Gene synthesis design: a pythonic approach
Researchers often need to synthesize genes of interest in this era of synthetic biology. Gene synthesis by PCR assembly of multiple DNA fragments is a quick and economical method that is widely applied. Up to now, there have been a few software solutions for designing fragments in gene synthesis. However, some of these software solutions use programming languages that are not popular now, other software products are commercial or require users to visit servers. In this study, we propose a Python program to design DNA fragments for gene synthesis. The algorithm is designed to meet the experimental needs. Also, the source code with detailed annotation is freely available for all users. Furthermore, the feasibility of the algorithm and the program is validated by experiments. Our program can be useful for the design of gene synthesis in the labs and help the study of gene structure and function.
Hu et al. (2024) Gene synthesis design: a pythonic approach. PeerJ 12:e17750 https://doi.org/10.7717/peerj.17750
An intense 60-day weight-loss course leads to an 18 kg body weight reduction and metabolic reprogramming of soldiers with obesity
Soldiers of the Mexican Army with obesity were subjected to an intense 60-day weight-loss course consisting of a controlled diet, daily physical training, and psychological sessions. The nutritional treatment followed the European Society of Cardiology (ESC) recommendations, incorporating elements of the traditional milpa diet in the nutritional intervention. The total energy intake was reduced by 200 kcal every 20 days, starting with 1,800 kcal and ending with 1,400 kcal daily. On average, the participants reduced their body weight by 18 kg. We employed an innovative approach to monitor the progress of the twelve soldiers who completed the entire program. We compared the untargeted metabolomics profiles of their urine samples, taken before and after the course. The data obtained through liquid chromatography and high-resolution mass spectrometry (LC-MS) provided insightful results. Classification models perfectly separated the profiles pre and post-course, indicating a significant reprogramming of the participants’ metabolism. The changes were observed in the C1-, vitamin, amino acid, and energy metabolism pathways, primarily affecting the liver, biliary system, and mitochondria. This study not only demonstrates the potential of rapid weight loss and metabolic pathway modification but also introduces a non-invasive method for monitoring the metabolic state of individuals through urine mass spectrometry data.
Albores-Méndez et al. (2024) An intense 60-day weight-loss course leads to an 18 kg body weight reduction and metabolic reprogramming of soldiers with obesity. PeerJ 12:e17757 https://doi.org/10.7717/peerj.17757
Genotypes and phenotypes in a Wolbachia-ant symbiosis
The fitness effects of overt parasites, and host resistance to them, are well documented. Most symbionts, however, are more covert and their interactions with their hosts are less well understood. Wolbachia, an intracellular symbiont of insects, is particularly interesting because it is thought to be unaffected by the host immune response and to have fitness effects mostly focussed on sex ratio manipulation. Here, we use quantitative PCR to investigate whether host genotype affects Wolbachia infection density in the leaf-cutting ant Acromyrmex echinatior, and whether Wolbachia infection density may affect host morphology or caste determination. We found significant differences between host colonies in the density of Wolbachia infections, and also smaller intracolonial differences in infection density between host patrilines. However, the density of Wolbachia infections did not appear to affect the morphology of adult queens or likelihood of ants developing as queens. The results suggest that both host genotype and environment influence the host-Wolbachia relationship, but that Wolbachia infections carry little or no physiological effect on the development of larvae in this system.
Frost et al. (2024) Genotypes and phenotypes in a Wolbachia-ant symbiosis. PeerJ 12:e17781 https://doi.org/10.7717/peerj.17781
Negative effects of agricultural open-channel irrigation system on vertebrate populations in central Mexico
Linear infrastructures such as agricultural irrigation channels produce physical changes and negative impacts to habitats, wildlife populations, communities, and ecosystems. Open irrigation channels act as a pitfall for wildlife and can affect vertebrates of all sizes. Nonetheless, small channels have received relatively little attention by conservation biologists. The objective of this study was to analyze vertebrate species richness and mortality in relation to different sections of an irrigation channel system and the surrounding landscape characteristics. For two years, we conducted monthly surveys along an open-channel irrigation system to estimate its effect on vertebrates through records of dead and alive individuals. We examined the spatial relation of species richness and mortality with transects using a canonical correspondence analysis and chi-squared tests to determine possible variations in the different structures of the channel and seasonality. Further, a landscape diversity index was used to analyze the importance of surrounding habitat structure and composition on these parameters. Most vertebrates (61%) were found dead, small mammals and reptiles were the most affected. Our results indicate that mortality of small vertebrates varies depending on species, structures of the open-channel agricultural irrigation system (i.e., concrete channel and floodgates), seasonality (i.e., wet, and dry), and landscape heterogeneity (i.e., high, medium, and low landscape diversity). The open-channel irrigation system is a threat to populations of small vertebrates in anthropized landscapes, conservation efforts should be directed at protecting water bodies and restructuring the open-channel agricultural irrigation system to avoid mortality of species such as small rodents (M. mexicanus) and reptiles (C. triseriatus, B. imbricata, and Thamnophis spp.).
Gómez-Ortiz et al. (2024) Negative effects of agricultural open-channel irrigation system on vertebrate populations in central Mexico. PeerJ 12:e17818 https://doi.org/10.7717/peerj.17818
Occurrence and abundance of microplastics in surface water of Songkhla Lagoon
Background Microplastic (MP) pollution is now a global critical issue and has been the subject of considerable worry for multiple various types of habitats, notably in lagoons which are coastal areas connected to the ocean. MPs are of concern, particularly because floating MP in surface water can be ingested by a number of marine organisms. There are several lagoons along Southeast Asia’s coastline, but Songkhla Lagoon is Thailand’s only exit with a rich biodiversity. To date, there has been little research undertaken on MP in this lagoon, so there is a pressing need to learn more about the presence of MP in the lagoon’s water. Methods We investigate MPs in the surface water of Songkhla Lagoon, Thailand. Sampling took place at ten stations in the lagoon during the wet season in December 2022 and the dry season in February 2023. Samples were digested with hydrogen peroxide to remove organic matter followed by density separation using saturated sodium chloride. MPs were visually examined under a stereo microscope to describe and determine the shape, size, and color. Polymer type was identified using a micro Fourier transform infrared (FTIR) spectrometer. Moreover, the in-situ of water quality of the surface water was measured using a multi-parameter probe. A Mann-Whitney U test was performed to investigate the variations in MP levels and water quality parameters between the wet and dry seasons. Correlation analysis (Spearman rho) was used to determine the significance of correlations between MP and water quality (p < 0.05). Results MPs were detected at all ten of the sites sampled. The most abundant MPs were small size class (<500 µm, primarily consisting of fibers). Five types of polymers were seen in surface water, including polyethylene terephthalate, rayon, polypropylene, polyester, and poly (ethylene:propylene). Rayon and polyester were the dominant polymers. Additionally, the most dominant color of MPs in the wet and dry season was black and blue, respectively. The mean contents of MPs in the wet and dry season were 0.43 ± 0.18 and 0.34 ± 0.08 items/L, respectively. The Mann-Whitney U test suggested a significant difference between water quality in the wet and dry seasons (p < 0.05). Correlation analysis (Spearman rho) indicated a negative significant difference relationship between the MPs and the values of total dissolved solid (TDS) in the wet season (r = −0.821, p = <0.05), revealing that the large amounts of MPs may possibly be dispersed within surface water bodies with low TDS concentrations. Based on the overall findings, MP pollution in the surface water of the lagoon is not found to be influenced by the seasonal context. Rivers flowing into the lagoon, especially the U-Taphao River, may be a principal pathway contributing to increased MP pollution loading in the lagoon. The results can be used as baseline data to undertake further research work relevant to sources, fates, distribution, and impacts of MPs in other coastal lagoons.
Environmental Contamination and Remediation
Pradit et al. (2024) Occurrence and abundance of microplastics in surface water of Songkhla Lagoon. PeerJ 12:e17822 https://doi.org/10.7717/peerj.17822
Association between the metabolic score for insulin resistance and prostate cancer: a cross-sectional study in Xinjiang
Background Insulin resistance is associated with the development and progression of various cancers. However, the epidemiological evidence for the association between insulin resistance and prostate cancer is still limited. Objectives To investigate the associations between insulin resistance and prostate cancer prevalence. Methods A total of 451 patients who were pathologically diagnosed with prostate cancer in the First Affiliated Hospital of Xinjiang Medical University were selected as the case population; 1,863 participants who conducted physical examinations during the same period were selected as the control population. The metabolic score for insulin resistance (METS-IR) was calculated as a substitute indicator for evaluating insulin resistance. The Chi-square test and Mann-Whitney U test were performed to compare the basic information of the case population and control population. Univariate and multivariate logistic regression analyses to define factors that may influence prostate cancer prevalence. The generalized additive model (GAM) was applied to fit the relationship between METS-IR and prostate cancer. Interaction tests based on generalized additive model (GAM) and contour plots were also carried out to analyze the interaction effect of each factor with METS-IR on prostate cancer. Results METS-IR as both a continuous and categorical variable suggested that METS-IR was negatively associated with prostate cancer prevalence. Smoothed curves fitted by generalized additive model (GAM) displayed a nonlinear correlation between METS-IR and prostate cancer prevalence (P < 0.001), and presented that METS-IR was negatively associated with the odds ratio (OR) of prostate cancer. The interaction based on the generalized additive model (GAM) revealed that METS-IR interacted with low-density lipoprotein cholesterol (LDL-c) to influence the prostate cancer prevalence (P = 0.004). Contour plots showed that the highest prevalence probability of prostate cancer was achieved when METS-IR was minimal and low-density lipoprotein cholesterol (LDL-c) or total cholesterol (TC) was maximal. Conclusions METS-IR is nonlinearly and negatively associated with the prevalence of prostate cancer. The interaction between METS-IR and low-density lipoprotein cholesterol (LDL-c) has an impact on the prevalence of prostate cancer. The study suggests that the causal relationship between insulin resistance and prostate cancer still needs more research to confirm.
Wang et al. (2024) Association between the metabolic score for insulin resistance and prostate cancer: a cross-sectional study in Xinjiang. PeerJ 12:e17827 https://doi.org/10.7717/peerj.17827
Gliding toward an understanding of the origin of flight in bats
Bats are the only mammals capable of powered flight and have correspondingly specialized body plans, particularly in their limb morphology. The origin of bat flight is still not fully understood due to an uninformative fossil record but, from the perspective of a functional transition, it is widely hypothesized that bats evolved from gliding ancestors. Here, we test predictions of the gliding-to-flying hypothesis of the origin of bat flight by using phylogenetic comparative methods to model the evolution of forelimb and hindlimb traits on a dataset spanning four extinct bats and 231 extant mammals with diverse locomotor modes. Our results reveal that gliders exhibit adaptive trait optima (1) toward relatively elongate forelimbs that are intermediate between those of bats and non-gliding arborealists, and (2) toward relatively narrower but not longer hindlimbs that are intermediate between those of non-gliders and bats. We propose an adaptive landscape based on limb length and width optimal trends derived from our modeling analyses. Our results support a hypothetical evolutionary pathway wherein glider-like postcranial morphology precedes a bat-like morphology adapted to powered-flight, setting a foundation for future developmental, biomechanical, and evolutionary research to test this idea.
Burtner et al. (2024) Gliding toward an understanding of the origin of flight in bats. PeerJ 12:e17824 https://doi.org/10.7717/peerj.17824
Escaping the benthos with Coral Reef Arks: effects on coral translocation and fish biomass
Anthropogenic stressors like overfishing, land based runoff, and increasing temperatures cause the degradation of coral reefs, leading to the loss of corals and other calcifiers, increases in competitive fleshy algae, and increases in microbial pathogen abundance and hypoxia. To test the hypothesis that corals would be healthier by moving them off the benthos, a common garden experiment was conducted in which corals were translocated to midwater geodesic spheres (hereafter called Coral Reef Arks or Arks). Coral fragments translocated to the Arks survived significantly longer than equivalent coral fragments translocated to Control sites (i.e., benthos at the same depth). Over time, average living coral surface area and volume were higher on the Arks than the Control sites. The abundance and biomass of fish were also generally higher on the Arks compared to the Control sites, with more piscivorous fish on the Arks. The addition of Autonomous Reef Monitoring Structures (ARMS), which served as habitat for sessile and motile reef-associated organisms, also generally significantly increased fish associated with the Arks. Overall, the Arks increased translocated coral survivorship and growth, and exhibited knock-on effects such as higher fish abundance.
Carilli et al. (2024) Escaping the benthos with Coral Reef Arks: effects on coral translocation and fish biomass. PeerJ 12:e17640 https://doi.org/10.7717/peerj.17640
Study on the inhibitory mechanism of fig leaf extract against postharvest Fusarium in melon
The objective of this study was to explore the fungistatic mechanism of fig leaf extract against Fusarium and to provide a theoretical basis for the development of new plant-derived fungicides. Methods The fungistaticity of fig leaf extract were analyzed by the ring of inhibition method. Fusarium equiseti was selected as the target for analyzing its fungistatic mechanism in terms of mycelial morphology, ultrastructure, cell membrane permeability, membrane plasma peroxidation, reactive oxygen species (ROS) content and changes in the activity of protective enzymes. The effect of this extract was verified in melon, and its components were determined by metabolite analysis using ultraperformance liquid chromatography‒mass spectrometry (UPLC‒MS). Results Fig leaf extract had an obvious inhibitory effect on Fusarium, and the difference was significant (P < 0.05) or highly significant (P < 0.01). Scanning and transmission electron microscopy revealed that F. equiseti hyphae exhibited obvious folding, twisting and puckering phenomena, resulting in an increase in the cytoplasmic leakage of spores, interstitial plasma, and the concentration of the nucleus, which seriously damaged the integrity of the fungal cell membrane. This phenomenon was confirmed by propidium iodide (PI) and fluorescein diacetate (FAD) staining, cell membrane permeability and malondialdehyde (MDA) content. Fig leaf extract also induced the mycelium to produce excessive H2O2,which led to lipid peroxidation of the cell membrane, promoted the accumulation of MDA, accelerated protein hydrolysis, induced an increase in antioxidant enzyme activity, and disrupted the balance of ROS metabolism; these findings showed that fungal growth was inhibited, which was verified in melons. A total of 1,540 secondary metabolites were detected by broad-targeted metabolomics, among which the fungistatic active substances flavonoids (15.45%), phenolic acids (15%), and alkaloids (10.71%) accounted for a high percentage and the highest relative content of these substances 1,3,7,8-tetrahydroxy-2- prenylxanthone, 8-hydroxyquinoline and Azelaic acid were analysed for their antimicrobial, anti-inflammatory, antioxidant, preventive effects against plant diseases and acquisition of resistance by plants. This confirms the reason for the fungicidal properties of fig leaf extracts. Conclusion Fig leaf extract has the potential to be developed into a plant-derived fungicide as a new means of postharvest pathogen prevention and control in melon.
Yao et al. (2024) Study on the inhibitory mechanism of fig leaf extract against postharvest Fusarium in melon. PeerJ 12:e17654 https://doi.org/10.7717/peerj.17654
Exploring the mediating roles of physical literacy and mindfulness on psychological distress and life satisfaction among college students
Background Psychological distress has been a growing challenge to healthy living worldwide. Special attention has been concentrated on examining the cost of psychological distress on the life satisfaction of college students who are vulnerable groups coping with the challenge. The purpose of this study is to explore the roles of physical literacy (PL) and mindfulness in mediating the impact of psychological distress on life satisfaction among college students in China. Methods A sample of 653 students from six universities across three cities in China participated in an online survey, which included measures of PL, mindfulness, life satisfaction, as well as stress, anxiety, and depression levels. Structural equation modeling (SEM) was implemented to analyze the survey data. Results The findings of the SEM analysis demonstrated an acceptable model fit (X2/df = 3.63, CFI = 0.951, TLI = 0.940, RMSEA = 0.068, 90% CI = [0.060, 0.075], SRMR = 0.051) with a large effect size (R2 = 0.36) for life satisfaction, indicating that 36% of the variation in life satisfaction could be explained by the model. In addition, significant partial-mediation effects of PL and mindfulness were observed in the relationship between psychological distress and life satisfaction. These findings provide empirical support for the notion that interventions targeting PL and mindfulness practices may effectively enhance well-being and alleviate psychological distress among college students. Furthermore, this study suggests that integrating PL and mindfulness components into physical education and activity programs could be beneficial in meeting individuals’ holistic health needs.
Kan et al. (2024) Exploring the mediating roles of physical literacy and mindfulness on psychological distress and life satisfaction among college students. PeerJ 12:e17741 https://doi.org/10.7717/peerj.17741