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Results for “Origin cell mapping”

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At least 19 recordsLinked to original sources
PubMed2026

Aqueous humour extracellular vesicle membrane protein profiling reveals pathological features of refractory macular edema.

BACKGROUND: Both diabetic macular edema (DME) and retinal vein occlusion-related macular edema (RVO-ME) can become refractory to anti-vascular endothelial growth factor (anti-VEGF) therapy, but the underlying mechanisms are unclear. Molecular discrimination of refractory disease could guide personalized treatment. This study examined whether aqueous humor-derived extracellular vesicle (EV) membrane proteins can characterize refractoriness and reveal etiology-specific pathways. METHODS: This prospective cohort study included 28 patients with DME or RVO-ME (14 each), further divided into treatment-naïve and refractory subgroups. Aqueous humour samples were collected before intravitreal anti-VEGF injection. EV membrane proteins were profiled using an EV Array chip targeting 435 antibodies. Differentially expressed proteins were analyzed by bioinformatics, including Gene Ontology, Kyoto encyclopaedia of genes and genomes (KEGG) pathway enrichment, Gene set enrichment analysis (GSEA), and cell-of-origin mapping using public single-cell RNA-seq data. RESULTS: VEGF/VEGFR2 were elevated in treatment-naïve DME and RVO-ME. Refractory DME showed upregulation of C5 and CD34 (complement/immune activation). Refractory RVO-ME exhibited increased CD68 and Annexin A1 with decreased PDGFR (chronic inflammation, vascular dysregulation). RANTES was commonly upregulated in refractory disease. Several EV proteins discriminated refractory cases with high accuracy (AUC 0.898-0.980). Cellular origin suggested immune cell-derived EVs in DME, retinal cell-derived EVs in RVO-ME. External validation confirmed key differences. CONCLUSION: Refractory ME involves distinct pathways: immune-inflammatory activation in DME versus chronic inflammation with vascular dysregulation in RVO-ME. EV membrane proteins from aqueous humor provide insights into therapeutic resistance and hold promise as biomarkers for personalized treatment decisions.

artificial intelligence↗
PubMed2025

MOADE: a multimodal autoencoder for dissociating bulk multi-omics data.

In single cell biology, the complexity of tissues may hinder lineage cell mapping or tumor microenvironment decomposition, requiring digital dissociation of bulk tissues. Many deconvolution methods focus on transcriptomic assay, not easily applicable to other omics due to ambiguous cell markers and reference-to-target difference. Here, we present MOADE, a multimodal autoencoder pipeline linking multi-dimensional features to jointly predict personalized multi-omic profiles and cellular compositions, using pseudo-bulk data constructed by internal non-transcriptomic reference and external scRNA-seq data. MOADE is evaluated through rigorous simulation experiments and real multi-omic data from multiple tissue types, outperforming nine deconvolution pipelines with superior generalizability and fidelity.

Humans↗
PubMed1992

Identification and characterization of a complex chromosomal replication origin in Schizosaccharomyces pombe.

In the budding yeast, S. cerevisiae, two-dimensional (2D) gel electrophoresis techniques permit mapping of DNA replication origins to short stretches of DNA (+/- 300 bp). In contrast, in mammalian cells and Drosophila, 2D gel techniques do not permit precise origin localization; the results have been interpreted to suggest that replication initiates in broad zones (several kbp or more). However, alternative techniques (replication timing, nascent strand polarity analysis, nascent strand size analysis) suggest that mammalian origins can be mapped to short DNA stretches, just like S. cerevisiae origins. Because the fission yeast, Schizosaccharomyces pombe, resembles higher organisms in several ways to a greater extent than does S. cerevisiae, we thought that S. pombe replication origins might prove to resemble--and thus be helpful models for--animal cell origins. An attempt to test this possibility using 2D gel techniques resulted in identification of a replication origin near the ura4 gene on chromosome III of S. pombe. The 2D gel patterns produced by this S. pombe origin indeed resemble the patterns produced by animal cell origins and show that the S. pombe origin cannot be precisely located. The data suggest an initiation zone of 3-5 kbp. Some aspects of the 2D gel patterns detected at the S. pombe origin cannot be explained by the rationale of initiation in broad zones, suggesting that future biochemical and genetic studies of this complex origin are likely to provide information useful in helping to understand the apparent conflict between the 2D gel mapping techniques and other mapping techniques at animal cell origins.

Chromosomes, Fungal↗
PubMed1979

Surface mapping of mouse thymocytes.

The blocking method used previously for determining the relative positions of different components of the cell surface was modified by first fixing the cells with paraformaldehyde. This technique was applied to the H-2K (K), H-2D (D), TL, Lyt-1, and Lyt-2 surface components of mouse thymocytes, and the results were compared in parallel with data obtained with the original technique with unfixed cells. Previous mapping data with unfixed cells, indicating the positions of these molecules relative to one another, were confirmed with paraformaldehyde-fixed cells, with one exception. On unfixed cells, D and TL appeared sufficiently adjacent to produce mutual interference in the attachment of anti-D and anti-TL antibodies. With paraformaldehyde-fixed cells this was not so, D and TL appearing sufficiently separated from one another to obviate interference in the attachment of anti-D and anti-TL antibodies. The previously reported close association of K with Lyt-1 and of D with Lyt-2 were demonstrable equally with unfixed and paraformaldehyde-fixed thymocytes. It is suggested that activation of D sites, and alternatively of TL sites, by antibody in the present experiments brings these two molecules into apposition and that this movement may exemplify a mechanism concerned in immunological recognition and response.

Animals↗
PubMed1991

Chemically distinct rat olivocochlear neurons.

We have produced a neurochemical map of the cell bodies of origin of the cochlear efferent terminals in rat by combining glutamic acid decarboxylase (GAD), choline acetyltransferase (ChAT), or calcitonin gene-related peptide (CGRP) immunocytochemistry with retrograde transport of horseradish peroxidase. The locations of cochlear efferent cell bodies are in general agreement with the medial and lateral systems described by White and Warr (J. Comp. Neurol. 219:203-214, 1983) with some minor modifications. The lateral system consists of at least two pools of chemically distinct neurons located within the lateral superior olive (LSO) ipsilateral to the injected cochlea. One pool immunostains with an antibody to GAD while the other immunostains with antibodies to ChAT and to CGRP. The medial efferent system consists of periolivary neurons that are almost exclusively large and ChAT-positive but CGRP-negative. They are located both ipsilateral and contralateral to the cochlea they project to. There are a few GAD-positive small neurons in the medioventral and rostral periolivary regions that project ipsilaterally, but these may prove tobe ectopic neurons. The ipsilateral lateroventral periolivary region (LVPO) contains some efferent neurons, all of which are ChAT-positive but CGRP-negative. Additional cochlear efferent neurons, some of which are ChAT-positive and others GAD-positive, are present within and immediately dorsal to the fiber capsule surrounding the medial limb, and to a lesser extent the lateral limb, of the ipsilateral LSO. Not all GAD-positive or ChAT-positive olivary cells project to the cochlea. We have complemented the results in the brainstem by demonstrating two immunocytochemically distinct populations of efferent terminals in the cochlea simultaneously, one CGRP-positive and the other GAD-positive. Approximately equal numbers of boutons immunoreactive for both markers are present beneath inner hair cells throughout the entire length of the cochlea. Surprisingly high numbers of GAD-positive and CGRP-positive boutons are also present on outer hair cells, with each class having its spatially and morphologically distinct features. The lack of CGRP-positive periolivary cells that are retrogradely labeled by cochlear injections of HRP suggests that the lateral olivocochlear system sends projections to outer hair cells. Our results raise questions about species differences in the organization of targets of the lateral and medial olivocochlear systems.

Animals↗
PubMed1991

Characterization of a second promoter for the mouse liver/bone/kidney-type alkaline phosphatase gene: cell and tissue specific expression.

The second leader exon and the relative promoter of the mouse liver/bone/kidney-type alkaline phosphatase gene were identified and characterized. The transcription initiation site was determined by S1 mapping analysis. The differential expression of the two alternatively spliced transcripts was assessed in cell lines of different origin and in various tissues by polymerase chain reaction and RNase mapping analysis. The first promoter is active in embryo derived cells, whereas the second promoter is silent in basal conditions but it is activated by dibutyryl cAMP in fibroblastic cells. In the whole animal, the transcript driven by the first promoter is found in most tissues albeit at different levels, while the one driven by the second promoter is specifically expressed at high levels only in the heart.

Alkaline Phosphatase↗
PubMed1992

Ewing's tumor X mouse hybrids expressing the MIC2 antigen: analyses using fluorescence CDD-banding and non-isotopic ISH.

We present a highly sensitive method that has been applied to map the chromosomal origin of the prominent cell surface antigen of Ewing's tumor cells recognized by monoclonal antibody HBA-71. The technique allows an unambiguous identification of human chromosomal material in interspecific cell hybrids. This is achieved by fluorescent in situ hybridization of biotinylated total human DNA, followed by high resolution fluorescence banding with the chromomycin/distamycin/DAPI triple stain. An advantage of this method is that all signals can be visualized in one single operation by simply switching the appropriate filter blocks. The protocol has proved extremely useful in gene mapping by means of interspecific cell hybrids, a technique that depends on the accurate and unambiguous recognition of the relevant (e.g., human) genetic material in the clonal genome. Our studies confirm that this antigen is the product of the MIC2 gene, which is so far the only well-studied pseudoautosomal gene in man, and which is located on the short arms of chromosomes X and Y. Furthermore, no influence of the Ewing's tumor-specific translocation t(11;22) on MIC2 expression could be discerned.

Animals↗
PubMed1978

Field potential and single unit analyses of the avian dorsal motor nucleus of the vagus and citeria for identifying vagal cardiac cells of origin.

Field potentials evoked by mid-cervical vagal stimulation were systematically mapped in the dorsal motor and solitary nuclei of the pigeon. Since responses varied predictably with microelectrode position, they could be used for localization in the dorsal medulla. By varying stimulus intensity and monitoring the vagal compound action potential, contributions of the different compound action potential waves were then established. Activation of the Bl-wave, which includes cardioinhibitory fiber activity, has its most prominent effect in the intermediate rostrocaudal zone of the dorsal motor nucleus in the region of subnuxleus b. This is where the cells of origin of the vagal cardiac fibers have previously been anatomically localized. Single unit experiments then established that (a) vagal motoneurons with axonal conduction velocities in the cardioinhibitory fiber range (8.0-14.5 m/sec) are primarily localized to the intermediate rostrocaudal zone of the dorsal motor nucleus in the region of subnucleus b, and (b) motoneurons in this zone that conduct at 8.0-14.5 m/sec distribute their axons in the cardiac branches. Furthermore, no error is introduced by identifying such neurons with mid-cervical rather than midthoracic vagal stimulation. Thus, the following criteria establish a neuron as giving rise to a vagal cardioinhibitory fiber: (a) localizing it to the intermediate rostrocaudal zone of the dorsal motor nucleus on the basis of the field potential evoked by mid-cervical vagal stimulation; (b) antidromically activating it with mid-cervical vagal stimulation; and (c) demonstrating that its axon conducts at 8.8-14.5 m/sec.

Animals↗
PubMed1991

Temporal analysis and spatial mapping of Lymantria dispar nuclear polyhedrosis virus transcripts and in vitro translation polypeptides.

Genomic expression of the Lymantria dispar multinucleocapsid nuclear polyhedrosis virus (LdMNPV) was studied. Viral specific transcripts expressed in cell culture at various times from 2 through 72 h postinfection were identified and their genomic origins mapped through Northern analysis. Sixty-five distinct transcripts were identified in this analysis. Most viral transcripts were expressed late in infection, and originated from throughout the viral genome. Viral polypeptides expressed in infected 652Y cells were labeled with [35S]methionine and identified by autoradiography after separation by SDS polyacrylamide gel electrophoresis. Viral protein synthesis was found to occur in a sequential manner. Four proteins were identified in the early phase of viral replication (4-12 h p.i.), 24 proteins in the intermediate phase (12-24 h p.i.), and 5 proteins during the late phase (greater than 24 h p.i.). Cytoplasmic RNAs were isolated from LdMNPV infected cells at 16, 24, and 48 h p.i., and used for hybrid selections with overlapping DNA fragments that covered the entire LdMNPV genome. The selected RNAs were translated in vitro, and 61 distinct viral polypeptides were identified and their genomic origins mapped. Temporal and spatial transcription and translation maps of the LdMNPV genome were generated with these data, and the expression pattern of the LdMNPV genome was compared to that of the Autographa californica nuclear polyhedrosis virus.

Animals↗
PubMed1979

On the progenitor cell migration velocity.

An attempt is presented to extract cell kinetic information from histomorphological features. It is applicable to rapidly proliferating tissues like the intestinal epithelium. Each replicating tissue has an origin where cells are formed and a periphery toward which cells migrate. The migration path along which they move is denominated as tissue radius on which all cell positions are mapped. Cell migration on the radius is associated with cell proliferation at tissue origin. Each mitosis there is associated with the displacement of all cells distal to it by one cell position. The more mitoses positioned between a cell and tissue origin, the greater its migration velocity. It is possible therefore to derive the cell migration velocity v(x) from the cumulative mitotic distribution on the radius, N(x). v(x) = N(x)/tm (tm = mitotic time). In this form v(x) represents also cell production at any point on the radius and may serve for the computation of other cell kinetic parameters like generation time. These arguments are illustrated on the rat incisor tooth inner enamel epithelium which has been studied in the normal and rapidly erupting tooth.

Ameloblasts↗
PubMed1975

Temporal genetic mapping in the blue-green alga Anacystis nidulans using ethyl methanesulphonate.

Cultures of the blue-green alga Anacytis nidulans were synchronized with respect to DNA synthesis as well as cell division. Application of ethyl methanesulphonate at different stages of replication resulted in a peak of mutation frequency for different genetic markers; this peak can be accounted for in terms of the involvement of repair processes. A temporal map of 19 markers has been constructed by this method. Comparison of gene position obtained by temporal mapping indicates that either bidirectional replication or unidirectional replication from more than one origin occurs.

Cell Division↗
PubMed1979

Epstein-Barr virus-specific RNA. III. Mapping of DNA encoding viral RNA in restringent infection.

Namalwa and Raji cells, originally obtained from a Burkitt tumor biopsy, grow as continuous cell lines in vitro and contain the Epstein-Barr virus (EBV)-related nuclear antigen EBNA (B. M. Reedman and G. Klein, Int. J. Cancer 11:499-520, 1973) and RNA homologous to at least 17 and 30% of the EBV genome, respectively (S. D. Hayward and E. Kieff, J. Virol. 18:518-525, 1976; T. Orellana and E. Kieff, J. Virol. 22:321-330, 1977). The polyribosomal and polyadenylated [poly(A)+] RNA fractions of Namalwa and Raji cells are enriched for a class of viral RNA homologous to 5 to 7% of EBV DNA (Hayward and Kieff, J. Virol. 18:518-525, 1976; Orellana and Kieff, J. Virol. 22:321-330, 1977). The objective of the experiments described in this communication was to determine the location within the map of the EBV genome (D. Given and E. Kieff, J. Virol. 28:524-542, 1978) of the DNA which encodes the viral RNA in the poly(A)+ and non-polyadenylated [poly(A)-] RNA fractions of Namalwa cells. Hybridization of labeled DNA homologous to Namalwa poly(A)+ or poly(A)- RNA to blots containing EcoRI, Hsu I, or Hsu I/EcoRI double-cut fragments of EBV (B95-8) or (W91) DNA indicated that these RNAs are encoded by DNA contained primarily in the Hsu I A/EcoRI A and Hsu I B/EcoRI A fragments and, to a lesser extent, in other fragments of the EBV genome. Hybridizations of Namalwa poly(A)+ and poly(A)- RNA in solution to denatured labeled EcoRI A or B fragments, Hsu I A, B, or D fragments, and Hsu I A/EcoRI A or Bam I S fragments and of Raji polyribosomal poly(A)+ RNA to the EcoRI A fragment indicated that (i) Namalwa poly(A)+ RNA is encoded primarily by 6 x 10(5) daltons of a 2 x 10(6)-dalton segment of DNA, Bam I S, which is tandemly reiterated, approximately 10 times, in the Hsu I A/EcoRI A fragment and is encoded to a lesser extent by DNA in the Hsu I B, EcoRI B, and Hsu I D fragments. Raji polyribosomal poly(A)+ RNA is encoded by a similar fraction of the EcoRI A fragment as that which encodes Namalwa poly(A)+ RNA. (ii) The fraction of the Bam I S fragment homologous to Namalwa poly(A)- RNA is similar to the fraction homologous to Namalwa poly(A)+ RNA. However, Namalwa poly(A)- RNA is homologous to a larger fraction of the DNA in the Hsu I B, Hsu I D, and EcoRI B fragments.

Cell Line↗
PubMed1991

Laser microdissection of the fragile X region: identification of cosmid clones and of conserved sequences in this region.

Laser microdissection has been used to dissect material from the X-chromosome region involved in fragile-X-linked mental retardation. After dissection, single chromosome slices corresponding to this fragile site were subjected to DNA amplification using either a vector ligation method (to provide known anchor sequences) or primer oligonucleotides corresponding to the ubiquitous Alu sequences. Amplified material was then cloned or, alternately, used to screen a gridded cosmid library. Eight cosmid clones identified in this way were regionally mapped using a panel of hybrid cell lines and shown to originate from a narrow interval centered on the fragile X site. Two clones are included in the approximately 6-cM interval defined by probes RNI (DXS369, 5 cM proximal) and VK21 (DXS 296, 1-2 cM distal) and which includes the fragile site, and at least one clone contains sequences conserved across species suggestive of a gene. This method combines the focused approach of microdissection and the convenience of obtaining cosmid (rather than small-insert) clones; it may be useful for studies of other defined chromosomal regions.

Animals↗
PubMed2025

CLADES: A Programmable Cascade of Genes for Cell Lineage Analysis and Manipulation.

In the Drosophila brain, neuronal diversity originates from approximately 100 neural stem cells, each dividing asymmetrically. Precise mapping of cell lineages at the single-cell resolution is crucial for understanding the mechanisms that direct neuronal specification. However, existing methods for high-resolution lineage tracing are notably time-consuming and labor-intensive. Here, we outline the best practices for lineage tracing using CLADES (cell lineage access driven by an edition sequence), a revolutionary approach to neuronal lineage tracing that addresses the limitations of previous methods. CLADES effectively traces the birth order of neurons using approximately 100 samples. The technique relies on a genetic cascade of reporter activations and deactivations that delineate lineage progression through color-coded markers. This system not only facilitates the detailed mapping of neuronal lineages but also holds the potential to be applied to tracking biological events and producing cell types for therapeutic purposes.

Animals↗
PubMed1975

Orientation of the complementary strands of polyoma virus DNA with respect to the DNA physical map.

The chemical polarities of the two strands of polyoma virus DNA with respect to the DNA physical map have been determined by hybridization of restriction endonuclease fragments specifically labeled with [125I]dCMP at their 3' termini to asymmetric polyoma complementary RNA (the product of in vitro transcription of viral DNA by Escherichia coli RNA polymerase). The orientations of the polyoma-specific stable RNA transcripts present in the cytoplasm of productively linfected mouse cells have been deduced from this result: the 5' ends of the early and late viral transcripts map very near the origin of viral DNA replication.

Cell-Free System↗
PubMed1975

The pontocerebellar projection onto the paramedian lobule in the cat: an experimental study with the use of horseradish peroxidase as a tracer.

Horseradish peroxidase (HRP) was injected into cerebellar cortex of the paramedian lobule in 12 cats, and the ensuing distribution of labeled cells in the pontine nuclei was mapped in some detail. The cells in the pontine gray which give origin to fibers to the paramedian lobule lie together, in part in groups, and in part in columns. The columns are situated both medial and ventrolateral to the peduncle, as well as in the dorsolateral pontine nucleus. The projection is bilateral with a clearcut contralateral preponderance, except in the lateralmost region in the dorsolateral nucleus, which projects mainly ipsilaterally. The column medial to the peduncle projects in a topographical pattern to the paramedian lobule. The dorsal part of this column projects to the rostral folia of the paramedian lobule, while successively more ventral parts in the column project to more caudal paramedian lobules. Within the other columns only a faint sign of a topographical organization is found. The location of the pontine columns projecting onto the paramedian lobule largely corresponds to the pontine terminal areas of fibers from the sensory cerebral cortex (SmI and SmII). The corresponding topography in these parts of the corticopontine and pontocerebellar pathways is suitable for a somatotopical impulse transmission from the sensory cortex to the paramedian lobule, in agreement with the results of physiological investigations. Furthermore, a correlation of the pontine areas projecting onto the paramedian lobule with the terminal areas of pontine afferents shows that the pons may be a relay station in mediating influences from other parts of the cortex (MsI, visual and acoustic), the cerebellar nuclei and the colliculi to the paramedian lobule.

Animals↗
PubMed1992

Genetic analysis of the herpes simplex virus type 1 UL9 gene: isolation of a LacZ insertion mutant and expression in eukaryotic cells.

HSV-1 host range mutants in complementation group 1-36 (hr27 and hr156) whose mutations map in the UL9 gene, encoding the origin binding protein, are unable to form plaques or synthesize viral DNA or late viral proteins when grown in nonpermissive Vero cells (Carmichael, E. P., Kosovsky, M. J., Weller, S. K., 1988, J. Virol. 62, 91-99). These defects are complemented efficiently by growth in the permissive cell line, S22, which contains the wild type version of several HSV genes including UL9. In this report the precise nature and location of the lesions in host range mutants hr27 and hr156 were determined by DNA sequencing; both mutants were found to contain identical single-base-pair substitutions at codons 309 and 311 in the UL9 open reading frame. This region lies within the putative helicase domain of the UL9 protein. The UL9 gene was disrupted by the insertion of an insertional mutagen ICP6::lacZ in which the Escherichia coli lacZ gene is expressed under control of the viral ICP6 promoter. Hr94, a viral mutant containing this insertion, does not form plaques or synthesize viral DNA when grown in Vero cells, although both defects are complemented efficiently on permissive cell lines. These results confirm that the UL9 gene product is essential for viral growth and DNA replication. Furthermore, since no detectable UL9 protein is synthesized in hr94-infected cells, this virus provides a useful genetic background for further structure-function analysis since no potentially interfering nonfunctional UL9 protein will be expressed. We have expressed the UL9 open reading frame under the control of the strong and inducible HSV-1 ICP6 promoter and have derived Vero cell lines containing variable copy numbers of the ICP6::UL9 construct. Cells whose copy number of this construct exceeded approximately 120 are unable to support efficient plaque formation by wild-type virus. Cell lines with low copy numbers of this construct are able to complement hr27, hr156, and hr94.

Amino Acid Sequence↗