Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “single cell analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 469 records · Page 26Linked to original sources
PubMed1993

Identification and cell lineage of individual neural precursors in the Drosophila CNS.

The Drosophila CNS is complex enough to serve as a model for many of the molecular, cellular and developmental functions of the vertebrate CNS, yet simple enough for single-cell analysis. Recent advances have provided molecular markers that allow most Drosophila CNS precursors to be uniquely identified, as well as methods for determining the complete cell lineage of each precursor. A detailed understanding of wild-type neurogenesis, combined with existing molecular genetic techniques, should provide insight into the fundamental mechanisms that generate neuronal and glial diversity.

Animals↗
PubMed1983

Spontaneous, rhythmic myoelectric activity induced by scorpion neurotoxin, reduced [calcium]0 and cadmium in chick striated muscle.

The cellular electrical activity accompanying the very slow resting-tension oscillation (period 4-13 min) in chick skeletal muscle caused by scorpion neurotoxin, reduced [Ca2+]0 and Cd2+ was investigated. All three oscillogenic treatments were found to induce spontaneous, periodically recurring, electrical activation of muscle cells, including periodic bursting activity of individual cells. The period of the recurrent electrical activation approximated the period of the resting-tension oscillation. The data suggest that the three oscillogenic treatments act by way of a common mechanism, possibly a critical Ca2+ moiety, to effect the periodic electrical activation of the cells. Analysis of single cell and group discharge activity suggests that the cells are coupled by non-specific, electrotonic interactions, resulting in the integration of their individual periodic activities into a resting-tension oscillation of the whole muscle.

Action Potentials↗
PubMed1983

Selective uptake of Lucifer Yellow into different cell populations of the developing chicken retina.

Whole chick embryo eyes at different stages of development were incubated in a solution of Lucifer Yellow (LY) and examined in frozen sections. Different cell populations selectively take up the dye during the course of development: from embryonic day 4 - day 8 of incubation (E4-E8) only a subpopulation of neuroepithelial cells are stained, which at E7-E8 are located mainly near the periphery between the prospective ora serrata and the outer edge of the retina. This staining disappears after E8. A second phase starts at E10, with a weak but specific staining of a small population of cells in the outer nuclear layer which becomes less pronounced by E12. Starting around E10.5 a bright staining of cells in the innermost part of the inner nuclear layer can be observed. Their size, shape and location suggest that most of them represent a subclass of amacrine cells (including all 'displaced amacrine cells'). Beginning at E15, the staining pattern becomes more complex. A single cell analysis of the percentage of LY-stained cells which are stained either before or after papain-treatment and dissociation of the intact tissue confirms and extends the histological findings.

Animals↗
PubMed1996

Determination of insulin in single pancreatic cells by capillary electrophoresis and laser-induced native fluorescence.

Development of a method for the determination of insulin based on capillary electrophoresis with laser-induced native fluorescence detection is described. Under optimal conditions, insulin as low as 73 amol can be detected with a good signal-to-noise ratio (S/N = 10 peak-to-peak). Application of this method for the determination of insulin content in single cells from the insulin-secreting cell lines RINm5F and beta TC3 is demonstrated. Non-bonded poly(ethylene oxide)-coated and bare capillaries are evaluated for this purpose, with the latter found to be more suitable for single-cell analysis.

Animals↗
PubMed2003

Cell-to-cell variability in the differentiation program of human megakaryocytes.

Differentiation of CD34(+) stem/progenitor cells into megakaryocytes is thought to be a uniform, unidirectional process, in which cells transform step by step from less differentiated precursor stages to more differentiated megakaryocytes. Here we propose the concept and present evidence based on single-cell analysis that differentiation occurs along multiple, partially asynchronous routes. In all CD34(+) cells cultured with thrombopoietin, surface appearance of glycoprotein IIIa (GPIIIa) preceded that of GPIb, indicating that the expression of these glycoproteins occurs in a timely ordered manner. Cellular F-actin content increased in parallel with GPIb expression. Only cells that expressed GPIb were polyploid, pointing to co-regulation of GPIb expression, actin cytoskeleton formation and polyploidization during megakaryocytopoiesis. On the other hand, most progenitor cells responded to thrombin but not to thromboxane A(2) analogue by rises in cytosolic [Ca(2+)](i). The appearance of thromboxane-induced responses during megakaryocytopoiesis was not strictly linked to glycoprotein expression, because cells showed responsiveness either before or after GPIb expression. The same non-strictly sequential pattern was observed for disappearance of the Ca(2+) response by prostacyclin mimetic; in some megakaryocytes it occurred before and in others after GPIb expression. Thus, megakaryocytic differentiation follows along independent routes that are either strictly sequential (GPIIIa and GPIb expression) or proceed at different velocities (Ca(2+) signal regulation).

Antigens, CD34↗
PubMed2006

Bioreporters: gfp versus lux revisited and single-cell response.

Genetically engineered organisms expressing spectroscopically active reporter molecules in response to chemical effectors display great potential as living transducers in sensing applications. Green fluorescent protein (gfp gene) bioreporters have distinct advantages over luminescent couterparts (lux gene), including applicability at the single-cell level, but are typically less sensitive. Here we describe a gfp-bearing bioreporter that is sensitive to naphthalene (a poorly water soluble pollutant behaving like a large class of hydrophobic compounds), is suitable for use in chemical assays and bioavailability studies, and has detection limits comparable to lux-bearing bioreporters for higher efficiency detection strategies. Simultaneously, we find that the exploitation of population response data from single-cell analysis is not an algorithmic conduit to enhanced signal detection and hence lower effector detection limits, as normally assumed. The assay reported functions to equal effect with or without biocide.

Biosensing Techniques↗
PubMed2006

Dual isotype expressing B cells [kappa(+)/lambda(+)] arise during the ontogeny of B cells in the bone marrow of normal nontransgenic mice.

Central to the clonal selection theory is the tenet that a single B cell expresses a single receptor with a single specificity. Previously, based on our work in anti-phosphocholine transgenic mouse models, we suggested that B cells escaped clonal deletion by coexpression of more than one receptor on their cell surface. We argued that "receptor dilution" was necessary when: (i) the expressed immunoglobulin receptor is essential for immune protection against pathogens and (ii) this protective receptor is autoreactive and would be clonally deleted, leaving a hole in the B cell repertoire. Here, we demonstrate that dual isotype expressing B cells arise during the normal ontogeny of B cells in the bone marrow and populate both the spleen and peritoneal cavity of nontransgenic mice. Furthermore, single cell analysis of the expressed immunoglobulin light chains suggests that receptor editing may play a role in the generation of a significant fraction of dual isotype expressing B cells.

Animals↗
PubMed2026

Endothelial PERK restricts lymphoid regeneration by reducing DLL4-NOTCH3 signaling at the Pre-B niche.

Delayed immune recovery after hematopoietic stem cell (HSC) transplantation is associated with a poor clinical outcome. We study the role of unfolded protein response (ER stress) in hematopoietic regeneration within the bone marrow (BM) microenvironment. We reveal that BM endothelium PERK activation is a prominent feature of patients with leukemia and is a hallmark response in mice following ionizing irradiation. Ablating endothelial Perk boosts NOTCH ligand DLL4 expression and promotes DLL4-dependent early HSC and B progenitor regeneration. Single-cell analysis reveals that endothelial DLL4 activates NOTCH3 expressed by mesenchymal stroma cells, and that the PERK-DLL4 axis coordinates the regulation of lymphoid commitment. NOTCH3 is critical for the upregulation of IL7 following irradiation and the expansion of lymphoid progenitors. These findings not only unveil an ER stress-controlled vascular-stroma signaling mechanism in regenerative hematopoiesis but also highlight PERK blockade as a promising strategy to improve immune recovery after myeloablative transplantation.

CP: cell biology↗
PubMed2005

Micro-separation toward systems biology.

Current biology is experiencing transformation in logic or philosophy that forces us to reevaluate the concept of cell, tissue or entire organism as a collection of individual components. Systems biology that aims at understanding biological system at the systems level is an emerging research area, which involves interdisciplinary collaborations of life sciences, computational and mathematical sciences, systems engineering, and analytical technology, etc. For analytical chemistry, developing innovative methods to meet the requirement of systems biology represents new challenges as also opportunities and responsibility. In this review, systems biology-oriented micro-separation technologies are introduced for comprehensive profiling of genome, proteome and metabolome, characterization of biomolecules interaction and single cell analysis such as capillary electrophoresis, ultra-thin layer gel electrophoresis, micro-column liquid chromatography, and their multidimensional combinations, parallel integrations, microfabricated formats, and nano technology involvement. Future challenges and directions are also suggested.

Chromatography, Liquid↗
PubMed2006

Phosphoproteomic approaches to elucidate cellular signaling networks.

Protein phosphorylation is crucial in the regulation of signaling pathways that control various biological responses. Recent progress in diverse methodologies to investigate protein phosphorylation in complex biological samples has resulted in more rapid, detailed and quantitative analyses of signaling networks. In particular, advances in mass spectrometry (MS) have enabled the identification and quantification of thousands of both known and novel phosphorylation sites. Initial MS-based information can be complemented with a variety of recently developed and improved phosphoproteomic techniques. These include multiplexed microbead or kinase activity assays, flow cytometry based single-cell analysis, protein microarrays and interaction studies. The combination of multiple approaches, coupled with phenotypic response measurements, computational modeling and biochemical manipulations, will ultimately reveal the mechanistic regulation of signaling networks.

Animals↗
PubMed2006

Origin and T cell receptor diversity of Foxp3+CD4+CD25+ T cells.

Foxp3(+)CD4(+)CD25(+) regulatory T cells can differentiate from Foxp3(-)CD4(+) medullary thymocytes and Foxp3(-)CD4(+) naive T cells. However, the impact of these two processes on size and composition of the peripheral repertoire of regulatory T cells is unclear. Here we followed the fate of individual Foxp3(+)CD4(+)CD25(+) thymocytes and T cells in vivo in T cell receptor (TCR) transgenic mice that express a restricted but polyclonal repertoire of TCRs. By utilizing high-throughput single-cell analysis, we showed that Foxp3(+)CD4(+) peripheral T cells were derived from thymic precursors that expressed a different TCRs than Foxp3(-)CD4(+) medullary thymocytes and Foxp3(-)CD4(+) T cells. Furthermore, the diversity of TCRs on Foxp3(+)CD4(+) regulatory T cells exceeded the diversity of TCRs on Foxp3(-)CD4(+) naive T cells, even in mice that lack expression of tissue-specific antigens. Our results imply that higher TCR diversity on Foxp3(+) regulatory T cells helps these cells to match the specificities of autoreactive and naive T cells.

Amino Acid Sequence↗
PubMed2005

IL-4-expressing bronchoalveolar T cells from asthmatic and healthy subjects preferentially express CCR 3 and CCR 4.

BACKGROUND: The concept of the polarization of chemokine receptor expression by T(H)1 and T(H)2 cells provides an attractive mechanism for their differential recruitment to tissue, which could be subject to disease-specific therapeutic intervention. The paradigm that T(H)1 cells preferentially express CXCR 3 and CCR 5 and T(H)2 cells preferentially express CCR 3, CCR 4, and CCR 8 has been well established in the setting of in vitro polarized cell lines; however, the situation in vivo appears less clear-cut. OBJECTIVE: We sought to investigate whether this pattern of polarization can be demonstrated in human lung tissue. METHODS: We used single-cell analysis to investigate the relationship between chemokine receptor expression and cytokine production on peripheral blood and bronchoalveolar lavage fluid T cells in patients with asthma, a putative T(H)2 disease, as well as in healthy control subjects. RESULTS: We have found in both asthmatic and control subjects that IL-4-expressing blood and bronchoalveolar lavage fluid T cells are significantly more likely to express the T(H)2 type 2 chemokine receptors CCR 3 and CCR 4, with 10-fold and 2-fold differences in expression, respectively, compared with IFN-gamma-expressing cells. CONCLUSION: We have provided evidence that polarization of T(H)2-type chemokine receptors on IL-4-expressing cells can be demonstrated in an in vivo setting and therefore that these cells might indeed be susceptible to differential patterns of recruitment as a result of expression of the relevant chemokines at inflammatory sites.

Adult↗
PubMed2005

Quantitatively distinct requirements for signaling-competent cell spreading on engineered versus natural adhesion ligands.

To design synthetic microenvironments that elicit desired cell behaviors, we must better understand the molecular mechanisms by which cells interact with candidate biomaterials. Using cell lines with distinct alpha5beta1 integrin expression profiles, we demonstrate that this integrin mediates cell spreading on substrata coated with genetically engineered artificial extracellular matrix (aECM) proteins containing the RGD sequence (RGD-containing aECM protein [aRGD]) but lacking the PHSRN synergy site. Furthermore, aRGD-mediated adhesion stimulates an intracellular focal adhesion kinase (FAK) signal that is indicative of integrin tethering. Although both aRGD and the natural ECM protein fibronectin (FN) support alpha5beta1 integrin-mediated cell spreading, quantitative single-cell analysis revealed that aRGD-mediated spreading requires ten-fold greater threshold amount of integrin expression than FN-mediated spreading. Our analysis demonstrates that aRGD-based substrata mediate both biophysical (cell spreading) and biochemical (FAK signaling) events via the alpha5beta1 integrin, albeit with efficacy quantitatively distinct from that of natural ECM proteins that possess the full spectrum of adhesion and synergy domains.

Amino Acid Sequence↗
PubMed2006

Endothelial and hematopoietic cell fate of human embryonic stem cells.

The endothelial cells, lining the inside of blood vessels, and the blood-forming hematopoietic cells play crucial roles in vasculogenesis. The establishment of human embryonic stem cells (hESCs) provides a unique tool to study the early development of endothelial and hematopoietic cells, opening new avenues of research to explore organ vascularization and regeneration. The current study demonstrates that a population of intermediate-stage precursors, which possesses primitive endothelial properties during hESC differentiation, is capable of giving rise to endothelial and hematopoietic cells. Single cell analysis reveals that these primitive endothelial-like precursors contain rare bipotent cells with hemangioblast properties, responsible for both endothelial and hematopoietic cell fates. These findings will facilitate the further study of cellular commitment, lineage restriction, and terminal differentiation of endothelial and hematopoietic compartments and may lead to novel regenerative therapies.

Animals↗
PubMed2026

A machine learning-derived and functionally validated circadian rhythm signature predicts clinical outcomes and in silico drug sensitivity in colorectal cancer.

BACKGROUND: Colorectal cancer (CRC) displays considerable heterogeneity in clinical outcomes, highlighting the need for reliable prognostic biomarkers. While the aberrant expression of circadian rhythm-related genes has been implicated in cancer pathogenesis, its comprehensive role in CRC progression and predicted therapeutic vulnerabilities remains inadequately characterized. METHODS: Bulk and single-cell RNA-sequencing data were integrated from multiple CRC cohorts. A circadian rhythm signature (CRS) was developed through machine learning algorithms and validated for prognostic value. Comprehensive analyses of tumor microenvironment, genomic alterations, and drug sensitivity were performed. Furthermore, the biological function of the core gene, BHLHE40, was validated in CRC cell lines through CCK-8, EdU, and wound healing assays. RESULTS: Single-cell analysis demonstrated an elevated expression signature of circadian rhythm-related genes in dendritic cells. The optimized CRS, comprising 14 circadian rhythm-related genes, successfully categorized patients into high- and low-risk groups. Patients with a high CRS showed markedly poorer overall survival and computationally inferred immunosuppressive features, including reduced CD8+ T cell infiltration and increased M2 macrophage polarization. Genomic analysis revealed enhanced mutation burden in TP53 and alterations in RTK-RAS/WNT pathways. Notably, in vitro assays confirmed that BHLHE40 is significantly overexpressed in CRC cells. Knockdown of BHLHE40 markedly inhibited tumor cell proliferation and migration. Drug sensitivity profiling identified bexarotene and SMER-3 as potential therapeutic options for high-CRS patients. A nomogram integrating CRS with clinical parameters demonstrated superior predictive accuracy for 1-, 3-, and 5-year survival. CONCLUSIONS: The CRS represents a promising prognostic biomarker that reflects tumor immune status and genomic features, providing valuable insights for personalized treatment strategies in CRC.

Circadian rhythm↗
PubMed2004

Tracking operator state fluctuations in gene expression in single cells.

We report the results of operator state fluctuations in gene expression for the entire bacterial growth cycle, using single-cell analysis and synthetic unregulated and negative-feedback transcription regulatory gene circuits. In the unregulated circuit, during the cell cycle, we observe a crossover from log-normal-to-normal distribution of expressed proteins and an unusual linear dependence of their standard deviation on the mean gene expression levels. With negative-feedback circuits we find the existence of bimodality as the cell cycle progresses. We suggest that such long-tail and bimodal distributions may be used as selection mechanisms in developmental switches and for assigning cell identity.

Anisotropy↗
PubMed2000

A novel genetic pathway for sudden cardiac death via defects in the transition between ventricular and conduction system cell lineages.

HF-1 b, an SP1 -related transcription factor, is preferentially expressed in the cardiac conduction system and ventricular myocytes in the heart. Mice deficient for HF-1 b survive to term and exhibit normal cardiac structure and function but display sudden cardiac death and a complete penetrance of conduction system defects, including spontaneous ventricular tachycardia and a high incidence of AV block. Continuous electrocardiographic recordings clearly documented cardiac arrhythmogenesis as the cause of death. Single-cell analysis revealed an anatomic substrate for arrhythmogenesis, including a decrease and mislocalization of connexins and a marked increase in action potential heterogeneity. Two independent markers reveal defects in the formation of ventricular Purkinje fibers. These studies identify a novel genetic pathway for sudden cardiac death via defects in the transition between ventricular and conduction system cell lineages.

Action Potentials↗
PubMed2001

A defect in the Kv channel-interacting protein 2 (KChIP2) gene leads to a complete loss of I(to) and confers susceptibility to ventricular tachycardia.

KChIP2, a gene encoding three auxiliary subunits of Kv4.2 and Kv4.3, is preferentially expressed in the adult heart, and its expression is downregulated in cardiac hypertrophy. Mice deficient for KChIP2 exhibit normal cardiac structure and function but display a prolonged elevation in the ST segment on the electrocardiogram. The KChIP2(-/-) mice are highly susceptible to the induction of cardiac arrhythmias. Single-cell analysis revealed a substrate for arrhythmogenesis, including a complete absence of transient outward potassium current, I(to), and a marked increase in action potential duration. These studies demonstrate that a defect in KChIP2 is sufficient to confer a marked genetic susceptibility to arrhythmias, establishing a novel genetic pathway for ventricular tachycardia via a loss of the transmural gradient of I(to).

Action Potentials↗