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14 recordsLinked to original sources
PubMed1978

Receptive-field properties of neurons in binocular and monocular segments of striate cortex in cats raised with binocular lid suture.

1. We studied the receptive fields of 171 striate cortical neurons from 17 cats raised with binocular lid suture. Of these, 102 fields were within 10 degrees of the area centralis and the remaining 69 were at least 38 degrees from the vertical meridian. 2. Based on their different response properties, cells were divided into three broad groups: the mappable cells (49%) had clearly defined receptive fields, the unmappable cells (31%) were activated by visual stimuli but had diffuse fields which could not be hand plotted, and the visually inexcitable cells (20%) could not be activated by visual stimuli. Very few (less than or equal to 12% of the total sample) normal simple or complex cells could be found. 3. Orientation selectivity was assessed in these cells. Only 12% displayed orientation selectivity within normal bounds, and these were all mappable cells. None of the unmappable cells had discernible orientation selectivity. 4. Ocular dominance was assessed for 62 of the centrally located receptive fields. Among mappable cells, there was an abnormally low proportion of binocular fields, while no such abnormality was seen for unmappable cells. 5. For 47 of the neurons, average response histograms were compiled for moving stimuli of various parameters in an effort to evoke the maximum discharge or peak response. This peak response was normal for mappable cells but reduced for unmappable cells. 6. We devised a technique for studying potential inhibitory receptive-field zones in these neurons, validated the method in normal striate cortex, and used it to test 20 mappable cells in the lid-sutured cats. None showed the pattern of strong inhibitory side bands seen in normal simple cells, although six showed weak or abnormal inhibitory zones. Interestingly, six of the seven visually inexcitable cells tested by this method had purely inhibitory receptive fields. 7. The effects of binocular suture were essentially identical for the binocular and monocular segments since the cell types and their response properties did not differ between these two areas of cortex. Furthermore, the cortical monocular segments of these cats seemed qualitatively different from the deprived cortical monocular segment after monocular suture. This extends an analogous difference for these cats reported for the monocular segments of the lateral geniculate nucleus. We thus conclude that monocularly and binocularly sutured cats develop by qualitatively different mechanisms. For the former, competition between central synapses related to each eye is a prominent feature of geniculocortical development, whereas, for the latter, such specific forms of geniculocortical development may not obtain.

Animals↗
PubMed1975

The prior probability of autosomal linkage.

An expression is derived for the prior probability of linkage between a random trait locus and any one of m random marker loci, and this probability is computed form=1, 10, 20, 30, 50 and 100. A similar expression is derived for two trait loci, and computed for m=1, 10, 20 and 30. When one trait locus and 30 marker loci are being studied, a priori there is over a three-quarter probability that the trait locus should be syntenic with at least one of the markers, and about a one-half probability that there should be a linkage mappable from recombination frequencies. If two traits are studied, then the prior probability that at least one should be syntenic with one of the 30 markers is 0-94, and there is a three-quarter probability that such a linkage should be mappable.

Chromosome Mapping↗
PubMed1984

Two healing patterns correlate with different adult neural connectivity patterns in regenerating embryonic Xenopus retina.

Nasal and temporal one-third-sized eye fragments, formed by ablation at stage 32-33 of Xenopus laevis embryos, heal and, in about 50% of the cases, survive to make eyes in the postmetamorphic animal which have mappable visuotectal projections. The majority of nasal one-third eyes have duplicate projections whereas the majority of temporal one-third eyes have unduplicated projections. Most nasal one-third eye fragments and a minority of temporal eye fragments heal by the extrusion of cells from the center of the cut edge into the region of the ablation, forming a tongue of cells between the distal cut edges. This healing pattern is correlated with duplicated visuotectal projections. Most temporal one-third fragments and a minority of nasal one-third fragments heal by rounding up; that is, the distal cut edges collapse to meet in the region of the ablation. This healing pattern is correlated with the formation of unduplicated visuotectal projections. During tongue formation, neurons and undifferentiated cells are transferred from the original fragment into the tongue in a disorderly array, but quickly re-form normal retinal order. We propose that the tongue cells retain their original determination to connect to the same tectal positions as the fragment from which they originated, despite their new positions, and that this mosaicism, coupled with cell movement into the tongue, established duplicate visuotectal projections.

Animals↗
PubMed1995

Predigestion of DNA template improves the level of polymorphism of random amplified polymorphic DNAs in wheat.

Random amplified polymorphic DNA (RAPD) analysis in wheat has proven to be poor in its levels of both reproducibility and polymorphism. By digesting the template, prior to performing PCR, with frequently cutting restriction enzymes, the level of polymorphism was improved. RAPD profiles from certain primers were not affected by this pretreatment of the template, but other primers produced distinct profiles from each of several restriction enzymes assayed. Some polymorphisms were specific to one or more restriction digests, but none involved the simple loss of bands from the unrestricted template profile. Genotypic comparisons enabled the selection of primer-restriction enzyme combinations that enabled polymorphic and mappable patterns to be produced both between wheat varieties and between wheats with and without chromosomal segments deriving from related species.

DNA Primers↗
PubMed2025

Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.

For the detection of somatic structural variation (SV) in cancer genomes, long-read sequencing is advantageous over short-read sequencing with respect to mappability and variant phasing. However, most current long-read SV detection methods are not developed for the analysis of tumor genomes characterized by complex rearrangements and heterogeneity. Here, we present Severus, a breakpoint graph-based algorithm for somatic SV calling from long-read cancer sequencing. Severus works with matching normal samples, supports unbalanced cancer karyotypes, can characterize complex multibreak SV patterns and produces haplotype-specific calls. On a comprehensive multitechnology cell line panel, Severus consistently outperforms other long-read and short-read methods in terms of SV detection F1 score (harmonic mean of the precision and recall). We also illustrate that compared to long-read methods, short-read sequencing systematically misses certain classes of somatic SVs, such as insertions or clustered rearrangements. We apply Severus to several clinical cases of pediatric leukemia/lymphoma, revealing clinically relevant cryptic rearrangements missed by standard genomic panels.

Humans↗
PubMed2026

Likelihood-based optimization enables accurate copy number estimation for paralogous genes using exome data.

MOTIVATION: Exome sequencing is widely used for genetic studies; however, accurate detection of copy number variants (CNV) in paralogous genes is challenging due to short-read mapping ambiguity and extensive copy-number variation. The human genome contains several hundred paralogous genes, many of which are known to harbor disease-associated CNVs. Existing exome CNV callers are primarily designed for rare CNV detection in uniquely mappable regions and are not well-suited for paralogous genes. METHODS: We describe a computational method (EdgeCopy) for copy number profiling of paralogous genes using whole-exome sequence data. EdgeCopy aggregates reads mapped to all copies of paralogous genes and relates observed read depth to copy number for multiple exome samples using an approximate composite likelihood function. The likelihood function is optimized using numerical optimization to obtain gene-level fractional copy number estimates that are discretized and refined using a Hidden Markov Model to obtain exon-level copy number estimates. RESULTS: Benchmarking of Edgecopy using experimental copy number data showed high concordance (mean = 0.973) for six disease-associated paralogous genes. We evaluated performance using whole-exome data from approximately 2400 samples across five continental populations from the 1000 Genomes Project. EdgeCopy shows robust concordance with whole-genome sequencing based estimates (0.974-0.982) across populations and 130 paralogous genes spanning a wide range of copy-number variation. In comparison, copy number analysis using a state-of-the-art exome CNV caller failed to estimate copy number for paralogous genes with very high mapping ambiguity and showed much lower concordance (0.565) for CNV events compared to EdgeCopy (0.908). AVAILABILITY: EdgeCopy is freely available at https://github.com/vibansal-lab/edgecopy.

Humans↗
PubMed2026

Integrating plant phenotypic and genotypic data in the AGENT project: a BrAPI service implementation.

MOTIVATION: The AGENT project established a network of actively cooperating European genebanks, integrating genomic and phenotypic data from accessions of wheat and barley. Due to specific storage demands for phenotypic and genotypic data, the project used separate database instances and backend technologies to manage integrated phenotypic and genotypic data. RESULTS: We discuss the challenges encountered when integrating dispersed data to serve through a single interface such as the Plant Breeding Application Programming Interface, BrAPI. We examine how the consistent mappability of genebank data to the BrAPI model can enable the implementation of effective services. The advantages of BrAPI in transparently linking distributed data entities through embedded, unique identifiers are highlighted. We present a technical solution involving a BrAPI proxy, which combines and merges separate BrAPI endpoints. Finally, we demonstrate the AGENT BrAPI implementation with an illustrative example that validates a suggested SNP for a trait from the literature by linking phenotypic, genotypic and passport data. AVAILABILITY AND IMPLEMENTATION: The BrAPI proxy implementation and documentation is available at the Python Package Index (https://pypi.org/project/brapi-proxy) and archived in Zenodo (doi: 10.5281/zenodo.19436445). SUPPLEMENTARY INFORMATION: A Jupyter Notebook file for the validation example using a marker-trait relationship found in the literature.

Phenotype↗
PubMed2026

AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates.

MOTIVATION: Satellite DNA has long posed challenges for genome assembly and analysis due to its low sequence complexity and poor mappability. These large heterochromatic arrays of tandem repeats are ubiquitous across eukaryotic genomes, yet remain understudied. Current methods for annotating satellite regions, and other classes of tandem repeat arrays, are limited in their ability to annotate divergent or novel sequences. RESULTS: In this work, we introduce AniAnn's, an algorithm for annotating large blocks of tandemly repeating DNAs. AniAnn's exploits the high Average Nucleotide Identity (ANI) shared between repeat units of the same array to quickly and accurately infer the boundaries of such arrays. We show that AniAnn's improves the annotation of satellites and other tandem repeats within a variety of plant and animal genomes, while requiring only a fraction of the runtime compared to previous approaches. We conclude by exploring several use cases of AniAnn's as a lightweight method for masking repeats prior to whole-genome alignment as well as the de novo annotation and classification of satellite repeats. AVAILABILITY: AniAnn's is open source software and available at github.com/marbl/anianns.

Algorithms↗
PubMed2025

A complete and near-perfect rhesus macaque reference genome: lessons from subtelomeric repeats and sequencing bias.

A truly complete, telomere-to-telomere (T2T), and error-free reference genome remains a foundational resource-and long-standing goal-for unbiased comparative and functional genomics. While recent T2T assemblies of humans and other primates have made substantial progress, most still contain thousands of base-level errors, particularly within highly repetitive regions. Here, we present T2T-MMU8v2.0, a near-perfect T2T assembly of the rhesus macaque (Macaca mulatta), representing the highest base-level accuracy reported in a primate genome to date. By employing an optimized ONT-only assembly strategy, we identify subtelomeric satellite-rich regions as the principal bottleneck to improving assembly quality, owing to technological biases in long-read platforms and limitations in current hybrid assembly frameworks. We discover 268 previously unannotated repeat families and resolve ~8 Mbp of SATR satellite arrays, with over 99-fold enrichment in historically misassembled subtelomeric regions. These satellites form four distinct genomic architectures, each with unique SATR satellite composition, segmental duplication organization, and epigenetic signatures, distinct from the subtelomeric architectures observed in hominid genomes. Notably, in contrast to the largely gene-poor subtelomeric regions in African hominids, the SATR architectures in macaques harbor 58 actively transcribed genes, supported by open chromatin and expression data, suggesting gene innovation within these repetitive regions. Functionally, T2T-MMU8v2.0 improves read mappability and accuracy across sequencing platforms, and results in a 19% improvement of transcription start site enrichment scores and 5,821 additional chromatin accessibility peaks on average, thereby enhancing variant detection, regulatory annotation, and transcriptomic resolution in population genetics or single-nucleus studies. Together, this work establishes a new benchmark for genomics, offers a roadmap for resolving complex repetitive regions, and reveals previously unrecognized features of subtelomeric genome structure and evolution.

Journal Article↗
PubMed1995

A survey of DNA polymorphism within the genus Capsicum and the fingerprinting of pepper cultivars.

Interspecific genetic variation was examined in the genus Capsicum based on shared restriction fragments in Southern analyses. Four distinct clusters were delineated among 21 accessions of cultivated and wild pepper (C. annuum, C. baccatum, C. chacoense, C. chinense, and C. frutescens). Three tight clusters comprised of accessions belonging to C. annuum, C. frutescens, and C. baccatum, respectively, were formed, along with a fourth cluster comprised of one accession each of C. chinense and C. chacoense. All accessions were differentiated by this technique, and the clusters corresponded closely to previous morphology-based classification. Sufficient DNA polymorphism exists among these accessions that segregating populations useful for restriction fragment length polymorphism (RFLP) mapping could be constructed using any two pepper accessions as parents. Regression analysis indicates that genetic distance is a good predictor (R2 = 0.872) of the level of mappable DNA polymorphism in Capsicum. Intraspecific variability was examined among four C. annuum cultivars (NuMex R Naky, Jupiter, Perennial, and Criollo de Morelos 334) using both RFLPs and randomly amplified polymorphic DNA (RAPDs), allowing a comparative evaluation of the two techniques. Seventeen percent of the clones used singly in RFLP analyses were sufficient for the differentiation of these varieties, as were 12.5% of the RAPD PCR amplifications. Dendrograms constructed from RFLP and RAPD analyses of the intraspecific data are similar but not identical. Southern analysis and RAPD PCR should be useful for DNA fingerprinting and the discrimination of closely related C. annuum genotypes.

Agriculture↗
PubMed1988

Surgical ablation of ventricular tachycardia with sequential map-guided subendocardial resection: electrophysiologic assessment and long-term follow-up.

A new operative technique of sequential map-guided subendocardial resection (SER) was used in 45 consecutive patients for the treatment of sustained ventricular tachycardia due to coronary artery disease. This technique is characterized by map-guided SER or cryothermic ablation during normothermic cardiopulmonary bypass, followed by repeated sequences of programmed stimulation to assess adequacy of resection. The patients' mean age was 59 +/- 10 years and the mean left ventricular ejection fraction was 34 +/- 12%. Twenty-five (56%) patients had a history of myocardial infarction within the previous 2 months. After ventriculotomy, 34 patients (76%) had inducible monomorphic ventricular tachycardia. These patients underwent repeated sequences of ventricular tachycardia induction and mapping during normothermic bypass followed by successive SER or cryothermic ablation until sustained monomorphic ventricular tachycardia was no longer inducible. Twenty-seven patients had a total of 60 discrete, mappable tachycardias induced and seven patients had 10 discrete tachycardias that were too fast to accurately map. In the remaining 11 patients, no ventricular tachycardia was inducible after ventriculotomy and SER, which included all visually identifiable scar, was performed. The mean cardiopulmonary bypass time was 102 +/- 27 min. Forty-one of 45 patients (91%) survived to hospital discharge, and 35 of 41 patients (85%) had no inducible ventricular tachycardia at postoperative electrophysiologic evaluation performed in the absence of all antiarrhythmic drugs. The remaining six patients had no inducible ventricular tachycardia with drug therapy. All four operative nonsurvivors had refractory cardiac collapse preoperatively. Over 19 +/- 12 months of follow-up, there were four sudden cardiac deaths and no nonfatal recurrences of ventricular tachycardia. There were seven additional cardiac deaths. Actuarial cardiac survival was 0.57, and freedom from arrhythmic events was 0.76 at 42 months. Thus, in the absence of cardiogenic shock, the technique of sequential map-guided SER achieves: (1) a high operative survival with acceptable perfusion times, (2) excellent long-term arrhythmia control, and (3) survival comparable to that in patients with similar left ventricular function and no history of ventricular tachyarrhythmia.

Aged↗
PubMed1991

Current role of catheter ablative procedures in patients with cardiac arrhythmias. A report for health professionals from the Subcommittee on Electrocardiography and Electrophysiology, American Heart Association.

Catheter ablative techniques have assumed an increasingly important role in the treatment of patients with drug-refractory cardiac arrhythmias. Catheter ablation of the AV junction is considered the procedure of choice for management of patients without bypass tracts with drug-resistant supraventricular arrhythmias. Catheter techniques have been used with increasing frequency in attempts to ablate accessory AV tracts. These techniques currently appear to be less effective than surgical techniques but involve less morbidity and expense. In some centers, accessory pathway ablation using catheter techniques is the procedure of first choice in selected patients with drug-refractory tachycardia mediated by an accessory pathway. Catheter ablation of ventricular tachycardia should be reserved for patients with mappable ventricular tachycardia who are not candidates for cardiac electrosurgery or insertion of an automatic defibrillator. The development of more flexible catheters and more manageable energy delivery systems holds promise for more effective catheter techniques.

Arrhythmias, Cardiac↗
PubMed1985

Native salivary chromosomes of Drosophila melanogaster: retrospect and prospect.

A method has been developed which, for the first time, allows the preparation of mappable cytological spreads of salivary chromosomes from D. melanogaster without exposure to acid fixatives. These isolated native chromosomes show the best preservation of ultrastructure observed to date--ribonucleoprotein particles may be seen to be organized in linear arrays in transcriptionally active puffs and the repeating nucleosome module is present. Native salivary chromosomes are proving useful for the localization of nuclear proteins both at the light microscope and ultrastructural levels. They display only background-level binding of antibodies specific for the Z-DNA conformation. However, Z-DNA immunoreactivity is activated by exposure to acid fixative, first in interbands and then in bands. The Z-conformation in the chromosomes is held in place by elastic torsional strain which appears in the DNA following acid fixation. Native D. melanogaster salivary chromosomes offer promise for enabling the probing of the chromatin of known genetic loci for properties dependent on the preservation of macromolecular integrity.

Animals↗
PubMed2025

Bioinformatics for the Structural Genomics of Poxviruses.

Poxviruses are large, complex viruses, and their host species are widespread across the tree of life. As a result, the bioinformatics analysis of their genomes can be complex. Here we show how a few helpful tools and strategies can be used to inform the analysis, leading to a better understanding of the structural properties of poxvirus genomes and to a more accurate quality control of, or comparison between, assembled sequences.

Poxviridae↗