PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Barley yield and malt quality affected by fall and spring planting under rainfed conditions
items: Degradation of zearalenone by microorganisms and enzymes
items: Prevalence and virulence genes of Staphylococcus aureus from food contact surfaces in Thai restaurants
items: Sex-specific differences in symbiotic microorganisms associated with an invasive mealybug (Phenacoccus solenopsis Tinsley) based on 16S ribosomal DNA
items: Prognostic and clinicopathological role of RACK1 for cancer patients: a systematic review and meta-analysis
items: Integrative models of histopathological images and multi-omics data predict prognosis in endometrial carcinoma
items: Integrated lipidomic and transcriptomic analysis reveals diacylglycerol accumulation in olive of Longnan (China)
items: Effects of passages through an insect or a plant on virulence and physiological properties of the fungus Metarhizium robertsii
items: Thalattosuchian crocodylomorphs from European Russia, and new insights into metriorhynchid tooth serration evolution and their palaeolatitudinal distribution
items: Development and validation of lumbar spine finite element model

Barley yield and malt quality affected by fall and spring planting under rainfed conditions
type: item
type: AcademicArticle
description: Background As 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. Methods Sixteen 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. Results Grain 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 ext…
format: application/pdf
format: text/html
creator: Ibrahim Saygili
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.15802
publisher: PeerJ Inc.
rights: © 2023 Saygili
abstract: Background As 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. Methods Sixteen 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. Results Grain 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 ext…
bibliographic citation: Saygili (2023) Barley yield and malt quality affected by fall and spring planting under rainfed conditions. PeerJ 11:e15802 https://doi.org/10.7717/peerj.15802
date submitted: 2023-04-26
date accepted: 2023-07-07
issued: 2023-08-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saygili
  given name: Ibrahim
doi: 10.7717/peerj.15802
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-14
copyright: ©2023 Saygili
attribution name: Saygili

Degradation of zearalenone by microorganisms and enzymes
type: item
type: AcademicArticle
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 …
format: application/pdf
format: text/html
creator: Jiregna Gari
creator: Rahma Abdella
subject: Biotechnology
subject: Microbiology
subject: Mycology
subject: Infectious Diseases
description: doi:10.7717/peerj.15808
publisher: PeerJ Inc.
rights: © 2023 Gari and Abdella
abstract: 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 …
bibliographic citation: Gari et al. (2023) Degradation of zearalenone by microorganisms and enzymes. PeerJ 11:e15808 https://doi.org/10.7717/peerj.15808
date submitted: 2023-03-03
date accepted: 2023-07-07
issued: 2023-08-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gari
  given name: Jiregna
author list: Agent
  family name: Abdella
  given name: Rahma
doi: 10.7717/peerj.15808
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-14
copyright: ©2023 Gari and Abdella
attribution name: Gari and Abdella

Prevalence and virulence genes of Staphylococcus aureus from food contact surfaces in Thai restaurants
type: item
type: AcademicArticle
description: Background Staphylococcus 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. Methods In 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. Results Two 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. Conclusion The 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 …
format: application/pdf
format: text/html
creator: Kannipa Tasanapak
creator: Siriwat Kucharoenphaibul
creator: Jintana Wongwigkarn
creator: Sutthirat Sitthisak
creator: Rapee Thummeepak
creator: Plykaeow Chaibenjawong
creator: Wassana Chatdumrong
creator: Kunsuda Nimanussornkul
subject: Food Science and Technology
subject: Genetics
subject: Microbiology
subject: Molecular Biology
subject: Environmental Health
description: doi:10.7717/peerj.15824
publisher: PeerJ Inc.
rights: © 2023 Tasanapak et al.
abstract: Background Staphylococcus 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. Methods In 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. Results Two 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. Conclusion The 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 …
bibliographic citation: Tasanapak et al. (2023) Prevalence and virulence genes of Staphylococcus aureus from food contact surfaces in Thai restaurants. PeerJ 11:e15824 https://doi.org/10.7717/peerj.15824
date submitted: 2022-12-14
date accepted: 2023-07-10
issued: 2023-08-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tasanapak
  given name: Kannipa
author list: Agent
  family name: Kucharoenphaibul
  given name: Siriwat
author list: Agent
  family name: Wongwigkarn
  given name: Jintana
author list: Agent
  family name: Sitthisak
  given name: Sutthirat
author list: Agent
  family name: Thummeepak
  given name: Rapee
author list: Agent
  family name: Chaibenjawong
  given name: Plykaeow
author list: Agent
  family name: Chatdumrong
  given name: Wassana
author list: Agent
  family name: Nimanussornkul
  given name: Kunsuda
doi: 10.7717/peerj.15824
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-14
copyright: © 2023 Tasanapak et al.
attribution name: Tasanapak et al.

Sex-specific differences in symbiotic microorganisms associated with an invasive mealybug (Phenacoccus solenopsis Tinsley) based on 16S ribosomal DNA
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Lu Wang
creator: Xia Liu
creator: Yongming Ruan
subject: Agricultural Science
subject: Bioinformatics
subject: Entomology
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.15843
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: 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.
bibliographic citation: Wang et al. (2023) Sex-specific differences in symbiotic microorganisms associated with an invasive mealybug (Phenacoccus solenopsis Tinsley) based on 16S ribosomal DNA. PeerJ 11:e15843 https://doi.org/10.7717/peerj.15843
date submitted: 2023-04-21
date accepted: 2023-07-12
issued: 2023-08-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Lu
author list: Agent
  family name: Liu
  given name: Xia
author list: Agent
  family name: Ruan
  given name: Yongming
doi: 10.7717/peerj.15843
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-14
copyright: © 2023 Wang et al.
attribution name: Wang et al.

Prognostic and clinicopathological role of RACK1 for cancer patients: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background The 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. Methodology PubMed, 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. Results Twenty-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. Conclusions RACK1 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.
format: application/pdf
format: text/html
creator: Qiuhao Wang
creator: Sixin Jiang
creator: Yuqi Wu
creator: You Zhang
creator: Mei Huang
creator: Yan Qiu
creator: Xiaobo Luo
subject: Evidence Based Medicine
subject: Oncology
subject: Translational Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.15873
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: Background The 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. Methodology PubMed, 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. Results Twenty-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. Conclusions RACK1 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.
bibliographic citation: Wang et al. (2023) Prognostic and clinicopathological role of RACK1 for cancer patients: a systematic review and meta-analysis. PeerJ 11:e15873 https://doi.org/10.7717/peerj.15873
date submitted: 2023-04-21
date accepted: 2023-07-18
issued: 2023-08-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Qiuhao
author list: Agent
  family name: Jiang
  given name: Sixin
author list: Agent
  family name: Wu
  given name: Yuqi
author list: Agent
  family name: Zhang
  given name: You
author list: Agent
  family name: Huang
  given name: Mei
author list: Agent
  family name: Qiu
  given name: Yan
author list: Agent
  family name: Luo
  given name: Xiaobo
doi: 10.7717/peerj.15873
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-14
copyright: ©2023 Wang et al.
attribution name: Wang et al.

Integrative models of histopathological images and multi-omics data predict prognosis in endometrial carcinoma
type: item
type: AcademicArticle
description: Objective This study aimed to predict the molecular features of endometrial carcinoma (EC) and the overall survival (OS) of EC patients using histopathological imaging. Methods The 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. Results Prognostic 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). Conclusions The 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.
format: application/pdf
format: text/html
creator: Yueyi Li
creator: Peixin Du
creator: Hao Zeng
creator: Yuhao Wei
creator: Haoxuan Fu
creator: Xi Zhong
creator: Xuelei Ma
subject: Bioinformatics
subject: Oncology
subject: Pathology
subject: Women’s Health
description: doi:10.7717/peerj.15674
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Objective This study aimed to predict the molecular features of endometrial carcinoma (EC) and the overall survival (OS) of EC patients using histopathological imaging. Methods The 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. Results Prognostic 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). Conclusions The 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.
bibliographic citation: Li et al. (2023) Integrative models of histopathological images and multi-omics data predict prognosis in endometrial carcinoma. PeerJ 11:e15674 https://doi.org/10.7717/peerj.15674
date submitted: 2023-04-14
date accepted: 2023-06-11
issued: 2023-08-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yueyi
author list: Agent
  family name: Du
  given name: Peixin
author list: Agent
  family name: Zeng
  given name: Hao
author list: Agent
  family name: Wei
  given name: Yuhao
author list: Agent
  family name: Fu
  given name: Haoxuan
author list: Agent
  family name: Zhong
  given name: Xi
author list: Agent
  family name: Ma
  given name: Xuelei
doi: 10.7717/peerj.15674
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-11
copyright: © 2023 Li et al.
attribution name: Li et al.

Integrated lipidomic and transcriptomic analysis reveals diacylglycerol accumulation in olive of Longnan (China)
type: item
type: AcademicArticle
description: Background Olive (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. Methods In 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. Results A 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. Conclusion We 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.
format: application/pdf
format: text/html
creator: Wei Hu
creator: Junyi Ma
creator: Hongjie Zhang
creator: Xin Miu
creator: Xin Miao
creator: Yu Deng
subject: Agricultural Science
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15724
publisher: PeerJ Inc.
rights: © 2023 Hu et al.
abstract: Background Olive (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. Methods In 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. Results A 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. Conclusion We 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.
bibliographic citation: Hu et al. (2023) Integrated lipidomic and transcriptomic analysis reveals diacylglycerol accumulation in olive of Longnan (China). PeerJ 11:e15724 https://doi.org/10.7717/peerj.15724
date submitted: 2023-03-15
date accepted: 2023-06-18
issued: 2023-08-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Wei
author list: Agent
  family name: Ma
  given name: Junyi
author list: Agent
  family name: Zhang
  given name: Hongjie
author list: Agent
  family name: Miu
  given name: Xin
author list: Agent
  family name: Miao
  given name: Xin
author list: Agent
  family name: Deng
  given name: Yu
doi: 10.7717/peerj.15724
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-11
copyright: © 2023 Hu et al.
attribution name: Hu et al.

Effects of passages through an insect or a plant on virulence and physiological properties of the fungus Metarhizium robertsii
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
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
subject: Ecology
subject: Entomology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.15726
publisher: PeerJ Inc.
rights: © 2023 Tomilova et al.
abstract: 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.
bibliographic citation: Tomilova et al. (2023) Effects of passages through an insect or a plant on virulence and physiological properties of the fungus Metarhizium robertsii. PeerJ 11:e15726 https://doi.org/10.7717/peerj.15726
date submitted: 2023-04-11
date accepted: 2023-06-18
issued: 2023-08-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tomilova
  given name: Oksana G.
author list: Agent
  family name: Kryukov
  given name: Vadim Y.
author list: Agent
  family name: Kryukova
  given name: Natalia A.
author list: Agent
  family name: Tolokonnikova
  given name: Khristina P.
author list: Agent
  family name: Tokarev
  given name: Yuri S.
author list: Agent
  family name: Rumiantseva
  given name: Arina S.
author list: Agent
  family name: Alekseev
  given name: Alexander A.
author list: Agent
  family name: Glupov
  given name: Viktor V.
doi: 10.7717/peerj.15726
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-11
copyright: © 2023 Tomilova et al.
attribution name: Tomilova et al.

Thalattosuchian crocodylomorphs from European Russia, and new insights into metriorhynchid tooth serration evolution and their palaeolatitudinal distribution
type: item
type: AcademicArticle
description: From the Middle Jurassic to the Early Cretaceous, metriorhynchid crocodylomorphs inhabited marine ecosystems across the European archipelago. Unfortunately, European metriorhynchids are only well known from Germany, France, and the UK, with the Eastern European fossil record being especially poor. This hinders our understanding of metriorhynchid biodiversity across these continuous seaways, and our ability to investigate provincialism. Here we describe eleven isolated tooth crowns and six vertebrae referable to Metriorhynchidae from the Callovian, Oxfordian, Volgian (Tithonian), and Ryazanian (Berriasian) or Valanginian of European Russia. We also describe an indeterminate thalattosuchian tooth from the lower Bajocian of the Volgograd Oblast, the first discovery of a marine reptile from the Bajocian strata of European Russia. These rare fossils, along with previous reports of Russian thalattosuchians, indicate that thalattosuchians have been common in the Middle Russian Sea since it was formed. Palaeolatitude calculations for worldwide metriorhynchid-bearing localities demonstrate that the occurrences in European Russia are the most northern, located mainly between 44–50 degrees north. However, metriorhynchids appear to be rare at these palaeolatitudes, and are absent from palaeolatitudes higher than 50°. These observations support the hypothesis that metriorhynchids evolved an elevated metabolism but were not endo-homeothermic, especially as endo-homeothermic marine reptiles (ichthyosaurs and plesiosaurs) remained abundant at much higher palaeolatitudes.
format: application/pdf
format: text/html
creator: Mark T. Young
creator: Nikolay G. Zverkov
creator: Maxim S. Arkhangelsky
creator: Alexey P. Ippolitov
creator: Igor A. Meleshin
creator: Georgy V. Mirantsev
creator: Alexey S. Shmakov
creator: Ilya M. Stenshin
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.15781
publisher: PeerJ Inc.
rights: © 2023 Young et al.
abstract: From the Middle Jurassic to the Early Cretaceous, metriorhynchid crocodylomorphs inhabited marine ecosystems across the European archipelago. Unfortunately, European metriorhynchids are only well known from Germany, France, and the UK, with the Eastern European fossil record being especially poor. This hinders our understanding of metriorhynchid biodiversity across these continuous seaways, and our ability to investigate provincialism. Here we describe eleven isolated tooth crowns and six vertebrae referable to Metriorhynchidae from the Callovian, Oxfordian, Volgian (Tithonian), and Ryazanian (Berriasian) or Valanginian of European Russia. We also describe an indeterminate thalattosuchian tooth from the lower Bajocian of the Volgograd Oblast, the first discovery of a marine reptile from the Bajocian strata of European Russia. These rare fossils, along with previous reports of Russian thalattosuchians, indicate that thalattosuchians have been common in the Middle Russian Sea since it was formed. Palaeolatitude calculations for worldwide metriorhynchid-bearing localities demonstrate that the occurrences in European Russia are the most northern, located mainly between 44–50 degrees north. However, metriorhynchids appear to be rare at these palaeolatitudes, and are absent from palaeolatitudes higher than 50°. These observations support the hypothesis that metriorhynchids evolved an elevated metabolism but were not endo-homeothermic, especially as endo-homeothermic marine reptiles (ichthyosaurs and plesiosaurs) remained abundant at much higher palaeolatitudes.
bibliographic citation: Young et al. (2023) Thalattosuchian crocodylomorphs from European Russia, and new insights into metriorhynchid tooth serration evolution and their palaeolatitudinal distribution. PeerJ 11:e15781 https://doi.org/10.7717/peerj.15781
date submitted: 2023-05-08
date accepted: 2023-07-03
issued: 2023-08-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Young
  given name: Mark T.
author list: Agent
  family name: Zverkov
  given name: Nikolay G.
author list: Agent
  family name: Arkhangelsky
  given name: Maxim S.
author list: Agent
  family name: Ippolitov
  given name: Alexey P.
author list: Agent
  family name: Meleshin
  given name: Igor A.
author list: Agent
  family name: Mirantsev
  given name: Georgy V.
author list: Agent
  family name: Shmakov
  given name: Alexey S.
author list: Agent
  family name: Stenshin
  given name: Ilya M.
doi: 10.7717/peerj.15781
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-11
copyright: ©2023 Young et al.
attribution name: Young et al.

Development and validation of lumbar spine finite element model
type: item
type: AcademicArticle
description: The functional biomechanics of the lumbar spine have been better understood by finite element method (FEM) simulations. However, there are still areas where the behavior of soft tissues can be better modeled or described in a different way. The purpose of this research is to develop and validate a lumbar spine section intended for biomechanical research. A FE model of the 50th percentile adult male (AM) Total Human Model for Safety (THUMS) v6.1 was used to implement the modifications. The main modifications were to apply orthotropic material properties and nonlinear stress-strain behavior for ligaments, hyperelastic material properties for annulus fibrosus and nucleus pulposus, and the specific content of collagenous fibers in the annulus fibrosus ground substance. Additionally, a separation of the nucleus pulposus from surrounding bones and tissues was implemented. The FE model was subjected to different loading modes, in which intervertebral rotations and disc pressures were calculated. Loading modes contained different forces and moments acting on the lumbar section: axial forces (compression and tension), shear forces, pure moments, and combined loading modes of axial forces and pure moments. The obtained ranges of motion from the modified numerical model agreed with experimental data for all loading modes. Moreover, intradiscal pressure validation for the modified model presented a good agreement with the data available from the literature. This study demonstrated the modifications of the THUMS v6.1 model and validated the obtained numerical results with existing literature in the sub-injurious range. By applying the proposed changes, it is possible to better model the behavior of the human lumbar section under various loads and moments.
format: application/pdf
format: text/html
creator: Tomasz Wiczenbach
creator: Lukasz Pachocki
creator: Karol Daszkiewicz
creator: Piotr Łuczkiewicz
creator: Wojciech Witkowski
subject: Computational Science
subject: Biomechanics
description: doi:10.7717/peerj.15805
publisher: PeerJ Inc.
rights: © 2023 Wiczenbach et al.
abstract: The functional biomechanics of the lumbar spine have been better understood by finite element method (FEM) simulations. However, there are still areas where the behavior of soft tissues can be better modeled or described in a different way. The purpose of this research is to develop and validate a lumbar spine section intended for biomechanical research. A FE model of the 50th percentile adult male (AM) Total Human Model for Safety (THUMS) v6.1 was used to implement the modifications. The main modifications were to apply orthotropic material properties and nonlinear stress-strain behavior for ligaments, hyperelastic material properties for annulus fibrosus and nucleus pulposus, and the specific content of collagenous fibers in the annulus fibrosus ground substance. Additionally, a separation of the nucleus pulposus from surrounding bones and tissues was implemented. The FE model was subjected to different loading modes, in which intervertebral rotations and disc pressures were calculated. Loading modes contained different forces and moments acting on the lumbar section: axial forces (compression and tension), shear forces, pure moments, and combined loading modes of axial forces and pure moments. The obtained ranges of motion from the modified numerical model agreed with experimental data for all loading modes. Moreover, intradiscal pressure validation for the modified model presented a good agreement with the data available from the literature. This study demonstrated the modifications of the THUMS v6.1 model and validated the obtained numerical results with existing literature in the sub-injurious range. By applying the proposed changes, it is possible to better model the behavior of the human lumbar section under various loads and moments.
bibliographic citation: Wiczenbach et al. (2023) Development and validation of lumbar spine finite element model. PeerJ 11:e15805 https://doi.org/10.7717/peerj.15805
date submitted: 2023-02-02
date accepted: 2023-07-07
issued: 2023-08-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wiczenbach
  given name: Tomasz
author list: Agent
  family name: Pachocki
  given name: Lukasz
author list: Agent
  family name: Daszkiewicz
  given name: Karol
author list: Agent
  family name: Łuczkiewicz
  given name: Piotr
author list: Agent
  family name: Witkowski
  given name: Wojciech
doi: 10.7717/peerj.15805
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-11
copyright: ©2023 Wiczenbach et al.
attribution name: Wiczenbach et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359