. Then, we evaluated the causalities of two missense mutations, c.1812C>T and c.1520A>G, with LDL‐C and TC. We revealed that the c.1812C>T SNP showed the strongest association with LDL‐C (P = 5.40 × 10^?11) and TC (P = 3.64 × 10^?8) and explained all the QTL effect in Sutai pigs. Haplotype analysis found that two missense SNPs locate within a 1.93‐Mb haplotype block. One major haplotype showed the strongest significant association with LDL‐C (P = 4.62 × 10^?18) and TC (P = 1.06 × 10^?9). However, the c.1812C>T SNP was not identified in the White Duroc × Erhualian intercross, and the association of c.1520A>G with both LDL‐C and TC did not achieve significance in this F₂ population, suggesting population heterogeneity. Both missense mutations were identified in the Duroc × (Landrace × Large White) population and showed significant associations with LDL‐C and TC. Our data give evidence that the LDLR gene should be a candidate causative gene for LDL‐C and TC in pigs, but heterogeneity exists in different populations.     

Methylation of SOCS3 is inversely associated with metabolic syndrome in an epigenome-wide association study of obesity

Epigenetic mechanisms, including DNA methylation, mediate the interaction between gene and environment and may play an important role in the obesity epidemic. We assessed the relationship between DNA methylation and obesity in peripheral blood mononuclear cells (PBMCs) at 485,000 CpG sites across the genome in family members (8-90 y of age) using a discovery cohort (192 individuals) and a validation cohort (1,052 individuals) of Northern European ancestry. After Bonferroni-correction (P_α=0.05 = 1.31 × 10^?7) for genome-wide significance, we identified 3 loci, cg18181703 (SOCS3), cg04502490 (ZNF771), and cg02988947 (LIMD2), where methylation status was associated with body mass index percentile (BMI%), a clinical index for obesity in children, adolescents, and adults. These sites were also associated with multiple metabolic syndrome (MetS) traits, including central obesity, fat depots, insulin responsiveness, and plasma lipids. The SOCS3 methylation locus was also associated with the clinical definition of MetS. In the validation cohort, SOCS3 methylation status was found to be inversely associated with BMI% (P = 1.75 × 10^?6), waist to height ratio (P = 4.18 × 10^?7), triglycerides (P = 4.01 × 10^?4), and MetS (P = 4.01 × 10^?7), and positively correlated with HDL-c (P = 4.57 × 10^?8). Functional analysis in a sub cohort (333 individuals) demonstrated SOCS3 methylation and gene expression in PBMCs were inversely correlated (P = 2.93 × 10^?4) and expression of SOCS3 was positively correlated with status of MetS (P = 0.012). We conclude that epigenetic modulation of SOCS3, a gene involved in leptin and insulin signaling, may play an important role in obesity and MetS.     

Characterization of 11 polymorphic tetranucleotide microsatellites for forensic applications in California elk (Cervus elaphus canadensis)

Eleven polymorphic tetranucleotide microsatellite loci have been developed for forensic use in the protection of California elk. Based on a reference sample of elk taken from three races throughout California, the loci consist of 4–9 alleles (average 6.125). Probabilities of identity ( Paetkau et al. 1995 ) range from 0.079 to 0.288, with an overall probability of identity of 1.3 × 10^?9 (one in 7.8 × 10⁸).     

Three‐dimensional (3‐D) fluorescence spectroscopy analysis of the fluorescent dissolved organic matter released by the marine toxic dinoflagellate Alexandrium catenella exposed to metal stress by zinc or lead

We investigated the effects of zinc or lead on growth and on exudation of fluorescent dissolved organic matter (FDOM) by the marine toxic dinoflagellate Alexandrium catenella (Whedon & Kofoid) Balech. The species was exposed to increasing free zinc (1.34 × 10^?7 M–3.98 × 10^?6 M) or lead (5.13 × 10^?9 M–1.82 × 10^?7 M) concentra‐tions. Low metal levels ([Zn²⁺] = 1.34 × 10^?7 M; [Pb²⁺] = 5.13 × 10^?9 M) had no effect on cell growth. Toxic effects were observed from higher metal contamination ([Zn²⁺] = 3.98 × 10^?6 M; [Pb²⁺] = 6.54 × 10^?8 M), as a conversion of vegetative cells into cysts. Analysis of the released FDOM by three‐dimensional (3‐D) fluorescence spectroscopy was achieved, using the parallel factor analysis (PARAFAC). The PARAFAC modeling revealed four components associated with two contributions: one related to the biological activity; the other linked to the organic matter decomposition in the culture medium. The C1 component combined a tryptophan peak and characteristics of humic substances, whereas the C2 component was considered as a tryptophan protein fluorophore. The two others C3 and C4 components were associated with marine organic matter production. Relea‐sed fluorescent substances were induced by low ([Zn²⁺]= 1.34 × 10^?7 M; [Pb²⁺] = 5.13 × 10^?9 M) and moderate ([Zn²⁺] = 6.21 × 10^?7 M; [Pb²⁺] = 2.64× 10^?9 M) metal concentrations, suggesting the activation of cellular mechanisms in response to metal stress, to exudate FDOM that could complex metal cations and reduce their toxicity toward A. catenella cells.     

Highly selective determination of phenolphthalein by flow injection chemiluminescence method based on a molecular imprinting polymer

The phenolphthalein‐imprinted polymer was prepared with methacrylic acid as functional monomer and ethylene glycol dimethacrylate as cross‐linker. Taking advantage of the quenching effect of phenolphthalein on the potassium permanganate–HCl–anhydrous alcohol chemiluminescence system, a new model was established to determine phenolphthalein by a highly selective flow injection chemiluminescence method. The traditional flow‐though cell was replaced with a novel flow path using a Y‐shaped polymethyl methacrylate column, through which the three reactants were injected simultaneously. The linear range of this assay was from 1.0 × 10^?8 to 1.0 × 10^?6 g/mL (r = 0.9978). The limit of detection was 8.9 × 10^?9 g/mL. The relative standard deviation for the determination of 1.0 × 10^?8 g/mL phenolphthalein solution was below 2.9% (n = 11). The proposed method was applied to the determination of phenolphthalein in real samples with satisfactory results. Copyright © 2009 John Wiley & Sons, Ltd.     

Isolation and characterization of ten novel microsatellite loci in the red-winged tinamou (<Emphasis Type="Italic">Rhynchotus rufescens</Emphasis>, Tinamiformes,Aves) and cross-amplification in other tinamous

We describe the isolation and characterization of ten microsatellite loci from the red-winged tinamou (Rhynchotus rufescens) and also evaluated the cross-amplification of these loci and other ten loci previously developed for the great tinamou (Tinamus major) in other tinamous. Genetic variability was assessed using 24 individuals. Six loci were polymorphic with moderate to high number of alleles per locus (2–12 alleles) and showed expected heterozygosity (HE) ranging from 0.267 to 0.860. All loci conformed to the Hardy–Weinberg expectation and linkage disequilibrium was not significant for any pair of loci. This battery of polymorphic loci showed high paternity exclusion probability (0.986) and low genetic identity probability (4.95 × 10⁻⁵), proving to be helpful for parentage tests and population analyses in the red-winged tinamou. The cross-amplification was moderate where of the 160 locus/taxon combinations, 46 (28.75%) successfully amplified.