黄杉属的分子系统发育与生物地理学

松科植物的叶绿体和线粒体基因分别为父系和母系遗传，二者的联合分析为系统发育重建，特别是揭示网状进化过程提供了便利条件。此外，松科中的多个属（如黄杉属、铁杉属等）呈洲际间断分布，是研究生物地理学问题的良好试材。 本文选择来自于叶绿体和线粒体基因组的5个DNA片段，通过序列分析对黄杉属的所有8个种进行了系统发育重建;同时结合已有的对黄杉属的各方面研究，讨论了该属典型的东亚-北美间断分布式样的形成过程。主要结果如下： (1) 叶绿体DNA片段trnfM-trnS、rpl20和trnP的序列分析 无论叶绿体基因两两组合分析还是3个叶绿体片段的联合分析均强烈支持东亚的6种黄杉属植物聚为一支（支持率>96%），其中日本黄杉位于最基部，其他分布于中国的5个种聚在一起。 (2) 线粒体基因nad5和cox1的序列分析 线粒体基因序列的进化速率较慢，信息位点相对较少，因此分辨率较低。本文中线粒体DNA序列在黄杉属的东亚物种间几乎没有分辨率，但是仍以>60%的Bootstrap支持率将该属分为东亚与北美两个姐妹支。 (3) 5个DNA片段的联合分析 5个细胞质DNA片段(trnfM-trnS, rpl20, trnP, nad5, cox1)的联合数据矩阵长4351 bp，其中含变异位点129个（3.0%），信息位点109个（2.5%）。利用最大简约法进行的系统发育分析表明：黄杉属分成北美和东亚两支，与地理分布相吻合，并分别得到了66%和100%的支持;中国的5个物种形成一个单系分支，该分支与日本黄杉为姐妹群关系。 根据上述叶绿体和线粒体DNA片段的序列分析结果，并结合前人的研究资料，我们认为黄杉属通过白令陆桥扩散后，在北美和东亚独立进化，但该属的起源地尚需要进一步研究。

Determinants of small-scale fishermen's income on Oman's Batinah Coast

The small-scale fishing industry of Oman is responsible for almost 90 percent of the total marine fishery production. It is also the main supplier of fish for Omani households. This study analyzes the factors that determine small-scale fishermen’s income on Oman’s Batinah Coast, which has almost 30 percent of Oman’s population and more than one-third of the small-scale fishermen. We find that fishermen’s income here can be explained broadly under four major blocks of variables: geographical region, fishing inputs and catch, socioeconomic and demographic characteristics, and the nature of the relationship with fisheries extension services. In general, the Wilayat (local administrative units) failed to make any significant impact on fishermen’s income. The variable “Fishing inputs and catch,” such as increases in engine power, boat length, weekly catch, and number of weekly trips, positively impacted fishermen’s income while increases in weekly fishing costs, number of crew members, and difficulty in getting ice had a significantly negative effect on the income. Furthermore, socioeconomic and demographic characteristics also contributed significantly in determining the fishermen’s income level. The other important findings were related to extension services. The variables “Fishermen’s exchange of information and cooperation with the ministry” and “Fishermen’s involvement in the extension activities” were found to have positive effects on fishermen’s income levels. Capitalizing on these findings could improve fishermen’s incomes and their lives across the region, as well as nationally.

Statistical analyses to support guidelines for marine avian sampling: Final report. [Digital Supplements A-G attached]

Interest in development of offshore renewable energy facilities has led to a need for high-quality, statistically robust information on marine wildlife distributions. A practical approach is described to estimate the amount of sampling effort required to have sufficient statistical power to identify species specific “hotspots” and “coldspots” of marine bird abundance and occurrence in an offshore environment divided into discrete spatial units (e.g., lease blocks), where “hotspots” and “coldspots” are defined relative to a reference (e.g., regional) mean abundance and/or occurrence probability for each species of interest. For example, a location with average abundance or occurrence that is three times larger the mean (3x effect size) could be defined as a “hotspot,” and a location that is three times smaller than the mean (1/3x effect size) as a “coldspot.” The choice of the effect size used to define hot and coldspots will generally depend on a combination of ecological and regulatory considerations. A method is also developed for testing the statistical significance of possible hotspots and coldspots. Both methods are illustrated with historical seabird survey data from the USGS Avian Compendium Database.

Diet shifts of juvenile red snapper (Lutjanus campechanus) with changes in habitat and fish size

We examined the diets and habitat shift of juvenile red snapper (Lutjanus campechanus) in the northeast Gulf of Mexico. Fish were collected from open sand-mud habitat (little to no relief), and artificial reef habitat (1-m3 concrete or PVC blocks), from June 1993 through December 1994. In 1994, fish settled over open habitat from June to September, as shown by trawl collections, then began shifting to reef habitat — a shift that was almost completed by December as observed by SCUBA visual surveys. Stomachs were examined from 1639 red snapper that ranged in size from 18.0 to 280.0 mm SL. Of these, 850 fish had empty stomachs, and 346 fish from open habitat and 443 fish from reef habitat contained prey. Prey were identified to the lowest possible taxon and quantified by volumetric measurement. Specific volume of particular prey taxa were calculated by dividing prey volume by individual fish weight. Red snapper shifted diets with increasing size. Small red snapper (<60 mm SL) fed mostly on chaetognaths, copepods, shrimp, and squid. Large red snapper (60–280 mm SL) shifted feeding to fish prey, greater amounts of squid and crabs, and continued feeding on shrimp. We compared red snapper diets for overlapping size classes (70–160 mm SL) of fish that were collected from both habitats (Bray-Curtis dissimilarity index and multidimensional scaling analysis). Red snapper diets separated by habitat type rather than fish size for the size ranges that overlapped habitats. These diet shifts were attributed to feeding more on reef prey than on open-water prey. Thus, the shift in habitat shown by juvenile red snapper was reflected in their diet and suggested differential habitat values based not just on predation refuge but food resources as well.

Small scale manufacture of crude agar from Gracilaria seaweeds

A simplified process was worked out to prepare crude agar from red seaweeds (Gracilaria sp.). The process required careful preliminary cleaning and bleaching (sun-drying) of the weed. The agar was extracted by boiling with water in a mixture (2%) strong enough to set as a jelly. Freezing the jelly over a 3—day period in an ice-making machine, adjusted to work slowly, separated out ice and agar. The blocks were thawed out and the agar dried in the sun. The efficiency of extraction was over 800/A.

40 Gbit/s optical communication system

The University of Bristol is studying the feasibility of deploying 40 Gbit/s optical time division multiplexed (OTDM) transmission networks to support new telecommunication services such the Internet and video-on-demand systems. Among the functional blocks being considered in the project are the optical pulse sources, signal multiplexers and demultiplexers, clock recovery subsystems, signal detection and dispersion accommodation methods.

A survey of process hygiene in the Sri Lankan prawn industry. 3. Critical control points

Of fifteen processing plants surveyed in Sri Lanka, only five were found to have a prawn process which was adequately controlled. Most common process faults were: inadequate chilling of prawns after a wash in 30°C, mains water, the use of large blocks of ice to cool prawns, and high ratios of prawns to ice. There was also ample scope for cross-contamination of the processed prawns.

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.

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.

Phylogenetic relationships of the macaques (Cercopithecidae : Macaca), inferred from mitochondrial DNA sequences

To study the phylogenetic relationships of the macaques, five gene fragments were sequenced from 40 individuals of eight species: Macaca mulatta, M. cyclopis, M. fascicularis, M. arctoides, M. assamensis, M. thibetana, M. silenus, and M. leonina. In addition, sequences of M. sylvanus were obtained from Genbank. A baboon was used as the outgroup. The phylogenetic trees were constructed using maximum-parsimony and Bayesian methods. Because five gene fragments were from the mitochondrial genome and were inherited as a single entity without recombination, we combined the five genes into a single analysis. The parsimony bootstrap proportions we obtained were higher than those from earlier studies based on the combined mtDNA dataset. Excluding M. arctoides, our results are generally consistent with the classification of Delson (1980). Our phylogenetic analyses agree with earlier studies suggesting that the mitochondrial lineages of M. arctoides share a close evolutionary relationship with the mitochondrial lineages of the fascicularis group of macaques (and M. fascicularis, specifically). M. mulatta (with respect to M. cyclopis), M. assamensis assamensis (with respect to M. thibetana), and M. leonina (with respect to M. silenus) are paraphyletic based on our analysis of mitochondrial genes.