Benchmarking of a time-saving and scalable protocol for the extraction of DNA from diverse viromes
The virome, composed of viruses inhabiting diverse ecosystems, significantly influences microbial community dynamics and host health. The phenol-chloroform DNA extraction protocol for viromes, though effective, is time-intensive and requires the use of multiple toxic chemicals. This study introduces a streamlined, scalable protocol for DNA extraction using a commercially-available kit as an alternative, assessing its performance against the phenol-chloroform method across human fecal, mouse fecal, and soil samples. No significant differences in virome diversity or community composition were seen between methods. Most viral operational taxonomic units (vOTUs) were common to both methods, with only a small percentage unique to either approach. Alpha- and beta-diversity analyses showed no significant impact of the extraction method on virome composition, confirming the kit’s efficacy and versatility on sample types beyond those officially supported by the manufacturer. While the kit approach offers benefits like reduced toxicity and increased throughput, it has limitations such as higher costs and potential issues reliably capturing low-abundance taxa. This protocol provides a viable option for large-scale virome studies, although the phenol-chloroform approach may still be preferable for specific sample types.
Shamash et al. (2025) Benchmarking of a time-saving and scalable protocol for the extraction of DNA from diverse viromes. PeerJ 13:e18785 https://doi.org/10.7717/peerj.18785
Do goats recognise humans cross-modally?
Recognition plays a key role in the social lives of gregarious species, enabling animals to distinguish among social partners and tailor their behaviour accordingly. As domesticated animals regularly interact with humans, as well as members of their own species, we might expect mechanisms used to discriminate between conspecifics to also apply to humans. Given that goats can combine visual and vocal cues to recognise one another, we investigated whether this cross-modal recognition extends to discriminating among familiar humans. We presented 26 goats (17 males and nine females) with facial photographs of familiar people and two repeated playbacks of a voice, either congruent (from the same person) or incongruent with that photograph (from a different person). When cues were incongruent, violating their expectations, we expected goats to show changes in physiological parameters and moreover, respond faster and for longer after playbacks. Accordingly, heart rate decreased as the playback sequence progressed, but only when the face and voice presented were incongruent. Heart rate variability was also affected by congruency, but we were unable to determine precisely where differences lay. However, goats showed no changes in time taken to respond, or how long they responded for (our primary variables of interest). We also found evidence to suggest that shifts in cardiac responses may not have been robust. Although our findings could imply that goats had successfully perceived differences in congruency between the visual and vocal identity information presented, further evidence is needed to determine whether they are capable of cross-modal recognition of humans.
Mason et al. (2025) Do goats recognise humans cross-modally?. PeerJ 13:e18786 https://doi.org/10.7717/peerj.18786
Sleep-wake patterns of fencing athletes: a long-term wearable device study
Objective Sleep is the most efficient means of recovery for athletes, guaranteeing optimal athletic performance. However, many athletes frequently experience sleep problems. Our study aims to describe the sleep-wake patterns of fencing athletes and determine whether factors, such as sex, competitive level and training schedules, could affect the sleep-wake rhythm. Methods Sleep data from 23 fencing athletes were collected using the Huawei Band 6, monitoring key sleep parameters such as bedtime, wake time, duration of deep and light sleep, wake periods, REM sleep duration, and nap duration. During this period, athletes were required to wear the band continuously for 24 hours daily, except bathing, charging, and competition times. Results Athletes averaged 7.97 hours of sleep per night, with significant differences observed in wake time (p = 0.015) and midpoint of sleep (p = 0.048) between high-level and low-level athletes, as well as a higher frequency of naps among high-level (χ2 = 11.97, p = 0.001) and female (χ2 = 3.88, p = 0.049) athletes. Nap duration was negatively correlated with night sleep duration (r = − 0.270, p < 0.001). Athletes were observed for changes in sleep-wake patterns from Monday to Sunday. On Mondays, Wednesdays, and Fridays, when there was no morning training, the athletes’ wake-up time and the midpoint of sleep were shifted significantly backward, and there were significant differences in sleep parameters between training days and rest days. Conclusion The sleep patterns of athletes differ according to level and gender. The sleep-wake patterns of athletes are influenced by training schedules, indicating the presence of sleep rhythm disruption.
Dai et al. (2025) Sleep-wake patterns of fencing athletes: a long-term wearable device study. PeerJ 13:e18812 https://doi.org/10.7717/peerj.18812
Identification and mechanistic insights of cell senescence-related genes in psoriasis
Background Psoriasis is a chronic inflammatory skin disease affecting 2–3% of the global population, characterised by red scaly patches that significantly affect patients’ quality of life. Recent studies have suggested that cell senescence, a state in which cells cease to divide and secrete inflammatory mediators, plays a critical role in various chronic diseases, including psoriasis. However, the involvement and mechanisms of action of senescence-related genes in psoriasis remain unclear. Methods This study aimed to identify senescence-related genes associated with psoriasis and explore their molecular mechanisms. RNA sequencing data from psoriasis and control samples were obtained from the GEO database. Differential expression analysis was performed using DESeq2 to identify differentially expressed genes (DEGs). The intersection of DEGs with cell senescence-related genes from the CellAge database was used to identify the candidate genes. Protein-protein interaction networks, Gene Ontology, and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted to explore the functions and pathways of these genes. Machine learning algorithms, including Least Absolute Shrinkage and Selection Operator (LASSO) regression and Support vector machine-recursive feature elimination (SVE-RFE), were used to select feature genes that were validated by qRT-PCR. Additionally, an immune cell infiltration analysis was performed to understand the roles of these genes in the immune response to psoriasis. Results This study identified 4,913 DEGs in psoriasis, of which 46 were related to cell senescence. Machine learning highlighted four key genes, CXCL1, ID4, CCND1, and IRF7, as significant. These genes were associated with immune cell infiltration and validated by qRT-PCR, suggesting their potential as therapeutic targets for psoriasis. Conclusions This study identified and validated key senescence-related genes involved in psoriasis, providing insights into their molecular mechanisms and potential therapeutic targets and offering a foundation for developing targeted therapies for psoriasis.
Deng et al. (2025) Identification and mechanistic insights of cell senescence-related genes in psoriasis. PeerJ 13:e18818 https://doi.org/10.7717/peerj.18818
Exploring freshwater soundscapes of tropical marshland habitats in Southeast Asia: insights into auditory sensory adaptation of wild Siamese fighting fish Betta splendens
While soundscapes shape the structure and function of auditory systems over evolutionary timescales, there is limited information regarding the adaptation of wild fish populations to their natural acoustic environments. This is particularly relevant for freshwater ecosystems, which are extremely diverse and face escalating pressures from human activities and associated noise pollution. The Siamese fighting fish Betta splendens is one of the most important cultured species in the global ornamental fish market and is increasingly recognized as a model organism for genetics and behavioural studies. This air-breathing species (Anabantoidei), characterized by the presence of a suprabranchial labyrinth organ that enhances auditory sensitivity, is native to Southeast Asia and inhabits low flow freshwater ecosystems that are increasingly threatened due to habitat destruction and pollution. We characterized the underwater soundscape, along with various ecological parameters, across five marshland habitats of B. splendens, from lentic waterbodies to small canals near a lake in Chiang Rai province (Thailand). All habitats exhibited common traits of low dissolved oxygen and dense herbaceous vegetation. Soundscapes were relatively quiet with Sound Pressure Level (SPL) around 102–105 dB re 1 µPa and most spectral energy below 1,000 Hz. Sound recordings captured diverse biological sounds, including potential fish vocalizations, but primarily insect sounds. Hearing thresholds were determined using auditory evoked potential (AEP) recordings, revealing best hearing range within 100–400 Hz. Males exhibited lower hearing thresholds than females at 400 and 600 Hz. This low-frequency tuning highlights the potential susceptibility of B. splendens to anthropogenic noise activities. This study provides first characterization of the auditory sensitivity and natural soundscape of B. splendens, establishing an important ground for future hearing research in this species. The information provided on the auditory sensory adaptation of B. splendens emphasizes the importance of preserving quiet soundscapes from lentic freshwater ecosystems.
Ramos et al. (2025) Exploring freshwater soundscapes of tropical marshland habitats in Southeast Asia: insights into auditory sensory adaptation of wild Siamese fighting fish Betta splendens. PeerJ 13:e18491 https://doi.org/10.7717/peerj.18491
Analysis of the anthropogenic effect on the Silencio River in Salvador Escalante, Michoacán, México
The average annual water availability worldwide is approximately 1,386 trillion cubic hectometers (hm3), of which 97.5% is saltwater and only 2.5% is freshwater. Nearly 70% is not available for human consumption as it is in glaciers, snow, and ice. It is estimated that only 0.77% is accessible freshwater for human use. Mexico has an availability of 451,584.7 million cubic meters (m3) of freshwater, with accessibility and distribution being unequal. The growth in urbanization, population, and industrialization has caused a decrease in water quality, and other parameters. Organic and inorganic contaminants evolved from various sources cause the degradation of water quality. The pollution of aquatic bodies, such as rivers and lakes, is one of the main problems in the world. In Salvador Escalante in México, the domestic wastewaters treatment plant (WWTP) is being exposed to effluents contaminated with metals like copper, cadmium, lead, and mercury. In this work, active sludges from the WWTP were analyzed. First, particle size distribution of flocs was measured by a sedimentation process. Secondly, analysis of the tolerance that microorganisms exhibit to metals (i.e., factors) was performed, based on a 2 $\hat {}$ ˆ (4-1) factorial design of experiments at laboratory-scale, measuring pH, chemical oxygen demand (COD) and electrical conductivity (responses). This aims to evaluate the capacity of the WWTP for improve the water quality. Microbiologic cultures were used for a qualitative study of the microorganisms contained in the active sludges; it was found that Enterobacterium does not grow in presence of heavy metals. Cadmium is the most harmful metal for microorganisms according to Pareto diagrams presented in this study.
Environmental Contamination and Remediation
Pérez-Méndez et al. (2025) Analysis of the anthropogenic effect on the Silencio River in Salvador Escalante, Michoacán, México. PeerJ 13:e18531 https://doi.org/10.7717/peerj.18531
Insecticides may facilitate the escape of weeds from biological control
Background Preventative pesticide seed treatments (hereafter preventative pest management or PPM) are common corn and soybean treatments, and often include both fungicides and neonicotinoid insecticides. While PPM is intended to protect crops from soil-borne pathogens and early season insect pests, these seed treatments may have detrimental effects on biological control of weed seeds by insects. Methods Here, in two 3-year corn-soy rotations in Pennsylvania USA, we investigated a PPM approach to insect management compared to an integrated pest management approach (IPM) and a “no (insect) pest management” (NPM) control. This was crossed with a grass cover crop to see if this conservation practice can help recover the ecosystem services affected by chemical pest management practices. We hypothesized that PPM and IPM approaches would release weed seeds from biological control by insects but cover crops would increase biological control. We measured the effect of these treatments on the weed-seed bank, mid-season weed biomass, granivorous insect activity-density, and weed-seed predation. Results We found that, contrary to our hypothesis, planting a cover crop decreased carabid activity-density without consistent differences in weed-seed predation. Pest management and cover crop treatments also had inconsistent effects on the weed-seed bank and mid-season weed biomass, but insecticide use without a cover crop increased the biomass of likely glyphosate-resistant marestail (Erigeron canadensis L.) at the end of the trial. Our results suggest that reducing insecticide use may be important when combating herbicide-resistant weeds. We found planting cover crops and/or avoiding the use of insecticides may combat these problematic weeds.
Rowen et al. (2025) Insecticides may facilitate the escape of weeds from biological control. PeerJ 13:e18597 https://doi.org/10.7717/peerj.18597
Thermal ecology of the Mexican Garter Snake (Thamnophis eques): temporal and spatial variations
Heterogeneous environments provide different daily and seasonal thermal conditions for snakes, resulting in temporal and spatial variations in body temperature (Tb). This study analyzes the Tb of Thamnophis eques in the forest and grassland of a Mexican locality through daily and seasonal profiling. The patterns were obtained from seminatural enclosures in the field with a point sampling strategy to analyze temporal and spatial variations in Tb. The variation of Tb throughout the day was correlated with air and substrate temperatures, both in the grassland and in the forest. The average Tb in the grassland was 0.88 °C greater than in the forest. Our results indicate that T. eques showed differences in Tb between grassland and forest, principally in late spring and early summer during the early rise and late plateau phases, coinciding with the presence of foliage on the willow trees present in the study area, while in late summer and early autumn, the Tb was similar when willow trees canopy cover was absent (May–September). Our results support the hypothesis that the Tb of snakes differ between forests when the willows have leaves and is similar when canopy cover is equivalent, in this case, when tree canopy cover was absent. Our results also shown that T. eques presented daily and seasonal warming patterns similar to other Arizona populations and like those of other northern Gartersnakes. However, this result may not be valid for the entire wide distribution and consequent diversity of habitats of T. eques. The information of Tb in T. eques through daily and seasonal profiles in different habitats could aid in understanding the effects of environmental conditions on the ecological strategies deployed by snakes on habitat selection.
Venegas-Barrera et al. (2025) Thermal ecology of the Mexican Garter Snake (Thamnophis eques): temporal and spatial variations. PeerJ 13:e18641 https://doi.org/10.7717/peerj.18641
Common insect pests in homes and cultural heritage sites
Insect pests represent a threat to the integrity of historic buildings and homes, causing serious losses and irreversible damage. These pests can cause extensive damage to organic materials, including wood, textiles, and paper. Beetles, termites, booklice, moths, and cockroaches are just some of the main insect pests that are frequently found in historic buildings and homes. Beetle species such as the furniture beetle and the powderpost beetle are well recognised for their capacity to infest and feed on wood. Termite infestations can remain undetected and cause considerable damage that may even lead to the complete destruction of a building’s structural integrity. Cloth moth larvae are known to damage textiles, including carpets, furniture, clothes, and tapestries. Some wood-destroying species of cockroaches have the potential to harm historic buildings. Booklice have the ability to eat cellulose fibres found in archived articles and artefacts stored in heritage buildings, causing deterioration and damage to documents over time. This article reviews the literature and presents an overview of the major insect pests belonging to five known orders Coleoptera, Blattodea, Lepidoptera, Zygentoma (long-tailed silverfish) and Psocoptera, which pose a threat to households, museums, depositories, libraries, and cultural heritage buildings. We also discuss their biology, their impact on human health, and the various potential approaches to identifying them.
Hasnaoui et al. (2025) Common insect pests in homes and cultural heritage sites. PeerJ 13:e18700 https://doi.org/10.7717/peerj.18700
Single-cell transcriptome analysis reveals cellular reprogramming and changes of immune cell subsets following tetramethylpyrazine treatment in LPS-induced acute lung injury
Background Acute lung injury (ALI) is a disordered pulmonary disease characterized by acute respiratory insufficiency with tachypnea, cyanosis refractory to oxygen and diffuse alveolar infiltrates. Despite increased research into ALI, current clinical treatments lack effectiveness. Tetramethylpyrazine (TMP) has shown potential in ALI treatment, and understanding its effects on the pulmonary microenvironment and its underlying mechanisms is imperative. Methods We established a mouse model of lipopolysaccharide (LPS)-induced ALI and performed single cell RNA sequencing (scRNA-seq). Bioinformatic analyses of the immune, epithelial and endothelial cells were then performed to explore the dynamic changes of the lung tissue microenvironment. We also analyzed the effects of TMP on the cell subtypes, differential gene expression and potential regulation of transcriptional factors involved. Immunohistochemistry and enzyme-linked immunosorbent assay were performed to identify the effects of TMP on immune inflammatory response. Results We found that TMP efficiently protected against LPS-induced acute lung injury. Results of scRNA-seq showed that the cells were divided into seven major cell clusters, including immune cells, fibroblasts, endothelial cells and epithelial cells. Neither dexamethasone (Dex) nor TMP treatment showed any significant protective effects in these clusters. However, TMP treatment in the LPS-induced ALI model significantly increased follicular helper T cells and reduced CD8+ naive T cells, Vcan-positive monocytes and Siva-positive NK cells. In addition, TMP treatment increased the number of basal epithelial cells and lymphatic endothelial cells (LECs), indicating its protective effects on these cell types. Scenic analysis suggested that TMP likely mitigates LPS-induced injury in epithelial and endothelial cells by promoting FOSL1 in basal epithelial cells and JunB in LECs. Conclusions Our findings suggest that TMP appears to alleviate LPS-induced lung injury by regulating the immune response, promoting epithelial cell survival and boosting the antioxidant potential of endothelial cells. This study highlights the potential therapeutic use of TMP in the management of ALI.
Wu et al. (2025) Single-cell transcriptome analysis reveals cellular reprogramming and changes of immune cell subsets following tetramethylpyrazine treatment in LPS-induced acute lung injury. PeerJ 13:e18772 https://doi.org/10.7717/peerj.18772