Isolation, characterisation and cross amplification of thirteen microsatellite loci for coral endo-symbiotic dinoflagellates (Symbiodinium clade C)

The health and productivity of coral reefs is underpinned by the symbiosis between corals and dinoflagellates (Symbiodinium spp.). To enable population genetic analyses of Symbiodinium spp, required for coral reef conservation, seven microsatellite loci were isolated from Symbiodinium clade C from the Great Barrier Reef, Australia. These microsatellite primer pairs consistently amplified between 1 and 8 alleles per coral host colony, with mean number of alleles ranging from 1.9 to 4.0 and generally high genetic diversities (Shannon’s Index = 0.71–2.76). The novel microsatellite loci amplified between 1 and 10 alleles in four other C strains, but did not amplify a D strain. Three of six previously published clade C microsatellite loci amplified 1–6 alleles in two or more of five C strains tested. The primers and cross amplifications presented here therefore provide a useful tool for elucidating the population genetic structure of clade C Symbiodinium populations.     

Microsatellite loci for Symbiodinium A3 (S. fitti) a common algal symbiont among Caribbean Acropora (stony corals) and Indo-Pacific giant clams (Tridacna)

We developed ten polymorphic microsatellite loci for S. fitti (type A3), and tested their utility on a Caribbean population associated with the coral Acropora palmata and an Indo-Pacific population harbored by the giant clam Tridacna maxima. Our analyses identified from 3 to 8 alleles for each haploid locus. Diversity (R) indices were 0.48 for the Indo-Pacific and 0.81 for the Caribbean. Greater than 95% of the samples possessed a single, symbiont, multilocus genotype (MLG). Among their many uses for the study of coral-algal symbioses, population genetic markers provide insight on the potential for symbiont dispersal, can be used to assess symbiont population stability/longevity in hospite, and partition symbiont diversity into reproductively isolated operational taxonomic units (i.e. species).     

Microsatellite loci for the plate-and-pillar coral, Porities rus.

Little is known about species and population-level genetic relatedness for many reef building corals, despite their critical importance as the foundation of coral reef ecosystems. We report the isolation and characterization of seven polymorphic microsatellites from the plate-and-pillar coral, Porites rus. Across all loci, there was a maximum of 18 alleles for the 37 individuals tested. We also tested these primers on 12 other species of Porites. At least one locus amplified in most of the species. These markers should be useful in various genetic applications involving Porities spp.     

Microsatellite loci development for rare Colorado Sclerocactus (Cactaceae)

The genus Sclerocactus (Cactaceae) consists of 15 species, which have a confused taxonomic history due to morphological similarities and distribution overlap. Habitat loss and hybridization are of concern and have established cause for genetic investigations to further understand the genus and develop conservation strategies. Thirteen variable microsatellite loci were identified using S. glaucus and S. parviflorus and were tested in three additional species: S. wetlandicus, S. brevispinus and S. cloverii. The mean number of alleles per locus ranged from 2 to 11, with an average of 6.6. The observed and expected mean heterozygosity ranged from 0.00 to 0.90 and 0.26 to 0.90, respectively. These loci will aid in determining levels of hybridization, diversity and taxonomy of Sclerocactus.     

Microsatellite loci for the endangered growling grass frog (Litoria raniformis), with cross amplification in other Australian frog species

The growling grass frog, Litoria raniformis, was once abundant in south-eastern Australia but has suffered severe declines over the past 20 years. Here we describe nine polymorphic microsatellite loci for L. raniformis. Genetic variation was assessed in 59 individuals from Somerton, Victoria in south-eastern Australia. The number of alleles per locus ranged from three to 16. Cross amplification was assessed in ten other Australian hylid frogs. These microsatellite markers will be used to investigate impacts of urbanization on dispersal and gene flow in L. raniformis.     

Microsatellite loci for studies of the common cuttlefish,Sepia officinalis

The common cuttlefish, Sepia officinalis, represents a model mobile marine species for studies of evolutionary processes occurring across a range of spatial and temporal scales. Such studies are relevant to sustainable fishery management and biodiversity conservation as the species is intensely exploited and an important component of inshore marine ecosystems. The isolation and preliminary characterisation of 10 dinucleotide repeat microsatellite loci is described. Genotyping of 48 adults from Agon Coutainville (France) revealed polymorphism at 9 of the loci. Among the polymorphic loci there was an average of 8.8 alleles per locus (range 3–14) with observed and expected heterozygosity per locus ranging from 0.104 to 0.792 and from 0.101 to 0.806, respectively. No evidence of linkage disequilibrium was detected between any locus pair. The loci described here represent a valuable addition to the suite of genetic markers applicable to S. officinalis research.     

Microsatellite loci for genetic analysis of the arctic gadids Boreogadus saida and Arctogadus glacialis

We report sets of 19 and 16 microsatellite loci for the examination of the population genetics of Boreogadus saida and Arctogadus glacialis, respectively. Six of these loci were developed from a collection of 9,497 expressed sequences from B. saida while the remaining loci were found in the literature and optimized for use in B. saida and A. glacialis. The numbers of alleles observed for each locus ranged from 3 to 33 in B. saida and 1–22 in A. glacialis. Observed heterozygosities ranged from 0.02 to 0.93 in B. saida and 0.17–1.0 in A. glacialis. Species specific differences were observed for the loci providing new tools for the identification of these two morphologically similar arctic gadids. The loci presented here can be used to distinguish between the two species and fill fundamental biological knowledge gaps, thus promoting conservation of these important fishes.     

Microsatellite loci for the carpenter bee Xylocopa frontalis (Apidae, Xylocopini)

In the present study, a microsatellite-enriched genomic library was constructed and primers for 14 microsatellite loci were designed for Xylocopa frontalis. Twenty unrelated individuals were screened. All loci were polymorphic and the number of alleles per locus ranged from 6 to 17 (x?=?10.43). Observed (H_o) and expected (H_e) heterozygosities ranged from 0.350 to 0.950 and 0.674 to 0.898, respectively. All loci were in Hardy?CWeinberg equilibrium, except one. The microsatellite loci described in this study will contribute towards general biology studies of X. frontalis, intranidal genetic relationships and nest management for the pollination of passion fruit.     

Microsatellite loci characterised in a megapode, the Australian brush-turkey Alectura lathami

We isolated 137 unique Australian brush-turkey (Alectura lathami) microsatellite sequences. Twenty-five loci when characterised in 24 individuals displayed 2–17 alleles per locus. Four loci were found to be Z-linked based on a complete lack of heterozygotes in females and sequence similarity to the chicken Z chromosome. Due to the small genetic distance among species within this family, a proportion of these loci are expected to be of utility for genetic studies of other megapodes, many of which are endangered.     

White-Matter damage in Clade C HIV-positive subjects: a diffusion tensor imaging study

The relationship between cognitive impairment and white-matter integrity in human immunodeficiency virus (HIV) remains poorly understood, particularly in clade C. The authors utilized diffusion tensor imaging (DTI) and a comprehensive neuropsychological evaluation to investigate the relationship between cognitive impairment and white-matter integrity in HIV-positive subjects with clade C HIV. Forty-four HIV-infected individuals and 10 seronegative subjects were compared, using a whole-brain, voxel-based approach to define fractional anisotropy (FA) and mean diffusion (MD). Compared with healthy-control subjects, the HIV-infected group exhibited decreased FA in the corpus callosum, superior longitudinal fasciculus, and cingulum and sagittal stratum. This study provides evidence that white-matter integrity is compromised in individuals infected with clade C HIV.     

Microsatellite markers for the Arctic copepod Calanus glacialis and cross-amplification with C. finmarchicus

Calanus glacialis is a major component of Arctic zooplankton and a keystone species in Arctic marine ecosystems. Due to the observed climate warming, its numbers are being reduced to the advantage of a sibling Atlantic species Calanus finmarchicus. We developed and characterized the first set of microsatellite markers in this species to investigate its population genetic structure and dispersal capabilities. Nine polymorphic loci displayed an average of 7.3 alleles (range between 2 and 13) and the levels of expected heterozygosity ranged from 0.039 to 0.806. These provide a valuable tool to understand present connectivity patterns across Arctic regions, look for signatures of past climate effects and predict the response to future climate-driven environmental changes. Additionally, due to the cross-amplification with C. finmarchicus, the markers can be used to discriminate between these sibling species.     

Microsatellite loci for testing temporal changes in the population genetics of the Florida mouse (Podomys floridanus)

The Florida mouse (Podomys floridanus) is endemic to Florida and is considered vulnerable by the IUCN due to extensive habitat loss. Here, we describe a panel of 76 microsatellite DNA markers for population genetic studies of this species. Fourteen of these loci were examined to estimate genetic diversity for 39 specimens collected in Florida in 1957 and 2006. DNA extractions from the 1957 specimens were carried out from snips of skin taken from museum voucher skins, whereas the 2006 samples were extracted from fresh liver tissue. The use of museum skins for reconstructing the genetics of historical populations is becoming a critical part of understanding past, present, and future genetic trends for threatened species. Mean expected heterozygosity for the two populations was 0.73 and mean observed heterozygosity was 0.75. The number of alleles per locus ranged from 2 to 15. All microsatellites were polymorphic, and exhibited variability across time.     

Characterization of novel microsatellite loci for Hetaerina americana damselflies, and cross-amplification in other species

Hetaerina damselflies are distributed throughout the neotropics. We developed eleven microsatellite loci for the damselfly Hetaerina americana. Microsatellites were tested for polymorphism on a panel of 24 individuals. The number of alleles ranged from 2 to 6, observed heterozygosity from 0.080 to 0.701, and the fixation index from ?0.266 to 1.000. Cross-amplification was tested in 7 different species in the genus Hetaerina from the United States and Mexico. These microsatellite loci will be useful for studies of population structure and gene flow in H. americana.     

Executive Dyscontrol of Learning and Memory: Findings from a Clade C HIV-positive South African Sample

Objective: Although pre-clinical work suggests there might be differences in neurovirulence across HIV-1 clades, few studies investigate neuropsychological deficits in the globally predominant clade C infection. The purpose of this study was to investigate verbal learning and memory performance in HIV-positive individuals in Cape Town, South Africa, where clade C is the most prevalent subtype of the virus. Method: Using a case-control design, we recruited 53 isiXhosa-speaking, cART-naïve HIV-positive adults and 53 demographically matched HIV-negative controls. Participants were administered a comprehensive neuropsychological test battery. The test of interest was the Hopkins Verbal Learning Test-Revised (HVLT-R); previous studies have used that instrument to identify executive dyscontrol of verbal learning and memory processes in clade B HIV-positive participants. Results: HIV-positive participants showed only partial impairment on the HVLT-R’s learning/memory components (e.g., they recalled significantly fewer words across learning trials, but displayed relatively intact performance on delayed recall trials). They also displayed little executive dyscontrol over encoding and retrieval processes (e.g., there were no significant between-group differences on measures of semantic or serial clustering). Conclusions: Post-cART era studies suggest that verbal learning and memory performance is impaired in clade B samples, at least partially due to executive dyscontrol over encoding and retrieval processes. We found few such impairments in the current clade C sample. These preliminary findings suggest different CNS vulnerability across clades that would have implications for delineating clade-specific neuropathological and neurocognitive clinical features.     

A new set of microsatellite loci for Leptonycteris yerbabuenae and cross species amplification with other glossophagines

A technique based on 454 sequencing of an enriched library was used to construct genomic libraries highly enriched for microsatellite loci for Leptonycteris yerbabuenae. Twenty-four polymorphic microsatellites were developed and tested as markers in the target species. We probed ascertainment bias in 5 different glossophagines (L. nivalis, Glossophaga leachii, G. soricina, Anoura geoffroyi, and Choeronycteris mexicana), indicating their potential utility for suitable studies of population genetics and other related analyses. Levels of expected heterozygosity were medium?Clow for all markers (mean H_E?=?0.147, range 0.008?C0.46).     

Characterization of new microsatellite loci for the South-American rodents Cavia aperea and C. magna

Based on the publicly available genome draft of Cavia porcellus and four other loci described for C. aperea, we characterized 16 microsatellite loci applicable for C. magna and 12 for C. aperea. We designed the primers to be used in a multiplex fluorescence array. The average number of alleles for each locus was 7.4 and the mean expected heterozygosity was 0.67. The use of these markers provides a good framework for population genetics, molecular ecology and other evolutionary studies in these species.     

Microsatellite loci isolated from the lowland tapir (Tapirus terrestris), one of the largest Neotropical mammal

We describe ten microsatellite loci from the lowland tapir (Tapirus terrestris), one of the last members of the Neotropical megafauna and considered a vulnerable species. A total of 74 alleles were detected, ranging from four to thirteen alleles per locus. The expected heterozygosity ranged from 0.34 to 0.88, with a mean of 0.635. All but one locus conformed to the Hardy–Weinberg expectations. These microsatellite loci can be used in population genetic studies of the genus Tapirus, in which all species are threatened globally.     

线虫中影响活动区形成遗传位点的遗传筛选

目的 筛选与鉴定线虫中影响神经突触活动区形成的遗传位点。方法 我们通过构建SYD-2：：GFP转基因动物作为活动区的标记进行正向遗传筛选,以鉴定影响活动区形成的系列遗传位点。结果 从15000筛选群体中,我们分离出8个感兴趣的遗传位点。其突变体的表现型主要反映在SYD-2：：GFP荧光标记数目、形态与分布的改变以及大缺口的出现。一些突变体还表现出明显的行为缺陷以及针对涕灭威（aldicarb）的抗性或者敏感性。结论 这些突变体为我们进一步系统研究活动区的形成与神经递质释放的机制提供了重要前提。     

线虫中影响活动区形成遗传位点的遗传筛选(英文)

目的筛选与鉴定线虫中影响神经突触活动区形成的遗传位点。方法我们通过构建SYD-2::GFP转基因动物作为活动区的标记进行正向遗传筛选,以鉴定影响活动区形成的系列遗传位点。结果从15 000筛选群体中,我们分离出8个感兴趣的遗传位点。其突变体的表现型主要反映在SYD-2::GFP荧光标记数目、形态与分布的改变以及大缺口的出现。一些突变体还表现出明显的行为缺陷以及针对涕灭威(aldicarb)的抗性或者敏感性。结论这些突变体为我们进一步系统研究活动区的形成与神经递质释放的机制提供了重要前提。