SEARCH · PubMed Health

Results for “reference mapping”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 199 records · Page 11Linked to original sources

PubMed2003

Genetic analysis and genome mapping in Raphanus.

The first genetic map of the Raphanus genome was developed based on meiosis in a hybrid between Raphanus sativus (cultivated radish) and Raphanus raphanistrum (wild radish). This hybrid was used to produce a BC1 population of 54 individuals and an F2 population of 85 individuals. A total of 236 marker loci were assayed in these populations using a set of 144 informative Brassica RFLP probes previously used for genetic mapping in other crucifer species. The genetic maps derived from the BC1 and F2 populations were perfectly collinear and were integrated to produce a robust Raphanus map. Cytological observations demonstrated strict bivalent pairing in the R. sativus x R. raphanistrum hybrids. Productive pairing along the length of each chromosome was confirmed by the identification of nine extensive linkage groups and the lack of clustering of marker loci. Indeed, the distributions of both marker loci and crossovers was more random than those reported for other crop species. The genetic markers and the reference map of Raphanus will be of considerable value for future trait mapping and marker-assisted breeding in this crop, as well as in the intergenomic transfer of Raphanus genes into Brassica crops. The future benefits of comparative mapping with Arabidopsis and Brassica species are also discussed.

Chromosome Mapping↗

PubMed2006

Characterization of cell wall associated proteins of a Staphylococcus aureus isolated from bovine mastitis case by a proteomic approach.

Staphylococcus aureus causes different pathologies in humans and animals. In particular, it is involved in intramammary infections in cows, causing economic losses and milk-safety problems. Although it is well-known that surface components (proteins and capsular polysaccharides) and exotoxins are virulence factors involved in the pathogenesis of bovine mastitis, less is known about the precise biochemical identity of such molecules. Therefore, mapping of surface proteins using specific disease- and environment-isolates provides a benchmark for strain comparison of pathogens with different pathogenic characteristics and antibiotic resistance mechanism and can aid in defining specific vaccine and therapeutic targets. In this study, we used a proteomic approach on protein extracts of lysostaphin-treated S. aureus in isotonic conditions, to produce a reproducible and well resolved 2-D electrophoresis (2-DE) reference map of surface associated proteins of isolated S. aureus from a case of bovine mastitis. The most abundant protein components were identified by Matrix assisted laser desorption ionisation-time of flight (MALDI-TOF) mass spectrometry.

Animals↗

PubMed1999

Probing for drug-induced multiplex signal transduction pathways using high resolution two-dimensional gel electrophoresis: application to beta-adrenoceptor stimulation in the rat C6 glioma cell.

Whole-cell [(32)P]-protein phosphorylation assays and two-dimensional gel electrophoresis (2-DGE) were applied to the analysis of the beta-adrenoceptor (betaAR)-linked signal transduction pathway. Rat C6 glioma cells were stimulated with isoproterenol and the protein lysates were resolved by 2-DGE. Two dimensional [(32)P]-phosphoprotein 'maps' were generated depicting the modulation of intracellular proteins after isoproterenol stimulation versus unstimulated cells. A total of 274 distinct phosphoprotein spots were detected, of which 200 were up-regulated, 69 were down-regulated, and 5 remained unchanged. An evaluation of isoproterenol's activity across several kinase pathways was performed using a computer-generated 2-DGE template incorporating the location and identification of individual signaling phosphoprotein intermediaries. The template served as a 'reference map' for drug treatment comparisons. We observed a significant increase in the phosphorylation states of several nuclear transcription factors, notably CREB-1, ATF-1, NFkappaB/IkappaBalpha and ELK-1, but not c-Jun. A parallel series of radioimmunoprecipitation studies confirmed our 2-DGE findings. Moreover, isoproterenol increased the phosphorylation state of PKC and of several MAPK-dependent pathway kinases which correlated with a significant increase in their endogenous kinase activity. Isoproterenol's effects on PKA, PKC and ERK-dependent activities were blocked by propranolol, a betaAR antagonist. In conclusion, an acute isoproterenol stimulus induced multiplex pathway modulation via the betaAR in the C6 glioma cell indicating that signaling pathway cross-talk is an essential feature for the regulation of cellular function. Moreover, the immediate advantages of the 2-DGE analytical approach were apparent, and further development of the protein database will provide a valuable tool to screen for broad-based drug-mediated signaling activities.

Animals↗

PubMed2006

2-D protein maps of rat gastrocnemius and soleus muscles: a tool for muscle plasticity assessment.

Functional characterization of muscle fibers relies on ATPase activity and on differential measurements of metabolic proteins, including mitochondrial and glycolytic enzymes, glucose, lactate and lactic acid transporters, calcium cycling proteins and components of the contractile machinery. The recent introduction of microarray technology has enabled detailed gene expression studies under different physiological and pathological conditions, thus generating novel hypotheses on muscle function. However, microarray approaches are limited by the incomplete genome coverage of currently available chips, and by poor correlation between mRNA concentration and protein expression level. We have used 2-DE and MS to build a reference map of proteins from rat mixed gastrocnemius and soleus muscle, and to assess qualitative and quantitative differences in protein distribution between these two functionally dissimilar muscles. More than 800 spots on each gel were detected by silver staining, of which 167 were excised, digested in-gel with trypsin and analyzed by ESI-MS/MS. One hundred and twenty eight distinct gene products were identified, including metabolic, transport and contractile proteins. Forty one spots displayed differences in relative expression level between mixed gastrocnemius and soleus samples. These data not only enable differentiation of functionally distinct slow-twitch and fast-twitch fiber types, but also provide tools for investigating muscle plasticity in response to physiological and environmental conditions such as aging or hypoxia.

Aging↗

PubMed2026

GRNContext: an interactive web platform for contextualized gene regulatory networks visualization across human cancers.

SUMMARY: While current Gene Regulatory Network (GRN) databases provide comprehensive reference maps of potential interactions between transcription factors and target genes, they do not specify which regulatory interactions are active within specific biological contexts. This limitation is particularly critical in cancer, where transcriptional programs are inherently tissue-specific. To address this gap, we developed GRNContext, an interactive web platform designed for the visualization, exploration, and comparative analysis of gene regulatory networks contextualized across 33 cancer types from The Cancer Genome Atlas (TCGA). Our approach uses the TFLink human reference GRN as a starting point and integrates TCGA transcriptomic profiles to infer cancer-specific regulatory activity. Regulatory relevance was assessed using complementary machine learning and statistical methods, which were unified into a consensus score to prioritize and filter the most relevant candidate regulators for each target gene. By providing both curated context-specific GRNs and a user-friendly platform, GRNContext constitutes a comprehensive and accessible resource that supports mechanistic investigations, hypothesis generation, and translational research focused on transcriptional regulation in cancer. AVAILABILITY AND IMPLEMENTATION: GRNContext is supported by all major browsers and freely available on the web at https://apps.cienciavida.org/grncontext. It is implemented as a client-server web application featuring a FastAPI backend and a React frontend utilizing Cytoscape.js for interactive network visualization, all containerized via Docker for cross-platform compatibility.

Humans↗

PubMed1996

Current role and future perspectives for radiofrequency catheter ablation of postmyocardial infarction ventricular tachycardia.

The most common substrate for ventricular tachycardia (VT) is a postmyocardial infarction (MI) scar. Radiofrequency catheter ablation (RFCA) in post-MI VT faces clinical, electrophysiologic, anatomic, and methodologic difficulties not found in many other human tachycardias. The pathophysiologic understanding of post-MI VT is incomplete; this influences the process of selecting RFCA target sites, which is time consuming, demands catheter stability, and has low sensitivity and predictive value for VT interruption by RF current. Improving and simplifying the methodology of RFCA in post-MI VT is badly needed. We review the pathophysiology of post-MI VT from the data reported on endocardial, epicardial, and intramural ventricular mapping obtained either intraoperatively or in a Langendorff perfused set-up in hearts from transplanted patients. From these studies we conclude that (1) some post-MI VT cases are not amenable to RFCA (reentry around the scar, VT having a subepicardial or deep intramural substrate, or a wide, extensive, subendocardial intrascar area of slow conduction); and (2) searching for the endocardial exit is advantageous for selecting the RFCA targets. We also comment on a new self-reference mapping catheter that allows the recording of high gain, noise-free, unfiltered and filtered unipolar signals as well as unipolar pacing. Among the unresolved issues in these patients is the meaning of fast nonclinical VT induced after successful RFCA of the clinical VT, which may explain why a substantial number of these patients still receive an implantable cardioverter-defibrillator.

Catheter Ablation↗

PubMed2004

Mapping of the Physcomitrella patens proteome.

The moss Physcomitrella patens is unique among land plants due to the high rate of homologous recombination in its nuclear DNA. The feasibility of gene targeting makes Physcomitrella an unrivalled model organism in the field of plant functional genomics. To further extend the potentialities of this seed-less plant we aimed at exploring the P. patens proteome. Experimental conditions had to be adopted to meet the special requirements connected to the investigations of this moss. Here we describe the identification of 306 proteins from the protonema of Physcomitrella. Proteins were separated by two dimensional electrophoresis, excised form the gel and analysed by means of mass spectrometry. This reference map will lay the basis for further profound studies in the field of Physcomitrella proteomics.

Amino Acid Sequence↗

PubMed2006

Proteome analysis of cultured fibroblasts from type 1 diabetic patients and normal subjects.

CONTEXT: Protein profiling of diabetic tissues could provide useful biomarkers for early diagnosis, therapeutic targets, and disease response markers. Cultured fibroblasts are a useful in vitro model for proteome analysis and study of the molecular mechanisms involved in diabetes. OBJECTIVE: The objective of the study was to isolate and characterize the proteins of cultured fibroblasts, obtained by skin biopsy, from long-term type 1 diabetic patients without complications and age- and sex-matched normal subjects as controls. DESIGN: Proteins were separated by two-dimensional electrophoresis (2-DE), and the gel images were qualitatively and quantitatively analyzed. Protein identification was performed by matrix-assisted laser desorption/ionization mass spectrometry. RESULTS: Reproducible protein maps of fibroblasts from diabetic and healthy subjects were obtained. A total of 125 protein spots were isolated and identified, among them 27 proteins not previously reported in published human fibroblast 2-DE maps, including 20 proteins never reported previously in the literature in human skin fibroblasts. Quantitative analyses revealed six protein spots differentially expressed in the fibroblasts from the diabetic vs. the control subjects (P < 0.05), representing glycolytic enzymes and structural proteins. An increase of triosephosphate I isomerase of two splice isoforms of pyruvate kinase and alpha-actinin 4 and a decrease of tubulin-beta2 and splice isoform 2 of tropomyosin beta-chain were detected. CONCLUSIONS: We generated 2-DE reference maps of the proteome of human skin fibroblasts from both normal and uncomplicated type 1 diabetic patients. Differences in glycolytic enzymes and structural proteins were found. The functional implications of the identified proteins are discussed.

Adult↗

PubMed2005

Molecular cloning and genetic mapping of perennial ryegrass casein protein kinase 2 alpha-subunit genes.

The alpha-subunit of the casein protein kinase CK2 has been implicated in both light-regulated and circadian rhythm-controlled plant gene expression, including control of the flowering time. Two putative CK2alpha genes of perennial ryegrass (Lolium perenne L.) have been obtained from a cDNA library constructed with mRNA isolated from cold-acclimated crown tissue. The genomic organisation of the two genes was determined by Southern hybridisation analysis. Primer designs to the Lpck2a-1 and Lpck2a-2 cDNA sequences permitted the amplification of genomic products containing large intron sequences. Amplicon sequence analysis detected single nucleotide polymorphisms (SNPs) within the p150/112 reference mapping population. Validated SNPs, within diagnostic restriction enzyme sites, were used to design cleaved amplified polymorphic sequence (CAPS) assays. The Lpck2a-1 CAPS marker was assigned to perennial ryegrass linkage group (LG) 4 and the Lpck2a-2 CAPS marker was assigned to LG2. The location of the Lpck2a-1 gene locus supports the previous conclusion of conserved synteny between perennial ryegrass LG4, the Triticeae homoeologous group 5L chromosomes and the corresponding segment of rice chromosome 3. Allelic variation at the Lpck2a-1 and Lpck2a-2 gene loci was correlated with phenotypic variation for heading date and winter survival, respectively. SNP polymorphism may be used for the further study of the role of CK2alpha genes in the initiation of reproductive development and winter hardiness in grasses.

Amino Acid Sequence↗

PubMed2004

Mapping of bovine skeletal muscle proteins using two-dimensional gel electrophoresis and mass spectrometry.

The large individual variation in meat quality seen both within and between animals is not fully understood. Consequently, our long-term goal is to identify reliable proteins which control or determine bovine meat quality. Using a proteomic approach, bovine skeletal muscle samples were analyzed by two-dimensional gel electrophoresis (2-DE) using an immobilized pH 4-7 gradient in the first dimension and mass spectrometry. We first tested the reproducibility of the method. These experiments showed slightly greater intersample than intrasample variability. In order to evaluate the type of visualized proteins in 2-DE, we initiated the construction of a protein reference map of bovine Semitendinosus muscle. In total, 129 protein spots corresponding to 75 different gene products were identified. Of these proteins, the largest portion is involved in metabolism (25.5%), cell structure (17%), cell defense (16%) and contractile apparatus (14.5%). One quarter of the identified proteins are represented by two or several protein spots and multiple isoforms of troponin T are present. Peptide mass fingerprint results indicate that these isoforms are partly generated by alternative splicing. The data presented here are an important step for further proteome analyses on bovine muscle. This may lead to progress in understanding the mechanisms controlling postmortem muscle metabolism and meat quality.

Alternative Splicing↗

PubMed1982

Some extensions to the GELLAB two-dimensional electrophoretic gel analysis system.

Several important extensions to the GELLAB 2D electrophoresis gel analysis system are discussed, including concepts that lead to the generation of consistent gel maps for a particular cell line, as illustrated by some recent results for the P388D1 cell system, GELLAB is an interactive graphics computer system that facilitates (a) image accessioning, (b) spot-data extraction from the image with position and density quantitation, (c) pairing of corresponding spots between gels, and (d) spot analysis for a large number of corresponding spots (over 3000 per gel) for up to 128 gels. Multiple gels are accessioned into the system used to create a composite gel data base. These then may be partitioned into multiple classes of gels and searched for statistically significant interclass spot differences, which can be visualized in reference map images of selected spot sets as well as mosaic images of particular spots in all gels. In addition to the visual feedback that is available during the gel analysis, various statistical, numerical, and other displays may be generated in the CGELP interactive program of the GELLAB system.

Animals↗

PubMed2006

Real-time rigid body motion correction and shimming using cloverleaf navigators.

Subject motion during scanning can greatly reduce MRI image quality and is a major reason for discarding data in both clinical and research scanning. The quality of the high-resolution structural data used for morphometric analysis is especially compromised by subject movement because high-resolution scans are of longer duration. A method is presented that measures and corrects rigid body motion and associated first-order shim changes in real time, using a pulse sequence with embedded cloverleaf navigators and a feedback control mechanism. The procedure requires a 12-s preliminary mapping scan. A single-path, 4.2-ms cloverleaf navigator is inserted every repetition time (TR) after the readout of a 3D fast low-angle shot (FLASH) sequence, requiring no additional RF pulses and minimally impacting scan duration. Every TR, a rigid body motion estimate is made and a correction is fed back to adjust the gradients and shim offsets. Images are corrected and reconstructed on the scanner computer for immediate access. Correction for between-scan motion can be accomplished by using the same reference map for each scan repetition. Human and phantom tests demonstrated a consistent improvement in image quality if motion occurred during the acquisition.

Algorithms↗

PubMed2025

Architectural transcription factors collectively shape nuclear radial positioning of chromatin contacts.

The measurement of three-dimensional genome folding in the nucleus, mostly through Hi-C methods, is expressed as contact frequencies between genomic segments, without anchoring to physical axes of the spherical nucleus. Here, we mapped the chromatin contacts along nuclear radial axis and built radial score by factoring in contact frequencies. The chromatin high-order structures exhibit rich diversity along radial axis. Furthermore, the proximal trans contacts retrieved by radial score reveal conserved active/inactive chromatin segregation across intra- and interchromosomal interactions. Ablation of CTCF proteins disrupts chromatin loops with mild changes to chromatin radial positioning. By acutely perturbing multiple transcription factor (TF) occupancy, chromatin loop dissolutions are often accompanied by radial dissociations between two anchors. Our work provides a genome architecture reference map adhering to nuclear physical axis and suggests that multiple architectural TFs collectively shape nuclear positioning of chromatin and their contacts, with contacts serving as forces on chromatin positioning as well.

Chromatin↗

PubMed2004

Microsatellite markers associated with two Aegilops tauschii-derived greenbug resistance loci in wheat.

A new source of greenbug (Schizaphis graminum Rondani) resistance derived from Aegilops tauschii (Coss.) Schmal was identified in W7984, a synthetic hexaploid wheat line and one parent of the International Triticeae Mapping Initiative (ITMI) mapping population. Segregation analysis of responses to greenbug feeding in a set of recombinant inbred lines (RILs) identified a single, dominant gene governing the greenbug resistance in W7984, which was placed in chromosome arm 7DL by linkage analysis with molecular markers in the ITMI population. Allelism tests based on the segregation of responses to greenbug feeding in F2 and testcross plants revealed that the greenbug resistance in W7984 and Largo, another synthetic line carrying the greenbug resistance gene Gb3, was controlled by different but linked loci. Using the ITMI reference map and a target mapping strategy, we have constructed a microsatellite map of Gb3 in a mapping population of 130 F7 RILs from Largo x TAM 107 and identified one marker (Xwmc634) co-segregating with Gb3 and four markers (Xbarc76, Xgwm037, Xgwm428 and Xwmc824) closely linked with Gb3. Deletion mapping of selected microsatellite markers flanking the Gb3 locus placed this resistance gene into the distal 18% region of 7DL. Comparative mapping in the ITMI and Largo x TAM 107 populations using the same set of microsatellite markers provided further evidence that greenbug resistance in W7984 and Largo is conditioned by two different loci. We suggest that the greenbug resistance gene in W7984 be designated Gb7. The microsatellite map of Gb3 constructed from this study should be a valuable tool for marker-assisted selection of Gb3-conferred greenbug resistance in wheat breeding.

Animals↗

PubMed1999

Use of a geographic information system to determine appropriate means of trauma patient transport.

OBJECTIVE: To determine whether a geographic information system (GIS) and historical transport data can be used to create a map that identifies locations (zones) from which either ambulance or helicopter transport will result in shorter out-of-hospital times. METHODS: A retrospective, cross-sectional review of a trauma registry was conducted in a two-county region served by a single trauma center. Data were gathered for all patients transported directly to the trauma center between 1993 and 1996. Incident locations and times from first 911 contact until arrival at the trauma center (out-of-hospital time) were extracted. A GIS was used to create a reference map with all incident locations plotted and given z-coordinates corresponding to out-of-hospital time. Two contour surfaces were interpolated: one for all helicopter transports and one for all ground transports. Areas where the helicopter surface was lower than the ambulance surface were designated air zones since helicopter transport resulted in shorter out-of-hospital times. The remaining area was designated a ground zone since ambulance transport resulted in shorter out-of-hospital times. The mean out-of-hospital times were calculated for each mode of transport in both zones and were compared using a two-tailed t-test. RESULTS: An air zone was identified beginning between 5 and 16 miles from the trauma center. Mean (+/-SD) out-of-hospital time from the air zone was 50 +/- 9 minutes for helicopter transport (n = 54) and 63 +/- 14 minutes for ambulance transport (n = 140). The difference between the means was 13 minutes (p < 0.000001; 95% CI = 8.95 to 17.05). Mean out-of-hospital time from the ground zone was 68 +/-16 minutes for helicopter transport (n = 122) and 32 +/- 14 minutes for ambulance transport (n = 2,047). The difference between the means was 36 minutes (p < 0.000001; 95% CI = 33.59 to 38.41). CONCLUSIONS: A GIS and historical transport data can be used to create a map identifying locations from which either helicopter or ambulance transport will minimize out-of-hospital time. Inappropriate choice of transport mode is associated with increased out-of-hospital time.

Aircraft↗

PubMed1993

Deletion mapping and a highly reduced radiation hybrid in the Xp22.3-p22.2 region.

The human Xp22.3-p22.2 region contains several known disease genes as well as distinctive families of low copy repetitive sequences. In this study, we have developed new tools to more finely map this area. We have characterized a mapping panel of various cell lines and hybrids with different molecular breakpoints as defined by previously mapped reference markers from this region. The panel subdivides this area into nine distinct regions from DXS41 through the pseudoautosomal boundary. We have also identified a radiation-reduced somatic cell hybrid, Z4-7, that contains DXS31, DXS452, STS, DXS143, and DXS85, but not PABX, DXS16, or other single-copy probes from proximal Xp and Xq. A phage library was constructed from Z4-7 and over 80,000 plaques were screened with total human DNA. More than 100 positive clones were identified as potential new markers in this region. Nine of these have been mapped to the hybrid panel, and unique subclones have been isolated from three of these markers. The panel has also allowed us to map several other DNA markers, genes (AMG, OA1), and repetitive elements of the DXF22S and DXF30S sequence families relative to the various breakpoints.

Albinism, Ocular↗

PubMed2004

Two-dimensional maps and databases of the human macrophage proteome and secretome.

Macrophages exert a crucial, but still incompletely known, role in complex disorders such inflammatory, immunological, and infectious diseases. A differential proteomic approach should help to elucidate the macrophage dysfunctions involved in these diseases. With this goal in mind, we established the first two-dimensional maps of the human macrophage proteome and secretome. Intracellular and secreted proteins were extracted from monocyte-derived macrophages obtained from healthy donors (n = 16), and separated by two-dimensional gel electrophoresis. Silver-stained gels were analyzed using Progenesis software. A high level of between-gel reproducibility was obtained, allowing us to generate two patterns specific of the macrophage proteome and secretome, respectively. A total of 127 and 66 distinct intracellular and secreted polypeptide spots, corresponding to 100 and 38 different proteins, respectively, were identified by matrix assisted laser desorption/ionisation-mass spectrometry. The two-dimensional reference maps and databases resulting from this study confirm that macrophages are involved in a wide range of biological functions, and that they provide a useful tool for a wide array of investigators involved in macrophage biology, allowing to investigate the macrophage protein changes associated with various disorders or environmental stimuli.

Databases, Protein↗

PubMed2006

Alternative workflows for plant proteomic analysis.

High-throughput separations are intrinsic to the detection and analysis of peptides and proteins by mass spectrometry (MS). Together, efficient separation and MS can lead to the identification of thousands of proteins in a sample, cell or tissue and help build proteome maps that can be used to define a cell type or cellular state. Although 2D gels have been successfully used to separate proteins for subsequent MS analysis, alternative separation efficiencies and, consequently deeper results could be obtained with HPLC or other separation techniques that improve throughput. This highlight is aimed toward plant scientists who have special separation needs due to the nature of plant cells and who could benefit from knowing options and requirements for adopting alternative separation protocols. Through the various sample processing and protein separation strategies, plant biologists should be able to improve the quality of their proteomic reference maps and gain new information about the proteins that define plant cells.

Chromatography, High Pressure Liquid↗