Genome-Wide Identification and Functional Analysis of the TIFY Family Genes in Response to Abiotic Stresses and Hormone Treatments in Tartary Buckwheat (Fagopyrum tataricum).

TIFY is a plant-specific gene family with four subfamilies: ZML, TIFY, PPD, and JAZ. Recently, this family was found to have regulatory functions in hormone stimulation, environmental response, and development. However, little is known about the roles of the TIFY family in Tartary buckwheat (Fagopyrum tataricum), a significant crop for both food and medicine. In this study, 18 TIFY family genes (FtTIFYs) in Tartary buckwheat were identified. The characteristics, motif compositions, and evolutionary relationships of the TIFY proteins, as well as the gene structures, cis-acting elements, and synteny of the TIFY genes, are discussed in detail. Moreover, we found that most FtTIFYs responded to various abiotic stresses (cold, heat, salt, or drought) and hormone treatments (ABA, MeJA, or SA). Through yeast two-hybrid assays, we revealed that two FtTIFYs, FtTIFY1 and FtJAZ7, interacted with FtABI5, a homolog protein of AtABI5 involved in ABA-mediated germination and stress responses, implying crosstalk between ABA and JA signaling in Tartary buckwheat. Furthermore, the overexpression of FtJAZ10 and FtJAZ12 enhanced the heat stress tolerance of tobacco. Consequently, our study suggests that the FtTIFY family plays important roles in responses to abiotic stress and provides two candidate genes (FtJAZ10 and FtJAZ12) for the cultivation of stress-resistant crops.

Trypanosomes have six mitochondrial DNA helicases with one controlling kinetoplast maxicircle replication.

Kinetoplast DNA (kDNA), the trypanosome mitochondrial DNA, contains thousands of minicircles and dozens of maxicircles interlocked in a giant network. Remarkably, Trypanosoma brucei's genome encodes 8 PIF1-like helicases, 6 of which are mitochondrial. We now show that TbPIF2 is essential for maxicircle replication. Maxicircle abundance is controlled by TbPIF2 level, as RNAi of this helicase caused maxicircle loss, and its overexpression caused a 3- to 6-fold increase in maxicircle abundance. This regulation of maxicircle level is mediated by the TbHslVU protease. Previous experiments demonstrated that RNAi knockdown of TbHslVU dramatically increased abundance of minicircles and maxicircles, presumably because a positive regulator of their synthesis escaped proteolysis and allowed synthesis to continue. Here, we found that TbPIF2 level increases following RNAi of the protease. Therefore, this helicase is a TbHslVU substrate and an example of a positive regulator, thus providing a molecular mechanism for controlling maxicircle replication.

A study on the influence of academic passion on PhD students' research engagement-The role of ambidextrous learning and academic climate.

The engagement in research, as the primary form of learning engagement for PhD students, is crucial for enhancing their competitive edge. Academic passion, a key determinant of learning engagement, plays a significant role in driving the research enthusiasm of PhD students. However, the "black box" concerning whether and how academic passion influences PhD students' research engagement remains to be explored. Addressing this gap, the present study draws upon self-determination theory, adopts the "motivation-behavior-effect" analytical framework, and incorporates ambidextrous learning as a mediator to elucidate the specific pathway through which academic passion impacts PhD students' engagement in research activities. Furthermore, it examines the facilitating role of the academic climate in this process. From December 2022 to March 2023, a questionnaire survey was conducted, collecting 522 responses from PhD students across 25 universities in China. The survey primarily assessed the PhD students' academic passion, ambidextrous learning behaviors (including tendencies towards exploratory and exploitative learning), and their perceived academic climate, investigating how these factors collectively influence their engagement in research activities. The questionnaire data were analyzed using a combination of SEM and bootstrapping with SPSS 26.0 and Mplus 8.3 software. The findings reveal that academic passion significantly positively affects PhD students' research engagement; ambidextrous learning (exploratory and exploitative learning) mediates the relationship between academic passion and PhD students' research engagement; and the academic climate effectively facilitates the transformation of PhD students' academic passion into ambidextrous learning (exploratory and exploitative learning). The study's conclusions not only foster PhD students' enthusiasm for research but also enhance learning effectiveness and innovation vitality, providing a theoretical basis for reforming the doctoral training system.

Transcriptomic analysis to identify genes associated with hypothalamus vulnerability in aging mice with cognitive decline.

The normal aging process is accompanied by cognitive decline, and previous studies have indicated the crucial role of the hypothalamus in regulating both aging and cognition. However, the precise molecular mechanism underlying this relationship remains unclear. Therefore, this present study aimed to identify potential predictors of cognitive decline associated with aging specifically within the hypothalamus. To achieve this, we employed Morris water maze (MWM) testing to assess learning and memory differences between young and aged mice. Additionally, transcriptome sequencing was conducted on the hypothalamus of young and aged mice to identify potential genes. Subsequently, GO and KEGG analyses were performed to investigate the functions of differentially expressed genes (DEGs) and their associated biological pathways. Finally, the results obtained from sequencing analysis were further validated using qRT-PCR. Notably, MWM testing revealed a significant decrease in spatial learning and memory ability among aged mice. According to KEGG analysis, the DEGs primarily encompassed various biochemical signaling pathways related to immune system (e.g., C3; C4b; Ccl2; Ccl7; Cebpb; Clec7a; Col3a1; Cxcl10; Cxcl2; Fosb; Fosl1; Gbp5; H2-Ab1; Hspa1a; Hspa1b; Icam1; Il1b; Itga5; Itgax; Lilrb4a; Plaur; Ptprc; Serpine1; Tnfrsf10b; Tnfsf10), neurodegenerative disease (e.g., Atp2a1; Creb5; Fzd10; Hspa1a; Hspa1b; Il1b; Kcnj10; Nxf3; Slc6a3; Tubb6; Uba1y; Wnt9b), nervous system function (e.g., Chrna4; Chrna6; Creb5; Slc6a3),and aging (e.g., Creb5; Hspa1a; Hspa1b) among others. These identified genes may serve as potential predictors for cognitive function in elderly individuals and will provide a crucial foundation for further exploration into the underlying molecular mechanisms.

Phytohormones regulate the non-redundant response of ω-3 fatty acid desaturases to low temperatures in Chorispora bungeana.

To explore the contributions of ω-3 fatty acid desaturases (FADs) to cold stress response in a special cryophyte, Chorispora bungeana, two plastidial ω-3 desaturase genes (CbFAD7, CbFAD8) were cloned and verified in an Arabidopsis fad7fad8 mutant, before being compared with the microsomal ω-3 desaturase gene (CbFAD3). Though these genes were expressed in all tested tissues of C. bungeana, CbFAD7 and CbFAD8 have the highest expression in leaves, while CbFAD3 was mostly expressed in suspension-cultured cells. Low temperatures resulted in significant increases in trienoic fatty acids (TAs), corresponding to the cooperation of CbFAD3 and CbFAD8 in cultured cells, and the coordination of CbFAD7 and CbFAD8 in leaves. Furthermore, the cold induction of CbFAD8 in the two systems were increased with decreasing temperature and independently contributed to TAs accumulation at subfreezing temperature. A series of experiments revealed that jasmonie acid and brassinosteroids participated in the cold-responsive expression of ω-3 CbFAD genes in both C. bungeana cells and leaves, while the phytohormone regulation in leaves was complex with the participation of abscisic acid and gibberellin. These results point to the hormone-regulated non-redundant contributions of ω-3 CbFADs to maintain appropriate level of TAs under low temperatures, which help C. bungeana survive in cold environments.

Comparative analysis of allele frequencies of 15 deafness gene variants between hearing-loss and normal populations in Henan, China.

Background: Hearing loss is found in more than 5 % of cases worldwide. Hearing loss is divided into three types: Sensorineural hearing loss, Combined hearing loss and Conductive hearing loss. Among them, no less than 50 % of pediatric cases of sensorineural hearing loss are genetic. In Henan, China, there are no statistics on the allele frequency of deafness gene variants. Methods: We divided 2178 subjects enrolled at the Third Affiliated Hospital of Zhengzhou College from January 2019 to March 2021 into a hearing loss group and a normal control group. We performed array and pathogenicity classification for screening the 15 deafness gene variants, calculated and compared the allele frequency of the deafness gene variants, and then compared the hearing loss diagnosis rate between the hearing loss group and the normal control group. Results: We found that in the hearing loss group, the overall allele frequency of all detected variants was 16.6 %. Comparative analysis showed that the allele frequencies of GJB2 c.235delC variant, GJB3 c.538C > T variant and SLC26A4 c.919-2A > G variant were significantly higher than those of the East Asian population average in the gnomAD database. At the same time, our study confirmed that GJB3 c.538C > T variant may not be the disease-causing variant of hearing loss. Conclusions: These results support genetic counseling and rational prediction of risk for deafness.

p166, a link between the trypanosome mitochondrial DNA and flagellum, mediates genome segregation.

Kinetoplast DNA (kDNA), the trypanosome mitochondrial genome, is a giant network containing several thousand interlocked DNA rings. Within the mitochondrion, kDNA is condensed into a disk-shaped structure positioned near the flagellar basal body. The disk is linked to the basal body by a remarkable transmembrane filament system named the tripartite attachment complex (TAC). Following kDNA replication, the TAC mediates network segregation, pulling the progeny networks into the daughter cells by their linkage to the basal bodies. So far TAC has been characterized only morphologically with no known protein components. By screening an RNAi library, we discovered p166, a protein localizing between the kDNA and basal body in intact cells and in isolated flagellum-kDNA complexes. RNAi of p166 has only small effects on kDNA replication, but it causes profound defects in network segregation. For example, kDNA replication without segregation causes the networks to grow to enormous size. Thus, p166 is the first reported molecular component of the TAC, and its discovery will facilitate study of kDNA segregation machinery at the molecular level.

Mn2+ Ions Capture and Uniform Composite Electrodes with PEI Aqueous Binder for Advanced LiMn2O4-Based Battery.

The electrode deterioration and capacity decay caused by the dissolution of transition metal ions have been criticized for a long time. The branched polyethyleneimine (PEI) was employed as a functional binder for spinel lithium manganese oxide (LiMn2O4, LMO) and layer structure lithium cobalt oxide (LiCoO2, LCO) to resolve the problem. Due to the chelation reaction of amine groups, PEI polymer binder can effectively absorb soluble transition metal ions, which is beneficial to reduce the loss of active materials. For PEI-based cathode, the uniform distribution of key components is achieved by the rapid curing process of water, which endow PEI-based cathode with a higher Li+ diffusion coefficient and improved electrochemical reaction kinetics. In addition, the fixed binder coating is favorable to protecting the active materials from parasitic reaction with the lithium hexafluorophosphate (LiPF6)-based electrolyte. Therefore, the PEI-based cell shows superior rate capability and long-term cycle performance. Functional binders of this study provide a simple and effective strategy to achieve higher capacity and longer cycle stability for transition metal oxide electrodes.

Protein arginine phosphorylation in organisms.

Protein arginine phosphorylation (pArg), a novel molecular switch, plays a key role in regulating cellular processes. The intrinsic acid lability, hot sensitivity, and hot-alkali instability of "high-energy" phosphoamidate (PN bond) in pArg, make the investigation highly difficult and challenging. Recently, the progress in identifying prokaryotic protein arginine kinase/phosphatase and assigning hundreds of pArg proteins and phosphosites has been made, which is arousing scientists' interest and passions. It shows that pArg is tightly connected to bacteria stress response and pathogenicity, and is probably implied in human diseases. In this review, we highlight the strategies for investigation of this mysterious modification and its momentous physiological functions, and also prospect for the potentiality of drugs development targeting pArg-relative pathways.

Solvophobic interaction promoted supramolecular helical assembly of building blocks of weak intermolecular halogen bonding.

We report supramolecular helical assembly in water of ß-turn structured bis(N-amidothioureas) containing Br-substitutes of moderate halogen bonding ability, promoted by stronger hydrophobic interaction. The helical polymers show an unusual negative nonlinear CD-ee dependence.

Yeast Template-Derived Multielectron Reaction NASICON Structure Na3MnTi(PO4)3 for High-Performance Sodium-Ion Batteries.

The sodium super ion conductor (NASICON) structure materials are essential for sodium-ion batteries (SIBs) due to their robust crystal structure, excellent ionic conductivity, and flexibility to regulate element and valence. However, the poor electronic conductivity and inferior energy density caused by the nature of these materials have always been obstacles to commercialization. Herein, using yeast as a template to derive NASICON structure Na3MnTi(PO4)3 (NMTP) materials (noted as Yeast@NMTP/C) is presented. The Yeast@NMTP/C material retains the microsphere morphology of the yeast template and not only controls the particle size (around 2 µm) to shorten the Na+ diffusion pathways but also improves the electronic conductivity to optimize the electrochemical kinetics. The Yeast@NMTP/C cathode delivers reversible multielectron redox reactions including Ti4+/3+, Mn3+/2+, and Mn4+/3+ and exhibits a high capacity of 108.5 mAh g-1 with a 79.2% capacity retention after 1000 cycles at a 2C rate. The sodium storage mechanism of Yeast@NMTP/C reveals that the addition of Ti4+/3+ redox plays a key role in improving the Na+ diffusion kinetics, and both solid-solution and two-phase reactions take place during the desodiation and sodiation process. Additionally, the high-rate and long-span cycle performance of Yeast@NMTP/C at 10C is ascribed to contribute to pseudocapacitance.

Role of metal cations and oxyanions in the regulation of protein arginine phosphatase activity of YwlE from Bacillus subtilis.

Protein arginine phosphorylation (pArg) is a relatively novel posttranslational modification. Protein arginine phosphatase YwlE negatively regulates arginine phosphorylation and consequently induces the expression of stress-response genes that are crucial for bacterial stress tolerance and pathogenic homolog Staphylococcus aureus virulence. However, little is known about the factors that affect the enzymatic activity of YwlE with the exception of the effect of oxidative stress. Herein, based on the hydrolysis of the chromogenic substrate p-nitrophenyl phosphate (pNPP) by YwlE, we investigate the role of metal cations and oxyanions in the regulation of YwlE activity. Interestingly, among the various cations that we tested, Ca2+ activates YwlE, while other cations, including Ag+, Co2+, Cd2+, and Zn2+, are inhibitory. Furthermore, as chemical analogues of phosphate, oxyanions play multiple roles in phosphatase activity. The regulatory switch Cys within the catalytic site regulates YwlE activity. Specifically, the thiol of this Cys could be alkylated by IAM (iodoacetamide) or oxidized by H2O2, resulting in enzymatic inhibition. Conversely, reducing reagents, such as DTT (dithiothreitol), ß-me (ß-mercaptoethanol), and TCEP (tris(2-carboxyethyl)phosphine) enhance YwlE activity. Additionally, as a stable analogue to pArg, pAIE binds to YwlE with a Kd of 149.1 nM and a binding stoichiometry n of 1.2 and inhibits YwlE with an IC50 of 316.3 ± 12.73 µM. The inhibition and activation of YwlE may have broad implications for the physiology, pharmacology and toxicology of metal cations and oxyanions.

Transmembrane Fluoride Transport by a Cyclic Azapeptide With Two ß-Turns.

Diverse classes of anion transporters have been developed, most of which focus on the transmembrane chloride transport due to its significance in living systems. Fluoride transport has, to some extent, been overlooked despite the importance of fluoride channels in bacterial survival. Here, we report the design and synthesis of a cyclic azapeptide (a peptide-based N-amidothiourea, 1), as a transporter for fluoride transportation through a confined cavity that encapsulates fluoride, together with acyclic control compounds, the analogs 2 and 3. Cyclic receptor 1 exhibits more stable ß-turn structures than the control compounds 2 and 3 and affords a confined cavity containing multiple inner -NH protons that serve as hydrogen bond donors to bind anions. It is noteworthy that the cyclic receptor 1 shows the capacity to selectively transport fluoride across a lipid bilayer on the basis of the osmotic and fluoride ion-selective electrode (ISE) assays, during which an electrogenic anion transport mechanism is found operative, whereas no transmembrane transport activity was found with 2 and 3, despite the fact that 2 and 3 are also able to bind fluoride via the thiourea moieties. These results demonstrate that the encapsulation of an anionic guest within a cyclic host compound is key to enhancing the anion transport activity and selectivity.

Effect of hydroxyurea on procyclic Trypanosoma brucei: an unconventional mechanism for achieving synchronous growth.

Procyclic Trypanosoma brucei cells were synchronized with 0.2 mM hydroxyurea. The cells did not arrest at the G(1)/S boundary but proceeded through one round of replication and arrested near the end of S phase. The mitochondrial genome (kinetoplast DNA network) replicated, forming two progeny networks, but the repair of minicircle gaps was inhibited.

Single-handed supramolecular double helix of homochiral bis(N-amidothiourea) supported by double crossed C-I···S halogen bonds.

The natural DNA double helix consists of two strands of nucleotides that are held together by multiple hydrogen bonds. Here we propose to build an artificial double helix from fragments of two strands connected by covalent linkages therein, but with halogen bonding as the driving force for self-assembling the fragments to the double helix. We succeed in building such a double helix in both solution and solid state, by using a bilateral N-(p-iodobenzoyl)alanine based amidothiourea which in its folded cis-form allows double and crossed C-I···S halogen bonds that lead to right- or left-handed double helix when the two alanine residues are of the same L,L- or D,D-configuration. The double helix forms in dilute CH3CN solution of the micromolar concentration level, e.g., 5.6 µM from 2D NOESY experiments and exhibits a high thermal stability in solution up to 75 °C, suggesting cooperative and thereby strong intermolecular double crossed halogen bonding that makes the double helix stable. This is supported by the observed homochiral self-sorting in solution.

A Cryophyte Transcription Factor, CbABF1, Confers Freezing, and Drought Tolerance in Tobacco.

Abscisic acid responsive element binding factors (ABFs) play crucial roles in plant responses to abiotic stress. However, little is known about the roles of ABFs in alpine subnival plants, which can survive under extreme environmental conditions. Here, we cloned and characterized an ABF1 homolog, CbABF1, from the alpine subnival plant Chorispora bungeana. Expression of CbABF1 was induced by cold, drought, and abscisic acid. Subcellular localization analysis revealed that CbABF1 was located in the nucleus. Further, CbABF1 had transactivation activity, which was dependent on the N-terminal region containing 89 residues. A Snf1-related protein kinase, CbSnRK2.6, interacted with CbABF1 in yeast two-hybrid analysis and bimolecular fluorescence complementation assays. Transient expression assay revealed that CbSnRK2.6 enhanced the transactivation of CbABF1 on ABRE cis-element. We further found that heterologous expression of CbABF1 in tobacco improved plant tolerance to freezing and drought stress, in which the survival rates of the transgenic plants increased around 40 and 60%, respectively, compared with wild-type plants. Moreover, the transgenic plants accumulated less reactive oxygen species, accompanied by high activities of antioxidant enzymes and elevated expression of stress-responsive genes. Our results thus suggest that CbABF1 is a transcription factor that plays an important role in cold and drought tolerance and is a candidate gene in molecular breeding of stress-tolerant crops.

Favorable Outcomes of Chinese HCV-Related Cirrhotic Patients with Sustained Virological Response after Pegylated Interferon Plus Ribavirin Treatment.

Few studies have conducted follow-up investigations of the clinical course in HCV-related cirrhotic patients who achieved a sustained virological response (SVR) with pegylated interferon plus ribavirin treatment (PegIFN + RBV). We investigated the clinical course and laboratory data in a prospective cohort study enrolling HCV-related cirrhotic patients who received PegIFN + RBV between August 2008 and July 2013 in China. Complete blood counts, liver function tests, and HCV-RNA were serially examined. Liver-related complications were recorded. To detect hepatocellular carcinoma (HCC), alpha-fetoprotein assays, and ultrasound scans were repeated at 6-month intervals. Twenty-five patients were enrolled, including 8 patients with decompensation events before treatment. Eighteen patients achieved SVR with a mean follow-up period of 25.78 months. During the follow-up period, only one patient exhibited HCV-RNA positivity and no decompensation events were detected, but 4 patients developed HCC after SVR. APRI decreased more in patients with SVR than in patients with non-SVR (median, -1.33 versus 0.86, P < 0.001). The albumin levels and platelet counts significantly increased during the follow-up period after SVR (44.27 ± 4.09 versus 42.63 ± 4.37, P = 0.037 and 173.89 ± 87.36 versus 160.11 ± 77.97, P = 0.047). These data indicated that HCV-related cirrhotic patients with SVR after PegIFN + RBV may have a favorable clinical course and improvements in laboratory data. Moreover, HCC should be monitored.

Viral Inactivation of Human Osteochondral Grafts with Methylene Blue and Light.

OBJECTIVE: Cartilage injury is one of the most common disorders of synovial joints. Fresh osteochondral allografts are becoming a standard treatment; however, they are supply constrained with a potential risk of disease transmission. There are no known virucidal processes available for osteochondral allografts and most methods presently available are detrimental to cartilage. Methylene blue light treatment has been shown to be successful in the literature for viral inactivation of fresh frozen plasma. The purpose of this study was to determine the capacity of methylene blue light treatment to inactivate a panel of clinically relevant viruses inoculated onto osteochondral allografts. DESIGN: Osteochondral grafts recovered from human cadaveric knees were inoculated with one of the following viruses: bovine viral diarrhea virus (BVDV), hepatitis A virus (HAV), human immunodeficiency virus type 1 (HIV-1), porcine parvovirus (PPV), and pseudorabies virus (PrV). The samples were processed through a methylene blue light treatment, which consisted of an initial soak in nonilluminated circulating methylene blue at ambient temperature, followed by light exposure with circulating methylene blue at cool temperatures. The final titer was compared with the recovery control for the viral log reduction. RESULTS: HIV-1, BVDV, and PrV were reduced to nondetectable levels while HAV and PPV were reduced by 3.1 and 5.6 logs, respectively. CONCLUSIONS: The methylene blue light treatment was effective in reducing (a) enveloped DNA and RNA viruses to nondetectable levels and (b) nonenveloped DNA and RNA viruses of inoculated human osteochondral grafts by 3.1 to 5.6 logs. This study demonstrates the first practical method for significantly reducing viral load in osteochondral implants.

Enhanced tissue regeneration potential of juvenile articular cartilage.

BACKGROUND: Articular cartilage undergoes substantial age-related changes in molecular composition, matrix structure, and mechanical properties. These age-related differences between juvenile and adult cartilage manifest themselves as markedly distinct potentials for tissue repair and regeneration. PURPOSE: To compare the biological properties and tissue regeneration capabilities of juvenile and adult bovine articular cartilage. STUDY DESIGN: Controlled laboratory study. METHODS: Articular cartilage harvested from juvenile (age, 4 months) and adult (age, 6-8 years) bovine femoral condyles was cultured for 4 weeks to monitor chondrocyte migration, glycosaminoglycan content conservation, and new tissue formation. The cartilage cell density and proliferative activity were also compared. Additionally, the effects of age-related changes on cartilage gene expression were analyzed using the Affymetrix GeneChip array. RESULTS: Compared with adult cartilage, juvenile bovine cartilage demonstrated a significantly greater cell density, higher cell proliferation rate, increased cell outgrowth, elevated glycosaminoglycan content, and enhanced matrix metallopeptidase 2 activity. During 4 weeks in culture, only juvenile cartilage was able to generate new cartilaginous tissues, which exhibited pronounced labeling for proteoglycan and type II collagen but not type I collagen. With over 19,000 genes analyzed, distinctive gene expression profiles were identified. The genes mostly involved in cartilage growth and expansion, such as COL2A1, COL9A1, MMP2, MMP14, and TGFB3, were upregulated in juvenile cartilage, whereas the genes primarily responsible for structural integrity, such as COMP, FN1, TIMP2, TIMP3, and BMP2, were upregulated in adult cartilage. CONCLUSION: As the first comprehensive comparison between juvenile and adult bovine articular cartilage at the tissue, cellular, and molecular levels, the results strongly suggest that juvenile cartilage possesses superior chondrogenic activity and enhanced regenerative potential over its adult counterpart. Additionally, the differential gene expression profiles of juvenile and adult cartilage suggest possible mechanisms underlying cartilage age-related changes in their regeneration capabilities, structural components, and biological properties. CLINICAL RELEVANCE: The results of this comparative study between juvenile and adult bovine articular cartilage suggest an enhanced regenerative potential of juvenile cartilage tissue in the restoration of damaged articular cartilage.