Genome-wide analysis of the CalS gene family in cotton reveals their potential roles in fiber development and responses to stress
Callose deposition occurs during plant growth and development, as well as when plants are under biotic and abiotic stress. Callose synthase is a key enzyme for the synthesis of callose. In this study, 27, 28, 16, and 15 callose synthase family members were identified in Gossypium hirsutum, Gossypium barbadense, Gossypium raimondii, and Gossypium arboreum using the sequence of Arabidopsis callose synthase. The CalSs were divided into five groups by phylogenetic, gene structure, and conservative motif analysis. The conserved motifs and gene structures of CalSs in each group were highly similar. Based on the analysis of cis-acting elements, it is inferred that GhCalSs were regulated by abiotic stress. WGD/Segmental duplication promoted the amplification of the CalS gene in cotton, and purification selection had an important function in the CalS family. The transcriptome data and qRT-PCR under cold, heat, salt, and PEG treatments showed that GhCalSs were involved in abiotic stress. The expression patterns of GhCalSs were different in various tissues. We predicted that GhCalS4, which was highly expressed in fibers, had an important effect on fiber elongation. Hence, these results help us understand the role of GhCalSs in fiber development and stress response.
Feng et al. (2021) Genome-wide analysis of the CalS gene family in cotton reveals their potential roles in fiber development and responses to stress. PeerJ 9:e12557 https://doi.org/10.7717/peerj.12557
FEM: mining biological meaning from cell level in single-cell RNA sequencing data
Background One goal of expression data analysis is to discover the biological significance or function of genes that are differentially expressed. Gene Set Enrichment (GSE) analysis is one of the main tools for function mining that has been widely used. However, every gene expressed in a cell is valuable information for GSE for single-cell RNA sequencing (scRNA-SEQ) data and not should be discarded. Methods We developed the functional expression matrix (FEM) algorithm to utilize the information from all expressed genes. The algorithm converts the gene expression matrix (GEM) into a FEM. The FEM algorithm can provide insight on the biological significance of a single cell. It can also integrate with GEM for downstream analysis. Results We found that FEM performed well with cell clustering and cell-type specific function annotation in three datasets (peripheral blood mononuclear cells, human liver, and human pancreas).
Liu et al. (2021) FEM: mining biological meaning from cell level in single-cell RNA sequencing data. PeerJ 9:e12570 https://doi.org/10.7717/peerj.12570
The gut microbiota of wild wintering great bustard (Otis tarda dybowskii): survey data from two consecutive years
Background The composition of the intestinal microbiota plays a significant role in modulating host health. It serves as a sensitive evaluation indicator and has substantial implications in protecting endangered species. Great Bustards are typical farmland-dependent wintering birds that are highly susceptible to the interference of human activities. However, information regarding their gut microbiota remains scarce. Methods To ensure a comprehensive analysis of this crucial data, we collected fecal samples from wild Great Bustards at their wintering habitat for two consecutive years. High-throughput sequencing of the 16S rRNA gene was subsequently applied to characterize their core gut microbiota and determine whether the gut microbial composition was similar or varied interannually. Results The gut microbiota of the Great Bustard was primarily comprised of four phyla: Firmicutes (82.87%), Bacteroidetes (7.98%), Proteobacteria (4.49%), and Actinobacteria (3.67%), accounting for 99.01% of the microbial community in all samples. Further analysis revealed 22 genera of core microbes and several pathogens. Notably, there were no significant differences in the alpha-diversity and beta-diversity between the two sample groups from different years. Conclusions This study provides essential information for assessing the health and developing targeted protective measures of this threatened species.
Lu et al. (2021) The gut microbiota of wild wintering great bustard (Otis tarda dybowskii): survey data from two consecutive years. PeerJ 9:e12562 https://doi.org/10.7717/peerj.12562
Lyophilized cell-free supernatants of Lactobacillus isolates exhibited antibiofilm, antioxidant, and reduces nitric oxide activity in lipopolysaccharide-stimulated RAW 264.7 cells
Background Probiotics can release bioactive substances known as postbiotics, which can inhibit pathogenic microorganisms, improve immunomodulation, reduce antioxidant production, and modulate the gut microbiota. Methods In this study, we evaluated the in vitro antimicrobial effects, antioxidant activity, and anti-inflammatory potential of 10 lyophilized cell-free supernatants (LCFS) of Lactobacillus isolates. LCFS was obtained via centrifugation and subsequent lyophilization of the supernatant collected from the culture medium ofeach isolate. The antibacterial and antibiofilm activities of the LCFS were determined using broth microdilution. The antioxidant potential was evaluated by measuring the total phenolic and flavonoid contents and 2,2-Diphennyl-1-picrylhydrazyl (DPPH) and 2,2’-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) radical cation (ABTS+) radical scavenging activities. Results All the isolates were able to inhibit the four tested pathogens. The isolates exhibited strong antibiofilm activity and eradicated the biofilms formed by Acinetobacter buamannii and Escherichia coli. All the prepared Lactobacillus LCFS contained phenols and flavonoids and exhibited antioxidant activities in the DPPH and ABTS+ radical scavenging assays. The MTT (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide) assay revealed that LCFS was not cytotoxic to RAW 264.7 cells. In addition, the ten Lactobacillus LCFS decreased the production of nitric oxide. Conclusions All the isolates have beneficial properties. This research sheds light on the role of postbiotics in functional fermented foods and pharmaceutical products. Further research to elucidate the precise molecular mechanisms of action of probiotics is warranted.
Sornsenee et al. (2021) Lyophilized cell-free supernatants of Lactobacillus isolates exhibited antibiofilm, antioxidant, and reduces nitric oxide activity in lipopolysaccharide-stimulated RAW 264.7 cells. PeerJ 9:e12586 https://doi.org/10.7717/peerj.12586
Influence of soil amendment of different concentrations of amino acid water-soluble fertilizer on physiological characteristics, yield and quality of “Hangjiao No.2” Chili Pepper
Amino acids are well known as natural stimulators of plant growth and are widely used to promote crop yield and quality. Several studies have been conducted to investigate the effects of amino acid (s) as a foliar spray on a variety of plant species. However, the effects of soil amendment of different concentrations of amino acid water-soluble fertilizer on the physiological characteristics, yield, and quality of pepper remain unclear. Following this, three experimental sets of amino acid water-soluble fertilizer in the ratio 1.8: 2.7: 3.6 kg including control (CK) were conducted in Lintao county, Gansu province. The treatments were applied through furrow method at 6 weeks after planting. The results showed that physiological characteristics of the pepper plants, such as chlorophyll a (1.35 mg g−1), and b (0.67 mg g−1), total chlorophyll (2.02 mg g−1), carotenoid (0.63 mg g−1), ETR (26.25 µmol m−2s−1), Fv/Fm (0.75), Qp (0.92) contents of the leaves were increased by the 1.8 kg treatment while NPQ (71.37%) and root activity (2185.52 µg g−1 h−1) were improved by the 3.6 kg treatment compared to the control. Fertilization with 2.7 kg of amino acid water-soluble fertilizer also had a significant influence on fruit length (25.50 cm), and yield of pepper (37.92 t ha−1) while fruit diameter (24.51 mm), firmness (5.30 kg cm−2), fresh (48.10 g) and dry (4.71 g) weights were higher in the 1.8 kg treatment compared to the control. The lowest rate of fertilizer (1.8 kg) applied again resulted in a significant increase in soluble protein (79.79%), capsaicin (5.80 mg g−1), dihydrocapsaicin (1.08 mg g−1), vitamin C (72.33%) and the essential and non-essential amino acid contents of the pepper which ranged from (235.15 to 11.16 µg g−1) and (1,605.10 to 16.63 µg g−1) respectively, while soluble sugar (9.02%) was enhanced by 3.6 kg treatment compared to the control. The findings suggest that soil amendment with low concentration of amino acid water-soluble fertilizer (1.8 kg) could be successfully used to improve the physiological characteristics and fruit quality of peppers in vegetable production.
Bakpa et al. (2021) Influence of soil amendment of different concentrations of amino acid water-soluble fertilizer on physiological characteristics, yield and quality of “Hangjiao No.2” Chili Pepper. PeerJ 9:e12472 https://doi.org/10.7717/peerj.12472
Effects of nitrogen topdressing and paclobutrazol at different stages on spike differentiation and yield of winter wheat
Background Optimal nitrogen (N) application and plant growth regulators can improve wheat productivity. This can help to improve yield level and ensure food security with limited resources in the Huang-Huai-Hai Plain of China (HPC). Methods A 2-year field experiment was conducted using a randomized block design with four treatments (TS-N topdressing at pseudostem erection stage ; TPS-N topdressing combined with paclobutrazol application at pseudostem erection stage; TJ-N topdressing at jointing stage; TPJ-N topdressing at combined with paclobutrazol application at jointing stage) in 2011–2013. Results The grain number per ear, thousand kernel weight and yield for the TJ and TPJ treatments were higher than those of the TS and TPS treatments. Grain number per ear, yield, and thousands kernel weigh for the TPJ treatment were significantly higher than for the TS and TPS in 2011–2012 (9.82% and 7.27%, 10.23% and 8.99%, 6.12% and 5.58%) and in 2012–2013 (10.21% and 11.55%, 8.00% and 6.58%, 0.00 and 0.00), respectively. Thousands kernel weight under TJ were significantly higher than those under TS and TPS by 13.21% and 14.03%, respectively in 2012–2013. The floret number, significantly correlated with cytokinin content, was also significantly increased under TJ and TPJ at connectivum differentiation stage. For TPJ treatment, the floret number was significantly higher than for the TS, TPS, and TJ by 19.92%, 10.21%, 6.10% in 2011–2012; it was higher than for the TS and TPS by 28.06% and 29.61% in 2012–2013, respectively. The relative expression level of cytokinin oxidase/dehydrogenase gene (TaCKX2.2) was improved during flowering, when cytokinin content was at high level and was also inhibited by paclobutrazol with different degrees. Conclusions Therefore, nitrogen topdressing at jointing stage had increased grain number per ear, thousand kernel weight, and grain yield of wheat. Paclobutrazol could delay spike differentiation and promote cytokinin accumulation that induced expression of TaCKX2.2, maintaining hormonal balance and affecting wheat spike morphogenesis.
Li et al. (2021) Effects of nitrogen topdressing and paclobutrazol at different stages on spike differentiation and yield of winter wheat. PeerJ 9:e12473 https://doi.org/10.7717/peerj.12473
Probabilistic risk assessment and water quality index of a tropical delta river
Water plays a major role in supporting the wellness and life processes in living things as well as in the ecological structure’s stabilities. However, several environmental scientists have recounted the alarming menace unfit water quality portends as well as the shortfalls of its global utilization in various spheres of life. This study aims to determine the fitness of the Ossiomo River and its likely health risk impact when consumed or used for other domestic purposes. The outcome of the physicochemical and heavy metal characterization showed that most of the parameters surpassed the slated benchmarks. Findings from the study revealed a significant difference (p < 0.05) for water temperature, color, TDS, BOD5, HCO3, Na, Fe, Mn, and THC across the four stations respectively. Meanwhile, pH, salinity, turbidity, TSS, DO, Cl, P, NH4H, NO2, NO3, SO4, Zn, Cu, Cr, Ni, Pb, and V showed no significant (p > 0.05) across the four stations respectively. The pH level of the water was slightly acidic at the range of 4.40–6.82. The outcome of the computed water quality index showed that station 1 (66.38) was poor for human ingestion which was above the set slated benchmarks of 26–50. However, stations 2–4 (163.79, 161.79, and 129.95) were unsuitable for drinking which was above the set slated benchmarks of 100. The outcome of the health risk evaluation revealed that the hazard quotients (HQs) were considered greater than 1 (>1) for Cr (2.55). The hazard index (0.46) via the dermal pathway was <1 while the ingestion (4.35) pathway was >1. The sum of the HQs (4.81) was also > 1. Thus, there are possible non-carcinogenic health risks via direct ingestion of the water. The outcome from the carcinogenic risk for Pb, Cr, and Cd (6 × 10–3, 4.00 × 10–1, and 1.22 × 100), was somewhat greater than the target goal (1.0 × 10–6 to 1.0 × 10–4) of carcinogenic risks stipulated by the United States Environmental Protection Agency for drinking water, respectively, especially for Cd. There might be a potential carcinogenic risk if the water is consumed when the metal contents are higher than the target limits set. Sustainable farming and treatment of wastes from industrial outputs should be the main management of this watercourse.
Environmental Contamination and Remediation
Anani et al. (2021) Probabilistic risk assessment and water quality index of a tropical delta river. PeerJ 9:e12487 https://doi.org/10.7717/peerj.12487
Molecular identification and diversity of adult arthropod carrion community collected from pig and sheep carcasses within the same locality during different stages of decomposition in the KwaZulu-Natal province of South Africa
The current study aimed at molecular identification and comparing the diversity of arthropods communities between pig and sheep carcasses during the cold and warm season in KwaZulu-Natal province of South Africa. Adult arthropods found on and around the carcasses were collected using either fly traps or forceps. Molecular analyses confirmed the identification of twelve arthropod species collected from both sheep and pig carcasses during the cold season. Results showed that 11 of 12 arthropod species were common in both sheep and pig carcasses, with exception to Onthophagus vacca (Coleoptera: Scarabaeidae) (Linnaeus, 1767) and Atherigona soccata (Diptera: Muscidae) (Rondani, 1871) species which were unique to sheep and pig carcasses respectively. However, during the warm season, the sheep carcass attracted more arthropod (n = 13) species as compared to the pig carcass. The difference in the obtained arthropod was due to the presence of O. vacca which was also unique to the sheep carcass during this season. Furthermore, there was an addition of a beetle species Hycleus lunatus (Coleoptera: Meloidae) (Pallas, 1782), which was collected from both sheep and pig carcasses but unique to the warm season. The pig carcass attracted more dipteran flies during both warm (n = 1,519) and cold season (n = 779) as compared to sheep carcass during the warm (n = 511) and cold season (n = 229). In contrast, coleopterans were more abundant on the sheep carcass during the warm season (n = 391) and cold season (n = 135) as compared to the pig carcass in both warm season (n = 261) and cold season (n = 114). In overall, more flies and beetles were collected on both sheep and pig carcasses during the warm season, and this further highlight that temperature influenced the observed difference in the abundance of collected arthropod between seasons.
Tembe et al. (2021) Molecular identification and diversity of adult arthropod carrion community collected from pig and sheep carcasses within the same locality during different stages of decomposition in the KwaZulu-Natal province of South Africa. PeerJ 9:e12500 https://doi.org/10.7717/peerj.12500
Detection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice
Background The panicle is the most important organ in rice, and all the panicle-related traits are correlated with rice grain yield. Understanding the underlying genetic mechanisms controlling panicle development is very important for improving rice production. Methods Nine panicle-related traits including heading date, panicle length, number of primary branches, number of secondary branches, number of grains per panicle, number of panicles per plant, number of filled grains per plant, seed-setting rate, and grain yield per plant were investigated. To map the quantitative trait loci (QTLs) for the nine panicle-related traits, a PCR-based genetic map with 208 markers (including 121 simple sequence repeats and 87 InDels) and a high-density linkage map with 18,194 single nucleotide polymorphism (SNP) markers were both used. Results Using a recombinant inbred line population derived from an indica variety Huanghuazhan and a japonica line Jizi 1560, a total of 110 and 112 QTLs were detected for panicle-related traits by PCR-based genetic map and by high-density linkage map, respectively. Most of the QTLs were clustered on chromosomes 1, 2, 3, 6, and 7 while no QTLs were detected on chromosome 10. Almost all the QTLs with LOD values of more than 5.0 were repeatedly detected, indicating the accuracy of the two methods and the stability of the QTL effects. No genes for panicle-related traits have been previously reported in most of these regions. QTLs found in JD1006–JD1007 and RM1148–RM5556 with high LOD and additive values deserved further research. The results of this study are beneficial for marker-assisted breeding and provide research foundation for further fine-mapping and cloning of these QTLs for panicle-related traits.
Li et al. (2021) Detection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice. PeerJ 9:e12504 https://doi.org/10.7717/peerj.12504
Does long-term fire suppression impact leaf litter breakdown and aquatic invertebrate colonization in pine flatwoods wetlands?
Ephemeral wetlands are commonly embedded within pine uplands of the southeastern United States. These wetlands support diverse communities but have often been degraded by a lack of growing-season fires that historically maintained the vegetation structure. In the absence of fire, wetlands develop a dense mid-story of woody vegetation that increases canopy cover and decreases the amount of herbaceous vegetation. To understand how reduced fire frequency impacts wetland processes, we measured leaf litter breakdown rates and invertebrate communities using three common plant species (Longleaf Pine (Pinus palustris), Pineland Threeawn Grass (Aristida stricta), and Black Gum (Nyssa sylvatica)) that occur in pine flatwoods wetlands located on Eglin Air Force Base, Florida. We also tested whether or not the overall habitat type within a wetland (fire maintained or fire suppressed) affected these processes. We placed leaf packs containing 15.0 g of dried leaf litter from each species in both fire-maintained and fire-suppressed sections of three wetlands, removing them after 103–104 days submerged in the wetland. The amount of leaf litter remaining at the end of the study varied across species (N. sylvatica = 7.97 ± 0.17 g, A. stricta = 11.84 ± 0.06 g, and P. palustris = 11.37 ± 0.07 g (mean ± SE)) and was greater in fire-maintained habitat (leaf type: F2,45 = 437.2, P < 0.001; habitat type: F1,45 = 4.6, P = 0.037). We identified an average of 260 ± 33.5 (SE) invertebrates per leaf pack (range: 19–1,283), and the most abundant taxonomic groups were Cladocera, Isopoda, Acariformes, and Diptera. Invertebrate relative abundance varied significantly among litter species (approximately 39.9 ± 9.4 invertebrates per gram of leaf litter remaining in N. sylvatica leaf packs, 27.2 ± 5.3 invertebrates per gram of A. stricta, and 14.6 ± 3.1 invertebrates per gram of P. palustris (mean ± SE)) but not habitat type. However, both habitat (pseudo-F1,49 = 4.30, P = 0.003) and leaf litter type (pseudo-F2,49 = 3.62, P = 0.001) had a significant effect on invertebrate community composition. Finally, this work was part of ongoing projects focusing on the conservation of the critically imperiled Reticulated Flatwoods Salamander (Ambystoma bishopi), which breeds exclusively in pine flatwoods wetlands, and we examined the results as they relate to potential prey items for larval flatwoods salamanders. Overall, our results suggest that the vegetation changes associated with a lack of growing-season fires can impact both invertebrate communities and leaf litter breakdown.
Chandler et al. (2021) Does long-term fire suppression impact leaf litter breakdown and aquatic invertebrate colonization in pine flatwoods wetlands?. PeerJ 9:e12534 https://doi.org/10.7717/peerj.12534