In Silico Structural Insights into a Glucanase from Clostridium perfringens and Prediction of Structural Stability Improvement Through Hydrophobic Interaction Network and Aromatic Interaction.

Glucanases are widely applied in industrial applications such as brewing, biomass conversion, food, and animal feed. Glucanases catalyze the hydrolysis of glucan to produce the sugar hemiacetal through hydrolytic cleavage of glycosidic bonds. Current study aimed to investigate structural insights of a glucanase from Clostridium perfringens through blind molecular docking, site-specific molecular docking, molecular dynamics (MD) simulation, and binding energy calculation.

Testing the kinetic tradeoff between bicarbonate versus phosphoenolpyruvate affinity and glucose-6 phosphate response of phosphoenolpyruvate carboxylase from two C grasses.

Phosphoenolpyruvate (PEP) carboxylase (PEPC) has an anaplerotic role in central plant metabolism but also initiates the carbon concentrating mechanism during C photosynthesis. The C PEPC has different binding affinities (K) for PEP (K) and HCO (K), and allosteric regulation by glucose-6-phosphate (G6-P) compared to non-photosynthetic isoforms. These differences are linked to specific changes in amino acids within PEPC.

Engineering Cascade Bio-solar Cells Inspired by the Z-Scheme of Oxygenic Photosynthesis: Layered Chlorophyll and Bacterio-chlorophyll Derivatives.

The natural Z-scheme of oxygenic photosynthesis efficiently drives electron transfer from photosystem II (PSII) to photosystem I (PSI) via an electron transport chain, despite the lower energy levels of PSII. Inspired by this sophisticated mechanism, we present a layered cascade bio-solar cell (CBSC) that emulates the Z-scheme. In this design, chlorophyll derivatives (Chl) act as PSI analogs, while bacteriochlorophyll derivatives (BChl) serve as PSII analogs in the active layer.

Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I.

Background: All chemical forms of energy and oxygen on Earth are generated via photosynthesis where light energy is converted into redox energy by two photosystems (PS I and PS II). There is an increasing number of PS I 3D structures deposited in the Protein Data Bank (PDB). The Triangular Spatial Relationship (TSR)-based algorithm converts 3D structures into integers (TSR keys).

Plasmon-Driven Gold Nanopillar Multiarrayed Gene Amplification Methodology for the High-Throughput Discrimination of Pathogens.

Molecular diagnosis limitations, including complex treatment processes, low cost-effectiveness, and operator-dependent low reproducibility, interrupt the timely prevention of disease spread and the development of medical devices for home and outdoor uses. A newly fabricated gold nanopillar array-based film is presented for superior photothermal energy conversion. Magnifying the metal film surface-to-volume ratio increases the photothermal energy conversion efficiency, resulting in a swift reduction in the gene amplification reaction time.

Predictive equation derived from 6,497 doubly labelled water measurements enables the detection of erroneous self-reported energy intake.

Nutritional epidemiology aims to link dietary exposures to chronic disease, but the instruments for evaluating dietary intake are inaccurate. One way to identify unreliable data and the sources of errors is to compare estimated intakes with the total energy expenditure (TEE). In this study, we used the International Atomic Energy Agency Doubly Labeled Water Database to derive a predictive equation for TEE using 6,497 measures of TEE in individuals aged 4 to 96 years.

A human skin-on-a-chip platform for microneedling-driven skin cancer treatment.

Skin-on-a-chip models provide physiologically relevant platforms for studying diseases and drug evaluation, replicating the native skin structures and functions more accurately than traditional 2D or simple 3D cultures. However, challenges remain in creating models suitable for microneedling applications and monitoring, as well as developing skin cancer models for analysis and targeted therapy. Here, we developed a human skin/skin cancer-on-a-chip platform within a microfluidic device using bioprinting/bioengineering techniques.

Enhancement of photoinduced reactive oxygen species generation in open-cage fullerenes.

Photodynamic therapy is an important tool in modern medicine due to its effectiveness, safety, and the ability to provide targeted treatment for a range of diseases. Photodynamic therapy utilizes photosensitizers to generate reactive oxygen species (ROS). Fullerenes can be used as photosensitizers to produce ROS in high quantum yields.

Insights into the separation, enantioseparation and recognition mechanisms of methamphetamine isotopologues on achiral and polysaccharide-based chiral columns in high-performance liquid chromatography.

Background: Isotopologues resulting from the labelling of molecules with deuterium have attracted interest due to the isotope effect observed in chemistry and biosciences. Isotope effect may also play out in noncovalent interactions and mechanisms leading to intermolecular recognition. In chromatography, differences in retention time between isotopologues, as well as between isotopomers have been observed resulting in two different elution sequences (isotope effects): the normal isotope effect when heavier isotopologues retain longer than lighter analogues, and the inverse isotope effect featuring the opposite elution order.

The effect of thermal stress on the X-organ/sinus gland proteome of the estuarine blue crab Callinectes sapidus during the intermolt and premolt stages.

Survival of brachyuran crabs is temperature-dependent and thermal stress promotes changes during molting. We aimed to decipher the impact of thermal stresses on the X-organ/sinus gland (XO/SG) complex, a temperature-sensitive neuroendocrine tissue involved in the molting regulation of Callinectes sapidus during the intermolt and premolt phases. We employed a proteogenomic approach using specimens subjected to control (24 °C), cold (19 °C), and heat (29 °C) temperatures.

Autophagy related 7 (ATG7) regulates food intake and liver health during asparaginase exposure.

Amino acid starvation by the chemotherapy agent asparaginase is a potent activator of the integrated stress response (ISR) in liver and can upregulate autophagy in some cell types. We hypothesized that autophagy related 7 (ATG7), a protein that is essential for autophagy and an ISR target gene, was necessary during exposure to asparaginase to maintain liver health. We knocked down Atg7 systemically (Atg7) or in hepatocytes only (ls-Atg7KO) in mice before exposure to pegylated asparaginase for 5 d.

Novel archaeal ribosome dimerization factor facilitating unique 30S-30S dimerization.

Protein synthesis (translation) consumes a substantial proportion of cellular resources, prompting specialized mechanisms to reduce translation under adverse conditions. Ribosome inactivation often involves ribosome-interacting proteins. In both bacteria and eukaryotes, various ribosome-interacting proteins facilitate ribosome dimerization or hibernation, and/or prevent ribosomal subunits from associating, enabling the organisms to adapt to stress.

Evidence for intrinsic DNA dynamics and deformability in damage sensing by the Rad4/XPC nucleotide excision repair complex.

Altered DNA dynamics at lesion sites are implicated in how DNA repair proteins sense damage within genomic DNA. Using laser temperature-jump (T-jump) spectroscopy combined with cytosine-analog Förster Resonance Energy Transfer (FRET) probes that sense local DNA conformations, we measured the intrinsic dynamics of DNA containing 3 base-pair mismatches recognized in vitro by Rad4 (yeast ortholog of XPC). Rad4/XPC recognizes diverse lesions from environmental mutagens and initiates nucleotide excision repair.

Exploring Feed Digestibility and Broiler Performance in Response to Dietary Supplementation of .

This study evaluated the feed digestibility of diets including autotrophic in 252 male broilers (Ross 308), comparing unprocessed biomass (trial 1) and pulsed electric field (PEF) processed biomass (trial 2) at inclusion levels up to 20%. In trial 2, performance and meat color were also evaluated. Each trial included seven treatments (0%, 1%, 2%, 5%, 10%, 15%, and 20% (%/ on dry matter (DM)) ) with six replicates (three birds per replicate) per treatment.

A quasi affine transformation evolution algorithm with evolution matrix selection operation for parameter estimation of proton exchange membrane fuel cells.

Electrochemical energy conversion technologies include proton exchange membrane fuel cells (PEMFCs) where proton interchange is an alternative to diesel distributed generation, and PEMFCs are considered as a promising backup power source and a tool to regulate power consumption. Some of the major benefits of these PEMFCs especially in power system applications include low emission of carbon, fast load following capability, no noise and high start-up reliability. It is challenging to find the best PEMFC parameters because the model is complex and the problem is nonlinear; not all optimization algorithms can solve this problem.

Acetogenesis to ethanologenesis: facilitating NADH oxidation via reductive acetate uptake.

(Homo)acetogens, including Clostridium spp., represent an enigma in metabolic flexibility and diversity. Eubacterium callanderi KIST612 is an acetogen that produces n-butyrate with carbon monoxide (CO) as the carbon and energy source; however, the production route is unknown.

Structural snapshots of the aldol condensation reaction of the enzyme trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from Pseudomonas fluorescens N3.

Aldolases are crucial enzymes that catalyze the formation of carbon-carbon bonds in the context of the anabolic and catabolic pathways of various metabolites. The bacterium Pseudomonas fluorescens N3 can use naphthalene as its sole carbon and energy source by using, among other enzymes, the trans-o-hydroxybenzylidenepyruvate (tHBP) hydratase-aldolase (HA), encoded by the nahE gene. In this study, we present the crystallographic structures of tHBP-HA in three different functional states: the apo enzyme with a phosphate ion in the active site, and the Schiff base adduct bound either to pyruvate or to the substitute with '(R)-4-hydroxy-4-(2-hydroxyphenyl)-2-oxobutanoate'(intermediate state).

Electron transfer in polysaccharide monooxygenase catalysis.

Polysaccharide monooxygenase (PMO) catalysis involves the chemically difficult hydroxylation of unactivated C-H bonds in carbohydrates. The reaction requires reducing equivalents and will utilize either oxygen or hydrogen peroxide as a cosubstrate. Two key mechanistic questions are addressed here: 1) How does the enzyme regulate the timely and tightly controlled electron delivery to the mononuclear copper active site, especially when bound substrate occludes the active site? and 2) How does this electron delivery differ when utilizing oxygen or hydrogen peroxide as a cosubstrate? Using a computational approach, potential paths of electron transfer (ET) to the active site copper ion were identified in a representative AA9 family PMO from (PMO9E).

α/β hydrolase domain-containing protein 1 acts as a lysolipid lipase and is involved in lipid droplet formation.

Lipid droplets (LDs) are the major sites of lipid and energy homeostasis. However, few LD biogenesis proteins have been identified. Using model microalga , we show that ABHD1, an α/β-hydrolase domain-containing protein, is localized to the LD surface and stimulates LD formation through two actions: one enzymatic and one structural.

Wireless power-up and readout from a label-free biosensor.

Wearable and implantable biosensors have rapidly entered the fields of health and biomedicine to diagnose diseases and physiological monitoring. The use of wired medical devices causes surgical complications, which can occur when wires break, become infected, generate electrical noise, and are incompatible with implantable applications. In contrast, wireless power transfer is ideal for biosensing applications since it does not necessitate direct connections between measurement tools and sensing systems, enabling remote use of the biosensors.

Harnessing nature's palette: Exploring photosynthetic pigments for sustainable biotechnology.

Photosynthetic microorganisms such as cyanobacteria, microalgae, and anoxygenic phototrophic bacteria (APB) have emerged as sustainable and economic biotechnology platforms due to their ability to transform energy from light into chemicals through photosynthesis. The light is absorbed by photosynthetic pigment-protein antenna complexes which are composed of pigments such as bacteriochlorophylls (BChl) and carotenoids in APB, and chlorophylls (Chl), phycobiliproteins (PBP), and carotenoids in cyanobacteria and microalgae. These photosynthetic pigments are essential in the physiology of photosynthetic microorganisms and offer significant health benefits due to their potent antioxidant activity, with properties that include anticancer, antiaging, antiproliferative, anti-inflammatory, and neuroprotective effects.

Phylogenomic insights into the taxonomy, ecology, and mating systems of the lorchel family Discinaceae (Pezizales, Ascomycota).

Lorchels, also known as false morels (Gyromitra sensu lato), are iconic due to their brain-shaped mushrooms and production of gyromitrin, a deadly mycotoxin. Molecular phylogenetic studies have hitherto failed to resolve deep-branching relationships in the lorchel family, Discinaceae, hampering our ability to settle longstanding taxonomic debates and to reconstruct the evolution of toxin production. We generated 75 draft genomes from cultures and ascomata (some collected as early as 1960), conducted phylogenomic analyses using 1542 single-copy orthologs to infer the early evolutionary history of lorchels, and identified genomic signatures of trophic mode and mating-type loci to better understand lorchel ecology and reproductive biology.

Reduced lipid and glucose oxidation and reduced lipid synthesis in AMPKα2 myotubes.

Adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK) plays a crucial role in regulation of metabolic homeostasis. To understand the role of the catalytic α2 subunit of AMPK in skeletal muscle energy metabolism, myotube cultures were established from and mice. Myotubes from mice had lower basal oleic acid and glucose oxidation compared to myotubes from mice.

Highly accurate Korean draft genomes reveal structural variation highlighting human telomere evolution.

Given the presence of highly repetitive genomic regions such as subtelomeric regions, understanding human genomic evolution remains challenging. Recently, long-read sequencing technology has facilitated the identification of complex genetic variants, including structural variants (SVs), at the single-nucleotide level. Here, we resolved SVs and their underlying DNA damage-repair mechanisms in subtelomeric regions, which are among the most uncharted genomic regions.

Combination of anaerobic digestion and sludge biochar for bioenergy conversion: Estimation and evaluation of energy production, CO emission, and cost analysis.

Waste-to-energy technologies involve the conversion of several wastes to useful energy forms like biogas and biochar, which include biological and thermochemical processes, as well as the combination of both systems. Assessing the economic and environmental impacts is an important step to integrate sustainability and economic viability at anaerobic digestion systems and its waste management. Energy production, CO emissions, cost analysis, and an overall process evaluation were conducted, relying on findings from both laboratory and pilot-scale experiments.