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Results for “Heterogeneity Mapping”

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At least 91 records · Page 5Linked to original sources
PubMed2026

Integrative analysis of single-cell sequencing identifies CD8+ TIM3+ CD101+ T cell-associated genes as prognostic biomarkers in breast cancer.

BACKGROUND: Breast cancer is a prevalent and deadly malignancy that significantly impacts women's quality of life and imposes financial burdens. Despite therapeutic advancements, tumour heterogeneity and frequent relapses remain major challenges. Accordingly, this study aimed to characterize immune features associated with CD8+ TIM3+ CD101+ T cells and develop a prognostic signature for breast cancer. METHODS: This study integrated single-cell and bulk transcriptomic datasets to characterize CD8+ TIM3+ CD101+ T cell (CCT)-related immune features and construct a prognostic signature in breast cancer. Single-cell RNA-seq data were sourced from the Gene Expression Omnibus (GEO) repository, and bulk transcriptomic data were from The Cancer Genome Atlas (TCGA) and GEO databases. Analytical methods included pseudo-time trajectory reconstruction (Monocle2), intercellular signalling analysis (CellChat), functional enrichment (ClusterProfiler), and immune profiling (ssGSEA). Prognostic modeling was conducted using least absolute shrinkage and selection operator (LASSO) Cox regression, with validation via Kaplan-Meier and time-dependent receiver operating characteristic (ROC) analyses. RESULTS: Single-cell analysis identified 17 clusters spanning seven cell types, including T cells, myeloid cells, and epithelial cells. T-cell sub-clustering revealed four subtypes. Pseudotime analysis suggested a potential state-transition relationship between CD8+ CD101- TIM3+ and CD8+ CD101+ TIM3+ T-cell states. A total of 121 differentially expressed genes were enriched in vital biological processes. An 11-gene prognostic model showed strong predictive power across cohorts. Single-cell T-cell reclustering identified a CD8+ CD101+ TIM3+ T-cell subpopulation, which was primarily characterized by the expression of markers such as CD101 and HAVCR2/TIM3. CONCLUSIONS: This study maps cellular heterogeneity and molecular networks in breast cancer, offering insights for targeted therapy and improved prognosis.

Breast invasive carcinoma↗
PubMed1998

Cellular protein hnRNP-A1 interacts with the 3'-end and the intergenic sequence of mouse hepatitis virus negative-strand RNA to form a ribonucleoprotein complex.

We previously showed that several cellular proteins specifically bind to the 3'-end and the intergenic sequences of the negative-strand RNA of mouse hepatitis virus (MHV), and proposed that these distant RNA sequences can be brought together by cellular and viral proteins (Furuya and Lai, 1993; Zhang et al., 1994; Zhang and Lai, 1995). The cellular protein p35 has been identified as a heterogeneous nuclear ribonucleoprotein (hnRNP) A1. We have now expressed hnRNP-A1 as a glutathione-S-transferase (GST) fusion protein and demonstrated that the amino terminal two-thirds of hnRNP-A1 interacted with the two MHV regulatory RNA sequences (3'-end and intergenic sequences) through protein-RNA interaction while its carboxy-terminal glycine-rich domain mediated homomeric (protein-protein) interactions. In a partially reconstituted reaction, in which the two MHV RNA fragments and the purified GST-hnRNP-A1 fusion protein were mixed, an RNP complex was formed. Depletion of either hnRNP-A1 or one of the RNA components abolished the complex formation. These results indicate that hnRNP-A1 can mediate the formation of an MHV RNP complex, which includes both the negative-strand leader and intergenic sequences. Site-directed mutagenesis revealed that mutations in the MHV intergenic sequences, which inhibited MHV RNA transcription, also inhibited the RNP complex formation. Deletion analysis showed that the amino terminal RNA-binding domains of hnRNP-A1 is essential for the RNP complex formation while the carboxy-terminal protein-binding domain enhanced the complex formation by 90-fold. These findings provide direct evidence demonstrating that the negative-strand leader RNA and intergenic sequences can form an RNP complex mediated by cellular protein hnRNP-A1.

Animals↗
PubMed2000

Contributions of mass spectrometry to structural immunology.

Mass spectrometry has made important contributions to the field of immunology in the past decade. A variety of mass spectrometric-based techniques have been applied to study the structures of macromolecules that play a vital role in the immune response. These include traditional molecular mass measurements to identify post-translational modifications and structural heterogeneity, mass mapping of proteolysis products, sequencing by tandem mass spectrometry and conformational analysis. Antigen-antibody and other immune complexes have been detected by mass spectrometry, providing an avenue to study macromolecular assemblies that are important to immune function. By virtue of the ability of mass spectrometry based techniques to analyze complex biological mixtures, mass spectrometry has also been employed to identify and sequence protein epitopes important in both the humoral and cellular immune responses. This has been achieved through a combination of immunoaffinity and mass spectrometric techniques, and the coupling of high-performance chromatographs to mass spectrometers. These approaches are important for the identification of pathogens and show promise for the early diagnosis of disease associated with viral and bacterial infection and malignancy. These investigations will enable the mechanisms associated with normal and impaired immune function to be elucidated. Mass spectrometry has been utilized to characterize the structure of peptide mimics, multiple antigenic peptides and other constructs in the design of synthetic immunogens. Information derived from these studies will aid in the development of novel therapeutics and vaccines.

Allergy and Immunology↗
PubMedDate not supplied

A genetic study of the human low-voltage electroencephalogram.

The studied phenotype, the low-voltage electroencephalogram (LVEEG), is characterized by the absence of an alpha rhythm from the resting EEG. In previous studies, evidence was found for a simple autosomal-dominant mode of inheritance of the LVEEG. Such a polymorphism in brain function can be used as a research model for the stepwise elucidation of the molecular mechanism involved in those aspects of neuronal activity that are reflected in the EEG. Linkage with the variable number of tandem repeats (VNTR) marker CMM6 (D20S19) and localization of an LVEEG (EEGV1) gene on 20q have previously been reported, and genetic heterogeneity has been demonstrated. This latter result has been corroborated by studying new marker (MS214). The phenotype of the LVEEG is described here in greater detail. Its main characteristic is the absence of rhythmic alpha activity, especially in occipital leads, whereas other wave forms such as beta or theta waves may be present. Analysis of 17 new families (some of them large), together with 60 previously described nuclear families, supports the genetic hypothesis of an autosomal-dominant mode of inheritance. Problems connected with the analysis of linkage heterogeneity, exclusion mapping, and the study of multipoint linkage are discussed. A possible explanation of the localization of LVEEG in the close vicinity of another gene influencing synchronization of the normal EEG, the gene for benign neonatal epilepsie, is given.

Aging↗
PubMed1979

The organization of the ribosomal RNA genes of Chironomus tentans and some closely related species.

Southern gel analysis of total DNA from Chironomus tentans showed that the rRNA genes (rDNA) are homogeneous in structure. After cloning in Escherichia coli plasmid pBR313, the rDNA organisation was further studied by restriction fragment analysis and R-loop mapping. No heterogeneity could be detected by heteroduplex analysis of six different cloned rRNA cistrons. R-loop sizes of 1.69 and 3.63 kilobases (kb) were measured for the 18S and 28S rRNA coding sequences. The two spacers are 0.75 and 1.77 kb long. Southern gel analysis showed also a homogeneous rDNA structure for a Canadian population of C. tentans and C. pallidivittatus. The same technique indicated, however, that the rDNA of two other closely related species of C. thummi and C. melanotus is heterogeneous in structure. A possible correlation between this heterogeneity and the presence of heterochromatin in these species is discussed.

Animals↗
PubMed2005

Changes in carotenoid content and distribution in living plant tissue can be observed and mapped in situ using NIR-FT-Raman spectroscopy.

Near-infrared (NIR) excited Fourier transform (FT) Raman spectroscopy has been applied for in situ analysis of carotenoids in living plant samples. Pelargonium x hortorum leaf has been mapped using a Raman mapping technique to illustrate heterogeneous distribution of carotenoids. Mapping has also been employed for visualization of carotenoid changes induced by abiotic and biotic stress. In a tomato (Lycopersicon esculentum Mill.) fruit, inhibition of lycopene biosynthesis and accumulation of beta-carotene are demonstrated in tissue affected by sunscald physiological disorder. Raman map of diseased sugarbeet (Beta vulgaris L.) leaf shows a local carotenoid decline at infection site while the carotenoid accumulation is evident in parsley (Petroselinum crispum Mill. Nym.) as a response to Septoria petroselini infestation. Additionally, occurrence of lutein, beta-carotene and capsanthin, and changes in their relative content during bell pepper (Capsicum annum L.) fruit ripening are described by single Raman spectra. Based on these examples, the potential application of NIR-FT-Raman spectroscopy for a non-destructive analysis of carotenoids in various living plant tissues of the size ranging from about 0.01 mm(2) to 35 cm(2) is discussed.

Beta vulgaris↗
PubMed2006

Spatial scaling between leaf area index maps of different resolutions.

We developed algorithms for spatial scaling of leaf area index (LAI) using sub-pixel information. The study area is located near Liping County, Guizhou Province, in China. Methods for LAI spatial scaling were investigated on LAI images with 960 m resolution derived in two ways. LAI from distributed calculation (LAID) was derived using Landsat ETM+ data (30 m), and LAI from lumped calculation (LAIL) was obtained from the coarse (960 m) resolution data derived through resampling the ETM+ data. We found that lumped calculations can be considerably biased compared to the distributed (ETM+) case, suggesting that global and regional LAI maps can be biased if surface heterogeneity within the mapping resolution is ignored. Based on these results, we developed algorithms for removing the biases in lumped LAI maps using sub-pixel land cover-type information, and applied these to correct one coarse resolution LAI product which greatly improved its accuracy.

China↗
PubMed2006

Dynamic mapping of hippocampal development in childhood onset schizophrenia.

Prior cross-sectional anatomic brain imaging studies of the hippocampus in schizophrenia have generally shown loss in total hippocampal volume although the progressive course of these changes remains unknown. We report the first prospective sub-regional maps of hippocampal development in childhood onset schizophrenia (COS), reconstructed from serial brain MRI scans of 29 children with COS scanned every 2 years (87 scans) and compared to 31 controls matched for age, sex, and scan interval (94 scans). As expected, the COS subjects showed significant bilateral deficits (9-10%) in total hippocampal volume which remained consistent between age 9 and 26. However sub-regional maps showed heterogeneous changes with loss of hippocampal volume in both anterior as well as posterior ends while the body of the hippocampus gained in volume suggesting that hippocampal subunits are differentially affected in schizophrenia.

Adolescent↗
PubMed1977

Evidence from UV transcription mapping in HeLa cells that heterogeneous nuclear RNA is the messenger RNA precursor.

The effects of UV irradiation on the incorporation of [3H]uridine in HeLa (human) cell mRNA, rRNA, heterogeneous nuclear RNA (hnRNA) and early mRNA from adenovirus type 2 have been compared. The UV target size of cell mRNA is at least 3 times larger than the average size of the mRNA itself and larger than the adenovirus-2 early mRNA, which is known to derive from transcription units of about 1.5-5.0 kilobases. The UV target size of hnRNA, in contrast, is about the same as its size determined by sedimentation and overlaps with the target size of mRNA. It is concluded that most mRNA derives from a higher molecular weight hnRNA molecule.

Adenoviridae↗
PubMed1982

Nucleotide sequence of the 5'- and 3'- domains for rabbit 18S ribosomal RNA.

By direct RNA sequence analysis we have determined the primary structures of both the 5' and 3' domains for rabbit 18S ribosomal RNA. Purified 18S rRNA was labeled in vitro at either its 5' or 3' terminus with 32P, base-specifically fragmented enzymatically and chemically, and the resulting fragments electrophoretically fractionated by size in adjacent lanes of 140 cm long polyacrylamide sequencing gels run in 90% formamide. A phylogenetic comparison of both the mammalian 5' proximal 400 residues and the 3' distal 301 nucleotides with the previously determined yeast and Xenopus laevis 18S rRNA sequence shows extensive conservation interspersed with tracts having little homology. Clusters of G + C rich sequences are present within the mammalian 5' domain which are entirely absent in both the Xenopus laevis and yeast 18S rRNAs. Most base differences and insertions within the mammalian 18S rRNA when compared with yeast or Xenopus rRNA result in an increase in the G + C content of these regions. We have found nucleotide sequence analysis of the ribosomal RNA directly permits detection of both cistron heterogeneities and mapping of many of the modified bases.

Animals↗
PubMed1994

BoLA class I charge heterogeneity reflects the expression of more than two loci.

Internationally recognized allo-antisera in lymphocyte microcytotoxicity assays are thought to detect allelic products of a single highly polymorphic class I locus. A recent report suggested that two bovine lymphocyte antigen (BoLA) class I loci are expressed at the protein level. However, 1D-IEF analysis of BoLA class I molecules reveals multi-band patterns which cannot be reconciled with the reported number of loci. The aim of this study was to investigate the origins of the charge diversity of BoLA class I molecules observed using 1D-IEF. BoLA class I molecules appear to be glycosylated at a single N-linked position with a complex type carbohydrate moiety which has up to three terminal sialic acid residues. Class I molecules immunoprecipitated from resting bovine PBL are not phosphorylated. Neither modification is responsible for the observed charge heterogeneity. Peptide mapping reveals that different BoLA charge variants have distinct digestion patterns. Furthermore, a number of different polypeptides are associated with each serological specificity. These polypeptides appear to be encoded by different loci which exist in linkage disequilibrium. The number of charge variants with different peptide maps indicates that the BoLA system has a minimum of three class I loci expressed at the protein level.

Alleles↗
PubMed1987

Initiation and termination of duck hepatitis B virus DNA synthesis during virus maturation.

We characterized a number of important features of the structure of the cohesive overlap region of the DNA genome of duck hepatitis B virus. The 5'-terminal nucleotide of minus-strand DNA was localized to nucleotide 2537, a G residue within the 12-base repeat sequence DR1. This G residue was shown to be the site of a covalent linkage to a protein, consistent with speculation that this protein is the primer of minus-strand synthesis, which occurs by reverse transcription. The 3' terminus of the minus strand was heterogeneous, being mapped to nucleotides 2530 and 2531, indicating that the minus strand is terminally redundant by seven or eight bases and ends at the putative 5' end of the transcribed RNA template (pregenome) for reverse transcription. We previously demonstrated that the presumptive RNA primer of plus-strand synthesis remains attached to plus-strand DNA during virus maturation; moreover, the sequence of this primer suggested an origin from the 5' end of the pregenome (J.-M. Lien, C. E. Aldrich, and W. S. Mason, J. Virol. 57:229-236, 1986). We show here that over 75% of plus-strand primers are capped, further supporting the idea that these primers are uniquely derived from the 5' end of the pregenome. Finally, we found that seemingly mature duck hepatitis B virus genomes are incomplete by at least 12 bases, in that the 12-base repeat sequence DR2 is not copied into plus-strand DNA during virus maturation. Since DR2 in virion DNA is duplexed with the RNA primer of plus-strand synthesis, it is possible that the failure to make complete plus strands is due to an inability of the viral DNA polymerase to carry out a displacement of the bound RNA primer.

Animals↗
PubMed1994

Structure and heterogeneity of the a sequences of human herpesvirus 6 strain variants U1102 and Z29 and identification of human telomeric repeat sequences at the genomic termini.

The unit-length genome of human herpesvirus 6 (HHV-6) consists of a single unique component (U) bounded by direct repeats DRL and DRR and forms head-to-tail concatemers during productive infection. cis-elements which mediate cleavage and packaging of progeny virions (a sequences) are found at the termini of all herpesvirus genomes. In HHV-6, DRL and DRR are identical and a sequences may therefore also occur at the U-DR junctions to give the arrangement aDRLa-U-aDRRa. We have sequenced the genomic termini, the U-DRR junction, and the DRR.DRL junction of HHV-6 strain variants U1102 and Z29. A (GGGTTA)n motif identical to the human telomeric repeat sequence (TRS) was found adjacent to, but did not form, the termini of both strain variants. The DRL terminus and U-DRR junction contained sequences closely related to that of the well-conserved herpesvirus packaging signal Cn-Gn-Nn-Gn (pac-1), followed by tandem arrays of TRSs separated by single copies of a hexanucleotide repeat. HHV-6 strain U1102 contained repeat sequences not found in HHV-6 Z29. In contrast, the DRR terminus of both variants contained a simple tandem array of TRSs and a close homolog of a herpesvirus pac-2 signal (GCn-Tn-GCn). The DRR.DRL junction was formed by simple head-to-tail linkage of the termini, yielding an intact cleavage signal, pac-2.x.pac-1, where x is the putative cleavage site. The left end of DR was the site of intrastrain size heterogeneity which mapped to the putative a sequences. These findings suggest that TRSs form part of the a sequence of HHV-6 and that the arrangement of a sequences in the genome can be represented as aDRLa-U-a-DRRa.

Base Sequence↗
PubMed2006

Quantitative membrane electrostatics with the atomic force microscope.

The atomic force microscope (AFM) is sensitive to electric double layer interactions in electrolyte solutions, but provides only a qualitative view of interfacial electrostatics. We have fully characterized silicon nitride probe tips and other experimental parameters to allow a quantitative electrostatic analysis by AFM, and we have tested the validity of a simple analytical force expression through numerical simulations. As a test sample, we have measured the effective surface charge density of supported zwitterionic dioleoylphosphatidylcholine membranes with a variable fraction of anionic dioleoylphosphatidylserine. The resulting surface charge density and surface potential values are in quantitative agreement with those predicted by the Gouy-Chapman-Stern model of membrane charge regulation, but only when the numerical analysis is employed. In addition, we demonstrate that the AFM can detect double layer forces at a separation of several screening lengths, and that the probe only perturbs the membrane surface potential by <2%. Finally, we demonstrate 50-nm resolution electrostatic mapping on heterogeneous model membranes with the AFM. This novel combination of capabilities demonstrates that the AFM is a unique and powerful probe of membrane electrostatics.

Algorithms↗
PubMedDate not supplied

[Genetic deafness: a brief review].

In this article, we present a brief literature review of hereditary deafness, considering the main historical aspects, genetic heterogeneity, gene mapping and the problems related to genetic counseling.

English Abstract↗
PubMed1990

Lectins and immunohistochemistry of colorectal cancer, its recurrences and metastases.

In 31 patients resected specimens from primary colorectal cancers, corresponding liver metastases and local recurrences were investigated for the staining pattern of lectins (PNL, UEA, WGA, HPA, SBA, RCA) and tissue antigens (CEA, SP, ACT) by immunohistochemistry. Comparison of staining patterns showed a loss of marker expression from normal colonic mucosa to colorectal primary carcinomas, and a tendency to marker loss from the primary tumour to liver metastases. However, even a neo-expression of markers not present in the primary tumour could be observed. For clinical use, serum markers observed in patient follow-up may be valuable even where the findings are negative at the time of primary tumour surgery. In contrast to the heterogenous marker map of primary tumours and metastases, comparison of primary and locally recurrent tumour revealed a staining pattern that was almost always identical. This supports the hypothesis that locoregional recurrences develop from remnant cells of the primary tumour left behind at surgery. There is no support for the thesis that locoregional recurrences arise from mucosal changes at the anastomosis or from suture material.

Adenocarcinoma↗
PubMed1999

A new locus for autosomal dominant "pure" hereditary spastic paraplegia mapping to chromosome 12q13, and evidence for further genetic heterogeneity.

Autosomal dominant pure hereditary spastic paraplegia (ADPHSP) is clinically characterized by slowly progressive lower-limb spasticity. The condition is genetically heterogeneous, and loci have been mapped at chromosomes 2p, 8q, 14q, and 15q. We have performed a genomewide linkage screen on a large family with ADPHSP, in which linkage to all four previously known loci was excluded. Analysis of markers on chromosome 12q gave a peak pairwise LOD score of 3.61 at D12S1691, allowing us to assign a new locus for ADPHSP (a locus that we have designated "SPG10") to this region. Haplotype construction and analysis of recombination events narrowed the SPG10 locus to a 9.2-cM region between markers D12S368 and D12S83. In addition, our data strongly suggest that there are at least six ADPHSP loci, since we describe a further family in which linkage to all five known ADPHSP loci has been excluded.

Adolescent↗