Hierarchical assembly and environmental enhancement of bacterial ice nucleators.

Bacterial ice nucleating proteins (INPs) are exceptionally effective in promoting the kinetically hindered transition of water to ice. Their efficiency relies on the assembly of INPs into large functional aggregates, with the size of ice nucleation sites determining activity. Experimental freezing spectra have revealed two distinct, defined aggregate sizes, typically classified as class A and C ice nucleators (INs).

Defluorination of Organofluorine Compounds Using Dehalogenase Enzymes from (D4B).

Organofluorine compounds have been widely used as pharmaceuticals, agricultural pesticides, and water-resistant coatings for decades; however, these compounds are recognized as environmental pollutants. The capability of microorganisms and enzymes to defluorinate organofluorine compounds is both rare and highly desirable to facilitate environmental remediation efforts. Recently, a strain of (D4B) was identified with potential biodegradation activity toward perfluoroalkyl substances (PFAS) and other organofluorine compounds.

AlphaFold2 modeling and molecular dynamics simulations of an intrinsically disordered protein.

We use AlphaFold2 (AF2) to model the monomer and dimer structures of an intrinsically disordered protein (IDP), Nvjp-1, assisted by molecular dynamics (MD) simulations. We observe relatively rigid dimeric structures of Nvjp-1 when compared with the monomer structures. We suggest that protein conformations from multiple AF2 models and those from MD trajectories exhibit a coherent trend: the conformations of an IDP are deviated from each other and the conformations of a well-folded protein are consistent with each other.

Enhanced humification of full-scale apple wood and cow manure by promoting lignocellulose degradation via biomass pretreatments.

Agroforestry waste and cow manure pollute the environment, of which, agroforestry waste is difficult to degrade. Compost is an effective way to dispose agroforestry waste; however, the low degradation efficiency of lignocellulose in agroforestry waste affects the process of composting humification. This study investigated lignocellulose degradation and composting humification in full-size apple wood and cow manure composting processes by applying different pretreatments (acidic, alkaline, and high-temperature) to apple wood.

Accurate prediction by AlphaFold2 for ligand binding in a reductive dehalogenase and implications for PFAS (per- and polyfluoroalkyl substance) biodegradation.

Despite the success of AlphaFold2 (AF2), it is unclear how AF2 models accommodate for ligand binding. Here, we start with a protein sequence from Acidimicrobiaceae TMED77 (T7RdhA) with potential for catalyzing the degradation of per- and polyfluoroalkyl substances (PFASs). AF2 models and experiments identified T7RdhA as a corrinoid iron-sulfur protein (CoFeSP) which uses a norpseudo-cobalamin (BVQ) cofactor and two FeS iron-sulfur clusters for catalysis.

Enhanced removal of tetrabromobisphenol A by Burkholderia cepacian Y17 immobilized on biochar.

Biochar-immobilized bacteria have been widely used to remove organic pollutants; however, the enhanced effect of biochar-immobilized bacteria on tetrabromobisphenol A (TBBPA) removal has not been fully investigated and the removal mechanism remains unclear. In this study, a bacterial strain with high TBBPA degradation ability, Burkholderia cepacian Y17, was isolated from an e-waste disassembly area, immobilized with biochar, and used for the removal of TBBPA. Comparisons were performed of the factors affecting the immobilization and TBBPA removal efficiency, including the biochar preparation temperature, immobilization temperature, and pH.

Agave REVEILLE1 regulates the onset and release of seasonal dormancy in Populus.

Deciduous woody plants like poplar (Populus spp.) have seasonal bud dormancy. It has been challenging to simultaneously delay the onset of bud dormancy in the fall and advance bud break in the spring, as bud dormancy, and bud break were thought to be controlled by different genetic factors.

TCA and SSRI Antidepressants Exert Selection Pressure for Efflux-Dependent Antibiotic Resistance Mechanisms in Escherichia coli.

Microbial diversity is reduced in the gut microbiota of animals and humans treated with selective serotonin reuptake inhibitors (SSRIs) and tricyclic antidepressants (TCAs). The mechanisms driving the changes in microbial composition, while largely unknown, is critical to understand considering that the gut microbiota plays important roles in drug metabolism and brain function. Using Escherichia coli, we show that the SSRI fluoxetine and the TCA amitriptyline exert strong selection pressure for enhanced efflux activity of the AcrAB-TolC pump, a member of the resistance-nodulation-cell division (RND) superfamily of transporters.

Biochar-goethite composites inhibited/enhanced degradation of triphenyl phosphate by activating persulfate: Insights on the mechanism.

In this study, the biochar-goethite composites (MBC@FH) were synthesized through co-ball milling and the degradation of triphenyl phosphate (TPhP) was compared in persulfate (PDS) alone system and MBC@FH&PDS systems. The results showed that TPhP can be effectively degraded in PDS alone system and degradation efficiency reached up to 90 % within reaction of 8 h, at a PDS concentration of 10 mM, a reaction temperature of 30 °C and a system pH of 6.12.

Highly stable cathodes for proton exchange membrane fuel cells: Novel carbon supported Au@PtNiAu concave octahedral core-shell nanocatalyst.

Despite the remarkable research efforts, the lack of ideal activity and state-of-the-art electrocatalysts remains a substantial challenge for the global application of fuel cell technology. Herein, is reported the synthesis of Au@PtNiAu concave octahedral core-shell nanocatalysts (Au@PtNiAu-COCS) via solvothermal synthesis modification and optimization approach. The special structure generating a large number of step atoms, enhancing the oxygen reduction reaction (ORR) and methanol oxidation reaction (MOR) activity and stability.

FeO loaded on ball milling biochar enhanced bisphenol a removal by activating persulfate: Performance and activating mechanism.

In this study, pristine biochar (BC), ball milling biochar (MBC), FeO modified BC (FeO@BC), and FeO modified MBC (FeO@MBC) were prepared to compare the Bisphenol A (BPA) removal efficiency by activating persulfate (PDS). All catalysts exhibited excellent degradation rather than adsorption in the PDS system, and FeO@MBC800 had the best BPA removal efficiency, with 96.73% degradation and negligible 1.

AlphaFold2 models indicate that protein sequence determines both structure and dynamics.

AlphaFold 2 (AF2) has placed Molecular Biology in a new era where we can visualize, analyze and interpret the structures and functions of all proteins solely from their primary sequences. We performed AF2 structure predictions for various protein systems, including globular proteins, a multi-domain protein, an intrinsically disordered protein (IDP), a randomized protein, two larger proteins (> 1000 AA), a heterodimer and a homodimer protein complex. Our results show that along with the three dimensional (3D) structures, AF2 also decodes protein sequences into residue flexibilities via both the predicted local distance difference test (pLDDT) scores of the models, and the predicted aligned error (PAE) maps.

A pH-Based Single-Sensor Array for Discriminating Metal Ions in Water.

Human activities, such as mining and manufacturing, expose society and the natural environment to harmful levels of metal ions. Recently, optical sensor arrays for metal ion detection have become popular owing to their favourable features, such as facile sample preparation and the requirement of less expensive instrumentation compared to traditional, spectrometry-based analysis techniques. Sensor arrays usually consist of numerous optical probes that are used in combination to generate unique analyte responses.

A quantitative yeast aging proteomics analysis reveals novel aging regulators.

Calorie restriction (CR) is the most robust longevity intervention, extending lifespan from yeast to mammals. Numerous conserved pathways regulating aging and mediating CR have been identified; however, the overall proteomic changes during these conditions remain largely unexplored. We compared proteomes between young and replicatively aged yeast cells under normal and CR conditions using the Stable-Isotope Labeling by Amino acids in Cell culture (SILAC) quantitative proteomics and discovered distinct signatures in the aging proteome.

Overexpression of an Phosphopyruvate Carboxylase Improves Plant Growth and Stress Tolerance.

It has been challenging to simultaneously improve photosynthesis and stress tolerance in plants. Crassulacean acid metabolism (CAM) is a CO-concentrating mechanism that facilitates plant adaptation to water-limited environments. We hypothesized that the ectopic expression of a CAM-specific phosphopyruvate carboxylase (PEPC), an enzyme that catalyzes primary CO fixation in CAM plants, would enhance both photosynthesis and abiotic stress tolerance.

Protein interaction potential landscapes for yeast replicative aging.

We proposed a novel interaction potential landscape approach to map the systems-level profile changes of gene networks during replicative aging in Saccharomyces cerevisiae. This approach enabled us to apply quasi-potentials, the negative logarithm of the probabilities, to calibrate the elevation of the interaction landscapes with young cells as a reference state. Our approach detected opposite landscape changes based on protein abundances from transcript levels, especially for intra-essential gene interactions.

Complementary performances of convolutional and capsule neural networks on classifying microfluidic images of dividing yeast cells.

Microfluidic-based assays have become effective high-throughput approaches to examining replicative aging of budding yeast cells. Deep learning may offer an efficient way to analyze a large number of images collected from microfluidic experiments. Here, we compare three deep learning architectures to classify microfluidic time-lapse images of dividing yeast cells into categories that represent different stages in the yeast replicative aging process.

Association study based on topological constraints of protein-protein interaction networks.

The non-random interaction pattern of a protein-protein interaction network (PIN) is biologically informative, but its potentials have not been fully utilized in omics studies. Here, we propose a network-permutation-based association study (NetPAS) method that gauges the observed interactions between two sets of genes based on the comparison between permutation null models and the empirical networks. This enables NetPAS to evaluate relationships, constrained by network topology, between gene sets related to different phenotypes.

Atomistic probing of aptameric binding of CD19 outer membrane domain reveals an "aptamer walking" mechanism.

We propose an integrated structural approach to search potential aptamer molecules for targeting cancer receptor proteins. We used the outer cellular domain of the B-lymphocyte antigen, CD19, as the target for this study. First, using available protein-aptamer structures deposited in the protein data bank as resources, structural annotation was performed to seek the most probable binding aptamer and its potential initial configuration to the CD19 structure.

Advancing Aptamers as Molecular Probes for Cancer Theranostic Applications-The Role of Molecular Dynamics Simulation.

Theranostics cover emerging technologies for cell biomarking for disease diagnosis and targeted introduction of drug ingredients to specific malignant sites. Theranostics development has become a significant biomedical research endeavor for effective diagnosis and treatment of diseases, especially cancer. An efficient biomarking and targeted delivery strategy for theranostic applications requires effective molecular coupling of binding ligands with high affinities to specific receptors on the cancer cell surface.

Characterisation of aptamer-anchored poly(EDMA-co-GMA) monolith for high throughput affinity binding.

Immobilisation of aptameric ligands on solid stationary supports for effective binding of target molecules requires understanding of the relationship between aptamer-polymer interactions and the conditions governing the mass transfer of the binding process. Herein, key process parameters affecting the molecular anchoring of a thrombin-binding aptamer (TBA) onto polymethacrylate monolith pore surface, and the binding characteristics of the resulting macroporous aptasensor were investigated. Molecular dynamics (MD) simulations of the TBA-thrombin binding indicated enhanced Guanine 4 (G4) structural stability of TBA upon interaction with thrombin in an ionic environment.

A Suggestion of Converting Protein Intrinsic Disorder to Structural Entropy Using Shannon's Information Theory.

We propose a framework to convert the protein intrinsic disorder content to structural entropy () using Shannon's information theory (IT). The structural capacity (), which is the sum of and structural information (), is equal to the amino acid sequence length of the protein. The structural entropy of the residues expands a continuous spectrum, ranging from 0 (fully ordered) to 1 (fully disordered), consistent with Shannon's IT, which scores the fully-determined state 0 and the fully-uncertain state 1.

Correction to: Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave.

Following publication of the original article.

Components and dispersion characteristics of organic and inorganic odorous gases in a large-scale dairy farm.

The rapid development of large-scale livestock husbandry has caused serious air pollution problems (e.g., The Tuzuoqi demonstration farm belonging to the Yili Group.

A New Calmodulin-Binding Protein Expresses in the Context of Secondary Cell Wall Biosynthesis and Impacts Biomass Properties in .

A greater understanding of biosynthesis, signaling and regulatory pathways involved in determining stem growth and secondary cell wall chemistry is important for enabling pathway engineering and genetic optimization of biomass properties. The present study describes a new functional role of , a gene belonging to the IQ67-Domain1 family of genes, in impacting biomass formation and chemistry. Expression studies showed that has enhanced expression in developing xylem and tension-stressed tissues in .