The effects of livestock grazing on physicochemical properties and bacterial communities of perlite-rich soil
Livestock grazing has been proposed as a cost-effective way to reclaim post-mining lands. It can enhance soil fertility and biodiversity, but its impacts on soil quality and microbial communities vary across soil types. Moreover, waste from grazing raises concerns about pathogens that could pose risks to animal and human health. This study investigated the effects of grazing on post-mining perlite-rich soil in central Thailand. A comparative analysis of soil physicochemical properties and bacterial diversity was conducted between grazed and ungrazed sites. Bacterial diversity was assessed using 16S amplicon sequencing. The perlite-rich soil was found to be sandy, acidic, and to have low nutritional content. Grazing significantly improved the soil texture and nutrient content, suggesting its potential as a cost-effective reclamation strategy. The 16S metagenomic sequencing analysis revealed that microbial communities were impacted by livestock grazing. Specifically, shifts in the dominant bacterial phyla were identified, with increases in Firmicutes and Chloroflexi and a decrease in Actinobacteria. Concerns about increased levels of pathogenic Enterobacteriaceae due to grazing were not substantiated in perlite-rich soil. These bacteria were consistently found at low levels in all soil samples, regardless of livestock grazing. This study also identified a diverse population of Streptomycetaceae, including previously uncharacterized strains/species. This finding could be valuable given that this bacterial family is known for producing antibiotics and other secondary metabolites. However, grazing adversely impacted the abundance and diversity of Streptomycetaceae in this specific soil type. In line with previous research, this study demonstrated that the response of soil microbial communities to grazing varies significantly depending on the soil type, with unique responses appearing to be associated with perlite-rich soil. This emphasizes the importance of soil-specific research in understanding how grazing affects microbial communities. Future research should focus on optimizing grazing practices for perlite-rich soil and characterizing the Streptomycetaceae community for potential antibiotic and secondary metabolite discovery. The obtained findings should ultimately contribute to sustainable post-mining reclamation through livestock grazing and the preservation of valuable microbial resources.
Premsuriya et al. (2024) The effects of livestock grazing on physicochemical properties and bacterial communities of perlite-rich soil. PeerJ 12:e18433 https://doi.org/10.7717/peerj.18433
A classification system for identifying persons with an unknown cardiovascular disease (CVD) status for a multiracial/ ethnic Caribbean population
Background The need for classification systems for cardiovascular disease (CVD) that is population-specific is important towards understanding the clinical disease and diagnostics associated with the disease. This paper presents the form and validation results of this classification system. Method The survey data used was captured from 778 participants, 526 persons with no prior CVD, and 252 who reported prior CVD. Binomial logistic regression and Discriminant analysis were utilised to develop classification models. This classification system provided a general measure of severity of disease by utilising scores estimated from two algorithms developed from 13 routine physiologic measurements, along with demographic information of age and ethnicity, inter alia, and previous health status. Results For each model, specific score ranges were identified, which gave the best classification for those with a prior CVD incident (higher scores) and for others labelled as non-CVD (lower scores). The two classification models (Logistic Regression Model and Discriminant Analysis Model) developed had high area under the receiver-operating characteristic (AUROC) values (98% & 99%) and sensitivity (86 and 90%), which improved discrimination between Non-CVD and CVD participants and, more importantly, correctly classified a greater proportion of CVD participants. New to this type of research was the estimation and detailed evaluation of a range of scores, labelled non-differentiating, which fell in the middle of the spectrum and which contained the higher-end scores for the non-CVD individuals and the lower-end scores for CVD patients, all of whom were incorrectly classified, based on their prior history. Conclusion The classification system of scores is able to differentiate the CVD status of individuals, with good predictability, and could assist physicians with recommending different treatment plans. The two models in this classification system each individually outperformed the three established models in terms of the strength of their correct classifications of individuals with or without prior reported CVD incidents. More importantly, they have smaller non-differentiating ranges than the three known models and, in that range, the two new models have lower CVD/non-CVD ratios suggesting they are more likely to misclassify non-CVD individuals compared to CVD patients, which is a more benign misclassification. Further, when used in combination, the two models increased the sensitivity, in classifying individuals of different ethnicities, beyond that of either one used independently or of any of the three standard European/North American models. These efforts will be instrumental in advancing personalised CVD management strategies and improving health outcomes across diverse populations.
Hosein et al. (2024) A classification system for identifying persons with an unknown cardiovascular disease (CVD) status for a multiracial/ ethnic Caribbean population. PeerJ 12:e17948 https://doi.org/10.7717/peerj.17948
Muscle synergies during the walk-run and run-walk transitions
Background Muscular synergies could represent the patterns of muscular activation used by the central nervous system (CNS) to simplify the production of movement. Studies in walking-running transitions described up to nine synergy modules, and an earlier activation of flexor and extension ankle muscular groups compared to running or walking. Our project aims to study the behaviour of muscle synergies in different stance and swing variations of walking-running (WRT) and running-walking (RWT) transitions. Methods Twenty-four trained men participated in this study. A variable speed protocol on a treadmill was developed to record the activity of 14 muscle during walking, running and relative transitions. The protocol was based on five ramps of 50 seconds each around ± 10 and 20% of the WRT speed. WRT and RWT were identified according to an abrupt change of the duty factor. Analysing surface electromyography using non-negative matrix factorization (NMF) we obtained synergy modules and temporal activation profiles. Alpha threshold for statistical tests set at 0.05. Results We described four different transition strides, two for increasing speed transitions, and two for decreasing speed transitions. Four to six synergy modules were found in each condition. According to the maximum cosine similarity results, the two identified WRT conditions shared five modules, while the two RWT conditions shared four modules. WRT and RWT overall shared 4.33 ± 0.58 modules. The activation profiles and centres of activation revealed differences among conditions. Discussion Transition occurred at step level, and transition strides were composed by walk-like and run-like steps. Compared with previous studies in running and walking, both transitions needed earlier activation of a comparable number of synergy modules. Synergies were affected by acceleration: during RWT the need to dissipate energy, to decrease the speed, was achieved by increasing the number of co-activating muscles. This was reflected in fewer synergy modules and different activation profiles compared to WRT. We believe that our results could be enforced in different applied fields, like clinical gait analysis, physiotherapy and rehabilitation, where plans including co-activation of specific muscular groups could be useful. Gait transitions are common in different sports, and therefore also application in training and sport science would be possible.
Lagos-Hausheer et al. (2024) Muscle synergies during the walk-run and run-walk transitions. PeerJ 12:e18162 https://doi.org/10.7717/peerj.18162
Ecological features and insecticide resistance of Aedes albopictus in Xi’an, a high-risk dengue transmission area in China
Background Dengue, a mosquito-borne viral disease, has occurred in many cities in China, and it tends to spread to higher latitudes (Huang et al., 2023). Xi’an, situated in central-west China, has witnessed an increase imported cases in the past few years, raising concerns of local dengue transmission. It is crucial to investigate the population density of Aedes albopictus and its insecticides resistance to enhance early warning of dengue fever. Methods Eight sampling sites in eight counties (YT, BL, WY, CH, YL, LN, LT, ZZ) of Xi’an city were surveyed by larval dipping and human-baited double net trap biweekly from June 2021 to September 2022. The Breteau Index (BI, number of positive containers per 100 houses) and Container Index (CI, the percentage of containers containing larvae or pupae) were used to assess larval density, and the human-baited double net trap (HDN, the number of Ae. albopictus females collected per person per hour) to indicate human bating rate (HBR). Meanwhile, the association between the meteorological factors and mosquito density was analyzed. The Ae. albopictus adult insecticides resistance was evaluated by the World Health Organization (WHO) standard resistance bioassay. Adult females were exposed to insecticide-impregnated paper for 1 h, then transferred to the recovery tube, and mortality rate was calculated after 24 h. According to the Implementation Plan for National Vector Surveillance (2016), resistance status was classified into three levels based on mortality: <80% mortality as resistant, between 80% and 98% mortality as possibly resistant, and >98% mortality as sensitive. Results From June 2021 to September 2022, a total of 1,065 houses were surveyed for water holding containers, and 99 of 430 water holding containers were checked to be positive for Ae. albopictus larvae and pupae. A total of 1,048 Ae. albopictus females were collected. The average BI, CI and HBR were 10.39, 21.41, and 11.20 female/man/hour in 2021 and 8.86, 20.86, and 11.63 f/m/h in 2022, respectively. The findings showed that the BI exceeded 5 in most months and reached above 20 in specific months. The CI varied in different months and monitoring sites, with the highest CI in August 2021 and July 2022. The discarded tires had the highest positivity rate, with up to 40.32% testing positive for Ae. albopictus larvae. The monthly average temperature showed a positive correlation with CI (r = 0.77), and the monthly BI was positively associated with CI (r = 0.93). The BI, CI, and HBR were significantly higher in the rainy season than other seasons. The bioassay results showed that the mortality rate of Ae. albopictus at the YT monitoring site was 76.92%, indicating resistance to deltamethrin. The mortality rate of Ae. Albopictus at BL, WY, CH, YL, LN, LT, and ZZ sampling sites were varying from 81.25%∼100%, suggesting possibly resistant or still sensitive to beta-cypermethrin, alpha-cypermethrin, malathion, chlorpyrifos, and propoxur.
Lei et al. (2024) Ecological features and insecticide resistance of Aedes albopictus in Xi’an, a high-risk dengue transmission area in China. PeerJ 12:e18246 https://doi.org/10.7717/peerj.18246
Identifying a cis-element in PtoCP1 promoter for efficiently controlling constitutive gene expression in Populus tomentosa
Gene expression is regulated by transcription factors binding to cis-elements in promoters. However, efficient cis-elements for genetic engineering are rarely reported. In this study, we identified an 11 bp cis-element in the PtoCP1 promoter that drives strong constitutive gene expression in Populus tomentosa. A 2,270 bp promoter region upstream of the PtoCP1 gene’s translation start site was cloned and named ProPtoCP1. This promoter controls GUS reporter gene expression in the roots, leaves, and stems of Arabidopsis seedlings. Based on the location and density of cis-elements, the PtoCP1 promoter was divided into four fragments by 5′-end deletions. GUS staining and RT-qPCR revealed a key cis-element at −466 to −441 bp essential for gene expression. Further analysis showed that the MYB-TGACG cis-element is a positive regulator, whereas neither MYB nor TGACG alone drove gene expression. This study enhances our understanding of gene expression regulation by cis-elements and provides a valuable tool for genetic engineering.
Peng et al. (2024) Identifying a cis-element in PtoCP1 promoter for efficiently controlling constitutive gene expression in Populus tomentosa. PeerJ 12:e18292 https://doi.org/10.7717/peerj.18292
Ecological and taxonomic dissimilarity in species and higher taxa of reptiles in western Mexico
Reptiles are one of the most diverse groups of vertebrates in the world that are distributed in almost all ecosystems. Many of these studies have focused on exploring their diversity patterns across different environments; and recent studies on reptile alpha and beta diversity have incorporated a multifaceted approach into their analysis to have more comprehensive evaluations. This study presents an assessment of the taxonomic diversity of reptile patterns using methods that incorporate the assessment of higher taxa. Likewise, the taxonomic dissimilarities between reptile communities in the physiographic regions of the state of Jalisco were analyzed. Evaluations for the groups of snakes and lizards independently are presented. We use the taxonomic distinctiveness index that assesses the complexity of the taxonomic structure of communities through hierarchical classification above the species level to measure the relationships between taxa. The dissimilarity of the taxonomic structure in each community was also analyzed. Beta diversity partitions were performed to identify the contribution of turnover and the differences in richness. We determined that alpha diversity of species and higher taxa maintain different patterns, indicating that Jalisco presents regions with overrepresentation of reptile families and genera, as well as regions with an opposite trend. The representation of higher taxa is higher in the lizard group, although in terms of species richness snakes are the most prominent group. The turnover is the most important component at species and higher taxa, with similar values for lizards and snakes. The findings presented show that incorporating phylogenetic information about species through taxonomic relationships provides complementary information that species diversity per se, especially at the level of alpha diversity.
Calderón-Patrón et al. (2024) Ecological and taxonomic dissimilarity in species and higher taxa of reptiles in western Mexico. PeerJ 12:e18343 https://doi.org/10.7717/peerj.18343
Spatiotemporal gait characteristics post-total hip arthroplasty and its impact on locomotive syndrome: a before-after comparative study in hip osteoarthritis patients
Background Understanding the gait pattern of patients eligible for total hip arthroplasty (THA) due to hip osteoarthritis (OA) offers valuable information for improving locomotive syndrome (LS). This study aims to measure the gait patterns of THA-eligible patients using an optical motion capture system and to analyze these patterns using principal component analysis (PCA). Additionally, this study examines the relationship between THA-induced gait patterns and LS. Methods This before-after study included 237 patients who underwent unilateral primary THA due to hip OA. The primary outcome measures were spatiotemporal gait parameters. Secondary outcome measures included three LS risk tests: a stand-up test, a two-step test, a 25-question Geriatric Locomotive Function Scale (GLFS-25), and total clinical decision limits stages. PCA was performed using 16 spatiotemporal gait parameters collected before and three months after THA. Principal components (PC) were selected to achieve a cumulative contribution rate of 90% (0.9) or higher. Each summarized PC was compared using a paired t-test before and three months after THA. Furthermore, multiple regression analysis was conducted to determine how changes in each PC between before and three months after THA related to changes in the four LS evaluation items. Results PCA identified three principal components (PC1, PC2, PC3) that accounted for a cumulative contribution rate of 0.910 using 16 spatiotemporal gait parameters. When comparing before and three months after THA for all three PCs, significant differences were observed in each PC (p < 0.001), with overall walking ability and stance phase being higher three months after THA than before THA, while the asymmetry of support time was lower three months after THA. The results of multiple regression analysis revealed that PC1, PC2, and PC3 were the most influential factors in total clinical decision limits stage. For each LS risk test, the factors related to the stand-up test were identified as PC1, PC2, and PC3, while the factors related to the two-step test were identified as PC1 and PC2. The factors related to the GLFS-25 were also identified as PC1 and PC2. Conclusions The most important findings of this study indicate that the three PCs represent over 90% of the 16 spatiotemporal gait parameters, which are associated with total clinical decision limits stage and LS risk tests. The present results suggest that PC1 represents overall walking ability, PC2 represents the stance phase, and PC3 represents asymmetry of support time. Gait pattern characteristics, such as overall walking ability, stance phase, and asymmetry of support time, were clearly defined by these PCs. Regarding the relationship between PC and LS, all three PCs are related to total clinical decision limits stage. In addition, PC1 and PC2 related to all three LS risk tests, and PC3 related only to the stand-up test.
Miyazaki et al. (2024) Spatiotemporal gait characteristics post-total hip arthroplasty and its impact on locomotive syndrome: a before-after comparative study in hip osteoarthritis patients. PeerJ 12:e18351 https://doi.org/10.7717/peerj.18351
The mitochondrial genome sequences of eleven leafhopper species of Batracomorphus (Hemiptera: Cicadellidae: Iassinae) reveal new gene rearrangements and phylogenetic implications
Batracomorphus is the most diverse and widely distributed genus of Iassinae. Nevertheless, there has been no systematic analysis of the genome structure and phylogenetic relationships of the genus. To determine the characteristics of the mitogenomes of Batracomorphus species as well as the phylogenetic relationships between them, we sequenced and compared the mitogenomes of 11 representative Batracomorphus species. The results revealed that the mitogenomes of the 11 Batracomorphus species exhibited highly similar gene and nucleotide composition, and codon usage compared with other reported mitogenomes of Iassinae. Of these 11 species, we found that the mitogenomes of four species were rearranged in the region from trnI-trnQ-trnM to trnQ-trnI-trnM, whereas the remaining species presented a typical gene order. The topologies of six phylogenetic trees were in agreement. Eurymelinae consistently formed paraphyletic groups. Ledrinae and Evacanthinae formed sister taxa within the same clade. Similarly, Typhlocybinae and Mileewinae consistently clustered together. All phylogenetic trees supported the monophyly of Iassinae, indicating its evolutionary distinctiveness while also revealing its sister relationship with Coelidiinae. Notably, the nodes for all species of the genus Batracomorphus were well supported and these taxa clustered into a large branch that indicated monophyly. Within this large branch, four Batracomorphus species with a gene rearrangement (trnQ-trnI-trnM) exhibited distinctive clustering, which divided the large branch into three minor branches. These findings expand our understanding of the taxonomy, evolution, genetics, and systematics of the genus Batracomorphus and broader Iassinae groups.
Lu et al. (2024) The mitochondrial genome sequences of eleven leafhopper species of Batracomorphus (Hemiptera: Cicadellidae: Iassinae) reveal new gene rearrangements and phylogenetic implications. PeerJ 12:e18352 https://doi.org/10.7717/peerj.18352
A Python program to merge Sanger sequences: an update
Gene cloning is an important step in investigating gene structure and function. To verify gene sequence, Sanger sequencing is used, which may produce several overlapping sequencing files that need to be merged before alignment to the target gene sequence is performed. Previously, we reported the Python program to Merge Sanger sequences (https://peerj.com/articles/11354/), which ran in command line and relied heavily on EMBOSS suite. In this updated version of the program, we have made several remarkable improvements. It provides a graphical user interface (GUI) written with tkinter, which is convenient and stable. It does not require users to rename the input sequences before performing merging. With regard to the implementation, the updated version utilizes Python function (Align.PairwiseAligner) to align adjacent sequences, which is more flexible (can adjust program parameter i.e., the number of first-time consecutive matching bases). The new version of the program makes merging Sanger sequences much more convenient and facilitates gene study.
Lin et al. (2024) A Python program to merge Sanger sequences: an update. PeerJ 12:e18363 https://doi.org/10.7717/peerj.18363
Exploring reported population differences in Norway lobster (Nephrops norvegicus) in the Pomo Pits region of the Adriatic Sea using genome-wide markers
The Norway lobster (Nephrops norvegicus) is one of the most important decapod crustacean seafood species in the Adriatic Sea. Previous research has identified significant differences in growth rates and maturation timing of Nephrops in the Pomo/Jabuka Pits area compared to other subpopulations in Adriatic fishing grounds. Here, we use 1,623 genome-wide single nucleotide polymorphisms (SNPs) to investigate whether the Pomo Pits subpopulation is genetically different from other sites in the Adriatic and neighbouring seas. We found no genetic differentiation among all sampled Adriatic sites, suggesting high gene flow between Pomo Pits Nephrops and those of surrounding areas. We also found genetic homogeneity between the Adriatic sites and single-site samples from the Aegean and Tyrrhenian Seas. However, we detected distinct genetic differentiation between all Mediterranean sites and an Atlantic site in western Scotland, which provides evidence for a phylogenetic break between the Atlantic and the Mediterranean. Our results indicate that Pomo Pits Nephrops are not genetically different from others sampled in the Adriatic and that key biological parameters in Pomo Pits Nephrops could be driven by spatial variation in fishing pressure and/or environmental factors rather than geographic isolation.
Jenkins et al. (2024) Exploring reported population differences in Norway lobster (Nephrops norvegicus) in the Pomo Pits region of the Adriatic Sea using genome-wide markers. PeerJ 12:e17852 https://doi.org/10.7717/peerj.17852