Glutamine metabolism-related genes and immunotherapy in nonspecific orbital inflammation were validated using bioinformatics and machine learning.

BACKGROUND: Nonspecific orbital inflammation (NSOI) is an idiopathic, persistent, and proliferative inflammatory condition affecting the orbit, characterized by polymorphous lymphoid infiltration. Its pathogenesis and progression have been linked to imbalances in tumor metabolic pathways, with glutamine (Gln) metabolism emerging as a critical aspect in cancer. Metabolic reprogramming is known to influence clinical outcomes in various malignancies. However, comprehensive research on glutamine metabolism's significance in NSOI is lacking. METHODS: This study conducted a bioinformatics analysis to identify and validate potential glutamine-related molecules (GlnMgs) associated with NSOI. The discovery of GlnMgs involved the intersection of differential expression analysis with a set of 42 candidate GlnMgs. The biological functions and pathways of the identified GlnMgs were analyzed using GSEA and GSVA. Lasso regression and SVM-RFE methods identified hub genes and assessed the diagnostic efficacy of fourteen GlnMgs in NSOI. The correlation between hub GlnMgs and clinical characteristics was also examined. The expression levels of the fourteen GlnMgs were validated using datasets GSE58331 and GSE105149. RESULTS: Fourteen GlnMgs related to NSOI were identified, including FTCD, CPS1, CTPS1, NAGS, DDAH2, PHGDH, GGT1, GCLM, GLUD1, ART4, AADAT, ASNSD1, SLC38A1, and GFPT2. Biological function analysis indicated their involvement in responses to extracellular stimulus, mitochondrial matrix, and lipid transport. The diagnostic performance of these GlnMgs in distinguishing NSOI showed promising results. CONCLUSIONS: This study successfully identified fourteen GlnMgs associated with NSOI, providing insights into potential novel biomarkers for NSOI and avenues for monitoring disease progression.

Comparative transcriptomic analysis primarily explores the molecular mechanism of compound eye formation in Neocaridina denticulata sinensis.

Compound eyes formation in decapod crustaceans occurs after the nauplius stage. However, the key genes and regulatory mechanisms of compound eye development during crustacean embryonic development have not yet been clarified. In this study, RNA-seq was used to investigate the gene expression profiles of Neocaridina denticulata sinensis from nauplius to zoea stage. Based on RNA-seq data analysis, the phototransduction and insect hormone biosynthesis pathways were enriched, and molting-related neuropeptides were highly expressed. There was strong cell proliferation in the embryo prior to compound eye development. The formation of the visual system and the hormonal regulation of hatching were the dominant biological events during compound eye development. The functional analysis of DEGs across all four developmental stages showed that cuticle formation, muscle growth and the establishment of immune system occurred from nauplius to zoea stage. Key genes related to eye development were discovered, including those involved in the determination and differentiation of the eye field, eye-color formation, and visual signal transduction. In conclusion, the results increase the understanding of the molecular mechanism of eye formation in crustacean embryonic stage.

A Sunlight-Driven Self-Cleaning CuCo-MOF Composite Membrane for Highly Efficient Emulsion Separation and Water Purification.

The fouling phenomenon of membranes has hindered the rapid development of separation technology in wastewater treatment. The integration of materials into membranes with both excellent separation performance and self-cleaning properties still pose challenges. Here, a self-assembled composite membrane with solar-driven self-cleaning performance is reported for the treatment of complex oil-water emulsions. The mechanical robustness of the composite membrane is enhanced by the electrostatic attraction between chitosan and metal-organic frameworks (MOF) CuCo-HHTP as well as the crosslinking effect of glutaraldehyde. Molecular dynamics (MD) simulations also revealed the hydrogen bonding interaction between chitosan and CuCo-HHTP. The composite membrane of CuCo-HHTP-5@CS/MPVDF exhibits a high flux ranging from 700.6 to 2350.6 L∙m-2∙h-1∙bar-1 and excellent separation efficiency (>99.0%) for various oil-water emulsions, including crude oil, kerosene, and other light oils. The addition of CuCo-HHTP shows remarkable photothermal effects, thus demonstrating excellent solar-driven self-cleaning capability and antibacterial performance (with an efficiency of ≈100%). Furthermore, CuCo-HHTP-5@CS/MPVDF can activate peroxomonosulfate (PMS) under sunlight, quickly removing oil-fouling and dyes. Density functional theory (DFT) calculations indicate that the bimetallic sites of Cu and Co in CuCo-HHTP effectively promoted the activation of PMS. This study provides distinctive insights into the multifaceted applications of MOFs-derived photothermal anti-fouling composite membranes.

Different machine learning methods based on maxillary sinus in sex estimation for northwestern Chinese Han population.

BACKGROUND & OBJECTIVE: Sex estimation is a critical aspect of forensic expertise. Some special anatomical structures, such as the maxillary sinus, can still maintain integrity in harsh environmental conditions and may be served as a basis for sex estimation. Due to the complex nature of sex estimation, several studies have been conducted using different machine learning algorithms to improve the accuracy of sex prediction from anatomical measurements. MATERIAL & METHODS: In this study, linear data of the maxillary sinus in the population of northwest China by using Cone-Beam Computed Tomography (CBCT) were collected and utilized to develop logistic, K-Nearest Neighbor (KNN), Support Vector Machine (SVM) and random forest (RF) models for sex estimation with R 4.3.1. CBCT images from 477 samples of Han population (75 males and 81 females, aged 5-17 years; 162 males and 159 females, aged 18-72) were used to establish and verify the model. Length (MSL), width (MSW), height (MSH) of both the left and right maxillary sinuses and distance of lateral wall between two maxillary sinuses (distance) were measured. 80% of the data were randomly picked as the training set and others were testing set. Besides, these samples were grouped by age bracket and fitted models as an attempt. RESULTS: Overall, the accuracy of the sex estimation for individuals over 18 years old on the testing set was 77.78%, with a slightly higher accuracy rate for males at 78.12% compared to females at 77.42%. However, accuracy of sex estimation for individuals under 18 was challenging. In comparison to logistic, KNN and SVM, RF exhibited higher accuracy rates. Moreover, incorporating age as a variable improved the accuracy of sex estimation, particularly in the 18-27 age group, where the accuracy rate increased to 88.46%. Meanwhile, all variables showed a linear correlation with age. CONCLUSION: The linear measurements of the maxillary sinus could be a valuable tool for sex estimation in individuals aged 18 and over. A robust RF model has been developed for sex estimation within the Han population residing in the northwestern region of China. The accuracy of sex estimation could be higher when age is used as a predictive variable.

Unlocking potential biomarkers bridging coronary atherosclerosis and pyrimidine metabolism-associated genes through an integrated bioinformatics and machine learning approach.

BACKGROUND: This study delves into the intricate landscape of atherosclerosis (AS), a chronic inflammatory disorder with significant implications for cardiovascular health. AS poses a considerable burden on global healthcare systems, elevating both mortality and morbidity rates. The pathological underpinnings of AS involve a marked metabolic disequilibrium, particularly within pyrimidine metabolism (PyM), a crucial enzymatic network central to nucleotide synthesis and degradation. While the therapeutic relevance of pyrimidine metabolism in diverse diseases is acknowledged, the explicit role of pyrimidine metabolism genes (PyMGs) in the context of AS remains elusive. Utilizing bioinformatics methodologies, this investigation aims to reveal and substantiate PyMGs intricately linked with AS. METHODS: A set of 41 candidate PyMGs was scrutinized through differential expression analysis. GSEA and GSVA were employed to illuminate potential biological pathways and functions associated with the identified PyMGs. Simultaneously, Lasso regression and SVM-RFE were utilized to distill core genes and assess the diagnostic potential of four quintessential PyMGs (CMPK1, CMPK2, NT5C2, RRM1) in discriminating AS. The relationship between key PyMGs and clinical presentations was also explored. Validation of the expression levels of the four PyMGs was performed using the GSE43292 and GSE9820 datasets. RESULTS: This investigation identified four PyMGs, with NT5C2 and RRM1 emerging as key players, intricately linked to AS pathogenesis. Functional analysis underscored their critical involvement in metabolic processes, including pyrimidine-containing compound metabolism and nucleotide biosynthesis. Diagnostic evaluation of these PyMGs in distinguishing AS showcased promising results. CONCLUSION: In conclusion, this exploration has illuminated a constellation of four PyMGs with a potential nexus to AS pathogenesis. These findings unveil emerging biomarkers, paving the way for novel approaches to disease monitoring and progression, and providing new avenues for therapeutic intervention in the realm of atherosclerosis.

Identification of clinical prognostic factors and analysis of ferroptosis-related gene signatures in the bladder cancer immune microenvironment.

BACKGROUND: Bladder cancer (BLCA) is a prevalent malignancy affecting the urinary system and poses a significant burden in terms of both incidence and mortality rates on a global scale. Among all BLCA cases, non-muscle invasive bladder cancer constitutes approximately 75% of the total. In recent years, the concept of ferroptosis, an iron-dependent form of regulated cell death marked by the accumulation of lipid peroxides, has captured the attention of researchers worldwide. Nevertheless, the precise involvement of ferroptosis-related genes (FRGs) in the anti-BLCA response remains inadequately elucidated. METHODS: The integration of BLCA samples from the TCGA and GEO datasets facilitated the quantitative evaluation of FRGs, offering potential insights into their predictive capabilities. Leveraging the wealth of information encompassing mRNAsi, gene mutations, CNV, TMB, and clinical features within these datasets further enriched the analysis, augmenting its robustness and reliability. Through the utilization of Lasso regression, a prediction model was developed, enabling accurate prognostic assessments within the context of BLCA. Additionally, co-expression analysis shed light on the complex relationship between gene expression patterns and FRGs, unraveling their functional relevance and potential implications in BLCA. RESULTS: FRGs exhibited increased expression levels in the high-risk cohort of BLCA patients, even in the absence of other clinical indicators, suggesting their potential as prognostic markers. GSEA revealed enrichment of immunological and tumor-related pathways specifically in the high-risk group. Furthermore, notable differences were observed in immune function and m6a gene expression between the low- and high-risk groups. Several genes, including MYBPH, SOST, SPRR2A, and CRNN, were found to potentially participate in the oncogenic processes underlying BLCA. Additionally, CYP4F8, PDZD3, CRTAC1, and LRTM1 were identified as potential tumor suppressor genes. Significant discrepancies in immunological function and m6a gene expression were observed between the two risk groups, further highlighting the distinct molecular characteristics associated with different prognostic outcomes. Notably, strong correlations were observed among the prognostic model, CNVs, SNPs, and drug sensitivity profiles. CONCLUSIONS: FRGs are associated with the onset and progression of BLCA. A FRGs signature offers a viable alternative to predict BLCA, and these FRGs show a prospective research area for BLCA targeted treatment in the future.

Integration of bioinformatics and machine learning approaches for the validation of pyrimidine metabolism-related genes and their implications in immunotherapy for osteoporosis.

BACKGROUND: Osteoporosis (OP), the "silent epidemic" of our century, poses a significant challenge to public health, predominantly affecting postmenopausal women and the elderly. It evolves from mild symptoms to pronounced severity, stabilizing eventually. Unique among OP's characteristics is the altered metabolic profile of affected cells, particularly in pyrimidine metabolism (PyM), a crucial pathway for nucleotide turnover and pyrimidine decomposition. While metabolic adaptation is acknowledged as a therapeutic target in various diseases, the specific role of PyM genes (PyMGs) in OP's molecular response remains to be clarified. METHODS: In pursuit of elucidating and authenticating PyMGs relevant to OP, we embarked on a comprehensive bioinformatics exploration. This entailed the integration of Weighted Gene Co-expression Network Analysis (WGCNA) with a curated list of 37 candidate PyMGs, followed by the examination of their biological functions and pathways via Gene Set Variation Analysis (GSVA). The Least Absolute Shrinkage and Selection Operator (LASSO) technique was harnessed to identify crucial hub genes. We evaluated the diagnostic prowess of five PyMGs in OP detection and explored their correlation with OP's clinical traits, further validating their expression profiles through independent datasets (GSE2208, GSE7158, GSE56815, and GSE35956). RESULTS: Our analytical rigor unveiled five PyMGs-IGKC, TMEM187, RPS11, IGLL3P, and GOLGA8N-with significant ties to OP. A deeper dive into their biological functions highlighted their roles in estrogen response modulation, cytosolic calcium ion concentration regulation, and GABAergic synaptic transmission. Remarkably, these PyMGs emerged as potent diagnostic biomarkers for OP, distinguishing affected individuals with substantial accuracy. CONCLUSIONS: This investigation brings to light five PyMGs intricately associated with OP, heralding new avenues for biomarker discovery and providing insights into its pathophysiological underpinnings. These findings not only deepen our comprehension of OP's complexity but also herald the advent of more refined diagnostic and therapeutic modalities.

Performance and protein conformation of thermally treated silver carp (Hypophthalmichthys molitrix) and scallop (Argopecten irradians) blended gels.

BACKGROUND: The quality of surimi-based products can be improved by combining the flesh of different aquatic organisms. The present study investigated the effects of incorporating diverse ratios of unwashed silver carp (H) and scallop (A) and using various thermal treatments on the moisture, texture, microstructure, and conformation of the blended gels and myofibrillar protein of surimi. RESULTS: A mixture ratio of A:H = 1:3 yielded the highest gel strength, which was 60.4% higher than that of scallop gel. The cooking losses of high-pressure heating and water-bath microwaving were significantly higher than those of other methods (P < 0.05). Moreover, the two-step water bath and water-bath microwaving samples exhibited a more regular spatial network structure compared to other samples. The mixed samples exhibited a microstructure with a uniform and ordered spatial network, allowing more free water to be trapped by the internal structure, resulting in more favorable gel properties. The thermal treatments comprehensively modified the tertiary and quaternary structures of proteins in unwashed mixed gel promoted protein unfurling, provided more hydrophobic interactions, enhanced protein aggregation and improved the gel performance. CONCLUSION: The findings of the present study improve our understanding of the interactions between proteins from different sources. We propose a new method for modifying surimi's gel properties, facilitating the development of mixed surimi products, as well as enhancing the efficient utilization of aquatic resources. © 2024 Society of Chemical Industry.

Sex estimation using maxillary sinus volume for Chinese subjects based on cone-beam computed tomography.

BACKGROUND: Sex estimate is a key stage in forensic science for identifying individuals. Some anatomical structures may be useful for sex estimation since they retain their integrity even after highly severe events. However, few studies are focusing on the Chinese population. Some researchers used teeth for sex estimation, but comparison with maxillary sinus were lack. As a result, the objective of this research is to develop a sex estimation formula for the northwestern Chinese population by the volume of the maxillary sinus and compare with the accuracy of sex estimation based on teeth through cone-beam computed tomography (CBCT). METHODS: CBCT images from 349 samples were used to establish and verify the formula. The volume of both the left and right maxillary sinuses was measured and examined for appropriate formula coefficients. To create the formula, we randomly picked 80% of the data as the training set and 20% of the samples as the testing set. Another set of samples, including 20 males and 20 females, were used to compare the accuracy of maxillary sinuses and teeth. RESULTS: Overall, sex estimation accuracy by volume of the left maxillary sinus can reach 78.57%, while by the volume of the right maxillary sinus can reach 74.29%. The accuracy for females, which can reach 91.43% using the left maxillary sinus, was significantly higher than that for males, which was 65.71%. The result also shows that maxillary sinus volume was higher in males. The comparison with the available results using measurements of teeth for sex estimation performed by our group showed that the accuracy of sex estimation using canines volume was higher than the one using maxillary sinus volume, the accuracies based on mesiodistal diameter of canine and first molar were the same or lower than the volume of maxillary sinus. CONCLUSIONS: The study demonstrates that measurement of maxillary sinus volume based on CBCT scans was an available and alternative method for sex estimation. And we established a method to accurately assess the sex of the northwest Chinese population. The comparison with the results of teeth measurements made the conclusion more reliable.

Electrochemical monitoring of 4-chlorophenol as a water pollutant via carbon paste electrode amplified with Fe3O4 incorporated cellulose nanofibers (CNF).

A crucial problem that needs to be resolved is the sensitive and selective monitoring of chlorophenol compounds, especifically 4-chlorophenol (4-CP), one of the most frequently used organic industrial chemicals. In light of this, the goal of this study was to synthesize Fe3O4 incorporated cellulose nanofiber composite (Fe3O4/CNF) as an amplifier in the development of a modified carbon paste electrode (CPE) for 4-CP detection. Transmission electron microscopy (TEM) was used to evaluate the morphology of the synthesized nanocatalyst, while differential pulse voltammetry (DPV), electrochemical impedance spectroscopy (EIS), and linear sweep voltammetry (LSV) techniques were implemented to illuminate the electrochemical characteristics of the fabricated sensor. The ultimate electrochemical sensor (Fe3O4/CNF/CPE) was used as a potent electrochemical sensor for monitoring 4-CP in the concentration range of 1.0 nM-170 µM with a limit of detection value of 0.5 nM. As a result of optimization studies, 8.0 mg Fe3O4/CNF was found to be the ideal catalyst concentration, whereas pH = 6.0 was chosen as the ideal pH. The 4-CP's oxidation current was found to be over 1.67 times greater at ideal operating conditions than it was at the surface of bare CPE, and its oxidation potential decreased by about 120 mV. By using the standard addition procedure on samples of drinking water and wastewater, the suggested capability of Fe3O4/CNF/CPE to detect 4-CP was further investigated. The recovery range was found to be 98.52-103.66%. This study paves the way for the customization of advanced nanostructure for the application in electrochemical sensors resulting in beneficial environmental impact and enhancing human health.

A multisectoral and multidisciplinary endeavor: a review of diabetes self-management apps in China.

BACKGROUND: While the use of self-management apps has considerable promise to efficiently reduce the diabetes burden that disproportionally affects low- and middle-income countries (LMICs), and the multisectoral and multidisciplinary approaches have been encouraged to be used in diabetes management, little is known about the status of the integration of these approaches in the existing diabetes self-management apps. This review examines the diabetes apps in China as an indication of the current status of integrating multisectoral and multidisciplinary approaches in diabetes mHealth care in LMICs. METHODS: Eligible diabetes apps were searched on major Chinese app stores up to December 23, 2022. The app comprehensiveness index (ranging 0-80) regarding the app functions and diabetes management domains was created. The multisectoral and multidisciplinary features were summarized using indices derived from current guidance. RESULTS: Sixty-six apps were reviewed, all developed by private companies. The average comprehensiveness score was 16, with many major self-management domains and functions not represented among the reviewed apps. Forty apps (61%) involved multiple sectoral entities, with public/private and private/private collaborations being the most common collaborative combinations. Thirty-seven apps (56%) involved multiple disciplines, among which endocrinology/metabolism, nutrition, and cardiovascular medicine were the top three most common disciplines. Compared to non-multidisciplinary apps, multidisciplinary apps tended to provide more comprehensive services in apps (6.14 vs. 5.18, p = 0.0345). Different sectors and disciplines tended to work independently, without robust interactions, in providing diabetes management services in the reviewed apps. CONCLUSION: Multisectoral and multidisciplinary features has presented in the current diabetes self-management apps in China; however, it is still in its infancy and significant limitations existed. More engagement of civil society organizations and community groups and innovative collaborations between sectors and disciplines are needed to provide comprehensive, continuous, and patient-centered mHealth care for patients with diabetes in LMICs like China. Clear guidance for integrating and evaluating the multisectoral and multidisciplinary efforts in self-management apps is necessary to ensure the effective use of mHealth solutions for diabetes management in LMICs.

How a raindrop gets shattered on biological surfaces.

Many biological surfaces of animals and plants (e.g., bird feathers, insect wings, plant leaves, etc.) are superhydrophobic with rough surfaces at different length scales. Previous studies have focused on a simple drop-bouncing behavior on biological surfaces with low-speed impacts. However, we observed that an impacting drop at high speeds exhibits more complicated dynamics with unexpected shock-like patterns: Hundreds of shock-like waves are formed on the spreading drop, and the drop is then abruptly fragmented along with multiple nucleating holes. Such drop dynamics result in the rapid retraction of the spreading drop and thereby a more than twofold decrease in contact time. Our results may shed light on potential biological advantages of hypothermia risk reduction for endothermic animals and spore spreading enhancement for fungi via wave-induced drop fragmentation.

Ovarian transcriptome and metabolic responses of RNAi-mediated farnesyl pyrophosphate synthase knockdown in Neocaridina denticulata sinensis.

Methyl farnesoate (MF) is considered the equivalent of JH in crustaceans and plays an essential role in many crucial physiological processes. It is believed that farnesyl pyrophosphate synthase (FPPS) plays an essential role in the biosynthesis of mevalonate, which is a branch of the JH/MF pathway. The full-length cDNA of FPPS (NdFPPS) from Neocaridina denticulata sinensis was isolated and characterized, and the deduced amino acid of NdFPPS contained a polyprenyl_synt domain. In addition to its ubiquitous tissue expression, NdFPPS was significantly expressed in the ovary. In vivo gene silencing with dsRNA interference was performed to further investigate the function of NdFPPS. An ovarian transcriptomic analysis of dsNdFPPS experimental and control groups was used to compare, annotate, and classify differentially expressed genes (DEGs). A total of 9230 DEGs were identified in the experimental and control groups based on FPKM values, of which 5082 were up-regulated genes and 4148 were down-regulated genes. 761 GO terms and 102 KEGG pathways were enriched for the DEGs. Our results suggest that NdFPPS might play an important role in ovarian development, however, further functional study is needed to elucidate physiological role of NdFPPS in reproduction.

Using Both Plasma and Urine Donor-Derived Cell-Free DNA to Identify Various Renal Allograft Injuries.

BACKGROUND: This study was designed to investigate the association between donor-derived cell-free DNA (dd-cfDNA) and renal allograft injuries. METHODS: This single-center study enrolled 113 adult kidney transplant recipients with kidney biopsies. Plasma and urine dd-cfDNA was detected by target region capture sequencing. RESULTS: Plasma dd-cfDNA fraction was increased in multiple types of injuries, but most significantly in antibody-mediated rejection. Plasma dd-cfDNA fraction in isolated antibody-mediated rejection (1.94%, IQR: 1.15%, 2.33%) was higher than in T cell-mediated rejection (0.55%, IQR: 0.50%, 0.73%, P = 0.002) and negative biopsies (0.58%, IQR: 0.42%, 0.78%, P < 0.001), but lower than in mixed rejection (2.49%, IQR: 1.16%, 4.90%, P = 0.342). Increased urine dd-cfDNA concentration was associated with several types of injury, but most significantly with BK polyomavirus-associated nephropathy. Urine dd-cfDNA concentration in BK polyomavirus-associated nephropathy (12.22 ng/mL, IQR: 6.53 ng/mL, 31.66 ng/mL) was respectively higher than that in T cell-mediated rejection (5.24 ng/mL, IQR: 3.22 ng/mL, 6.99 ng/mL, P = 0.001), borderline change (3.93 ng/mL, IQR: 2.45 ng/mL, 6.30 ng/mL, P < 0.001), and negative biopsies (3.09 ng/mL, IQR: 1.94 ng/mL, 5.05 ng/mL, P < 0.001). Plasma dd-cfDNA fraction was positively associated with glomerulitis (r = 0.365, P < 0.001) and peri-tubular capillaritis (r = 0.344, P < 0.001), while urine dd-cfDNA concentration correlated with tubulitis (r = 0.302, P = 0.002). CONCLUSIONS: Both plasma and urine dd-cfDNA are sensitive markers for renal allograft injuries. The interpretation of a specific disease by dd-cfDNA should be combined with other clinical indicators.

Rice ACID PHOSPHATASE 1 regulates Pi stress adaptation by maintaining intracellular Pi homeostasis.

The concentration and homeostasis of intracellular phosphate (Pi) are crucial for sustaining cell metabolism and growth. During short-term Pi starvation, intracellular Pi is maintained relatively constant at the expense of vacuolar Pi. After the vacuolar stored Pi is exhausted, the plant cells induce the synthesis of intracellular acid phosphatase (APase) to recycle Pi from expendable organic phosphate (Po). In this study, the expression, enzymatic activity and subcellular localization of ACID PHOSPHATASE 1 (OsACP1) were determined. OsACP1 expression is specifically induced in almost all cell types of leaves and roots under Pi stress conditions. OsACP1 encodes an acid phosphatase with broad Po substrates and localizes in the endoplasmic reticulum (ER) and Golgi apparatus (GA). The phylogenic analysis demonstrates that OsACP1 has a similar structure with human acid phosphatase PHOSPHO1. Overexpression or mutation of OsACP1 affected Po degradation and utilization, which further influenced plant growth and productivity under both Pi-sufficient and Pi-deficient conditions. Moreover, overexpression of OsACP1 significantly affected intracellular Pi homeostasis and Pi starvation signalling. We concluded that OsACP1 is an active acid phosphatase that regulates rice growth under Pi stress conditions by recycling Pi from Po in the ER and GA.

Characterization of the PHOSPHATE RESPONSE 2-dependent and -independent Pi-starvation response secretome in rice.

Many proteins secreted from plant cells into the surrounding extracellular space help maintain cell structure and regulate stress responses in the external environment. In this study, under Pi-replete and depleted conditions, 652 high-confidence secreted proteins were quantified from wild-type (WT) and PHOSPHATE RESPONSE 2 (OsPHR2)-overexpressing suspension-cultured cells (SCCs). These proteins were functionally grouped as phosphatases, signal transduction proteins, pathogen-related (PR) proteins, cell wall-remodeling proteins, and reactive oxygen species (ROS) metabolism proteins. Although PHOSPHATE RESPONSE (PHR) transcription factors regulate two-thirds of Pi-responsive genes at the transcriptional level, only 30.6% of the Pi-starvation-regulated secreted proteins showed significant changes in OsPHR2-overexpressing SCCs. The OsPHR2-dependent systemic Pi signaling pathway mainly regulates phosphatases and PR proteins, which are involved in the utilization of organophosphate, pathogen resistance, and colonization by rhizosphere microorganisms. The OsPHR2-independent local Pi signaling pathway, on the other hand, largely regulated ROS metabolism proteins, cell wall-remodeling proteins, and signal transduction proteins, which are involved in modifying cell wall structure and root architecture. The functions of differentially expressed secreted proteins between WT and OsPHR2-overexpressing plants under Pi-sufficient and Pi-deficient conditions were further confirmed by analysis of the acid phosphatase activity, ROS content, and cell wall composition.

RNA-seq analysis revealing the immune response of Neocaridina denticulata sinensis gill to Vibrio parahaemolyticus infection.

Vibrio parahaemolyticus causes serious economic losses to the shrimp farming industry. There is still a lack of adequate understanding of the changes in the overall response of N. denticulata sinensis caused by V. parahaemolyticus, particularly with respect to gill tissue, which is severely damaged by the pathogen. In this study, a total of 1358 differentially expressed genes were identified between the PBS control and Vibrio stimulation groups using transcriptome sequencing techniques. After further screening and analysis, many immune-related genes were obtained, involving lysosome pathway, metabolic process, chitin-binding protein, and serine protease family members. In addition, we randomly selected six DEGs in the lysosome pathway for qRT-PCR verification, and the results showed that their expression patterns were consistent with the RNA-seq. The results demonstrate the molecular regulation of the gill tissue response to V. parahaemolyticus infection in N. denticulata sinensis, contributing to the understand of the complex and efficient innate immune system and defense mechanisms in crustaceans.

An extracellular Cu/Zn superoxide dismutase from Neocaridina denticulata sinensis: cDNA cloning, mRNA expression and characterizations of recombinant protein.

Neocaridina denticulata sinensis possesses characters of rapid growth, tenacious vitality, short growth cycle, transparent, and easy feeding. Therefore, it is gradually being developed into an animal model for basic research on decapod crustaceans. Herein, a Cu/Zn superoxide dismutase (Cu/Zn-SOD), named as Nd-ecCu/Zn-SOD, was identified and characterized from N. denticulata sinensis. The full-length cDNA sequence of Nd-ecCu/Zn-SOD is 829 bp containing a 684 bp open reading frame, which encodes a protein of 227 amino acid residues with a typical Sod_Cu domain. The quantitative real-time PCR analysis showed that Nd-ecCu/Zn-SOD mRNA was expressed in all the tested tissues. Under challenge with copper, the mRNA expression of Nd-ecCu/Zn-SOD reached the maximum at 6 h, and decreased until 24 h. After 24 h of exposure, its expression was up-regulated significantly at 36 h. After then its expression sharply decreased with a comeback at 48 h. The result indicated that Nd-ecCu/Zn-SOD might play an important role in the stress response of N. denticulata sinensis. The expression of Nd-ecCu/Zn-SOD in gills challenged with Vibrio parahaemolyticus changed in a time-dependent manner. Nd-ecCu/Zn-SOD was lowly expressed in early developmental stages by RNA-Seq technology, yet it showed that a cyclical rise and fall occurred between middle stages and late stages. In addition, Nd-ecCu/Zn-SOD was recombinantly expressed using E. coli and the recombinant protein was purified as a single band on SDS-PAGE. The recombinant Nd-ecCu/Zn-SOD (rNd-ecCu/Zn-SOD) existed enzymatic activity under a wide range of temperature and pH. The exposure of metal ions was found that Zn2+, Mg2+, Ca2+, Ba2+, and Cu2+ could inhibit the enzymatic activity of rNd-ecCu/Zn-SOD, and Mn2+ increased the enzymatic activity of rNd-ecCu/Zn-SOD. These results indicate that Nd-ecCu/Zn-SOD may play a pivotal role in resistant against oxidative damage and act as a biomarker under stressful environment.

Potential biomarkers for predicting the overall survival outcome of kidney renal papillary cell carcinoma: an analysis of ferroptosis-related LNCRNAs.

BACKGROUND: Kidney renal papillary cell carcinoma (KIRP) is a dangerous cancer, which accounts for 15-20% of all kidney malignancies. Ferroptosis is a rare kind of cell death that overcomes medication resistance. Ferroptosis-related long non-coding RNAs (LNCRNAs) in KIRP, remain unknown. METHOD: We wanted to express how ferroptosis-related LNCRNAs interact with immune cell infiltration in KIRP. Gene set enrichment analysis in the GO and KEGG databases were used to explore gene expression enrichment. The prognostic model was constructed using Lasso regression. In addition, we also analyzed the modifications in the tumor microenvironment (TME) and immunological association. RESULT: The expression of LNCRNA was closely connected to the ferroptosis, according to co-expression analyses. CASC19, AC090197.1, AC099850.3, AL033397.2, LINC00462, and B3GALT1-AS1 were found to be significantly increased in the high-risk group, indicating that all of these markers implicates the malignancy processes for KIRP patients and may be cancer-promoting variables. LNCTAM34A and AC024022.1 were shown to be significantly elevated in the low-risk group; these might represent as the KIRP tumor suppressor genes. According to the TCGA, CCR, and inflammation-promoting genes were considered to be significantly different between the low-risk and high-risk groups. The expression of CD160, TNFSF4, CD80, BTLA, and TNFRSF9 was different in the two risk groups. CONCLUSION: LNCRNAs associated with ferroptosis were linked to the occurrence and progression of KIRP. Ferroptosis-related LNCRNAs and immune cell infiltration in the TME may be potential biomarkers in KIRP that should be further investigated.

Neuroprotection of Triptolide against Amyloid-Beta1-42-induced toxicity via the Akt/mTOR/p70S6K-mediated Autophagy Pathway.

Triptolide is a natural active compound that has significant neuroprotective properties and shows promising effects in the treatment of Alzheimer's disease (AD). Recent studies have shown that autophagy occurs in AD. In this study, we determined whether autophagy regulated by triptolide ameliorates neuronal death caused by amyloid-Beta1-42 (Aß1-42). We examined the effects of triptolide on cell viability, autophagy, apoptosis, and the protein kinase B/mammalian target of the rapamysin/70 kDa ribosomal protein S6 kinase (Akt/mTOR/p70S6K) signaling pathway in PC12 cells. The results indicated that triptolide treatment exhibited a cytoprotective effect against cell injury induced by Aß1-42. Triptolide also reduced apoptosis and enhanced cell survival by decreasing autophagosome accumulation and inducing autophagic degradation. Furthermore, our results also showed that activating the Akt/mTOR/p70S6K mechanism was one reason for the protection of triptolide. Triptolide treatment protected against Aß1-42-induced cytotoxicity by decreasing autophagosome accumulation, and inducing autophagic degradation in PC12 cells. These findings also suggest that the reduction of autophagosome accumulation observed in triptolide-treated cells was Akt/mTOR/p70S6K pathway dependent. Overall, triptolide exhibits a neuron protective effect and this study provides new insight into AD prevention and treatment.