Extracted Eucalyptus globulus Bark Fiber as a Potential Substrate for Pinus radiata and Quillaja saponaria Germination

This study aimed to explore alternative substrates for growing forest species using eucalyptus bark. It evaluated the potential of extracted Eucalyptus globulus fiber bark as a substitute for commercial growing media such as coconut fiber, moss, peat, and compost pine. We determined the physicochemical parameters of the growing media, the germination rate, and the mean fresh and dry weights of seedlings. We used the Munoo-Liisa Vitality Index (MLVI) test to evaluate the phytotoxicity of the bark alone and when mixed with commercial substrates. Generally, the best mixture for seed growth was 75% extracted eucalyptus bark fiber and 25% commercial substrates. In particular, the 75E-25P (peat) mixture is a promising substitute for seedling growth of Pinus radiata, achieving up to 3-times higher MLVI than the control peat alone. For Quillaja saponaria, the best growth substrate was the 50E-50C (coconut fiber) mixture, which had the most significant MLVI values (127%). We added chitosan and alginate-encapsulated fulvic acid phytostimulants to improve the performance of the substrate mixtures. The fulvic acid, encapsulated or not, significantly improved MLVI values in Q. saponaria species and P. radiata in concentrations between 0.05 and 0.1% w/v. This study suggests that mixtures with higher levels of extracted fiber are suitable for growing forest species, thus promoting the application of circular economy principles in forestry.

Prior acute exercise restores postprandial fat oxidation in active cannabis users

Data suggest cannabis users have similar or lower levels of blood lipids compared to nonusers. However, the extent to which cannabis users experience postprandial lipemia is not known. Eleven cannabis users and 11 nonusers completed either rest or 1 h of exercise at their ventilatory threshold the evening before a meal tolerance test (MTT). Substrate oxidation, blood pressure, and capillary blood were obtained before and every 30-60 min post-meal for 3 h. Linear mixed models were utilized to examine differences in variables between groups, conditions, across time, and their interactions. Exercise led to increased fat oxidation post-MTT (p < 0.05), with cannabis users exhibiting higher AUC compared to the control trial (p < 0.05). Exercise also caused significantly lower levels of triglycerides (p < 0.05). Metabolic flexibility was improved in cannabis users in the exercise trial only (p < 0.05). No effect of group, trial, or interactions were detected for other variables of interest (all p > 0.05). This study indicated that prior exercise improves lipid metabolism in cannabis users and nonusers after a high-fat meal test. Cannabis users appear sensitive to the effects of exercise. Future studies should incorporate additional meals and variables related to cardiovascular health and metabolism.

Almond By-Products Substrates as Sustainable Amendments for Green Bean Cultivation

Almond processing generates a high quantity of by-products, presenting the untapped potential for alternative applications and improved sustainability in production. This study aimed to evaluate whether the incorporation of almond by-products (hulls/shells) can improve the biochemical characteristics of green bean pods when used as an alternative to traditional growing media in green bean plants. Four substrates were prepared: the Control substrate (C): 70% peat + 30% perlite; substrate (AS): 70% peat + 30% shells; substrate (AH): 70% peat + 30% perlite + 1 cm hulls as mulch; substrate (MIX): 70% peat + 15% shells + 15% hulls. Plants were grown in each of these substrates and subjected to two irrigation levels, 100% and 50% of their water-holding capacity. Biochemical parameters (photosynthetic pigments, total phenolics, flavonoids, ortho-diphenols, soluble proteins, antioxidant capacity) and color were evaluated in the harvested pods. Results showed that pods from plants growing in AH substrate presented statistically significant higher values in their total phenolic content, while AS and MIX substrates did not reveal significant benefits. Summarily, this study highlights the potential of almond hulls as a promising medium for green bean cultivation, particularly when employed as mulch. Further research is recommended to gain a more comprehensive understanding of the application of almond by-products as natural fertilizers/mulch.

The MOVECLIM - AZORES project: Bryophytes from Pico Island along an elevation gradient

Background

In September 2012, a comprehensive survey of Pico Island was conducted along an elevational transect, starting at Manhenha (10 m a.s.l.) and culminating at the Pico Mountain caldera (2200 m a.s.l.). The primary objective was to systematically inventory the bryophytes inhabiting the best-preserved areas of native vegetation environments. Twelve sites were selected, each spaced at 200 m elevation intervals. Within each site, two 10 m x 10 m plots were established in close proximity (10-15 m apart). Within these plots, three 2 m x 2 m quadrats were randomly selected and sampled for bryophytes using microplots measuring 10 cm x 5 cm, which were then collected into paper bags. Six substrates were surveyed in each quadrat: rock, soil, humus, organic matter, tree bark and leaves/fronds. Three replicates were obtained from all substrates available and colonised by bryophytes, resulting in a maximum of 18 microplots per quadrat, 54 microplots per plot, 108 microplots per site, and a total of 1296 microplots across the 12 sites on Pico Island.

New information

Two-thirds of the maximum expected number of microplots (n = 878; 67.75%) were successfully collected, yielding a total of 4896 specimens. The vast majority (n = 4869) were identified at the species/subspecies level. The study identified a total of 70 moss and 71 liverwort species or subspecies. Elevation levels between 600-1000 m a.s.l., particularly in the native forest plots, exhibited both a higher number of microplots and greater species richness. This research significantly enhanced our understanding of Azorean bryophyte diversity and distribution, contributing valuable insights at both local and regional scales. Notably, two new taxa for the Azores were documented during the MOVECLIM study, namely the pleurocarpous mosses Antitrichiacurtipendula and Isotheciuminterludens.

Evaluation of Rice Straw, Corncob, and Soybean Straw as Substrates for the Cultivation of Lepista sordida

Lepista sordida is a type of high-quality rare edible and medicinal mushroom, and its research boom is just beginning. More than 80 million tons of grain crop residues are produced each year in Heilongjiang Province. To realize the exploration and utilization of wild L. sordida mushrooms and also provide a theoretical support for the high-value utilization of these resources in Heilongjiang Province, we evaluated the cultivation of L. sordida mushrooms using rice straw, corncob, and soybean straw as substrates. L. sordida grew on all three substrates, and the biological efficiency and yield of the mushrooms grown on soybean straw and corncob were 32.33 ± 1.78% and 4.20 ± 0.23 kg m-2, and 30.15 ± 0.93% and 3.92 ± 0.12 kg m-2, respectively, which increased by 9.38% and 2.08% compared with that on the rice straw substrate with 3.84 ± 0.12 kg m-2 and 29.56 ± 0.89%. The time it took for the mycelia to colonize and initiate primordia on the soybean straw substrate was 22.33 ± 0.58 d and 19.67 ± 0.58 d, respectively, which was delayed by 2 d and 3 d compared with that on the rice straw substrate with 20.67 ± 2.08 d and 16.33 ± 0.58 d, respectively. The fruiting bodies grown on corncob and soybean straw substrates were relatively larger than those on the rice straw substrate. The highest amount of crude protein was 57.38 ± 0.08 g 100 g-1, and the lowest amount of crude polysaccharide was 6.03 ± 0.01 g 100 g-1. They were observed on mushrooms collected from the corncob substrate. The contents of the heavy metal mercury, lead, arsenic, and cadmium in the fruiting bodies grown on each substrate were within the national safety range.

Phosphatase specificity principles uncovered by MRBLE:Dephos and global substrate identification

Phosphoprotein phosphatases (PPPs) regulate major signaling pathways, but the determinants of phosphatase specificity are poorly understood. This is because methods to investigate this at scale are lacking. Here, we develop a novel in vitro assay, MRBLE:Dephos, that allows multiplexing of dephosphorylation reactions to determine phosphatase preferences. Using MRBLE:Dephos, we establish amino acid preferences of the residues surrounding the dephosphorylation site for PP1 and PP2A-B55, which reveals common and unique preferences. To compare the MRBLE:Dephos results to cellular substrates, we focused on mitotic exit that requires extensive dephosphorylation by PP1 and PP2A-B55. We use specific inhibition of PP1 and PP2A-B55 in mitotic exit lysates coupled with phosphoproteomics to identify more than 2,000 regulated sites. Importantly, the sites dephosphorylated during mitotic exit reveal key signatures that are consistent with MRBLE:Dephos. Furthermore, integration of our phosphoproteomic data with mitotic interactomes of PP1 and PP2A-B55 provides insight into how binding of phosphatases to substrates shapes dephosphorylation. Collectively, we develop novel approaches to investigate protein phosphatases that provide insight into mitotic exit regulation.

P450Rdb: a manually curated database of reactions catalyzed by cytochrome P450 enzymes

INTRODUCTION

Cytochrome P450 enzymes (P450s) are recognized as the most versatile catalysts worldwide, playing vital roles in numerous biological metabolism and biosynthesis processes across all kingdoms of life. Despite the vast number of P450 genes available in databases (over 300,000), only a small fraction of them (less than 0.2%) have undergone functional characterization.

OBJECTIVES

To provide a convenient platform with abundant information on P450s and their corresponding reactions, we introduce the P450Rdb database, a manually curated resource compiles literature-supported reactions catalyzed by P450s.

METHODS

All the P450s and Reactions were manually curated from the literature and known databases. Subsequently, the P450 reactions organized and categorized according to their chemical reaction type and site. The website was developed using HTML and PHP languages, with the MySQL server utilized for data storage.

RESULTS

The current version of P450Rdb catalogs over 1,600 reactions, involving more than 590 P450s across a diverse range of over 200 species. Additionally, it offers a user-friendly interface with comprehensive information, enabling easy querying, browsing, and analysis of P450s and their corresponding reactions. P450Rdb is free available at http://www.cellknowledge.com.cn/p450rdb/.

CONCLUSIONS

We believe that this database will significantly promote structural and functional research on P450s, thereby fostering advancements in the fields of natural product synthesis, pharmaceutical engineering, biotechnological applications, agricultural and crop improvement, and the chemical industry.

Crucial roles of the BRCA1-BARD1 E3 ubiquitin ligase activity in homology-directed DNA repair

The tumor-suppressor breast cancer 1 (BRCA1) in complex with BRCA1-associated really interesting new gene (RING) domain 1 (BARD1) is a RING-type ubiquitin E3 ligase that modifies nucleosomal histone and other substrates. The importance of BRCA1-BARD1 E3 activity in tumor suppression remains highly controversial, mainly stemming from studying mutant ligase-deficient BRCA1-BARD1 species that we show here still retain significant ligase activity. Using full-length BRCA1-BARD1, we establish robust BRCA1-BARD1-mediated ubiquitylation with specificity, uncover multiple modes of activity modulation, and construct a truly ligase-null variant and a variant specifically impaired in targeting nucleosomal histones. Cells expressing either of these BRCA1-BARD1 separation-of-function alleles are hypersensitive to DNA-damaging agents. Furthermore, we demonstrate that BRCA1-BARD1 ligase is not only required for DNA resection during homology-directed repair (HDR) but also contributes to later stages for HDR completion. Altogether, our findings reveal crucial, previously unrecognized roles of BRCA1-BARD1 ligase activity in genome repair via HDR, settle prior controversies regarding BRCA1-BARD1 ligase functions, and catalyze new efforts to uncover substrates related to tumor suppression.

Teline monspessulana Can Harm the Chilean Native Tree Nothofagus obliqua: Effects on Germination and Initial Growth

Teline monspessulana is highly invasive in several countries around the world. This species pressurizes and displaces several native and endemic tree species in south-central Chile such as Nothofagus obliqua, the native species of greatest timber interest. We determined the effects induced by allelochemical stress of T. monspessulana on N. obliqua germination and initial growth. Germination was evaluated under in vitro conditions and in natural substrate obtained from sites inhabited by N. obliqua and from nearby areas invaded by T. monspessulana. Controls irrigated with tap water and treatments with aqueous extracts of aerial organs of the invasive species were used. Morphometric and morphological variables were evaluated, and the composition of alkaloids and phenols from the plant organs used for the aqueous extracts was determined. The substrates were also chemically characterized. Allelochemicals synthesized by T. monspessulana caused germination and growth inhibition and tissue-level alterations, as well as leaf and root damage in N. obliqua seedlings. In the aerial organs of T. monspessulana, the quinolizidine alkaloids aphylline, caulophylline, anagyrine, and sophocarpine were mainly detected. In addition, 21 phenolic compounds were identified, including gallic acid, vanillic acid, chlorogenic acid, p-coumaric acid, and quercetin. The phytotoxic potential of T. monspessulana can compromise the natural multiplication of N. obliqua and its survival from its first phenological stages. This interdisciplinary study model facilitated the clarification of the plant-plant relationship mediated by allelochemicals. The model can be replicated to investigate other interspecific interactions between invasive and native species.

Optimization of Production Methods for Black Soldier Fly Larvae (Hermetia illucens L.) in Burkina Faso

Larvae of Hermetia illucens are a valuable source of protein for animal feed that can be produced by exposing animal and agro-industrial wastes to naturally occurring flies. The objective of this study was to improve techniques for obtaining H. illucens larvae to feed livestock in Burkina Faso. An experiment was conducted to determine the most favourable substrates and seasons for larval production. The substrates used were poultry manure, local beer waste, local beer waste mixed with poultry manure, cottonseed cake, and industrial brewery waste mixed with poultry manure. The production of larvae was carried out in four different seasons. The effect of the container's oviposition area (0.07 m2, 0.09 m2, and 0.11 m2) and the type of container (terracotta, plastic, and iron) on larval production was also assessed. The produced larval biomass was high during, or just after, the rainy season but very low during the cool dry and hot dry seasons. Yields were higher with local beer waste mixed with poultry manure followed by local beer waste and cottonseed cake. The average mass of H. illucens larvae increased slightly with the oviposition area for the same amount of substrate. Iron and terracotta containers provided better results than plastic containers. The suitability of this production method for H. illucens larvae production is discussed.

Fungal Glycosidases in Sporothrix Species and Candida albicans

Glycoside hydrolases (GHs) are enzymes that participate in many biological processes of fungi and other organisms by hydrolyzing glycosidic linkages in glycosides. They play fundamental roles in the degradation of carbohydrates and the assembly of glycoproteins and are important subjects of studies in molecular biology and biochemistry. Based on amino acid sequence similarities and 3-dimensional structures in the carbohydrate-active enzyme (CAZy), they have been classified in 171 families. Members of some of these families also exhibit the activity of trans-glycosydase or glycosyl transferase (GT), i.e., they create a new glycosidic bond in a substrate instead of breaking it. Fungal glycosidases are important for virulence by aiding tissue adhesion and colonization, nutrition, immune evasion, biofilm formation, toxin release, and antibiotic resistance. Here, we review fungal glycosidases with a particular emphasis on Sporothrix species and C. albicans, two well-recognized human pathogens. Covered issues include a brief account of Sporothrix, sporotrichosis, the different types of glycosidases, their substrates, and mechanism of action, recent advances in their identification and characterization, their potential biotechnological applications, and the limitations and challenges of their study given the rather poor available information.

Performance and Durability of Non-Stick Coatings Applied to Stainless Steel: Subtractive vs. Additive Manufacturing

This study compares subtractive manufacturing (SM) and additive manufacturing (AM) techniques in the production of stainless-steel parts with non-stick coatings. While subtractive manufacturing involves the machining of rolled products, additive manufacturing employs the FFF (fused filament fabrication) technique with metal filament and sintering. The applied non-stick coatings are commercially available and are manually sprayed with a spray gun, followed by a curing process. They are an FEP (fluorinated ethylene propylene)-based coating and a sol-gel ceramic coating. Key properties such as surface roughness, water droplet sliding angle, adhesion to the substrate and wear resistance were examined using abrasive blasting techniques. In the additive manufacturing process, a higher roughness of the samples was detected. In terms of sliding angle, variations were observed in the FEP-based coatings and no variations were observed in the ceramic coatings, with a slight increase for FEP in AM. In terms of adhesion to the substrate, the ceramic coatings applied in the additive process showed a superior behavior to that of subtractive manufacturing. On the other hand, FEP coatings showed comparable results for both techniques. In the wear resistance test, ceramic coatings outperformed FEP coatings for both techniques. In summary, additive manufacturing of non-stick coatings on stainless steel showed remarkable advantages in terms of roughness, adhesion and wear resistance compared to the conventional manufacturing approach. These results are of relevance in fields such as medicine, food industry, chemical industry and marine applications.

Three-Phase Motor Inverter and Current Sensing GaN Power IC

A three-phase GaN-based motor inverter IC with three integrated phase current mirror sensors (sense-FETs or sense-HEMTs, 1200:1 ratio), a temperature sensor, and an amplifier is presented and experimentally operated. The three low-side currents are read out by virtual grounding transimpedance amplifiers. A modified summed DC current readout circuit using only one amplifier is also discussed. During continuous 24 V motor operation with space-vector pulse width modulation (SVPWM), the sensor signal is measured and a bidirectional measurement capability is verified. The measured risetime of the sensor signal is 51 ns, indicating around 7 MHz bandwidth (without intentional optimization for high bandwidth). The IC is operated up to 32 V on DC-biased semi-floating substrate to limit negative static back-gating of the high-side transistors to around -7% of the DC-link voltage. Analysis of the capacitive coupling from the three switch-nodes to the substrate is calculated for SVPWM based on capacitance measurement, resulting in four discrete semi-floating substrate voltage levels, which is experimentally verified. Integrated advanced power converter topologies with sensors improve the power density of power electronics applications, such as for low-voltage motor drive.

Inhibiting Polyamide Intrusion of Thin Film Composite Membranes: Strategies and Environmental Implications

Thin film composite polyamide (TFC) nanofiltration (NF) membranes represent extensive applications at the water-energy-environment nexus, which motivates unremitting efforts to explore membranes with higher performance. Intrusion of polyamide into substrate pores greatly restricts the overall membrane permeance because of the excessive hydraulic resistance, while the effective inhibition of intrusion remains technically challenging. Herein, we propose a synergetic regulation strategy of pore size and surface chemical composition of the substrate to optimize selective layer structure, achieving the inhibition of polyamide intrusion effective for the membrane separation performance enhancement. Although reducing the pore size of the substrate prevented polyamide intrusion at the intrapore, the membrane permeance was adversely affected due to the exacerbated "funnel effect". Optimizing the polyamide structure via surface chemical modification of the substrate, where reactive amino sites were in situ introduced by the ammonolysis of polyethersulfone substrate, allowed for maximum membrane permeance without reducing the substrate pore size. The optimal membrane exhibited excellent water permeance, ion selectivity, and emerging contaminants removal capability. The accurate optimization of selective layer is anticipated to provide a new avenue for the state-of-the-art membrane fabrication, which opens opportunities for promoting more efficient membrane-based water treatment applications.

[Interaction of DNA Methyltransferase Dnmt3a with Phosphorus Analogs of S-Adenosylmethionine and S-Adenosylhomocysteine]

Enzymatic methyltransferase reactions are of crucial importance for cell metabolism. S-Adenosyl-L-methionine (AdoMet) is a main donor of the methyl group. DNA, RNA, proteins, and low-molecular-weight compounds are substrates of methyltransferases. In mammals, DNA methyltransferase Dnmt3a de novo methylates the C5 position of cytosine residues in CpG sequences in DNA. The methylation pattern is one of the factors that determine the epigenetic regulation of gene expression. Here, interactions with the catalytic domain of Dnmt3a was for the first time studied for phosphonous and phosphonic analogs of AdoMet and S-adenosyl-L-homocysteine (AdoHcy), in which the carboxyl group was substituted for respective phosphorus-containing group. These AdoMet analogs were shown to be substrates of Dnmt3a, and the methylation efficiency was only halved as compared with that of natural AdoMet. Both phosphorus-containing analogs of AdoHcy, which is a natural methyltransferase inhibitor, showed similar inhibitory activities toward Dnmt3a and were approximately four times less active than AdoHcy. The finding that the phosphonous and phosphonic analogs are similar in activity was quite unexpected because the geometry and charge of their phosphorus-containing groups differ substantially. The phosphorus-containing analogs of AdoMet and AdoHcy are discussed as promising tools for investigation of methyltransferases.

Underwater Bonding with a Biobased Adhesive from Tannic Acid and Zein Protein

Herein are presented several adhesive formulations made from zein protein and tannic acid that can bind to a wide range of surfaces underwater. Higher performance comes from more tannic acid than zein, whereas dry bonding required the opposite case of more zein than tannic acid. Each adhesive works best in the environment that it was designed and optimized for. We show underwater adhesion experiments done on different substrates and in different waters (sea water, saline solution, tap water, deionized water). Surprisingly, the water type does not influence the performance to a great deal but the substrate type does. An additional unexpected result was bond strength increasing over time when exposed to water, contradicting general experiments of working with glues. Initial adhesion underwater was stronger compared to benchtop adhesion, suggesting that water helps to make the glue stick. Temperature effects were determined, indicating maximum bonding at about 30 °C and then another increase at higher temperatures. Once the adhesive was placed underwater, a protective skin formed on the surface, keeping water from entering the rest of the material immediately. The shape of the adhesive could be manipulated easily and, once in place, the skin could be broken to induce faster bond formation. Data indicated that underwater adhesion was predominantly induced by tannic acid, cross-linking within the bulk for adhesion and to the substrate surfaces. The zein protein provided a less polar matrix that helped to keep the tannic acid molecules in place. These studies provide new plant-based adhesives for working underwater and for creating a more sustainable environment.

Unlocking the Mysteries of Alpha-N-Terminal Methylation and its Diverse Regulatory Functions

Protein post-translation modifications (PTMs) are a critical regulatory mechanism of protein function. Protein α-N-terminal (Nα) methylation is a conserved PTM across prokaryotes and eukaryotes. Studies of the Nα methyltransferases responsible for Να methylation and their substrate proteins have shown that the PTM involves diverse biological processes, including protein synthesis and degradation, cell division, DNA damage response, and transcription regulation. This review provides an overview of the progress toward the regulatory function of Να methyltransferases and their substrate landscape. More than 200 proteins in humans and 45 in yeast are potential substrates for protein Nα methylation based on the canonical recognition motif, XP[KR]. Based on recent evidence for a less stringent motif requirement, the number of substrates might be increased, but further validation is needed to solidify this concept. A comparison of the motif in substrate orthologs in selected eukaryotic species indicates intriguing gain and loss of the motif across the evolutionary landscape. We discuss the state of knowledge in the field that has provided insights into the regulation of protein Να methyltransferases and their role in cellular physiology and disease. We also outline the current research tools that are key to understanding Να methylation. Finally, challenges are identified and discussed that would aid in unlocking a system-level view of the roles of Να methylation in diverse cellular pathways.

The Pleiotropic Ubiquitin-Specific Peptidase 16 and Its Many Substrates

Ubiquitin-specific peptidase 16 (USP16) is a deubiquitinase that plays a role in the regulation of gene expression, cell cycle progression, and various other functions. It was originally identified as the major deubiquitinase for histone H2A and has since been found to deubiquitinate a range of other substrates, including proteins from both the cytoplasm and nucleus. USP16 is phosphorylated when cells enter mitosis and dephosphorylated during the metaphase/anaphase transition. While much of USP16 is localized in the cytoplasm, separating the enzyme from its substrates is considered an important regulatory mechanism. Some of the functions that USP16 has been linked to include DNA damage repair, immune disease, tumorigenesis, protein synthesis, coronary artery health, and male infertility. The strong connection to immune response and the fact that multiple oncogene products are substrates of USP16 suggests that USP16 may be a potential therapeutic target for the treatment of certain human diseases.

Analysis of Nanostar Reshaping Kinetics for Optimal Substrate Fabrication

Gold nanostars (NS) are emerging as a versatile tool in surface-enhanced Raman scattering (SERS) applications because of their wide localized surface plasmon resonance (LSPR) tunability, simple synthesis procedure, and high SERS enhancement. These particles are commonly used in solutions with a stabilizing coating shell (e.g., thiolated molecules or silver shell). However, coatings cannot be used for the fabrication of SERS substrates as the NS have to interact with the substrate planar surface. Without coating, NS have been observed to change over time, leading to a hypochromic shift of the LSPR. To understand this shift, we synthesized surfactant-free gold NS with different spike morphologies and investigated their reshaping morphology and kinetics. Using TEM, the NS sharp spike features were observed to reshape over time. The kinetics of this process were analyzed and determined by monitoring the LSPR, which was observed to follow an exponential decay over time. We used an empirical fit for the LSPR-shift data as a function of time, which permits to predict the LSPR at a specific time based only on the initial LSPR (independently of the initial spike morphology). We show the effect of the LSPR on the SERS signal for the NS and how the SERS signal correlated to our prediction. Finally, we evaluated our approach by fabricating SERS substrates with immobilized NS and collecting the reflectance spectra. We were able to predict the substrate LSPR and aim for an optimal LSPR with an average 3% deviation. These new insights on NS reshaping can permit the fabrication of NS-based substrates with desirable optical/plasmonic properties.

[Effects of Different Colored Polycarbonate Plastics on Growth and Community Structure of Periphytic Algae]

Periphytic algae are important primary producers in water bodies, which play an important role in maintaining ecological function and water purification. Previous studies have shown that plastic is a good substrate for periphytic algae, and different plastic materials have different effects on the colonization of periphytic algae; however, there are few reports on the effects of plastic color on the growth of periphytic algae. In this study, polycarbonate plastic (PC) of various colors were used as the substrate to study the effects of different colors on the growth and community structure of periphytic algae by measuring the biomass, photosynthetic activity, and community composition. The results showed that the growth of periphytic algae was inhibited by the brown PC plastic, and the contents of chlorophyll a and dry weight in this group were significantly lower than those in other groups. Green PC plastic inhibited the photosynthetic activity of periphytic algae, and the actual photosynthetic efficiency (Yield) of the group was significantly lower than that of the other groups. The influence of PC plastic with different colors on periphytic algae occurred mainly in the early colonization/development stage but was not significant in the late community maturity stage. On day seven of the experiment, the community composition of periphytic algae was significantly different between the transparent PC plastic group and the green PC plastic group. By contrast, on days 25 and 40, there were no significant differences in the community structure of periphytic algae. In the early stage of the experiment, the dominant genus was Pseudoranea (Cyanophyta), and in the middle and mature stages, the dominant genus was Mougeotia (Chlorophyta). In this study, the effects of different colors of polycarbonate plastics on periphytic algae were investigated, which provided new insights for selecting suitable substrates for water pollution treatment by using periphyton biotechnology.

Cellular functions of the ClpP protease impacting bacterial virulence

Proteostasis mechanisms significantly contribute to the sculpting of the proteomes of all living organisms. ClpXP is a central AAA+ chaperone-protease complex present in both prokaryotes and eukaryotes that facilitates the unfolding and subsequent degradation of target substrates. ClpX is a hexameric unfoldase ATPase, while ClpP is a tetradecameric serine protease. Substrates of ClpXP belong to many cellular pathways such as DNA damage response, metabolism, and transcriptional regulation. Crucially, disruption of this proteolytic complex in microbes has been shown to impact the virulence and infectivity of various human pathogenic bacteria. Loss of ClpXP impacts stress responses, biofilm formation, and virulence effector protein production, leading to decreased pathogenicity in cell and animal infection models. Here, we provide an overview of the multiple critical functions of ClpXP and its substrates that modulate bacterial virulence with examples from several important human pathogens.

Explicit Thermal Resistance Model of Self-Heating Effects of AlGaN/GaN HEMTs with Linear and Non-Linear Thermal Conductivity

We presented an explicit empirical model of the thermal resistance of AlGaN/GaN high-electron-mobility transistors on three distinct substrates, including sapphire, SiC, and Si. This model considered both a linear and non-linear thermal resistance model of AlGaN/GaN HEMT, the thickness of the host substrate layers, and the gate length and width. The non-linear nature of channel temperature-visible at the high-power dissipation stage-along with linear dependency, was constructed within a single equation. Comparisons with the channel temperature measurement procedure (DC) and charge-control-based device modeling were performed to verify the model's validity, and the results were in favorable agreement with the observed model data, with only a 1.5% error rate compared to the measurement data. An agile expression for the channel temperature is also important for designing power devices and monolithic microwave integrated circuits. The suggested approach provides several techniques for investigation that could otherwise be impractical or unattainable when utilizing time-consuming numerical simulations.

Cesium Lead Bromide Nanocrystals: Synthesis, Modification, and Application to O2 Sensing

The fluorescence intensity of inorganic CsPbBr₃ (CPB) perovskite nanocrystals (NCs) decreases in the presence of O₂. In this study, we synthesized CPB NCs with various shapes and sizes for use as optical gas sensing materials. We fabricated O₂ gas sensors from the various CPB NCs on several porous and nonporous substrates and examined the effects of the NC shapes and aggregate sizes and the substrate pore size on the device response. Our sensor fabricated from CPB nanocrystals on a porous substrate exhibited the highest response; the porous substrate allowed the rapid diffusion of O₂ such that the NC surface was exposed effectively to the gas. Thus, the interfacial interaction between NC surfaces and substrates is a critical factor for consideration when preparing gas sensors with a high response.

Atypical Substrates of the Organic Cation Transporter 1

The human organic cation transporter 1 (OCT1) is expressed in the liver and mediates hepatocellular uptake of organic cations. However, some studies have indicated that OCT1 could transport neutral or even anionic substrates. This capability is interesting concerning protein-substrate interactions and the clinical relevance of OCT1. To better understand the transport of neutral, anionic, or zwitterionic substrates, we used HEK293 cells overexpressing wild-type OCT1 and a variant in which we changed the putative substrate binding site (aspartate474) to a neutral amino acid. The uncharged drugs trimethoprim, lamivudine, and emtricitabine were good substrates of hOCT1. However, the uncharged drugs zalcitabine and lamotrigine, and the anionic levofloxacin, and prostaglandins E2 and F2α, were transported with lower activity. Finally, we could detect only extremely weak transport rates of acyclovir, ganciclovir, and stachydrine. Deleting aspartate474 had a similar transport-lowering effect on anionic substrates as on cationic substrates, indicating that aspartate474 might be relevant for intra-protein, rather than substrate-protein, interactions. Cellular uptake of the atypical substrates by the naturally occurring frequent variants OCT1*2 (methionine420del) and OCT1*3 (arginine61cysteine) was similarly reduced, as it is known for typical organic cations. Thus, to comprehensively understand the substrate spectrum and transport mechanisms of OCT1, one should also look at organic anions.

Materials Perspectives of Integrated Plasmonic Biosensors

With the growing need for portable, compact, low-cost, and efficient biosensors, plasmonic materials hold the promise to meet this need owing to their label-free sensitivity and deep light-matter interaction that can go beyond the diffraction limit of light. In this review, we shed light on the main physical aspects of plasmonic interactions, highlight mainstream and future plasmonic materials including their merits and shortcomings, describe the backbone substrates for building plasmonic biosensors, and conclude with a brief discussion of the factors affecting plasmonic biosensing mechanisms. To do so, we first observe that 2D materials such as graphene and transition metal dichalcogenides play a major role in enhancing the sensitivity of nanoparticle-based plasmonic biosensors. Then, we identify that titanium nitride is a promising candidate for integrated applications with performance comparable to that of gold. Our study highlights the emerging role of polymer substrates in the design of future wearable and point-of-care devices. Finally, we summarize some technical and economic challenges that should be addressed for the mass adoption of plasmonic biosensors. We believe this review will be a guide in advancing the implementation of plasmonics-based integrated biosensors.

Major implications of single nucleotide polymorphisms in human carboxylesterase 1 on substrate bioavailability

The number of studies and reviews conducted for the Carboxylesterase gene is limited in comparison with other enzymes. Carboxylesterase (CES) gene or human carboxylesterases (hCES) is a multigene protein belonging to the α/β-hydrolase family. Over the last decade, two major carboxylesterases (CES1 and CES2), located at 16q13-q22.1 on human chromosome 16 have been extensively studied as important mediators in the metabolism of a wide range of substrates. hCES1 is the most widely expressed enzyme in humans, and it is found in the liver. In this review, details regarding CES1 substrates include both inducers (e.g. Rifampicin) and inhibitors (e.g. Enalapril, Diltiazem, Simvastatin) and different types of hCES1 polymorphisms (nsSNPs) such as rs2244613 and rs71647871. along with their effects on various CES1 substrates were documented. Few instances where the presence of nsSNPs exerted a positive influence on certain substrates which are hydrolyzed via hCES1, such as anti-platelets like Clopidogrel when co-administered with other medications such as angiotensin-converting enzyme (ACE) inhibitors were also recorded. Remdesivir, an ester prodrug is widely used for the treatment of COVID-19, being a CES substrate, it is a potent inhibitor of CES2 and is hydrolyzed via CES1. The details provided in this review could give a clear-cut idea or information that could be used for further studies regarding the safety and efficacy of CES1 substrate.

Secretion into Milk of the Main Metabolites of the Anthelmintic Albendazole Is Mediated by the ABCG2/BCRP Transporter

Albendazole (ABZ) is an anthelmintic with a broad-spectrum activity, widely used in human and veterinary medicine. ABZ is metabolized in all mammalian species to albendazole sulfoxide (ABZSO), albendazole sulfone (ABZSO₂) and albendazole 2-aminosulphone (ABZSO₂-NH₂). ABZSO and ABZSO₂ are the main metabolites detected in plasma and all three are detected in milk. The ATP-binding cassette transporter G2 (ABCG2) is an efflux transporter that is involved in the active secretion of several compounds into milk. Previous studies have reported that ABZSO was in vitro transported by ABCG2. The aim of this work is to correlate the in vitro interaction between ABCG2 and the other ABZ metabolites with their secretion into milk by this transporter. Using in vitro transepithelial assays with cells transduced with murine Abcg2 and human ABCG2, we show that ABZSO₂ and ABZSO₂-NH₂ are in vitro substrates of both. In vivo assays carried out with wild-type and Abcg2^-/- lactating female mice demonstrated that secretion into milk of these ABZ metabolites was mediated by Abcg2. Milk concentrations and milk-to-plasma ratio were higher in wild-type compared to Abcg2^-/- mice for all the metabolites tested. We conclude that ABZ metabolites are undoubtedly in vitro substrates of ABCG2 and actively secreted into milk by ABCG2.

Attributes of High-Performance Electron Transport Layers for Perovskite Solar Cells on Flexible PET versus on Glass

Electron transport layers (ETLs) play a fundamental role in perovskite solar cells (PSCs) through charge extraction. Here, we developed flexible PSCs on 12 different kinds of ETLs based on SnO₂. We show that ETLs need to be specifically developed for plastic substrates in order to attain 15% efficient flexible cells. Recipes developed for glass substrates do not typically transfer directly. Among all the ETLs, ZnO/SnO₂ double layers delivered the highest average power conversion efficiency of 14.6% (best cell 14.8%), 39% higher than that of flexible cells of the same batch based on SnO₂-only ETLs. However, the cells with a single ETL made of SnO₂ nanoparticles were found to be more stable as well as more efficient and reproducible than SnO₂ formed from a liquid precursor (SnO₂-LP). We aimed at increasing the understanding of what makes a good ETL on polyethylene terephthalate (PET) substrates. More so than ensuring electron transport (as seen from on-current and series resistance analysis), delivering high shunt resistances (R _SH) and lower recombination currents (I _off) is key to obtain high efficiency. In fact, R _SH of PSCs fabricated on glass was twice as large, and I _off was 76% lower in relative terms, on average, than those on PET, indicating considerably better blocking behavior of ETLs on glass, which to a large extent explains the differences in average PCE (+29% in relative terms for glass vs PET) between these two types of devices. Importantly, we also found a clear trend for all ETLs and for different substrates between the wetting behavior of each surface and the final performance of the device, with efficiencies increasing with lower contact angles (ranging between ∼50 and 80°). Better wetting, with average contact angles being lower by 25% on glass versus PET, was conducive to delivering higher-quality layers and interfaces. This cognizance can help further optimize flexible devices and close the efficiency gap that still exists with their glass counterparts.

Characterization of the class IIa histone deacetylases substrate specificity

Class IIa histone deacetylases (HDACs) play critical roles in vertebrate development and physiology, yet direct evidence of their intrinsic deacetylase activity and on substrate specificity regarding the peptide sequence is still missing. In this study, we designed and synthesized a combinatorial peptide library allowing us to profile class IIa HDACs sequence specificity at positions +3 through -3 from the central lysine modified by the well-accepted trifluoroacetyl function. Our data revealed a strong preference for bulky aromatic acids directly flanking the central trifluoroacetyllysine, while all class IIa HDACs disfavor positively charged residues and proline at the +1/-1 positions. The chemical nature of amino acid residues N-terminally to the central trifluoroacetyllysine has a more profound effect on substrate recognition as compared to residues located C-terminally. These findings were validated by designing selected favored and disfavored peptide sequences, with the favored ones are accepted with catalytic efficacy of 75 000 and 525 000 M^-1  s^-1 for HDAC7 and HDAC5, respectively. Results reported here could help in developing class IIa HDACs inhibitors and also in the search for new natural class IIa HDACs substrates.

Recombinant Porcine 12-Lipoxygenase Catalytic Domain: Effect of Inhibitors, Selectivity of Substrates and Specificity of Oxidation Products of Linoleic Acid

Lipoxygenase (LOX) is a major endogenous enzyme for the enzymatic oxidation of lipids during meat storage and meat product manufacturing. In the present work, some characteristics, i.e., effects of inhibitors, selectivity of substrates and specificity of oxidation products, were studied using recombinant porcine 12-lipoxygenase catalytic domain (12-LOXcd). Several familiar inhibitors were found inhibit the activity of recombinant porcine 12-LOXcd;nordihydroguaiaretic acid demonstrated the strongest inhibitory effect. The enzyme could oxygenate common polyunsaturated fatty acids, and showed the highest affinity to linoleic acid (LA), followed by arachidonic acid (AA), linolenic acid (LN) and docosahexaenoic acid (DHA). Under the action of porcine 12-LOXcd, LA was oxidized into four hydroxyoctadecadienoic acid (HODE) isomers, i.e., 13-Z,E-HODE, 13-E,E-HODE, 9-Z,E-HODE and 9-E,E-HODE. Variation of pH not only affected the yield of LA oxidation products, but also the distribution of HODE isomers. These results indicated that endogenous LOX activity and LOX-catalyzed lipid oxidation can be regulated during meat storage and meat product manufacturing.

A PON for All Seasons: Comparing Paraoxonase Enzyme Substrates, Activity and Action including the Role of PON3 in Health and Disease

Paraoxonases (PONs) are a family of hydrolytic enzymes consisting of three members, PON1, PON2, and PON3, located on human chromosome 7. Identifying the physiological substrates of these enzymes is necessary for the elucidation of their biological roles and to establish their applications in the biomedical field. PON substrates are classified as organophosphates, aryl esters, and lactones based on their structure. While the established native physiological activity of PONs is its lactonase activity, the enzymes’ exact physiological substrates continue to be elucidated. All three PONs have antioxidant potential and play an important anti-atherosclerotic role in several diseases including cardiovascular diseases. PON3 is the last member of the family to be discovered and is also the least studied of the three genes. Unlike the other isoforms that have been reviewed extensively, there is a paucity of knowledge regarding PON3. Thus, the current review focuses on PON3 and summarizes the PON substrates, specific activities, kinetic parameters, and their association with cardiovascular as well as other diseases such as HIV and cancer.

Mitogen-Activated Protein Kinase and Substrate Identification in Plant Growth and Development

Mitogen-activated protein kinases (MAPKs) form tightly controlled signaling cascades that play essential roles in plant growth, development, and defense response. However, the molecular mechanisms underlying MAPK cascades are still very elusive, largely because of our poor understanding of how they relay the signals. The MAPK cascade is composed of MAPK, MAPKK, and MAPKKK. They transfer signals through the phosphorylation of MAPKKK, MAPKK, and MAPK in turn. MAPKs are organized into a complex network for efficient transmission of specific stimuli. This review summarizes the research progress in recent years on the classification and functions of MAPK cascades under various conditions in plants, especially the research status and general methods available for identifying MAPK substrates, and provides suggestions for future research directions.

The Bioanalytical and Biomedical Applications of Polymer Modified Substrates

Polymers with different structures and morphology have been extensively used to construct functionalized surfaces for a wide range of applications because the physicochemical properties of polymers can be finely adjusted by their molecular weights, polydispersity and configurations, as well as the chemical structures and natures of monomers. In particular, the specific functions of polymers can be easily achieved at post-synthesis by the attachment of different kinds of active molecules such as recognition ligand, peptides, aptamers and antibodies. In this review, the recent advances in the bioanalytical and biomedical applications of polymer modified substrates were summarized with subsections on functionalization using branched polymers, polymer brushes and polymer hydrogels. The review focuses on their applications as biosensors with excellent analytical performance and/or as nonfouling surfaces with efficient antibacterial activity. Finally, we discuss the perspectives and future directions of polymer modified substrates in the development of biodevices for the diagnosis, treatment and prevention of diseases.

Composite Detectors Based on Single-Crystalline Films and Single Crystals of Garnet Compounds

This manuscript summarizes recent results on the development of composite luminescent materials based on the single-crystalline films and single crystals of simple and mixed garnet compounds obtained by the liquid-phase epitaxy growth method. Such composite materials can be applied as scintillating and thermoluminescent (TL) detectors for radiation monitoring of mixed ionization fluxes, as well as scintillation screens in the microimaging techniques. The film and crystal parts of composite detectors were fabricated from efficient scintillation/TL materials based on Ce³⁺-, Pr³⁺-, and Sc³⁺-doped Lu₃Al₅O₁₂ garnets, as well as Ce³⁺-doped Gd_3−xA_xAl_5−yGa_yO₁₂ mixed garnets, where A = Lu or Tb; x = 0–1; y = 2–3 with significantly different scintillation decay or positions of the main peaks in their TL glow curves. This work also summarizes the results of optical study of films, crystals, and epitaxial structures of these garnet compounds using absorption, cathodoluminescence, and photoluminescence. The scintillation and TL properties of the developed materials under α- and β-particles and γ-quanta excitations were studied as well. The most efficient variants of the composite scintillation and TL detectors for monitoring of composition of mixed beams of ionizing radiation were selected based on the results of this complex study.

Characteristics of respiratory microdroplet nuclei on common substrates

To evaluate the role of common substrates in the transmission of respiratory viruses, in particular SARS-CoV-2, uniformly distributed microdroplets (approx. 10 µm diameter) of artificial saliva were generated using an advanced inkjet printing technology to replicate the aerosol droplets and subsequently deposited on five substrates, including glass, polytetrafluoroethylene, stainless steel, acrylonitrile butadiene styrene and melamine. The droplets were found to evaporate within a short timeframe (less than 3 s), which is consistent with previous reports concerning the drying kinetics of picolitre droplets. Using fluorescence microscopy and atomic force microscopy, we found that the surface deposited microdroplet nuclei present two distinctive morphological features as the result of their drying mode, which is controlled by both interfacial energy and surface roughness. Nanomechanical measurements confirm that the nuclei deposited on all substrates possess similar surface adhesion (approx. 20 nN) and Young's modulus (approx. 4 MPa), supporting the proposed core-shell structure of the nuclei. We suggest that appropriate antiviral surface strategies, e.g. functionalization, chemical deposition, could be developed to modulate the evaporation process of microdroplet nuclei and subsequently mitigate the possible surface viability and transmissibility of respiratory virus.

Comparison between the kinematics for kangaroo rat hopping on a solid versus sand surface

In their natural habitats, animals move on a variety of substrates, ranging from solid surfaces to those that yield and flow (e.g. sand). These substrates impose different mechanical demands on the musculoskeletal system and may therefore elicit different locomotion patterns. The goal of this study is to compare bipedal hopping by desert kangaroo rats (Dipodomys deserti) on a solid versus granular substrate under speed-controlled conditions. To accomplish this goal, we developed a rotary treadmill, which is able to have different substrates or uneven surfaces. We video recorded six kangaroo rats hopping on a solid surface versus sand at the same speed (1.8 m s^-1) and quantified the differences in the hopping kinematics between the two substrates. We found no significant differences in the hop period, hop length or duty cycle, showing that the gross kinematics on the two substrates were similar. This similarity was surprising given that sand is a substrate that absorbs mechanical energy. Measurements of the penetration resistance of the sand showed that the combination of the sand properties, toe-print area and kangaroo rat weight was probably the reason for the similarity.

Ultrathin Two-Dimensional Metal-Organic Framework Nanosheets with Activated Ligand-Cluster Units for Enhanced SERS

Ultrathin two-dimensional (2D) metal-organic framework (MOF) nanosheets (MOFNs) comprise an emerging family of attractive materials with excellent potential for use in different catalytic, electrochemical, and sensing applications owing to their striking features such as ultrathin thickness, a large surface area, and highly ordered network structures. However, to the best of our knowledge, the ligand-cluster units activated through exfoliation into the MOFNs have rarely been realized, which is indeed crucial for surface-enhanced Raman scattering (SERS) analysis. Herein, we emphasize that the activated ligand-cluster units are based on the accessible coordination sites at the exposed cluster nodes accompanied by a complete excitation of the ligand-cluster units under incident photons, which make MOFNs highly effective SERS substrates, significantly outperforming their bulk counterparts. The SERS enhancement of MOFNs is further illustrated by an efficient integration of the inherent ligand-cluster charge-transfer (LCCT) transitions in MOFNs into interfacial charge-transfer processes through an "L"-type charge-transfer (CT) pathway, as further evidenced by an ultrahigh degree (0.98) of CT contributed to the SERS enhancement. This study provides an efficient strategy of exfoliating MOFs into ultrathin nanosheets for the design of highly efficient MOF-based SERS substrates.

γ-Secretase modulators show selectivity for γ-secretase-mediated amyloid precursor protein intramembrane processing

The aggregation of β‐amyloid peptide 42 results in the formation of toxic oligomers and plaques, which plays a pivotal role in Alzheimer's disease pathogenesis. Aβ42 is one of several Aβ peptides, all of Aβ30 to Aβ43 that are produced as a result of γ‐secretase–mediated regulated intramembrane proteolysis of the amyloid precursor protein. γ‐Secretase modulators (GSMs) represent a promising class of Aβ42‐lowering anti‐amyloidogenic compounds for the treatment of AD. Gamma‐secretase modulators change the relative proportion of secreted Aβ peptides, while sparing the γ‐secretase–mediated processing event resulting in the release of the cytoplasmic APP intracellular domain. In this study, we have characterized how GSMs affect the γ‐secretase cleavage of three γ‐secretase substrates, E‐cadherin, ephrin type A receptor 4 (EphA4) and ephrin type B receptor 2 (EphB2), which all are implicated in important contexts of cell signalling. By using a reporter gene assay, we demonstrate that the γ‐secretase–dependent generation of EphA4 and EphB2 intracellular domains is unaffected by GSMs. We also show that γ‐secretase processing of EphA4 and EphB2 results in the release of several Aβ‐like peptides, but that only the production of Aβ‐like proteins from EphA4 is modulated by GSMs, but with an order of magnitude lower potency as compared to Aβ modulation. Collectively, these results suggest that GSMs are selective for γ‐secretase–mediated Aβ production.

Interplay between DsbA1, DsbA2 and C8J_1298 Periplasmic Oxidoreductases of Campylobacter jejuni and Their Impact on Bacterial Physiology and Pathogenesis

The bacterial proteins of the Dsb family catalyze the formation of disulfide bridges between cysteine residues that stabilize protein structures and ensure their proper functioning. Here, we report the detailed analysis of the Dsb pathway of Campylobacter jejuni. The oxidizing Dsb system of this pathogen is unique because it consists of two monomeric DsbAs (DsbA1 and DsbA2) and one dimeric bifunctional protein (C8J_1298). Previously, we showed that DsbA1 and C8J_1298 are redundant. Here, we unraveled the interaction between the two monomeric DsbAs by in vitro and in vivo experiments and by solving their structures and found that both monomeric DsbAs are dispensable proteins. Their structures confirmed that they are homologs of EcDsbL. The slight differences seen in the surface charge of the proteins do not affect the interaction with their redox partner. Comparative proteomics showed that several respiratory proteins, as well as periplasmic transport proteins, are targets of the Dsb system. Some of these, both donors and electron acceptors, are essential elements of the C. jejuni respiratory process under oxygen-limiting conditions in the host intestine. The data presented provide detailed information on the function of the C. jejuni Dsb system, identifying it as a potential target for novel antibacterial molecules.

Overlap and Specificity in the Substrate Spectra of Human Monoamine Transporters and Organic Cation Transporters 1, 2, and 3

Human monoamine transporters (MATs) are cation transporters critically involved in neuronal signal transmission. While inhibitors of MATs have been intensively studied, their substrate spectra have received far less attention. Polyspecific organic cation transporters (OCTs), predominantly known for their role in hepatic and renal drug elimination, are also expressed in the central nervous system and might modulate monoaminergic signaling. Using HEK293 cells overexpressing MATs or OCTs, we compared uptake of 48 compounds, mainly phenethylamine and tryptamine derivatives including matched molecular pairs, across noradrenaline, dopamine and serotonin transporters and OCTs (1, 2, and 3). Generally, MATs showed surprisingly high transport activities for numerous analogs of neurotransmitters, but their substrate spectra were limited by molar mass. Human OCT2 showed the broadest substrate spectrum, and also the highest overlap with MATs substrates. Comparative kinetic analyses revealed that the radiotracer meta-iodobenzylguanidine had the most balanced uptake across all six transporters. Matched molecular pair analyses comparing MAT and OCT uptake using the same methodology could provide a better understanding of structural determinants for high cell uptake by MATs or OCTs. The data may result in a better understanding of pharmacokinetics and toxicokinetics of small molecular organic cations and, possibly, in the development of more specific radiotracers for MATs.

Novel solid-phase microextraction fiber coatings: A review

The materials used for the fabrication of solid-phase microextraction fiber coatings in the past five years are summarized in the current review, including carbon, metal-organic frameworks, covalent organic frameworks, aerogel, polymer, ionic liquids/poly (ionic liquids), metal oxides, and natural materials. The preparation approaches of different coatings, such as sol-gel technique, in-situ growth, electrodeposition, and glue methods, are briefly reviewed together with the evolution of the supporting substrates. In addition, the limitations of the current coatings and the future development directions of solid-phase microextraction are presented.

ATP binding cassette transporters and cancer: revisiting their controversial role

The expression of ATP-binding cassette transporter (ABC transporters) has been reported in various tissues such as the lung, liver, kidney, brain and intestine. These proteins account for the efflux of different compounds and metabolites across the membrane, thus decreasing the concentration of the toxic compounds. ABC transporter genes play a vital role in the development of multidrug resistance, which is the main obstacle that hinders the success of chemotherapy. Preclinical and clinical trials have investigated the probability of overcoming drug-associated resistance and substantial toxicities. The focus has been put on several strategies to overcome multidrug resistance. These strategies include the development of modulators that can modulate ABC transporters. This knowledge can be translated for clinical oncology treatment in the future.

Baseline Data of the Fungal Phytobiome of Three Sorghum (Sorghum bicolor) Cultivars in South Africa using Targeted Environmental Sequencing

Plant-associated fungi, or the mycobiome, inhabit plant surfaces above ground, reside in plant tissues as endophytes, or are rhizosphere in the narrow zone of soil surrounding plant roots. Studies have characterized mycobiomes of various plant species, but little is known about the sorghum mycobiome, especially in Africa, despite sorghum being one of the most important indigenous and commercial cereals in Africa. In this study, the mycobiome associated with above- and below-ground tissues of three commercial sorghum cultivars, as well as from rhizosphere and surrounding bulk soil samples, were sequenced using targeted sequencing with the Illumina MiSeq platform. Relative abundance differences between fungal communities were found between above-ground and below-ground niches, with most differences mostly in the dominant MOTUs, such as Davidiellaceae sp. (Cladosporium), Didymellaceae sp. 1 (Phoma), Fusarium, Cryptococcus and Mucor. Above-ground communities also appeared to be more diverse than below-ground communities, and plants harboured the most diversity. A considerable number of MOTUs were shared between the cultivars although, especially for NS5511, their abundances often differed. Several of the detected fungal groups include species that are plant pathogens of sorghum, such as Fusarium, and, at low levels, Alternaria and the Ustilaginomycetes. Findings from this study illustrate the usefulness of targeted sequencing of the ITS rDNA gene region (ITS2) to survey and monitor sorghum fungal communities and those from associated soils. This knowledge may provide tools for disease management and crop production and improvement.

Mechanistic insights into COVID-19 by global analysis of the SARS-CoV-2 3CLpro substrate degradome

The main viral protease (3CLpro) is indispensable for SARS-CoV-2 replication. We delineate the human protein substrate landscape of 3CLpro by TAILS substrate-targeted N-terminomics. We identify more than 100 substrates in human lung and kidney cells supported by analyses of SARS-CoV-2-infected cells. Enzyme kinetics and molecular docking simulations of 3CLpro engaging substrates reveal how noncanonical cleavage sites, which diverge from SARS-CoV, guide substrate specificity. Cleaving the interactors of essential effector proteins, effectively stranding them from their binding partners, amplifies the consequences of proteolysis. We show that 3CLpro targets the Hippo pathway, including inactivation of MAP4K5, and key effectors of transcription, mRNA processing, and translation. We demonstrate that Spike glycoprotein directly binds galectin-8, with galectin-8 cleavage disengaging CALCOCO2/NDP52 to decouple antiviral-autophagy. Indeed, in post-mortem COVID-19 lung samples, NDP52 rarely colocalizes with galectin-8, unlike in healthy lungs. The 3CLpro substrate degradome establishes a foundational substrate atlas to accelerate exploration of SARS-CoV-2 pathology and drug design.

Mechanistic understanding of the pollutant removal and transformation processes in the constructed wetland system

Constructed wetland systems (CWs) are biologically and physically engineered systems to mimic the natural wetlands which can potentially treat the wastewater from the various point and nonpoint sources of pollution. The present study aims to review the various mechanisms involved in the different types of CWs for wastewater treatment and to elucidate their role in the effective functioning of the CWs. Several physical, chemical, and biological processes substantially influence the pollutant removal efficiency of CWs. Plants species Phragmites australis, Typha latifolia, and Typha angustifolia are most widely used in CWs. The rate of nitrogen (N) removal is significantly affected by emergent vegetation cover and type of CWs. Hybrid CWs (HCWS) removal efficiency for nutrients, metals, pesticides, and other pollutants is higher than a single constructed wetland. The contaminant removal efficiency of the vertical subsurface flow constructed wetlands (VSSFCW) commonly used for the treatment of domestic and municipal wastewater ranges between 31% and 99%. Biochar/zeolite addition as substrate material further enhances the wastewater treatment of CWs. Innovative components (substrate materials, plant species) and factors (design parameters, climatic conditions) sustaining the long-term sink of the pollutants, such as nutrients and heavy metals in the CWs should be further investigated in the future. PRACTITIONER POINTS: Constructed wetland systems (CWs) are efficient natural treatment system for on-site contaminants removal from wastewater. Denitrification, nitrification, microbial and plant uptake, sedimentation and adsorption are crucial pollutant removal mechanisms. Phragmites australis, Typha latifolia, and Typha angustifolia are widely used emergent plants in constructed wetlands. Hydraulic retention time (HRT), water flow regimes, substrate, plant, and microbial biomass substantially affect CWs treatment performance.

CYPstrate: A Set of Machine Learning Models for the Accurate Classification of Cytochrome P450 Enzyme Substrates and Non-Substrates

The interaction of small organic molecules such as drugs, agrochemicals, and cosmetics with cytochrome P450 enzymes (CYPs) can lead to substantial changes in the bioavailability of active substances and hence consequences with respect to pharmacological efficacy and toxicity. Therefore, efficient means of predicting the interactions of small organic molecules with CYPs are of high importance to a host of different industries. In this work, we present a new set of machine learning models for the classification of xenobiotics into substrates and non-substrates of nine human CYP isozymes: CYPs 1A2, 2A6, 2B6, 2C8, 2C9, 2C19, 2D6, 2E1, and 3A4. The models are trained on an extended, high-quality collection of known substrates and non-substrates and have been subjected to thorough validation. Our results show that the models yield competitive performance and are favorable for the detection of CYP substrates. In particular, a new consensus model reached high performance, with Matthews correlation coefficients (MCCs) between 0.45 (CYP2C8) and 0.85 (CYP3A4), although at the cost of coverage. The best models presented in this work are accessible free of charge via the "CYPstrate" module of the New E-Resource for Drug Discovery (NERDD).

Effects of Particle Size on the Dielectric, Mechanical, and Thermal Properties of Recycled Borosilicate Glass-Filled PTFE Microwave Substrates

Low dielectric loss and low-cost recycled borosilicate (BRS) glass-reinforced polytetrafluoroethylene (PTFE) composites were fabricated for microwave substrate applications. The composites were prepared through a dry powder processing technique by dispersing different micron sizes (25 µm, 45 µm, 63 µm, 90 µm, and 106 µm) of the recycled BRS filler in the PTFE matrix. The effect of the filler sizes on the composites' thermal, mechanical, and dielectric properties was studied. The dielectric properties of the composites were characterised in the frequency range of 1-12 GHz using an open-ended coaxial probe (OCP) connected to a vector network analyser (VNA). XRD patterns confirmed the phase formation of PTFE and recycled BRS glass. The scanning electron microscope also showed good filler dispersion at larger filler particle sizes. In addition, the composites' coefficient of thermal expansion and tensile strength decreased from 12.93 MPa and 64.86 ppm/°C to 7.12 MPa and 55.77 ppm/°C when the filler size is reduced from 106 μm to 25 μm. However, moisture absorption and density of the composites increased from 0.01% and 2.17 g/cm3 to 0.04% and 2.21 g/cm3. The decrement in filler size from 106 μm to 25 μm also increased the mean dielectric constant and loss tangent of the composites from 2.07 and 0.0010 to 2.18 and 0.0011, respectively, while it reduced the mean signal transmission speed from 2.088 × 108 m/s to 2.031 × 108 m/s. The presented results showed that PTFE/recycled BRS composite exhibited comparable characteristics with commercial high-frequency laminates.

Structural and Functional Connectivity Substrates of Cognitive Impairment in Multiple Sclerosis

Cognitive impairment (CI) occurs in 43 to 70% of multiple sclerosis (MS) patients at both early and later disease stages. Cognitive domains typically involved in MS include attention, information processing speed, memory, and executive control. The growing use of advanced magnetic resonance imaging (MRI) techniques is furthering our understanding on the altered structural connectivity (SC) and functional connectivity (FC) substrates of CI in MS. Regarding SC, different diffusion tensor imaging (DTI) measures (e.g., fractional anisotropy, diffusivities) along tractography-derived white matter (WM) tracts showed relevance toward CI. Novel diffusion MRI techniques, including diffusion kurtosis imaging, diffusion spectrum imaging, high angular resolution diffusion imaging, and neurite orientation dispersion and density imaging, showed more pathological specificity compared to the traditional DTI but require longer scan time and mathematical complexities for their interpretation. As for FC, task-based functional MRI (fMRI) has been traditionally used in MS to brain mapping the neural activity during various cognitive tasks. Analysis methods of resting fMRI (seed-based, independent component analysis, graph analysis) have been applied to uncover the functional substrates of CI in MS by revealing adaptive or maladaptive mechanisms of functional reorganization. The relevance for CI in MS of SC–FC relationships, reflecting common pathogenic mechanisms in WM and gray matter, has been recently explored by novel MRI analysis methods. This review summarizes recent advances on MRI techniques of SC and FC and their potential to provide a deeper understanding of the pathological substrates of CI in MS.

Approaching transglutaminase from Streptomyces bacteria over three decades

Transglutaminases are protein cross-linking and protein-modifying enzymes that have attracted considerable interest due to their causal involvement in various diseases and versatility in industrial applications. In particular, microbial transglutaminases (MTG) from Streptomyces bacteria have managed in recent years to evolve from simple food additives to specialized enzymes for the site-directed modification of therapeutic proteins. The review summarizes relevant studies from the beginning dealing with the occurrence, production, structure, catalysis, and substrate molecules of MTG enzymes. It also addresses biotechnological procedures with MTG from S. mobaraensis (SmMTG) as the most prominent representative in focus. Reassessment of the available data revealed unexpected insights into catalysis of SmMTG and other transglutaminases, suggesting selection of glutamine donor proteins by subsites at the front vestibule and the existence of distinct lysine pockets. Flexibility of the SmMTG-accessible glutamine donor substrate regions seems to be more important than the glutamine environment. Nevertheless, residues in close vicinity to glutamines also determine interaction with the SmMTG subsites. The apparent lack of subsites for lysine donor proteins suggests self-assembly of the substrate proteins prior to enzymatic cross-linking. The study of natural substrate proteins, especially their mutual interaction, is proposed to further illuminate catalysis of SmMTG. To this end, structure and function of the characterized substrate proteins from S. mobaraensis are discussed in conclusion.