Genotyping of TRIM5 locus in northern pig-tailed macaques (Macaca leonina), a primate species susceptible to Human Immunodeficiency Virus type 1 infection

Background: The pig-tailed macaques are the only Old World monkeys known to be susceptible to human immunodeficiency virus type 1 (HIV-1) infection. We have previously reported that the TRIM5-Cyclophilin A (TRIMCyp) fusion in pig-tailed macaques (Macaca n

A multi-locus phylogeny of Nectogalini shrews and influences of the paleoclimate on speciation and evolution

Nectogaline shrews are a major component of the small mammalian fauna of Europe and Asia, and are notable for their diverse ecology, including utilization of aquatic habitats. So far, molecular phylogenetic analyses including nectogaline species have been unable to infer a well-resolved, well-supported phylogeny, thus limiting the power of comparative evolutionary and ecological analyses of the group. Here, we employ Bayesian phylogenetic analyses of eight mitochondrial and three nuclear genes to infer the phylogenetic relationships of nectogaline shrews. We subsequently use this phylogeny to assess the genetic diversity within the genus Episoriculus, and determine whether adaptation to aquatic habitats evolved independently multiple times. Moreover, we both analyze the fossil record and employ Bayesian relaxed clock divergence dating analyses of DNA to assess the impact of historical global climate change on the biogeography of Nectogalini. We infer strong support for the polyphyly of the genus Episoriculus. We also find strong evidence that the ability to heavily utilize aquatic habitats evolved independently in both Neomys and Chimarrogale + Nectogale lineages. Our Bayesian molecular divergence analysis suggests that the early history of Nectogalini is characterized by a rapid radiation at the Miocene/Pliocene boundary, thus potentially explaining the lack of resolution at the base of the tree. Finally, we find evidence that nectogalines once inhabited northern latitudes, but the global cooling and desiccating events at the Miocene/Pliocene and Pliocene/Pleistocene boundaries and Pleistocene glaciation resulted in the migration of most Nectogalini lineages to their present day southern distribution. (C) 2010 Elsevier Inc. All rights reserved.

Improving productivity - Opening the black box

Hourly productivity levels in the UK still remain behind those in some competitor countries. The government devotes much policy attention to enhancing productivity and continues to emphasise its five drivers - investment, innovation, skills, enterprise, and competition. This article argues that it is investment broadly defined that is the key to sustained productivity improvement. The emphasis should be on improving productivity simultaneously with improving the quality of production. Only thus will the gains be widely shared. In achieving these aims there are two prerequisites for policy-makers. The first is to ensure better coordination of policy than appears to be currently achieved by the present departmental structures in Whitehall. The second is to recognize fully the long and complex chain of causation that can be triggered by pulling on one policy lever. Such complexity can only be fully understood by more research on what actually goes on inside the black box of the organization. © 2006 Oxford University Press.

Developpement de la peche artisanale dans les eaux Burundaises du Lac Tanganyika

A light fishery for "Ndagala" (Strolothrissa tanganicae) has been practised for many years on Lake Tanganyika. Initially this had a low catch rate, but has since been developed by the introduction of an artisanal fishery unit based on the catamaran. A unit consists of a pair of metal canoes joined together. The fish are attracted by three lights mounted on the structure, and are caught with a pyramid-shaped lift net. Selected beaches have been reserved for the artisanal fishery and the numher of units operating has increased from 12 in 1957 to 538 in 1972. The mean annual catch per unit is 11,000 kg, which is not sufficient for the fishery to be economic. However, prediction of a possible mean catch as high as 40 tons year encouraged the Burundi Government to launch a project with help from the Freedom from Hunger Campaign. This was designed to develop the fishery by the creation of artisanal fishing centres, and to make available a large number of fully equipped catamarans which could be paid for by a system of hire-purchase. The success of the project has illustrated that the furnishing of adequate equipment can bring about a transformation of the traditional fishery.

Clustering user data for user modelling in the GUIDE multi-modal set-top box

Chapter 20 Clustering User Data for User Modelling in the GUIDE Multi-modal Set- top Box PM Langdon and P. Biswas 20.1 ... It utilises advanced user modelling and simulation in conjunction with a single layer interface that permits a ...

The unidirectional emptying box

A theoretical description of the turbulent mixing within and the draining of a dense fluid layer from a box connected to a uniform density, quiescent environment through openings in the top and the base of the box is presented in this paper. This is an extension of the draining model developed by Linden et al. (Annu. Rev. Fluid Mech. vol. 31, 1990, pp. 201-238) and includes terms that describe localized mixing within the emptying box at the density interface. Mixing is induced by a turbulent flow of replacement fluid into the box and as a consequence we predict, and observe in complementary experiments, the development of a three-layer stratification. Based on the data collated from previous researchers, three distinct formulations for entrainment fluxes across density interfaces are used to account for this localized mixing. The model was then solved numerically for the three mixing formulations. Analytical solutions were developed for one formulation directly and for a second on assuming that localized mixing is relatively weak though still significant in redistributing buoyancy on the timescale of the draining process. Comparisons between our theoretical predictions and the experimental data, which we have collected on the developing layer depths and their densities show good agreement. The differences in predictions between the three mixing formulations suggest that the normalized flux turbulently entrained across a density interface tends to a constant value for large values of a Froude number FrT, based on conditions of the inflow through the top of the box, and scales as the cube of FrT for small values of FrT. The upper limit on the rate of entrainment into the mixed layer results in a minimum time (tD) to remove the original dense layer. Using our analytical solutions, we bound this time and show that 0.2tE ≈tD tE, i.e. the original dense layer may be depleted up to five times more rapidly than when there is no internal mixing and the box empties in a time tE. © 2010 Cambridge University Press.

金鱼DEAD-box家族基因p68和p110在配子发生中的表达特征

利用组织原位杂交技术,以地高辛标记的反义RNA为探针,检测了金鱼(Carassius auratus)DEAD-box家族基因p68和p110在卵子发生及精子发生中的表达分布特点。结果表明:在金鱼配子发生中,p68基因在各个时期的卵母细胞均有表达,Ⅰ、Ⅱ期卵母细胞中的表达水平较Ⅲ、Ⅳ期卵母细胞中更高。p68基因的表达只限于精原细胞和初级精母细胞中。p110基因在金鱼精子发生各阶段持续表达,其中精原细胞和初级精母细胞中表达水平较高;在卵子发生中,Ⅰ期卵母细胞中没有p110 RNA阳性信号,Ⅱ期卵母细胞中信号

黄鳝DEAD-box家族PL10基因的克隆与序列分析

通过PCR克隆的方法,从黄鳝(Monopterus albus)中得到两个PL10 基因的cDNA片段Mo PL10A和Mo PL10B,长度均为1.127 kb,推测其编码375个氨基酸的蛋白片段.结合其他PL10类同源物序列,对这两条cDNA进行了分析和初步的功能推测.根据此片段的氨基酸序列构建的系统发育树与形态分类结果一致.在不同组织中的RT PCR结果表明Mo PL10A和Mo PL10B的mRNA在各组织中的分布有差异.

Comparative study and expression analysis of the interferon gamma gene locus cytokines in Xenopus tropicalis

Using bioinformatics approach, the genome locus containing interleukin (IL)-22, IL-26, and interferon gamma (IFN-gamma) genes has been identified in the amphibian, Xenopus tropicalis. Like that in other vertebrates such as fish, birds, and mammals, the Xenopus IL-22, IL-26, and IFN-gamma are clustered in the same chromosome and the adjacent genes are conserved. The genomic structures of the Xenopus IL-22, IL-26, and IFN-gamma gene were identical to that of their mammalian counterparts. The Xenopus IL-22 and IL-26 genes contained five exons and four introns while the Xenopus IFN-gamma gene consisted of four exons and three introns. The Xenopus IL-22, IL-26, and IFN-gamma share 14.1-41.6%, 14.6-31.2%, and 23.7-36.5% identity to their counterparts in other species, respectively. Reverse-transcription polymerase chain reaction (PCR) and real-time quantitative PCR analyses revealed that the expression of IL-22, IL-26, and IFN-gamma genes was significantly upregulated after simulation with bacterial polyliposaccharide and/or synthetic double-stranded poly(I:C), suggesting these cytokines like those in other vertebrates play an important role in regulating immune response in Xenopus.

Development and characterization of polymorphic microsatellite loci in the endangered Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis)

The finless porpoise (Neophocaena phocaenoides) is one of the smallest cetacean species widely distributed in the shallow coastal waters of the Indo-Pacific Oceans. The population size of the Yangtze subspecies (N. p. asiaeorientalis) has sharply decreased in the last two decades and access to objective data on its population structure and genetic diversity would be of great assistance for their proper management. Here we report on the isolation of nine polymorphic microsatellite using the "Fast Isolation by AFLP of Sequences Containing repeats" (FIASCO) protocol. Polymorphism was assessed using 30 porpoise individuals randomly sampled in the Yangtze River. The number of alleles per locus varies from 2 to 9, with an average value of 5.56, whereas the ranges of observed and expected heterozygosi ties were 0.300-0.633 (mean 0.496) and 0.473-0.804 (mean 0.659), respectively.

Construction and characterization of a Lipotes vexillifer genomic DNA BAC library

We constructed a genomic DNA library for Lipotes vexillifer (L. vexillifer), the Baiji or Yangtze River dolphin, one of the most endangered mammals in the world. The library consists of 149,000 BAC clones, with an average insert size of 83 kb, representing approximately 3.4 haploid genome equivalents. PCR amplification of four known L. vexillifer genes yielded two to four positive clones each. To demonstrate the utility of this library, we isolated and sequenced the L. vexillifer alpha lactalbumin gene, which is a gene specific to mammals and one which has been widely used as molecular tool in phylogenetic analysis. We also end-sequenced 20 randomly selected clones, resulting in the identification of at least five new L. vexilliter genes, five SSR loci, and one SINE locus. These results suggest that this library is a valuable resource for candidate gene cloning, physical mapping, and genome sequencing of this important and threatened species.

Complex mutation at a microsatellite locus in sturgeons: Acipenser sinensis, A-schrenckii, A-gueldenstaedtii and A-baerii

Cross-species amplifications of microsatellite locus Spl-106, which was originally screened from the genome of shovelnose sturgeon (Scaphirhynchus platorynchus) with a perfect TAGA repeat motif, were carried out in four other species of the genera Acipenser. A total of 34 polymerase chain reaction (PCR) products representing 16 different alleles of this locus was sequenced. Sequence analysis results showed that besides the number changes of repeat units, many mutational events, such as single-base substitutions and various insertion/deletion (indels) occurred not only at species level but also at individual level, even among the different alleles within the same individual. The repeat motifs varied from perfect (TAGA)n array to perfect compound (TAAA)m (GAAA)n and perfect or imperfect compound (TAAA)m (TAGA)n (TAAA)x arrays in different species and different individuals. The evolution dynamics of this locus in sturgeons was inferred in that it may evolve from a single perfect to different perfect or imperfect compounds.

Predictive entropy search for efficient global optimization of black-box functions

We propose a novel information-theoretic approach for Bayesian optimization called Predictive Entropy Search (PES). At each iteration, PES selects the next evaluation point that maximizes the expected information gained with respect to the global maximum. PES codifies this intractable acquisition function in terms of the expected reduction in the differential entropy of the predictive distribution. This reformulation allows PES to obtain approximations that are both more accurate and efficient than other alternatives such as Entropy Search (ES). Furthermore, PES can easily perform a fully Bayesian treatment of the model hyperparameters while ES cannot. We evaluate PES in both synthetic and real-world applications, including optimization problems in machine learning, finance, biotechnology, and robotics. We show that the increased accuracy of PES leads to significant gains in optimization performance.