Computational modeling of chromosome re-replication in mutant strains of fission yeast

Typically cells replicate their genome only once per division cycle, but under some circumstances, both natural and unnatural, cells synthesize an overabundance of DNA, either in a disorganized manner (“overreplication”) or by a systematic doubling of chromosome number (“endoreplication”). These variations on the theme of DNA replication and division have been studied in strains of fission yeast, Schizosaccharomyces pombe, carrying mutations that interfere with the function of mitotic cyclin-dependent kinase (Cdk1:Cdc13) without impeding the roles of DNA-replication loading factor (Cdc18) and S-phase cyclin-dependent kinase (Cdk1:Cig2). Some of these mutations support endoreplication, and some overreplication. In this paper, we propose a dynamical model of the interactions among the proteins governing DNA replication and cell division in fission yeast. By computational simulations of the mathematical model, we account for the observed phenotypes of these re-replicating mutants, and by theoretical analysis of the dynamical system, we provide insight into the molecular distinctions between overreplicating and endoreplicating cells. In the case of induced overproduction of regulatory proteins, our model predicts that cells first switch from normal mitotic cell cycles to growth-controlled endoreplication, and ultimately to disorganized overreplication, parallel to the slow increase of protein to very high levels.     

Reduced IgG anti-small nuclear ribonucleoprotein autoantibody production in systemic lupus erythematosus patients with positive IgM anti-cytomegalovirus antibodies

Introduction

In rheumatoid arthritis (RA), synovial fluid (SF) contains a large number of neutrophils that contribute to the inflammation and destruction of the joints. The SF also contains granulocyte-macrophage colony-stimulating factor (GM-CSF), which sustains viability of neutrophils and activates their functions. Using proteomic surveillance, we here tried to elucidate the effects of GM-CSF on neutrophils.

Methods

Neutrophils stimulated by GM-CSF were divided into four subcellular fractions: cytosol, membrane/organelle, nuclei, and cytoskeleton. Then, proteins were extracted from each fraction and digested by trypsin. The produced peptides were detected using matrix-assisted laser desorption ionisation-time-of-flight mass spectrometry (MALDI-TOF MS).

Results

We detected 33 peptide peaks whose expression was upregulated by more than 2.5-fold in GM-CSF stimulated neutrophils and identified 11 proteins out of the 33 peptides using MALDI-TOF/TOF MS analysis and protein database searches. One of the identified proteins was neutrophil gelatinase-associated lipocalin (NGAL). We confirmed that the level of NGAL in SF was significantly higher in patients with RA than in those with osteoarthritis. We next addressed possible roles of the increased NGAL in RA. We analysed proteome alteration of synoviocytes from patients with RA by treatment with NGAL in vitro. We found that, out of the detected protein spots (approximately 3,600 protein spots), the intensity of 21 protein spots increased by more than 1.5-fold and the intensity of 10 protein spots decreased by less than 1 to 1.5-fold as a result of the NGAL treatment. Among the 21 increased protein spots, we identified 9 proteins including transitional endoplasmic reticulum ATPase (TERA), cathepsin D, and transglutaminase 2 (TG2), which increased to 4.8-fold, 1.5-fold and 1.6-fold, respectively. Two-dimensional electrophoresis followed by western blot analysis confirmed the upregulation of TERA by the NGAL treatment and, moreover, the western blot analysis showed that the NGAL treatment changed the protein spots caused by post-translational modification of TERA. Furthermore, NGAL cancelled out the proliferative effects of fibroblast growth factor (FGF)-2 and epidermal growth factor (EGF) on chondrocytes from a patient with RA and proliferative effect of FGF-2 on chondrosarcoma cells.

Conclusions

Our results indicate that GM-CSF contributes to the pathogenesis of RA through upregulation of NGAL in neutrophils, followed by induction of TERA, cathepsin D and TG2 in synoviocytes. NGAL and the upregulated enzymes may therefore play an important role in RA.     

Posttranslational regulation of I-Ed by affinity for CLIP

Several MHC class II alleles linked with autoimmune diseases form unusually low stability complexes with CLIP, leading us to hypothesize that this is an important feature contributing to autoimmune pathogenesis. To investigate cellular consequences of altering class II/CLIP affinity, we evaluated invariant chain (Ii) mutants with varying CLIP affinity for a mouse class II allele, I-E(d), which has low affinity for wild-type CLIP and is associated with a mouse model of spontaneous, autoimmune joint inflammation. Increasing CLIP affinity for I-E(d) resulted in increased cell surface and total cellular abundance and half-life of I-E(d). This reveals a post-endoplasmic reticulum chaperoning capacity of Ii via its CLIP peptides. Quantitative effects on I-E(d) were less pronounced in DM-expressing cells, suggesting complementary chaperoning effects mediated by Ii and DM, and implying that the impact of allelic variation in CLIP affinity on immune responses will be highest in cells with limited DM activity. Differences in the ability of cell lines expressing wild-type or high-CLIP-affinity mutant Ii to present Ag to T cells suggest a model in which increased CLIP affinity for class II serves to restrict peptide loading to DM-containing compartments, ensuring proper editing of antigenic peptides.     

Metabolic rate does not scale with body mass in cultured mammalian cells

The allometric scaling of metabolic rate with organism body mass can be partially accounted for by differences in cellular metabolic rates. For example, hepatocytes isolated from horses consume almost 10-fold less oxygen per unit time as mouse hepatocytes [Porter and Brand, Am J Physiol Regul Integr Comp Physiol 269: R226-R228, 1995]. This could reflect a genetically programmed, species-specific, intrinsic metabolic rate set point, or simply the adaptation of individual cells to their particular in situ environment (i.e., within the organism). We studied cultured cell lines derived from 10 mammalian species with donor body masses ranging from 5 to 600,000 g to determine whether cells propagated in an identical environment (media) exhibited metabolic rate scaling. Neither metabolic rate nor the maximal activities of key enzymes of oxidative or anaerobic metabolism scaled significantly with donor body mass in cultured cells, indicating the absence of intrinsic, species-specific, cellular metabolic rate set points. Furthermore, we suggest that changes in the metabolic rates of isolated cells probably occur within 24 h and involve a reduction of cellular metabolism toward values observed in lower metabolic rate organisms. The rate of oxygen delivery has been proposed to limit cellular metabolic rates in larger organisms. To examine the effect of oxygen on steady-state cellular respiration rates, we grew cells under a variety of physiologically relevant oxygen regimens. Long-term exposure to higher medium oxygen levels increased respiration rates of all cells, consistent with the hypothesis that higher rates of oxygen delivery in smaller mammals might increase cellular metabolic rates.     

Wetland development in a previously mined landscape of East Texas,USA

We studied wetland development in a chronosequence of created wetlands in a reclaimed landscape in east Texas seasonally for 1 year. The purpose of the study was to identify features (i.e., indicators) that best reflected changes in wetland ecosystem state through time and could serve as indicators of “maturity” for bond-release. Features considered included surface water nutrients, soil nutrients, soil redox potential, vegetative biomass and diversity, and benthic invertebrate biomass and diversity. Our sampling focused on nine wetlands representing three different-age classes (n = 3 for each) as a surrogate for time. All wetland sites were created with the same homogenized mine spoil and had similar hydrology and climate. Age-specific changes in all parameters were observed, except for surface water nutrients. The oldest wetlands (i.e., “mature”) exhibited highest soil concentrations of N, C, K, P, and Ca. Soil redox potential was significantly lower in the mature wetlands, in addition to within-wetland (lowest in deepest sampling zones) and intra-annual variability (i.e., lowest during the summer). Mature created wetlands supported the highest vegetative biomass and species richness and highest densities of invertebrates; however, taxa richness was similar across all age groups. Of all parameters we measured, vegetation metrics were among the simplest and most cost-effective measures used to track the early development of mitigated wetlands. This study provides the basis from which to track the development of these reclaimed ecosystems in a more rigorous and easily replicated manner. With further validation, select use of these parameter sets in east Texas and other similar landscapes could aid both in determining compliance for regulatory purposes as well as tracking success of ecological mitigation.     

Frequent coexistence of anti-topoisomerase I and anti-U1RNP autoantibodies in African American patients associated with mild skin involvement: a retrospective clinical study

Introduction  

The presence of anti-topoisomerase I (topo I) antibodies is a classic scleroderma (SSc) marker presumably associated with a unique clinical subset. Here the clinical association of anti-topo I was reevaluated in unselected patients seen in a rheumatology clinic setting.     

Stochastic exit from mitosis in budding yeast: Model predictions and experimental observations

Unlike many mutants that are completely viable or inviable, the CLB2-dbΔ clb5Δ mutant of Saccharomyces cerevisiae is inviable in glucose but partially viable on slower growth media such as raffinose. On raffinose, the mutant cells can bud and divide but in each cycle there is a chance that a cell will fail to divide (telophase arrest), causing it to exit the cell cycle. This effect gives rise to a stochastic phenotype that cannot be explained by a deterministic model. We measure the interbud times of wild-type and mutant cells growing on raffinose and compute statistics and distributions to characterize the mutant''s behavior. We convert a detailed deterministic model of the budding yeast cell cycle to a stochastic model and determine the extent to which it captures the stochastic phenotype of the mutant strain. Predictions of the mathematical model are in reasonable agreement with our experimental data and suggest directions for improving the model. Ultimately, the ability to accurately model stochastic phenotypes may prove critical to understanding disease and therapeutic interventions in higher eukaryotes.Key words: stochastic phenotype, mitotic exit, non-genetic variability, cell cycle modeling, computational biology, stochastic modeling, deterministic modeling     

Genetic diversity, social structure, and conservation value of the elephants of the Nakai Plateau, Lao PDR, based on non-invasive sampling

The Lao People??s Democratic Republic (PDR) may have the largest Asian elephant population in Indochina. However, elephants on Lao PDR??s Nakai Plateau are potentially threatened by the construction of a hydropower dam that will flood important habitat. We conducted a non-invasive genetic study of elephants in this region to provide baseline data on genetic diversity and social structure prior to dam construction. For the 102 elephants we detected, values of observed heterozygosity (0.711) and allelic diversity (8.0 alleles/locus) at microsatellite loci were higher than those found in elephant populations in India and Vietnam, while mitochondrial diversity (haplotype diversity 0.741; nucleotide diversity 0.011) was similar to that reported for the Lao/Vietnam region. Six mitochondrial haplotypes were detected, representing both major clades previously reported in this species. Relatedness estimates between females and young detected near each other are consistent with familial relationships, and relatedness estimates between adult males and females suggest male locational dispersal. Since family group structure appears to be intact in the Nakai region, these elephants will likely move as relatively large family groups in response to habitat disturbance. These results have positive implications for the viability of the elephant population in this region, demonstrate its conservation significance, and will be valuable for predicting and monitoring the effects of the hydropower dam over time.     

The two domains of centrin have distinct basal body functions in Tetrahymena

The basal body is a microtubule-organizing center responsible for organizing the cilium, a structure important for cell locomotion and sensing of the surrounding environment. A widely conserved basal body component is the Ca(2+)-binding protein centrin. Analyses of centrin function suggest a role in basal body assembly and stability; however, its molecular mechanisms remain unclear. Here we describe a mutagenic strategy to study the function and essential nature of the various structural features of Cen1 in the ciliate Tetrahymena. We find that the two domains of Cen1 are both essential, and examination of strains containing mutant CEN1 alleles indicates that there are two predominant basal body phenotypes: misorientation of newly assembled basal bodies and stability defects. The results also show that the two domains of Cen1 are able to bind Ca(2+) and that perturbation of Ca(2+) binding affects Cen1 function. In all, the data suggest that the two domains of Cen1 have distinct functions.