scholarly journals A computational model of mitochondrial AZT metabolism

2005 ◽  
Vol 392 (2) ◽  
pp. 363-373 ◽  
Author(s):  
Patrick C. Bradshaw ◽  
Jiaxin Li ◽  
David C. Samuels
Keyword(s):  
Computational Model ◽  
Competitive Inhibition ◽  
Peak Plasma ◽  
Cell Types ◽  
Mitochondrial Toxicity ◽  
Postmitotic Cells ◽  
Dividing Cells ◽  
Mtdna Replication ◽  
Low Levels ◽  
Postmitotic Cell

The mechanisms of the mitochondrial toxicity of AZT (azidothymidine; zidovudine) are not clear. The two main contenders are the incorporation of phosphorylated AZT into the mtDNA (mitochondrial DNA) and the competitive inhibition of natural deoxynucleotide metabolism. We have built a computational model of AZT metabolism in mitochondria in order to better understand these toxicity mechanisms. The model includes the transport of non-phosphorylated and phosphorylated forms of AZT into mitochondria, phosphorylation, and incorporation into mtDNA. The model also includes the mitochondrial metabolism of the natural deoxynucleotides. We define three simulated cell types, i.e. rapidly dividing, slowly dividing and postmitotic cells. Our standard simulation indicates that incorporation of AZT into mtDNA is highest in rapidly dividing cells because of the higher mitochondrial AZTTP (3′-azidothymidine-5′-triphosphate)/dTTP ratio in this cell type. However, under these standard conditions the rate of incorporation into mtDNA is too low to be a major cause of toxicity. These simulations relied on the assumption that phosphorylated AZT is transported with the same kinetics as phosphorylated thymidine. In simulations with mitochondria set to have a limited ability to transport phosphorylated AZT, AZTTP accumulates to toxic levels in the mitochondria of postmitotic cells, while low levels are maintained in mitochondria from rapidly dividing cells. This result is more consistent with the tissue toxicities observed in patients. Our model also predicts that inhibition by AZT of mitochondrial deoxycytidine phosphorylation by thymidine kinase 2 may contribute to the mitochondrial toxicity, since in simulations using a typical peak plasma AZT level the mtDNA replication rate is decreased by 30% in postmitotic cell simulations.

scholarly journals A computational model of mitochondrial deoxynucleotide metabolism and DNA replication

2005 ◽  
Vol 288 (5) ◽  
pp. C989-C1002 ◽  
Author(s):  
Patrick C. Bradshaw ◽  
David C. Samuels
Keyword(s):  
Computational Model ◽  
Cell Types ◽  
Matrix Space ◽  
Previous Hypothesis ◽  
Postmitotic Cells ◽  
Dividing Cells ◽  
Mtdna Replication ◽  
Time Required ◽  
Almost All ◽  
Different Cell Types

We present a computational model of mitochondrial deoxynucleotide metabolism and mitochondrial DNA (mtDNA) synthesis. The model includes the transport of deoxynucleosides and deoxynucleotides into the mitochondrial matrix space, as well as their phosphorylation and polymerization into mtDNA. Different simulated cell types (cancer, rapidly dividing, slowly dividing, and postmitotic cells) are represented in this model by different cytoplasmic deoxynucleotide concentrations. We calculated the changes in deoxynucleotide concentrations within the mitochondrion during the course of a mtDNA replication event and the time required for mtDNA replication in the different cell types. On the basis of the model, we define three steady states of mitochondrial deoxynucleotide metabolism: the phosphorylating state (the net import of deoxynucleosides and export of phosphorylated deoxynucleotides), the desphosphorylating state (the reverse of the phosphorylating state), and the efficient state (the net import of both deoxynucleosides and deoxynucleotides). We present five testable hypotheses based on this simulation. First, the deoxynucleotide pools within a mitochondrion are sufficient to support only a small fraction of even a single mtDNA replication event. Second, the mtDNA replication time in postmitotic cells is much longer than that in rapidly dividing cells. Third, mitochondria in dividing cells are net sinks of cytoplasmic deoxynucleotides, while mitochondria in postmitotic cells are net sources. Fourth, the deoxynucleotide carrier exerts the most control over the mtDNA replication rate in rapidly dividing cells, but in postmitotic cells, the NDPK and TK2 enzymes have the most control. Fifth, following from the previous hypothesis, rapidly dividing cells derive almost all of their mtDNA precursors from the cytoplasmic deoxynucleotides, not from phosphorylation within the mitochondrion.

scholarly journals Platelet and Erythrocyte Extravasation across Inflamed Corneal Venules Depend on CD18, Neutrophils and Mast Cell Degranulation

2021 ◽  
Vol 22 (14) ◽  
pp. 7360
Author(s):  
Angie De La Cruz ◽  
Aubrey Hargrave ◽  
Sri Magadi ◽  
Justin A. Courson ◽  
Paul T. Landry ◽  
...  
Keyword(s):  
Mast Cell ◽  
Cell Types ◽  
Mast Cell Degranulation ◽  
Wild Type ◽  
Delayed Wound Healing ◽  
Corneal Epithelial ◽  
Corneal Abrasion ◽  
Low Levels ◽  
Endothelial Pores

Platelet extravasation during inflammation is under-appreciated. In wild-type (WT) mice, a central corneal epithelial abrasion initiates neutrophil (PMN) and platelet extravasation from peripheral limbal venules. The same injury in mice expressing low levels of the β2-integrin, CD18 (CD18hypo mice) shows reduced platelet extravasation with PMN extravasation apparently unaffected. To better define the role of CD18 on platelet extravasation, we focused on two relevant cell types expressing CD18: PMNs and mast cells. Following corneal abrasion in WT mice, we observed not only extravasated PMNs and platelets but also extravasated erythrocytes (RBCs). Ultrastructural observations of engorged limbal venules showed platelets and RBCs passing through endothelial pores. In contrast, injured CD18hypo mice showed significantly less venule engorgement and markedly reduced platelet and RBC extravasation; mast cell degranulation was also reduced compared to WT mice. Corneal abrasion in mast cell-deficient (KitW-sh/W-sh) mice showed less venule engorgement, delayed PMN extravasation, reduced platelet and RBC extravasation and delayed wound healing compared to WT mice. Finally, antibody-induced depletion of circulating PMNs prior to corneal abrasion reduced mast cell degranulation, venule engorgement, and extravasation of PMNs, platelets, and RBCs. In summary, in the injured cornea, platelet and RBC extravasation depends on CD18, PMNs, and mast cell degranulation.

scholarly journals Pathway-dependent regulation of sleep dynamics in a network model of the sleep-wake cycle

2019 ◽  
Author(s):  
Charlotte Héricé ◽  
Shuzo Sakata
Keyword(s):  
Computational Model ◽  
Eye Movement ◽  
Network Model ◽  
Rem Sleep ◽  
Synaptic Weight ◽  
Nrem Sleep ◽  
Cell Types ◽  
Brain Areas ◽  
Neuronal Populations ◽  
Neural Populations

AbstractSleep is a fundamental homeostatic process within the animal kingdom. Although various brain areas and cell types are involved in the regulation of the sleep-wake cycle, it is still unclear how different pathways between neural populations contribute to its regulation. Here we address this issue by investigating the behavior of a simplified network model upon synaptic weight manipulations. Our model consists of three neural populations connected by excitatory and inhibitory synapses. Activity in each population is described by a firing-rate model, which determines the state of the network. Namely wakefulness, rapid eye movement (REM) sleep or non-REM (NREM) sleep. By systematically manipulating the synaptic weight of every pathway, we show that even this simplified model exhibits non-trivial behaviors: for example, the wake-promoting population contributes not just to the induction and maintenance of wakefulness, but also to sleep induction. Although a recurrent excitatory connection of the REM-promoting population is essential for REM sleep genesis, this recurrent connection does not necessarily contribute to the maintenance of REM sleep. The duration of NREM sleep can be shortened or extended by changes in the synaptic strength of the pathways from the NREM-promoting population. In some cases, there is an optimal range of synaptic strengths that affect a particular state, implying that the amount of manipulations, not just direction (i.e., activation or inactivation), needs to be taken into account. These results demonstrate pathway-dependent regulation of sleep dynamics and highlight the importance of systems-level quantitative approaches for sleep-wake regulatory circuits.Author SummarySleep is essential and ubiquitous across animal species. Over the past half-century, various brain areas, cell types, neurotransmitters, and neuropeptides have been identified as part of a sleep-wake regulating circuitry in the brain. However, it is less explored how individual neural pathways contribute to the sleep-wake cycle. In the present study, we investigate the behavior of a computational model by altering the strength of connections between neuronal populations. This computational model is comprised of a simple network where three neuronal populations are connected together, and the activity of each population determines the current state of the model, that is, wakefulness, rapid-eye-movement (REM) sleep or non-REM (NREM) sleep. When we alter the connection strength of each pathway, we observe that the effect of such alterations on the sleep-wake cycle is highly pathway-dependent. Our results provide further insights into the mechanisms of sleep-wake regulation, and our computational approach can complement future biological experiments.

Dynamic Computational Model of the Human Spinal Cord Connectome

2019 ◽  
Vol 31 (2) ◽  
pp. 388-416 ◽  
Author(s):  
Jeffrey E. Arle ◽  
Nicolae Iftimia ◽  
Jay L. Shils ◽  
Longzhi Mei ◽  
Kristen W. Carlson
Keyword(s):  
Spinal Cord ◽  
Computational Model ◽  
Cell Types ◽  
Neural Circuitry ◽  
Simulation Software ◽  
Cross Sectional ◽  
Human Spinal Cord ◽  
Starting Point ◽  
The Many ◽  
Future Work

Connectomes abound, but few for the human spinal cord. Using anatomical data in the literature, we constructed a draft connectivity map of the human spinal cord connectome, providing a template for the many calibrations of specialized behavior to be overlaid on it and the basis for an initial computational model. A thorough literature review gleaned cell types, connectivity, and connection strength indications. Where human data were not available, we selected species that have been studied. Cadaveric spinal cord measurements, cross-sectional histology images, and cytoarchitectural data regarding cell size and density served as the starting point for estimating numbers of neurons. Simulations were run using neural circuitry simulation software. The model contains the neural circuitry in all ten Rexed laminae with intralaminar, interlaminar, and intersegmental connections, as well as ascending and descending brain connections and estimated neuron counts for various cell types in every lamina of all 31 segments. We noted the presence of highly interconnected complex networks exhibiting several orders of recurrence. The model was used to perform a detailed study of spinal cord stimulation for analgesia. This model is a starting point for workers to develop and test hypotheses across an array of biomedical applications focused on the spinal cord. Each such model requires additional calibrations to constrain its output to verifiable predictions. Future work will include simulating additional segments and expanding the research uses of the model.

Sch-28080 inhibits bafilomycin-sensitive H+ secretion in turtle bladder independently of luminal [K+]

1993 ◽  
Vol 265 (2) ◽  
pp. F174-F179
Author(s):  
O. F. Kohn ◽  
P. P. Mitchell ◽  
P. R. Steinmetz
Keyword(s):  
Competitive Inhibition ◽  
Short Circuit ◽  
Short Circuit Current ◽  
Atpase Inhibitor ◽  
Turtle Bladder ◽  
High K ◽  
Ph Stat ◽  
Low Levels ◽  
K Concentration ◽  
Removal Studies

To explore the possible contribution of an H-K-adenosine-triphosphatase (H-K-ATPase) to H+ secretion (JH) in the isolated turtle bladder, we measured electrogenic JH (JeH) as short-circuit current and total JH (JTH) by pH stat titration in the presence of ouabain at different ambient K+ concentration ([K+]) and during luminal addition of a known gastric H-K-ATPase inhibitor, Schering (Sch)-28080. JH was not reduced by decreasing ambient [K+] to undetectable or very low levels (< 0.05 mM by atomic absorption) and luminal BaCl2 addition to further reduce local [K+] at the apical membrane. These K(+)-removal studies indicate that H+ transport is not coupled to countertransport of K+. JTH did not exceed JeH at any point: in K(+)-free solutions JTH was 0.73 +/- 0.05, and JeH was 0.95 +/- 0.08 mumol/h; in standard (3.5 mM) K+ solutions JTH was 0.72 +/- 0.05 and JeH 0.98 +/- 0.06 mumol/h; in high (118 mM) K+ solutions JTH was 0.65 +/- 0.07 and JeH 0.94 +/- 0.08 mumol/h. Sch-28080 caused a rapid inhibition of JH, with similar half-maximal inhibitory concentrations (IC50) in K(+)-free, standard [K+], and high [K+] solutions. Bafilomycin inhibited JeH and JTH with an IC50 of approximately 100 nM. The observed non-potassium-competitive inhibition of JH by Sch-28080 and the bafilomycin sensitivity distinguish the H-ATPase of the turtle bladder from the gastric H-K-ATPase. The rapidity of the inhibition by Sch-28080 suggests that it acts at an accessible luminal site of the ATPase.

scholarly journals Methods to Enhance Signal Using Isotopic In Situ Hybridization

2002 ◽  
Vol 50 (8) ◽  
pp. 1031-1037 ◽  
Author(s):  
Betty Ky ◽  
Paul J. Shughrue
Keyword(s):  
Gene Expression ◽  
In Situ Hybridization ◽  
Cell Types ◽  
Oxytocin Receptor ◽  
Specific Cell ◽  
Rat Hypothalamus ◽  
Low Levels ◽  
Tuberoinfundibular Peptide ◽  
Cryostat Sections

Isotopic in situ hybridization (ISH) has been established as a uniquely powerful tool for the study of gene expression in specific cell types. This technique allows the visualization and quantification of gene expression and gene expression changes in cells. In our study of biological and molecular phenomena, we have increasingly encountered the need to detect small changes in gene expression as well as genes of low abundance, such as the oxytocin receptor (OTR) and the tuberoinfundibular peptide of 39 residues (Tip39). To increase the sensitivity of isotopic ISH for detection of rare mRNAs, we performed ISH on cryostat sections of rat hypothalamus and thalamus with 35S-labeled riboprobes and amplified the signal by hybridizing over 2 nights as well as labeling the probe with both [35S]-UTP and [35S]-ATP. These two methods of enhancement independently and in combination demonstrated a dramatic increase in signal, allowing the visualization of low levels of gene expression previously undetectable by conventional methods.

scholarly journals Atypical Cristae Morphology of Human Syncytiotrophoblast Mitochondria

2011 ◽  
Vol 286 (27) ◽  
pp. 23911-23919 ◽  
Author(s):  
Daniela De Los Rios Castillo ◽  
Mariel Zarco-Zavala ◽  
Sofia Olvera-Sanchez ◽  
Juan Pablo Pardo ◽  
Oscar Juarez ◽  
...  
Keyword(s):  
Atp Synthase ◽  
Physiological Function ◽  
Cell Types ◽  
Dimeric Complex ◽  
Inhibitory Protein ◽  
Low Levels ◽  
Mitochondrial Complexes

Mitochondrial complexes I, III2, and IV from human cytotrophoblast and syncytiotrophoblast associate to form supercomplexes or respirasomes, with the following stoichiometries: I1:(III2)1 and I1:(III2)1–2:IV1–4. The content of respirasomes was similar in both cell types after isolating mitochondria. However, syncytiotrophoblast mitochondria possess low levels of dimeric complex V and do not have orthodox cristae morphology. In contrast, cytotrophoblast mitochondria show normal cristae morphology and a higher content of ATP synthase dimer. Consistent with the dimerizing role of the ATPase inhibitory protein (IF1) (García, J. J., Morales-Ríos, E., Cortés-Hernandez, P., and Rodríguez-Zavala, J. S. (2006) Biochemistry 45, 12695–12703), higher relative amounts of IF1 were observed in cytotrophoblast when compared with syncytiotrophoblast mitochondria. Therefore, there is a correlation between dimerization of complex V, IF1 expression, and the morphology of mitochondrial cristae in human placental mitochondria. The possible relationship between cristae architecture and the physiological function of the syncytiotrophoblast mitochondria is discussed.

scholarly journals Evidence for a stem cell hierarchy in the adult human breast

2007 ◽  
Vol 177 (1) ◽  
pp. 87-101 ◽  
Author(s):  
René Villadsen ◽  
Agla J. Fridriksdottir ◽  
Lone Rønnov-Jessen ◽  
Thorarinn Gudjonsson ◽  
Fritz Rank ◽  
...  
Keyword(s):  
Stem Cell ◽  
Progenitor Cells ◽  
Functional Characterization ◽  
Cell Activity ◽  
Cell Types ◽  
Human Breast ◽  
Mammosphere Formation ◽  
Adult Human ◽  
Dividing Cells ◽  
Stem Cell Hierarchy

Cellular pathways that contribute to adult human mammary gland architecture and lineages have not been previously described. In this study, we identify a candidate stem cell niche in ducts and zones containing progenitor cells in lobules. Putative stem cells residing in ducts were essentially quiescent, whereas the progenitor cells in the lobules were more likely to be actively dividing. Cells from ducts and lobules collected under the microscope were functionally characterized by colony formation on tissue culture plastic, mammosphere formation in suspension culture, and morphogenesis in laminin-rich extracellular matrix gels. Staining for the lineage markers keratins K14 and K19 further revealed multipotent cells in the stem cell zone and three lineage-restricted cell types outside this zone. Multiparameter cell sorting and functional characterization with reference to anatomical sites in situ confirmed this pattern. The proposal that the four cell types are indeed constituents of an as of yet undescribed stem cell hierarchy was assessed in long-term cultures in which senescence was bypassed. These findings identify an adult human breast ductal stem cell activity and its earliest descendants.

scholarly journals A Spindle Checkpoint Functions during Mitosis in the Early Caenorhabditis elegans Embryo

2005 ◽  
Vol 16 (3) ◽  
pp. 1056-1070 ◽  
Author(s):  
Sandra E. Encalada ◽  
John Willis ◽  
Rebecca Lyczak ◽  
Bruce Bowerman
Keyword(s):  
Caenorhabditis Elegans ◽  
Chromosome Segregation ◽  
Spindle Checkpoint ◽  
Metaphase Plate ◽  
Time Lapse ◽  
Cell Types ◽  
Embryonic Cells ◽  
Mitotic Spindles ◽  
Animal Cells ◽  
Dividing Cells

During mitosis, chromosome segregation is regulated by a spindle checkpoint mechanism. This checkpoint delays anaphase until all kinetochores are captured by microtubules from both spindle poles, chromosomes congress to the metaphase plate, and the tension between kinetochores and their attached microtubules is properly sensed. Although the spindle checkpoint can be activated in many different cell types, the role of this regulatory mechanism in rapidly dividing embryonic animal cells has remained controversial. Here, using time-lapse imaging of live embryonic cells, we show that chemical or mutational disruption of the mitotic spindle in early Caenorhabditis elegans embryos delays progression through mitosis. By reducing the function of conserved checkpoint genes in mutant embryos with defective mitotic spindles, we show that these delays require the spindle checkpoint. In the absence of a functional checkpoint, more severe defects in chromosome segregation are observed in mutants with abnormal mitotic spindles. We also show that the conserved kinesin CeMCAK, the CENP-F-related proteins HCP-1 and HCP-2, and the core kinetochore protein CeCENP-C all are required for this checkpoint. Our analysis indicates that spindle checkpoint mechanisms are functional in the rapidly dividing cells of an early animal embryo and that this checkpoint can prevent chromosome segregation defects during mitosis.

scholarly journals Characterization of DNA-Bound Histone in the Cells of The Avian Erythropoietic Series

1972 ◽  
Vol 10 (1) ◽  
pp. 47-59
Author(s):  
R. APPELS ◽  
J. R. E. WELLS ◽  
A. F. WILLIAMS
Keyword(s):  
Polyacrylamide Gel Electrophoresis ◽  
Cell Types ◽  
Erythroid Cell ◽  
Macromolecular Synthesis ◽  
Polychromatic Erythrocytes ◽  
Rna And Protein Synthesis ◽  
Dividing Cells ◽  
Cell Series

The distribution of DNA-bound histone from purified cell populations of the avian erythroid cell series was studied to examine the possible relationship between these molecules and the in vivo activity of cells. High-resolution polyacrylamide gel electrophoresis of histones indicated that the 3 main cell types, namely, erythrocytes (inactive in macromolecular synthesis), polychromatic erythrocytes (active in RNA and protein synthesis) and erythroblasts (dividing cells) all contained the same histone components. This result is contrary to previous reports that the f2c histone (characteristic of avian erythroid cells) was absent from erythroblasts; in addition it does not support the proposition that dividing cells contain a unique f1 histone component. Quantitation of histone analyses showed that erythroblasts contain relatively less f2c histone than the non-dividing cells of the series and that there was a slight redistribution of f1 histone components between polychromatic and mature erythrocytes.

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