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.     

Polymorphism and selection in the major histocompatibility complex <Emphasis Type="Italic">DRA</Emphasis> and <Emphasis Type="Italic">DQA</Emphasis> genes in the family Equidae

The major histocompatibility complex genes coding for antigen binding and presenting molecules are the most polymorphic genes in the vertebrate genome. We studied the DRA and DQA gene polymorphism of the family Equidae. In addition to 11 previously reported DRA and 24 DQA alleles, six new DRA sequences and 13 new DQA alleles were identified in the genus Equus. Phylogenetic analysis of both DRA and DQA sequences provided evidence for trans-species polymorphism in the family Equidae. The phylogenetic trees differed from species relationships defined by standard taxonomy of Equidae and from trees based on mitochondrial or neutral gene sequence data. Analysis of selection showed differences between the less variable DRA and more variable DQA genes. DRA alleles were more often shared by more species. The DQA sequences analysed showed strong amongst-species positive selection; the selected amino acid positions mostly corresponded to selected positions in rodent and human DQA genes.     

Forage selection by mule deer: does niche breadth increase with population density?

Effects of population density of mule deer Odocoileus hemionus on forage selection were investigated by comparing diet characteristics of two subpopulations of deer in southern California, USA, that differed in population density during winter. Quality of diet for deer, as indexed by faecal crude protein, was higher at the low-density site than at the high-density site in winter, when deer densities were different. Quality of diet was similar in summer when both areas had comparable densities of deer. Both outcomes are consistent with predictions from density-dependent selection of diets by deer. Dietary niche breadth, however, differed in a manner opposite to predictions of niche theory based on diet selection under an ideal-free distribution. During winter, when differences in density between the two study sites were pronounced, niche breadth along the dietary axis in the low-density area was twice that of the high-density site. Generalist herbivores feeding primarily on low-quality browse at high population density in winter would be expected to increase their dietary breadth by feeding on additional species of plants as they depleted their food supply. Mule deer in our study, however, decreased the breadth of their dietary niche as population density increased. We hypothesize that by rapidly eliminating high-quality forages from an area by heavy grazing, deer at higher population densities narrowed their dietary niche. Theoretical models for changes in niche dimensions, including the ideal-free distribution, need to consider such empirical outcomes.     

马的骨髓间充质干细胞诱导为软骨 细胞和成骨细胞及其鉴定

本研究旨在将建立的马(Equuscaballus)骨髓间充质干细胞诱导分化为成骨细胞和软骨细胞。通过原代细胞培养获取马的骨髓间充质干细胞,并对第3代(P3)纯化细胞进行干细胞特性鉴定,之后诱导其向不同细胞分化并对诱导分化的细胞进行染色和特异性基因表达的鉴定。实验结果显示,获得的马骨髓细胞表达了干细胞转录因子和间充质干细胞表面标记物,确定获得的细胞为马骨髓间充质干细胞。P3代细胞经诱导培养后由长梭形转变为"骨结节"形态的成骨细胞和"铺路石"形态的软骨细胞。茜素红将诱导的成骨细胞团染成红色,并随着时间的递增红色"骨结节"逐步增大;阿尔新蓝则将蛋白聚糖和透明质酸等含量丰富的诱导细胞染为蓝色,并且随着诱导天数的增加被染成蓝色的软骨细胞逐渐增多,而对照组细胞未见着色。实时荧光定量PCR检测发现,成骨细胞中Col和ALPL基因的表达量随诱导时间的延长发生明显变化;普通PCR结果显示,在诱导的软骨细胞中扩增获得了collagenⅡ、aggrecan和Sox9软骨特异基因,而对照组细胞不表达特异基因。综上所述,本实验建立了马骨髓间充质干细胞并成功将其诱导分化为成骨细胞和软骨细胞,为骨组织缺损修复和软骨细胞的治疗提供了实验基础。     

新疆卡拉麦里山有蹄类野生动物自然保护区夏季蒙古野驴适宜生境与种群数量评估

蒙古野驴(Equus hemionus hemionus)是亚洲内陆荒漠、半荒漠和荒漠草原区域的代表性物种。开展其种群数量调查和适宜生境研究可以为该物种的保护管理提供科学决策依据。本研究于2018和2019年夏季,采用样线法对新疆卡拉麦里山有蹄类自然保护区蒙古野驴的地理分布现状和种群数量进行了调查,采用Distance 7.0软件估算了蒙古野驴的种群密度和数量,并通过MaxEnt模型分析筛选环境变量,确定保护区蒙古野驴的适宜生境及其主要影响因子。结果表明: 调查中发现蒙古野驴718群、共4782头,有效分布位点363个。夏季蒙古野驴适宜生境主要位于保护区的中东部,面积为6737.5 km²,占整个保护区的45.4%,估算保护区夏季蒙古野驴的种群密度为(0.5±0.1)头·km^-2,保护区内蒙古野驴种群数量为(3246±575)头。MaxEnt模型的预测准确性较高,AUC的平均值为0.890。影响蒙古野驴分布的主要环境因子依次为: 距水源点距离、植被类型、距人类活动区距离、距G216国道的距离、海拔和最干季的降水量。最后,从水源点保护、核心区调整、野生动物通道监测和交通建设4个方面,对蒙古野驴种群的保护管理提出了建议。     

Temporal Overlap Among Feral Horses,Cattle, and Native Ungulates at Water Sources

Feral horse (Equus ferus caballus) populations on public rangelands in the western United States threaten forage production for livestock and wildlife habitat. Interference competition between feral horses and heterospecifics at watering sources can have negative effects on livestock and wildlife. Researchers have documented altered timing and behavior of wild ungulates at water sources when horses were present. The few studies examining these interactions have infrequently occurred within areas specifically managed for feral equids and have not occurred in sites with cattle. We used motion-sensitive cameras at 8 watering sources to document watering activity patterns and construct indices of temporal overlap among feral horses, cattle, elk (Cervus canadensis), mule deer (Odocoileus hemionus), and pronghorn (Antilocapra americana) within the Adobe Town Herd Management Area in southern Wyoming, USA, between June and September 2018 and 2019. Feral horses, cattle, and pronghorn exhibited a high degree of temporal overlap (>79%) in water use, with feral horses and pronghorn exhibiting the highest estimated percent overlap (88.1%, 95% CI = 86.5–89.6%). Mule deer and elk watering activity also overlapped with horses and cattle but to a lesser degree (<55%). Feral horses spent a mean of 16.7 ± 30.5 (SD) minutes during a watering event and were present at a given water source on average 4.5 ± 6.3% and up to 34.9% of the day, which is less than reported in previous studies. Cattle spent on average 23.5 ± 44.9 minutes during a watering event, and were present on average 4.2 ± 7.7% and up to 42.4% of the day at a single water source. Results of generalized linear mixed-effects models indicated that number of conspecifics was the strongest predictor of visit duration for pronghorn and horses; hour of the day and group size of heterospecifics were informative, but less important, variables. There was no difference in peak visitation time for any species between sites of high versus low horse or cattle use. Despite temporal overlap, we did not find evidence of interference competition between feral horses, cattle, and pronghorn. We recommend future examination of interference competition and its biological consequences between introduced and native ungulates at water sources of varying size across sites, equid population levels, and livestock stocking rates. © 2020 The Wildlife Society.     

Feral Horse Space Use and Genetic Characteristics from Fecal DNA

Feral horses (Equus ferus caballus) in the western United States are managed by the Bureau of Land Management (BLM) and United States Forest Service in designated areas on public lands with a goal of maintaining populations in balance with multiple uses of the landscape. Small, isolated populations can be at risk of extirpation from stochastic events and deleterious genetic effects resulting from inbreeding and reduced heterozygosity. The genetic diversity of feral horse herds is periodically monitored using blood or hair samples collected during management gathers (i.e., occasions when the herd is rounded up). We conducted a study to examine genetic characteristics of the feral horse population at the BLM Little Book Cliffs Herd Management Area (HMA) in Colorado, USA, using non-invasively collected fecal samples. Additionally, we explored whether genotypes could be used to document space use and potential sub-population development. We used a random sampling scheme, walking transects in sampling areas covering most of the HMA to find and collect fecal samples of all ages, except those that were deteriorating. We collected >1,800 fecal samples from across the study area in May, August, and October 2014. We then identified unique individuals using a suite of microsatellite loci. Our estimates of genetic diversity from fecal samples were higher than those reported from blood and hair samples taken during recent horse gathers, likely because our sample size and spatial distribution was larger. Genotypes revealed that some individuals were found only in certain parts of the study area and at a higher proportion than random; thus, they could be considered residents in those sampling areas. Using discriminant function analyses, we detected 5 genetic groups in the sample population, but these did not correspond to individuals in specific parts of the study area. Our results support the use of fecal DNA to augment direct observations of horse presence and could be used to detect habitat use and areas of high density. Non-invasive techniques such as fecal DNA sampling can help managers decide whether new individuals need to be translocated to a closed population to maintain genetic diversity without the human safety and animal welfare concerns associated with gathers and invasive techniques. © 2021 The Wildlife Society.     

Using Fecal DNA and Closed-Capture Models to Estimate Feral Horse Population Size

Accurate population estimates provide the foundation for managing feral horses (Equus caballus ferus) across the western United States. Certain feral horse populations are protected by the Wild and Free-Roaming Horses and Burros Act of 1971 and managed by the Bureau of Land Management (BLM) or the United States Forest Service on designated herd management areas (HMAs) or wild horse territories, respectively. Horses are managed to achieve an appropriate management level (AML), which represents the number of horses determined by BLM to contribute to a thriving natural ecological balance and avoid deterioration of the range. To achieve AML for each HMA, BLM resource managers need accurate and precise population estimates. We tested the use of non-invasive fecal samples in a genetic capture-recapture framework to estimate population size in a closed horse population at the Little Book Cliffs HMA, Colorado, USA, with a known size of 153 individuals. We collected 1,957 samples over 3 independent sampling periods in 2014 and amplified them at 8 microsatellite loci. We applied mark-recapture models to determine population size using 954 samples that amplified at all 8 loci. We subsampled and reanalyzed our dataset to simulate different data collection protocols and evaluated effects on accuracy and precision of estimates using N-mixture modeling, full likelihood closed-capture modeling, and capwire single-occasion modeling that used data from all 3 sampling periods. Our model results were accurate and precise for analyses that used data from all 3 occasions; however, capwire single-occasion modeling was not accurate when we analyzed each sampling period separately. For all subsampling analysis scenarios, reducing sample size decreased precision, whether by reducing number of field staff, field days, or geographic areas surveyed on each period. Reducing spatial coverage of the survey area did not result in accurate population estimates and only marginally lowered the number of samples that would need to be collected to maintain accuracy. Because laboratory analysis contributes the greatest expense for this method ($80 U.S./sample), reducing fecal sample size is advantageous. Our results demonstrate that non-invasive sampling combined with good survey design and careful genetic and capture-recapture analyses can provide an alternative method to estimate the number of feral horses in a closed population. This method may be especially appropriate in situations where aerial inventories are not practical or accurate because of low sighting conditions. But the higher costs associated with laboratory sample analyses may reduce the method's feasibility compared to helicopter surveys. © 2021 The Wildlife Society. This article has been contributed to by US Government employees and their work is in the public domain in the USA.     

卡拉麦里山有蹄类野生动物自然保护区蒙古野驴生境格局动态及其成因分析

人类干扰导致的生境丧失与破碎化严重影响野生动物生存。基于2005年至2019年在新疆卡拉麦里山有蹄类野生动物自然保护区开展野外调查所获数据,选取影响蒙古野驴生境选择的关键环境因子,采用最大熵模型（MaxEnt）模拟矿业开发前（2005年）、矿业开发顶峰时（2011年）以及矿区生态修复和道路修建（2019年）三个时期的蒙古野驴适宜生境空间分布。选取相关的景观格局指数,分析了近15年来保护区内蒙古野驴生境格局的变化趋势。结果显示蒙古野驴的适宜生境主要分布于保护区中部,水源是影响蒙古野驴生境质量的关键自然因素。2005-2019年间该保护区蒙古野驴的生境经历了由较好状态到恶化,随后逐渐恢复的过程。矿业开发前蒙古野驴高适宜生境面积最大（2022.31 km²）,生境破碎化程度低,总体生境质量较好。矿业开发顶峰时蒙古野驴的适宜生境向保护区北部转移,适宜生境大面积丧失,其中高适宜生境面积减少了30.28%,且生境斑块面积小,形状不规则、离散和破碎化程度高,严重威胁蒙古野驴生存。矿区生态修复和道路建设后,大多数已修复的矿区重新成为蒙古野驴的适宜生境,保护区内蒙古野驴适宜生境面积较矿业开发时增加了556.31 km²,但仍处于破碎隔离状态;道路沿线适宜生境丧失严重,蒙古野驴对其明显回避。基于上述研究结果,针对蒙古野驴生境保护提出了具体措施,为卡山保护区蒙古野驴生境恢复及保护提供了科学依据。