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PubMed1997

Genome organization of Pseudomonas stutzeri and resulting taxonomic and evolutionary considerations.

In order to determine the genome variability within Pseudomonas stutzeri, 20 strains representing the seven described genomovars and strain JM300 were analyzed by using various resolution levels of rare cutting enzymes. XbaI and SpeI fingerprints revealed a high degree of heterogeneity of restriction patterns that did not correlate with the division into genomovars. However, a fragment pattern comparison led to the establishment of several groups of clonal variants within genomovars. One circular chromosome ranging in size from 3.75 to 4.64 Mb constitutes the genome of P. stutzeri strains. The I-CeuI, PacI, and SwaI low-resolution map of P. stutzeri type strain CCUG 11256 shows the locations of 12 genes, including rrn operons and the origin of replication. I-CeuI digests of the 20 strains studied plus the positions of six genes allowed a comparison of the rrn backbone organization within genomovars; the four rrn operons seemed to be at similar locations with respect to the origin of replication, as did the rest of the genes. However, a comparison of I-CeuI cleavage maps of the genomovar reference strains revealed a diverse genome organization in the genomovars relative to rrn operons and gene locations. In most genomovars, rrn operons are not arranged around the origin of replication but are equally distributed on the chromosome. Strain JM300 does not belong to any described genomovar, as determined from the organization of its genome. Large chromosomal rearrangements seem to be responsible for the differences in superordinate genome structure and must have played an important role in P. stutzeri diversification and niche colonization. An ancestral chromosome is suggested, and some plausible pathways for the generation of the various genome structures are proposed.

Blotting, Southern↗

PubMed2002

[Construction of linkage map of chromosomes 1 and 3 in large white x Meishan reference family].

A three-generation family of pigs has been constructed by using three Large White boars and seven sows of Meishan pigs as parents. In this family, five F1 males and twenty-three F1 females were intercrossed to generate 147 F2 offspring. According to the pig linkage map of USDA-MARC, eight and nine microsatellite markers selected on chromosomes 1 and 3 were chosen to span the entire chromosomes. The members of this family were genotyped. The characterization of these microsatellites was shown that they were polymorphic and could be used to construct linkage map and detect quantitative trait loci (QTLs). Linkage analyses were performed using the CRI-MAP software package. The lengths of the sex-averaged linkage map were 182.3 cM and 180.2 cM on chromosomes 1 and 3, respectively. There were some differences between the linkage maps in this study and of USDA-MARC. The linkage map of chromosome 1 in female was found to be shorter than in male, and the contrary was on chromosome 3.

Animals↗

PubMed2002

Characterization of the porcine melanocortin 2 receptor gene (MC2R ).

A porcine bacterial artificial chromosome (BAC) clone, containing the melanocortin 2 receptor gene (MC2R) was isolated. The complete coding sequence of the MC2R gene, contained in 1 exon, was determined. Polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) was performed on a 241-bp coding fragment. An AluI polymorphism, detecting a silent mutation, was found and typed on unrelated animals of five different pig breeds. The Meishan, Piétrain and Large White breeds differ significantly in allele frequencies from the Landrace and Czech Meat Pig breeds. The melanocortin 5 receptor gene (MC5R) was detected by PCR in the same BAC clone, as could be expected from the human and porcine mapping data. PCR-SSCP was performed on a 200-bp coding of MC5R, but no polymorphisms were detected. The BAC clone was mapped to Sscr6q27 by fluorescent in situ hybridization (FISH). A (CA)n microsatellite (SGU0002), isolated from the BAC, was localized on chromosome 6 by RH mapping near marker SW1473 and by linkage mapping on the MARC reference family at the same position as the marker SW2173 (97 cM). Allele frequencies, heterozygosity and polymorphism information contents (PIC) values were calculated for the five different pig breeds examined. The transcription of both genes in porcine liver, heart, kidney, fat, brain, pancreas, stomach, bladder, ovaries, lung, spleen, skin, adrenal gland and muscle tissues was examined by reverse transcriptase-polymerase chain reaction. Transcription was detected in skin and adrenal gland tissues for MC2R, while a positive signal was detected for MC5R in kidney, fat, pancreas, skin, adrenal gland and spleen tissues.

Amino Acid Sequence↗

PubMed2001

Estimation of DNA sequence diversity in bovine cytokine genes.

DNA sequence variation provides the fundamental material for improving livestock through selection. In cattle, single nucleotide polymorphisms and small insertions/deletions (collectively referred to here as SNPs) have been identified in cytokine genes and scored in a reference population to determine linkage map positions. The aim of the present study was twofold: first, to estimate the SNP frequency in a reference population of beef cattle, and second, to determine cytokine haplotypes in a group of sires from commercial populations. Forty-five SNP markers in DNA segments from nine cytokine gene loci were analyzed in 26 reference parents. Comparison of all 52 haploid genomes at each PCR amplicon locus revealed an average of one SNP per 143 bp of sequence, whereas comparison of any two chromosomes identified heterozygous sites, on average, every 443 bp. The combination of these 45 SNP genotypes was sufficient to uniquely identify each of the 26 animals. The average number of haplotype alleles (4.4) per PCR amplicon (688 bp) and the percentage heterozygosity among founding parents (50%) were similar to those for microsatellite markers in the same population. For 49 sires from seven common breeds of beef cattle, SNP genotypes (1,225 total) were obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) at three amplicon loci. All three of the amplicon haplotypes were correctly deduced for each sire without the use of parent or progeny genotypes. The latter allows a wide range of genetic studies in commercial populations of cattle where genotypic information from relatives may not be available.

Alleles↗

PubMed1995

COL5A1: fine genetic mapping and exclusion as candidate gene in families with nail-patella syndrome, tuberous sclerosis 1, hereditary hemorrhagic telangiectasia, and Ehlers-Danlos Syndrome type II.

COL5A1, the gene for the alpha 1 chain of type V collagen, has been considered a candidate gene for certain diseases based on chromosomal location and/or disease phenotype. We have employed 3'-untranslated region RFLPs to exclude COL5A1 as a candidate gene in families with tuberous sclerosis 1, Ehlers-Danlos syndrome type II, and nail-patella syndrome. In addition, we describe a polymorphic simple sequence repeat (SSR) within a COL5A1 intron. This SSR is used to exclude COL5A1 as a candidate gene in hereditary hemorrhagic telangiectasia (Osler-Rendu-Weber disease) and to add COL5A1 to the existing map of "index" markers of chromosome 9 by evaluation of the COL5A1 locus on the CEPH 40-family reference pedigree set. This genetic mapping places COL5A1 between markers D9S66 and D9S67.

Base Sequence↗

PubMed1998

Optical mapping of neural responses in the embryonic rat brainstem with reference to the early functional organization of vagal nuclei.

We examined the functional organization of the vagal nuclei of the rat embryo during morphogenesis, using multiple-site optical recording with a voltage-sensitive dye. Slice preparations with vagus nerve fibers were dissected from 13- to 16-d-old embryonic (E13-E16) rat brainstems, and they were stained with the dye. Electrical activity in response to vagal stimulation was recorded optically from many sites. In the E13-E14 preparations, two types of spike-like optical signals were recorded: one was a narrow signal (type I), and the other was a broader signal (type II). Comparison with the morphology revealed by DiI labeling suggests that the type I signal response area corresponds to the nucleus of the tractus solitarius, and the type II signal response area corresponds to the dorsal motor nucleus of the vagus nerve. In the E15-E16 preparations, type I signals were followed by a slow signal related to glutamate-mediated excitatory postsynaptic potentials, suggesting that synaptic function is organized in the nucleus of the tractus solitarius by the 15-d-old embryonic stage. In the E14 preparation, a small, slow signal was evoked only in Mg2+-free solution, implying that postsynaptic function related to NMDA receptors emerges, in latent form, at the 14-d-old embryonic stage. In the E15 and E16 preparations, although the nucleus ambiguus is identified morphologically, no neural response-related optical signal was observed there, indicating that the embryonic organization of morphology and physiological function is not necessarily temporally coincident. We have mapped the dynamic spatiotemporal patterns of the evoked optical signals and have outlined the early phase of the functional organization of the cranial nuclei related to the vagus.

Animals↗

PubMed1994

Spectral pattern recognition of improved voice quality.

The self-organizing map (a neural network) was applied to the spectral pattern recognition of voice quality in 34 subjects: 15 patients operated on because of insufficient glottal closure and 19 subjects not treated for voice disorders. The voice samples, segments of sustained /a/, were perceptually rated by six experts. A self-organized acoustic feature map was first computed from tokens of /a/ and then used for the analysis of the samples. The locations of the samples on the map were determined and the distances from a normal reference were compared with the perceptual ratings. The map locations corresponded to the degree of audible disorder: the samples judged as normal were overlapping or close to the normal reference, whereas the samples judged as dysphonic were located further away from it. The comparison of pre- and postoperative samples of the patients showed that the perceived improvement of voice quality was also detected by the map.

Adult↗

PubMed2005

Inferring gene transcriptional modulatory relations: a genetical genomics approach.

Bayesian network modeling is a promising approach to define and evaluate gene expression circuits in diverse tissues and cell types under different experimental conditions. The power and practicality of this approach can be improved by restricting the number of potential interactions among genes and by defining causal relations before evaluating posterior probabilities for billions of networks. A newly developed genetical genomics method that combines transcriptome profiling with complex trait analysis now provides strong constraints on network architecture. This method detects those chromosomal intervals responsible for differences in mRNA expression using quantitative trait locus (QTL) mapping. We have developed an efficient Bayesian approach that exploits the genetical genomics method to focus computational effort on the most plausible gene modulatory networks. We exploit a dense marker map for a genetic reference population (GRP) that consists of 32 BXD strains of mice made by intercrossing two progenitor strains--C57BL/6J and DBA/2J. These progenitors differ at approximately 1.3 million known single nucleotide polymorphisms (SNPs), all of which can be exploited to estimate the probability that a gene contains functional polymorphisms that segregate within the GRP. We constructed 66 candidate networks that include all the candidate modulator genes located in the 209 statistically significant trans-acting QTL regions. SNPs that distinguish between the two progenitor strains were used to further winnow the list of candidate modulators. Bayesian network was then used to identify the genetic modulatory relations that best explain the microarray data.

Algorithms↗

PubMed1994

Three-dimensional molecular shape analysis-quantitative structure-activity relationship of a series of cholecystokinin-A receptor antagonists.

The three-dimensional molecular shape analysis-quantitative structure-activity relationship (3D-MSA-QSAR) technique has been applied to develop correlations between the calculated physicochemical properties and the in vitro activities of a series of 3-(acylamino)-5-phenyl-2H-1,4-benzodiazepine cholecystokinin-A (CCK-A) antagonists. 3D-MSA-QSARs were developed for varying subsets of 53 analogs (J. Med. Chem. 1988, 31, 2235-2246). An active conformation is hypothesized for these compounds using the loss in biological activity-loss in conformational stability principle. After placing all compounds in the active conformation and performing pairwise molecular shape analysis, it was determined that not any one analog serves as the best shape reference compound. Nonidentical volumes of allowed receptor space are mapped out by different antagonists. A shape reference compound that consists of selected overlapped structures expands the definition of the accessible receptor space. This type of mutant improves the predicted activity of analogs over the value predicted if only one compound is chosen as the reference. Molecular shape, as represented by common overlap steric volume and nonoverlap steric volume, is the major factor contributing to the affinity of this class of compounds. Intramolecular conformational stability, as measured by the difference in energy of the active conformation and the global minimum energy conformation, is also important. It is further concluded from the 3D-MSA-QSAR models that part of the binding pocket for the 3-amido substituent has a preference for lipophilicity. The method used in this study of fragmenting the antagonist into spheres of varying radii and measuring lipophilicity isolates the substructure with highest probability of interacting with the receptor. Two indicator variables marking the presence of an N-methyl group and an o-fluoro atom on the 5'-phenyl substituent of the benzodiazepine ring structure also contribute significantly to the 3D-MSA-QSAR models. The 3D-MSA-QSAR results have led to the proposal of a 3D pharmacophore model for the benzodiazepine CCK-A antagonists.

Animals↗

PubMedDate not supplied

A human genome map of comparative anchor tagged sequences.

Effective comparative mapping inference utilizing developing gene maps of animal species requires the inclusion of anchored reference loci that are homologous to genes mapped in the more "gene-dense" mouse and human maps. Nominated anchor loci, termed comparative anchor tagged sequences (CATS), have been ordered in the mouse linkage map, but due to the dearth of common polymorphisms among human coding genes have not been well represented in human linkage maps. We present here an ordered framework map of 314 comparative anchor markers in humans based on mapping analysis in the Genebridge 4 panel of radiation hybrid cell lines, plus empirically optimized CATS PCR primers which detect these markers. The ordering of these homologous gene markers in human and mouse maps provides a framework for comparative gene mapping of representative mammalian species.

Animals↗

PubMed2000

Areas 3a, 3b, and 1 of human primary somatosensory cortex. Part 2. Spatial normalization to standard anatomical space.

Interindividual topographical variability of cytoarchitectonically defined somatosensory areas 3a, 3b, and 1 was analyzed in the standard anatomical format of a computerized brain atlas. T1-weighted magnetic resonance images were obtained from 10 postmortem brains. The brains were serially sectioned at 20 mcm, sections were stained for cell bodies, and areas 3a, 3b, and 1 were defined with an observer-independent cytoarchitectonic technique. After correction of the sections for deformations due to histological processing, the 3-D reconstructed histological volumes of the individual brains and the volume representations of the cytoarchitectonic areas were adapted to the reference brain of a computerized atlas. Corresponding areas were superimposed in the 3-D space of the reference brain. These population maps describe, for each voxel, how many brains have a representation of one particular cytoarchitectonic area. Each area's extent is very variable across different brains, but representations of areas 3a, 3b, and 1 in >/=50% of the brains were found in the fundus of the central sulcus, its caudal bank, and on the crown of the postcentral gyrus, respectively. Volumes of interest (VOIs) were defined for each area in which >/=50% of the brains have a representation of that area. Despite close spatial relationship of areas 3a, 3b, and 1 in the postcentral gyrus, the three VOIs overlap by <1% of their volumes. Functional imaging data can now be brought into the same standard anatomical format, and changes in regional cerebral blood flow can be calculated in VOIs of areas 3a, 3b, and 1, which are derived from genuine cytoarchitectonic data.

Adult↗

PubMed2002

Complexities in ETS-domain transcription factor function and regulation: lessons from the TCF (ternary complex factor) subfamily. The Colworth Medal Lecture.

The ETS-domain transcription factor family can be divided into a series of subfamilies. Elk-1 represents the founding member of the ternary complex factor (TCF) subfamily. By focusing on the TCF subfamily, we can demonstrate the complexities that exist in the function and regulation of ETS-domain transcription factors. This article focuses on Elk-1 in detail and summarizes the functions of other TCFs. The key themes covered include the domain structure of the TCFs, the mechanisms of complex formation with serum response factor, regulation of TCFs by mitogen-activated protein kinase cascades, and transcriptional regulatory properties of the TCFs. Finally, the emerging role of the TCFs in vivo is discussed. A picture is developing indicating that, while these proteins exhibit significant sequence and functional conservation, key differences in their structure and regulation are being identified which may relate to unique functions of these proteins in vivo.

Amino Acid Sequence↗

PubMed2005

Optic radiation changes after optic neuritis detected by tractography-based group mapping.

Postmortem data suggest that trans-synaptic degeneration occurs in the lateral geniculate nucleus after optic nerve injury. This study investigated in vivo the optic radiations in patients affected by optic neuritis using fast marching tractography (FMT), a diffusion magnetic resonance imaging (MRI) fiber tracking method, and group mapping techniques, which allow statistical comparisons between subjects. Seven patients, 1 year after isolated unilateral optic neuritis, and ten age and gender-matched controls underwent whole-brain diffusion tensor MR imaging. The FMT algorithm was used to generate voxel-scale connectivity (VSC) maps in the optic radiations in each subject in native space. Group maps of the left and right optic radiations were created in the patient and control group in a standardized reference frame using statistical parametric mapping (SPM99). The reconstructed optic radiations in the patient group were localized more laterally in the posterior part of the tracts and more inferiorly than in the control group. Patients showed reduced VSC values in both tracts compared with controls. These findings suggest that the group mapping techniques might be used to assess changes in the optic radiations in patients after an episode of optic neuritis. The changes we have observed may be secondary to the optic nerve damage.

Adult↗

PubMed1993

Dinucleotide repeat loci contribute highly informative genetic markers to the human chromosome 2 linkage map.

Microsatellite repeat loci can provide informative markers for genetic linkage. Currently, the human chromosome 2 genetic linkage map has very few highly polymorphic markers. Being such a large chromosome, it will require a large number of informative markers for the dense coverage desired to allow disease genes to be mapped quickly and accurately. Dinucleotide repeat loci from two anonymous chromosome 2 genomic DNA clones were sequenced so that oligonucleotide primers could be designed for amplifying each locus using the polymerase chain reaction (PCR). Five sets of PCR primers were also generated from nucleotide sequences in the GenBank Database of chromosome 2 genes containing dinucleotide repeats. In addition, one PCR primer pair was made that amplifies a restriction fragment length polymorphism on the TNP1 gene (Hoth and Engel, 1991). These markers were placed on the CEPH genetic linkage map by screening the CEPH reference DNA panel with each primer set, combining these data with those of other markers previously placed on the map, and analyzing the combined data set using CRI-MAP and LINKAGE. The microsatellite loci are highly informative markers and the TNP1 locus, as expected, is only moderately informative. A map was constructed with 38 ordered loci (odds > or = 1000:1) spanning 296 cM (male) and 476 cM (female) of chromosome 2 compared with 306 cM (male) and 529 cM (female) for a previous map of 20 markers.

Animals↗

PubMed2001

By any other name: when will preschoolers produce several labels for a referent?

Two experiments investigated why preschool children sometimes produce multiple words for a referent (i.e. polynomy), but other times seem to allow only one word. In Experiment 1, 40 three- and four-year-olds completed a modification of Deák & Maratsos' (1998) naming task. Although social demands to produce multiple words were reduced, children produced, on average, more than two words per object. Number of words produced was predicted by receptive vocabulary. Lexical insight (i.e. knowing that a word refers to function or appearance) and metalexical beliefs (i.e. that a hypothetical referent has one label, or more than one) were not preconditions of polynomy. Polynomy was independent of bias to map novel words to unfamiliar referents. In Experiment 2, 40 three- and four-year-olds learned new words for nameable objects. Children showed a correction effect, yet produced more than two words per object. Children do not have a generalized one-word-per-object bias, even during word learning. Other explanations (e.g. contextual restriction of lexical access) are discussed.

Child Language↗

PubMed1997

Analysis of the genetic polymorphism between three Streptococcus thermophilus strains by comparing their physical and genetic organization.

The physical maps of Streptococcus thermophilus CNRZ368 and NST2280 strains were constructed by analysing PFGE patterns obtained with the low-frequency-cutting enzymes SmaI, BssHII and SfiI. Their chromosomes are 1864 and 1840 kb circular molecules, respectively. Comparison of their physical maps with that of the reference A054 strain revealed a relatively conserved organization of the restriction sites. Three variable regions were detected with the map of CNRZ368 whereas 15 were found with the map of NST2280. To construct the genetic maps, probes corresponding to 10 single-copy genes, the rrn genes and the insertion sequences IS1191, IS981 and ISS1 were hybridized to Southern blots of chromosomal DNA digested with the different mapping enzymes. Comparison of the genetic maps of the three strains showed a conserved location of the mapped single-copy genes. However, six rrn loci were present in the chromosome of A054 and CNRZ368 whereas five were present in the NST2280 chromosome. A polymorphism was also found in the copy number of the insertion sequences between the three strains.

Chromosome Mapping↗

PubMed1985

Mapping of cholinoceptive(nicotinoceptive)neurons in the lower brainstem: with special reference to the ventral surface of the medulla.

The distribution of cholinoceptive neurons in the lower brainstem of the rat was investigated by means of a histochemical method for specific acetylcholinesterase. Nicotinoceptive neurons were characterized using an alpha-bungarotoxin-horseradish peroxidase conjugate for the detection of nicotinic acetylcholine receptors. For the first time a nearly complete mapping of the location of cholinoceptive (nicotinoceptive) neurons of the lower brainstem was achieved. Special attention was focused on the organization of the cholinoceptive neuronal matrix of the ventral surface of the medulla, where regulative centers for vasomotor and respiratory control are located.

Acetylcholinesterase↗

PubMed2000

Ion trap MS(n) genealogical mapping-approaches for structure elucidation of novel products of consecutive fragmentations of morphinans

The analysis of data within multi-generational, genealogical, electrospray ionization/MS(n) fragmentation maps is discussed in reference to the structure elucidation of morphinans, an important class of pharmacological compounds. Various general approaches to separate and understand observed processes are discussed. These include: (1) Simple synthetic schemes incorporating deuterium and (13)C into morphinans to study later-generation, O-methyl group migration; (2) labeling to understand 'intense' signals for even-electron to odd-electron ion 'switching' events; (3) gas phase 'synthesis' of proposed MS(3) ions via an independent route, using chemical ionization (CI) MS/MS of naphthalenes and analysis via a bench-top El/Cl ion trap; (4) a useful synthetic paradigm for generating proposed carbonium ion structures at MS(4) via electrospray ionization (ESI) of easily synthesized amines; (5) the analysis of an oxidation product and correlation of MS(n) data of a switched, odd-electron species with electron ionization and low-pressure, low-energy charge exchange data; and (6) a new way of summarizing MS(n) data. Copyright -Copyright 2000 John Wiley & Sons, Ltd.

Journal Article↗