Targeting Sirt-1 controls GVHD by inhibiting T-cell allo-response and promoting Treg stability in mice.

Graft-versus-host disease (GVHD) remains one of the major complications after allogeneic bone marrow transplantation (allo-BMT). Sirtuin-1 (Sirt-1) plays a crucial role in various biological processes including cellular senescence, metabolism, and inflammatory responses. Sirt-1 deacetylation regulates different transcription factors that are important for modulating immune responses. In the current study, we addressed the role of Sirt-1 in GVHD induction by employing Sirt-1 conditional knockout mice as well as a pharmacological Sirt-1 inhibitor. Using major histocompatibility complex (MHC)-mismatched and MHC-matched murine BMT models, we found that Sirt-1-/- T cells had a reduced ability to induce acute GVHD (aGVHD) via enhanced p53 acetylation. Sirt-1-deficient T cells also promoted induced regulatory T cell (iTreg) differentiation and inhibited interferon-γ production after allo-BMT. Sirt-1 deletion in iTregs increased Foxp3 stability and restrained iTreg conversion into pathogenic T cells. Furthermore, we found that administration with a Sirt-1 inhibitor, Ex-527, significantly improved recipient survival and clinical scores, with no signs of tumor relapse. These results indicate that Sirt-1 inhibition can attenuate GVHD while preserving the graft-versus-leukemia effect. Consistently, Sirt-1-deficient T cells also displayed a remarkably reduced ability to induce chronic GVHD (cGVHD). Mechanistic studies revealed that Sirt-1 deficiency in T cells enhanced splenic B-cell reconstitution and reduced follicular T helper cell development. Sirt-1 deficiency in T cells modulated donor B-cell responses reducing both B-cell activation and plasma cell differentiation. In addition, therapeutic Sirt-1 inhibition could both prevent cGVHD and reduce established cGVHD. In conclusion, Sirt-1 is a promising therapeutic target for the control of aGVHD and cGVHD pathogenesis and possesses high potential for clinical application.

Length-Independent Charge Transport in Chimeric Molecular Wires.

Advanced molecular electronic components remain vital for the next generation of miniaturized integrated circuits. Thus, much research effort has been devoted to the discovery of lossless molecular wires, for which the charge transport rate or conductivity is not attenuated with length in the tunneling regime. Herein, we report the synthesis and electrochemical interrogation of DNA-like molecular wires. We determine that the rate of electron transfer through these constructs is independent of their length and propose a plausible mechanism to explain our findings. The reported approach holds relevance for the development of high-performance molecular electronic components and the fundamental study of charge transport phenomena in organic semiconductors.

Solvent effects on kinetic mechanisms of self-assembly by peptide amphiphiles via molecular dynamics simulations.

Peptide amphiphiles are known to form a variety of distinctive self-assembled nanostructures (including cylindrical nanofibers in hydrogels) dependent upon the solvent conditions. Using a novel coarse-grained model, large-scale molecular dynamics simulations are performed on a system of 800 peptide amphiphiles (sequence, palmitoyl-Val3Ala3Glu3) to elucidate kinetic mechanisms of molecular assembly as a function of the solvent conditions. The assembly process is found to occur via a multistep process with transient intermediates that ultimately leads to the stabilized nanostructures including open networks of ß-sheets, cylindrical nanofibers, and elongated micelles. Different kinetic mechanisms are compared in terms of peptide secondary structures, solvent-accessible surface area, radius of gyration, relative shape anisotropy, intra/intermolecular interactions, and aggregate size dynamics to provide insightful information for the design of functional biomaterials.

Sequence-Dependent Structural Stability of Self-Assembled Cylindrical Nanofibers by Peptide Amphiphiles.

Three-dimensional networks of nanofibers, which are formed through self-assembly of peptide amphiphiles, serve as a biomimetic hydrogel scaffold for tissue engineering. With an emphasis to improve hydrogel properties for cell-specific behavior, a better understanding between structural characteristics and physical properties of the macroscopic gel is sought. Large-scale molecular dynamics simulations were performed on two PA sequences with identical composition (palmitoyl-V3A3E3 and palmitoyl-A3V3E3) showing different self-assembly kinetic mechanisms. While both sequences yielded cylindrical nanofibers, these structures have contrasting internal arrangement with respect to the hydrophobic core; the former is continuous with predominately alkyl tails, whereas the latter is disjointed with interconnecting micelles. Two additional sequences (palmitoyl-V6E3 and palmitoyl-A6E3) were examined to determine the effects of a homogeneous ß-sheet forming segment that is either strongly or mildly hydrophobic on self-assembly. Results from this study indicate that internal structural arrangement of nanofibers can provide a correlation with structural stability and mechanical behavior of hydrogel nanostructures.

Role of hydrophobicity on self-assembly by peptide amphiphiles via molecular dynamics simulations.

Using a novel coarse-grained model, large-scale molecular dynamics simulations were performed to examine self-assembly of 800 peptide amphiphiles (sequence palmitoyl-V3A3E3). Under suitable physiological conditions, these molecules readily assemble into nanofibers leading to hydrogel construction as observed in experiments. Our simulations capture this spontaneous self-assembly process, including formation of secondary structure, to identify morphological transitions of distinctive nanostructures. As the hydrophobic interaction is increased, progression from open networks of secondary structures toward closed cylindrical nanostructures containing either ß-sheets or random coils are observed. Moreover, temperature effects are also determined to play an important role in regulating formation of secondary structures within those nanostructures. These understandings of the molecular interactions involved and the role of environmental factors on hydrogel formation provide useful insight for development of innovative smart biomaterials for biomedical applications.

A tail of two peptide amphiphiles: effect of conjugation with hydrophobic polymer on folding of peptide sequences.

Peptide amphiphiles (PA) offer the potential of incorporating biological function into synthetic materials for tissue engineering in regenerative medicine. These hybrid conjugates are known to undergo self-assembly starting from single molecules to nanofibers before turning into hydrogel scaffolds-such a process involves conformational changes in secondary structures of peptides. Therefore, insights on the ability of peptide amphiphiles to form secondary structure as single molecules are useful for understanding self-assembly behavior. We report here a molecular simulation study of peptide folding by two PA sequences, each contains an alkyl tail and short peptide segment. The alkyl tail is observed to play two opposing roles in modulating sequence-dependent folding kinetics and thermodynamics. On one hand, it restricts conformational freedom reducing the entropic cost of folding, which is thus promoted. On the other hand, it acts as an interaction site with nonpolar peptide residues, blocking the peptide from helix nucleation, which reduces folding.

A stochastic B cell affinity maturation model to characterize mechanisms of protection for tetravalent dengue vaccine constructs.

Dengue annually infects millions of people from a regionally and seasonally varying dengue virus population circulating as four distinct serotypes. Effective protection against dengue infection and disease requires tetravalent vaccine formulations to stimulate a balanced protective immune response to all four serotypes. However, this has been a challenge to achieve, and several clinical trials with different leading vaccine candidates have demonstrated unbalanced replication and interference of interindividual serotype components, leading to low efficacy and enhanced disease severity for dengue-naïve populations. Production of serotype-specific neutralizing antibodies is largely viewed as a correlate of protection against severe dengue disease. However, the underlying mechanisms that lead to these protective immune responses are not clearly elucidated. In this work, using a stochastic model of B cell affinity maturation, we tested different live-attenuated vaccine constructs with varied viral replication rates and contrasted the initiation and progress of adaptive immune responses during tetravalent vaccination and after dengue virus challenge. Comparison of our model simulations across different disease-severity levels suggested that individual production of high levels of serotype-specific antibodies together with a lower cross-reactive antibody are better correlates for protection. Furthermore, evolution of these serotype-specific antibodies was dependent on the percent of viral attenuation in the vaccine, and production of initial B cell and T cell populations pre- and post-secondary dengue infection was crucial in providing protective immunity for dengue-naïve populations. Furthermore, contrasting disease severity with respect to different dengue serotypes, our model simulations showed that tetravalent vaccines fare better against DENV-4 serotype when compared to other serotypes.

Sr doped TiO2 photocatalyst for the removal of Janus Green B dye under visible light.

Hydrothermal synthesis of pristine and Sr doped TiO2 is proposed. The synthesized products were studied for their physiochemical properties. 3% Sr-TiO2 showed a narrow bandgap, which facilitate an increase in oxygen vacancies. The agglomerated morphology was tuned to a nanoball structure after doping with Sr ions. Surface area was increased for the Sr doped TiO2. The samples were used to reduce Janus Green B (JG) dye as a model pollutant. The pure TiO2 showed poor efficiency, while the prepared Sr-TiO2 photocatalyst showed enhanced efficiency with a corresponding increase in the rate constant values of the samples. Tuning of the bandgap, an improvement in the morphology and an increase in the surface area were the major positives of the Sr doped TiO2 samples compared to pure TiO2, 3% Sr-TiO2 is emerging as the best photocatalyst in reducing toxic pollutants. The 3% Sr-TiO2 is a promising candidate for water remediation in the future.

A static and dynamic copula-based ARIMA-fGARCH approach to determinants of carbon dioxide emissions in Argentina.

This paper attempts to model both static and dynamic dependence structures and measure impacts of energy consumptions (both renewable (EC) and non-renewable (REN) energies), economic globalization (GLO), and economic growth (GDP) on carbon dioxide (CO2) emissions in Argentina over the period 1970-2020. For analyses purpose, the current research deploys the novel static and dynamic copula-based ARIMA-fGARCH with different submodels. The static bivariate copula results show that the growth rates of the pairs EC-CO2 and GDP-CO2 are asymmetrically positive co-movements and have high left tail (extreme) dependencies, implying that the increase in non-renewable energy and economic growth can critically contribute to the environmental degradation, and the decrease in the consumption of non-renewable energy at a high level will consequently reduce the CO2 emissions at the same level. Based on several copula-based dependence measures, we document that between the two factors, the non-renewable energy has a stronger impact than the economic growth regarding the CO2 emissions. On the other hand, the growth rates of both economic globalization and renewable energy symmetrically negatively co-move with the growth rates of the CO2 emissions, but they have no extreme dependencies, indicating that these factors contribute to Argentina's environmental quality, in which the factor of renewable energy has a greater impact. Furthermore, the dynamic copula outcomes show that the (tail) dependencies of CO2 emissions on the non-renewable energy and economic growth are time-varying, while the pairs REN-CO2 and GLO-CO2 possess only dynamic dependencies, but no dynamic tail dependencies. Moreover, through the dynamic copula-based dependence, the environmental Kuznets curve (EKC) hypothesis can be estimated and illustrated explicitly. In addition, we leverage multivariate vine copulas for modelling dependence structures of the five variables simultaneously, which can reveal rich information regarding conditional associations among the relevant variables. Some policy implications are also provided to mitigate CO2 emissions.

Stochastic Model of the Adaptive Immune Response Predicts Disease Severity and Captures Enhanced Cross-Reactivity in Natural Dengue Infections.

The dengue virus circulates as four distinct serotypes, where a single serotype infection is typically asymptomatic and leads to acquired immunity against that serotype. However, the developed immunity to one serotype is thought to underlie the severe manifestation of the disease observed in subsequent infections from a different serotype. We developed a stochastic model of the adaptive immune response to dengue infections. We first delineated the mechanisms initiating and sustaining adaptive immune responses during primary infections. We then contrasted these immune responses during secondary infections of either a homotypic or heterotypic serotype to understand the role of pre-existing and reactivated immune pathways on disease severity. Comparison of non-symptomatic and severe cases from heterotypic infections demonstrated that overproduction of specific antibodies during primary infection induces an enhanced population of cross-reactive antibodies during secondary infection, ultimately leading to severe disease manifestations. In addition, the level of disease severity was found to correlate with immune response kinetics, which was dependent on beginning lymphocyte levels. Our results detail the contribution of specific lymphocytes and antibodies to immunity and memory recall that lead to either protective or pathological outcomes, allowing for the understanding and determination of mechanisms of protective immunity.

Lysosomal Acid Lipase Is Required for Donor T Cells to Induce Graft-versus-Host Disease.

Graft-versus-host disease (GVHD) limits the success of allogeneic hematopoietic cell transplantation (allo-HCT). Lysosomal acid lipase (LAL) mediates the intrinsic lipolysis of cells to generate free fatty acids (FFAs), which play an essential role in the development, proliferation, and function of T cells. Here, we find that LAL is essential for donor T cells to induce GVHD in murine models of allo-HCT. Specifically, LAL is required for donor T cell survival, differentiation, and alloreactivity in GVHD target organs, but not in lymphoid organs. LAL induces the differentiation of donor T cells toward GVHD pathogenic Th1/Tc1 and Th17 while suppressing regulatory T cell generation. LAL-/- T cells succumb to oxidative stress and become anergic in target organs. Pharmacologically targeting LAL effectively prevents GVHD development while preserving the GVL activity. Thus, the present study reveals the role of LAL in T cell alloresponse and pathogenicity and validates LAL as a target for controlling GVHD and tumor relapse after allo-HCT.

A review and notes on the phylogenetic relationship of the centipede genus Otostigmus Porat, 1876 (Chilopoda: Scolopendromorpha: Scolopendridae) from Vietnam.

The genus Otostigmus Porat, 1876 is reviewed based on recent material collected from parts of Vietnam. A total of nine species are documented and imaged. The phylogeny of the genus Otostigmus is analyzed based on a 603-bp dataset of the cytochrome c oxidase subunit I (COI) gene. The average K2P genetic distance between Otostigmus species is 19%, and eight of nine species are considered to be monophyletic, except O. amballae. The phylogenetic relationship between Otostigmus species necessitates a deeper study with more samples and genetic data. In addition, an identification key to all Otostigmus species is provided for the fauna of Vietnam.

Bone Marrow Transplantation Platform to Investigate the Role of Dendritic Cells in Graft-versus-Host Disease.

Allogeneic bone marrow transplantation (BMT) is an effective therapy for hematological malignancies due to the graft-versus-leukemia (GVL) effect to eradicate tumors. However, its application is limited by the development of graft-versus-host disease (GVHD), a major complication of BMT. GVHD is evoked when T-cells in the donor grafts recognizealloantigen expressed by recipient cells and mount unwanted immunological attacks against recipient healthy tissues. Thus, traditional therapies are designed to suppress donor T-cell alloreactivity. However, these approaches substantially impair the GVL effect so that the recipient's survival is not improved. Understanding the effects of therapeutic approaches on BMT, GVL, and GVHD, is thus essential. Due to the antigen-presenting and cytokine-secreting capacities to stimulate donor T-cells, recipient dendritic cells (DCs) play a significant role in the induction of GVHD. Therefore, targeting recipient DCs becomes a potential approach for controlling GVHD. This work provides a description of a novel BMT platform to investigate how host DCs regulate GVH and GVL responses after transplantation. Also presented is an effective BMT model to study the biology of GVHD and GVL after transplantation.

Emerging Role of Circulating Tumor Cells in Gastric Cancer.

With over 1 million incidence cases and more than 780,000 deaths in 2018, gastric cancer (GC) was ranked as the 5th most common cancer and the 3rd leading cause of cancer deaths worldwide. Though several biomarkers, including carcinoembryonic antigen (CEA), cancer antigen 19-9 (CA19-9), and cancer antigen 72-4 (CA72-4), have been identified, their diagnostic accuracies were modest. Circulating tumor cells (CTCs), cells derived from tumors and present in body fluids, have recently emerged as promising biomarkers, diagnostically and prognostically, of cancers, including GC. In this review, we present the landscape of CTCs from migration, to the presence in circulation, biologic properties, and morphologic heterogeneities. We evaluated clinical implications of CTCs in GC patients, including diagnosis, prognosis, and therapeutic management, as well as their application in immunotherapy. On the one hand, major challenges in using CTCs in GC were analyzed, from the differences of cut-off values of CTC positivity, to techniques used for sampling, storage conditions, and CTC molecular markers, as well as the unavailability of relevant enrichment and detection techniques. On the other hand, we discussed future perspectives of using CTCs in GC management and research, including the use of circulating tumor microembolies; of CTC checkpoint blockade in immunotherapy; and of organoid models. Despite the fact that there are remaining challenges in techniques, CTCs have potential as novel biomarkers and/or a non-invasive method for diagnostics, prognostics, and treatment monitoring of GC, particularly in the era of precision medicine.

Invariant polymorphism in virus capsid assembly.

Directed self-assembly of designed viral capsids holds significant potential for applications in materials science and medicine. However, the complexity of preparing these systems for assembly and the difficulty of quantitative experimental measurements on the assembly process have limited access to critical mechanistic questions that dictate the final product yields and isomorphic forms. Molecular simulations provide a means of elucidating self-assembly of viral proteins into icosahedral capsids and are the focus of the present study. Using geometrically realistic coarse-grained models with specialized molecular dynamics methods, we delineate conditions of temperature and coat protein concentration that lead to the spontaneous self-assembly of T = 1 and T = 3 icosahedral capsids. In addition to the primary product of icosahedral capsids, we observe a ubiquitous presence of nonicosahedral yet highly symmetric and enclosed aberrant capsules in both T = 1 and T = 3 systems. This polymorphism in assembly products recapitulates the scope and morphology of particle types that have been observed in mis-assembly experiments of virus capsids. Moreover, we find that this structural polymorphism in the end point structures is an inherent property of the coat proteins and arises from condition-dependent kinetic mechanisms that are independent of the elemental mechanisms of capsid growth (as long as the building blocks of the coat proteins are all monomeric, dimeric, or trimeric) and the capsid T number. The kinetic mechanisms responsible for self-assembly of icosahedral capsids and aberrant capsules are deciphered; the self-assembly of icosahedral capsids requires a high level of assembly fidelity, whereas self-assembly of nonicosahedral capsules is a consequence of an off-pathway mechanism that is prevalent under nonoptimal conditions of temperature or protein concentration during assembly. The latter case involves kinetically trapped dislocations of pentamer-templated proteins with hexameric organization. These findings provide insights into the complex processes that govern viral capsid assembly and suggest some features of the assembly process that can be exploited to control the assembly of icosahedral capsids and nonicosahedral capsules.

Analysis of ribosomal protein gene structures: implications for intron evolution.

Many spliceosomal introns exist in the eukaryotic nuclear genome. Despite much research, the evolution of spliceosomal introns remains poorly understood. In this paper, we tried to gain insights into intron evolution from a novel perspective by comparing the gene structures of cytoplasmic ribosomal proteins (CRPs) and mitochondrial ribosomal proteins (MRPs), which are held to be of archaeal and bacterial origin, respectively. We analyzed 25 homologous pairs of CRP and MRP genes that together had a total of 527 intron positions. We found that all 12 of the intron positions shared by CRP and MRP genes resulted from parallel intron gains and none could be considered to be "conserved," i.e., descendants of the same ancestor. This was supported further by the high frequency of proto-splice sites at these shared positions; proto-splice sites are proposed to be sites for intron insertion. Although we could not definitively disprove that spliceosomal introns were already present in the last universal common ancestor, our results lend more support to the idea that introns were gained late. At least, our results show that MRP genes were intronless at the time of endosymbiosis. The parallel intron gains between CRP and MRP genes accounted for 2.3% of total intron positions, which should provide a reliable estimate for future inferences of intron evolution.

Microscopic Behaviors of Tri- n-Butyl Phosphate, n-Dodecane, and Their Mixtures at Air/Liquid and Liquid/Liquid Interfaces: An AMBER Polarizable Force Field Study.

In solvent extraction processes for recovering metal ions from used nuclear fuel, as well as other industrial applications, a better understanding of the metal complex phase transfer phenomenon would greatly aid ligand design and process optimization. We have approached this challenge by utilizing the classical molecular dynamics simulations technique to gain visual appreciation of the vapor/liquid and liquid/liquid interface between tri- n-butyl phosphate (TBP) and n-dodecane with air and water. In this study, we successfully reparameterized polarizable force fields for TBP and n-dodecane that accurately reproduced several of their thermophysical properties such as density, heat of vaporization, and dipole moment. Our models were able to predict the surface and interfacial tension of different systems when compared to experimental results that were also performed by us. Through this study, we gained atomistic understanding of the behaviors of TBP and n-dodecane at the interface against air and water, useful in further computational studies of such systems. Finally, our studies indicate that the initial configuration of a simulation may have a large effect on the final result.

Vitamin C stabilizes CD8+ iTregs and enhances their therapeutic potential in controlling murine GVHD and leukemia relapse.

Adoptive transfer of induced regulatory T cells (iTregs) can ameliorate graft-versus-host disease (GVHD) after allogeneic hematopoietic cell transplantation (allo-HCT). CD4+ iTregs can effectively prevent GVHD but impair the graft-versus-leukemia (GVL) effect, whereas CD8+ iTregs preserve the GVL effect but have limited efficacy in GVHD control because of their instability under inflammatory conditions. Thus, we aimed to stabilize CD8+ iTregs via treatment with vitamin C (Vit C) to improve their efficacy in controlling GVHD. We found that addition of Vit C significantly improved the stability of forkhead box P3 (Foxp3) expression in CD8+ iTregs. Moreover, Vit C-treated CD8+ iTregs exhibited high efficacy in attenuating acute and chronic GVHD. The mechanistic study revealed that addition of Vit C to CD8+ iTreg culture markedly increased DNA demethylation in the conserved noncoding sequence 2 region and, hence, maintained higher Foxp3 expression levels compared with untreated controls. In acute GVHD, Vit C-treated CD8+ iTregs were able to inhibit pathogenic T-cell expansion and differentiation while reducing thymus damage and B-cell activation in cGVHD. Importantly, in contrast to CD4+ iTregs, Vit C-treated CD8+ iTregs retained the ability to control tumor relapse. These results provide a strong rationale to use Vit C in the clinic to stabilize CD8+ iTregs for the control of GVHD and preservation of GVL after allo-HCT.

High prevalence of colonisation with carbapenem-resistant Enterobacteriaceae among patients admitted to Vietnamese hospitals: Risk factors and burden of disease.

BACKGROUND: Carbapenem-resistant Enterobacteriaceae (CRE) is an increasing problem worldwide, but particularly problematic in low- and middle-income countries (LMIC) due to limitations of resources for surveillance of CRE and infection prevention and control (IPC). METHODS: A point prevalence survey (PPS) with screening for colonisation with CRE was conducted on 2233 patients admitted to neonatal, paediatric and adult care at 12 Vietnamese hospitals located in northern, central and southern Vietnam during 2017 and 2018. CRE colonisation was determined by culturing of faecal specimens on selective agar for CRE. Risk factors for CRE colonisation were evaluated. A CRE admission and discharge screening sub-study was conducted among one of the most vulnerable patient groups; infants treated at an 80-bed Neonatal ICU from March throughout June 2017 to assess CRE acquisition, hospital-acquired infection (HAI) and treatment outcome. RESULTS: A total of 1165 (52%) patients were colonised with CRE, most commonly Klebsiella pneumoniae (n = 805), Escherichia coli (n = 682) and Enterobacter spp. (n = 61). Duration of hospital stay, HAI and treatment with a carbapenem were independent risk factors for CRE colonisation. The PPS showed that the prevalence of CRE colonisation increased on average 4.2% per day and mean CRE colonisation rates increased from 13% on the day of admission to 89% at day 15 of hospital stay. At the NICU, CRE colonisation increased from 32% at admission to 87% at discharge, mortality was significantly associated (OR 5·5, P < 0·01) with CRE colonisation and HAI on admission. CONCLUSION: These data indicate that there is an epidemic spread of CRE in Vietnamese hospitals with rapid transmission to hospitalised patients.

Molecular Dynamics Investigations of Dibutyl-phosphoric Acid-Parameterization and Dimerization.

A reparameterized molecular dynamics force field for dibutyl-phosphoric acid (HDBP) has been developed. Parameterization was done using the general Amber force field, as a starting point. The density and dipole moment of bulk phase simulations compare well to that of known experimental values, and the heat of vaporization is comparable to an estimated empirical value. All values have been optimized to within 4%. The newly optimized force field was validated against the self-diffusion coefficient, matching experimental data to within 18%, which is a significant improvement compared to the nonoptimized force field. Further, a potential of mean force study was carried out to understand the behavior of hydrogen bonds in HDBP dimers. This required the determination of hydrogen bonding criteria that captures the behavior of the HDBP dimer and is reported in this work as well.