Assessing the impact of shallow subsurface pipe drainage on soil salinity and crop yield in arid zone
Purpose Soil salinization is one of the key problems of sustainable development of arid agricultural land. Exploring the use of shallow subsurface pipe drainage to improve soil salinization. Methods This study investigates the desalinization effect of shallow subsurface pipe drainage, in combination with drip irrigation under plastic mulch, in an arid region in China. Field data collection was conducted in 2010. Soil salinity at a range of soil depths, water EC and pH of subsurface pipe drainage and crop yield during crop growth stages in salinized farmlands were measured. Results and Conclusion The results show that soil salinity was reduced significantly on mildly (1–3 dS m−1) and moderately (3–6 dS m−1) salinized farmlands. The highest desalinization rate of mildly and moderately salinized soils was 51% and 91% respectively. The desalinization in upper soil layers, to a depth of 60 cm, was more significant than that in lower soil layers. Drainage water salinity was much higher than irrigation water salinity. Crop yield on mildly and moderately salinized land increased about 25% and 50%, respectively. This indicates that the combination of drip irrigation and shallow subsurface pipe drainage on farmlands is potential feasible to desalt farmlands and to improve crop yield. The study has led to a desalinization of 330 ha year−1 in Xinjiang.
Yang et al. (2021) Assessing the impact of shallow subsurface pipe drainage on soil salinity and crop yield in arid zone. PeerJ 9:e12622 https://doi.org/10.7717/peerj.12622
Transcriptome analysis identifies candidate genes in the biosynthetic pathway of sex pheromones from a zygaenid moth, Achelura yunnanensis (Lepidoptera: Zygaenidae)
In most moth species, sex pheromones responsible for mating and communication of both sexes are primarily produced by the pheromone glands (PGs) of female moths. Although the PG transcriptomes and pheromone production related genes from 24 moth species have been characterized, studies on the related information remain unknown in the Zygaenidae family. Here, we sequenced the PG transcriptome of a zygaenid moth, Achelura yunnanensis. Such the sequencing resulted in the yields of 47,632,610 clean reads that were assembled into 54,297 unigenes, coupled with RNA sequencing data from 12 other tissues. Based on the transcriptome, a total of 191 genes encoding pheromone biosynthesis and degradation enzymes were identified, 161 of which were predicted to have full-length sequences. A comparative analysis among 24 moth species of nine families indicated that the numbers of the genes were variable, ranging from 14 in two Grapholita species to 191 in A. yunnanensis. Phylogenetic analysis in parallel with the expression data highlighted some key genes, including three △9 and four △11 desaturases, four fatty acyl-CoA reductases (FARs) clustering in the pgFAR clade, and three significantly antennae-enriched aldehyde oxidases. An extensive tissue- and sex- expression profile revealed a broad distribution of the genes, in which 128 relatives were detected in the PGs and 127 in the antennae. This study reports, for the first time, the gene repertoires associated with the pheromone production in Zygaenidae, and provides a valuable resource for exploring putative roles of the PG-enriched genes in A. yunnanensis.
Nuo et al. (2021) Transcriptome analysis identifies candidate genes in the biosynthetic pathway of sex pheromones from a zygaenid moth, Achelura yunnanensis (Lepidoptera: Zygaenidae). PeerJ 9:e12641 https://doi.org/10.7717/peerj.12641
Comprehensive analysis of ceRNA network of ERCC4 in colorectal cancer
Objective ERCC4 is one of the most significant molecules of Nucleotide Excision Repair (NER), which has been researched due to its high expression in colorectal cancer (CRC). This study aimed to find out the ceRNA (competitive endogenous RNA) network of ERCC4 in CRC. Methods and Materials Pan cancer mRNA expression of ERCC4 was evaluated using TCGA database. The protein expression of ERCC4 was evaluated based on the Human Protein Atlas (HPA). We screened DElncRNAs and DEmiRNAs in two groups of ERCC4high and ERCC4low expression in CRC. Then a lncRNA-miRNA-ERCC4 regulatory network was constructed based on DElncRNAs and DEmiRNAs using Starbase database and visualized by Cytoscape software. Kaplan-Meier analysis was performed to evaluate the prognostic value of the ceRNA network. Further, RT-PCR was performed to validate the expression of the representative molecules in the ceRNA network in CRC and normal tissues. The relationship between drug sensitivity and these molecules were also evaluated using RNAactDrug database. Results ERCC4 was overexpressed in a variety of tumors at mRNA levels, including CRC. High expression of ERCC4 was also observed on protein level in CRC. A total of 1,885 DElncRNAs and 68 DEmiRNAs were identified from CRC samples in ERCC4high and ERCC4low expression groups. Predicted by the Starbase database, we got interacting miRNAs and lncRNAs of ERCC4 from the DEmiRNAs and DElncRNAs, and a lncRNA-miRNA-ERCC4 regulatory network was constructed. Kaplan-Meier survival curves results showed that miR-200c-3p (hazard ratio [HR] = 0.62, P = 0.032), MALAT1 (HR = 1.54, P = 0.016), and AC005520.2 (hazard ratio [HR] = 1.75, P = 0.002) were significantly associated with the prognosis of CRC. After validation by RT-PCR, we found that ERCC4 and MALAT1 were up-regulated in CRC compared with normal tissues, while miR-200c-3p was down-regulated. A strong negative correlation was observed between MALAT1 and miR-200c-3p. Drug sensitivity analysis showed that ERCC4, miR-200c and MALAT1 were all associated with Cisplatin. Conclusion We constructed a ceRNA network of ERCC4 in CRC, of which the MALAT1-miR-200c-3p-ERCC4 axis may be involved in the development, prognosis and chemotherapy sensitivity of CRC. These findings might provide novel clues and insights on the molecular mechanisms of ERCC4 and NER pathway in CRC.
Hu et al. (2021) Comprehensive analysis of ceRNA network of ERCC4 in colorectal cancer. PeerJ 9:e12647 https://doi.org/10.7717/peerj.12647
Comparison of African savanna elephant (Loxodonta africana) fatty acid profiles in whole blood, whole blood dried on blood spot cards, serum, and plasma
Background African elephants in managed care have presented differences in the balance between omega-3 and omega-6 fatty acids, a situation primarily thought to be due to dietary differences between the managed animals and their free-ranging counterparts. Because of this, circulating fatty acid status is included in routine monitoring of elephant health. A method of blood collection that requires only a few drops of whole blood, dried on filter paper (DBS) and can be used for analyzing full fatty acid profiles offers advantages in clinical application. Methods This study compared the use of whole blood, and whole blood DBS, serum or plasma for use in evaluating circulating fatty acid composition in African savannah elephants. Samples from six African elephants (two males and four females) were collected during the same week at the NC Zoo, Asheboro, NC. Results Results found only 2 of 36 individual fatty acids and none of the 10 fatty acid groupings were different when comparing the four blood fraction sample types to each other with Mann-Whitney U-Test pairwise comparisons. Myristic acid (14:0) was lower in the DBS samples than in whole blood, serum, and plasma and pentadecaenoic acid (15:1) was slightly more concentrated in DBS and whole blood. Discussion Results indicate that fatty acid profile of serum, plasma, whole blood, and DBS are comparable in African elephants. The DBS method offers advantages in acquisition and handling and may be preferable to other methods in both routine health assessment of captive animals and field research on free ranging animals.
Wood et al. (2021) Comparison of African savanna elephant (Loxodonta africana) fatty acid profiles in whole blood, whole blood dried on blood spot cards, serum, and plasma. PeerJ 9:e12650 https://doi.org/10.7717/peerj.12650
Spatial and temporal distribution patterns of tick-borne diseases (Tick-borne Encephalitis and Lyme Borreliosis) in Germany
Background In the face of ongoing climate warming, vector-borne diseases are expected to increase in Europe, including tick-borne diseases (TBD). The most abundant tick-borne diseases in Germany are Tick-Borne Encephalitis (TBE) and Lyme Borreliosis (LB), with Ixodes ricinus as the main vector. Methods In this study, we display and compare the spatial and temporal patterns of reported cases of human TBE and LB in relation to some associated factors. The comparison may help with the interpretation of observed spatial and temporal patterns. Results The spatial patterns of reported TBE cases show a clear and consistent pattern over the years, with many cases in the south and only few and isolated cases in the north of Germany. The identification of spatial patterns of LB disease cases is more difficult due to the different reporting practices in the individual federal states. Temporal patterns strongly fluctuate between years, and are relatively synchronized between both diseases, suggesting common driving factors. Based on our results we found no evidence that weather conditions affect the prevalence of both diseases. Both diseases show a gender bias with LB bing more commonly diagnosed in females, contrary to TBE being more commonly diagnosed in males. Conclusion For a further investigation of of the underlying driving factors and their interrelations, longer time series as well as standardised reporting and surveillance system would be required.
Cunze et al. (2021) Spatial and temporal distribution patterns of tick-borne diseases (Tick-borne Encephalitis and Lyme Borreliosis) in Germany. PeerJ 9:e12422 https://doi.org/10.7717/peerj.12422
Overexpression of SKA3 correlates with poor prognosis in female early breast cancer
Background Spindle and kinetochore associated complex subunit 3 (SKA3) plays an important role in tumorigenesis and the progression of various tumors. But the relationship between SKA3 and early breast cancer remains unclear. The study aimed to explore the prognostic significance of SKA3 in breast cancer. Methods In the study, SKA3 expression was initially assessed using the Oncomine database and The Cancer Genome Atlas database (TCGA). Then, we presented validation results for RT-qPCR (quantitative reverse transcription PCR) and ELISA (enzyme-linked immunosorbent assay). The relationship between clinical characteristics and SKA3 expression was assessed by Chi-square test and Fisher’s exact test. Kaplan–Meier method and Cox regression analysis were conducted to evaluate the prognostic value of SKA3. Gene set enrichment analysis (GSEA) was performed to screen biological pathways using the TCGA dataset. Besides, single sample gene set enrichment analysis (ssGSEA) was utilized to identify immune infiltration cells about SKA3. Results SKA3 mRNA was expressed at high levels in breast cancer tissues compared with normal tissues. Chi-square test and Fisher’s exact test showed SKA3 expression was related to age, tumor (T) classification, node (N) classification, tumor-node-metastasis (TNM) stage, estrogen receptor (ER), progesterone receptor (PR), molecular subtype, and race. RT-qPCR results showed that SKA3 expression was overexpressed in ER, PR status, and molecular subtype in Chinese people. Kaplan–Meier curves implicated that high SKA3 expression was related to a poor prognosis in female early breast cancer patients. Cox regression models showed that high SKA3 expression could be used as an independent risk factor for female early breast cancer. Four signaling pathways were enriched in the high SKA3 expression group, including mTORC1 signaling pathway, MYC targets v1, mitotic spindle, estrogen response early. Besides, the SKA3 expression level was associate with infiltrating levels of activated CD4 T cells and eosinophils in breast cancer. Conclusion High SKA3 expression correlates with poor prognosis and immune infiltrates in breast cancer. SKA3 may become a biomarker for the prognosis of breast cancer.
Zhong et al. (2021) Overexpression of SKA3 correlates with poor prognosis in female early breast cancer. PeerJ 9:e12506 https://doi.org/10.7717/peerj.12506
Identification of high protein kinase CK2α in HPV(+) oropharyngeal squamous cell carcinoma and correlation with clinical outcomes
Background Oropharyngeal squamous cell carcinoma (OPSCC) incidence is rising worldwide, especially human papillomavirus (HPV)-associated disease. Historically, high levels of protein kinase CK2 were linked with poor outcomes in head and neck squamous cell carcinoma (HNSCC), without consideration of HPV status. This retrospective study examined tumor CK2α protein expression levels and related clinical outcomes in a cohort of Veteran OPSCC patient tumors which were determined to be predominantly HPV(+). Methods Patients at the Minneapolis VA Health Care System with newly diagnosed primary OPSCC from January 2005 to December 2015 were identified. A total of 119 OPSCC patient tumors were stained for CK2α, p16 and Ki-67 proteins and E6/E7 RNA. CK2α protein levels in tumors and correlations with HPV status and Ki-67 index were assessed. Overall survival (OS) analysis was performed stratified by CK2α protein score and separately by HPV status, followed by Cox regression controlling for smoking status. To strengthen the limited HPV(−) data, survival analysis for HPV(−) HNSCC patients in the publicly available The Cancer Genome Atlas (TCGA) PanCancer RNA-seq dataset was determined for CSNK2A1. Results The patients in the study population were all male and had a predominant history of tobacco and alcohol use. This cohort comprised 84 HPV(+) and 35 HPV(−) tumors. CK2α levels were higher in HPV(+) tumors compared to HPV(−) tumors. Higher CK2α scores positively correlated with higher Ki-67 index. OS improved with increasing CK2α score and separately OS was significantly better for those with HPV(+) as opposed to HPV(−) OPSCC. Both remained significant after controlling for smoking status. High CSNK2A1 mRNA levels from TCGA data associated with worse patient survival in HPV(−) HNSCC. Conclusions High CK2α protein levels are detected in HPV(+) OPSCC tumors and demonstrate an unexpected association with improved survival in a strongly HPV(+) OPSCC cohort. Worse survival outcomes for high CSNK2A1 mRNA levels in HPV(−) HNSCC are consistent with historical data. Given these surprising findings and the rising incidence of HPV(+) OPSCC, further study is needed to understand the biological roles of CK2 in HPV(+) and HPV(−) HNSCC and the potential utility for therapeutic targeting of CK2 in these two disease states.
Trembley et al. (2021) Identification of high protein kinase CK2α in HPV(+) oropharyngeal squamous cell carcinoma and correlation with clinical outcomes. PeerJ 9:e12519 https://doi.org/10.7717/peerj.12519
Transcriptomic analysis of melon/squash graft junction reveals molecular mechanisms potentially underlying the graft union development
Oriental melon (Cucumis melo var. makuwa Makino) has become a widely planted horticultural crop in China especially in recent years and has been subjected to the grafting technique for the improvement of cultivation and stress resistance. Although grafting has a long history in horticulture, there is little known about the molecular mechanisms of the graft healing process in oriental melon. This study aims to reveal the molecular changes involved in the graft healing process. In the present work, anatomical observations indicated that the 2, 6, and 9 DAG were three critical stages for the graft healing and therefore, were selected for the subsequent high-throughput RNA-seq analysis. A total of 1,950 and 1,313 DEGs were identified by comparing IL vs. CA and CA vs. VB libraries, respectively. More DEGs in the melon scion exhibited abundant transcriptional changes compared to the squash rootstock, providing increased metabolic activity and thus more material basis for the graft healing formation in the scion. Several DEGs were enriched in the plant hormone signal transduction pathway, phenylpropanoid biosynthesis, and carbon metabolism. In addition, the results showed that concentrations of IAA, GA3, and ZR were induced in the graft junctions. In conclusion, our study determined that genes involved in the hormone-signaling pathway and lignin biosynthesis played the essential roles during graft healing. These findings expand our current understandings of the molecular basis of the graft junction formation and facilitate the improvement and success of melon grafting in future production.
Xu et al. (2021) Transcriptomic analysis of melon/squash graft junction reveals molecular mechanisms potentially underlying the graft union development. PeerJ 9:e12569 https://doi.org/10.7717/peerj.12569
The influence of rhizosphere soil fungal diversity and complex community structure on wheat root rot disease
Wheat root rot disease due to soil-borne fungal pathogens leads to tremendous yield losses worth billions of dollars worldwide every year. It is very important to study the relationship between rhizosphere soil fungal diversity and wheat roots to understand the occurrence and development of wheat root rot disease. A significant difference in fungal diversity was observed in the rhizosphere soil of healthy and diseased wheat roots in the heading stage, but the trend was the opposite in the filling stage. The abundance of most genera with high richness decreased significantly from the heading to the filling stage in the diseased groups; the richness of approximately one-third of all genera remained unchanged, and only a few low-richness genera, such as Fusarium and Ceratobasidium, had a very significant increase from the heading to the filling stage. In the healthy groups, the abundance of most genera increased significantly from the heading to filling stage; the abundance of some genera did not change markedly, or the abundance of very few genera increased significantly. Physical and chemical soil indicators showed that low soil pH and density, increases in ammonium nitrogen, nitrate nitrogen and total nitrogen contributed to the occurrence of wheat root rot disease. Our results revealed that in the early stages of disease, highly diverse rhizosphere soil fungi and a complex community structure can easily cause wheat root rot disease. The existence of pathogenic fungi is a necessary condition for wheat root rot disease, but the richness of pathogenic fungi is not necessarily important. The increases in ammonium nitrogen, nitrate nitrogen and total nitrogen contributed to the occurrence of wheat root rot disease. Low soil pH and soil density are beneficial to the occurrence of wheat root rot disease.
Zhang et al. (2021) The influence of rhizosphere soil fungal diversity and complex community structure on wheat root rot disease. PeerJ 9:e12601 https://doi.org/10.7717/peerj.12601
Development and primary validation of the School Health Assessment Tool for Primary Schools (SHAT-PS)
Background School health programs need to target all aspects of physical, psychological, and social well-being. Using a slightly modified version of the COSMIN Risk of Bias checklist, we developed and conducted the first validation of the School Health Assessment Tool for Primary Schools (SHAT-PS). Method The exploratory sequential mixed method was used in this study. In the first phase, scientific databases were systematically searched to find school health models and instruments and 65 interviews were conducted with school stakeholders. The Colaizzi’s method was used to code the qualitative data into themes. Then, a pool of items was created for each theme, rechecked by psychometric experts and then validated for content (i.e., relevance, clarity, and comprehensiveness) by psychometric experts and individuals of the target population (i.e., school personnel). In the second phase, classical test theory was utilized to analyze the validity and reliability of the resulting items from phase 1 among 400 individuals working at primary schools. Results The coding of the interviews resulted in ten themes that we labeled based on the theoretical literature: school health policies, community connections, health education, physical activity, health services, nutrition, psychological services, physical environment, equipment and facilities, and school staff’s health. The items created for each theme ended up in an initial pool of 76 items. In the final stage of phase 1, 69 items remained after the content validity assessment by experts and school personnel. In phase 2, the SHAT-PS items were tested using maximum likelihood exploratory factor analysis and confirmatory factor analysis. Of the 69 items from phase 1, 22 items were removed due to low factor loadings. The results showed that the 8-factor model was the best solution (chi-square/df = 2.41, CFI = .98, TLI = .97, RMSEA = .06). The discriminant and convergent validity of the SHAT-PS were evaluated as satisfactory and the scale had high internal consistency (Cronbach’s alpha for all subscales > .93). The test-retest reliability was satisfactory—the intraclass correlation coefficient pooled was .95 (99% CI [.91–.98]). Moreover, the standard error of measurement resulted in an SEM pooled equal to 4.4. No discrepancy was found between subgroups of gender and subgroups of staffs’ positions at schools. Conclusion The SHAT-PS is a valid and reliable tool that may facilitate school staff, stakeholders and researchers to evaluate the presence of the factors that promote health at primary schools. Nevertheless, in the process of validation, many of the items related to staff’s health were eliminated due to poor factor loadings. Obviously, staff health is an important factor in the measurement of school health. Hence, we recommend that the validity and reliability of the SHAT-PS in other cultures should be done using the original 76-item version.
Kazemitabar et al. (2021) Development and primary validation of the School Health Assessment Tool for Primary Schools (SHAT-PS). PeerJ 9:e12610 https://doi.org/10.7717/peerj.12610