Pharmacological and biological antiviral therapeutics for cardiac coxsackievirus infections

Subtype B coxsackieviruses (CVB) represent the most commonly identified infectious agents associated with acute and chronic myocarditis, with CVB3 being the most common variant. Damage to the heart is induced both directly by virally mediated cell destruction and indirectly due to the immune and autoimmune processes reacting to virus infection. This review addresses antiviral therapeutics for cardiac coxsackievirus infections discovered over the last 25 years. One group represents pharmacologically active low molecular weight substances that inhibit virus uptake by binding to the virus capsid (e.g., pleconaril) or inactivate viral proteins (e.g., NO-metoprolol and ribavirin) or inhibit cellular proteins which are essential for viral replication (e.g., ubiquitination inhibitors). A second important group of substances are interferons. They have antiviral but also immunomodulating activities. The third and most recently discovered group includes biological and cellular therapeutics. Soluble receptor analogues (e.g., sCAR-Fc) bind to the virus capsid and block virus uptake. Small interfering RNAs, short hairpin RNAs and antisense oligonucleotides bind to and led to degradation of the viral RNA genome or cellular RNAs, thereby preventing their translation and viral replication. Most recently mesenchymal stem cell transplantation has been shown to possess antiviral activity in CVB3 infections. Taken together, a number of antiviral therapeutics has been developed for the treatment of myocardial CVB infection in recent years. In addition to low molecular weight inhibitors, biological therapeutics have become promising anti-viral agents.     

On the origin and evolution of SARS-CoV-2

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the ongoing global outbreak of a coronavirus disease (herein referred to as COVID-19). Other viruses in the same phylogenetic group have been responsible for previous regional outbreaks, including SARS and MERS. SARS-CoV-2 has a zoonotic origin, similar to the causative viruses of these previous outbreaks. The repetitive introduction of animal viruses into human populations resulting in disease outbreaks suggests that similar future epidemics are inevitable. Therefore, understanding the molecular origin and ongoing evolution of SARS-CoV-2 will provide critical insights for preparing for and preventing future outbreaks. A key feature of SARS-CoV-2 is its propensity for genetic recombination across host species boundaries. Consequently, the genome of SARS-CoV-2 harbors signatures of multiple recombination events, likely encompassing multiple species and broad geographic regions. Other regions of the SARS-CoV-2 genome show the impact of purifying selection. The spike (S) protein of SARS-CoV-2, which enables the virus to enter host cells, exhibits signatures of both purifying selection and ancestral recombination events, leading to an effective S protein capable of infecting human and many other mammalian cells. The global spread and explosive growth of the SARS-CoV-2 population (within human hosts) has contributed additional mutational variability into this genome, increasing opportunities for future recombination.Subject terms: Evolutionary biology, Infectious diseases     

First-principles-based calculations of vibrational normal modes in polyatomic materials with translational symmetry: application to PETN molecular crystal

Numerical studies of vibrational energy transport and associated (non)linear infrared and Raman response in polyatomic materials require knowledge of the multidimensional vibrational potential-energy surface and the ability to perform normal-mode analysis on that potential. The presence of translational symmetry, as in crystals, leads to the observed dispersion of the unit cell normal modes and has to be accounted for in calculations of energy transfer rates and other spectroscopic quantities. Here we report on the implementation of a computational approach that combines the generalized supercell method and density functional theory electronic structure calculations to investigate the vibrational structure in translationally symmetric materials containing relatively large numbers of atoms in the unit cell (58 atoms in the present study). The method is applied to calculate the phonon and vibron dispersion relations and the vibrational density of states in pentaerythritol tetranitrate (PETN) molecular crystal which is an important energetic material. The results set the stage for future investigations of vibrational energy transport and associated nonlinear spectroscopic signatures in this class of materials.     

Thermal effects in collision-free infrared multiphoton absorption by SF6 and CF3Br

An opto-thermal molecular beam study has been carried out to investigate the multiple-photon laser excitation of SF₆ and CF₃Br. The molecular beam was produced by means of a supersonic expansion through a nozzle at variable temperature. The opto-thermal signal was measured by means of a high-sensitivity superconducting bolometer. The multiple-photon excitation of SF₆ has been measured as a function of the initial ro-vibrational population of the molecule. The experimental results have been compared with both previously published data of molecular beam and gas cell experiments and theoretical calculations. A satisfactory agreement has been found between some of our experimental results and the theoretical spectra obtained by means of the heat-bath feed-back model.     

Determination of cell type‐specific proteome signatures of primary human leukocytes,endothelial cells,keratinocytes, hepatocytes,fibroblasts and melanocytes by comparative proteome profiling

Cells gain their functional specialization by different protein synthesis. A lot of knowledge with respect to cell type‐specific proteins has been collected during the last thirty years. This knowledge was built mainly by using antibodies. Nowadays, modern MS, which supports comprehensive proteome analyses of biological samples, may render possible the search for cell type‐specific proteins as well. However, a therefore necessary systematic MS study comprising many different cell types has not been performed until now. Here we present a proteome analysis strategy supporting the automated and meaningful comparison of any biological samples. We have presently applied this strategy to six different primary human cell types, namely leukocytes, endothelial cells, keratinocytes, hepatocytes, fibroblasts, and melanocytes. Comparative analysis of the resulting proteome profiles allowed us to select proteins specifically identified in one of the six cell types and not in any of the five others. Based on these results, we designated cell type‐specific proteome signatures consisting each of six such characteristic proteins. These signatures independently reproduced well‐known marker proteins already established for FACS analyses in addition to novel candidate marker proteins. We applied these signatures for the interpretation of proteome profiles obtained from the analyses of hepatocellular carcinoma‐associated tissue homogenates and normal liver tissue homogenates. The identification of members of the above described signatures gave us an indication of the presence of characteristic cells in the diseased tissues and thus supported the interpretation of the proteomics data of these complex biological samples.     

A new vision of evaluating gene expression signatures

Gene expression profiles based on high-throughput technologies contribute to molecular classifications of different cell lines and consequently to clinical diagnostic tests for cancer types and other diseases. Statistical techniques and dimension reduction methods have been devised for identifying minimal gene subset with maximal discriminative power. For sets of in silico candidate genes, assuming a unique gene signature or performing a parsimonious signature evaluation seems to be too restrictive in the context of in vitro signature validation. This is mainly due to the high complexity of largely correlated expression measurements and the existence of various oncogenic pathways. Consequently, it might be more advantageous to identify and evaluate multiple gene signatures with a similar good predictive power, which are referred to as near-optimal signatures, to be made available for biological validation. For this purpose we propose the bead-chain-plot approach originating from swarm intelligence techniques, and a small scale computational experiment is conducted in order to convey our vision. We simulate the acquisition of candidate genes by using a small pool of differentially expressed genes derived from microarray-based CNS tumour data. The application of the bead-chain-plot provides experimental evidence for improved classifications by using near-optimal signatures in validation procedures.     

CRISPR‐Cas: From the Bacterial Adaptive Immune System to a Versatile Tool for Genome Engineering

The field of biology has been revolutionized by the recent advancement of an adaptive bacterial immune system as a universal genome engineering tool. Bacteria and archaea use repetitive genomic elements termed clustered regularly interspaced short palindromic repeats (CRISPR) in combination with an RNA‐guided nuclease (CRISPR‐associated nuclease: Cas) to target and destroy invading DNA. By choosing the appropriate sequence of the guide RNA, this two‐component system can be used to efficiently modify, target, and edit genomic loci of interest in plants, insects, fungi, mammalian cells, and whole organisms. This has opened up new frontiers in genome engineering, including the potential to treat or cure human genetic disorders. Now the potential risks as well as the ethical, social, and legal implications of this powerful new technique move into the limelight.     

Polarized Raman spectroscopy of oligothiophene crystals to determine unit cell orientation

Raman spectra were recorded experimentally and calculated theoretically for bithiophene, terthiophene, and quaterthiophene samples as a function of excitation polarization. Distinct spectral signatures were assigned and correlated to the molecular/unit cell orientation as determined by X-ray diffraction. The ability to predict molecular/unit cell orientation within organic crystals using polarized Raman spectroscopy was evaluated by predicting the unit cell orientation in a simulated terthiophene crystal given a random set of simulated polarized Raman spectra. Polarized Raman spectroscopy offers a promising tool to quickly and economically determine the unit cell orientation in known organic crystals and crystalline thin films. Implications of our methodologies for studying individual molecule conformations are discussed.     

Crosstalk Among UV‐Induced Inflammatory Mediators,DNA Damage and Epigenetic Regulators Facilitates Suppression of the Immune System

The suppression of the immune system by overexposure to ultraviolet (UV) radiation has been implicated in the initiation and progression of photocarcinogenesis. Numerous changes occur in the skin on UVB exposure, including the generation of inflammatory mediators, DNA damage, epigenetic modifications, and migration and functional alterations in the antigen‐presenting dendritic cells. Although each of these alterations can elicit a cascade of events that have the potential to modulate immune sensitivity alone, there is emerging evidence that there is considerable crosstalk between these cascades. The development of an understanding of UV‐induced changes in the skin that culminate in UV‐induced immunosuppression, which has been implicated in the risk of nonmelanoma skin cancer, as a network of events has implications for the development of more effective chemopreventive strategies. In the current review article, we discuss the evidence of interactions between the various molecular targets and signaling mechanisms associated with UV‐induced immunosuppression.     

Contributions of mass spectrometry to structural immunology

Mass spectrometry has made important contributions to the field of immunology in the past decade. A variety of mass spectrometric-based techniques have been applied to study the structures of macromolecules that play a vital role in the immune response. These include traditional molecular mass measurements to identify post-translational modifications and structural heterogeneity, mass mapping of proteolysis products, sequencing by tandem mass spectrometry and conformational analysis. Antigen-antibody and other immune complexes have been detected by mass spectrometry, providing an avenue to study macromolecular assemblies that are important to immune function. By virtue of the ability of mass spectrometry based techniques to analyze complex biological mixtures, mass spectrometry has also been employed to identify and sequence protein epitopes important in both the humoral and cellular immune responses. This has been achieved through a combination of immunoaffinity and mass spectrometric techniques, and the coupling of high-performance chromatographs to mass spectrometers. These approaches are important for the identification of pathogens and show promise for the early diagnosis of disease associated with viral and bacterial infection and malignancy. These investigations will enable the mechanisms associated with normal and impaired immune function to be elucidated. Mass spectrometry has been utilized to characterize the structure of peptide mimics, multiple antigenic peptides and other constructs in the design of synthetic immunogens. Information derived from these studies will aid in the development of novel therapeutics and vaccines.     

The Course of Immune Stimulation by Photodynamic Therapy: Bridging Fundamentals of Photochemically Induced Immunogenic Cell Death to the Enrichment of T‐Cell Repertoire

Photodynamic therapy (PDT) is a potentially immunogenic and FDA‐approved antitumor treatment modality that utilizes the spatiotemporal combination of a photosensitizer, light and oftentimes oxygen, to generate therapeutic cytotoxic molecules. Certain photosensitizers under specific conditions, including ones in clinical practice, have been shown to elicit an immune response following photoillumination. When localized within tumor tissue, photogenerated cytotoxic molecules can lead to immunogenic cell death (ICD) of tumor cells, which release damage‐associated molecular patterns and tumor‐specific antigens. Subsequently, the T‐lymphocyte (T cell)–mediated adaptive immune system can become activated. Activated T cells then disseminate into systemic circulation and can eliminate primary and metastatic tumors. In this review, we will detail the multistage cascade of events following PDT of solid tumors that ultimately lead to the activation of an antitumor immune response. More specifically, we connect the fundamentals of photochemically induced ICD with a proposition on potential mechanisms for PDT enhancement of the adaptive antitumor response. We postulate a hypothesis that during the course of the immune stimulation process, PDT also enriches the T‐cell repertoire with tumor‐reactive activated T cells, diversifying their tumor‐specific targets and eliciting a more expansive and rigorous antitumor response. The implications of such a process are likely to impact the outcomes of rational combinations with immune checkpoint blockade, warranting investigations into T‐cell diversity as a previously understudied and potentially transformative paradigm in antitumor photodynamic immunotherapy.     

Artificial evolution with adeno-associated viral libraries

After attracting the attention of the scientific community due to a number of favourable characteristics that make it an attractive vector for human gene therapy [1,2], AAV has been thoroughly investigated in the past two decades. Standard technologies for the manipulation of the viral genome and for efficient packaging and purification protocols have paved the road for trial and error manipulation by educated guesses to study viral infectious biology by reverse genetics and to generate improved vectors for human gene transfer. However, despite remarkable progress, our limited knowledge of molecular mechanisms implicated in virus-cell interactions has been a limiting factor. Combinatorial engineering and high-throughput selection techniques hold the potential to boost technological improvement by offering the possibility to screen large numbers of randomly generated clones by appropriate selection protocols. These approaches not only require lesser knowledge of viral biology, but can also be employed as valuable tools to investigate molecular mechanisms that drive the infection process. In this review we recapitulate the rationale for employment of combinatorial methods in AAV vector development and the accomplishments achieved so far, discussing current limitations and interesting developments that are in sight.     

Discrimination of Excited States of Acetylacetone through Theoretical Molecular-Frame Photoelectron Angular Distributions

Photoelectron angular distribution (PAD) in the laboratory frame for randomly oriented molecules is typically described by a single anisotropy parameter, the so-called asymmetry parameter. However, especially from a theoretical perspective, it is more natural to consider molecular photoionization by using a molecular frame. The molecular frame PADs (MFPADs) may be used to extract information about the electronic structure of the system studied. In the last decade, significant experimental efforts have been directed to MFPAD measurements. MFPADs are highly characterizing signatures of the final ionic states. In particular, they are very sensitive to the nature of the final state, which is embodied in the corresponding Dyson orbital. In our previous work on acetylacetone, a prototype system for studying intra-molecular hydrogen bond interactions, we followed the dynamics of the excited states involved in the photoexcitation–deexcitation process of this molecule. It remains to be explored the possibility of discriminating between different excited states through the MFPAD profiles. The calculation of MFPADs to differentiate excited states can pave the way to the possibility of a clear discrimination for all the cases where the recognition of excited states is otherwise intricate.     

Concluding remarks and the challenge from the immune system

This meeting has covered a wide range of approaches to the study of interactions of biomembranes and one is struck by the progress in their analysis and the application of many new methods. The main theme of the meeting has been the structure of biomembranes and their components. Rather than pick highlights of these or attempt to summarise the findings in these Concluding remarks, I will instead summarise some of the interactions of the cells of the immune systems for which immunologists would like explanations at a molecular level. One of the features of the immune system is that it involves a variety of populations of cells that have complex migratory patterns and interactions that occur throughout life. The surfaces of these cells--the leukocytes--mediate interactions that are essential for the fine control of the immune system that ensures the rapid but controlled rejection of foreign materials such as viruses and bacteria. At the same time it must ensure that reactivity against self is prevented, otherwise autoimmune diseases such as rheumatoid arthritis and multiple sclerosis may result. Some of the features of the interactions involved are outlined in this short overview with more detailed analysis of the leukocyte cell surface given in ref. 1.     

Etude des systemes ternaires: polymere-polymere-solvant. Application au systeme polystyrene-polydimethylsiloxane-benzene

The ternary system benzene-polydimethylsiloxane-polystyrene has been investigated by light scattering. Apparent molecular weight and solvation coefficient have been determined by applying the relations established for the ternary system of polymer in mixed solvents. The range of validity of these relations for our system has been discussed. We have also determined the χ₂₃ parameter (interaction between the both polymers), following the variations of apparent molecular weight or the compositions at the spinodal.     

Imaging mass spectrometry data reduction: Automated feature identification and extraction

Imaging MS now enables the parallel analysis of hundreds of biomolecules, spanning multiple molecular classes, which allows tissues to be described by their molecular content and distribution. When combined with advanced data analysis routines, tissues can be analyzed and classified based solely on their molecular content. Such molecular histology techniques have been used to distinguish regions with differential molecular signatures that could not be distinguished using established histologic tools. However, its potential to provide an independent, complementary analysis of clinical tissues has been limited by the very large file sizes and large number of discrete variables associated with imaging MS experiments. Here we demonstrate data reduction tools, based on automated feature identification and extraction, for peptide, protein, and lipid imaging MS, using multiple imaging MS technologies, that reduce data loads and the number of variables by >100×, and that highlight highly-localized features that can be missed using standard data analysis strategies. It is then demonstrated how these capabilities enable multivariate analysis on large imaging MS datasets spanning multiple tissues.     

Atomic motions in the alphabeta-merging region of 1,4-polybutadiene: a molecular dynamics simulation study

We present fully atomistic molecular dynamics simulations on 1,4-polybutadiene in a wide temperature range from 200 to 280 K, i.e., in the region where the alpha- and beta-relaxations merge and above. A big computational effort has been performed-especially for the lowest temperatures investigated-to extend the simulation runs to very long times (up to 1 mus for 200 K). The simulated sample has been carefully validated by using previous neutron scattering data on the real sample with similar microstructure. Inspecting the trajectories of the different hydrogens in real space, we have observed a heterogeneous dynamical behavior (each kind of hydrogen moves in a different way) with signatures of combined hopping and diffusive motions in the whole range investigated. The application of a previously proposed model [Colmenero et al., Europhys. Lett. 71, 262 (2005)] is successful and a characterization of the local motions and diffusion is possible. The comparison of our results to those reported in the literature provides a consistent scenario for polybutadiene dynamics and puts into a context the different experimental observations. We also discuss the impact of the hopping processes on the observation and interpretation of experimentally accessible magnitudes and the origin of the deviations from Gaussian behavior in this system.     

Construction of Recombinant Modified Vaccinia Ankara （MVA） Expressing Hepatitis B Virus Surface Antigen

Introduction Despitetheexistenceofeffectiveprophylacticvac cinesagainstthehepatitisBvirus(HBV)formany years,HBVinfectionremainsaserioushealthproblem worldwide.Approximatetwobillionpeoplehavebeen infectedbyHBVanditisestimatedthatmorethan350millionofthemare…