Overview of chicken embryo genes related to sex differentiation
Sex determination in chickens at an early embryonic stage has been a longstanding challenge in poultry production due to the unique ZZ:ZW sex chromosome system and various influencing factors. This review has summarized the genes related to the sex differentiation of chicken early embryos (mainly Dmrt1, Sox9, Amh, Cyp19a1, Foxl2, Tle4z1, Jun, Hintw, Ube2i, Spin1z, Hmgcs1, Foxd1, Tox3, Ddx4, cHemgn and Serpinb11 in this article), and has found that these contributions enhance our understanding of the genetic basis of sex determination in chickens, while identifying potential gene targets for future research. This knowledge may inform and guide the development of sex screening technologies for hatching eggs and support advancements in gene-editing approaches for chicken embryos. Moreover, these insights offer hope for enhancing animal welfare and promoting conservation efforts in poultry production.
Luo et al. (2024) Overview of chicken embryo genes related to sex differentiation. PeerJ 12:e17072 https://doi.org/10.7717/peerj.17072
Endosymbiont and gut bacterial communities of the brown-banded cockroach, Supella longipalpa
The brown-banded cockroach (Supella longipalpa) is a widespread nuisance and public health pest. Like the German cockroach (Blattella germanica), this species is adapted to the indoor biome and completes the entirety of its life cycle in human-built structures. Recently, understanding the contributions of commensal and symbiotic microbes to the biology of cockroach pests, as well as the applications of targeting these microbes for pest control, have garnered significant scientific interest. However, relative to B. germanica, the biology of S. longipalpa, including its microbial associations, is understudied. Therefore, the goal of the present study was to quantitatively examine and characterize both the endosymbiont and gut bacterial communities of S. longipalpa for the first time. To do so, bacterial 16S rRNA gene amplicon sequencing was conducted on DNA extracts from whole adult females and males, early instar nymphs, and late instar nymphs. The results demonstrate that the gut microbiome is dominated by two genera of bacteria known to have beneficial probiotic effects in other organisms, namely Lactobacillus and Akkermansia. Furthermore, our data show a significant effect of nymphal development on diversity and variation in the gut microbiome. Lastly, we reveal significant negative correlations between the two intracellular endosymbionts, Blattabacterium and Wolbachia, as well as between Blattabacterium and the gut microbiome, suggesting that Blattabacterium endosymbionts could directly or indirectly influence the composition of other bacterial populations. These findings have implications for understanding the adaptation of S. longipalpa to the indoor biome, its divergence from other indoor cockroach pest species such as B. germanica, the development of novel control approaches that target the microbiome, and fundamental insect-microbe interactions more broadly.
Guse et al. (2024) Endosymbiont and gut bacterial communities of the brown-banded cockroach, Supella longipalpa. PeerJ 12:e17095 https://doi.org/10.7717/peerj.17095
Beliefs, barriers, and promotion practices of Indian nurses’ regarding healthy eating for cancer survivors in a tertiary care hospital—A cross sectional survey
Purpose To describe the beliefs, barriers and promotion practices of Indian nurses’ regarding healthy eating (HE) behaviours amongst cancer survivors, and to gain insights into whether their educational qualifications might affect the promotion of HE. Methods Data was gathered using a validated questionnaire, 388 of the approached 400 nurses who worked at a tertiary care hospital in India gave informed consent to participate in the study. The Mann-Whitney U test and the Chi square analysis (for continuous and categorical variables respectively) were performed to carry out sub-group comparisons based on the qualification of the nurses i.e., Bachelor of Science in Nursing (BSc) and General Nursing and Midwifery (GNM). Results The nurses believed that dieticians/nutritionists were primarily responsible for educating the cancer survivors regarding HE. HE was promoted by nurses’ relatively equally across multiple treatment stages (“during” treatment 24.4%, “post” treatment 23.1%; and “pre” treatment 22.3%). Nurses’ believed HE practices had numerous benefits, with improved health-related quality of life (HRQoL) (75.7%), and mental health (73.9%) being the most frequent responses. The most frequently cited barriers by the nurses in promoting HE were lack of time (22.2%), and lack of adequate support structure (19.9%). Sub-group comparisons generally revealed no significant difference between the BSc and GNM nurses in their perceptions regarding HE promotion to cancer survivors. Exceptions were how the GNM group had significantly greater beliefs regarding whether HE can “reduce risk of cancer occurrence” (p = 0.004) and “whether or not I promote HE is entirely up to me” (p = 0.002). Conclusion The nurses in India believe in the promotion of HE practices among cancer survivors across various stages of cancer treatments. However, they do face a range of barriers in their attempt to promote HE. Overcoming these barriers might facilitate effective promotion of HE among cancer survivors and help improve survivorship outcomes. Implications for cancer survivors Indian nurses employed in the two tertiary care hospitals wish to promote HE among cancer survivors, but require further knowledge and support services for more effective promotion of HE.
Pai et al. (2024) Beliefs, barriers, and promotion practices of Indian nurses’ regarding healthy eating for cancer survivors in a tertiary care hospital—A cross sectional survey. PeerJ 12:e17107 https://doi.org/10.7717/peerj.17107
TBX5 genetic variants and SCD-CAD susceptibility: insights from Chinese Han cohorts
Background The prevention and prediction of sudden cardiac death (SCD) present persistent challenges, prompting exploration into common genetic variations for potential insights. T-box 5 (TBX5), a critical cardiac transcription factor, plays a pivotal role in cardiovascular development and function. This study systematically examined variants within the 500-bp region downstream of the TBX5 gene, focusing on their potential impact on susceptibility to SCD associated with coronary artery disease (SCD-CAD) in four different Chinese Han populations. Methods In a comprehensive case-control analysis, we explored the association between rs11278315 and SCD-CAD susceptibility using a cohort of 553 controls and 201 SCD-CAD cases. Dual luciferase reporter assays and genotype-phenotype correlation studies using human cardiac tissue samples as well as integrated in silicon analysis were applied to explore the underlining mechanism. Result Binary logistic regression results underscored a significantly reduced risk of SCD-CAD in individuals harboring the deletion allele (odds ratio = 0.70, 95% CI [0.55–0.88], p = 0.0019). Consistent with the lower transcriptional activity of the deletion allele observed in dual luciferase reporter assays, genotype-phenotype correlation studies on human cardiac tissue samples affirmed lower expression levels associated with the deletion allele at both mRNA and protein levels. Furthermore, our investigation revealed intriguing insights into the role of rs11278315 in TBX5 alternative splicing, which may contribute to alterations in its ultimate functional effects, as suggested by sQTL analysis. Gene ontology analysis and functional annotation further underscored the potential involvement of TBX5 in alternative splicing and cardiac-related transcriptional regulation. Conclusions In summary, our current dataset points to a plausible correlation between rs11278315 and susceptibility to SCD-CAD, emphasizing the potential of rs11278315 as a genetic risk marker for aiding in molecular diagnosis and risk stratification of SCD-CAD.
Rui et al. (2024) TBX5 genetic variants and SCD-CAD susceptibility: insights from Chinese Han cohorts. PeerJ 12:e17139 https://doi.org/10.7717/peerj.17139
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.
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
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.
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
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.
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
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.
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
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.
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
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.
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