title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1149 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Estimating food resource availability in arid environments with Sentinel 2 satellite imagery link: https://peerj.com/articles/9209 last-modified: 2020-05-26 description: BackgroundIn 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.MethodsWe 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.ResultsWe 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.DiscussionMSAVI2 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.ConclusionsOverall, 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). creator: Caterina Funghi creator: René H.J. Heim creator: Wiebke Schuett creator: Simon C. Griffith creator: Jens Oldeland uri: https://doi.org/10.7717/peerj.9209 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Funghi et al. title: Genome-wide identification and characterization of the fibrillin gene family in Triticum aestivum link: https://peerj.com/articles/9225 last-modified: 2020-05-26 description: BackgroundThe 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.MethodsIn 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.ResultsThe 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. creator: Yaoyao Jiang creator: Haichao Hu creator: Yuhua Ma creator: Junliang Zhou uri: https://doi.org/10.7717/peerj.9225 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jiang et al. title: A new nematode species, Chromadorina tangaroa sp. nov. (Chromadorida: Chromadoridae) from the hull of a research vessel, New Zealand link: https://peerj.com/articles/9233 last-modified: 2020-05-26 description: 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. creator: Daniel Leduc uri: https://doi.org/10.7717/peerj.9233 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Leduc title: Hamstring extensibility differences among elite adolescent and young dancers of different dance styles and non-dancers link: https://peerj.com/articles/9237 last-modified: 2020-05-26 description: BackgroundHamstrings 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.MethodsThe 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.ResultsThe 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).ConclusionsThe systematic practice of dance, regardless of the style, seems to lead to high ranges of hamstring extensibility. Ballet dancers have the greatest hamstring extensibility. creator: Raquel Vaquero-Cristóbal creator: Patricia Molina-Castillo creator: Pedro A. López-Miñarro creator: Mario Albaladejo-Saura creator: Francisco Esparza-Ros uri: https://doi.org/10.7717/peerj.9237 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Vaquero-Cristóbal et al. title: Transcultural adaptation and validation of the questionnaire “Urgency, Weak stream, Incomplete emptying and Nocturia (UWIN)” for the Brazilian Portuguese link: https://peerj.com/articles/9039 last-modified: 2020-05-25 description: 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. creator: Caroline S. Silva creator: Katia S. Freitas creator: Anna Paloma R. Ribeiro creator: Cristiano M. Gomes creator: Jose Bessa Junior uri: https://doi.org/10.7717/peerj.9039 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Silva et al. title: Identifying multiple collagen gene family members as potential gastric cancer biomarkers using integrated bioinformatics analysis link: https://peerj.com/articles/9123 last-modified: 2020-05-25 description: BackgroundGastric cancer is one of the most common malignant cancers worldwide. Despite substantial developments in therapeutic strategies, the five-year survival rate remains low. Therefore, novel biomarkers and therapeutic targets involved in the progression of gastric tumors need to be identified.MethodsWe obtained the mRNA microarray datasets GSE65801, GSE54129 and GSE79973 from the Gene Expression Omnibus database to acquire differentially expressed genes (DEGs). We used the Database for Annotation, Visualization, and Integrated Discovery (DAVID) to analyze DEG pathways and functions, and the Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape to obtain the protein–protein interaction (PPI) network. Next, we validated the hub gene expression levels using the Oncomine database and Gene Expression Profiling Interactive Analysis (GEPIA), and conducted stage expression and survival analysis.ResultsFrom the three microarray datasets, we identified nine major hub genes: COL1A1, COL1A2, COL3A1, COL5A2, COL4A1, FN1, COL5A1, COL4A2, and COL6A3.ConclusionOur study identified COL1A1 and COL1A2 as potential gastric cancer prognostic biomarkers. creator: Zhaoxing Li creator: Zhao Liu creator: Zhiting Shao creator: Chuang Li creator: Yong Li creator: Qingwei Liu creator: Yifei Zhang creator: Bibo Tan creator: Yu Liu uri: https://doi.org/10.7717/peerj.9123 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Herbicide applications increase greenhouse gas emissions of alfalfa pasture in the inland arid region of northwest China link: https://peerj.com/articles/9231 last-modified: 2020-05-25 description: Herbicides are used to control weeds in agricultural crops such as alfalfa (Medicago sativa L.), which is a forage crop. It is unclear what, if any, effect herbicides have on greenhouse gas (GHG) emissions when used on alfalfa. Our study was conducted in 2017 and 2018 to investigate the effects of two herbicides (Quizalofop-p-ethyl, QE and Bentazone, BT) on methane (CH4), carbon dioxide (CO2) and nitrous oxide (N2O) emissions from soil planted with alfalfa. QE is used to control grasses and BT is used for broadleaf weed control. Soil CO2 emissions and soil uptake of CH4 increased significantly in both years following the QE and BT treatments, although CO2 emissions differed significantly between the trial years. N2O emissions decreased relative to the control and showed no significant differences between the trial years. The application of QE and BT on alfalfa resulted in a significant increase in CO2 emissions which contributed to a significant increase in GHG emissions. The application of QE influenced GHG emissions more than BT. We demonstrated the potential effect that herbicide applications have on GHG fluxes, which are important when considering the effect of agricultural practices on GHG emissions and the potential for global warming over the next 100 years. creator: Lina Shi creator: Yarong Guo creator: Jiao Ning creator: Shanning Lou creator: Fujiang Hou uri: https://doi.org/10.7717/peerj.9231 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Shi et al. title: Revealing the selective mechanisms of inhibitors to PARP-1 and PARP-2 via multiple computational methods link: https://peerj.com/articles/9241 last-modified: 2020-05-25 description: BackgroundResearch has shown that Poly-ADP-ribose polymerases 1 (PARP-1) is a potential therapeutic target in the clinical treatment of breast cancer. An increasing number of studies have focused on the development of highly selective inhibitors that target PARP-1 over PARP-2, its closest isoform, to mitigate potential side effects. However, due to the highly conserved and similar binding sites of PARP-1 and PARP-2, there is a huge challenge for the discovery and design of PARP-1 inhibitors. Recently, it was reported that a potent PARP-1 inhibitor named NMS-P118 exhibited greater selectivity to PARP-1 over PARP-2 compared with a previously reported drug (Niraparib). However, the mechanisms underlying the effect of this inhibitor remains unclear.MethodsIn the present study, classical molecular dynamics (MD) simulations and accelerated molecular dynamics (aMD) simulations combined with structural and energetic analysis were used to investigate the structural dynamics and selective mechanisms of PARP-1 and PARP-2 that are bound to NMS-P118 and Niraparib with distinct selectivity.ResultsThe results from classical MD simulations indicated that the selectivity of inhibitors may be controlled by electrostatic interactions, which were mainly due to the residues of Gln-322, Ser-328, Glu-335, and Tyr-455 in helix αF. The energetic differences were corroborated by the results from aMD simulations.ConclusionThis study provides new insights about how inhibitors specifically bind to PARP-1 over PARP-2, which may help facilitate the design of highly selective PARP-1 inhibitors in the future. creator: Hongye Hu creator: Buran Chen creator: Danni Zheng creator: Guanli Huang uri: https://doi.org/10.7717/peerj.9241 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hu et al. title: Agreement between the GAITRite® System and the Wearable Sensor BTS G-Walk® for measurement of gait parameters in healthy adults and Parkinson’s disease patients link: https://peerj.com/articles/8835 last-modified: 2020-05-22 description: BackgroundNowadays, the most widely used types of wearable sensors in gait analysis are inertial sensors. The aim of the study was to assess the agreement between two different systems for measuring gait parameters (inertial sensor vs. electronic walkway) on healthy control subjects (HC) and patients with Parkinson’s disease (PD).MethodsForty healthy volunteers (26 men, 14 women, mean age 58.7 ± 7.7 years) participated in the study and 24 PD patients (19 men, five women, mean age 62.7 ± 9.8 years). Each participant walked across an electronic walkway, GAITRite, with embedded pressure sensors at their preferred walking speed. Concurrently a G-Walk sensor was attached with a semi-elastic belt to the L5 spinal segment of the subject. Walking speed, cadence, stride duration, stride length, stance, swing, single support and double support phase values were compared between both systems.ResultsThe Passing-Bablock regression slope line manifested the values closest to 1.00 for cadence and stride duration (0.99 ≤ 1.00) in both groups. The slope of other parameters varied between 0.26 (double support duration in PD) and 1.74 (duration of single support for HC). The mean square error confirmed the best fit of the regression line for speed, stride duration and stride length. The y-intercepts showed higher systematic error in PD than HC for speed, stance, swing, and single support phases.ConclusionsThe final results of this study indicate that the G-Walk system can be used for evaluating the gait characteristics of the healthy subjects as well as the PD patients. However, the duration of the gait cycle phases should be used with caution due to the presence of a systematic error. creator: Slávka Vítečková creator: Hana Horáková creator: Kamila Poláková creator: Radim Krupička creator: Evžen Růžička creator: Hana Brožová uri: https://doi.org/10.7717/peerj.8835 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Vítečková et al. title: Maternal trauma and fear history predict BDNF methylation and gene expression in newborns link: https://peerj.com/articles/8858 last-modified: 2020-05-22 description: Trauma and related fear exert significant influence on mental and physical health throughout the lifespan and are associated with intergenerational patterns of development, health, and behavior. DNA methylation and gene expression are involved in our developmental adaptations to our experiences and can be influenced by social interventions. Patterns of DNA methylation and expression of a gene involved in neurodevelopment and psychiatric risk (BDNF) have been linked with childhood trauma. Given the intergenerational patterns of health and behavior, and previous links between childhood trauma and BDNF methylation and expression, this study investigated the potential for maternal history of traumatic experiences to influence development in her newborn, via changes in her newborn’s BDNF methylation and expression. We found that mothers’ trauma history was associated with epigenetic regulation of BDNF in their newborns. Moreover, the association between maternal trauma and BDNF methylation and expression patterns were moderated by newborn sex. Male newborns showed increased BDNF expression with maternal exposure to child abuse (p = .001), and increased BDNF methylation with greater maternal fear (p = .001). Female newborns showed reduced BDNF expression with greater maternal fear (p = .004). Practitioners strive to identify prevention and intervention avenues that will reduce the harmful effects of trauma. Future research should consider the potential for maternal historical trauma experiences to influence offspring DNA methylation and gene expression in a manner that could alter development and inform novel prevention strategies. creator: Stefanie R. Pilkay creator: Terri Combs-Orme creator: Frances Tylavsky creator: Nicole Bush creator: Alicia K. Smith uri: https://doi.org/10.7717/peerj.8858 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Pilkay et al.