不同海拔饲育的麦洼牦牛肺脏组织转录组学分析

为了探讨牦牛适应高海拔低氧环境的基因表达特征与规律,对在高海拔（3 560 m）和低海拔地区（478 m）饲育4个月的2.5~3岁健康雄性麦洼牦牛肺组织进行转录组测序。转录组测序采用Illumina高通量测序平台(HiSeqTM2500/4000)进行,并以qRT-PCR验证差异表达基因的表达量。结果显示,高海拔组牦牛肺脏转录组平均每个测序样本得到约5.76亿条Clean Reads,低海拔组牦牛中得到约6.10亿条Clean Reads,比对到参考基因组上的Reads数分别占91.74%和91.28%以上,共发现了2 047个新转录本。低海拔组与高海拔组牦牛肺脏组织之间共有199个差异表达基因,其中含89个差异上调表达基因和110个差异下调表达基因。所得差异表达基因富集在297个GO条目和146个KEGG通路中,包含62个低氧适应相关的GO条目和35个低氧适应相关代谢通路。其中低氧适应相关GO条目在生物过程、细胞组成和分子功能三种类别中占比最多的分别为细胞粘附、蛋白复合物和钙离子结合。低氧适应相关KEGG通路中占比最多的为肿瘤坏死因子(TNF)信号通路,其次为低氧诱导因子1(HIF-1)信号通路。qRT-PCR验证结果显示,Ⅱ类人类白细胞抗原α链(HLA-DOA、HLA-DRA)、补体因子 (C2)和甘露糖结合凝集素相关丝氨酸蛋白酶1（MASP1）基因的表达量变化与转录组测序结果相符。本研究为全局和深入理解牦牛肺组织转录本表达对高海拔低氧的响应提供了有价值的切入点。     

Hypoxic regulation of the 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase gene family (PFKFB-1-4) expression in vivo

When oxygen becomes limiting, cells shift primarily to a glycolytic mode for generation of energy. A key regulator of glycolytic flux is fructose-2,6-bisphosphate (F-2,6-BP), a potent allosteric regulator of 6-phosphofructo-1-kinase (PFK-1). The levels of F-2,6-BP are maintained by a family of bifunctional enzymes, 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFKFB or PFK-2), which have both kinase and phosphatase activities. Each member of the enzyme family is characterized by their phosphatase:kinase activity ratio (K:B) and their tissue-specific expression. Previous work demonstrated that one of the PFK-2 isozyme genes, PFKFB-3, was induced by hypoxia through the hypoxia-inducible factor-1 (HIF-1) pathway. In this study we examined the basal and hypoxic expression of three members of this family in different organs of mice. Our findings indicate that all four isozymes (PFKFB-1-4) are responsive to hypoxia in vivo. However, their basal level of expression and hypoxia responsiveness varies in the different organs studied. Particularly, PFKFB-1 is highly expressed in liver, heart and skeletal muscle, with the highest response to hypoxia found in the testis. PFKFB-2 is mainly expressed in the lungs, brain and heart. However, the highest hypoxia responses are found only in liver and testis. PFKFB-3 has a variable low basal level of expression in all organs, except skeletal muscle, where it is highly expressed. Most importantly, its hypoxia responsiveness is the most ample of all three genes, being strongly induced in the lungs, liver, kidney, brain, heart and testis. Further studies showed that PFKFB-1 and PFKFB-2 were highly responsive to hypoxia mimics such as transition metals, iron chelators and inhibitors of HIF hydroxylases, suggesting that the hypoxia responsiveness of these genes is also regulated by HIF proteins. In summary, our data demonstrate that PFK-2 genes are responsive to hypoxia in vivo, indicating a physiological role in the adaptation of the organism to environmental or localized hypoxia/ischemia.     

Anoxia- and hypoxia-induced expression of LDH-A* in the Amazon Oscar, Astronotus crassipinis

Adaptation or acclimation to hypoxia occurs via the modulation of physiologically relevant genes, such as erythropoietin, transferrin, vascular endothelial growth factor, phosphofructokinase and lactate dehydrogenase A. In the present study, we have cloned, sequenced and examined the modulation of the LDH-A gene after an Amazonian fish species, Astronotus crassipinis (the Oscar), was exposed to hypoxia and anoxia. In earlier studies, we have discovered that adults of this species are extremely tolerant to hypoxia and anoxia, while the juveniles are less tolerant. Exposure of juveniles to acute hypoxia and anoxia resulted in increased LDH-A gene expression in skeletal and cardiac muscles. When exposed to graded hypoxia juveniles show decreased LDH-A expression. In adults, the levels of LDH-A mRNA did not increase in hypoxic or anoxic conditions. Our results demonstrate that, when given time for acclimation, fish at different life-stages are able to respond differently to survive hypoxic episodes.     

牦牛Atg5基因克隆及其在输卵管、卵巢和子宫中的表达定位

自噬是一种保守的细胞内降解过程,在多种生物体内证实自噬有重要的生物学意义。但是自噬在牦牛这一高原特色物种体内的研究未见报道。因此为探索正常生理条件下自噬相关基因在牦牛生殖过程中的表达,本研究分别采集牦牛不同繁殖周期（卵泡期、黄体期及妊娠期）的主要生殖器官（输卵管、卵巢、子宫）,克隆牦牛自噬相关基因5（Autophagy related 5,Atg5）基因并进行生物信息学分析;利用qRT-PCR检测Atg5 基因在组织中的相对表达量;并采用蛋白质免疫印迹（Western-blot, WB）检测Atg5和Atg5-Atg12（Autophagy related 12,自噬相关基因12）复合体在不同组织中的表达水平;免疫组织化学方法分析Atg5在各生殖器官中的分布特征。结果显示,成功克隆牦牛Atg5基因在进化过程中高度保守,编码的蛋白质为可溶性的非跨膜蛋白;qRT-PCR和WB检测结果显示Atg5和Atg5-Atg12复合体在牦牛输卵管、卵巢和子宫中均有表达。其中卵泡期卵巢Atg5-Atg12表达显著高于黄体期和妊娠期,卵泡期Atg5的表达却显著低于黄体期和妊娠期;黄体期输卵管Atg5-Atg12表达量显著高于卵泡期和妊娠期,妊娠期输卵管中Atg5的表达量显著高于卵泡期和黄体期;卵泡期和妊娠期子宫中Atg5-Atg12的表达量显著高于黄体期,而黄体期子宫中的Atg5的表达量又显著高于妊娠期和卵泡期,在蛋白水平上Atg5和Atg5-Atg12的表达呈负相关。免疫组织化学结果显示Atg5在输卵管黏膜上皮,卵巢卵泡膜、颗粒层、生殖上皮、黄体细胞,子宫内膜和子宫腺体均有表达。研究结果表明自噬在牦牛体内与其他物种相似具有保守性,通过检测Atg5-Atg12复合体在牦牛生殖器官中的表达,推测自噬可能参与牦牛生殖生理过程的调控。该研究结果对自噬在其他大型哺乳动物以及高寒低氧环境中动物的研究具有借鉴意义,有助于自噬参与其他动物生殖生理作用机制的研究。       

The pulmonary circulation of some domestic animals at high altitude

Pulmonary haemodynamics and the histology of the pulmonary vasculature have been studied at high altitude in the yak, in interbreeds between yaks and cattle, and in domestic goats and sheep indigenous to high altitudes together with crosses between them and low-altitude strains. Cattle at high altitude had a higher pulmonary arterial pressure than cattle at low altitude. The yak and two interbreeds with cattle (dzos and stols) had a low pulmonary arterial pressure compared with cattle, while the medial thickness of the small pulmonary arteries was less than would be expected in cattle, suggesting that the yak has a low capacity for hypoxic pulmonary vasoconstriction and that this characteristic is transmitted genetically. Goats and sheep showed haemodynamic evidence of a limited response of the pulmonary circulation to high altitude, but no evidence that the high altitude breeds had lost this response. There were no measurable differences in the thickness of the media of the small pulmonary arteries between high- and low-altitude breeds of goats and sheep. All these species showed prominent intimal protrusions of muscle into the pulmonary veins but no specific effect of high altitude in this respect.     

高原低氧胁迫对小鼠肝脏功能及基因表达的影响

低氧作为青藏高原最为特殊的环境因素之一,对高原动物的适应进化产生了深刻的影响。持续的低氧暴露会损伤肝脏功能,引起动物机体代谢紊乱,但连续低氧处理对子代肝脏的影响仍缺乏相关研究。本研究将成年小鼠转移至高原低氧环境 (海拔3 220 m) 饲养并繁殖,以常氧条件下饲养小鼠为对照,统计低氧处理小鼠 (低氧第0代) 及其子代 (低氧第1 ~ 5代) 生长数据,发现长期低氧暴露导致小鼠肝脏比重增加,肝细胞肿胀,肝索间红细胞浸润,并且子一代小鼠肝小叶出现脂肪变性。血液生化指标显示,相比于对照组 (常氧第0代),低氧第0代和低氧第1代的谷丙转氨酶和谷草转氨酶水平显著上升 (P < 0.05);血清白蛋白、球蛋白、总胆红素和总胆固醇水平在低氧第0代中下降,低氧第1代中上升 (P < 0.05)。空腹注射葡萄糖和胰岛素后低氧组小鼠的葡萄糖耐受能力和胰岛素敏感性显著减弱 (P < 0.05)。常氧第0代、低氧第0代及低氧第1代肝脏RNA-seq分析发现,低氧第0代和低氧第1代共有的459个差异基因显著富集在MAPK、细胞凋亡、脂质代谢和内质网等信号通路。本研究发现低氧胁迫对子代小鼠肝脏具有重要影响,此结果对肝脏低氧生理和高原肝脏疾病的研究具有重要的借鉴意义。     

高原鼢鼠肺组织细胞凋亡相关 基因的进化分析及其在不同 海拔条件下的表达模式

高原鼢鼠（Myospalax baileyi）是青藏高原特有的地下鼠,其地下洞道严重缺氧。一般来说,低氧会促进细胞凋亡。为了探讨高原鼢鼠适应低氧环境的分子机制,本文应用生物信息学方法对p53下游凋亡促进基因Pidd、Fas、Bax、Puma、Apaf-1、Scotin、Perp、Igfbp3和凋亡抑制基因Bcl-2的序列和编码的氨基酸序列进行了进化分析,并以SD大鼠（Rattus norvegicus）为对照,研究了这些基因在不同海拔环境条件下（3 300 m和2 260 m）的表达模式。结果表明：（1）高原鼢鼠细胞凋亡基因的序列与以色列鼹鼠（Nannospalax galili）同源性最高;预测的PIDD、PUMA、Apaf-1、IGFBP3和BCL-2编码蛋白结构域与以色列鼹鼠的存在明显的趋同进化位点;SIFT评估发现,高原鼢鼠和以色列鼹鼠与其他物种相比,p53、PIDD、PUMA、Apaf-1和IGFBP3氨基酸序列分别在78、853、157、320和285号位点的变异对其功能有显著影响;（2）在高海拔条件下（3 300 m）,高原鼢鼠肺组织中凋亡促进基因Pidd、Bax、Puma和Apaf-1表达水平显著下降,凋亡抑制基因Bcl-2表达水平显著升高,而在SD大鼠中凋亡促进基因和凋亡抑制基因的表达水平均没有变化;高原鼢鼠中Bcl-2/Bax比值随海拔的升高显著上升,而在SD大鼠中没有变化。以上结果提示,高原鼢鼠p53结构变异可能导致其下游基因表达模式与SD大鼠不同,其中凋亡促进基因Pidd、Bax、Puma和Apaf-1表达水平下降,凋亡抑制基因Bcl-2表达水平上升,从而抑制了细胞在低氧条件下的凋亡;在长期低氧的作用下,高原鼢鼠p53下游基因产物PIDD、PUMA、Apaf-1和IGFBP3产生了影响其功能的变异位点,这可能改变了它们与发挥功能的复合物的结合力,从而抑制了细胞凋亡。因此,通过长期的低氧适应,高原鼢鼠肺组织中与细胞凋亡相关的基因产物结构发生变异,导致其基因表达水平发生变化,从而抑制细胞凋亡,这是高原鼢鼠适应地下低氧洞道生境的分子机制之一。     

Effects of embryonic hypoxia on lip formation

The upper lip is formed by the fusion of facial processes, a process in which many genetic and environmental factors are involved. Embryonic hypoxia is induced by uterine anemia and the administration of vasoconstrictors during pregnancy. To define the relationship between hypoxia and upper lip formation, hypoxic conditions were created in a whole embryo culture system. Hypoxic embryos showed a high frequency of impaired fusion, reflecting failure in the growth of the lateral nasal process (LNP). In hypoxic embryos, cell proliferation activity in the LNP mesenchyme was decreased following downregulation of genes that are involved in lip formation. We also observed upregulation of vascular endothelial growth factor expression along with the induction of apoptosis in the LNP. These results suggest that embryonic hypoxia during lip formation induces apoptosis in physiologically hypoxic regions, hypoxia-induced gene expression and downregulation of the genes involved in maxillofacial morphogenesis as immediate responses, followed by reduction of mesenchymal cell proliferation activity, resulting in insufficient growth of the facial processes.     

Evidence for species-specific clock gene expression patterns in hamster peripheral tissues

Rhythmic oscillations that repeat every 24 h can be found in numerous behavioral and physiological functions. Beside the endogenous master clock in the suprachiasmatic nucleus (SCN), peripheral oscillators exist that can disengage from the master clock rhythm by different mechanisms. The fact that core clock genes in peripheral tissues do not always have the same characteristics as in the SCN suggests that their function may vary in different organs. Additionally, suggestions about species-specific variation in expression peak and nadir times, especially in the testis, led to the need for systematical investigations on clock gene expression patterns in different organs and species under standardized methodological conditions. Therefore, daily gene expression patterns of the clock genes Bmal1, Period1, Period2, Clock, Cryptochrome1 and Cryptochrome2 were recorded at each of eight time points during a 24 hour period in the testis, kidney, liver, spleen and heart of three hamster species (Phodopus sungorus, Phodopus roborovskii and Cricetulus griseus; family: Cricetidae). Clock gene expression was found to be rhythmic in all investigated organs, however with inconsistent results in the testis. Complex cosinor analysis revealed species differences in temporal gene expression patterns regarding their orthophase, number of peaks, and amplitude for all genes and organs with most pronounced differences in the testis. The results of this study strongly indicate that clock gene expression in peripheral tissues is species-specific and that their functions might be at least partly connected to clock-unrelated traits that vary between the investigated species. Further studies should aim at clarifying the specific roles of clock genes in the testis.     

牦牛水通道蛋白AQP1和AQP3基因克隆及在不同组织中表达和定位

水通道蛋白（Aquaporin,AQP）广泛存在于生物体的各组织部位,影响着生物体水代谢的过程。为进一步研究水通道蛋白1（AQP1）和水通道蛋白3（AQP3）生物学功能,本文对牦牛（Bos grunniens）不同组织中AQP1和AQP3基因的表达与定位进行了研究。采用PCR方法扩增牦牛AQP1和AQP3基因,对其序列进行生物信息学分析,采用qPCR方法检测2个基因在牦牛不同种组织中的表达量,采用免疫组织化学的方法分析AQP1和AQP3蛋白在组织中的定位和表达。结果表明,牦牛AQP1和AQP3基因CDS区分别为816 bp和840 bp,与野牦牛的同源性最高为99%。AQP1和AQP3基因的表达量在肾脏中最高,显著高于心脏、肝脏、脾脏、肺脏、肌肉、小肠和瘤胃,AQP1基因在各组织中的表达均高于AQP3基因的表达。AQP1和AQP3蛋白定位发现其主要分布于肾脏近曲小管、小肠固有层细胞和瘤胃颗粒层细胞中,均在肾脏中的表达量最高。AQP1蛋白在脾脏、小肠和肌肉组织中的表达极显著高于AQP3蛋白表达。该研究结果对高寒低氧环境中动物的研究具有借鉴意义,有助于牦牛AQP1和AQP3功能研究。     

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.     

Differences in mitochondrial gene expression profiles, enzyme activities and myosin heavy chain types in yak versus bovine skeletal muscles

Hypoxia can affect energy metabolism. We examined gene expression and enzyme activity related to mitochondrial energy metabolism, as well as myosin heavy chain (MyHC) types in yaks (Bos grunniens) living at high altitudes. Real-time quantitative PCR assays indicated that the yak has significantly lower levels of carnitine palmitoyltransferase (CPT) mRNA in the biceps femoris and lower levels of uncoupling protein 3 (UCP3) mRNA in both biceps femoris and longissimus dorsi than in Yellow cattle. No significant differences between yak and Yellow cattle were observed in the activities of mitochondrial β-hydroxyacyl-CoA dehydrogenase, isocitrate dehydrogenase and cytochrome oxidase in the same muscles. Semi-quantitative RT-PCR analysis showed that the MyHC 1 mRNA levels in yak biceps femoris was lower than in Yellow cattle. We conclude that the yak has significantly lower mRNA levels of CPT, UCP3, and MyHC 1 in biceps femoris than in Yellow cattle, suggesting that the yak biceps femoris has lower fatty acid oxidation capacity and greater glycolytic metabolic potential.     

Lung-selective gene responses to alveolar hypoxia: potential role for the bone morphogenetic antagonist gremlin in pulmonary hypertension

Pulmonary hypoxia is a common complication of chronic lung diseases leading to the development of pulmonary hypertension. The underlying sustained increase in vascular resistance in hypoxia is a response unique to the lung. Thus we hypothesized that there are genes for which expression is altered selectively in the lung in response to alveolar hypoxia. Using a novel subtractive array strategy, we compared gene responses to hypoxia in primary human pulmonary microvascular endothelial cells (HMVEC-L) with those in cardiac microvascular endothelium and identified 90 genes (forming 9 clusters) differentially regulated in the lung endothelium. From one cluster, we confirmed that the bone morphogenetic protein (BMP) antagonist, gremlin 1, was upregulated in the hypoxic murine lung in vivo but was unchanged in five systemic organs. We also demonstrated that gremlin protein was significantly increased by hypoxia in vivo and inhibited HMVEC-L responses to BMP stimulation in vitro. Furthermore, significant upregulation of gremlin was measured in lungs of patients with pulmonary hypertensive disease. From a second cluster, we showed that CXC receptor 7, a receptor for the proangiogenic chemokine CXCL12, was selectively upregulated in the hypoxic lung in vivo, confirming that our subtractive strategy had successfully identified a second lung-selective hypoxia-responsive gene. We conclude that hypoxia, typical of that encountered in pulmonary disease, causes lung-specific alterations in gene expression. This gives new insights into the mechanisms of pulmonary hypertension and vascular loss in chronic lung disease and identifies gremlin 1 as a potentially important mediator of vascular changes in hypoxic pulmonary hypertension.