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PubMed2003

A two-dimensional proteome map of Shigella flexneri.

Shigella flexneri is a Gram-negative facultatively intracellular pathogen responsible for bacillary dysentery in humans. In this study, extracellular proteins from the culture medium and whole cell proteins in cellular extracts of S. flexneri 2a strain 2457T were examined by two-dimensional (2-D) gel electrophoresis using immobilized pH gradient (IPG) technology. Proteins were identified by matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) in combination with Mascot search program. In total, among the 488 proteins spots processed, 388 proteins were identified. The identified proteins represented 169 genes. By comparing results of Mascot search against databases of Escherichia coli and genomes of S. flexneri 2a, one S. flexneri-specific protein was identified and one possible gap was found in 2457T genome sequences. Although this proteome map is still incomplete, it is already a useful reference for future studies involving pathogenicity, vaccine development, design of novel antibacterial drugs, etc. Proteome maps and a table of all identified proteins are available on the internet at www.proteomics.com.cn.

Bacterial Proteins↗

PubMed1989

Human ret proto-oncogene mapped to chromosome 10q11.2.

Using cosmid clones derived from human ret protooncogene as probes, we determined its chromosome localization by fluorescence in situ hybridization. Two overlapping clones, cret-1 and -2, which were cloned using the most 5' part of human ret proto-oncogene cDNA, hybridized to chromosome 10q11.2. Sixty-three and 52% of the grains obtained by cret-1 and -2, respectively, were localized to the same site. No other specific hybridization site was observed. From these data, we assigned the site of ret proto-oncogene to chromosome 10q11.2, where the possible locus responsible for multiple endocrine neoplasia type 2A (MEN2A) was mapped by linkage analysis using interstitial retinol binding protein cDNA and D10S5. These findings suggest that ret proto-oncogene might be a suitable probe for approaching the MEN2A locus.

Chromosome Mapping↗

PubMed1997

Computer simulation of centration effects on corneal-topography analysis of excimer laser photorefractive keratectomy ablations.

Excimer laser photorefractive keratectomy (PRK) procedures photoablate the central optical zone, potentially altering the corneal vertex normal and thus the corneal topography (CT) system reference axis. Anterior corneal surface coordinates (x, y, and z) were computer generated to simulate spherical and PRK-ablated corneal surfaces. Power maps were reconstructed by using surface tangents relative to various assumed CT reference axes, the original and displaced vertex normals. The simulation process eliminated focus, alignment, and surface-reconstruction errors. A simulated 5.00-D myopic PRK decentered 1 mm from the vertex produced a new corneal vertex 0.13 mm from the original position. Axial power-map generation by using this new reference axis produced a spherical keratectomy with astigmatic untreated periphery. This computer simulation demonstrates that reference axis changes are significant for even modest PRK decentration and can explain apparent steepening in untreated corneal areas. CT users should be aware that pre- and postoperative CT power maps may not be directly comparable.

Computer Simulation↗

PubMed1996

Hypermethylation-associated inactivation indicates a tumor suppressor role for p15INK4B.

The recently identified cyclin-dependent kinase inhibitor p15INK4B is localized to a region on chromosome 9p21 frequently deleted in human tumors. Previous evidence has pointed to a related gene, p16INK4A, as the principal target of this deletion. We report that in gliomas and, to a striking degree, in leukemias, the p15 gene is commonly inactivated in association with promoter region hypermethylation involving multiple sites in a 5'-CpG island. In some gliomas and all of the primary leukemias, this event occurs without alteration of the adjacent gene, p16INK4A. In other tumors, including lung, head and neck, breast, prostate, and colon cancer, inactivation of p15INK4B occurs only rarely and only with concomitant inactivation of p16. Aberrant methylation of p15INK4B is associated with transcriptional loss of this gene. Treatment with the demethylating agent 5-aza-2'-deoxycytidine leads to re-expression of p15 mRNA. In selected leukemia cell lines, p15 inactivation correlates with known resistance to the growth-suppressive effects of transforming growth factor-beta. These results suggest that p15INK4B is inactivated selectively in leukemias and gliomas and seems to constitute an important tumor suppressor gene loss in these neoplasms.

Adult↗

PubMed1987

Relationships between interhemispheric cortical connections and visual areas in hooded rats.

The correlation between visual topography within striate and lateral extrastriate visual cortex and the pattern of callosal connections to those areas has been studied in gray rats. The procedure was to put multiple injections of horseradish peroxidase (HRP) into the occipital cortex of the right hemisphere. The cortical areas 17 and 18a in the left hemisphere were electrophysiologically mapped upon stimulation of the right eye. Reference lesions were placed at selected recording sites. Horizontal sections of the left cortex were reacted for the demonstration of HRP. This permitted the comparison of the visual and callosal maps in the same animal. Like in other mammals, the callosal projections coincide with the cortical representations of the vertical midline and the more central regions of the visual field. The heavy line of labelled neurons and terminations embedded within the primary callosal band at the 17/18a border coincides with the representation of the vertical meridian. It provides the boundary between V1 and the maps located lateral to it. In area 18a, the anterolateral is contained in its anterior half, whereas areas lateromedial and laterointermediate are contained in its posterior half. The acallosal 'island', caudal to the acallosal 'body', contains the map known as posterolateral. There are two laterolateral (LL) maps which coincide with the acallosal 'islands' lateral to the acallosal 'body'; laterolateral anterior is more rostral than LL and these are retinotopically organized as mirror images of each other. Lateral to LL, there is a suggestion of an additional map, which could correspond to a pararhinal area. These results may be useful to understand aspects of a basic mammalian plan in the organization of visual cortex.

Animals↗

PubMed1978

Location of the cleavage sites on the SV 40 DNA map produced by the restriction endonucleases Pst 1 and Bam 1.

Restriction endonucleases from Providencia stuartii (Pst 1) and Bacillus amyloliquefaciens H (Bam 1) cleave SV 40 DNA at two and one specific sites, respectively. Using EcoRI and Hind III endonuclease restriction sites as reference, the two Pst I sites were mapped at 0.050; 0.265 and the Bam I site was mapped at 0.170 of the genome length, clockwise, from the single EcoRI cleavage site.

DNA Restriction Enzymes↗

PubMed1993

Physically mapped, cosmid-derived microsatellite markers as anchor loci on bovine chromosomes.

To identify physical and genetic anchor loci on bovine chromosomes, 13 cosmids, obtained after the screening of partial bovine cosmid libraries with the (CA)n microsatellite motif, were mapped by fluorescence in situ hybridization (FISH). Eleven cosmid probes yielded a specific signal on one of the bovine chromosomes and identified the following loci: D5S2, D5S3, D6S3, D8S1, D11S5, D13S1, D16S5, D17S2, D19S2, D19S3, D21S8. Two cosmids produced centromeric signals on many chromosomes. The microsatellite-containing regions were subcloned and sequenced. The sequence information revealed that the two centromeric cosmids were derived from bovine satellites 1.723 and 1.709, respectively. A cosmid located in the subtelomeric region of Chromosome (Chr) 17 (D17S2) had features of a chromosome-specific satellite. Primers were designed for eight of the nonsatellite cosmids, and seven of these microsatellites were polymorphic with between three and eight alleles on a set of outbred reference families. The polymorphic and chromosomally mapped loci can now be used to physically anchor other bovine polymorphic markers by linkage analysis. The microsatellite primers were also applied to DNA samples of a previously characterized panel of somatic hybrid cell lines, allowing the assignment of seven microsatellite loci to defined syntenic groups. These assignments confirmed earlier mapping results, revealed a probable case of false synteny, and placed two formerly unassigned syntenic groups on specific chromosomes.

Animals↗

PubMed2001

The ARKdb: genome databases for farmed and other animals.

The ARKdb genome databases provide comprehensive public repositories for genome mapping data from farmed species and other animals (http://www.thearkdb.org) providing a resource similar in function to that offered by GDB or MGD for human or mouse genome mapping data, respectively. Because we have attempted to build a generic mapping database, the system has wide utility, particularly for those species for which development of a specific resource would be prohibitive. The ARKdb genome database model has been implemented for 10 species to date. These are pig, chicken, sheep, cattle, horse, deer, tilapia, cat, turkey and salmon. Access to the ARKdb databases is effected via the World Wide Web using the ARKdb browser and Anubis map viewer. The information stored includes details of loci, maps, experimental methods and the source references. Links to other information sources such as PubMed and EMBL/GenBank are provided. Responsibility for data entry and curation is shared amongst scientists active in genome research in the species of interest. Mirror sites in the United States are maintained in addition to the central genome server at Roslin.

Animals↗

PubMed1996

BCR gene recombines with genomically distinct sites on band 11Q13 in complex BCR-ABL translocations of chronic myeloid leukemia.

We have analysed a cloned 11q13/3'BCR junction fragment, one recombination product of a complex t(9;11;22) translocation in a patient with chronic myeloid leukemia. 3'M-Bcr recombined with chromosome band 11q13 at a specific point between two Alu elements lying in opposite orientation. We present new molecular data comparing the genomic location of the 11q13 breakpoint in our patient with that of one other recently reported to lie within the GSTP1 gene. This is the first time that specific breakpoint sites within a chromosomal region highly involved in complex Ph translocations have been relatively mapped. These early results argue against a precise site in 11q13 with which M-Bcr preferentially recombines and favour instead a larger recombination-prone domain. Both of the 11q13 breakpoint regions show Alu repeat elements in close proximity to the site of recombination.

Base Sequence↗

PubMed2001

Linkage disequilibrium in the human genome.

With the availability of a dense genome-wide map of single nucleotide polymorphisms (SNPs), a central issue in human genetics is whether it is now possible to use linkage disequilibrium (LD) to map genes that cause disease. LD refers to correlations among neighbouring alleles, reflecting 'haplotypes' descended from single, ancestral chromosomes. The size of LD blocks has been the subject of considerable debate. Computer simulations and empirical data have suggested that LD extends only a few kilobases (kb) around common SNPs, whereas other data have suggested that it can extend much further, in some cases greater than 100 kb. It has been difficult to obtain a systematic picture of LD because past studies have been based on only a few (1-3) loci and different populations. Here, we report a large-scale experiment using a uniform protocol to examine 19 randomly selected genomic regions. LD in a United States population of north-European descent typically extends 60 kb from common alleles, implying that LD mapping is likely to be practical in this population. By contrast, LD in a Nigerian population extends markedly less far. The results illuminate human history, suggesting that LD in northern Europeans is shaped by a marked demographic event about 27,000-53,000 years ago.

Alleles↗

PubMed2001

The cream dilution gene, responsible for the palomino and buckskin coat colours, maps to horse chromosome 21.

The colour locus historically referred to as C in the horse is linked to microsatellites markers on horse chromosome 21. Preliminary results demonstrated linkage of Ccr, thought to be the cream dilution variant of the C locus, to HTG10. An analysis of horse chromosome 21 using additional families confirmed and established a group of markers linked to Ccr. This work also improved the resolution of previously reported linkage maps for this chromosome. Linkage analysis unambiguously produced the map order: SGCV16-(19.1 cM)-HTG10-(3.8 cM)-LEX60/COR73-(1.3 cM)-COR68-(4.5 cM)- Ccr-(11.9 cM)-LEX31. Comparative and synteny data suggested that the horse C locus is not tyrosinase (TYR).

Animals↗

PubMed2003

Sentinel lymph node mapping in colorectal cancer.

BACKGROUND: Ultrastaging, by serial sectioning combined with immunohistochemical techniques, improves detection of lymph node micrometastases. Sentinel lymph node mapping and retrieval provides a representative node(s) to facilitate ultrastaging. The impact on staging of carcinoma of the colon and rectum in all series emphasizes the importance of this technique in cancer management. Now the challenge is to determine the biological relevance and prognostic implications. METHODS: The electronic literature (1966 to present) on sentinel node mapping in carcinoma of the colon and rectum was reviewed. Further references were obtained by cross-referencing from key articles. RESULTS: Lymphatic mapping appears to be readily applicable to colorectal cancer and identifies those lymph nodes most likely to harbour metastases. Sentinel node mapping carries a false-negative rate of approximately 10 per cent in larger studies, but will also potentially upstage a proportion of patients from node negative to node positive following the detection of micrometastases. The prognostic implication of these micrometastases requires further evaluation. CONCLUSION: Further follow-up to assess the prognostic significance of micrometastases in colorectal cancer is required before the staging benefits of sentinel node mapping can have therapeutic implications.

Colorectal Neoplasms↗

PubMed2005

Multimodal architectonic mapping of human superior temporal gyrus.

Although it is generally accepted that human superior temporal gyrus is activated by a huge variety of auditory and linguistic tasks, little is known about the exact positions and extents of cortical areas that are located on the lateral convexity of the gyrus (e.g., Brodmann's area 22). Such information, however, is relevant for a rigorous testing of structural-functional relationships in both normal volunteers and patients suffering from disorders of auditory and language perception. The present combined cytoarchitectonic and receptorarchitectonic study identifies a distinct area (Te3) in the lateral bulge of the superior temporal gyrus by using an algorithm-based approach for the detection of cortical borders. Our mapping data show that, in contrast to Brodmann's area (BA) 22, only small portions of Te3 reach the dorsal and ventral banks of the gyrus. Therefore, we labelled the newly defined area as "Te3" and not as "BA 22". The cytoarchitectonically defined borders of Te3 coincide with abrupt changes in the receptorarchitecture of several classical neurotransmitters, suggesting that Te3 represents a functionally relevant area of the human superior temporal gyrus. Since position and extent of area Te3 varied considerably between subjects, probability maps were created that show for each voxel of the standard references space, the frequency with which Te3 was present in it. These maps, in combination with previously published maps of the primary auditory cortex, can directly be compared with functional imaging data, and may open new perspectives for the analysis of structural-functional correlations in the human auditory and language systems.

Algorithms↗

PubMed2026

A High-Resolution Stereo-Seq Spatial Transcriptomic Resource for Adult Holstein Cattle Liver.

The bovine liver is a highly compartmentalized organ that plays essential roles in continuous gluconeogenesis and nitrogen recycling; however, its spatial molecular architecture has remained largely uncharacterized due to the limitations of traditional bulk and single-cell approaches. To address this gap, Spatial Enhanced Resolution Omics-sequencing (Stereo-seq) was utilized to generate a subcellular-resolution (500 nm) transcriptomic map of an adult Holstein cattle liver, and a refined reference-guided workflow was implemented to overcome standard annotation limitations in livestock. Raw sequencing data were processed using the Stereo-seq Analysis Workflow and analyzed with Stereopy, Seurat, SingleR, and reference-guided workflows. Spatial aggregation was evaluated at Bin20, Bin50, Bin100, Bin150, and Bin200. Increasing bin size increased molecular identifier counts and detected-gene complexity while progressively reducing spatial granularity. Bin50, corresponding to 50 × 50 DNA nanoballs and an approximate nominal footprint of 25 × 25 µm, was therefore selected as a practical intermediate aggregation level for the primary analyses. Quality-control assessment, Leiden clustering, UMAP visualization, reference-based cell-type annotation, cluster-marker analysis, and spatial mapping of canonical hepatic genes demonstrated preservation of biologically interpretable liver transcriptional organization. Raw sequencing data processed spatial matrices, annotated objects, and analysis code are publicly available to support reanalysis and computational benchmarking. In summary, we present a Stereo-seq spatial transcriptomic resource generated from liver tissue of an adult Holstein cow. This initial resource provides a valuable foundation for future studies of bovine liver biology, comparative genomics, and the spatial basis of livestock health and production traits.

Animals↗

PubMed1998

Integration of chicken cytogenetic and genetic maps: 18 new polymorphic markers isolated from BAC and PAC clones.

As an approach to integrate the chicken genetic and cytogenetic maps, bacterial artificial chromosome (BAC) and P1-derived artificial chromosome (PAC) clones were localized by fluorescence in situ hybridization (FISH) on chromosomes and by genetic mapping on the East Lansing and Compton reference families. Some of the clones used in this study were previously selected for the presence of potentially polymorphic (CA)n repeats and a microsatellite marker was developed when possible for genetic mapping. For other clones, a single strand conformational polymorphism (SSCP) was developed and used for this purpose. Between the two approaches, 18 markers linking the cytogenetic and genetic maps, seven on macrochromosomes and 11 on microchromosomes, were generated. Our results enabled the assignment and orientation of a linkage group to chromosome 3, together with the assignment of linkage groups to eight different microchromosomes, a fraction of the genome lacking mapping data and for which the degree of coverage by the genetic map was not well estimated previously.

Animals↗

PubMed2004

Using sequential indicator simulation to assess the uncertainty of delineating heavy-metal contaminated soils.

Mapping the spatial distribution of soil pollutants is essential for delineating contaminated areas. Currently, geostatistical interpolation, kriging, is increasingly used to estimate pollutant concentrations in soils. The kriging-based approach, indicator kriging (IK), may be used to model the uncertainty of mapping. However, a smoothing effect is usually produced when using kriging in pollutant mapping. The detailed spatial patterns of pollutants could, therefore, be lost. The local uncertainty of mapping pollutants derived by the IK technique is referred to as the conditional cumulative distribution function (ccdf) for one specific location (i.e. single-location uncertainty). The local uncertainty information obtained by IK is not sufficient as the uncertainty of mapping at several locations simultaneously (i.e. multi-location uncertainty or spatial uncertainty) is required to assess the reliability of the delineation of contaminated areas. The simulation approach, sequential indicator simulation (SIS), which has the ability to model not only single, but also multi-location uncertainties, was used, in this study, to assess the uncertainty of the delineation of heavy metal contaminated soils. To illustrate this, a data set of Cu concentrations in soil from Taiwan was used. The results show that contour maps of Cu concentrations generated by the SIS realizations exhausted all the spatial patterns of Cu concentrations without the smoothing effect found when using the kriging method. Based on the SIS realizations, the local uncertainty of Cu concentrations at a specific location of x', refers to the probability of the Cu concentration z(x') being higher than the defined threshold level of contamination (z(c)). This can be written as Prob(SIS)[z(x')>z(c)], representing the probability of contamination. The probability map of Prob(SIS)[z(x')>z(c)] can then be used for delineating contaminated areas. In addition, the multi-location uncertainty of an area A,delineated as contaminated based on the probability map of Prob(SIS)[z(x')>z(c)], can be calculated to assess the reliability of delineation. Multi-location uncertainty refers to the probability of Cu concentrations in several locations, x'(1), x'(2), em leader, x'(m,) in the area A, being higher than the threshold (z(c)) as denoted by Prob(SIS)[z(x'(1))>z(c), z(x'(2))>z(c), em leader, andz(x'(m))>z(c)] or Prob(SIS)[z(A)>z(c)]. The multi-location uncertainty Prob(SIS)[z(A)>z(c)], obtained from the SIS, can be used to assess the reliability of delineation for regions suspected of contamination, (A), which has been delineated as contaminated. Reliance on this information facilitates the decision making process in determining which areas are contaminated and require cleanup action.

Copper↗

PubMed1991

Mapping of human chromosome 5 microsatellite DNA polymorphisms.

Thirteen moderately to highly informative microsatellite DNA polymorphisms based on (dC-dA)n.(dG-dT)n repeats were mapped to segments of human chromosome 5 using both linkage analysis and a panel of somatic cell hybrids which contained rearranged chromosomes. The markers were distributed throughout most of the length of the chromosome from the regions p15.3-p15.1 to q33.3-qter. Maps of the sites of meiotic recombination within the reference families proved particularly useful for the purpose of integrating new polymorphisms into the existing linkage map.

Base Sequence↗

PubMed1989

Fine structure DNA mapping studies of the chromosomal region harboring the genetic defect in neurofibromatosis type I.

To better map the location of the von Recklinghausen neurofibromatosis (NF1) gene, we have characterized a somatic cell hybrid designated 7AE-11. This microcell-mediated, chromosome-transfer construct harbors a centromeric segment and a neo-marked segment from the distal long arm of human chromosome 17. We have identified 269 cosmid clones with human sequences from a 7AE-11 library and, using a panel of somatic cell hybrids with a total of six chromosome 17q breakpoints, have mapped 240 of these clones on chromosome 17q. The panel included a hybrid (NF13) carrying a der(22) chromosome that was isolated from an NF1 patient with a balanced translocation, t(17;22) (q11.2;q11.2). Fifty-three of the cosmids map into a region spanning the NF13 breakpoint, as defined by the two closest flanking breakpoints (17q11.2 and 17q11.2-q12). RFLP clones from a subset of these cosmids have been mapped by linkage analysis in normal reference families, to localize the NF1 gene more precisely and to enhance the potential for genetic diagnosis of this disorder. The cosmids in the NF1 region will be an important resource for testing DNA blots of large-fragment restriction-enzyme digests from NF1 patient cell lines, to detect rearrangements in patients' DNA and to identify the 17;22 NF1 translocation breakpoint.

Animals↗