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The clinical spectrum of Down syndrome (DS) ranges from congenital malformations to premature aging and early-onset senescence. Excessive immunoreactivity and oxidative stress are thought to accelerate the pace of aging in DS patients; however, the immunological profile remains elusive. We investigated whether peripheral blood monocyte-derived dendritic cells (MoDCs) in DS patients respond to lipopolysaccharide (LPS) distinctly from non-DS control MoDCs. Eighteen DS patients (age 2–47 years, 12 males) and 22 controls (age 4–40 years, 15 males) were enrolled. CD14-positive monocytes were immunopurified and cultured for 7 days in the presence of granulocyte-macrophage colony-stimulating factor and IL-4, yielding MoDCs in vitro. After the LPS-stimulation for 48 hours from days 7 to 9, culture supernatant cytokines were measured by multiplex cytokine bead assays, and bulk-prepared RNA from the cells was used for transcriptomic analyses. MoDCs from DS patients produced cytokines/chemokines (IL-6, IL-8, TNF-α, MCP-1, and IP-10) at significantly higher levels than those from controls in response to LPS. RNA sequencing revealed that DS-derived MoDCs differentially expressed 137 genes (74 upregulated and 63 downregulated) compared with controls. A gene enrichment analysis identified 5 genes associated with Toll-like receptor signaling (KEGG: hsa04620, P = 0.00731) and oxidative phosphorylation (hsa00190, P = 0.0173) pathways. MoDCs obtained from DS patients showed higher cytokine or chemokine responses to LPS than did control MoDCs. Gene expression profiles suggest that hyperactive Toll-like receptor and mitochondrial oxidative phosphorylation pathways configure the immunoreactive signature of MoDCs in DS patients. Excessive immunoreactivity and oxidative stress are associated with aging in patients with Down syndrome; however, their immunological profiles remain elusive. Gene expression profiling in this study illustrates that hyperactive toll-like receptor and mitochondrial oxidative phosphorylation pathways configure the immunoreactive signature in monocyte-derived dendritic cells from patients with Down syndrome. Graphical Abstract [ABSTRACT FROM AUTHOR]

RIPK1 is a multi-functional kinase that regulates cell death and inflammation and has been implicated in the pathogenesis of inflammatory diseases. RIPK1 acts in a kinase-dependent and kinase-independent manner to promote or suppress apoptosis and necroptosis, but the underlying mechanisms remain poorly understood. Here, we show that a mutation (R588E) disrupting the RIPK1 death domain (DD) caused perinatal lethality induced by ZBP1-mediated necroptosis. Additionally, these mice developed postnatal inflammatory pathology, which was mediated by necroptosis-independent TNFR1, TRADD, and TRIF signaling, partially requiring RIPK3. Our biochemical mechanistic studies revealed that ZBP1- and TRIF-mediated activation of RIPK3 required RIPK1 kinase activity in wild-type cells but not in Ripk1 R588E/R588E cells, suggesting that DD-dependent oligomerization of RIPK1 and its interaction with FADD determine the mechanisms of RIPK3 activation by ZBP1 and TRIF. Collectively, these findings revealed a critical physiological role of DD-dependent RIPK1 signaling that is important for the regulation of tissue homeostasis and inflammation. [Display omitted] • ZBP1 and TRIF induce necroptosis-mediated perinatal death in Ripk1 R588E/R588E mice • TRADD induces inflammation and early postnatal death in Ripk1 R588E/R588E Mlkl −/− • RIPK3 causes MLKL-independent postnatal inflammation in Ripk1 R588E/R588E mice • The RIPK1 DD determines how ZBP1 and TRIF engage and activate RIPK3 RIPK1 regulates cell death via kinase-dependent and kinase-independent mechanisms. Utilizing mice expressing RIPK1 with a point mutation disrupting its death domain, Imai et al. show that RIPK1 death domain interactions are critical to suppress ZBP1- and TRIF-induced activation of RIPK3 and necroptosis. [ABSTRACT FROM AUTHOR]

The development of atherosclerotic plaques is the result of a chronic inflammatory response coordinated by stromal and immune cellular components of the vascular wall. While endothelial cells and leukocytes are well-recognised mediators of inflammation in atherosclerosis, the role of smooth muscle cells (SMCs) remains incompletely understood. Here we aimed to address the role of canonical NF-κB signalling in SMCs in the development of atherosclerosis. We investigated the role of NF-κB signalling in SMCs in atherosclerosis by employing SMC-specific ablation of NEMO, an IKK complex subunit that is essential for canonical NF-κB activation, in ApoE−/− mice. We show that SMC-specific ablation of NEMO (NEMOSMCiKO) inhibited high fat diet induced atherosclerosis in ApoE−/− mice. NEMOSMCiKO/ApoE−/− mice developed less and smaller atherosclerotic plaques, which contained fewer macrophages, decreased numbers of apoptotic cells and smaller necrotic areas and showed reduced inflammation compared to the plaques of ApoE−/− mice. In addition, the plaques of NEMOSMCiKO/ApoE−/− mice showed higher expression of α-SMA and lower expression of the transcriptional factor KLF4 compared to those of ApoE−/− mice. Consistently, in vitro, NEMO-deficient SMCs exhibited reduced proliferation and migration, as well as decreased KLF4 expression and lower production of IL-6 and MCP-1 upon inflammatory stimulus (TNF or LPS) compared to NEMO-expressing SMCs. In conclusion, NEMO-dependent activation of NF-κB signalling in SMCs critically contributes to the pathogenesis of atherosclerosis by regulating SMC proliferation, migration and phenotype switching in response to inflammatory stimuli. [ABSTRACT FROM AUTHOR]

Objectives: Immunoglobulin A vasculitis/Henoch–Schönlein purpura (IgAV/HSP) is a major cause of vasculitis in children. It is often accompanied by nephritis (HSPN) and could progress to chronic kidney disease. Galactose‐deficient IgA1 was recently reported to be involved in the pathogenesis of HSPN, for which immunosuppressive drugs are considered key treatment. However, the involvement of immune cells in the development of HSPN remains unclear. Methods: We compared gene expressions of peripheral blood mononuclear cells (PBMCs) among healthy controls (n = 10), IgAV/HSP patients (n = 21) and HSPN patients (n = 8), which required nephritis development within 3 months of IgAV/HSP onset. Immunohistochemistry analysis and flow cytometry were performed to assess renal biopsy specimens and PBMCs, respectively. Serum CX3CL1 levels were measured by ELISA. Results: GNLY and GZMB expressions increased in HSPN patients, consistent with increased number of glomerular granulysin‐ and/or granzyme B‐positive cells demonstrated by immunohistochemistry analysis. Additionally, circulating cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells were activated with the up‐regulated surface expressions of human leucocyte antigen DR (HLA‐DR) and CX3CR1 in HSPN patients with severe proteinuria. Renal biopsies demonstrated increased number of CD8+ cells and/or CD56+ cells and up‐regulated expression of glomerular CX3CL1, a specific ligand for CX3CR1, along with increased serum CX3CL1 level. Conclusion: Activated CTLs and NK cells play roles in the development of nephritis in IgAV/HSP patients and can be used as novel biomarkers for HSPN. [ABSTRACT FROM AUTHOR]

The partial molar volume changes in the transfer of several hydrophobic molecules, which are composed of aromatic rings and an aliphatic chain of different lengths, from carbon tetrachloride to water (ΔVhyd) are calculated using the three-dimensional interaction site model theory of molecular solvation. The theory reproduces recent experimental observations: the addition of a methyl group decreases ΔVhyd; in contrast, the addition of an aromatic ring increases ΔVhyd. The discrepancy is found to originate from the difference between chain and ring structures rather than that between aliphaticity and aromaticity. Furthermore, a general rule of the variation in ΔVhyd due to the addition of a hydrocarbon is found through the theoretical analysis. An outward addition at the trans position, which is to form chain structure, decreases ΔVhyd, while an inward addition at the cis position, which is to form ring structure, increases ΔVhyd. This is explained in terms of solvent packing rather than the so-called hydrophobic hydration. The present findings argue against the traditional idea that the hydrophobic hydration can be represented by the observed values of ΔVhyd. [ABSTRACT FROM AUTHOR]

The free energy change associated with the coil-to-native structural transition of protein G in aqueous solution is calculated by using the molecular theory of solvation, also known as the three-dimensional reference interaction site model theory, to uncover the molecular mechanism of protein folding. The free energy is decomposed into the protein intramolecular energy, the hydration energy, and the hydration entropy. The folding is accompanied with a large gain in the protein intramolecular energy. However, it is almost canceled by the correspondingly large loss in the hydration energy due to the dehydration, resulting in the total energy gain about an order of magnitude smaller than might occur in vacuum. The hydration entropy gain is found to be a substantial driving force in protein folding. It is comparable with or even larger than the total energy gain. The total energy gain coupled with the hydration entropy gain is capable of suppressing the conformational entropy loss in the folding. Based on careful analysis of the theoretical results, the authors present a challenging physical picture of protein folding where the overall folding process is driven by the water entropy effect. [ABSTRACT FROM AUTHOR]

The hydration free energy (HFE) of several proteins modeled using the all-atom force field is calculated by employing the three-dimensional reference interaction site model theory, a recently developed integral equation theory of molecular solvation. The HFE is decomposed into the energetic and entropic components under the isochoric condition. The former comprises the protein-water interaction energy and the water reorganization energy arising from the structural changes induced in water. Each component is further decomposed into the nonelectrostatic and electrostatic contributions. It is found that the HFE is governed by the nonelectrostatic hydration entropy and the electrostatic hydration energy. The nonelectrostatic hydration entropy is almost exclusively ascribed to the translational entropy loss of water upon the protein insertion. It asymptotically becomes proportional to the excluded volume (EV) for water molecules as the protein size increases. The hydration energy is determined by the protein-water interaction energy which is half compensated by the water reorganization energy. These energy terms are approximately proportional to the water-accessible surface area (ASA). The energetic and entropic contributions are balanced with each other and the HFE has no apparent linear relation with the EV and ASA. [ABSTRACT FROM AUTHOR]

The hydrophobic effects on partial molar volume (PMV) are investigated as a PMV change in the transfer of a benzenelike nonpolar solute from the nonpolar solvent to water, using an integral equation theory of liquids. The volume change is divided into two effects. One is the “packing” effect in the transfer from the nonpolar solvent to hypothetical “nonpolar water” without hydrogen bonding networks. The other is the “iceberg” effect in the transfer from nonpolar water to water. The results indicate that the packing effect is negative and a half compensated by the positive iceberg effect. The packing effect is explained by the difference in the solvent compressibility. Further investigation shows that the sign and magnitude of the volume change depend on the solute size and the solvent compressibility. The finding gives a significant implication that the exposure of a hydrophobic residue caused by protein denaturation can either increase or decrease the PMV of protein depending on the size of the residue and the fluctuation of its surroundings. [ABSTRACT FROM AUTHOR]

Statistical mechanical expressions for the partial molar volume (PMV) and the partial molar compressibility (PMC) of a solute molecule with internal degrees of freedom are derived. The equilibrium PMV is expressed simply by the conformational ensemble average of PMV. The equilibrium PMC consists of two terms: the conformational ensemble average of PMC and the mean square fluctuation of PMV along conformational axis. As an illustrative application of the theory, the equilibrium PMV and PMC of butane in aqueous solution are calculated from the relations, in which the thermodynamic quantities of each conformer appearing in the relations are obtained by the reference interaction site model theory. The conformational ensemble average of PMC is the predominant contribution to the equilibrium PMC in this particular example. Possibility of shedding light on the protein conformation in terms of PMV and PMC is discussed. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A Kirkwood-Buff equation for the partial molar volumes of polyatomic molecules in solutions is derived based on the reference interaction site model (RISM) theory of molecular liquids. The partial molar volume of the twenty amino acids in aqueous solution at infinite dilution are calculated using the equation, and the results are discussed in comparison with the experimental data. The results indicate that ionizations of the C- and N-terminus groups give negative contributions to the volume ranging from -3.2 cm[sup 3]/mol to -9.7 cm[sup 3]/mol depending on the amino acid. Ionization of the dissociable residues also give negative contribution which ranges from -3.0 cm[sup 3]/mol to -6.0 cm[sup 3]/mol. On the other hand, contribution of the fractional charges on atoms to the volume is not necessarily negative, but rather slightly positive with few exceptions. It is clarified that contribution from an atom group to the volume is largely dependent on the situation where the group is placed. Therefore, it is concluded that the conventional way of determining the partial molar volume from group contributions is not reliable. The theoretical results for the partial molar volume exhibit a systematic deviation from corresponding experimental data, which increases nearly proportionally with increasing temperature and with the number of atoms in the amino acids. In order to account for the deviation, a concept of the "ideal fluctuation volume" is proposed, which is the ideal gas contribution to the volume, originating from the intramolecular fluctuation of solute. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Abstract: Colossal negative thermal expansion (NTE) with a volume contraction of about 8 %, the largest value reported so far for NTE materials, was observed in an electron‐doped giant tetragonal perovskite compound Pb1−xBixVO3 (x=0.2 and 0.3). A polar tetragonal (P4mm) to non‐polar cubic structural transition took place upon heating. The coefficient of thermal expansion (CTE) and the working temperature could be tuned by changing the Bi content, and La substitution decreased the transition temperature to room temperature. Pb0.76La0.04Bi0.20VO3 exhibited a unit cell volume contraction of 6.7 % from 200 K to 420 K. Interestingly, further gigantic NTE of about 8.5 % was observed in a dilametric measurement of a Pb0.76La0.04Bi0.20VO3 polycrystalline sample. The pronounced NTE in the sintered body should be attributed to an anisotropic lattice parameter change. [ABSTRACT FROM AUTHOR]

Abstract: Colossal negative thermal expansion (NTE) with a volume contraction of about 8 %, the largest value reported so far for NTE materials, was observed in an electron‐doped giant tetragonal perovskite compound Pb1−xBixVO3 (x=0.2 and 0.3). A polar tetragonal (P4mm) to non‐polar cubic structural transition took place upon heating. The coefficient of thermal expansion (CTE) and the working temperature could be tuned by changing the Bi content, and La substitution decreased the transition temperature to room temperature. Pb0.76La0.04Bi0.20VO3 exhibited a unit cell volume contraction of 6.7 % from 200 K to 420 K. Interestingly, further gigantic NTE of about 8.5 % was observed in a dilametric measurement of a Pb0.76La0.04Bi0.20VO3 polycrystalline sample. The pronounced NTE in the sintered body should be attributed to an anisotropic lattice parameter change. [ABSTRACT FROM AUTHOR]

• We propose a time series clustering method based on mixtures of state space models. • Our method performs clustering while modeling each cluster with a state space model. • Our method incorporates a new EM algorithm for mixtures of state space models. • Experiments showed our method is effective in clustering non-stationary time series. In this paper, we consider the task of clustering a set of individual time series while modeling each cluster, that is, model-based time series clustering. The task requires a parametric model with sufficient flexibility to describe the dynamics in various time series. To address this problem, we propose a novel model-based time series clustering method with mixtures of linear Gaussian state space models, which have high flexibility. The proposed method uses a new expectation-maximization algorithm for the mixture model to estimate the model parameters, and determines the number of clusters using the Bayesian information criterion. Experiments on a simulated dataset demonstrate the effectiveness of the method in clustering, parameter estimation, and model selection. The method is applied to real datasets commonly used to evaluate time series clustering methods. Results showed that the proposed method produces clustering results that are as accurate or more accurate than those obtained using previous methods. [ABSTRACT FROM AUTHOR]

The article offers the authors insights about the existence of quantum spin liquids (QSL), and the search for the hypothetical state of QSL. Topics discussed include the implications of the discovery of cuprate superconductors in physics, the issue over antiferromagnetism, and the paper of physicist Philip Anderson, proposing that the insulating phase of the cuprates is QSL.

The kagome Heisenberg antiferromagnet is a leading candidate in the search for a spin system with a quantum spin-liquid ground state. The nature of its ground state remains a matter of active debate. We conducted oxygen-17 single-crystal nuclear magnetic resonance (NMR) measurements of the spin-1/2 kagome lattice in herbertsmithite [ZnCu3(OH)6Cl2], which is known to exhibit a spinon continuum in the spin excitation spectrum.We demonstrated that the intrinsic local spin susceptibility χkagome, deduced from the oxygen-17 NMR frequency shift, asymptotes to zero below temperatures of 0.03J, where J ∼ 200 kelvin is the copper-copper superexchange interaction. Combined with the magnetic field dependence of χkagome that we observed at low temperatures, these results imply that the kagome Heisenberg antiferromagnet has a spin-liquid ground state with a finite gap. [ABSTRACT FROM AUTHOR]

Mucopolysaccharidosis type II (MPS II) is caused by deficiency of lysosomal enzyme iduronate-2-sulfatase. Insufficient activity of the enzyme results in accumulation of glycosaminoglycans leading to progressive multisystem pathologies. MPS II is less likely to be complicated by kidney and urinary tract problems. We report a boy with MPS II, who developed left hydronephrosis. His hydronephrosis improved after starting enzyme replacement therapy. It was suggested that MPS II was closely associated with the pathogenesis of hydronephrosis. [ABSTRACT FROM AUTHOR]

Cerebral malaria is a fatal complication of malaria. Conventional methods for evaluating experimental cerebral malaria have several drawbacks. Therefore, we aimed to develop an easy-to-use method for evaluating experimental cerebral malaria using OKD48 (Keap1-dependent Oxidative stress Detector, No-48-luciferase) mice to evaluate oxidative stress. OKD48 mice infected with Plasmodium berghei ANKA strain (PbA) suffered from experimental cerebral malaria and oxidative stress was successfully detected in the brains of living OKD48 mice developing experimental cerebral malaria. Oxidative stress in the brain was dependent on the development of experimental cerebral malaria, as prevention of experimental cerebral malaria did not elicit oxidative stress. We provide a novel evaluation method for experimental cerebral malaria using oxidative stress indicator OKD48 mice. [ABSTRACT FROM AUTHOR]

Recent studies show that some human malaria parasite species Plasmodium falciparum and P.vivax parasitize erythroblasts; however, the biological and clinical significance of this is unclear. To investigate further, we generated a rodent malaria parasite (P. yoelii 17XNL) expressing GFP-ovalbumin (OVA). Its infectivity to erythroblasts was confirmed and parasitized erythroblasts were capable of initiating malaria infections. Experiments showed that MHC class I molecules were highly expressed on parasitized erythroblasts. As CD8+ T cells recognize MHC class I and peptide complexes on target cells and are involved in protection or pathology against malaria, we examined whether erythroblasts are targeted by CD8+ T cells. Purified non-parasitized erythroblasts pulsed with OVA peptides were recognized by OVA-specific CD8+ T cells. Crucially, parasitized erythroblasts isolated from GFP-OVA-, but not GFP- infected-mice, activated OT-I CD8+ T cells, indicating that CD8+ T cells recognize parasitized erythroblasts in an antigen-specific manner. [ABSTRACT FROM AUTHOR]

General cellular functions of proteasomes occur through protein degradation, whereas the specific function of immunoproteasomes is the optimization of antigen processing associated with MHC class I. We and others previously reported that deficiency in subunits of immunoproteasomes impaired the activation of antigen-specific CD8+ T cells, resulting in higher susceptibility to tumor and infections. We demonstrated that CD8+ T cells contributed to protection against malaria parasites. In this study, we evaluated the role of immunoproteasomes in the course of infection with rodent malaria parasites. Unexpectedly, Plasmodium yoelii infection of mice deficient in LMP7, a catalytic subunit of immunoproteasomes, showed lower parasite growth in the early phase of infection and lower lethality compared with control mice. The protective characteristics of LMP7-deficient mice were not associated with enhanced immune responses, as the mutant mice showed comparable or diminished activation of innate and acquired immunity. The remarkable difference was observed in erythrocytes instead of immune responses. Parasitized red blood cells (pRBCs) purified from LMP7-deficient mice were more susceptible to phagocytosis by macrophages compared with those from wild-type mice. The susceptibility of pRBC to phagocytosis appeared to correlate with deformity of the membrane structures that were only observed after infection. Our results suggest that RBCs of LMP7-deficient mice were more likely to deform in response to infection with malaria parasites, presumably resulting in higher susceptibility to phagocytosis and in the partial resistance to malaria. [ABSTRACT FROM AUTHOR]

In antigen (Ag) cross-presentation, dendritic cells (DCs) take up extracellular Ag and translocate them from the endosome to the cytosol for proteasomal degradation. The processed peptides can enter the conventional MHC I pathway. The molecules responsible for the translocation of Ag across the endosomal membrane into the cytosol are unknown. Here we demonstrate that heat shock protein 90 (HSP90) is critical for this step. Cross-presentation and -priming were decreased in both HSP90a-null DCs and mice. CD8a+ DC apoptosis mediated by translocation of exogenous cytochrome c to the cytosol was also eliminated in HSP90a-null mice. Ag translocation into the cytosol was diminished in HSP90a-null DCs and in DCs treated with an HSP90 inhibitor. Internalized Ag was associated with HSP90 and translocated to the cytosol, a process abrogated by the HSP90 inhibitor. Ag within purified phagosomes was released in an HSP90-dependent manner. These results demonstrate the important role of HSP90 in cross-presentation by pulling endosomal Ag out into the cytosol. [ABSTRACT FROM AUTHOR]

AcrB is a membrane protein and a multidrug efflux transporter. Although the recently solved X-ray crystal structures of AcrB provide a rough sketch of how drugs efflux, the pathway and mechanism have not been completely elucidated. In this study, a ligand-mapping method based on the 3D-RISM molecular theory of solvation, which we recently developed, is applied to AcrB in order to identify the drug efflux pathway. We use a fragment-based approach as a strategy to map chemical functionality on the internal surfaces. A few “multifunctional” ligand-binding sites, which recognize various types of functional groups, are detected inside the porter domain. Spatial links between the multifunctional sites indicate a probable multidrug efflux pathway. The frustrated environment of the protein cavity constructed of weak interactions between ligand and protein may be a mechanism for allowing smooth transportation through the protein. Guided diffusion appears to be the main mechanism for efflux. [ABSTRACT FROM AUTHOR]

Reversible phosphorylation of proteins is a post-translational modification that regulates diverse biological processes. The molecular mechanism underlying phosphoryl transfer catalyzed by enzymes remains a subject of active debate. In particular, the nature of transition state (TS), whether it has an associative or dissociative character, has been one of the most controversial issues. Structural evidence supports associative TS, whereas physical organic studies point to a dissociative character. Here we perform hybrid quantum mechanics/molecular mechanics simulations for the reversible phosphorylation of phosphoserine phosphatase (PSP) to study the nature of the TS. Both phosphorylation and dephosphorylation reactions are investigated based on the two-dimensional energy surfaces along phosphoryl and proton transfer coordinates. The structures of the active site at TS in both reactions reveal compact geometries, consistent with crystal structures of PSP with phosphate analogues. However, the electron density of the phosphoryl group in both TS structures slightly decreases compared with that in the reactant states. These findings suggest that the TS of PSP has a geometrically associative yet electronically dissociative character and strongly depends on proton transfer being coupled with phosphoryl transfer. Structure and literature database, which searches on phosphotransferases, suggest that such a hybrid TS is consistent with many structures and physical organic studies and likely holds for most enzymes catalyzing phosphoryl transfer. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011 [ABSTRACT FROM AUTHOR]

In line with the recent development of fragment-based drug design, a new computational method for mapping of small ligand molecules on protein surfaces is proposed. The method uses three-dimensional (3D) spatial distribution functions of the atomic sites of the ligand calculated using the molecular theory of solvation, known as the 3D reference interaction site model (3D-RISM) theory, to identify the most probable binding modes of ligand molecules. The 3D-RISM-based method is applied to the binding of several small organic molecules to thermolysin, in order to show its efficiency and accuracy in detecting binding sites. The results demonstrate that our method can reproduce the major binding modes found by X-ray crystallographic studies with sufficient precision. Moreover, the method can successfully identify some binding modes associated with a known inhibitor, which could not be detected by X-ray analysis. The dependence of ligand-binding modes on the ligand concentration, which essentially cannot be treated with other existing computational methods, is also investigated. The results indicate that some binding modes are readily affected by the ligand concentration, whereas others are not significantly altered. In the former case, it is the subtle balance in the binding affinity between the ligand and water that determines the dominant ligand-binding mode. [ABSTRACT FROM AUTHOR]

Abstract: We have developed a DNA vaccine encoding a fusion protein of ubiquitin (Ub) and target proteins at the N-terminus for effective induction of antigen-specific CD8+ T cells. A series of expression plasmids encoding a model antigen, ovalbumin (OVA), fused with mutated Ub, was constructed. Western blotting analyses using COS7 cells transfected with these plasmids revealed that there were three types of amino acid causing different binding capacities between Ub and OVA. Natural Ub with a C-terminal glycine readily dissociated from OVA; on the other hand, artificially mutated Ub, the C-terminal amino acid of which had been exchanged to valine or arginine, stably united with the polypeptide, while Ub with a C-terminal alanine partially dissociated. The ability of DNA vaccination to induce OVA-specific CD8+ T cells closely correlated with the stability of Ub fusion to OVA. Our strategy could be used to optimize the effect of genetic vaccines on the induction of CD8+ T cells. [Copyright &y& Elsevier]

Abstract: The pressure effect on conformational equilibria of simple organic compounds and the pressure denaturation of proteins have been well investigated by using vibrational spectroscopy. However, there was no systematic investigation of the pressure effect on conformational equilibria of oligopeptides, which are located between the simple organic compounds and proteins. Here, we review the recent vibrational spectroscopic and theoretical studies of the pressure effect on conformational equilibria of model oligopeptides and helix bundle protein in aqueous solution. [Copyright &y& Elsevier]

The partial molar volume and the solvation free energy of five globular proteins in aqueous solutions are calculated by the three-dimensional reference interaction site model theory, a modern integral equation theory of molecular liquids. The partial molar volume calculated by the theory shows quantitative agreement with the corresponding experimental data. Concerning the solvation free energy, the theoretical results are compared with estimations by an empirical method which uses the accessible surface area of atoms, because the corresponding experimental data are not available. Possible applications of the method to problems related to the solvation thermodynamics of protein are discussed. [Copyright &y& Elsevier]

Collagen abnormalities in the skin and spinal cord have been reported in amyotrophic lateral sclerosis (ALS) patients. Serum carboxyterminal propeptide of type I procollagen (PICP) and the carboxyterminal cross-linked telopeptide of type I collagen (ICTP) reflect type I collagen synthesis and degradation, respectively. However, there has been no study concerning PICP or ICTP in ALS. We studied collagen contents of the skin and measured serum levels of PICP and ICTP in patients with ALS and control subjects. Serum PICP levels were significantly lower in ALS patients than in controls. Serum ICTP levels were significantly higher in ALS patients than in controls, and there was an appreciable positive correlation between serum ICTP levels and the duration of illness in ALS patients. In ALS patients, the collagen content of the skin was significantly smaller than in controls and indicated a progressive decrease in relation to illness. In addition, there was a significant negative correlation between serum ICTP concentrations and the collagen content of the skin in ALS patients. These data suggest that increased ICTP levels and decreased serum PICP levels may reflect unique changes in the skin, with a predominance of degradation compared to the synthesis of type I collagen in ALS.Copyright © 2000 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

BACKGROUND: Abnormalities hyaluronic acid (HA) of skin have been reported in patients with amyotrophic lateral sclerosis (ALS). However, little is known concerning the changes of serum HA in ALS. The purpose of this study was to investigate skin HA content and serum HA levels in ALS patients. METHODS: We measured skin HA content and serum HA levels in patients with ALS, and compared the results with those of control subjects. RESULTS: Skin HA content in ALS patients was significantly higher than in diseased control subjects and control subjects without neurological disorders, and of increased significantly, the longer the duration of illness. Serum HA concentrations in patients with ALS were significantly higher than in diseased control subjects and in healthy control subjects, and were positively and significantly associated with duration of illness. There was an appreciable positive correlation between serum HA concentrations and skin HA content in ALS patients. CONCLUSION: These data suggest that a metabolic alteration of HA may take place in ALS and increased levels of serum HA may reflect an increased content of skin HA in ALS. (ALS 2000; 1:213-218). [ABSTRACT FROM AUTHOR]

Abnormalities of collagen and glycosaminoglycans of skin have been reported in patients with amyotrophic lateral sclerosis (ALS). However, little is known concerning laminin in ALS. The aim of this study is to evaluate laminin 1 immunohistochemistry of skin in ALS patients. We studied laminin 1 immunoreactivity of skin from 17 patients with ALS, 17 patients with other neurological or muscular diseases (control group A) and 10 patients without neurological or muscular disorders (control group B). The dermis, the epithelial basement membrane of the epidermal layer and the basement membrane of skin appendages and blood vessels of skin in ALS patients were significantly higher than in control groups A and B, and showed a significant positive correlation with the duration of illness in the optical density for laminin 1 immunoreactivity. In addition, there was an appreciable positive relationship in the laminin 1 immunoreactivity between the dermis and the basement membrane in ALS patients. These data suggest that alterations of laminin 1 in the skin of ALS patients could be related to the pathogenesis of ALS and may contribute to changes in the mechanical properties of the skin, resulting in the absence of bedsores in ALS patients.Copyright © 2000 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

In the Comment on our paper [J. Chem. Phys. 123, 167103 (2005), preceding paper], Graziano argues based on the scaled particle theory that the partial molar volume change in the transfer of a hydrophobic solute from “hypothetical nonpolar water” to water can be explained simply by the difference in the effective size of solvent molecules. Opposing to the argument, we clarify using the reference interaction site model theory that the attractive interactions represented by the hydrogen bonding play an essential role for the volume change, and that the explanation given by Graziano replaces the real physics by a fake model based on an “effective” molecular diameter. We also make a general argument against the use of hard-sphere models when one considers the properties of hydration. [ABSTRACT FROM AUTHOR]

Ciliary neurotrophic factor (CNTF), a potent survival factor in spinal motoneurons of embryonic chick and rat, is currently being investigated in humans as a treatment for amyotrophic lateral sclerosis (ALS). However, its physiological and pathological activities in ALS remain unclear. We measured CNTF contents in the cervical enlargement of the spinal cord from 9 ALS patients and 12 age-matched control subjects using a sensitive enzyme-linked immunoassay. CNTF genotypes were determined by the polymerase chain reaction-restriction fragment length polymorphism method. In control subjects, there were 8 homozygotes and 4 heterozygotes, while in ALS patients there were 6 and 3, respectively. In both homozygotes and heterozygotes, CNTF expression in the spinal cord from ALS patients tended to decrease compared to control subjects. In homozygotes, the decrease was significant (p < 0.05). Concerning the regional concentrations of CNTF, in homozygotes, CNTF contents in the lateral corticospinal tract were markedly lower (p < 0.001) in ALS patients than in controls. The decrease in CNTF expression in the lateral corticospinal tract of the spinal cord from ALS patients may be a feature of ALS and could be related to motor neuron loss. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

An integral equation for rigid-body molecules with respect to site-density distribution function under arbitrary external fields is derived by the density-functional theory. Using a grand canonical partition function of molecular systems, we extend original Percus’ idea to molecular fluids. The extended Percus’ idea provides a relation between the site–site pair distribution function and site–density distribution function under an external field composed of the site–site interaction potentials of a molecule fixed at the origin. The site–density integral equation combined with the extended Percus’ relation to molecular fluids gives a closure relation of reference interaction site model equation. The site–site pair distribution functions of homonuclear diatomic Lennard-Jones fluids obtained by the integral equation agree well with those of Monte Carlo simulation. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We calculate the partial molar volume (PMV) of 20 amino acids in aqueous solution at infinite dilution by using the Kirkwood-Buff equation and the three-dimensional reference interaction site model (3D-RISM) integral equation theory for molecular liquids. As compared to the conventional, one-dimensional (1D-RISM) approach, the results exhibit drastic improvement for the quantitative agreement with experiments. The deviation from the experimental data seen for the relatively large amino acids is discussed in terms of the "ideal fluctuation volume" introduced in the previous study based on the 1D-RISM. Robustness of the new approach is further demonstrated by applying it to the PMV of polyglutamic acids in aqueous solution. The method provides reasonable account for the PMV increase with the chain length, both in α-helical and extended structures, whereas the 1D-RISM approach gives an unnatural decrease of the PMV for the α helix with a complete turn of the backbone. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Three dimensional (3D) hydration structure is informative to clarify the functions of hydrated waters around a protein. We develop a new approach to calculate 3D solvation structure with reasonable computational cost. In the present method, the total solvation structure is obtained using conventional one dimensional reference interaction site model (RISM) followed by integrating the 3D fragment data, which are evaluated around each atom (site) of solute. Thanks to this strategy, time-consuming 3D fast Fourier transformation, which is required in 3D-RISM theory, can be avoided and high-parallel performance is achieved. The method is applied to small molecular systems for comparison with 3D-RISM. The obtained results by the present method and by 3D-RISM show good agreement. The hydration structures for a large protein computed by the present method are also consistent with those obtained by x-ray crystallography. [ABSTRACT FROM AUTHOR]

This article focuses on a study according to which water molecules in a protein cavity were detected by a statistical-mechanical theory. Water molecules confined inside cavities in a protein are of great importance in understanding the structure, stability, and functions of the biomolecule. The simulation of such water molecules is as difficult as the protein folding itself. The study proves unambiguously that the common understanding was really a prejudice. It is interesting to compare the hydration structure obtained by the 3D-RISM theory with crystallographic water sites of X-ray structure.

The rate of electron transfer is critical in determining the efficiency of photoenergy conversion systems and is controlled by changing the relative energy gap of components, their geometries, or surroundings. However, the rate of electron transfer has not been controlled by the remote input of an external field without changing the geometries or materials of the systems. We demonstrate here that an applied microwave field can enhance the photocatalytic reduction of bipyridinium ion using CdS quantum dots (QDs) by accelerating electron transfer. Analysis of the time-resolved emission decay profiles of CdS quantum dots immersed in aqueous solutions of bipyridinium exhibited the shortening of their emission lifetimes, because of the accelerated electron transfer from QDs to bipyridinium under microwave irradiation. This discovery leads us to a new methodology using microwaves as an external field to enhance photocatalytic reactions. [ABSTRACT FROM AUTHOR]

Reports on a study which looked at the expression of inhibitory factor in the skin of patients with amyotrophic lateral sclerosis (ALS). Role played by the leukemia inhibitory factor (LIF) which belongs to a group of cytokines; Details of the study which involved 10 patients; The strongly positive nature of LIF immunoreactivity seen in the epidermis; The potential for LIF to be used in treating ALS.

Discusses ciliary neurotropic factor (CNTF) in skin biopsies of patients with amyotropic lateral sclerosis (ALS). Results from tests of biopsy samples taken from the upper arm of 10 ALS patients; Loss of CNTF being proposed as a possible mechanism for the sporadic form of ALS.

The CRISPR/Cas9 system is a powerful genome editing technique employed in a wide variety of organisms including recently the human malaria parasite, P. falciparum. Here we report on further improvements to the CRISPR/Cas9 transfection constructs and selection protocol to more rapidly modify the P. falciparum genome and to introduce transgenes into the parasite genome without the inclusion of drug-selectable marker genes. This method was used to stably integrate the gene encoding GFP into the P. falciparum genome under the control of promoters of three different Plasmodium genes (calmodulin, gapdh and hsp70). These genes were selected as they are highly transcribed in blood stages. We show that the three reporter parasite lines generated in this study (GFP@cam, GFP@gapdh and GFP@hsp70) have in vitro blood stage growth kinetics and drug-sensitivity profiles comparable to the parental P. falciparum (NF54) wild-type line. Both asexual and sexual blood stages of the three reporter lines expressed GFP-fluorescence with GFP@hsp70 having the highest fluorescent intensity in schizont stages as shown by flow cytometry analysis of GFP-fluorescence intensity. The improved CRISPR/Cas9 constructs/protocol will aid in the rapid generation of transgenic and modified P. falciparum parasites, including those expressing different reporters proteins under different (stage specific) promoters. [ABSTRACT FROM AUTHOR]

Cancer patients without metastasis are generally considered as candidates for curative localized radiation therapy. However, while the benefits of localized radiation have been demonstrated by many clinical studies, recurrences or distant metastases that develop after local treatment remain a major therapeutic challenge. Several in vitro and in vivo studies have reported that irradiation may subsequently alter tumor aggression by reducing or promoting the invasiveness of the remaining cancer cells after radiation, which appears to differ depending on the form of radiation, as well as the investigated cell lines. Cell lines recapitulate cancer heterogeneity based on the characteristics reflected in their genetic abnormalities, and thus can be used as a tool to investigate the genetic basis of cancer aggression. Importantly, molecular insights into this process would allow us to tailor drug treatments for use in combination with local radiation treatment. This review summarizes the diverse responses of cancer cell invasiveness induced by radiation, and discusses the possible molecular pathways and the genetic variations that may affect radiation-altered invasion. [ABSTRACT FROM AUTHOR]

Malaria remains a significant global public health concern, with a recent increase in the number of zoonotic malaria cases in Southeast Asian countries. However, limited reports on the vector for zoonotic malaria exist owing to difficulties in detecting parasite DNA in Anopheles mosquito vectors. Herein, we demonstrate for the first time that several Anopheles mosquitoes contain simian malaria parasite DNA using droplet digital PCR (ddPCR), a highly sensitive PCR method. An entomological survey was conducted to identify simian malaria vector species at Phra Phothisat Temple (PPT), central Thailand, recognized for a high prevalence of simian malaria in wild cynomolgus macaques. A total of 152 mosquitoes from six anopheline species were collected and first analyzed by a standard 18S rRNA nested-PCR analysis for malaria parasite which yielded negative results in all collected mosquitoes. Later, ddPCR was used and could detect simian malaria parasite DNA, i.e. Plasmodium cynomolgi , in 25 collected mosquitoes. And this is the first report of simian malaria parasite DNA detection in Anopheles sawadwongporni. This finding proves that ddPCR is a powerful tool for detecting simian malarial parasite DNA in Anopheles mosquitoes and can expand our understanding of the zoonotic potential of malaria transmission between monkeys and humans. [Display omitted] • An entomological survey to identify simian malaria in Anopheles vectors. • Six Anopheles spp. were collected at a location of high simian malaria prevalence. • All mosquitos were negative by standard nested PCR, but were 25 positives by ddPCR. • First report of simian malaria parasite DNA detection in An. sawadwongporni. • ddPCR is a powerful tool for detecting simian malarial parasite DNA in Anopheles. [ABSTRACT FROM AUTHOR]

The Plasmodium life cycle involves differentiation into multiple morphologically distinct forms, a process regulated by developmental stage-specific gene expression. Histone proteins are involved in epigenetic regulation in eukaryotes, and the histone variant H3.3 plays a key role in the regulation of gene expression and maintenance of genomic integrity during embryonic development in mice. However, the function of H3.3 through multiple developmental stages in Plasmodium remains unknown. To examine the function of H3.3, h3.3 -deficient mutants (Δh3.3) were generated in P. berghei. The deletion of h3.3 was not lethal in blood stage parasites, although it had a minor effect of the growth rate in blood stage; however, the in vitro ookinete conversion rate was significantly reduced, and the production of the degenerated form was increased. Regarding the mosquito stage development of Δh3.3 , oocysts number was significantly reduced, and no sporozoite production was observed. The h3.3 gene complemented mutant have normal development in mosquito stage producing mature oocysts and salivary glands contained sporozoites, and interestingly, the majority of H3.3 protein was detected in female gametocytes. However, Δh3.3 male and female gametocyte production levels were comparable to the wild-type levels. Transcriptome analysis of Δh3.3 male and female gametocytes revealed the upregulation of several male-specific genes in female gametocytes, suggesting that H3.3 functions as a transcription repressor of male-specific genes to maintain sexual identity in female gametocytes. This study provides new insights into the molecular biology of histone variants H3.3 which plays a critical role on zygote-to-oocyst development in primitive unicellular eukaryotes. [Display omitted] • Characterization of two histone H3 proteins in P. berghei. • H3.3 plays a critical role on zygote-to-oocyst development. • Δh3.3 mutants showed no sporozoite production. • The majority of H3.3-HA protein was detected in female gametocytes. • Several male-specific genes were upregulated in Δh3.3 female gametocytes. [ABSTRACT FROM AUTHOR]

Purpose: The goal of this study is to clarify the underlying mechanisms of metastasis suppression by carbon-ion radiotherapy combined with immature dendritic cell immunotherapy (CiDC), which was shown previously to suppress pulmonary metastasis in an NR-S1-bearing C3H/He mouse model.Methods and Materials: Mouse carcinoma cell lines (LLC, LM8, Colon-26, and Colon-26MGS) were grafted into the right hind paw of syngeneic mice (C57BL/6J, C3H/He, and BALB/c). Seven days later, the tumors on the mice were locally irradiated with carbon ions (290 MeV/n, 6 cm spread-out Bragg peak, 1 or 2 Gy). At 1.5 days after irradiation, bone marrow-derived immature dendritic cells (iDCs) were administrated intravenously into a subset of the mice. The number of lung metastases was evaluated within 3 weeks after irradiation. In vitro-cultured cancer cells were irradiated with carbon ions (290 MeV/n, mono-energy, LET approximately 70-80 keV/µm), and then cocultured with iDCs for 3 days to determine the DC maturation.Results: CiDC effectively repressed distant lung metastases in cancer cell (LLC and LM8)-bearing C57BL/6J and C3H/He mouse models. However, Colon-26- and Colon-26MGS-bearing BALB/c models did not show enhancement of metastasis suppression by combination treatment. This result was evaluated further by comparing LM8-bearing C3H/He and LLC-bearing C57BL/6J models with a Colon-26-bearing BALB/c model. In vitro coculture assays demonstrated that all irradiated cell lines were able to activate C3H/He- or C57BL/6J-derived iDCs into mature DCs, but not BALB/c-derived iDCs.Conclusions: The genetic background of the host could have a strong effect on the potency of combination therapy. Future animal and clinical testing should evaluate host genetic factors when evaluating treatment efficacy. [ABSTRACT FROM AUTHOR]

Abstract: Cerebral malaria (CM) is the most severe complication of Plasmodium infection. Although inappropriate immune responses to Plasmodium falciparum are reported as the major causes of CM, the precise mechanisms for development remain unclear. IL-23 and IL-17 have critical roles in the onset of autoimmunity and inflammatory diseases triggered by microbial infections. Thus, we investigated the influence of IL-23 and IL-17 on experimental CM (ECM) using Plasmodium berghei ANKA infection of C57BL/6 mice. Both IL-23 deficient mice and wild-type (WT) mice developed ECM. IL-17 deficient mice also developed ECM, while IL-17 producing cells other than CD4+ T cells (Th17) were increased in WT mice that developed ECM. In conclusion, this study showed that IL-23 and IL-17 are not involved in ECM development. [ABSTRACT FROM AUTHOR]

• A new method to evaluate the integrity of the blood–cerebrospinal fluid barrier (BCSFB) was developed. • BCSFB permeability was increased specifically in cerebral malaria (CM), but not in non-CM. • CD8+ T cells are involved in the BCSFB breakdown during CM. • Hemozoin was found in the choroid plexus in CM. Cerebral malaria is one of the most severe pathologies of malaria; it induces neuro-cognitive sequelae and has a high mortality rate. Although many factors involved in the development of cerebral malaria have been discovered, its pathogenic mechanisms are still not completely understood. Most studies on cerebral malaria have focused on the blood–brain barrier, despite the importance of the blood–cerebrospinal fluid barrier, which protects the brain from peripheral inflammation. Consequently, the pathological role of the blood–cerebrospinal fluid barrier in cerebral malaria is currently unknown. To examine the status of the blood–cerebrospinal fluid barrier in cerebral malaria and malaria without this pathology (non-cerebral malaria), we developed a new method for evaluating the permeabilization of the blood–cerebrospinal fluid barrier during cerebral malaria in mice, using Evans blue dye and a software-assisted image analysis. Using C57BL/6J (B6) mice infected with Plasmodium berghei ANKA strain as an experimental cerebral malaria model and B6 mice infected with P. berghei NK65 strain or Plasmodium yoelii as non-cerebral malaria models, we revealed that the permeability of the blood–cerebrospinal fluid barrier increased during experimental cerebral malaria but not during non-cerebral malaria. We observed haemorrhaging in the cerebral ventricles and hemozoin-like structures in the choroid plexus, which is a key component of the blood–cerebrospinal fluid barrier, in cerebral malaria mice. Taken together, this evidence indicates that the blood–cerebrospinal fluid barrier is disrupted in experimental cerebral malaria, whereas it remains intact in non-cerebral malaria. We also found that P. berghei ANKA parasites and CD8+ T cells are involved in the blood–cerebrospinal fluid barrier disruption in experimental cerebral malaria. An understanding of the mechanisms underlying cerebral malaria might help in the development of effective strategies to prevent and manage cerebral malaria in humans. [ABSTRACT FROM AUTHOR]

Background: Acute kidney injury (AKI) often occurs in pediatric patients who received allogeneic hematopoietic cell transplantation (HCT). We evaluated the risk and effect of HCT-related AKI in pediatric patients. Methods: We retrospectively studied the survival and renal outcome of 69 children 100 days and 1-year posttransplant in our institution in 2004–2016. Stage-3 AKI developed in 34 patients (49%) until 100 days posttransplant. Results: The 100-day overall survival (OS) rates of patients with stage-3 AKI were lower than those without it (76.5% vs. 94.3%, P = 0.035). The 1-year OS rates did not differ markedly between 21 post-100-day survivors with stage-3 AKI and 29 without it (80.8% vs. 87.9%, P = 0.444). The causes of 19 deaths included the relapse of underlying disease or graft failure (n = 11), treatment-related events (4), and second HCT-related events (4). Underlying disease of malignancy (crude hazard ratio (HR) 5.7; 95% confidence interval (CI), 2.20 to 14.96), > 1000 ng/mL ferritinemia (crude HR 4.29; 95% CI, 2.11 to 8.71), stem cell source of peripheral (crude HR 2.96; 95% CI, 1.22 to 7.20) or cord blood (crude HR 2.29; 95% CI, 1.03 to 5.06), and myeloablative regimen (crude HR 2.56; 95% CI, 1.24 to 5.26), were identified as risk factors for stage-3 AKI until 100 days posttransplant. Hyperferritinemia alone was significant (adjusted HR 5.52; 95% CI, 2.21 to 13.76) on multivariable analyses. Conclusions: Hyperferritinemia was associated with stage-3 AKI and early mortality posttransplant. Pretransplant iron control may protect the kidney of pediatric HCT survivors. [ABSTRACT FROM AUTHOR]

Intestinal helminths induce immune suppressive responses thought to regulate inflammatory diseases including allergies and autoimmune diseases. This study was designed to evaluate whether helminthic infections suppress the natural development of systemic lupus erythematosus (SLE) in NZBWF1 mice. Infection of NZBWF1 SLE-prone mice with two nematodes failed to establish long-lasting settlement. However, the Hymenolepis microstoma (Hm) rodent tapeworm successfully established long-term parasitization of NZBWF1 mice and was used to evaluate the suppressive effects of helminth infection. Ten-month-old NZBWF1 mice developed symptoms including autoantibody generation, proteinuria, glomerular histopathology, and splenomegaly, but mice infected with Hm at 2 months of age did not show any clinical signs. Furthermore, infection with Hm reduced lymphocyte activation and increased regulatory T cells in the spleen and mesenteric lymph nodes. These results indicate that infection with Hm protects NZBWF1 mice from naturally developing SLE and suggest that pathological immunity is attenuated, presumably because of the induction of regulatory T cells. Unlabelled Image • SLE-prone NZBWF1 mice were refractory to Hp and Tm but susceptible to Hm. • Hm prevents natural development of SLE and prolonged survival of NZBWF1 mice • Hm infection increases Tregs and decreased plasma cells and Tfh in NZBWF1 mice. [ABSTRACT FROM AUTHOR]