Mathematical model for early development of the sea urchin embryo

In Xenopus and Drosophila, the nucleocytoplasmic ratio controls many aspects of cell-cycle remodeling during the transitory period that leads from fast and synchronous cell divisions of early development to the slow, carefully regulated growth and divisions of somatic cells. After the fifth cleavage in sea urchin embryos, there are four populations of differently sized blastomeres, whose interdivision times are inversely related to size. The inverse relation suggests nucleocytoplasmic control of cell division during sea urchin development as well. To investigate this possibility, we developed a mathematical model based on molecular interactions underlying early embryonic cell-cycle control. Introducing the nucleocytoplasmic ratio explicitly into the molecular mechanism, we are able to reproduce many physiological features of sea urchin development.     

Nucleocytoplasmic protein translocation during mitosis in the social amoebozoan Dictyostelium discoideum

Mitosis is a fundamental and essential life process. It underlies the duplication and survival of all cells and, as a result, all eukaryotic organisms. Since uncontrolled mitosis is a dreaded component of many cancers, a full understanding of the process is critical. Evolution has led to the existence of three types of mitosis: closed, open, and semi‐open. The significance of these different mitotic species, how they can lead to a full understanding of the critical events that underlie the asexual duplication of all cells, and how they may generate new insights into controlling unregulated cell division remains to be determined. The eukaryotic microbe Dictyostelium discoideum has proved to be a valuable biomedical model organism. While it appears to utilize closed mitosis, a review of the literature suggests that it possesses a form of mitosis that lies in the middle between truly open and fully closed mitosis—it utilizes a form of semi‐open mitosis. Here, the nucleocytoplasmic translocation patterns of the proteins that have been studied during mitosis in the social amoebozoan D. discoideum are detailed followed by a discussion of how some of them provide support for the hypothesis of semi‐open mitosis.     

Towards understanding the control of the division cycle in animal cells.

The author reviewed the historical process by which classical knowledge of cell division accumulated, to give rise to the molecular biology of the cell cycle, and discussed the perspective of this field of research. The study of the control of cell division began at the turn of the century. It was hypothesized that cell division was a physiological regulation necessary for growing cells to maintain a proper nucleocytoplasmic ratio to survive, which was later substantiated by the finding that amoeba cells could be prevented from dividing by repeated excision of the cytoplasm. However, the observation in Tetrahymena that heat-shocked cells grow exceedingly, but fail to divide, suggested that the cell required the accumulation of a labile "division protein" to initiate division. Mechanisms that control the cell cycle were studied in oocytes by nuclear transplantation and cytoplasmic transfer, and in cultured mammalian cells, protozoa, and Physarum plasmodia by cell fusion. These experiments demonstrated the existence of cytoplasmic factors that control the cell cycle. Maturation promoting factor (MPF) thus discovered in frog oocytes became known to be an ubiquitous cytoplasmic factor that causes the transition from interphase to metaphase in all organisms. The insight into the molecular control of cell growth and division was gained from yeast cell genetics. For biochemical analysis of the cell cycle control, the method to observe the cell cycle in vitro was developed using frog egg extracts. Thus, MPF was identified as a cdc2--cyclin protein complex. Its activity was found to depend on synthesis and phosphorylation of these proteins. However, recently it was found that there were cell cycle phenomena that were difficult to explain in these terms. Various other cellular factors, including nucleocytoplasmic ratio and microtubule assembly, were also found to control MPF, as well as the cell cycle. It remained open to future how these factors control MPF to alter the pattern of the cell cycle.     

Nucleotide excision repair in chromatin: the shape of things to come

Much of our mechanistic understanding of nucleotide excision repair (NER) has been derived from biochemical studies that have analysed the reaction as it occurs on DNA substrates that are not representative of DNA as it exists in the living cell. These studies have been extremely useful in deciphering the core mechanism of the NER reaction, but efforts to understand how NER operates in chromatin have been hampered in part because assembling DNA into nucleosomes, the first level of chromatin compaction, is inhibitory to NER in vitro. However, recent research using biochemical, genetic and cell-based studies is now providing us with the first insights into the molecular mechanism of NER as it occurs in the cellular context. A number of recent studies have provided glimpses of a chromatin--NER connection. Here I review this literature and evaluate how it might aid our understanding, and shape our future research into NER.     

Genetic control of cell size

Over the past 25 years, the genetic control of cell size has mainly been addressed in yeast, a single-celled organism. Recent insights from Drosophila have shed light on the signalling pathways responsible for adjusting and maintaining cell size in metazoans. Evidence is emerging for a signalling cascade conserved in evolution that links external nutrient sources to cell size.     

Monitoring biomolecular interactions by time-lapse atomic force microscopy

The atomic force microscope (AFM) is a unique imaging tool that enables the tracking of single macromolecule events in response to physiological effectors and pharmacological stimuli. Direct correlation can therefore be made between structural and functional states of individual biomolecules in an aqueous environment. This review explores how time-lapse AFM has been used to learn more about normal and disease-associated biological processes. Three specific examples have been chosen to illustrate the capabilities of this technique. In the cell, actin polymerizes into filaments, depolymerizes, and undergoes interactions with numerous effector molecules (i.e., severing, capping, depolymerizing, bundling, and cross-linking proteins) in response to many different stimuli. Such events are critical for the function and maintenance of the molecular machinery of muscle contraction and the dynamic organization of the cytoskeleton. One goal is to use time-lapse AFM to examine and manipulate some of these events in vitro, in order to learn more about how these processes occur in the cell. Aberrant protein polymerization into amyloid fibrils occurs in a multitude of diseases, including Alzheimer's and type 2 diabetes. Local amyloid deposits may cause organ dysfunction and cell death; hence, it is of interest to learn how to interfere with fibril formation. One application of time-lapse AFM in this area has been the direct visualization of amyloid fibril growth in vitro. This experimental approach holds promise for the future testing of potential therapeutic drugs, for example, by directly visualizing at which level of fibril assembly (i.e., nucleation, elongation, branching, or lateral association of protofibrils) a given active compound will interfere. Nuclear pore complexes (NPCs) are large supramolecular assemblies embedded in the nuclear envelope. Transport of ions, small molecules, proteins, RNAs, and RNP particles in and out of the nucleus occurs via NPCs. Time-lapse AFM has been used to structurally visualize the response of individual NPC particles to various chemical and physical effectors known to interfere with nucleocytoplasmic transport. Taken together, such time-lapse AFM studies could provide novel insights into the molecular mechanisms of fundamental biological processes under both normal and pathological conditions at the single molecule level.     

The effect of the nucleocytoplasmic ratio on protein synthesis and expression of a stage-specific antigen in early cleaving mouse embryos

The nucleocytoplasmic ratio of fertilized mouse eggs was manipulated by removing or injecting cytoplasm by micropipette, and bisection of denuded eggs to obtain both pronuclei in one half of the eggs cytoplasm. The experimental eggs were capable of cleavage to the morula stage and, in some instances, developed to the blastocyst stage similar to unmanipulated eggs. The removal of large quantities of cytoplasm by micropipette and injecting them into a recipient egg did not provide sufficient numbers of viable eggs, whereas transfer of smaller quantities (about a quarter of the cytoplasm) was less deleterious, at least for recipient eggs. However, the alteration of the nucleocytoplasmic ratio by this method was not of the correct magnitude for the purpose of this experiment. Therefore, bisection was the preferred method whereby the nucleocytoplasmic ratio was doubled. This resulted in both pronuclei residing in one half of the egg's cytoplasm. Half eggs with one pronucleus (haploid) but retaining a nucleocytoplasmic ratio similar to unmanipulated control eggs served as additional controls for the bisection experiments. Protein synthesis was analysed by two-dimensional gel electrophoresis, showing that the 2-cell- and 4-cell-stage bisected embryos with double and normal nucleocytoplasmic ratio expressed equivalent protein synthesis patterns as control embryos of the same stage. Likewise, the stage-specific surface antigen SSEA-1 did not appear before the 6- to 8-cell stage. Also in cytoplasm transfer experiments, there was no indication that altering the nucleocytoplasmic ratio in either direction changed the timing of stage-specific gene expression. These results support the idea that stage-specific gene activity during early mouse cleavage might proceed in parallel to DNA replication cycles and is independent of the nucleocytoplasmic ratio.     

Cellular dimensions affecting the nucleocytoplasmic volume ratio

Although it has long been appreciated that larger eukaryotic cells have larger nuclei, little is known about how this size relationship is maintained. Here we describe a method for measuring the aqueous volume ratio of nucleus to cytoplasm, two compartments which are interconnected via the pores in the nuclear envelope. We then use that method to identify proportional cellular dimensions in variously treated cells and in different cell types. Cells were scrape loaded with a mixture of fluorescent dextrans: Texas red dextran, average mol wt = 10,000 (TRDx10), and fluorescein isothiocyanate dextran, average mol wt = 70,000 (FDx70). After introduction into the cytoplasmic space, the TRDx10 distributed into both the nucleus and cytoplasm, whereas the FDx70 was restricted to cytoplasm, due to size exclusion by the nuclear pores. The aqueous nucleocytoplasmic volume ratio (RN/C) was determined by measuring, from fluorescence images of spread cells, total cellular fluorescence of each of the two probes and the fluorescence ratio of those probes in the cytoplasm. RN/C was unaffected by the measurement procedure or by varying temperatures between 23 degrees and 37 degrees C. Loading excess unlabeled dextrans had little effect on RN/C, with the single exception that high concentrations of large dextrans could lower RN/C in endothelial cells. Expanding intracellular membranous compartments of macrophages by phagocytosis of latex beads decreased RN/C. Expanding the same compartment by pinocytosis of sucrose, which nearly doubled total cell volume, had little effect on RN/C, indicating that nuclear volume was more closely linked to the cytoplasmic volume, exclusive of vesicular organelles, than to total cell volume. RN/C was the same in mononucleate and binucleate endothelial cells. Finally, measurements of RN/C in murine bone marrow-derived macrophages, bovine aortic endothelial cells, Swiss 3T3 fibroblasts, PtK2 cells, and CV-1 cells revealed that nuclear volume scaled allometrically with cell volume. The allometric relationship indicated that cell volume was proportional to nuclear surface area.     

Some aspects of haematology of an Indian grass snake Natrix stolata in relation to sex and size.

Studies have been made on the erythrocyte counts per mm3 of blood, total differential leucocyte counts per mm3 of blood, concentration of haemoglobin per 100 ml of blood, haematocrit values and nucleocytoplasmic ratio in a common Indian grass snake, Natrix stolata, in relation to body weight of both the sexes in the same month of the year (during breeding phase). Logarithmic transformations have been used in case of erythrocyte counts and haemoglobin concentrations. From log/log calculation it seems that the correlation between body weight and erythrocyte is more prounounced in females than in males. The concentration of haemoglobin shows a very high degree of correlation in both the sexes. The haematocrit values show a clear trend of increase with increasing body weight in both the sexes. The nucleocytoplasmic ratio does not show much variation in different weight groups whereas in females the variation is well marked in different weight groups and the size of erythrocyte also becomes larger in higher weight groups. In both the sexes the leucocyte counts have been found that along with the increase in body weights, the number of leucocyte increases in juveniles but in adults the leucocyte number decreases with the increasing body weights.     

A model for persistent infection with Epstein-Barr virus: the stealth virus of human B cells.

Most adult humans are infected benignly and for life with the herpesvirus Epstein-Barr virus. EBV has been a focus of research because of its status as a candidate tumor virus for a number of lymphomas and carcinomas. In vitro EBV has the ability to establish a latent infection in proliferating B lymphoblasts. This is the only system available for studying human herpesvirus latency in culture and has been extremely useful for elucidating how EBV promotes cellular growth. However, to understand how EBV survives in the healthy host and what goes awry, leading to disease, it is essential to know how EBV establishes and maintains a persistent infection in vivo. Early studies on the mechanism of EBV persistence produced inconclusive and often contradictory results because the techniques available were crude and insensitive. Recent advances in PCR technology and the application of sophisticated cell fractionation techniques have now provided new insights into the behavior of the virus. Most dramatically it has been shown that EBV in vivo does not establish latency in a proliferating lymphoblast, but in a resting memory B cell. The contrasting behaviors of being able to establish a latent infection in proliferating B blasts and resting memory B cells can be resolved in terms of a model where EBV performs its complete life cycle in B lymphocytes. The virus achieves this not by disrupting normal B cell biology but by using it.     

Morphologically-structured models of growing budding yeast populations

It has been well recognized that many key aspects of cell cycle regulation are encoded into the size distributions of growing budding yeast populations due to the tight coupling between cell growth and cell division present in this organism. Several attempts have been made to model the cell size distribution of growing yeast populations in order to obtain insight on the underlying control mechanisms, but most were based on the age structure of asymmetrically dividing populations. Here we propose a new framework that couples a morphologically-structured representation of the population with population balance theory to formulate a dynamic model for the size distribution of growing yeast populations. An advantage of the presented framework is that it allows derivation of simpler models that are directly identifiable from experiments. We show how such models can be derived from the general framework and demonstrate their utility in analyzing yeast population data. Finally, by employing a recently proposed numerical scheme, we proceed to integrate numerically the full distributed model to provide predictions of dynamics of the cell size structure of growing yeast populations.     

A new role of ran GTPase.

Ran is a G protein similar to Ras, but it has no membrane binding site. RanGEF, RCC1, is on chromatin and RanGAP, RanGAP1/Rna1p is in cytoplasm. Ran, thus, shuttles between the nucleus and the cytoplasm to complete its GTPase cycle, carrying out nucleocytoplasmic transport of macromolecules. A majority of Ran binding proteins, thus far found, are required for this process. A recently found novel Ran-binding protein, RanBPM, however, is localized in the centrosome. Subsequently, four groups reported that RanGTP, but not RanGDP, can induce microtubule self-organization in Xenopus egg extracts where no nuclear membrane is present. Thus, Ran is suggested to have a new role beyond the nucleocytoplasmic transport of macromolecules. In both microtubule assembly and nucleocytoplasmic transport, chromosomal localization of RCC1 is important to carry out the functions of RanGTPase. In this regard, a future intriguing question is how RCC1 interacts with chromatin DNA.     

Programmed cell death in fission yeast

Recently a metacaspase, encoded by YCA1, has been implicated in a primitive form of apoptosis or programmed cell death in yeast. Previously it had been shown that over-expression of mammalian pro-apoptotic proteins can induce cell death in yeast, but the mechanism of how cell death occurred was not clearly established. More recently, it has been shown that DNA or oxidative damage, or other cell cycle blocks, can result in cell death that mimics apoptosis in higher cells. Also, in fission yeast deletion of genes required for triacylglycerol synthesis leads to cell death and expression of apoptotic markers. A metacaspase sharing greater than 40% identity to budding yeast Yca1 has been identified in fission yeast, however, its role in programmed cell death is not yet known. Analysis of the genetic pathways that influence cell death in yeast may provide insights into the mechanisms of apoptosis in all eukaryotic organisms.     

Distinct phospho-forms of cortactin differentially regulate actin polymerization and focal adhesions

Cortactin is an actin-binding protein that is overexpressed in many cancers and is a substrate for both tyrosine and serine/threonine kinases. Tyrosine phosphorylation of cortactin has been observed to increase cell motility and invasion in vivo, although it has been reported to have both positive and negative effects on actin polymerization in vitro. In contrast, serine phosphorylation of cortactin has been shown to stimulate actin assembly in vitro. Currently, the effects of cortactin serine phosphorylation on cell migration are unclear, and furthermore, how the distinct phospho-forms of cortactin may differentially contribute to cell migration has not been directly compared. Therefore, we tested the effects of different tyrosine and serine phospho-mutants of cortactin on lamellipodial protrusion, actin assembly within cells, and focal adhesion dynamics. Interestingly, while expression of either tyrosine or serine phospho-mimetic cortactin mutants resulted in increased lamellipodial protrusion and cell migration, these effects appeared to be via distinct processes. Cortactin mutants mimicking serine phosphorylation appeared to predominantly affect actin polymerization, whereas mutation of cortactin tyrosine residues resulted in alterations in focal adhesion turnover. Thus these findings provide novel insights into how distinct phospho-forms of cortactin may differentially contribute to actin and focal adhesion dynamics to control cell migration.     

Wake of the flood: ascribing functions to the wave of type III effector proteins of phytopathogenic bacteria

Plant pathogenic bacteria use waves of type III effector proteins, delivered into the eukaryotic host cell, to modulate the host cell for the pathogen's benefit. This is evidenced by the flood of effector genes that have recently been uncovered from the genome sequence of several plant pathogenic bacteria. However, pathogens are unwilling to easily reveal the mechanisms by which these effectors function. Nevertheless, persistent scrutiny has led to the successful characterization of a handful of effectors and it is beginning to provide insights into how phytopathogenic bacteria cause disease on their hosts.     

A Nucleotide-Dependent Conformational Switch Controls the Polymerization of Human IMP Dehydrogenases to Modulate their Catalytic Activity

Inosine 5′-monophosphate dehydrogenase (IMPDH) catalyzes the rate-limiting step in the de novo GTP biosynthetic pathway and plays essential roles in cell proliferation. As a clinical target, IMPDH has been studied for decades, but it has only been within the last years that we are starting to understand the complexity of the mechanisms of its physiological regulation. Here, we report structural and functional insights into how adenine and guanine nucleotides control a conformational switch that modulates the assembly of the two human IMPDH enzymes into cytoophidia and allosterically regulates their catalytic activity. In vitro reconstituted micron-length cytoophidia-like structures show catalytic activity comparable to unassembled IMPDH but, in turn, are more resistant to GTP/GDP allosteric inhibition. Therefore, IMPDH cytoophidia formation facilitates the accumulation of high levels of guanine nucleotides when the cell requires it. Finally, we demonstrate that most of the IMPDH retinopathy-associated mutations abrogate GTP/GDP-induced allosteric inhibition and alter cytoophidia dynamics.