title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=477 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Response surface methodology for the mixed fungal fermentation of Codonopsis pilosula straw using Trichoderma reesei and Coprinus comatus link: https://peerj.com/articles/15757 last-modified: 2023-08-14 description: The objective of this study was to investigate the cellulose degradation rate (CDR) and lignin degradation rate (LDR) of Codonopsis pilosula straw (CPS) and the optimal fermentation parameters for mixed fungal fermentation. Single-factor tests were used to study the effects of the fungal ratio (Trichoderma reesei: Coprinus comatus), fungal inoculum, corn flour content, and fermentation time on the degradation rate of cellulose and lignin. Based on the results of this experiment, the optimal fermentation factors were identified, and the effects of various factors and their interactions on the degradation rates of cellulose and lignin were further evaluated using the response surface method. The quadratic polynomial mathematical model of degradation rates of the cellulose and lignin in CPS by mixed fungus fermentation was established using Design Expert software v8.0.6. Under the optimal parameters for fungal fermentation of CPS straw (fungal ratio 4:6, fungal inoculum 8%, corn flour content 10%, fermentation time of 15 d), the CDR and LDR reached 13.65% and 10.73%, respectively. Collectively, the mixed fungal fermentation of CPS resulted in decreased lignin and cellulose content, better retention of nutrients, and enhanced fermentation quality. The results of this study indicate that fermentation using Trichoderma reesei and Coprinus comatus is a productive method for straw degradation, providing a theoretical basis for the development of CPS as feed. creator: Ti Wei creator: Hongfu Chen creator: Dengyu Wu creator: Dandan Gao creator: Yong Cai creator: Xin Cao creator: Hongwei Xu creator: Jutian Yang creator: Penghui Guo uri: https://doi.org/10.7717/peerj.15757 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wei et al. title: Tailored modulation of S100A1 and RASSF8 expression by butanediamide augments healing of rotator cuff tears link: https://peerj.com/articles/15791 last-modified: 2023-08-14 description: ObjectivesThis investigation sought to elucidate promising treatment modalities for rotator cuff tears (RCTs) by delving into the molecular machinations instigating the affliction. The focus was on differentially expressed genes (DEGs) linked to RCTs, and the exploration of their roles and operative pathways.MethodsDEGs were discerned from GEO datasets, followed by the establishment of a protein-protein interaction (PPI) network. Subsequently, the network’s core genes were determined employing a Venn diagram. Enrichment analysis facilitated the unveiling of the biological roles and signal transduction pathways of these pivotal genes, thus shedding light on molecular strategies for RCT-targeted treatment. The Discovery Studio 2019 software was employed to sift through FDA-sanctioned drugs targeting these essential proteins. Moreover, the efficaciousness of these FDA-endorsed drugs vis-à-vis RCTs was corroborated by the construction of an in vivo animal model of the injury and the in vitro cultivation of tendon-derived stem cells.ResultsBioinformatics outcomes revealed a significant overexpression of S100A1 and RASSF8 in RCT patients. The FDA drug repository indicated that Butanediamide has a selective affinity for S100A1 and RASSF8. Subsequent in vivo and in vitro experimentation demonstrated that Butanediamide could suppress S100A1 expression and bolster TDSC proliferation, thereby facilitating RCT healing.ConclusionsS100A1 and RASSF8 are pivotal genes implicated in RCTs, and their roles have been elucidated. The FDA-approved compound, Butanediamide, may represent a prospective therapeutic agent for RCTs by targeting S100A1 and RASSF8, respectively. creator: Yuan Lin creator: Ruipeng Guo creator: Geng R creator: Bin Xu uri: https://doi.org/10.7717/peerj.15791 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lin et al. title: Barley yield and malt quality affected by fall and spring planting under rainfed conditions link: https://peerj.com/articles/15802 last-modified: 2023-08-14 description: BackgroundAs a result of the changing climate characteristics, it is necessary to reevaluate the planting time for crop plants. The aim of the present study was to determine the quality characteristics of malting barley cultivars in fall and spring plantings.MethodsSixteen malting barley cultivars were used. Two fall-planted and two spring-planted trials were conducted in two consecutive years. The field trials were carried out in a randomized complete block design with four replications in Tokat province of Turkey under rainfed conditions.ResultsGrain yields varied between 4.38 and 5.71 t/ha in fall-planted trials and between 3.12 and 4.89 t/ha in spring-planted trials. Malt extracts were between 77.0% and 78.0% kg in fall-planted trials and between 73.9% and 76.9% in spring-planted trials. Alpha amylase activities ranged from 77.9 to 81.4 Ceralpha unit (CU)/g in fall-planted trials and from 80.8 to 100.9 CU/g in spring-planted trials. Diastatic power ranged from 194.5 to 331.1 Windisch-Kolbach unit (°WK) in fall-planted trials and from 129.0 to 259.8 °WK in spring-planted trials. GGE biplot analysis indicated that winter barley cultivar Durusu and facultative barley cultivar Ince-04 were the best with consistent grain yields while Ince-04 was the best with stable malt extract across the trials. In scatter plot graphics, winter barley cultivars Durusu, Aydanhanim, Yildiz and facultative Ince-04 had superior performance in fall-plantings for grain yield and malt extract. In spring planting, facultative Ince-04 had higher performance than those of other cultivars. In spring plantings, facultative or winter barley cultivars that do not have strong vernalization requirement had better yield and malt quality. Appropriate planting time and cultivars can allow a better use of available water in malt barley production under rainfed conditions. Lastly, instead of evaluating the grain yield or malt quality alone, it would be best to evaluate the target product (malt extract percentage) obtained from a particular region, process, or production methodology. creator: Ibrahim Saygili uri: https://doi.org/10.7717/peerj.15802 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Saygili title: Degradation of zearalenone by microorganisms and enzymes link: https://peerj.com/articles/15808 last-modified: 2023-08-14 description: Mycotoxins are toxic metabolites produced by fungi that may cause serious health problems in humans and animals. Zearalenone is a secondary metabolite produced by fungi of the genus Fusarium, widely exists in animal feed and human food. One concern with the use of microbial strains and their enzyme derivatives for zearalenone degradation is the potential variability in the effectiveness of the degradation process. The efficiency of degradation may depend on various factors such as the type and concentration of zearalenone, the properties of the microbial strains and enzymes, and the environmental conditions. Therefore, it is important to carefully evaluate the efficacy of these methods under different conditions and ensure their reproducibility. Another important consideration is the safety and potential side effects of using microbial strains and enzymes for zearalenone degradation. It is necessary to evaluate the potential risks associated with the use of genetically modified microorganisms or recombinant enzymes, including their potential impact on the environment and non-target organisms. Additionally, it is important to ensure that the degradation products are indeed harmless and do not pose any health risks to humans or animals. Furthermore, while the use of microbial strains and enzymes may offer an environmentally friendly and cost-effective solution for zearalenone degradation, it is important to explore other methods such as physical or chemical treatments as well. These methods may offer complementary approaches for zearalenone detoxification, and their combination with microbial or enzyme-based methods may improve overall efficacy. Overall, the research on the biodegradation of zearalenone using microorganisms and enzyme derivatives is promising, but there are important considerations that need to be addressed to ensure the safety and effectiveness of these methods. Development of recombinant enzymes improves enzymatic detoxification of zearalenone to a non-toxic product without damaging the nutritional content. This review summarizes biodegradation of zearalenone using microorganisms and enzyme derivatives to nontoxic products. Further research is needed to fully evaluate the potential of these methods for mitigating the impact of mycotoxins in food and feed. creator: Jiregna Gari creator: Rahma Abdella uri: https://doi.org/10.7717/peerj.15808 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Gari and Abdella title: Prevalence and virulence genes of Staphylococcus aureus from food contact surfaces in Thai restaurants link: https://peerj.com/articles/15824 last-modified: 2023-08-14 description: BackgroundStaphylococcus aureus is one of the most common pathogens responsible for food poisoning due to its ability to produce staphylococcal enterotoxin (SE). S. aureus can form biofilms on the surfaces of food processing devices, enabling the distribution of SE on foods through cross-contamination events. Thailand is known for its exotic cuisine, but there is no data on the prevalence of SE-harboring S. aureus in restaurants in Thailand.MethodsIn this study, we conducted surface swabs on surfaces of kitchen utensil that come into contact with food and on the hands of food handlers working in restaurants in the north part of Thailand. Isolated S. aureus was investigated for biofilm formation, virulence, and SE genes.ResultsTwo hundred S. aureus were isolated from 650 samples. The highest prevalence of S. aureus contamination was detected on the hands of food handlers (78%), followed by chopping boards (26%), plates (23%), knives (16%), spoons (13%), and glasses (5%). All of them were methicillin-sensitive S. aureus (MSSA) and the mecA gene was not present in any strains. Biofilm formation was detected using the CRA method, and 49 (24.5%) were identified as biofilm-producing strains, with the hands of food handlers identified as the primary source of biofilm-producing strains. The prevelence of biofilm-related adhesion genes detected were: icaAD (13%), fnbA (14.5%), cna (6.5%), and bap (0.5%). Two classical enterotoxin genes, sec and sed, were also found in four and six of the S. aureus isolates, respectively, from hands and utensils.ConclusionThe highest prevelence of S. aureus was detected on the hands of food handlers. S. aureus strains with biofilm and enterotoxin production abilities were discovered on food contact surfaces and the hands of food handlers, implying significant risk of food contamination from these sources that could be harmful to consumers. To avoid cross-contamination of food with food contact items, the food handlers’ hands should be properly washed, and all food preparation equipment should be thoroughly cleaned. creator: Kannipa Tasanapak creator: Siriwat Kucharoenphaibul creator: Jintana Wongwigkarn creator: Sutthirat Sitthisak creator: Rapee Thummeepak creator: Plykaeow Chaibenjawong creator: Wassana Chatdumrong creator: Kunsuda Nimanussornkul uri: https://doi.org/10.7717/peerj.15824 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Tasanapak et al. title: Sex-specific differences in symbiotic microorganisms associated with an invasive mealybug (Phenacoccus solenopsis Tinsley) based on 16S ribosomal DNA link: https://peerj.com/articles/15843 last-modified: 2023-08-14 description: The ability of Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae) to utilize a wide range of host plants is closely related to the symbiotic bacteria within its body. This study investigated the diversity of symbiotic microorganisms associated with the sap-sucking hemipteran insect. Using deep sequencing of the 16S rDNA gene and subsequent analysis with the Qiime software package, we constructed a comprehensive library of bacterial operational taxonomic units (OTUs). We compared the microbial communities of female and male adult mealybugs. Our results showed significant differences in bacterial composition between the sexes, with Proteobacteria, Firmicutes, and Bacteroidetes being the dominant phyla in both female and male mealybugs. These results suggest that the diverse assemblage of symbiotic bacteria in P. solenopsis may be critical in enabling this insect to utilize a wide range of host plants by facilitating carbohydrate digestion and energy uptake. creator: Lu Wang creator: Xia Liu creator: Yongming Ruan uri: https://doi.org/10.7717/peerj.15843 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wang et al. title: Prognostic and clinicopathological role of RACK1 for cancer patients: a systematic review and meta-analysis link: https://peerj.com/articles/15873 last-modified: 2023-08-14 description: BackgroundThe receptor for activated C kinase 1 (RACK1) expression is associated with clinicopathological characteristics and the prognosis of various cancers; however, the conclusions are controversial. As a result, this study aimed to explore the clinicopathological and prognostic values of RACK1 expression in patients with cancer.MethodologyPubMed, Embase, Web of Science, Cochrane Library, and Scopus were comprehensively explored from their inception to April 20, 2023, for selecting studies on the clinicopathological and prognostic role of RACK1 in patients with cancer that met the criteria for inclusion in this review. Pooled hazard ratios (HRs) and 95% confidence intervals (CIs) were used to assess the prognosis-predictive value of RACK1 expression, while pooled odds ratios (ORs) and 95% CIs were used to evaluate the correlation between RACK1 expression and the clinicopathological characteristics of patients with cancer. The quality of the included studies was evaluated using the Newcastle-Ottawa Scale.ResultsTwenty-two studies (13 on prognosis and 20 on clinicopathological characteristics) were included in this systematic review and meta-analysis. The findings indicated that high RACK1 expression was significantly associated with poor overall survival (HR = 1.62; 95% CI, 1.13–2.33; P = 0.009; I2 = 89%) and reversely correlated with disease-free survival/recurrence-free survival (HR = 1.87; 95% CI, 1.22–2.88; P = 0.004; I2 = 0%). Furthermore, increased RACK1 expression was significantly associated with lymphatic invasion/N+ stage (OR = 1.74; 95% CI, 1.04–2.90; P = 0.04; I2 = 79%) of tumors.ConclusionsRACK1 may be a global predictive marker of poor prognosis in patients with cancer and unfavorable clinicopathological characteristics. However, further clinical studies are required to validate these findings. creator: Qiuhao Wang creator: Sixin Jiang creator: Yuqi Wu creator: You Zhang creator: Mei Huang creator: Yan Qiu creator: Xiaobo Luo uri: https://doi.org/10.7717/peerj.15873 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang et al. title: Integrative models of histopathological images and multi-omics data predict prognosis in endometrial carcinoma link: https://peerj.com/articles/15674 last-modified: 2023-08-11 description: ObjectiveThis study aimed to predict the molecular features of endometrial carcinoma (EC) and the overall survival (OS) of EC patients using histopathological imaging.MethodsThe patients from The Cancer Genome Atlas (TCGA) were separated into the training set (n = 215) and test set (n = 214) in proportion of 1:1. By analyzing quantitative histological image features and setting up random forest model verified by cross-validation, we constructed prognostic models for OS. The model performance is evaluated with the time-dependent receiver operating characteristics (AUC) over the test set.ResultsPrognostic models based on histopathological imaging features (HIF) predicted OS in the test set (5-year AUC = 0.803). The performance of combining histopathology and omics transcends that of genomics, transcriptomics, or proteomics alone. Additionally, multi-dimensional omics data, including HIF, genomics, transcriptomics, and proteomics, attained the largest AUCs of 0.866, 0.869, and 0.856 at years 1, 3, and 5, respectively, showcasing the highest discrepancy in survival (HR = 18.347, 95% CI [11.09–25.65], p < 0.001).ConclusionsThe results of this experiment indicated that the complementary features of HIF could improve the prognostic performance of EC patients. Moreover, the integration of HIF and multi-dimensional omics data might ameliorate survival prediction and risk stratification in clinical practice. creator: Yueyi Li creator: Peixin Du creator: Hao Zeng creator: Yuhao Wei creator: Haoxuan Fu creator: Xi Zhong creator: Xuelei Ma uri: https://doi.org/10.7717/peerj.15674 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Li et al. title: Integrated lipidomic and transcriptomic analysis reveals diacylglycerol accumulation in olive of Longnan (China) link: https://peerj.com/articles/15724 last-modified: 2023-08-11 description: BackgroundOlive (Olea europaea L.) oil accumulate more diacylglycerols (DAG) than mostly vegetable oils. Unsaturated fatty acids-enriched DAG consumption enhanced wellness in subjects. However, the mechanism of DAG accumulation is not yet fully understood.MethodsIn this study, gene network of DAG accumulation and fatty acid composition in the two olive mesocarps (“Chenggu 32” (CG) and “Koroneiki” (QJ)) were investigated by integrating lipidome and transcriptome techniques.ResultsA total of 1,408 lipid molecules were identified by lipidomic analysis in olive mesocarp, of which DAG (DAG36:3, DAG36:4 and DAG36:5) showed higher content, and triacylglycerols (TAG54:3, TAG54:4) exhibited opposite trend in CG. Specifically, DAG was rich in polyunsaturated fatty acids (especially C18:2) at the sn-2 position, which was inconsistent with TAG at the same positions (Primarily C18:1). Transcriptomic analysis revealed that phospholipase C (NPC, EC 3.1.4.3) were up-regulated relative to QJ, whereas diacylglycerol kinase (ATP) (DGK, EC 2.7.1.107), diacylglycerol acyltransferase (DGAT, EC 2.3.1.20), and phospholipid: diacylglycerol acyltransferase (PDAT, EC 2.3.1.158) were down-regulated.ConclusionWe speculated that the non-acyl coenzyme A pathway played a significant role in DAG biosynthesis. Additionally, fatty acyl-ACP thioesterase B (FATB, EC 3.1.2.14), stearoyl [acyl-carrier-protein] 9-desaturase (SAD, EC 1.14.19.2) and omega-6 fatty acid desaturase (FAD2, EC 1.14.19.6) were highly expressed in CG and may be involved in regulating fatty acid composition. Meanwhile, phospholipase A1 (LCAT, EC 3.1.1.32) involved in the acyl editing reaction facilitated PUFA linkage at the sn-2 position of DAG. Our findings provide novel insights to increase the DAG content, improve the fatty acid composition of olive oil, and identify candidate genes for the production of DAG-rich oils. creator: Wei Hu creator: Junyi Ma creator: Hongjie Zhang creator: Xin Miu creator: Xin Miao creator: Yu Deng uri: https://doi.org/10.7717/peerj.15724 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Hu et al. title: Effects of passages through an insect or a plant on virulence and physiological properties of the fungus Metarhizium robertsii link: https://peerj.com/articles/15726 last-modified: 2023-08-11 description: Species of the genus Metarhizium are characterized by a multitrophic lifestyle of being arthropod parasites, rhizosphere colonizers, endophytes, and saprophytes. The process of adaptation to various organisms and substrates may lead to specific physiological alterations that can be elucidated by passaging through different hosts. Changes in virulence and cultivation properties of entomopathogenic fungi subcultured on different media or passaged through a live insect host are well known. Nevertheless, comparative in-depth physiological studies on fungi after passaging through insect or plant organisms are scarce. Here, virulence, plant colonization, hydrolytic enzymatic activities, toxin production, and antimicrobial action were compared between stable (nondegenerative) parent strain Metarhizium robertsii MB-1 and its reisolates obtained after eight passages through Galleria mellonella larvae or Solanum lycopersicum or after subculturing on the Sabouraud medium. The passaging through the insect caused similar physiological alterations relative to the plant-based passaging: elevation of destruxin A, B, and E production, a decrease in protease and lipase activities, and lowering of virulence toward G. mellonella and Leptinotarsa decemlineata as compared to the parent strain. The reisolates passaged through the insect or plant showed a slight trend toward increased tomato colonization and enhanced antagonistic action on tomato-associated bacterium Bacillus pumilus as compared to the parental strain. Meanwhile, the subculturing of MB-1 on the Sabouraud medium showed stability of the studied parameters, with minimal alterations relative to the parental strain. We propose that the fungal virulence factors are reprioritized during adaptation of M. robertsii to insects, plants, and media. creator: Oksana G. Tomilova creator: Vadim Y. Kryukov creator: Natalia A. Kryukova creator: Khristina P. Tolokonnikova creator: Yuri S. Tokarev creator: Arina S. Rumiantseva creator: Alexander A. Alekseev creator: Viktor V. Glupov uri: https://doi.org/10.7717/peerj.15726 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Tomilova et al.