Influence of finite-sites mutation, population subdivision and sampling schemes on patterns of nucleotide polymorphism for species with molecular hyperdiversity

Molecular hyperdiversity has been documented in viruses, prokaryotes and eukaryotes. Such organisms undermine the assumptions of the infinite-sites mutational model, because multiple mutational events at a site comprise a non-negligible portion of polymorphisms. Moreover, different sampling schemes of individuals from species with subdivided populations can profoundly influence resulting patterns and interpretations of molecular variation. Inspired by molecular hyperdiversity in the nematode Caenorhabditis sp. 5, which exhibits average pairwise differences among synonymous sites of >5% as well as modest population structure, we investigated via coalescent simulation the joint effects of a finite-sites mutation (FSM) process and population subdivision on the variant frequency spectrum. From many demes interconnected through a stepping-stone migration model, we constructed local samples from a single deme, pooled samples from several demes and scattered samples of a single individual from numerous demes. Compared with a single panmictic population at equilibrium, we find that high population mutation rates induce a deficit of rare variants (positive Tajima's D) under a FSM model. Population structure also induces such a skew for local samples when migration is high and for pooled samples when migration is low. Contrasts of sampling schemes for C. sp. 5 imply high mutational input coupled with high migration. We propose that joint analysis of local, pooled and scattered samples for species with subdivided populations provides a means of improving inference of demographic history, by virtue of the partially distinct patterns of polymorphism that manifest when sequences are analyzed according to differing sampling schemes.     

Molecular farming of pharmaceutical proteins

Molecular farming is the production of pharmaceutically important and commercially valuable proteins in plants. Its purpose is to provide a safe and inexpensive means for the mass production of recombinant pharmaceutical proteins. Complex mammalian proteins can be produced in transformed plants or transformed plant suspension cells. Plants are suitable for the production of pharmaceutical proteins on a field scale because the expressed proteins are functional and almost indistinguishable from their mammalian counterparts. The breadth of therapeutic proteins produced by plants range from interleukins to recombinant antibodies. Molecular farming in plants has the potential to provide virtually unlimited quantities of recombinant proteins for use as diagnostic and therapeutic tools in health care and the life sciences. Plants produce a large amount of biomass and protein production can be increased using plant suspension cell culture in fermenters, or by the propagation of stably transformed plant lines in the field. Transgenic plants can also produce organs rich in a recombinant protein for its long-term storage. This demonstrates the promise of using transgenic plants as bioreactors for the molecular farming of recombinant therapeutics, including vaccines, diagnostics, such as recombinant antibodies, plasma proteins, cytokines and growth factors. This revised version was published online in August 2006 with corrections to the Cover Date.     

hIL-6·hIL-6Rα·gp130三元复合物的结构预测

通过Ｄｅｌｐｈｉ方法分析人白介素６（ｈｕｍａｎ ｉｎｔｅｒｌｅｕｋｉｎ－６,ｈＩＬ－６）／人白介素６受体α亚基（ｈｕｍａｎ ｉｎｔｅｒｌｅｕｋｉｎ－６ ｒｅｃｅｐｔｏｒ α ｓｕｂｕｎｉｔ,ｈＩＬ－６Ｒα）复合物、ｇｐ１３０（βｓｕｂｕｎｉｔ）的空间构象的表现静电分布,利用分子对接方法研究ｇｐ１３０和ｈＩＬ－６／ｈＩＬ－６Ｒα复合物作用成三元复合物的空间构象,经过分子力学优化、分子动力学常温动态模     

DNA重排及体外分子进化

ＤＮＡ重排是目前为止最简便、最有效的体外定向进化技术,可以对单一基因、质粒、代谢途径、部分甚至整个基因组进行改造。本综述了ＤＮＡ重排的基本原理、特点、与其它体外进化技术的不同,着重介绍了其在体外分子进化上的广泛应用,并对应用前景进行了展望。     

Taxonomic investigation of five streptomycete cultures belonging to ISP standards

The taxonomic investigation of five streptomycete cultures belonging to the International Streptomyces Project (ISP) standards was carried out using the methods of population analysis, DNA-DNA hybridization, and multilocus DNA fingerprinting. Two species with names considered to be synonymous,S. alboviridis ISP 5326 andS. oligocarbophilus ISP 5589, were found to be actually identical. Three other species investigated,S. krainskii ISP 5321,S. craterifer ISP 5296, and 5.anulatus ISP 5361, whose names are usually referred to as synonymous, were shown to be different species.     

Stereotactic radiosurgery for patients with breast cancer brain oligometastases — molecular subtypes and clinical outcomes

BackgroundWe sought to determine the clinical outcomes of patients with breast cancer (BC) who had undergone stereotactic radiosurgery (SRS) for a limited number of brain metastases (BM) and to identify factors influencing overall survival (OS) and local control.Materials and methodsThe records of 45 patients who underwent SRS for 72 brain lesions were retrospectively evaluated. Statistics included the chi-squared test, Kaplan-Meier method, and the multivariate Cox model.ResultsThe median number of treated BM was 2 (range 1–10). Median OS from BM diagnosis and post-SRS were 27.6 [95% confidence interval (CI): 14.8–40.5) and 18.5 months (95% CI: 11.1–25.8), respectively. One-year and two-year survival rates after BM diagnosis were 55% and 41%, respectively. In a univariate analysis, the Luminal-B-human-epidermal-growth-receptor-positive (HER2+) subtype had the longest median OS at 39.1 months (95% CI: 34.1–44.1, p = 0.004). In an adjusted analysis, grade 2 [hazard ratio (HR): 0.1; 95% CI: 0.1–0.6, p = 0.005), craniotomy (HR: 0.3; 95% CI: 0.1–0.7; p = 0.006), and ≥ 2 systemic therapies received (HR: 0.3; 95% CI: 0.1–0.9, p = 0.028) were associated with improved OS. One-year and two-year intracranial progression-free survival rates were 85% and 63%, respectively. Four factors for a higher risk of any intracranial recurrence remained significant in the adjusted analysis, as follows: age < 50 years (HR: 4.2; 95% CI: 1.3–36.3; p = 0.014), grade 3 (HR: 3.7; 95% CI: 1.1–13.2; p = 0.038), HER2+ (HR: 6.9; 95% CI: 1.3–36.3; p = 0.023), and whether the brain was the first metastatic site (HR: 4.7; 95% CI: 1.6–14.5; p = 0.006).ConclusionIntrinsic BC characteristics are important determinants for both survival and intracranial control for patients undergoing SRS for oligometastatic brain disease.     

嗜肺巴斯德杆菌研究进展

嗜肺巴斯德杆菌(Pasteurella pneumotropica)是一种条件致病菌,人兽共患。主要危害啮齿类动物,特别是免疫缺陷或抑制的动物,可引起炎症和脓肿等症状。该菌是实验动物中感染率最高的病原菌之一,多呈隐性感染,给动物实验带来了极大的干扰。本文针对嗜肺巴斯德杆菌的流行病学、检测和鉴定、分子分型和防治等方面进行综述。     

神经钙蛋白δ的功能及其分子作用机制

神经钙蛋白δ(neurocalcinδ)作为神经钙敏感蛋白(neuronal calcium sensors,NCSs)家族的重要成员之一,具有分布广泛、结构较保守的特性.早期研究发现,神经钙蛋白δ具有两对EF手结构(EF1,EF2,EF3和EF4).EF1不能结合Ca2+,而EF2、EF3和EF4与Ca2+结合能促使其N端豆蔻酰暴露,进而实现其由细胞质到细胞质膜的转移定位以及与靶蛋白的结合,从而发挥重要效应.本综述根据神经钙蛋白δ的"Ca2+-豆蔻酰基开关"特性,一方面介绍其能与膜鸟苷酸环化酶反应,参与cGMP信号转导,进而影响视觉和嗅觉,甚至血压等生物学活动;另一方面,介绍神经钙蛋白δ通过与S100β、网格蛋白、肌动蛋白、微管等蛋白质之间的相互作用,并参与细胞内囊泡运输,从而影响细胞内大分子包装、运输等过程.本文还阐明了神经钙蛋白δ参与精子发生、细胞癌变、肾病发生等过程.由于神经钙蛋白δ对了解某些疾病的发生原理、信号转导过程、细胞内信息调控网络等具有重要意义,本综述将为研究相关疾病提供新的研究方向与理论基础.     

河北省华北落叶松河北群体遗传多样性分析

以来自河北8个群体共312个华北落叶松天然个体为材料,利用10对SSR引物对群体进行扩增,所得数据用于其遗传多样性和遗传结构的研究。结果表明:10对SSR位点共检测到42个位点,平均每个位点有4.2个等位基因,位点的等位基因数(Na)为2~6个。群体平均等位基因数为3.36,Shannon指数(I)平均为0.749,观察杂合度Ho为0.405、期望杂合度He为0.423,来自河北北部的围场台子水和吉字以及兴隆雾灵山的多样性水平最高,南部的阜平群体多样性水平最低。AMOVA分子差异分析显示3%的遗传变异存在于群体间,97%的遗传变异则存在于群体内,基因分化系数Gst仅为0.028,表明华北落叶松在河北的群体分化很低。聚类结果表明河北围场两个群体为一类,蔚县、隆化和涿鹿为一类,阜平和赤城为一类,兴隆雾灵山群体距离其他较远。多样性北部群体较高,南部较低,表明华北落叶松可能的衍化方向是从北向南,印证了北部可能是起源中心的结论。     

Multiple glacial refugia and complex postglacial range shifts of the obligatory woodland plant Polygonatum verticillatum (Convallariaceae)

The phylogeography of typical alpine plant species is well understood in Europe. However, the genetic patterns of boreo-montane species are mostly unstudied. Therefore, we analysed the AFLPs of 198 individuals of Polygonatum verticillatum over a major part of its European distribution. We obtained a total of 402 reproducible fragments, of which 96.8% were polymorphic. The average Φ _ST over all samples was high (73.0%). The highest number of private fragments was observed in the Cantabrian Mountains; the highest genetic diversities of the populations were detected in populations from the Alps. BAPS, Principal Coordinates and Cluster analyses revealed a deep split between the Cantabrian population and all other samples. The latter further distinguished two major groups in western and eastern Europe. These results suggest a complex biogeographical history of P. verticillatum . The Cantabrian population was most probably isolated for the longest time. Furthermore, putative glacial survival centres might have existed in the western group around the glaciated Alps and in the eastern group in the foothills of the Carpathian and Balkan mountain systems. The origin of the Scandinavian populations is still unresolved, but an origin from the southeastern Alps or the western Balkans appears the most likely scenario.