title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=688 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genome-wide identification and functional analysis of class III peroxidases in Gossypium hirsutum link: https://peerj.com/articles/13635 last-modified: 2022-07-01 description: Class III peroxidase (PRX) genes play essential roles in various processes, such as auxin catabolism, removal of H2O2, crosslinking cell wall components, and response to biotic and abiotic stresses. In this study, we identified 166, 78 and 89 PRX genes from G. hirsutum, G. arboretum and G. raimondii, respectively. These PRX genes were classified into seven subfamilies based on phylogenetic tree analysis and the classification of PRX genes in Arabidopsis. Segmental duplication and purifying selection were the major factors driving the evolution of GhPRXs. GO and KEGG enrichment analysis revealed that GhPRX genes were mainly associated with responding to oxidative stresses, peroxidase activities and phenylpropanoid biosynthesis pathways. Transcriptome data analysis showed that GhPRX genes expression were significantly different in microspore development between the sterility line-JinA and the maintainer line MB177. We confirmed the up-regulation of GhPRX107 and down-regulation of GhPRX128 in the sterile line compared to its maintainer line using qRT-PCR, suggesting their roles in pollen fertility. In addition, silencing GhPRX107 in cotton showed a significant decrease of the reactive oxygen species (ROS) levels of microsporocyte stage anthers compared to control. Overexpressing GhPRX107 in Arabidopsis significantly increased the ROS levels of anthers compared to wild type. In conclusion, we identified GhPRX107 as a determinant of ROS levels in anther. This work sets a foundation for PRX studies in pollen development. creator: Yi Chen creator: Jiajia Feng creator: Yunfang Qu creator: Jinlong Zhang creator: Li Zhang creator: Dong Liang creator: Yujie Yang creator: Jinling Huang uri: https://doi.org/10.7717/peerj.13635 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chen et al. title: Recent advances in methods for in situ root phenotyping link: https://peerj.com/articles/13638 last-modified: 2022-07-01 description: Roots assist plants in absorbing water and nutrients from soil. Thus, they are vital to the survival of nearly all land plants, considering that plants cannot move to seek optimal environmental conditions. Crop species with optimal root system are essential for future food security and key to improving agricultural productivity and sustainability. Root systems can be improved and bred to acquire soil resources efficiently and effectively. This can also reduce adverse environmental impacts by decreasing the need for fertilization and fresh water. Therefore, there is a need to improve and breed crop cultivars with favorable root system. However, the lack of high-throughput root phenotyping tools for characterizing root traits in situ is a barrier to breeding for root system improvement. In recent years, many breakthroughs in the measurement and analysis of roots in a root system have been made. Here, we describe the major advances in root image acquisition and analysis technologies and summarize the advantages and disadvantages of each method. Furthermore, we look forward to the future development direction and trend of root phenotyping methods. This review aims to aid researchers in choosing a more appropriate method for improving the root system. creator: Anchang Li creator: Lingxiao Zhu creator: Wenjun Xu creator: Liantao Liu creator: Guifa Teng uri: https://doi.org/10.7717/peerj.13638 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Li et al. title: Genetic diversity of enterotoxigenic Bacillus cereus strains in coriander in southwestern Mexico link: https://peerj.com/articles/13667 last-modified: 2022-07-01 description: BackgroundCoriander, like other leafy green vegetables, is available all year round and is commonly consumed raw in Mexico as in other countries in the preparation of street or homemade food. Bacillus cereus (B. cereus) is a microorganism that can reach coriander because it is usually found in the soil and in some regions the vegetables are irrigated with polluted water. Therefore, the aim of this study was to determinate the presence of B. cereus in coriander used for human consumption in southwestern Mexico and determine the toxigenic profile, biofilm production, genes associated with the production of biofilms, sporulation rates, enzymatic profile, psychotropic properties, and genetic diversity of B. cereus.MethodsFresh coriander samples were collected from several vegetable retailers in different markets, microbiological analysis was performed. Molecular identification, genes related to the production of biofilm, and toxin gene profiling of B. cereus isolates were determined by PCR. The biofilm formation was measured by performing a crystal violet assay. The genetic diversity of B. cereus strains was determined by PCR of repetitive elements using oligonucleotide (GTG) 5.ResultsWe found a frequency of B. cereus in vegetables was 20% (13/65). In this study, no strains with genes for the HBL toxin were found. In the case of genes related to biofilms, the frequency was low for sipW [5.8%, (1/17)] and tasA [11.7%, (2/17)]. B. cereus strains produce a low amount of biofilm with sporulation rates around 80%. As for genetic diversity, we observed that strains isolated from the same market, but different vegetable retailers are grouped into clusters. In the coriander marketed in southwestern Mexico, were found B. cereus strains with genes associated with the production of diarrheal toxins. Together, these results show actual information about the state of art of B. cereus strains circulating in the southwestern of Mexico. creator: Daniel Alexander Castulo-Arcos creator: Roberto Adame-Gómez creator: Natividad Castro-Alarcón creator: Aketzalli Galán-Luciano creator: María Cristina Santiago Dionisio creator: Marco A. Leyva-Vázquez creator: Jose-Humberto Perez-Olais creator: Jeiry Toribio-Jiménez creator: Arturo Ramirez-Peralta uri: https://doi.org/10.7717/peerj.13667 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Castulo-Arcos et al. title: Manipulation of light quality is an effective tool to regulate photosynthetic capacity and fruit antioxidant properties of Solanum lycopersicum L. cv. ‘Microtom’ in a controlled environment link: https://peerj.com/articles/13677 last-modified: 2022-07-01 description: Light quality plays an essential role in setting plant structural and functional traits, including antioxidant compounds. This paper aimed to assess how manipulating the light spectrum during growth may regulate the photosynthetic activity and fruit bioactive compound synthesis in Solanum lycopersicum L. cv. ‘Microtom’ to improve plant physiological performance and fruit nutritional value. Plants were cultivated under three light quality regimes: red-green-blue LEDs (RGB), red-blue LEDs (RB) and white fluorescent lamps (FL), from sowing to fruit ripening. Leaf functional traits, photosynthetic efficiency, Rubisco and D1 protein expression, and antioxidant production in fruits were analyzed. Compared to FL, RGB and RB regimes reduced height and increased leaf number and specific leaf area, enhancing plant dwarf growth. The RGB regime improved photosynthesis and stomatal conductance despite lower biomass, favoring Rubisco synthesis and carboxylation rate than RB and FL regimes. The RB light produced plants with fewer flowers and fruits with a lower ascorbic acid amount but the highest polyphenol content, antioxidant capacity and SOD and CAT activities. Our data indicate that the high percentage of the green wavelength in the RGB regime promoted photosynthesis and reduced plant reproductive capacity compared to FL and RB. Conversely, the RB regime was the best in favoring the production of health-promoting compounds in tomato berries. creator: Ermenegilda Vitale creator: Violeta Velikova creator: Tsonko Tsonev creator: Giulia Costanzo creator: Roberta Paradiso creator: Carmen Arena uri: https://doi.org/10.7717/peerj.13677 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Vitale et al. title: Spatial distribution of soil nutrients and evaluation of cultivated land in Xuwen county link: https://peerj.com/articles/13239 last-modified: 2022-06-30 description: It is of great significance to promote the quantitative research of soil science and the implementation of precision agriculture. On this basis, taking Xuwen County as the research object, this paper comprehensively analyzed the soil characteristics of cultivated land in Xuwen County and clarify the soil nutrient content and spatial distribution characteristics of cultivated land in Xuwen County, this paper comprehensively applied the methods of geostatistics, geographic information system (GIS) and fuzzy mathematics, and referred to the cultivated land quality grade standard (GB/T 33469-2016), to analyze the soil characteristics and evaluate the soil fertility of this region. The results show that the optimal interpolation model of soil pH and available phosphorus (AP) is a Gaussian model, and the optimal interpolation model of soil organic matter (SOM), available nitrogen (AN) and available potassium (AK) is a J-Bessel model. In addition, the spatial correlation of AK is weak, whereas pH, SOM, AN and AP show moderate spatial correlation. The proportion of excellent, good, average, medium and poor comprehensive fertility index are 26.00%, 32.67%, 19.33%, 19.00% and 3.00%, respectively. The overall level of soil fertility in Xuwen County is above the average, and the fertility quality presents an obvious trend of high in the South and low in the North. Areas that above average fertility are mainly distributed in Maichen Town, Qujie Town, Nanshan Town and Chengbei Town. The results can provide theoretical basis for improving the utilization rate of chemical fertilizer, fine management of cultivated land and ecological environment in this region, which can help in decision-making of precision fertilization. creator: Chao Zheng creator: Xiaofei Yang creator: Zhiqiang Liu creator: Kexing Liu creator: Yongxiang Huang uri: https://doi.org/10.7717/peerj.13239 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zheng et al. title: Soil organic carbon and nitrogen storage under a wheat (Triticum aestivum L.)—maize (Zea mays L.) cropping system in northern China was modified by nitrogen application rates link: https://peerj.com/articles/13568 last-modified: 2022-06-30 description: Field cultivation practices have changing the carbon and nitrogen cycles in farmland ecosystem, soil organic carbon (SOC) and total nitrogen (TN) were the important parameters in maintaining soil quality and increasing agricultural productivity, however, N application’s effects on the SOC and TN storage capacity under intensive wheat-maize cropping system remain unclear. Therefore, we investigated the characteristics and relationships of SOC and TN for wheat-maize cropping system under nitrogen treatments. In doing so, continuous applications of four nitrogen application rates were examined: 0, 180, 240 and 300 kg ha−1 (N0, N180, N240 and N300, respectively). Wheat yields under N180 and N240 were significantly higher than that under N300, while the maize yields under N180, N240 and N300 were significantly higher than that under N0 by 79.79, 85.23 and 86.85%, respectively; the TN content and storage were significantly higher under N240 than that under other N levels in 40–60 cm soil layer after wheat growing season; the SOC content and storage under N180 and N240 were significant higher than that under N300 in 20–40 cm after maize growing season. The correlations between SOC and TN contents (or storage) were stronger after wheat planting than maize planting. These findings provide a basis for further studies on the effect of long-term N application on SOC and TN storage, crop quality and nitrogen use efficiency under wheat-maize cropping systems. creator: Lifang Wang creator: Shijie Liu creator: Geng Ma creator: Chenyang Wang creator: Jutao Sun uri: https://doi.org/10.7717/peerj.13568 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Electromyographic analysis of the serratus anterior and upper trapezius in closed kinetic chain exercises performed on different unstable support surfaces: a systematic review and meta-analysis link: https://peerj.com/articles/13589 last-modified: 2022-06-30 description: BackgroundMultiple investigations have compared the electromyographic (EMG) activity of the scapular muscles between stable and unstable support surfaces during the execution of closed kinetic chain exercises. However, these comparative analyses have grouped different unstable surfaces (wobble board, BOSU, therapeutic ball, and suspension equipment) into a single data pool, without considering the possible differences in neuromuscular demand induced by each unstable support surface. This study aimed to analyze the individual effect of different unstable support surfaces compared to a stable support surface on scapular muscles EMG activity during the execution of closed kinetic chain exercises.MethodologyA literature search was conducted of the Pubmed Central, ScienceDirect and SPORTDiscus databases. Studies which investigated scapular muscles EMG during push-ups and compared at least two support surfaces were included. The risk of bias of included articles was assessed using a standardized quality assessment form for descriptive, observational and EMG studies, and the certainty of the evidence was measured with the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach. A random-effects model was used to calculate effect sizes (ES, Hedge’s g).ResultsThirty studies were selected in the systematic review. Of these, twenty-three low-to-high quality studies (498 participants) were included in the meta-analysis. The main analyzes revealed, in decreasing order, greater UT EMG activity during push-ups performed on suspension equipment (ES = 2.92; p = 0.004), therapeutic ball (ES = 1.03; p < 0.001) and wobble board (ES = 0.33; p = 0.003); without effect on the BOSU ball. In addition, no effect was observed for SA on any unstable device. The certainty of the evidence ranged from low to very low due to the inclusion of descriptive studies, as well as high imprecision, inconsistency, and risk of publication bias.ConclusionThese findings could be applied in scapular muscles strengthening in healthy individuals. The use of suspension equipment achieves higher UT activation levels. Conversely, the use of any type of unstable devices to increase the activation levels of the SA in shoulder musculoskeletal dysfunctions is not recommended. These conclusions should be interpreted with caution as the available evidence showed a low to very low certainty of evidence, downgraded mostly by inconsistency and imprecision. creator: Guillermo Mendez-Rebolledo creator: Ignacio Orozco-Chavez creator: Juan Morales-Verdugo creator: Rodrigo Ramirez-Campillo creator: Ann M.J. Cools uri: https://doi.org/10.7717/peerj.13589 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Mendez-Rebolledo et al. title: Thrombocytopenia and increased risk of adverse outcome in COVID-19 patients link: https://peerj.com/articles/13608 last-modified: 2022-06-30 description: BackgroundThrombocytopenia was common in the coronavirus disease 2019 (COVID-19) patients during the infection, while the role of thrombocytopenia in COVID-19 pathogenesis and its relationship with systemic host response remained obscure. The study aimed to systematically evaluate the relationship between thrombocytopenia in COVID-19 patients and clinical, haematological and biochemical markers of the disease as well as adverse outcomes.MethodsTo assess the relationship between abnormal platelet levels and disease progression, a multi-center retrospective cohort study was conducted. COVID-19 patients with thrombocytopenia and a sub-cohort of matched patients without thrombocytopenia were compared for their clinical manifestations, haematological disorders, biochemical parameters, inflammatory markers and clinical outcome.ResultsThrombocytopenia was present in 127 of 2,209 analyzed patients on admission. Compared with the control group, thrombocytopenia patients developed significantly higher frequency of respiratory failure (41.9% vs. 22.6%, P = 0.020), intensive care unit entrance (25.6% vs. 11.5%, P = 0.012), disseminated intravascular coagulation (45.2% vs. 10.6%, P < 0.001), more altered platelet morphology indexes and coagulation perturbation, higher levels of inflammatory markers. In addition, a significantly increased all-cause mortality (hazard ratio 3.08, 95% confidence interval 2.26–4.18, P < 0.001) was also observed in the patients with thrombocytopenia. Late development of thrombocytopenia beyond 14 days post-symptom was observed in 61 patients, from whom a comparable mortality rate yet longer duration to death was observed compared to those with early thrombocytopenia.ConclusionsOur finding from this study adds to previous evidence that thrombocytopenia is associated with adverse outcome of the disease and recommend that platelet count and indices be included alongside other haematological, biochemical and inflammatory markers in COVID-19 patients’ assessment during the hospital stay. creator: Yang Yuan creator: Gang Wang creator: Xi Chen creator: Xiao-Lei Ye creator: Xiao-Kun Li creator: Rui Li creator: Wan-Li Jiang creator: Hao-Long Zeng creator: Juan Du creator: Xiao-Ai Zhang creator: Hao Li creator: Li-Qun Fang creator: Qing-Bin Lu creator: Wei Liu uri: https://doi.org/10.7717/peerj.13608 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yuan et al. title: Influence of Nordic walking with poles with an integrated resistance shock absorber on carbohydrate and lipid metabolic indices and white blood cell subpopulations in postmenopausal women link: https://peerj.com/articles/13643 last-modified: 2022-06-30 description: BackgroundRegular and individualised physical activities have been shown to prevent adverse changes associated with the aging process. The main purpose of this study was to evaluate changes in carbohydrate and lipid metabolism and white blood cell (WBC) subpopulations in postmenopausal women participating in Nordic walking (NW) training and to compare the use of poles with an integrated resistance shock absorber (RSA) with the use of classic poles.Materials & MethodsA total of 23 postmenopausal women participated in a 8-week programme of systematic physical activity between February and April. Before and after the training programme, somatic features and serum concentrations of 25-hydroxyvitamin D, glucose, and insulin, were assessed, as well as lipid profile and WBC count and its specific subpopulations.ResultsAnalysis of differences in somatic features and biochemical indices before and after training in the group of women who used RSA poles showed significant decreases in fat mass content (p < 0.05), insulin (p < 0.05), homeostatic model assessment of insulin resistance (p < 0.05), triglycerides (p < 0.05), total cholesterol (p < 0.05) and monocytes (p ≤ 0.01). In the group of women who used classic poles (NW), there was a significant decrease in WBC (p ≤ 0.01), lymphocytes (p < 0.05), monocytes (p ≤ 0.01) and granulocytes (p < 0.05).ConclusionIncreasing the training load through the use of RSA poles resulted in greater changes in carbohydrate and lipid metabolic indices compared to the use of classic NW poles. In turn, the more significant effect on WBC and its specific subpopulations count in the NW, compared to the RSA training programme, may indicate that specificity of training load is an important factor in modifying the immune system response. creator: Anna Huta-Osiecka creator: Krystian Wochna creator: Rafał Stemplewski creator: Katarzyna Marciniak creator: Tomasz Podgórski creator: Zbigniew Kasprzak creator: Piotr Leszczyński creator: Alicja Nowak uri: https://doi.org/10.7717/peerj.13643 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Huta-Osiecka et al. title: Taxonomic and functional nematode diversity in Maldivian coral degradation zones: patterns across reef typologies and depths link: https://peerj.com/articles/13644 last-modified: 2022-06-30 description: The intensification of dredging and infilling activities in lagoons and on coral reefs are common practices in the Maldivian archipelago, and these activities alter the biodiversity of the bioconstructors and the functioning of the ecosystem. The alteration of environmental factors can also affect inconspicuous fauna, such as free-living nematodes. The implications of a reduction in biodiversity may transcend decreased taxonomic diversity, resulting in changes in functional diversity and redundancy; however, how the environmental conditions and human pressure affects the functionality of nematodes in Maldivian coral degradation zones (CDZs) remain poorly understood. In this paper, we examined changes in the taxonomic and functional diversity and the functional redundancy in nematode communities regarding the geographic location (atolls with various levels of human pressure), the exposure and topography of the reef (lagoon and ocean), the slope of the reef, and the depth. The functional diversity and redundancy were evaluated by considering two main biological traits of nematodes: i) the trophic strategy, and ii) the life strategy. The extremely high number of nematode genera observed in the Maldives is supported by the high complexity of the carbonate sediments. The reef exposure and depth were the most relevant environmental factors that influenced the taxonomic and functional diversity. The functional diversity, according to the trophic strategies, mirrored the taxonomic diversity because the adaptive plasticity of nematode buccal cavity structures is closely associated with the high biodiversity of the phylum. The high abundance of k-strategists in ocean reefs may indicate a higher ecological quality when compared to lagoon reefs; however, the absence of significant differences in life strategy functional diversity and functional redundancy indicates that a recovery process is underway. Analyses of nematode communities should be combined with standard investigations of reef bioconstructors during monitoring activities to assess the vulnerability of CDZ systems to future disturbances and facilitate the adoption of the most appropriate preventative actions. creator: Eleonora Grassi creator: Monica Montefalcone creator: Lucia Cesaroni creator: Loretta Guidi creator: Maria Balsamo creator: Federica Semprucci uri: https://doi.org/10.7717/peerj.13644 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Grassi et al.