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PubMed1990

A genetic map of human chromosome 17p.

A genetic linkage map was constructed with 18 loci from the short arm and pericentric region of chromosome 17 typed on the CEPH reference families. The genetic map includes three markers extracted from the CEPH public database. Nine loci could be ordered using a threshold of odds of at least 1000:1 against alternative orders during the map construction process. With a reduced tolerance of 100:1, a total of 13 loci could be placed on the map spanning a distance of approximately 60 cM in females and 46 cM in males. There were statistically significant differences between the male and the female genetic maps. The order inferred from the genetic data was consistent with the physical localizations of these probes obtained from somatic cell hybrids and tumor deletion studies. This map should be useful for genetic fine mapping of 17p loci.

Alleles↗

PubMed1991

Processing and termination of 23S rRNA-5S rRNA-tRNA(Gly) primary transcripts in Thermus thermophilus HB8.

The two 23S rRNA-5S rRNA-tRNAGly operons from the extreme thermophilic eubacterium Thermus thermophilus HB8 were used to characterized the in vivo processing and termination of 23S rRNA-5S rRNA-tRNAGly primary transcripts in this organism by nuclease S1 mapping. A processing site in the pre-23S rRNA 3'-flanking region is located approximately 25 nucleotides upstream of 5S rRNA and precedes a putative 23S-5S rRNA spacer antitermination box A. Cleavage at this site and 5S rRNA 5' end formation were shown to be inseparable events. Termination of transcription at the uridine cluster following the termination-associated hairpin was shown to be efficient but leaky. Subsequent to the operon, a functional promoter was detected whose -35 box coincided with the uridine-rich termination region. The promoter directed synthesis of a beta-galactosidase fusion protein in Escherichia coli.

Base Sequence↗

PubMed1988

Proprioceptors and their contribution to somatosensory mapping: complex messages require complex processing.

This review of other people's work concentrates on two matters. First, which of the various receptors are chiefly involved in creating the central representations or maps of the body that both underlie the conscious perception of our body image and are needed to control our motor performance. Second, how are these relatively well-charted signals used in sensorimotor mapping, with particular attention paid to various human psychophysical observations and illusions that throw light on the central integrative mechanisms involved. Detailed citation is largely restricted to developments since earlier reviews.

Animals↗

PubMed2026

Developmental and cellular vulnerabilities underlie genetic architecture of schizophrenia.

Schizophrenia (SZ) is a highly heritable neuropsychiatric condition with complex polygenic architecture. Elucidating the cellular and developmental substrates vulnerable to the genetic risk is essential for understanding the underlying neurobiological mechanisms. Here, we integrated genome-wide association study (GWAS) and whole-exome sequencing (WES) data with a developmental multi-omics atlas of the human cortex (including 5 cortical regions), comprising about 3 million single-nucleus RNA sequencing (snRNA-Seq) and single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-Seq) profiles across 8 neurodevelopmental processes, to map cell-type-specific enrichment of SZ genetic risk. Our enrichment analyses revealed that both common and rare genetic liabilities converged on broad excitatory and inhibitory neuronal classes. Across different statistical frameworks, we identified genetic enrichment within intratelencephalic (IT) projection neurons and layer 6b excitatory neurons (Ex-L6b) networks across multiple cortical regions. Stage-resolved developmental mapping in the frontal cortex showed that genetic liabilities, particularly the rare variants, are predominantly concentrated within early developmental processes, namely neurogenesis and neuronal migration. Differential expression analysis in postmortem frontal cortex snRNA-Seq datasets cross-validated the cellular substrates of the genetic liabilities. Collectively, our findings establish a high-resolution cellular and temporal framework of SZ susceptibility, implicating mature associative IT microcircuits, deep-layer thalamocortical-regulating networks, and early developmental specification windows as primary points of genetic convergence in SZ.

Journal Article↗

PubMed1991

Combination of in situ hybridization and immunocytochemistry to detect messenger RNAs in identified CNS neurons and glia in tissue culture.

We have developed a technique in which immunofluorescence is combined with in situ hybridization using cDNA and RNA probes to assess the expression and distribution of messenger RNAs (mRNA) by neurons and neuroglia in tissue cultures of the rat dentate gyrus. The probes used in this study include a cDNA probe for ribosomal RNA (rRNA) and an RNA probe (cRNA) for glial fibrillary acidic protein (GEAP), an intermediate filament protein subunit expressed by astrocytes in the central nervous system. Both ubiquitous (tubulin) and cell type-specific (MAP-2 and GEAP) antibodies were used to identify neurons and neuroglia in culture. Using this procedure, the mRNA for rRNA was found in the cell bodies and large processes of MAP-2-positive neurons and throughout the cytoplasm of GEAP-positive flat astrocytes. In process-bearing astrocytes, GEAP mRNA is concentrated in the cell body, although some hybridization also occurred in astrocyte cell processes. With this combined in situ hybridization-immunofluorescence technique, the expression and distribution of an mRNA can be examined in different immunocytochemically identified cell types under identical culture and hybridization conditions. It is also possible to determine if there is a differential subcellular distribution of an mRNA in a single cell and if the distribution of the mRNA reflects the distribution of the protein itself. Finally, this technique can be utilized to verify the specificity of probes for cell type-specific mRNAs and to determine appropriate hybridization conditions to produce a specific signal.

Animals↗

PubMed1987

[Optimization of the method of cyanogen bromide mapping of polypeptides separated by polyacrylamide gel electrophoresis].

Two highly efficient methods of CNBr-peptide mapping of polypeptides divided by polyacrylamide gel electrophoresis are described. The first is elaborated on the basis of peptide mapping of collagen proposed by G. Barsh et al. The following three modifications diminish wasting the material essential for the method. 1. CNBr treatment takes place in the absence of CNBr solution outside the gel, excluding the peptides elution from the gel fragments in the process of mapping. 2. After CNBr treatment the solution of CNBr is substituted by the samples buffer before electrophoresis by means of drying and subsequent addition of minimal volumes of the buffer. The latter procedures substitute the gel washing out by the buffer solution. 3. The step of washing the gel fragments by the 70% strong solution of formic acid before CNBr treatment is excluded. The second method of CNBr-peptide mapping is notable for extracting peptides from the gel fragments in the process of CNBr-treatment and permits obtaining of the high quality peptide electrophoregrams.

Collagen↗

PubMed1987

Stereotactic computer graphic system with brain maps.

We have developed a stereotactic computer graphic system with brain maps that runs on a personal computer. This system consists of three parts: 1. firmware for dizitizing radiological films with a TV camera or scanner (when digital image is not directly obtained from floppy disks); 2. software for introducing or processing brain maps by matching them with CT or NMR images; 3. hardware. Our system is designed to: 1. recognize the relevant frame points and calculate targets, their volume and surgical instrument trajectory; 2. match between brain maps of an ideal brain and patient's CT or NMR images with visible and invisible pathology; 3. monitor during surgery the position of the surgical instrument or target modification. The whole procedure and processed images are stored in a data-base for further study.

Brain Mapping↗

PubMed1990

Phosphorylation of microtubule proteins in rat brain at different developmental stages: comparison with that found in neuronal cultures.

The phosphorylation of rat brain microtubule protein on intracranial injection of labeled phosphate has been analyzed. The major microtubule protein components phosphorylated in vivo in rat brain are the high-molecular-weight microtubule-associated proteins (MAPs) MAP-1A, MAP-1B, and MAP-2. A slight phospholabeling of beta-tubulin, which corresponds to the phosphorylation of a minor neuronal beta-tubulin isotype, is also observed. Whereas MAP-1B, MAP-2, and beta-tubulin are phosphorylated in the brain of 5-day-old rat pups, when most neurons of the CNS are extending processes, MAP-1A phosphorylation is observed only after neuronal maturation takes place. The phosphorylation of MAP-1A, MAP-1B, and beta-tubulin may be due mainly to casein kinase II or a related enzyme, whereas MAP-2 appears to be modified by other enzymes such as the cyclic AMP-dependent protein kinase (protein kinase A) and the calcium/phospholipid-dependent protein kinase (protein kinase C). Microtubule protein phosphorylation has also been studied in neuronal cultures. In differentiated neuroblastoma cells, only MAP-1B and beta-tubulin are phosphorylated in a manner coupled to neurite outgrowth. In primary cultures of fetal rat brain neurons, the pattern of microtubule protein phosphorylation resembles that found in vivo in rat pup brain. As phosphorylated MAP-1A and MAP-1B are present mainly on assembled microtubules, whereas the phosphorylation of MAP-2 decreases its interaction with microtubules, a role can be suggested for the phosphorylation of these proteins in the regulation of microtubule assembly and disassembly during neuronal development.

Aging↗

PubMed1992

Networks formed by dorsal root ganglion neurites within spinal cord explants: a computer-aided analysis of HRP intracellularly labeled neurons.

Dorsal root ganglion (DRG) neurons from rat embryos were explanted either alone or with the attached spinal cord (SC). Neuritic processes were mapped out histologically using an intracellular iontophoretic HRP method. Computer reconstructions and morphometric parameters allowed a comparative quantitative analysis of the DRG neurons and of their neuritic processes in both models. The first model, strongly dependent on nerve growth factor (NGF) for its survival, developed large multidirectional processes. The second model showed a bipolar distribution of its neuritic processes, the central one entering predominantly the dorsolateral part of the cord explant and ramifying both homo- and heterolaterally. The quantitative data revealed a significant decrease in the overall size of the neuritic networks of the second model (with attached SC). A discriminant analysis permitted the recognition of these two populations of DRG neurons. The role of the spinal cord explant, and more precisely the target cells of the dorsal horn, was considered to be a prominent factor in the development of the DRG neuritic networks.

Animals↗

PubMed1995

Nonstationary vortexlike reentrant activity as a mechanism of polymorphic ventricular tachycardia in the isolated rabbit heart.

BACKGROUND: Ventricular tachycardia may result from vortexlike reentrant excitation of the myocardium. Our general hypothesis is that in the structurally normal heart, these arrhythmias are the result of one or two nonstationary three-dimensional electrical scroll waves activating the heart muscle at very high frequencies. METHODS AND RESULTS: We used a combination of high-resolution video imaging, electrocardiography, and image processing in the isolated rabbit heart, together with mathematical modeling. We characterized the dynamics of changes in transmembrane potential patterns on the epicardial surface of the ventricles using optical mapping. Image processing techniques were used to identify the surface manifestation of the reentrant organizing centers, and the location of these centers was used to determine the movement of the reentrant pathway. We also used numerical simulations incorporating Fitzhugh-Nagumo kinetics and realistic heart geometry to study how stationary and nonstationary scroll waves are manifest on the epicardial surface and in the simulated ECG. We present epicardial surface manifestations (reentrant spiral waves) and ECG patterns of nonstationary reentrant activity that are consistent with those generated by scroll waves established at the right and left ventricles. We identified the organizing centers of the reentrant circuits on the epicardial surface during polymorphic tachycardia, and these centers moved during the episodes. In addition, the arrhythmias that showed the greatest movement of the reentrant centers displayed the largest changes in QRS morphology. The numerical simulations showed that stationary scroll waves give rise to monomorphic ECG signals, but nonstationary meandering scroll waves give rise to undulating ECGs characteristic of torsade de pointes. CONCLUSIONS: Polymorphic ventricular tachycardia in the healthy, isolated rabbit heart is the result of either a single or paired ("figure-of-eight") nonstationary scroll waves. The extent of the scroll wave movement corresponds to the degree of polymorphism in the ECG. These results are consistent with our numerical simulations that showed monomorphic ECG patterns of activity for stationary scroll waves but polymorphic patterns for scroll waves that were nonstationary.

Animals↗

PubMed1994

Genetic map construction with constraints.

A pilot program, CME, is described for generating a physical genetic map from hybridization fingerprinting data. CME is implemented in the parallel constraint logic programming language ElipSys. The features of constraint logic programming are used to enable the integration of pre-existing mapping information (partial probe orders from cytogenetic maps and local physical maps) into the global map generation process, while parallelism enables the search space to be traversed more efficiently. CME was tested using data from chromosome 2 of Schizosaccharomyces pombe and was found able to generate maps as well as (and sometimes better than) a more traditional method. This paper illustrates the practical benefits of using a symbolic logic programming language and shows that the features of constraint handling and parallel execution bring the development of practical systems based on AI programming technologies nearer to being a reality.

Algorithms↗

PubMed1991

The extracellular domain of p185/neu is released from the surface of human breast carcinoma cells, SK-BR-3.

The human breast carcinoma cell line SK-BR-3, expresses the neu oncogene product, p185, which is a receptor tyrosine kinase. Using a double monoclonal antibody capture enzyme-linked immunosorbent assay for p185, activity was detected in conditioned media from cultures of SK-BR-3 cells. Two monoclonal antibodies specific for the extracellular domain of p185/neu immunoprecipitated a protein with a molecular mass of approximately 105 kDa. p105 was further shown to compete with p185 for binding to monoclonal antibodies and pulse-chase experiments indicate that it was generated by post-translational processing. Peptide maps showed that p105 and p185 are related polypeptides. Since p105 is close to the predicted size for the extracellular domain of p185/neu, we propose that SK-BR-3 cells specifically process and release this portion of the receptor into the medium. The release of the extracellular domain may have implications in oncogenesis and its detection could prove useful as a cancer diagnostic.

Adenocarcinoma↗

PubMed1988

Developments in processing image sequences for elemental mapping.

Elemental mapping consists in searching the distribution of a given chemical species over an extended specimen area, with relation to topographical or structural features. It can be done with EELS core signals from a combination of several energy filtered images. One major problem encountered in the processing of such sequences of images lies in the extrapolation errors due to a difficult estimate of the background below the characteristic signal. The chosen method must be sufficiently reliable to avoid the risk of both "false positive" and "false negative" values: the first category may stem from spurious signals or from a non-satisfactory fit of the background. The second category is mainly due to a limited sensitivity. The EELS signal is often much weaker than the background intensity; an extrapolation error can therefore transform a negative value into a positive one, or vice versa. The purpose of the present contribution is to check the validity of the processing at different levels: i) different mathematical models of background; ii) different types of fitting procedures (one-parameter and two-parameters fits); iii) different fitting methods and several associated manipulations, such as a quasi local estimation of the involved fitting parameters. The statistical validity of those techniques is discussed through several tests on real images obtained from different specimens (Co/CeO2 catalysts, ferritin molecules, U and Tb staining clusters). Progress is made on the way of quantitative elemental mapping at a given confidence level, and towards the identification of single atoms.

Electron Probe Microanalysis↗

PubMed1989

Different anisotropies of movement direction in upper and lower layers of the cat's area 18 and their implications for global optic flow processing.

Cells in Area 18 of awake and behaving cats were tested for directional preference with a large visual noise pattern. Upper and lower layer cells were found to exhibit different anisotropies for movement direction, offset by 90 degrees. These findings could reflect different functions for the global mapping and processing of optic flow field in upper and lower layers.

Animals↗

PubMed1988

Activity sharpens the regenerating retinotectal projection in goldfish: sensitive period for strobe illumination and lack of effect on synaptogenesis and on ganglion cell receptive field properties.

The regenerating optic nerve of goldfish first reestablishes a rough retinotopic map on the contralateral tectum and then sharpens it. Disruption of visual activity, either by blocking activity with intraocular tetrodotoxin (TTX; Schmidt and Edwards, 1983) or by synchronizing activity with strobe illumination (Schmidt and Eisele, 1985), disrupts the sharpening process: the map is correctly oriented but the multiunit receptive fields at each point average 25-40 degrees in diameter. In order to test whether strobe and TTX interfere with the same mechanism, we have tested whether their sensitive periods are the same, and whether strobe, like TTX treatment, does not affect either ganglion cell receptive field properties or synaptogenesis. In parallel studies, we exposed fish to 2 weeks of either strobe illumination or intraocular TTX beginning at various times after crush and determined via electrophysiological recordings that the periods of sensitivity were nearly identical. There was no effect of either treatment during the first 2 weeks (before the fibers arrive at the tectum), maximal disruption of sharpening between 14 and 50 days (the period of rapid synaptogenesis), decreasing disruption between 50 and 125 days, and no effect beyond that point or in the normal projection. In addition, long strobe exposures of up to 142 days produced no greater disruptions than shorter 2-3-week exposures, indicating no cumulative effect. The reestablishment of synaptic transmission in tectum, assayed by recording field potentials elicited by optic nerve shock, was not affected by stroboscopic illumination. Finally, individual ganglion cells, recorded intraretinally following long-term strobe exposure, had receptive fields that were normal both in size and in their characteristic responses to light-on, to light-off, or to both on and off. These findings support the hypothesis that strobe-like TTX prevents retinotopic refinement by preventing the correction of errors initially made by the ingrowing optic axons (Schmidt et al., 1988).

Animals↗

PubMed2025

Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment.

Ultrafast mapping of short reads via lightweight mapping techniques such as pseudoalignment has significantly accelerated transcriptomic and metagenomic analyses, often with minimal accuracy loss compared to alignment-based methods. However, applying pseudoalignment to large genomic references, like chromosomes, is challenging due to their size and repetitive sequences. We introduce a new and modified pseudoalignment scheme that partitions each reference into "virtual colors…. These are essentially overlapping bins of fixed maximal extent on the reference sequences that are treated as distinct "colors" from the perspective of the pseudoalignment algorithm. We apply this modified pseudoalignment procedure to process and map single-cell ATAC-seq data in our new tool alevin-fry-atac . We compare alevin-fry-atac to both Chromap and Cell Ranger ATAC . Alevin-fry-atac is highly scalable and, when using 32 threads, is approximately 2.8 times faster than Chromap (the second fastest approach) while using approximately one third of the memory and mapping slightly more reads. The resulting peaks and clusters generated from alevin-fry-atac show high concordance with those obtained from both Chromap and the Cell Ranger ATAC pipeline, demonstrating that virtual colorenhanced pseudoalignment directly to the genome provides a fast, memory-frugal, and accurate alternative to existing approaches for single-cell ATAC-seq processing. The development of alevin-fry-atac brings single-cell ATAC-seq processing into a unified ecosystem with single-cell RNA-seq processing (via alevin-fry ) to work toward providing a truly open alternative to many of the varied capabilities of CellRanger . Furthermore, our modified pseudoalignment approach should be easily applicable and extendable to other genome-centric mapping-based tasks and modalities such as standard DNA-seq, DNase-seq, Chip-seq and Hi-C.

Journal Article↗

PubMed1979

Nucleotide sequence of the EcoRI-F fragment of adenovirus 2 genome.

Using the DNA sequence method of Maxam and Gilbert the entire nucleotide sequence of the adenovirus 2 EcoRI-F fragment was determined. Information contained in that nucleotide sequence, which is 1743 base pairs long, is interpreted with respect to the mapping and processing of the three mRNAs partly encoded by the EcoRI-F fragment. A method to rapidly determine the cleavage site of restriction endonucleases is also reported.

Adenoviridae↗

PubMed1992

Gonadotropin-releasing hormone neurons and pathways in the brain of the female mink (Mustela vison).

The distribution of gonadotropin-releasing hormone-immunoreactive neurons and processes was mapped in the female mink brain using coronal, horizontal and sagittal sections. Perikarya were found along a ventral continuum including the olfactory tubercle, the diagonal band of Broca, the lateral septum, the preoptic and anterior hypothalamic area and the mediobasal hypothalamus; 80% of the perikarya were counted in the mediobasal hypothalamus. Fibres were mainly observed in the organum vasculosum of the lamina terminalis and the median eminence. A few processes terminated in the ependymal cells lining the third and lateral ventricles. The total number of immunoreactive perikarya was the highest in the brains of females sacrificed in July; it then significantly decreased until December. This variation is discussed in relation to the annual breeding cycle.

Animals↗