A preliminary genetic map of Zhikong scallop (Chlamys farreri Jones et Preston 1904)

Zhikong scallop (Chlamys farreri Jones et Preston 1904) is one of the most important aquaculture species in China. The development of a genetic linkage map would provide a powerful tool for the genetic improvement of this species. Amplified fragment length polymorphism (AFLP) is a PCR-based technique that has proven to be powerful in genome fingerprinting and mapping, and population analysis. Genetic maps of C. farreri were constructed using AFLP markers and a full-sib family with 60 progeny. A total of 503 segregating AFLP markers were obtained, with 472 following the Mendelian segregation ratio of 1:1 and 31 markers showing significant (P< 0.05) segregation distortion. The male map contained 166 informative AFLP markers in 23 linkage groups covering 2468 cM. The average distance between markers was 14.9 cM. The female genetic map consisted of 198 markers in 25 linkage groups spanning 3130 cM with an average inter-marker spacing of 15.8 cM. DNA polymorphisms that segregated in a 3:1 ratio as well as the AFLP markers that were heterozygous in both parents were included to construct combined linkage genetic map. Five shared linkage groups, ranging from 61.1 to 162.5 cM, were identified between the male and female maps, covering 431 cM. Amplified fragment length polymorphism markers appeared to be evenly distributed within the linkage groups. Although preliminary, these maps provide a starting point for the mapping of the functional genes and quantitative trait loci in C. farreri.

Construction of AFLP-based genetic linkage map for Zhikong scallop, Chlamys farreri Jones et Preston and mapping of sex-linked markers

Zhikong scallop (Chlamys farreri) is an economically important aquaculture species in China; however, frequent mass mortality seriously affects the development of its industry. Genetic linkage map is useful for genetic improvement and selective breeding of C. farreri. Linkage maps were constructed using an intraspecific F-1 cross and amplified fragment length polymorphism (AFLP) markers. Thirty-two selected AFLP primer combinations produced 545 AFLP markers that were polymorphic in either of the parents and segregated in the progeny. Of these segregating markers, 166 were mapped to 19 linkage groups of the female framework map, covering a total of 1503.9 cM, with an average marker spacing of 10.2 cM; and 197 markers were assigned to 20 linkage groups of the male map, covering a total of 1630.7 cM, with 9.2 cM per marker. A sex-linked marker was mapped on the female map with zero recombination and a LOD of 27.3. The genetic length of C farreri genome was estimated as 1889.0 cM for the female and 1995.9 cM for the male. The coverage of the framework map was calculated as 79.6% for the female and 81.7% for the male. When the triplets and doublets were considered, the observed length of the map was calculated as 1610.2 cM with coverage of 85.2% for the female, and 1880.5 cM with coverage of 94.2% for the male. The genetic maps presented here will serve as a basis for the construction of a high-resolution genetic map and mapping of economically important genes. (C) 2004 Published by Elsevier B.V.

Triploid and tetraploid Zhikong scallop, Chlamys farreri Jones et Preston, produced by inhibiting polar body I

Triploid scallops are valuable for aquaculture because of their enlarged adductor muscle, and tetraploids are important for the commercial production of triploids. We tested tetraploid induction in the zhikong scallop by inhibiting polar body I in newly fertilized eggs. The ploidy of resultant embryos was determined by chromosome counting at 2- to 4-cell stage and by flow cytometry thereafter. Embryos from the control groups were mostly diploids (79%), along with some aneuploids. Embryos from the treated groups were 13% diploids, 18% triploids, 26% tetraploids, 13% pentaploids, and 36% aneuploids. Tetraploids, pentaploids, and most aneuploids suffered heavy mortality during the first week and became undetectable among the larvae at day 14. Five tetraploids (2%) were found among a sample of 267 spat from one of the replicates, and none was detected at day 450. The adductor muscle of triploid scallops was 44% heavier (P < .01) than that of diploids, confirming the value of the triploid technology in this species.

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.

Growth, survival and immune activity of scallops, Chlamys farreri Jones et Preston, compared between suspended and bottom culture in Haizhou Bay, China

We examined the growth, survival and immune response of the scallop, Chlamys farreri, during a 1-year period in deep water of Haizhou Bay. Scallops were cultured using two methods: (1) in lantern nets at a 5 m depth and (2) in a bottom culture system (sleeves) on the seabed at about a 25 m depth. Shell heights, meat dry weight and immune activities in the haemolymph (superoxide dismutase and myeloperoxidase) were measured bimonthly or quarterly from July 2007 to June 2008. Survival was measured at the end of the study and environmental parameters in the experimental layers were monitored during the experiment. The growth and immune activities of scallops were lower when the water temperature was high, which was consistent with the main mortality occurring in summer. The growth and immunity of scallops were higher in the suspended culture than in the bottom culture during the experiment, with the exception of shell growth during the last study period. Survival of scallops in the suspended culture (54.6 +/- 12.3%) was significantly lower than that in the bottom culture (86.8 +/- 3.5%) at the end of this study. We conclude from our results that the high mortality of C. farreri can be prevented by culturing them in a bottom culture system before November of the first year, and then transferring them to a suspended culture to improve scallop production.

Studies on mass summer mortality of cultured zhikong scallops (Chlamys farreri Jones et Preston) in China

Mass mortalities of cultured zhikong scallops (Chlamys farreri) have occurred each summer in most culture areas of northern China since 1996. Among the hypothesized causes are high culture density, infectious disease and genetic inbreeding. To investigate these potential agents, C. farreri were deployed at three densities (low, medium and high) at three sites (Jiaonan, Penglai and Yantai) in the summer of 2000. Scallops were sampled for survival, growth and histopathology before, during and after a mortality episode. Most of the mortality occurred in July and August, during and toward the later part of the spawning season, when water temperature reached 23-26 degrees C. Final cumulative mortalities reached 85% to 90% at all three sites. Scallops in the medium and high densities had higher initial death rates than did those at the low density. High densities also inhibited growth. Ciliates from the genus Trichodina, larvae of various organisms and anomalous secretions were observed in sections of the gill cavity, with highest prevalence during and at the end of the mortality period. Prokaryotic inclusion bodies were found in the soft tissues, but their prevalence was low and apparently without correlation with mortalities. Genetic analysis with random amplified polymorphic DNA markers showed slightly lower heterozygosity in the cultured stocks (0.301) than in the wild stocks (0.331). It is possible that the mortalities are caused by a combination of several factors such as stress associated with reproduction, high temperature, overcrowding and poor circulation in the growout cages, opportunistic invaders or pathogens, and possibly inbreeding. (c) 2005 Elsevier B.V. All rights reserved.

Bu fy mywyd yn un diliw o hapus: them?u yn Atgofion John Gwilym Jones

Morgan, M. (2004). Bu fy mywyd yn un diliw o hapus: them?u yn Atgofion John Gwilym Jones. Y Traethodydd. 159, pp.235-251.

James Evans : inventor of the syllabic system of the Cree language / by John McLean ... (Robin Rustler).

http://www.archive.org/details/jamesevans00maclrich

Discussion of "On families of distributions with shape parameters", by M.C. Jones

SCOPUS: ar.j

Simulating one of the CIB W14 round robin test cases using the SMARTFIRE fire field model

Numerical predictions produced by the SMARTFIRE fire field model are compared with experimental data. The predictions consist of gas temperatures at several locations within the compartment over a 60 min period. The test fire, produced by a burning wood crib attained a maximum heat release rate of approximately 11MW. The fire is intended to represent a nonspreading fire (i.e. single fuel source) in a moderately sized ventilated room. The experimental data formed part of the CIB Round Robin test series. Two simulations are produced, one involving a relatively coarse mesh and the other with a finer mesh. While the SMARTFIRE simulations made use of a simple volumetric heat release rate model, both simulations were found capable of reproducing the overall qualitative results. Both simulations tended to overpredict the measured temperatures. However, the finer mesh simulation was better able to reproduce the qualitative features of the experimental data. The maximum recorded experimental temperature (12141C after 39 min) was over-predicted in the fine mesh simulation by 12%. (C) 2001 Elsevier Science Ltd. All rights reserved.

Reviews: Private Passions with Robin Wilson [Radio review]

Tony Mann reviews Robin Wilson's appearance as Michael Berkeley's guest on Private Passions. Broadcast on BBC Radio 3, on 9 September 2007.

The Ocean Colour Climate Change Initiative: III. A round-robin comparison on in-water bio-optical algorithms

Satellite-derived remote-sensing reflectance (Rrs) can be used for mapping biogeochemically relevant variables, such as the chlorophyll concentration and the Inherent Optical Properties (IOPs) of the water, at global scale for use in climate-change studies. Prior to generating such products, suitable algorithms have to be selected that are appropriate for the purpose. Algorithm selection needs to account for both qualitative and quantitative requirements. In this paper we develop an objective methodology designed to rank the quantitative performance of a suite of bio-optical models. The objective classification is applied using the NASA bio-Optical Marine Algorithm Dataset (NOMAD). Using in situRrs as input to the models, the performance of eleven semi-analytical models, as well as five empirical chlorophyll algorithms and an empirical diffuse attenuation coefficient algorithm, is ranked for spectrally-resolved IOPs, chlorophyll concentration and the diffuse attenuation coefficient at 489 nm. The sensitivity of the objective classification and the uncertainty in the ranking are tested using a Monte-Carlo approach (bootstrapping). Results indicate that the performance of the semi-analytical models varies depending on the product and wavelength of interest. For chlorophyll retrieval, empirical algorithms perform better than semi-analytical models, in general. The performance of these empirical models reflects either their immunity to scale errors or instrument noise in Rrs data, or simply that the data used for model parameterisation were not independent of NOMAD. Nonetheless, uncertainty in the classification suggests that the performance of some semi-analytical algorithms at retrieving chlorophyll is comparable with the empirical algorithms. For phytoplankton absorption at 443 nm, some semi-analytical models also perform with similar accuracy to an empirical model. We discuss the potential biases, limitations and uncertainty in the approach, as well as additional qualitative considerations for algorithm selection for climate-change studies. Our classification has the potential to be routinely implemented, such that the performance of emerging algorithms can be compared with existing algorithms as they become available. In the long-term, such an approach will further aid algorithm development for ocean-colour studies.