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At least 1,711 records · Page 95Linked to original sources
PubMed2006

Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites.

The identification of cis-regulatory elements is central to understanding gene transcription. Hypersensitivity of cis-regulatory elements to digestion with DNaseI remains the gold-standard approach to locating such elements. Traditional methods used to identify DNaseI hypersensitive sites are cumbersome and can only be applied to short stretches of DNA at defined locations. Here we report the development of a novel genomic array-based approach to DNaseI hypersensitive site mapping (ADHM) that permits precise, large-scale identification of such sites from as few as 5 million cells. Using ADHM we identified all previously recognized hematopoietic regulatory elements across 200 kb of the mouse T-cell acute lymphocytic leukemia-1 (Tal1) locus, and, in addition, identified two novel elements within the locus, which show transcriptional regulatory activity. We further validated the ADHM protocol by mapping the DNaseI hypersensitive sites across 250 kb of the human TAL1 locus in CD34+ primary stem/progenitor cells and K562 cells and by mapping the previously known DNaseI hypersensitive sites across 240 kb of the human alpha-globin locus in K562 cells. ADHM provides a powerful approach to identifying DNaseI hypersensitive sites across large genomic regions.

Algorithms↗
PubMed2002

New frontiers in molecular pediatric cardiology.

Numerous advances in understanding the molecular basis of congenital heart disease have been published in the past year. Highlights are reviewed, focusing on two major topics: genetic syndromes and cardiac organogenesis. Genetic syndromes are discussed in the context of complementary data from targeted mutations in animals and genetic mapping studies in humans. These include the DiGeorge, Holt-Oram, Alagille, familial primary pulmonary hypertension, and Noonan syndromes. Novel concepts in cardiac organogenesis are discussed, including the existence and contribution of an anterior heart field to the developing cardiac outflow tract, novel cell-cell signaling involving migrating neural crest, the origins of the conduction system and initial embryonic heartbeat, and the possibility of a population of cardiac stem cells in the adult heart. The studies reviewed have potential clinical relevance in the near future and will be of interest to the clinician interested in congenital heart disease.

Age Factors↗
PubMed1991

Human genome research in an interdependent world.

This has been the year of agenda-setting conferences for the ambitious ELSI (ethical, legal and social issues) program of the Human Genome Project (HGP). But of the dozen or more major meetings of this sort held across the country, the one held at the National Institutes of Health (NIH) in Bethesda, MD, June 2-4, 1991, was distinctive in several respects. As its name implies, "Human Genome Research in an Interdependent World" was a global look at the issues raised by gene mapping and sequencing. Unlike previous conferences, however, this meeting looked beyond a comparative analysis of clinical and domestic legal issues, and concentrated on topics that may require responses on a truly international level if they are to be successfully resolved....[Capron served as general chairman of the conference]

DNA Fingerprinting↗
PubMed2006

Chagas disease in Mexico: an analysis of geographical distribution during the past 76 years--a review.

Literature from 1928 through 2004 was compiled from different document sources published in Mexico or elsewhere. From these 907 publications, we found 19 different topics of Chagas disease study in Mexico. The publications were arranged by decade and also by state. This information was used to construct maps describing the distribution of Chagas disease according to different criteria: the disease, vectors, reservoirs, and strains. One of the major problems confronting study of this zoonotic disease is the great biodiversity of the vector species; there are 30 different species, with at least 10 playing a major role in human infection. The high variability of climates and biogeographic regions further complicate study and understanding of the dynamics of this disease in each region of the country. We used a desktop Genetic Algorithm for Rule-Set Prediction procedure to provide ecological models of organism niches, offering improved flexibility for choosing predictive environmental and ecological data. This approach may help to identify regions at risk of disease, plan vector-control programs, and explore parasitic reservoir association. With this collected information, we have constructed a data base: CHAGMEX, available online in html format.

Animals↗
PubMed2004

[Establishment of protein profile of human small cell lung cancer cell line NCI-H446].

BACKGROUND & OBJECTIVE: Small cell lung cancer (SCLC) is particularly aggressive, and characterized by rapid growth and early metastasis. At present, there is no data concerning SCLC two-dimensional polyacrylamide gel electrophoresis (2-DE) reference map,and its protein profiles in public databases. This study was to establish a well-resolved, reproducible 2-DE map of proteome in SCLC cell line NCI-H446, and analyze its protein profiles. METHODS: Two-DE was applied to separate the total proteins of NCI-H446 cells, which were then silver-stained in the gel. Well-separated protein spots were selected from the gel by ImageMaster 2D analysis system. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS), peptide map fingerprinting (PMF),and database searching were used to identify the protein spots. RESULTS: Clear,well-resolved, reproducible 2-DE patterns of proteome in NCI-H446 cells were obtained. The average protein spots of 3 gels were 1506+/-74; and 1412+/-56 spots were matched with an average matching rate of 93.4%. The average deviation of spot position was (0.96+/-0.27) mm in IEF direction, and (1.24+/-0.41) mm in SDS-PAGE direction indicating relatively good reproducibility of the protein spots. Fifty-eight proteins were identified, certain proteins were products of oncogenes, and others were involved in cell cycle regulation, and signal transduction. CONCLUSIONS: A reference map of NCI-H446 cells was established,certain proteins were identified by MALDI-TOF-MS and PMF. These data will be useful for establishing human SCLC proteome database.

Amino Acid Sequence↗
PubMed2001

Establishment of a root proteome reference map for the model legume Medicago truncatula using the expressed sequence tag database for peptide mass fingerprinting.

We have established a proteome reference map for Medicago truncatula root proteins using two-dimensional gel electrophoresis combined with peptide mass fingerprinting to aid the dissection of nodulation and root developmental pathways by proteome analysis. M. truncatula has been chosen as a model legume for the study of nodulation-related genes and proteins. Over 2,500 root proteins could be displayed reproducibly across an isoelectric focussing range of 4-7. We analysed 485 proteins by peptide mass fingerprinting, and 179 of those were identified by matching against the current M. truncatula expressed sequence tag (EST) database containing DNA sequences of approximately 105,000 ESTs. Matching the EST sequences to available plant DNA sequences by BLAST searches enabled us to predict protein function. The use of the EST database for peptide identification is discussed. The majority of identified proteins were metabolic enzymes and stress response proteins, and 44% of proteins occurred as isoforms, a result that could not have been predicted from sequencing data alone. We identified two nodulins in uninoculated root tissue, supporting evidence for a role of nodulins in normal plant development. This proteome map will be updated continuously (http://semele.anu.edu.au/2d/2d.html) and will be a powerful tool for investigating the molecular mechanisms of root symbioses in legumes.

Databases as Topic↗
PubMed2006

Identifying biological concepts from a protein-related corpus with a probabilistic topic model.

BACKGROUND: Biomedical literature, e.g., MEDLINE, contains a wealth of knowledge regarding functions of proteins. Major recurring biological concepts within such text corpora represent the domains of this body of knowledge. The goal of this research is to identify the major biological topics/concepts from a corpus of protein-related MEDLINE titles and abstracts by applying a probabilistic topic model. RESULTS: The latent Dirichlet allocation (LDA) model was applied to the corpus. Based on the Bayesian model selection, 300 major topics were extracted from the corpus. The majority of identified topics/concepts was found to be semantically coherent and most represented biological objects or concepts. The identified topics/concepts were further mapped to the controlled vocabulary of the Gene Ontology (GO) terms based on mutual information. CONCLUSION: The major and recurring biological concepts within a collection of MEDLINE documents can be extracted by the LDA model. The identified topics/concepts provide parsimonious and semantically-enriched representation of the texts in a semantic space with reduced dimensionality and can be used to index text.

Abstracting and Indexing↗
PubMed2000

Linkage and associated studies of schizophrenia.

Genetic epidemiology has provided consistent evidence over many years that schizophrenia has a genetic component, and that this genetic component is complex, polygenic, and involves epistatic interaction between loci. Molecular genetics studies have, however, so far failed to identify any DNA variant that can be demonstrated to contribute to either liability to schizophrenia or to any identifiable part of the underlying pathology. Replication studies of positive findings have been difficult to interpret for a variety of reasons. First, few have reproduced the initial findings, which may be due either to random variation between two samples in the genetic inputs involved, or to a lack of power to replicate an effect at a given alpha level. Where positive data have been found in replication studies, the positioning of the locus has been unreliable, leading no closer to positional cloning of genes involved. However, an assessment of all the linkage studies performed over the past ten years does suggest a number of regions where positive results are found numerous times. These include regions on chromosomes 1, 2, 4, 5, 6, 7, 8, 9, 10, 13, 15, 18, 22 and the X. All of these data are critically reviewed and their locations compared. Reasons for the difficulty in obtaining consistent results and possible strategies for overcoming them are discussed. Am. J. Med. Genet. (Semin. Med. Genet.) 97:23-44, 2000.

Chromosome Mapping↗
PubMed2002

Genome-wide linkage analysis of families with obsessive-compulsive disorder ascertained through pediatric probands.

The goal of this study was to identify chromosomal regions likely to contain susceptibility alleles for early-onset obsessive-compulsive disorder (OCD). A genome scan was done in 56 individuals from seven families ascertained through pediatric OCD probands; 27 of the 56 subjects had a lifetime diagnosis of definite OCD. Denser mapping of regions on chromosomes 2, 9, and 16 was subsequently done with those subjects and ten additional subjects from the largest family in the study. Direct interviews were completed with 65 of the 66 genotyped individuals. Relatives were interviewed blind to proband status. Of the 65 interviewed individuals, 32 had a lifetime diagnosis of definite OCD. Three of the seven probands had a history of Tourette disorder. Two of the 25 relatives with OCD had a tic history, whereas none of the 33 relatives without OCD had tics. The genome scan consisted of 349 microsatellite markers with an average between-marker distance of 11.3 centiMorgan (cM). Fine mapping was done with 24 additional markers at an average spacing of 1.6 cM. Parametric and nonparametric linkage analyses were conducted using GENEHUNTER(+). The maximum multipoint LOD score with a dominant model was 2.25 on 9p. However, with fine mapping and additional subjects, that LOD score decreased to 1.97. The maximum multipoint nonparametric LOD* score was 1.73 on 19q. The maximum multipoint LOD score with a recessive model was 1.40 on 6p. The results provide suggestive evidence for linkage on 9p and identify regions requiring further study with much larger samples.

Adolescent↗
PubMedDate not supplied

Nomenclature guidelines for X-linked mental retardation.

Nomenclature guidelines are proposed for non-specific and for syndromal forms of X-linked mental retardation. Non-specific mental retardations (MRX) are given unique symbols for each family (MRX1, MRX2, MRX3 ...). Syndromal mental retardations (MRXS) which do not as yet have specific symbols are given unique interim symbols for each syndrome (MRXS1, MRXS2, MRXS3 ...). The prerequisite for assignment of serial MRX and MRXS gene symbols is a minimum lod score (or multipoint lod score) of +2 between the MR locus and one or more X chromosome markers. Prior approval of availability for proposed gene symbols must be obtained from the Nomenclature Committee of the Human Gene Mapping Workshops.

Chromosome Mapping↗
PubMed1976

Fiber trajectories of olfactory bulb efferents in the hamster.

Olfactory bulb efferents sweep caudally over the surface of the piriform lobe in a broad fiber sheet. The internal organization of this axon population was analysed by topologically transforming the cortical surface from its in situ cylindrical form into an unrolled (flattened) map. The distribution of degeneration elicited by restricted bulb lesions and fiber transections was then reconstructed onto this map. Most of the projection cortex of the main olfactory bulb is innervated in a widespread, non-topographic manner by axons that collect in the compact bundle of the lateral olfactory tract (LOT). LOT collateral branches bound for the prepiriform cortex veer laterally off the main trajectory of the tract at an angle of 50 degrees or less. Thus, transection of discrete fiber populations leaves only a small wedge-shaped pocket of totally denervated cortex distal to the cut. The medial half of the olfactory tubercle and the hippocampal rudiment receive their bulbar input along medially disposed fibers that do not join the LOT proper. The lateral half of the olfactory tubercle, however, receives an input from LOT fiber collaterals as well as these medial bulb efferents. Finally, much of the corticomedial amygdaloid complex receives fibers from the accessory olfactory bulb along a specialized subdivision of the LOT, the accessory olfactory tract. These observations are expressed in a schematic summary of the trajectories of olfactory bulb efferents as they appear in the unrolled map and in the more standard ventral view of the hamster brain.

Animals↗
PubMed1995

Intrinsic connections of the rat amygdaloid complex: projections originating in the basal nucleus.

The amygdaloid complex is involved in associational processes, such as the formation of emotional memories about sensory stimuli. However, the anatomical connections through which the different amygdaloid nuclei process incoming information and communicate with the other amygdaloid nuclei, is poorly understood. As part of an ongoing project aimed at elucidating the intrinsic connections of the rat amygdaloid complex, we injected the anterograde tracer PHA-L (Phaseolus vulgaris-leucoagglutinin) into different rostrocaudal levels of the basal nucleus of the amygdala in 21 rats and analyzed the distribution of labeled fibers and terminals throughout the amygdaloid complex. The connectional analysis, together with cytoarchitectonic observations, suggested that contrary to previous notions the basal nucleus in the rat has three divisions: magnocellular, intermediate, and parvicellular. The magnocellular division has heavy reciprocal connections with the lateral portion of the parvicellular division and the intermediate division projects weakly to the parvicellular division, whereas the projection from the medial portion of the parvicellular division to the intermediate division is heavy and the lateral and medial portions of the parvicellular division are only weakly interconnected, as are the magnocellular and intermediate divisions. The main intraamygdaloid targets of the basal nucleus projections are the nucleus of the lateral olfactory tract, the anterior amygdaloid area, the medial and capsular divisions of the central nucleus, the anterior cortical nucleus, and the amygdalohippocampal area. Our findings provide the most detailed understanding of the intra-amygdala connections of the basal nucleus to date and show that the connections within the basal nucleus and between the basal nucleus and other amygdaloid areas are more widespread and topographically organized than previously recognized.

Amygdala↗
PubMed1995

Two-locus approach of segregation and linkage analysis in the study of complex traits.

A two-locus segregation and linkage-analysis approach was used to characterize the genetic control of a complex trait (Q1) and to localize the genes that have detectable effects. The results suggested that a two-locus Mendelian model fit the data significantly better than a one-locus model. The linkage results based on the most parsimonious two-locus model revealed linkage of Q1 to two areas (MG2 and MG3), while there was less evidence for linkage using one-locus models. Results also suggested that the subphenotypes (Q2 and Q3) provided useful information for further analysis of Q1 using two-locus models.

Alleles↗
PubMed2005

Approaches to detecting gene x gene interaction in Genetic Analysis Workshop 14 pedigrees.

Whether driven by the general lack of success in finding single-gene contributions to complex disease, by increased knowledge about the potential involvement of specific biological interactions in complex disease, or by recent dramatic increases in computational power, a large number of approaches to detect locus x locus interactions were recently proposed and implemented. The six Genetic Analysis Workshop 14 (GAW14) papers summarized here each applied either existing or refined approaches with the goal of detecting gene x gene, or locus x locus, interactions in the GAW14 data. Five of six papers analyzed the simulated data; the other analyzed the Collaborative Study on the Genetics of Alcoholism data. The analytic strategies implemented for detecting interactions included multifactor dimensionality reduction, conditional linkage analysis, nonparametric linkage correlation, two-locus parametric linkage analysis, and a joint test of linkage and association. Overall, most of the groups found limited success in consistently detecting all of the simulated interactions due, in large part, to the nature of the generating model.

Alcoholism↗
PubMed2003

Neural correlates of segmental and tonal information in speech perception.

The Chinese language provides an optimal window for investigating both segmental and suprasegmental units. The aim of this cross-linguistic fMRI study is to elucidate neural mechanisms involved in extraction of Chinese consonants, rhymes, and tones from syllable pairs that are distinguished by only one phonetic feature (minimal) vs. those that are distinguished by two or more phonetic features (non-minimal). Triplets of Chinese monosyllables were constructed for three tasks comparing consonants, rhymes, and tones. Each triplet consisted of two target syllables with an intervening distracter. Ten Chinese and English subjects were asked to selectively attend to targeted sub-syllabic components and make same-different judgments. Direct between-group comparisons in both minimal and non-minimal pairs reveal increased activation for the Chinese group in predominantly left-sided frontal, parietal, and temporal regions. Within-group comparisons of non-minimal and minimal pairs show that frontal and parietal activity varies for each sub-syllabic component. In the frontal lobe, the Chinese group shows bilateral activation of the anterior middle frontal gyrus (MFG) for rhymes and tones only. Within-group comparisons of consonants, rhymes, and tones show that rhymes induce greater activation in the left posterior MFG for the Chinese group when compared to consonants and tones in non-minimal pairs. These findings collectively support the notion of a widely distributed cortical network underlying different aspects of phonological processing. This neural network is sensitive to the phonological structure of a listener's native language. Hum. Brain Mapping 20:185-200, 2003.

Adult↗
PubMed2005

Automated quality assurance routines for fMRI data applied to a multicenter study.

Standard procedures to achieve quality assessment (QA) of functional magnetic resonance imaging (fMRI) data are of great importance. A standardized and fully automated procedure for QA is presented that allows for classification of data quality and the detection of artifacts by inspecting temporal variations. The application of the procedure on phantom measurements was used to check scanner and stimulation hardware performance. In vivo imaging data were checked efficiently for artifacts within the standard fMRI post-processing procedure by realignment. Standardized and routinely carried out QA is essential for extensive data amounts as collected in fMRI, especially in multicenter studies. Furthermore, for the comparison of two different groups, it is important to ensure that data quality is approximately equal to avoid possible misinterpretations. This is shown by example, and criteria to quantify differences of data quality between two groups are defined.

Artifacts↗
PubMed2002

Surgery of the motor thalamus: problems with the present nomenclatures.

The literature on thalamic surgery is difficult to read because different nomenclatures are in use. Neurosurgeons mostly use the stereotactic atlas of Schaltenbrand with Hassler's nomenclature of the thalamus. Neuroanatomists use different nomenclatures for the primate thalamus. The cytoarchitectonic definition of nuclei is difficult in the motor thalamus, and it would be best to define the nuclei based on their subcortical afferents. However, tracing studies are not available in humans. Thus, human thalamic nomenclature is based entirely on cytoarchitectonic subdivisions and transfer of knowledge by analogy from monkey to man. Problems arise when trying to transfer the detailed knowledge from monkey to the human brain. By doing so, different authors have come to different conclusions concerning the subcortical afferents of Hassler's motor nuclei, which inevitably leads to confusion when attempting neurophysiological interpretations of the surgical data. The present review draws attention to the discrepancies and open questions in the literature. There is a need to better define the limits of the sensory and cerebellar afferent receiving thalamic nuclei as well as those of the cerebellar and pallidal afferent receiving territories in humans.

Animals↗
PubMed1998

Fingertip representation in the human somatosensory cortex: an fMRI study.

Eight right-handed adult humans underwent functional magnetic resonance imaging (fMRI) of their brain while a vibratory stimulus was applied to an individual digit tip (digit 1, 2, or 5) on the right hand. Multislice echoplanar imaging techniques were utilized during digit stimulation to investigate the organization of the human primary somatosensory (SI) cortex, cortical regions located on the upper bank of the Sylvian fissure (SII region), insula, and posterior parietal cortices. The t test and cluster size analyses were performed to produce cortical activation maps, which exhibited significant regions of interest (ROIs) in all four cortical regions investigated. The frequency of significant ROIs was much higher in SI and the SII region than in the insula and posterior parietal region. Multiple digit representations were observed in the primary somatosensory cortex, corresponding to the four anatomic subdivisions of this cortex (areas 3a, 3b, 1, and 2), suggesting that the organization of the human somatosensory cortex resembles that described in other primates. Overall, there was no simple medial to lateral somatotopic representation in individual subject activity maps. However, the spatial distance between digit 1 and digit 5 cortical representations was the greatest in both SI and the SII region within the group. Statistical analyses of multiple activity parameters showed significant differences between cortical regions and between digits, indicating that vibrotactile activations of the cortex are dependent on both the stimulated digit and cortical region investigated.

Adolescent↗