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PubMed1987

Histone H4 from cuttlefish testis is sequentially acetylated. Comparison with acetylation of calf thymus histone H4.

The differently acetylated subfractions of histone H4 isolated from cuttlefish testis and from calf thymus were separated by ion exchange chromatography on sulfopropyl-Sephadex, using a shallow linear gradient of guanidine hydrochloride in the presence of 6 M urea at pH 3.0. The tetra-, tri-, di-, mono-, and nonacetylated forms of cuttlefish H4 represent 2, 6.4, 18, 32.2, and 41.4% of the whole histone, respectively. The di-, mono-, and nonacetylated forms of calf H4 represent 11.7, 41.3, and 44% of the whole histone, respectively. The acetylation sites were determined in each subfraction by identification of the acetylated peptides. In each acetylated H4 subfraction, the acetylated tryptic peptides were identified by peptide mapping and amino acid analysis with reference to the peptide map of nonacetylated H4. In cuttlefish testis H4, lysine 12 is the main site of acetylation in the monoacetylated subfraction; lysines 5 and 12 are found acetylated in diacetylated H4; lysines 5, 12, and 16 are found acetylated in triacetylated H4. From these results and the stoichiometry of the different H4 subfractions, it can be concluded that lysine 5 is acetylated after lysine 12. In calf thymus, lysine 16 is the only site of acetylation in the monoacetylated subfraction. All the diacetylated forms are acetylated in lysine 16, the second site of acetylation being, in decreasing order, lysine 12, lysine 5, or lysine 8. These observations suggest that acetylation occurs in a sequential manner. Moreover, the sites of acetylation depend upon the biological event in which acetylation is involved.

Acetylation↗
PubMed1989

Understanding maps as symbols: the development of map concepts in children.

We expect that many readers encountered this article with the beliefs that maps are highly specialized devices primarily used for wayfinding; that they represent the spatial world in a single, correct form; that they are readily transparent; and that their sole contribution to psychology is their role in externalizing environmental cognition. By discussing the myriad functions and forms of maps, by highlighting their symbolic nature, and by considering some of the misconceptions about maps, we have attempted to demonstrate the value of maps for addressing a wide range of developmental questions. Our review of past research literature suggests that research conducted within individual disciplines has both strengths and limitations. Work in the psychological tradition is characterized by attention to important subject characteristics and to carefully described and implemented research designs, procedures, coding, and analyses. At the same time, this work reveals, at best, highly restricted views about maps, and at worst, fundamental misconceptions about maps. Work in the geographic and environmental traditions, in contrast, samples a broader range of map forms and functions, but it suffers from inattention to procedural details that makes the conclusions less compelling than they might otherwise be. A conventional wisdom is emerging from the work in both traditions: That children's map understanding occurs extremely early and extremely easily. The limitations of both research traditions, however, suggest the need for caution in accepting this view. Developmental and cartographic theories provide a compelling reason to reexamine the early and easy view and suggest the need for alternative conceptual and empirical approaches. We have argued that future work should integrate the traditions of psychology and geography. Illustrative data from an interdisciplinary program of research were presented. We described work demonstrating the gradual and difficult process of mastering the representational and geometric correspondences that link the map to its referent in the world. Our data suggest that there are significant achievements in map conceptualization (the understanding of the concept of a map), map identification (understanding the formal components of a map), and map utilization (the ability to use maps). Our data support the view that maps are not transparent and that children's abilities to understand, use, and create maps are linked to their developing representational and spatial skills. In concluding, we should acknowledge that we have deliberately pushed interpretations about understanding maps as symbolic representations to the extreme. The reason for this strategy is simple: We believe that work on maps--both in the public schools and in academia--is assumed to be an expendable and irrelevant luxury.(ABSTRACT TRUNCATED AT 400 WORDS)

Child Development↗
PubMed1990

Topographic analysis in brain mapping can be compromised by the average reference.

The average reference introduces ghost potential fields at the latencies for which the integral of scalp-recorded potentials differs from zero. These spurious effects occur because the average reference is computed from a limited number of (scalp) electrodes which do not survey the bottom half of the head. By arbitrarily re-setting the zero at each latency in the maps to be compared, it can also obliterate or even reverse topographical differences in the case of focal brain potentials enhancements thereby defeating the purpose of brain mapping.

Adult↗
PubMed1985

Mapping of different neuropeptides in the lower brainstem of the rat: with special reference to the ventral surface.

A neuropeptide map of beta-endorphin-, vasoactive intestinal peptide-, substance P-, and somatostatin-like reactive neurons and nerve fibers was made by means of immunohistochemistry. Indirect immunofluorescence was carried out in parallel to peroxidase-antiperoxidase reaction using a modified fixation technique. Special interest was directed to the superficial ventral regions of the medulla oblongata where regulative centers for respiration and circulation have been localized. The atlas presented offers a reliable tool for a precise neuromorphological localization of these neuropeptides in pharmacophysiological experiments.

Animals↗
PubMed1988

A mapped set of DNA markers for human chromosome 15.

A primary genetic linkage map for human chromosome 15 has been constructed from 16 arbitrary DNA markers genotyped in 59 large reference families. The map spans a genetic distance of 146 cM in males and 187 cM in females. The ratio of female/male genetic distance was approximately 2.1 overall within the region of the chromosome covered by our map, but three segments showed a significant male excess in recombination frequency. A subset of seven of the linked markers would be enough to detect linkage of a genetic defect within the mapped region of chromosome 15, if at least 48 phase-known meioses in affected families were available for analysis.

Alleles↗
PubMed1991

A genetic linkage map of 41 restriction fragment length polymorphism markers for human chromosome 3.

A genetic linkage map for human chromosome 3 has been constructed using 41 polymorphic DNA markers genotyped in 40 CEPH reference families. The map spans a genetic distance of 261 cM in males and 413 cM in females; the ratio of these distances (approximately 1.6 in favor of female meioses) was fairly constant across the map. Frequency of recombination was relatively uniform throughout much of the chromosome, except that in both telomeric regions recombination was more frequent than the physical distances would predict. The genetic map was basically in agreement with physical localization of 24 loci that were mapped by fluorescent in situ hybridization. This map can be used for linkage studies for genetic diseases, and it will serve as a step toward a high-resolution map for human chromosome 3.

Chromosome Mapping↗
PubMed1976

Cleavage maps of the filamentous bacteriophages M13, fd, fl, and ZJ/2.

The replicative form DNAs of bacteriophage M13, fd, f1, and ZJ/2 were found to be sensitive to cleavage by the restriction endonucleases endoR-HapII, endoR-HaeII, endoR-HaeIII, endoR-HindII, endoR-AluI, endoR-Hha, and endoR-Hinf. With respect to M13 DNA the number of cleavage sites varied from 21 for endoR-Hinf, 18 for endoR-AluI, 15 for endoR-Hha, 13 for endoR-HapII, 10 for endoR-HaeIII, 3 for endoR-HaeII, to only a single site for endoR-HindII. In contrast to M13, fd and f1, the ZJ/2 DNA molecule was not cleaved by the endoR-HindII endonuclease. No cleavage site on either phage DNA was detected for the endonucleases endoR-Hsu, endoR-EcoRI and endoR-Sma. When compared with M13 DNA, several differences were noted in the number and size of cleavage products obtained with DNA of phage fd, f1, and ZJ/2. From the results of these analyses, using the M13 enzyme cleavage maps as a reference, the endoR-HapII, endoR-HaeII, endoR-HaeIII, endoR-HindII and endoR-AluI maps of phage fd, f1, and ZJ/2 could be constructed. As is expected for very closely related phages, the enzyme cleavage patterns exhibit a high degree of homology. Phage f1 and ZJ/2 are most related since an identical pattern was obtained with seven different restriction endonucleases. Evidence is provided also that f1 is more similar to M13 than to fd. Furthermore, characteristic differences exist within the endoR-Hinf enzyme cleavage pattern of all the four phages tested. Digestion of phage DNA with this enzyme, therefore, provides a new and sensitive method of distinguishing these closely related filamentous coliphages .

Chromosome Mapping↗
PubMed1991

Sensitivity and speed of colour Doppler flow mapping compared with continuous wave Doppler for the detection of ventricular septal defects.

Twenty nine patients (aged from three months to 37 years) with confirmed or suspected ventricular septal defects were studied separately by three examiners who used colour flow mapping and imaging, or continuous wave Doppler and imaging, or a combined reference examination. Colour flow mapping identified 19 of the 25 patients with a ventricular septal defect, continuous wave Doppler echocardiography identified 18, and the combined reference examination identified 24. Two of four patients without ventricular septal defect had a false positive result with colour flow mapping and none had a false positive result with continuous wave Doppler examination. During the reference examination continuous wave Doppler identified 24 patients with ventricular septal defects and colour flow mapping identified 23. In two patients a second ventricular septal defect was found by colour flow mapping, and confirmed by continuous wave Doppler. There was no significant difference in time to diagnosis between the two techniques. Colour flow mapping aids identification of multiple ventricular septal defects but is not faster and has lower specificity than continuous wave Doppler. A combination of the two techniques gave the highest sensitivity and specificity.

Adolescent↗
PubMed2025

AdDeam: a fast and scalable tool for estimating and clustering reference-level damage profiles.

MOTIVATION: DNA damage patterns, such as increased frequencies of C→T and G→A substitutions at fragment ends, are widely used in ancient DNA studies to assess authenticity and detect contamination. In metagenomic studies, fragments can be mapped against multiple references or de novo assembled contigs to identify those likely to be ancient. Generating and comparing damage profiles, however, can be both tedious and time-consuming. Although tools exist for estimating damage in single reference genomes and metagenomic datasets, none efficiently cluster damage patterns. RESULTS: To address this methodological gap, we developed AdDeam, a tool that combines rapid damage estimation with clustering for streamlined analyses and easy identification of potential contaminants or outliers. Our tool takes aligned ancient DNA (aDNA) fragments from various samples or contigs as input, computes damage patterns, clusters them, and outputs representative damage profiles per cluster, a probability of each sample pertaining to a cluster, as well as a Principal Component Analysis of the damage patterns for each sample for fast visualisation. We evaluated AdDeam on both simulated and empirical datasets. AdDeam effectively distinguishes different damage levels, such as uracil-DNA glycosylase-treated samples, sample-specific damages from specimens of different time periods, and can also distinguish between contigs containing modern or ancient fragments, providing a clear framework for aDNA authentication and facilitating large-scale analyses. AVAILABILITY AND IMPLEMENTATION: AdDeam is publicly available at https://github.com/LouisPwr/AdDeam and can also be installed via Bioconda. It is implemented in Python and C++. All analysis scripts and datasets are available at https://github.com/LouisPwr/AdDeamAnalysis and on Zenodo under: 10.5281/zenodo.15052427.

Software↗
PubMed1989

A genetic linkage map of markers for human chromosome 20.

A continuous genetic linkage map with five polymorphic DNA markers, including one that defines a locus containing a variable number of tandem repeats (VNTR), has been constructed from genotypic analysis of 59 large reference families. The map spans a genetic distance of 105 cM in males and 115 cM in females and provides initial anchor points for a high-resolution map of human chromosome 20.

Alleles↗
PubMed2026

Meta-PseU: A meta-classifier for robust prediction of RNA pseudouridine modification sites from long sequences.

BACKGROUND AND OBJECTIVES: Pseudouridine (Ψ) represents one of the most abundant and conserved RNA modifications. Ψ provides an additional hydrogen-bond donor that enhances RNA structural stability and modulates translation. It participates in diverse biological processes, including RNA-protein interactions, splicing, translational control, and stress responses. Aberrant pseudouridylation is implicated in cancer, neurodegenerative disorders, and autoimmune diseases. Despite its biological importance, experimental identification of Ψ sites remains time-consuming and costly, limiting the feasibility of transcriptome-wide profiling. Computational approaches have therefore become essential complements to experimental techniques. However, state-of-the-art machine-learning and deep-learning predictors often suffer from limited generalizability due to small training datasets. To overcome these issues, we aim at constructing new long-sequence datasets and developing a novel Ψ site predictor. METHODS: New long-sequence datasets were constructed as benchmarks for RNA Ψ-site prediction. The Ψ modification sites in RMBase 3.0 were mapped to the reference genomes across three species of human, mouse, and yeast, and the RNA sequences with a length of 201 were generated by extending the upstream and downstream from the mapped, central sites. To eliminate sequence redundancy, the sequences were clustered using CD-HIT with a 70% sequence identity threshold. We developed Meta-PseU, a logistic regression-based meta-classifier that considered 118 machine learning and deep learning classifiers. The datasets and programs are freely accessible at https://github.com/kuratahiroyuki/MetaPseU. RESULTS: By optimizing model configuration, we proposed the Meta-PseU model stacking 32 machine learning and deep learning classifiers out of 118 classifiers. Meta-PseU substantially improved model generalizability, overcoming a key limitation of existing approaches. It greatly outperformed state-of-the-art predictors and achieved increasing accuracy with increasing sequence length. CONCLUSIONS: Long-sequence datasets were newly constructed as benchmarks for RNA Ψ-site prediction. Meta-PseU offers a new framework for robust Ψ-site identification by using long sequences.

Pseudouridine↗
PubMed1991

Detailed physical map of human chromosomal region 11q12-13 shows high meiotic recombination rate around the MEN1 locus.

We have constructed a physical map of the region q12-13 on chromosome 11 by combining data generated from a panel of radiation-reduced somatic cell hybrids and pulsed-field gel electrophoresis (PFGE). Twenty different genetic markers have been sublocalized and ordered within this region and a total of 8.0 megabases has been mapped in detail using rare-cutting restriction endonucleases and PFGE. In two instances, the long-range restriction PFGE map spans the total distance between pairs of loci that have been previously mapped by genetic linkage in reference families. Comparison of this physical map with the available linkage map indicates a great variation in the recombination frequency over the region. The recombination rate is higher than expected, particularly for markers flanking the MEN1 region. Thus, for the closest pair of linked markers on the centromeric side, one centimorgan corresponds to approximately 300 kilobases, and for markers on the telomeric side, one centimorgan corresponds to approximately 350-600 kilobases.

Animals↗
PubMedDate not supplied

Physical and genetic mapping of the CDR gene with particular reference to its position with respect to the FRAXA site.

This study narrows down the localization of the gene coding for the cerebellar degeneration-related protein (CDR 34) to the upper boundary of the FRAXA and reports the finding of two common RFLPs respectively identified at an RsaI site flanking the 3' end of the gene and at a Hincll site flanking its 5' end. Segregation analysis carried out in the CEPH-pedigrees for the new CDR/RsaI-RFLP versus other polymorphic loci of the region has established a tight linkage with the markers DXS105/DX98 and absence of measurable linkage with two clusters of markers respectively located proximally to the FRAXA (F9, DXS102, DXS51, and DXS369) or distally to it (DXS52, DXS304). In addition, two recombinants were found among 23 scorable sibs identified in the Sardinian pedigrees segregating for the Martin-Bell Syndrome (MBS) and the CDR/RsaI variants. The overall evaluation of the in situ and genetic data reported suggest that the CDR locus 1) is located at the upper boundary of the FRAXA site; 2) is distal to DXS51 and proximal to DXS 389; and 3) segregates in a close linkage association with the loci DXS98 and DXS105 and, to a lesser extent, with the locus for MBS.

Antigens, CD34↗
PubMed1986

Plasmid map: a microcomputer program for display and storage of plasmid data.

We describe a plasmid map program which runs on an IBM PC microcomputer and facilitates the drawing of circular plasmid maps. The user enters information from the keyboard in the form of restriction enzyme sites, genes and their locations, and other plasmid markers such as promoters, origins, or other sites. This information can then be stored in a file for future reference. The plasmid map can be displayed on the screen, printed on a dot-matrix printer, or plotted on a Hewlett Packard HP7475A plotter.

Base Sequence↗
PubMed2026

Ambient temperature storage of individual parasitic nematode larvae for whole genome sequencing.

Soil-transmitted helminth (STH) infections are a major public health burden, and there are programmes of mass drug administration that attempt to ameliorate the harm that they cause. There has been increasing use of genomics to study STH infections and other parasitic nematodes, with particular interest in whole genome sequencing (WGS). For such studies, samples are commonly stored frozen, but in settings where these infections are endemic this can be difficult, and so there would be advantages to having ambient temperature storage methods. We investigated two ambient temperature storage methods - FTA cards and DESS buffer - for infective larvae of the rat parasites Nippostrongylus brasiliensis and Strongyloides ratti, prior to DNA extraction and then WGS. Our results showed that for individual larvae stored on FTA cards or in DESS buffer, this resulted in a lower proportion of sequence reads that mapped to the reference genomes, compared to the frozen control samples. Generally, for individual larvae, DESS-storage resulted in better sequencing results than FTA-storage. However, for pools of 10 or 50 larvae, then these ambient temperature storage methods generally resulted in comparable sequence read mapping to the frozen control samples.

Animals↗
PubMed2026

Comparison of paralog identification methods and their impact on species tree topologies in target capture phylogenomics within the Sindora clade (Detarioideae: Leguminosae).

Target capture is a common method of generating high throughput DNA sequencing data for phylogenetic reconstruction of species relationships, for which single copy genes are usually most informative. However, a pervasive problem with target capture is that putatively single copy genes may in fact be paralogs resulting from gene duplication, which are problematic for phylogenetic inference because their evolutionary history may differ from the divergence history of species. Here, we use as a case study a target enrichment dataset of 88 species of Detarioideae (Leguminosae) with a focus on the Sindora clade to examine approaches for handling paralogs, including the built-in paralog handling functions in HybPiper and CAPTUS, plus subsequent steps using Putative Paralog Detection and the tree-based Yang & Smith orthology inference approach. We compare the paralogs flagged using these methods and verify their performance with BLAST mapping against a reference genome sequence of Sindora glabra, and then subsequently compare the species tree topologies produced across these methods. Our comparisons of paralogs flagged across the Sindora clade show that the Putative Paralog Detection pipeline was the most accurate in identifying paralogs in terms of its similarity to the BLAST mapping, followed by the built-in paralog identification function of CAPTUS. However, the results we recovered for the Detarioideae subfamily suggest that the largest differences in species tree topology resulted from the use of paralog-filtered alignments (such as with the Putative Paralog Detection pipeline and the Yang & Smith orthology inference approaches) rather than just by removing the sequences of identified paralogous genes. This was the true for HybPiper-assembled datasets but was not seen in CAPTUS-assembled datasets. In all comparisons, the topological differences caused by different paralog handling methods tended to be confined to clades where processes such as hybridisation and introgression are prevalent. Our study provides a roadmap to establish the best approach to identify, eliminate or separate paralogs in the absence of a chromosomally contiguous reference genome for a study group, and highlights the importance of careful data inspection and processing in addition to understanding the extent of paralogy and paralog characteristics (e.g. sequence divergence between copies) for their study group.

Phylogeny↗
PubMed1991

Deletion of 20p 11.23----pter with normal growth hormone-releasing hormone genes.

Using a molecular analysis of the DNA from a patient with a deletion of chromosome 20 [46,XX,del(20)(p 11.23)], we have excluded the growth hormone-releasing hormone (GHRH) gene from the region 20p11.23----pter. The patient had minor facial anomalies. Rieger eye anomaly, a congenital heart defect, severe failure to thrive, and a neurosecretory problem in growth hormone (GH) secretion. Since the GHRH gene was previously mapped to chromosome 20, we used molecular genetic methods to determine whether the growth abnormalities were due to the deletion of this gene. DNAs of the patient and 2 normal control subjects were analyzed by quantitative Southern blotting using a DNA probe for the GHRH gene and 2 reference DNA probes mapping to chromosome 21. The GHRH gene was found to be present in 2 copies in the patient. This indicates that the gene for GHRH maps to the region outside the patient's deletion, in 20p11.23----qter. Furthermore, our results suggest that genes other than GHRH on 20p are important for developmental steps leading to normal neurosecretory function of GH and may also be involved in generating Rieger eye anomaly. Finally, GH deficiency and Rieger eye anomaly should be sought in other patients with deletions of 20p.

Child↗