Parvovirus Capsid-Antibody Complex Structures Reveal Conservation of Antigenic Epitopes Across the Family

The parvoviruses are small nonenveloped single stranded DNA viruses that constitute members that range from apathogenic to pathogenic in humans and animals. The infection with a parvovirus results in the generation of antibodies against the viral capsid by the host immune system to eliminate the virus and to prevent re-infection. For members currently either being developed as delivery vectors for gene therapy applications or as oncolytic biologics for tumor therapy, efforts are aimed at combating the detrimental effects of pre-existing or post-treatment antibodies that can eliminate therapeutic benefits. Therefore, understanding antigenic epitopes of parvoviruses can provide crucial information for the development of vaccination applications and engineering novel capsids able to escape antibody recognition. This review aims to capture the information for the binding regions of ∼30 capsid-antibody complex structures of different parvovirus capsids determined to date by cryo-electron microscopy and three-dimensional image reconstruction. The comparison of all complex structures revealed the conservation of antigenic regions among parvoviruses from different genera despite low sequence identity and indicates that the available data can be used across the family for vaccine development and capsid engineering.

Understanding The Role of Reline, a Natural DES, on Temperature-Induced Conformational Changes of C-Kit G-Quadruplex DNA: A Molecular Dynamics Study

The noncanonical guanine-rich DNAs have drawn particular attention to the scientific world due to their controllable diverse and polymorphic structures. Apart from biological and medical significance, G-quadruplex DNAs are widely used in various fields such as nanotechnology, nanomachine, biosensors, and biocatalyst. So far, the applications of the G-quadruplex DNA are mainly limited in the water medium. Recently, a new generation of solvent named deep eutectic solvent (DES) has become very popular and has been widely used as a reaction medium of biocatalytic reactions and long-term storage medium for nucleic acids, even at high temperature. Hence, it is essential to understand the role of DES on temperature-induced conformational changes of a G-quadruplex DNA. In this research work, we have explored the temperature-mediated conformational dynamics of c-kit oncogene promoter G-quadruplex DNA in reline medium in the temperature range of 300-500 K, using a total of 10 μs unbiased all-atom molecular dynamics simulation. Here, from RMSD, RMSF, R_g and principal component analyses, we notice that the c-kit G-quadruplex DNA is stable up to 450 K in reline medium. However, it unfolds in water medium at 450 K. It is found that the hydrogen bonding interactions between c-kit G-quadruplex DNA and reline play a key role in the stabilization of the G-quadruplex DNA even at high temperature. Furthermore, in this work we have observed a very interesting and distinctive phenomenon of the central cation of the G-quadruplex DNA. Its position was seen to fluctuate between the two tetrad cores, that is, the region between tetrad-1 and tetrad-2 and that between tetrad-2 and tetrad-3 and vice versa at 450 and 500 K in reline medium which is absent in water medium at 450 K. Moreover, the rate of its oscillation is increased when temperature is increased.

The Application of Regulatory Cascades in Streptomyces: Yield Enhancement and Metabolite Mining

Streptomyces is taken as an important resource for producing the most abundant antibiotics and other bio-active natural products, which have been widely used in pharmaceutical and agricultural areas. Usually they are biosynthesized through secondary metabolic pathways encoded by cluster situated genes. And these gene clusters are stringently regulated by interweaved transcriptional regulatory cascades. In the past decades, great advances have been made to elucidate the regulatory mechanisms involved in antibiotic production in Streptomyces. In this review, we summarized the recent advances on the regulatory cascades of antibiotic production in Streptomyces from the following four levels: the signals triggering the biosynthesis, the global regulators, the pathway-specific regulators and the feedback regulation. The production of antibiotic can be largely enhanced by rewiring the regulatory networks, such as overexpression of positive regulators, inactivation of repressors, fine-tuning of the feedback and ribosomal engineering in Streptomyces. The enormous amount of genomic sequencing data implies that the Streptomyces has potential to produce much more antibiotics for the great diversities and wide distributions of biosynthetic gene clusters in Streptomyces genomes. Most of these gene clusters are defined cryptic for unknown or undetectable natural products. In the synthetic biology era, activation of the cryptic gene clusters has been successfully achieved by manipulation of the regulatory genes. Chemical elicitors, rewiring regulatory gene and ribosomal engineering have been employed to crack the potential of cryptic gene clusters. These have been proposed as the most promising strategy to discover new antibiotics. For the complex of regulatory network in Streptomyces, we proposed that the discovery of new antibiotics and the optimization of industrial strains would be greatly promoted by further understanding the regulatory mechanism of antibiotic production.

Spiro-Indole-Coumarin Hybrids: Synthesis, ADME, DFT, NBO Studies and In Silico Screening through Molecular Docking on DNA G-Quadruplex

New series of hybrids were synthesized by combination of 4-hydroxycoumarin with spiro[indol-indazole-thiazolidine]-diones and spiro[indol-pyrazole-thiazolidine]-diones, via hitherto unknown Schiff bases. The effects of substituents, such as -F, -Br and -CH3, on the crucial characteristics pertaining to the hybrids were investigated through computational studies. In silico or virtual screening through molecular docking studies on the library of 22 compounds, including reference compounds, precursors, non-hybrid and hybrid derivatives, was performed on DNA G-quadruplex of the human genome. All six freshly synthesized hybrids showed high binding energy as compared to non-hybrids as well as reference compounds. The presence of substituents at 5-position of indole enhanced the binding tendency of the ligand. ADME studies indicated good oral bioavailability and absorption of these compounds. Density Functional Theory (DFT) calculations of hybrids were done at B3LYP/6-311G++(d,p) level of computation. Their HOMO and LUMO energy plots reflected the presence of high charge transfer and chemical potential. Natural bond order (NBO) calculations predicted hyperconjugative interactions. The Molecular Electrostatic Potential (MEP) surface plots showed possible electrophilic and nucleophilic attacking sites of the hybrids. Compound 10 a (5-fluoro-spiro[indol-indazole-thiazolidine]-dione-coumarin hybrid), on the basis of global reactivity descriptors, was filtered to be chemically most reactive with the highest binding energy of -8.23 kcal/mol with DNA G-quadruplex. The synthesized hybrid coumarin derivatives in correlation with theoretical docking studies validate that hybrid derivatives are more reactive compared to their non-hybrid counterparts.

Targeting the Inositol Pyrophosphate Biosynthetic Enzymes in Metabolic Diseases

In mammals, a family of three inositol hexakisphosphate kinases (IP6Ks) synthesizes the inositol pyrophosphate 5-IP7 from IP6. Genetic deletion of Ip6k1 protects mice from high fat diet induced obesity, insulin resistance and fatty liver. IP6K1 generated 5-IP7 promotes insulin secretion from pancreatic β-cells, whereas it reduces insulin signaling in metabolic tissues by inhibiting the protein kinase Akt. Thus, IP6K1 promotes high fat diet induced hyperinsulinemia and insulin resistance in mice while its deletion has the opposite effects. IP6K1 also promotes fat accumulation in the adipose tissue by inhibiting the protein kinase AMPK mediated energy expenditure. Genetic deletion of Ip6k3 protects mice from age induced fat accumulation and insulin resistance. Accordingly, the pan IP6K inhibitor TNP [N2-(m-trifluorobenzyl), N6-(p-nitrobenzyl)purine] ameliorates obesity, insulin resistance and fatty liver in diet induced obese mice by improving Akt and AMPK mediated insulin sensitivity and energy expenditure. TNP also protects mice from bone loss, myocardial infarction and ischemia reperfusion injury. Thus, the IP6K pathway is a potential target in obesity and other metabolic diseases. Here, we summarize the studies that established IP6Ks as a potential target in metabolic diseases. Further studies will reveal whether inhibition of this pathway has similar pleiotropic benefits on metabolic health of humans.

Fully automated platelet isolation on a centrifugal microfluidic device for molecular diagnostics

Platelets play crucial roles in hemostasis and immunity. Over the last decades, clinical evidence has revealed the significance of platelets as complementary biomarkers for the detection and treatment of various diseases, including cancer. Due to a lack of well standardized convenient isolation methods for platelets, pre-analytical factors such as complex handling procedures negatively impact the quality of the platelet samples, including overactivation, low purity, and poor reproducibility. This may lead to biased interpretation of various downstream analyses, such as proteomic and genomic analyses. Herein, we describe a fully automated lab-on-a-disc-based method of platelet isolation from a small volume of blood (<1 mL). This method provides higher yields (>4 folds) and purity (>99%) and lower platelet activation than the conventional method. Moreover, it was also superior in the detection of platelet-related RNAs CD41, PF4, and P2Y12 due to lower contamination with white blood cells.

A Supramolecular Approach to Structure-Based Design with A Focus on Synthons Hierarchy in Ornithine-Derived Ligands: Review, Synthesis, Experimental and in Silico Studies

The success of innovative drugs depends on an interdisciplinary and holistic approach to their design and development. The supramolecular architecture of living systems is controlled by non-covalent interactions to a very large extent. The latter are prone to extensive cooperation and like a virtuoso play a symphony of life. Thus, the design of effective ligands should be based on thorough knowledge on the interactions at either a molecular or high topological level. In this work, we emphasize the importance of supramolecular structure and ligand-based design keeping the potential of supramolecular H-bonding synthons in focus. In this respect, the relevance of supramolecular chemistry for advanced therapies is appreciated and undisputable. It has developed tools, such as Hirshfeld surface analysis, using a huge data on supramolecular interactions in over one million structures which are deposited in the Cambridge Structure Database (CSD). In particular, molecular interaction surfaces are useful for identification of macromolecular active sites followed by in silico docking experiments. Ornithine-derived compounds are a new, promising class of multi-targeting ligands for innovative therapeutics and cosmeceuticals. In this work, we present the synthesis together with the molecular and supramolecular structure of a novel ornithine derivative, namely N-α,N-δ)-dibenzoyl-(α)-hydroxymethylornithine, 1. It was investigated by modern experimental and in silico methods in detail. The incorporation of an aromatic system into the ornithine core induces stacking interactions, which are vital in biological processes. In particular, rare C=O…π intercontacts have been identified in 1. Supramolecular interactions were analyzed in all structures of ornithine derivatives deposited in the CSD. The influence of substituent was assessed by the Hirshfeld surface analysis. It revealed that the crystal packing is stabilized mainly by H…O, O…H, C…H, Cl (Br, F)…H and O…O interactions. Additionally, π…π, C-H…π and N-O…π interactions were also observed. All relevant H-bond energies were calculated using the Lippincott and Schroeder H-bond model. A library of synthons is provided. In addition, the large synthons (Long-Range Synthon Aufbau Module) were considered. The DFT optimization either in vacuo or in solutio yields very similar molecular species. The major difference with the relevant crystal structure was related to the conformation of terminal benzoyl C15-C20 ring. Furthermore, in silico prediction of the extensive physicochemical ADME profile (absorption, distribution, metabolism and excretion) related to the drug-likeness and medicinal chemistry friendliness revealed that a novel ornithine derivative 1 has the potential to be a new drug candidate. It has shown good in silico absorption and very low toxicity.

Comparative Transcriptome Analysis of Two Cucumber Cultivars with Different Sensitivity to Cucumber Mosaic Virus Infection

Cucumber mosaic virus (CMV), with extremely broad host range including both monocots and dicots around the world, belongs to most important viral crop threats. Either natural or genetically constructed sources of resistance are being intensively investigated; for this purpose, exhaustive knowledge of molecular virus-host interaction during compatible and incompatible infection is required. New technologies and computer-based “omics” on various levels contribute markedly to this topic. In this work, two cucumber cultivars with different response to CMV challenge were tested, i.e., sensitive cv. Vanda and resistant cv. Heliana. The transcriptomes were prepared from both cultivars at 18 days after CMV or mock inoculation. Subsequently, four independent comparative analyses of obtained data were performed, viz. mock- and CMV-inoculated samples within each cultivar, samples from mock-inoculated cultivars to each other and samples from virus-inoculated cultivars to each other. A detailed picture of CMV-influenced genes, as well as constitutive differences in cultivar-specific gene expression was obtained. The compatible CMV infection of cv. Vanda caused downregulation of genes involved in photosynthesis, and induction of genes connected with protein production and modification, as well as components of signaling pathways. CMV challenge caused practically no change in the transcription profile of the cv. Heliana. The main differences between constitutive transcription activity of the two cultivars relied in the expression of genes responsible for methylation, phosphorylation, cell wall organization and carbohydrate metabolism (prevailing in cv. Heliana), or chromosome condensation and glucan biosynthesis (prevailing in cv. Vanda). Involvement of several genes in the resistant cucumber phenotype was predicted; this can be after biological confirmation potentially applied in breeding programs for virus-resistant crops.

Pharmaceutical Co-Crystallization: Regulatory Aspects, Design, Characterization, and Applications

Pharmaceutical co-crystals are novel class of pharmaceutical substances, which possess an apparent probability of advancement of polished physical properties offering stable and patentable solid forms. These multi-component crystalline forms influence pertinent physicochemical parameters like solubility, dissolution rate, chemical stability, physical stability, etc. which in turn result in the materials with superior properties to those of the free drug. Co-crystallization is a process by which the molecular interactions can be altered to optimize the drug properties. Co-crystals comprise a multicomponent system of active pharmaceutical ingredient (API) with a stoichiometric amount of a pharmaceutically acceptable coformer incorporated in the crystal lattice. By manufacturing pharmaceutical co-crystals, the physicochemical properties of a drug can be improved thus multicomponent crystalline materials have received renewed interest in the current scenario due to the easy administration in the pharmaceutical industry. There is an immense amount of literature available on co-crystals. However, there is a lack of an exhaustive review on a selection of coformers and regulations on co-crystals. The review has made an attempt to bridge this gap. The review also describes the methods used to prepare co-crystals with their characterization. Brief description on the pharmaceutical applications of co-crystals has also been incorporated here. Efforts are made to include reported works on co-crystals, which further help to understand the concept of co-crystals in depth.

Direct Measurement of the Elastohydrodynamic Lift Force at the Nanoscale

We present the first direct measurement of the elastohydrodynamic lift force acting on a sphere moving within a viscous liquid, near and along a soft substrate under nanometric confinement. Using atomic force microscopy, the lift force is probed as a function of the gap size, for various driving velocities, viscosities, and stiffnesses. The force increases as the gap is reduced and shows a saturation at small gap. The results are in excellent agreement with scaling arguments and a quantitative model developed from the soft lubrication theory, in linear elasticity, and for small compliances. For larger compliances, or equivalently for smaller confinement length scales, an empirical scaling law for the observed saturation of the lift force is given and discussed.

Interaction and Polarization Energy Relationships in σ-Hole and π-Hole Bonding

We demonstrate that a wide range of σ- and π-hole interaction energies can be related to (a) the electrostatic potentials and electric fields of the σ- and π-hole molecules at the approximate positions of the negative sites and (b) the electrostatic potentials and polarizabilities of the latter. This is consistent with the Coulombic nature of these interactions, which should be understood to include both electrostatics and polarization. The energies associated with polarization were estimated and were shown to overall be greater for the stronger interactions; no new factors need be introduced to account for these. All of the interactions can be treated in the same manner.

Non-covalent interactions with inverted carbon: a carbo-hydrogen bond or a new type of hydrogen bond?

Crystal structure analysis and quantum chemical calculations enabled us to discover a new non-covalent interaction, coined as carbo-hydrogen bond (C_H-bond).

Identification of a previously unreported co-crystal form of acetazolamide: a combination of multiple experimental and virtual screening methods

In this work, we demonstrate an approach of trying multiple methods in a more comprehensive search for co-crystals of acetazolamide.

Phase-controlled field-effect micromixing using AC electroosmosis

The exploration and application of electrokinetic techniques in micro total analysis systems have become ubiquitous in recent years, and scientists are expanding the use of such techniques in areas where comparable active or passive methods are not as successful. In this work, for the first time, we utilize the concept of AC electroosmosis to design a phase-controlled field-effect micromixer that benefits from a three-finger sinusoidally shaped electrodes. Analogous to field-effect transistor devices, the principle of operation for the proposed micromixer is governed by the source-gate and source-drain voltage potentials that are modulated by introducing a phase lag between the driving electrodes. At an optimized flow rate and biasing scheme, we demonstrate that the source, gate, and drain voltage phase relations can be configured such that the micromixer switches from an unmixed state (phase shift of 0°) to a mixed state (phase shift of 180°). High mixing efficiencies beyond 90% was achieved at a volumetric flow rate of 4 µL/min corresponding to ~13.9 mm/s at optimized voltage excitation conditions. Finally, we employed the proposed micromixer for the synthesis of nanoscale lipid-based drug delivery vesicles through the process of electrohydrodynamic-mediated nanoprecipitation. The phase-controlled electrohydrodynamic mixing utilized for the nanoprecipitation technique proved that nanoparticles of improved monodispersity and concentration can be produced when mixing efficiency is enhanced by tuning the phase shifts between electrodes.

Biological activity tuning of antibacterial urotropine via co-crystallization: synthesis, biological activity evaluation and computational insight

Urotropine (1) is a synthetic heterocyclic antibacterial agent.

Two-dimensional halogen-bonded organic frameworks based on the tetrabromobenzene-1,4-dicarboxylic acid building molecule

2D halogen-bonded organic frameworks were readily engineered by strong and directional effects of the primary Br⋯O and the secondary Br⋯π halogen bonding interactions from the tetrabromobenzene-1,4-dicarboxylic acid building molecule involving 100% supramolecular yields.

R. S, Gonnade RG. Drug–drug cocrystals of anticancer drugs erlotinib–furosemide and gefitinib–mefenamic acid for alternative multi-drug treatment

Drug–drug cocrystals of anticancer drugs erlotinib and gefitinib with furosemide and mefenamic acid, respectively, have been synthesized, characterized and their solubilities and dissolution rates were correlated with crystal structures.

A high energy phosphate jump - From pyrophospho-inositol to pyrophospho-serine

Inositol pyrophosphates (PP-IPs) are a class of energy rich metabolites present in all eukaryotic cells. The hydroxyl groups on these water soluble derivatives of inositol are substituted with diphosphate and monophosphate moieties. Since the discovery of PP-IPs in the early 1990s, enormous progress has been made in uncovering pleiotropic roles for these small molecules in cellular physiology. PP-IPs exert their effect on proteins in two ways - allosteric regulation by direct binding, or post-translational regulation by serine pyrophosphorylation, a modification unique to PP-IPs. Serine pyrophosphorylation is achieved by Mg²⁺-dependent, but enzyme independent transfer of a β-phosphate from a PP-IP to a pre-phosphorylated serine residue located in an acidic motif, within an intrinsically disordered protein sequence. This distinctive post-translational modification has been shown to regulate diverse cellular processes, including rRNA synthesis, glycolysis, and vesicle transport. However, our understanding of the molecular details of this phosphotransfer from pyrophospho-inositol to generate pyrophospho-serine, is still nascent. This review discusses our current knowledge of protein pyrophosphorylation, and recent advances in understanding the mechanism of this important yet overlooked post-translational modification.

Patient-Specific Bone Multiscale Modelling, Fracture Simulation and Risk Analysis-A Survey

This paper provides a starting point for researchers and practitioners from biology, medicine, physics and engineering who can benefit from an up-to-date literature survey on patient-specific bone fracture modelling, simulation and risk analysis. This survey hints at a framework for devising realistic patient-specific bone fracture simulations. This paper has 18 sections: Section 1 presents the main interested parties; Section 2 explains the organzation of the text; Section 3 motivates further work on patient-specific bone fracture simulation; Section 4 motivates this survey; Section 5 concerns the collection of bibliographical references; Section 6 motivates the physico-mathematical approach to bone fracture; Section 7 presents the modelling of bone as a continuum; Section 8 categorizes the surveyed literature into a continuum mechanics framework; Section 9 concerns the computational modelling of bone geometry; Section 10 concerns the estimation of bone mechanical properties; Section 11 concerns the selection of boundary conditions representative of bone trauma; Section 12 concerns bone fracture simulation; Section 13 presents the multiscale structure of bone; Section 14 concerns the multiscale mathematical modelling of bone; Section 15 concerns the experimental validation of bone fracture simulations; Section 16 concerns bone fracture risk assessment. Lastly, glossaries for symbols, acronyms, and physico-mathematical terms are provided.

Theory of the flow-induced deformation of shallow compliant microchannels with thick walls

Long, shallow microchannels embedded in thick, soft materials are widely used in microfluidic devices for lab-on-a-chip applications. However, the bulging effect caused by fluid-structure interactions between the internal viscous flow and the soft walls has not been completely understood. Previous models either contain a fitting parameter or are specialized to channels with plate-like walls. This work is a theoretical study of the steady-state response of a compliant microchannel with a thick wall. Using lubrication theory for low-Reynolds-number flows and the theory for linearly elastic isotropic solids, we obtain perturbative solutions for the flow and deformation. Specifically, only the channel's top wall deformation is considered, and the ratio between its thickness t and width w is assumed to be (t/w)²≫1. We show that the deformation at each stream-wise cross section can be considered independently, and that the top wall can be regarded as a simply supported rectangle subject to uniform pressure at its bottom. The stress and displacement fields are found using Fourier series, based on which the channel shape and the hydrodynamic resistance are calculated, yielding a new flow rate-pressure drop relation without fitting parameters. Our results agree favourably with, and thus rationalize, previous experiments.

An experimental study of the influence of orientation on water condensation of a thermoelectric cooling heatsink

An experimental investigation of thermoelectric cooling using a Peltier element to dehumidify moist air under controlled, high relative humidity conditions has been conducted. The influence of the cold side heatsink orientation on the water collection rate was experimentally determined. One finned heatsink-fan combination was used on the heat rejection side. On the cold side flat plates, uncoated and Polytetrafluoroethylene (PTFE) coated, a fanned plate with four fins, and a heatsink having 15 fins were used. The PTFE coated plate showed up to a 30% higher water collection rate (expressed in L/kWh) compared to the uncoated flat plate that has the same surface area. Clearing the surfaces-removing all condensate every hour-increased the water collection rate by up to 18% for the flat plates. The finned heatsink and the PTFE coated flat plate were used for the orientation experiments. The finned heatsink was rotated from 0° to 90°, as well as tilted from 0° to 90° (vertical to horizontal). To investigate the effect of surface orientation on a single-side collection surface in isolation, the PTFE coated flat plate was tilted from 15° to 165° in 15° increments. The highest collection rates are found for a rotation angle of 60° and a tilted angle of 75° for the finned heatsink, 0.249 L/kWh and 0.221 L/kWh respectively. The highest measured collection rate for the PTFE coated plate is 0.319 L/kWh at an orientation of 15° from the horizontal. Experiments for the horizontal orientation of the finned heatsink show that once the spaces between the fins are completely filled with water the collection rate drops by an order of magnitude, from 0.203 L/kWh to 0.026 L/kWh. The experiments show that the orientation of a thermoelectric heatsink should be considered when optimizing the water collection rates under high humidity conditions for thermoelectric cooling heatsinks.

Paper Stacks for Uniform Rehydration of Dried Reagents in Paper Microfluidic Devices

Spatially uniform reconstitution of dried reagents is critical to the function of paper microfluidic devices. Advancing fluid fronts in paper microfluidic devices drive (convect) and concentrate rehydrated reagents to the edges, causing steep chemical gradients and imperfect mixing. This largely unsolved problem in paper microfluidics is exacerbated by increasing device dimensions. In this article, we demonstrate that mixing of dried reagents with a rehydrating fluid in paper microfluidics may be significantly enhanced by stacking paper layers having different wicking rates. Compared to single-layer paper membranes, stacking reduced the “non-reactive area”, i.e. area in which the reconstituted reagents did not interact with the rehydrating fluid, by as much as 97% in large (8 cm × 2 cm) paper membranes. A paper stack was designed to collect ~0.9 ml liquid sample and uniformly mix it with dried reagents. Applications of this technology are demonstrated in two areas: (i) collection and dry storage of sputum samples for tuberculosis testing, and (ii) salivary glucose detection using an enzymatic assay and colorimetric readout. Maximizing the interaction of liquids with dried reagents is central to enhancing the performance of all paper microfluidic devices; this technique is therefore likely to find important applications in paper microfluidics.

Autophagy and apoptosis are regulated by stress on Bcl2 by AMBRA1 in the endoplasmic reticulum and mitochondria

BACKGROUND

Autophagy and apoptosis are two important physiological processes that determine cell survival or death in response to different stress signals. The regulatory mechanisms of these two processes share B-cell lymphoma-2 family proteins and AMBRA1, which are present in both the endoplasmic reticulum and mitochondria. B-cell lymphoma-2 family proteins sense different stresses and interact with AMBRA1 to regulate autophagy and apoptosis, which are respectively mediated by Beclin1 and Caspases. Therefore, we investigated how different levels of stress on B-cell lymphoma-2 family proteins that bind to AMBRA1 in the endoplasmic reticulum and mitochondria regulate the switch from autophagy to apoptosis.

METHODS

In this paper, we considered the responses of B-cell lymphoma-2 family proteins, which bind to AMBRA1 in both the endoplasmic reticulum and mitochondria, to two different levels of stress in a model originally proposed by Kapuy et al. We investigated how these two stress levels affect the transition from autophagy to apoptosis and their effects on apoptosis activation over time. Additionally, we analyzed how the feedback regulation in this model affects the bifurcation diagrams of two levels of stress and cell fate decisions between autophagy and apoptosis.

RESULTS

Autophagy is activated for minor stress in mitochondria regardless of endoplasmic reticulum stress, while apoptosis is activated for only significant stress in mitochondria. Apoptosis is only sensitive to mitochondria stress. The time duration before apoptosis activation is longer in the presence of high AMBRA1 levels with high endoplasmic reticulum and mitochondria stress. AMBRA1 can compete with B-cell lymphoma-2 family proteins to bind and activate Beclin1 and thus promote the autophagy process for a long time before apoptosis. Furthermore, apoptosis is prone to occur with increasing activation of Caspases, inactivation of Beclin1-A and the Michaelis constant of Caspases.

CONCLUSION

A novel mathematical model has been developed to understand the complex regulatory mechanisms of autophagy and apoptosis. Our model may be applied to further autophagy-apoptosis dynamic modeling experiments and simulations.

Designing Microfluidic Devices to Sort Haematopoietic Stem Cells Based on Their Mechanical Properties

Aim

Few haematopoietic stem cells (HSCs) injected systemically for therapeutic purposes actually reach sites of injury as the vast majority become entrapped within pulmonary capillaries. One promising approach to maintain circulating HSC numbers would be to separate subpopulations with smaller size and/or greater deformability from a heterogeneous population. This study tested whether this could be achieved using label-free microfluidic devices.

Methods

2 straight (A-B) and 3 spiral (C-E) devices were fabricated with different dimensions. Cell sorting was performed at different flow rates after which cell diameter and stiffness were determined using micromanipulation. Cells isolated using the most efficient device were tested intravitally for their ability to home to the mouse injured gut.

Results

Only straight Device B at a high flow rate separated HSCs with different mechanical properties. Side outlets collected mostly deformable cells (nominal rupture stress/σ_R = 6.81 kPa; coefficient of variation/CV = 0.31) at a throughput of 2.3 × 10⁵ cells/min. All spiral devices at high flow rates separated HSCs with different stiffness and size. Inner outlets collected mostly deformable cells in Devices C (σ_R = 25.06 kPa; CV = 0.26), D (σ_R = 22.21 kPa; CV = 0.41), and E (σ_R = 29.26 kPa; CV = 0.27) at throughputs of 2.3 × 10⁵ cells/min, 1.5 × 10⁵ cells/min, and 1.6 × 10⁵ cells/min, respectively. Since Device C separated cells with higher efficiency and throughput, it was utilized to test the homing ability of separated cells in vivo. Significantly more deformable cells were observed trafficking through the injured gut—interestingly, increased retention was not observed.

Conclusion

This study applied microfluidics to separate subpopulations from one stem cell type based on their intrinsic mechanical heterogeneity. Fluid dynamics within curved devices most effectively separated HSCs. Such devices may benefit cellular therapy.

A Review on Deterministic Lateral Displacement for Particle Separation and Detection

The separation and detection of particles in suspension are essential for a wide spectrum of applications including medical diagnostics. In this field, microfluidic deterministic lateral displacement (DLD) holds a promise due to the ability of continuous separation of particles by size, shape, deformability, and electrical properties with high resolution. DLD is a passive microfluidic separation technique that has been widely implemented for various bioparticle separations from blood cells to exosomes. DLD techniques have been previously reviewed in 2014. Since then, the field has matured as several physics of DLD have been updated, new phenomena have been discovered, and various designs have been presented to achieve a higher separation performance and throughput. Furthermore, some recent progress has shown new clinical applications and ability to use the DLD arrays as a platform for biomolecules detection. This review provides a thorough discussion on the recent progress in DLD with the topics based on the fundamental studies on DLD models and applications for particle separation and detection. Furthermore, current challenges and potential solutions of DLD are also discussed. We believe that a comprehensive understanding on DLD techniques could significantly contribute toward the advancements in the field for various applications. In particular, the rapid, low-cost, and high-throughput particle separation and detection with DLD have a tremendous impact for point-of-care diagnostics.

Polyhedra, spindles, phage nucleus and pyramids: Structural biology of viral superstructures

Viral infection causes comprehensive rearrangements of the cell that reflect as much host defense mechanisms as virus-induced structures assembled to facilitate infection. Regardless of their pro- or antiviral role, large intracellular structures are readily detectable by microscopy and often provide a signature characteristic of a specific viral infection. The structural features and localization of these assemblies have thus been commonly used for the diagnostic and classification of viruses since the early days of virology. More recently, characterization of viral superstructures using molecular and structural approaches have revealed very diverse organizations and roles, ranging from dynamic viral factories behaving like liquid organelles to ultra-stable crystals embedding and protecting virions. This chapter reviews the structures, functions and biotechnological applications of virus-induced superstructures with a focus on assemblies that have a regular organization, for which detailed structural descriptions are available. Examples span viruses infecting all domains of life including the assembly of virions into crystalline arrays in eukaryotic and bacterial viruses, nucleus-like compartments involved in the replication of large bacteriophages, and pyramid-like structures mediating the egress of archaeal viruses. Among these superstructures, high-resolution structures are available for crystalline objects produced by insect viruses: viral polyhedra which function as the infectious form of occluded viruses, and spindles which are potent virulence factors of entomopoxviruses. In turn, some of these highly symmetrical objects have been used to develop and validate advanced structural approaches, pushing the boundary of structural biology.

Structure and Gating Dynamics of Na+/Cl- Coupled Neurotransmitter Transporters

Neurotransmitters released at the neural synapse through vesicle exocytosis are spatiotemporally controlled by the action of neurotransmitter transporters. Integral membrane proteins of the solute carrier 6 (SLC6) family are involved in the sodium and chloride coupled uptake of biogenic amine neurotransmitters including dopamine, serotonin, noradrenaline and inhibitory neurotransmitters including glycine and γ-amino butyric acid. This ion-coupled symport works through a well-orchestrated gating of substrate through alternating-access, which is mediated through movements of helices that resemble a rocking-bundle. A large array of commercially prescribed drugs and psychostimulants selectively target neurotransmitter transporters thereby modulating their levels in the synaptic space. Drug-induced changes in the synaptic neurotransmitter levels can be used to treat depression or neuropathic pain whereas in some instances prolonged usage can lead to habituation. Earlier structural studies of bacterial neurotransmitter transporter homolog LeuT and recent structure elucidation of the Drosophila dopamine transporter (dDAT) and human serotonin transporter (hSERT) have yielded a wealth of information in understanding the transport and inhibition mechanism of neurotransmitter transporters. Computational studies based on the structures of dDAT and hSERT have shed light on the dynamics of varied components of these molecular gates in affecting the uphill transport of neurotransmitters. This review seeks to address structural dynamics of neurotransmitter transporters at the extracellular and intracellular gates and the effect of inhibitors on the ligand-binding pocket. We also delve into the effect of additional factors including lipids and cytosolic domains that influence the translocation of neurotransmitters across the membrane.

Structural and Reactivity Analyses of Nitrofurantoin–4-dimethylaminopyridine Salt Using Spectroscopic and Density Functional Theory Calculations

Pharmaceutical salt, nitrofurantoin–4-dimethylaminopyridine (NF-DMAP), along with its native components NF and DMAP are scrutinized by FT-IR and FT-Raman spectroscopy along with density functional theory so that an insight into the H-bond patterns in the respective crystalline lattices can be gained. Two different functionals, B3LYP and wB97X-D, have been used to compare the theoretical results. The FT-IR spectra obtained for NF-DMAP and NF clearly validate the presence of C33–H34⋅⋅⋅O4 and N23–H24⋅⋅⋅N9 hydrogen bonds by shifting in the stretching vibration of –NH and –CH group of DMAP+ towards the lower wavenumber side. To explore the significance of hydrogen bonding, quantum theory of atoms in molecules (QTAIM) has been employed, and the findings suggest that the N23–H24⋅⋅⋅N9 bond is a strong intermolecular hydrogen bond. The decrement in the HOMO-LUMO gap, which is calculated from NF → NF-DMAP, reveals that the active pharmaceutical ingredient is chemically less reactive compared to the salt. The electrophilicity index (ω) profiles for NF and DMAP confirms that NF is acting as electron acceptor while DMAP acts as electron donor. The reactive sites of the salt are plotted by molecular electrostatic potential (MEP) surface and calculated using local reactivity descriptors.

Artificial High Density Lipoprotein Nanoparticles in Cardiovascular Research

Lipoproteins are endogenous nanoparticles which are the major transporter of fats and cholesterol in the human body. They play a key role in the regulatory mechanisms of cardiovascular events. Lipoproteins can be modified and manipulated to act as drug delivery systems or nanocarriers for contrast agents. In particular, high density lipoproteins (HDL), which are the smallest class of lipoproteins, can be synthetically engineered either as nascent HDL nanodiscs or spherical HDL nanoparticles. Reconstituted HDL (rHDL) particles are formed by self-assembly of various lipids and apolipoprotein AI (apo-AI). A variety of substances including drugs, nucleic acids, signal emitting molecules, or dyes can be loaded, making them efficient nanocarriers for therapeutic applications or medical diagnostics. This review provides an overview about synthesis techniques, physicochemical properties of rHDL nanoparticles, and structural determinants for rHDL function. We discuss recent developments utilizing either apo-AI or apo-AI mimetic peptides for the design of pharmaceutical rHDL formulations. Advantages, limitations, challenges, and prospects for clinical translation are evaluated with a special focus on promising strategies for the treatment and diagnosis of atherosclerosis and cardiovascular diseases.

Conformational changes influence clogging behavior of micrometer-sized microgels in idealized multiple constrictions

Clogging of porous media by soft particles has become a subject of extensive research in the last years and the understanding of the clogging mechanisms is of great importance for process optimization. The rise in the utilization of microfluidic devices brought the possibility to simulate membrane filtration and perform in situ observations of the pore clogging mechanisms with the aid of high speed cameras. In this work, we use microfluidic devices composed by an array of parallel channels to observe the clogging behavior of micrometer sized microgels. It is important to note that the microgels are larger than the pores/constrictions. We quantify the clog propensity in relation to the clogging position and particle size and find that the majority of the microgels clog at the first constriction independently of particle size and constriction entrance angle. We also quantify the variations in shape and volume (2D projection) of the microgels in relation to particle size and constriction entrance angle. We find that the degree of deformation increases with particle size and is dependent of constriction entrance angle, whereas, changes in volume do not depend on entrance angle.

A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts

The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.

Self-Construal Priming Modulates Ensemble Perception of Multiple-Face Identities

This study explored the modulatory role of independent/interdependent self-construal on ensemble perception. Two experiments were conducted to study the effect of self-construal on ensemble coding of multiple-face identities (Experiment 1) and dot size (Experiment 2) separately. Before the implicit ensemble perception task, participants in both experiments were either primed with independent or interdependent self-construal via a well-validated pronoun circle task, in which they were exposed to either singular ("I," "me," and "my") or plural ("We," "us," and "our") pronouns in essays. The results showed that interdependent self-construal (vs. independent self-construal) featured as global processing and emphasizing interconnectedness with others enhanced the ensemble coding of high-level features (e.g., identity in Experiment 1) but not of low-level features (e.g., size in Experiment 2). To the best of our knowledge, this study was the first to investigate the role of self-construal on ensemble representations. In sum, the results of the current study supported the domain-specific mechanism of ensemble perception on one hand, and extended the effect of self-construal on single face recognition to multiple face recognition on the other hand.

Research on a Mixed Gas Classification Algorithm Based on Extreme Random Tree

Because of the low accuracy of the current machine olfactory algorithms in detecting two mixed gases, this study proposes a hybrid gas detection algorithm based on an extreme random tree to greatly improve the classification accuracy and time efficiency. The method mainly uses the dynamic time warping algorithm (DTW) to perform data pre-processing and then extracts the gas characteristics from gas signals at different concentrations by applying a principal component analysis (PCA). Finally, the model is established by using a new extreme random tree algorithm to achieve the target gas classification. The sample data collected by the experiment was verified by comparison experiments with the proposed algorithm. The analysis results show that the proposed DTW algorithm improves the gas classification accuracy by 26.87%. Compared with the random forest algorithm, extreme gradient boosting (XGBoost) algorithm and gradient boosting decision tree (GBDT) algorithm, the accuracy rate increased by 4.53%, 5.11% and 8.10%, respectively, reaching 99.28%. In terms of the time efficiency of the algorithms, the actual runtime of the extreme random tree algorithm is 66.85%, 90.27%, and 81.61% lower than that of the random forest algorithm, XGBoost algorithm, and GBDT algorithm, respectively, reaching 103.2568 s.

[Ozone oxidizes oleic fatty acid with the highest rate constant and does not oxidize palmitic acid. Different physicochemical parameters of substrates and their role in phylogenesis.]

Physicochemical differences between О3 oxidation parameters for palmitic and oleic fatty acids (FA) during phylogenesis (evolution) are fundamental for а) production of palmitoleic monounsaturated fatty (MFA), b) formation of carnitine palmitoyltransferase as a FA transporter to mitochondria, and c) in vivo production of oleic MFA under humoral regulatory effect of insulin. In the strive for the best kinetic parameters of biological organisms without a possibility of modifying physicochemical and biochemical reactions in the mitochondrial matrix, the mitochondria can be provided with a substrate that increases energy production efficiency and the amount of ATP. Physicochemical parameters of oleic MFA has become the standard of an oxidation substrate for in vivo energy production; this MFA was synthesized in organisms for millions of years. Environmental influences are the second factor which determines kinetic perfection of biological organisms during phylogenesis. Are these influences always beneficial? Mostly, they are not. However, they largely stimulate adaptive functions of the organism, including the biological function of locomotion, cognitive function and the function of positioning in the environment. Biological, energy and kinetic perfection formed in vivo can be easily destroyed if phylogenetically herbivorous Homo sapiens abuses the diet of carnivorous animals (meat) which was not consumed by him and his ancestors during phylogenesis. This abuse is the major cause of metabolic pandemias in human population. They are: insulin resistance, atherosclerosis and atheromatosis, obesity and nonalcoholic liver disease. The most effective measures preventing metabolic pandemias, cardiac heart disease and myocardial infarction are extremely simple. People should remain herbivorous.

Reaction Time Improvements by Neural Bistability

The often reported reduction of Reaction Time (RT) by Vision Training) is successfully replicated by 81 athletes across sports. This enabled us to achieve a mean reduction of RTs for athletes eye-hand coordination of more than 10%, with high statistical significance. We explain how such an observed effect of Sensorimotor systems' plasticity causing reduced RT can last in practice for multiple days and even weeks in subjects, via a proof of principle. Its mathematical neural model can be forced outside a previous stable (but long) RT into a state leading to reduced eye-hand coordination RT, which is, again, in a stable neural state.

FEF Excitability in Attentional Bias: A TMS-EEG Study

The role of distinct cortical regions in guiding social orienting needs further investigation. Our aim was to explore the contribution of the frontal eye field (FEF) in early orienting of attention towards stimuli with social value. We used a TMS-EEG approach to investigate event related potentials (ERPs; no-TMS block) and TMS evoked potentials (TEPs; TMS block) during the cueing phase of a modified version of the dot-probe task, comparing competing (face vs. house) and not competing (house vs. house) conditions. Our results revealed an increased amplitude of ERP components in the competing condition, showing greater posterior N170 and fronto-central vertex positive potential (VPP) and an enhanced frontal negative component at 250-270 ms from cue onset. TMS pulses over the FEF induced similar N170 and VPP amplified components. In addition, in the ERPs, a reduced positivity at 400 ms was shown when the face appeared on the left side vs. the right side of space. In contrast, in the TMS blocks, we found lateralized effects on N170 depending on the side of face presentation. The enhanced cortical excitability induced by TMS over the right FEF significantly correlated with the performance on the behavioral task, suggesting a link between the FEF activity during the cueing phase of the dot-probe task and the subsequent behavioral response times to the targets.

The thermal expansion properties of halogen bond containing 1,4 dioxane halogen complexes

Strong halogen bonds formed between 1,4 dioxane and dihalogens lead to minimum expansion in the direction of these bonds.

Influence of molecular width on the thermal expansion in solids

It has been shown that the thermal expansion would be higher in a direction along which the molecular width is shorter and it would be smaller if the molecular width is longer along that direction.