Characterization of the complete chloroplast genome sequences of six Dalbergia species and its comparative analysis in the subfamily of Papilionoideae (Fabaceae)
Dalbergia spp. are numerous and widely distributed in pantropical areas in Asia, Africa and America, and most of the species have important economic and ecological value as precious timber. In this study, we determined and characterized six complete chloroplast genomes of Dalbergia species (Dalbergia obtusifolia, D. hupeana, D. mimosoides, D. sissoo, D. hancei, D. balansae), which displayed the typical quadripartite structure of angiosperms. The sizes of the genomes ranged from 155,698 bp (D. hancei) to 156,419 bp (D. obtusifolia). The complete chloroplast genomes of Dalbergia include 37 tRNA genes, eight rRNA genes and 84 protein-coding genes. We analysed the sequence diversity of Dalberigia chloroplast genomes coupled with previous reports. The results showed 12 noncoding regions (rps16-accD, trnR-UCU-trnG-UCC, ndhE-ndhG, trnG-UCC-psbZ, rps8-rpl14, trnP-UGG-psaJ, ndhH-rps15, trnQ-UUG-rps16, trnS-GCU-psbI, rps12-clpP, psbA-trnK-UUU, trnK-UUU-intron), and four coding regions (rps16, ycf1, rps15 and ndhF) showed many nucleotide variations that could be used as potential molecular markers. Based on a site-specific model, we analysed the selective pressure of chloroplast genes in Dalbergia species. Twenty-two genes with positively selected sites were detected, involving the photosynthetic system (ndhC, adhD, ndhF, petB, psaA, psaB, psbB, psbC, psbK and rbcL), self-replication category of genes (rpoA, rpoC2, rps3, rps12 and rps18) and others (accD, ccsA, cemA, clpP, matK, ycf1 and ycf2). Additionally, we identified potential RNA editing sites that were relatively conserved in the genus Dalbergia. Furthermore, the comparative analysis of cp genomes of Dalbergieae species indicated that the boundary of IRs/SSC was highly variable, which resulted in the size variation of cp genomes. Finally, phylogenetic analysis showed an inferred phylogenetic tree of Papilionoideae species with high bootstrap support and suggested that Amorpheae was the sister of the clade Dalbergieae. Moreover, three genera of the Pterocarpus clade showed a nested evolutionary relationship. These complete cp genomes provided valuable information for understanding the genetic variation and phylogenetic relationship of Dalbergia species with their relatives.
Li et al. (2022) Characterization of the complete chloroplast genome sequences of six Dalbergia species and its comparative analysis in the subfamily of Papilionoideae (Fabaceae). PeerJ 10:e13570 https://doi.org/10.7717/peerj.13570
Genome-wide identification and functional analysis of class III peroxidases in Gossypium hirsutum
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.
Chen et al. (2022) Genome-wide identification and functional analysis of class III peroxidases in Gossypium hirsutum. PeerJ 10:e13635 https://doi.org/10.7717/peerj.13635
Recent advances in methods for in situ root phenotyping
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.
Li et al. (2022) Recent advances in methods for in situ root phenotyping. PeerJ 10:e13638 https://doi.org/10.7717/peerj.13638
Genetic diversity of enterotoxigenic Bacillus cereus strains in coriander in southwestern Mexico
Background Coriander, 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. Methods Fresh 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. Results We 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.
Castulo-Arcos et al. (2022) Genetic diversity of enterotoxigenic Bacillus cereus strains in coriander in southwestern Mexico. PeerJ 10:e13667 https://doi.org/10.7717/peerj.13667
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
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.
Vitale et al. (2022) 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. PeerJ 10:e13677 https://doi.org/10.7717/peerj.13677
Spatial distribution of soil nutrients and evaluation of cultivated land in Xuwen county
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.
Spatial and Geographic Information Science
Zheng et al. (2022) Spatial distribution of soil nutrients and evaluation of cultivated land in Xuwen county. PeerJ 10:e13239 https://doi.org/10.7717/peerj.13239
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
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.
Wang et al. (2022) 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. PeerJ 10:e13568 https://doi.org/10.7717/peerj.13568
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
Background Multiple 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. Methodology A 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). Results Thirty 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. Conclusion These 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.
Mendez-Rebolledo et al. (2022) 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. PeerJ 10:e13589 https://doi.org/10.7717/peerj.13589
Thrombocytopenia and increased risk of adverse outcome in COVID-19 patients
Background Thrombocytopenia 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. Methods To 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. Results Thrombocytopenia 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. Conclusions Our 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.
Yuan et al. (2022) Thrombocytopenia and increased risk of adverse outcome in COVID-19 patients. PeerJ 10:e13608 https://doi.org/10.7717/peerj.13608
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
Background Regular 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 & Methods A 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. Results Analysis 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). Conclusion Increasing 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.
Huta-Osiecka et al. (2022) 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. PeerJ 10:e13643 https://doi.org/10.7717/peerj.13643