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Articles published in PeerJ
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PeerJ
2167-8359
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https://peerj.com/articles/16733
Biochar’s role in improving pakchoi quality and microbial community structure in rhizosphere soil
Background
Biochar amendments enhance crop productivity and improve agricultural quality. To date, studies on the correlation between different amounts of biochar in pakchoi (Brassica campestris L.) quality and rhizosphere soil microorganisms are limited, especially in weakly alkaline soils. The experiment was set up to explore the effect of different concentrations of biochar on vegetable quality and the correlation between the index of quality and soil bacterial community structure changes.
Methods
The soil was treated in the following ways via pot culture: the blank control (CK) without biochar added and with biochar at different concentrations of 1% (T1), 3% (T2), 5% (T3), and 7% (T4). Here, we investigatedthe synergistic effect of biochar on the growth and quality of pakchoi, soil enzymatic activities, and soil nutrients. Microbial communities from pakchoi rhizosphere soil were analyzed by Illumina MiSeq.
Results
The results revealed that adding 3% biochar significantly increased plant height, root length, and dry weight of pakchoi and increased the contents of soluble sugars, soluble proteins, Vitamin C (VC), cellulose, and reduced nitrate content in pakchoi leaves. Meanwhile, soil enzyme activities and available nutrient content in rhizosphere soil increased. This study demonstrated that the the microbial community structure of bacteria in pakchoi rhizosphere soil was changed by applying more than 3% biochar. Among the relatively abundant dominant phyla, Gemmatimonadetes, Anaerolineae, Deltaproteobacteria and Verrucomicrobiae were reduced, and Alphaproteobacteria, Gammaproteobacteria, Bacteroidia, and Acidimicrobiia relative abundance increased. Furthermore, adding 3% biochar reduced the relative abundance of Gemmatimonas and increased the relative abundances of Ilumatobacter, Luteolibacter, Lysobacter, Arthrobacter, and Mesorhizobium. The nitrate content was positively correlated with the abundance of Gemmatimonadetes, and the nitrate content was significantly negatively correlated with the relative abundance of Ilumatobacter. Carbohydrate transport and metabolism in the rhizosphere soil of pakchoi decreased, and lipid transport and metabolism increased after biochar application.
Conclusion
Overall, our results indicated that applying biochar improved soil physicochemical states and plant nutrient absorption, and affected the abundance of dominant bacterial groups (e.g., Gemmatimonadetes and Ilumatobacter), these were the main factors to increase pakchoi growth and promote quality of pakchoi. Therefore, considering the growth, quality of pakchoi, and soil environment, the effect of using 3% biochar is better.
application/pdf
text/html
doi:10.7717/peerj.16733
Biochar’s role in improving pakchoi quality and microbial community structure in rhizosphere soil
Xia Wu
Fengjun Yang
Jili Zhang
Feng Gao
Yi Chen Hu
Kejun Yang
Peng Wang
Agricultural Science
Microbiology
Molecular Biology
Plant Science
Soil Science
doi:10.7717/peerj.16733
PeerJ Inc.
© 2024 Wu et al.
Background
Biochar amendments enhance crop productivity and improve agricultural quality. To date, studies on the correlation between different amounts of biochar in pakchoi (Brassica campestris L.) quality and rhizosphere soil microorganisms are limited, especially in weakly alkaline soils. The experiment was set up to explore the effect of different concentrations of biochar on vegetable quality and the correlation between the index of quality and soil bacterial community structure changes.
Methods
The soil was treated in the following ways via pot culture: the blank control (CK) without biochar added and with biochar at different concentrations of 1% (T1), 3% (T2), 5% (T3), and 7% (T4). Here, we investigatedthe synergistic effect of biochar on the growth and quality of pakchoi, soil enzymatic activities, and soil nutrients. Microbial communities from pakchoi rhizosphere soil were analyzed by Illumina MiSeq.
Results
The results revealed that adding 3% biochar significantly increased plant height, root length, and dry weight of pakchoi and increased the contents of soluble sugars, soluble proteins, Vitamin C (VC), cellulose, and reduced nitrate content in pakchoi leaves. Meanwhile, soil enzyme activities and available nutrient content in rhizosphere soil increased. This study demonstrated that the the microbial community structure of bacteria in pakchoi rhizosphere soil was changed by applying more than 3% biochar. Among the relatively abundant dominant phyla, Gemmatimonadetes, Anaerolineae, Deltaproteobacteria and Verrucomicrobiae were reduced, and Alphaproteobacteria, Gammaproteobacteria, Bacteroidia, and Acidimicrobiia relative abundance increased. Furthermore, adding 3% biochar reduced the relative abundance of Gemmatimonas and increased the relative abundances of Ilumatobacter, Luteolibacter, Lysobacter, Arthrobacter, and Mesorhizobium. The nitrate content was positively correlated with the abundance of Gemmatimonadetes, and the nitrate content was significantly negatively correlated with the relative abundance of Ilumatobacter. Carbohydrate transport and metabolism in the rhizosphere soil of pakchoi decreased, and lipid transport and metabolism increased after biochar application.
Conclusion
Overall, our results indicated that applying biochar improved soil physicochemical states and plant nutrient absorption, and affected the abundance of dominant bacterial groups (e.g., Gemmatimonadetes and Ilumatobacter), these were the main factors to increase pakchoi growth and promote quality of pakchoi. Therefore, considering the growth, quality of pakchoi, and soil environment, the effect of using 3% biochar is better.
Wu et al. (2024) Biochar’s role in improving pakchoi quality and microbial community structure in rhizosphere soil. PeerJ 12:e16733 https://doi.org/10.7717/peerj.16733
2023-05-01
2023-12-07
2024-03-18
Wu
Xia
Yang
Fengjun
Zhang
Jili
Gao
Feng
Hu
Yi Chen
Yang
Kejun
Wang
Peng
10.7717/peerj.16733
https://peerj.com/articles/16733
12
https://peerj.com/articles/16733
10.7717/peerj.16733
2167-8359
12
PeerJ
2024-03-18
©2024 Wu et al.
Wu et al.
-
https://peerj.com/articles/16817
Anti-ENO1 antibody combined with metformin against tumor resistance: a novel antibody-based platform
Background
Antibody-based platforms (i.e., ADC) have emerged as one of the most encouraging tools for the cancer resistance caused by cancer stem cells (CSCs) enrichment. Our study might provide a promising therapeutic direction against drug resistance and serve as a potential precursor platform for screening ADC.
Methods
The cell migration, invasion, drug resistance, and self-renewal were assessed by the cell invasion and migration assay, wound healing assay, CCK-8 assay, colony formation assay, and sphere formation assay, respectively. The expression profiles of CSCs (ALDH+ and CD44+) subpopulations were screened by flow cytometry. The western blot and cell immunofluorescence assay were used to evaluate pathway-related protein expression in both anti-ENO1 antibody, MET combined with DPP/CTX-treated CSCs.
Results
In the present study, western blot and flow cytometry verified that anti-ENO1 antibody target the CD44+ subpopulation by inhibiting the PI3K/AKT pathway, while metformin might target the ALDH+ subpopulation through activation of the AMPK pathway and thus reverse drug resistance to varying degrees. Subsequently, in vitro investigation indicated that anti-ENO1 antibody, metformin combined with cisplatin/cetuximab could simultaneously target ALDH+ and CD44+ subpopulations. The combination also inhibited the CSCs proliferation, migration, invasion, and sphere formation; which may result in overcoming the drug resistance. Then, molecular mechanism exploration verified that the anti-ENO1 antibody, metformin combined with cisplatin/cetuximab inhibited the Wnt/β-catenin signaling.
Conclusions
The study preliminarily revealed anti-ENO1 antibody combined with metformin could overcome drug resistance against CSCs by inhibiting the Wnt//β-catenin pathway and might serve as a potential precursor platform for screening ADC. More importantly, it is reasonably believed that antibody-based drug combination therapy might function as an encouraging tool for oncotherapy.
application/pdf
text/html
doi:10.7717/peerj.16817
Anti-ENO1 antibody combined with metformin against tumor resistance: a novel antibody-based platform
Xiong Shu
Hui Wen Zhang
Shi Ya Liu
Li Xin Sun
Tao Zhang
Yu Liang Ran
Biochemistry
Cell Biology
Molecular Biology
Oncology
Pharmacology
doi:10.7717/peerj.16817
PeerJ Inc.
© 2024 Shu et al.
Background
Antibody-based platforms (i.e., ADC) have emerged as one of the most encouraging tools for the cancer resistance caused by cancer stem cells (CSCs) enrichment. Our study might provide a promising therapeutic direction against drug resistance and serve as a potential precursor platform for screening ADC.
Methods
The cell migration, invasion, drug resistance, and self-renewal were assessed by the cell invasion and migration assay, wound healing assay, CCK-8 assay, colony formation assay, and sphere formation assay, respectively. The expression profiles of CSCs (ALDH+ and CD44+) subpopulations were screened by flow cytometry. The western blot and cell immunofluorescence assay were used to evaluate pathway-related protein expression in both anti-ENO1 antibody, MET combined with DPP/CTX-treated CSCs.
Results
In the present study, western blot and flow cytometry verified that anti-ENO1 antibody target the CD44+ subpopulation by inhibiting the PI3K/AKT pathway, while metformin might target the ALDH+ subpopulation through activation of the AMPK pathway and thus reverse drug resistance to varying degrees. Subsequently, in vitro investigation indicated that anti-ENO1 antibody, metformin combined with cisplatin/cetuximab could simultaneously target ALDH+ and CD44+ subpopulations. The combination also inhibited the CSCs proliferation, migration, invasion, and sphere formation; which may result in overcoming the drug resistance. Then, molecular mechanism exploration verified that the anti-ENO1 antibody, metformin combined with cisplatin/cetuximab inhibited the Wnt/β-catenin signaling.
Conclusions
The study preliminarily revealed anti-ENO1 antibody combined with metformin could overcome drug resistance against CSCs by inhibiting the Wnt//β-catenin pathway and might serve as a potential precursor platform for screening ADC. More importantly, it is reasonably believed that antibody-based drug combination therapy might function as an encouraging tool for oncotherapy.
Shu et al. (2024) Anti-ENO1 antibody combined with metformin against tumor resistance: a novel antibody-based platform. PeerJ 12:e16817 https://doi.org/10.7717/peerj.16817
2023-03-31
2023-12-30
2024-03-18
Shu
Xiong
Zhang
Hui Wen
Liu
Shi Ya
Sun
Li Xin
Zhang
Tao
Ran
Yu Liang
10.7717/peerj.16817
https://peerj.com/articles/16817
12
https://peerj.com/articles/16817
10.7717/peerj.16817
2167-8359
12
PeerJ
2024-03-18
© 2024 Shu et al.
Shu et al.
-
https://peerj.com/articles/17002
Integrating single-cell and bulk sequencing data to identify glycosylation-based genes in non-alcoholic fatty liver disease-associated hepatocellular carcinoma
Background
The incidence of non-alcoholic fatty liver disease (NAFLD) associated hepatocellular carcinoma (HCC) has been increasing. However, the role of glycosylation, an important modification that alters cellular differentiation and immune regulation, in the progression of NAFLD to HCC is rare.
Methods
We used the NAFLD-HCC single-cell dataset to identify variation in the expression of glycosylation patterns between different cells and used the HCC bulk dataset to establish a link between these variations and the prognosis of HCC patients. Then, machine learning algorithms were used to identify those glycosylation-related signatures with prognostic significance and to construct a model for predicting the prognosis of HCC patients. Moreover, it was validated in high-fat diet-induced mice and clinical cohorts.
Results
The NAFLD-HCC Glycogene Risk Model (NHGRM) signature included the following genes: SPP1, SOCS2, SAPCD2, S100A9, RAMP3, and CSAD. The higher NHGRM scores were associated with a poorer prognosis, stronger immune-related features, immune cell infiltration and immunity scores. Animal experiments, external and clinical cohorts confirmed the expression of these genes.
Conclusion
The genetic signature we identified may serve as a potential indicator of survival in patients with NAFLD-HCC and provide new perspectives for elucidating the role of glycosylation-related signatures in this pathologic process.
application/pdf
text/html
doi:10.7717/peerj.17002
Integrating single-cell and bulk sequencing data to identify glycosylation-based genes in non-alcoholic fatty liver disease-associated hepatocellular carcinoma
Zhijia Zhou
Yanan Gao
Longxin Deng
Xiaole Lu
Yancheng Lai
Jieke Wu
Shaodong Chen
Chengzhong Li
Huiqing Liang
Biochemistry
Bioinformatics
Molecular Biology
Gastroenterology and Hepatology
Histology
doi:10.7717/peerj.17002
PeerJ Inc.
© 2024 Zhou et al.
Background
The incidence of non-alcoholic fatty liver disease (NAFLD) associated hepatocellular carcinoma (HCC) has been increasing. However, the role of glycosylation, an important modification that alters cellular differentiation and immune regulation, in the progression of NAFLD to HCC is rare.
Methods
We used the NAFLD-HCC single-cell dataset to identify variation in the expression of glycosylation patterns between different cells and used the HCC bulk dataset to establish a link between these variations and the prognosis of HCC patients. Then, machine learning algorithms were used to identify those glycosylation-related signatures with prognostic significance and to construct a model for predicting the prognosis of HCC patients. Moreover, it was validated in high-fat diet-induced mice and clinical cohorts.
Results
The NAFLD-HCC Glycogene Risk Model (NHGRM) signature included the following genes: SPP1, SOCS2, SAPCD2, S100A9, RAMP3, and CSAD. The higher NHGRM scores were associated with a poorer prognosis, stronger immune-related features, immune cell infiltration and immunity scores. Animal experiments, external and clinical cohorts confirmed the expression of these genes.
Conclusion
The genetic signature we identified may serve as a potential indicator of survival in patients with NAFLD-HCC and provide new perspectives for elucidating the role of glycosylation-related signatures in this pathologic process.
Zhou et al. (2024) Integrating single-cell and bulk sequencing data to identify glycosylation-based genes in non-alcoholic fatty liver disease-associated hepatocellular carcinoma. PeerJ 12:e17002 https://doi.org/10.7717/peerj.17002
2023-07-28
2024-02-05
2024-03-18
Zhou
Zhijia
Gao
Yanan
Deng
Longxin
Lu
Xiaole
Lai
Yancheng
Wu
Jieke
Chen
Shaodong
Li
Chengzhong
Liang
Huiqing
10.7717/peerj.17002
https://peerj.com/articles/17002
12
https://peerj.com/articles/17002
10.7717/peerj.17002
2167-8359
12
PeerJ
2024-03-18
©2024 Zhou et al.
Zhou et al.
-
https://peerj.com/articles/17049
Changes in hamstring contractile properties during the competitive season in young football players
Background
The study aimed to examine alterations and imbalances in hamstring muscle contractile properties among young football players throughout their competitive season, and to understand how these changes might contribute to the risk of muscle injuries. Hamstring injuries are particularly common in football, yet the underlying causes and effective prevention methods remain unclear.
Methods
The research involved 74 young footballers who were assessed before the season (pre-test) and after 12 weeks of training (post-test). To evaluate changes in hamstring muscle contractile properties, specifically the left and right biceps femoris (BF) and semitendinosus (ST), tensiomyography (TMG) parameters were utilized.
Results
In comparison to the BF muscle, significant differences in time delay (Td) between the left and right sides in the post-test (p = 0.0193), and maximal displacement (Dm) between the left and right sides at the pre-test (p = 0.0395). However, significant differences in Dm were observed only in the left ST muscle between the pre- and post-tests (p = 0.0081). Regarding lateral symmetry, BF registered measurements of 79.7 ± 13.43 (pre-test) and 77.4 ± 14.82 (post-test), whereas ST showed measurements of 87.0 ± 9.79 (pre-test) and 87.5 ± 9.60 (post-test).
Conclusions
These assessments provided TMG reference data for hamstring muscles in young footballers, both before the season and after 12 weeks of in-season training. The observed changes in the contractile properties and decrease in lateral symmetry of the BF in both tests suggest an increased risk of injury.
application/pdf
text/html
doi:10.7717/peerj.17049
Changes in hamstring contractile properties during the competitive season in young football players
Paweł Pakosz
Mariusz Konieczny
Przemysław Domaszewski
Tomasz Dybek
Mariusz Gnoiński
Elżbieta Skorupska
Anatomy and Physiology
Kinesiology
Biomechanics
Sports Injury
Sports Medicine
doi:10.7717/peerj.17049
PeerJ Inc.
© 2024 Pakosz et al.
Background
The study aimed to examine alterations and imbalances in hamstring muscle contractile properties among young football players throughout their competitive season, and to understand how these changes might contribute to the risk of muscle injuries. Hamstring injuries are particularly common in football, yet the underlying causes and effective prevention methods remain unclear.
Methods
The research involved 74 young footballers who were assessed before the season (pre-test) and after 12 weeks of training (post-test). To evaluate changes in hamstring muscle contractile properties, specifically the left and right biceps femoris (BF) and semitendinosus (ST), tensiomyography (TMG) parameters were utilized.
Results
In comparison to the BF muscle, significant differences in time delay (Td) between the left and right sides in the post-test (p = 0.0193), and maximal displacement (Dm) between the left and right sides at the pre-test (p = 0.0395). However, significant differences in Dm were observed only in the left ST muscle between the pre- and post-tests (p = 0.0081). Regarding lateral symmetry, BF registered measurements of 79.7 ± 13.43 (pre-test) and 77.4 ± 14.82 (post-test), whereas ST showed measurements of 87.0 ± 9.79 (pre-test) and 87.5 ± 9.60 (post-test).
Conclusions
These assessments provided TMG reference data for hamstring muscles in young footballers, both before the season and after 12 weeks of in-season training. The observed changes in the contractile properties and decrease in lateral symmetry of the BF in both tests suggest an increased risk of injury.
Pakosz et al. (2024) Changes in hamstring contractile properties during the competitive season in young football players. PeerJ 12:e17049 https://doi.org/10.7717/peerj.17049
2023-10-06
2024-02-13
2024-03-18
Pakosz
Paweł
Konieczny
Mariusz
Domaszewski
Przemysław
Dybek
Tomasz
Gnoiński
Mariusz
Skorupska
Elżbieta
10.7717/peerj.17049
https://peerj.com/articles/17049
12
https://peerj.com/articles/17049
10.7717/peerj.17049
2167-8359
12
PeerJ
2024-03-18
© 2024 Pakosz et al.
Pakosz et al.
-
https://peerj.com/articles/17126
Deciphering the genomes of motility-deficient mutants of Vibrio alginolyticus 138-2
The motility of Vibrio species plays a pivotal role in their survival and adaptation to diverse environments and is intricately associated with pathogenicity in both humans and aquatic animals. Numerous mutant strains of Vibrio alginolyticus have been generated using UV or EMS mutagenesis to probe flagellar motility using molecular genetic approaches. Identifying these mutations promises to yield valuable insights into motility at the protein structural physiology level. In this study, we determined the complete genomic structure of 4 reference specimens of laboratory V. alginolyticus strains: a precursor strain, V. alginolyticus 138-2, two strains showing defects in the lateral flagellum (VIO5 and YM4), and one strain showing defects in the polar flagellum (YM19). Subsequently, we meticulously ascertained the specific mutation sites within the 18 motility-deficient strains related to the polar flagellum (they fall into three categories: flagellar-deficient, multi-flagellar, and chemotaxis-deficient strains) by whole genome sequencing and mapping to the complete genome of parental strains VIO5 or YM4. The mutant strains had an average of 20.6 (±12.7) mutations, most of which were randomly distributed throughout the genome. However, at least two or more different mutations in six flagellar-related genes were detected in 18 mutants specifically selected as chemotaxis-deficient mutants. Genomic analysis using a large number of mutant strains is a very effective tool to comprehensively identify genes associated with specific phenotypes using forward genetics.
application/pdf
text/html
doi:10.7717/peerj.17126
Deciphering the genomes of motility-deficient mutants of Vibrio alginolyticus 138-2
Kazuma Uesaka
Keita Inaba
Noriko Nishioka
Seiji Kojima
Michio Homma
Kunio Ihara
Bioinformatics
Genetics
Genomics
Microbiology
doi:10.7717/peerj.17126
PeerJ Inc.
© 2024 Uesaka et al.
The motility of Vibrio species plays a pivotal role in their survival and adaptation to diverse environments and is intricately associated with pathogenicity in both humans and aquatic animals. Numerous mutant strains of Vibrio alginolyticus have been generated using UV or EMS mutagenesis to probe flagellar motility using molecular genetic approaches. Identifying these mutations promises to yield valuable insights into motility at the protein structural physiology level. In this study, we determined the complete genomic structure of 4 reference specimens of laboratory V. alginolyticus strains: a precursor strain, V. alginolyticus 138-2, two strains showing defects in the lateral flagellum (VIO5 and YM4), and one strain showing defects in the polar flagellum (YM19). Subsequently, we meticulously ascertained the specific mutation sites within the 18 motility-deficient strains related to the polar flagellum (they fall into three categories: flagellar-deficient, multi-flagellar, and chemotaxis-deficient strains) by whole genome sequencing and mapping to the complete genome of parental strains VIO5 or YM4. The mutant strains had an average of 20.6 (±12.7) mutations, most of which were randomly distributed throughout the genome. However, at least two or more different mutations in six flagellar-related genes were detected in 18 mutants specifically selected as chemotaxis-deficient mutants. Genomic analysis using a large number of mutant strains is a very effective tool to comprehensively identify genes associated with specific phenotypes using forward genetics.
Uesaka et al. (2024) Deciphering the genomes of motility-deficient mutants of Vibrio alginolyticus 138-2. PeerJ 12:e17126 https://doi.org/10.7717/peerj.17126
2023-12-08
2024-02-27
2024-03-18
Uesaka
Kazuma
Inaba
Keita
Nishioka
Noriko
Kojima
Seiji
Homma
Michio
Ihara
Kunio
10.7717/peerj.17126
https://peerj.com/articles/17126
12
https://peerj.com/articles/17126
10.7717/peerj.17126
2167-8359
12
PeerJ
2024-03-18
© 2024 Uesaka et al.
Uesaka et al.
-
https://peerj.com/articles/17130
Validation of CDC45 as a novel biomarker for diagnosis and prognosis of gastric cancer
Background
Cell division cycle protein 45 (CDC45) has been demonstrated to play vital roles in the progression of various malignancies. However, the clinical significance of CDC45 in gastric cancer (GC) remains unreported.
Method
In this study, we employed the TCGA database and the TCGA & GTEx dataset to compare the mRNA expression levels of CDC45 between gastric cancer tissues and adjacent or normal tissues (p < 0.05 was considered statistically significant), which was further validated in multiple datasets including GSE13911, GSE29272, GSE118916, GSE66229, as well as RT-qPCR. Furthermore, we harnessed the Human Protein Atlas (HPA) to evaluate the protein expression of CDC45, which was subsequently verified through immunohistochemistry (IHC). To ascertain the diagnostic utility of CDC45, receiver operating characteristic (ROC) curves and the area under the ROC curve (AUC) were calculated in TCGA database, and further validated it in TCGA & GTEx and GSE66229 datasets. The Kaplan–Meier method was used to reveal the prognostic importance of CDC45 in The Cancer Genome Atlas (TCGA) database and authenticated through the GSE66229, GSE84433, and GSE84437 datasets. Through cBioPortal, we identified co-expressed genes of CDC45, and pursued enrichment analysis. Additionally, we availed gene set enrichment analysis (GSEA) to annotate the biological functions of CDC45.
Results
Differential expression analysis revealed that CDC45 was significantly upregulated at both the mRNA and protein levels in GC (all p < 0.05). Remarkably, CDC45 emerged as a promising prognostic indicator and a novel diagnostic biomarker for GC. In a comprehensive the drug susceptibility analysis, we found that patients with high expression of CDC45 had high sensitivity to various chemotherapeutic agents, among which 5-fluorouracil, docetaxel, cisplatin, and elesclomol were most evident. Furthermore, our findings suggested a plausible association between CDC45 and immune cell infiltration. Enrichment analysis revealed that CDC45 and its associated genes may play crucial roles in muscle biofunction, whereas GSEA demonstrated significant enrichment of gene sets pertaining to G protein-coupled receptor ligand binding and G alpha (i) signaling events.
Conclusion
Our study elucidates that upregulation of CDC45 is intricately associated with immune cell infiltration and holds promising potential as a favorable prognostic marker and a novel diagnostic biomarker for GC.
application/pdf
text/html
doi:10.7717/peerj.17130
Validation of CDC45 as a novel biomarker for diagnosis and prognosis of gastric cancer
Lihua Wu
Gan Gao
Hui Mi
Zhou Luo
Zheng Wang
Yongdong Liu
Liangyan Wu
Haihua Long
Yongqi Shen
Computational Biology
Genomics
Gastroenterology and Hepatology
Oncology
doi:10.7717/peerj.17130
PeerJ Inc.
© 2024 Wu et al.
Background
Cell division cycle protein 45 (CDC45) has been demonstrated to play vital roles in the progression of various malignancies. However, the clinical significance of CDC45 in gastric cancer (GC) remains unreported.
Method
In this study, we employed the TCGA database and the TCGA & GTEx dataset to compare the mRNA expression levels of CDC45 between gastric cancer tissues and adjacent or normal tissues (p < 0.05 was considered statistically significant), which was further validated in multiple datasets including GSE13911, GSE29272, GSE118916, GSE66229, as well as RT-qPCR. Furthermore, we harnessed the Human Protein Atlas (HPA) to evaluate the protein expression of CDC45, which was subsequently verified through immunohistochemistry (IHC). To ascertain the diagnostic utility of CDC45, receiver operating characteristic (ROC) curves and the area under the ROC curve (AUC) were calculated in TCGA database, and further validated it in TCGA & GTEx and GSE66229 datasets. The Kaplan–Meier method was used to reveal the prognostic importance of CDC45 in The Cancer Genome Atlas (TCGA) database and authenticated through the GSE66229, GSE84433, and GSE84437 datasets. Through cBioPortal, we identified co-expressed genes of CDC45, and pursued enrichment analysis. Additionally, we availed gene set enrichment analysis (GSEA) to annotate the biological functions of CDC45.
Results
Differential expression analysis revealed that CDC45 was significantly upregulated at both the mRNA and protein levels in GC (all p < 0.05). Remarkably, CDC45 emerged as a promising prognostic indicator and a novel diagnostic biomarker for GC. In a comprehensive the drug susceptibility analysis, we found that patients with high expression of CDC45 had high sensitivity to various chemotherapeutic agents, among which 5-fluorouracil, docetaxel, cisplatin, and elesclomol were most evident. Furthermore, our findings suggested a plausible association between CDC45 and immune cell infiltration. Enrichment analysis revealed that CDC45 and its associated genes may play crucial roles in muscle biofunction, whereas GSEA demonstrated significant enrichment of gene sets pertaining to G protein-coupled receptor ligand binding and G alpha (i) signaling events.
Conclusion
Our study elucidates that upregulation of CDC45 is intricately associated with immune cell infiltration and holds promising potential as a favorable prognostic marker and a novel diagnostic biomarker for GC.
Wu et al. (2024) Validation of CDC45 as a novel biomarker for diagnosis and prognosis of gastric cancer. PeerJ 12:e17130 https://doi.org/10.7717/peerj.17130
2023-10-25
2024-02-27
2024-03-18
Wu
Lihua
Gao
Gan
Mi
Hui
Luo
Zhou
Wang
Zheng
Liu
Yongdong
Wu
Liangyan
Long
Haihua
Shen
Yongqi
10.7717/peerj.17130
https://peerj.com/articles/17130
12
https://peerj.com/articles/17130
10.7717/peerj.17130
2167-8359
12
PeerJ
2024-03-18
© 2024 Wu et al.
Wu et al.
-
https://peerj.com/articles/16627
Mammal dung–dung beetle trophic networks: an improved method based on gut-content DNA
Background
Dung beetles provide many important ecosystem services, including dung decomposition, pathogen control, soil aeration, and secondary seed dispersal. Yet, the biology of most dung beetles remains unknown. Natural diets are poorly studied, partly because previous research has focused on choice or attraction experiments using few, easily accessible dung types from zoo animals, farm animals, or humans. This way, many links within natural food webs have certainly been missed. In this work, we aimed to establish a protocol to analyze the natural diets of dung beetles using DNA gut barcoding.
Methods
First, the feasibility of gut-content DNA extraction and amplification of 12s rDNA from six different mammal dung types was tested in the laboratory. We then applied the method to beetles caught in pitfall traps in Ecuador and Germany by using 12s rDNA primers. For a subset of the dung beetles caught in the Ecuador sampling, we also used 16s rDNA primers to see if these would improve the number of species we could identify. We predicted the likelihood of amplifying DNA using gut fullness, DNA concentration, PCR primer, collection method, and beetle species as predictor variables in a dominance analysis. Based on the gut barcodes, we generated a dung beetle-mammal network for both field sites (Ecuador and Germany) and analyzed the levels of network specificity.
Results
We successfully amplified mammal DNA from dung beetle gut contents for 128 specimens, which included such prominent species as Panthera onca (jaguar) and Puma concolor (puma). The overall success rate of DNA amplification was 53%. The best predictors for amplification success were gut fullness and DNA concentration, suggesting the success rate can be increased by focusing on beetles with a full gut. The mammal dung–dung beetle networks differed from purely random network models and showed a moderate degree of network specialization (H2′: Ecuador = 0.49; Germany = 0.41).
Conclusion
We here present a reliable method of extracting and amplifying gut-content DNA from dung beetles. Identifying mammal dung via DNA reference libraries, we created mammal dung-dung beetle trophic networks. This has benefits over previous methods because we inventoried the natural mammal dung resources of dung beetles instead of using artificial mammal baits. Our results revealed higher levels of specialization than expected and more rodent DNA than expected in Germany, suggesting that the presented method provides more detailed insights into mammal dung–dung beetle networks. In addition, the method could have applications for mammal monitoring in many ecosystems.
application/pdf
text/html
doi:10.7717/peerj.16627
Mammal dung–dung beetle trophic networks: an improved method based on gut-content DNA
Karen M. Pedersen
Christoph von Beeren
Arianna Oggioni
Nico Blüthgen
Biodiversity
Ecology
Entomology
Molecular Biology
Zoology
doi:10.7717/peerj.16627
PeerJ Inc.
© 2024 Pedersen et al.
Background
Dung beetles provide many important ecosystem services, including dung decomposition, pathogen control, soil aeration, and secondary seed dispersal. Yet, the biology of most dung beetles remains unknown. Natural diets are poorly studied, partly because previous research has focused on choice or attraction experiments using few, easily accessible dung types from zoo animals, farm animals, or humans. This way, many links within natural food webs have certainly been missed. In this work, we aimed to establish a protocol to analyze the natural diets of dung beetles using DNA gut barcoding.
Methods
First, the feasibility of gut-content DNA extraction and amplification of 12s rDNA from six different mammal dung types was tested in the laboratory. We then applied the method to beetles caught in pitfall traps in Ecuador and Germany by using 12s rDNA primers. For a subset of the dung beetles caught in the Ecuador sampling, we also used 16s rDNA primers to see if these would improve the number of species we could identify. We predicted the likelihood of amplifying DNA using gut fullness, DNA concentration, PCR primer, collection method, and beetle species as predictor variables in a dominance analysis. Based on the gut barcodes, we generated a dung beetle-mammal network for both field sites (Ecuador and Germany) and analyzed the levels of network specificity.
Results
We successfully amplified mammal DNA from dung beetle gut contents for 128 specimens, which included such prominent species as Panthera onca (jaguar) and Puma concolor (puma). The overall success rate of DNA amplification was 53%. The best predictors for amplification success were gut fullness and DNA concentration, suggesting the success rate can be increased by focusing on beetles with a full gut. The mammal dung–dung beetle networks differed from purely random network models and showed a moderate degree of network specialization (H2′: Ecuador = 0.49; Germany = 0.41).
Conclusion
We here present a reliable method of extracting and amplifying gut-content DNA from dung beetles. Identifying mammal dung via DNA reference libraries, we created mammal dung-dung beetle trophic networks. This has benefits over previous methods because we inventoried the natural mammal dung resources of dung beetles instead of using artificial mammal baits. Our results revealed higher levels of specialization than expected and more rodent DNA than expected in Germany, suggesting that the presented method provides more detailed insights into mammal dung–dung beetle networks. In addition, the method could have applications for mammal monitoring in many ecosystems.
Pedersen et al. (2024) Mammal dung–dung beetle trophic networks: an improved method based on gut-content DNA. PeerJ 12:e16627 https://doi.org/10.7717/peerj.16627
2023-01-07
2023-11-16
2024-03-15
Pedersen
Karen M.
von Beeren
Christoph
Oggioni
Arianna
Blüthgen
Nico
10.7717/peerj.16627
https://peerj.com/articles/16627
12
https://peerj.com/articles/16627
10.7717/peerj.16627
2167-8359
12
PeerJ
2024-03-15
©2024 Pedersen et al.
Pedersen et al.
-
https://peerj.com/articles/16876
Clinical significance of small nuclear ribonucleoprotein U1 subunit 70 in patients with hepatocellular carcinoma
Background & Aims
Small nuclear ribonucleoprotein U1 subunit 70 (SNRNP70) as one of the components of the U1 small nuclear ribonucleoprotein (snRNP) is rarely reported in cancers. This study aims to estimate the application potential of SNRNP70 in hepatocellular carcinoma (HCC) clinical practice.
Methods
Based on the TCGA database and cohort of HCC patients, we investigated the expression patterns and prognostic value of SNRNP70 in HCC. Then, the combination of SNRNP70 and alpha-fetoprotein (AFP) in 278 HCC cases was analyzed. Next, western blotting and immunohistochemistry were used to detect the expression of SNRNP70 in nucleus and cytoplasm. Finally, Cell Counting Kit-8 (CCK-8) and scratch wound healing assays were used to detect the effect of SNRNP70 on the proliferation and migration of HCC cells.
Results
SNRNP70 was highly expressed in HCC. Its expression was increasingly high during the progression of HCC and was positively related to immune infiltration cells. Higher SNRNP70 expression indicated a poor outcome of HCC patients. In addition, nuclear SNRNP70/AFP combination could be a prognostic biomarker for overall survival and recurrence. Cell experiments confirmed that knockdown of SNRNP70 inhibited the proliferation and migration of HCC cells.
Conclusion
SNRNP70 may be a new biomarker for HCC progression and HCC diagnosis as well as prognosis. SNRNP70 combined with serum AFP may indicate the prognosis and recurrence status of HCC patients after operation.
application/pdf
text/html
doi:10.7717/peerj.16876
Clinical significance of small nuclear ribonucleoprotein U1 subunit 70 in patients with hepatocellular carcinoma
Dong Jiang
Xia-Ling Zhu
Yan An
Yi-ran Li
Bioinformatics
Cell Biology
Molecular Biology
Gastroenterology and Hepatology
Oncology
doi:10.7717/peerj.16876
PeerJ Inc.
© 2024 Jiang et al.
Background & Aims
Small nuclear ribonucleoprotein U1 subunit 70 (SNRNP70) as one of the components of the U1 small nuclear ribonucleoprotein (snRNP) is rarely reported in cancers. This study aims to estimate the application potential of SNRNP70 in hepatocellular carcinoma (HCC) clinical practice.
Methods
Based on the TCGA database and cohort of HCC patients, we investigated the expression patterns and prognostic value of SNRNP70 in HCC. Then, the combination of SNRNP70 and alpha-fetoprotein (AFP) in 278 HCC cases was analyzed. Next, western blotting and immunohistochemistry were used to detect the expression of SNRNP70 in nucleus and cytoplasm. Finally, Cell Counting Kit-8 (CCK-8) and scratch wound healing assays were used to detect the effect of SNRNP70 on the proliferation and migration of HCC cells.
Results
SNRNP70 was highly expressed in HCC. Its expression was increasingly high during the progression of HCC and was positively related to immune infiltration cells. Higher SNRNP70 expression indicated a poor outcome of HCC patients. In addition, nuclear SNRNP70/AFP combination could be a prognostic biomarker for overall survival and recurrence. Cell experiments confirmed that knockdown of SNRNP70 inhibited the proliferation and migration of HCC cells.
Conclusion
SNRNP70 may be a new biomarker for HCC progression and HCC diagnosis as well as prognosis. SNRNP70 combined with serum AFP may indicate the prognosis and recurrence status of HCC patients after operation.
Jiang et al. (2024) Clinical significance of small nuclear ribonucleoprotein U1 subunit 70 in patients with hepatocellular carcinoma. PeerJ 12:e16876 https://doi.org/10.7717/peerj.16876
2023-04-07
2024-01-11
2024-03-15
Jiang
Dong
Zhu
Xia-Ling
An
Yan
Li
Yi-ran
10.7717/peerj.16876
https://peerj.com/articles/16876
12
https://peerj.com/articles/16876
10.7717/peerj.16876
2167-8359
12
PeerJ
2024-03-15
©2024 Jiang et al.
Jiang et al.
-
https://peerj.com/articles/16891
Conspecific and heterospecific cueing in shelter choices of Blaptica dubia cockroaches
Background
Like many cockroaches, Argentinian wood roaches, Blaptica dubia, prefer darker shelters over lighter shelters. In three experiments, we asked whether chemical cues from other roaches might influence shelter choice, a process known as conspecific or heterospecific cueing, depending on whether the cues come from an individual of the same or a different species, respectively.
Methods
Each experiment involved trials with focal B. dubia cockroaches in testing arenas containing plastic shelters of varying levels of darkness, with filter paper under each shelter acting as a carrier for chemical cues. In Experiment 1, we tested female and male B. dubia cockroaches with two shelters matched for darkness but differing in cues (conspecific vs. none). The shelter with no cue contained a blank filter paper as a control. In Experiment 2 (conspecific cueing) and Experiment 3 (heterospecific cueing), we tested B. dubia cockroach choices for lighter or darker shelters with filter papers containing chemical cues of other roaches or no chemical cues. For the conspecific cueing study of Experiment 2, we used chemical cues from other B. dubia cockroaches. In contrast, for the heterospecific cueing study of Experiment 3, we used chemical cues from a different species, the death’s head cockroach, Blaberus craniifer.
Results
In Experiment 1, B. dubia cockroaches overwhelmingly preferred shelters with conspecific chemical cues over darkness-matched shelters without cues. In Experiments 2 and 3, they strongly preferred darker shelters, especially when chemical cues were present. Additionally, they were more likely to be under the lighter shelter when chemical cues were present there. These results reveal that the public information B. dubia cockroaches gain from chemical cues—including those from other species—can drive shelter choices in this species.
application/pdf
text/html
doi:10.7717/peerj.16891
Conspecific and heterospecific cueing in shelter choices of Blaptica dubia cockroaches
Todd M. Freeberg
S. Ryan Risner
Sarah Y. Lang
Sylvain Fiset
Animal Behavior
Ecology
Entomology
Zoology
doi:10.7717/peerj.16891
PeerJ Inc.
© 2024 Freeberg et al.
Background
Like many cockroaches, Argentinian wood roaches, Blaptica dubia, prefer darker shelters over lighter shelters. In three experiments, we asked whether chemical cues from other roaches might influence shelter choice, a process known as conspecific or heterospecific cueing, depending on whether the cues come from an individual of the same or a different species, respectively.
Methods
Each experiment involved trials with focal B. dubia cockroaches in testing arenas containing plastic shelters of varying levels of darkness, with filter paper under each shelter acting as a carrier for chemical cues. In Experiment 1, we tested female and male B. dubia cockroaches with two shelters matched for darkness but differing in cues (conspecific vs. none). The shelter with no cue contained a blank filter paper as a control. In Experiment 2 (conspecific cueing) and Experiment 3 (heterospecific cueing), we tested B. dubia cockroach choices for lighter or darker shelters with filter papers containing chemical cues of other roaches or no chemical cues. For the conspecific cueing study of Experiment 2, we used chemical cues from other B. dubia cockroaches. In contrast, for the heterospecific cueing study of Experiment 3, we used chemical cues from a different species, the death’s head cockroach, Blaberus craniifer.
Results
In Experiment 1, B. dubia cockroaches overwhelmingly preferred shelters with conspecific chemical cues over darkness-matched shelters without cues. In Experiments 2 and 3, they strongly preferred darker shelters, especially when chemical cues were present. Additionally, they were more likely to be under the lighter shelter when chemical cues were present there. These results reveal that the public information B. dubia cockroaches gain from chemical cues—including those from other species—can drive shelter choices in this species.
Freeberg et al. (2024) Conspecific and heterospecific cueing in shelter choices of Blaptica dubia cockroaches. PeerJ 12:e16891 https://doi.org/10.7717/peerj.16891
2023-06-01
2024-02-19
2024-03-15
Freeberg
Todd M.
Risner
S. Ryan
Lang
Sarah Y.
Fiset
Sylvain
10.7717/peerj.16891
https://peerj.com/articles/16891
12
https://peerj.com/articles/16891
10.7717/peerj.16891
2167-8359
12
PeerJ
2024-03-15
© 2024 Freeberg et al.
Freeberg et al.
-
https://peerj.com/articles/17055
Comparing the effects of empagliflozin and liraglutide on lipid metabolism and intestinal microflora in diabetic mice
Background and Objectives
Recent studies have shown that the imbalance of intestinal flora is related to the occurrence and progression of diabetic nephropathy (DN) and can affect lipid metabolism. Sodium-dependent glucose transporters 2 (SGLT2) inhibitor and glucagon-like peptide-1 (GLP-1) receptor agonist are commonly used hypoglycemic drugs and have excellent renal safety. The purpose of this study was to compare the protective effects of empagliflozin and liraglutide on kidneys, lipid metabolism, and intestinal microbiota in diabetic mice.
Methods
We established a mouse model of type two diabetes by feeding rats a high-fat diet (HFD) followed by an intraperitoneal injection of STZ. The mice were randomly divided into groups: normal control (NC), diabetic model (DM), liraglutide treatment (LirT), empagliflozin treatment (EmpT), and liraglutide combined with empagliflozin treatment (Emp&LirT) groups. Blood glucose, lipids, creatinine, and uric acid, as well as urinary nitrogen and albumin levels were measured. The renal tissues were subjected to HE, PAS and Masson’s staining. These parameters were used to evaluate renal function and histopathological changes in mice. Mice feces were also collected for 16sRNA sequencing to analyze the composition of the intestinal flora.
Results
All the indexes related to renal function were significantly improved after treatment with drugs. With respect to lipid metabolism, both drugs significantly decreased the serum triglyceride levels in diabetic mice, but the effect of liraglutide on reducing serum cholesterol was better than that of empagliflozin. However, empagliflozin had a better effect on the reduction of low-density lipoproteins (LDL). The two drugs had different effects on intestinal flora. At the phylum level, empagliflozin significantly reduced the ratio of Firmicutes to Bacteroidota, but no effect was seen with liraglutide. At the genus level, both of them decreased the number of Helicobacter and increased the number of Lactobacillus. Empagliflozin also significantly increased the abundance of Muribaculaceae, Muribaculum, Olsenella, and Odoribacter, while liraglutide significantly increased that of Ruminococcus.
Conclusion
Liraglutide and empagliflozin were both able to improve diabetes-related renal injury. However, the ability of empagliflozin to reduce LDL was better compared to liraglutide. In addition, their effects on the intestine bacterial flora were significantly different.
application/pdf
text/html
doi:10.7717/peerj.17055
Comparing the effects of empagliflozin and liraglutide on lipid metabolism and intestinal microflora in diabetic mice
Qiong Yang
Ling Deng
Changmei Feng
Jianghua Wen
Biochemistry
Molecular Biology
Histology
doi:10.7717/peerj.17055
PeerJ Inc.
© 2024 Yang et al.
Background and Objectives
Recent studies have shown that the imbalance of intestinal flora is related to the occurrence and progression of diabetic nephropathy (DN) and can affect lipid metabolism. Sodium-dependent glucose transporters 2 (SGLT2) inhibitor and glucagon-like peptide-1 (GLP-1) receptor agonist are commonly used hypoglycemic drugs and have excellent renal safety. The purpose of this study was to compare the protective effects of empagliflozin and liraglutide on kidneys, lipid metabolism, and intestinal microbiota in diabetic mice.
Methods
We established a mouse model of type two diabetes by feeding rats a high-fat diet (HFD) followed by an intraperitoneal injection of STZ. The mice were randomly divided into groups: normal control (NC), diabetic model (DM), liraglutide treatment (LirT), empagliflozin treatment (EmpT), and liraglutide combined with empagliflozin treatment (Emp&LirT) groups. Blood glucose, lipids, creatinine, and uric acid, as well as urinary nitrogen and albumin levels were measured. The renal tissues were subjected to HE, PAS and Masson’s staining. These parameters were used to evaluate renal function and histopathological changes in mice. Mice feces were also collected for 16sRNA sequencing to analyze the composition of the intestinal flora.
Results
All the indexes related to renal function were significantly improved after treatment with drugs. With respect to lipid metabolism, both drugs significantly decreased the serum triglyceride levels in diabetic mice, but the effect of liraglutide on reducing serum cholesterol was better than that of empagliflozin. However, empagliflozin had a better effect on the reduction of low-density lipoproteins (LDL). The two drugs had different effects on intestinal flora. At the phylum level, empagliflozin significantly reduced the ratio of Firmicutes to Bacteroidota, but no effect was seen with liraglutide. At the genus level, both of them decreased the number of Helicobacter and increased the number of Lactobacillus. Empagliflozin also significantly increased the abundance of Muribaculaceae, Muribaculum, Olsenella, and Odoribacter, while liraglutide significantly increased that of Ruminococcus.
Conclusion
Liraglutide and empagliflozin were both able to improve diabetes-related renal injury. However, the ability of empagliflozin to reduce LDL was better compared to liraglutide. In addition, their effects on the intestine bacterial flora were significantly different.
Yang et al. (2024) Comparing the effects of empagliflozin and liraglutide on lipid metabolism and intestinal microflora in diabetic mice. PeerJ 12:e17055 https://doi.org/10.7717/peerj.17055
2023-09-18
2024-02-14
2024-03-15
Yang
Qiong
Deng
Ling
Feng
Changmei
Wen
Jianghua
10.7717/peerj.17055
https://peerj.com/articles/17055
12
https://peerj.com/articles/17055
10.7717/peerj.17055
2167-8359
12
PeerJ
2024-03-15
© 2024 Yang et al.
Yang et al.
PeerJ
https://peerj.com/articles/index.rss1?journal=peerj
2167-8359