Activation of CTU2 expression by LXR promotes the development of hepatocellular carcinoma.

Cytosolic thiouridylase 2 (CTU2) is an enzyme modifying transfer RNAs post-transcriptionally, which has been implicated in breast cancer and melanoma development. And we found CTU2 participated in hepatocellular carcinoma (HCC) progression here. HepG2 cells as well as xenograft nude mice model were employed to investigate the role of CTU2 in HCC development in vitro and in vivo respectively. Further, we defined CTU2 as a Liver X receptor (LXR) targeted gene, with a typical LXR element in the CTU2 promoter. CTU2 expression was activated by LXR agonist and depressed by LXR knockout. Interestingly, we also found CTU2 took part in lipogenesis by directly enhancing the synthesis of lipogenic proteins, which provided a novel mechanism for LXR regulating lipid synthesis. Meanwhile, lipogenesis was active during cell proliferation, particularly in tumor cells. Reduction of CTU2 expression was related to reduced tumor burden and synergized anti-tumor effect of LXR ligands by inducing tumor cell apoptosis and inhibiting cell proliferation. Taken together, our study identified CTU2 as an LXR target gene. Inhibition of CTU2 expression could enhance the anti-tumor effect of LXR ligand in HCC, identifying CTU2 as a promising target for HCC treatment and providing a novel strategy for the application of LXR agonists in anti-tumor effect.

Response of Chlorella vulgaris to exposure to CuO NPs: Contributions of particulate and dissolved metal forms as modulated by tannic acid and pH.

A suspension of copper oxide nanoparticles (CuO NPs) is a mixture of dissolved and particulate Cu, the relative proportions of which highly depend on the water chemistry. However, the relationship between different proportions of particulate and dissolved Cu and the overall toxicity of CuO NPs is still unknown. This study investigated the response of Chlorella vulgaris to CuO NPs at varying solution pH and at different tannic acid (TA) additions, with a focus on exploring whether and how dissolved and particulate Cu contribute to the overall toxicity of CuO NPs. The results of the exposure experiments demonstrated the involvement of both dissolved and particulate Cu in inducing toxicity of CuO NPs, and the inhibition of CuO NPs on cell density of Chlorella vulgaris was found to be significantly (p < 0.05) alleviated with increased levels of TA and pH (< 8). Using the independent action model, the contribution to toxicity of particulate Cu was found to be enhanced with increasing pH values and TA concentrations. The toxic unit indicator better (R2 = 0.86, p < 0.001) explained impacts of CuO NPs on micro-algae cells than commonly used mass concentrations (R2 = 0.27-0.77, p < 0.05) across different levels of pH and TA. Overall, our study provides an additivity-based method to improve the accuracy of toxicity prediction through including contributions to toxicity of both dissolved and particulate Cu and through eliminating the uneven distribution of data due to large variations in total Cu, particulate Cu, dissolved Cu, Cu2+ activities, Cu-TA complexes and other Cu-complexes concentrations with varying water chemistry conditions.

Insulator-to-metal transition in the black diamond from molecular-dynamics-Landauer method.

The critical condition and mechanism of the insulator-to-metal transition (IMT) for the black diamond were studied by the molecular-dynamics-Landauer method. The IMT will occur at sufficiently high contents of vacancies in the diamond. The critical concentration of vacancies for the IMT might be between V:C143 (0.69%) and V:C127 (0.78%). At a low concentration of vacancies (below 0.69%), the intermediate band (IB) consists of a filled band and a separate empty band, which makes the material to be an insulator. The IMT of the black diamond is due to the mergence between the two isolated IBs when the concentration of vacancies is high, and the merged IB is partially filled by electrons. The distribution of vacancies also influences the IMT of the black diamond.

Early diagnosis and prognostic potential of RAC3 in bladder tumor.

BACKGROUND AND PURPOSE: Bladder tumors are among the most prevalent malignancies in the urinary system, and RAC3 has been linked to various types of cancer. This article seeks to explore the potential of RAC3 as both an early diagnostic marker for bladder tumors and a novel therapeutic target. METHODS/PATIENTS: The expression of RAC3 in bladder tissue was detected using immunohistochemical staining. Additionally, the protein expression of RAC3 was measured and quantified through enzyme-linked immunosorbent assay (ELISA). Subsequently, the correlation between the expression level of RAC3 and bladder tumors was investigated through multifactorial analysis and survival analysis. RESULTS: Our findings revealed that RAC3 expression was upregulated in bladder tumor tissues. Moreover, we observed higher levels of RAC3 expression in the serum and urine of patients with bladder tumors compared to those with non-bladder tumors. Additionally, we identified a significant positive correlation between RAC3 expression levels and the stage, degree of differentiation, and infiltration of bladder tumors. Importantly, high RAC3 expression emerged as an influential factor in the poor prognosis of bladder tumors, as patients with high RAC3 expression exhibited a lower overall survival rate than those with low RAC3 expression. CONCLUSION: Based on our results, RAC3 shows promise as both a marker for early diagnosis of bladder tumors and a potential therapeutic target.

The role of extracellular polymeric substances (EPS) in chemical-degradation of persistent organic pollutants in soil: A review.

Persistent organic pollutants (POPs) in soil show high environmental risk due to their high toxicity and low biodegradability. Studies have demonstrated the degradation function of microbial extracellular polymeric substances (EPS) on POPs in various matrices. However, the degradation mechanisms and the factors that influence the process in soil have not been clearly illustrated. In this review, the characteristics of EPS were introduced and the possible mechanisms of EPS on degradation of organic pollutants (e.g., external electron transfer, photodegradation, and enzyme catalysis) were comprehensively discussed. In addition, the environmental conditions (e.g., UV, nutrients, and redox potential) that could influence the production and degradation-related active components of EPS were addressed. Moreover, the current approaches on the application of EPS in biotechnology were summarized. Further, the future perspectives of enhancement on degradation of POPs by regulating EPS were discussed. Overall, this review could provide a new thought on remediation of POPs by widely-existing EPS in soil with low-cost and minimized eco-disturbance.

Biochar-based materials as remediation strategy in petroleum hydrocarbon-contaminated soil and water: Performances, mechanisms, and environmental impact.

Petroleum contamination is considered as a major risk to the health of humans and environment. Biochars as low-cost and eco-friendly carbon materials, have been widely used for the removal of petroleum hydrocarbon in the environment. The purpose of this paper is to review the performance, mechanisms, and potential environmental toxicity of biochar, modified biochar and its integration use with other materials in petroleum contaminated soil and water. Specifically, the use of biochar in oil-contaminated water and soil as well as the factors that could influence the removal ability of biochar were systematically evaluated. In addition, the modification and integrated use of biochar for improving the removal efficiency were summarized from the aspects of sorption, biodegradation, chemical degradation, and reusability. Moreover, the functional impacts and associated ecotoxicity of pristine and modified biochars in various environments were demonstrated. Finally, some shortcoming of current approaches, and future research needs were provided for the future direction and challenges of modified biochar research. Overall, this paper gain insight into biochar application in petroleum remediation from the perspectives of performance enhancement and environmental sustainability.

Association between N, N-diethyl-m-toluamide exposure and the odds of kidney stones in US adults: a population-based study.

Background: Currently, there is limited research on the specific relationship between N, N-diethyl-m-toluamide (DEET) exposure and the odds of kidney stones. We aimed to investigate the relationship between DEET exposure and the prevalence of kidney stones. Methods: We included 7,567 qualified participants in our research from the 2007-2016 NHANES survey. We carried out three logistic regression models to explore the potential association between DEET exposure and the odds of kidney stones. Spline smoothing with generalized additive models (GAM) was utilized to assess the non-linear relationship and restricted cubic spline (RCS) curves was to determine the dose-response association. Multivariate regression models were used to conduct stratified analysis and sensitivity analysis. Results: Baseline characteristics of study participants presented the distribution of covariables. Regression analysis revealed that the odds of kidney stones were positively associated with the main metabolites of 3-diethyl-carbamoyl benzoic acid (DCBA) (log2) (OR = 1.05, 95% CI 1.02 to 1.08). The fourth quartile of urine DCBA showed a greater risk of kidney stones in the fully adjusted model (OR = 1.36, 95% CI 1.08 to 1.72). Another DEET metabolite of N, N-diethyl-3-hydroxymethylbenzamide (DHMB) was used to confirm the accuracy and stability of the results. The spline smoothing curve represented two main DEET metabolites had similar no-linear relationships and a positive trend with kidney stones proportion. RCS implied that the incidence of kidney stones rose with increasing levels of DEET exposure. High-risk groups on kidney stones were exhibited by stratified analysis under DEET exposure. Conclusion: Our study suggests that DEET exposure is positively associated with odds of kidney stones. Further investigation into the underlying processes of this association is required to guide the prevention and treatment of kidney stones.

Single Ni Atom-Dispersed WSe2 Monolayer for Sensing Typical Fault Gases in Dry-Type Transformers: A First-Principles Study.

This work, using the first-principles theory, uses the Ni-decorated WSe2 (Ni-WSe2) monolayer as a novel gas sensing material upon CO and HCHO in the dry-type transformers in order to evaluate their operation status. Results indicate that the Ni atom can be stably adsorbed on the TW site of the pristine WSe2 monolayer with the binding force of -4.33 eV. Via the gas adsorption analysis, it is found that the Ni-WSe2 monolayer performs chemisorption upon CO and HCHO molecules, with adsorption energies of -2.27 and -1.37 eV, respectively. The analyses of the band structure and Frontier molecular orbital manifest the potential of the Ni-WSe2 monolayer as a resistance-type gas sensor upon CO and HCHO, with sensing responses of 55.9 and 30.9% based on the band gap change and of 55.0 and 38.5% based on the energy gap change. The analysis of the density of state clearly shows the modified electronic property of the Ni-WSe2 monolayer in gas adsorptions. On the other hand, the analysis of the work function (WF) reveals the limited possibility to explore the Ni-WSe2 monolayer as a WF-based gas sensor for CO and HCHO detections. This work systemically studies the sensing potential of the Ni-WSe2 monolayer upon two typical gas species in the dry-type transformers, which is meaningful to explore novel nanomaterial-based gas sensors to monitor the operation condition of electrical equipment.

Phenoloxidases: catechol oxidase - the temporary employer and laccase - the rising star of vascular plants.

Phenolics are vital for the adaptation of plants to terrestrial habitats and for species diversity. Phenoloxidases (catechol oxidases, COs, and laccases, LACs) are responsible for the oxidation and polymerization of phenolics. However, their origin, evolution, and differential roles during plant development and land colonization are unclear. We performed the phylogeny, domain, amino acids, compositional biases, and intron analyses to clarify the origin and evolution of COs and LACs, and analysed the structure, selective pressure, and chloroplast targeting to understand the species-dependent distribution of COs. We found that Streptophyta COs were not homologous to the Chlorophyta tyrosinases (TYRs), and might have been acquired by horizontal gene transfer from bacteria. COs expanded in bryophytes. Structural-functionality and selective pressure were partially responsible for the species-dependent retention of COs in embryophytes. LACs emerged in Zygnemaphyceae, having evolved from ascorbate oxidases (AAOs), and prevailed in the vascular plants and strongly expanded in seed plants. COs and LACs coevolved with the phenolic metabolism pathway genes. These results suggested that TYRs and AAOs were the first-stage phenoloxidases in Chlorophyta. COs might be the second key for the early land colonization. LACs were the third one (dominating in the vascular plants) and might be advantageous for diversified phenol substrates and the erect growth of plants. This work provided new insights into how phenoloxidases evolved and were devoted to plant evolution.

Efficient Removal of Nitrate in Neutral Solution Using Zero-Valent Al Activated by Soaking.

Nitrate is a contaminant widely found in surface water, and a high concentration of nitrate can pose a serious threat to human health. Zero-valent iron is widely used to reduce nitrate in aqueous solution, but an acidic condition is required. Zero-valent aluminum has a much lower redox potential (E0(Al3+/Al0) = -1.662 V) than zero-valent iron (E0(Fe2+/Fe0) = -0.44 V), making it a better choice for reduction of nitrate. However, a passive oxide film covering on Al surfaces inhibits its electron transfer. In this work, metal Al powder was activated by a soaking procedure in deionized water. It was found that nitrate in neutral solution can be efficiently and completely reduced by soaked Al, even if the concentration of nitrate-N was up to 100 mg L-1. Using an optimal soaking time, the soaked Al can remove >90% of nitrate in aqueous solution within ∼2 h at 50 °C. Furthermore, the nitrate reduction efficiency increased with increasing reaction temperature and dosage of Al powder. After reaction, only ∼50% of pristine N content was left in the form of ammonia ions (NH4+) in aqueous solution. Mechanism analyses showed that after soaking, Al particle surfaces were covered by a layer of loose and fine Al(OH)3 grains, which can shorten the induction time for the beginning of the reaction between inner Al and outside ions or molecules. This is the reason why soaked Al has a high efficiency for nitrate removal. The present results indicate that soaking is an effective way to activate Al to remove nitrate in water.

Transcriptome Analysis of the Salt-Treated Actinidia deliciosa (A. Chev.) C. F. Liang and A. R. Ferguson Plantlets.

The area of saline land in the world is quite large, and there is broad room for its development and usage. 'Xuxiang' is an Actinidia deliciosa variety that is tolerant to salt and can be planted in an area of light-saline land, and has good comprehensive characteristics and high economic value. However, the molecular mechanism of salt tolerance is unknown at present. To understand the molecular mechanism of salt tolerance, the leaves of A. deliciosa 'Xuxiang' were used as explants to establish a sterile tissue culture system, and plantlets were obtained using this system. One percent concentration (w/v) of sodium chloride (NaCl) was employed to treat the young plantlets cultured in Murashige and Skoog (MS) medium, then RNA-seq was used for transcriptome analysis. The results showed that the genes related to salt stress in the phenylpropanoid biosynthesis pathway and the anabolism of trehalose and maltose pathways were up-regulated; however, those genes in the plant hormone signal transduction and metabolic pathways of starch, sucrose, glucose, and fructose were down-regulated after salt treatment. The expression levels of ten genes that were up-regulated and down-regulated in these pathways were confirmed by real-time quantitative polymerase chain reaction (RT-qPCR) analysis. The salt tolerance of A. deliciosa might be related to the expression level changes in the genes in the pathways of plant hormone signal transduction, phenylpropanoid biosynthesis, and starch, sucrose, glucose, and fructose metabolism. The increased expression levels of the genes encoding alpha-trehalose-phosphate synthase, trehalose-phosphatase, alpha-amylase, beta-amylase, feruloyl-CoA 6-hydroxylase, ferulate 5-hydroxylase, and coniferyl-alcohol glucosyl transferase might be vital to the salt stress response of the young A. deliciosa plants.

Distribution of environmentally persistent free radicals in size-segregated PMs emitted from residential biomass fuel combustion.

Environmentally persistent free radicals (EPFRs) are considered as an emerging pollutant due to their potential environmental risks, but the distribution characteristics of particulate matters (PMs)-EPFRs from residential combustion source are poorly understood. In this study, biomass (corn straw, rice straw, pine and jujube wood) combustion was studied in lab-controlled experiments. More than 80% of PM-EPFRs were distributed in PMs with aerodynamic diameter (dae) ≤ 2.1 µm, and their concentration in fine PMs was about 10 times that in coarse PM (2.1 µm ≤ dae ≤ 10 µm). The detected EPFRs were carbon-centered free radicals adjacent to oxygen atoms or a mixture of oxygen- and carbon-centered radicals. The concentrations of EPFRs in coarse and fine PMs were positively correlated with char-EC, but the EPFRs in fine PMs exhibited a negative correlation with soot-EC (p < 0.05). The increase of PM-EPFRs signals with the increased dilution ratio during pine wood combustion was more significant than that from rice straw, which may be resulted from the interactions between the condensable volatiles and the transition metals. Our study provides useful information for better understanding the formation of combustion-derived PM-EPFRs, and will be instructive for its purposeful emissions control.

Serum estradiol to testosterone ratio as a novel predictor of severe preeclampsia in the first trimester.

Preeclampsia (PE) is the most common medical complication during pregnancy and the second leading cause of maternal death worldwide. However, a better predictive model of PE remains to be explored. A total of 15 severe preeclampsia (sPE) and 75 healthy control patients were included in this study. Patient data was obtained from September 2019 to September 2021. Nuchal translucency (NT) and crown-rump length (CRL) of the fetus were acquired by ultrasound. Maternal blood samples were collected at 11+0 to 13+6  weeks of gestation. Chemiluminescent immunoassays were used to detect serum testosterone (T) and estradiol (E2) levels. Time-resolved fluorescence analysis was used to examine the levels of serum pregnancy-associated plasma protein A (PAPPA) and ß-human chorionic gonadotrophin (ß-HCG) protein. The sPE group exhibited increased T levels, and decreased E2 levels and E2/T ratios from 11 to 14 weeks of gestation, compared with the control group. E2 and the E2/T ratio showed positive linear correlation with CRL in pregnant women. Body-mass-index (BMI), T, and E2 were determined to be the main factors that affected the occurrence of sPE at the 12-week gestation period time point. The receiver operating characteristic (ROC) curve revealed that the AUC of the E2/T ratio was .717. The imbalanced T and E2 levels in the patients had a specific intrinsic relevance with sPE, which suggests them as novel predictors of the sPE.

Synergistic effect and mechanisms of ultrasound and AlOOH suspension on Al hydrolysis for hydrogen production.

Ultrasound can accelerate and change the reaction process and is widely used in the field of hydrogen production and storage. In this study, ultrasound (US) and AlOOH suspension (AH) are used to promote hydrogen production from Al hydrolysis. The results indicate that both US and AH greatly shorten the induction time and enhance the hydrogen production rate and yield. The promoting effect of US and AH on Al hydrolysis originates from the acoustic cavitation effect and catalytic effect, respectively. When AH is used in combination with US, Al hydrolysis has the best hydrogen production performance and the hydrogen yield can reach 96.6 % within 1.2 h, because there is a synergistic effect on Al hydrolysis between AH and US. Mechanism analyses reveal that the micro-jets and local high temperature environment arising from acoustic cavitation improve the catalytic activity of AlOOH, while the suspended AlOOH particles enhance the cavitation effect of US. This work provides a novel and feasible method to promote hydrogen production from Al hydrolysis.

Transcriptome Analysis of Low-Temperature-Treated Tetraploid Yellow Actinidia chinensis Planch. Tissue Culture Plantlets.

The cold-resistant mechanism of yellow kiwifruit associated with gene regulation is poorly investigated. In this study, to provide insight into the causes of differences in low-temperature tolerance and to better understand cold-adaptive mechanisms, we treated yellow tetraploid kiwifruit 'SWFU03' tissue culture plantlets at low temperatures, used these plantlets for transcriptome analysis, and validated the expression levels of ten selected genes by real-time quantitative polymerase chain reaction (RT-qPCR) analysis. A number of 1630 differentially expressed genes (DEGs) were identified, of which 619 pathway genes were up-regulated, and 1011 were down-regulated in the cold treatment group. The DEGs enriched in the cold tolerance-related pathways mainly included the plant hormone signal transduction and the starch and sucrose metabolism pathway. RT-qPCR analysis confirmed the expression levels of eight up-regulated genes in these pathways in the cold-resistant mutants. In this study, cold tolerance-related pathways (the plant hormone signal transduction and starch and sucrose metabolism pathway) and genes, e.g., CEY00_Acc03316 (abscisic acid receptor PYL), CEY00_Acc13130 (bZIP transcription factor), CEY00_Acc33627 (TIFY protein), CEY00_Acc26744 (alpha-trehalose-phosphate synthase), CEY00_Acc28966 (beta-amylase), CEY00_Acc16756 (trehalose phosphatase), and CEY00_Acc08918 (beta-amylase 4) were found.

The value of contrast-enhanced ultrasonography in differential diagnosis of benign and malignant ovarian sex cord stromal tumors.

Background: Sex cord-stromal tumors (SCSTs) are uncommon neoplasms that are typically difficult to diagnose before surgery due to limited experience in their medical imaging. Contrast-enhanced ultrasonography (CEUS) can evaluate the microvessel density of tumors, and the microvessel density of malignant tumors is significantly greater than that of benign tumors, so this provides a method for CEUS to differentiate benign and malignant tumors. Methods: The CEUS diagnoses of 31 patients with pathologically confirmed SCSTs were retrospectively analyzed and compared to conventional ultrasound-based diagnoses. Based on the pathological results, the patients were divided into benign and non-benign groups. Using pathology as the gold standard, four-table data were used to evaluate the authenticity of conventional ultrasonography and CEUS. Results: Among these 31 SCST patients, only the size of the lesion and the stripy hypoenhancement on CEUS differed significantly between the benign group and the non-benign group (P<0.05). In the benign group (n=25), 22 patients showed sparse stripes of hypoenhancement, 1 showed no enhancement, and 2 showed hyperenhancement. In 5 cases of malignant SCSTs, 4 showed hyperenhancement (with non-enhanced areas inside the tumor), and 1 showed sparse strips of hypoenhancement; in 1 case of borderline SCST, the tumor showed uniform hyperenhancement. The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy rate of the conventional ultrasound diagnoses for the 31 SCST patients were 52.0%, 16.7%, 72.2%, 7.7%, and 45.2%, respectively. In relation to CEUS, sparse strips of hypoenhancement or no enhancement were valuable diagnostic criteria for diagnosing benign SCSTs. The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy rate of CEUS were 92.0%, 83.3%, 95.8%, 71.4%, and 90.3%, respectively. The accuracy of CEUS was higher than that of conventional US, and the difference was statistically significant (χ2=14.467, P=0.000). Conclusions: Sparse strips of hypoenhancement or no enhancement on CEUS are the characteristic manifestations of benign SCSTs, and hyperenhancement (with a non-enhanced area observable inside the mass) may be suggestive of malignant tumors. CEUS significantly improved the differentiation of benign and malignant SCSTs.

Analysis of fungal dynamic changes in the natural fermentation broth of 'Hongyang' kiwifruit.

'Hongyang' kiwifruit (Actinidia chinensis Planch.) is an ideal kiwifruit wine variety. At present, there is no research on the dynamic changes of yeast during the natural fermentation of kiwifruit wine. In this study, a high-throughput was employed to analyze the fungal population composition and diversity in the samples cultured in yeast extract peptone dextrose (YPD) medium and enriched in the natural fermentation process of 'Hongyang' kiwifruit at four time points, day one (D1T), day three (D3T), day five (D5T), and day fifteen (D15T). Five hundred and eighty-two operational taxonomic units (OTUs) were obtained from 131 genera and 178 species samples. The diversity analysis results showed that in the early natural fermentation stage, the dominant species was Aureobasidium pullulans, and as natural fermentation proceeded, the genus Pichia became the dominant species. Pichia kluyveri was an important species at the later stages of natural fermentation. An analysis of the metabolic pathways shows that P. kluyveri plays an aromatic-producing role in the natural fermentation of 'Hongyang' kiwifruit. These results could provide a theoretical basis for the studies of kiwifruit fungal diversity and fungal changes during fermentation. The findings could fix a major deficiency in the production of kiwifruit fruit wine, which lacks a specific flavor-producing yeast species or strain.

Identification and validation of a ferroptosis-related gene signature for predicting survival in skin cutaneous melanoma.

PURPOSE: Ferroptosis plays a crucial role in the initiation and progression of melanoma. This study developed a robust signature with ferroptosis-related genes (FRGs) and assessed the ability of this signature to predict OS in patients with skin cutaneous melanoma (SKCM). METHODS: RNA-sequencing data and clinical information of melanoma patients were extracted from TCGA, GEO, and GTEx. Univariate, multivariate, and LASSO regression analyses were conducted to identify the gene signature. A 10 FRG signature was an independent and strong predictor of survival. The predictive performance was assessed using ROC curve. The functions of this gene signature were assessed by GO and KEGG analysis. The statuses of low-risk and high-risk groups according to the gene signature were compared by GSEA. In addition, we investigated the possible relationship of FRGs with immunotherapy efficacy. RESULTS: A prognostic signature with 10 FRGs (CYBB, IFNG, FBXW7, ARNTL, PROM2, GPX2, JDP2, SLC7A5, TUBE1, and HAMP) was identified by Cox regression analysis. This signature had a higher prediction efficiency than clinicopathological features (AUC = 0.70). The enrichment analyses of DEGs indicated that ferroptosis-related immune pathways were largely enriched. Furthermore, GSEA showed that ferroptosis was associated with immunosuppression in the high-risk group. Finally, immune checkpoints such as PDCD-1 (PD-1), CTLA4, CD274 (PD-L1), and LAG3 were also differential expression in two risk groups. CONCLUSIONS: The 10 FRGs signature were a strong predictor of OS in SKCM and could be used to predict therapeutic targets for melanoma.

Overexpression of MET4 Leads to the Upregulation of Stress-Related Genes and Enhanced Sulfite Tolerance in Saccharomyces uvarum.

Saccharomyces uvarum is one of the few fermentative species that can be used in winemaking, but its weak sulfite tolerance is the main reason for its further use. Previous studies have shown that the expression of the methionine synthase gene (MET4) is upregulated in FZF1 (a gene encoding a putative zinc finger protein, which is a positive regulator of the transcription of the cytosolic sulfotransferase gene SSU1) overexpression transformant strains, but its exact function is unknown. To gain insight into the function of the MET4 gene, in this study, a MET4 overexpression vector was constructed and transformed into S. uvarum strain A9. The MET4 transformants showed a 20 mM increase in sulfite tolerance compared to the starting strain. Ninety-two differential genes were found in the transcriptome of A9-MET4 compared to the A9 strain, of which 90 were upregulated, and two were downregulated. The results of RT-qPCR analyses confirmed that the expression of the HOMoserine requiring gene (HOM3) in the sulfate assimilation pathway and some fermentation-stress-related genes were upregulated in the transformants. The overexpression of the MET4 gene resulted in a significant increase in sulfite tolerance, the upregulation of fermentation-stress-related gene expression, and significant changes in the transcriptome profile of the S. uvarum strain.

pValid 2: A deep learning based validation method for peptide identification in shotgun proteomics with increased discriminating power.

Tandem mass spectrometry has been the principal method in shotgun proteomics for peptide and protein identification. However, incorrect identifications reported by proteome search engines are still unknown, and further validation methods are needed. We have proposed a validation method pValid before, but its scope of application is limited because two features used in pValid are related to open database search and sub-optimal peptide candidates for tandem mass spectra, and the performance on complex datasets still has room for improvement. In this study, we developed a more comprehensive validation method, pValid 2, to break these limitations by removing the two features and bringing in a new feature related to the retention time predicted by a deep learning-based method pPredRT. pValid 2 yielded an average false positive rate of 0.03% and an average false negative rate of 1.37% on three testing datasets, better than those of pValid, and flagged 8.47% to 11.31% more incorrect identifications than pValid on two complex datasets. Moreover, pValid 2 flagged almost all decoy identifications in validating the open-search datasets. In addition, the function of validating identifications given by MaxQuant and MS-GF+ was implemented in pValid 2, and the validation results showed that pValid 2 performed dramatically better than three metabolic labeling validation methods. Further considering its cost-effectiveness as a pure computational approach, pValid 2 has the potential to be a widely used validation tool for peptide identifications of any proteome search engines in shotgun proteomics. SIGNIFICANCE: Identification results given by shotgun proteomics are vital to life science research. The correctness of identifications deeply affects the precision of the subsequent studies about protein structures and functions, protein-protein interactions, pathogenic mechanism, and targeted drugs. Thus, validating the correctness of identifications is crucial and urgent. In 2019, we developed an identification credibility validation method named pValid, whose false positive rate (FPR) is 0.03% and false negative rate (FNR) is 1.79%, comparable to those of the gold standard, i.e., the Synthetic-peptide validation method. However, pValid can only be used for validating the results from pFind, and its validation performance on a few complex datasets still has room for improvement. So, in this submission, we proposed pValid 2, a more comprehensive computational validation method that can validate identifications from any proteome search engines with increased discriminating power.