Deciphering the Thermal Stability of Bacteriophage MS2-Derived Virus-like Particle and Its Engineered Variant.

RNA bacteriophage MS2-derived virus-like particles (VLPs) have been widely used in biomedical research as model systems to study virus assembly, structure-function relationships, vaccine development, and drug delivery. Considering the diverse utility of these VLPs, a systemic engineering approach has been utilized to generate smaller particles with optimal serum stability and tissue penetrance. Additionally, it is crucial to demonstrate the overall stability of these mini MS2 VLPs, ensuring cargo protection until they reach their target cell/organ. However, no detailed analysis of the thermal stability and heat-induced disassembly of MS2 VLPs has yet been attempted. In this work, we investigated the thermal stability of both wild-type (WT) MS2 VLP and its "mini" variant containing S37P mutation (mini MS2 VLP). The mini MS2 VLP exhibits a higher capsid melting temperature (Tm) when compared to its WT MS2 VLP counterpart, possibly attributed to its smaller interdimer angle. Our study presents that the thermal unfolding of MS2 VLPs follows a sequential process involving particle destabilization, nucleic acid exposure/melting, and disassembly of VLP. This observation underscores the disruption of cooperative intersubunit interactions and protein-nucleic acid interactions, shedding light on the mechanism of heat-induced VLP disassembly.

Cooperative interactions between invader and resident microbial community members weaken the negative diversity-invasion relationship.

The negative diversity-invasion relationship observed in microbial invasion studies is commonly explained by competition between the invader and resident populations. However, whether this relationship is affected by invader-resident cooperative interactions is unknown. Using ecological and mathematical approaches, we examined the survival and functionality of Aminobacter niigataensis MSH1 to mineralize 2,6-dichlorobenzamide (BAM), a groundwater micropollutant affecting drinking water production, in sand microcosms when inoculated together with synthetic assemblies of resident bacteria. The assemblies varied in richness and in strains that interacted pairwise with MSH1, including cooperative and competitive interactions. While overall, the negative diversity-invasion relationship was retained, residents engaging in cooperative interactions with the invader had a positive impact on MSH1 survival and functionality, highlighting the dependency of invasion success on community composition. No correlation existed between community richness and the delay in BAM mineralization by MSH1. The findings suggest that the presence of cooperative residents can alleviate the negative diversity-invasion relationship.

pH-triggered hydrophility-adjustable fluorescent probes for simultaneously imaging lipid droplets and lysosomes and the application in fatty liver detection.

To study the collaboration between lipid droplets (LDs) and lysosomes, and the lipid change in nonalcoholic fatty liver disease (NAFLD), herein two pH-triggered hydrophility-adjustable fluorescent probes (LD-Lyso and LD-Lyso 1) are designed. The mechanism is based on cyclization and ring-opening with thorough consideration of pH and hydrophilic differences between LDs and lysosomes. Both of the two probes exist in ring-opening form and emit red fluorescence in acidic environment, while they exist in cyclized form and the emission is blueshifted in alkaline environment due to reduced conjugate planes. Moreover, LD-Lyso exhibits near infrared fluorescence at 740 nm under ring-opening form, which facilitates further cell, tissue, and in vivo imaging. The cell imaging results show that LD-Lyso can simultaneously target LDs and lysosomes by two different colors. Impressively, LD-Lyso cannot only detect NAFLD tissues from the normal tissue, but also distinguish different degrees of NAFLD tissues and mice, which provides a very promising tool for timely diagnosis of early NAFLD.

Characterisation of Indian gut microbiome for B-vitamin production and its comparison with Chinese cohort.

The human gut microbiota can biosynthesize essential micronutrients such as B-vitamins and is also known for its metabolic cooperative behaviour. The present study characterises such B-vitamin biosynthesizers, their biosynthetic pathways, explores their prevalence and abundance, examines how lifestyle or diet affects them in multiple Indian cohorts and compares it with the Chinese cohort. To achieve this, publicly available faecal metagenome data of healthy individuals from multiple Indian (two urban and three tribal populations) and a Chinese cohort were analysed. The distribution of prevalence and abundance of B-vitamin biosynthesizers showed similar profiles to that of the entire gut community of the Indian cohort, and there were 28 B-vitamin biosynthesizers that had modest or higher prevalence and abundance. The omnivorous diet affected only the prevalence of a few B-vitamin biosynthesizers; however, lifestyle and/or location affected both prevalence and abundance. A comparison with the Chinese cohort showed that fourteen B-vitamin biosynthesizers were significantly more prevalent and abundant in Chinese as compared with Indian samples (False Discovery Rate (FDR) <= 0·05). The metabolic potential of the entire gut community for B-vitamin production showed that within India, the tribal cohort has a higher abundance of B-vitamin biosynthesis pathways as compared with two urban cohorts namely, Bhopal and Kasargod, and comparison with the Chinese cohort revealed a higher abundance in the latter group. Potential metabolic cooperative behaviour of the Indian gut microbiome for biosynthesis of the B-vitamins showed multiple pairs of species showed theoretical complementarity for complete biosynthetic pathways genes of thiamine, riboflavin, niacin and pantothenate.

The Use of the Statistical Entropy in Some New Approaches for the Description of Biosystems.

Some problems of describing biological systems with the use of entropy as a measure of the complexity of these systems are considered. Entropy is studied both for the organism as a whole and for its parts down to the molecular level. Correlation of actions of various parts of the whole organism, intercellular interactions and control, as well as cooperativity on the microlevel lead to a more complex structure and lower statistical entropy. For a multicellular organism, entropy is much lower than entropy for the same mass of a colony of unicellular organisms. Cooperativity always reduces the entropy of the system; a simple example of ligand binding to a macromolecule carrying two reaction centers shows how entropy is consistent with the ambiguity of the result in the Bernoulli test scheme. Particular attention is paid to the qualitative and quantitative relationship between the entropy of the system and the cooperativity of ligand binding to macromolecules. A kinetic model of metabolism. corresponding to Schrödinger's concept of the maintenance biosystems by "negentropy feeding", is proposed. This model allows calculating the nonequilibrium local entropy and comparing it with the local equilibrium entropy inherent in non-living matter.

Comprehensive Pore Tuning in an Ultrastable Fluorinated Anion Cross-Linked Cage-Like MOF for Simultaneous Benchmark Propyne Recovery and Propylene Purification.

Propyne/propylene (C3 H4 /C3 H6 ) separation is an important but challenging industrial process to produce polymer-grade C3 H6 and recover high-purity C3 H4 . Herein, we report an ultrastable TiF6 2- anion cross-linked metal-organic framework (ZNU-2) with precisely controlled pore size, shape and functionality for benchmark C3 H4 storage (3.9/7.7 mmol g-1 at 0.01/1.0 bar and 298 K) and record high C3 H4 /C3 H6 (10/90) separation potential (31.0 mol kg-1 ). The remarkable C3 H4 /C3 H6 (1/99, 10/90, 50/50) separation performance was fully demonstrated by simulated and experimental breakthroughs under various conditions with excellent recyclability and high productivity (42 mol kg-1 ) of polymer-grade C3 H6 from a 1/99 C3 H4 /C3 H6 mixture. A modelling study revealed that the symmetrical spatial distribution of six TiF6 2- on the icosahedral cage surface provides two distinct binding sites for C3 H4 adsorption: one serves as a tailored single C3 H4 molecule trap and the other boosts C3 H4 accommodation by cooperative host-guest and guest-guest interactions.

Field study of microbial community structure and dechlorination activity in a multi-solvents co-contaminated site undergoing natural attenuation.

BTEX and chlorinated aliphatic hydrocarbons (CAHs) are the common pollutants found at contaminated sites, and natural attenuation (NA) of CAHs was widely observed where they coexist. In this work, the groundwater in a site co-contaminated with BTEX and CAHs was monitored for 1 year. The compositions and activities of the microfloras, especially dechlorinators and their relationships with the contaminants, geochemical properties, seasons and depth were evaluated. The results are consistent with the well-known NA conceptual model where CAHs are not able to stimulate the enrichment of dechlorinators alone, but BTEX does promote dechlorination. The higher temperature, rather than ORP in the deeper groundwater of the wet season became a key factor to promote the abundance of dechlorinators, but only when BTEX was available, indicating that the substrates from the BTEX biodegradation played an important role in the dechlorinator enrichment. The elevated ORP in the shallower groundwater exceeded the optimum conditions for reductive dechlorination and no significant seasonal variation of dechlorinators was found. The co-occurrence network revealed the cooperative interactions among the functional microfloras in which dechlorinators, BTEX degraders, and fermentative bacteria jointly promoted the dechlorination. These findings provided us a further understanding of the NA processes in a commingled plume.

Microbial profiles associated improving bioelectricity generation from sludge fermentation liquid via microbial fuel cells with adding fruit waste extracts.

This first-attempt study illustrated the microbial cooperative interactions related to bioelectricity generation from the mixture of sludge fermentation liquid (SFL) and fruit waste extracts (FWEs) via microbial fuel cells (MFCs). The optimal output voltages of 0.65 V for SFL-MFCs, 0.51 V for FWEs-MFCs and 0.75 V for mixture-MFCs associated with bioelectricity conversion efficiencies of 1.061, 0.718 and 1.391 kWh/kg COD were reached, respectively. FWEs addition for substrates C/N ratio optimization contributed considerably to increase SFL-fed MFCs performance via triggering a higher microbial diversity, larger relatively abundance of functional genes and microbial synergistic interactions with genera enrichment of Clostridium, Alicycliphilus, Thermomonas, Geobacter, Paludibaculum, Pseudomonas, Taibaiella and Comamonas. Furthermore, a conceptual illustration of co-locating scenario of wastewater treatment plant(s), waste sludge in situ acidogenic fermentation, fruit waste collection/crushing station and MFC plant was proposed for the first time, which provided new thinking for future waste sludge treatment toward maximizing solid reduction and power recovery.

Understanding and Controlling the Crystallization Process in Reconfigurable Plasmonic Superlattices.

The crystallization of nanomaterials is a primary source of solid-state, photonic structures. Thus, a detailed understanding of this process is of paramount importance for the successful application of photonic nanomaterials in emerging optoelectronic technologies. While colloidal crystallization has been thoroughly studied, for example, with advanced in situ electron microscopy methods, the noncolloidal crystallization (freezing) of nanoparticles (NPs) remains so far unexplored. To fill this gap, in this work, we present proof-of-principle experiments decoding a crystallization of reconfigurable assemblies of NPs at a solid state. The chosen material corresponds to an excellent testing bed, as it enables both in situ and ex situ investigation using X-ray diffraction (XRD), transmission electron microscopy (TEM), high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), atomic force microscopy (AFM), and optical spectroscopy in visible and ultraviolet range (UV-vis) techniques. In particular, ensemble measurements with small-angle XRD highlighted the dependence of the correlation length in the NPs assemblies on the number of heating/cooling cycles and the rate of cooling. Ex situ TEM imaging further supported these results by revealing a dependence of domain size and structure on the sample preparation route and by showing we can control the domain size over 2 orders of magnitude. The application of HAADF-STEM tomography, combined with in situ thermal control, provided three-dimensional single-particle level information on the positional order evolution within assemblies. This combination of real and reciprocal space provides insightful information on the anisotropic, reversibly reconfigurable assemblies of NPs. TEM measurements also highlighted the importance of interfaces in the polydomain structure of nanoparticle solids, allowing us to understand experimentally observed differences in UV-vis extinction spectra of the differently prepared crystallites. Overall, the obtained results show that the combination of in situ heating HAADF-STEM tomography with XRD and ex situ TEM techniques is a powerful approach to study nanoparticle freezing processes and to reveal the crucial impact of disorder in the solid-state aggregates of NPs on their plasmonic properties.

Mesoporous Iron-doped MoS2/CoMo2S4 Heterostructures through Organic-Metal Cooperative Interactions on Spherical Micelles for Electrochemical Water Splitting.

Mesoporous metal sulfide hybrid (meso-MoS2/CoMo2S4) materials via a soft-templating approach using diblock copolymer polystyrene-block-poly(acrylic acid) micelles are reported. The formation of the meso-MoS2/CoMo2S4 heterostructures is based on the sophisticated coassembly of dithiooxamide and metal precursors (i.e., Co2+, PMo12), which are subsequently annealed in nitrogen atmosphere to generate the mesoporous material. Decomposing the polymer leaves behind mesopores throughout the spherical MoS2/CoMo2S4 hybrid particles, generating numerous electrochemical active sites in a network of pores that enable faster charge transfer and mass/gas diffusion that enhance the electrocatalytic performance of MoS2/CoMo2S4. Doping the spherical meso-MoS2/CoMo2S4 heterostructures with iron improves the electronic properties of the hybrid meso-Fe-MoS2/CoMo2S4 material and consequently results in its superior electrochemical activities for both hydrogen evolution reaction and oxygen evolution reaction.

Competitive and/or Cooperative Interactions of Listeria monocytogenes With Bacillus cereus in Dual-Species Biofilm Formation.

Microorganisms in dairy industries can form monospecies, dual-species, or multispecies biofilms, showing cooperative or competitive behaviors, which might contribute to the reduction of efficiency of cleaning and sanitization processes and eventually turn into a potential source of contamination. This study proposes to evaluate the behavior of Listeria monocytogenes in monospecies biofilms, cocultured with Bacillus cereus. The isolates were of dairy origin, and the selection occurred after studies of competition among species. The biofilm formations on AISI 304 stainless steel at 25°C in a stationary culture were analyzed to observe the cooperative or competitive interactions among species, as well as the effect of pre-adhered cells. Biofilm formation assays were performed in four experiments: Experiment 1: in the presence of strains of antagonistic substance producer B. cereus (+); Experiment 2: extract of the antagonistic substance of B. cereus; Experiment 3: pre-adhered cells of B. cereus; and Experiment 4: pre-adhered cells of L. monocytogenes. Subsequently, cooperative behavior was observed by scanning electron microscopy. The L. monocytogenes monospecies biofilm counts of greater than 5 log colony-forming units (CFU)/cm2 were also observed in dual-species biofilms in the presence of B. cereus (non-producers of antagonist substance), showing cooperative behavior between species. However, in the presence of antagonistic substance produced by B. cereus, the counts were lower, 1.39 and 1.70 log CFU/cm2 (p > 0.05), indicating that the antagonistic substance contributes to competitive interactions. These data are relevant for the development of new studies to control L. monocytogenes in the dairy industry.

Iron(II) Spin Crossover Complexes with 4,4'-Dipyridylethyne-Crystal Structures and Spin Crossover with Hysteresis.

Three new iron(II) 1D coordination polymers with cooperative spin crossover behavior showing thermal hysteresis loops were synthesized using N2O2 Schiff base-like equatorial ligands and 4,4'-dipyridylethyne as a bridging, rigid axial linker. One of those iron(II) 1D coordination polymers showed a 73 K wide hysteresis below room temperature, which, upon solvent loss, decreased to a still remarkable 30 K wide hysteresis. Single crystal X-ray structures of two iron(II) coordination polymers and T-dependent powder XRD patterns are discussed to obtain insight into the structure property relationship of those materials.

Shaping Liquid Crystals with Gold Nanoparticles: Helical Assemblies with Tunable and Hierarchical Structures Via Thin-Film Cooperative Interactions.

The availability of helical assemblies of plasmonic nanoparticles with precisely controlled and tunable structures can play a key role in the future development of chiral plasmonics and metamaterials. Here, a strategy to efficiently yield helical structures based on the cooperative interactions of liquid crystals and gold nanoparticles in thin films is developed. These nanocomposites exhibit exceptional long-range hierarchical order across length scales, which results from the growth mechanism of nanoparticle-coated twisted nanoribbons and their ability to form organized bundles. The helical assembly formation is governed by the presence of rationally functionalized nanoparticles. Importantly, the thickness of the achieved nanocomposites can be reversibly reconfigured owing to the polymorphic nature of the liquid crystal. The versatility of the proposed approach is demonstrated by preparing helices assembled from nanoparticles of different geometries and dimensions (spherical and rod-like). The described strategy may become an enabling technology for structuring nanoparticle assemblies with high precision and fabricating optically active materials.

Two-dimensional Ising model for microarray hybridization: cooperative interactions between bound target molecules.

The Langmuir adsorption model is widely used for description and quantification of microarray oligo-target hybridization. According to the model, the binding centers for adsorption of target molecules from solution are represented by oligo-probes. However, the Langmuir model does not consider the interactions between the targets adsorbed at the neighboring binding centers, which are possible due to high-density of array-bound probes. We have shown that the two-dimensional Ising model, which takes into account the nearest neighboring target molecules interactions, better describes the experimental data of oligo-target hybridization in comparison with the Langmuir model. Thus, we found an evidence for existence of positive cooperative interactions between adsorbed target molecules: so, binding of the first target molecules facilitates the binding of subsequent ones to the neighboring probes. Communicated by Ramaswamy H. Sarma.

Evolution of weak cooperative interactions for biological specificity.

A hallmark of biological systems is that particular functions and outcomes are realized in specific contexts, such as when particular signals are received. One mechanism for mediating specificity is described by Fisher's "lock and key" metaphor, exemplified by enzymes that bind selectively to a particular substrate via specific finely tuned interactions. Another mechanism, more prevalent in multicellular organisms, relies on multivalent weak cooperative interactions. Its importance has recently been illustrated by the recognition that liquid-liquid phase transitions underlie the formation of membraneless condensates that perform specific cellular functions. Based on computer simulations of an evolutionary model, we report that the latter mechanism likely became evolutionarily prominent when a large number of tasks had to be performed specifically for organisms to function properly. We find that the emergence of weak cooperative interactions for mediating specificity results in organisms that can evolve to accomplish new tasks with fewer, and likely less lethal, mutations. We argue that this makes the system more capable of undergoing evolutionary changes robustly, and thus this mechanism has been repeatedly positively selected in increasingly complex organisms. Specificity mediated by weak cooperative interactions results in some useful cross-reactivity for related tasks, but at the same time increases susceptibility to misregulation that might lead to pathologies.

Interdependence theory of tissue failure: bulk and boundary effects.

The mortality rate of many complex multicellular organisms increases with age, which suggests that net ageing damage is accumulative, despite remodelling processes. But how exactly do these little mishaps in the cellular level accumulate and spread to become a systemic catastrophe? To address this question we present experiments with synthetic tissues, an analytical model consistent with experiments, and a number of implications that follow the analytical model. Our theoretical framework describes how shape, curvature and density influences the propagation of failure in a tissue subjected to oxidative damage. We propose that ageing is an emergent property governed by interaction between cells, and that intercellular processes play a role that is at least as important as intracellular ones.

Quaternized Cellulose Hydrogels as Sorbent Materials and Pickering Emulsion Stabilizing Agents.

Quaternized (QC) and cross-linked/quaternized (CQC) cellulose hydrogels were prepared by cross-linking native cellulose with epichlorohydrin (ECH), with subsequent grafting of glycidyl trimethyl ammonium chloride (GTMAC). Materials characterization via carbon, hydrogen and nitrogen (CHN) analysis, thermogravimetric analysis (TGA), and Fourier transform infrared (FTIR)/13C solid state NMR spectroscopy provided supportive evidence of the hydrogel synthesis. Enhanced thermal stability of the hydrogels was observed relative to native cellulose. Colloidal stability of octanol and water mixtures revealed that QC induces greater stabilization over CQC, as evidenced by the formation of a hexane-water Pickering emulsion system. Equilibrium sorption studies with naphthenates from oil sands process water (OSPW) and 2-naphthoxy acetic acid (NAA) in aqueous solution revealed that CQC possess higher affinity relative to QC with the naphthenates. According to the Langmuir isotherm model, the sorption capacity of CQC for OSPW naphthenates was 33.0 mg/g and NAA was 69.5 mg/g. CQC displays similar affinity for the various OSPW naphthenate component species in aqueous solution. Kinetic uptake of NAA at variable temperature, pH and adsorbent dosage showed that increased temperature favoured the uptake process at 303 K, where Qm = 76.7 mg/g. Solution conditions at pH 3 or 9 had a minor effect on the sorption process, while equilibrium was achieved in a shorter time at lower dosage (ca. three-fold lower) of hydrogel (100 mg vs. 30 mg). The estimated activation parameters are based on temperature dependent rate constants, k1, which reveal contributions from enthalpy-driven electrostatic interactions. The kinetic results indicate an ion-based associative sorption mechanism. This study contributes to a greater understanding of the adsorption and physicochemical properties of cellulose-based hydrogels.

Mechanistic stochastic model of histone modification pattern formation.

BACKGROUND: The activity of a single gene is influenced by the composition of the chromatin in which it is embedded. Nucleosome turnover, conformational dynamics, and covalent histone modifications each induce changes in the structure of chromatin and its affinity for regulatory proteins. The dynamics of histone modifications and the persistence of modification patterns for long periods are still largely unknown. RESULTS: In this study, we present a stochastic mathematical model that describes the molecular mechanisms of histone modification pattern formation along a single gene, with non-phenomenological, physical parameters. We find that diffusion and recruitment properties of histone modifying enzymes together with chromatin connectivity allow for a rich repertoire of stochastic histone modification dynamics and pattern formation. We demonstrate that histone modification patterns at a single gene can be established or removed within a few minutes through diffusion and weak recruitment mechanisms of histone modification spreading. Moreover, we show that strong synergism between diffusion and weak recruitment mechanisms leads to nearly irreversible transitions in histone modification patterns providing stable patterns. In the absence of chromatin connectivity spontaneous and dynamic histone modification boundaries can be formed that are highly unstable, and spontaneous fluctuations cause them to diffuse randomly. Chromatin connectivity destabilizes this synergistic system and introduces bistability, illustrating state switching between opposing modification states of the model gene. The observed bistable long-range and localized pattern formation are critical effectors of gene expression regulation. CONCLUSION: This study illustrates how the cooperative interactions between regulatory proteins and the chromatin state generate complex stochastic dynamics of gene expression regulation.

Rethinking quasispecies theory: From fittest type to cooperative consortia.

Recent investigations surprisingly indicate that single RNA "stem-loops" operate solely by chemical laws that act without selective forces, and in contrast, self-ligated consortia of RNA stem-loops operate by biological selection. To understand consortial RNA selection, the concept of single quasi-species and its mutant spectra as drivers of RNA variation and evolution is rethought here. Instead, we evaluate the current RNA world scenario in which consortia of cooperating RNA stem-loops (not individuals) are the basic players. We thus redefine quasispecies as RNA quasispecies consortia (qs-c) and argue that it has essential behavioral motifs that are relevant to the inherent variation, evolution and diversity in biology. We propose that qs-c is an especially innovative force. We apply qs-c thinking to RNA stem-loops and evaluate how it yields altered bulges and loops in the stem-loop regions, not as errors, but as a natural capability to generate diversity. This basic competence-not error-opens a variety of combinatorial possibilities which may alter and create new biological interactions, identities and newly emerged self identity (immunity) functions. Thus RNA stem-loops typically operate as cooperative modules, like members of social groups. From such qs-c of stem-loop groups we can trace a variety of RNA secondary structures such as ribozymes, viroids, viruses, mobile genetic elements as abundant infection derived agents that provide the stem-loop societies of small and long non-coding RNAs.