CHIIMP: An automated high‐throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees

Short tandem repeats (STRs), also known as microsatellites, are commonly used to noninvasively genotype wild‐living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq‐based approach and tested its performance using previously genotyped fecal samples from long‐term studied chimpanzees in Gombe National Park, Tanzania. Using data from eight microsatellite loci as a reference, we designed a bioinformatics platform that converts raw MiSeq reads into locus‐specific files and automatically calls alleles after filtering stutter sequences and other PCR artifacts. Applying this method to the entire Gombe population, we confirmed previously reported genotypes, but also identified 31 new alleles that had been missed due to sequence differences and size homoplasy. The new genotypes, which increased the allelic diversity and heterozygosity in Gombe by 61% and 8%, respectively, were validated by replicate amplification and pedigree analyses. This demonstrated inheritance and resolved one case of an ambiguous paternity. Using both singleplex and multiplex locus amplification, we also genotyped fecal samples from chimpanzees in the Greater Mahale Ecosystem in Tanzania, demonstrating the utility of the MiSeq‐based approach for genotyping nonhabituated populations and performing comparative analyses across field sites. The new automated high‐throughput analysis platform (available at https://github.com/ShawHahnLab/chiimp ) will allow biologists to more accurately and effectively determine wildlife population size and structure, and thus obtain information critical for conservation efforts.     

Using high throughput screening to define virus clearance by chromatography resins

High throughput screening (HTS) of chromatography resins can accelerate downstream process development by rapidly providing information on product and impurity partitioning over a wide range of experimental conditions. In addition to the removal of typical product and process‐related impurities, chromatography steps are also used to remove potential adventitious viral contaminants and non‐infectious retrovirus‐like particles expressed by rodent cell lines used for production. This article evaluates the feasibility of using HTS in a 96‐well batch‐binding format to study removal of the model retrovirus xenotropic murine leukemia virus (xMuLV) from product streams. Two resins were examined: the anion exchange resin Q Sepharose Fast Flow? (QSFF) and Capto adhere?, a mixed mode resin. QSFF batch‐binding HTS data was generated using two mAbs at various pHs, NaCl concentrations, and levels of impurities. Comparison of HTS data to that generated using the column format showed good agreement with respect to virus retentation at different pHs, NaCl concentrations and impurity levels. Results indicate that NaCl concentration and impurity level, but not pH, are key parameters that can impact xMuLV binding to both resins. Binding of xMuLV to Capto adhere appeared to tolerate higher levels of NaCl and impurity than QSFF, and showed some product‐specific impact on binding that was not observed with QSFF. Overall, the results demonstrate that the 96‐well batch‐binding HTS technique can be an effective tool for rapidly defining conditions for robust virus clearance on chromatographic resins. Biotechnol. Bioeng. 2013; 110: 1984–1994. © 2013 Wiley Periodicals, Inc.     

Synthesis and assessment of the relative toxicity of the oxidised derivatives of campesterol and dihydrobrassicasterol in U937 and HepG2 cells

The cytotoxic effects of the oxidised derivatives of the phytosterols, stigmasterol and β-sitosterol, have previously been shown to be similar but less potent than those of the equivalent cholesterol oxides in the U937 cell line. The objective of the present study was to compare the cytotoxic effects of the oxidised derivatives of synthetic mixtures of campesterol and dihydrobrassicasterol in both the U937 and HepG2 cell lines. The parent compounds consisted of a campesterol: dihydrobrassicasterol mix at a ratio of 2:1 (2CMP:1DHB) and a dihydrobrassicasterol:campesterol mix at a ratio of 3:1 (3DHB:1CMP). The 2CMP:1DBH oxides were more cytotoxic in the U937 cells than the 3DBH:1CMP oxides but the difference in cytotoxicity was less marked in the HepG2 cells. The order of toxicity of the individual oxidation products was found to be similar to that previously observed for cholesterol, β-sitosterol and stigmasterol oxidation products in the U937 cell line. There was an increase in apoptotic nuclei in U937 cells incubated with the 7-keto and 7β-OH derivatives of both 2CMP:1DHB and 3DHB:1CMP and also in the presence of 3DHB:1CMP-3β,5α,6β-triol and 2CMP:1DHB-5β,6β-epoxide. An additional oxidation product synthesised from 2CMP:1DHB, 5,6,22,23-diepoxycampestane, was cytotoxic but did not induce apoptosis. These results signify the importance of campesterol oxides in the overall paradigm of phytosterol oxide cytotoxicity.     

Conditional and unconditional QTL mapping of drought-tolerance-related traits of wheat seedling using two related RIL populations

For discovering the quantitative trait loci (QTLs) contributing to early seedling growth and drought tolerance during germination, conditional and unconditional analyses of 12 traits of wheat seedlings: coleoptile length, seedling height, longest root length, root number, seedling fresh weight, stem and leaves fresh weight, root fresh weight, seedling dry weight, stem and leaves dry weight, root dry weight, root to shoot fresh weight ratio, root-to-shoot dry weight ratio, were conducted under two water conditions using two F_8:9 recombinant inbred line (RIL) populations. The results of unconditional analysis are as follows: 88 QTLs accounting for 3.33–77.01% of the phenotypic variations were detected on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 4D, 5A, 5B, 5D, 6A, 6B, 6D, 7A, 7B and 7D. Among these QTLs, 19 were main-effect QTLs with a contribution rate greater than 10%. The results of the conditional QTL analysis of 12 traits under osmotic stress on normal water conditions were as follows: altogether 22 QTLs concerned with drought tolerance were detected on chromosomes 1B, 2A, 2B, 3B, 4A, 5D, 6A, 6D, 7B, and 7D. Of these QTLs, six were main-effect QTLs. These 22 QTLs were all special loci directly concerned with drought tolerance and most of them could not be detected by unconditional analysis. The finding of these QTLs has an important significance for fine-mapping technique, map-based cloning, and molecular marker-assisted selection of early seedling traits, such as growth and drought tolerance.     

Two new cytotypes reinforce that <Emphasis Type="Italic">Micronycteris hirsuta</Emphasis> Peters, 1869 does not represent a monotypic taxon

Background

The genus Micronycteris is a diverse group of phyllostomid bats currently comprising 11 species, with diploid number (2n) ranging from 26 to 40 chromosomes. The karyotypic relationships within Micronycteris and between Micronycteris and other phyllostomids remain poorly understood. The karyotype of Micronycteris hirsuta is of particular interest: three different diploid numbers were reported for this species in South and Central Americas with 2n?=?26, 28 and 30 chromosomes. Although current evidence suggests some geographic differentiation among populations of M. hirsuta based on chromosomal, morphological, and nuclear and mitochondrial DNA markers, the recognition of new species or subspecies has been avoided due to the need for additional data, mainly chromosomal data.

Results

We describe two new cytotypes for Micronycteris hirsuta (MHI) (2n?=?26 and 25, NF?=?32), whose differences in diploid number are interpreted as the products of Robertsonian rearrangements. C-banding revealed a small amount of constitutive heterochromatin at the centromere and the NOR was located in the interstitial portion of the short arm of a second pair, confirmed by FISH. Telomeric probes hybridized to the centromeric regions and weakly to telomeric regions of most chromosomes. The G-banding analysis and chromosome painting with whole chromosome probes from Carollia brevicauda (CBR) and Phyllostomus hastatus (PHA) enabled the establishment of genome-wide homologies between MHI, CBR and PHA.

Conclusions

The karyotypes of Brazilian specimens of Micronycteris hirsuta described here are new to Micronycteris and reinforce that M. hirsuta does not represent a monotypic taxon. Our results corroborate the hypothesis of karyotypic megaevolution within Micronycteris, and strong evidence for this is that the entire chromosome complement of M. hirsuta was shown to be derivative with respect to species compared in this study.

     

Areas of high diversity for the world’s inland-breeding waterbirds

Waterbirds are a globally-distributed, species-rich group of birds that are critically dependent upon wetland habitats. They can be used as ecosystem sentinels for wetlands, which as well as providing ecosystem services and functions essential to humans, are important habitats for a wide range of plant and animal taxa. Here we carry out the first global analysis of inland-breeding waterbird distributions using data from 471 waterbird species in 28 families to identify global areas of high waterbird diversity. First we identify the primary area of high diversity for all inland-breeding waterbird species to be in Eastern Africa. For globally threatened inland-breeding waterbirds, the area of highest diversity is in Eastern China. Second, we show that the current network of protected areas provides poor coverage for threatened waterbirds in Eastern and Central Asia, and Northern India. In contrast, there is a higher protected area coverage in most of Europe and Brazil. Targeting the specific areas that have the highest numbers of species and the poorest coverage of protected areas is vital for both waterbird and wetland conservation.     

Characteristics of cases with unknown stage prostate cancer in a population-based cancer registry

BackgroundThe New South Wales Central Cancer Registry (NSW CCR) is the only population-based cancer registry in Australia that has routinely collected summary stage at diagnosis since its inception in 1972. However, a large proportion of prostate cancer cases have “unknown” stage recorded by the registry. We investigated the characteristics of prostate cancer cases with “unknown” stage recorded by the NSW CCR, and examined survival for this group.MethodsData were obtained from the NSW CCR for all first primary prostate cancer cases diagnosed in 1999–2007. Summary stage was recorded as localised, regional, distant or “unknown”. Associations between disease stage and patient characteristics (age, place of residence at diagnosis, year of diagnosis and country of birth) and prostate cancer specific survival were investigated using multivariable logistic regression and Cox proportional hazards models respectively.ResultsOf 39 852 prostate cancer cases, 41.8% had “unknown” stage recorded by the NSW CCR. This proportion decreased significantly over time, increased with increasing age at diagnosis and was higher for those living in socio-economically disadvantaged areas. The proportion with “unknown” stage varied across area health services. Prostate cancer specific survival for cases with “unknown” stage was significantly poorer than for those with localised stage but better than for those with regional or distant stage.ConclusionsResearchers or others using cancer registry stage data to examine prostate cancer outcomes need to consider the differences between cases with “unknown” stage at diagnosis and those with known stage recorded by the registry, and what impact this may have on their results.