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Results for “cell state transition”

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At least 19 recordsLinked to original sources
PubMed1992

Identification of a transitional cell state in the developmental pathway to carrot somatic embryogenesis.

We have located a novel carbohydrate epitope in the cell walls of certain single cells in embryogenic, but not in non-embryogenic, suspension cultures of carrot. Expression of this epitope, recognized by the mAb JIM8, is regulated during initiation, proliferation, and prolonged growth of suspension cultures such that changes in the abundance of JIM8-reactive cells always precede equivalent changes in embryogenic potential. Therefore, a direct correlation exists between the presence of the JIM8-reactive cell wall epitope and somatic embryo formation. The JIM8-reactive cell wall epitope is expressed in the cell walls of three types of single cells and one type of cell cluster. One of the single cell types seems able to follow one of two phytohormone-controlled developmental pathways, either a cell elongation pathway that eventually leads to cell death, or a cell division pathway that gives rise to proembryogenic masses. We demonstrate that all JIM8-reactive cell types in embryogenic carrot suspension cultures are developmentally related, and that the switch by one of them to somatic embryogenesis is accompanied by the immediate dissipation of the JIM8-reactive cell wall epitope. The cell wall carbohydrate epitope recognized by JIM8 therefore represents a cell wall marker for a very early transitional cell state in the developmental pathway to carrot somatic embryogenesis.

Antibodies, Monoclonal↗
PubMed2026

Identifying fate-determining transcription factors with single-cell omics.

Single-cell sequencing enables the systematic discovery of cell fate-determining transcription factors (TFs), or key TFs, that define cellular identity or drive cell state transitions. A wide range of computational methods have been developed for this goal, but they differ substantially in the input data and the biological questions they address. In this article, we systematically review computational approaches for key TF identification and organize them from three perspectives: whether they identify TFs defining cell state identity or driving state transitions, whether transitions are modeled as discrete or continuous processes, and whether TFs act individually or combinatorially. We summarize key features and application scenarios of relevant methods to guide tool selection and discuss emerging trends in this field toward programmable and active control of cell fate.

Transcription Factors↗
PubMedDate not supplied

Spontaneously active cells induce state transitions in a model of olfactory cortex.

The existence of neurons with intrinsic oscillations does not in itself explain the synchronization of local populations of neurons, but it is likely to pace population rhythms when the neurons are suitably coupled by chemical and/or electrical synapses. In the present study, we have investigated the role of spontaneously active cells as noisy or pacemaker units in setting global oscillations in a three-layered cortical model. The presence of a small number of noisy (spontaneously active) units induce oscillations at the network level in the range of the gamma rhythm. The number of noisy units in the network and their type (excitatory or inhibitory or excitatory and inhibitory together) determines the emergence of regular oscillations or aperiodic (chaotic) behaviour. It also determines the onset of the global behaviour. On replacing a noisy unit by a pacemaker unit, similar gamma oscillations were generated. With both noisy and pacemaker units, we found that certain characteristics of the spontaneous activity determine the delay period for the onset of global activity. Preliminary studies have been carried out with spontaneously active units having a chaotic dynamics but the results are much similar to that with a noisy burst. Different functional roles have been suggested for cortical oscillations, such as determining global functional states and specifying connectivity during development. Oscillations at different frequency bands, in particular in the gamma band (around 40 Hz), have also been associated with memory and attention. The presence of spontaneously active neurons, either with noisy or oscillatory activity, could be responsible for global oscillations in the absence of external stimuli in certain cortical areas in the mature brain.

Models, Neurological↗
PubMed2025

Trajectory inference from single-cell genomics data with a process time model.

Single-cell transcriptomics experiments provide gene expression snapshots of heterogeneous cell populations across cell states. These snapshots have been used to infer trajectories and dynamic information even without intensive, time-series data by ordering cells according to gene expression similarity. However, while single-cell snapshots sometimes offer valuable insights into dynamic processes, current methods for ordering cells are limited by descriptive notions of "pseudotime" that lack intrinsic physical meaning. Instead of pseudotime, we propose inference of "process time" via a principled modeling approach to formulating trajectories and inferring latent variables corresponding to timing of cells subject to a biophysical process. Our implementation of this approach, called Chronocell, provides a biophysical formulation of trajectories built on cell state transitions. The Chronocell model is identifiable, making parameter inference meaningful. Furthermore, Chronocell can interpolate between trajectory inference, when cell states lie on a continuum, and clustering, when cells cluster into discrete states. By using a variety of datasets ranging from cluster-like to continuous, we show that Chronocell enables us to assess the suitability of datasets and reveals distinct cellular distributions along process time that are consistent with biological process times. We also compare our parameter estimates of degradation rates to those derived from metabolic labeling datasets, thereby showcasing the biophysical utility of Chronocell. Nevertheless, based on performance characterization on simulations, we find that process time inference can be challenging, highlighting the importance of dataset quality and careful model assessment.

Single-Cell Analysis↗
PubMed2025

Deciphering Cell Fate and Clonal Dynamics via Integrative Single-Cell Lineage Modeling.

Through natural or synthetic lineage barcodes, single-cell technologies now enable the joint measurement of molecular states and clonal identities, providing an unprecedented opportunity to study cell fate and dynamics. Yet, most computational methods for inferring cell development and differentiation rely exclusively on transcriptional similarity, overlooking the lineage information encoded by lineage barcodes. This limitation is exemplified by T cells, where subtle transcriptional differences mark divergent fates with distinct biological activity. Single-cell RNA and matched TCR sequencing is now ubiquitous in the analysis of clinical samples, where the TCR sequence provides an endogenous clonal barcode and could reveal clonal T cell responses. We present Clonotrace, a computational framework that jointly models gene expression and clonotype information to infer cell state transitions and fate biases with higher fidelity. While motivated by challenges in analyzing T cell populations, especially in the tumor microenvironment and immunotherapy settings, Clonotrace is broadly applicable to any lineage-barcoded single-cell dataset. Across diverse systems including T cells, hematopoietic differentiation, and cancer therapy resistance models, Clonotrace reveals differentiation hierarchies, distinguishes unipotent from multipotent states, and identifies candidate fate-determining genes driving lineage commitment.

Journal Article↗
PubMed2025

Deciphering Cell Fate and Clonal Dynamics via Integrative Single-Cell Lineage Modeling.

Through natural or synthetic lineage barcodes, single-cell technologies now enable the joint measurement of molecular states and clonal identities, providing an unprecedented opportunity to study cell fate and dynamics. Yet, most computational methods for inferring cell development and differentiation rely exclusively on transcriptional similarity, overlooking the lineage information encoded by lineage barcodes. This limitation is exemplified by T cells, where subtle transcriptional differences mark divergent fates with distinct biological activity. Single-cell RNA and matched TCR sequencing is now ubiquitous in the analysis of clinical samples, where the TCR sequence provides an endogenous clonal barcode and could reveal clonal T cell responses. We present Clonotrace, a computational framework that jointly models gene expression and clonotype information to infer cell state transitions and fate biases with higher fidelity. While motivated by challenges in analyzing T cell populations, especially in the tumor microenvironment and immunotherapy settings, Clonotrace is broadly applicable to any lineage-barcoded single-cell dataset. Across diverse systems including T cells, hematopoietic differentiation, and cancer therapy resistance models, Clonotrace reveals differentiation hierarchies, distinguishes unipotent from multipotent states, and identifies candidate fate-determining genes driving lineage commitment.

Journal Article↗
PubMed2026

Spatial proximity sequencing maps developmental dynamics in the germinal center.

Spatial profiling of proteins and protein interactions facilitates understanding of cell functions within tissues and is essential for studies in signaling, immunity, and cancer. We present spatial proximity sequencing (Sprox-seq) for simultaneous profiling of surface proteins, protein complexes, and mRNAs, recording the tissue location of each molecule. Sprox-seq profiled 32 proteins, 528 pairwise interactions, and thousands of mRNAs with spatial resolution across human tonsils and germinal centers. Mapping tissue-wide protein interactions recapitulated RNA-defined tissue architecture but also revealed higher interaction complexity in the light zone. Protein-interaction trajectories uncovered a B cell state transition distinct from that inferred by RNA. Integrated protein-complex and mRNA analysis related spatially enriched complexes with mitotic pathways. Sprox-seq captured cell-cell interactions, such as B cell-follicular dendritic cell interactions mediated by the receptor complex VLA-4-VCAM1. Sprox-seq provides a spatially resolved multi-modal view of cell states and an integrated study of protein and cellular interactions across tissues.

Humans↗
PubMed2025

Cell-type-specific defense priming and NHP-dependent systemic immunity against Pectobacterium in Chinese cabbage.

Defense priming is an effective strategy for mounting the defensive capacity of plants. Primed plants undergo minimal changes, enabling rapid, robust responses to subsequent pathogen attack. The cell-type-specific mechanisms underlying priming and systemic immunity remain unclear. Using single-nucleus RNA sequencing (snRNA-seq), we reveal how primed Chinese cabbage coordinates N-hydroxypipecolic acid (NHP)-dependent systemic immunity against Pectobacterium carotovorum. NHP accumulates as a phloem-mobile priming signal. snRNA-seq identified a priming-specific epidermal cell state transition and transcriptional cascade: BrWRKY18-1 activates BrWRKY33-1 expression during priming, initiating NHP-dependent systemic immunity. At post-challenge primed state, pathogenesis-related genes (PRs), such as BrPR3, BrPR4-1, and BrPR4-2, are predominantly expressed in systemic tissues to inhibit infection. Notably, the functionality of these PR genes in immunity necessitates their expression in all cells to effectively enhance defensive resistance. This NHP-transcription factor-PR axis couples mobile signaling to systemic immunity, elucidating cell-type-specific defense priming.

Plant Immunity↗
PubMed1985

Effects of the free radical generator paraquat on differentiation, superoxide dismutase, glutathione and inorganic peroxides in microplasmodia of Physarum polycephalum.

The herbicide paraquat was used to investigate the effects of oxidative stress on the spherulation of Physarum polycephalum microplasmodia. The responses of a white non-differentiating strain of Physarum were compared with those of a common yellow strain that readily spherulates in salts-only starvation medium. The addition of paraquat to the salts medium increased the specific activity of superoxide dismutase in both strains; it also induced an increase in the intracellular inorganic peroxide concentration in both strains. Glutathione concentration was higher in the paraquat-treated yellow strain than in the controls. Paraquat had no effect on glutathione concentration in white microplasmodia. Paraquat accelerated spherulation in yellow microplasmodia. The white microplasmodia responded to the herbicide by cleaving into structures similar to immature spherules; however, these structures were not viable. The results of this study support the hypothesis that free radicals are involved in cell state transitions.

Free Radicals↗
PubMed2000

Excitation energy transfer from phycobilisomes to photosystems: a phenomenon associated with the temporal separation of photosynthesis and nitrogen fixation in a cyanobacterium, Plectonema boryanum.

Plectonema boryanum shows temporal separation of photosynthesis and nitrogen fixation under diazotrophic conditions. Low temperature fluorescence studies have shown that in vivo the nitrogen fixing and photosynthesizing cells are adapted to 'state 2' and 'state 1', respectively. During nitrogen fixation phycobilisomes seem to transfer excitation energy to photosystem I whereas during oxygenic photosynthesis the energy is transferred to photosystem II. The state 2 adapted N-phase cells failed to undergo transition to state 1 while P-phase cells exhibited state 1 to state 2 transition. The nitrogen fixing cells showed a decreased level ofpsbC transcript, lack of CP47 in thylakoid membrane, and presence of the F685 peak but absence of the F695 peak in 77 K fluorescence spectra. These results suggest that the metabolic and molecular changes associated with nitrogen fixation may favor direct energy transfer from the phycobilisomes to photosystem I. This should help the organism to achieve low photosystem II and high photosystem I activity to set temporal separation of nitrogen fixation and photosynthesis for photoautotrophic growth under diazotrophic conditions.

Bacterial Proteins↗
PubMed2000

Excitation energy transfer from phycobilisomes to photosystems: a phenomenon associated with the temporal separation of photosynthesis and nitrogen fixation in a cyanobacterium, Plectonema boryanum(1).

Plectonema boryanum shows temporal separation of photosynthesis and nitrogen fixation under diazotrophic conditions. Low temperature fluorescence studies have shown that in vivo the nitrogen fixing and photosynthesizing cells are adapted to 'state 2' and 'state 1', respectively. During nitrogen fixation phycobilisomes seem to transfer excitation energy to photosystem I whereas during oxygenic photosynthesis the energy is transferred to photosystem II. The state 2 adapted N-phase cells failed to undergo transition to state 1 while P-phase cells exhibited state 1 to state 2 transition. The nitrogen fixing cells showed a decreased level of psbC transcript, lack of CP47 in thylakoid membrane, and presence of the F685 peak but absence of the F695 peak in 77 K fluorescence spectra. These results suggest that the metabolic and molecular changes associated with nitrogen fixation may favor direct energy transfer from the phycobilisomes to photosystem I. This should help the organism to achieve low photosystem II and high photosystem I activity to set temporal separation of nitrogen fixation and photosynthesis for photoautotrophic growth under diazotrophic conditions.

Journal Article↗
PubMed2003

Magnetic field exposure during gestation: pineal and cerebral cortex serotonin in the rat.

Extremely low frequency (ELF) magnetic fields seem to have a reproducible influence on cells in transitional states, such as cells during the embryonic and early postnatal periods. Intense and continuous serotonergic synaptic growth is present during the first 2 weeks of postnatal development, paralleled by 5-HT content in the brain, so, the effect of ELF on 5-HT content in the cerebral cortex and pineal gland was determined in growing rats exposed during pregnancy, and in normal controls. The results showed a significant 5-HT increase at birth, 15 and 21 days, in the cerebral cortex. No differences were found in the pineal gland. These short MF exposures had a long term effect on cerebral cortex 5-HT, possibly starting since the fetal period. The relevance of the present findings are discussed as related to the serotonin trophic role on the brain cortex.

Age Factors↗
PubMed2001

Intracellular pH homeostasis during cell-cycle progression and growth state transition in Schizosaccharomyces pombe.

Accurate measurement of intracellular pH in unperturbed cells is fraught with difficulty. Nevertheless, using a variety of methods, intracellular pH oscillations have been reported to play a regulatory role in the control of the cell cycle in several eukaryotic systems. Here, we examine pH homeostasis in Schizosaccharomyces pombe using a non-perturbing ratiometric pH sensitive GFP reporter. This method allows for accurate intracellular pH measurements in living, entirely undisturbed, logarithmically growing cells. In addition, the use of a flow cell allows internal pH to be monitored in real time during nutritional, or growth state transition. We can find no evidence for cell-cycle-related changes in intracellular pH. By contrast, all data are consistent with a very tight homeostatic regulation of intracellular pH near 7.3 at all points in the cell cycle. Interestingly, pH set point changes are associated with growth state. Spores, as well as vegetative cells starved of either nitrogen, or a carbon source, show a marked reduction in their internal pH compared with logarithmically growing vegetative cells. However, in both cases, homeostatic regulation is maintained.

Cell Cycle↗
PubMed1992

Glucose sensing of individual pancreatic beta-cells involves transitions between steady-state and oscillatory cytoplasmic Ca2+.

Glucose stimulation of individual pancreatic beta-cells is associated with a rise of the cytoplasmic Ca2+ concentration ([Ca2+]i) manifested either as large amplitude oscillations (0.2-0.5/min) or as a sustained increase. Determinants for the transitions between the basal and the two stimulated states have now been studied using dual-wavelength fluorometric measurements on individual ob/ob mouse beta-cells loaded with the Ca2+ indicator Fura-2. The transition from the basal state to large amplitude oscillations was induced by raising the glucose concentration to 7 mM or above. The frequencies and shapes of the [Ca2+]i cycles remained largely unaffected when raising glucose as high as 40 mM. However, in some cells the oscillatory pattern was transformed into a sustained increase of [Ca2+]i at high glucose concentrations. Although the peak values for the oscillations exceeded the steady-state increase, the time average [Ca2+]i was higher during the latter phase. Both types of glucose-induced transitions were facilitated by the presence of 1-100 nM glucagon. Protein kinase C activation by 10 nM of the phorbol ester TPA resulted in a transformation of the glucose-induced oscillations into a sustained increase of [Ca2+]i but the levels reached were considerably lower than obtained with glucose alone. It is concluded that the glucose sensing of the individual beta-cell is based on sudden transitions between steady-state and oscillating cytoplasmic Ca2+. It is these transitions rather than alterations of the oscillatory characteristics which determine the average [Ca2+]i regulating insulin release.

Animals↗
PubMed1977

Inhibition of ribonucleases by ribonucleotides and transition state analogs in cell-free extracts from Ehrlich ascites tumor cells.

We investigated the ribonucleolytic breakdown of poly(U), poly(A), RNA trascribed from calf thymus DNA with E. coli RNA polymerase, ribosomal RNA, tRNA and mengovirus RNA by an enzyme fraction obrained from a postribosomal supernatant of Ehrlich ascites tumor cells. The single-stranded homopolyribonucleotides are preferentially degraded by the enzyme fraction with the production of ribonucleoside 5'-monophosphates. The RNase activity is completely dependent on the presence of Mg2+ ions and is highest at Mg2+ and K+ concentrations optimal for cell-free protein synthesis. Ribonucleoside 5'-monophosphates, ribonucleoside 2'(3')-monophosphates, ribonucleoside 2'(3'),5'-bisphosphates and transition state analogs consisting of vanadyl sulfate and either ribonucleosides or ribonucleoside 5'-monophosphates in a molar ratio 1:1 inhibit the ribonucleolytic activity of the enzyme fraction. The ribonucleoside 2'(3'),5'-bisphosphates and the transition state analogs are the most effective inhibitors. However, only in the presence of ribonucleoside 2'(3'),5'-bisphosphates a concomitant stimulation by 50 to 60% of poly(U)-directed polyphenylalanine synthesis is observed; all the other RNase inhibitors tested also inhibit polypeptide synthesis. The results of preliminary experiments show that poly(U) and ribonucleoside 2'(3'),5'-bisphosphates are well suited as ligands for affinity chromatography of ribonucleases from Ehrlich ascites tumor cells.

Animals↗
PubMed1986

The kinetics of in vivo state transitions in mesophyll and guard cell chloroplasts monitored by 77 k fluorescence emission spectra.

Fluorescence emission spectral peaks at 685, 695 and 730 nanometers (F685, F695, and F730) were recorded 77 K from diluted leaf tissue and epidermal powders prepared from Saxifraga cernua. The time course for state 1 to state 2 transitions was monitored as changes in the ratios of the three emission peaks. During illumination with light 2 (580 nm) the F730/F695 and F730/F685 ratios increased within minutes to establish a condition characteristic of state 2. A major difference between the two chloroplast types was the more rapid establishment of state 2 by mesophyll chloroplasts. An increase in light 2 intensity caused an increase in the magnitude of the F730/F695 ratio for both chloroplast types and, for guard cell chloroplasts, a decrease in the time required to establish the new ratio. The role of reversible phosphorylation of the light-harvesting chlorophyll a/b protein complex in regulating state transitions for both mesophyll and guard cell chloroplasts was assessed using DCMU and sodium fluoride, a specific phosphatase inhibitor. DCMU-treated mesophyll and epidermal tissues failed to show a state 1-state 2 transition. NaF-treated tissues attained state 2 but lacked the ability to revert back to state 1.

Journal Article↗
PubMed1977

PH-dependent changes of 2,3-bisphosphoglycerate in human red cells during transitional and steady states in vitro.

A systematic study of the pH-dependent changes in the range 6.6--7.4 of 2,3-bisphosphoglycerate and the adenine nucleotides was performed in the presence and absence of glucose during transitional and steady states. 1. The results indicatethat 2,3-gisphosphoglycerate phosphatase breaks down 2,3-bisphosphoglycerate nearly independent of pH at a rate of 480 mumol 2,3-bisphosphoglycerate x1 cells-1xh-1.2,3-Bisphosphoglycerate mutase is practically completely inhibited below pH value increases in long-term experiments with lower 2,3-bisphosphoglycerate levels. The formation of pyruvate corresponds to the breakdown of 2,3-bisphosphoglycerate afterconsumption of an unknown reducing substance.

Adenosine Diphosphate↗