bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Rhodium Analogue of Coenzyme B12 as an Anti‐Photoregulatory Ligand Inhibiting Bacterial CarH Photoreceptors
Authors: Pérez‐Castaño Ricardo , Aranda Juan , Widner Florian J. , Kieninger Christoph , Deery Evelyne , Warren Martin J. , Orozco Modesto , Elías‐Arnanz Montserrat , Padmanabhan S. , Kräutler Bernhard 
Published: February 2024

AbstractCoenzyme B12 (AdoCbl; 5′‐deoxy‐5′‐adenosylcobalamin), the quintessential biological organometallic radical catalyst, has a formerly unanticipated, yet extensive, role in photoregulation in bacteria. The light‐responsive cobalt‐corrin AdoCbl performs this nonenzymatic role by facilitating the assembly of CarH photoreceptors into DNA‐binding tetramers in the dark, suppressing gene expression. Conversely, exposure to light triggers the decomposition of this AdoCbl‐bound complex by a still elusive photochemical mechanism, activating gene expression. Here, we have examined AdoRhbl, the non‐natural rhodium analogue of AdoCbl, as a photostable isostructural surrogate for AdoCbl. We show that AdoRhbl closely emulates AdoCbl in its uptake by bacterial cells and structural functionality as a regulatory ligand for CarH tetramerization, DNA binding, and repressor activity. Remarkably, we find AdoRhbl is photostable even when bound “base‐off/His‐on” to CarH in vitro and in vivo. Thus, AdoRhbl, an antivitamin B12, also represents an unprecedented anti‐photoregulatory ligand, opening a pathway to precisely target biomimetic inhibition of AdoCbl‐based photoregulation, with new possibilities for selective antibacterial applications. Computational biomolecular analysis of AdoRhbl binding to CarH yields detailed structural insights into this complex, which suggest that the adenosyl group of photoexcited AdoCbl bound to CarH may specifically undergo a concerted non‐radical syn‐1,2‐elimination mechanism, an aspect not previously considered for this photoreceptor.
Hydrogen‐Induced Formation of Surface Acid Sites on Pt/Al(PO3)3 Enables Remarkably Efficient Hydrogenolysis of C−O Bonds in Alcohols and Ethers
Authors: Oshida Kento , Yuan Kang , Yamazaki Yukari , Tsukimura Rio , Nishio Hidenori , Nomoto Katsutoshi , Miura Hiroki , Shishido Tetsuya , Jin Xiongjie , Nozaki Kyoko 
Published: February 2024

AbstractThe hydrogenolysis of oxygenates such as alcohols and ethers is central to the biomass valorization and also a valuable transformation in organic synthesis. However, a mild and efficient catalyst system for the hydrogenolysis of a large variety of alcohols and ethers with various functional groups is still underdeveloped. Here, we report an aluminum metaphosphate‐supported Pt nanoparticles (Pt/Al(PO3)3) for the hydrogenolysis of a wide variety of primary, secondary, and tertiary alkyl and benzylic alcohols, and dialkyl, aryl alkyl, and diaryl ethers, including biomass‐derived furanic compounds, under mild conditions (0.1–1 atm of H2, as low as 70 °C). Mechanistic studies suggested that H2 induces formation of the surface Brønsted acid sites via its cleavage by supported Pt nanoparticles. Accordingly, the high efficiency and the wide applicability of the catalyst system are attributed to the activation and cleavage of C−O bonds by the hydrogen‐induced Brønsted acid sites with the assistance of Lewis acidic Al sites on the catalyst surface. The high efficiency of the catalyst implies its potential application in energy‐efficient biomass valorization or fine chemical synthesis.
N‐methyl‐d‐aspartate receptors: Structure, function, and role in organophosphorus compound poisoning
Authors: Kolić Dora , Kovarik Zrinka 
Published: February 2024

AbstractAcute organophosphorus compound (OP) poisoning induces symptoms of the cholinergic crises with the occurrence of severe epileptic seizures. Seizures are induced by hyperstimulation of the cholinergic system, but are enhanced by hyperactivation of the glutamatergic system. Overstimulation of muscarinic cholinergic receptors by the elevated acetylcholine causes glutamatergic hyperexcitation and an increased influx of Ca2+ into neurons through a type of ionotropic glutamate receptors, N‐methyl‐d‐aspartate (NMDA) receptors (NMDAR). These excitotoxic signaling processes generate reactive oxygen species, oxidative stress, and activation of the neuroinflammatory response, which can lead to recurrent epileptic seizures, neuronal cell death, and long‐term neurological damage. In this review, we illustrate the NMDAR structure, complexity of subunit composition, and the various receptor properties that change accordingly. Although NMDARs are in normal physiological conditions important for controlling synaptic plasticity and mediating learning and memory functions, we elaborate the detrimental role NMDARs play in neurotoxicity of OPs and focus on the central role NMDAR inhibition plays in suppressing neurotoxicity and modulating the inflammatory response. The limited efficacy of current medical therapies for OP poisoning concerning the development of pharmacoresistance and mitigating proinflammatory response highlights the importance of NMDAR inhibitors in preventing neurotoxic processes and points to new avenues for exploring therapeutics for OP poisoning.
Development of an integrated and project‐based laboratory course in upper‐level biochemistry and molecular biology
Authors: Liu Yange , Tu Shuo , Hu Xiaojuan , Xiong Xiangyang , Pan Zezheng , Liu Zhuoqi , Zhu Weifeng , Luo Daya , Cui Xiangpei , Huang Chunhong , Xie Caifeng 
Published: February 2024

AbstractAn integrated and projected‐based laboratory course was described, integrating interconnected knowledge points and biochemistry and molecular biology techniques on a research project‐based system. The program, which served as an essential extension of theoretical courses to practice, was conducted with a sophomore of basic medical science who had completed the course in medical biochemistry and molecular biology. This course engaged students in learning “genetic manipulation” and “recombinant DNA technology” to understand the target gene's role in disease mechanics, thus altering evaluation and treatment for clinical disease. Students could master applied and advanced techniques, such as cell culture, transfection, inducing exogenous fusion protein expression, purifying protein and its concentration assay, quantitative polymerase chain reaction, and western bot analysis. This laboratory exercise links laboratory practices with the methods of current basic research. Students need to complete the experimental design report and laboratory report, which could be advantageous for improving their ability to write lab summaries and scientific papers in the future. The reliability and validity analyses were conducted on the questionnaire, and we examined students' satisfaction with the course and their gains from the course. The student feedback was generally positive, indicating that the exercise helped consolidate theoretical knowledge, increase scientific research enthusiasm, and provide a powerful tool to be a better person and make informed decisions.
Modulating the acetylation of α‐tubulin by LncRNAs and microRNAs helps in the progression of cancer
Authors: Kar Sneha , Mukherjee Rimi , Guha Subhabrata , Talukdar Debojit , Das Gaurav , Murmu Nabendu 
Published: February 2024

AbstractMalignant tumor cells go through morphological and gene expression alterations, including rearrangement of cytoskeleton proteins that promote invasion and metastasis. Microtubules form a major cytoskeleton component that plays a significant role in regulating multiple cellular activities and function depending on the presence of posttranslational modification (PTM). Acetylation is a type of PTM that generally occurs in the lysine 40 region of α‐tubulin and is known to be critically associated with cancer metastasis. Current evidence demonstrates that noncoding RNAs, such as long noncoding RNA (lncRNA) and microRNA (or miRNA), which are correlated with gene regulation modulate the expression of acetylated tubulin in the development and metastasis of cancer. This review provides an overview about the role of lncRNA and miRNA in regulation of tubulin acetylation in various types of cancer.
Amine‐Carbamate Self‐Immolative Spacers Counterintuitively Release 3° Alcohol at Much Faster Rates than 1° Alcohol Payloads
Authors: Mason Mattia , Bisbal Lopez Lydia , Bashiri Fazel , Herrero Aurélie , Baron Aurélien , Bucci Raffaella , Pignataro Luca , Gennari Cesare , Dal Corso Alberto 
Published: February 2024

AbstractSelf‐immolative (SI) spacers are degradable chemical connectors widely used in prodrugs and drug conjugates to release pharmaceutical ingredients in response to specific stimuli. Amine‐carbamate SI spacers are particularly versatile, as they have been used to release different hydroxy cargos, ranging from 2° and 3° alcohols to phenols and oximes. In this work, we describe the ability of three amine‐carbamate SI spacers to release three structurally similar imidazoquinoline payloads, bearing either a 1°, a 2° or a 3° alcohol as the leaving group. While the spacers showed comparable efficacy at releasing the 2° and 3° alcohols, the liberation of the 1° alcohol was much slower, unveiling a counterintuitive trend in nucleophilic acyl substitutions. The release of the 1° alcohol payload was only possible using a SI spacer bearing a pyrrolidine ring and a tertiary amine handle, which opens the way to future applications in drug delivery systems.
Thermally Activated Delayed Fluorescent Binuclear Copper(I) Alkynyl Complexes with Cuprophilic Interactions
Authors: Zhang Xi , Song Jia‐Xi , Chang Xiaoyong , Li Kai , Chen Yong 
Published: February 2024

AbstractCopper(I)‐based thermally activated delayed fluorescence (TADF) emitters have been conceived to be promising candidates for display and lighting applications because of their multifarious structures and strong photoluminescence. Herein a string of binuclear Cu(I) complexes bearing pronounced cuprophilic interactions have been designed and synthesized. [Cu2(dppb)2(μ2‐η1‐C≡C−Ph)2] (1 a) and [Cu2(dppb)2(μ2‐η1‐C≡C−PPXZ)2] (1 b) display photoluminescence quantum yields of up to 67 % in doped films and solid states via TADF and exhibit reversible bicolor luminescence switching upon mechanical stimuli. Computational studies manifest that the metal‐to‐ligand charge transfer predominant transitions ensure a small energy splitting (ΔEST) between the lowest singlet (S1) and triplet (T1) excited states and cuprophilic interactions promote the spin‐orbit coupling (SOC), favoring the reverse intersystem crossing (RISC) process. This study provides a new strategy for the construction of stimuli‐responsive metal‐based TADF materials.
Highly efficient supported bimetallic Au‐Pd catalysts for oxidative esterification of methacrolein to methyl methacrylate
Authors: Yang Yubo , Zheng Yanxia , Cai Lu , Li Yuchao , Xu Rui , Zuo Cuncun , Huang Haofei , Wang Ming , Dai Ruihui , Zhang Liping , Zhao Yansong 
Published: February 2024

AbstractAu‐Pd alloy particles supported on TiO2 were synthesized by the sol‐immobilized method and their confirmation was achieved through transmission electron microscope (TEM) and energy dispersive spectrometer (EDS) mapping. The samples were subjected to oxidative esterification of methacrolein with methanol to methyl methacrylate (MMA). Notably, a remarkable enhancement of catalytic performance was found in the presence of Pd. Among the samples tested, the sample Au0.25Pd0.75/TiO2 exhibited the highest catalytic performance. The interaction between Au and Pd demonstrated a synergistic effect, with Pd contributing to the stability of Au nanoparticles and strengthening the production of active oxygen species, which facilitated the efficient removal of hydrogen from intermediate hemiacetal. Furthermore, a probable reaction mechanism was proposed to explain these observations.
CFD study on flow characteristics of sieve tray columns with circular downcomers
Authors: Su Huihui , Wang Enlu , Xu Yifei 
Published: February 2024

AbstractTo investigate the flow characteristics of sieve tray columns with circular downcomers, the Euler–Euler gas–liquid two‐phase flow model is used to simulate a three‐dimensional sieve tray column. Each phase is regarded as an interpenetrating continuum with independent transport equations. The velocity distribution, clear liquid height, and foam layer height are predicted by the model. The correlation is established for predicting the clear liquid height on the sieve tray. The results show the following: (1) The sensitivity of the clear liquid height to the gas phase load is greater than that of the liquid phase load. (2) When the gas–liquid distribution is stable, the flow on the round sieve tray column presents a piston flow pattern. (3) The average liquid holdup of the circular downcomer of the three heights all showed a slow decrease at first, and then an inflection point appeared near the height of 0.02 m, after which the liquid holdup dropped sharply. (4) The established correlation has good predictive performance for calculating the clear liquid height in the column, and the relative error between the calculated value and the actual value is less than 10%.
Nitrile Furanics via Copper‐Catalyzed Dehydration of Aldoximes and Knoevenagel Condensation
Authors: Annatelli Mattia , Sadraoui Chaimaa , Trapasso Giacomo , Aricò Fabio 
Published: February 2024

AbstractIn this work two synthetic approaches to introduce nitrile moieties into bio‐based derived furanic compounds were investigated, i. e., dehydration of aldoximes and Knoevenagel condensation. Both methodologies have been first tested and optimized on furfural and thus exploited on 5‐hydroxymethyl‐2‐furfural (HMF) and 5,5’‐oxy(bismethylene)‐2‐furaldehyde (OBMF). The syntheses of furfural, HMF and OBMF aldoximes were efficiently conducted (also in large scale) under mild reaction conditions and short reaction time. The subsequent dehydration to nitrile furanic compounds was carried out in the presence of catalytic amount of copper acetate monohydrate. Furthermore, Knoevenagel condensations were performed on furfural, HMF and OBMF with different Activated Methylene Group compounds, using for the first‐time dimethyl carbonate as the reaction media. Most of the resulting products were isolated as pure via simple liquid‐liquid extraction in good to excellent yields. Future applications of these compounds might include aldoxime reduction into amine furanics ‐ herein also preliminary investigated ‐ and hydrolysis of the nitrile derivatives in the related carboxylic acid (or ester) furanics. All these products are interesting monomers for the preparation of bio‐based polymers.
Derivation of transcriptomics-based points of departure for 20 Per- or polyfluoroalkyl substances using a larval fathead minnow (Pimephales promelas) reduced transcriptome assay
Authors: Villeneuve Daniel L , Bush Kendra , Hazemi Monique , Hoang John X , Le Michelle , Blackwell Brett R , Stacy Emma , Flynn Kevin M 
Published: February 2024

Abstract
Traditional toxicity testing has been unable to keep pace with the introduction of new chemicals into commerce. Consequently, there are limited or no toxicity data for many chemicals to which fish and wildlife may be exposed. Per- and polyfluoroalkyl substances (PFAS) are emblematic of this issue in that ecological hazards of most PFAS remain uncharacterized. The present study employed a high-throughput assay to identify the concentration at which 20 PFAS, with diverse properties, elicited a concerted gene expression response (termed a transcriptomics-based point of departure [tPOD]) in larval fathead minnows (Pimephales promelas; 5–6 days postfertilization) exposed for 24 h. Based on a reduced transcriptome approach that measured whole-body expression of 1832 genes, the median tPOD for the 20 PFAS tested was 10 µM. Longer-chain carboxylic acids (12–13 C–F); an eight-C–F dialcohol, N-alkyl sulfonamide; and telomer sulfonic acid were among the most potent PFAS, eliciting gene expression responses at concentrations &lt;1 µM. With a few exceptions, larval fathead minnow tPODs were concordant with those based on whole-transcriptome response in human cell lines. However, larval fathead minnow tPODs were often greater than those for Daphnia magna exposed to the same PFAS. The tPODs overlapped concentrations at which other sublethal effects have been reported in fish (available for 10 PFAS). Nonetheless, fathead minnow tPODs were orders of magnitude higher than aqueous PFAS concentrations detected in tributaries of the North American Great Lakes, suggesting a substantial margin of safety. Overall, results broadly support the use of a fathead minnow larval transcriptomics assay to derive screening-level potency estimates for use in ecological risk-based prioritization.
In Silico Acute Aquatic Hazard Assessment and Prioritization Using a Grouped Target Site Model: A Case Study of Organic Substances Reported in Permian Basin Hydraulic Fracturing Operations
Authors: Boone Kathleen S. , Di Toro Dominic M. , Davis Craig W. , Parkerton Thomas F. , Redman Aaron 
Published: February 2024

Abstract
Hydraulic fracturing (HF) is commonly used to enhance onshore recovery of oil and gas during production. This process involves the use of a variety of chemicals to support the physical extraction of oil and gas, maintain appropriate conditions downhole (e.g., redox conditions, pH), and limit microbial growth. The diversity of chemicals used in HF presents a significant challenge for risk assessment. The objective of the present study is to establish a transparent, reproducible procedure for estimating 5th percentile acute aquatic hazard concentrations (e.g., acute hazard concentration 5th percentiles [HC5s]) for these substances and validating against existing toxicity data. A simplified, grouped target site model (gTSM) was developed using a database (n = 1696) of diverse compounds with known mode of action (MoA) information. Statistical significance testing was employed to reduce model complexity by combining 11 discrete MoAs into three general hazard groups. The new model was trained and validated using an 80:20 allocation of the experimental database. The gTSM predicts toxicity using a combination of target site water partition coefficients and hazard group-based critical target site concentrations. Model performance was comparable to the original TSM using 40% fewer parameters. Model predictions were judged to be sufficiently reliable and the gTSM was further used to prioritize a subset of reported Permian Basin HF substances for risk evaluation. The gTSM was applied to predict hazard groups, species acute toxicity, and acute HC5s for 186 organic compounds (neutral and ionic). Toxicity predictions and acute HC5 estimates were validated against measured acute toxicity data compiled for HF substances. This case study supports the gTSM as an efficient, cost-effective computational tool for rapid aquatic hazard assessment of diverse organic chemicals. Environ Toxicol Chem 2024;43:1161–1172. © 2024 ExxonMobil Petroleum and Chemical BV. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
A Multicompartment Assessment of Microplastic Contamination in Semi-remote Boreal Lakes
Authors: McIlwraith Hayley K. , Dias Minoli , Orihel Diane M. , Rennie Michael D. , Harrison Anna L. , Hoffman Matthew J. , Provencher Jennifer F. , Rochman Chelsea M. 
Published: February 2024

Abstract
Microplastic contamination is ubiquitous across the globe, even in remote locations. Still, the sources and pathways of microplastics to such locations are largely unknown. To investigate microplastic contamination in a semi-remote location, we measured microplastic concentrations in nine oligotrophic lakes within and around the International Institute for Sustainable Development—Experimental Lakes Area in northwestern Ontario, Canada. Our first objective was to establish ambient concentrations of microplastics in bottom sediments, surface water, and atmospheric deposition in semi-remote boreal lakes. Across all lakes, mean shallow and deep sediment microplastic concentrations, near-surface water microplastic concentrations from in situ filtering, and dry atmospheric microplastic deposition rates were 551 ± 354 particles kg−1, 177 ± 103 particles kg−1, 0.2 ± 0.3 particles L−1, and 0.4 ± 0.2 particles m−2 day−1, respectively. Our second objective was to investigate whether microplastic contamination of these lakes is driven by point sources including local runoff and direct anthropogenic inputs or nonpoint sources such as atmospheric deposition. Lakes were selected based on three levels of anthropogenic activity—low, medium, and high—though activity levels were minimal across all study lakes compared with highly populated areas. Whereas a positive correlation would indicate that point sources were a likely pathway, we observed no relationship between the level of anthropogenic activity and microplastic contamination of surface water. Moreover, the composition of microplastics in surface water and atmospheric deposition were similar, comprising mostly polyester and acrylic fibers. Together, these results suggest that atmospheric deposition may be the main pathway of microplastics to these remote boreal lakes. Environ Toxicol Chem 2024;43:999–1011. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
Marine Microbiota Responses to Shipping Scrubber Effluent Assessed at Community Structure and Function Endpoints
Authors: Genitsaris Savvas , Stefanidou Natassa , Hatzinikolaou Dimitris , Kourkoutmani Polyxeni , Michaloudi Evangelia , Voutsa Dimitra , Gros Meritxell , García-Gómez Elisa , Petrović Mira , Ntziachristos Leonidas , Moustaka-Gouni Maria 
Published: February 2024

Abstract
The use of novel high-throughput sequencing (HTS) technologies to examine the responses of natural multidomain microbial communities to scrubber effluent discharges to the marine environment is still limited. Thus, we applied metabarcoding sequencing targeting the planktonic unicellular eukaryotic and prokaryotic fraction (phytoplankton, bacterioplankton, and protozooplankton) in mesocosm experiments with natural microbial communities from a polluted and an unpolluted site. Furthermore, metagenomic analysis revealed changes in the taxonomic and functional dominance of multidomain marine microbial communities after scrubber effluent additions. The results indicated a clear shift in the microbial communities after such additions, which favored bacterial taxa with known oil and polycyclic aromatic hydrocarbons (PAHs) biodegradation capacities. These bacteria exhibited high connectedness with planktonic unicellular eukaryotes employing variable trophic strategies, suggesting that environmentally relevant bacteria can influence eukaryotic community structure. Furthermore, Clusters of Orthologous Genes associated with pathways of PAHs and monocyclic hydrocarbon degradation increased in numbers at treatments with high scrubber effluent additions acutely. These genes are known to express enzymes acting at various substrates including PAHs. These indications, in combination with the abrupt decrease in the most abundant PAHs in the scrubber effluent below the limit of detection—much faster than their known half-lives—could point toward a bacterioplankton-initiated rapid ultimate biodegradation of the most abundant toxic contaminants of the scrubber effluent. The implementation of HTS could be a valuable tool to develop multilevel biodiversity indicators of the scrubber effluent impacts on the marine environment, which could lead to improved impact assessment. Environ Toxicol Chem 2024;43:1012–1029. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.