Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “compartmentalization”

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 163 records · Page 9Linked to original sources
PubMed2003

Eukaryotic genome evolution: rearrangement and coevolution of compartmentalized genetic information.

The plant cell operates with an integrated, compartmentalized genome consisting of nucleus/cytosol, plastids and mitochondria that, in its entirety, is regulated in time, quantitatively, in multicellular organisms and also in space. This genome, as do genomes of eukaryotes in general, originated in endosymbiotic events, with at least three cells, and was shaped phylogenetically by a massive and highly complex restructuring and intermixing of the genetic potentials of the symbiotic partners and by lateral gene transfer. This was accompanied by fundamental changes in expression signals in the entire system at almost all regulatory levels. The gross genome rearrangements contrast with a highly specific compartmental interplay, which becomes apparent in interspecific nuclear-plastid cybrids or hybrids. Organelle exchanges, even between closely related species, can greatly disturb the intracellular genetic balance ("hybrid bleaching"), which is indicative of compartmental coevolution and is of relevance for speciation processes. The photosynthetic machinery of plastids, which is embedded in that genetic machinery, is an appealing model to probe into genomic and organismic evolution and to develop functional molecular genomics. We have studied the reciprocal Atropa belladonna-Nicotiana tabacum cybrids, which differ markedly in their phenotypes, and found that transcriptional and post-transcriptional processes can contribute to genome/plastome incompatibility. Allopolyploidy can influence this phenomenon by providing an increased, cryptic RNA editing potential and the capacity to maintain the integrity of organelles of different taxonomic origins.

Atropa belladonna↗
PubMed2002

Oscillatory and chaotic dynamics in compartmentalized geometries.

The effects of spatial compartmentalization of a multistep reaction mechanism (Willamowski-Rössler model) whose mass action rate law shows oscillations and chaotic dynamics are explored. The mechanism is decomposed into subsets of reactions that are then assumed to take place in distinct regularly or randomly distributed spatial domains in the system. The reactive domains are coupled by diffusion. The spatiotemporal system states are investigated as a function of the system size and geometrical arrangement of the domains. A compartmentalization is chosen where the isolated domain attractors are simple steady states. It is then shown that changes in the system size or domain geometry can produce bifurcations leading to simple or period-doubled oscillatory attractors as well as chaotic states. These bifurcations are analyzed by direct simulations of the compartmentalized reaction-diffusion equations and by an analysis in terms of integral equations.

Journal Article↗
PubMed1975

Compartmentation in Vicia faba Leaves: II. Kinetics of C-Sucrose Redistribution among Individual Tissues following Pulse Labeling.

Leaflets of Vicia faba L. were pulse labeled with (14)CO(2) and the kinetics of (14)C-sucrose redistribution among individual tissues was followed. Sucrose specific activity in the whole leaf peaked about 15 minutes after labeling and declined with a half-time of about 80 minutes. In one experiment, leaflet discs taken at various times during the (12)CO(2) chase were quick frozen, freeze-substituted, and embedded in plastic. The tissue was sectioned paradermally and sections of palisade parenchyma, of spongy parenchyma, and of spongy parenchyma that contained veins were collected. Water extracts from these sections were assayed for sucrose specific activity. Sucrose specific activity in the palisade parenchyma was higher than that of the spongy parenchyma and reached a maximum in both tissues 9 to 15 minutes after labeling. Sucrose specific activity initially declined rapidly in the palisade parenchyma followed by a period during which little or no loss occurred. Sucrose specific activity in sections containing veins peaked at 15 minutes with a maximum value substantially higher than either mesophyll tissue, indicating that recently synthesized sucrose was preferentially exported from the mesophyll. Decline of activity in these sections containing veins continued for the remainder of the experiment. Sucrose specific activity in lower epidermal peels peaked several minutes after that of the whole leaflet and remained lower. Sucrose specific activity in upper epidermal peels was variable (probably due to contamination), but the limited data suggest that the sucrose specific activity there reached somewhat higher values than those of the lower epidermis. The experiments indicate that each leaf tissue contains a kinetically identifiable sucrose pool (which we refer to as "histological compartmentation"), and that further compartmentation may occur at the intracellular level. A simulation of leaf sucrose compartmentation is presented.

Journal Article↗
PubMed1986

Sodium Transport and Compartmentation in Spergularia marina: Partial Characterization of a Functional Symplasm.

In this paper, a combination of tracer uptake, efflux, and pulse-chase techniques is applied to the problem of compartmentation of Na(+) ((24)Na(+)) in the roots of intact, midvegetative Spergularia marina (L.) Griseb. plants. An approach is presented for conducting useful compartmental analysis when it is known that the assumptions required for straightforward interpretations of influx and efflux studies are invalid. Linear rates of (24)Na(+) accumulation in both roots and shoots were attained within at most a few minutes following the start of labeling. Shoot (24)Na(+) contents equaled root contents within about 20 minutes. Analysis of root accumulation rates, and compartmental and pulse-chase efflux studies indicated that the unidirectional flux rates involved were at least an order of magnitude greater than linear rates of root and shoot accumulation. These rapid fluxes involved only a small portion of the total root Na(+) (about 1%). The results suggest the existence of a small symplastic compartment, distinct from the ;bulk cytoplasm,' rapidly exchanging with the medium, and responsible for delivery of Na(+) to the xylem. The physical identity of this compartment and its physiological significance are discussed with respect to precedents in the literature.

Journal Article↗
PubMed1988

Intracellular compartmentation of ions in salt adapted tobacco cells.

Na(+) and Cl(-) are the principal solutes utilized for osmotic adjustment in cells of Nicotiana tabacum L. var Wisconsin 38 (tobacco) adapted to NaCl, accumulating to levels of 472 and 386 millimolar, respectively, in cells adapted to 428 millimolar NaCl. X-ray microanalysis of unetched frozen-hydrated cells adapted to salt indicated that Na(+) and Cl(-) were compartmentalized in the vacuole, at concentrations of 780 and 624 millimolar, respectively, while cytoplasmic concentrations of the ions were maintained at 96 millimolar. The morphometric differences which existed between unadapted and salt adapted cells, (cytoplasmic volume of 22 and 45% of the cell, respectively), facilitated containment of the excited volume of the x-ray signal in the cytoplasm of the adapted cells. Confirmation of ion compartmentation in salt adapted cells was obtained based on kinetic analyses of (22)Na(+) and (36)Cl(-) efflux from cells in steady state. These data provide evidence that ion compartmentation is a component of salt adaptation of glycophyte cells.

Journal Article↗
PubMed1998

Global identifiability of linear compartmental models--a computer algebra algorithm.

A priori global identifiability deals with the uniqueness of the solution for the unknown parameters of a model and is, thus, a prerequisite for parameter estimation of biological dynamic models. Global identifiability is however difficult to test, since it requires solving a system of algebraic nonlinear equations which increases both in nonlinearity degree and number of terms and unknowns with increasing model order. In this paper, a computer algebra tool, GLOBI (GLOBal Identifiability) is presented, which combines the topological transfer function method with the Buchberger algorithm, to test global identifiability of linear compartmental models. GLOBI allows for the automatic testing of a priori global identifiability of general structure compartmental models from general multi input-multi output experiments. Examples of usage of GLOBI to analyze a priori global identifiability of some complex biological compartmental models are provided.

Algorithms↗
PubMed1975

Compartmentation of acetyl-coA in rat-liver mitochondria.

The ratio of the specific radioactivities of 3-hydroxybutyrate: citrate was determined in rat liver mitochondria which were incubated in the presence of [1-14C]palmitate, pyruvate, bicarbonate, ATP, phosphate and malonate. Without compartmentation this ratio would maximally be 2, however, under our conditions values of 2.5-3.7 were observed. In further experiments with mitochondria, the sensitivity of pyruvate carboxylase for acetyl-CoA produced from various precursors was tested. It was found that acetyl-CoA produced from L-acetylcarnitine or by oxidation from either pyruvate, octanoate or palmitylcarnitine but not from leucine led to a stimulation of pyruvate carboxylation. These results demonstrate a compartmentation of acetyl-CoA in liver mitochondria. The further finding that different mitochondrial fractions showed varying ratios of specific radioactivities of 3-hydroxybutyrate:citrate indicates that the observed compartmentation may be explained by the existence of different types of mitochondria with varying enzyme patterns and acetyl-CoA pools.

Acetoacetates↗
PubMed1972

A compartmental analysis of 24 Na kinetics in rat cerebrum, sciatic nerve and cerebrospinal fluid.

1. The kinetics of (24)Na exchange in rat cerebrospinal fluid, brain and sciatic nerve were studied during steady-state plasma isotope conditions. The entrance of (24)Na into brain and sciatic nerve was found to fit a three compartmental model. Using newly derived equations for compartmental analysis, the first compartment (24)Na space of brain was found to be about 22% and the second compartment space about 6%; the corresponding sciatic nerve spaces were 26 and 11%, respectively. In the discussion, arguments are presented that suggest that the first compartment is the extracellular space (ECS) and the second compartment is the intracellular space. The t((1/2)) for compartmental equilibration between plasma and brain ECS was 2 hr and from ECS to intracellular space 14 hr; in nerve the respective t((1/2))'s were (2/3) hr and 10 hr.2. A third compartment of 18% was found in sciatic nerve which was interpreted to be anatomically confined to the epi- and perineurium; in brain the corresponding space was 2% and was felt to be anatomically and kinetically an inactive closed compartment in parallel with the blood.3. There were two t((1/2))'s for plasma-c.s.f. (24)Na equilibration of less than 10 min and 2 hr.4. Profiles of brain, from cortex to ventricle, at 6 min, demonstrated a gradient of decreasing (24)Na radioactivity from ventricle to cortex.

Animals↗
PubMed1993

Compartmentalization of defined epitopes expressed in Escherichia coli has only a minor influence on efficiency of phagocytic processing for presentation by class I and class II major histocompatibility complex molecules to T cells.

The effect of abundance and compartmentalization of antigenic epitopes expressed in Escherichia coli on phagocytic processing was studied by expressing fusion proteins containing the epitope from positions 52 to 61 of hen egg white lysozyme [HEL(52-61)], which binds the I-Ak murine major histocompatibility complex class II (MHC-II) molecule or the epitope from positions 257 to 264 of chicken egg ovalbumin [OVA(257-264]), which binds the Kb murine MHC-I molecule. Epitopes expressed as fusion proteins in the outer membrane protein LamB allowed exposure of the epitopes either at the bacterial surface, in the periplasmic space, or in the cytoplasm. Regardless of epitope compartmentalization within the bacterium, MHC-II-restricted or MHC-I-restricted presentation to T hybridoma cells occurred after macrophages phagocytosed bacteria producing the HEL(52-61) epitope or the OVA(257-264) epitope, respectively. Increased epitope abundance within a given microbial compartment resulted in increased processing and presentation to epitope-specific T hybridoma cells. Minor differences in the efficiency of epitope processing between the constructs was observed, and the HEL or OVA epitope exposed in the periplasmic space was processed most efficiently compared with the surface- or cytoplasm-localized epitopes. These differences could be overcome by increasing the amount of epitope per bacterium as little as two to five times. The minor differences in processing efficiency may be due to differing protein contexts of the epitope as well as differing epitope compartmentalizations within the bacteria. Thus, production of abundant epitope is the important parameter influencing processing of epitopes expressed in E. coli to induce T-cell responses rather than targeting of an epitope to a specific bacterial compartment.

Amino Acid Sequence↗
PubMed2005

Human immunodeficiency virus type 1 genomic RNA sequences in the female genital tract and blood: compartmentalization and intrapatient recombination.

Investigation of human immunodeficiency virus type 1 (HIV-1) in the genital tract of women is crucial to the development of vaccines and therapies. Previous analyses of HIV-1 in various anatomic sites have documented compartmentalization, with viral sequences from each location that were distinct yet phylogenetically related. Full-length RNA genomes derived from different compartments in the same individual, however, have not yet been studied. Furthermore, although there is evidence that intrapatient recombination may occur frequently, recombinants comprising viruses from different sites within one individual have rarely been documented. We compared full-length HIV-1 RNA sequences in the plasma and female genital tract, focusing on a woman with high HIV-1 RNA loads in each compartment who had been infected heterosexually and then transmitted HIV-1 by the same route. We cloned and sequenced 10 full-length HIV-1 RNA genomes from her genital tract and 10 from her plasma. We also compared viral genomes from the genital tract and plasma of four additional heterosexually infected women, sequencing 164 env and gag clones obtained from the two sites. Four of five women, including the one whose complete viral sequences were determined, displayed compartmentalized HIV-1 genomes. Analyses of full-length, compartmentalized sequences made it possible to document complex intrapatient HIV-1 recombinants that were composed of alternating viral sequences characteristic of each site. These findings demonstrate that the genital tract and blood harbor genetically distinct populations of replicating HIV-1 and provide evidence that recombination between strains from the two compartments contributes to rapid evolution of viral sequence variation in infected individuals.

Female↗
PubMed2005

Compartmentalization of hepatitis C virus quasispecies in blood mononuclear cells of patients with mixed cryoglobulinemic syndrome.

The aim of this study was to investigate the quasispecies heterogeneity of hepatitis C virus (HCV) in the plasma, cryoprecipitate, and peripheral lymphocytes of chronically infected HCV patients with mixed cryoglobulinemia (MC). We studied 360 clones from 10 HCV-positive patients with MC and 8 age-, gender- and HCV genotype-matched subjects with chronic HCV infection but without MC. A partial nucleotide sequence encompassing the E1/E2 region, including hypervariable region 1 (HVR1), was amplified and cloned from plasma, cryoprecipitates, and peripheral blood mononuclear cells (PBMC), and the genetic diversity and complexity and synonymous and nonsynonymous substitution rates were determined. Heterogeneous selection pressure at codon sites was evaluated. Compartmentalization was estimated by phylogenetic and phenetic (Mantel's test) approaches. The patients with MC had 3.3 times lower nonsynonymous substitution rates (1.7 versus 5.7 substitutions/100 sites). Among the subjects with HCV genotype 1, the MC patients had significantly less complexity than the controls, whereas the diversity and complexity were similar in the genotype 2 patients and controls. Site-specific selection analysis confirmed the low frequency of MC patients showing positive selection. There was a significant correlation between positive selection and the infecting HCV genotype. The quasispecies were less heterogeneous in PBMC than in plasma. Significant compartmentalization of HCV quasispecies was observed in the PBMC of four of nine subjects (three with MC) and seven of nine cryoprecipitates. In one subject with MC, we detected a 5-amino-acid insertion at codons 385 to 389 of HVR1. Our results suggest reduced quasispecies heterogeneity in MC patients that is related to a low selection pressure which is probably due to an impaired immune response, the HCV genotype, and/or the duration of the infection. The frequent HCV quasispecies compartmentalization in patients' PBMC suggests a possible pathogenetic significance.

Aged↗
PubMed2005

Sites that direct nuclear compartmentalization are near the 5' end of the mouse immunoglobulin heavy-chain locus.

VDJ rearrangement in the mouse immunoglobulin heavy chain (Igh) locus involves a combination of events, including a large change in its nuclear compartmentalization. Prior to rearrangement, Igh moves from its default peripheral location near the nuclear envelope to an interior compartment, and after rearrangement it returns to the periphery. To identify any sites in Igh responsible for its association with the periphery, we systematically analyzed the nuclear positions of the Igh locus in mouse non-B- and B-cell lines and, importantly, in primary splenic lipopolysaccharide-stimulated B cells and plasmablasts. We found that a broad approximately 1-Mb region in the 5' half of the variable-gene region heavy-chain (Vh) locus regularly colocalizes with the nuclear lamina. The 3' half of the Vh gene region is less frequently colocalized with the periphery, while sequences flanking the Vh gene region are infrequently so. Importantly, in plasmacytomas, VDJ rearrangements that delete most of the Vh locus, including part of the 5' half of the Vh gene region, result in loss of peripheral compartmentalization, while deletion of only the proximal half of the Vh gene region does not. In addition, when Igh-Myc translocations move the Vh genes to a new chromosome, the distal Vh gene region is still associated with the nuclear periphery. Thus, the Igh region that interacts with the nuclear periphery is localized but is likely comprised of multiple sites that are distributed over approximately 1 Mb in the 5' half of the Vh gene region. This 5' Vh gene region that produces peripheral compartmentalization is the same region that is distinguished by requirements for interleukin-7, Pax5, and Ezh2 for rearrangement of the Vh genes.

5' Flanking Region↗
PubMed2005

Intracellular compartmentation in planctomycetes.

The phylum Planctomycetes of the domain Bacteria consists of budding, peptidoglycan-less organisms important for understanding the origins of complex cell organization. Their significance for cell biology lies in their possession of intracellular membrane compartmentation. All planctomycetes share a unique cell plan, in which the cell cytoplasm is divided into compartments by one or more membranes, including a major cell compartment containing the nucleoid. Of special significance is Gemmata obscuriglobus, in which the nucleoid is enveloped in two membranes to form a nuclear body that is analogous to the structure of a eukaryotic nucleus. Planctomycete compartmentation may have functional physiological roles, as in the case of anaerobic ammonium-oxidizing anammox planctomycetes, in which the anammoxosome harbors specialized enzymes and is wrapped in an envelope possessing unique ladderane lipids. Organisms in phyla other than the phylum Planctomycetes may possess compartmentation similar to that of some planctomycetes, as in the case of members of the phylum Poribacteria from marine sponges.

Anaerobiosis↗
PubMed1991

Cut set analysis of compartmental models with applications to experiment design.

Conventional compartmental analysis typically involves equations derived from mass-rate balance considerations for each compartment (pool), with each equation associated with a single pool. However, alternative mathematical descriptions, which effectively group pools into various other configurations, facilitate model analysis in certain applications, e.g., for kinetic experiment design or analysis. Such equivalent models are usually obtained using (often) complex matrix operations. An alternative approach, cut set analysis, can be applied directly to the graph of the compartmental model to readily generate alternative mathematical descriptions in which the needed equivalence transformations are easily performed graphically. This graphical transformation is developed here for linear, time-invariant multicompartmental models in which particular parameter values are the experimental objective. The method potentially provides greater flexibility in analyzing complex compartmental models in theory and practice, and it is exemplified here by application to the design of steady-state kinetic endocrine system studies in experimental animals.

Animals↗
PubMed2002

Phosphatidylinositol 3-kinase functionally compartmentalizes the concurrent G(s) signaling during beta2-adrenergic stimulation.

Compartmentation of intracellular signaling pathways serves as an important mechanism conferring the specificity of G protein-coupled receptor (GPCR) signaling. In the heart, stimulation of beta2-adrenoceptor (beta2-AR), a prototypical GPCR, activates a tightly localized protein kinase A (PKA) signaling, which regulates substrates at cell surface membranes, bypassing cytosolic target proteins (eg, phospholamban). Although a concurrent activation of beta2-AR-coupled G(i) proteins has been implicated in the functional compartmentation of PKA signaling, the exact mechanism underlying the restriction of the beta2-AR-PKA pathway remains unclear. In the present study, we demonstrate that phosphatidylinositol 3-kinase (PI3K) plays an essential role in confining the beta2-AR-PKA signaling. Inhibition of PI3K with LY294002 or wortmannin enables beta2-AR-PKA signaling to reach intracellular substrates, as manifested by a robust increase in phosphorylation of phospholamban, and markedly enhances the receptor-mediated positive contractile and relaxant responses in cardiac myocytes. These potentiating effects of PI3K inhibitors are not accompanied by an increase in beta2-AR-induced cAMP formation. Blocking G(i) or Gbetagamma signaling with pertussis toxin or betaARK-ct, a peptide inhibitor of Gbetagamma, completely prevents the potentiating effects induced by PI3K inhibition, indicating that the pathway responsible for the functional compartmentation of beta2-AR-PKA signaling sequentially involves G(i), Gbetagamma, and PI3K. Thus, PI3K constitutes a key downstream event of beta2-AR-G(i) signaling, which confines and negates the concurrent beta2-AR/G(s)-mediated PKA signaling.

Adrenergic beta-Agonists↗
PubMed2005

Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization.

BACKGROUND: Compartmentalization is a key feature of eukaryotic cells, but its evolution remains poorly understood. GTPases are the oldest enzymes that use nucleotides as substrates and they participate in a wide range of cellular processes. Therefore, they are ideal tools for comparative genomic studies aimed at understanding how aspects of biological complexity such as cellular compartmentalization evolved. RESULTS: We describe the identification and characterization of a unique family of circularly permuted GTPases represented by the human orthologue of yeast Lsg1p. We placed the members of this family in the phylogenetic context of the YlqF Related GTPase (YRG) family, which are present in Eukarya, Bacteria and Archea and include the stem cell regulator Nucleostemin. To extend the computational analysis, we showed that hLsg1 is an essential GTPase predominantly located in the endoplasmic reticulum and, in some cells, in Cajal bodies in the nucleus. Comparison of localization and siRNA datasets suggests that all members of the family are essential GTPases that have increased in number as the compartmentalization of the eukaryotic cell and the ribosome biogenesis pathway have evolved. CONCLUSION: We propose a scenario, consistent with our data, for the evolution of this family: cytoplasmic components were first acquired, followed by nuclear components, and finally the mitochondrial and chloroplast elements were derived from different bacterial species, in parallel with the formation of the nucleolus and the specialization of nuclear components.

Cell Nucleus↗
PubMed2005

Influence of Notch on dorsoventral compartmentalization and actin organization in the Drosophila wing.

Compartment boundaries play key roles in tissue organization by separating cell populations. Activation of the Notch receptor is required for dorsoventral (DV) compartmentalization of the Drosophila wing, but the nature of its requirement has been controversial. Here, we provide additional evidence that a stripe of Notch activation is sufficient to establish a sharp separation between cell populations, irrespective of their dorsal or ventral identities. We further find that cells at the DV compartment boundary are characterized by a distinct shape, a smooth interface, and an accumulation of F-actin at the adherens junction. Genetic manipulation establishes that a stripe of Notch activation is both necessary and sufficient for this DV boundary cell phenotype, and supports the existence of a non-transcriptional branch of the Notch pathway that influences F-actin. Finally, we identify a distinct requirement for a regulator of actin polymerization, capulet, in DV compartmentalization. These observations imply that Notch effects compartmentalization through a novel mechanism, which we refer to as a fence, that does not depend on the establishment of compartment-specific cell affinities, but does depend on the organization of the actin cytoskeleton.

Actins↗
PubMed1997

Compartmental organization of the Drosophila genital imaginal discs.

We have investigated the anterior and posterior compartmental organization of the genital imaginal disc. Unlike the thoracic discs, the genital disc is a compound disc consisting of three primordia--the female genital, male genital, and anal primordia. Here we provide evidence that each primordium is divided into anterior and posterior compartments. Genes that are known to be expressed in compartment-specific manners in other discs (engrailed, hedgehog, patched, decapentaplegic, wingless and cubitus interruptus) are expressed in analogous patterns in each primordium of the genital disc. Specifically, engrailed and cubitus interruptus are expressed in complementary domains, while patched, decapentaplegic and wingless are expressed along the border between the two domains. Mitotic clones induced at the beginning of the second larval instar do not cross the boundary between the engrailed-expressing and cubitus interruptus-expressing domains, indicating that these domains are true genetic compartments. Furthermore, we examined the phenotypes of mutant clones of the cAMP-dependent protein kinase A and engrailed-invected, genes that are known to play compartment-specific functions in other discs. These experiments demonstrate that the anterior/posterior patterning functions of these genes are conserved in the genital disc. The adult clonal phenotypes of protein kinase A and engrailed-invected mutants also provide a more detailed map of the adult genitalia and analia with respect to the anterior/posterior compartmental subdivision. Our results lead us to propose a new model to describe the anterior and posterior compartmental organization of the genital disc.

Animals↗