title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=767 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Carbon isotope discrimination and the factors affecting it in a summer maize field under different tillage systems link: https://peerj.com/articles/12891 last-modified: 2022-02-11 description: Based on two years of field experiments, under different soil tillage methods and straw management practices, which included conventional tillage (CT), subsoiling (SS), rotary tillage (RT), and no-tillage (NT), combined with either straw return (S) or straw removal (0), we characterized the dynamic changes in Δ13C among three height layers [upper (U, 240 cm above the ground), middle (M, 120 cm above the ground), and lower (L, 30 cm above the ground)] of the summer maize canopy. The Δ13C, the factors affecting it, and the relationships between Δ13C and soil water content (SWC), the leaf area index (LAI), canopy microclimate, and the CO2 concentration were elucidated. The results indicated that the Δ13C of summer maize at the pre-filling stage was greater than that at the post-filling stage. Δ13C also varied at different heights, with the order of the Δ13C values being L > U > M. Among the different tillage methods, the Δ13C values were ordered SSS > CTS > RTS > NTS. SSS and NTS significantly increased the LAI; air temperature and relative humidity tended to gradually decrease with the increase in height of summer maize. Correlation analyses of the various influencing factors and Δ13C showed that SWC, LAI, air temperature, and CO2 concentration were all positively correlated with Δ13C, in which LAI and air temperature were significantly or extremely significantly positively correlated with Δ13C. In addition, we show that Δ13C can be used as a prediction index for summer maize yield, providing a theoretical basis for future yield research that may save precious time in summer maize breeding efforts. creator: Jichao Cui creator: Huifang Han uri: https://doi.org/10.7717/peerj.12891 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Cui and Han title: Genetic variability studies for tuber yield and yield attributes in Ethiopian released potato (Solanum tuberosum L.) varieties link: https://peerj.com/articles/12860 last-modified: 2022-02-10 description: Information on the extent of genetic variability and association among quantitative traits are vital for any crop improvement program and the development of suitable selection strategies. Limited research has been carried out thus far on potato genetic variability and trait association. This study on genetic variability and association among quantitative traits was conducted to assess the extent of genetic variability among yield and agronomic traits to identify superior varieties for the breeding program. To this effect, 20 improved varieties and a local cultivar were planted at two locations in central Ethiopia during the main cropping season of 2017/18 in a randomized complete block design using three replications. Analysis of variance of tuber yield and yield traits at each location and over locations, revealed the existence of highly significant (P < 0.01) differences among varieties in all agronomic and yield traits. Phenotypic coefficient of variation values ranged from 0.75% (specific gravity) to 32.22% (total starch yield) while the genotypic coefficient of variation values ranged between 0.70% (specific gravity) to 30.22% (total starch yield). Maximum difference between phenotypic and genotypic coefficient of variation values were noted for stem number, average tuber number, average tuber weight, number of leaves per plant and tuber yield. Hence, these traits are substantially influenced by the physiological status of the seed tuber at planting and by the environment, post emergence. Range of variability for most of the traits was high, indicating ample scope for selection and improvement in these traits. The estimated values for broad sense heritability and genetic advance, as percent of mean, ranged from 33.52% to 98.66% and 1.35% to 58.26%, respectively. All the traits had high heritability values, except average tuber number per hill, days to physiological maturity, average tuber weight and number of leaves per plant with moderate heritability values. creator: Gebrehanna Lemma Tessema creator: Ali Wassu Mohammed creator: Desta Tesfaye Abebe uri: https://doi.org/10.7717/peerj.12860 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gebrehanna et al. title: Vertical and temporal variations of soil bacterial and archaeal communities in wheat-soybean rotation agroecosystem link: https://peerj.com/articles/12868 last-modified: 2022-02-10 description: Soil microbes are an essential component of terrestrial ecosystems and drive many biogeochemical processes throughout the soil profile. Prior field studies mainly focused on the vertical patterns of soil microbial communities, meaning their temporal dynamics have been largely neglected. In the present study, we investigated the vertical and temporal patterns of soil bacterial and archaeal communities in a wheat-soybean rotation agroecosystem at a depth of millions of sequences per sample. Our results revealed different vertical bacterial and archaeal richness patterns: bacterial richness was lowest in the deep soil layer and peaked in the surface or middle soil layer. In contrast, archaeal richness did not differ among soil layers. PERMANOVA analysis indicated that both bacterial and archaeal community compositions were significantly impacted by soil depth but unaffected by sampling time. Notably, the proportion of rare bacteria gradually decreased along with the soil profile. The rare bacterial community composition was the most important indicator for soil nutrient fertility index, as determined by random forest analysis. The soil prokaryotic co-occurrence networks of the surface and middle soil layers are more connected and harbored fewer negative links than that of the deep soil layer. Overall, our results highlighted soil depth as a more important determinant than temporal variation in shaping the soil prokaryotic community and interspecific interactions and revealed a potential role of rare taxa in soil biogeochemical function. creator: Mika Yokota creator: Yupeng Guan creator: Yi Fan creator: Ximei Zhang creator: Wei Yang uri: https://doi.org/10.7717/peerj.12868 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yokota et al. title: Determinants of quality of life and well-being in cognitively unimpaired older adults: a systematic review link: https://peerj.com/articles/12900 last-modified: 2022-02-10 description: ObjectiveIt is important to know the psychological variables that are related to quality of life and well-being in healthy elderly people. The main objective of the present review is to analyse which factors, through psychological variables, are determinant on the adaptive processes that acquire relevance in the last stage of life.Data sourcesAn electronic search was conducted in WOS, Science Direct, PsycARTICLES, Psychology Database and Psycinfo.Study selectionThe search terms used were derived from the combination of the following search string: ((“Emotional Factors” OR “Emotional Effects”) AND (“Emotional Intelligence” OR “Emotional Regulation”) AND (“Quality of Life” OR “Personal Satisfaction”) AND (“Healthy Old People” OR “Healthy Old Adults”) AND (“Healthy Aging” OR “Successful Aging”)).Data extraction11th April 2021.Data synthesisIn total, 13 articles were selected.ConclusionsThe articles showed the importance of social support, proactive coping strategies (emotional regulation) and emotional intelligence as key factors in the elderly population for their positive influence on variables such as quality of life and well-being.Prospero ID: CRD42021224789 creator: María Dolores Frías-Luque creator: Abel Toledano-González uri: https://doi.org/10.7717/peerj.12900 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Frías-Luque and Toledano-González title: The effect of farmland on the surface water of the Aral Sea Region using Multi-source Satellite Data link: https://peerj.com/articles/12920 last-modified: 2022-02-10 description: BackgroundThe improper land utilization has brought tremendous pressure on the surface water of the Aral Sea Region in the past decades. It was seriously hindered for construction of the Green Silk Road Economic Belt by the fragile environment. Therefore, it is of great necessity for environmental protection and social development to monitor the change of surface water in the Aral Sea Region.MethodsIn this study, LandTrendr algorithm was used on Landsat time-series data to characterize the change in farmland on the Google Earth Engine platform. Based on multi-source data, the water area changes of the Aral Sea were extracted based on the Google Earth Engine, and the mean method was utilized to extract the changes in water level and water storage. Finally, a water-farmland coupling degree model was utilized to evaluate the impact of farmland changes on the surface water in the Aral Sea Region.ResultsAs a result, the change of farmland is as follows: the farmland area of the Aral Sea Region has abandoned 3,129 km2 from 1987 to 2019, with overall accuracy of 85.3%. The farmland change had increased the drainage downstream of the Amu Darya River and the Syr Darya River. It has led area of the Aral Sea to decrease each year continuously. The area of the Aral Sea shrank by 1,606.36 km2 per year from 1987 to 2019. Furthermore, Aral Sea’s water level decreased by 0.13 m per year from 2003 to 2009. The amount of water storage in the Aral Sea Region also showed a downward trend from 2002 to 2016. There was a high-quality coupling coordination 0.903 relationship between surface water and farmland. It will increase the burden of water for people’s normal daily life by the water loss resources caused by abandoned farmland. This study emphasized threat of unreasonable farmland management to surface water of the Aral Sea Region. The findings contributed for decision makers to formulating effective reasonable policies to protect surface water and use land of the Aral Sea Region. Meanwhile, the application of coupling degree model can provide a new method for studying the connection of independent systems in the farmland, water, environment and more. creator: Jiancong Shi creator: Qiaozhen Guo creator: Shuang Zhao creator: Yiting Su creator: Yanqing Shi uri: https://doi.org/10.7717/peerj.12920 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Shi et al. title: Clinical predictors and electrodiagnostic characteristics in patients with Guillain-Barré syndrome with respiratory failure: a retrospective, matched case-control study link: https://peerj.com/articles/12930 last-modified: 2022-02-10 description: BackgroundRespiratory failure is a common complication of Guillain-Barré syndrome (GBS). This study aimed to determine the clinical predictors and electrodiagnostic (EDx) characteristics in patients with Guillain-Barré syndrome (GBS) with respiratory failure.MethodsThe retrospective study included 29 confirmed GBS cases with respiratory failure and age- (±5 years) and sex-matched controls (1:1). The dependent t-test and McNemar–Bowker test were used to analyse the continuous and categorical data, respectively. In addition, a multiple logistic regression analysis was used to analyse the predictive factors for respiratory failure.ResultsAmong both cases and controls, the majority were male (72.4%), and the average age was 50.9 years. The data showed that patients with respiratory failure had higher GBS disability scores, lower motor power (≤3) of the hip flexors and ankle dorsiflexors, and experienced facial and bulbar palsy. In the multivariate analysis, the significant predictive factors were bulbar palsy (AOR 10.4 [95% CI [2.6–41.4]) and motor power of hip flexors ≤ 3 (AOR 31.4 [95% CI [3.1–314.5]). Patients with respiratory failure had lower compound muscle action potential amplitude of the ulnar and tibial nerves. The median, ulnar, and tibial nerve conduction studies were more likely to reflect inexcitability. The GBS subtypes in GBS patients with and without respiratory failure were not significantly different.ConclusionsBulbar palsy and motor power of the hip flexors ≤ 3 were significant predictors for respiratory failure. The GBS subtypes in patients with and without respiratory failure were not significantly different. creator: Kanchana Charoentanyarak creator: Apiradee Singjam creator: Jittima Saengsuwan uri: https://doi.org/10.7717/peerj.12930 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Charoentanyarak et al. title: Depletion of RIPK4 parallels higher malignancy potential in cutaneous squamous cell carcinoma link: https://peerj.com/articles/12932 last-modified: 2022-02-10 description: BackgroundThe RIPK4 (receptor-interacting protein kinase 4), a member of the RIPK family, acts as an important regulator of epidermal differentiation, cutaneous inflammation, and cutaneous wound repair. However, Until now, the role of RIPK4 in tumorigenesis remains elusive. There have been no studies exploring the effects of RIPK4 on the signaling pathway in cutaneous squamous cell carcinoma (SCC). It remains unknown whether RIPK4 expression, which can affect the degree of epidermal differentiation can also influence the radiosensitivity of skin SCC. It is urgent to fully elucidate the biological mechanism by which RIPK4 promotes carcinogenesis in skin SCC and determine whether RIPK4 expression levels predicts the sensitivity to radiotherapy in skin SCC. MethodsHuman skin SCC cell line, A431, was transfected with either small interfering RNAs (siRNAs) targeting RIPK4 (siR-RIPK4) or negative control siRNA (siR-NC). Western blotting was used to detect the expression of RIPK4 and Raf/MEK/ERK pathway-related proteins. The cells were irradiated using an X-ray irradiator at 6 MV with different radiation doses (0, 2, 6, and 10 Gy). Cell proliferation analysis, colony formation assay, transwell cell migration and invasion assay, cell cycle and apoptosis analysis were conducted to investigate the effect of RIPK4 silencing on skin SCC malignancy and radiosensitivity.ResultsRIPK4 protein expression was significantly decreased in the A431 cells transfected with siR-RIPK4, compared with the A431 cells transfected with siR-NC. RIPK4 silencing facilitated the proliferation, colony formation, migration, and invasion ability of A431 cell line, while cell cycle progression or cell apoptosis were not significantly influenced. In contrast with the previous literature, Raf/MEK/ERK pathway was not effected by RIPK4 knockdown in skin SCC. RIPK4 knockdown could not reverse the radiation resistance of A431 cells to irradiation in vitro.ConclusionsIn general, although depletion of RIPK4 cannot reverse the radiation resistance of A431 cells in vitro, it parallels higher malignancy potential in cutaneous SCC. To our knowledge, this is the first report of the effects of RIPK4 expression on the Raf/MEK/ERK signaling pathway and radiosensitivity in cutaneous SCC. The better understanding of the molecular mechanism of RIPK4 in cutaneous SCC may provide a promising biomarker for skin SCC prognosis and treatment. creator: Jing Xu creator: Dongping Wu creator: Bicheng Zhang creator: Chi Pan creator: Yinglu Guo creator: Qichun Wei uri: https://doi.org/10.7717/peerj.12932 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Xu et al. title: Genome-wide identification and expression analysis of serine hydroxymethyltransferase (SHMT) gene family in tomato (Solanum lycopersicum) link: https://peerj.com/articles/12943 last-modified: 2022-02-10 description: Serine hydroxymethyltransferase (SHMT) is one of the most important enzyme families in one-carbon metabolic pathway and photorespiration within plant cells. Recently studies reported the active roles of plant SHMTs in defending abiotic stresses. However, genome-scale analysis of SHMT in tomato is currently unknown. In this study, seven SHMT genes were identified in the tomato genome using a genome-wide search approach. In addition, their physicochemical properties, protein secondary structure, subcellular localization, gene structure, conserved motifs, phylogenetic and collinear relationships were analyzed. Our results demonstrated that tomato SHMT members were divided into two group and four subgroups, and they were conserved with the orthologs of other plants. Analysis of cis-acting elements showed that each of the SlSHMT genes contained different kinds of hormones and stress-related cis-acting elements in their promoter regions. Finally, qRT-PCR analysis indicated that SlSHMTs were expressed at different levels in different tissues, and they responded to UV, cold, heat, NaCl, H2O2, ABA and PEG treatments. These results provided definite evidence that SlSHMTs might involve in growth, development and stress responses in tomato, which laid a foundation for future functional studies of SlSHMTs. creator: Zesheng Liu creator: Xuejuan Pan creator: Chunlei Wang creator: Fahong Yun creator: Dengjing Huang creator: Yandong Yao creator: Rong Gao creator: Fujin Ye creator: Xingjuan Liu creator: Weibiao Liao uri: https://doi.org/10.7717/peerj.12943 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: A comparative study of bacterial diversity based on effects of three different shade shed types in the rhizosphere of Panax quiquefolium L. link: https://peerj.com/articles/12807 last-modified: 2022-02-09 description: BackgroundShading is an important factor affecting the cultivation of American ginseng, as it influences crop quality and yield. Rhizosphere microorganisms are also crucial for normal plant growth and development. However, whether different shade types significantly change American ginseng rhizosphere microorganisms is unknown.MethodsThis study evaluated the rhizosphere soils of American ginseng under traditional, high flag and high arch shade sheds. High-throughput 16S rRNA gene sequencing determined the change of rhizosphere bacterial communities.ResultsThe microbial diversity in rhizosphere soils of American ginseng significantly changed under different shading conditions. The bacteria diversity was more abundant in the high arch shade than flat and traditional shades. Different bacterial genera, including Bradyrhizobium, Rhizobium, Sphingomonas, Streptomyces and Nitrospira, showed significantly different abundances. Different shading conditions changed the microbial metabolic function in the American ginseng rhizosphere soils. The three types of shade sheds had specific enriched functional groups. The abundance of ATP-binding cassette (ABC) transporters consistently increased in the bacterial microbiota. These results help understand the influence of shading systems on the rhizosphere microecology of American ginseng, and contribute to the American ginseng cultivation. creator: Xianchang Wang creator: Xu Guo creator: Lijuan Hou creator: Jiaohong Zhang creator: Jing Hu creator: Feng Zhang creator: Jilei Mao creator: Zhifen Wang creator: Congjing Zhang creator: Jinlong Han creator: Yanwei Zhu creator: Chao Liu creator: Jinyue Sun creator: Chenggang Shan uri: https://doi.org/10.7717/peerj.12807 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Unraveling the hidden paleobiodiversity of the Middle Devonian (Emsian) crinoids (Crinoidea, Echinodermata) from Poland link: https://peerj.com/articles/12842 last-modified: 2022-02-09 description: Most previous publications on Devonian crinoids from the Holy Cross Mountains in Poland have concentrated on crinoid columns, and until now, little has been published about crinoid cups and calyxes. Herein, five crinoid taxa are described from an abundant occurrence of aboral cups and partial crowns from the Bukowa Góra Member (Emsian) in the Holy Cross Mountains of southern Poland. The following taxa are described: Bactrocrinites sp., Codiacrinus sevastopuloi sp. nov., Halocrinites geminatus (Bohatý, 2005), Halocrinites schlotheimiiSteininger, 1831, and a single brachial plate from a flexible crinoid placed in Flexibilia incertae sedis. Simple discoid holdfasts are also present encrusted to cylindrical stromatoporoids. These taxa are the first crinoids described from the remains of partial crowns from Emsian strata of Poland. creator: William I. Ausich creator: Mariusz A. Salamon creator: Bartosz J. Płachno creator: Tomasz Brachaniec creator: Wojciech Krawczyński creator: Andrzej Boczarowski creator: Karolina Paszcza creator: Magdalena Łukowiak creator: Przemysław Gorzelak uri: https://doi.org/10.7717/peerj.12842 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ausich et al.