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 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 p107 is active in the nucleolus in non-dividing human granulosa lutein cells

2000 ◽  
Vol 25 (3) ◽  
pp. 275-286 ◽  
Author(s):  
C Green ◽  
R Chatterjee ◽  
HH McGarrigle ◽  
F Ahmed ◽  
NS Thomas
Keyword(s):  
Cell Cycle ◽  
Cell Types ◽  
Quiescent State ◽  
Cdk Inhibitor ◽  
Proliferating Cells ◽  
Dividing Cells ◽  
E2f Transcription Factors ◽  
Almost All ◽  
Different Cell Types ◽  
P27 Kip1

Cells are maintained in a quiescent state by members of the retinoblastoma protein family, pRb and p130. Both are phosphoproteins and hypophosphorylated forms of pRb and p130 bind and repress the activity of E2F transcription factors, thereby preventing entry into the cell cycle. Mitogenic stimulation causes activation of cyclin dependent kinases (cdk) that phosphorylate both pRb and p130, thereby releasing E2F factors which stimulate the transcription of a number of genes that are required for DNA synthesis and for regulating the cell cycle. In non-dividing cells, cdks are maintained in an inactive state by cdk inhibitor proteins such as p27(Kip1). The aim of our study was to determine how E2F complexes are regulated during the differentiation of human primary granulosa lutein cells (GLC) of the corpus luteum (CL). The CL is formed in the ovary after ovulation at the terminal stage of folliculogenesis after completion of maturation and differentiation of Graafian follicles. As shown by flow cytometry GLC are not dividing, being predominantly in the G(0)/G(1) phase of the cell cycle and, consistent with this, they contain the cdk inhibitor protein, p27(Kip1), but not E2F-1 which is normally expressed only in proliferating cells. The GLC do express E2F-4, hypophosphorylated pRb, p130 forms 1 and 2 and, surprisingly, hypophosphorylated p107. p107 is normally present only in dividing cells where it regulates E2F activity during the cell cycle. These forms of pRb, p130 as well as p107, together with E2F-4 are all active in that they can bind an E2F DNA-binding site in a pull-down assay. Immunocytochemistry shows that these proteins are expressed in almost all GLC but have different sub-cellular distribution: p107 is concentrated in nucleoli, while p130 and E2F-4 show relatively even nuclear and cytoplasmic distributions. Both pRb and p130 have been implicated previously in repressing E2F activity in many different cell types during cell cycle arrest in G(0)/G(1). We conclude that p107 is active in human primary GLC but its nucleolar localisation would suggest that it represses ribosomal RNA synthesis rather than E2F activity.

scholarly journals Therapeutic Exosomes in Prognosis and Developments of Coronary Artery Disease

2021 ◽  
Vol 8 ◽  
Author(s):  
Ai-Qun Chen ◽  
Xiao-Fei Gao ◽  
Zhi-Mei Wang ◽  
Feng Wang ◽  
Shuai Luo ◽  
...  
Keyword(s):  
Coronary Artery Disease ◽  
Coronary Artery ◽  
Cell Types ◽  
Biological Functions ◽  
Stent Restenosis ◽  
Artery Disease ◽  
Almost All ◽  
Different Cell Types ◽  
Insight Into ◽  
Systematic Knowledge

Exosomes, with an diameter of 30~150 nm, could be released from almost all types of cells, which contain diverse effective constituent, such as RNAs, proteins, lipids, and so on. In recent years, exosomes have been verified to play an important role in mechanism, diagnosis, treatment, and prognosis of cardiovascular disease, especially coronary artery disease (CAD). Moreover, it has also been shown that exosomes derived from different cell types have various biological functions based on the cell stimulation and microenvironment. However, therapeutic exosomes are currently far away from clinical translation, despite it is full of hope. In this review, we summarize an update of the recent studies and systematic knowledge of therapeutic exosomes in atherosclerosis, myocardial infarction, and in-stent restenosis, which might provide a novel insight into the treatment of CAD and promote the potential clinical application of therapeutic exosomes.

Turnover of the carboxy-terminal tyrosine of alpha-tubulin and means of reaching elevated levels of detyrosination in living cells

1987 ◽  
Vol 88 (2) ◽  
pp. 185-203
Author(s):  
J. Wehland ◽  
K. Weber
Keyword(s):  
Primary Cultures ◽  
Neuroblastoma Cells ◽  
Cell Types ◽  
Morphological Transformation ◽  
Alpha Tubulin ◽  
Tubulin Antibodies ◽  
Cell Processes ◽  
Carboxy Terminal ◽  
Almost All ◽  
Different Cell Types

Monoclonal antibodies specific for either the tyrosinated (Tyr) or the detyrosinated (Glu) form of alpha-tubulin were elicited with synthetic peptides spanning the carboxy-terminal sequences of the two forms. While almost all microtubules (MTs) are usually of the Tyr-tubulin type (Tyr-rich MTs) some MTs containing noticeable amounts of Glu-tubulin (Glu-rich MTs) were found in many but not all cell lines studied. Glu-rich MTs seemed absent from proliferating CHO and N115 neuroblastoma cells. When differentiation of these cells was initiated by the addition of forskolin for CHO, or by serum deprivation for N115, elevated levels of microtubular Glu-tubulin were observed. In differentiated N115 cells Glu-tubulin was restricted to MT of elongated cell processes and was not found in growth cones and many MT of the cell body. Elevated levels of Glu-tubulin were also characteristic of other differentiated cell types, including neurones and myotubes but were not found in glial cells, astrocytes and fibroblasts in the same primary cultures. Additional experiments suggested that the restricted distribution of Glu-tubulin is the result of MT subsets with different stabilities. Results with mitotic drugs indicated that detyrosination occurs on MTs rather than on soluble tubulin and that stabilization of MTs usually favours the detyrosination process. Evidence for a functional alpha-tubulin cycle involving an inherent carboxypeptidase and a recharging ligase was apparent in 3T3 cells from the preponderance of Glu-rich MTs induced by taxol treatment or the micro-injection of certain antibodies either protecting the detyrosinated form (Glu-tubulin antibodies) or inhibiting retyrosination (ligase antibodies). As the same treatment of CHO cells resulted in comparable arrays of Glu-rich MTs only when forskolin was also present, different cell types may differ in the level of active carboxypeptidase. The results are discussed in terms of possible functions of the tyrosination/detyrosination cycle of alpha-tubulin. While most results can be explained on the basis of ‘older’ and, consequently, more detyrosinated MTs, others raise the possibility that cyclic-AMP-dependent events and certain environmental influences known to induce either a morphological transformation or a differentiation event may influence the carboxypeptidase inherent in the alpha-tubulin cycle.

scholarly journals Targeting GRK5 for Treating Chronic Degenerative Diseases

2021 ◽  
Vol 22 (4) ◽  
pp. 1920
Author(s):  
Federica Marzano ◽  
Antonio Rapacciuolo ◽  
Nicola Ferrara ◽  
Giuseppe Rengo ◽  
Walter J. Koch ◽  
...  
Keyword(s):  
Neurological Diseases ◽  
Cell Types ◽  
Cardiac Cells ◽  
Multifunctional Protein ◽  
Surface Receptors ◽  
Extracellular Signals ◽  
Degenerative Disorders ◽  
Almost All ◽  
Related Proteins ◽  
Different Cell Types

G protein-coupled receptors (GPCRs) are the largest family of cell-surface receptors and they are responsible for the transduction of extracellular signals, regulating almost all aspects of mammalian physiology. These receptors are specifically regulated by a family of serine/threonine kinases, called GPCR kinases (GRKs). Given the biological role of GPCRs, it is not surprising that GRKs are also involved in several pathophysiological processes. Particular importance is emerging for GRK5, which is a multifunctional protein, expressed in different cell types, and it has been found located in single or multiple subcellular compartments. For instance, when anchored to the plasma membrane, GRK5 exerts its canonical function, regulating GPCRs. However, under certain conditions (e.g., pro-hypertrophic stimuli), GRK5 translocates to the nucleus of cells where it can interact with non-GPCR-related proteins as well as DNA itself to promote “non-canonical” signaling, including gene transcription. Importantly, due to these actions, several studies have demonstrated that GRK5 has a pivotal role in the pathogenesis of chronic-degenerative disorders. This is true in the cardiac cells, tumor cells, and neurons. For this reason, in this review article, we will inform the readers of the most recent evidence that supports the importance of targeting GRK5 to prevent the development or progression of cancer, cardiovascular, and neurological diseases.

DNA Polymerase in Avian Erythroid Cells

1972 ◽  
Vol 11 (3) ◽  
pp. 785-798
Author(s):  
A. F. WILLIAMS
Keyword(s):  
Cell Division ◽  
Dna Synthesis ◽  
Dna Polymerase ◽  
Cell Types ◽  
Polymerase Activity ◽  
Erythroid Cells ◽  
Isolated Nuclei ◽  
Dividing Cells ◽  
Different Cell Types

The level and properties of DNA polymerase activity assayable in extracts of avian erythroid cells was studied. The enzyme was detectable in the dividing cells (erythroblasts) of the erythropoietic series and also the immature non-dividing erythrocytes. It could not be assayed in mature erythrocytes. Investigations showed that activity began to decline at the time of the last cell division of the erythroid series. Properties of the enzyme did change in different cell types; however, the changes did not correlate with cessation of DNA synthesis. Some preliminary results on DNA synthesis by isolated nuclei are also reported and these showed that only nuclei from erythroblasts could synthesize DNA in vitro in the absence of primer.

Platelet Toll-Like Receptors: Bridging Inflammation and Immunity

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. SCI-45-SCI-45
Author(s):  
Paul Kubes
Keyword(s):  
Immune Cells ◽  
Conflicts Of Interest ◽  
Detection System ◽  
Vascular Dysfunction ◽  
Cell Types ◽  
Neutrophil Extracellular Traps ◽  
Extracellular Traps ◽  
Almost All ◽  
Different Cell Types

Abstract Since the discovery that there is a series of pattern recognition receptors that allow the immune system to detect pathogens, there has been a lot of work to elucidate the signaling molecules that contribute to this detection system. Although the cell types involved would seem to be just as important, our understanding of which cells are critical remains less well explored. Using intravital imaging to visualize the different cell types, we were surprised to find that in almost all conditions that we examined, platelets were rapidly recruited to afflicted tissues. Under some conditions, platelets bound vascular macrophage including Kupffer cells and helped contain bacteria. These were instantaneous responses. At later times, platelets bound neutrophils and induced the production of neutrophil extracellular traps (NETs) that helped to catch bacteria as well as viruses but did induce some local vascular injury. In some scenarios, platelets bound endothelial cells and whether this was to wall off and contain infections or a hijacking of platelets by bacteria to induce vascular dysfunction and poor perfusion remains unclear. Visualizing platelets in sterile injury also revealed important contributions to helping recruit other immune cells that help to heal. The role of the platelet as an effector in infections and inflammation will be discussed. Disclosures No relevant conflicts of interest to declare.

AVP and dDAVP in rabbit cortical collecting tubule: a comparative time-course study

1990 ◽  
Vol 258 (1) ◽  
pp. R99-R103
Author(s):  
M. Leite ◽  
W. N. Suki
Keyword(s):  
Time Course ◽  
Cell Types ◽  
Receptor Activation ◽  
Osmotic Water ◽  
Significant Difference ◽  
Time Course Study ◽  
Time Required ◽  
Collecting Tubules ◽  
Different Cell Types

The V2-selective analogue of arginine vasopressin (AVP), dDAVP, has been used to distinguish between the effects of V1- and V2-receptor activation by AVP in different cell types of the kidney. Based on studies showing different effects of AVP and dDAVP on prostaglandin secretion, and also on cytosolic Ca2+, we designed a comparative time-course study of both agonists on rabbit microdissected cortical collecting tubules (CCT) microperfused in vitro at 38 degrees C. Plots of the effects of AVP (10 microU/ml or 2.2 x 10(-11) M and 100 microU/ml or 2.2 x 10(-10) M) and dDAVP (10 microU/ml or 0.8 x 10(-11) M) on osmotic water permeability (Pf) at comparable antidiuretic activities, revealed an increase of Pf that was maintained for as long as 170 min of hormone exposure. Also the magnitude of increase in Pf and the time required to achieve the more sustained phase of response were comparable, with no significant difference between the two agonists. These results clearly demonstrate a stable response of rabbit CCT to AVP and dDAVP at physiological temperature, and they reveal no evidence for a difference between the native hormone AVP and its V2 selective analogue on the net hydrosmotic response of the CCT.

scholarly journals Exosomal MiRNAs in Pediatric Cancers

2019 ◽  
Vol 20 (18) ◽  
pp. 4600 ◽  
Author(s):  
Angela Galardi ◽  
Marta Colletti ◽  
Virginia Di Paolo ◽  
Patrizia Vitullo ◽  
Loretta Antonetti ◽  
...  
Keyword(s):  
Biological Fluids ◽  
Regulation Of Gene Expression ◽  
Cell Types ◽  
Aberrant Expression ◽  
Pediatric Cancers ◽  
Exosomal Mirnas ◽  
Rhabdoid Tumors ◽  
Almost All ◽  
Invasive Techniques ◽  
Different Cell Types

MicroRNAs (miRNAs) have generated great attention in oncology as they play a fundamental role in the regulation of gene expression and their aberrant expression is present in almost all types of tumors including pediatric ones. The discovery that miRNAs can be transported by exosomes, which are vesicles of 40–120 nm involved in cellular communication, that are produced by different cell types, and that are present in different biological fluids, has opened the possibility of using exosomal miRNAs as biomarkers. The possibility to diagnose and monitor the progression and response to drugs through molecules that can be easily isolated from biological fluids represents a particularly important aspect in the pediatric context where invasive techniques are often used. In recent years, the idea of liquid biopsy as well as studies on the possible role of exosomal miRNAs as biomarkers have developed greatly. In this review, we report an overview of all the evidences acquired in recent years on the identification of exosomal microRNAs with biomarker potential in pediatric cancers. We discuss the following herein: neuroblastoma, hepatoblastoma, sarcomas (osteosarcoma, Ewing’s sarcoma and rhabdoid tumors, and non-rhabdomyosarcoma soft tissue sarcoma), brain tumors, lymphomas, and leukemias.

scholarly journals Creative destruction: a basic computational model of cortical layer formation

2020 ◽  
Author(s):  
Roman Bauer ◽  
Gavin J Clowry ◽  
Marcus Kaiser
Keyword(s):  
Computational Model ◽  
State Diagram ◽  
Physical Space ◽  
Cell Types ◽  
Cortical Layer ◽  
Neural Systems ◽  
Layer Formation ◽  
Wide Range ◽  
The Central Nervous System ◽  
Different Cell Types

AbstractOne of the most characteristic properties of many vertebrate neural systems is the layered organization of different cell types. This cytoarchitecture exists in the cortex, the retina, the hippocampus and many other parts of the central nervous system. The developmental mechanisms of neural layer formation have been subject to substantial experimental efforts. Here, we provide a general computational model for cortical layer formation in 3D physical space. We show that this multi-scale, agent-based model comprising two distinct stages of apoptosis, can account for the wide range of neuronal numbers encountered in different cortical areas and species. Our results demonstrate the phenotypic richness of a basic state diagram structure, and suggest a novel function for apoptosis. Moreover, slightly changed gene regulatory dynamics recapitulate characteristic properties observed in neurodevelopmental diseases. Overall, we propose a novel computational model using gene-type rules, exhibiting many characteristics of normal and pathological cortical development.

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