GPGPU加速生物序列比对研究进展

序列比对是生物信息学中最常用和最经典的研究手段。生物序列比对需要有强大计算能力的硬件支撑,而近年快速发展起来的GPGPU正好可堪此任。本文首先介绍GPGPU的发展过程,进而讲述GPGPU硬件设备与其编程环境,然后对GPGPU做科学计算时需要的数学库函数做一介绍,最后综述近年来国内外基于GPGPU的生物序列比对软件和相关研究工作,并总结和展望其辉煌前景。     

陕南早寒武世ANABARITES壳体内部结构及亲缘关系探讨

陕南灯影组宽川铺段的小壳化石具完好的三维保存方式。Anabarites是三辐射对称、单管底栖群居生物,亲缘关系不明。作者通过对陕南宁强下寒武统宽川铺段进行数次系统采样,经过对样品的醋酸溶蚀处理和电子扫描电镜照像后,发现Anabarites壳体内部具螺旋状微结构;经测试分析后认为该结构可能与中槽的深浅成正相关,两者的形成可能与微环境中水体的变化有关。探讨其可能的亲缘关系及其演化序列。     

冬眠和非冬眠状态达乌尔黄鼠肾单位及相关功能因子的比较

冬眠是动物应对冬季低温和食物匮乏的一种生存策略。达乌尔黄鼠(Spermophilus dauricus)是典型的贮脂类冬眠动物。为研究冬眠动物肾脏的适应机制,本实验采用组织学、血液生化分析及酶联免疫方法检测了夏季活动期(7月)、冬眠期(12月)和早春出眠后(3月)达乌尔黄鼠肾单位形态学及血清肌酐、尿素和抗利尿激素(ADH)的变化,并用qPCR方法检测了肾脏水通道蛋白基因(AQP1、AQP2和AQP3)、ADH受体(V2R)及内皮型一氧化氮合酶基因(eNOS)的表达。结果发现,冬眠期和早春出眠期的达乌尔黄鼠肾小球密度、近曲小管和远曲小管的相对管径、皮质部近曲小管数与远曲小管数比值均低于夏季活动期;冬眠期血清肌酐和尿素浓度高于夏季活动期和早春出眠期,ADH浓度及其受体V2R基因表达低于夏季活动期;冬眠期AQP1基因表达高于早春出眠期,AQP3基因表达低于夏季活动期,AQP2基因表达无显著差异;冬眠期eNOS基因表达低于早春出眠期。这些结果表明冬眠的达乌尔黄鼠表现出较低的肾功能;不同时期的水通道蛋白,eNOS及ADH表现出适应性的功能调节。该实验结果丰富了对冬眠动物肾脏适应机制的认识。     

Amino acid starvation‐induced LDLR trafficking accelerates lipoprotein endocytosis and LDL clearance

Mammalian cells utilize Akt‐dependent signaling to deploy intracellular Glut4 toward cell surface to facilitate glucose uptake. Low‐density lipoprotein receptor (LDLR) is the cargo receptor mediating endocytosis of apolipoprotein B‐containing lipoproteins. However, signaling‐controlled regulation of intracellular LDLR trafficking remains elusive. Here, we describe a unique amino acid stress response, which directs the deployment of intracellular LDLRs, causing enhanced LDL endocytosis, likely via Ca²⁺ and calcium/calmodulin‐dependent protein kinase II‐mediated signalings. This response is independent of induction of autophagy. Amino acid stress‐induced increase in LDL uptake in vitro is comparable to that by pravastatin. In vivo, acute AAS challenge for up to 72 h enhanced the rate of hepatic LDL uptake without changing the total expression level of LDLR. Reducing dietary amino acids by 50% for 2 to 4 weeks ameliorated high fat diet‐induced hypercholesterolemia in heterozygous LDLR‐deficient mice, with reductions in both LDL and VLDL fractions. We suggest that identification of signaling‐controlled regulation of intracellular LDLR trafficking has advanced our understanding of the LDLR biology, and may benefit future development of additional therapeutic strategies for treating hypercholesterolemia.     

美国白蛾在我国发生的世代变化分析

美国白蛾是原产于北美地区的世界性植物检疫性害虫,自1979年发现入侵我国以来,严重威胁我国的生态安全。近年来,随着全球气候变暖,美国白蛾疫情不断南扩,其化性在一些地区出现新的变化。本文根据1979—2021年该虫发生扩散情况和各地区监测普查结果,结合部分地区温度变化数据,全面分析了美国白蛾入侵我国以来的发生扩散过程,对比分析了各地区发生世代数及变化情况,阐明部分地区世代数增加的原因。针对美国白蛾世代数演变规律和反复暴发成灾的情况,提出了当前应关注的几个重点问题:世代数增加引发的扩张速率显著上升;扩张潜力与沿长江地区扩散趋势减缓关系;暴发成灾时有发生与本土化趋势不明显。鉴于当前外来入侵物种管理要求提高及多年来美国白蛾防控工作中暴露的一些问题,提出要在守护国家生物安全底线前提下制定防治策略、在统筹生物多样性保护下实现控制目标、在做好应急准备下摸清暴发成灾规律、在强化疫情检疫管理中提高疫情认定效率等对策。     

稻-渔共作农田一株优势真菌LW-1对土壤碱解氮、有效磷、土壤酶活性及镉生物有效性的影响

为了探讨稻-鳅-蛙共作农田优势真菌对土壤碱解氮、有效磷、土壤酶活性及镉污染土壤镉生物有效性的影响,本研究分离、纯化及初步鉴定稻-鳅-蛙农田土壤中的优势真菌LW-1,并将其扩繁后制成1×10³、1×10⁵、1×10⁷个/mL孢子3种浓度的菌液,最后将3种浓度的菌液和空白菌液分别添加至0、5、10、20 mg/kg镉污染的土壤中,每10天取土壤样本检测土壤有效磷、碱解氮、转化酶、过氧化氢酶、脲酶有效态镉含量。结果表明,随着菌液浓度的增加,土壤中碱解氮和有效磷的含量显著增加(P<0.05),土壤转化酶和脲酶活性均显著性提高(P<0.05),而有效态镉的含量显著降低(P<0.05)。这说明稻-鳅-蛙共作农田中的优势真菌可提高土壤肥力并降低镉污染土壤的生物有效性,研究结果为该模式在土壤改良和修复中的应用提供理论依据,也为理解稻-鳅-蛙共作农田土壤肥力高于常规稻田的机制提供了新的视角。     

在实验动物水平通过恢复和改善胰岛β细胞功能的糖尿病治疗新进展

糖尿病是一个世界性问题,在中国就有超过1.3亿人患有糖尿病.糖尿病主要分为1型糖尿病和2型糖尿病.遗憾的是,糖尿病至今尚未达成有效的预防和治愈手段.但是,近年来的一系列突破性的研究成果,让我们看到了治愈糖尿病的希望.在这里我们回顾了目前关于1型糖尿病和2型糖尿病可能的治愈途径的研究进展.这些途径包括胰岛移植和1型糖尿病...     

PRIMORDIAL GERM CELL-DERIVED MOUSE EMBRYONIC GERM (EG) CELLSIN VITRORESEMBLE UNDIFFERENTIATED STEM CELLS WITH RESPECT TO DIFFERENTIATION CAPACITY AND CELL CYCLE DISTRIBUTION

Embryonic germ (EG) cells of line EG-1 derived from mouse primordial germ cells were investigated for theirin vitrodifferentiation capacity. By cultivation as embryo-like aggregates EG-1 cells differentiated into cardiac, skeletal muscle and neuronal cells accompanied by the expression of tissue-specific genes and proteins as shown by RT-PCR analysis and indirect immunofluorescence. In comparison to embryonic stem (ES) cells of line D3 the efficiency of differentiation into cardiac and muscle cells was comparatively low, whereas spontaneous neuronal differentiation was more efficient than in D3 cells. Furthermore, the distribution of cell cycle phases as a parameter for the differentiation state was analysed in undifferentiated EG cells and ES cells and compared to data obtained for embryonic carcinoma (EC) cells of line P19 and differentiated, epithelioid EPI-7 cells. Flow cytometric analysis revealed similar cell cycle phase distributions in EG, EC and ES cells. In contrast, the somatic differentiated EPI-7 cells showed a longer G₁-phase and shorter S- and G₂/M-phases. Together, our results demonstrate that the differentiation state and capacity of EG cellsin vitroresemble that of totipotent ES cells.     

The intermediary metabolite pyruvate attenuates stunning and reduces infarct size in in vivo porcine myocardium

The intermediary metabolite pyruvate has been shown to exert significant beneficial effects in in vitro models of myocardial oxidative stress and ischemia-reperfusion injury. However, there have been few reports of the ability of pyruvate to attenuate myocardial stunning or reduce infarct size in vivo. This study tested whether supraphysiological levels of pyruvate protect against reversible and irreversible in vivo myocardial ischemia-reperfusion injury. Anesthetized, open-chest pigs (n = 7/group) underwent 15 min of left anterior descending coronary artery (LAD) occlusion and 3 h of reperfusion to induce stunning. Load-insensitive contractility measurements of regional preload recruitable stroke work (PRSW) and PRSW area (PRSWA) were generated. Vehicle or pyruvate (100 mg/kg i.v. bolus + 10 mg x kg(-1) x min(-1) intra-atrial infusion) was administered during ischemia and for the first hour of reperfusion. In infarct studies, pigs (n = 6/group) underwent 1 h of LAD ischemia and 3 h of reperfusion. Group I pigs received vehicle or pyruvate for 30 min before and throughout ischemia. In group II, the infusion was extended through 1 h of reperfusion. In the stunning protocol, pyruvate significantly improved the recovery of PRSWA at 1 h (50 +/- 4% vs. 23 +/- 3% in controls) and 3 h (69 +/- 5% vs. 39 +/- 3% in controls) reperfusion. Control pigs exhibited infarct sizes of 66 +/- 1% of the area at risk. The pyruvate I protocol was associated with an infarct size of 49 +/- 3% (P < 0.05), whereas the pyruvate II protocol was associated with an infarct size of 30 +/- 2% (P < 0.05 vs. control and pyruvate I). These findings suggest that pyruvate attenuates stunning and decreases myocardial infarction in vivo in part by reduction of reperfusion injury. Metabolic interventions such as pyruvate should be considered when designing the optimal therapeutic strategies for limiting myocardial ischemia-reperfusion injury.     

北祁连山东段早石炭世棘鱼类、辐鳍鱼类和软骨鱼类--北祁连山东段石炭纪鱼类序列研究之一

对甘肃靖远一带和内蒙古自治区黑山地区早石炭世前黑山组、臭牛沟组和靖远组中三亚纲鱼类微体化石进行了形态学和古组织学研究。这些化石涉及 7个目或亚目 ,含 4属 4种 ,其中有 2新种。文中记述的属均为全球广布的属。建立了 3个早石炭世鱼类组合 ,这是我国早石炭世第一个鱼类组合序列。辐鳍鱼类和软骨鱼类中 2个目的化石均为我国早石炭世鱼类的首次记录