Multiscale modeling of red blood cell mechanics and blood flow in malaria

Red blood cells (RBCs) infected by a Plasmodium parasite in malaria may lose their membrane deformability with a relative membrane stiffening more than ten-fold in comparison with healthy RBCs leading to potential capillary occlusions. Moreover, infected RBCs are able to adhere to other healthy and parasitized cells and to the vascular endothelium resulting in a substantial disruption of normal blood circulation. In the present work, we simulate infected RBCs in malaria using a multiscale RBC model based on the dissipative particle dynamics method, coupling scales at the sub-cellular level with scales at the vessel size. Our objective is to conduct a full validation of the RBC model with a diverse set of experimental data, including temperature dependence, and to identify the limitations of this purely mechanistic model. The simulated elastic deformations of parasitized RBCs match those obtained in optical-tweezers experiments for different stages of intra-erythrocytic parasite development. The rheological properties of RBCs in malaria are compared with those obtained by optical magnetic twisting cytometry and by monitoring membrane fluctuations at room, physiological, and febrile temperatures. We also study the dynamics of infected RBCs in Poiseuille flow in comparison with healthy cells and present validated bulk viscosity predictions of malaria-infected blood for a wide range of parasitemia levels (percentage of infected RBCs with respect to the total number of cells in a unit volume).     

Mitochondrial matrix calcium is an activating signal for hormone secretion

Mitochondrial Ca(2+) signals have been proposed to accelerate oxidative metabolism and ATP production to match Ca(2+)-activated energy-consuming processes. Efforts to understand the signaling role of mitochondrial Ca(2+) have been hampered by the inability to manipulate matrix Ca(2+) without directly altering cytosolic Ca(2+). We were able to selectively buffer mitochondrial Ca(2+) rises by targeting the Ca(2+)-binding protein S100G to the matrix. We find that matrix Ca(2+) controls signal-dependent NAD(P)H formation, respiration, and ATP changes in intact cells. Furthermore, we demonstrate that matrix Ca(2+) increases are necessary for the amplification of sustained glucose-dependent insulin secretion in β cells. Through the regulation of NAD(P)H in adrenal glomerulosa cells, matrix Ca(2+) also acts as a positive signal in reductive biosynthesis, which stimulates aldosterone secretion. Our dissection of cytosolic and mitochondrial Ca(2+) signals reveals the physiological importance of matrix Ca(2+) in energy metabolism required for signal-dependent hormone secretion.     

Prion diseases of yeast: amyloid structure and biology

Prion "variants" or "strains" are prions with the identical protein sequence, but different characteristics of the prion infection: e.g. different incubation periods for scrapie strains or different phenotype intensities for yeast prion variants. We have shown that infectious amyloids of the yeast prions [PSI+], [URE3] and [PIN+] each have an in-register parallel β-sheet architecture. Moreover, we have pointed out that this amyloid architecture can explain how one protein can faithfully transmit any of several conformations to new protein monomers. This explains how proteins can be genes.     

Development of the downstream process in the production of the recombinant histone H1.3 variant

It was shown that H1 type histones possess anticancer activity and could be utilized in therapy of acute myeloid leukemia. We developed an experimental pilot-scale technology of the recombinant histone H1.3 variant production. The downstream process includes acidic extraction of the target protein from the culture broth, ion-exchange, reversed-phase and size-exclusion chromatography, and freeze-drying. The accent was made on the reduction of bacterial endotoxin contamination of the active pharmaceutical ingredient. Highly efficient downstream strategy of the target protein depyrogenation is discussed in the paper. The developed technology allows the production of the protein with high yield (approx. 110 g per 1000 L of the culture broth) and of high purity (estimated productivity is 75–100 g/month). The activity and purity of the active pharmaceutical ingredients produced for clinical trials were confirmed by different tests including ultra performance liquid chromatography, size exclusion chromatography, ELISA, SDS–PAGE, gel-clot LAL-test. Clinical trials were started in the Russian Federation.     

Macrophage activation and differentiation signals regulate schlafen-4 gene expression: evidence for Schlafen-4 as a modulator of myelopoiesis

Background

The ten mouse and six human members of the Schlafen (Slfn) gene family all contain an AAA domain. Little is known of their function, but previous studies suggest roles in immune cell development. In this report, we assessed Slfn regulation and function in macrophages, which are key cellular regulators of innate immunity.

Methodology/Principal Findings

Multiple members of the Slfn family were up-regulated in mouse bone marrow-derived macrophages (BMM) by the Toll-like Receptor (TLR)4 agonist lipopolysaccharide (LPS), the TLR3 agonist Poly(I∶C), and in disease-affected joints in the collagen-induced model of rheumatoid arthritis. Of these, the most inducible was Slfn4. TLR agonists that signal exclusively through the MyD88 adaptor protein had more modest effects on Slfn4 mRNA levels, thus implicating MyD88-independent signalling and autocrine interferon (IFN)-β in inducible expression. This was supported by the substantial reduction in basal and LPS-induced Slfn4 mRNA expression in IFNAR-1^−/− BMM. LPS causes growth arrest in macrophages, and other Slfn family genes have been implicated in growth control. Slfn4 mRNA levels were repressed during macrophage colony-stimulating factor (CSF-1)-mediated differentiation of bone marrow progenitors into BMM. To determine the role of Slfn4 in vivo, we over-expressed the gene specifically in macrophages in mice using a csf1r promoter-driven binary expression system. Transgenic over-expression of Slfn4 in myeloid cells did not alter macrophage colony formation or proliferation in vitro. Monocyte numbers, as well as inflammatory macrophages recruited to the peritoneal cavity, were reduced in transgenic mice that specifically over-expressed Slfn4, while macrophage numbers and hematopoietic activity were increased in the livers and spleens.

Conclusions

Slfn4 mRNA levels were up-regulated during macrophage activation but down-regulated during differentiation. Constitutive Slfn4 expression in the myeloid lineage in vivo perturbs myelopoiesis. We hypothesise that the down-regulation of Slfn4 gene expression during macrophage differentiation is a necessary step in development of this lineage.     

Photoperiodic and temperature control of diapause induction and colour change in the southern green stink bug Nezara viridula

Abstract. The effect of photoperiod and temperature on the duration of the nymphal period, diapause induction and colour change in adults of Nezara viridula (L.) (Heteroptera: Pentatomidae) from Japan was studied in the laboratory. At 20 °C, the developmental period for nymphs was significantly shorter under LD 10 : 14 h (short day) and LD 16 : 8 h (long day) than under intermediate photoperiods, whereas at 25 °C it was slightly shorter under intermediate than short- and long-day conditions. It is assumed that photoperiod-mediated acceleration of nymphal growth takes place in autumn when day-length is short and it is unlikely that nymphal development is affected by day-length under summer long-day and hot conditions. Nezara viridula has an adult diapause controlled by a long-day photoperiodic response. At 20 °C and 25 °C in both sexes, photoperiodic responses were similar and had thresholds close to 12.5 h, thus suggesting that the response is thermostable within this range of temperatures and day-length plays a leading role in diapause induction. Precopulation and preoviposition periods were significantly longer under near-critical regimes than under long-day ones. Short-day and near-critical photoperiods induced a gradual change of adult colour from green to brown/russet. The rate of colour change was significantly higher under LD 10 : 14 h than under LD 13 : 11 h, suggesting that the colour change is strongly associated with diapause induction. The incidences of diapause or dark colour did not vary among genetically determined colour morphs, indicating that these morphs have a similar tendency to enter diapause and change colour in response to short-day conditions.     

Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility

Escherichia coli endonuclease VIII (Nei) excises oxidized pyrimidines from DNA. It shares significant sequence homology and similar mechanism with Fpg, a bacterial 8-oxoguanine glycosylase. The structure of a covalent Nei-DNA complex has been recently determined, revealing critical amino acid residues which are important for DNA binding and catalysis. Several Fpg structures have also been reported; however, analysis of structural dynamics of Fpg/Nei family proteins has been hindered by the lack of structures of uncomplexed and DNA-bound enzymes from the same source. We report a 2.8 A resolution structure of free wild-type Nei and two structures of its inactive mutants, Nei-E2A (2.3 A) and Nei-R252A (2.05 A). All three structures are virtually identical, demonstrating that the mutations did not affect the overall conformation of the protein in its free state. The structures show a significant conformational change compared with the Nei structure in its complex with DNA, reflecting a approximately 50 degrees rotation of the two main domains of the enzyme. Such interdomain flexibility has not been reported previously for any DNA glycosylase and may present the first evidence for a global DNA-induced conformational change in this class of enzymes. Several local but functionally relevant structural changes are also evident in other parts of the enzyme.     

How to Find Decision Makers in Neural Networks

Nervous systems often face the problem of classifying stimuli and making decisions based on these classifications. The neurons involved in these tasks can be characterized as sensory or motor, according to their correlation with sensory stimulus or motor response. In this study we define a third class of neurons responsible for making perceptual decisions. Our mathematical formalism enables the weighting of neuronal units according to their contribution to decision making, thus narrowing the field for more detailed studies of underlying mechanisms. We develop two definitions of a contribution to decision making. The first definition states that decision making activity can be found at the points of emergence for behavioral correlations in the system. The second definition involves the study of propagation of noise in the network. The latter definition is shown to be equivalent to the first one in the cases when they can be compared. Our results suggest a new approach to analyzing decision making networks An erratum to this article can be found at