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18 recordsLinked to original sources
PubMed2025

MIA-Jet: Multi-scale Identification Algorithm of Chromatin Jets.

The mammalian genome is organized into large-scale chromosome territories, compartments, domains, and at the smallest scale, chromatin loops and stripes. The newest element is a chromatin jet, a diffused line perpendicular to the main diagonal in the Hi-C contact map, which was reported in quiescent mammalian lymphocytes supporting a two-sided symmetric cohesin loop extrusion model. A similar structure is observed in Repli-HiC data, where relatively thin and straight chromatin fountains indicate coupling of DNA replication forks. However, the precise biological implications of these jet-like structures are unknown due to the limitations in computational methods. We developed MIA-Jet, a multi-scale ridge detection algorithm that can accurately detect jets of variable lengths, widths, and angles. When tested on Hi-C, Repli-HiC, ChIA-PET, ChIA-Drop, and Micro-C data in mouse, human, roundworm, and zebrafish cells, MIA-Jet outperformed existing methods. In human cells, jets were enriched in cohesin loading sites and early replication initiation zones. Applying MIA-Jet to Hi-C data generated from protein-degraded cells revealed that jets are dependent on cohesin but not YY1, and jet signals are strengthened after depleting WAPL. We envision MIA-Jet to be broadly applicable to any 3D genome mapping data, thereby providing new insights into the functional roles of chromatin jets.

3D genome mapping↗
PubMed1979

Recovery of sensibility after suture of digital nerves.

A group of 49 patients with 74 injured digital nerves was studied more than 5 years following epineurial nerve suture. Three tests of return of sensibility were used: von Frey plastic filaments, a modified Weber two-point discrimination device, and a dynamic test--the plastic ridge. The correlation between two-point discrimination and tactilegnosis in the range of 8 to 12 mm was poor. The plastic ridge device detects the presence or absence of tactilegnosis in patients in the intermediate range of two-point discrimination between 8 and 12 mm. Of the factors studied, the patient's age at the time of nerve suture was found to be directly related to the return of sensibility by both two-point discrimination and ridge criteria.

Adolescent↗
PubMed2024

GRable Version 1.0: A Software Tool for Site-Specific Glycoform Analysis With Improved MS1-Based Glycopeptide Detection With Parallel Clustering and Confidence Evaluation With MS2 Information.

High-throughput intact glycopeptide analysis is crucial for elucidating the physiological and pathological status of the glycans attached to each glycoprotein. Mass spectrometry-based glycoproteomic methods are challenging because of the diversity and heterogeneity of glycan structures. Therefore, we developed an MS1-based site-specific glycoform analysis method named "Glycan heterogeneity-based Relational IDentification of Glycopeptide signals on Elution profile (Glyco-RIDGE)" for a more comprehensive analysis. This method detects glycopeptide signals as a cluster based on the mass and chromatographic properties of glycopeptides and then searches for each combination of core peptides and glycan compositions by matching their mass and retention time differences. Here, we developed a novel browser-based software named GRable for semi-automated Glyco-RIDGE analysis with significant improvements in glycopeptide detection algorithms, including "parallel clustering." This unique function improved the comprehensiveness of glycopeptide detection and allowed the analysis to focus on specific glycan structures, such as pauci-mannose. The other notable improvement is evaluating the "confidence level" of the GRable results, especially using MS2 information. This function facilitated reduced misassignment of the core peptide and glycan composition and improved the interpretation of the results. Additional improved points of the algorithms are "correction function" for accurate monoisotopic peak picking; one-to-one correspondence of clusters and core peptides even for multiply sialylated glycopeptides; and "inter-cluster analysis" function for understanding the reason for detected but unmatched clusters. The significance of these improvements was demonstrated using purified and crude glycoprotein samples, showing that GRable allowed site-specific glycoform analysis of intact sialylated glycoproteins on a large-scale and in-depth. Therefore, this software will help us analyze the status and changes in glycans to obtain biological and clinical insights into protein glycosylation by complementing the comprehensiveness of MS2-based glycoproteomics. GRable can be freely run online using a web browser via the GlyCosmos Portal (https://glycosmos.org/grable).

Glycopeptides↗
PubMed1979

Cell junctions in the cyst envelope in the silkworm testis, Bombyx mori Linné.

The cell junctions of the cyst envelope in the testes of Bombyx mori were examined by electron miscroscopy utilizing a thin-sectioning technique following conventional fixation, tannic acid fixation and lanthanum tracer study, and also using a freeze-fracture technique. There are three kinds of junctions; septate junctions, gap junctions and tight junctions. Septate junctions are of the pleated type. Gap junctions are characterized by four electron-dense lines and three electron-lucent lines in the reduced intercellular spaces seen by thin-sectioning. They are of the "E" type, having clusters of intramembraneous particles on the E-fracture face. The most striking finding is the frequent presence of tight junctions on the fracture planes, while focally fused outer leaflets of the junctional unit membranes are rarely detected on thin-sectioned preparations. Tight junctions are characterized by branching zigzag ridges on the P-fracture face and complementary grooves on the E-fracture face. It is proposed that tight junctions are new morphological evidence of blood-germ cell barrier in an insect.

Animals↗
PubMed1979

[Double-contrast arthrography in chondropathia patellae--clinical and experimental study on pathogenesis and diagnosis (author's transl)].

This study is based on the evaluation of 250 arthrographies of the patellofemoral joint ("défilé" arthrographs in Ficat's terminology) which were performed because of clinical suspicion of chondropathia patellae and which could be controlled intraoperatively in 30 cases, as well as on examinations employing an etching paste as used in metallurgy and performed on 20 knee-joints of corpses. 46% of the arthrographies showed a ridge-shaped cartilaginous thickening which was not pre-modelled in the osseous structure and which separated the medial facette into a paramedian and a marginal segment and correlated with chondromalacia to a greater degree than patellar dysplasias or secondary osseous changes. This variant, which could not be detected by plain roentgenography, must be considered as a pre-arthrotic deformity on account of the high point-shaped pressure load on the ridge. The findings were fully confirmed by macroscopic examination of the postmortem material.

Adolescent↗
PubMed1978

Toward less hazardous cigarettes. Current advances.

Critical levels of selected cigarette smoke constituents have been expressed in terms of maximum numbers of pre-1960 cigarettes that a smoker may consume daily without increasing his mortality risk substantially above that of a nonsmoker. This could still imply an important risk, although it may be difficult to detect. We relate these levels to the yields of 27 current low tar and nicotine commercial cigarettes, as measured at the Oak Ridge National Laboratory. In addition, the yields of these selected constituents concomitant with the yield of 1 mg of nicotine are provided as a guide for the smoker who titrates or adjusts his smoking pattern to accommodate a fixed daily intake of nicotine.

Acrolein↗
PubMed2026

PScnv: personalized self-normalizing CNV detection with a hierarchical multi-phase framework.

MOTIVATION: Accurate detection of copy number variations (CNVs) from targeted panel sequencing remains challenging due to limited genomic coverage and pronounced sample-specific biases. Existing normalization strategies, including baseline-cohort, matched-control, and single-sample approaches, often struggle to balance noise suppression with adaptability, leading to inconsistent performance across heterogeneous samples. RESULTS: We present PScnv, a personalized self-normalizing framework for robust CNV detection from panel sequencing data. PScnv integrates a pre-built panel-of-normals (PoN) with sample-intrinsic stable chromosomes through ridge-regression normalization to generate individualized log2 ratio profiles with reduced systematic variation. CNVs are then identified using a hierarchical multi-phase segmentation pipeline incorporating z-score pre-partitioning, kernel-based correction, and circular binary segmentation. In 139 clinical tumor samples with orthogonal FISH validation at MET, ERBB2, and MTAP, PScnv showed improved accuracy and robustness over existing methods that do not require patient-matched normal samples, provided that a pre-built PoN cohort is available. AVAILABILITY: Source code is available for academic use at https://github.com/lvws/PScnv.

DNA Copy Number Variations↗
PubMed1978

A maturation change detected in the semilunar cartilages with the scanning electron microscope.

The surface of rabbit, cat, monkey and human semilunar cartilages was examined with the scanning electron microscope. A common feature was the occurrence of numerous ridges, undulations and furrows on the surface, but this was thought to be due to marked shrinkage and distortion of cartilage not firmly attached to bone. Humps were seen on the semilunar cartilages of young animals, but pits occurred in adults. This is thought to reflect a maturation change. Humps were seen in a young human semilunar cartilage, but pits were not seen in adult specimens. It is not clear whether pits are truly absent or just masked by the severe ridging produced during the preparation of large human specimens.

Aging↗
PubMed2026

Chromosome-scale genome assembly and genomic prediction of essential oil compounds in Atractylodes lancea for genomics-assisted breeding.

Atractylodes lancea rhizomes are used as crude drugs. Essential oil compounds, including atractylodin, hinesol, β-eudesmol, and atractylon, are key determinants of crude drug quality. Conventional breeding of A. lancea is difficult because of its perennial growth. In this study, a chromosome-scale reference genome of A. lancea (4.79 Gb) was generated, and genome-wide association studies (GWAS) and genomic predictions of essential oil compounds were conducted to explore the potential for genome-assisted breeding. Genotyping of 480 lines using double-digest restriction-site-associated DNA-sequencing yielded 29,136 high-quality SNPs. All the compounds showed high genomic heritability (h2 = 0.758-0.915), indicating strong genetic control. Despite the high genomic heritability, GWAS detected only one weak association with atractylon and no significant loci for the three compounds. However, genomic prediction achieved moderate to high accuracy across multiple models, particularly the ridge regression, genomic best linear unbiased prediction, and Bayesian approaches. The prediction accuracy, measured as the Pearson correlation coefficient between the observed and predicted values, exceeded 0.6 for all four essential oil compounds. These results demonstrate the efficacy of genomic selection for improving essential oil compound levels in A. lancea and provide a foundation for genome-assisted breeding of medicinal plants with long breeding cycles.

Atractylodes lancea↗
PubMed1979

Tight junction development between cultured hepatoma cells: possible stages in assembly and enhancement with dexamethasone.

Freeze-fracture and thin-section methods were used to study tight junction formation between confluent H4-II-E hepatoma cells that were plated in monolayer culture in media with and without dexamethasone, a synthetic glucocorticoid. Three presumptive stages in the genesis of tight junctions were suggested by these studies: 1) "formation zones" (smooth P-fracture face ridges deficient in intramembranous particles), apparently matched across a partially reduced extracellular space, develop between adjacent cells; 2) linear strands and aggregates of 9--11 nm particles collect along the ridges of the formation zones. The extracellular space was always reduced when these structures were found matched with pits in gentle E-face depressions; 3) the linear arrays of particles on the ridges associate within the membranes to form the fibrils characteristic of mature tight junctions. The formation zones resemble tight junctions in terms of size, complexity and the patterns of membrane ridges. Although some of the beaded particle specializations may actually be gap junctions, it is unlikely that all can be interpreted in this way. No other membrane structures were detected that could represent developmental stages of tight junctions. Dexamethasone (at 2 x 10(-6)M) apparently stimulated formation of tight junctions. Treated cultures had a greater number of formation zones and mature tight junctions, although no differences in qualitative features of the junctions were noted.

Animals↗
PubMed1979

Cell death during the development of the truncus and conus of the chick embryo heart.

The presence of cell death in the walls of the truncus and conus of the developing chick heart was investigated by a variety of light and electron microscopic techniques. Necrotic areas were observed in the myocardial layer of the truncus and conus and within the mesenchymal cells of the truncoconal ridges and aortopulmonary septum. These necrotic zones appeared first at Stage 25-26 and reached their maximum extent at Stages 29-32 undergoing later progressive disappearance. The morphological changes of the degenerating cells detectable under both transmission and scanning electron microscopy are also reported. The possible role of cell death in the morphogenesis of the truncus and conus is discussed.

Animals↗
PubMed1977

A naphthol yellow S and erythrosin B staining procedure for use in studies of the acrosome reaction of rabbit spermatozoa.

Rabbit spermatozoa suspended in Krebs-Ringer-phosphate containing 0.25% glucose were smeared on polylysine-coated slides and dried in air at room temperature for 30 min at room temperature, blotted, rinsed in 1.0% aqueous acetic acid for 10-15 sec, drained and stained for 7 min in a mixture of equal parts of aqueous naphthol yellow S and erythrosin B (final concentration of each dye 0.1% w/v) at pH 4.6-5.0 (pH adjusted with acetic acid). Stained slides were well rinsed in distilled water adjusted to pH 4.6-5.0 with acetic acid, blotted, allowed to dry completely, rinsed in xylene and mounted in synthetic resin. Acrosomal caps were stained cherry-red (apical ridge) to pink (dorsal and ventral aspects); postnuclear caps stained pale pink; nuclei were either unstained or stained a very faint yellowish-pink. The mid-piece and flagellum were stained different shades of pink. The procedure is simple, rapid, and gives highly reproducible results. When present, acrosomes are easily detected regardless of the density of the smear.

Acrosome↗
PubMed1978

A maturation change in the surface of cat articular cartilage detected by the scanning electron microscope.

The articular surface of the femoral condyle of kittens (2 days to 2 months old) and cats (6 months to 20 months old) was studied by examining air dried and critical point dried specimens in the scanning electron microscope. The surface of kitten cartilage was found to be populated by innumerable humps which were more prominent in air dried than in critical point dried specimens. Undulations and ridges were seen on air dried kitten cartilage, which was markedly shrunken and distorted, but undulations and ridges were absent from critical point dried specimens where shrinkage was more modest or even undetectable. The surface of the articular cartilage of 12 months and 20 months old cats was populated by innumerable pits. A rare hump in a pit was seen in specimens from the 12 months old cat, but not from the 20 months old animal. In 6--8 months old cats an intermediate situation prevails, for in some specimens pits were present on the posterior part of the condyle but humps and humps in pits were present on the anterior aspect. This study shows that the surface of young articular cartilage is populated by humps, but as the cartilage matures these formations are either transformed into pits or replaced by pits.

Age Factors↗
PubMed1978

Electron microscopic study of measles virus infection: cell fusion and hemadsorption.

Virus-induced cell fusion has been studied after infection of Vero cells with measles virus. Scanning and transmission electron microscopy were combined with immunoperoxidase labeling of measles antigens to correlate viral production and distribution of virus-induced erythrocyte binding sites with progress of fusion. Release of infectious virus started before syncytia were detected and decreased while the number and size of syncytia were increasing. Most virions were seen budding from mononucleated cells or from the periphery of syncytia where cells were being recruited. Moving inward, the surfaces of syncytia where cells were being recruited. Moving inward, the surfaces of syncytia were covered with numerous ridges containing viral antigen, but few viral buds were seen, suggesting that syncytia might be sites of defective viral formation. Hemadsorption occurred predominantly within the confines of syncytia. Erythrocytes were scattered sparsely over immature syncytia but were densely packed in the center of mature syncytia. Active binding sites for erythrocytes were located on cell villi and ridges covered with measles antigens. Hemadsorption was completely inhibited in measles virus-infected cultures pretreated with virus-specific immunoglobulin G for 1 h at 4 degrees C. However, when these cultures were shifted to 37 degrees C, hemadsorbing sites were recovered at the periphery of enlarging syncytia. Virus-induced sites for erythrocyte adsorption were found to move centripetally on syncytium membranes as fusion progressed.

Antigens, Viral↗
PubMed1979

Scanning electron microscopy of peripheral blood leukocytes of the chickens.

Polymorphonuclear leukocytes, e.g., neutrophilic granulocytes, were enriched from heparinized blood by a Ficoll-step-gradient centrifugation procedure. Scanning electron microscopy (SEM) revealed a surface morphology of narrow ridge-like profiles and small ruffles with occasional microprocesses. Mononuclear leukocytes were isolated by centrifugation over a Ficoll-Metrizoat gradient. The lymphocytes showed varying numbers of microvilli of different length, size and shape. B lymphocytes, characterized by their capability of "sheep red blood cell (SRBC)-rosette formation", displayed a similar surface morphology. Completely smooth lymphocytes, described in the literature as T lymphocytes, could not be detected, although many lymphocytes with few microprocesses were observed. Thus, SEM is not a useful tool for distinguishing between B and T lymphocytes in the peripheral blood of chickens. Monocytes were characterized by prominent membrane-like ruffles, but in some cases they closely resembled granulocytes. An influence of the various separation media on the surface morphology of the isolated cells could not be detected when compared with cells isolated by the buffy-coat method.

Animals↗
PubMed1977

Possible genetic predisposition for alcohol addiction.

In a group of male addictive alcoholics, some palmar and fingerprint characteristics were determined, as well as the ABO, MN, Ss, Kell, Duffy, Lewis, and P blood groups, Rh and Hp phenotypes, HLA and Au antigens, immunoglobulins, blood sugar, cholesterol, SGOT, SGPT, and karyotypes. In comparison with the normal population the alcoholics show increased occurrence of whorls and arches on the fingers, decrease in the total ridge count, sharpening of the atd angle, and separation of the lower from the upper transverse line. Genetic markers in the blood of alcoholics show different frequencies of A, Lewis a-b+, Lewis a-b-, Duffy a-, Duffy a+, SS, and M blood groups, CcD-ee, Hpl-1, Hp2-1 phenotypes, and HLA-5, HLA-7, w10, w16, and w5 antigens. These findings may be expected to lead soon to detection of the predisposition to the development of alcohol addiction caused by some genetic malformations.

ABO Blood-Group System↗
PubMed1978

Intramembrane changes occurring during maturation of herpes simplex virus type 1: freeze-fracture study.

During the maturation of two strains of herpes simplex virus type 1 (VR3 and Patton), intramembrane changes were detected with the freeze-fracture technique in the viral envelope and the infected cell plasma membrane, and these changes were compared with data obtained from thin sections. Regardless of the strain, the inner leaflet of the viral envelope of extracellular virions was characterized by a density of intramembrane particles (IMP) three times larger than the host nuclear and plasma membrane. Addition of IMP, which probably represent virus-coded proteins, was detected in the viral envelope only after budding from the nuclear membrane, whereas it occurred during envelopment of capsids at cytoplasmic vacuoles. Fused membranes also showed one of their fracture faces covered with a high density of IMP similar to that of the mature virion envelope. The internal side of the membrane leaflet bearing these numerous particles was always characterized by the presence of an electron-dense material in thin sections. In addition, the plasma membrane of fibroblasts and Vero cells showed strain-specific changes: patches of closely packed IMP were observed with the VR3 strain, whereas ridges almost devoid of IMP characterized the plasmalemma of cells infected with the Patton strain. These intramembrane changes, however, were not observed as early as herpes membrane antigens. Thus, application of the freeze-fracture technique to herpes simplex virus type 1-infected cells revealed striking structural differences between viral and uninfected cell membranes. These differences are probably related to insertion and clustering of virus-coded proteins in the hydrophobic part of the membrane bilayer.

Capsid↗
PubMed1977

Effects of filipin on the structure and biological activity of enveloped viruses.

The interaction of the polyene antibiotic filipin with membrane-bound cholesterol in vesicular stomatitis (VS), influenza, and Rauscher leukemia virions was studied. Exposure of virions to filipin resulted in a series of depressions and ridges in the envelope of VS virions, with a periodicity of 15 to 20 nm perpendicular to the long axis of the particle; similar morphological alterations were observed in negatively stained preparations, in thin-sectioned virions, and in protease-treated virions that lack surface glycoproteins. This morphological effect was specific for filipin, since the envelopes of VS virions that had been treated with another polyene antibiotic, amphotericin B, exhibited markedly different morphology. Morphological alterations induced by filipin in influenza and Rauscher leukemia virions differed from those seen in VS virions. The infectivity of filipin-treated VS virions was reduced up to 500-fold, whereas influenza virions were resistant to filipin treatment. Incorporation of filipin into the virions was demonstrated, and no release of either lipids or proteins from virions was detected after filipin treatment. A stoichiometry of approximately 1 mol of bound filipin per mol of cholesterol was found in both intact and protease-treated VS virions. The equilibrium dissociation constant for filipin-cholesterol interaction was approximately 74-fold larger in intact than in protease-treated VS virions. The initial rate of association of filipin with cholesterol in intact virions was slower than that in protease-treated particles. The fluidity of lipids in VS viral membranes, as probed by a stearic acid derivative spin label, was markedly reduced when either intact or protease-treated virions were treated with filipin.

Amphotericin B↗