Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “RNA Aggregation”

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 1,171 records · Page 65Linked to original sources
PubMed1998

MEMD, a new cell adhesion molecule in metastasizing human melanoma cell lines, is identical to ALCAM (activated leukocyte cell adhesion molecule).

From a differential mRNA display comparing a non- and a highly metastasizing human melanoma cell line, we isolated and characterized memD. memD is preferentially expressed in the highly metastasizing melanoma cell lines of a larger panel. The encoded protein, MEMD, is identical to activated leukocyte cell adhesion molecule (ALCAM), a recently identified ligand of CD6. ALCAM is involved in homophylic (ALCAM-ALCAM) and heterophylic (ALCAM-CD6) cell adhesion interactions. We have studied MEMD/ALCAM cell-cell interactions between human melanoma cells. The expression of this cell adhesion molecule not only correlates with enhanced metastatic properties and with aggregational behavior of human melanoma cells as tested by FACS analysis, but transfection experiments also make clear that MEMD/ALCAM expression is essential for cell-cell interaction of the investigated human melanoma cells. As the melanoma cell lines analyzed are all CD6 negative, these results strongly suggest that MEMD/ALCAM is an adhesion molecule mediating homophylic clustering of melanoma cells. MEMD/ALCAM expression is not restricted to subsets of leukocytes and melanoma cells, it can also be found in healthy organs and in several other malignant tumor cell lines. Besides, MEMD/ALCAM is also expressed in cultured endothelial cells, pericytes and melanocytes, in xenografts derived from the radial and vertical growth phase and in 4 of 13 melanoma metastasis lesions. The potential role is discussed of MEMD/ALCAM mediated cell-cell interactions in migration of mobile cells (ie, activated leukocytes, metastasizing tumor cells) through tissues.

Activated-Leukocyte Cell Adhesion Molecule↗
PubMed2026

DPAS-Graph: adaptive spatial-feature relation learning for spatial RNA-to-protein prediction and virtual protein profiling.

Paired spatial multi-omics provides a supervised basis for learning RNA-protein correspondence in situ, but predicting protein abundance from spatial transcriptomic data alone remains challenging across tissue contexts and protein panels. Here, we present DPAS-Graph, an adaptive relation-learning framework for spatial RNA-to-protein prediction. Rather than directly merging spatial proximity and transcriptomic similarity as fixed graph priors, DPAS-Graph represents them as two relation channels on a shared edge support and updates their contributions during representation learning for protein prediction. Its Niche-Coupled Field Encoder combines layer-wise edge-relation modeling, intra-branch relation refinement, and cross-branch residual correction to learn spot representations for protein abundance prediction. In a leave-one-dataset-out benchmark across seven paired spatial multi-omics datasets, DPAS-Graph achieved lower aggregate prediction errors and improved spot-level agreement of protein expression profiles, with gains mainly reflected in error-based metrics and PCC-Spot. Spatial autocorrelation and protein-derived domain agreement analyses were further used to characterize the spatial behavior of the predicted protein maps. When applied to external RNA-only spatial sections, DPAS-Graph generated qualitatively interpretable marker-level virtual protein maps, illustrating its use as a complementary tool for protein-level interpretation of transcriptomics-only spatial data.

RNA↗
PubMed1992

Effects of the extracellular matrix on fetal choroid plexus epithelial cells: changes in morphology and multicellular organization do not affect gene expression.

We have developed a primary culture system for fetal mouse choroid plexus epithelial cells which maintains their differentiated phenotype. When grown on a reconstituted basement membrane substrate (Matrigel) epithelial cells formed aggregates which became embedded in the matrix and developed into characteristic and highly reproducible multicellular vesicular structures. These vesicles consisted of a squamous layer of epithelial cells with extensive attachment to the matrix substrate, surrounding a fluid-filled lumen. Electron microscopy showed that cells comprising these vesicles had a high degree of membrane specialization and polarized morphology which in many respects mimicked the in vivo morphology. Biochemical analyses demonstrated that under these culture conditions the tissue-specific pattern of gene expression of fetal choroid plexus epithelium was maintained. After 6 days in culture these cells contained approximately the same amount of transthyretin mRNA as the 12.5-day choroid plexus in vivo, and the level of total RNA per cell, which is proportional to the protein synthetic capability of the cells, was also maintained. The pattern of protein secretion was also very similar to that generated by fetal mouse choroid plexus cells in vivo. In contrast choroid plexus epithelial cells attached poorly to collagen I gels. Heterogeneous aggregates were formed in which cell-cell interactions were more extensive than cell-substrate interactions, and in no cases was a central lumen observed. Cells on the surface of large aggregates showed some evidence of membrane polarization, while the majority of cells in the cultures exhibited little evidence of polarized morphology. Despite the striking difference in morphology and multicellular organization these cells still expressed high levels of transthyretin mRNA and maintained the same pattern of protein synthesis as cells cultured on Matrigel. These results indicate that the basement membrane is important for the organization of choroid plexus epithelial cells into a functional epithelium in vitro and thus presumably the maintenance of the integrity of the blood-brain barrier in vivo. In contrast to several other epithelial systems which have been studied, the type of extracellular matrix does not appear to directly influence tissue-specific gene expression by choroid plexus epithelial cells. Thus the level of gene expression is not dependent on the cytoarchitecture and multicellular organization of this cell type.

Animals↗
PubMed1994

Purification, properties, and subcellular localization of foxtail mosaic potexvirus 26-kDa protein.

The open reading frame 2 (ORF2) of the potexviral genome encodes a 24- to 26-kDa protein which is part of the "triple gene block," a group of overlapping ORFs also present in the genomes of the carla-, hordei-, and furoviruses. The product of these ORFs is believed to play a role in the cell-to-cell movement of the viruses in host plants. The amino acid sequences of the homologous ORF2 products encoded by these related viruses suggest that they specify NTP binding and possibly helicase activities. We have used an Escherichia coli expression system to produce significant amounts of the 26-kDa protein (p26) encoded by foxtail mosaic potexvirus ORF2. p28 was purified to near homogeneity by conventional purification methods and some of its biochemical properties were determined. We present evidence that p26 is an ATP, CTP, and RNA binding protein with apparent ATPase activity. Western blot analysis of infected plant extracts using a polyclonal antiserum produced against p26 indicates that it is a relatively stable protein maintained at high levels for at least 6 days following its peak level of expression. Moreover, it is found predominantly in the soluble fraction of infected tissues. An immunocytochemical analysis of infected Chenopodium quinoa leaves reveals that p26 is exclusively associated with cytoplasmic inclusions in proximity to but distinct from aggregates of viral particles.

Adenosine Triphosphatases↗
PubMed2006

The impact of genetic variation in the region of the GPIIIa gene, on Pl expression bias and GPIIb/IIIa receptor density in platelets.

Some studies have suggested that genetic variability in the glycoprotein (GP) IIIa gene modulates expression of platelet GPIIb/IIIa (alpha(2b)beta(3)). We sought to determine as to whether combinations of genetic variants within the GPIIIa gene (haplotypes) influenced the expression of GPIIIa RNA and protein levels in human platelets. Three promoter polymorphisms, Pl(A1/A2) genotype and platelet receptor densities were determined in 207 acute coronary syndrome (ACS) patients. Allele-specific quantitative reverse transcription-polymerase chain reaction of platelet RNA from Pl(A1/A2) heterozygotes identified a greater expression of Pl(A2) bearing transcripts among heterozygotes. Among the patients studied, the ratio of Pl(A1)/Pl(A2) RNA expression was significantly influenced by promoter haplotype (P < 0.01). However, this effect reflected carriership of rare not common haplotypes (P = 0.2). There was a threefold variation between subjects in the number of GPIIb/IIIa receptors expressed per platelet, although no association between receptor density and the Pl(A2) (P = 0.93) or promoter polymorphisms was demonstrated (-468A, P = 0.52; -425C, P = 0.59; -400A, P = 0.52). Among common haplotypes, Pl(A1)/Pl(A2) RNA expression was negatively correlated with adjusted GPIIb/IIIa receptor density (P = 0.04). The overall trend towards higher expression of Pl(A2) bearing message in Pl(A1/A2) heterozygotes, and the existence of rare haplotypes with more pronounced changes indicate the existence of cis-acting genetic factors that remain to be identified.

Analysis of Variance↗
PubMed2004

Characterization of a multicopper oxidase gene cluster in Phanerochaete chrysosporium and evidence of altered splicing of the mco transcripts.

A cluster of multicopper oxidase genes (mco1, mco2, mco3, mco4) from the lignin-degrading basidiomycete Phanerochaete chrysosporium is described. The four genes share the same transcriptional orientation within a 25 kb region. mco1, mco2 and mco3 are tightly grouped, with intergenic regions of 2.3 and 0.8 kb, respectively, whereas mco4 is located 11 kb upstream of mco1. All are transcriptionally active, as shown by RT-PCR. Comparison of cDNAs and the corresponding genomic sequences identified 14-19 introns within each gene. Based on homology and intron composition, two subfamilies of mco sequences could be identified. The sequences have copper-binding motifs similar to ferroxidase proteins, but different from fungal laccases. Thus, these sequences constitute a novel branch of the multicopper oxidase family. Analysis of several cDNA clones obtained from poly(A) RNA revealed the presence of transcripts of various lengths. Splice variants from mco2, mco3 and mco4 were characterized. They generally exhibited the presence of one to five introns, whereas other transcripts lacked some exons. In all cases, the presence of introns leads to frame shifts that give rise to premature stop codons. In aggregate, these investigations show that P. chrysosporium possesses a novel family of multicopper oxidases which also feature clustering and incomplete processing of some of their transcripts, a phenomenon referred to in this paper as 'altered splicing'.

Alternative Splicing↗
PubMed2005

Isolation and identification of an EPS-producing Rhizobium strain from arid soil (Algeria): characterization of its EPS and the effect of inoculation on wheat rhizosphere soil structure.

The production of exopolysaccharides (EPSs) by bacterial populations in the rhizosphere has been demonstrated to contribute to water and nutrient uptake by plant roots through the modification of the physical properties of rhizosphere soil. We report here the characterization of a new EPS produced by a bacterial strain (KYGT207) isolated from an arid soil in southern Algeria (Gassi Touil), and the effect of inoculation of this strain on soil physical properties in the rhizosphere of Triticum durum L. Strain KYGT207 was assigned to the genus Rhizobium by 16S ribosomal DNA sequencing and belongs to a new species closely related to Rhizobium sullae. The EPS produced by this strain was found to be composed of glucose (Glc), galactose (Gal), and mannuronic acid (ManA) in a molar ratio of 2:1:1. The primary structure of the EPS was determined by sugar analysis, 1D and 2D NMR spectroscopy, consisting of a tetrasaccharide repeating unit with the following original structure: [structure: see text]. A rheological analysis showed that this EPS could be considered as a thickening agent with polyelectrolyte properties. Inoculation of wheat plantlets with strain KYGT207 caused significant promotion of plant growth (+85% for shoot dry mass and +56% for root dry mass), a significant increase in root-adhering soil (RAS) dry mass (dm) per root dm (RAS/RT) up to 137%, and in RAS aggregate water stability. We demonstrate that EPS-producing bacteria were present in sandy soils subjected to water stress and that EPS-producing Rhizobium populations play an important role in the rhizosphere through their contribution to soil aggregation.

Algeria↗
PubMed1995

The effect of histone H1 and DNA methylation on transcription.

We have previously shown that DNA methylation acts as a focus for the formation of inactive chromatin in vivo. We have investigated the mechanism further by in vitro transcription of a template containing two tRNA genes and an extensive (G+C)-rich sequence characteristic of a CpG island. The extent of transcription from the unmethylated or fully methylated template was assayed in the presence of varied levels of histone H1. The transcriptional activity of both templates was inhibited by increasing amounts of histone H1, although inhibition with the methylated template occurs at a lower H1:DNA ratio. The H1c variant shows the greatest preferential inhibition of the methylated template. We demonstrated that histone H1 complexed to DNA is one of the factors that inhibits transcription by preventing the formation of initiation complexes, particularly on methylated template, rather than the formation of disordered H1.DNA aggregates.

Ammonium Sulfate↗
PubMed2025

Multi-criteria decision making and its application to in silico discovery of vaccine candidates for Toxoplasma gondii.

Vaccine discovery against eukaryotic parasites is not trivial and few exist. Reverse vaccinology is an in silico vaccine discovery approach, designed to identify vaccine candidates from the thousands of protein sequences encoded by a target genome. Previously, we produced the Vacceed bioinformatics pipeline for identification of parasite membrane and excreted/secreted proteins that were likely be exposed to the hosts immune system. More recently, we improved upon machine learning as the final decision-making process to identify parasite proteins that induce a protective response in an animal model. Subsequently, we combined Vacceed with metrics on B and T cell epitope types to produce a new in silico discovery workflow. In this study we extend this in silico workflow to the developability of proteins as vaccines by the incorporation of metrics on the physicochemical properties of proteins. To demonstrate this process, every Toxoplasma gondii protein was ranked in its capacity to provide exposure to the immune system (Vacceed exposure score), presence of epitopes and solubility characteristics by several multicriteria decision making (MCDM) tools (such as TOPSIS, VIKOR and MABAC). A consensus rank was subsequently generated from the results of these tools using a variety of aggregate ranking methods. Levels of uncertainty in the aggregate protein rankings was assessed by conformal interval prediction in association with a machine learning model. Several of the top ranked proteins identified by this approach were novel, uncharacterized membrane transporters or proteins associated with RNA metabolism. In conclusion, MCDM automated the decision making using well known algorithms while conformal prediction intervals varied significantly across the 8000+ proteins of T. gondii. Highly ranked proteins (e.g. the top 100) typically generated low prediction intervals, providing high levels of confidence in their ranks.

Toxoplasma↗
PubMed2004

Nuclear body movement is determined by chromatin accessibility and dynamics.

Promyelocytic leukemia (PML) and Cajal bodies are mobile subnuclear organelles, which are involved in activities like RNA processing, transcriptional regulation, and antiviral defense. A key parameter in understanding their biological functions is their mobility. The diffusion properties of PML and Cajal bodies were compared with a biochemically inactive body formed by aggregates of murine Mx1 by using single-particle tracking methods. The artificial Mx1-yellow fluorescent protein body showed a very similar mobility compared with PML and Cajal bodies. The data are described quantitatively by a mechanism of nuclear body movement consisting of two components: diffusion of the body within a chromatin corral and its translocation resulting from chromatin diffusion. This finding suggests that the body mobility reflects the dynamics and accessibility of the chromatin environment, which might target bodies to specific nuclear subcompartments where they exert their biological function.

Adenosine Triphosphate↗
PubMed2001

Studies on the role of the minor capsid protein in transport of Beet western yellows virus through Myzus persicae.

Beet western yellows virus (BWYV), family Luteoviridae, is an icosahedral plant virus which is strictly transmitted by aphids in a persistent and circulative manner. Virions cross two cellular barriers in the aphid by receptor-based mechanisms involving endocytosis and exocytosis. Particles are first transported across intestinal cells into the haemolymph and then across accessory salivary gland cells for delivery to the plant via saliva. We identified the midgut part of the digestive tract as the site of intestinal passage by BWYV virions. To analyse the role in transmission of the minor capsid component, the readthrough (RT) protein, the fate of a BWYV RT-deficient non-transmissible mutant was followed by transmission electron microscopy in the vector Myzus persicae. This mutant was observed in the gut lumen but was never found inside midgut cells. However, virion aggregates were detected in the basal lamina of midgut cells when BWYV antiserum was microinjected into the haemolymph. The presence of virions in the haemolymph was confirmed by a sensitive molecular technique for detecting viral RNA. Thus, transport of the mutant virions through intestinal cells occurred but at a low frequency. Even when microinjected into the haemolymph, the RT protein mutant was never detected near or in the accessory salivary gland cells. We conclude that the RT protein is not strictly required for the transport of virus particles through midgut cells, but is necessary for the maintenance of virions in the haemolymph and their passage through accessory salivary gland cells.

Animals↗
PubMed1967

Studies on ribosomes from barley leaves. Changes during senescence.

The effect of sucrose, Mg(2+) and deoxycholate on the yield of ribosomes from barley leaves was determined and the changes in the amount and the composition of ribosomes during senescence of intact and excised first seedling leaves were examined.The extraction medium containing 20 mm tris-HCl, 0.25 m sucrose, 1 mm MgCl(2) and 0.5% deoxycholate (pH 7.8) gave the maximum yield of polyribosomes and ribosomes. That polyribosomes were not non-specific aggregates was suggested by their capacity to synthesize nascent protein. During senescence of both intact and excised leaves polyribosomes and ribosomes were lost and the ribosomes-polyribosomes which originally contained 48% protein and 52% RNA showed substantial decline in the protein content during senescence indicating the degradation of ribosomes and the loss of their function.

Journal Article↗
PubMed2000

Stromal cell-derived factor-1 and macrophage-derived chemokine: 2 chemokines that activate platelets.

Platelets play roles in both thrombosis and inflammation, and chemokines that are released at sites of inflammation could potentially activate platelets. Among the chemokine receptors expressed on platelets, the CXCR4 is the receptor for chemokine stromal cell-derived factor-1 (SDF-1), and the CCR4 is the receptor for macrophage-derived chemokine (MDC). Of the chemokines tested, SDF-1 and MDC were the only 2 that activated platelets. Both are weak agonists, but they enhanced response to low-dose adenosine 5'-diphosphate (ADP), epinephrine, or serotonin. When SDF-1 and MDC were added together, full and brisk platelet aggregation occurred. Platelet activation by these 2 chemokines appears to involve distinct pathways: SDF-1 inhibited an increase in cyclic adenosine monophosphate (cAMP) following prostaglandin (PG) I(2), while MDC had no effect. In contrast, MDC, but not SDF-1, lead to Ca(++) mobilization by platelets. Further, second-wave aggregation induced by MDC in platelet-rich plasma was inhibited by aspirin, ADP scavenger creatine phosphate/creative phosphokinase (CP/CPK), and ARL-66096, an antagonist of the ADP P2T(AC) receptor involved in adenylyl cyclase inhibition. But the aggregation was not affected by A3P5PS, an inhibitor of the ADP P2Y receptor. SDF-1-induced aggregation was inhibited by aspirin, but it was only slightly affected by CP/CPK, ARL-66096, or A3P5PS. Finally, the presence of chemokines in platelets was determined. Reverse transcriptase-polymerase chain reaction studies with platelet RNA did not detect the presence of SDF-1 or MDC. In summary, SDF-1 and MDC are platelet agonists that activate distinct intracellular pathways. Their importance in the development of thrombosis at sites of inflammation needs to be further evaluated.

Actins↗
PubMed1989

DNA binding protein from Streptomyces hygroscopicus: detection of binding by gel retardation, sedimentation and effects on the transcriptional activity in vitro.

The binding to supercoiled plasmid DNA as well as to double-stranded short DNA fragments of the DNA binding protein. ASBIII, from S. hygroscopicus has been demonstrated by gel retardation asay. As further revealed by sedimentation analysis, the protein-DNA complex formation also involves condensation of DNA and an aggregation step at higher total protein-to-DNA ratio (w/w). In vitro studies of the transcriptional activity of DNA-protein complexes showed that the ASBIII protein inhibits the overall template activity in the RNA polymerase II system to nearly similar extents for various DNA's. Preincubation of ASBIII-DNA complexes of different GC content, however, suggested a selective inhibitory effect on GC-rich DNA due to the higher stability of this complex. The results also indicate that the initiation of transcription of the GC-rich DNA template is affected by the ASBIII protein. The present results on the DNA binding properties and inactivation of the transcription of the ASBIII protein suggest that this protein may be a potential candidate for the local compaction of chromosomal DNA in Streptomyces hygroscopicus.

Animals↗
PubMed1983

Repair of a calcium-dependent adhesive mechanism of embryonic neural retina cells: kinetic and molecular analysis.

In this paper, we examine the restitution of a Ca2+-dependent adhesive system of embryonic chick neural retina cells following trypsinization in the absence of divalent cations. The processes involved in the restitution of this system are dissected by monitoring the effects of various drugs, alone and in specific combinations, on the kinetics of adhesion and the morphology of 24-h aggregates. In agreement with prior observations, aggregate formation can be separated into two distinct phases: the formation of adhesions and their ultimate stabilization. The formation of adhesions appears to involve two processes, de novo synthesis of protein and mobilization of an endogenous pool, while stabilization requires de novo synthesis of RNA and protein glycosylation. We also examine the appearance of two cell surface molecules previously implicated in the function of the Ca2+-dependent adhesive system. The cells repaired in the presence or absence of the inhibitors and surface-iodinated at 3 and 5 h. The labelled molecules are then separated by two-dimensional polyacrylamide gel electrophoresis. The appearance of the two molecules, gp130/4.8 and gp70/4.8, is affected by the various drugs in a manner consistent with the effects of these agents on the kinetics of adhesion. These molecules appear to exist in endogenous pools and they are also synthesized de novo during the repair period.

Animals↗
PubMed2003

Microanatomic relationships between CD8+ cells and HIV-1-producing cells in human lymphoid tissue in vivo.

OBJECTIVE: Host immune responses are unable to fully suppress HIV-1 replication in lymphoid tissues. Microanatomic relationships between HIV-1-producing cells and CD8+ cells in lymphoid tissues were analyzed to determine whether there was evidence for an immune privileged site or impaired recognition of virus-producing cells. METHODS: CD8+ cell phenotypes were determined on disaggregated inguinal lymph node cells by flow cytometry for seven untreated HIV-1-infected subjects. Microanatomic relationships between HIV-1-producing cells and CD8+ cells were analyzed in lymph node sections from 15 HIV-1-infected individuals using in situ hybridization and immunohistochemical staining. RESULTS: Most (median, 96%) lymph node CD8+ cells coexpressed CD3. Frequencies of virus-producing cells detected by in situ hybridization correlated with plasma HIV-1 RNA concentration (Spearman rho = 0.70; p =.02; n = 11). The percentage of lymph node cells adjacent to virus-producing cells that were CD8+ (median, 29%) was not statistically different from the percentage of CD8+ cells in lymphoid tissue overall (median, 34%; p =.09). CONCLUSIONS: Multiple explanations could account for the observation that CD8+ cells do not preferentially accumulate around virus-producing cells including the possibility that HIV-1-specific CD8+ cells cannot recognize virus-producing cells. Further studies are necessary to determine whether HIV-1-specific CD8+ T cells aggregate around virus-producing cells in lymphoid tissue.

CD8-Positive T-Lymphocytes↗