Refined genome-wide comparative map of the domestic horse, donkey and human based on cross-species chromosome painting: insight into the occasional fertility of mules

We have made a complete set of painting probes for the domestic horse by degenerate oligonucleotide-primed PCR amplification of flow-sorted horse chromosomes. The horse probes, together with a full set of those available for human, were hybridized onto metaphase chromosomes of human, horse and mule. Based on the hybridization results, we have generated genome-wide comparative chromosome maps involving the domestic horse, donkey and human. These maps define the overall distribution and boundaries of evolutionarily conserved chromosomal segments in the three genomes. Our results shed further light on the karyotypic relationships among these species and, in particular, the chromosomal rearrangements that underlie hybrid sterility and the occasional fertility of mules.

A preliminary genetic linkage map of the pacific abalone Haliotis discus hannai Ino

Preliminary genetic linkage maps were constructed for the Pacific abalone (Haliotis discus hannai Ino) using amplified fragment length polymorphism (AFLP), randomly amplified polymorphic DNA (RAPD), and microsatellite markers segregating in a F, family. Nine microsatellite loci, 41 RAPD, and 2688 AFLP markers were genotyped in the parents and 86 progeny of the mapping family. Among the 2738 markers, 384 (including 365 AFLP markers, 10 RAPD markers, and 9 microsatellite loci) were polymorphic and segregated in one or both parents: 241 in the female and 146 in the male. The majority of these markers, 232 in the female and 134 in the male, segregated according to the expected 1:1 Mendelian ratio (alpha = 0.05). Two genetic linkage maps were constructed using markers segregating in the female or the male parent. The female framework map consisted of 119 markers in 22 linkage groups, covering 1773.6 cM with an average intermarker space of 18.3 cM. The male framework map contained 94 markers in 19 linkage groups, spanning 1365.9 cM with an average intermarker space of 18.2 cM. The sex determination locus was mapped to the male map but not to the female map, suggesting a XY-male determination mechanism. Distorted markers showing excess of homozygotes were mapped in clusters, probably because of their linkage to a gene that is incompatible between two parental populations.

Reciprocal chromosome painting illuminates the history of genome evolution of the domestic cat, dog and human

Domestic cats and dogs are important companion animals and model animals in biomedical research. The cat has a highly conserved karyotype, closely resembling the ancestral karyotype of mammals, while the dog has one of the most extensively rearranged mammalian karyotypes investigated so far. We have constructed the first detailed comparative chromosome map of the domestic dog and cat by reciprocal chromosome painting. Dog paints specific for the 38 autosomes and the X chromosomes delineated 68 conserved chromosomal segments in the cat, while reverse painting of cat probes onto red fox and dog chromosomes revealed 65 conserved segments. Most conserved segments on cat chromosomes also show a high degree of conservation in G-banding patterns compared with their canine counterparts. At least 47 chromosomal fissions (breaks), 25 fusions and one inversion are needed to convert the cat karyotype to that of the dog, confirming that extensive chromosome rearrangements differentiate the karyotypes of the cat and dog. Comparative analysis of the distribution patterns of conserved segments defined by dog paints on cat and human chromosomes has refined the human/cat comparative genome map and, most importantly, has revealed 15 cryptic inversions in seven large chromosomal regions of conserved synteny between humans and cats.

Tectonic geomorphology of the Ryukyu Trench-Arc-Backarc System: geological-geophysical exploration and mapping

OKINAWA TROUGH; BASIN

Single base-resolution methylome of the silkworm reveals a sparse epigenomic map

Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic cytosines are methylcytosines, all of which probably occur in CG dinucleotides. CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. We find that transposable elements, promoters and ribosomal DNAs are hypomethylated, but in contrast, genomic loci matching small RNAs in gene bodies are densely methylated. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis(1) and human(2), demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.

Heroin impairs map-picture-following and memory tasks dependent on gender and orientation of the tasks

Male and female heroin-dependent patients (HDPs) matched with "normal" people were tested on 4 topographical orientation tasks: schematic map-following, map-memory, schematic picture-following, and picture-memory tasks. The results showed that, in general

Sensitivity map of laser tweezers Raman spectroscopy for single-cell analysis of colorectal cancer

Raman spectroscopy on single, living epithelial cells captured in a laser trap is shown to have diagnostic power over colorectal cancer. This new single-cell technology comprises three major components: primary culture processing of human tissue samples to produce single-cell suspensions, Raman detection on singly trapped cells, and diagnoses of the cells by artificial neural network classifications. it is compared with DNA flow cytometry for similarities and differences. Its advantages over tissue Raman spectroscopy are also discussed. In the actual construction of a diagnostic model for colorectal cancer, real patient data were taken to generate a training set of 320 Raman spectra and, a test set of 80. By incorporating outlier corrections to a conventional binary neural classifier, our network accomplished significantly better predictions than logistic regressions, with sensitivity improved from 77.5% to 86.3% and specificity improved from 81.3% to 86.3% for the training set and moderate improvements for the test set. Most important, the network approach enables a sensitivity map analysis to quantitate the relevance of each Raman band to the normal-to-cancer transform at the cell level. Our technique has direct clinic applications for diagnosing cancers and basic science potential in the study of cell dynamics of carcinogenesis. (C) 2007 Society of Photo-Optical Instrumentation Engineers.

Sensitivity map of laser tweezers Raman spectroscopy for single-cell analysis of colorectal cancer

Raman spectroscopy on single, living epithelial cells captured in a laser trap is shown to have diagnostic power over colorectal cancer. This new single-cell technology comprises three major components: primary culture processing of human tissue samples to produce single-cell suspensions, Raman detection on singly trapped cells, and diagnoses of the cells by artificial neural network classifications. it is compared with DNA flow cytometry for similarities and differences. Its advantages over tissue Raman spectroscopy are also discussed. In the actual construction of a diagnostic model for colorectal cancer, real patient data were taken to generate a training set of 320 Raman spectra and, a test set of 80. By incorporating outlier corrections to a conventional binary neural classifier, our network accomplished significantly better predictions than logistic regressions, with sensitivity improved from 77.5% to 86.3% and specificity improved from 81.3% to 86.3% for the training set and moderate improvements for the test set. Most important, the network approach enables a sensitivity map analysis to quantitate the relevance of each Raman band to the normal-to-cancer transform at the cell level. Our technique has direct clinic applications for diagnosing cancers and basic science potential in the study of cell dynamics of carcinogenesis. (C) 2007 Society of Photo-Optical Instrumentation Engineers.

Comparative map between the domestic pig and dog

Cross-species chromosome painting with probes derived from flow-sorted dog and human chromosomes was used to construct a high-resolution comparative map for the pig. In total 98 conserved autosomal segments between pig and dog were detected by probes specific for the 38 autosomes and X Chromosome of the dog. Further integration of our results with the published human-dog and cat-dog comparative maps, and with data from comparative gene mapping, increases the resolution of the current pig-human comparative map. It allows for the conserved syntenies detected in the pig, human, and cat to be aligned against the putative ancestral karyotype of eutherian mammals and for the history of karyotype evolution of the pig lineage to be reconstructed. Fifteen fusions, 17 fissions, and 23 inversions are required to convert the ancestral mammalian karyotype into the extant karyotype of the pig.

Phylogenomic study of the subfamily Caprinae by cross-species chromosome painting with Chinese muntjac paints

Chromosomal homologies have been established between the Chinese muntjac (Muntiacus reevesi, MRE, 2n = 46) and five ovine species: wild goat (Capra aegagrus, CAE, 2n = 60), argall (Ovis ammon, OAM, 2n = 56), snow sheep (Ovis nivicola, ONI, 2n = 52), red goral (Naemorhedus cranbrooki, NCR, 2n = 56) and Sumatra serow (Capricornis sumatraensis, CSU, 2n = 48) by chromosome painting with a set of chromosome-specific probes of the Chinese muntjac. In total, twenty-two Chinese muntjac autosomal painting probes detected thirty-five homologous segments in the genome of each species. The chromosome X probe hybridized to the whole X chromosomes of all ovine species while the chromosome Y probe gave no signal. Our results demonstrate that almost all homologous segments defined by comparative painting show a high degree of conservation in G-banding patterns and that each speciation event is accompanied by specific chromosomal rearrangements. The combined analysis of our results and previous cytogenetic and molecular systematic results enables us to map the chromosomal rearrangements onto a phylogenetic tree, thus providing new insights into the karyotypic evolution of these species.

Defining the orientation of the tandem fusions that occurred during the evolution of Indian muntjac chromosomes by BAC mapping

The Indian muntjac (Muntiacus muntjak vaginalis) has a karyotype of 2n=6 in the female and 7 in the male, the karyotypic evolution of which through extensive tandem fusions and several centric fusions has been well-documented by recent molecular cytogenetic studies. In an attempt to define the fusion orientations of conserved chromosomal segments and the molecular mechanisms underlying the tandem fusions, we have constructed a highly redundant (more than six times of whole genome coverage) bacterial artificial chromosome (BAC) library of Indian muntjac. The BAC library contains 124,800 clones with no chromosome bias and has an average insert DNA size of 120 kb. A total of 223 clones have been mapped by fluorescent in situ hybridization onto the chromosomes of both Indian muntjac and Chinese muntjac and a high-resolution comparative map has been established. Our mapping results demonstrate that all tandem fusions that occurred during the evolution of Indian muntjac karyotype from the acrocentric 2n=70 hypothetical ancestral karyotype are centromere-telomere (head-tail) fusions.

A genetic map of large yellow croaker Pseudosciaena crocea

Genetic linkage maps were constructed for large yellow croaker Pseudosciaena crocea (Richardson, 1846) using AFLP and microsatellite markers in an F-1 family. Five hundred and twenty-three AFLP markers and 36 microsatellites were genotyped in the parents and 94 F-1 progeny. Among these, 362 AFLP markers and 13 SSR markers followed the 1:1 Mendelian segregation ratio (P > 0.05). The female genetic map contained 181 AFLP and 7 microsatellite markers forming 24 linkage groups spanning 2959.1 cM, while the male map consisted of 153 AFLP and 8 microsatellite markers in 23 linkage groups covering 2205.7 cM. One sex linked marker was mapped to the male map and co-segregated with the AFLP marker agacta355, suggesting an XY-male determination mechanism and this may be useful in the breeding of monosex populations. (c) 2007 Elsevier B.V. All rights reserved.

A linkage map of common carp (Cyprinus carpio) based on AFLP and microsatellite markers

P>Common carp (Cyprinus carpio) is an important fish for aquaculture, but genomics of this species is still in its infancy. In this study, a linkage map of common carp based on Amplified Fragment Length Polymorphism (AFLP) and microsatellite (SSR) markers has been generated using gynogenetic haploids. Of 926 markers genotyped, 151 (149 AFLPs, two SSRs) were distorted and eliminated from the linkage analyses. A total of 699 AFLP and 20 microsatellite (SSR) markers were assigned to the map, which comprised 64 linkage groups and covered 5506.9 cM Kosambi, with an average interval distance of 7.66 cM Kosambi. The normality tests on interval map distances showed a non-normal marker distribution. Visual inspection of the map distance distribution histogram showed a cluster of interval map distances on the left side of the chart, which suggested the occurrence of AFLP marker clusters. On the other hand, the lack of an obvious cluster on the right side showed that there were a few big gaps which need more markers to bridge. The correlation analysis showed a highly significant relatedness between the length of linkage group and the number of markers, indicating that the AFLP markers in this map were randomly distributed among different linkage groups. This study is helpful for research into the common carp genome and for further studies of genetics and marker-assisted breeding in this species.

Research and compilation of the Geomorphologic Atlas of the People's Republic of China (1:1,000,000)

National Natural Science Foundation of China [40871177, 40830529]

Wear mechanism map of uncoated HSS tools during drilling die-cast magnesium alloy

A wear mechanism map of uncoated high-speed steel (HSS) tools was constructed under the conditions of dry-drilling die-cast magnesium alloys. Three wear mechanisms appear in the map based on the microanalysis of drilled HSS tools by SEM, including adhesive wear, abrasive wear and diffusion wear. In the map, there exists a minor wear region which is called "safety zone". This wear mechanism map will be a good reference for choosing suitable drilling parameters when drilling die-cast magnesium alloys.