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Cytogenetic maps depict the location and order of markers along chromosomes. Cytogenetic maps are important in genome research as they relate the genetic data and molecular sequences to the morphological features of chromosomes. In this paper, we discuss various methods used in cytogenetic mapping in maize, with special reference to fluorescence in situ hybridization (FISH) of single-copy sequences on meiotic pachytene chromosomes.
We studied the factors precipitating spontaneous recurrences of methamphetamine (MAP)-induced paranoid-hallucinatory states (referred to as "flashbacks") in 28 flashbackers, along with 18 non-flashbackers with a history of MAP psychosis. Plasma levels of catecholamines and their metabolites were assayed in the 28 flashbackers, the 18 non-flashbackers, 8 subjects with persistent MAP psychosis, and 33 normal controls (22 MAP users and 11 non-users). The flashbackers had been exposed to significantly higher numbers of stressful events, and/or MAP-induced frightening paranoid-hallucinatory states during previous MAP use, than the non-flashbackers. Factors triggering the flashbacks met the DSM-III-R criteria for a mild psychosocial stressor. During flashbacks, plasma norepinephrine levels increased and plasma levels of 3-methoxytyramine, which is an indicator of dopamine release, showed a smaller increase. It follows that stressful experiences together with MAP use may induce sensitization to mild psychosocial stressors. Noradrenergic hyperactivity and some degree of increased dopamine release may be involved in this process. Stress sensitization may elicit memories of MAP psychosis associated with stressful experiences in response to mild psychosocial stressors, leading to the occurrence of flashbacks. Sensitization to stress associated with noradrenergic hyperactivity, involving increased dopamine release may be central to spontaneous recurrences of MAP psychosis.
Three physical mapping methods, radiation hybrid (RH) mapping, pulsed-field gel electrophoresis (PFGE), and fluorescence in situ hybridization (FISH) of interphase nuclei, were used to determine the order and relative distances between 12 loci in the q31-q33 region of human chromosome 5. The information obtained by each of the methods was compared to determine whether they gave consistent results. Based upon a combination of data, the predicted order of the 12 loci is cen-ADRB2-PDEA-CSF1R-RPS14-ANX6-SPARC++ +-GLRA1-GLUR1-ADRA1B-IL12- GABRG2-GABRA1-tel. Over the 5-Mb region spanned by these loci, we determined that an RH mapping unit (centiray, cR6500) is equivalent to 21 kb, in good agreement with previous estimates of 27-34 kb/cR6500 using the same set of radiation hybrids to map other regions. Of the three methods, RH mapping was by far the easiest and most efficient method for determining both order and distances. In addition, the range of resolution of RH mapping was the broadest, ranging from approximately 200 kb to several megabasepairs. Interphase FISH was the most informative method for clarifying the order of closely linked markers. The FISH distances obtained in this study will be useful as an internal reference for high-resolution mapping studies of other regions on the long arm of human chromosome 5. In contrast to RH mapping and FISH, PFGE was the least reliable of the three methods, producing some data that were inconsistent with the distances determined by the other two methods.
Programming events in the stage 28-31 clawed frog embryo partly determine the organization of the future retinotectal map by specifying the permanent reference axes for cellular positional information in the retina. Thus, when transplanted in 180 degrees -rotated orientation into a stage 27/28 orbit, an unspecified (stage 28 or younger) eye can acquire new axes and develop a normally-oriented retinotectal map, whereas a specified (stage 31 or older) eye retains its original axes and develops an inverted map. We have used the retinotectal map to determine when (and under what conditions) specification with changes in orientation occurred in eye primordia serially transplanted between embryos of different stages. Specification was not precipitated when stage 22/23 eyes were grafted into stage 28-32 embryos or explanted in vitro, nor was specification delayed when stage 28 eyes were grafted into embryos younger than stage 28. Control experiments confirmed the general correlation between the time of specification and the stage of the eye primordium. We infer that intraocular regulatory mechanisms control the time of specification.
A comprehensive genetic linkage map of the porcine genome has been developed by typing 128 genetic markers in a cross between the European Wild Boar and a domestic breed (Large White). The marker set includes 68 polymerase chain reaction-formatted microsatellites, 60 anchored reference markers informative for comparative mapping and 47 markers which have been physically assigned by in situ hybridization. Novel multipoint assignments are provided for 54 of the markers. The map covers about 1800 cM, and the average spacing between markers is 11 cM. We used the map data to estimate the genome size in pigs, thereby addressing the total recombination distance in a third mammalian species. A sex-average genome length of 1873 +/- 139 cM was obtained by comparing the recombinational and physical distances in defined regions of the genome. This is strikingly different from the length of the human genome (3800-4000 cM) and is more similar to the mouse estimate (1600 cM). The recombination rate in females was significantly higher than in males.
BACKGROUND: Whole-genome sequencing efforts, have during the past decade, unveiled the central role of genomic rearrangements-such as chromosomal inversions-in evolutionary processes, including local adaptation in a wide range of taxa. However, employment of reference genomes from distantly or even closely related species for mapping and the subsequent variant calling can lead to errors and/or biases in the datasets generated for downstream analyses. RESULTS: Here, we capitalize on the recently generated chromosome-anchored genome assemblies for Arctic cod (Arctogadus glacialis), polar cod (Boreogadus saida), and Atlantic cod (Gadus morhua) to evaluate the extent and consequences of reference bias on population sequencing datasets (approx. 15-20 × coverage) for both Arctic cod and polar cod. Our findings demonstrate that the choice of reference genome impacts the mapping statistics, including mapping depth and mapping quality, as well as core population genetic estimates, such as heterozygosity levels, nucleotide diversity (π), and cross-species genetic divergence (DXY). Furthermore, using a more distantly related reference genome can lead to inaccurate detection and characterization of chromosomal inversions, i.e., in terms of size (length) and location (position), due to inter-chromosomal reorganizations between species. Additionally, we observe that some of the verified species-specific inversions are split across multiple genomic regions when mapped against a heterospecific reference. CONCLUSIONS: Inaccurate identification of chromosomal rearrangements as well as biased population genetic measures could potentially lead to erroneous interpretation of species-specific genomic diversity, impede the resolution of local adaptation, and thus, impact predictions of their genomic potential to respond to climatic and other environmental perturbations.
We isolated deletion mutants of Pseudomonas aeruginosa plasmid R91-5 by both in vitro and in vivo means. Many of the deletion mutants selected on the basis of resistance to donor-specific phages fell into a few groups of apparently identical mutants, although the mutants were nonsibs. By analyzing plasmids with large deletions, we found that the essential replication genes of R91-5 were within a 3.85-kilobase region between coordinates 45.5 and 48.9. The origin of plasmid transfer (oriT) was mapped to a 4.5-kilobase region between coordinates 1.7 and 6.2. We indirectly determined the direction of plasmid transfer from oriT. By combining the data from our analysis of the deletions with data from complementation tests between cloned R91-5 fragments and known reference mutants, we ordered and mapped the 10 known transfer (tra) cistrons of R91-5. All of the tra cistrons mapped within the Tra2 region, and their order was as follows: traX, -Y, -T, -Q, -(V, R), -U, -(S, Z), -W (the cistrons in parentheses could not be ordered with respect to each other).
To define the position of a 13q12 breakpoint from a patient with ganglioneuroblastoma, a series of somatic cell hybrids carrying human chromosome translocations with breakpoints in the proximal part of chromosome 13 has been compiled. Sequence-tagged sites (STS) have been generated from a series of Alu-PCR probes previously shown to be in the 13q12 region. Together with an STS for the oncogene FLT1, these have been used to define the relative positions of the translocation breakpoints in the hybrids. In this way, four markers have been ordered in three subregions of 13q12 and reference breakpoints established. The refined physical map of 13q12 provides a series of reference markers with known locations and will be invaluable in the further characterization of breakpoints in this region.
The current autosomal version (4.2) of the sheep genetic map comprises 1175 loci and spans approximately 3540 cM. This corresponds to almost complete coverage of the sheep genome. Each chromosome is represented by a single linkage group, with the largest gap between adjacent loci being 19.8 cM. In contrast the 1998 goat genetic map (the most recently published) is much less well developed spanning 2737 cM and comprising only 307 loci. Only one of the goat chromosomes appears to have complete coverage (chromosome 27), and 16 of the chromosomes are comprised of two or more linkage groups, or a linkage group and one or more unlinked markers. The two maps share 218 loci, and the maps have been aligned using the shared loci as reference points. Overall there is good agreement between the maps in terms of homologous loci mapping to equivalent chromosomes in the two species, with only four markers mapping to non-equivalent chromosomes. However, there are lots of inversions in locus order between the sheep and goat chromosomes. Whilst some of these differences in locus order may be genuine, the majority are likely to be a consequence of the paucity of genetic information for the goat map.
The famous rice cultivar (cv.), St. No. 1, confers complete resistance to many isolates collected from the South China region. To effectively utilize the resistance, a linkage assay using microsatellite markers (SSR) was performed in the three F2 populations derived from crosses between the donor cv. St. No. 1 and each of the three susceptible cvs. C101PKT, CO39 and AS20-1, which segregated into 3R:1S (resistant/susceptible) ratio, respectively. A total of 180 SSR markers selected from each chromosome equally were screened. The result showed that the two markers RM128 and RM486 located on chromosome 1 were linked to the resistance gene in the respective populations above. This result is not consistent with those previously reported, in which a well-known resistance gene Pif in the St. No. 1 is located on chromosome 11. To confirm this result, additional four SSR markers, which located in the region lanked by RM128 and RM486, were tested. The results showed that markers RM543 and RM319 were closer to, and RM302 and RM212 completely co-segregated with the resistance locus detected in the present study. These results indicated that another resistance gene involved in the St. No. 1, which is located on chromosome 1, and therefore tentatively designated as Pi37(t). To narrow down genomic region of the Pi37(t) locus, eight markers were newly developed in the target region through bioinformatics analysis (BIA) using the publicly available sequences. The linkage analysis with these markers showed that the Pi37(t) locus was mapped to a approximately 0.8 centimorgans (cM) interval flanked by RM543 and FPSM1, where a total of seven markers co-segregated with it. To physically map the locus, the Pi37(t)-linked markers were landed on the reference sequence of cv. Nipponbare through BIA. A contig map corresponding to the locus was constructed based on the reference sequence aligned by the Pi37(t)-linked markers. Consequently, the Pi37(t) locus was defined to 374 kb interval flanking markers RM543 and FPSM1, where only four candidate genes with the resistance gene conserved structure (NBS-LRR) were further identified to a DNA fragment of 60 kb in length by BIA.
An echo-planar spectroscopic imaging method of temperature mapping is proposed. This method is sufficiently faster than the so-called 3D magnetic resonance spectroscopic imaging (3D-MRSI) method and does not require image subtractions, unlike the conventional phase mapping method when an internal reference signal is detectable. The water proton chemical shift measured by using the tissue lipid as an internal reference clearly visualized the temperature change in a porcine liver sample in vitro. It was also demonstrated that the internally referenced echo-planar spectroscopic imaging method could markedly reduce a temperature error caused by a simple, translational motion between scans compared with the phase-mapping method.
Experiments are described that have lead to the development of a highly reproducible tryptic map of recombinant DNA derived bovine somatotropin (rbSt). Tryptic digestion of rbSt at 37 degrees C results in the formation of a precipitate. Preliminary characterization of the precipitate suggests that its formation is due to the association of intermediate tryptic fragments. An examination of the temperature dependence of the digestion has revealed that precipitate formation is inhibited when digestion is performed at 10 degrees C or less. The combination of a 5-mg sample, the use of highly purified trypsin, and digestion at 5 degrees C generate a tryptic map that exhibits an average 1.3% RSD (0.5-3.6%) for all anticipated fragments. Validation studies demonstrate that while the peak response precision is rugged to daily variation of operators or chromatographic systems, the fragment retention is not. This dictates that peaks be assigned by qualitative pattern recognition. Assay ruggedness in the peak response domain allows for the implementation of quantitative methods for the comparison of rbSt reference standard and sample tryptic maps. The assay is linear for all anticipated fragments within 50-150% of the operating range. Specificity is established by assay of pituitary somatotropins from other species and rbSt analogs produced by site-specific mutagenesis. The data demonstrate that all single amino acid substitutions examined are identified by using the technique. Assay sensitivity is validated for selected tryptic fragments through analysis of reference standard digests spiked with known amounts of rbSt analog digests. The data indicate that potential impurities of 3.2, 2.0, and 4.5% can be quantitated with statistical confidence in the tryptic fragments T1, T10, and T23 + 25, respectively.
Probabilistic maps of neocortical areas and subcortical fiber tracts, warped to a common reference brain, have been published using microscopic architectonic parcellations in ten human postmortem brains. The maps have been successfully applied as topographical references for the anatomical localization of activations observed in functional imaging studies. Here, for the first time, we present stereotaxic, probabilistic maps of the hippocampus, the amygdala and the entorhinal cortex and some of their subdivisions. Cytoarchitectonic mapping was performed in serial, cell-body stained histological sections. The positions and the extent of cytoarchitectonically defined structures were traced in digitized histological sections, 3-D reconstructed and warped to the reference space of the MNI single subject brain using both linear and non-linear elastic tools of alignment. The probability maps and volumes of all structures were calculated. The precise localization of the borders of the mapped regions cannot be predicted consistently by macroanatomical landmarks. Many borders, e.g. between the subiculum and entorhinal cortex, subiculum and Cornu ammonis, and amygdala and hippocampus, do not match sulcal landmarks such as the bottom of a sulcus. Only microscopic observation enables the precise localization of the borders of these brain regions. The superposition of the cytoarchitectonic maps in the common spatial reference system shows a considerably lower degree of intersubject variability in size and position of the allocortical structures and nuclei than the previously delineated neocortical areas. For the first time, the present observations provide cytoarchitectonically verified maps of the human amygdala, hippocampus and entorhinal cortex, which take into account the stereotaxic position of the brain structures as well as intersubject variability. We believe that these maps are efficient tools for the precise microstructural localization of fMRI, PET and anatomical MR data, both in healthy and pathologically altered brains.
Hepatocellular carcinoma (HCC) is a common malignancy worldwide and is a leading cause of death. To contribute to the development and improvement of molecular markers for diagnostics and prognostics and of therapeutic targets for the disease, we have largely expanded the currently available human liver tissue maps and studied the differential expression of proteins in normal and cancer tissues. Reference two-dimensional electrophoresis (2-DE) maps of human liver tumor tissue include labeled 2-DE images for total homogenate and soluble fraction separated on pH 3-10 gels, and also images for soluble fraction separated on pH 4-7 and pH 6-9 gels for a more detailed map. Proteins were separated in the first dimension by isoelectric focusing on immobilized pH gradient (IPG) strips, and by 7.5-17.5% gradient sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gels in the second dimension. Protein identification was done by peptide mass fingerprinting with delayed extraction-matrix assisted laser desorption/ionization-time of flight-mass spectrometry (DE-MALDI-TOF-MS). In total, 212 protein spots (117 spots in pH 4-7 map and 95 spots in pH 6-9) corresponding to 127 different polypeptide chains were identified. In the next step, we analyzed the differential protein expression of liver tumor samples, to find out candidates for liver cancer-associated proteins. Matched pairs of tissues from 11 liver cancer patients were analyzed for their 2-DE profiles. Protein expression was comparatively analyzed by use of image analysis software. Proteins whose expression levels were different by more than three-fold in at least 30% (four) of the patients were further analyzed. Numbers of protein spots overexpressed or underexpressed in tumor tissues as compared with nontumorous regions were 9 and 28, respectively. Among these 37 spots, 1 overexpressed and 15 underexpressed spots, corresponding to 11 proteins, were identified. The physiological significance of the differential expressions is discussed.
Monoclonal antibodies referred to as Am1, Am2 and Am3 against highly purified bovine tryptophanyl-tRNA synthetase were prepared. Am2 antibodies inhibit the Trp-tRNA synthetase activity and interact with the active truncated enzyme forms (dimers of either 40-kDa or 51-kDa fragments) produced by limited proteolysis. Am1 and Am3 antibodies exert no effect on the Trp-tRNA synthetase activity; epitopes recognized by them are mapped close to one another and reside at the dispensable part of the Trp-tRNA synthetase molecule. Am1 cross-reacts with Trp-tRNA synthetases of eukaryotic, prokaryotic and archaebacterial species, as revealed by immunoblot analysis. A rapid two-step technique was developed for isolating electrophoretically homogeneous Trp-tRNA synthetase from Escherichia coli. The purified enzyme interacted with Am1, but not with Am2 and Am3 antibodies taken at the same concentrations. As in the case of eukaryotic Trp-tRNA synthetase, Am1 did not influence the activity of Trp-tRNA synthetase from E. coli. From the aforementioned results it follows that: (a) the conservation of part of the Trp-tRNA synthetase structure which is not directly involved in the formation of the catalytic centre of prokaryotic and eukaryotic Trp-tRNA synthetases suggests that the dispensable part of the molecule might be involved in some additional biological function(s) of Trp-tRNA synthetase besides tRNA(Trp) charging; (b) the common antigenic determinant in Trp-tRNA synthetase of eukaryotes, prokaryotes and archaebacteria indicates that this enzyme was presumably present in the common ancestor of the above organisms.
PURPOSE: To describe and evaluate new statistical techniques for detecting topographic changes in series of retinal and optic nerve head images acquired by scanning laser tomography (Heidelberg Retinal Tomograph [HRT]; Heidelberg Engineering, Heidelberg, Germany). METHODS: Proven quantitative techniques, collectively referred to as statistic image mapping (SIM), are widely used in neuroimaging. These techniques are applied to HRT images. A pixel-by-pixel analysis of topographic height over time yields a statistic image that is generated by using permutation testing, derives significance limits for change wholly from the patient's own data, and removes the need for reference data sets. These novel techniques were compared to the Topographic Change Analysis (TCA super-pixel analysis) available in the current HRT software, by means of an extensive series of computer experiments. The SIM and TCA techniques were further tested and compared to linear regression of rim area (RA) against time, in real longitudinal HRT series of eyes of 20 normal subjects and 30 ocular hypertensive (OHT) patients that were known to have converted to glaucoma, on the basis of visual field criteria. RESULTS: Computer simulation indicated that SIM has better diagnostic precision at detecting change. In the real longitudinal series, SIM flagged false-positive structural progression in two (10%) of normal subjects, whereas TCA identified three (15%), and linear regression of RA against time identified two (10%). SIM identified 22 (73%) of the OHT converters as having structural progression, whereas the TCA and linear regression of RA against time each identified 16 (53%) over the course of the follow-up. CONCLUSIONS: SIM has better diagnostic precision in detecting change in series of HRT images when compared to current quantitative techniques. The clinical utility of these techniques will be established on further longitudinal data sets.
Meiotic recombination in flow-sorted single sperm was used to analyze four highly polymorphic microsatellite markers on the long arm of chromosome 9. The microsatellites comprised three tightly linked markers: 9CMP1 (D9S109), 9CMP2 (D9S127), and D9S53, which map to 9q31, and a reference marker, ASS, which is located in 9q34.1. Haplotypes of single sperm were assessed by using PCR in a single-step multiplex reaction to amplify each locus. Recombinant haplotypes were identified by their relative infrequency and were analyzed using THREELOC, a maximum-likelihood-analysis program, and an adaptation of CRI-MAP. The most likely order of these markers was cen-D9S109-D9S127-D9S53-ASS-tel with D9S109, D9S127, and D9S53 being separated by a genetic distance of approximately 3%. The order of the latter three markers did not however achieve statistical significance using the THREELOC program.
High temporal resolution and sensitivity to index different functional brain states makes the EEG a powerful tool in psychophysiology. Its full potential can now be utilized since recording technology and computational power for the large data masses has become affordable. However, basic traditional strategies in EEG need reviewing. Conventional, spontaneous or evoked EEG traces which are used for various complex analyses give ambiguous information on EEG power (amplitude) and phase for a given point on the scalp. Principally, analysis should first be done over space, then over time, to avoid ambiguities or pre-selections. First or second spatial derivative computations can provide "reference-free" data for analyses over time. We propose to use direct, spatial approaches for the analysis of the scalp EEG field distributions when simultaneous recordings in several EEG channels can be examined. The ambiguity of the conventional EEG waveshapes results in different, equally "correct" scalp maps of EEG power of the same multichannel data for different reference electrodes. An exception are scalp maps of EEG power computed against the common, average reference, as they are related to the reference-free spatial distribution (maps) of the maximal and minimal (extreme) field values over time, and thus are directly interpretable in terms of net orientation of the generator process. A proposed, reference-free EEG segmentation into epochs of periodically stationary spatial distributions of the mapped scalp EEG fields uses the locations of maximal and minimal (extreme) field values at each moment in time as classifiers, and thus avoids the priviledging of two arbitrarily chosen recording points in the field.