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PubMed2000

Compartmentalization of RNA processing factors within nuclear speckles.

In the mammalian cell nucleus pre-mRNA splicing factors are organized in a speckled pattern. The fluorescence signal within speckles appears homogeneous when cells are immunolabeled with antibodies directed against pre-mRNA splicing factors and examined by fluorescence microscopy. We have reexamined the speckled domains using serial dilutions of antibodies against SR proteins, snRNPs, and a 3' end processing protein by immunofluorescence and confocal laser scanning microscopy. Using higher antibody dilutions, the speckled domains consist of numerous subdomains that are spherical and heterogeneous in size ranging from 0.2 to 0.5 micrometer in diameter. We refer to these subdomains as "subspeckles." Each speckle is composed of 5 to 50 subspeckles and in some cases in actively transcribing cells, strings and loops of subspeckles were observed to extend from the speckled domains. Upon inhibition of RNA polymerase II transcription, the strings and loops of subspeckles were no longer observed. Subspeckles were also not observed in coiled bodies. Using fluorescence in situ hybridization we found subspeckles to be colocalized with transiently expressed beta-tropomyosin RNA transcripts. The compartmentalization into subspeckles may represent an efficient way of organizing these factors for their subsequent transport to transcription/RNA processing sites.

Animals↗

PubMed2002

A compartmental model for oxygen transport in brain microcirculation in the presence of blood substitutes.

A compartmental model is developed for oxygen (O(2)) transport in brain microcirculation in the presence of blood substitutes (hemoglobin-based oxygen carriers). The cerebrovascular bed is represented as a series of vascular compartments, on the basis of diameters, surrounded by a tissue compartment. A mixture of red blood cells (RBC) and plasma/extracellular hemoglobin solution flows through the vascular bed from the arterioles through the capillaries to the venules. Oxygen is transported by convection in the vascular compartments and by diffusion in the surrounding tissue where it is utilized. Intravascular resistance and the diffusive loss of oxygen from the arterioles to the tissue are incorporated in the model. The model predicts that most of the O(2) transport occurs at the level of capillaries. Results computed from the present model in the presence of hemoglobin-based oxygen carriers are consistent with those obtained from the earlier validated model (Sharan et al., 1989, 1998a) on oxygen transport in brain circulation in the absence of extracellular hemoglobin. We have found that: (a) precapillary PO(2) gradients increase as PO(2) in the arterial blood increases, P(50 p) (oxygen tension at 50% saturation of hemoglobin with O(2) in plasma) decreases, i.e. O(2) affinity of the extracellular hemoglobin is increased, the flow rate of the mixture decreases, hematocrit decreases at constant flow, metabolic rate increases, and intravascular transport resistance in the arterioles is neglected; (b) precapillary PO(2) gradients are not sensitive to (i) intracapillary transport resistance, (ii) cooperativity (n(p)) of hemoglobin with oxygen in plasma, (iii) hemoglobin concentration in the plasma and (iv) hematocrit when accounting for viscosity variation in the flow; (c) tissue PO(2) is not sensitive to the variation of intravascular transport resistance in the arterioles. We also found that tissue PO(2) is a non-monotonic function of the Hill coefficient n(p) for the extracellular hemoglobin with a maximum occurring when n(p) equals the blood Hill coefficient. The results of the computations give estimates of the magnitudes of the increases in tissue PO(2) as arterial PO(2) increases,P(50 p) increases, flow rate increases, hematocrit increases, hemoglobin concentration in the plasma increases, metabolic rate decreases, the capillary mass transfer coefficient increases or the intracapillary transport resistance decreases.

Animals↗

PubMed2003

Modelling the dynamics of LCMV infection in mice: II. Compartmental structure and immunopathology.

In this study, we develop a mathematical model for analysis of the compartmental aspects and immunopathology of lymphocytic choriomeningitis virus (LCMV) infection in mice. We used sets of original and published data on systemic (extrasplenic) virus distribution to estimate the parameters of virus growth and elimination for spleen and other anatomical compartments, such as the liver, kidney, thymus and lung as well as transfer rates between blood and the above organs. A mathematical model quantitatively integrating the virus distribution kinetics in the host, the specific cytotoxic T lymphocyte (CTL) response in spleen and the re-circulation of effector CTL between spleen, blood and liver is advanced to describe the CTL-mediated immunopathology (hepatitis) in mice infected with LCMV. For intravenous and "peripheral" routes of infection we examine the severity of the liver disease, as a function of the virus dose and the host's immune status characterized by the numbers of precursor and/or cytolytic effector CTL. The model is used to predict the efficacy of protection against virus persistence and disease in a localized viral infection as a function of the composition of CTL population. The modelling analysis suggests quantitative demands to CTL memory for maximal protection against a wide range of doses of infection with a primarily peripheral site of virus replication without the risk of favoring immunopathology. It specifies objectives for CTL vaccination to ensure virus elimination with minimal immunopathology vs. vaccination for disease.

Animals↗

PubMed1999

Compartmental analysis revisited.

This paper gives a precise definition of compartment and shows that even when a compartmental model is not exactly identifiable, a range of its pharmacokinetic parameters can be determined. It is thus better to know approximate values of clearly defined parameters than exact values of quantities with no physical or physiological content.

Mathematics↗

PubMed2002

Compartmentalization of HIV-1 between breast milk and blood of HIV-infected mothers.

HIV-1 variants in breast milk and peripheral blood have been compared in three HIV-1 infected mothers. Analysis of DNA and RNA env C2-V3 sequences showed a differential distribution of HIV variants between the two compartments. The major provirus variant found in breast milk corresponds to a minor variant in the blood of two mothers. In the third mother, the predominant proviral variant detected in breast milk was not represented in the HIV-1 blood population. The major RNA variant in breast milk was not represented in the blood of two mothers. The predominant RNA variant in breast milk and blood was however the same for the third mother. Unexpectedly, the pattern of free virus variants in breast milk of three mothers did not correspond to that of the proviral form, suggesting that free viruses do not derive from infected cells in breast milk. The observation of a compartmentalization of HIV-1 between peripheral blood and breast milk emphasizes that postnatal transmission of HIV occurs with variants that may not be predicted from the analysis of circulating viral populations.

Amino Acid Sequence↗

PubMed1987

A model of the compartmentalization of taurine in rat hypothalmaic neuronal and glial cell particles.

We conclude that the high affinity taurine uptake system is located on neuronal membranes in the hypothalamus and that the low affinity taurine uptake system is located on glial membranes. The evoked release of taurine by either K+ and/or veratridine is Ca2+-independent and thus taurine, according to classical criteria, does not function as a neurotransmitter in the hypothalamus. This model for the differential cellular transport and compartmentalization of taurine into neuronal and glial cells and for a cytoplasmic location has important implications concerning its possible role in the central nervous system, specifically as a neuromodulator of neuronal activity.

Animals↗

PubMed1998

Compartmental modeling of human lactation.

A difficult task for a novice modeler is beginning a modeling project. The methods described here delineate the modeling process step by step. Aristole is quoted as having said "One learns to play the flute by playing the flute," and the same principle holds somewhat for modeling. An excellent means for understanding modeling is to work with example models, altering rate coefficients and model structure, to learn first-hand the mechanics of the process. An excellent resource for viewing and downloading published models is the Library of Mathematical Models of Biological Systems, and can be accessed via the World Wide Web at the address http://gopher.dml.georgetown.edu/model/model.html++ + . This modeling library provides access to working models of biological systems. Experimenting with available examples of models, such as those presented in this volume and those available through the Modeling Library, provides an excellent opportunity for new modelers to get started in compartmental modeling.

Breast Feeding↗

PubMed1998

Development and application of a compartmental model of 3-methylhistidine metabolism in humans and domestic animals.

Measurement of urinary 3-methylhistidine (3MH) excretion is the primary in vivo method to measure skeletal muscle (myofibrillar) protein breakdown. This method requires quantitative collection of urine and is based on the assumption that no metabolism of 3MH occurs once it is released from actin and myosin. This is true in most species, but in sheep and swine a proportion is retained in muscle as a dipeptide, balenine. In neither of these species does urine 3MH yield any data on the metabolism of 3MH. We have conducted studies that propose that 3MH metabolism in humans, cattle, dogs, swine, and sheep can be defined from a single bolus infusion of a stable isotope 3-[methyl-2H3]-methylhistidine. Following the bolus dose of the stable isotope tracer, serial blood samples and/or urine was collected over three to five days. A minimum of three exponentials were required to describe the plasma decay curve adequately. The kinetic linear-time-invariant models of 3MH metabolism in the whole animal were constructed by using the SAAM/CONSAM modeling program. Three different configurations of a three-compartment model are described: (A) A simple three-compartment model for humans, cattle, and dogs, in which plasma kinetics (3-[methyl-2H3]-MH/3MH) are described by compartment 1 and with one urinary exit from compartment 1. (B) A plasma-urinary kinetic three-compartment model with two exits was used for sheep with a urinary exit out of compartment 1 and a balenine exit out of a tissue compartment 3. (C) A plasma three-compartment model was used in swine with an exit out of a tissue compartment 3. The kinetic parameters reflect the differences in known physiology of humans, cattle, and dogs as compared to sheep and swine that do not quantitatively excrete 3MH into the urine. Steady-state model calculations define masses and fluxes of 3MH between three compartments and, importantly, the de novo production of 3MH. The de novo production of 3MH for humans, cattle, dogs, sheep, and swine are 3.1, 6.0, 12.1, 10.3, and 7.2 mumol x kg-1 x d-1, respectively. The de novo production of 3MH as calculated by the compartmental model was not different when compared to 3MH production as calculated via traditional urinary collection. Additionally, data suggest that steady-state compartment masses and mass transfer rates may be related to fat free mass and muscle mass in humans and swine, respectively. In conclusion, models of 3MH metabolism have been developed in numerous species, and these models can be used for the assessment of muscle proteolysis and 3MH kinetics without the collection of urine. This methodology is less evasive and will be useful in testing further experimental designs that alter myofibrillar protein breakdown.

Actins↗

PubMed1994

Compartmental analysis of brain edema using magnetic resonance imaging.

The potential exists for increasing the sensitivity of magnetic resonance imaging (MRI) to white matter (WM) pathologies by identifying compartments of tissue water. We have found the physical equivalents of myelin-associated biological water compartments in normal and pathologic states by using multiexponential analysis of T2 relaxation. In addition, we have applied this multi-parametric technique for the definition of various types of white matter edemas. We were able to identify some changes in physical compartments visible by MRI with simultaneous changes in biological compartments. We conclude that MRI is a very sensitive method to quantify abnormal accumulation of intracerebral water; however, it is a somewhat limited probe for identifying the biologic compartmentation of edema among the various biological compartments of the brain.

Animals↗

PubMed1991

Eicosanoid production by brain tumours in vivo--evidence for intracranial compartmentation.

Brain tumours produce prostaglandins in vitro; their in vivo production has been studied by determining the levels of prostaglandin F2 alpha, prostaglandin E2, 6-ketoprostaglandin F1 alpha and thromboxane B2 in tumour cyst fluid and ventricular CSF taken from 21 patients with a variety of intracranial tumours. The levels were high in tumour cyst fluid but there was no overall increase in ventricular CSF. Hence, brain tumours do not produce a consistent pattern of abnormality of eicosanoid concentrations in the ventricular CSF that would be useful for diagnosis. If brain tumours produce excess quantities of these prostaglandins in vivo as they do in vitro, these prostaglandins may be rapidly cleared by the cerebral microvasculature unless compartmentalized within a tumour cyst.

6-Ketoprostaglandin F1 alpha↗

PubMed1988

On the compartmentalization of catalase, fatty acyl-CoA oxidase and urate oxidase in mammalian livers, and the influence of clofibrate treatment on this microlocalization.

The compartmentalization of catalase, fatty acyl-CoA oxidase and urate oxidase was examined in the livers of mice, rats and guinea pigs, using the technique of digitonin extraction in order to avoid the trauma associated with centrifugation procedures. The results are interpreted as indicating that an appreciable proportion of catalase activity occurs in the cytoplasmic compartment of these cells. Following treatment of the animals with clofibrate, the specific activity in both peroxisomal and cytoplasmic compartments was increased, with a higher proportion of cytoplasmic catalase being evident in mice. The results for catalase were compared with those for fatty acyl-CoA oxidase and urate oxidase both of which were indicated as showing a closer association with the peroxisomal compartment than was the case for catalase. These data have been discussed in relation to their significance on present understanding of peroxisomal structure and function.

Acyl-CoA Oxidase↗

PubMed1992

Anatomical and functional compartmentalization of the subparafascicular thalamic nucleus in the rat.

The localization and the transmitter phenotype of subparafascicular thalamic nucleus (Spf) neurons projecting to the inferior colliculus (IC) and to the spinal cord (Sp) were studied by using a retrograde fluorescent double labeling technique, and a combined technique of retrograde tracing and immunohistochemistry for tyrosine hydroxylase (TH) and glutamate decarboxylase (GAD). The cell population of Spf-IC neurons was totally differentiated from that of Spf-Sp neurons which have been reported to be dopaminergic. The former were densely distributed, small to medium sized cells and localized in the central portion of the Spf, while the latter were sparsely distributed, large cells and localized in the marginal portion of the Spf. Spf-IC neurons were completely devoid of TH immunoreactivity and, instead, approximately half of them showed GAD immunoreactivity. From these findings, it is concluded that the Spf is distinctly compartmentalized by the presence at least two separate neuronal subpopulations, which are distinguishable in terms of their cell size, distribution patterns, transmitter phenotypes and trajectories.

Animals↗

PubMed1991

Extreme endurance training: evidence of capillary and mitochondria compartmentalization in human skeletal muscle.

Biopsies from the medial gastrocnemius muscle of three experienced endurance runners who had completed an ultramarathon run (160 km) the previous day were assessed for their oxidative characteristics (fibre types, capillarization and mitochondria content). Also, a regional comparison was made for fibres located centrally (completely surrounded by other fibres) versus fibres located peripherally (next to the interfascicular space) and the capillarization of these peripheral fibres was determined. Subsarcolemmal mitochondria were abundant and 'compartmentalized' close to the capillaries. The number of capillaries around fibres ranged from 5.8 to 8.5 and 5.7 to 8.5, and the number of capillaries.mm-2 ranged from 665 to 810 and 727 to 762, for type I (slow twitch) and type II (fast twitch) fibres, respectively. Central fibres contained a greater number of capillaries and more capillaries.mm-2 than their peripheral counterparts. Peripheral fibres contained more capillaries.micron-1 between fibres than at the interfascicular space. Type I fibres were more distributed (63%-78%) and larger than type II fibres. An abundance of subsarcolemmal mitochondria located close to the capillaries, efficient capillary proliferation between fibres where sharing can occur and greater relative distribution and size of type I fibres are, collectively, efficient characteristics of extreme endurance training.

Adenosine Triphosphatases↗

PubMed1980

Quantitation of thyroidal binding of iodide by compartmental analysis verified by an intravenous perchlorate discharge test.

Compartmental analysis was applied to 123I-iodide uptake data to quantitate iodine binding in the human thyroid gland. The method allowed for arterio/venous differences in plasma tracer level and for an "instantaneous" phase of thyroid uptake. Results were checked by an intravenous perchlorate discharge test. Observations in eleven normal and untreated thyrotoxic subjects confirmed earlier findings that iodine binding takes place rapidly, the binding rate constant being much greater than the exit rate constant. A lower limit of 0.15 min-1 for the binding rate constant in the uninhibited gland was estimated from the observations in one subject who demonstrated a small perchlorate discharge. The method was used in the study of eight subjects with an intrinsic binding defect and of twenty-four thyrotoxic subjects being treated with 5 mg or 20 mg carbimazole, twice daily. Binding rate constants (range 0.003--0.105 min-1) were typically less than the exit rate constants (range 0.027--0.156 min-1), the net clearance of iodide ranging from 1.5 to 67.9% of the unidirectioinal clearance, compared to 72% in the uninhibited gland. The method proved useful in assessing the severity of an intrinsic binding defect and in the investigation of lack of response to antithyroid drug therapy.

Computers↗

PubMed1980

Measurement of cerebral blood flow in the pig by the Xe-133 clearance technique. Failure of the two-compartmental clearance model.

The Xe-133 clearance technique is used to measure cerebral blood flow in the pig, which often serves as an experimental animal for cardiovascular research. The clearance curves are fitted by a two-exponential model. However, the fitted parameters are incompatible with a two-compartmental model: the values found for the parameters depend on the length of the clearance curve analysed. The discrepancies are thought to be consequences of the heterogeneity of cerebral blood flow and of mathematical problems of parameter identification. The non-validity of the relative weight of the fast clearance component as an anatomical or functional parameter is demonstrated. The use of the mean time constant, mean transit time, mean decay constant and initial slope for determination of cerebral blood flow rates is discussed. The mean cerebral blood flow of the anaesthetized pig measured by the clearance technique is found to be lower than the blood flow measured by means of a flow probe around the common carotid artery (with the external carotid artery tied off). The existence of a significant arteriovenous shunt flow is postulated.

Animals↗

PubMed1989

On stochastic compartmental models.

The statistical averaging of compartmental models with parameters being random processes is derived for the case of vanishing input and uniformly bounded input. The difference of resulting models is discussed.

Models, Theoretical↗

PubMed1979

The grasshopper X chromosome. II. Negative heteropycnosis, transcription activities and compartmentation during spermatogonial stages.

The X chromosome can be identified with the light microscope throughout all stages of the gonial cell cycle (including interphase) in the grasshopper Brachystola magna. At gonial mitotic stages the X chromosome gives the appearance of being undercondensed or negatively heteropycnotic. At interphase the X projects out from the body of the nucleus.--Examination with the electron microscope reveals that the X is compartmentalized at least two gonial cell cycles prior to the entry of the cells into meiotic prophase. The membrane layers that envelope the X chromatin at interphase remain associated with the X chromosome throughout gonial mitotic stages providing the ultrastructural basis for the apparent negative heteropycnosis observed with the light microscope.--The X chromosome is inactive in RNA synthesis during gonial mitotic stages but is hyperactive in RNA synthesis when compared to autosomes at gonial interphase.--X-chromosome condensation which reaches its maximum at premieotic interphase is initiated at or prior to the pre-pentultimate gonial division.

Animals↗

PubMed1988

Reproducible compartmentalization of individual chromosome domains in human CNS cells revealed by in situ hybridization and three-dimensional reconstruction.

Specific chromosome domains in interphase nuclei of neurons and glia were studied by three-dimensional (3-D) reconstruction of serial optical sections from in situ hybridized human CNS tissue. Overall patterns of centromere organization, delineated with alphoid repeats, were comparable to those seen in mouse, and are clearly conserved in mammalian evolution. Cloned probes from other individual chromosome domains were used to define interphase organization more precisely. Homologous chromosomes were spatially separated in nuclei. In large neurons, probes specific for 9q12, or 1q12 showed that at least one homolog was always compartmentalized together with centromeres on the nucleolus, while the second signal either abutted the nucleolus or was on the nuclear membrane. A telomeric Yq12 sequence also localized together with perinucleolar centromeres in a completely non-Rabl orientation. In astrocytes, these three chromosome regions were on the membrane and not necessarily associated with nucleoli. Therefore there are different patterns of interphase chromosome organization in functionally distinct cell types. In contrast to the above domains, a 1p36.3 telomeric sequence embedded in a large Alu-rich and early replicating chromosome region, was always found in an interior euchromatic nuclear compartment in both neurons and glial cells. In double hybridizations with 1q12 and 1p36.3 probes, 1p arms were clearly separated in all cells, and arms projected radially into the interior nucleoplasm with non-Rabl orientations. There was no absolute or rigid position for each 1p arm with respect to each other or to the major dendrite, indicating that individual chromosome arms may be dynamically positioned even in highly differentiated cell types. We suggest that centromeric and other highly repeated non-transcribed sequence domains may act as general organizing centers for cell type specific interphase patterns that are conserved in mammalian evolution. Such centers would allow selected groups of chromosome arms to extend into (and contract from) an interior, presumably transcriptionally active, nuclear compartment.

Astrocytes↗