Reciprocal chromosome painting among human, aardvark, and elephant (superorder Afrotheria) reveals the likely eutherian ancestral karyotype

The Afrotheria, a supraordinal grouping of mammals whose radiation is rooted in Africa, is strongly supported by DNA sequence data but not by their disparate anatomical features. We have used flow-sorted human, aardvark, and African elephant chromosome painting probes and applied reciprocal painting schemes to representatives of two of the Afrotherian orders, the Tubulidentata (aardvark) and Proboscidea (elephants), in an attempt to shed additional light on the evolutionary affinities of this enigmatic group of mammals. Although we have not yet found any unique cytogenetic signatures that support the monophyly of the Afrotheria, embedded within the aardvark genome we find the strongest evidence yet of a mammalian ancestral karyotype comprising 2n = 44. This karyotype includes nine chromosomes that show complete conserved synteny to those of man, six that show conservation as single chromosome arms or blocks in the human karyotype but that occur on two different chromosomes in the ancestor, and seven neighbor-joining combinations (i.e., the synteny is maintained in the majority of species of the orders studied so far, but which corresponds to two chromosomes in humans). The comparative chromosome maps presented between human and these Afrotherian species provide further insight into mammalian genome organization and comparative genomic data for the Afrotheria, one of the four major evolutionary clades postulated for the Eutheria.

Cross-species chromosome painting in the golden mole and elephant-shrew: support for the mammalian clades Afrotheria and Afroinsectiphillia but not Afroinsectivora

Cross-species painting (fluorescence in situ hybridization) with 23 human (Homo sapiens (HSA)) chromosome-specific painting probes (HSA 1-22 and the X) was used to delimit regions of homology on the chromosomes of the golden mole (Ghrysochloris asiaticus) and elephant-shrew (Elephantulus rupestris). A cladistic interpretation of our data provides evidence of two unique associations, HSA 1/19p and 5/21/3, that support Afrotheria. The recognition of HSA 5/3/21 expands on the 3/21 synteny originally designated as an ancestral state for all eutherians. We have identified one adjacent segment combination (HSA2/8p/4) that is supportive of Afroinsectiphillia (aardvark, golden mole, elephant-shrew). Two segmental combinations (HSA 10q/17 and HSA 3/20) unite the aardvark and elephant-shrews as sister taxa. The finding that segmental syntenies in evolutionarily distant taxa can improve phylogenetic resolution suggests that they may be useful for testing sequence-based phylogenies of the early eutherian mammals. They may even suggest clades that sequence trees are not recovering with any consistency and thus encourage the search for additional rare genomic changes among afrotheres.

Characterization and Comparison of the Tissue-Related Modules in Human and Mouse

Background: Due to the advances of high throughput technology and data-collection approaches, we are now in an unprecedented position to understand the evolution of organisms. Great efforts have characterized many individual genes responsible for the interspecies divergence, yet little is known about the genome-wide divergence at a higher level. Modules, serving as the building blocks and operational units of biological systems, provide more information than individual genes. Hence, the comparative analysis between species at the module level would shed more light on the mechanisms underlying the evolution of organisms than the traditional comparative genomics approaches. Results: We systematically identified the tissue-related modules using the iterative signature algorithm (ISA), and we detected 52 and 65 modules in the human and mouse genomes, respectively. The gene expression patterns indicate that all of these predicted modules have a high possibility of serving as real biological modules. In addition, we defined a novel quantity, "total constraint intensity,'' a proxy of multiple constraints (of co-regulated genes and tissues where the co-regulation occurs) on the evolution of genes in module context. We demonstrate that the evolutionary rate of a gene is negatively correlated with its total constraint intensity. Furthermore, there are modules coding the same essential biological processes, while their gene contents have diverged extensively between human and mouse. Conclusions: Our results suggest that unlike the composition of module, which exhibits a great difference between human and mouse, the functional organization of the corresponding modules may evolve in a more conservative manner. Most importantly, our findings imply that similar biological processes can be carried out by different sets of genes from human and mouse, therefore, the functional data of individual genes from mouse may not apply to human in certain occasions.

A practical demonstration of scalable, parallel mesh generation

Cambridge Flow Solutions Ltd, Compass House, Vision Park, Cambridge, CB4 9AD, UK Real-world simulation challenges are getting bigger: virtual aero-engines with multistage blade rows coupled with their secondary air systems & with fully featured geometry; environmental flows at meta-scales over resolved cities; synthetic battlefields. It is clear that the future of simulation is scalable, end-to-end parallelism. To address these challenges we have reported in a sequence of papers a series of inherently parallel building blocks based on the integration of a Level Set based geometry kernel with an octree-based cut-Cartesian mesh generator, RANS flow solver, post-processing and geometry management & editing. The cut-cells which characterize the approach are eliminated by exporting a body-conformal mesh driven by the underpinning Level Set and managed by mesh quality optimization algorithms; this permits third party flow solvers to be deployed. This paper continues this sequence by reporting & demonstrating two main novelties: variable depth volume mesh refinement enabling variable surface mesh refinement and a radical rework of the mesh generation into a bottom-up system based on Space Filling Curves. Also reported are the associated extensions to body-conformal mesh export. Everything is implemented in a scalable, parallel manner. As a practical demonstration, meshes of guaranteed quality are generated for a fully resolved, generic aircraft carrier geometry, a cooled disc brake assembly and a B747 in landing configuration. Copyright © 2009 by W.N.Dawes.

Control of Arabidopsis flowering: the chill before the bloom.

The timing of the floral transition has significant consequences for reproductive success in plants. Plants gauge both environmental and endogenous signals before switching to reproductive development. Many temperate species only flower after they have experienced a prolonged period of cold, a process known as vernalization, which aligns flowering with the favourable conditions of spring. Considerable progress has been made in understanding the molecular basis of vernalization in Arabidopsis. A central player in this process is FLC, which blocks flowering by inhibiting genes required to switch the meristem from vegetative to floral development. Recent data shows that many regulators of FLC alter chromatin structure or are involved in RNA processing.

Freezing and cold storage of cat fish fillets

The freezing and cold storage changes occurring in skinless fillets of cat fish and the effect of packaging on the quality of frozen fillets during storage at -18°C were studied. Maximum shelf-life of 27 weeks was shown by fillets frozen as glazed (water) blocks and packed in polythene lined waxed cartons.

Investigations on long distance transportation of fish 1. Transportation of frozen fish from Cochin to Calcutta

Oil Sardine (Sardinella longiceps), mackerel (Rastrelliger kanagurta), cat fish (Arius sp.), threadfin bream (Nemipterus japonicus) and ribbon fish (Trichurus sp.) were frozen in glazed/unglazed blocks, packed in expanded polystyrene (EPS) insulated plywood boxes with and without additional ice and despatched in uninsulated parcel vans of trains from Cochin to Calcutta. The consignments reached the destination in excellent condition and were readily disposed off.

Studies on frozen storage of minced fish from threadfin bream

Minced fish prepared from threadfin bream (Nemipterus japonicus) was frozen as blocks, packed in polythene lined waxed cartons and stored at -23°C. The changes taking place during storage were followed. There was good correlation between the organoleptic quality, extractability of protein, cook drip loss and weight loss on thawing. The frozen minced fish was acceptable up to 28 weeks under frozen storage.

The propagation of the mud crab Scylla serrata (F.) de Haan

The mud crab Scylla serrata is an important commercial species found in many brackish areas in the Philippines. During spawning and hatching, the berried females migrate to the sea. Seeds for pond stocking are obtained from the wild. Because of the unpredictability of seed supply, there is a need to propagate the species artificially. Thus, spawning, larval rearing, maturation, and rematuration of the species are being studied. The first attempts at hatching S. serrata were successful with rates varying between 75% and 90%. Two out of three trials on larval rearing yielded a few megalops. The first zoeal stages were fed diatoms, rotifers, Artemia salina, and bread yeast. Overfeeding programs were implemented during the critical premolting periods to prevent weakening of the larvae and lessen cannibalism. Larval weakening during the premolt makes them susceptible to attacks by fungi like Lagenidium and ciliates like Vorticella. S. serrata larvae survived salinity levels as low as 15 ppt until the 14th day of rearing. Other larvae were able to survive in salinities of 30-32 ppt for 8 to 13 days. Zoeal molting was hastened by lowering the salinity to 25-27 ppt. Artificial broodstocking of juveniles and adult crabs has been made possible using a simple refuge system made of three-compartmented hollow blocks. This system has been helpful in minimizing fighting among crabs. Remarkable growth rates have been observed with feeds like mussel meat and trash fish. Average growth increments of 11 mm carapace length and 20 . 35 g body weight have been observed every fortnight. A newly spent spawner could gain additional weight of 22 . 5 g in only 6 days. Feeding rates of juveniles and adult crabs have been established based on the average body weight from an experiment using mussel meat. Crabs feed more at night. In another experiment, eyestalk ablation was found to be effective in inducing growth and mating. Aside from hastening the molting process, copulation is induced even among the small crabs (average carapace length = 55 mm). Natural mating lasts about 26 hr. A copulation which lasted for seven days with a break in between was observed.

Studies on frozen characteristics of individually quick frozen and block frozen mackerel

Studies on mackerel (Rastrelliger kanagurta) of medium (4%) and high (11%) lipid contents quick frozen individually (IQF) and as blocks (BF) and stored at -23°C showed that block frozen mackerel had higher frozen storage shelf-life than individually quick frozen samples. IQF samples of medium and high lipid contents had shelf-lives of 17 and 20 weeks whereas BF samples of both series had 23 and 24 weeks respectively based on sensory evaluation.

顶体反应抑制剂4'- 乙酰胺苯基4-胍基苯甲酸酯(AGB)具有阻断HIV-1进入细胞的作用

】目的: 研究4'- 乙酰胺苯基4- 胍基苯甲酸酯(AGB)抗 HIV-1 活性及作用靶点。方法: 通过 AGB对宿主细胞的毒性实验、合胞体抑制实验、融合阻断实验、对HIV-1感染细胞的保护作用实 验和对HIV-1急性感染细胞p24抗原产生的抑制作用等试验，观察AGB对HIV-1复制的影响和作 关键词: AGB; HIV-1; 病毒进入; 杀微生物剂; 杀精子活性 中图分类号: R967; 文献标识码: A 文章编号: 0253-357X(2005)11-0660-05 本研究为国家高技术研究发展计划(2003AA219142)、国 家科技攻关计划 (2004BA719A14)、中国科学院知识创新 工程重要方向(KSCX2-SW-216; KSCX12-SW-11)、云南 省科技攻关计划(2004NG12)和云南省生育调节与少数民 族优生研究重点实验室资助项目 通讯作者: 郑永唐; Tel: +86-871-5195684; Fax:+86-871-5191823; E-mail: zhengyt@mail.kiz.ac.cn 在我国, 人免疫缺陷病毒(human immunodeficiency virus, HIV)危害日趋严重，处在全国低流行 与局部地区及特定人群高流行并存的态势。卫生部 的数据显示，截止2005 年3 月底，全国累计报告 HIV 感染者114 703 例。专家估计我国实际HIV 感 染者超过100 万人。预计到2010 年, 全国HIV感染 者将突破千万。截止2004 年底, 云南省累计报告的 HIV 感染者已达28 391 人, 是全国流行最严重的地 区。艾滋病流行正由高危人群向一般人群传播。 新的证据显示近年来由性传播途径感染的比例有所 上升, 女性感染者的比例有较大幅度的上升, 迫切需 要发展一种女性可自主控制的方法 [1]。杀微生物剂 是可以局部用药于阴道和宫颈、能够杀灭或抑制 包括HIV等病毒性和细菌性病原体、人工合成或天 然的药物。具有避孕作用的杀微生物剂更是近年 来的研究热点，也具有广阔的应用前景[2,3]。 顶体酶是存在于精子顶体内的一种类胰蛋白 酶, 它是受精过程中的一种重要的蛋白水解酶, 此酶 能水解卵细胞的透明带, 使精子能够与卵细胞相融 合; 顶体酶还能促进生殖系统中激肽的释放, 后者能 够增强精子的活力和促进精子的运动, 顶体酶的失 活将导致不孕[4]。AGB(4'- 乙酰胺苯基 4- 胍基苯甲 酸酯)是顶体酶的抑制剂, 实验表明在多种动物中有 很好的杀精子作用[5-7]。Bourimbaiar等[8]曾报道AGB 还具有体外抗HIV-1的作用, 活性较N-9高, 且毒性 较小。在本实验中, 我们发现AGB 的体外抗HIV-1 活性主要是阻断HIV-1 进入细胞。 用机制。结果: AGB抑制HIV-1IIIB诱导C8166细胞形成合胞体, EC50为39.5 μg/ml; 抑制HIV-1感染 细胞上清中HIV-1 p24抗原的表达, EC50为33.36 μg/ml; 阻断HIV-1慢性感染H9细胞与正常C8166 细胞间融合的作用。结论: AGB具有阻断HIV-1 进入宿主细胞的作用，是一种有前景的具杀精子 作用的杀微生物剂。

The Genomes of Oryza sativa: A history of duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped superscaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000 - 40,000. Only 2% - 3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism ( SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication

Background: Various evolutionary models have been proposed to interpret the fate of paralogous duplicates, which provides substrates on which evolution selection could act. In particular, domestication, as a special selection, has played important role in crop cultivation with divergence of many genes controlling important agronomic traits. Recent studies have indicated that a pair of duplicate genes was often sub-functionalized from their ancestral functions held by the parental genes. We previously demonstrated that the rice cell-wall invertase (CWI) gene GIF1 that plays an important role in the grain-filling process was most likely subjected to domestication selection in the promoter region. Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function through independent selection. Results: Through synteny analysis, we show that GIF1 and another cell-wall invertase gene OsCIN1 were paralogues derived from a segmental duplication originated during genome duplication of grasses. Results based on analyses of population genetics and gene phylogenetic tree of 25 cultivars and 25 wild rice sequences demonstrated that OsCIN1 was also artificially selected during rice domestication with a fixed mutation in the coding region, in contrast to GIF1 that was selected in the promoter region. GIF1 and OsCIN1 have evolved into different expression patterns and probable different kinetics parameters of enzymatic activity with the latter displaying less enzymatic activity. Overexpression of GIF1 and OsCIN1 also resulted in different phenotypes, suggesting that OsCIN1 might regulate other unrecognized biological process. Conclusion: How gene duplication and divergence contribute to genetic novelty and morphological adaptation has been an interesting issue to geneticists and biologists. Our discovery that the duplicated pair of GIF1 and OsCIN1 has experiencedsub-functionalization implies that selection could act independently on each duplicate towards different functional specificity, which provides a vivid example for evolution of genetic novelties in a model crop. Our results also further support the established hypothesis that gene duplication with sub-functionalization could be one solution for genetic adaptive conflict.

Technology for the community: SEAFDEC-designed artificial reefs

An account is given of the fabrication and deployment of artificial reefs used in the SEAFDEC/AQD's Community Fishery Resource Management project, which focused on Malalison Island located in west Central Philippines. The project aimed to apply community-based techniques of fishery resource management through the collaboration of community organizations, biologists and social scientists. The 3 types of reefs (building blocks, concrete pipe culvert, and modified concrete pipe culvert) were deployed at Gui-ob reef covering an area of less than 1 ha.

A critical reassessment of the role of mitochondria in tumorigenesis

Background Mitochondrial DNA (mtDNA) is being analyzed by an increasing number of laboratories in order to investigate its potential role as an active marker of tumorigenesis in various types of cancer. Here we question the conclusions drawn in most of these investigations, especially those published in high-rank cancer research journals, under the evidence that a significant number of these medical mtDNA studies are based on obviously flawed sequencing results. Methods and Findings In our analyses, we take a phylogenetic approach and employ thorough database searches, which together have proven successful for detecting erroneous sequences in the fields of human population genetics and forensics. Apart from conceptual problems concerning the interpretation of mtDNA variation in tumorigenesis, in most cases, blocks of seemingly somatic mutations clearly point to contamination or sample mix-up and, therefore, have nothing to do with tumorigenesis. Conclusion The role of mitochondria in tumorigenesis remains unclarified. Our findings of laboratory errors in many contributions would represent only the tip of the iceberg since most published studies do not provide the raw sequence data for inspection, thus hindering a posteriori evaluation of the results. There is no precedent for such a concatenation of errors and misconceptions affecting a whole subfield of medical research.