Chromosomal mapping of 5S ribosomal RNA genes in the eastern oyster, Crassostrea virginica gmelin by fluorescence in situ hybridization

Chromosomal location of the 5S ribosomal RNA gene was studied in the eastern oyster, Crassostrea virginica Gmelin. using fluorescence in situ hybridization (FISH). Metaphase chromosomes were obtained from early embryos, and the FISH probe was made by PCR (polymerase chain reaction) amplification of the 5S rRNA gene and labeled by incorporation of digoxigenin-1 1-dUTP during PCR. Hybridization was detected with fluorescein-labeled antidigoxigenin antibodies. Two pairs of FISH signals were observed on metaphase chromosomes. Karyotypic analysis showed that the 5S rRNA gene cluster is interstitially located on short arms of chromosomes 5 and 6. On chromosome 5, the 5S rRNA genes were located immediately next to the centromere, whereas on chromosome 6, they were located approximately half way between the telomere and the centromere. Chromosomes of C. virginica are difficult to identify because of their similarities in size and arm ratio, and the chromosomal location of 5S rRNA genes provides unambiguous identification of chromosomes 5 and 6. Previous studies have mapped the major rRNA gene cluster (18S-5.8S-28S) to chromosome 2. and this study shows that the 5S rRNA gene cluster is not linked to the major rRNA genes and duplicated during evolution.

Genetic mapping of size-related quantitative trait loci (QTL) in the bay scallop (Argopecten irradians) using AFLP and microsatellite markers

We constructed genetic linkage maps for the bay scallop Argopecten irradians using AFLP and microsatellite markers and conducted composite interval mapping (CIM) of body-size-related traits. Three hundred seventeen AFLP and 10 microsatellite markers were used for map construction. The female parent map contained 120 markers in 15 linkage groups, spanning 479.6 cM with an average interval of 7.0 cM. The male parent map had 190 markers in 17 linkage groups, covering 883.8 cM at 7.2 cM per marker. The observed coverage was 70.4% for the female and 81.1% for the male map. Markers that were distorted toward the same direction were closely linked to each other on the genetic maps, suggesting the presence of genes important for survival. Six size-related traits, shell length, shell height, shell width, total weight, soft tissue weight, and shell weight, were measured for QTL mapping. The size data were significantly correlated with each other. We subjected the data, log transformed firstly, to a principle component analysis and use the first principle component for QTL mapping. CIM analysis revealed one significant QTL (LOD=2.69, 1000 permutation, P<0.05) in linkage group 3 on the female parent map. The mapping of size-related QTL in this study raises the possibility of improving the growth of bay scallops through marker-assisted selection. (c) 2007 Published by Elsevier B.V.

Identification and mapping of amplified fragment length polymorphism markers linked to shell color in bay scallop, Argopecten irradians irradians (Lamarck, 1819)

Amplified fragment length polymorphisms (AFLP) were used to study the inheritance of shell color in Argopecten irradians. Two scallops, one with orange and the other with white shells, were used as parents to produce four F-1 families by selfing and outcrossing. Eighty-eight progeny, 37 orange and 51 white, were randomly selected from one of the families for segregation and mapping analysis with AFLP and microsatellite markers. Twenty-five AFLP primer pairs were screened, yielding 1138 fragments, among which 148 (13.0%) were polymorphic in two parents and segregated in progeny. Six AFLP markers showed significant (P < 0.05) association with shell color. All six loci were mapped to one linkage group. One of the markers, F1f335, is completely linked to the gene for orange shell, which we designated as Orange1, without any recombination in the progeny we sampled. The marker was amplified in the orange parent and all orange progeny, but absent in the white parent and all the white progeny. The close linkage between F1f335 and Orange1 was validated using bulk segregation analysis in two natural populations, and all our data indicate that F1f335 is specific for the shell color gene, Orange1. The genomic mapping of a shell color gene in bay scallop improves our understanding of shell color inheritance and may contribute to the breeding of molluscs with desired shell colors.

Chromosomal mapping of major ribosomal rRNA genes in the hard clam (Mercenaria mercenaria) using fluorescence in situ hybridization

Karyotype and chromosomal location of the major ribosomal RNA genes were studied in the hard clam (Mercenaria mercenaria Linnaeus) using fluorescence in situ hybridization (FISH). Metaphase chromosomes were obtained from early embryos. Internal transcribed spacers (ITS) between major RNA genes were amplified and used as FISH probes. The probes were labeled with digoxigenin-11-dUTP by polymerase chain reaction and detected with fluorescein-labeled anti-digoxigenin antibodies. FISH with the ITS probes produced two to four signals per nucleus or metaphase. M. mercenaria had a haploid number of 19 chromosomes with a karyotype of seven metacentric, four metacentric or submetacentric, seven submetacentric, and one submetacentric or subtelocentric chromosomes (7M + 4M/SM + 7SM + 1SM/ST). Two ITS loci were observed: one located near the centromere on the long arm of Chromosome 10 and the other at the telomere of the short arm of Chromosome 12. FISH signals on Chromosome 10 are strong and consistent, while signals on Chromosome 12 are variable. This study provides the first karyotype and chromosomal assignment of the major RNA genes in M. mercenaria. Similar studies in a wide range of species are needed to understand the role of chromosomal changes in bivalve evolution.

Chromosomal mapping of the major ribosomal RNA genes in the dwarf surfclam (Mulinia lateralis Say)

Chromosomal location of the major ribosomal RNA genes (rRNA) were studied in the dwarf surfclam (Mulinia lateralis, Say) using fluorescence in situ hybridization (FISH). FISH probes for the rRNA genes were made by polymerase chain reaction (PCR), labeled with digoxigenin-11-dUTP and detected with fluorescein-labeled antidigoxigenin antibodies. Mulinia lateralis had a diploid number of 38 chromosomes and all chromosomes were telocentric. FISH with the rRNA probe produced positive and consistent signals on two pairs of chromosomes: Chromosome 15 with a relative length of 4.6% and Chromosome 19, the shortest chromosome. Both loci were telomeric. The rRNA location provides the first physical landmark of the M. lateralis genome.

Assessing the potential of VEGETATION sensor data for mapping snow and ice cover: a Normalized Difference Snow and Ice Index

The VEGETATION (VGT) sensor in SPOT 4 has four spectral bands that are equivalent to Landsat Thematic Mapper (TM) bands (blue, red, near-infrared and mid-infrared spectral bands) and provides daily images of the global land surface at a 1-km spatial resolution. We propose a new index for identifying and mapping of snow ice cover, namely the Normalized Difference Snow/Ice Index (NDSII), which uses reflectance values of red and mid-infrared spectral bands of Landsat TM and VGT. For Landsat TM data, NDSII is calculated as NDSIITM =(TM3 -TM5)/(TM3 +TM5); for VGT data, NDSII is calculated as NDSIIVGT =(B2- MIR)/(B2 + MIR). As a case study we used a Landsat TM image that covers the eastern part of the Qilian mountain range in the Qinghai-Xizang (Tibetan) plateau of China. NDSIITM gave similar estimates of the area and spatial distribution of snow/ice cover to the Normalized Difference Snow Index (NDSI=(TM2-TM5)/(TM2+TM5)) which has been proposed by Hall et al. The results indicated that the VGT sensor might have the potential for operational monitoring and mapping of snow/ice cover from regional to global scales, when using NDSIIVGT.

Phylogenetic relationships of five pika species (genus Ochotona) based on mitochondrial DNA restriction maps

Restriction site mapping of mitochondrial DNA (mtDNA) with 16 restriction endonucleases was used to examine the phylogenetic relationships of Ochotona cansus, O. huangensis, O. thibetana, O. curzoniae and O. erythrotis. A 1-kb length variation between O. erythrotis of subgenus Pika and other four species of subgenus Ochotona was observed, which may be a useful genetic marker for identifying the two subgenera. The phylogenetic tree constructed using PAUP based on 61 phylogenetically informative sites suggests that O. erythrotis diverged first, followed by O. cansus, while O. curzoniae and O. huangensis are sister taxa related to O. thibetana, The results indicate that both O. cansus and O. huangensis should be treated as independent species. If the base substitution rate of pikas mtDNA was 2% per million years, then the divergence time of the two subgenera, Pika and Ochotana, is about 8.8 Ma ago of late Miocence, middle Bao-dian of Chinese mammalian age, and the divergence of the four species in subgenus Ochotona would have occurred about 2.5 - 4.2 Ma ago, Yushean of Chinese mammalian age. This calculation appears to be substantiated by the fossil record.

滑坡泥石流信息遥感获取与空间预测

On the issue of geological hazard evaluation（GHE）, taking remote sensing and GIS systems as experimental environment, assisting with some programming development, this thesis combines multi-knowledges of geo-hazard mechanism, statistic learning, remote sensing (RS), high-spectral recognition, spatial analysis, digital photogrammetry as well as mineralogy, and selects geo-hazard samples from Hong Kong and Three Parallel River region as experimental data, to study two kinds of core questions of GHE, geo-hazard information acquiring and evaluation model. In the aspect of landslide information acquiring by RS, three detailed topics are presented, image enhance for visual interpretation, automatic recognition of landslide as well as quantitative mineral mapping. As to the evaluation model, the latest and powerful data mining method, support vector machine (SVM), is introduced to GHE field, and a serious of comparing experiments are carried out to verify its feasibility and efficiency. Furthermore, this paper proposes a method to forecast the distribution of landslides if rainfall in future is known baseing on historical rainfall and corresponding landslide susceptibility map. The details are as following: (a) Remote sensing image enhancing methods for geo-hazard visual interpretation. The effect of visual interpretation is determined by RS data and image enhancing method, for which the most effective and regular technique is image merge between high-spatial image and multi-spectral image, but there are few researches concerning the merging methods of geo-hazard recognition. By the comparing experimental of six mainstream merging methods and combination of different remote sensing data source, this thesis presents merits of each method ,and qualitatively analyzes the effect of spatial resolution, spectral resolution and time phase on merging image. (b) Automatic recognition of shallow landslide by RS image. The inventory of landslide is the base of landslide forecast and landslide study. If persistent collecting of landslide events, updating the geo-hazard inventory in time, and promoting prediction model incessantly, the accuracy of forecast would be boosted step by step. RS technique is a feasible method to obtain landslide information, which is determined by the feature of geo-hazard distribution. An automatic hierarchical approach is proposed to identify shallow landslides in vegetable region by the combination of multi-spectral RS imagery and DEM derivatives, and the experiment is also drilled to inspect its efficiency. (c) Hazard-causing factors obtaining. Accurate environmental factors are the key to analyze and predict the risk of regional geological hazard. As to predict huge debris flow, the main challenge is still to determine the startup material and its volume in debris flow source region. Exerting the merits of various RS technique, this thesis presents the methods to obtain two important hazard-causing factors, DEM and alteration mineral, and through spatial analysis, finds the relationship between hydrothermal clay alteration minerals and geo-hazards in the arid-hot valleys of Three Parallel Rivers region. (d) Applying support vector machine (SVM) to landslide susceptibility mapping. Introduce the latest and powerful statistical learning theory, SVM, to RGHE. SVM that proved an efficient statistic learning method can deal with two-class and one-class samples, with feature avoiding produce ‘pseudo’ samples. 55 years historical samples in a natural terrain of Hong Kong are used to assess this method, whose susceptibility maps obtained by one-class SVM and two-class SVM are compared to that obtained by logistic regression method. It can conclude that two-class SVM possesses better prediction efficiency than logistic regression and one-class SVM. However, one-class SVM, only requires failed cases, has an advantage over the other two methods as only "failed" case information is usually available in landslide susceptibility mapping. (e) Predicting the distribution of rainfall-induced landslides by time-series analysis. Rainfall is the most dominating factor to bring in landslides. More than 90% losing and casualty by landslides is introduced by rainfall, so predicting landslide sites under certain rainfall is an important geological evaluating issue. With full considering the contribution of stable factors (landslide susceptibility map) and dynamic factors (rainfall), the time-series linear regression analysis between rainfall and landslide risk mapis presented, and experiments based on true samples prove that this method is perfect in natural region of Hong Kong. The following 4 practicable or original findings are obtained: 1) The RS ways to enhance geo-hazards image, automatic recognize shallow landslides, obtain DEM and mineral are studied, and the detailed operating steps are given through examples. The conclusion is practical strongly. 2) The explorative researching about relationship between geo-hazards and alteration mineral in arid-hot valley of Jinshajiang river is presented. Based on standard USGS mineral spectrum, the distribution of hydrothermal alteration mineral is mapped by SAM method. Through statistic analysis between debris flows and hazard-causing factors, the strong correlation between debris flows and clay minerals is found and validated. 3) Applying SVM theory (especially one-class SVM theory) to the landslide susceptibility mapping and system evaluation for its performance is also carried out, which proves that advantages of SVM in this field. 4) Establishing time-serial prediction method for rainfall induced landslide distribution. In a natural study area, the distribution of landslides induced by a storm is predicted successfully under a real maximum 24h rainfall based on the regression between 4 historical storms and corresponding landslides.

An investigation of the roles of surface aluminum and acid sites in the zeolite MCM-22

Ammonia adsorption studies reveal that the observed Lewis acidity in the zeolite MCM-22 is derived from at least two types of framework aluminum sites (Al(F)), that is, octahedral Al(F) and three-coordinate Al(F). Comparative ammonia or trimethylphosphine (TMP) adsorption experiments with MCM-22 confirm that octahedral Al species gives rise to the signal at delta(ISO) approximate to 0 in the (27)Al NMR spectrum; this is a superposition of two NMR signals from the different Al species on the water-re constructed zeolite surface. A sharp resonance assigned to framework Al reversibly transforms on ammonia adsorption to delta(ISO) (27)Al approximate to 55 from tetrahedral Al(F), while the broad peak is assigned to nonframework aluminium which results from hydrothermal treatment. This study also demonstrates the effectiveness of (27)Al magic angle spinning (MAS) and multiple quantum (MQ) MAS NMR spectroscopy as a technique for the study of zeolite reactions.