Non-synchronized Cells Research Articles

Novel transformation strategies improve efficiency up to 10-fold in stramenopile algae

Stramenopile algae have the potential to become the light-driven photosynthetic biofactories of the future, but the transformation technologies required to reach this goal remain sub-optimal. Nannochloropsis oceanica and Phaeodactylum tricornutum were used as experimental systems for electroporation-mediated transformation. Two transformation approaches were developed; 1) timed transformation of synchronized cells and 2) addition of saponins as transformation adjuvants. Transformation efficiency was increased ~8 times using synchronized N. oceanica cultures transformed in the G2/M phase, in comparison to state-of-the-art methods based on transformation of non-synchronized cells. For P. tricornutum the transformation was up to 5 times more efficient in non-synchronized conditions. N. oceanica and P. tricornutum responded differently upon exposure to different saponin plant extracts. Saponin treatments enhanced P. tricornutum and N. oceanica transformation efficiencies ~2 and ~2.5 times, respectively. Combining cell synchronization and saponin transformation adjuvant treatment, improves transformation efficiency in N. oceanica, results in a >10-fold improvement of the transformation efficiency for N. oceanica. In addition, a protocol for directed ribonucleoprotein (RNP)-mediated genome engineering of DNA constructs with short flanking arms (50 bp) in N. oceanica was established, enabling improved RNP targeted non-homologous end-joining (NHEJ) gene editing. In conclusion, this study expands the toolbox for stramenopile genome engineering, promoting their use as model organisms and sustainable biofactories.

Division behaviours and their effects on pre-implantation development of pig embryos.

The quality of pre-implantation embryos could affect developmental efficiency after embryo transfer. However, the assessment of pre-implantation embryos was unsatisfactory, especially in pig embryos to date. Therefore, this study was designed to investigate available and applicable parameters that indicate developmental potential and quality of porcine pre-implantation embryos produced by handmade cloning (HMC), and parthenogenetic activation without zona pellucida (PAZF) and with zona pellucida (PAZI). Firstly, a common division behaviour was detected, that is the formation of uneven division with two unequal size blastomeres (UD 2-cell), especially in HMC embryos; then, the proportion of UD 2-cell was found to be significantly higher than that of even division with equal size blastomeres (ED 2-cell) (72.56 ± 4.56 vs. 24.57 ± 1.92). The formation of UD 2-cell might be due to the spindle migration along the long axis in 1-cell stage, and the cleavage furrow was not formed in the centre of cytoplasm. In the two sister blastomeres of UD 2-cell, uneven distribution of organelles (mitochondria and lipid droplet) was observed with lower proportion in the smaller one (p<.05). Although no difference in blastocyst rate was observed between UD and ED 2-cell embryos, the cell number per blastocyst from UD 2-cell embryos was lower than that from ED 2-cell embryos (44.15 ± 2.05 vs. 51.55 ± 1.83). Besides, because of non-synchronized division of each blastomere, the following three cleavage routes were observed in all HMC/PAZF/PAZI embryos: T1 (2-cell → 3-cell → 4-cell → ≥5-cell → morula → blastocyst), T2 (2-cell → 3-cell → 4-cell → morula → blastocyst) and T3 (2-cell → 3-cell/4-cell → morula → blastocyst). Therefore, in pig in vitro-produced embryos, division behaviours of uneven volume of cytoplasm and non-synchronized cell cycles were observed at the early embryonic developmental stage, which might be another potential factor to evaluate embryonic development.

Synchronization of Cultured Cells to G1, S, G2, and M Phases by Double Thymidine Block.

The typical cell cycle in eukaryotes is composed of four phases including the G1, S, G2, and M phases. G1, S, and G2 together are called interphase. Cell synchronization is a process that brings cultured cells at different stages of the cell cycle to the same phase. For many experiments, it is desirable to have a population of cells that are traversing the cell cycle synchronously, as it allows population-wide data to be collected rather than relying solely on single-cell experiments. While there are various drugs that can be used to arrest the cell at each specific phase of the cell cycle, they may cause undesired side effects. Here, we describe a protocol to synchronize cells to each cell cycle phase by using only one chemical: thymidine. Non-synchronized cells are synchronized to early S phase by a double thymidine block. The release of the double thymidine block allows the cells to progress through the cell cycle in a synchronized pace. By collecting the cells at various time intervals following the release of double thymidine block, we are able to harvest cells synchronized to the G2, M, and G1 phases. This synchronization can be assessed by various methods, including flow cytometry to examine the DNA content, Western blotting to examine the expression of various cell phase-specific markers, and microscopy to examine the morphology of the chromosome.

Enhancement of biotransformation of ginsenosides in white ginseng roots by aerobic co-cultivation of Bacillus subtilis and Trichoderma reesei.

In the present work, the biotransformation of ginsenosides in white ginseng roots was innovatively investigated using the aerobic fermentation by the co-cultivation of Bacillus subtilis and Trichoderma reesei. It is found that in the co-cultivation mode, the optimal nitrogen source was corn steep liquor, and the loading of ginseng powder and inoculation proportion of B. subtilis and T. reesei were 15g/L and 1:4, respectively. The total ginsenoside yield and production of minor ginsenosides in the co-cultivation mode obviously enhanced in comparison to the monoculture mode. Meanwhile, the maximal total ginsenoside yield of 21.79% and high hydrolase activities were achieved using the staged inoculation at the inoculation proportion of 1:4 in the co-cultivation mode, the production of minor ginsenosides such as Rg3 and Rh1, Rh2 was significantly strengthened, and the pharmacological activities of the fermented solution obviously improved. The enhancement of ginsenoside transformation can be mainly attributed to hydrolysis of the produced hydrolases and metabolism of two probiotics. This result clearly reveals that using the staged inoculation in co-cultivation fermentation mode was favor of the ginsenoside biotransformation in ginseng due to non-synchronous cell growth and different metabolic pathways of both probiotics. This work can provide a novel method for enhancing ginsenoside transformation of ginseng.Key points• Co-cultivation fermentation significantly promoted ginsenoside biotransformation.• The staged inoculation in co-culture mode was an optimal operation method.• The pharmacological activity of the co-cultured solution was significantly enhanced.

Cell Cycle-Dependent Expression of Bk Channels in Human Mesenchymal Endometrial Stem Cells

The study of ion channels in stem cells provides important information about their role in stem cell fate. Previously we have identified the activity of calcium-activated potassium channels of big conductance (BK channels) in human endometrium-derived mesenchymal stem cells (eMSCs). BK channels could have significant impact into signaling processes by modulating membrane potential. The membrane potential and ionic permeability dynamically changes during cycle transitions. Here, we aimed at verification of the role of BK channels as potassium transporting pathway regulating cell cycle passageway of eMSCs. The functional expression of native BK channels was confirmed by patch-clamp and immunocytochemistry. In non-synchronized cells immunofluorescent analysis revealed BK-positive and BK-negative stained eMSCs. Using cell synchronization, we found that the presence of BK channels in plasma membrane was cell cycle-dependent and significantly decreased in G2M phase. However, the study of cell cycle progression in presence of selective BK channel inhibitors showed no effect of pore blockers on cycle transitions. Thus, BK channel-mediated K+ transport is not critical for the fundamental mechanism of passageway through cell cycle of eMSCs. At the same time, the dynamics of the presence of BK channels on plasma membrane of eMSCs can be a novel indicator of cellular proliferation.

A single-cell micro-trench platform for automatic monitoring of cell division and apoptosis after chemotherapeutic drug administration

Cells vary in their dynamic response to external stimuli, due to stochastic fluctuations and non-uniform progression through the cell cycle. Hence, single-cell studies are required to reveal the range of heterogeneity in their responses to defined perturbations, which provides detailed insight into signaling processes. Here, we present a time-lapse study using arrays of micro-trenches to monitor the timing of cell division and apoptosis in non-adherent cells at the single-cell level. By employing automated cell tracking and division detection, we precisely determine cell cycle duration and sister-cell correlations for hundreds of individual cells in parallel. As a model application we study the response of leukemia cells to the chemostatic drug vincristine as a function of cell cycle phase. The time-to-death after drug addition is found to depend both on drug concentration and cell cycle phase. The resulting timing and dose-response distributions were reproduced in control experiments using synchronized cell populations. Interestingly, in non-synchronized cells, the time-to-death intervals for sister cells appear to be correlated. Our study demonstrates the practical benefits of micro-trench arrays as a platform for high-throughput, single-cell time-lapse studies on cell cycle dependence, correlations and cell fate decisions in general.

Modeling Tumor Microenvironment Interactions of Imid Sensitive and Resistant Cells in 3D Organotypic Culture Models

Background: Organotypic culture models developed using 3D conditions recapitulate tissue-specific structural features and cell-cell interactions more accurately than conventional 2D cultures. Our ultimate goal is to optimize culture conditions which promote the survival and proliferation of multiple myeloma (MM) cells and could serve as a platform for molecular mechanistic, clinical biomarker and pharmacodynamic marker studies using immune-modulatory compounds (IMIDs) and other myeloma drugs alone and in combination.Design/Results: Using gas permeable microfluidic devices, we cultured and compared growth/morphologic properties of six multiple myeloma cell lines, MM1.S, MM1.SPR, H929, H929PR, H929-220R and RPMI-8226 in 2D and 3D conditions. Collagen type IV was used as an extra-cellular matrix source to grow these cells. Cell growth and morphology was captured at regular intervals. Ten days post culture, cells were harvested from the device and stained for proliferation (Ki67 staining) index and expression of key MM oncogenic molecules, CD138, CD38 and BCMA. Cell lines grown in 3D conditions had, with some exceptions, higher proliferation index compared to 2D conditions. Thus, Ki67-mean fluorescence intensity (MFI) for 3D vs 2D were: 2038 vs 1130 for MM1.S; 1614 vs 1912 for MM1.PR; 2067 vs 1169 for H929; 2057 vs 1702 for H929PR; 2300 vs 1889 for H929-220R; 2018 vs 1220 for RPMI-8226. Similar trends for higher proliferation under 3D conditions were observed for the CD138, CD38 and BCMA cell subsets. Expression of FOXM1, a potential marker of IMID resistance, was reduced in Pomalidomide sensitive non-synchronous cells compared to resistant cells, although a few clusters with higher FOXM1 expression were observed among sensitive cells. To further study the effects of other components of MM tumor micro-environment on Pomalidomide response, we optimized the culture conditions to co-culture MM cell lines with bone marrow stromal cells. The co-culture of bone marrow stromal cells, HS5 with MM cell line H929 protected Ikaros degradation induced by Pomalidomide. Interestingly, CD44 expression in H929 cells was upregulated in co-culture conditions with stromal cells.Future Directions: These culture conditions are currently being optimized to study the (1) drug effects in MM and immune cells alone and in combination and (2) use the co-culture derived cells for single cell level evaluation of genetic, transcriptomic or proteomic changes associated with drug treatment and (3) ultimately grow primary Myeloma cells in these conditions for ex vivo manipulation and downstream molecular and biological effects. DisclosuresAhsan:celgene: Employment, Equity Ownership. Jeyaraju:Celgene Corporation: Employment, Equity Ownership. Bisht:Celgene Corporation: Employment, Equity Ownership. Hagner:Celgene Corporation: Employment, Equity Ownership. Bjorklund:Celgene Corporation: Employment, Equity Ownership. Pierceall:Celgene: Employment, Equity Ownership. Thakurta:Celgene Corporation: Employment, Equity Ownership.

Beneficial Metabolic Consequences of Acyl‐CoA Synthetase ACSVL3 Knockout in Glioma Cells

We previously reported that knockdown or knockout (KO) of the fatty acid metabolic enzyme Very Long Chain Acyl‐CoA Synthetase 3 (ACSVL3; SLC27A3) in glioblastoma cells was beneficial. KO U87 glioma cells grew at a slower rate, became adherence‐dependent, and produced fewer, slower‐growing subcutaneous and intracranial tumors when implanted in NOD‐SCID mice. To understand the mechanisms underlying these changes, we investigated several possibilities. We initially demonstrated that lack of ACSVL3 did not slow the synthesis of membrane phospholipids necessary for the rapid proliferation of tumor cells in culture. We then investigated the possibility that ACSVL3 KO affected either apoptosis or autophagy. However, no differences in these processes between control and KO U87 cells were found. We next looked at cell cycle, and found that KO produced significant changes. In non‐synchronized cells, control U87 cells were mainly in G0/G1, while ACSVL3 KO cells were mainly in S‐phase. Both control and KO cells synchronized by serum starvation started out mainly in G0/G1, but by 12 hours KO cells shifted significantly toward S‐phase. Identification of the cyclins and cyclin‐dependent kinases that may be involved is in progress. Proteomic and metabolomic profiling indicated that in addition to effects on lipid metabolism, ACSVL3 KO produced changes in glucose and energy metabolism. Although glucose transporters GLUT1 and GLUT3 protein levels were reduced by KO, cellular uptake of labeled 2‐deoxyglucose was unaffected. However, oxidation of glucose to CO2 was reduced 40% by ACSVL3 depletion, and the cellular glucose level was 25% higher in KO cells. Glycolytic enzymes were upregulated by KO, but metabolic intermediates were essentially unchanged. Interestingly, lactate production and the levels of both LDHA and LDHB were elevated by ACSVL3 KO, and pentose phosphate pathway activity was lower in KO cells. Citric acid cycle enzymes, electron transport chain complexes, and ATP synthase protein levels were all reduced by ACSVL3 depletion. Mitochondria had a more punctate morphology in U87 cells, but were more elongated in KO cells. In conclusion, depletion of ACSVL3 affects many metabolic processes not directly related to lipid metabolism in human glioblastoma cells.Support or Funding InformationKennedy Krieger Research Administration fundsThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Sulforaphane as an adjunctive to everolimus counteracts everolimus resistance in renal cancer cell lines

BackgroundThe mechanistic target of rapamycin (mTOR) inhibitors, everolimus and temsirolimus, have widened therapeutic options to treat renal cell carcinoma (RCC). However, chronic treatment with these inhibitors often induces resistance, leading to therapeutic failure. PurposeThe natural compound, sulforaphane (SFN), was added to an everolimus based regime in vitro in the hopes of preventing resistance development. MethodsA panel of RCC cell lines (A498, Caki-1, KTCTL-26) was treated with everolimus or SFN or with an everolimus-SFN-combination, either short- (24h) or long-term (8 weeks), and cell growth, proliferation, apoptosis, and cell cycle phases were measured. The cell cycle regulating proteins cdk1, cdk2, cyclin A, cyclin B, akt and raptor (both total and activated) were also evaluated. ResultsShort-term incubation with everolimus (1nM) or SFN (5µM) significantly reduced RCC cell growth. Additive effects on tumor growth and proliferation were evoked by the SFN-everolimus combination. Long-term everolimus-incubation led to resistance development in Caki-1 cells, evidenced by elevated growth and proliferation, associated with an increased percentage of G2/M (non-synchronized cell model) or S-phase (synchronized cell model) cells. Molecular analysis revealed up-regulation of the cdk1-cyclin B and cdk2-cyclin A axis, along with elevated phosphorylation of the mTOR sub-member, raptor. In contrast, resistance development was not observed with the long-term combination of SFN-everolimus. The combination suppressed Caki-1 growth and proliferation, and was associated with an increase in G0/G1-phase cells, diminished cdk1 and akt (both total and activated), cyclin B and raptor expression. ConclusionAdding SFN to an everolimus based RCC treatment regimen in vitro delayed resistance development observed with chronic everolimus monotherapy. Ongoing in vivo studies are necessary to verify the in vitro data.

Identification of Mitosis-Specific Phosphorylation in Mitotic Chromosome-Associated Proteins.

During mitosis, phosphorylation of chromosome-associated proteins is a key regulatory mechanism. Mass spectrometry has been successfully applied to determine the complete protein composition of mitotic chromosomes, but not to identify post-translational modifications. Here, we quantitatively compared the phosphoproteome of isolated mitotic chromosomes with that of chromosomes in nonsynchronized cells. We identified 4274 total phosphorylation sites and 350 mitosis-specific phosphorylation sites in mitotic chromosome-associated proteins. Significant mitosis-specific phosphorylation in centromere/kinetochore proteins was detected, although the chromosomal association of these proteins did not change throughout the cell cycle. This mitosis-specific phosphorylation might play a key role in regulation of mitosis. Further analysis revealed strong dependency of phosphorylation dynamics on kinase consensus patterns, thus linking the identified phosphorylation sites to known key mitotic kinases. Remarkably, chromosomal axial proteins such as non-SMC subunits of condensin, TopoIIα, and Kif4A, together with the chromosomal periphery protein Ki67 involved in the establishment of the mitotic chromosomal structure, demonstrated high phosphorylation during mitosis. These findings suggest a novel mechanism for regulation of chromosome restructuring in mitosis via protein phosphorylation. Our study generated a large quantitative database on protein phosphorylation in mitotic and nonmitotic chromosomes, thus providing insights into the dynamics of chromatin protein phosphorylation at mitosis onset.

Effect of ATM on low-dose hyper-radiosensitivity in A549 cells synchronized at G2 phase

Objective To investigate the low-dose hyper-radiosensitivity (HRS)/induced radioresistance (IRR) in A549 cells synchronized at G2 phase and the role of ATM kinase in the process. Methods Human lung adenocarcinoma cell line A549 was synchronized at G2 phase by aphidicolin. The ATM-specific activator and inhibitor, chloroquine and KU55933, were used to regulate the activity of ATM. The colony formation assay was used to evaluate cell survival. Flow cytometry was used to determine the cell cycle of radiation-exposed A549 cells synchronized at G2 phase. Immunofluorescence was used to observe the dynamics of γ-H2AX fluorescence and evaluate the efficiency of DNA repair in A549 cells synchronized at G2 phase. Western blot was used to detect the expression of phosphorylated ATM (Ser1981) and ATM. Results A549 cells synchronized at G2 phase had substantially enhanced HRS than non-synchronized cells. The dose-induced transition from HRS to IRR was in accordance with the dose-response pattern of early G2/M checkpoint. However, with the same threshold dose, the activation of early checkpoint occurred earlier and lasted longer than normal. The activation of ATM kinase inhibited HRS and enhanced DNA repair, while the inhibition of ATM kinase enhanced HRS and hindered DNA repair. Conclusions ATM kinase-mediated early G2+ M checkpoint is a molecular switch for HRS in synchronized A549 cells. Low-dose irradiation with G2-phase synchronization and ATM inhibitor can enhance the low-dose radiosensitivity. Key words: Low-dose radiation sensitivity/increased radiation resistance; Early G2/M checkpoint; Cell cycle

Hepatitis B virus X protein-regulated expression of Plk1

To investigate the ability and underlying mechanism of hepatitis B virus X protein (HBx) regulation of Polo-like kinase 1 (Plk1) expression. The human HCC cell line HepG2 was transfected (transiently and stably) with an HBx plasmid expression vector (pCMV-HA-HBx) or empty plasmid vector (control), with and without expression plasmids with the Plk1 promoter. Effects on Plk1 expression were assessed by western blotting. Functional effects on the Plk1 promoter were assessed by luciferase reporter assay. Effects on the mRNA level of Plk1 in S phase HepG2 cells were assessed by quantitative real-time reverse transcriptase polymerase chain reaction. After blocking protein synthesis by treatment with cycloheximide (CHX), the turnover rate of Plk1 was assessed by western blotting. Lastly, the effect of HBx on cell cycle was assessed by flow cytometry. HBx did not increase the protein expression of Plk1 in non-synchronized HepG2 cells, but did significantly up-regulate the Plk1 protein level in the synchronized S phase cells (P = 0.026 and P = 0.003, respectively). Ectopic expression of HBx did not increase the mRNA level of Plk1 in HepG2 cells, but did inhibit the degradation of Plk1, as evidenced by an increased half-life of Plk1 protein (from 30 to 90 minutes). The HBx-expressing HepG2 cells showed more frequent entry into the S or G(2)/M phase than the control cells (31.65% vs. 24.56% or 9.43% vs. 4.47%, respectively) and less in the G(0)/G(1) phase (decrease from 70.97% to 58.92% for the HBx-expressing HepG2 cells). HBx is able to up-regulate the expression of Plk1 in HepG2 cells by a mechanism involving stabilization of the Plk1 protein primarily in the S phase of the cell cycl.

CBM-09CD15 AND CD15S EXPRESSION IS CORRELATED WITH CELL CYCLE ARREST AT G1-PHASE IN GLIOMA

BACKGROUND: CD15 and sialyl-CD15 are cell surface epitopes, known for their ability to bind specific ligands. They are over-expressed on many non-central nervous system (CNS) cancers. Few reports show CD15 expression in CNS neoplasms and in fact, early studies reported the absence of CD15 expression. Recent published reports, however, have identified CD15 as a potential marker for cancer stem-like cells in glioblastomas (GBM). To obtain a better understanding, CD15 and CD15s expression was re-examined in glioma cell lines. METHOD: Extracellular expression of CD15 and CD15s were determined by Immunocytochemistry Western blot and flow cytometry in GBM cells (UP-007 and SNB-19). Non-neoplastic astrocytes (SC-1800) served as controls. Cells were synchronised at G1, S or G2/M phases via serum starvation, Hydroxyurea and Colcemid, respectively followed by validation using the fluorescence ubiqutination cell cycle indicator (FUCCI) system. RESULTS: In non-synchronised GBM cell cultures, approximately 5% of cells express CD15 or CD15s compared to 1% of CD15 or CD15s positivity in SC-1800. When GBM cell lines were synchronised in specific phases, there was a significant increase in CD15 (20%) and CD15s (46.3%) expression, especially G1 phase. The population of CD15 positive cells was significantly increased (p < 0.001) in UP-007 (CD15: 15% and CD15s:36%) and SNB-19 (CD15:20% and CD15s:15%) compared to non-synchronised GBM cells and synchronised SC-1800 (CD15:1.5% and CD15s:1.8). CONCLUSION: CD15 and CD15s expression is cell cycle dependent in glioma cells and may account for the discrepancy of previous experimental data.

Cytological characterization of anther development in Panax ginseng Meyer.

Ginseng (Panax ginseng), a valued medicinal herb, is a slow-growing plant that flowers after 3years of growth with the formation of a solitary terminal umbel inflorescence. However, little is known about cytological events during ginseng reproduction, such as the development of the male organ, the stamen. To better understand the mechanism controlling ginseng male reproductive development, here, we investigated the inflorescence and flower structure of ginseng. Moreover, we performed cytological analysis of anther morphogenesis and showed the common and specialized cytological events including the formation of four concentric cell layers surrounding male reproductive cells followed by subsequent cell differentiation and degeneration of tapetal cells, as well as the formation of mature pollen grains via meiosis and mitosis during ginseng anther development. Particularly, our transverse section and microscopic observations showed that the ginseng tapetal layer exhibits obvious nonsynchronous cell division evidenced by the observation of one or two tapetal layers frequently observed in one anther lobe, suggesting the unique control of cell division. To facilitate the future study on ginseng male reproduction, we grouped the anther development into 10 developmental stages according to the characterized cytological events.

Human fucci pancreatic Beta cell lines: new tools to study Beta cell cycle and terminal differentiation.

Regulation of cell cycle in beta cells is poorly understood, especially in humans. We exploited here the recently described human pancreatic beta cell line EndoC-βH2 to set up experimental systems for cell cycle studies. We derived 2 populations from EndoC-βH2 cells that stably harbor the 2 genes encoding the Fucci fluorescent indicators of cell cycle, either from two vectors, or from a unique bicistronic vector. In proliferating non-synchronized cells, the 2 Fucci indicators revealed cells in the expected phases of cell cycle, with orange and green cells being in G1 and S/G2/M cells, respectively, and allowed the sorting of cells in different substeps of G1. The Fucci indicators also faithfully red out alterations in human beta cell proliferative activity since a mitogen-rich medium decreased the proportion of orange cells and inflated the green population, while reciprocal changes were observed when cells were induced to cease proliferation and increased expression of some beta cell genes. In the last situation, acquisition of a more differentiated beta cell phenotype correlates with an increased intensity in orange fluorescence. Hence Fucci beta cell lines provide new tools to address important questions regarding human beta cell cycle and differentiation.

Understanding the sub-cellular dynamics of silicon transportation and synthesis in diatoms using population-level data and computational optimization.

Controlled synthesis of silicon is a major challenge in nanotechnology and material science. Diatoms, the unicellular algae, are an inspiring example of silica biosynthesis, producing complex and delicate nano-structures. This happens in several cell compartments, including cytoplasm and silica deposition vesicle (SDV). Considering the low concentration of silicic acid in oceans, cells have developed silicon transporter proteins (SIT). Moreover, cells change the level of active SITs during one cell cycle, likely as a response to the level of external nutrients and internal deposition rates. Despite this topic being of fundamental interest, the intracellular dynamics of nutrients and cell regulation strategies remain poorly understood. One reason is the difficulties in measurements and manipulation of these mechanisms at such small scales, and even when possible, data often contain large errors. Therefore, using computational techniques seems inevitable. We have constructed a mathematical model for silicon dynamics in the diatom Thalassiosira pseudonana in four compartments: external environment, cytoplasm, SDV and deposited silica. The model builds on mass conservation and Michaelis-Menten kinetics as mass transport equations. In order to find the free parameters of the model from sparse, noisy experimental data, an optimization technique (global and local search), together with enzyme related penalty terms, has been applied. We have connected population-level data to individual-cell-level quantities including the effect of early division of non-synchronized cells. Our model is robust, proven by sensitivity and perturbation analysis, and predicts dynamics of intracellular nutrients and enzymes in different compartments. The model produces different uptake regimes, previously recognized as surge, externally-controlled and internally-controlled uptakes. Finally, we imposed a flux of SITs to the model and compared it with previous classical kinetics. The model introduced can be generalized in order to analyze different biomineralizing organisms and to test different chemical pathways only by switching the system of mass transport equations.

Organization of the mitotic chromosome.

Mitotic chromosomes are among the most recognizable structures in the cell, yet for over a century their internal organization remains largely unsolved. We applied chromosome conformation capture methods, 5C and Hi-C, across the cell cycle and revealed two distinct three-dimensional folding states of the human genome. We show that the highly compartmentalized and cell type-specific organization described previously for nonsynchronous cells is restricted to interphase. In metaphase, we identified a homogenous folding state that is locus-independent, common to all chromosomes, and consistent among cell types, suggesting a general principle of metaphase chromosome organization. Using polymer simulations, we found that metaphase Hi-C data are inconsistent with classic hierarchical models and are instead best described by a linearly organized longitudinally compressed array of consecutive chromatin loops.

The effects of 56MESS on mitochondrial and cytoskeletal proteins and the cell cycle in MDCK cells

56MESS has been shown to be cytotoxic but the mode of this action is unclear. In order to probe the mechanism of action for 56MESS, MDCK cells were utilised to investigate the effect on treated cells. IC50 values for 56MESS and cisplatin in the MDCK cell line, determined by a SRB assay, were 0.25 ± 0.03 and 18 ± 1.2 μM respectively. In a preliminary study, cells treated with 56MESS displayed no caspase-3/7 activity, suggesting that the mechanism of action is caspase independent. Protein expression studies revealed an increase the expression in the MTC02 protein associated with mitochondria in cells treated with 56MESS and cisplatin. Non-synchronised 56MESS-treated cells caused an arrest in the G2/M phase of the cell cycle, in comparison to the S phase arrest of cisplatin. In G0/G1 synchronised cells, both 56MESS and cisplatin both appeared to arrest within the S phase. these results suggest that 56MESS is capable of causing cell-cycle arrest, and that mitochondrial and cell cycle proteins may be involved in the mode of action of cytotoxicity of 56MESS.

Nuclear localization of DMP1 proteins suggests a role in intracellular signaling

Dentin matrix protein 1 (DMP1) is highly expressed in odontoblasts and osteoblasts/osteocytes and plays an essential role in tooth and bone mineralization and phosphate homeostasis. It is debatable whether DMP1, in addition to its function in the extracellular matrix, can enter the nucleus and function as a transcription factor. To better understand its function, we examined the nuclear localization of endogenous and exogenous DMP1 in C3H10T1/2 mesenchymal cells, MC3T3-E1 preosteoblast cells and 17IIA11 odontoblast-like cells. RT-PCR analyses showed the expression of endogenous Dmp1 in all three cell lines, while Western-blot analysis detected a major DMP1 protein band corresponding to the 57kDa C-terminal fragment generated by proteolytic processing of the secreted full-length DMP1. Immunofluorescent staining demonstrated that non-synchronized cells presented two subpopulations with either nuclear or cytoplasmic localization of endogenous DMP1. In addition, cells transfected with a construct expressing HA-tagged full-length DMP1 also showed either nuclear or cytoplasmic localization of the exogenous DMP1 when examined with an antibody against the HA tag. Furthermore, nuclear DMP1 was restricted to the nucleoplasm but was absent in the nucleolus. In conclusion, these findings suggest that, apart from its role as a constituent of dentin and bone matrix, DMP1 might play a regulatory role in the nucleus.

Activation of DNA damage response pathways as a consequence of anthracycline-DNA adduct formation

The cytotoxicity of doxorubicin, a clinically used anti-neoplastic drug, can be enhanced by formaldehyde (either endogenous or exogenous) to promote the formation of doxorubicin-DNA adducts. Formaldehyde supplies the carbon required for the covalent linkage of doxorubicin to one strand of DNA, with hydrogen bonds stabilising the doxorubicin mono-adduct to the other strand of DNA, to act much like an interstrand crosslink. Interstrand crosslinks present a major challenge for cellular repair processes, requiring the activation of numerous DNA damage response proteins for resolution of the resulting DNA intermediates and damage. This work investigates DNA damage response proteins activated by doxorubicin-DNA adducts. Although p53 was phosphorylated at Serine 15 in response to adducts, long term growth inhibition of mammalian cells was not affected by p53 status. Using siRNA technology and kinase inhibitors we observed enhanced cellular sensitivity to doxorubicin-DNA adducts when the activity of the signalling protein kinases ATM and ATR were lost. Cells synchronised using a double thymidine block were sensitised to adduct-initiated cell death upon ATR knockdown, but relatively unaffected by ATM knockdown. Loss of ATR was associated with abrogation of a drug-induced G2/M block and induction of mitotic catastrophe, while loss of ATM was associated with drug-induced apoptosis in non-synchronised cells. These proteins may therefore be potential drug targets to achieve synergistic cytotoxic responses to doxorubicin-DNA adduct forming therapies. The analysis of these protein kinases with respect to cell cycle progression indicates that ATR is required for G2/M checkpoint responses while ATM appears to function in G1 mediated responses to anthracycline adducts.