Whole genome sequencing reveals a novel deletion variant in the KIT gene in horses with white spotted coat colour phenotypes

White spotting phenotypes in horses can range in severity from the common white markings up to completely white horses. EDNRB, KIT, MITF, PAX3 and TRPM1 represent known candidate genes for such phenotypes in horses. For the present study, we re‐investigated a large horse family segregating a variable white spotting phenotype, for which conventional Sanger sequencing of the candidate genes’ individual exons had failed to reveal the causative variant. We obtained whole genome sequence data from an affected horse and specifically searched for structural variants in the known candidate genes. This analysis revealed a heterozygous ~1.9‐kb deletion spanning exons 10–13 of the KIT gene (chr3:77,740,239_77,742,136del1898insTATAT). In continuity with previously named equine KIT variants we propose to designate the newly identified deletion variant W22. We had access to 21 horses carrying the W22 allele. Four of them were compound heterozygous W20/W22 and had a completely white phenotype. Our data suggest that W22 represents a true null allele of the KIT gene, whereas the previously identified W20 leads to a partial loss of function. These findings will enable more precise genetic testing for depigmentation phenotypes in horses.     

卡拉麦里山有蹄类自然保护区蒙古野驴和鹅喉羚种群密度和数量

2006年9月至2007年12月, 在卡拉麦里山有蹄类自然保护区采用截线取样法调查了蒙古野驴(Equus hemionus)和鹅喉羚(Gazella subgutturosa sairensis)的种群密度。蒙古野驴野外调查样线总长6,696.4 km, 发现7,758 匹蒙古野驴; 鹅喉羚样线总长8,428.84 km, 发现8,586头鹅喉羚。采用Distance 5.0估算了蒙古野驴和鹅喉羚的密度和遇见率。从春季到秋季, 蒙古野驴遇见率在0.058–0.092匹/km之间变化, 而鹅喉羚遇见率则在0.096–0.342头/ km之间变化。春季蒙古野驴种群密度为0.55 ± 0.20 匹/km2 (平均数 ± 标准差,下同), 夏季为0.60 ± 0.13 匹/km2, 秋季为0.78 ± 0.19匹/km2和冬季为0.54 ± 0.14 匹/km2。蒙古野驴适宜栖息面积5,800 km2。春季到冬季, 蒙古野驴种群数量在3,379到5,318匹之间变化。鹅喉羚春季、夏季、秋季和冬季种群密度分别为1.14 ± 0.18头/km2, 0.95 ± 0.12头/km2, 1.08 ± 0.18头/km2和1.54 ± 0.31头/km2。该保护区的鹅喉羚冬季和春季适宜栖息面积均为10,000 km2, 夏季为12,000 km2, 秋季为15,000 km2。估算该区域春季鹅喉羚数量为14,286头, 夏季为6,628头, 秋季为8,337头, 冬季为19,677头。本研究的结果将为卡拉麦里山有蹄类自然保护区蒙古野驴和鹅喉羚长期监测提供基础数据。     

Purification and crystallization of haemoglobin from donkey (Equus asinus)

Haemoglobin acts as an important protein for oxygen carrier in all living beings. Purification of donkey haemoglobin was done using PEG 4000 as a separating medium. Crystallization was achieved using hanging drop vapor diffusion method using 2.8 M phosphate buffer, pH 6.8. Data collection was done using mar345 image plate detector system. The crystals grown under 2.8 M phosphate buffer are monoclinic with space group C2 and cell dimensions a=107.664 A, b=63.084 A, c=54.042 A, and beta=111.747 degrees.     

Feral donkey Equus asinus populations on the Karpaz peninsula, Cyprus

Numerous researchers have documented the adverse effects of feral donkeys Equus asinus introduced to semi-arid ecosystems. With the release of feral donkeys and potential increasing populations in natural habitats in northern Cyprus, there is concern for negative impacts on vegetation and native species. In the north of the island, there has been only one published study of feral donkey populations, and population estimators were relatively subjective. We estimated feral donkey populations on the Karpaz Peninsula using line transect surveys and quantitative distance sampling estimators. We stratified the sampling by using 11 sample units within the study area. We evaluated potential biases associated with habitat, topography, and perpendicular distance from the transect line and found that these variables did not bias donkey detections during our surveys. Using program DISTANCE, we found that a hazard rate cosine model was the best model that described our distance data based on model selection criterion (Akaikes Information Criteria adjusted for small sample bias). Estimated effective strip width was 280.19 m and detection probability was 0.47 with this model. Estimated donkey density was 6.7 donkeys/km², and estimated total abundance was 800 donkeys for the entire 132.5 km² study area. Of 95 donkey groups detected: 16% were detected in agricultural habitats with flat topography, 9% were detected in agricultural habitats with sloped topography, 24% were detected in shrub/forest habitats with flat topography, and 51% were detected in shrub/forest habitats with sloped topography. Of 102 behavioral observations recorded (multiple behaviors were detected in groups), frequencies of behaviors were 1% bedded, 70% standing, 22% grazing, 6% moving, and 2% other. Our estimated donkey population density in the Karpaz Peninsula was >2 times densities reported in arid regions of the United States and Australia, but slightly lower than earlier density estimates reported for the Karpaz region. These estimates of feral donkey populations in the Karpaz Peninsula provide a quantitative baseline from which to make population management decisions.     

Does Removing Coyotes for Livestock Protection Benefit Free-Ranging Ungulates?

Abstract: We studied the effects of coyote (Canis latrans) control for livestock protection on native ungulates during 2003 and 2004 on 7 sites in Utah and Colorado, USA, totaling over 1,900 km². We found no relationships between coyote control variables and offspring/female deer ratios. However, control effort (no. of hr spent aerial gunning for coyotes) and success (no. of coyotes taken) were positively correlated with numbers of mule deer (Odocoileus hemionus) and pronghorn (Antilocapra americana) observed per kilometer of transect. Our results suggest that coyote control for livestock protection may increase densities of mule deer and pronghorn in areas where it is conducted.     

Influence of Well Pad Activity on Winter Habitat Selection Patterns of Mule Deer

ABSTRACT Conversion of native winter range into producing gas fields can affect the habitat selection and distribution patterns of mule deer (Odocoileus hemionus). Understanding how levels of human activity influence mule deer is necessary to evaluate mitigation measures and reduce indirect habitat loss to mule deer on winter ranges with natural gas development. We examined how 3 types of well pads with varying levels of vehicle traffic influenced mule deer habitat selection in western Wyoming during the winters of 2005–2006 and 2006–2007. Well pad types included producing wells without a liquids gathering system (LGS), producing wells with a LGS, and well pads with active directional drilling. We used 36,699 Global Positioning System locations collected from a sample (n = 31) of adult (>1.5-yr-old) female mule deer to model probability of use as a function of traffic level and other habitat covariates. We treated each deer as the experimental unit and developed a population-level resource selection function for each winter by averaging coefficients among models for individual deer. Model coefficients and predictive maps for both winters suggested that mule deer avoided all types of well pads and selected areas further from well pads with high levels of traffic. Accordingly, impacts to mule deer could probably be reduced through technology and planning that minimizes the number of well pads and amount of human activity associated with them. Our results suggested that indirect habitat loss may be reduced by approximately 38–63% when condensate and produced water are collected in LGS pipelines rather than stored at well pads and removed via tanker trucks. The LGS seemed to reduce long-term (i.e., production phase) indirect habitat loss to wintering mule deer, whereas drilling in crucial winter range created a short-term (i.e., drilling phase) increase in deer disturbance and indirect habitat loss. Recognizing how mule deer respond to different types of well pads and traffic regimes may improve the ability of agencies and industry to estimate cumulative effects and quantify indirect habitat losses associated with different development scenarios.     

A challenge for miRNA: multiple isomiRs in miRNAomics

Accumulating evidence suggests that a single microRNA (miRNA) locus can generate a series of sequences during miRNA maturation process. These multiple sequences, called miRNA variants, or isomiRs, have different lengths and different 5′ and 3′ ends. Some of these isomiRs are detected as varied nucleotides and 3′ additional non-template nucleotides. As physiological miRNA isoforms, they have drawn attention for possible regulatory biological roles. The present work mainly reviews miRNA/isomiR biogenesis, isomiR expression patterns, and functional and evolutionary implications, especially between isomiRs from homologous and clustered miRNA loci. The phenomenon of multiple isomiRs and their biological roles indicates that analysis performed at the miRNA and isomiR levels should be included in miRNA studies. This may enrich and complicate miRNA biogenesis and coding–non-coding RNA regulatory networks.