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PubMed1995

A 2D crossover-based map of the human X chromosome as a model for map integration.

We have constructed a two-dimensional map of 243 markers on the X chromosome. The average distance between markers ordered by two recombinants is 5.4 centiMorgans (cM), which is reduced to 3.2 cM using a less stringent criterion of one recombinant. Map resolution is enhanced by replacing the usual reference marker format with a 2D format, and the two-recombinant rule is more conservative than the lod 3.0 criterion for order. Taken together, crossover mapping and the 2D format produces maps with greater reliability and higher resolution than maps constructed using currently accepted standards. This first high-density crossover-based map of an entire human chromosome provides a model for integrating physical and genetic maps.

Chromosome Mapping↗
PubMed1999

A complete comparative chromosome map for the dog, red fox, and human and its integration with canine genetic maps.

Cross-species reciprocal chromosome painting was used to delineate homologous chromosomal segments between domestic dog, red fox, and human. Whole sets of chromosome-specific painting probes for the red fox and dog were made by PCR amplification of flow-sorted chromosomes from established cell cultures. Based on their hybridization patterns, a complete comparative chromosome map of the three species has been built. Thirty-nine of the 44 synteny groups from the published radiation hybrid map and 33 of the 40 linkage groups in the linkage map of the dog have been assigned to specific chromosomes by fluorescence in situ hybridization and PCR-based genotyping. Each canine chromosome has at least one DNA marker assigned to it. The human-canid map shows that the canid karyotypes are among the most extensively rearranged karyotypes in mammals. Twenty-two human autosomal paints delineated 73 homologous regions on 38 canine autosomes, while paints from 38 dog autosomes detected 90 homologous segments in the human genome. Of the 22 human autosomes, only the syntenies of three chromosomes (14, 20, and 21) have been maintained intact in the canid genome. The dog-fox map and DAPI banding comparison demonstrate that the remarkable karyotype differences between fox (2n = 34 + 0-8 Bs) and dog (2n = 78) are due to 26 chromosomal fusion events and 4 fission events. It is proposed that the more easily karyotyped fox chromosomes can be used as a common reference and control system for future gene mapping in the DogMap project and CGH analysis of canine tumor DNA.

Animals↗
PubMed1981

Alignment of a restriction map with the genetic map of bacteriophage T4.

A restriction map of the bacteriophage T4 genome was aligned with the T4 genetic map. Included were the cleavage sites for BamHI, BglII, KpnI, PvuI, SalI, and XbaI. The alignment utilized the fact that the T4 genetic map had been oriented previously with respect to a T2/T4 heteroduplex map. DNA fragments from a BglII digestion of cytosine-containing DNA from a T4 dCTPase- denA denB(rIIH23B) alc mutant were hybridized with full-length chromosomal strands of bacteriophage T2, and the heteroduplexes were examined by electron microscopy. From their lengths and patterns of substitution and deletion loops, the heteroduplexes formed with 6 of the 13 BglII fragments could be unambiguously identified and positioned on the T2/T4 heteroduplex map. The ends of the T4 DNA strands in the heteroduplexes directly identified the location of 10 BglII cleavage sites. The remaining three BglII cleavage sites could be assigned to the T2/T4 heteroduplex map based on their relative locations on the restriction map. It was also possible to identify the source of the DNA strands (i.e., T2 or T4) in four previously unassigned deletion loops on the T2/T4 heteroduplex. Among the BglII fragments identified in heteroduplexes was the fragment containing the rIIH23B deletion; this deletion was used as the primary point of reference for alignment of the T4 restriction map with the T2/T4 heteroduplex map and, hence, with the T4 genetic map.

Chromosome Mapping↗
PubMed2006

[Characteristics of references between GSCC and CST for Semi-Luvisols].

In this paper, the references between Genetic Soil Classification of China (GSCC) and the Chinese Soil Taxonomy (CST) for GSCC-Semi-Luvisols were conducted, and their quantitative and spatial distribution characteristics within CST were studied, based on the 1 : 1 M Soil Database of China, which consists of 1 : 1 M digital soil map, soils profiles attribution database and soil reference system of China. Being a reference system for converting soil names in GSCC into those in CST, ST and WRB, respectively, Chinese Soil Reference System was a computerized retrieving system jointly developed by the experienced scientists of pedology and computer science. The comparison fields and laboratory investigation data of their soil profiles with diagnostic horizons and characteristics related in the target soil classification systems, and 2,540 typical soil species names corresponding in CST, ST and WRB systems were determined, respectively, which were selected from Soil Attributes Database because of their complete sets of attribute data. Finally, the system and reference database were established. "GIS linkage based soil type" method linked the records in the Soil Reference Database to the Soil Spatial Database. In this method, all records of soil profiles in Soil Reference Database as well as their soil reference name in other classification systems were allocated one by one onto corresponding soil type polygons in Soil Spatial Database on the GIS platform, according to the principles of soil type identity and similarity, parent material identity and likeness, and the location of soil profiles relative to linked target polygons. Area statistcs of all soils were conducted based on the polygons. The results showed that GSCC-Semi-Luvisols was a type of GSCC soil with a total area of 427,843.1 km2,which could be sorted to 4 CST Orders, i. e., Luvisols (51.3%), Cambosols (35.2%), Isohumosols (10.7%) and Anthrosols (2.8%), and further into CST 22 Groups and 38 Subgroups. All dark grey forest soil, superficial gleyed black soil, and leached dry red soil of GSCC subgroups could be sorted to Calcaric Hapli-Gelic Cambosols, Pachic Argi-Udic Cambosols and Typic Ferri-Ustic Luvisols of CST subgroups, respectively, and all grey cinnamon-like soil, calcareous grey cinnamonic soil and dry cinnamon soil could be sorted to Typic Ustic Cambosols. Making the reference was so complicated that there was no one to one reference relationship among other soils. The analysis of the area ratios and standard deviations of a certain GSCC soil classified by CST showed that the lower the unit for reference, the easier the reference would be. The results of this study were of high reference value to proper reference GSCC and CST, and to the application and development of CST.

China↗
PubMed1990

Gene mapping and other tools for discovery.

Genetic mapping provides a means of understanding the molecular basis of inherited diseases whose biochemistry is unknown. Adequate pedigrees, informative genetic markers, and accurate identification of the disease phenotype are necessary. For dominant inheritance, mapping studies can be done in a single large pedigree; the larger the number of affected individuals sampled the better the estimate of recombination between the gene causing the disease and one or more nearby genetic markers. For recessive inheritance, nuclear families with more than one affected sibling provide the best information. The development of many polymorphic DNA markers on the human genome has contributed to the success of mapping unknown genes because, as the genome is now densely covered with markers, the probability is good that at least one marker will be linked to the disease locus in a family that is segregating a disease allele. Most genetic markers now in use depend upon restriction fragment length polymorphisms (RFLPs), which are either the result of single-base-pair substitution or the presence of a variable number of tandemly repeated oligonucleotide units at a locus (VNTRs). RFLPs can be recognized by digesting DNA with restriction enzymes and separating the fragments by size on an electrophoretic gel. VNTRs can vary widely among individuals, and they provide more linkage information than single-site polymorphic markers because family members are more likely to be heterozygous. Genetic maps of each chromosome, constructed from linkage data relating marker loci to one another in normal reference families, permit rational choices of markers for disease-mapping studies.(ABSTRACT TRUNCATED AT 250 WORDS)

Chromosome Mapping↗
PubMed1998

Developing microsatellite markers from cDNA: a tool for adding expressed sequence tags to the genetic linkage map of the chicken.

A chicken embryonic cDNA library was screened with a (TG)13 probe in order to develop polymorphic microsatellite markers. The redundancy of the embryonic cDNA library with a chicken brain cDNA library, which was used for microsatellite development in a previous study, was extremely high. Of the 300 (TG)13 positive clones, only 80 were unique for the embryonic cDNA library. Still, nine expressed sequences derived from the embryonic cDNA library were mapped in the Wageningen (WAU) resource population. In addition seven microsatellite markers from the chicken brain cDNA library, which were monomorphic or unlinked in the two international reference families in the previous study, were also mapped in the WAU population. Three of the 16 mapped chicken expressed sequence tags (ESTs) showed relatively high percentages of sequence similarity to sequences found in other species. As two of these genes, RAB6 and ZFX/ZFY, have been mapped in humans, they contribute to the comparative map of the chicken.

Animals↗
PubMed1991

Mapping irradiation hybrids to cosmid and yeast artificial chromosome libraries by direct hybridization of Alu-PCR products.

A direct hybridization protocol is described for screening cosmid and yeast artificial chromosome libraries with pools of Alu-PCR products from somatic cell or irradiation hybrids. This method eliminates purification, cloning and analysis of each individual Alu-PCR product before library screening. A series of human X chromosome irradiation hybrids were mapped by this method, using a cosmid reference library for comparisons between overlapping hybrids to identify interesting clones for further analysis.

Base Sequence↗
PubMed2005

Functional heterogeneity of the supplementary motor area.

BACKGROUND AND PURPOSE: The purpose of this study was to assess supplementary motor area (SMA) activation during motor, sensory, word generation, listening comprehension, and working memory tasks by using functional MR imaging (fMRI). Human supplementary motor area (SMA) has been shown to play roles in motor control and other various functions such as sensory, speech expression, and memory. However, topographical localizations of these functions in the SMA remain unclear. The purpose of this study was to assess SMA activation during motor, sensory, word generation, listening comprehension, and working memory tasks by using functional MR imaging (fMRI). METHODS: Sixteen healthy right-handed subjects (nine men and seven women) were imaged on a Siemens 1.5T system. Whole-brain functional maps were acquired by using blood oxygenation level-dependent echo-planar imaging sequences in the axial plane. Each paradigm consisted of five epochs of activation versus the control condition. The activation tasks consisted of left-finger complex movement, heat sensory stimulation of the left hand, word generation, listening comprehension, and working memory. The reference function was a boxcar waveform. Activation maps were thresholded at an uncorrected P = .0001. The thresholded activation maps were placed into MNI (Montreal Neurologic Institute) stereotactic coordinates, and the anatomic localization of activation within the SMA was compared across tasks. RESULTS: SMA activation was observed in 16 volunteers for the motor task, 11 for the sensory task, 15 for the word generation task, five for the listening comprehension task, and 15 for the working memory task. Although not statistically significant, qualitative differences in the location of activation within the SMA were present by task. The rostral aspects of the SMA tended to activate during word generation and working memory tasks, and the caudal aspect of the SMA tended to activate during the motor and sensory tasks. Right (contralateral) SMA activation was observed during the motor and sensory tasks, and left SMA activation during the word generation and memory tasks. CONCLUSION: Our results suggest that SMA is involved in a variety of functional tasks, including motor, sensory, word generation, and working memory. Some are tasks that are traditionally associated with this area (such as motor and sensory), and others are not (such as word generation and working memory). Qualitatively, the anterior and posterior portions of the SMA appeared to be engaged by different types of tasks.

Adult↗
PubMed1995

A strategy for constructing high-resolution genetic maps of the human genome: a genetic map of chromosome 17p, ordered with meiotic breakpoint-mapping panels.

Genetic linkage analyses with genotypic data obtained from four CEPH reference families initially assigned 24 new PCR-based markers to chromosome 17 and located the markers at specific intervals of an existing genetic map of chromosome 17p. Each marker was additionally genotyped with an ordered set of obligate, phase-known recombinant chromosomes. The breakpoint-mapping panels for each family consisted of two parents, one sib with a nonrecombinant chromosome, and one or more sibs with obligate recombinant chromosomes. The relative order of markers was determined by sorting segregation patterns of new markers and ordered anchor markers and by minimizing double-recombination events. Consistency of segregation patterns with multiple flanking loci constituted support for order. A genetic map of chromosome 17p was completed with 39 markers in 23 clusters, with an average space of 3 cM between clusters. The collection of informative genotypes was highly efficient, requiring fivefold fewer genotypes than would be collected with all the CEPH families. Given the availability of large numbers of highly informative PCR-based markers, meiotic breakpoint mapping should facilitate construction of a human genomic map with 1-cM resolution.

Base Sequence↗
PubMed2004

Identification and fine mapping of quantitative trait loci for growth traits on bovine chromosomes 2, 6, 14, 19, 21, and 23 within one commercial line of Bos taurus.

We report the identification and fine mapping of QTL for birth weight (BWT), preweaning ADG (PWADG), and postweaning ADG on feed (ADGF) in a commercial line of Bos taurus using an identical-by-descent haplotype sharing method. One hundred seventy-six calves of 12 bulls (9 to 30 male calves from each sire) of the Beefbooster, Inc., M1 line were typed using 71 genetic markers from bovine chromosomes (BTA) 2, 6, 14, 19, 21, and 23 (8 to 16 markers from each chromosome). Sixteen haplotypes were found to have significant (P <0.05) associations with BWT at the comparison-wise threshold. The 16 haplotypes span 13 chromosomal regions, two on BTA 2 (9.1 to 22.5 cM and 95.0 to 100.3 cM), three on BTA 6 (8.2 to 11.8 cM, 35.5 to 49.7 cM, and 83.0 to 86.2 cM), three on BTA 14 (26.0 to 26.7 cM, 36.2 to 46.2 cM, and 52.0 to 67.7 cM), one on BTA 19 (52.0 to 52.7 cM), two on BTA 21 (9.9 to 20.4 cM and 28.2 to 46.1 cM), and two on BTA 23 (23.9 to 36.0 cM and 45.1 to 50.9 cM). Thirteen haplotypes spanning seven chromosomal regions significantly affected (P <0.05) PWADG at the comparison-wise threshold. The seven chromosomal regions include two regions on BTA 6 (11.8 to 44.2 cM and 83.0 to 86.2 cM), one on BTA 14 (26.7 to 50.8 cM), one on BTA 19 (4.8 to 15.9 cM), one on BTA 21 (9.9 to 20.4 cM), and two on BTA 23 (17.3 to 36.0 cM and 45.1 to 50.9 cM). For ADGF, 11 haplotypes were identified to have significant associations (P <0.05) at the comparison-wise threshold. The 11 haplotypes represented eight chromosomal regions, one on BTA 2 (9.1 to 22.5 cM), two on BTA 6 (49.7 to 50.1 cM and 59.6 to 63.6 cM), two on BTA 14 (17.0 to 24.0 cM and 36.2 to 46.2 cM), two on BTA 19 (52.0 to 52.7 cM and 65.1 to 65.7 cM), and one on BTA 21 (46.1 to 53.1 cM). The QTL regions identified and fine mapped in this study will provide a reference for future positional candidate gene research and marker-assisted selection of various growth traits.

Alleles↗
PubMed1988

Phosphorylation of the 20,000-Da myosin light chain isoforms of arterial smooth muscle by myosin light chain kinase and protein kinase C.

Phosphorylation of myosin light chain (LC) isoforms in arterial actomyosin can be induced by endogenous kinases upon addition of Mg2+ and ATP. The extent of phosphorylation in the presence of 2 mM ethylene glycol bis(beta-aminoethyl ether)N,N'-tetraacetic acid (EGTA), 0.2 mM Ca2+, or 0.2 mM Ca2+ plus calmodulin is 1.6, 2.1, and 2.3 mol phosphate/mol LC, respectively. Two-dimensional gel electrophoresis of actomyosin shows that the LC isoforms may be mono-, di-, and triphosphorylated. Tryptic phosphopeptide mapping of LC indicates that the radioactive phosphate is distributed to six peptides referred to as A through F. Phosphoamino acid analyses and the phosphopeptide maps of isolated LC, phosphorylated by either purified myosin light chain kinase or protein kinase C, reveal that myosin light chain kinase phosphorylates a serine residue in peptides A and B, and threonine plus serine residues in peptides C and D. Peptides E and F are phosphorylated by protein kinase C in serine and threonine residues, respectively. In actomyosin, with EGTA, phosphorylation of peptides E and F proceeds while phosphorylation of peptides A, B, C, and D is inhibited. Ca2+ and calmodulin enhance the phosphorylation of peptides A, B, C, and D, while phosphorylation of peptides E and F is decreased. In isolated LC, myosin light chain kinase preferentially phosphorylates the peptides A and B over C and D. Phosphorylation of peptides E and F in LC by protein kinase C promotes additional phosphorylation of peptides C and D by myosin light chain kinase, whereas phosphorylation of peptides A and B is diminished. The present data suggest that the phosphorylation of distinct sites in arterial myosin light chain by myosin light chain kinase and protein kinase C is interrelated.

Adenosine Triphosphate↗
PubMed2005

A rhesus macaque radiation hybrid map and comparative analysis with the human genome.

The genomes of nonhuman primates are powerful references for better understanding the recent evolution of the human genome. Here we compare the order of 802 genomic markers mapped in a rhesus macaque (Macaca mulatta) radiation hybrid panel with the human genome, allowing for nearly complete cross-reference to the human genome at an average resolution of 3.5 Mb. At least 23 large-scale chromosomal rearrangements, mostly inversions, are needed to explain the changes in marker order between human and macaque. Analysis of the breakpoints flanking inverted chromosomal segments and estimation of their duplication divergence dates provide additional evidence implicating segmental duplications as a major mechanism of chromosomal rearrangement in recent primate evolution.

Animals↗
PubMed1992

A genetic linkage map of human chromosome 21: analysis of recombination as a function of sex and age.

A genetic linkage map of human chromosome 21 has been constructed using 22 anonymous DNA markers and five complementary DNAs (cDNAs) encoding the amyloid beta protein precursor (APP), superoxide dismutase 1 (SOD1), the ets-2 proto-oncogene (ETS2), the estrogen inducible breast cancer locus (BCEI), and the leukocyte antigen, CD18 (CD18). Segregation of RFLPs detected by these DNA markers was traced in the Venezuelan Reference Pedigree (VRP). A comprehensive genetic linkage map consisting of the 27 DNA markers spans 102 cM on the long arm of chromosome 21. We have confirmed our initial findings of a dramatically increased rate of recombination at the telomere in both females and males and of significantly higher recombination in females in the pericentromeric region. By comparing patterns of recombination in specific regions of chromosome 21 with regard to both parental sex and age, we have now identified a statistically significant downward trend in the frequency of crossovers in the most telomeric portion of chromosome 21 with increasing maternal age. A less significant decrease in recombination with increasing maternal age was observed in the pericentromeric region of the chromosome. These results may help in ultimately understanding the physical relationship between recombination and nondisjunction in the occurrence of trisomy 21.

Adolescent↗
PubMed1990

Some of the factors involved in the Sarvazyan method for recording ultrasound field distributions with special reference to the application of ultrasound in physiotherapy.

The mapping of ultrasound fields using the dye paper method is described. The mode of action by which the dye concentration is increased has been investigated. Microbubbles on the paper surface and microstreaming of dye solution seem to be essential features of the mapping method. The streaming is thought to inhibit the formation of a dye depletion layer near the paper to an extent dependent on local sound intensity A linear relation between streaming velocity and intensity is derived.

Coloring Agents↗
PubMed2005

Whaleworms as a tag to map zones of heavy-metal pollution.

Biological monitoring refers to the use of living organisms to evaluate environmental conditions. Of particular relevance to the health of marine ecosystems is the improvement of methodologies of biological monitoring to provide highly ecologically sensitive indices of exposure. We have shown that anisakid nematodes, a parasite group widely distributed in oceans that infects a wide range of host species, can accumulate essential and non-essential metals to levels far in excess of their host tissues. The fact that they could be used as biomarkers of trace-metal contamination in studies of environmental impact suggests a potential use as a monitor species in a marine ecosystem under anthropogenic stress because they might produce a warning or alert signal of high ecological relevance.

Animals↗
PubMed2002

Chaos control by using Motor Maps.

In this paper a new method for chaos control is proposed, consisting of an unsupervised neural network, namely a Motor Map. In particular a feedback entrainment scheme is adopted: a chaotic system with a given parameter set generates the reference trajectory for another chaotic system with different parameters to be controlled: the Motor Map is required to provide the appropriate time-varying gain value for the feedback signal. The state of the controlled system is considered as input to the Motor Map. Particular efforts have been paid to the feasibility of the implementation. Indeed, the simulations performed have been oriented to design a Motor Map suitable for an hardware realization, thus some restrictive hypotheses, such as for example a low number of neurons, have been assumed. A huge number of simulations has been carried out by considering as system to be controlled a Double Scroll Chua Attractor as well as other chaotic attractors. Several reference trajectories have also been considered: a limit cycle generated by a Chua's circuit with different parameters values, a double scroll Chua attractor, a chaotic attractor of the family of the Chua's circuit attractors. In all the simulations instead of controlling the whole state space, only two state variables have been fed back. Good results in terms of settling time (namely, the period in which the map learns the control task) and steady state errors have been obtained with a few neurons. The Motor Map based adaptive controller offers high performances, specially in the case when the reference trajectory is switched into another one. In this case, a specialization of the neurons constituting the Motor Map is observed: while a group of neurons learns the appropriate control law for a reference trajectory, another group specializes itself to control the system when the other trajectory is used as a reference. A discrete components electronic realization of the Motor Map is presented and experimental results confirming the simulation results are shown. (c) 2002 American Institute of Physics.

Journal Article↗
PubMed2005

Quantifying and evaluating ecosystem health: a case study from Moreton Bay, Australia.

As part of the program monitoring the ecosystem health of Moreton Bay, Queensland, Australia, we developed a means for assessing ecosystem health that allows quantitative evaluation and spatial representations of the assessments. The management objectives for achieving ecosystem health were grouped into ecosystem objectives, water quality objectives, and human health objectives. For the first two groups, aspects of the ecosystem (e.g., trophic status) were identified, and an indicator was chosen for each aspect. Reference values for each indicator were derived from management objectives and compared with the mapped survey values. Subregions for which the indicator statistic was equal to or better than the assigned reference value are referred to as "compliant zones." High-resolution surface maps were created from spatial predictions on a fine hexagonal grid for each of the indicators. Eight reporting subregions were established based on the depth and predicted residence times of the water. Within each reporting subregion, the proportion that was compliant was calculated. These results then were averaged to create an integrated ecosystem health index. The ratings by a team of ecosystem experts and the calculated ecosystem health indices had good correspondence, providing assurance that the approach was internally consistent, and that the management objectives covered the relevant biologic issues for the region. This method of calculating and mapping ecosystem health, relating it directly to management objectives, may have widespread applicability for ecosystem assessment.

Conservation of Natural Resources↗