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At least 37 records · Page 2Linked to original sources
PubMed1977

Role of cell surface carbohydrates and proteins in cell behavior: studies on the biochemical reversion of an N-acetylglucosamine-deficient fibroblast mutant.

AD6, a mutant derived from 3T3 Balb/c cells, is characterized by low adhesion to substratum, round shape, increase in surface microvilli, increase in agglutinability by concanavalin A, and loss of directional motility. These properties are often observed in transformed cells. However, the mutant has normal growth properties and anchorage-dependence of growth, and it does not form tumors. In AD6, the biosynthesis of complex carbohydrates and glycoproteins is impaired because of a block in the acetylation of GlcN-6-P. This defect is responsible for all the surface alterations because feeding of GlcNAc to AD6 cells corrects the defects in the synthesis of complex carbohydrates and the exposure of glycoproteins at the outer surface of the plasma membrane. Parallel to this biochemical reversion, there is full restoration of the altered biological properties. In contrast, GlcNAc has no effect on the morphologic features of two lines of transformed cells. Our results suggest that the carbohydrate portion of cell surface proteins has an important role in adhesion and related aspects of cell behavior. The fact that a defined alteration of the cell surface induces many properties often encountered in transformed cells, without affecting control of cell division, strongly suggests that these alterations in properties are not sufficient to account for the loss of growth regulation.

Acetylglucosamine↗
PubMed1975

Myxospore induction in a nondispersed growing mutant of Myxococcus xanthus.

Myxococcus xanthus RB5, a rough-colony-forming, nondispersed growing mutant of strain FBt, forms macroscopic, multicellular masses of radially oriented cells in shake cultures. The cells appear to be held together by slime fibrils. Physical and enzymatic methods to disrupt the spheres were unsuccessful as were attempts to isolate dispersed growing mutants. During incubation of the spheres in starvation medium, the cells within convert to myxospores, indistinguishable from those formed in fruiting bodies. Myxospores were also induced in artifically constructed, dense masses of cells of a nonmotile strain.

Agar↗
PubMed1976

Effect of polymyxin on the ultrastructure of the outer membrane of wild-type and polymyxin-resistant strain of Salmonella.

The effect of polymyxin on two sets of Salmonella mutants was studied by thin-section and scanning electron microscopy. Polymyxin (in increasing concentrations, starting just below bactericidal effect) caused the appearance of the previously described rodlike projections on the cell surface of wild-type (smooth, polymyxin-sensitive) bacteria. These projections seemed to involve the outer membrane of the cell wall. In rough mutants, which are deficient in lipopolysaccharide, the projections were much smaller and flat. Higher concentrations of polymyxin were required to produce morphological effects in polyxmin-resistant mutants of both smooth and rough forms. Furthermore, in these mutants polymyxin caused vesicle-like bulging of the total outer membrane quite different in appearance from the rodlike projections of the wild type.

Cell Membrane↗
PubMed2026

LDLR Variant Classification Through Activity-Normalized Prime Editing Screening.

BACKGROUND: Inherited variants in the LDL (low-density lipoprotein) receptor (LDLR) gene are the most common cause of familial hypercholesterolemia, significantly increasing coronary artery disease risk. Early identification of pathogenic LDLR variants enables prompt lipid-lowering therapy and cascade testing of at-risk relatives; however, most LDLR variants observed in the population have uncertain or absent clinical classifications, leaving many patients without actionable information. METHODS: We developed the first activity-normalized prime editing screening pipeline to measure the impact of 5184 LDLR coding variants on LDL-cholesterol (LDL-C) uptake. Each prime editing guide RNA is paired with a genotypic outcome reporter to correct for variable editing efficiency, overcoming a key limitation of previous pooled genome editing screens. A statistical framework further improves variant effect estimates by jointly analyzing all missense variants at each amino acid position. RESULTS: We show that prime editing of the reporter construct correlates with endogenous variant installation frequency, validating the activity normalization approach. The resulting scores capture a continuous spectrum of functional effects, robustly separate pathogenic versus benign ClinVar variants, and show concordance with LDL-C levels in UK Biobank participants. We calibrate functional evidence strengths to the ACMG/AMP variant interpretation framework, enabling integration into a clinical variant classification workflow. By combining functional, computational, population, and contextual evidence, 322 of 434 LDLR variants currently classified as variants of uncertain significance, conflicting, or absent from ClinVar appear to meet evidence thresholds for reclassification and can be prioritized for expert review, substantially expanding the pool of actionable variant classifications. The screen also reveals a cluster of gain-of-function variants in LDLR class A repeat 5, at least some of which enhance LDL-C uptake through increased apolipoprotein B interaction, with implications for therapeutic genome editing. Last, prime editing uniquely detects splice-altering coding variants missed by cDNA-based screens and pathogenicity predictors, revealing an advantage of endogenous variant installation. CONCLUSIONS: Altogether, activity-normalized prime editing provides a scalable framework for LDLR variant classification that substantially expands the proportion of variants with evidence for genetic diagnosis and reveals novel biology with therapeutic relevance.

CRISPR screening↗
PubMed1978

Comparative susceptibility to amylases of starch granules of several single endosperm mutants representative of floury-opaque, starch-deficient, and modified starch types and their double-mutant combinations with opaque-2 in four inbred lines of maize.

Starch granules were prepared from kernels of eight single endosperm mutants, brittle-1, (bt1), brittle-2 (bt2), floury-1, floury-2, soft starch, opaque-1 (o1), shrunken-2 (sh2), and sugary-2 (su2), and their double-mutant combinations with opaque-2 (o2) of four inbred lines of maize (Zea mays L.), B37, C103, Oh43 and W64A. We compared the susceptibility of various starch granules to Rhizopus glucoamylase and pancreatin. Starch granules of the su2 and su2o2 mutants were digested by amylases much faster than those of the normal counterparts. Starch granules of the bt1, bt2, o1 and sh2 mutants tended to be digested by amylases faster than those of normal maize. Starch granules of double-mutant combinations with the o2 gene were, in general, digested to an extent very comparable to their respective non-opaque single mutant counterparts in each of their four inbred backgrounds. We followed the relative digestion of starch granules by using scanning electron microscopy. Starch granules of endosperm mutants susceptible to amylases showed numerous pin holes on the surface layer and the pores penetrated into the inner layers of the granules during the attack by amylases. In some of the granules the inner portion, which appeared terraced or step-shaped, could be seen. This may be indicative of layered internal structures of the granules.

Amylases↗
PubMed1979

Comparative susceptibility of starch granules of double- and triple-mutants containing amylose-extender, waxy, sugary-1, sugary-2 and dull genes of maize inbred OH43 (Zea mays L.) to amylase.

Starch granules were prepared from 14 double- and 26 triple-mutants containing amylose-extender (ae), 14 double- and 18 triple-mutants containing waxy (wx), 15 double- and 20 triple-mutants containing sugary-1 (su1), 13 double- and 23 triple-mutants containing sugary-2 (su2), and 14 double- and 19 triple-mutants containing dull (du) of maize inbred Oh43 (Zea mays L.). The relative susceptibilities of these starch granules to fungal glucoamylase were determined and the starch granules were examined by scanning electron microscopy. A commercial normal maize starch was used as a control. Starch granules of the double- and triple-mutants containing su1 and su2 were digested two to eight times faster than normal. The ae gene reduced susceptibility and seems to be epistatic to su1 and su2. Starch granules of the double- and triple-mutants containing wx were digested about two times faster than normal and those containing shrunken-2 (sh2) were digested 1.2 to eight times faster than normal. Starch granules of triple-mutant combinations with opaque-2 (o2) showed digestion properties which were comparable to those of their respective monopaque double-mutant counterpart.

Glucan 1,4-alpha-Glucosidase↗
PubMed1978

Regional differences in the morphology and motility of mesodermal cells from the early wing-bud of normal and talpid3 mutant chick embryos.

A method of culturing has been employed to compare the properties of cells migrating from small mesodermal explants taken from different regions of normal and mutant limb-buds at different stages of development. An analysis by time-lapse cinematography of the morphology and mobility of cells migrating from explants defines a distal region within the limb-bud where these properties are distinct from those of cells from more proximal regions. In the normal wing-bud distal cells subjacent to the apical ectodermal ridge possess a characteristic multipolar morphology and translocate slowly in vitro. Cells from more proximal regions tend to be bipolar and translocate more rapidly. Distal and proximal cells also probably differ in their adhesive strengths. In the mutant, talpid3, distal and proximal cells do not differ in the above properties and cells from all regions of the limb-bud are multipolar, translocate slowly and are more adhesive than normal cells. A study of light micrographs and scanning electron micrographs suggests that these regional differences are found in the limb-bud in vivo and are not merely an effect produced by the in vitro culturing system.

Animals↗
PubMed1976

Characterization of a temperature-sensitive mutant of Saccharomyces cerevisiae that undergoes uncontrolled protein synthesis.

A mutant of Saccharomyces cerevisiae, DW137, isolated after treatment of a wild-type strain with ICR-170. The mutant was respiration-deficient and showed abnormal cell division when grown at 30 degrees C. In addition, the mutant was temperature-sensitive and underwent lysis when grown at 37 degrees C. Random spore analysis, induced reversion profiles, and complementation analysis indicated that the abnormal phenotypes were under the control of a single recessive mutation caused by a base-pair substitution in a nuclear gene. Macromolecular analysis of the mutant at permissive and restrictive temperatures showed that at restrictive temperatures the mutant cannot synthesize DNA. Surprisingly, at restrictive temperatures, protein synthesis in the mutant continued at a rate greater than that observed at permissive temperatures. Cell death and lysis of the mutant could be prevented by treatment of cultures with cycloheximide, an inhibitor of protein synthesis. The data suggest that the abnormally high rate of protein synthesis and the inability to synthesize DNA are jointly responsible for death of the cells, and most probably play and integrating role in the incipient cell lysis.

Cell Division↗
PubMed2025

Structural and thermodynamic impact of oncogenic mutations on the nucleosome core particle.

The nucleosome core particle is essential for chromatin structure and function, serving as the fundamental unit of eukaryotic chromatin. Oncogenic mutations in core histones disrupt chromatin dynamics, altering DNA repair and transcription processes. Here, we investigate the molecular consequences of two mutations-H2BE76K and H4R92T-using 36 μs of all-atom molecular dynamics simulations and experimental biophysical assays. These mutations destabilize the H2B-H4 interface by disrupting critical salt bridges and hydrogen bonds, reducing binding free energy at this interface. Principal-component analysis reveals altered helix conformations and increased interhelical distances in mutant systems. Thermal stability assays and differential scanning calorimetry confirm that these mutations lower the dimer dissociation temperature and reduce enthalpy compared with the wild-type. Taken together, our results elucidate how these mutations compromise nucleosome stability and propose mechanisms through which they could modulate chromatin accessibility and gene dysregulation in cancer.

Nucleosomes↗
PubMed1976

Ultrastructure of melanin formation in Verticillium dahliae with (+)-scytalone as a biosynthetic intermediate.

Transmission and scanning electron microscopy showed that melanin of wild-type Verticillium dahliae occurred as granules in microsclerotial cell walls and in a fibrillar network encapsulating the walls. An albino microsclerotial mutant and a brown microsclerotial mutant of V. dahliae did not form melanin granules. When albino microsclerotia were treated with (+)-scytalone (a metabolite that the brown mutant accumulates), they formed melanin granules and turned black. These granules were similar in appearance and distribution to those in the wild type. Melanin granules of the wild-type isolate and the scytalone-treated albino mutant were formed at a maximum rate in microsclerotia from 5- to 8-day-old cultures. These observations suggest that scytalone is a natural intermediate of melanin synthesis in V. dahliae.

Cell Wall↗
PubMed1979

A mutant of Tetrahymena thermophila with a partial mirror-image duplication of cell surface pattern. I. Analysis of the phenotype.

Cells of a mutant clone, CU-127, of Tetrahymena thermophila (formerly T. pyriformis, syngen 1) manifest three anatomical abnormalities. First, the stable number of ciliary meridians is 21-25, above the usual number (17-21) in this species. Second, up to 30% of the cells have two oral apparatuses (OAs), one normal and the other abnormal. Third, more than one-half of the cells possess two distinct sets of contractile vacuole pores (CVPs). In some living cells two contractile vacuoles are seen. These abnormalities have persisted unchanged during more than 500 generations of vegetative propagation, and are similarly expressed in subclones. The normal and abnormal OAs are topographically segregated, with normal OAs developing along the "primary oral axis" and abnormal OAs developing along a "secondary oral axis" that is situated 170 degrees of the cell circumference to the cell's right of the primary oral axis. CVPs always appear within this 170 degree arc and never within the complementary 190 degrees arc to the left of the primary oral axis. A unique feature of the CU-127 clone is the commonly expressed mirror image reversal of the structural pattern of OAs that develop along the secondary oral axis. The primordia of such OAs initially appear (as usual) to the cell's left of a ciliary meridian, but as membranelles develop the frequently come to be oriented in a mirror image of the normal pattern, and an undulating membrane sometimes develops on the wrong (left) side of the oral primordium. When two sets of CVPs are formed, their average positions are roughly equidistant with respect to the two oral axes, with the two sets located 50-60 degrees to the right and left respectively of the primary and secondary oral axis. Such cells are thus bilaterally symmetrical about a plane defined by the central longitudinal axis and the halfway point between the two CVP sets (see Fig. 25). This plane bisects the cell into a normal and a "reversed" half-cell. However, only oral asymmetry and large-scale CVP positioning are subject to such reversal; all ciliary meridians remain of normal asymmetry and all CVPs are situated on the left side of CVP meridians. The fact that major aspects of large-scale cellular organization can be reversed while the "fine-positioning" associated with the ciliary meridians remains normal indicates that the two aspects of cell organization are distinct.

Animals↗
PubMed1978

Facial development in the mouse; a comparison between normal and mutant (amputated) mouse embryos.

This work extends previous investigations into cell interactions involved in specific morphogenetic events during the development of normal and mutant (amputated) mouse embryos. In the mutant mesenchyme, cells tend to clump together and form far more extensive areas of cell contact than are found in normal mesenchyme. This is confirmed for mutant facial mesenchyme. Facial outgrowth in the mutant is retarded. The first stages of this abnormality can be seen in the naso-frontal region at 10.5 days after conception. Neither the quantity of cells contributing to naso-frontal outgrowth nor cell proliferation in the naso-frontal region differ from normal in the mutant, and these factors can be eliminated as causes of the anomaly. Instead, cell clumping and increased areas of contact in the mutant arrest the normal expansion of the naso-frontal mesenchyme which presumably occurs as a result of increased secretion of intercellular matrix material between 9.5 and 10.5 days of development. The importance of this early expansion phase for facial development has not previously been recognized.

Animals↗
PubMed2024

Comparative Studies on Bulky DNA Damage Binding by Nucleotide Excision Repair Proteins Using Surface Plasmon Resonance, Differential Scanning Fluorometry, and DNase I Footprinting.

Nucleotide excision repair is a crucial cellular mechanism that ensures genomic stability, thereby preventing mutations that can lead to cancer. The human XPC and its yeast ortholog Rad4 protein complexes are central to this process and were the focus of the study. We used surface plasmon resonance and differential scanning fluorimetry to study the binding characteristics of XPC and Rad4 when bound to the bulky cluster di-FAAF-containing 55-mer duplex DNA. Our findings revealed that XPC binds 10 times more significant affinity to control and di-FAAF-modified DNA than Rad4 with greater protein-DNA interactions. Differential scanning fluorimetry indicates that Rad4 causes comparatively more significant conformational changes upon complexation with the damaged DNA. We conducted DNase I footprinting of the Rad4/DNA complex for the first time by determining the regions protected from DNase I digestion. The DNA at the lesion is entirely resistant to digestion by DNase I in the absence of Rad4 several nucleotides to the 3'-side of the first FAAF lesion. The lack of DNase I cleavage at the lesions did not change upon adding Rad4. However, in the presence of Rad4, a footprint is observed on the 7-nucleotide region (5'-TGGTGAT-3') of the complementary strand to the 3' side of the lesion.

Surface Plasmon Resonance↗
PubMed2026

Sexual selection purges mutation load, but not overall genetic diversity, decreasing vulnerability to extinction.

Theory suggests sexual selection will enhance population viability by purging deleterious alleles. However, direct genomic evidence for this fundamental idea is scarce and contradictory. We combined long-term experimental evolution with whole-genome resequencing to directly test how sexual selection affects mutation load, genomic divergence, and extinction risk in small populations (maximum Ne = 40) of Tribolium castaneum. After 156 generations, populations evolving under strong sexual selection carried substantially fewer deleterious alleles than populations under weak sexual selection, based on both individual-level estimates of missense and nonsense variants and population-level Rxy analyses, indicating more efficient purging of deleterious alleles. In contrast, nucleotide diversity and runs of homozygosity were similar across treatments, indicating that purging acted most strongly on deleterious variation, and that reduced mutation load in these small populations under strong sexual selection was not explained by demographic effects. Importantly, population-level mutation load estimates best explained extinction risk under inbreeding, directly linking sexual selection to purging and population viability. Genome scans of high and low sexual selection populations revealed peaks of divergence, which included genes involved in courtship, sex discrimination, and seminal fluid proteins. Our results provide direct genomic evidence that sexual selection can reduce mutation load without eroding standing genetic diversity and thus adaptive potential, while driving adaptive divergence in reproductive traits. This beneficial purging may help explain the widespread prevalence of sexual reproduction in nature despite inherent costs and have important ramifications as to how we manage populations of conservation concern.

Animals↗
PubMed2026

EscaPRRS-ORF5: a structure-aware evolutionary framework for prioritizing immune escape-prone variants in porcine reproductive and respiratory syndrome virus.

MOTIVATION: Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is a rapidly evolving RNA virus causing significant economic losses, posing a formidable challenge to vaccine efficacy due to its high mutational variability and immune escape. As the viral mutants evolve, their ability to sustain in population is driven by a range of host biology factors such as receptor binding, fusion, and uncoating. Existing tools that predict viral fitness and escape propensities rely heavily on extensive, up-to-date sequence data and lack integration of biochemical host interactions, limiting mechanistic understanding of the mutational landscape. We introduce Esca, a sequence-only toolchain framework that identifies immune escape-prone residues by exhaustively scanning each residue position for all amino acid substitutions using a Bayesian Variational Autoencoder (VAE) trained on protein language model embeddings. We demonstrate Esca on the GP5(ORF5) glycoprotein of PRRSV (EscaPRRS-ORF5) by training on ESM-2 embeddings of 32 146 GP5 sequences (2015-2022) spanning 140 sub-lineages. RESULTS: Despite being trained only on GP5 sequence data, EscaPRRS-ORF5 recovered 85.7% of the surface-exposed receptor binding interfaces as escape-prone regions. We use a mutation-sensitive fitness scoring scheme that goes beyond Hamming distances, to predict antibody escape tendencies, supporting surveillance of (re) emerging PRRSV variants. We do not claim that ORF5 alone captures PRRSV evolution or serves as a surveillance endpoint; rather, Esca offers a scalable path toward whole-genome, structure-aware surveillance. AVAILABILITY AND IMPLEMENTATION: EscaPRRS-ORF5 is freely available at https://doi.org/10.6084/m9.figshare.32661033 with an interactive Colab notebook at https://colab.research.google.com/drive/1TEgzAhPwvNAZ01VXeJbIFibfri2jnDA5? usp=sharing.

Porcine respiratory and reproductive syndrome viru↗
PubMed2026

SCAN: A sample-to-answer cross-priming isothermal assay for on-site virus detection with RT-qPCR sensitivity and genomically similar virus differentiation specificity.

Genomically similar viruses often differ in pathogenicity and host tropism due to specific mutations, and failure to distinguish them risks misdiagnosis and ineffective control. Molecular methods can differentiate such viruses but require laboratory settings and skilled personnel, while field-deployable immunological methods suffer from cross-reactivity. To address this challenge, we developed SCAN (Sample-to-answer Cross-priming isothermal amplification Assay with Nucleic acid strip), a general framework for on-site detection of genomically similar viruses. Comparative bioinformatics of isolation and sequencing data identifies key conserved differential determinants for primer design, ensuring specificity and reducing non-specific amplification. A one-tube cross-priming isothermal amplification (CPA) enables rapid target amplification without thermal cycling, and the products are visually detected on a nucleic acid strip. All steps are integrated into a handheld, lightweight device (9.9&#x202f;&#xd7;&#x202f;4.4&#x202f;&#xd7;&#x202f;3.3&#x202f;cm, <200&#x202f;g) that also prevents aerosol contamination. Using transmissible gastroenteritis virus (TGEV) and porcine respiratory coronavirus (PRCV), the latter a natural mutant of TGEV, as a model, SCAN achieves a detection limit of 102 copies/&#x3bc;L with sensitivity comparable to RT-qPCR and supports sample-to-answer testing within 80&#x202f;min and simple operations. With verified high sensitivity, specificity, and accuracy, as well as field usability, SCAN provides a generalizable route for developing point-of-care tests (PoCT) that require precise field differentiation of closely related pathogens.

Cross-priming isothermal amplification↗