Sequence and structure analyses of lytic polysaccharide monooxygenases mined from metagenomic DNA of humus samples around white-rot fungi in Cuc Phuong tropical forest, Vietnam
Background White-rot fungi and bacteria communities are unique ecosystems with different types of symbiotic interactions occurring during wood decomposition, such as cooperation, mutualism, nutritional competition, and antagonism. The role of chitin-active lytic polysaccharide monooxygenases (LPMOs) in these symbiotic interactions is the subject of this study. Method In this study, bioinformatics tools were used to analyze the sequence and structure of putative LPMOs mined by hidden Markov model (HMM) profiles from the bacterial metagenomic DNA database of collected humus samples around white-rot fungi in Cuc Phuong primary forest, Vietnam. Two genes encoding putative LPMOs were expressed in E. coli and purified for enzyme activity assay. Result Thirty-one full-length proteins annotated as putative LPMOs according to HMM profiles were confirmed by amino acid sequence comparison. The comparison results showed that although the amino acid sequences of the proteins were very different, they shared nine conserved amino acids, including two histidine and one phenylalanine that characterize the H1-Hx-Yz motif of the active site of bacterial LPMOs. Structural analysis of these proteins revealed that they are multidomain proteins with different functions. Prediction of the catalytic domain 3-D structure of these putative LPMOs using Alphafold2 showed that their spatial structures were very similar in shape, although their protein sequences were very different. The results of testing the activity of proteins GL0247266 and GL0183513 show that they are chitin-active LPMOs. Prediction of the 3-D structures of these two LPMOs using Alphafold2 showed that GL0247266 had five functional domains, while GL0183513 had four functional domains, two of which that were similar to the GbpA_2 and GbpA_3 domains of protein GbpA of Vibrio cholerae bacteria. The GbpA_2 - GbpA_3 complex was also detected in 11 other proteins. Based on the structural characteristics of functional domains, it is possible to hypothesize the role of chitin-active GbpA-like LPMOs in the relationship between fungal and bacterial communities coexisting on decomposing trees in primary forests.
Truong et al. (2024) Sequence and structure analyses of lytic polysaccharide monooxygenases mined from metagenomic DNA of humus samples around white-rot fungi in Cuc Phuong tropical forest, Vietnam. PeerJ 12:e17553 https://doi.org/10.7717/peerj.17553
Population structure and diversification of Gymnospermium kiangnanense, a plant species with extremely small populations endemic to eastern China
Background Gymnospermium kiangnanense is the only species distributed in the subtropical region within the spring ephemeral genus Gymnospermium. Extensive human exploitation and habitat destruction have resulted in a rapid shrink of G. kiangnanense populations. This study utilizes microsatellite markers to analyze the genetic diversity and structure and to deduce historical population events of extant populations of G. kiangnanense. Methods A total of 143 individuals from eight extant populations of G. kiangnanense, including two populations from Anhui Province and six populations from Zhejiang Province, were analyzed with using 21 pairs of microsatellite markers. Genetic diversity indices were calculated using Cervus, GENEPOP, GenALEX. Population structure was assessed using genetic distance (UPGMA), principal coordinate analysis (PCoA), Bayesian clustering method (STRUCTURE), and molecular variation analysis of variance (AMOVA). Population history events were inferred using DIYABC. Results The studied populations of G. kiangnanense exhibited a low level of genetic diversity (He = 0.179, I = 0.286), but a high degree of genetic differentiation (FST = 0.521). The mean value of gene flow (Nm) among populations was 1.082, indicating prevalent gene exchange via pollen dispersal. Phylogeographic analyses suggested that the populations of G. kiangnanense were divided into two lineages, Zhejiang (ZJ) and Anhui (AH). These two lineages were separated by the Huangshan-Tianmu Mountain Range. AMOVA analysis revealed that 36.59% of total genetic variation occurred between the two groups. The ZJ lineage was further divided into the Hangzhou (ZJH) and Zhuji (ZJZ) lineages, separated by the Longmen Mountain and Fuchun River. DIYABC analyses suggested that the ZJ and AH lineages were separated at 5.592 ka, likely due to the impact of Holocene climate change and human activities. Subsequently, the ZJZ lineage diverged from the ZJH lineage around 2.112 ka. Given the limited distribution of G. kiangnanense and the significant genetic differentiation among its lineages, both in-situ and ex-situ conservation strategies should be implemented to protect the germplasm resources of G. kiangnanense.
Liu et al. (2024) Population structure and diversification of Gymnospermium kiangnanense, a plant species with extremely small populations endemic to eastern China. PeerJ 12:e17554 https://doi.org/10.7717/peerj.17554
Sex difference in the association between triglyceride and intracerebral bleeding risk after intravenous thrombolysis for acute ischemic stroke, a multi-center retrospective study
Background Whether the relationship of intracerebral bleeding risk with lipid profile may vary by sex remains unclear. This study aims to investigate potential sex differences in the association between lipid profile and the risk of symptomatic intracerebral hemorrhage (sICH) in patients with acute ischemic stroke (AIS) who received intravenous thrombolysis using recombinant tissue plasminogen activator (r-tPA). Methods This multicenter retrospective observational study analyzed patients with AIS treated with intravenous r-tPA. sICH was defined as a worsening of 4 or higher points in the National Institutes of Health Stroke Scale (NIHSS) score within 36 hours after intravenous thrombolysis in any hemorrhage subtype. We assessed the odds ratio (OR) with 95% confidence interval (CI) of lipid profile for sICH for each sex using logistic regression models adjusted for potential confounding factors. Results Of 957 participants (median age 68 (interquartile range, 59–75), men 628 (65.6%)), 56 sICH events (36 (5.7%) in men and 20 (6.1%) in women) were observed. The risk of sICH in men decreased with increasing serum levels of triglyceride after adjustment for confounding factors (vs lowest tertile, medium tertile OR 0.39, 95% CI [0.17–0.91], top tertile OR 0.33, 95% CI [0.13–0.84], overall p = 0.021; per point increase, adjusted OR 0.29, 95% CI [0.13–0.63], p = 0.002). Neither serum levels of total cholesterol nor low-density lipoprotein (LDL) was associated with sICH in men. In women, there was no association between any of the lipid levels and the risk of sICH. Conclusions This study indicated that the association between serum levels of triglyceride and sICH may vary by sex. In men, increased triglyceride levels decrease the risk of sICH; in women, this association was lost. Further studies on the biological mechanisms for sex differences in stroke risk associated with triglyceride are needed.
Yuan et al. (2024) Sex difference in the association between triglyceride and intracerebral bleeding risk after intravenous thrombolysis for acute ischemic stroke, a multi-center retrospective study. PeerJ 12:e17558 https://doi.org/10.7717/peerj.17558
Associations between fundamental movement skills and accelerometer-measured physical activity in Chinese children: the mediating role of cardiorespiratory fitness
Background and purpose The associations of fundamental motor skills (FMS), health-related physical fitness (e.g., cardiorespiratory fitness, CRF), and moderate-vigorous physical activity (MVPA) have been demonstrated in Western children, but these associations have not yet been validated in a sample of Chinese children. The aims of this study, therefore, were to examine the association between FMS subdomains and MVPA in a sample of Chinese children and to evaluate whether this association is mediated by CRF. Methods A cross-sectional study consisting of 311 children aged 8–12 years (49.2% girls; mean age = 9.9 years) from Shanghai was conducted. FMS, CRF and MVPA were assessed using the Test of Gross Motor Development-3rd Edition, Progressive Aerobic Cardiovascular Endurance Run and ActiGraph GT3X accelerometers. Preacher & Hayes’s bootstrap method was used to test the mediating effects of CRF on the association between FMS and MVPA. Results CRF fully mediated the association between total FMS and MVPA in girls (indirect effects, b = 0.21, 95% CI [0.07–0.37]), while the mediation was only partial in boys (indirect effects, b = 0.12, 95% CI [0.01–0.26]). CRF fully mediated the association between locomotor skills and MVPA in girls (indirect effects, b = 0.27, 95% CI [0.09– 0.51]), whereas CRF partially mediated the association between object control skills and MVPA in boys (indirect effects, b = 0.15, 95% CI [0.18–0.35]). Conclusion In order to better design and implement sex-specific interventions aiming to increase MVPA, it is essential to consider FMS subdomains and CRF alongside the sex differences in the association between them.
Zhang et al. (2024) Associations between fundamental movement skills and accelerometer-measured physical activity in Chinese children: the mediating role of cardiorespiratory fitness. PeerJ 12:e17564 https://doi.org/10.7717/peerj.17564
Squatting biomechanics following physiotherapist-led care or hip arthroscopy for femoroacetabular impingement syndrome: a secondary analysis from a randomised controlled trial
Background Femoroacetabular impingement syndrome (FAIS) can cause hip pain and chondrolabral damage that may be managed non-operatively or surgically. Squatting motions require large degrees of hip flexion and underpin many daily and sporting tasks but may cause hip impingement and provoke pain. Differential effects of physiotherapist-led care and arthroscopy on biomechanics during squatting have not been examined previously. This study explored differences in 12-month changes in kinematics and moments during squatting between patients with FAIS treated with a physiotherapist-led intervention (Personalised Hip Therapy, PHT) and arthroscopy. Methods A subsample (n = 36) of participants with FAIS enrolled in a multi-centre, pragmatic, two-arm superiority randomised controlled trial underwent three-dimensional motion analysis during squatting at baseline and 12-months following random allocation to PHT (n = 17) or arthroscopy (n = 19). Changes in time-series and peak trunk, pelvis, and hip biomechanics, and squat velocity and maximum depth were explored between treatment groups. Results No significant differences in 12-month changes were detected between PHT and arthroscopy groups. Compared to baseline, the arthroscopy group squatted slower at follow-up (descent: mean difference −0.04 m∙s−1 (95%CI [−0.09 to 0.01]); ascent: −0.05 m∙s−1 [−0.11 to 0.01]%). No differences in squat depth were detected between or within groups. After adjusting for speed, trunk flexion was greater in both treatment groups at follow-up compared to baseline (descent: PHT 7.50° [−14.02 to −0.98]%; ascent: PHT 7.29° [−14.69 to 0.12]%, arthroscopy 16.32° [−32.95 to 0.30]%). Compared to baseline, both treatment groups exhibited reduced anterior pelvic tilt (descent: PHT 8.30° [0.21–16.39]%, arthroscopy −10.95° [−5.54 to 16.34]%; ascent: PHT −7.98° [−0.38 to 16.35]%, arthroscopy −10.82° [3.82–17.81]%), hip flexion (descent: PHT −11.86° [1.67–22.05]%, arthroscopy −16.78° [8.55–22.01]%; ascent: PHT −12.86° [1.30–24.42]%, arthroscopy −16.53° [6.72–26.35]%), and knee flexion (descent: PHT −6.62° [0.56– 12.67]%; ascent: PHT −8.24° [2.38–14.10]%, arthroscopy −8.00° [−0.02 to 16.03]%). Compared to baseline, the PHT group exhibited more plantarflexion during squat ascent at follow-up (−3.58° [−0.12 to 7.29]%). Compared to baseline, both groups exhibited lower external hip flexion moments at follow-up (descent: PHT −0.55 N∙m/BW∙HT[%] [0.05–1.05]%, arthroscopy −0.84 N∙m/BW∙HT[%] [0.06–1.61]%; ascent: PHT −0.464 N∙m/BW∙HT[%] [−0.002 to 0.93]%, arthroscopy −0.90 N∙m/BW∙HT[%] [0.13–1.67]%). Conclusion Exploratory data suggest at 12-months follow-up, neither PHT or hip arthroscopy are superior at eliciting changes in trunk, pelvis, or lower-limb biomechanics. Both treatments may induce changes in kinematics and moments, however the implications of these changes are unknown. Trial registration details Australia New Zealand Clinical Trials Registry reference: ACTRN12615001177549. Trial registered 2/11/2015.
Grant et al. (2024) Squatting biomechanics following physiotherapist-led care or hip arthroscopy for femoroacetabular impingement syndrome: a secondary analysis from a randomised controlled trial. PeerJ 12:e17567 https://doi.org/10.7717/peerj.17567
Optimization of polysaccharide conditions and analysis of antioxidant capacity in the co-culture of Sanghuangporus vaninii and Pleurotus sapidus
Fungal polysaccharides are commonly utilized in the food industry and biomedical fields as a natural and safe immune modulator. Co-culturing is a valuable method for enhancing the production of secondary metabolites. This study used intracellular polysaccharide (IPS) content as a screening index, co-culturing seven different fungi with Sanghuangporus vaninii. The seed pre-culture liquid culture time was selected through screening, and conditions were assessed using single factor experimentation, a Plackett-Burman (PB) design, and response surface methodology (RSM) optimization. RSM optimization was conducted, leading to the measurement of antioxidant capacity. Results indicated that the co-culture of S. vaninii and Pleurotus sapidus exhibited the most effective outcome. Specifically, pre-culturing S. vaninii and P. sapidus seed cultures for 2 days and 0 days, respectively, followed by co-culturing, significantly increased IPS content compared to single-strain culturing. Further optimization of co-culture conditions revealed that yeast extract concentration, liquid volume, and S. vaninii inoculum ratio notably influenced IPS content in the order of yeast extract concentration > liquid volume > S. vaninii inoculum ratio. Under the optimal conditions, IPS content reached 69.9626 mg/g, a 17.04% increase from pre-optimization co-culture conditions. Antioxidant capacity testing demonstrated that co-cultured IPS exhibited greater scavenging abilities for DPPH and ABTS free radicals compared to single strain cultures. These findings highlight the potential of co-culturing S. vaninii and P. sapidus to enhance IPS content and improve antioxidant capacity, presenting an effective strategy for increasing fungal polysaccharide production.
Lu et al. (2024) Optimization of polysaccharide conditions and analysis of antioxidant capacity in the co-culture of Sanghuangporus vaninii and Pleurotus sapidus. PeerJ 12:e17571 https://doi.org/10.7717/peerj.17571
Mammalian lures monitored with time-lapse cameras increase detection of pythons and other snakes
Background Enhancing detection of cryptic snakes is critical for the development of conservation and management strategies; yet, finding methods that provide adequate detection remains challenging. Issues with detecting snakes can be particularly problematic for some species, like the invasive Burmese python (Python bivittatus) in the Florida Everglades. Methods Using multiple survey methods, we predicted that our ability to detect pythons, larger snakes and all other snakes would be enhanced with the use of live mammalian lures (domesticated rabbits; Oryctolagus cuniculus). Specifically, we used visual surveys, python detection dogs, and time-lapse game cameras to determine if domesticated rabbits were an effective lure. Results Time-lapse game cameras detected almost 40 times more snakes (n = 375, treatment = 245, control = 130) than visual surveys (n = 10). We recorded 21 independent detections of pythons at treatment pens (with lures) and one detection at a control pen (without lures). In addition, we found larger snakes, and all other snakes were 165% and 74% more likely to be detected at treatment pens compared to control pens, respectively. Time-lapse cameras detected almost 40 times more snakes than visual surveys; we did not detect any pythons with python detection dogs. Conclusions Our study presents compelling evidence that the detection of snakes is improved by coupling live mammalian lures with time-lapse game cameras. Although the identification of smaller snake species was limited, this was due to pixel resolution, which could be improved by changing the camera focal length. For larger snakes with individually distinctive patterns, this method could potentially be used to identify unique individuals and thus allow researchers to estimate population dynamics.
McCampbell et al. (2024) Mammalian lures monitored with time-lapse cameras increase detection of pythons and other snakes. PeerJ 12:e17577 https://doi.org/10.7717/peerj.17577
Unraveling the complexities of drought stress in cotton: a multifaceted analysis of selection criteria and breeding approaches
Abiotic stress tolerance breeding programs present a spectrum of perspectives, yet definitive solutions remain elusive, with each approach carrying its own set of advantages and disadvantages. This study systematically evaluates extant methodologies, comparing plant performance across varied genotypes and selection traits under optimal and stress conditions. The objective is to elucidate prevailing ambiguities. Ten homozygous lines (F8 generation) were assessed using a randomized block design alongside five control varieties, with four replicates cultivated under well-watered and deficit water conditions. It is noteworthy that six of the ten homozygous lines were cultivated exclusively under well-watered conditions (F3 to F7), while four lines experienced deficit water conditions (F3 to F7). All five control varieties underwent cultivation under both conditions. These findings underscore the necessity for tailored breeding programs attuned to specific environmental exigencies, recognizing that individual traits manifest divergent responses to varying conditions. It is evident that certain traits exhibit marked disparities under well-watered conditions, while others evince heightened differentiation under water deficit conditions. Significantly, our analysis reveals a pronounced interaction between irrigation regimes and selection traits, which serves to underscore the nuanced interplay between genotype and environmental stress.
Gören et al. (2024) Unraveling the complexities of drought stress in cotton: a multifaceted analysis of selection criteria and breeding approaches. PeerJ 12:e17584 https://doi.org/10.7717/peerj.17584
Genomic organization and expression profiles of nitrogen assimilation genes in Glycine max
Background Glutamine synthetase (GS), glutamate synthase (GOGAT), and nitrate reductase (NR) are key enzymes involved in nitrogen assimilation and metabolism in plants. However, the systematic analysis of these gene families lacked reports in soybean (Glycine max (L.) Merr.), one of the most important crops worldwide. Methods In this study, we performed genome-wide identification and characterization of GS, GOGAT, and NR genes in soybean under abiotic and nitrogen stress conditions. Results We identified a total of 10 GS genes, six GOGAT genes, and four NR genes in the soybean genome. Phylogenetic analysis revealed the presence of multiple isoforms for each gene family, indicating their functional diversification. The distribution of these genes on soybean chromosomes was uneven, with segmental duplication events contributing to their expansion. Within the nitrogen assimilation genes (NAGs) group, there was uniformity in the exon-intron structure and the presence of conserved motifs in NAGs. Furthermore, analysis of cis-elements in NAG promoters indicated complex regulation of their expression. RT-qPCR analysis of seven soybean NAGs under various abiotic stresses, including nitrogen deficiency, drought-nitrogen, and salinity, revealed distinct regulatory patterns. Most NAGs exhibited up-regulation under nitrogen stress, while diverse expression patterns were observed under salt and drought-nitrogen stress, indicating their crucial role in nitrogen assimilation and abiotic stress tolerance. These findings offer valuable insights into the genomic organization and expression profiles of GS, GOGAT, and NR genes in soybean under nitrogen and abiotic stress conditions. The results have potential applications in the development of stress-resistant soybean varieties through genetic engineering and breeding.
Elsanosi et al. (2024) Genomic organization and expression profiles of nitrogen assimilation genes in Glycine max. PeerJ 12:e17590 https://doi.org/10.7717/peerj.17590
Ecotoxicological effects of tungsten on celery (Apium graveolens L) and pepper (Capsicum spp.)
Background Tungsten (W) is an emerging heavy metal pollutant, yet research remains scarce on the biomonitor and sensitive biomarkers for W contamination. Methods In this study, celery and pepper were chosen as study subjects and subjected to exposure cultivation in solutions with five different levels of W. The physiological and biochemical toxicities of W on these two plants were systematically analyzed. The feasibility of utilizing celery and pepper as biomonitor organisms for W contamination was explored and indicative biomarkers were screened. Results The results indicated that W could inhibit plants’ root length, shoot height, and fresh weight while concurrently promoting membrane lipid peroxidation. Additionally, W enhanced the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and total antioxidant capacity (TAOC) to counteract oxidative damage. From a physiological perspective, pepper exhibited potential as a biomonitor for W contamination. Biochemical indicators suggested that SOD could serve as a sensitive biomarker for W in celery, while TAOC and POD were more suitable for the roots and leaves of pepper. In conclusion, our study investigated the toxic effects of W on celery and pepper, contributing to the understanding of W’s environmental toxicity. Furthermore, it provided insights for selecting biomonitor organisms and sensitive biomarkers for W contamination.
Environmental Contamination and Remediation
Li et al. (2024) Ecotoxicological effects of tungsten on celery (Apium graveolens L) and pepper (Capsicum spp.). PeerJ 12:e17601 https://doi.org/10.7717/peerj.17601