Structural Variants Selected during Yak Domestication Inferred from Long-Read Whole-Genome Sequencing

Structural variants (SVs) represent an important genetic resource for both natural and artificial selection. Here we present a chromosome-scale reference genome for domestic yak (Bos grunniens) that has longer contigs and scaffolds (N50 44.72 and 114.39 Mb, respectively) than reported for any other ruminant genome. We further obtained long-read resequencing data for 6 wild and 23 domestic yaks and constructed a genetic SV map of 372,220 SVs that covers the geographic range of the yaks. The majority of the SVs contains repetitive sequences and several are in or near genes. By comparing SVs in domestic and wild yaks, we identified genes that are predominantly related to the nervous system, behavior, immunity, and reproduction and may have been targeted by artificial selection during yak domestication. These findings provide new insights in the domestication of animals living at high altitude and highlight the importance of SVs in animal domestication.     

海拔高度对青藏高原放牧牦牛肠道菌群多样性的影响

[背景]肠道菌群与宿主健康及环境适应性密切相关,牦牛为青藏高原特有的草食性反刍动物,不同海拔高度如何影响牦牛肠道菌群组成及肠道菌群在牦牛适应高海拔生境中的作用尚不清楚.[目的]探究青藏高原放牧牦牛肠道菌群多样性及其与海拔高度间的关系.[方法]采集青海省玛沁县(海拔4220 m)和乐都县(2745 m)2个海拔高度放牧牦...     

牦牛的分类学地位及起源研究:mtDNA D-loop序列的分析

牦牛的起源与属级分类学地位至今仍然存在一定的争议。我们测定了家养牦牛和野生牦牛线粒体控制区(D-loop)序列,并以此构建牦牛和牛属、野牛属、水牛属以及非洲水牛属相关种的系统发育树。研究结果表明线粒体D-loop区与Cytb基因序列在构建牛族的系统发育具有同样重要的价值。系统发育关系显示野牛属的灭绝种草原野牛与现存种美洲野牛先聚合为一单系群,然后再和牦牛形成一单系分支,表明牦牛与野牛属的草原野牛、美洲野牛亲缘关系最近,具有最近的共同祖先,而与牛属的其它亚洲物种亲缘关系较远。因此,本研究不支持将牦牛独立为牦牛属———Poephagus,牛属与野牛属在分类上也应合并为一个属。基于上述研究结果和化石证据,我们进一步对牦牛起源的历史背景进行了讨论,认为牦牛与野牛属的分化是由于第四纪气候变化在欧亚大陆发生的,野牛通过白令陆桥进入北美;冰期结束后,由于欧亚大陆其它地区温度升高,牦牛只能局限分布在较为寒冷的青藏高原;而野牛属在北美先后分化为草原野牛和美洲野牛,前者可能是后者的直接祖先。     

The effect of the cationic proteins of human blood cells on the growth of Escherichia coli

The antibacterial effect of cationic proteins (CP) on donor leukocytes and thrombocytes with respect to the growth of E. coli has been demonstrated in vitro, the maximum recorded inhibition being caused by the action of leukocytic CP. Differences in the inhibitory action may be linked with the presence of anomalies in the amino acid composition of leukocytic CP and thrombocytic CP, manifested by the deterioration of the basic properties of the latter, as well as by the fractional composition whose characteristic features for thrombocytic CP are the appearance of high-molecular components and a decrease in the proportion of low-molecular fractions. In patients with different forms of leukosis (chronic myeloleukemia, chronic lympholeukemia, acute myelomonoblastic leukosis) leukocytic CP retain their antibacterial activity. Under the action of blood cell CP changes in the outer and cytoplasmic membranes have been noted.     

A new method for the determination of thrombocyte function in patients and in preserved blood]

In a circulating thrombocytic plasma the pressure in front of a defined mesh filter depends on the combined capacity of adhesion and aggregation of thrombocytes. A new clinical in vitro test is based on this principle which comes nearest to the conditions to be found in hemostasis dependent on thrombocytes. Judging from the preliminary results of investigations performed on stored blood, blood donors, patients with thrombocytopenia, disturbances of blood flow and patients under anticoagulant therapy, the time until the pressure rise after administering ADP and the maximal pressure amplitude proved to be the most significant parameters of the new procedure.     

贺兰山牦牛冬春季的生境选择

在2009年12月－2010年1月和2010年4－5月,采用样线法结合直接观察法对贺兰山牦牛的冬春季生境选择进行了研究。结果表明,牦牛冬季对11种生境因子有选择性,偏爱山地针叶林带,海拔小于2 000 m,优势乔木为灰榆,坡度小于10,下坡位,距水源距离大于1 200 m,人为干扰距离2 000－4 000 m,隐蔽级大于70 %;春季牦牛对13种利用生境生态因子有选择性,偏爱于亚高山灌丛和草甸带,海拔大于3 000 m,乔木密度小于1株,乔木高度小于3 m,乔木距离大于3 m,灌木密度大于4 0株,灌木距离小于1 m,植被盖度大于7 0 %,上坡位,距水源的距离小于8 00 m,人为干扰距离大于4 000 m,隐蔽级大于7 0 %。冬春季牦牛在海拔、植被类型、地形特征、优势乔木、灌木种类、坡位、坡向、人为干扰距离、距水源距离上存在显著差异。主成分分析表明冬季第一主成分的贡献率21.100 %,其中绝对值较大的相关系数是乔木距离、优势乔木、乔木高度和乔木密度;春季第一主成分的贡献率是31.247 %,其中绝对值较大的相关系数是植被类型、海拔高度、地形特征和灌木密度。与其他分布地区的牦牛相比,贺兰山地区的牦牛能适应当地的地理特征和气候环境。     

Lysosomes-like thrombocyte alpha-granules: the activation and inhibition of the release of the contents in blood coagulation]

The mechanism of the release of alpha-granules constituents of thrombocytes was studied in the course of blood coagulation utilizing the fluorometric technique. The release reaction can be induced by proteolytic enzymes. The process is stimulated by the presence of extracellular Ca2+. This pattern of release reaction belongs to "release II" type. Aminazin can also induced release of alpha-granules constituents. Heparin inhibited release II induced by Ca2+ in citrated plasma, whereas streptase had no effect.     

Introgression,admixture, and selection facilitate genetic adaptation to high-altitude environments in cattle

Domestication and subsequent selection of cattle to form breeds and biological types that can adapt to different environments partitioned ancestral genetic diversity into distinct modern lineages. Genome-wide selection particularly for adaptation to extreme environments left detectable signatures genome-wide. We used high-density genotype data for 42 cattle breeds and identified the influence of Bos grunniens and Bos javanicus on the formation of Chinese indicine breeds that led to their divergence from India-origin zebu. We also found evidence for introgression, admixture, and migration in most of the Chinese breeds. Selection signature analyses between high-altitude (≥1800 m) and low-altitude adapted breeds (<1500 m) revealed candidate genes (ACSS2, ALDOC, EPAS1, EGLN1, NUCB2) and pathways that are putatively involved in hypoxia adaptation. Immunohistochemical, real-time PCR and CRISPR/cas9 ACSS2-knockout analyses suggest that the up-regulation of ACSS2 expression in the liver promotes the metabolic adaptation of cells to hypoxia via the hypoxia-inducible factor pathway. High altitude adaptation involved the introgression of alleles from high-altitude adapted yaks into Chinese Bos taurus taurus prior to their formation into recognized breeds and followed by selection. In addition to selection, adaptation to high altitude environments has been facilitated by admixture and introgression with locally adapted cattle populations.     

Carbonic anhydrase activity in the red blood cells of sea level and high altitude natives

Red blood cell carbonic anhydrase (CA) activity has not been studied in high altitude natives. Because CA is an intraerythocytic enzyme and high altitude natives are polycythemic, it is important to know if the activity of CA per red cell volume is different from that of their sea level counterparts. Blood was collected from healthy subjects living in Lima (150m) and from twelve subjects from Cerro de Pasco (4330m), and hematocrit and carbonic anhydrase activity were measured. As expected, the high altitude natives had significantly higher hematocrits than the sea level controls (p = 0.0002). No difference in the CA activity per milliliter of red cells was found between the two populations. There was no correlation between the hematocrit and CA activity.     

Thrombocytes Correlate with Lymphangiogenesis in Human Esophageal Cancer and Mediate Growth of Lymphatic Endothelial Cells In Vitro

Recent data provide evidence for an important role of thrombocytes in lymphangiogenesis within human malignant disease. The aim of this study was to investigate the role of thrombocytes in lymphangiogenesis in human esophageal cancer. Perioperative peripheral blood platelet counts (PBPC) were evaluated retrospectively in 320 patients with esophageal cancer, comprising 184 adenocarcinomas (AC), and 136 squamous cell carcinomas (SCC). Data on lymphangiogenesis evaluated by anti-podoplanin immunostaining were available from previous studies, platelets within the tumor tissue were assessed by CD61 immunostaining. For in vitro studies, human lymphatic endothelial cells (LECs) were isolated and co-cultured with peripheral blood platelets. Stromal thrombocytic clusters (STC) were evident in 82 samples (25.6%), and vascular thrombocytic clusters (VTC) in 56 (17.5%). STC and VTC were associated with a significantly higher PBPC at investigation of all cases. The presence of STC was associated with higher lymphatic microvessel density (p<0.001), PBPC and STC were associated with lymphovascular invasion of tumor cells in a regression model. The presence of STCs was associated with shorter DFS of all patients (p = 0.036, Breslow test), and VTC with shorter DFS in in SCC (p = 0.025, Breslow test). In cell culture, LEC proliferation was enhanced by co-culture with human platelets in a dose- and time-dependent manner mediated by the release of PDGF-BB and VEGF-C. Platelets play an important role in lymphangiogenesis and lymphovascular invasion in esophageal cancer, influencing prognosis. So the disruption of signaling pathways between platelets, tumor cells and lymphatic endothelium might be of benefit for patients.     

Diurnal variation and oscillatory patterns in physiological responses and HSP70 profile in heat stressed yaks at high altitude

The present study was carried out at altitude of 3000 m above sea level (asl) to evaluate the impact of heat stress on yak adaptability. Sixteen healthy yaks of different age were randomly divided into two groups, calf (GI; n = 8) and adult (GII; n = 8). Experimental yaks were exposed to heat stress in the open paddock. THI ranged between 61.60 and 64.17 which were beyond the comfortable limit for yak. Post-exposure, rectal temperature increased (p < 0.01) by 2.97 °F and 2.42 °F in calf and adult yaks as compared to pre-exposure (100.08 ± 0.04 °F, 100.06 ± 0.05 °F). Respiration rate increased (p < 0.01) by 2.96 and 2.40 fold in calf and adult yaks with increased pulse rate on post-exposure to heat stress. The oscillatory patterns of physiological responses indicated that the level of heat stress increment was higher (p < 0.05) in calves than adult yaks. Plasma HSP70 increased (p < 0.01) by 7 fold in calf and 5 fold in adult yaks in comparison to pre-exposure level of 83.67 ± 1.11pg/ml and 80.65 ± 1.35 pg/ml. Thus, the yaks were experiencing heat stress at high altitude of 3000 m asl during the warmer months of the year and calves were more prone to heat stress as compared to adults.     

Nocturnal periodic breathing at altitudes of 6,300 and 8,050 m

Nocturnal periodic breathing was studied in eight well-acclimatized subjects living at an altitude of 6,300 m [barometric pressure (PB) 350-352 Torr] for 3-5 wk and in four subjects during one night at 8,050 m altitude (PB 281-285 Torr). The measurements at 6,300 m included tidal volume by inductance plethysmography, arterial O2 saturation by ear oximetry (calibrated by arterial blood samples), electrocardiogram (ECG), and electrooculogram. At 8,050 m, periodic breathing was inferred from the cyclical variation in heart rate obtained from a night-long ECG record. All subjects at 6,300 m altitude showed well-marked periodic breathing with apneic periods. Cycle length averaged 20.5 s with 7.9 s apnea. Minimal arterial O2 saturation averaged 63.4% corresponding to a PO2 of approximately 33 Torr, i.e., approximately 6 Torr lower than the normal value at rest during daytime. This was probably the most severe hypoxemia of the 24-h period. At 8,050 m altitude, the cycle length averaged 15.4 s, much longer than predicted by a theoretical model. Cyclical variations in heart rate caused by periodic breathing occurred in all subjects, but abnormal cardiac rhythms such as ventricular premature contractions were uncommon. The severe arterial hypoxemia caused by periodic breathing may be an important determinant of tolerance to these great altitudes.     

Ultrastructural bases of intravascular thrombosis in the liver in mechanical jaundice

Electron microscopic studies of a rat liver blood circulatory bed at the experimentally induced 20-day cholestasis demonstrated that the biliary cirrhosis was accompanied by the development of intravascular thrombosis in the liver in a number of cases. Appearance of "pure" thrombocytic thrombi in the lumen of interlobular veins having continuous intact vascular walls was the morphologic feature of the thrombosis. These thrombi are characterized by absence of fibrin fibres. Presence of the intravascular thrombi indicated the higher aggregative ability of thrombocytes which in complex with haemostasis disorders, was one of the causes of hypertension and hemorrhage at the liver pathology.     

Granular pneumocytes and altitude: A stereological evaluation

Summary Stereological analysis demonstrates that the granular pneumocytes of mice native to high altitude (4660 m) are significantly larger than those of the same species (Phyllotis darwini) living at sea level. Such cells have larger nuclei and a significantly greater volume of mitochondria. There are both more and larger lamellar bodies in high altitude granular pneumocytes, resulting in about four times more surfactant per cell at high altitude.     

急性低氧对高原土生动物藏系绵羊血气的影响

为了探讨急性低氧时藏系绵羊(Ovis aries)的血气特点,揭示其低氧适应机制,将7只雄性藏系绵羊和5只雄性移居绵羊分别置于高低压氧舱内,测定模拟海拔0、2 300和4 500 m时各动物清醒状态下的血气指标。用热稀释法测定心输出量。使用血气分析仪和EG7血样板,测定动脉及混合静脉血的血气指标,按Ficks方法计算氧耗量。结果显示,随着模拟海拔高度的升高,藏羊和移居羊的动静脉血氧饱和度(So2)、氧分压(Po2)、二氧化碳分压(Pco2)都呈明显下降趋势(P<0.05),血红蛋白浓度(Hb)、血液pH、心输出量及氧耗量虽无明显的差异性改变,但它们在4 500 m处的绝对值是增加的。在相同海拔,藏羊的Hb明显低于移居羊(P<0.05),4 500 m时藏羊的动脉血氧饱和度(Sao2)及组织摄氧量显著高于移居羊(P<0.05)。表明藏羊在急性低氧时表现出的高Sao2及高组织摄氧量,低Hb、低pH是它适应高原低氧的生理基础。     

Profiling of the yak skeletal muscle tissue gene expression and comparison with the domestic cattle by genome array

Of all the mammals of the world, the yak lives at the highest altitude area of more than 3000 m. Comparison between yak and cattle of the low-altitude areas will be informative in studying animal adaptation to higher altitudes. To investigate the molecular mechanism involved in meat quality differences between the two Chinese special varieties Qinghai yak and Qinchuan cattle, 12 chemical–physical characteristics of the longissimus dorsi muscle related to meat quality were compared at the age of 36 months, and the gene expression profiles were constructed by utilizing the bovine genome array. Significant analysis of microarrays was used to identify the differentially expressed genes. Gene ontology and pathway analysis were performed by a free Web-based Molecular Annotation System 2.0. The results reveal ~11 000 probes representing about 10 000 genes that were detected in both the Qinghai yak and Qinchuan cattle. A total of 1922 genes were shown to be differentially expressed, 633 probes were upregulated and 1259 probes were downregulated in the muscle tissue of Qinghai yak that were mainly involved in ubiquitin-mediated proteolysis, muscle growth regulation, glucose metabolism, immune response and so on. Quantitative real-time PCR (qRT-PCR) was performed to validate some differentially expressed genes identified by microarray. Further analysis implied that animals living at a high altitude may supply energy by more active protein catabolism and glycolysis compared with those living in the plain areas. Our results establish the groundwork for further studies on yaks’ meat quality and will be beneficial in improving the yaks’ breeding by molecular biotechnology.     

The effect of ”living high–training low” on physical performance in rats

In this research, we hypothesized that, in rats, adaptation to high altitude (2500 m) plus training at low altitude (610 m), ”living high–training low”, improves physical performance at low altitude more than living and training at low altitude (610 m). Rats were divided into four groups: (1) living at low altitude (LL, n=12), (2) living and training at low altitude (LLTL, n=13), (3) living at high altitude (LH, n=12), (4) living at high altitude and training at low altitude (LHTL, n=13). The program for living at high altitude involved raising rats under hypobaric hypoxia (equivalent to 2500 m), and the training program consisted of running on a tread-mill at low altitude. All groups were raised at each altitude and trained to run at 35 m/min for 40 min/day, 6 days/week for 6 weeks. During this program, we measured heart rates both at rest and during exercise, and performed running-time trials. The mean heart rate during exercise was lower in groups with training than in groups without training, and the groups receiving training could run longer than the untrained groups. The LHTL group especially showed the lowest mean heart rate during exercise and the longest running time among all groups. After 6 weeks of the training program, all rats had a catheter implanted into the carotid artery, and the mean systemic arterial pressure was continuously measured during treadmill running. The rate of increase of this pressure as the running intensity increased was lower in groups with training than in groups without training, especially in the LHTL group. Finally, we anesthetized all the rats and extracted both the right and left ventricles, and the triceps surae and liver. Training increased the weight of the left ventricle, triceps surae, and liver. The increase in weight of the left ventricle and triceps surae was higher in the LHTL group than in the LLTL group in particular. It appeared that living high– training low may be an effective strategy to improve performance ability at low altitude. Received: 16 July 1999 / Revised: 24 January 2000 / Accepted: 25 January 2000     

Phylogeographical analysis shows the need to protect the wild yaks' last refuge in Nepal

The wild yak Bos mutus was believed to be regionally extinct in Nepal for decades until our team documented two individuals from Upper Humla, north‐western Nepal, in 2014. The International Union for Conservation of Nature (IUCN) seeks further evidence for the conclusive confirmation of that sighting. We conducted line transects and opportunistic sign surveys in the potential wild yak habitats of Humla, Dolpa, and Mustang districts between 2015 and 2017 and collected genetic samples (present and historic) of wild and domestic yaks Bos grunniens. We also sighted another wild yak in Upper Humla in 2015. Phylogenetic and haplotype network analyses based on mitochondrial D‐loop sequences (~450 bp) revealed that wild yaks in Humla share the haplotype with wild yaks from the north‐western region of the Qinghai‐Tibetan Plateau in China. While hybridization with domestic yaks is a major long‐term threat, illegal hunting for meat and trophy put the very small populations of wild yaks in Nepal at risk. Our study indicates that the unprotected habitat of Upper Humla is the last refuge for wild yaks in Nepal. We recommend wild yak conservation efforts in the country to focus on Upper Humla by (i) assigning a formal status of protected area to the region, (ii) raising awareness in the local communities for wild yak conservation, and (iii) providing support for adaptation of herding practice and pastureland use to ensure the viability of the population.     

Muscular blood flow in human highlanders and in lowlanders living at altitude (3 800 m) (author's transl)]

Muscular blood flow (MBF) was measured in the tibialis anteiror muscle by the 133Xe washout technique. Measurements were made in lowlanders at sea level, in native highlanders at 3 800 m and in lowlanders who had been living at this altitude for less than 6 months. At rest and during exercise, MBF is smaller in highlanders and in the high altitude visitors than in lowlanders. If, instead of total blood flow, the red cell flow is calculated (by multiplying MBF by the haematocrit) these differences are no longer significant at rest and are minimized during exercice. These results are consistent with reduction of cardiac output and blood supply to other regions in subjects who are acclimatized to altitude.     

Dynamics of morphometric indicators of rat testes during adaptation to high-altitude in the Antarctic regions with subsequent dysadaptation

In the experiments performed on 100 white non-inbred male rats (some of them have been kept at the altitude of 3.488 m in the station Vostok, and others--at the coastal level in the station Mirny) testes have been studied, as well as morphometric analysis of convoluted seminiferous tubules and estimation of spermatogenesis activity. During the first month of living at the altitude the section area of the convoluted seminiferous tubules decreases, while the area of their lumen increases. During subsequent periods in the animals, living at the altitude, differences in the parameters, in comparison with the control, disappear. During the first 6 months of their living at the altitude a sharp decrease in spermatogenesis activity is observed. A month of life at the coastal level (after 10 months of hypoxic effect) does not result in normalization of the spermatogenesis activity.