Construction, characterization and chromosomal mapping of bacterial artificial chromosome (BAC) library of Yunnan snub-nosed monkey (Rhinopithecus bieti)

We constructed a high redundancy bacterial artificial chromosome library of a seriously endangered Old World Monkey, the Yunnan snub-nosed monkey (Rhinopithecus bieti) from China. This library contains a total of 136 320 BAC clones. The average insert size of BAC clones was estimated to be 148 kb. The percentage of small inserts (50-100 kb) is 2.74%, and only 2.67% non-recombinant clones were observed. Assuming a similar genome size with closely related primate species, the Yunnan snub-nosed monkey BAC library has at least six times the genome coverage. By end sequencing of randomly selected BAC clones, we generated 201 sequence tags for the library. A total of 139 end-sequenced BAC clones were mapped onto the chromosomes of Yunnan snub-nosed monkey by fluorescence in-situ hybridization, demonstrating a high degree of synteny conservation between humans and Yunnan snub-nosed monkeys. Blast search against human genome showed a good correlation between the number of hit clones and the size of the chromosomes, an indication of unbiased chromosomal distribution of the BAC library. This library and the mapped BAC clones will serve as a valuable resource in comparative genomics studies and large-scale genome sequencing of nonhuman primates. The DNA sequence data reported in this paper were deposited in GenBank and assigned the accession number CG891489-CG891703.

Compressive response of glass fiber composite sandwich structures

Sandwich panels with crushable foam cores have attracted significant interest for impulsive load mitigation. We describe a method for making a lightweight, energy absorbing, glass fiber composite sandwich structure and explore it is through thickness (out-of-plane) compressive response. The sandwich structure utilized corrugated composite cores constructed from delamination resistant 3D woven E-glass fiber textiles folded over triangular cross section prismatic closed cell, PVC foam inserts. The corrugated structure was stitched to 3D woven S2-glass fiber face sheets and infiltrated with a rubber toughened, impact resistant epoxy. The quasi-static compressive stress-strain response of the panels was experimentally investigated as a function of the strut width to length ratio and compared to micromechanical predictions. Slender struts failed by elastic (Euler) buckling which transitioned to plastic microbuckling as the strut aspect ratio increased. Good agreement was observed between experimental results and micromechanical predictions over the wide range of core densities investigated in the study.

Effects of adrenergic agonists on the extrahepatic expression of vitellogenin Ao1 in heart and brain of the Chinese rare minnow (Gobiocypris rarus)

Teleost vitellogenins (VTGs) are large multidomain apolipoproteins and traditionally considered as the estrogen responsive precursors of the major egg yolk proteins. We identified five clones encoding VTGs, about 16% of the random EST clones from our constructed cDNA library from Chinese rare minnow liver tissue treated with 17 beta-estradiol (E2). Full-length vtgAo1 has been obtained based on the sequence information of four partial cDNA inserts by RACE. The inducibility of the vtgAo1 expression in liver by E2 was confirmed by RT-PCR. The presence of vtgAo1 transcripts have been observed primarily in liver. However. a significant level of the vtgAo1 was found in an unexpected location, heart, particularly in atrial cells by RT-PCR and whole mount in situ hybridization analyses. The vtgAo1 mRNA expression in heart and liver tissue could be suppressed by both alpha-adrenergic agonist, phenylephrine (PE) and beta-adrenergic agonist, isoproterenol (ISO). The expression of VTG in the heart observed in the present studies suggested it may provide protection from surplus intracellular lipids in fish cardiomyocytes as triglyceride transport proteins do in mammals. The results also indicated that the production of teleost vtg in vivo can be regulated by riot only estrogenic agents, but adrenergic signals as well. (c) 2008 Elsevier B.V. All rights reserved.

大赖草总DNA转化小麦引起的HMW-GS基因变化及大赖草HMW-GS基因的克隆

应用花粉管通道技术将新疆大赖草总DNA导入小麦，用高重序列分析方法，已为大赖草总DNA转入小麦提供了初步的分子证据。在转 化后代中选育出稳定遗传的大穗变异株系，分析表明，这些转化株中蛋白质含量明显增高(13%-17%)。对基因供体新疆大赖草、受 体春麦761、转化株的高分子量谷蛋白亚基(HMW-GS)进行了SDS-PAGE分析，发现这些转化株中HMW-GS发生了很大变化，并在此基础 上，用来自小麦基因组的四对特异引物，以PCR方法扩增供体、受体以及转化株的1Ax、1Bx、1Dx及1Ay、1By、1Dy型HMW-GS全基因 ，比较他们扩增产物的差异，结果表明，受体与转化株在HMW-GS基因1Ax、1Bx位点上的扩增产物差异不大，在HMW-GS基因位点1Dx 和y型基因上的扩增产物有较大差异，说明了受体在基因位点1Dx、1Ay、1By和1Dy上可能发生了多位点插入，可能由于这些基因位 点上的插入引起了转化株的高分子量谷蛋白亚基(HMW-GS)的变化，这就再一次为大赖草总DNA导入提供了直接的分子证据。虽然大 赖草总DNA导入提高了小麦蛋白质的含量，改变了HMW-GS的组成，部分改变了品质评分，但我们感到这些转化株在品质改良方面仍 有很大余地，如何更好地利用新疆大赖草蛋白质的优良特性及避免总DNA导入给转化株带来的不良性状，一个大赖草HMW-GS基因正 被分离及克隆，并准备将其利用于未来的品质育种当中。Total DNA of Leymus racemosus had been transformed into wheat through pollen tube pathway. Analysis of the repeated gene sequence had provided an elementary proof. Some variant cultivars with big ear were screened from their offsprings, and their protein content increased greatly from 13% (receptor)to 17%(transformed). The result from SDS-PAGE analysis of high-molecular-weight glutenin subunits(HMW- GS) respectively in donor(Xinjiang Leymus racemosus), receptor(spring wheat cultivar 761)and transformed wheats, showed the HMW-GS composition changed in the transformed plants. On the basis of the research, Four special pairs primers from wheat(T.aestivum L.) genome were used to amplify complete coding regions of HMW-GS genes on 1Ax、1Bx 、1Dx and 1Ay、1By、1Dy loci of donor、receptor and the big ear transformed cultivars. By comparing amplified PCR products. Faint differences were found among receptor and transformed cultivar's 1Ax、1Bx PCR amplifed products and apparent differences on those of 1Dx、y-typePCR product. We gueseed that there may be some DNA inserts in 1Dx 、1By、1Dy loci resulted in the changes of the HMW-GS among transformed cultivars. This provides second direct molecular witness to the exogenous DNA introduction. Even though the transformed plants have higher protein content, changed HMW-GS composition, partially improved process quality, there still leave much work to improve quality. In order to make full use of the excellent property of Leymus racemosus protein and avoid the disadvantages introducced by total DNA transformation, a HMW-GS gene of Leymus racemosus was being isolated and cloned.

CSR闭轨测量系统的建立

本文给出用于CSR系统的闭轨测量系统，内容包括shoe-box类型的位置探针介绍、宽带信号处理系统介绍、实验室刻度结果和在线测试结果。论文首先介绍了基于不同工作原理的几种位置探针和信号处理方式，探针包括容式探针、感式探针、条带型探针和wave-guide类型。考虑到CSR系统的实际情况，确定CSR系统的闭轨测量系统选用容式探针以及宽带信号处理系统。比较常用的几种容式探针的性能，可以看出linear-cut类型的shoe-box位置探针在灵敏度和线性方面较为理想，因此选定shoe-box位置探针作为CSR系统的位置探针。电子学系统采用分路信号处理，信号通过宽带低噪声放大器放大之后直接使用采样率为60MS/s的采样卡采样，数字信号的处理使用软件作离线处理，方便灵活且各种功能容易扩展。接下来给出了实验室标定和在线测量的结果。实验室测试结果表明，在实验室噪声水平下，在整个CSR系统束流回旋频率范围内，由于频率的不同对位置测量带来的误差小于40μm；而由于信号强度变化带来的误差小于20μm；在固定频率条件下系统的分辨率好于20μm。在线测量结果表明，系统的分辨率好于20μm；系统除了能够实现闭轨测量以外，还可以实现对束团的监测、tune值的测量以及频率分散的测量。在此基础之上的其他工作，比如闭轨反馈控制系统、逐束团位置测量以及束团中心的横向相空间测量正在进行之中。最后，论文介绍了作者在博士论文期间所作的其他一些工作，包括束运线上的环形位置探针、CSR系统中的单丝剖面测量系统以及HIRFL浅层肿瘤治疗系统中的束诊控制系统

The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration

Sulfide: quinone oxidoreductase (SQR) is a flavoprotein with homologues in all domains of life except plants. It plays a physiological role both in sulfide detoxification and in energy transduction. We isolated the protein from native membranes of the hyperthermophilic bacterium Aquifex aeolicus, and we determined its X-ray structure in the "as-purified,'' substrate-bound, and inhibitor-bound forms at resolutions of 2.3, 2.0, and 2.9 angstrom, respectively. The structure is composed of 2 Rossmann domains and 1 attachment domain, with an overall monomeric architecture typical of disulfide oxidoreductase flavoproteins. A. aeolicus SQR is a surprisingly trimeric, periplasmic integral monotopic membrane protein that inserts about 12 angstrom into the lipidic bilayer through an amphipathic helix-turn-helix tripodal motif. The quinone is located in a channel that extends from the si side of the FAD to the membrane. The quinone ring is sandwiched between the conserved amino acids Phe-385 and Ile-346, and it is possibly protonated upon reduction via Glu-318 and/or neighboring water molecules. Sulfide polymerization occurs on the re side of FAD, where the invariant Cys-156 and Cys-347 appear to be covalently bound to polysulfur fragments. The structure suggests that FAD is covalently linked to the polypeptide in an unusual way, via a disulfide bridge between the 8-methyl group and Cys-124. The applicability of this disulfide bridge for transferring electrons from sulfide to FAD, 2 mechanisms for sulfide polymerization and channeling of the substrate, S2-, and of the product, S-n, in and out of the active site are discussed.

Construction and characterization of a bacterial artificial chromosome library of marine macroalga Porphyra yezoensis (Rhodophyta)

A large-DNA-fragment library is necessary for research into the Porphyra genome. In this study, a bacterial artificial chromosome (BAC) library of Porphyra yezoensis was constructed and characterized. The library contains 54,144 BAC clones with an average insert size of about 65 kb and fewer than 0.7% of clones without large inserts. Therefore, its capacity is more than 6.6 P. yezoensis genome equivalents, and the probability of recovering any nuclear DNA sequence from the library is higher than 99%. The library shows good fidelity and stability. A putative trehalose-6-phosphate synthase (TPS) gene was successfully screened out from the library. The above results show that the library is useful for gene cloning and genomic research in P. yezoensis.

Construction and characterization of two bacterial artificial chromosome libraries of Zhikong scallop, Chlamys farreri Jones et Preston, and identification of BAC clones containing the genes involved in its innate immune system

Large-insert bacterial artificial chromosome (BAC) libraries are necessary for advanced genetics and genomics research. To facilitate gene cloning and characterization, genome analysis, and physical mapping of scallop, two BAC libraries were constructed from nuclear DNA of Zhikong scallop, Chlamys farreri Jones et Preston. The libraries were constructed in the BamHI and MboI sites of the vector pECBAC1, respectively. The BamHI library consists of 73,728 clones, and approximately 99% of the clones contain scallop nuclear DNA inserts with an average size of 110 kb, covering 8.0x haploid genome equivalents. Similarly, the MboI library consists of 7680 clones, with an average insert of 145 kb and no insert-empty clones, thus providing a genome coverage of 1.1x. The combined libraries collectively contain a total of 81,408 BAC clones arrayed in 212 384-well microtiter plates, representing 9.1x haploid genome equivalents and having a probability of greater than 99% of discovering at least one positive clone with a single-copy sequence. High-density clone filters prepared from a subset of the two libraries were screened with nine pairs of Overgos designed from the cDNA or DNA sequences of six genes involved in the innate immune system of mollusks. Positive clones were identified for every gene, with an average of 5.3 BAC clones per gene probe. These results suggest that the two scallop BAC libraries provide useful tools for gene cloning, genome physical mapping, and large-scale sequencing in the species.

Construction of bacterial artificial chromosome libraries for Zhikong Scallop Chlamys farreri

Two Large-insert genomic bacterial artificial chromosome (BAC) libraries of Zhikong scallop Chlamys farreri were constructed to promote our genetic and genomic research. High-quality megabase-sized DNA was isolated from the adductor muscle of the scallop and partially digested by BamH I and Mbo I, respectively. The BamH I library consisted of 53 760 clones while the Mbo I library consisted of 7 680clones. Approximately 96 % of the clones in BamH I library contained nuclear DNA inserts in average size of 100 kb, providing a coverage of 5.3 haploid genome equivalents. Similarly, the Mbo I library with an average insert of 145 kb and no insert-empty clones, thus providing a genome coverage of 1.1 haploid genome equivalents.

Motion Planning with Six Degrees of Freedom

The motion planning problem is of central importance to the fields of robotics, spatial planning, and automated design. In robotics we are interested in the automatic synthesis of robot motions, given high-level specifications of tasks and geometric models of the robot and obstacles. The Mover's problem is to find a continuous, collision-free path for a moving object through an environment containing obstacles. We present an implemented algorithm for the classical formulation of the three-dimensional Mover's problem: given an arbitrary rigid polyhedral moving object P with three translational and three rotational degrees of freedom, find a continuous, collision-free path taking P from some initial configuration to a desired goal configuration. This thesis describes the first known implementation of a complete algorithm (at a given resolution) for the full six degree of freedom Movers' problem. The algorithm transforms the six degree of freedom planning problem into a point navigation problem in a six-dimensional configuration space (called C-Space). The C-Space obstacles, which characterize the physically unachievable configurations, are directly represented by six-dimensional manifolds whose boundaries are five dimensional C-surfaces. By characterizing these surfaces and their intersections, collision-free paths may be found by the closure of three operators which (i) slide along 5-dimensional intersections of level C-Space obstacles; (ii) slide along 1- to 4-dimensional intersections of level C-surfaces; and (iii) jump between 6 dimensional obstacles. Implementing the point navigation operators requires solving fundamental representational and algorithmic questions: we will derive new structural properties of the C-Space constraints and shoe how to construct and represent C-Surfaces and their intersection manifolds. A definition and new theoretical results are presented for a six-dimensional C-Space extension of the generalized Voronoi diagram, called the C-Voronoi diagram, whose structure we relate to the C-surface intersection manifolds. The representations and algorithms we develop impact many geometric planning problems, and extend to Cartesian manipulators with six degrees of freedom.

Molecular analysis of the anaerobic rumen fungus Orpinomyces - insights into an AT-rich genome

Matthew J. Nicholson, Michael K. Theodorou and Jayne L. Brookman. (2005). Molecular analysis of the anaerobic rumen fungus Orpinomyces - insights into an AT-rich genome. Microbiology, 151 (1), 121-133. Sponsorship: BBSRC RAE2008

Plantar Loading During Cutting While Wearing a Rigid Carbon Fiber Insert.

Context : Stress fractures are one of the most common injuries in sports, accounting for approximately 10% of all overuse injuries. Treatment of fifth metatarsal stress fractures involves both surgical and nonsurgical interventions. Fifth metatarsal stress fractures are difficult to treat because of the risks of delayed union, nonunion, and recurrent injuries. Most of these injuries occur during agility tasks, such as those performed in soccer, basketball, and lacrosse. Objective : To examine the effect of a rigid carbon graphite footplate on plantar loading during 2 agility tasks. Design :  Crossover study. Setting : Laboratory. Patients or Other Participants : A total of 19 recreational male athletes with no history of lower extremity injury in the past 6 months and no previous metatarsal stress fractures were tested. Main Outcome Measure(s) :  Seven 45° side-cut and crossover-cut tasks were completed in a shoe with or without a full-length rigid carbon plate. Testing order between the shoe conditions and the 2 cutting tasks was randomized. Plantar-loading data were recorded using instrumented insoles. Peak pressure, maximum force, force-time integral, and contact area beneath the total foot, the medial and lateral midfoot, and the medial, middle, and lateral forefoot were analyzed. A series of paired t tests was used to examine differences between the footwear conditions (carbon graphite footplate, shod) for both cutting tasks independently (α = .05). Results : During the side-cut task, the footplate increased total foot and lateral midfoot peak pressures while decreasing contact area and lateral midfoot force-time integral. During the crossover-cut task, the footplate increased total foot and lateral midfoot peak pressure and lateral forefoot force-time integral while decreasing total and lateral forefoot contact area. Conclusions : Although a rigid carbon graphite footplate altered some aspects of the plantar- pressure profile during cutting in uninjured participants, it was ineffective in reducing plantar loading beneath the fifth metatarsal.