title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=135 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Three new species of the spider genus Naphrys Edwards (Araneae, Salticidae) under morphology and molecular data with notes in the distribution of Naphrys acerba (Peckham & Peckham) from Mexico link: https://peerj.com/articles/18775 last-modified: 2025-01-31 description: Herein, we describe three new species of the spider genus Naphrys Edwards, 2003 from Mexico: Naphrys echerisp. nov., Naphrys tecoxquinsp. nov., and Naphrys tuucasp. nov. An integrative taxonomic approach was applied, utilizing data from morphology, ultra-morphology, the mitochondrial gene COI, and distribution records. Four molecular methods for species delimitation were implemented under the corrected p-distance Neighbor-Joining (NJ) criteria: (1) Assemble Species by Automatic Partitioning (ASAP); (2) general mixed Yule coalescent (GMYC); (3) Bayesian Poisson tree process (bPTP); and (4) multi-rate Poisson tree process (mPTP). Both morphological and molecular data supported the delimitation and recognition of the three new species. The average interspecific genetic distance (p-distance) within the genus Naphrys is 14%, while the intraspecific genetic distances (p-distance) is <2% for most species. We demonstrate that the natural distribution of Naphrys is not restricted to the Nearctic region. Furthermore, the reported localities herein represent the first with precise locations in the country for Naphrys acerba. In addition, a taxonomic identification key is provided for the species in the genus. creator: Juan Maldonado-Carrizales creator: Alejandro Valdez-Mondragón creator: María L. Jiménez-Jiménez creator: Javier Ponce-Saavedra uri: https://doi.org/10.7717/peerj.18775 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Maldonado-Carrizales et al. title: Harnessing the potential of chloroplast-derived expression elements for enhanced production of cellulases in Escherichia coli link: https://peerj.com/articles/18616 last-modified: 2025-01-31 description: Thermophilic cellulases can play a crucial part in the efficient breakdown of cellulose—a major component of lignocellulosic plant biomass, however, their commercial production needs simple and robust biomanufacturing biosystems. In this study, two cellulases (β-glucosidase and endoglucanase) were heterologously expressed in Escherichia coli under a chloroplast-derived constitutive promoter and expression-enhancing terminator. The genes encoding the cellulases were sourced from a thermophilic bacterium Thermotoga maritima to exploit their industrially needed thermotolerance potential. The codon-optimized gene sequences were synthesized and placed under a tobacco chloroplast 16S rRNA promoter (Prrn), along with the 5′ UTR (untranslated region) from gene 10 of phage T7 (T7g10). A six-residue long histidine tag (His6-tag) was attached to the N-terminus for protein detection. A high-level of expression of β-glucosidase and endoglucanase in E. coli was recorded from the chloroplast promoter and terminator. Furthermore, the activity assays confirmed that the recombinant enzymes maintained their activity at elevated temperatures. Thermostability analysis showed that recombinant enzymes retained their thermotolerance even after being expressed in a non-native host. Where, β-glucosidase and endoglucanase showed their optimum activities at 90 °C and 100 °C, respectively. Examination of the 3D structures of T. maritima cellulases revealed differential ionic interactions contributing to this high degree of thermotolerance. The study highlights the feasibility of producing thermostable versions of recombinant enzymes in E. coli at high levels. Our finding underscores the potential of this approach to meet industrial demands for efficient enzyme production employing E. coli as a robust biomanufacturing platform. creator: Ayesha Siddiqui creator: Muhammad Mudassar Iqbal creator: Asad Ali creator: Iqra Fatima creator: Hazrat Ali creator: Aamir Shehzad creator: Sameer H. Qari creator: Ghulam Raza creator: Muhammad Aamer Mehmood creator: Peter J. Nixon creator: Niaz Ahmad uri: https://doi.org/10.7717/peerj.18616 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Siddiqui et al. title: Life expectancy of cats in Britain: moggies and mollies live longer link: https://peerj.com/articles/18869 last-modified: 2025-01-30 description: The domestic cat (Felis catus) has been a popular companion animal for about 12,000 years, initially valued for rodent control before evolving into pets that provide affection and companionship. Unlike dogs, cats were not selectively bred for specific roles until the late 1800s, resulting in breeds defined primarily by appearance, which sometimes leads to genetic disorders. Modern animal welfare concerns emphasize longevity and health, prompting research into factors affecting cat lifespans, including sex, reproductive status, and breed. This study aims to expand on previous UK research by analyzing these interactions and highlighting the potential negative impacts of pure breeding on cat health. Data from 7,708 cats receiving veterinary care in the UK during 2019 were analyzed, focusing on reproductive status, breeding status, age at death, and sex. Data were analyzed using ANOVA and Cox proportional hazards models to assess survival differences. The overall mean lifespan of cats in the UK is 11.83 years. Analysis indicates that male cats live shorter lives than females, attributed to higher trauma rates and health issues among males. Neutered/spayed cats generally exhibit longer lifespans compared to entire cats. Tom cats have the shortest lifespan, while spayed females (mollies) live the longest. Moggies tend to outlive both pure and cross-bred cats, suggesting that genetic diversity may contribute to greater longevity. The results of this study emphasize the influence of sex, reproductive status, and cat type on feline lifespan, highlighting the need for targeted health interventions, particularly for male cats. The findings underscore the complex interplay of genetic and environmental factors in determining the health and longevity of domestic cats. This research not only contributes to existing knowledge but also advocates for the consideration of these variables in future studies and veterinary practices. creator: Fernando Mata uri: https://doi.org/10.7717/peerj.18869 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Mata title: Prediction of influenza A virus-human protein-protein interactions using XGBoost with continuous and discontinuous amino acids information link: https://peerj.com/articles/18863 last-modified: 2025-01-30 description: Influenza A virus (IAV) has the characteristics of high infectivity and high pathogenicity, which makes IAV infection a serious public health threat. Identifying protein-protein interactions (PPIs) between IAV and human proteins is beneficial for understanding the mechanism of viral infection and designing antiviral drugs. In this article, we developed a sequence-based machine learning method for predicting PPI. First, we applied a new negative sample construction method to establish a high-quality IAV-human PPI dataset. Then we used conjoint triad (CT) and Moran autocorrelation (Moran) to encode biologically relevant features. The joint consideration utilizing the complementary information between contiguous and discontinuous amino acids provides a more comprehensive description of PPI information. After comparing different machine learning models, the eXtreme Gradient Boosting (XGBoost) model was determined as the final model for the prediction. The model achieved an accuracy of 96.89%, precision of 98.79%, recall of 94.85%, F1-score of 96.78%. Finally, we successfully identified 3,269 potential target proteins. Gene ontology (GO) and pathway analysis showed that these genes were highly associated with IAV infection. The analysis of the PPI network further revealed that the predicted proteins were classified as core proteins within the human protein interaction network. This study may encourage the identification of potential targets for the discovery of more effective anti-influenza drugs. The source codes and datasets are available at https://github.com/HVPPIlab/IVA-Human-PPI/. creator: Binghua Li creator: Xin Li creator: Xiaoyu Li creator: Li Wang creator: Jun Lu creator: Jia Wang uri: https://doi.org/10.7717/peerj.18863 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Li et al. title: Serum salusin levels in diarrhea- and constipation-predominant irritable bowel syndrome link: https://peerj.com/articles/18859 last-modified: 2025-01-30 description: ObjectiveInflammation and immunity play major roles in the etiopathogenesis of functional intestinal disorders. The salusins that were identified in this study are important because of their ease of collection, sensitivity and reliability. For that reason, the aim of this study was to analyze the importance of the levels of salusin in the blood, an inflammation-related parameter, in the diagnosis and prediction of irritable bowel disease.MethodologyThe study participants included 28 diagnosed with constipation-predominant IBS, 29 (34.1%) diagnosed with diarrhea-predominant IBS (D-IBS), and 28 (32.9%) controls. Enzyme-linked immune-sorbent assay (ELISA) method has been used for the measurement of salusin levels.ResultsParticipants were 50 (58.8%) female and 35 (41.2%) male. The serum levels of salusin-α were substantially reduced in the diarrhea-predominant IBS group vs controls. There was also no major difference in the levels of salusin between the constipation-predominant-IBS and the diarrhea-predominant IBS group.ConclusionA major prognostic relationship was found between the level of salusins and the subgroup of D-IBS. It is well known that salusins have been related to inflammatory processes and oxidative injury in previous studies. The relationship between salusin and gastrointestinal diseases should be further investigated. Low-grade submucosal intestinal inflammation is also associated with irritable bowel syndrome. It is our belief that salusins may be useful in diagnosing, predicting or treating IBS. creator: Elif Tugba Tuncel creator: Seda Sabah Ozcan creator: Mehmet Korkmaz creator: Elif Börekci uri: https://doi.org/10.7717/peerj.18859 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Tuncel et al. title: Acidity, sugar, and alcohol contents during the fermentation of Osmanthus-flavored sweet rice wine and microbial community dynamics link: https://peerj.com/articles/18826 last-modified: 2025-01-30 description: Sweet rice wine is a popular traditional Chinese rice wine widely loved by Chinese people for its high nutritional value. Osmanthus flower petals contain various nutrients and have good medicinal value. However, the dynamics of the sugar level, acidity, alcohol content, and microbial community during the fermentation of Osmanthus-flavored sweet rice wine have not been evaluated, which can lead to the unstable quality of Osmanthus flower sweet rice wine (OFSRW). In this study, the dynamic changes in sugar level, acidity, alcohol content, microbial community composition, and microbial metabolic pathways during traditional fermentation of OFSRW at four-time points—0 h (AG0), 24 h (AG24), 36 h (AG36), and 43 h (AG43)—were analyzed via direct titration, total acid assays, alcoholometry, and high-throughput macrogenomic techniques. First, we found that bacteria were the dominant microorganisms in the early stage of OFSRW fermentation (AG0), fungi were the dominant microorganisms in the middle and late stages of fermentation (AG24 and AG36), and Rhizopus was the main fungal genus throughout fermentation. Acidity and total sugars increased with fermentation time, and alcohol was not detected until the end of fermentation. Diversity analysis revealed that the dominant species at the beginning of natural fermentation was A. johnsonii, and R. delemar became the dominant species as natural fermentation progressed. Metabolic pathway analysis revealed that energy production and conversion, carbohydrate transport, amino acid transport, and metabolic pathways were the most active metabolic pathways in the fermenter. These results provide a reference basis for changes in the microbial community during the fermentation of cinnamon-flavored sweet rice wine. creator: Ping Tian creator: Jiaqiong Wan creator: Tuo Yin creator: Li Liu creator: Hongbing Ren creator: Hanbing Cai creator: Xiaozhen Liu creator: Hanyao Zhang uri: https://doi.org/10.7717/peerj.18826 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Tian et al. title: Freshwater sponges in the southeastern U.S. harbor unique microbiomes that are influenced by host and environmental factors link: https://peerj.com/articles/18807 last-modified: 2025-01-30 description: Marine, and more recently, freshwater sponges are known to harbor unique microbial symbiotic communities relative to the surrounding water; however, our understanding of the microbial ecology and diversity of freshwater sponges is vastly limited compared to those of marine sponges. Here we analyzed the microbiomes of three freshwater sponge species: Radiospongilla crateriformis, Eunapius fragilis, and Trochospongilla horrida, across four sites in western North Carolina, U.S.A. Our results support recent work indicating that freshwater sponges indeed harbor a distinct microbiome composition compared to the surrounding water and that these varied across sampling site indicating both environmental and host factors in shaping this distinct community. We also sampled sponges at one site over 3 months and observed that divergence in the microbial community between sponge and water occurs at least several weeks after sponges emerge for the growing season and that sponges maintain a distinct community from the water as the sponge tissue degrades. Bacterial taxa within the Gammproteobacteria, Alphproteobacteria, Bacteroidota (Flavobacteriia in particular), and Verrucomicrobia, were notable as enriched in the sponge relative to the surrounding water across sponge individuals with diverging microbial communities from the water. These results add novel information on the assembly and maintenance of microbial communities in an ancient metazoan host and is one of few published studies on freshwater sponge microbial symbiont communities. creator: Jacqueline G. Keleher creator: Taylor A. Strope creator: Noah E. Estrada creator: Allison M. Griggs Mathis creator: Cole G. Easson creator: Cara Fiore uri: https://doi.org/10.7717/peerj.18807 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Keleher et al. title: An analysis of the 24-hour on-call experience and treatment decision of a dental resident, a retrospective study link: https://peerj.com/articles/18678 last-modified: 2025-01-30 description: ObjectivesTo analyze the 24-hour on-call experience and factors influencing the treatment decisions of a dental resident for dental emergencies, particularly pulpitis, during on-call hours.MethodsThis retrospective study was conducted at a public stomatology hospital from January 1 to December 30, 2023. Each consultation was documented, recording the date and time, patient age and gender, diagnosis, and any emergent interventions. Statistical analyses were conducted using univariate analysis to explore the association between various factors and the incidence of dental interventions for pulpitis, with significance set at p < 0.05.ResultsOver 1 year, 81 residents from seven specialties managed 2,717 consultations during 365 instances of 24-h call duty. The busiest months were October (n = 297). Most consultations occurred during extended hours (1,856 consultations) compared to normal hours (8:00–17:00) (861 consultations). The busiest consultation periods were between 20:00 and 22:00. Pulpitis was the most frequently diagnosed condition (n = 988). Univariate analysis showed no significant impact of patient gender (p = 0.896) or age (p = 0.632) on the likelihood of receiving a dental intervention. However, consultations during extended hours were twice as likely (OR = 2.028, 95% CI [1.510–2.723]) to result in no intervention compared to normal hours. Endodontics and pediatric dentistry residents were more likely to perform interventions compared to other specialties, with postgraduate year (PGY) six residents being less likely to perform interventions compared to PGY4 residents.ConclusionResidents exhibit lower willingness to perform dental interventions during extended working hours and in higher grade levels, with significant variability across different specialties. Enhanced training and fatigue risk management for residents may help to ensure effective patient care during on-call hours. creator: Jiaoer Zheng creator: Ji Xu creator: Denghui Zhang uri: https://doi.org/10.7717/peerj.18678 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zheng et al. title: A new species of parrot snake, Leptophis (Serpentes: Colubridae) from the Brazilian Cerrado link: https://peerj.com/articles/18528 last-modified: 2025-01-30 description: We describe a new species of Leptophis (parrot snake) from the Cerrado ecoregion of Brazil. The new species, L. mystacinus sp. nov., differs from all other congeners in the following unique character combination: two Spectrum Green (129) to Light Parrot Green (133) dorsolateral stripes separated by a Buff (5) vertebral stripe, usually continuous onto the tail; loreal scale absent; postocular stripe Jet Black (300), wide and long (up 11 scales long onto nuchal region); maxillary teeth 21–25; ventrals 158–173; subcaudals 141–164; black spots on head absent; supracephalic plates of head not edged with black pigment; adult color pattern lacking dark oblique bands; keels absent on first dorsal scale rows; hemipenis unilobed, noncapitate, with undivided sulcus spermaticus, and first row of hemipenial body with four spines. Phylogenetic analysis of 16S mtDNA sequences indicate the new species is the sister taxon of L. dibernardoi, a species occurring in the neighboring Caatinga ecoregion. creator: Nelson R. Albuquerque creator: Roullien H. Martins creator: Priscila S. Carvalho creator: Donald B. Shepard creator: Diego J. Santana uri: https://doi.org/10.7717/peerj.18528 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Albuquerque et al. title: Biocontrol efficacy of Bacillus licheniformis and Bacillus amyloliquefaciens against rice pathogens link: https://peerj.com/articles/18920 last-modified: 2025-01-29 description: Biocontrol is a cost-effective and eco-friendly approach to control plant pathogens using natural enemies. Antagonistic microorganisms or their derivatives specifically target the plant pathogens while minimizing the harm to non-target organisms. Bacterial blight and brown spot are the major rice diseases caused by Xanthomonas oryzae pv. oryzae (Xoo) and Bipolaris oryzae (Bo), respectively. This study was conducted to assess the plant growth-promoting potential and biocontrol activity of root-associated bacteria against the rice pathogens, Xoo and Bo. A total of 98 bacteria were isolated from rice roots and characterized for plant growth-promoting properties including phosphate solubilization, indole-3-acetic acid production, nitrogen fixation and biofilm formation. Based on these properties, 36 bacteria were selected and tested for biocontrol potential against rice pathogens via co-culturing antagonism assay. LE7 exhibited the maximum inhibition of 79%, while FR8, PE2, LE7, LR22 and LR28 also significantly reduced the growth of Xoo. Likewise, FR2, LR22, LR35 and LE7 significantly inhibited the growth of Bo, in which LR22 exhibited the maximum inhibition of 81%. Under controlled-conditions, LE7 and LR22 significantly reduced the disease incidence of Xoo and Bo, respectively, and improved the growth of rice. Full-length 16S rRNA gene sequencing of most potential bacterial isolates, LE7 and LR22, revealed their maximum identity with Bacillus amyloliquefaciens and Bacillus licheniformis, respectively. Application of Bacillus spp. as biocontrol agent represents enormous potential in rice farming. The most promising bacterial isolates could be used as bioinoculants for rice disease management and improved production in a sustainable manner. creator: Mohsin Tariq creator: Mehvish Zahoor creator: Tahira Yasmeen creator: Tahir Naqqash creator: Muhammad Abdul Rehman Rashid creator: Muhammad Abdullah creator: Abdul Rafay Rafiq creator: Marriam Zafar creator: Iqra Irfan creator: Ijaz Rasul uri: https://doi.org/10.7717/peerj.18920 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Tariq et al.