Structure Analysis Research Articles

Comparative genomics and bioinformatics approaches revealed the role of CC-NBS-LRR genes under multiple stresses in passion fruit.

Passion fruit is widely cultivated in tropical, subtropical regions of the world. The attack of bacterial and fungal diseases, and environmental factors heavily affect the yield and productivity of the passion fruit. The CC-NBS-LRR (CNL) gene family being a subclass of R-genes protects the plant against the attack of pathogens and plays a major role in effector-triggered immunity (ETI). However, no information is available regarding this gene family in passion fruit. To address the underlying problem a total of 25 and 21 CNL genes have been identified in the genome of purple (Passiflora edulis Sims.) and yellow (Passiflora edulis f. flavicarpa) passion fruit respectively. Phylogenetic tree was divided into four groups with PeCNLs present in 3 groups only. Gene structure analysis revealed that number of exons ranged from 1 to 9 with 1 being most common. Most of the PeCNL genes were clustered at the chromosome 3 and underwent strong purifying selection, expanded through segmental (17 gene pairs) and tandem duplications (17 gene pairs). PeCNL genes contained cis-elements involved in plant growth, hormones, and stress response. Transcriptome data indicated that PeCNL3, PeCNL13, and PeCNL14 were found to be differentially expressed under Cucumber mosaic virus and cold stress. Three genes were validated to be multi-stress responsive by applying Random Forest model of machine learning. To comprehend the biological functions of PeCNL proteins, their 3D structure and gene ontology (GO) enrichment analysis were done. Our research analyzed the CNL gene family in passion fruit to understand stress regulation and improve resilience. This study lays the groundwork for future investigations aimed at enhancing the genetic composition of passion fruit to ensure robust growth and productivity in challenging environments.

Ethnic and functional differentiation of copy number polymorphisms in Tunisian and HapMap population unveils insights on genome organizational plasticity

Admixture mapping has been useful in identifying genetic variations linked to phenotypes, adaptation and diseases. Copy number variations (CNVs) represents genomic structural variants spanning large regions of chromosomes reaching several megabases. In this investigation, the “Canary” algorithm was applied to 102 Tunisian samples and 991 individuals from eleven HapMap III populations to genotype 1279 copy number polymorphisms (CNPs). In this present work, we investigate the Tunisian population structure using the CNP makers previously identified among Tunisian. The study revealed that Sub-Saharan African populations exhibited the highest diversity with the highest proportions of allelic CNPs. Among all the African populations, Tunisia showed the least diversity. Individual ancestry proportions computed using STRUCTURE analysis revealed a major European component among Tunisians with lesser contribution from Sub-Saharan Africa and Asia. Population structure analysis indicated the genetic proximity with Europeans and noticeable distance from the Sub-Saharan African and East Asian clusters. Seven genes harbouring Tunisian high-frequent CNPs were identified known to be associated with 9 Mendelian diseases and/or phenotypes. Functional annotation of genes under selection highlighted a noteworthy enrichment of biological processes to receptor pathway and activity as well as glutathione metabolism. Additionally, pathways of potential concern for health such as drug metabolism, infectious diseases and cancers exhibited significant enrichment. The distinctive genetic makeup of the Tunisians might have been influenced by various factors including natural selection and genetic drift, resulting in the development of distinct genetic variations playing roles in specific biological processes. Our research provides a justification for focusing on the exclusive genome organization of this population and uncovers previously overlooked elements of the genome.

Influence of reaction cell electrodes on organic electrochemical transistors

Organic electrochemical transistors (OECTs) hold great potential in various applications, including biosensing and neural network computation. Traditional “all-in-one” OECT device architecture faces the problems of unclear amplification mechanisms and complex side reactions, to name a few. The reaction cell OECT (RC-OECT) device architecture, proposed by Ting et al. [Adv. Funct. Mater. 31(19), 2010868 (2021)], effectively resolves these problems. Furthermore, in many applications of OECTs, such as high throughput (bio)sensing, an OECT device array instead of a single OECT is needed. Therefore, the size (area) of the OECT device, which represents the amount of occupied chip real estate and the integration of the device, matters. In this paper, we developed a hydrogen peroxide sensor based on the RC-OECT. We utilized an RC cathode modified by the poly(3,4-ethylenedioxythiophene) polystyrene sulfonate film and a Ag/AgCl OECT gate electrode for facilitating device integration, varied RC anode area, and achieved optimization of at least one of the two parameters, sensitivity and lower limit of detection (LLoD), in conjunction with the level of integration of the device. Multiple quantitative sensitivity metrics have been adopted in this work. We also evaluated the correlation between RC anode area and LLoD. In addition, a mechanistic analysis of the RC-OECT device structure, in terms of faradic and non-faradaic currents, was carried out to illustrate the interplay between sensing performance and the electrode area of the reaction cell. This mechanistic analysis provides insights for miniaturizing OECT devices with the RC-OECT architecture.

Analysis and comparison of water vapor transport features and circulation anomalies during the super-strong Meiyu period of 2020 and 1998*

2020 and 1998 are the strongest Meiyu years in recent decades. The characteristics of the super-strong Meiyu precipitation and water vapor sources in 2020 and 1998 were compared, and the atmospheric circulation anomalies and the forcing factor SST were examined. (1) In 2020, the Meiyu duration, accumulated precipitation, and number of rainstorm days were greater than in 1998, and the highest since 1961. The Meiyu period in 2020 experienced 11 rainstorm processes. In 1998, a typical “second Meiyu” phenomenon occurred, and the area of heavy rainfall in 1998 was located further southward than that in 2020 (2) The contribution of the Bay of Bengal-South China Sea (BOB-SCS) to the total supply of water vapor in 2020 and 1998 was 43.0% and 42.0%, respectively, i.e., much higher than that of the climatological mean (25.5%). In 2020, the sources that provide most water vapor were the BOB, SCS, and central Pacific Ocean, while in 1998 were the Arabian Sea, BOB, and the western Pacific Ocean. (3) During the Meiyu period in 2020 and 1998, the position of atmospheric circulation pattern “two ridges and one trough” are different. Analysis of the vertical structure revealed that the specific humidity intensity above the area of heavy rainfall in 1998 was weaker than that in 2020, and the low-level convergence zone was further south and not as strong as in 2020. The positions of the western Pacific subtropical high (WPSH) and the western North Pacific anticyclone (WNPAC) in 1998 were both further south than those in 2020, which resulted in the more southerly locations of the southwesterly jet stream and rain belt. It should be pointed out that, the important contributions of the SST anomalies in the equatorial central eastern Pacific and the tropical Indian Ocean to the anomalous WNPAC in 1998 and 2020, respectively.

Фреймовая структура аллюзивного антропонима как художественного концепта (на материале романа Донны Тартт «Тайная история» / Donna Tartt “The Secret History”)

The aim of the paper is to establish and describe the frame structure of an allusive anthroponym as a representative of an literary concept on the basis of Donna Tartt’s novel “The Secret History”. It is shown that allusive anthroponyms belong to onomastic realities, connotative lexicon, activating the concepts of the literary text. The scientific novelty of the work consists in the cognitive approach to the analysis of the literary concept through the establishment of the frame structure of an allusive anthroponym as a representative of the textual concept on the material of Donna Tartt’s novel “The Secret History” and working out a methodological model of analysis of the frame structure of allusive anthroponym. It is shown that an allusive anthroponym has a frame structure including a number of cognitive components. An allusive anthroponym can represent a text frame and can act as a component of it, representing the author’s worldview, and contributing to the creation of an literary image. The obtained results have shown that an allusive anthroponym can serve as a means of verbalising a text frame, which has a structure including such conceptual componenets as the frame name, time, place of action, the subject of the frame, the relation between objects / participants of the action, the characteristic of the action (with the involvement of encyclopaedic information).

Genome-wide identification of the N6-methyladenosine regulatory genes reveals NtFIP37B increases drought resistance of tobacco (Nicotiana tabacum L.)

BackgroundN6-methyladenosine (m6A) is one of the common internal RNA modifications found in eukaryotes. The m6A modification can regulate various biological processes in organisms through the modulation of alternative splicing, alternative polyadenylation, folding, translation, localization, transport, and decay of multiple types of RNA, without altering the nucleotide sequence. The three components involved in m6A modification, namely writer, eraser, and reader, mediate the abundance of RNA m6A modification through complex collaborative actions. Currently, research on m6A regulatory genes in plants is still in its infancy.ResultsIn this study, we identified 52 candidate m6A regulatory genes in common tobacco (Nicotiana tabacum L.). Gene structure, conserved domains, and motif analysis showed structural and functional diversity among different subgroups of tobacco m6A regulatory genes. The amplification of m6A regulatory genes were mainly driven by polyploidization and dispersed duplication, and duplicated genes evolved through purified selection. Based on the potential regulatory network and expression pattern analysis of m6A regulatory genes, a significant number of m6A regulatory genes might play important roles in growth, development, and stress response processes. Furthermore, we have confirmed the critical role of NtFIP37B, an m6A writer gene in tobacco, in enhancing drought resistance.ConclusionsThis study provides useful information for better understanding the evolution of m6A regulatory genes and the role of m6A modification in tobacco stress response, and lays the foundation for further elucidating the function of m6A regulatory genes in tobacco.

Effect of fast heating rate and alkaline catalyst on composition and characteristic of volatile products during catalytic upgrading of oil sand bitumen

The study was devoted to exploring the fundamental study on the upgrading of Buton oil sand bitumen (OSB) via fast alkaline catalytic pyrolysis based on the fluid pyrolysis technology. The effect of fast heating rate on the composition and molecular distribution of volatile products from the high-temperature fast pyrolysis of OSB was investigated by Py-GC/TOF-MS that could simulate the fast heating rate of industrial fluid pyrolysis process. The results showed that the volatile products of OSB under heating rates ranging from 10 to 1000 °C/s had the similar species composition. It was found that there were the highest relative content of low-carbon alkenes (C2-C4) and light aromatics (C6-C8) in volatile products under the 1000 °C/s, indicating that the fast heating rate favored the production of light alkenes and aromatics. Subsequently, a laboratory-scale fluidized bed apparatus was employed to further gain insight into fast alkaline catalytic pyrolysis behaviors of OSB. The investigation on the yield distribution, fractional- and molecular-level chemical characteristic of volatile products obtained from the fast alkaline catalytic upgrading of OSB over calcium aluminate was carried out with the aid of the comparison with that over Y zeolite-based FCC catalyst and silica sand. The results revealed that three-phase products over calcium aluminate possessed the larger selectivity of C2−C4 alkenes, larger yield of light oil and the lower coke output, which were 51.88%, 45.49% and 7.96%, respectively. On basis of the chemical structure analysis of liquid products, the alkaline catalytic upgrading of OSB over calcium aluminate could heighten the content of chain alkyl structures as well as alkyl-substituents attached to aromatic ring in liquid products. This indicated that the fast heating rate and alkaline catalyst that adopted in catalytic upgrading process of OSB could play an energetic role in optimizing the composition of volatile products. The alkaline catalytic upgrading of OSB based on fluid pyrolysis technology with the fast heating rate could heighten the yield of low-carbon olefins and light oil and lessen coke yield, meanwhile modify the chemical structure characteristics of liquid products that were conducive to the generation of valuable chemicals (light alkanes and BTX) during secondary processing of liquid products.

Detection of driver mutations and genomic signatures in endometrial cancers using artificial intelligence algorithms.

Analyzed endometrial cancer (EC) genomes have allowed for the identification of molecular signatures, which enable the classification, and sometimes prognostication, of these cancers. Artificial intelligence algorithms have facilitated the partitioning of mutations into driver and passenger based on a variety of parameters, including gene function and frequency of mutation. Here, we undertook an evaluation of EC cancer genomes deposited on the Catalogue of Somatic Mutations in Cancers (COSMIC), with the goal to classify all mutations as either driver or passenger. Our analysis showed that approximately 2.5% of all mutations are driver and cause cellular transformation and immortalization. We also characterized nucleotide level mutation signatures, gross chromosomal re-arrangements, and gene expression profiles. We observed that endometrial cancers show distinct nucleotide substitution and chromosomal re-arrangement signatures compared to other cancers. We also identified high expression levels of the CLDN18 claudin gene, which is involved in growth, survival, metastasis and proliferation. We then used in silico protein structure analysis to examine the effect of certain previously uncharacterized driver mutations on protein structure. We found that certain mutations in CTNNB1 and TP53 increase protein stability, which may contribute to cellular transformation. While our analysis retrieved previously classified mutations and genomic alterations, which is to be expected, this study also identified new signatures. Additionally, we show that artificial intelligence algorithms can be effectively leveraged to accurately predict key drivers of cancer. This analysis will expand our understanding of ECs and improve the molecular toolbox for classification, diagnosis, or potential treatment of these cancers.

The dopamine D2 receptors antagonist Veralipride inhibits carbonic anhydrases: solution and crystallographic insights on human isoforms.

The inhibitory effects of veralipride, a benzamide-class antipsychotic acting as dopamine D2 receptors antagonist incorporates a primary sulfonamide moiety and was investigated for its interactions with carbonic anhydrase (CA) isoforms. In vitro profiling using the stopped-flow technique revealed that veralipride exhibited potent inhibitory activity across all tested hCA isoforms, with exception of hCA III. Comparative analysis with standard inhibitors, acetazolamide (AAZ), and sulpiride, provided insights for understanding the relative efficacy of veralipride as CA inhibitor. The study reports the X-ray crystal structure analysis of the veralipride adduct with three human (h) isoforms, hCA I, II, and CA XII mimic, allowing the understanding of the molecular interactions rationalizing its inhibitory effects against each isoform. These findings contribute to our understanding of veralipride pharmacological properties and for the design of structural analogs endowed with polypharmacological properties.

Validitas Modul Pembelajaran Biologi Materi Jaringan Pada Tumbuhan Kelas XI. IPA MAN 1 Solok Selatan

A module is a type of teaching material that is packaged completely and systematically. MAN 1 Solok Selatan already has teaching materials, namely textbooks. In terms of the availability of textbooks at the school, it is not sufficient for the number of students, so not all students can borrow textbooks. There are shortcomings in the package book, namely that the material in the book is still minimal, as well as a lack of pictures of plant tissue. This research aims to produce a module on tissue material in plants for class XI. IPA MAN 1 Solok Selatan which is very valid and very practical. This research was conducted in the odd semester of the 2023/2024 academic year in class XI. IPA at MAN 1 Solok Selatan. This research is development research using a 4-D model which includes 4 stages, namely the define, design, develop and disseminate stages. This research was only carried out at the develop stage, namely validity testing. In the define stage, front end analysis is carried out (using questionnaires and interviews), student analysis, and task analysis starting from content structure analysis, concept analysis and learning objective analysis. The design stage is carried out by designing modules. In the develop stage, a validity test was carried out by filling out a questionnaire by 2 lecturers and 1 Biology teacher. Data were analyzed using percentage techniques and processed using descriptive analysis. The validity results by lecturers and teachers obtained an average of 91.81% with very valid criteria. It can be concluded that the module on plant tissue material for class XI IPA MAN 1 South Solok that was developed is very valid.

Analysis of Genetic Diversity and Structure of Eight Populations of Nerita yoldii along the Coast of China Based on Mitochondrial COI Gene.

Nerita yoldii is a euryhaline species commonly found in the intertidal zone. To investigate the genetic diversity of 233 N. yoldii individuals from eight locations along the coast of China, we utilized the mitochondrial COI gene as a molecular marker. A total of 34 haplotypes were detected, exhibiting a mean haplotype diversity (Hd) of 0.5915 and a mean nucleotide diversity (Pi) of 0.0025, indicating high levels of genetic diversity among all populations. An analysis of molecular variance (AMOVA) indicated that the primary source of genetic variation occurs within populations. In addition, neutral tests and mismatch analyses suggested that N. yoldii populations may have experienced bottleneck events. Moderate genetic differentiation was observed between Xiapu and other populations, excluding the Taizhou population, and may be attributed to the ocean currents. Intensively studying the genetic variation and population structure of N. yoldii populations contributes to understanding the current population genetics of N. yoldii in the coastal regions of China. This not only provides a reference for the study of other organisms in the same region but also lays the foundation for the systematic evolution of the Neritidae family.

Unveiling the dynamic expression of PR-1 during Musa spp. infection by Fusarium oxysporum fsp. Cubense: a cloning and characterization study.

Pathogen-related proteins (PR) are pivotal in plant defense, combating diverse biotic and abiotic stresses. While multiple gene families contribute to banana resistance against Fusarium oxysporum f sp. cubense (Foc), Pseudocercospora eumusae, and Pratylenchus coffeae, the significance of PR-1 genes in defense is paramount. Three PR-1 genes, up-regulated under diverse biotic stresses, were cloned from both resistant and susceptible cultivars of Foc, P. eumusae, and P. coffeae. Molecular characterization, phylogenetic analysis, and docking studies with the Foc TR4 CP gene were conducted. Through transcriptomic and real-time studies, three PR-1 genes (Ma02_g15050, Ma02_g15060, and Ma04_g34800) from Musa spp. were identified. These genes exhibited significant up-regulation in resistant cultivars when exposed to Foc, P. eumusae, and P. coffeae. Cloning of these genes was successfully performed from both resistant and susceptible cultivars of Foc race 1 and TR4, P. eumusae, and P. coffeae. Distinct characteristics were observed among the PR-1 genes, with groups 1 and 2 being acidic with signal peptides, and group 3 being basic without signal peptides. All cloned PR-1 proteins belonged to the CAP superfamily (PF00188). Phylogenetic analysis revealed clustering patterns for acidic PR-1 proteins, and KEGG orthology showed associations with vital pathways, including MAPK signaling, plant hormone signal transduction, and plant-pathogen interaction. Secondary and tertiary structure analyses confirmed sequence conservation across studied species. Docking studies explored interactions between the cerato-platanin (CP) gene from Foc TR4 and Ma02_g15060 from banana, suggesting the potential hindrance of PR-1 antifungal activity through direct interaction. The findings underscore the crucial role of cloned PR-1 genes in banana plant defense mechanisms against a broad spectrum of biotic stresses. These genes, especially those in groups 1 and 2, hold promise as candidates for developing stress-tolerant banana cultivars. The study provides valuable insights into the molecular aspects of banana defense strategies, emphasizing the potential applications of PR-1 genes in enhancing banana resilience.

Do phylogenetic community metrics reveal the South African quartz fields as terrestrial-habitat islands?

The quartz fields of the Greater Cape Floristic Region (GCFR) are arid and island-like special habitats, hosting ~142 habitat-specialized plant species, of which 81 % are local endemics, characterized by a rapid turnover of species between and among sites. We use several phylogenetic community metrics: (1) to examine species diversity and phylogenetic structure within and among quartz fields; (2) to investigate whether quartz field specialists are evolutionarily drawn from local species pools, whereas the alternative hypothesis posits that there is no significant evolutionary connection between quartz field specialists and the local species pools; and (3) to determine whether there is an association between certain traits and the presence of species in quartz fields. We sampled and developed dated phylogenies for six species-rich angiosperm families (Aizoaceae, Asteraceae, Crassulaceae, Cyperaceae, Fabaceae and Santalaceae) represented in the quartz field floras of southern Africa. Specifically, we focused on the flora of three quartz field regions in South Africa (Knersvlakte, Little Karoo and Overberg) and their surrounding species pools to address our research questions by scoring traits associated with harsh environments. We found that the Overberg and Little Karoo had the highest level of species overlap for families Aizoaceae and Fabaceae, whereas the Knersvlakte and the Overberg had the highest species overlap for families Asteraceae, Crassulaceae and Santalaceae. Although our phylogenetic community structure and trait analyses showed no clear patterns, relatively low pairwise phylogenetic distances between specialists and their local species pools for Aizoaceae suggest that quartz species could be drawn evolutionarily from their surrounding areas. We also found that families Aizoaceae and Crassulaceae in Knersvlakte and Little Karoo were phylogenetically even. Despite their proximity to one another within the GCFR, the studied areas differ in their species pools and the phylogenetic structure of their specialists. Our work provides further justification for increased conservation focus on these unique habitats under future scenarios of global change.

Biofloc supplementation improves growth performances, nutrient utilization, and histological status of Nile tilapia (Oreochromis niloticus) while enhancing zooplankton diversity, community, and abundance

The present work investigates the effect of biofloc supplementation, as an environmentally clean aqua-feed technique, on water quality, growth performance, feed utilization, and histological status of Nile tilapia (Oreochromis niloticus). Moreover, indicators of zooplankton diversity, community structure, abundance, similarities, and cluster analysis were studied during the experiment. A 60-day growth experiment based on biofloc supplementation was performed to evaluate, in addition to the control group (BF0), the effects of five groups of biofloc supplementation (BF1 = 14.20, BF2 = 28.40, BF3 = 42.60, BF4 = 56.80, and BF5 = 71.0 g L−1, respectively) on Nile tilapia juveniles (initial body weight: 13.30 ± 0.01 g fish−1). During the 15 days of acclimation, the juveniles in all groups were fed twice daily on the same control diet (a commercial diet containing 28% protein). Then, the juveniles were randomly distributed to 18 tanks (each 0.5 m3 with a stocking of 40 fish/tank). The feed rate was 3% of the total fish biomass, adjusted weekly. The water quality indicators were in the ideal range recommended for Nile tilapia culture. The results found that the highest weight gain, specific growth rate and survival rate, and the lowest feed conversion ratio of fish were reported in the BF5 group. Moreover, this group achieved the highest zooplankton abundance (20,706 Ind. L−1) compared to the control group (457 Ind. L−1). The results showed that sections of the muscles in the control group (BF0) revealed fibers arranged into bundles. Comparisons between the muscles in the control group (BF0) and the bioflocs groups (BF1–BF5) showed unclear differences. However, sections of the muscle group BF1 showed increased splitting of muscle fibers and the separation of individual muscle fibers into smaller units. The liver showed multiple pathological lesions in all experimental groups (BF0–BF5). Zooplankton diversity indicators and cluster analysis data also reported a significant difference between the control group (BF0) and the biofloc groups, especially the BF5 group. The present study concluded that the addition of biofloc (71 g L−1) to culture ponds significantly improves the growth, feed utilization, and survival rates of Nile tilapia while enhancing zooplankton diversity, community, and abundance.

Electronic structure analysis of Bi2WO6 and observation of near infrared emission on Nd3+doping

A simple solid-state reaction method is used to synthesize novel Nd3+doped Bi2WO6 materials and some novel results are reported for the first time. The samples of pristine and Nd3+ doped Bi2WO6, prepared by the precipitation and combustion methods, exhibit poor crystallinity. The pattern remains similar indicating that there is little change in the overall crystal structure after doping. We noticed that luminescence studies on Bi2WO6 are rare. The characteristic line emission with most intense emission at 1071 nm is observed in Nd3+doped Bi2WO6. Most intense excitation can be derived from f-f transitions. The emission can be excited using various wavelengths throughout the visible and NIR region. Transfer among activator ions restricts the luminescence intensity by concentration quenching. There is also a weak excitation band which corresponds to host sensitization. This band in the range 320–440 nm arises from Bi3+-W6+metal-to-metal charge transfer. The calculated critical distance for such transfer is found to be 22.65 Å. Thus, intense NIR emission around 1071 nm which can be pumped using various wavelengths throughout the visible and NIR region is observed in Bi2WO6:Nd3+. This can be useful in various applications like telecommunication, bio-imaging with the second biological window (NIR II: 1000–1500 nm), fluorescent cooling, photo morphogenesis etc. The density functional theory (DFT) simulations also support the experimental findings, confirming the electronic properties, nonmagnetic state, and the band gap of pristine and Nd3+doped Bi2WO6 after adding proper electron correlations for W-d states and Nd-f states.

New insights for simultaneous nutrient removal enhancement and greenhouse gas emissions reduction of constructed wetland by optimizing its redox environment through manganese oxide addition

Manganese oxide (MnOx) is receiving increased interest in the nutrient removal of constructed wetlands (CWs); however, its service effectiveness for simultaneous greenhouse gas (GHG) emissions reduction is still vague. In this study, three vertical flow CWs, i.e., volcanics (CCW), manganese sand uniformly mixing with volcanics (Mn-CW) and MnOx doped volcanics (MnV-CW), were constructed to investigate the underlying mechanisms of MnOx on nutrient removal enhancement and greenhouse gas (GHG) emissions reduction. The results showed that the MnOx doped volcanics optimized the oxidation–reduction potential surrounding the substrate (-164.0 ∼ +141.1 mv), and resulted in the lowest GHG emissions (CO2-equivalent) from MnV-CW, 16.8–36.5 % lower than that of Mn-CW and CCW. This was mainly ascribed to mitigation of N2O produced during the NO3−-N reduction process, according to results of 15N stable isotope labeling. Analysis of the microbial community structure revealed that due to the optimized redox conditions through chemical doping of MnOx on volcanics, the abundance of microbe involved in denitrification and Mn-oxidizing process in the MnV-CW was significantly increased at genus level, which led to a higher Mn cycling efficiency between biogenic MnOx and Mn2+, and enhanced denitrification efficiency and N2O emission reduction. This study would help to understand and provide a preferable reference for future applications for manganese-based CW.

Structural determinants of cold activity and glucose tolerance of a family 1 glycoside hydrolase (GH1) from Antarctic Marinomonas sp. ef1.

Cold-active enzymes support life at low temperatures due to their ability to maintain high activity in the cold and can be useful in several biotechnological applications. Although information on the mechanisms of enzyme cold adaptation is still too limited to devise general rules, it appears that very diverse structural and functional changes are exploited in different protein families and within the same family. In this context, we studied the cold adaptation mechanism and the functional properties of a member of the glycoside hydrolase family 1 (GH1) from the Antarctic bacterium Marinomonas sp. ef1. This enzyme exhibits all typical functional hallmarks of cold adaptation, including high catalytic activity at 5 °C, broad substrate specificity, low thermal stability, and higher lability of the active site compared to the overall structure. Analysis of the here-reported crystal structure (1.8 Å resolution) and molecular dynamics simulations suggest that cold activity and thermolability may be due to a flexible region around the active site (residues 298-331), whereas the dynamic behavior of loops flanking the active site (residues 47-61 and 407-413) may favor enzyme-substrate interactions at the optimal temperature of catalysis (Topt) by tethering together protein regions lining the active site. Stapling of the N-terminus onto the surface of the β-barrel is suggested to partly counterbalance protein flexibility, thus providing a stabilizing effect. The tolerance of the enzyme to glucose and galactose is accounted for by the presence of a "gatekeeping" hydrophobic residue (Leu178), located at the entrance of the active site.

Catalytic mechanism of sulfur-nitrogen doping metal single-atom graphene-based catalysts for the conversion of CO2 to CH4: A computational study

The conversion of CO2 into renewable fuel (CH4) has significant environmental and economic benefits. Graphene-supported single-atom catalysts (SACs) show promise as electrocatalysts for the carbon dioxide reduction reaction (CO2RR). In this study, using spin-polarized density functional theory (DFT) calculations, we investigate the potential for converting CO2 to CH4 on the representative SACs, specifically graphene-supported TM-N-S (transition metal-nitrogen-sulfur). The results show that TM-N-S can break the scaling relationship between the adsorption energy of *CHO and *OCH2. The free energy profiles indicate that among the candidate TM-N-S SACs, Fe, Co, and Ni-N-S stand out with low overpotentials of 0.23, 0.40, and 0.39 V, respectively. Compared with the competing hydrogen evolution reaction (HER), they exhibit higher CO2 selectivity and catalytic activity. Analysis of electronic structure and charge variations reveals the origin of CO2RR activity and the binding strength between catalyst and intermediate. This work uncovers the potential mechanism of CO2RR, providing valuable insights into the conversion of CO2 to CH4 via TM-N-S catalysis and offering novel perspectives for the design and screening of efficient SACs for CO2RR.

Effects of Different Antioxidant Intercalated Layered Double Hydroxides on Anti-Aging Properties of Asphalt Binders

This research aims to prepare different antioxidant intercalated layered double hydroxides (LDHs) and compare the thermal oxidation and ultraviolet (UV) aging resistances of different modified asphalts. The ion exchange technique was used to intercalate three different antioxidants: 3-(3,5-di-tert-butyl-4-carboxyphenyl) propionic acid, antioxidant 1222, and sodium dibutyl dithiocarbamate (rubber accelerator TP) into the interlayer of LDHs. The morphology, structures, UV blocking, and free radical scavenging properties of different antioxidant intercalated LDHs were characterized, respectively. The effects of the anti-aging agents on the physical properties (penetration, softening point, ductility, and viscosity); rheological behaviors (complex modulus and phase angle); and functional groups (C=O and S=O) of asphalt both before and after thermal oxidation aging and UV aging were systematically investigated. The results of the crystal structure and functional group analysis show that the three different antioxidants can be successfully inserted into the interlayer of LDHs without destroying their layered structures. Antioxidant intercalated LDHs exhibit a remarkable capacity for absorbing UV rays, coupled with a moderate ability to reflect UV light. Moreover, the inclusion of antioxidants into the interlayers of LDHs confers upon them the ability to scavenge free radicals. After 2 h of reaction, the free radical scavenging rates of LDHs-3, LDHs-1222, and LDHs-TP were 57.7%, 35.6%, and 17.1%, respectively. With an increase in the content of the antioxidant intercalated LDHs, the performance of the modified asphalt varies, and 4% is the optimal content of the anti-aging agents. Asphalts with the three antioxidant intercalated LDHs all had favorable storage stability, and their physical and rheological properties were improved after aging compared to LDHs-modified asphalt. The LDHs-3-modified asphalt showed the best anti-ultraviolet aging effect, while LDHs-1222-modified asphalt showed the best anti-thermal oxidation aging effect. This research lays the foundation for developing aging-resistant asphalt and improving the durability of asphalt pavement.

Evaluation of Genetic Diversity and Agronomic Traits of Germplasm Resources of Stropharia rugosoannulata

China possesses abundant wild germplasm resources and a wide range of cultivated strains of Stropharia rugosoannulata. However, issues such as genetic diversity and unclear genetic relationships have had an impact on the classification and preservation of germplasm resources, the breeding of new varieties, and the promotion of superior strains. There is an urgent need for genetic diversity analysis and assessment of germplasm resources. In this study, we conducted whole-genome resequencing of 50 cultivated and wild strains collected from various regions across the country. After applying a series of filtering parameters, we obtained 888,536 high-quality Single Nucleotide Polymorphism (SNP) markers. Using these SNP markers, we performed principal component analysis, population structure analysis, and phylogenetic clusters analysis on the 50 strains. Most cultivated strains exhibited high genetic similarity, while significant genetic diversity was observed among wild strains. Based on factors such as marker distribution throughout the entire genome and marker quality, we selected 358 core SNP markers to construct SNP fingerprints. Two-dimensional barcodes were generated for each strain to enable specific identification. Additionally, the mycelial growth rate of strains was evaluated on Potato Dextrose Agar (PDA) and substrate culture media. We also assessed their lignin degradation capability using guaiacol agar plates assay. It was observed that the mycelial growth rate on PDA and substrate culture medium exhibited a significant correlation with the diameter of the mycelial colony on guaiacol agar medium. Additionally, the correlation between the mycelial growth rate on the substrate medium and that on the guaiacol agar plate was stronger than that on PDA medium. This study provided molecular-level identification and assessment of germplasm resources. It clarified the genetic relationships among strains and the characteristics of mycelium growth-related agronomic traits of each strain. This research contributed to the enrichment and development of utilizable germplasm resources and breeding materials for S. rugosoannulata, offering a scientific basis for further research.