The combined impacts of wheat spatial position and phenology on cereal aphid abundance
Background Wheat is a staple crop that suffers from massive yield losses caused by cereal aphids. Many factors can determine the abundance of cereal aphids and the damage they cause to plants; among them are the plant’s genetic background, as well as environmental conditions such as spatial position within the plot, the composition and the distance from neighboring vegetation. Although the effects of these factors have been under scrutiny for many years, the combined effect of both factors on aphid populations is not fully understood. The goal of this study was to examine the collective impact of genotype and environment on wheat phenology (developmental stages), chemical diversity (metabolites), and insect susceptibility, as manifested by cereal aphid abundance. Methods To determine the influence of plant genotype on the metrics mentioned above, we measured the phenology, chemical profile, and aphid abundance of four wheat genotypes, including the tetraploid wild emmer (Triticum turgidum ssp. dicoccoides cv. Zavitan), tetraploid durum (Triticum turgidum ssp. durum cv. Svevo), and two hexaploid spring bread (Triticum aestivum), ‘Rotem’ and ‘Chinese Spring’. These genotypes are referred to as “focal” plants. To evaluate the impact of the environment, we scored the distance of each focal plant (spatial position) from two neighboring vegetation types: (i) natural resource and (ii) monoculture wheat resource. Results The results demonstrated that the wild emmer wheat was the most aphid-resistant, while the bread wheat Rotem was most aphid-susceptible. Aphids were more abundant in plants that matured early. The spatial position analysis demonstrated that aphids were more abundant in focal plants located closer to the margin monoculture wheat resource rather than to the natural resource, suggesting a resource concentration effect. The analysis of metabolic diversity showed that the levels of three specialized metabolites from the flavonoid class, differed between the wheat genotypes and some minor changes in central metabolites were shown as well. Altogether, these results demonstrate a combined effect of genetic background and spatial position on wheat phenology and aphid abundance on plants. This exposes the potential role of the marginal vegetation environment in shaping the insect population of desirable crops. These findings highlight the importance of maintaining plant intra-specific variation in the agriculture system because of its potential applications in reducing pest density.
Batyrshina et al. (2020) The combined impacts of wheat spatial position and phenology on cereal aphid abundance. PeerJ 8:e9142 https://doi.org/10.7717/peerj.9142
Isolation and functional analyses of PvFAD2 and PvFAD3 involved in the biosynthesis of polyunsaturated fatty acids from Sacha Inchi (Plukenetia volubilis)
The development of ω-3 fatty acid-rich vegetable oils is essential to enrich the production of functional foods. Sacha Inchi (Plukenetia volubilis L.) is a unique oilseed crop with much potential. Its seeds contain rich polyunsaturated fatty acids (PUFAs), especially linoleic acid (LA, C18:2) and α-linolenic acid (ALA, C18:3). Endoplasmic reticulum -located ω-6 and ω-3 fatty acid desaturases (FAD) are responsible for the biosynthesis of LA and ALA, respectively, in plant seeds. Here, we isolated two full-length FAD genes from Sacha Inchi, named PvFAD2 and PvFAD3, which encoded predicted amino acid residues of 384 and 379 in protein, respectively. Protein sequence and subcellular localization analysis revealed that they were located in the endoplasmic reticulum (ER). Heterologous expression in Saccharomyces cerevisiae confirmed that PvFAD2 and PvFAD3 could catalyze LA and ALA synthesis, respectively. The stability and catalytic efficiency of the PvFAD3 protein may be closely related to temperature. In transgenic tobacco, using seed-specific expression promoters, PvFAD2 and PvFAD3 significantly promotes the production of LA (from 68% to 70.5%) and ALA (from 0.7% to 3.1%) in seed oil. These results show that PvFAD2 and PvFAD3 do, indeed, function as crucial enzymes for PUFAs biosynthesis, and provide a key gene source for the sustainable production of lipids with tailored fatty acid compositions via genetic engineering in other oil crops.
Yang et al. (2020) Isolation and functional analyses of PvFAD2 and PvFAD3 involved in the biosynthesis of polyunsaturated fatty acids from Sacha Inchi (Plukenetia volubilis). PeerJ 8:e9169 https://doi.org/10.7717/peerj.9169
Effects of mining on the molybdenum absorption and translocation of plants in the Luanchuan molybdenum mine
Background There is a critical need to examine whether mining of molybdenum (Mo) ore will affect Mo absorption and translocation by plants at a community level. Methods Indigenous plants and their rhizospheric soil (0–20 cm) growing in two different areas including the mining and the unexploited areas were collected from the Luanchuan Mo mine—one of the largest Mo mines in Asia. The concentrations of Mo and other heavy metals of plants or soil were measured by ICP-AES. Mo absorption and translocation in plants growing in two areas were investigated and compared. Heavy metal pollution in soil was also evaluated by the potential ecological hazard index method. Results Mo concentration in mining soils was higher with the changes from 108.13 to 268.13 mg kg−1 compared to unexploited area. Mo concentrations in shoots and roots of plants growing in the mining area were also significant higher than those growing in the unexploited area with 2.59 and 2.99 times, respectively. The Mo translocation factor of plants growing in the unexploited area was 1.61, which reached 1.69 times that of plants growing in the mining area. Mo was the main heavy metal pollutant in the soil of both the mining and the unexploited areas. Conclusion Mining of Mo had changed not only the Mo concentration in soil but also Mo absorption and translocation in plants. Plants growing in the mining area absorbed more Mo from the soil but translocated relatively less to shoots than plants of the unexploited area. However, the mechanisms of Mo absorption and translocation of plants in mining area should be further studied in the future.
Environmental Contamination and Remediation
Yin et al. (2020) Effects of mining on the molybdenum absorption and translocation of plants in the Luanchuan molybdenum mine. PeerJ 8:e9183 https://doi.org/10.7717/peerj.9183
The high expression of MTH1 and NUDT5 predict a poor survival and are associated with malignancy of esophageal squamous cell carcinoma
Background MTH1 and NUDT5 effectively degrade nucleotides containing 8-oxoguanine. MTH1 and NUDT5 have been linked to the malignancy of multiple cancers. However, their functions in tumor growth and metastasis in esophageal squamous carcinoma (ESCC) remain obscure. Our present study aims to explore their prognostic value in ESCC and investigate their function in MTH1 or NUDT5-knockout tumor cells. Methods MTH1 and NUDT5 protein expression in ESCC adjacent normal tissues and tumor tissues was examined by immunohistochemistry staining. Kaplan–Meier curves were used to assess the association between their expression and overall survival (OS) in ESCC patients. Univariate and Multivariate Cox regression analyses were generated to determine the correlation between these protein expression and OS of ESCC patients. Protein expression in ESCC cell lines were measured by Western blotting. To explore the potential effects of the MTH1 and NUDT5 protein in ESCC, cell models with MTH1 or NUDT5 depletion were established. CCK-8, cell cycle, Western blotting, migration and invasion assays were performed. Results Our present study demonstrated that the levels of MTH1 and NUDT5 were upregulated in ESCC cell lines and ESCC tissues, the expression of MTH1 and NUDT5 in ESCC tissues was significantly higher than in adjacent non-tumorous, and higher levels of MTH1 and NUDT5 predicted a worse prognosis in patients with ESCC. MTH1 and NUDT5 are novel biomarkers of the progression of ESCC and a poor prognosis. We also found for the first time that the high expression of NUDT5 independently predicted lower OS in patients with ESCC (hazard ratio (HR) 1.751; 95% confidence interval (CI) [1.056–2.903]; p = 0.030). In addition, the depletion of MTH1 and NUDT5 strongly suppressed the proliferation of ESCC cells and significantly delayed the G1 phase of the cell cycle. Furthermore, we found that MTH1 and NUDT5 silencing inhibited epithelial–mesenchymal transition mainly by the MAPK/MEK/ERK dependent pathway, which in turn significantly decreased the cell migration and invasion of ESCC cells. Our results suggested that the overexpression of MTH1 and NUDT5 is probably involved in the tumor development and poor prognosis of ESCC.
Wang et al. (2020) The high expression of MTH1 and NUDT5 predict a poor survival and are associated with malignancy of esophageal squamous cell carcinoma. PeerJ 8:e9195 https://doi.org/10.7717/peerj.9195
Comprehensive analysis reveals a metabolic ten-gene signature in hepatocellular carcinoma
Background Due to the complicated molecular and cellular heterogeneity in hepatocellular carcinoma (HCC), the morbidity and mortality still remains high level in the world. However, the number of novel metabolic biomarkers and prognostic models could be applied to predict the survival of HCC patients is still small. In this study, we constructed a metabolic gene signature by systematically analyzing the data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and International Cancer Genome Consortium (ICGC). Methods Differentially expressed genes (DEGs) between tumors and paired non-tumor samples of 50 patients from TCGA dataset were calculated for subsequent analysis. Univariate cox proportional hazard regression and LASSO analysis were performed to construct a gene signature. The Kaplan–Meier analysis, time-dependent receiver operating characteristic (ROC), Univariate and Multivariate Cox regression analysis, stratification analysis were used to assess the prognostic value of the gene signature. Furthermore, the reliability and validity were validated in four types of testing cohorts. Moreover, the diagnostic capability of the gene signature was investigated to further explore the clinical significance. Finally, Go enrichment analysis and Gene Set Enrichment Analysis (GSEA) have been performed to reveal the different biological processes and signaling pathways which were active in high risk or low risk group. Results Ten prognostic genes were identified and a gene signature were constructed to predict overall survival (OS). The gene signature has demonstrated an excellent ability for predicting survival prognosis. Univariate and Multivariate analysis revealed the gene signature was an independent prognostic factor. Furthermore, stratification analysis indicated the model was a clinically and statistically significant for all subgroups. Moreover, the gene signature demonstrated a high diagnostic capability in differentiating normal tissue and HCC. Finally, several significant biological processes and pathways have been identified to provide new insights into the development of HCC. Conclusion The study have identified ten metabolic prognostic genes and developed a prognostic gene signature to provide more powerful prognostic information and improve the survival prediction for HCC.
Zhu et al. (2020) Comprehensive analysis reveals a metabolic ten-gene signature in hepatocellular carcinoma. PeerJ 8:e9201 https://doi.org/10.7717/peerj.9201
Estimating food resource availability in arid environments with Sentinel 2 satellite imagery
Background In arid environments, plant primary productivity is generally low and highly variable both spatially and temporally. Resources are not evenly distributed in space and time (e.g., soil nutrients, water), and depend on global (El Niño/ Southern Oscillation) and local climate parameters. The launch of the Sentinel2-satellite, part of the European Copernicus program, has led to the provision of freely available data with a high spatial resolution (10 m per pixel). Here, we aimed to test whether Sentinel2-imagery can be used to quantify the spatial variability of a minor tussock grass (Enneapogon spp.) in an Australian arid area and whether we can identify different vegetation cover (e.g., grass from shrubs) along different temporal scenarios. Although short-lasting, the Enneapogon grassland has been identified as a key primary food source to animals in the arid environment. If we are able to identify and monitor the productivity of this species remotely, it will provide an important new tool for examining food resource dynamics and subsequent animal responses to them in arid habitat. Methods We combined field vegetation surveys and Sentinel2-imagery to test if satellite spectral data can predict the spatial variability of Enneapogon over time, through GLMMs. Additionally, a cluster analysis (‘gower’ distance, ‘complete’ method), based on Enneapogon seed-productivity, and total vegetation cover in October 2016, identified three clusters: bare ground, grass dominated and shrub dominated. We compared the vegetation indices between these different clusters from October 2016 to January 2017. Results We found that MSAVI2 and NDVI correlated with the proportion of Enneapogon with seeds across the landscape and this relationship changed over time. Both vegetation indices (MSAVI2 and NDVI) were higher in patches with high seed-productivity of Enneapogon than in bare soil, but only in October, a climatically-favorable period during which this dominant grass reached peak seed-productivity. Discussion MSAVI2 and NDVI provided reliable estimates of the heterogeneity of vegetation type across the landscape only when measured in the Austral spring. This means that grass cover is related to seed-productivity and it is possible to remotely and reliably predict food resource availability in arid habitat, but only in certain conditions. The lack of significant differences between clusters in the summer was likely driven by the short-lasting nature of the vegetation in the study and the sparseness of the grass-dominated vegetation, in contrast to the shrub vegetation cluster that was particularly well measured by the NDVI. Conclusions Overall, our study highlights the potential for Sentinel2-imagery to estimate and monitor the change in grass seed availability remotely in arid environments. However, heterogeneity in grassland cover is not as reliably measured as other types of vegetation and may only be well detected during periods of peak productivity (e.g., October 2016).
Funghi et al. (2020) Estimating food resource availability in arid environments with Sentinel 2 satellite imagery. PeerJ 8:e9209 https://doi.org/10.7717/peerj.9209
Genome-wide identification and characterization of the fibrillin gene family in Triticum aestivum
Background The fibrillin (FBN) gene family is highly conserved and widely distributed in the photosynthetic organs of plants. Members of this gene family are involved in the growth and development of plants and their response to biotic and abiotic stresses. Wheat (Triticum aestivum), an important food crop, has a complex genetic background and little progress has occurred in the understanding of its molecular mechanisms. Methods In this study, we identified 26 FBN genes in the whole genome of T. aestivum through bioinformatic tools and biotechnological means. These genes were divided into 11 subgroups and were distributed on 11 chromosomes of T. aestivum. Interestingly, most of the TaFBN genes were located on the chromosomes 2A, 2B and 2D. The gene structure of each subgroup of gene family members and the position and number of motifs were highly similar. Results The evolutionary analysis results indicated that the affinities of FBNs in monocots were closer together. The tissue-specific analysis revealed that TaFBN genes were expressed in different tissues and developmental stages. In addition, some TaFBNs were involved in one or more biotic and abiotic stress responses. These results provide a basis for further study of the biological function of FBNs.
Jiang et al. (2020) Genome-wide identification and characterization of the fibrillin gene family in Triticum aestivum. PeerJ 8:e9225 https://doi.org/10.7717/peerj.9225
A new nematode species, Chromadorina tangaroa sp. nov. (Chromadorida: Chromadoridae) from the hull of a research vessel, New Zealand
Chromadorina is a globally distributed, largely marine nematode genus frequently found on a variety of organisms, including macro- and microalgae and crustaceans, as well as artificial substrates such as settlement plates and ship hulls. Here, Chromadorina tangaroa sp. nov. is described from filamentous seaweed growing on the hull of RV Tangaroa anchored in Wellington, North Island of New Zealand. It is characterized by body length 763–1,086 μm, and pore of secretory-excretory system located at or near level of teeth. Males have spicules with rounded capitulum followed by a narrower shaft and blade tapered distally, a gubernaculum as long as the spicules, and three cup-shaped precloacal supplements, and females are characterized by a cuticularized prevulvar pad, vagina located at 46–48% of body length from anterior, and vagina anteriorly directed. Chromadorina tangaroa sp. nov. is the first species of the genus to be described from New Zealand, but it is unclear whether it is native to the region because it may have dispersed as part of ship hull biofouling communities. Long-distance transport of nematodes through ship hull biofouling may be a common occurrence, but too little is known about the occurrence of nematodes on ship hulls to gauge the potential effect of shipping on nematode species distributions.
Leduc (2020) A new nematode species, Chromadorina tangaroa sp. nov. (Chromadorida: Chromadoridae) from the hull of a research vessel, New Zealand. PeerJ 8:e9233 https://doi.org/10.7717/peerj.9233
Hamstring extensibility differences among elite adolescent and young dancers of different dance styles and non-dancers
Background Hamstrings have been analyzed extensively due to their tendency to shorten and their effect in the lumbo-pelvic dynamics and the sagittal position of the spine in trunk flexion with extended knees positions. It has been demonstrated that practicing a certain sport results in long-term changes in hamstring extensibility. Despite this, adequate extensibility of the hamstring musculature is essential for the dancer’s performance. Several studies have found differences in the extensibility of the hamstrings depending on the dance style, but none have compared ballet, Spanish dance and modern dance. The purpose of the present research was to analyze the differences in hamstring extensibility among professional dance students based on dance style practiced and non-dancers. Methods The sample was comprised of 210 students from the Professional Dance Conservatory (70 for ballet, 70 for Spanish dance and 70 for modern dance) and 70 non-dancers. For the assessment of hamstring extensibility, the angle in the passive and active straight leg raise (PSLR and ASLR, respectively) test, and the scores of the pelvic tilt in sit-and-reach (SR) test and the toe-touch (TT) test were randomly conducted. Results The results showed significant differences for all the tests according to group (p < 0.001). In the PSLR and ASLR test, for both legs, and in the pelvic tilt in the SR test, the ballet dancers showed greater ranges of hamstring extensibility than the modern dancers and Spanish dancers (p ≤ 0.001). In the distance in the SR test and in the pelvic tilt in the TT test, the ballet dancers obtained higher values than the Spanish dancers (p = 0.004 and p = 0.003, respectively). The modern dancers showed higher ranges of hip flexion than the Spanish dancers in the ASLR test for both legs and in the pelvic tilt in the SR test (p from 0.007 to <0.001). Dancers showed significantly higher hamstring extensibility than non-dancers in all the tests (p < 0.001). Conclusions The systematic practice of dance, regardless of the style, seems to lead to high ranges of hamstring extensibility. Ballet dancers have the greatest hamstring extensibility.
Vaquero-Cristóbal et al. (2020) Hamstring extensibility differences among elite adolescent and young dancers of different dance styles and non-dancers. PeerJ 8:e9237 https://doi.org/10.7717/peerj.9237
Transcultural adaptation and validation of the questionnaire “Urgency, Weak stream, Incomplete emptying and Nocturia (UWIN)” for the Brazilian Portuguese
Lower urinary tract symptoms (LUTS) are common complaints in the adult male population and have a negative affect in the quality of life and represent an economic burden for the healthcare system worldwide. The International Prostatism Symptom Score (IPSS) is a validated tool for assessing these symptoms, but patients with low literacy may have difficulties comprehending and completing it accurately. The Urgency, Weak Stream, Incomplete Emptying, and Nocturia (UWIN) questionnaire was developed as a shorter tool in the assessment of LUTS to improve accuracy and minimize error. This study aimed at performing cross-cultural adaptation to Brazilian Portuguese and validation of UWIN questionnaire for patients with LUTS. The cross-cultural adaptation followed the steps of conceptual, item, semantic, operational, and pre-test equivalence to obtain the UWIN-Br version. The IPSS (gold standard) and UWIN-Br were coadministered, and information regarding the uroflowmetry examination was also recorded. We evaluated 306 men, median age 59 [52-66] years. There was a positive correlation r = 0.804 (p < 0.001) between the total IPSS score and the total UWIN-Br score, as well as the quality of life question (r = 0.761) (p < 0.001). The Bland-Altman plot showed good agreement between. Also, we observed that the maximum flow values decreased with the severity of the LUTS. UWIN-Br demonstrated excellent diagnostic accuracy in detecting the most severe cases. The area under the ROC curve was 89% [81–97%] 95% CI. 280 (91.5%) subjects completed the questionnaires without help, while 26 (8.5%) did so through an interview. The response time was 1.2 [1.0–1.5] min for UWIN-Br and 2.8 [2.2–3.4] min for IPSS (p < 0.001). UWIN-Br presents satisfactory and similar psychometric properties to the IPSS in the evaluation of LUTS and quality of life and is suitable for use in both clinical practice and research in our country.
Silva et al. (2020) Transcultural adaptation and validation of the questionnaire “Urgency, Weak stream, Incomplete emptying and Nocturia (UWIN)” for the Brazilian Portuguese. PeerJ 8:e9039 https://doi.org/10.7717/peerj.9039