Gene tree correction for reconciliation and species tree inference: Complexity and algorithms

Reconciliation consists in mapping a gene tree T into a species tree S, and explaining the incongruence between the two as evidence for duplication, loss and other events shaping the gene family represented by the leaves of T. When S is unknown, the Species Tree Inference Problem is to infer, from a set of gene trees, a species tree leading to a minimum reconciliation cost. As reconciliation is very sensitive to errors in T, gene tree correction prior to reconciliation is a fundamental task. In this paper, we investigate the complexity of four different combinatorial approaches for deleting misplaced leaves from T. First, we consider two problems (Minimum Leaf Removal and Minimum Species Removal) related to the reconciliation of T with a known species tree S. In the former (latter respectively) we want to remove the minimum number of leaves (species respectively) so that T is “MD-consistent” with S. Second, we consider two problems (Minimum Leaf Removal Inference and Minimum Species Removal Inference) related to species tree inference. In the former (latter respectively) we want to remove the minimum number of leaves (species respectively) from T so that there exists a species tree S such that T is MD-consistent with S. We prove that Minimum Leaf Removal and Minimum Species Removal are APX-hard, even when each label has at most two occurrences in the input gene tree, and we present fixed-parameter algorithms for the two problems. We prove that Minimum Leaf Removal Inference is not only NP-hard, but also W[2]-hard and inapproximable within factor $c\ln n$, where n is the number of leaves in the gene tree. Finally, we show that Minimum Species Removal Inference is NP-hard and W[2]-hard, when parameterized by the size of the solution, that is the minimum number of species removals.     

H9N2亚型禽流感病毒细胞适应株细胞致病性和HA、NA基因序列分析

对分离自中国南方的H9N2亚型禽流感病毒A/Chicken/Guangxi/KMⅢ/99(H9N2)进行了MDCK细胞的连续传代和NA基因序列的初步分析.研究发现,病毒接种细胞36 h左右出现细胞病变(CPE),细胞肿胀变圆,聚集,脱落.流感病毒经MDCK细胞连续传代19代后,HA效价与亲代病毒相当.将传代获得的第19代病毒进行基因克隆,与亲代病毒进行序列比较,发现经传代后其HA1羧基端的分子特征是:R-S-S-R,仍属于非低致病力毒株.     

随机交配群体两对连锁杂合基因频率的演变模型

用差分方程组建立具有两对连锁杂合基因的随机交配群体4种基因10种基因型频率逐代演变的数学模型,把它们看成影射,发现不动点集位于一个超平面与一个超曲面的交集.超平面具有类似分岔点的性质,故逐代计算中需进行归一化处理.对育种工作中在哪一代选种有指导意义.     

草原兔尾鼠透明带3(lZP3)基因序列同源性比较

透明带3作为精子的初级受体是透明带的一种主要糖蛋白,而抗ZP3抗体能够阻止精卵结合.因此,ZP3被认为是避孕疫苗的候选免疫原.草原兔尾鼠是新疆的重要害鼠,将它的ZP3基因序列与GenBank上已发表的几种鼠的ZP3基因序列进行同源性比较,将有助于哺乳动物受精机理的阐明与免疫不育疫苗的设计,同时也有助于了解这些鼠在系统进化中的相对地位.     

Solving coupled Dyson-Schwinger equations on a compact manifold

We present results for the gluon and ghost propagators in SU (N) Yang-Mills theory on a four-torus at zero and non-zero temperatures from a truncated set of Dyson-Schwinger equations. When compared to continuum solutions at zero temperature sizeable modifications due to the finite volume of the manifold, especially in the infrared, are found. Effects due to non-vanishing temperatures T, on the other hand, are minute for T < 250 MeV.     

人nov基因全长cDNA克隆、测序及其组织表达谱分析

采用特异性mRNA富集技术，从人早期胚胎中得到人nov基因(novH)的cDNA克隆，序列分析表明，该基因cDNA序列由2389个碱基对组成，包含一段长1071bp的开放阅读框(ORF)，3′端含有加尾信号AATAAA和ply(A)尾巴。Northern杂交显示，在Hela细胞和肾上腺组织中有表达的novHmRNA，大小约为2．5kb；多组织RNA点杂交分析结果进一步表明，novH基因在肾上腺和主动脉中的表达水平相对较高，在成人肾、肝、肺和小肠组织中亦有少量的表达。     

一个新的凋亡抑制蛋白P49的表达及氨基酸序列分析

从海灰翅夜蛾核型多角体病毒（SpliNPV)中新发现的p49基因可抑制病毒感染引起的草地贪夜蛾细胞Sf9的凋亡，用杆状病毒表达系统Bac to Bac克隆表达并收获P49蛋白，发现所测定的表达蛋白的氨基酸序列与由核苷酸推导的氨基酸序列一致，证明p49基因经克隆转染后得到正确表达，P49蛋白上－^91TVTDG^95－氨基酸序列为Caspase识别结构，比较P35与P49蛋白，两蛋白同源性约为48．8％，且都具Caspase识别和切割的氨基酸序列。     

嗜麦芽假单胞菌质粒pSH1的限制图谱及km~r标记的克隆

对嗜麦芽假单胞菌Ｐ２菌株（ＰｓｅｕｄｏｍｏｎａｓｍａｌｔｏｏｈｉｌｉａＰ２）的质粒ｐＳＨ１进行了限制酶切分析，确定了ＢｇｌⅡ、ＥｃｏＲⅠ、ＰｓｔⅠ、ＸｂａⅠ、ＢａｍＨⅠ、ＢｇｌⅠ、及ＰｖｕⅡ共７种限制性内切酶在ｐＳＨ１、质粒上的切割位点，前４种酶均为单一切点；后３种依次为２、７、５个切点．通过双酶切和部分酶切的方法绘制了ｐＳＨ１质粒的限制酶切图谱．将ｐＧＰ１－２质粒上的卡那霉素抗性基因（ｋｍｒ）片段插入ｐＳＨ１，获得了重组质粒ｐＳＨ２．ｐＳＨ２是由ｐＧＰ１－２质粒上大小为２．９０ｋｂ的ＤＮＡ片段（含ｋｍｒ）和ｇｈＨ１经ＢａｍＨⅠ－ＰｓｔⅠ双酶切产生５．７０ｋｂ大片段组成，它能够重新转化到喀麦芽假单胞菌受体（ｋｍｒ）中，其ｋｍｒ标记能够得到稳定的表达．