SNPlexing the human Y-chromosome: a single-assay system for major haplogroup screening

SNPs are one of the main sources of DNA variation among humans. Their unique properties make them useful polymorphic markers for a wide range of fields, such as medicine, forensics, and population genetics. Although several high-throughput techniques have been (and are being) developed for the vast typing of SNPs in the medical context, population genetic studies involve the typing of few and select SNPs for targeted research. This results in SNPs having to be typed in multiple reactions, consuming large amounts of time and of DNA. In order to improve the current situation in the area of human Y-chromosome diversity studies, we decided to employ a system based on a multiplex oligo ligation assay/PCR (OLA/PCR) followed by CE to create a Y multiplex capable of distinguishing, in a single reaction, all the major haplogroups and as many subhaplogroups on the Y-chromosome phylogeny as possible. Our efforts resulted in the creation of a robust and accurate 35plex (35 SNPs in a single reaction) that when tested on 165 human DNA samples from different geographic areas, proved capable of assigning samples to their corresponding haplogroup.     

双光子激发荧光成像技术对小鼠植入前胚胎的实时观测

双光子激发的蓝移效应可使利用同一束超快激光同时激发多种不同荧光特性的生物荧光染料的设想得以实现。选取锁模飞秒掺钛蓝宝石(Ti-sapphire)激光器输出的730nm激光,分别激发Hoechst33342,Fluo-4,PI和Indo-1四种常用生物荧光染料,分别利用(455±15)nm,(540±15)nm,(580±16)nm和(500±15)nm四种滤光片获得特异性荧光图像。结合双光子激发荧光成像技术穿透深,光损伤小,信噪比好等优势,选取合适的荧光染料组,应用单束激光激发、双染双通道成像方法,对小鼠植入前胚胎内细胞中的钙信号和染色体进行三维、四维实时成像,为探究小鼠植入前胚胎发育规律提供一种全新的多参数观测手段。     

Chromosome segregation in Escherichia coli division: a free energy-driven string model

Although the mechanisms of eukaryotic chromosome segregation and cell division have been elucidated to a certain extent, those for bacteria remain largely unknown. Here we present a computational string model for simulating the dynamics of Escherichia coli chromosome segregation. A novel thermal-average force field accounting for stretching, bending, volume exclusion, friction and random fluctuation is introduced. A Langevin equation is used to simulate the chromosome structural changes. The mechanism of chromosome segregation is thereby postulated as a result of free energy-driven structural optimization with replication introduced chromosomal mass increase. Predictions of the model agree well with observations of fluorescence labeled chromosome loci movement in living cells. The results demonstrate the possibility of a mechanism of chromosome segregation that does not involve cytoskeletal guidance or advanced apparatus in an E. coli cell. The model also shows that DNA condensation of locally compacted domains is a requirement for successful chromosome segregation. Simulations also imply that the shape-determining protein MreB may play a role in the segregation via modification of the membrane pressure.     

Karyotype differentiation patterns in species of the subfamily Scarabaeinae (Scarabaeidae, Coleoptera)

The aim of this study was to describe the karyotype of species belonging to the subfamily Scarabaeinae (Coleoptera, Scarabaeidae) and to compile the conventional cytogenetic data available in the literature for this group. The karyotypes of ten species belonging to the tribes Canthonini, Coprini, Onthophagini and Phanaeini were analyzed by conventional staining. Eight of these species were described for the first time (Canthon aff carbonarius, Canthon chalybaeus, Coprophanaeus dardanus, Deltochilum aff amazonicum, Dichotomius geminatus, Oxysternon silenus, Phanaeus chalcomelas and Malagoniella aff astyanax) and two were redescribed (Diabroctis mimas and Digitonthophagus gazella) since their karyotypes differed from those previously published in the literature. Four species studied showed a diploid number of 2n = 20 and a parachute type sex determining system and the karyotype was 2n = 20,Xy in two species and 2n = 18,Xy_p, 2n = 19,X0, 2n = 12,XY and 2n = 14,neoXY in one each. The chromosome morphology of the different species varied, with the observation of metacentric, submetacentric, subacrocentric and acrocentric chromosomes. The X chromosome was predominantly meta or submetacentric in the species analyzed, whereas the y chromosome presented two arms or was punctiform. In conclusion, the subfamily Scarabaeinae comprises 120 species analyzed cytogenetically, and are observed the occurrence of five chromosome rearrangements (autosome–autosome and X-autosome fusions, pericentric inversions, fissions and loss of the y chromosome) that are related to the chromosome variability and evolution in the group.     

Linking topology of large DNA molecules

Double helix DNA molecules, the carriers of genetic instructions in cells, are strongly affected by their topological properties. Two distinct and biologically important types of linking are associated with double helix DNAs: ‘internal’ linking of the two strands of individual double helices, and ‘external’ linking of separate double helix DNAs. The constraint of internal linking gives rise to internal torsional stress and supercoiling of circular DNAs. External linking is a likely outcome of DNA replication, and must be eliminated by the cell in order to separate duplicated DNAs. I outline some of the physics and biology connected with both internal and external linking.     

玉米（Zea mays L．）cdc2基因的染色体原位杂交物理定位

首次报道了玉米低拷贝ｃｄｃ２基因非放射性标记的探针染色体原位杂交的物理定位．供试探针为玉米，ｐ３４ｃｄｃ２的ｃＤＮＡ克隆ｃｄｃ２ＺｍＡ，片段长度仅为１．３ｋｂ．原位杂交检测结果表明，该基因位置在第４染色体及第９染色体长臂，同时在第８染色体长臂亦有杂交信号检出．３处信号检出位置距着丝粒距离和长臂长度百分比分别为５４．７９±２．５１６，８７．９４±１．５３７和２５．８６±０．８５６在第４、９和８染色体上信号检出率分别为２４．６％，１２．３％和６．６％．本文还就非放射原位杂交技术以及ｃｄｃ２基因在玉米基因组中的物理位置与其功能间的关系作了探讨     

Effect of nuclear magnetic resonance on chromosomes of mouse bone marrow cells

Three groups of six male Balb/c mice, subjected to 30 MHz continuous wave NMR exposure in a static magnetic field of 7.05 K Gauss for one hour, were each compared to another group of ten unexposed mice with respect to chromatid and chromosomal aberrations. The exposed groups were sacrificed at two hours, 24 hours and 48 hours following NMR exposure respectively. Control mice were sacrificed 24 hours after sham-exposure. All groups had approximately 0.02 apparent aberrations per cell. These apparent aberrations were in the form of metacentric chromosomes, possibly resulting from a union of chromosomes at their centromeres or possibly simply chromosomes in association. The results are consistent with earlier in vitro findings that NMR exposure causes no adverse cytogenetic effects.     

“组合—矩阵法”推算j—j耦合谱项

首次应用组合一矩阵法推引ｊ－ｊ耦合谱项。     

Global and local real-coded genetic algorithms based on parent-centric crossover operators

Parent-centric real-parameter crossover operators create the offspring in the neighbourhood of one of the parents, the female parent. The other parent, the male one, defines the range of the neighbourhood. With the aim of improving the behaviour of these crossover operators, we present three processes that are performed before their application. First, a female and male differentiation process determines the individuals in the population that may become female or/and male parents. Then, two different selection mechanisms choose the female and male parents from each group. In addition, we tackle the election of the most adequate evolution model to take out profit from these parent selection mechanisms. The experimental results confirm that these three processes may enhance the operation of the parent-centric crossover operators.