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Results for “reference mapping”

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PubMed1997

Mapping of repetitive and non-repetitive DNA probes to chromosomes of the microsporidian Encephalitozoon cuniculi.

The molecular karyotype of a murine isolate of Encephalitozoon cuniculi, a microsporidian with a wide range of mammalian hosts, comprises eleven chromosomes ranging in size between 217 and 315 kb. To determine specific chromosomal markers, a partial genomic library was constructed and cloned DNA fragments were hybridized to chromosomal bands separated by pulsed-field gel electrophoresis. Most probes were assigned to single chromosomes, indicating prevalence of low-copy number nucleotide sequences within the very small genome of E. cuniculi (2.9 Mb). A few probes were shown to hybridize to all chromosomes. These repetitive DNA fragments corresponded to either rRNA genes or some non-coding regions whose sequences were characterized by short micro- and minisatellites. The chromosomal locations of beta-tubulin genes and six newly identified protein-encoding genes were determined. Genes encoding dihydrofolate reductase, thymidylate synthase, serine hydroxymethyl transferase, a cdc2 kinase-like protein and helicase ERCC6-like protein were each located on a single chromosome whereas genes for both beta-tubulin and aminopeptidase were on two different chromosomes. The mapping will serve as a reference for further analysis of intraspecific karyotype polymorphism in different isolates from different host species.

Animals↗

PubMed2004

The Opportunities Map at Cornell University: finding direction in dairy production medicine.

Discussion between faculty and interested students revealed the existence of a multitude of opportunities in dairy production medicine at the College of Veterinary Medicine at Cornell University. Many of these were not well known to students, or even to some of the faculty, and the means of accessing specific learning experiences were sometimes obscure. Together, an informal group of faculty, students, and alumni set about cataloging available educational opportunities, resulting in a 31-page publication referred to as the "Opportunities Map." Essentially a student handbook for production medicine students, the Opportunities Map at Cornell helps guide the travel of food animal-interested students through the curriculum without missing the important highlights along the way. The map was originally developed to chronicle the opportunities and resources available to students, but it has also been used to foster face-to-face communications between students and faculty, to welcome incoming students with production animal interests, and to provide a baseline description for further discussion about the curriculum.

Animals↗

PubMed1993

Identification of carbohydrate structures in glycoprotein peptide maps by the use of LC/MS with selected ion extraction with special reference to tissue plasminogen activator and a glycosylation variant produced by site directed mutagenesis.

Electrospray ionization mass spectrometry utilizing a single quadrupole on line with reversed-phase HPLC (LC/MS) enables the characterization of glycoproteins in a relatively short period of time. In this approach the protein is digested with a suitable protease and the peptides are separated by reversed-phase HPLC and detected by electrospray ionization mass spectrometry. The glycopeptides are initially observed as a cluster of negatively sloping ions in a contour plot of data from the LC/MS run (m/z vs retention time) or as a characteristics series of masses at different elution times. The search for a particular glycopeptide is based on previously known carbohydrate structures and on consensus glycosylation sites. Further structural information is obtainable with glycosidase digestion and LC/MS analysis. The mass shifts following glycosidase digestion allow further confirmation of the structure. This approach identifies the site of attachment of two hybrid glycoforms to the T11 tryptic peptide in a reversed-phase tryptic map of recombinant tissue plasminogen activator (rt-PA). Use of selected ion extraction of the LC/MS data files allows one to graphically describe the elution order of closely related glycopeptides. The potential of LC/MS for the characterization of small amounts of unknown glycoproteins is shown by the study of an rt-PA mutant. A new potential site for glycosylation is created by site directed mutagenesis of wild type rt-PA with replacement of a threonine residue with asparagine at residue 103. An examination of a tryptic map shows that the mutant contains two new complex carbohydrate chains. The introduction of the new asparagine proximal to asparagine 117 changes this native high-mannose site in rt-PA to a complex-type glycosylation. This method allows rapid identification of carbohydrate containing peptides and yields useful structural information on microgram amounts of material.

Amino Acid Sequence↗

PubMed1989

Critical role of the D21S55 region on chromosome 21 in the pathogenesis of Down syndrome.

The duplication of a specific region of chromosome 21 could be responsible for the main features of Down syndrome. To define and localize this region, we analyzed at the molecular level the DNA of two patients with partial duplication of chromosome 21. These patients belong to two groups of Down syndrome patients characterized by different partial trisomies 21: (i) duplication of the long arm, proximal to 21q22.2, and (ii) duplication of the end of the chromosome, distal to 21q22.2 We assessed the copy number of five chromosome 21 sequences (SOD1, D21S17, D21S55, ETS2, and D21S15) and found that D21S55 was duplicated in both cases. By means of pulsed-field gel analysis and with the knowledge of regional mapping of the probes D21S17, D21S55 and ETS2, we estimated the size of the common duplicated region to be between 400 and 3000 kilobases. This region, localized on the proximal part of 21q22.3, is suspected to contain genes the overexpression of which is crucial in the pathogenesis of Down syndrome.

Chromosome Banding↗

PubMed2000

[Refined chromosome assignment of human novel H-RalGDS gene on chromosome 9q34.1 by using radiation hybrid genebridge 4 panel].

OBJECTIVE: Refined chromosome assignment of a novel Ras-related H-RalGDS gene (the human homology of rat RalGDS, Ral guanine nucleotide dissociation stimulator recently cloned and characterized by our laboratory) by using human/rodent radiation somatic cell hybrid panel GB4. METHODS: According to the sequence of the 3'-untranslated region of H-RalGDS cDNA, forward and reverse primers were designed and used to amplify the human/rodent somatic radiation hybrid Genebridge 4 panel. The PCR result of each cell line of the panel was scored in a certain way and put into the related internet site of WI/MIT Radiation Hybrid Mapper for RH mapping and comprehensive analysis. RESULTS: The H-RalGDS gene was successfully localized to the framework of chromosome 9. After referring to literature and further integrated mapping analysis of the physical, genetic linkage and cytological mappings, the gene was assigned precisely between the markers SURF5 and RPL7A which had already been assigned to human chromosome 9q34.1. CONCLUSION: The localization of H-RalGDS not only contributed much to the construction of refined gene map and cytogenetic map within the region of chromosome 9q34, but also made clear that RH mapping of human novel genes is a simple, convenient and reliable method which can provide even more genetic information of genes within chromosomal regions.

Animals↗

PubMed1995

Filling the gaps in the porcine linkage map: isolation of microsatellites from chromosome 18 using flow sorting and SINE-PCR.

Flow-sorted chromosome 18 material from the pig (SSC18) was amplified with SINE-PCR to generate DNA for molecular cloning. An SSC18-enriched library was constructed and subsequently screened with a (CA)15 probe to identify polymorphic microsatellites. Eleven unique microsatellites were obtained, six of which constituted direct extensions of SINE poly(A) tracts. Eight primer pairs amplified polymorphic loci in unrelated pigs. The polymorphic markers were typed in a Swedish reference pedigree for porcine genome mapping, but only two of them (S0177 and S0179) mapped to SSC18. The remaining markers mapped to chromosomes 3, 4, 7, 9, and 11. Together with two markers from other sources (S0062 and sw787), a four-point linkage group on SSC18 could be established.

Animals↗

PubMedDate not supplied

Comparison of event related potentials (ERPs) distributions obtained with three reference systems: linked binaural, mean reference, extracephalic.

Event related potentials (ERPs) to auditory and visual oddball paradigms were recorded from 19 scalp derivations in 10 controls. Three different reference systems were used: the linked earlobes (LE), the computer calculated mean reference (MR), and a calibrated sterno-vertebral extracephalic reference (EC). The distribution of ERPs was represented on single plane maps (quadratic interpolation, 4-NN method). With LE reference N2, P3a-P3b had no polarity reverted counterparts on the scalp. With EC reference a negativity was recorded on T3-T4 (and partly T5-T5) derivations with the same latency as P3a-P3b vertex component. With MR the N2, P3a-P3b components at vertex were paralleled by polarity reverted counterparts on anterior frontal, temporal and occipital derivations.

Acoustic Stimulation↗

PubMed2006

Transcription factor map alignment of promoter regions.

We address the problem of comparing and characterizing the promoter regions of genes with similar expression patterns. This remains a challenging problem in sequence analysis, because often the promoter regions of co-expressed genes do not show discernible sequence conservation. In our approach, thus, we have not directly compared the nucleotide sequence of promoters. Instead, we have obtained predictions of transcription factor binding sites, annotated the predicted sites with the labels of the corresponding binding factors, and aligned the resulting sequences of labels--to which we refer here as transcription factor maps (TF-maps). To obtain the global pairwise alignment of two TF-maps, we have adapted an algorithm initially developed to align restriction enzyme maps. We have optimized the parameters of the algorithm in a small, but well-curated, collection of human-mouse orthologous gene pairs. Results in this dataset, as well as in an independent much larger dataset from the CISRED database, indicate that TF-map alignments are able to uncover conserved regulatory elements, which cannot be detected by the typical sequence alignments.

Algorithms↗

PubMed2025

Diploid genome assembly of human fibroblast cell lines enables clone specific variant calling, improved read mapping and accurate phasing.

Human cell lines are fundamental tools in biomedical research and are widely used in disease modeling, drug development, and many other domains. Here, we present chromosome-level, phased diploid genome assemblies of two popular human cell lines: the BJ foreskin fibroblast line and the IMR-90 fetal lung fibroblast line. Our high-quality assemblies, generated using long-read and Hi-C sequencing data, reveal substantial structural variation, including more than 50,000 insertions, deletions, duplications, and inversions compared to the recent T2T-CHM13v2.0 reference. Our assemblies provide detailed maps of genetic variation, enabling more accurate variant calling and the ability to phase reads when using newly generated or historical sequencing data on these cell lines or their derivatives. All assemblies and associated data have been made available as a resource for the research community. We envision that diploid genome assembly will become a cornerstone approach for personalized medicine in the near future.

Journal Article↗

PubMed2005

Quantitative architectural analysis: a new approach to cortical mapping.

Recent progress in anatomical and functional MRI has revived the demand for a reliable, topographic map of the human cerebral cortex. Till date, interpretations of specific activations found in functional imaging studies and their topographical analysis in a spatial reference system are, often, still based on classical architectonic maps. The most commonly used reference atlas is that of Brodmann and his successors, despite its severe inherent drawbacks. One obvious weakness in traditional, architectural mapping is the subjective nature of localising borders between cortical areas, by means of a purely visual, microscopical examination of histological specimens. To overcome this limitation, more objective, quantitative mapping procedures have been established in the past years. The quantification of the neocortical, laminar pattern by defining intensity line profiles across the cortical layers, has a long tradition. During the last years, this method has been extended to enable a reliable, reproducible mapping of the cortex based on image analysis and multivariate statistics. Methodological approaches to such algorithm-based, cortical mapping were published for various architectural modalities. In our contribution, principles of algorithm-based mapping are described for cyto- and receptorarchitecture. In a cytoarchitectural parcellation of the human auditory cortex, using a sliding window procedure, the classical areal pattern of the human superior temporal gyrus was modified by a replacing of Brodmann's areas 41, 42, 22 and parts of area 21, with a novel, more detailed map. An extension and optimisation of the sliding window procedure to the specific requirements of receptorarchitectonic mapping, is also described using the macaque central sulcus and adjacent superior parietal lobule as a second, biologically independent example. Algorithm-based mapping procedures, however, are not limited to these two architectural modalities, but can be applied to all images in which a laminar cortical pattern can be detected and quantified, e.g. myeloarchitectonic and in vivo high resolution MR imaging. Defining cortical borders, based on changes in cortical lamination in high resolution, in vivo structural MR images will result in a rapid increase of our knowledge on the structural parcellation of the human cerebral cortex.

Algorithms↗

PubMed2005

Grammatical gender effects on cognition: implications for language learning and language use.

In 4 experiments, the authors addressed the mechanisms by which grammatical gender (in Italian and German) may come to affect meaning. In Experiments 1 (similarity judgments) and 2 (semantic substitution errors), the authors found Italian gender effects for animals but not for artifacts; Experiment 3 revealed no comparable effects in German. These results suggest that gender effects arise as a generalization from an established association between gender of nouns and sex of human referents, extending to nouns referring to sexuated entities. Across languages, such effects are found when the language allows for easy mapping between gender of nouns and sex of human referents (Italian) but not when the mapping is less transparent (German). A final experiment provided further constraints: These effects during processing arise at a lexical-semantic level rather than at a conceptual level.

Adult↗

PubMed2000

Mapping motor cortex projections to single motor units in humans with transcranial magnetic stimulation.

We devised a method to investigate the cortical organization of corticomotoneurons (CMs) to upper limb muscles. A spike-triggering technique was used, in which a tonically discharging single motor unit (SMU) triggered transcranial magnetic stimulation (TMS) of motor cortex, and the probability of producing short-latency discharges (primary excitatory responses [PERs]) was measured. PER probabilities were mapped in 34 SMUs, using a 16 cm(2) scalp grid with the central reference point having a probability of 0.5. Maps showed a single optimum point of scalp stimulation and significant decreases in PER probability with shifts of 2 cm from this point, for all subjects. These findings suggest that the colony of CMs projecting to an individual SMN is contained within a small volume of motor cortex. Changes in PER probability with shifts in stimulation site may reflect the organization of other intracortical neurons mediating TMS activation of these CMs.

Adult↗

PubMed1991

Restriction site mapping of subgenus D adenoviruses, prototypes 42-47, intermediate and atypical strains.

Restriction site maps with the endonucleases BamHI, BgIII, and HindIII were elaborated for 19 adenovirus strains of subgenus D, namely candidates AV42 to 47, 6 intermediate and 7 atypical strains. On the basis of several types mapped by biochemical methods, the physical maps for the 19 strains were constructed by adapting restriction fragments of defined molecular weight to the known maps, as the homology among strains within this subgenus is considerable. Other prototypes mapped by adaptation were also used for reference. The localization of the restriction sites on the genome was analyzed for all mapped types or strains of subgenus D (except AV8). The sites appeared to be randomly distributed; only one site was common to all strains.

Adenoviruses, Human↗

PubMed2005

Making two-level standards work in legacy communication frameworks.

The research presented deals with the problem of how information technology can support the interconnection of medical information systems in practice. We apply a two-part structural standard that consists of a fixed Information Reference (IR) Model, and an Archetype Reference (AR) Model that uses the structures of the IR model. A very important problem with the real-world application of such a two-level model is that the high level (abstract) entities, structures and their connections must be somehow translated into lower level equivalents that legacy database information systems can actually use to program their standardised interface. Our choice for the lower level medium is XML, such that the standard appears as an XSD schema that can be used, in the usual way, to validate a message document. To test the viability of the above paradigm, we developed an archetype-XSD translator tool in the form of Protégé/OWL plugins and tested it on an industrial interface for exchanging medical episodes (MedQuery), using an implementation of openEHR. We found that the most important features: Containment, Cardinality, Named references to other instances, and References to external terminologies, could all be mapped to standard XSD constructs. We also developed a validator plugin to check external references. We plan to put the system at work in a heterogeneous medical messaging system (a descendant of the Budapest based MediNet system) in the near future.

Communication↗

PubMed1996

Identification of two candidate tumor suppressor genes on chromosome 17p13.3.

A second tumor suppressor locus on 17p that is distinct from TP53 has been identified in brain, breast, lung, and ovarian tumors. Using allelic loss mapping and positional cloning methods, we have recently identified two novel genes, which we refer to as OVCA1 and OVCA2, that map to 17p13.3. The two genes are ubiquitously expressed and encode proteins of 443 and 227 amino acids, respectively, with no known functional motifs. Sequence comparison of OVCA1 and OVCA2 revealed extensive sequence identity and similarity to hypothetical proteins from Saccharomyces cerevisiae, Caenorhabditis elegans, and Rattus species. Northern blot analysis reveals that OVCA1 and OVCA2 mRNA were expressed in normal surface epithelial cells of the ovary, but the level of this transcript is significantly reduced or is undetectable in 92% (11/12) of the ovarian tumors and tumor cell lines analyzed. The location, high degree of amino acid conservation, and reduced expression in ovarian tumors and tumor cell lines suggest that decreased expression of these two genes contributes to ovarian tumorigenesis and should be considered candidate tumor suppressor genes.

Alleles↗

PubMed2001

Identification of protective epitopes by sequencing of the major outer membrane protein gene of a variant strain of Chlamydia psittaci serotype 1 (Chlamydophila abortus).

Protective monoclonal antibodies (MAbs) to the major outer membrane protein (MOMP) of species of the family Chlamydiaceae, which is the primary vaccine candidate antigen, recognize nonlinear epitopes conferred by the oligomeric conformation of the molecule. Protective MAbs failed to recognize oligomeric MOMP of the variant strain LLG, which bears amino acid substitutions in variable segments (VSs) 1, 2, and 4, and competed with monomer-specific MAbs mapping to these VSs in reference strain 577. The results suggest that multiple sites located in the three VSs contribute to the epitope of protective MAbs.

Amino Acid Sequence↗

PubMed1995

Random subcloning.

Random subcloning strategies are commonly employed for analyzing pieces of DNA that are too large for direct analysis. Such strategies are applicable to gene finding, physical mapping, and DNA sequencing. Random subcloning refers to the generation of many small, directly analyzable fragments of DNA that represent random fragments of a larger whole, such as a genome. Following analysis of these fragments, a map or sequence of the original target may be reconstructed. Mathematical modeling is useful in planning such strategies and in providing a reference for their evaluation, both during execution and following completion. The statistical theory necessary for constructing these models has been developed independently over the last century. This paper brings this theory together into a statistical model for random subcloning strategies. This mathematical model retains its utility even at high subclone redundancies, which are necessary for project completion. The discussion here centers on shotgun sequencing, a random subcloning strategy envisioned as the method of choice for sequencing the human genome.

Chromosome Mapping↗

PubMed1995

Developing mossy fiber terminal fields in the rat cerebellar cortex may segregate because of Purkinje cell compartmentation and not competition.

Many mossy fiber afferent projections to the rat cerebellar cortex terminate in parasagittal bands. In particular, the anterior lobe vermis of the cerebellum contains alternating bands of mossy fibers from the spinal cord and external cuneate nuclei. The cerebellar cortical efferents, the Purkinje cells, are also organized in parasagittal bands. These can be revealed by immunochemical staining for the antigen zebrin II, which is selectively expressed by bands of Purkinje cells. In some cases, the boundaries between mossy fiber terminal fields align with identified transitions between zebrin+/- sets of Purkinje cells, whereas others are located within apparently homogeneous Purkinje cell compartments. Two theories can explain the terminal-field topography: In one view, mossy fiber terminals segregate during development, because growth cones from different sources compete for common territory. Alternatively, mossy fiber growth cones directly recognize chemically distinct target territories, and activity-dependent mechanisms play only minor roles. To explore these issues, two sets of experiments were performed. First, the terminal-field map of the neonatal spinocerebellar projection was compared to the Purkinje cell compartmentation as revealed by anticalbindin immunocytochemistry. Second, subsets of spinocerebellar mossy fiber afferents were ablated early in postnatal development, and the consequences for the neighboring cuneocerebellar terminal fields were mapped in the adult with reference to the zebrin II+/- compartments. These experiments revealed no evidence that competitive interactions constrain the mossy fiber terminal-field distribution but, rather, suggest that the organization of the mossy fiber projections follows the compartmentation of the Purkinje cells.

Analysis of Variance↗