Comprehensive analysis of fatty acid metabolism-related gene signatures for predicting prognosis in patients with prostate cancer
Fatty acid metabolism (FAM) is an important factor in tumorigenesis and development. However, whether fatty acid metabolism (FAM)-related genes are associated with prostate cancer (PCa) prognosis is not known. Therefore, we established a novel prognostic model based on FAM-related genes to predict biochemical recurrence in PCa patients. First, PCa sequencing data were acquired from TCGA as the training cohort and GSE21032 as the validation cohort. Second, a prostate cancer prognostic model containing 10 FAM-related genes was constructed using univariate Cox and LASSO. Principal component analysis and t-distributed stochastic neighbour embedding analysis showed that the model was highly effective. Third, PCa patients were divided into high- and low-risk groups according to the model risk score. Survival analysis, ROC curve analysis, and independent prognostic analysis showed that the high-risk group had short recurrence-free survival (RFS), and the risk score was an independent diagnostic factor with diagnostic value in PCa patients. External validation using GSE21032 also showed that the prognostic model had high reliability. A nomogram based on a prognostic model was constructed for clinical use. Fourth, tumor immune correlation analyses, such as the ESTIMATE, CIBERSORT algorithm, and ssGSEA, showed that the high-risk group had higher immune cell infiltration, lower tumour purity, and worse RFS. Various immune checkpoints were expressed at higher levels in high-risk patients. In summary, this prognostic model is a promising prognostic biomarker for PCa that should improve the prognosis of PCa patients. These data provide new ideas for antitumour immunotherapy and have good potential value for the development of targeted drugs.
Wang et al. (2023) Comprehensive analysis of fatty acid metabolism-related gene signatures for predicting prognosis in patients with prostate cancer. PeerJ 11:e14646 https://doi.org/10.7717/peerj.14646
CMTM6 is highly expressed in lung adenocarcinoma and can be used as a biomarker of a poor diagnosis
Background CMTM6 which is chemokine-like factor (CKLF)-like Marvel transmembrane domain containing family member 6 is involved in the occurrence and progression of various tumors. However, the role of CMTM6 is still unclear in lung adenocarcinoma (LUAD). Methods Immunohistochemical, Western blotting and RT‒PCR methods were used to detect the expression of CMTM6 in LUAD. Cox regression and the Kaplan‒Meier method were performed to assess overall survival. Immunogenic features were evaluated according to immune cell infiltrations, immune checkpoints. The sensitivity to chemotherapy agents was estimated using the pRRophetic package. Results In LUAD, the expression of CMTM6 was obviously upregulated and was significantly associated with T stage (p = 0.008) and lymph node metastasis (p = 0.018). Multivariate Cox regression analysis demonstrated that CMTM6 was a specialty prognostic risk factor. Based on GSEA enrichment analysis, we found that high expression of CMTM6 is associated with multiple immune signaling pathways. The group with high CMTM6 expression showed a positive association with various types of tumor-infiltrating cells. Moreover, a total of 36 chemotherapeutic drugs were significantly correlated with the expression of CMTM6. Among them, two chemotherapeutic drugs had better therapeutic effects in the high CMTM6 expression group, while 34 chemotherapeutic drugs had therapeutic effects in the low CMTM6 expression group. Conclusion This study confirmed that CMTM6 is highly expressed in LUAD and is a new independent poor prognostic factor. In addition, the high expression of CMTM6 is closely related to the tumor microenvironment and immunotherapy, providing new ideas for the treatment of posterior LUAD.
Jia et al. (2023) CMTM6 is highly expressed in lung adenocarcinoma and can be used as a biomarker of a poor diagnosis. PeerJ 11:e14668 https://doi.org/10.7717/peerj.14668
The complex role of transcription factor GAGA in germline death during Drosophila spermatogenesis: transcriptomic and bioinformatic analyses
The GAGA protein (also known as GAF) is a transcription factor encoded by the Trl gene in D. melanogaster. GAGA is involved in the regulation of transcription of many genes at all stages of fly development and life. Recently, we investigated the participation of GAGA in spermatogenesis and discovered that Trl mutants experience massive degradation of germline cells in the testes. Trl underexpression induces autophagic death of spermatocytes, thereby leading to reduced testis size. Here, we aimed to determine the role of the transcription factor GAGA in the regulation of ectopic germline cell death. We investigated how Trl underexpression affects gene expression in the testes. We identified 15,993 genes in three biological replicates of our RNA-seq analysis and compared transcript levels between hypomorphic TrlR85/Trl362 and Oregon testes. A total of 2,437 differentially expressed genes were found, including 1,686 upregulated and 751 downregulated genes. At the transcriptional level, we detected the development of cellular stress in the Trl-mutant testes: downregulation of the genes normally expressed in the testes (indicating slowed or abrogated spermatocyte differentiation) and increased expression of metabolic and proteolysis-related genes, including stress response long noncoding RNAs. Nonetheless, in the Flybase Gene Ontology lists of genes related to cell death, autophagy, or stress, there was no enrichment with GAGA-binding sites. Furthermore, we did not identify any specific GAGA-dependent cell death pathway that could regulate spermatocyte death. Thus, our data suggest that GAGA deficiency in male germline cells leads to an imbalance of metabolic processes, impaired mitochondrial function, and cell death due to cellular stress.
Fedorova et al. (2023) The complex role of transcription factor GAGA in germline death during Drosophila spermatogenesis: transcriptomic and bioinformatic analyses. PeerJ 11:e14063 https://doi.org/10.7717/peerj.14063
Substantial changes in Gaseous pollutants and health effects during COVID-19 in Delhi, India
Background Coronavirus disease has affected the entire population worldwide in terms of physical and environmental consequences. Therefore, the current study demonstrates the changes in the concentration of gaseous pollutants and their health effects during the COVID-19 pandemic in Delhi, the national capital city of India. Methodology In the present study, secondary data on gaseous pollutants such as nitrogen dioxide (NO2), carbon monoxide (CO), sulfur dioxide (SO2), ammonia (NH3), and ozone (O3) were collected from the Central Pollution Control Board (CPCB) on a daily basis. Data were collected from January 1, 2020, to September 30, 2020, to determine the relative changes (%) in gaseous pollutants for pre-lockdown, lockdown, and unlockdown stages of COVID-19. Results The current findings for gaseous pollutants reveal that concentration declined in the range of 51%–83% (NO), 40%–69% (NOx), 31%–60% (NO2), and 25%–40% (NH3) during the lockdown compared to pre-lockdown period, respectively. The drastic decrease in gaseous pollutants was observed due to restricted measures during lockdown periods. The level of ozone was observed to be higher during the lockdown periods as compared to the pre-lockdown period. These gaseous pollutants are linked between the health risk assessment and hazard identification for non-carcinogenic. However, in infants (0–1 yr), Health Quotient (HQ) for daily and annual groups was found to be higher than the rest of the exposed group (toddlers, children, and adults) in all the periods. Conclusion The air quality values for pre-lockdown were calculated to be “poor category to “very poor” category in all zones of Delhi, whereas, during the lockdown period, the air quality levels for all zones were calculated as “satisfactory,” except for Northeast Delhi, which displayed the “moderate” category. The computed HQ for daily chronic exposure for each pollutant across the child and adult groups was more than 1 (HQ > 1), which indicated a high probability to induce adverse health outcomes.
Environmental Contamination and Remediation
Singh et al. (2023) Substantial changes in Gaseous pollutants and health effects during COVID-19 in Delhi, India. PeerJ 11:e14489 https://doi.org/10.7717/peerj.14489
Clasnip: a web-based intraspecies classifier and multi-locus sequence typing for pathogenic microorganisms using fragmented sequences
Bioinformatic approaches for the identification of microorganisms have evolved rapidly, but existing methods are time-consuming, complicated or expensive for massive screening of pathogens and their non-pathogenic relatives. Also, bioinformatic classifiers usually lack automatically generated performance statistics for specific databases. To address this problem, we developed Clasnip (www.clasnip.com), an easy-to-use web-based platform for the classification and similarity evaluation of closely related microorganisms at interspecies and intraspecies levels. Clasnip mainly consists of two modules: database building and sample classification. In database building, labeled nucleotide sequences are mapped to a reference sequence, and then single nucleotide polymorphisms (SNPs) statistics are generated. A probability model of SNPs and classification groups is built using Hidden Markov Models and solved using the maximum likelihood method. Database performance is estimated using three replicates of two-fold cross-validation. Sensitivity (recall), specificity (selectivity), precision, accuracy and other metrics are computed for all samples, training sets, and test sets. In sample classification, Clasnip accepts inputs of genes, short fragments, contigs and even whole genomes. It can report classification probability and a multi-locus sequence typing table for SNPs. The classification performance was tested using short sequences of 16S, 16–23S and 50S rRNA regions for 12 haplotypes of Candidatus Liberibacter solanacearum (CLso), a regulated plant pathogen associated with severe disease in economically important Apiaceous and Solanaceous crops. The program was able to classify CLso samples with even only 1–2 SNPs available, and achieved 97.2%, 98.8% and 100.0% accuracy based on 16S, 16–23S, and 50S rRNA sequences, respectively. In comparison with all existing 12 haplotypes, we proposed that to be classified as a new haplotype, given samples have at least 2 SNPs in the combined region of 16S rRNA (OA2/Lsc2) and 16–23S IGS (Lp Frag 4–1611F/Lp Frag 4–480R) regions, and 2 SNPs in the 50S rplJ/rplL (CL514F/CL514R) regions. Besides, we have included the databases for differentiating Dickeya spp., Pectobacterium spp. and Clavibacter spp. In addition to bacteria, we also tested Clasnip performance on potato virus Y (PVY). 251 PVY genomes were 100% correctly classified into seven groups (PVYC, PVYN, PVYO, PVYNTN, PVYN:O, Poha, and Chile3). In conclusion, Clasnip is a statistically sound and user-friendly bioinformatic application for microorganism classification at the intraspecies level. Clasnip service is freely available at www.clasnip.com.
Chuan et al. (2023) Clasnip: a web-based intraspecies classifier and multi-locus sequence typing for pathogenic microorganisms using fragmented sequences. PeerJ 11:e14490 https://doi.org/10.7717/peerj.14490
How to measure ego-resiliency in the face of various life-changing crises: Measurement invariance, convergent and discriminant validity and reliability of the Polish version of the Revised Ego-Resiliency Scale (ER89-R12)
This study examines the generalizability of the latent structure of the Polish version of the Ego-Resiliency Scale (ER89-R12), a brief self-report scale that measures ego-resiliency. We investigated the measurement invariance, validity, and reliability of ER89-R12 among three groups of individuals who were facing various major, long-term, life-changing crises (N = 512): parents of children with Down’s syndrome, women with breast cancer, and individuals after divorce. The analysis of the measurement invariance confirmed the two-factor structure of the questionnaire and the high reliability of this measure in those studied groups. A multigroup confirmatory factor analysis provided evidence of configural, metric, scalar, and residual invariance across the three groups. Moreover, the correlation patterns were similar across the groups. Ego-resiliency was strongly and consistently positively correlated with mental health: psychological well-being, perceived social support, self-esteem, and post-traumatic growth, and negatively correlated with perceived stress. The presented results indicate the potential usefulness of the ER89-R12 tool in studies on people experiencing various crises in their lives.
Kołodziej-Zaleska et al. (2023) How to measure ego-resiliency in the face of various life-changing crises: Measurement invariance, convergent and discriminant validity and reliability of the Polish version of the Revised Ego-Resiliency Scale (ER89-R12). PeerJ 11:e14499 https://doi.org/10.7717/peerj.14499
Co-circulation of all the four Dengue virus serotypes during 2018–2019: first report from Eastern Uttar Pradesh, India
Dengue fever is an endemic disease in India, transmitted by an infected mosquito bite. In India, the number of concurrent infections and the circulation of multiple dengue virus (DENV) serotypes has increased in recent decades. Molecular surveillance among the DENV serotype is important to keep track of the circulating serotypes, evolutionary changes, and key mutations that can alter the diagnostics. The current study included patients admitted for dengue in the Eastern Uttar Pradesh (E-UP) region during 2018–2019. The genetic characterization of the circulating DENV was accomplished through partial CprM (511 bp) gene amplification via reverse transcriptase polymerase chain reaction and sequencing. Phylogenetic analysis revealed the circulation of all four DENV1-4 serotypes. DENV-2 was the most abundant serotype (44%, 27/61), followed by DENV-3 (32%, 20/61). DENV-1 had a 16% (10/61) predominance, while DENV-4 (6%, 4/61) was found to be the least abundant serotype. DENV-2 genotypes were distributed among lineages I (7.4%), II (85%) and III (7.4%) of genotype IV, DENV-3 to lineage III of genotype III, DENV-1 to genotype III; DENV-2 to lineage B (75%) and C (25%) of genotype I. This primary report on the co-circulation of DENV1-4 serotypes from the E-UP region highlights the requirement of continuous molecular surveillance for monitoring circulating DENV serotypes.
Behera et al. (2023) Co-circulation of all the four Dengue virus serotypes during 2018–2019: first report from Eastern Uttar Pradesh, India. PeerJ 11:e14504 https://doi.org/10.7717/peerj.14504
The impacts of math anxiety, science anxiety, and gender on arts versus sciences choices in Qatari secondary schools
Previous studies showed small-to-moderate associations between students’ performances in math and science and math anxiety and science anxiety, respectively. Accordingly, the high prevalence of these two forms of topic anxiety represent severe obstructions to the worldwide demand calling for improving the quality of math and science achievements and, subsequently, increasing career success in science, technology, engineering, and math (STEM) domains. Therefore, this study examined math anxiety and science anxiety among female and male students who were enrolled in Sciences vs Arts tracks in Grades 11 and 12 in a Middle Eastern Arabic-speaking country (Qatar), and investigated how gender, math anxiety and science anxiety could predict this enrollment. Results showed that students in the Arts track experienced higher levels of math anxiety and science anxiety than those in the Sciences track, regardless of the students’ gender. However, a binary logistic regression analysis showed that science learning anxiety, but not evaluation science anxiety nor math learning or evaluation anxieties, significantly predicts students’ enrollment in Arts and Sciences tracks. Therefore, STEM career success is associated with good knowledge of STEM domains and positive emotions towards math and science.
Megreya et al. (2023) The impacts of math anxiety, science anxiety, and gender on arts versus sciences choices in Qatari secondary schools. PeerJ 11:e14510 https://doi.org/10.7717/peerj.14510
Assessing factors influencing students’ perceptions towards animal species conservation
Background The way humans perceive and interact with non-human animals is particular to each person, from antipathetic interactions evidenced by fear, aversion or repulsion, to empathy evidenced by feelings of affection, enchantment and interest in the animal. In this sense, herein we investigated the perception of university students about species belonging to different classes of wild vertebrates and the influence of social and educational factors on that. Methods Data were obtained through online forms answered by 700 university students from nine Brazilian states, 328 females and 372 males, aged between 18 and 65 years. The form had eight sentences to be answered in relation to 17 species of wild vertebrates. The agreement level for each of these sentences was to be indicated using a five-point Likert scale. The sentences were designed to assess aesthetic, risk, utilitarian, and preservation perceptions attributed to each species by students. Results We found that species perceived as useful by the students are generally also perceived as beautiful and as those that should be preserved. On the other hand, we found similarity between the species perceived as ugly and those that should not be preserved; and between the species perceived as harmful and those considered dangerous. Female and lower-income students more often agree that animals are harmful. We found that perceptions of danger in relation to animals were predominantly associated with younger respondents. However, this did not lead to less support for conservation among these students, as students of all age groups agree that species should be preserved. Our results show that students’ knowledge area was an important predictor associated with empathetic and antipathetic perceptions. Environmental area students showed greater empathy in all analyzed categories (beauty, usefulness, harmlessness, and preservation) than non-environmental areas students. On the other hand, students from the area of the exact sciences showed greater dislike in all analyzed categories than students from other areas. We found a strong relationship between the areas “Environmental” and “Humanities, Languages and Arts” for the attitudinal factors associated with utility and preservation, suggesting a similar empathetic worldview for students in these areas. Conclusions We found that the perception directed towards wild vertebrates varies according to the gender, age, income and study area of the students, in addition to the taxon considered. Finally, our results indicate that negative perceptions should be taken into account in environmental education efforts, educational policies and in planning fauna conservation plans which should incorporate the most diverse audiences, and not only encompass charismatic species but extend to animals that arouse great aversion from the part of people.
Mota Pereira et al. (2023) Assessing factors influencing students’ perceptions towards animal species conservation. PeerJ 11:e14553 https://doi.org/10.7717/peerj.14553
Differences in histomorphology and expression of key lipid regulated genes of four adipose tissues from Tibetan pigs
Tibetan pigs, an indigenous pig breed in China, have high overall fat deposition and flavorful and tasty meat. They are thus good models for studying adipogenesis. Few studies have been conducted focusing on expression of lipid regulated genes in different adipose tissues of Tibetan pigs. Therefore, we compared the difference of histomorphology and expression level of lipid regulated genes through qPCR and western blot in subcutaneous fat, perirenal fat, omental adipose tissue, and inguinal fat of Tibetan pigs. Our results showed that the area of subcutaneous adipocytes in Tibetan pigs was smaller, while the other three adipose tissues (perirenal fat, greater omentum fat, inguinal fat) had cell areas of similar size. The gene expression of FABP4, FASN, FABP3, and ME1 in subcutaneous fat was significantly higher than that in perirenal fat. Furthermore, the protein expression of FABP4 was significantly lower in subcutaneous fat than in perirenal fat (p < 0.05), and the expression of FASN was higher in greater omentum fat than in subcutaneous fat (p = 0.084). The difference in adipocyte cell size and expression of lipid-regulated genes in adipose tissues from the various parts of the pig body is likely due to the different cellular lipid metabolic processes. Specially, FABP4 and FASN may be involved in the regulation of fat deposition in different adipose tissues of Tibetan pigs.
Lin et al. (2023) Differences in histomorphology and expression of key lipid regulated genes of four adipose tissues from Tibetan pigs. PeerJ 11:e14556 https://doi.org/10.7717/peerj.14556