Exploring phytochemicals as potential pharmacological inhibitors for NS1 protein of Kyasanur forest disease virus using virtual screening, molecular docking, and molecular simulation approach
Background Kyasanur forest disease virus (KFDV) remains a significant public health challenge due to the limitations of existing vaccines, creating a critical need for effective antiviral treatments. KFDV is a tick-borne virus responsible for 400–500 new cases annually, with a mortality rate of 3–5%. The nonstructural protein 1 (NS1), which plays crucial roles in host cell interactions, immune evasion, and viral replication, represents a promising target for antiviral drug development. Objective This study aims to identify potential antiviral compounds that inhibit the activity of KFDV NS1 protein using a computational pharmacological drug design approach. The objectives include determining the 3D structure of the NS1 protein through homology modeling, conducting virtual screening of phytochemicals to identify potential inhibitors, and performing molecular dynamics simulations to assess the stability and binding free energies of the selected compounds. Methods The 3D structure of KFDV NS1 protein was predicted using homology modeling and validated using Ramachandran plot analysis. Virtual screening of phytochemicals from the Indian Medicinal Plants, Phytochemistry And Therapeutics (IMPPAT) database was performed to identify potential NS1 inhibitors. The top 15 compounds with the highest binding affinities were selected and subjected to absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis. Molecular dynamics simulations were conducted in duplicates for 200 ns to evaluate the stability of the ligand-NS1 complexes, and an additional independent simulation with randomized initial velocities was performed to ensure statistical robustness. Binding free energies were calculated using the molecular mechanics-generalized born surface area (MM-GBSA) method to determine the binding strength of each compound. Results The 3D structure of the KFDV NS1 protein was determined using I-Tasser-MTD, Robetta, and Swiss Model servers, and a minimized model of I-Tasser, achieving an ERRAT score of 94.37, was selected. Virtual screening of 11,530 phytochemicals from the IMPPAT database identified the top 115 compounds after three screening phases. Out of the 15 screened compounds, L2, L3, and L5 demonstrated notable binding affinities of −9.34, −9.12, and −9.08 kcal/mol, respectively, compared to the FDA-approved antiviral dasabuvir, which had a binding affinity of −8.0 kcal/mol. Molecular dynamics simulations confirmed the stability of compounds L2 (IMPHY010294), L3 (IMPHY001281), L5 (IMPHY011162), and dasabuvir, with free-energy binding values of −62.97 ± 4.0, −77.22 ± 4.71, −62.07 ± 2.88, and −87.68 ± 4.31 kcal/mol, respectively. Conclusion The computational analysis suggests that compounds L2 and L3 have strong binding affinities comparable to dasabuvir, indicating their potential as pharmacological inhibitors of the KFDV NS1 protein. Further validation through in vitro assays would complement these in silico findings.
Achappa et al. (2025) Exploring phytochemicals as potential pharmacological inhibitors for NS1 protein of Kyasanur forest disease virus using virtual screening, molecular docking, and molecular simulation approach. PeerJ 13:e19954 https://doi.org/10.7717/peerj.19954
Scanning electron microscopy (SEM) reveals high diversity of setae on the hind tibiae and basitarsi of Peruvian Stingless Bees (Apidae: Meliponini)
Stingless bees belong to the group of corbiculate bees, all characterized by the presence of a corbicula, a specialized structure of the hind tibia used for pollen collection. This group exhibits significant variation in foraging behavior, from flower-visiting foragers to kleptoparasites and obligate necrophagous. So far, scanning electron microscopy (SEM) studies have been mainly focused on the hind leg setae of Apis spp. and Bombus spp. Here, we performed a comparative morphological analysis of the setae and the pollen handling structures in the hind tibiae and basitarsi of seven stingless bee species: the floral pollen collector bees Melipona cf. eburnea, Partamona testacea, Scaura cf. latitarsis, Trigonisca cf. atomaria, Trigona dallatorreana, the robber bee Lestrimelitta sp. and the obligate necrophagous Trigona cf. hypogea, collected in Peruvian forests in 2020. The setae were classified into simple and branched types, subdivided into five and seven subtypes, respectively. In addition, we described three types of penicillum, five types of rastellum, three types of pollen brush, two types of setae covering the auricular area, and show the setae forming the sericeous area of Trigona spp. Finally, seven types of keirotrichia are described. We highlight that certain types of setae show a high degree of conservation across species, while others are unique and potentially indicative of adaptive specialization. Among species that have abandoned pollen foraging on flowers, we observed a simplification in the number of setal types and the absence of pollen handling structures in Lestrimelitta sp., whereas T. cf. hypogea exhibits the highest diversity of setae and retains most of these structures. Finally, based on these two species, we reflect on the link between reduced corbicula and functional corbicula. The study highlights the importance of further exploring the mechanical and sensory roles of setae and expanding this research in Meliponini. Such investigations can improve our understanding of their adaptive functions and provide valuable insights into the functional ecology, taxonomy and phylogenetic studies of these tropical pollinators.
Marconi et al. (2025) Scanning electron microscopy (SEM) reveals high diversity of setae on the hind tibiae and basitarsi of Peruvian Stingless Bees (Apidae: Meliponini). PeerJ 13:e19749 https://doi.org/10.7717/peerj.19749
Retrospective study: anthropometric and metabolic characteristics of patients with metabolic syndrome–a gender-specific analysis of clinical and correlation patterns
Background Metabolic syndrome (MetS) is a prevalent condition associated with increased cardiometabolic risk. Despite its clinical significance, the relationships between anthropometric indices and metabolic markers—particularly in a gender-specific context—remain inadequately explored. Methods This retrospective study included 104 patients diagnosed with MetS between 2016 and 2022. Anthropometric indices, including body roundness index (BRI), body mass index (BMI), waist-to-height ratio (WHtR), and weight-to-waist index (WWI), were analyzed for their associations with metabolic markers reflecting insulin resistance and glucose metabolism: fasting blood glucose (FBG), fasting insulin (FIns), and homeostatic model assessment of insulin resistance (HOMA-IR). These markers represent key components of MetS, although other diagnostic elements such as dyslipidemia and hypertension were beyond the scope of this analysis. Gender-specific subgroup analyses were conducted for 57 female and 47 male patients. Results Significant differences in anthropometric and metabolic characteristics were observed between genders. Male patients exhibited higher BMI (40.4 [37.5, 44.2] vs. 37.2 [33.6, 40.3], p = 0.022), waist circumference (128.0 [120.2, 137.5] cm vs. 115.0 [106.0, 120.0] cm, p < 0.001), and FIns levels (22.8 [16.4, 29.5] μIU/mL vs. 17.8 [15.0, 23.4] μIU/mL, p = 0.107). Correlation analyses revealed that BMI and BRI were strongly associated with HOMA-IR and FIns in both genders, with stronger associations observed in males (e.g., BMI vs. FIns, r = 0.60, p < 0.001). WHtR was significantly correlated with metabolic markers in males but not in females. WWI showed limited correlations across both genders. Discussion This study highlights distinct gender-specific patterns in the relationships between anthropometric indices and metabolic markers in MetS patients. These findings underscore the importance of tailored strategies in managing MetS, particularly considering gender-based differences in clinical and metabolic profiles.
Li et al. (2025) Retrospective study: anthropometric and metabolic characteristics of patients with metabolic syndrome–a gender-specific analysis of clinical and correlation patterns. PeerJ 13:e20183 https://doi.org/10.7717/peerj.20183
Barriers to care and the need for dental educational materials for the Lowe syndrome community: a survey of dentists
Background This study aimed to assess dentists’ experience in treating individuals with Lowe syndrome (LS), reasons they may be unable to provide dental care for individuals with LS, and perceptions of the need for educational materials tailored to the LS community regarding the dental setting. Methods A link to an electronic Qualtrics survey addressing these topics was emailed to the Tufts University School of Dental Medicine Alumni Network listserv. Results Data from 73 respondents were analyzed. Of the 57 who answered the question about having treated a patient with LS, three (5.3%) responded affirmatively. Among the 61 who answered why they might not be able to treat an individual with LS, the most common reasons were lack of experience treating children with special needs and not accepting medical assistance such as Medicaid/Medicare (both 31.1%). Of the 58 who responded to the item regarding the need for educational materials to support patients with LS in the dental setting, 47 (81.0%) agreed or strongly agreed. Conclusion Substantial barriers to dental care exist for individuals with LS. Educational materials about the dental setting should be developed for the LS community.
Lowenstein et al. (2025) Barriers to care and the need for dental educational materials for the Lowe syndrome community: a survey of dentists. PeerJ 13:e20174 https://doi.org/10.7717/peerj.20174
Impact of two field preservation methods on genotyping success of feces
Non-invasive samples, such as feces, remain an important source of DNA for genetic analyses in molecular ecology and conservation genetics, especially when working with elusive or endangered species. However, as labs transition to higher throughput and genomic-based technologies, many protocols that have been used for decades are becoming obsolete. New approaches have been developed for high-quality samples, now low-quality samples require further technical advances. Fecal samples obtained for non-invasive wildlife studies are typically of very low quality and sampling methods need to be optimized to reduce work and costs per sample. Preservation methods in the field affect the workload in the lab required to obtain genetic data, as well as the final genotype quality. Liquid preservation methods, such as nucleic acid preservation (NAP) buffer and ethanol, have been used during sampling to maintain DNA quality at room temperature until samples can reach the lab. NAP buffer is a non-hazardous, non-flammable solution (easy to send through post), and avoids having to dry the feces before DNA extraction (saving time and increasing safety). Here we compare two different liquid preservation methods (NAP buffer and 96% ethanol) for microsatellite genotyping by next generation sequencing of wolf fecal samples collected in the field and shipped at ambient temperature. Samples preserved in ethanol showed a higher rate of amplification and genotyping success than in NAP buffer, especially due to a higher rate of allelic dropout in NAP. Consequently, the number of replicates required to achieve high quality genotypes was slightly higher for fecal samples preserved in NAP buffer than for those preserved in ethanol. These results are important for the planning and optimization of projects that involve microsatellite genotyping from feces using high throughput technologies.
Valencia-Montoya et al. (2025) Impact of two field preservation methods on genotyping success of feces. PeerJ 13:e20154 https://doi.org/10.7717/peerj.20154
Solubilization of skin collagen improves the accuracy and reliability of stable isotope measurements
Stable isotope analysis of skin collagen is useful for detecting short-term or seasonal diet. Preparation of skin for stable isotope analysis varies across laboratories, and this may impact the comparability of data. It is important to understand the effects of different preparatory protocols on the stable isotopic and elemental compositions of skin samples. Using a Eurovector 3,300 elemental analyzer coupled to a Nu Horizon isotope ratio mass spectrometer, we tested the impact of three treatment variants (refluxing at three temperatures to remove non-collagenous proteins, treatment with sodium hydroxide (NaOH), and chemical lipid extraction using 2:1 chloroform:methanol) on the stable isotope (δ13carbon (C) and δ15nitrogen (N)) and elemental (wt% C, and wt% N) composition of pig (Sus scrofa domesticus) skin. The refluxing step produced pig skin with higher δ13C values, lower C:NAtomic ratios, less variable C:NAtomic ratios, wt% C, and wt% N. The chemical lipid extraction also produced higher, more reliable δ13C values and lower, less variable C:NAtomic ratios. The isotopic data in the lipid-extracted and refluxed samples were more consistent in the refluxed samples than the non-refluxed and non-lipid-extracted samples, as determined by the elemental compositions.
Derian et al. (2025) Solubilization of skin collagen improves the accuracy and reliability of stable isotope measurements. PeerJ 13:e20152 https://doi.org/10.7717/peerj.20152
Quality assessment from biobank plasma and serum specimens: a systematic review
Accurate assessment of serum and plasma quality is essential for reliable biobanking and research. This systematic review synthesizes 46 studies and shows that current evaluation methods prioritize sample processing delays, freeze-thaw cycles, storage duration, and temperature variations, while neglecting preanalytical factors like medication and diet. Temperature critically affected stability: non-refrigerated samples (8–37 °C) showed 3.2 times more biomarker alterations than refrigerated samples after >24 h delays. Freeze-thaw cycles caused dose-dependent instability, with >10 cycles triggering severe degradation (70% altered biomarkers) and universal enzyme impairment. Even ≤5 cycles significantly altered enzymes (43% affected). Enzymes also degraded over time at <−20 °C, with alteration rates rising from 20% (1–5 years) to 55% (>10 years). The analysis consolidates stability data for enzymes, sterols, cytokines, and metabolites across conditions, providing an evidence-based foundation for quality control. Standardizing procedures to address these gaps will enhance sample integrity, research reliability, and clinical utility. Critically, this review underscores that preexisting biobank collections may have inherent limitations, necessitating careful evaluation of sample history when designing studies.
Liang et al. (2025) Quality assessment from biobank plasma and serum specimens: a systematic review. PeerJ 13:e20122 https://doi.org/10.7717/peerj.20122
Evaluation of NEUROG1 methylation status in stool specimens in the advanced adenomas and colorectal cancer
Background To assess the status of NEUROG1 methylation in the advanced adenoma and colorectal cancer. Methods The NEUROG1 methylation in tissue and stool samples from patients with colorectal cancer (CRC), advanced adenoma (AA), and non-advanced adenoma (NAA) were evaluated using methylation-specific quantitative polymerase chain reaction (PCR). Results In tissue samples, the NEUROG1 methylation detection rates were 36% for CRC, 24% for NAA, and 88% for AA. In stool samples, the NEUROG1 methylation detection had a sensitivity of 63.46% for CRC with a positive predictive value (PPV) of 85.94%. The overall diagnostic specificity of the test for the NAA and the healthy control was 76.32%, with a negative predictive value (NPV) of 40.28%. Conclusion NEUROG1 methylation detection can potentially be used in the CRC and AA screening.
Zhang et al. (2025) Evaluation of NEUROG1 methylation status in stool specimens in the advanced adenomas and colorectal cancer. PeerJ 13:e19968 https://doi.org/10.7717/peerj.19968
Optimal treatment options for acne scars in patients with historic acne: a systematic review and network meta-analysis
Background Acne is a common skin condition that can cause permanent scarring and profoundly affect patients’ quality of life. Despite the increasing diversity of acne scar treatments, there is a dearth of comprehensive evidence-based guidelines to help clinicians and patients make the best choices. This study aimed to comprehensively assess the efficacy and safety of existing acne scar treatments through a network meta-analysis. Method PubMed, Embase, Cochrane Library, and Web of Science were thoroughly searched for relevant studies from database establishment to September 19, 2024. Outcome included Echelle d’evaluation clinique des cicatrices d’acne (ECCA), Goodman and Baron Scale (GBS), pain, patient satisfaction, and adverse events. Bayesian network meta-analyses were performed using the gemtc package in R. Risk of bias was assessed using Cochrane Risk of Bias (RoB 2) tool, while publication bias was assessed via funnel plots. The study protocol was registered with PROSPERO (CRD42024598780). Results A total of 68 randomized controlled trials were enrolled, comprising 4,480 patients with acne scarring. Laser + platelet-rich plasma (PRP) ranked best in reducing ECCA scores (surface under cumulative ranking curve to the total area (SUCRA): 98.4%), laser + filler injection ranked best in reducing GBS (SUCRA: 72.1%), and laser + chemical peels ranked the best in patient satisfaction (SUCRA: 89.6%). Microneedling was ranked as the most tolerable in terms of pain (SUCRA: 72.6%). In addition, no strong evidence suggesting a treatment reduced the risk of erythema nor post-inflammatory hyperpigmentation compared to the other treatments. Conclusions The evidence suggests laser combined with PRP or filler injections are the best options for reducing scar severity, while laser combined with chemical peeling yields the best patient satisfaction. Laser combined with other therapies should be considered to optimize treatment of acne scarring.
Wu et al. (2025) Optimal treatment options for acne scars in patients with historic acne: a systematic review and network meta-analysis. PeerJ 13:e19938 https://doi.org/10.7717/peerj.19938
Unveiling water quality and health risks from groundwater chemicals in Poyang Lake basin of China: a sophisticated analysis
Background Groundwater is a critical water resource in the Poyang Lake basin, especially given the increasing frequency of extreme drought events. However, comprehensive assessments of its chemical characteristics and associated health risks remain insufficient. This study aims to provide a comprehensive assessment of groundwater quality and associated health risks in the Poyang Lake basin, China. Methods This study collected 670 groundwater samples from domestic and agricultural wells across the basin during the 2022 dry season. Hydrochemical parameters, including manganese (Mn), ammonia nitrogen (NH4+), iron (Fe3+), aluminum (Al3+), chemical oxygen demand (COD), fluoride (F−), and nitrate (NO3−), were analyzed and compared against China’s Class III groundwater quality standards. Spatial variations in water quality were evaluated using the Entropically Weighted Water Quality Index (EWQI). Non-carcinogenic health risks via ingestion and dermal contact pathways were quantified through deterministic risk assessment models, with uncertainty and probability analyzed via Monte Carlo simulations (10,000 iterations). Sensitivity analysis was conducted to identify dominant factors influencing risk outcomes, ensuring a robust probabilistic interpretation of health hazards. Results The results unveils pronounced spatial variability across key hydrochemical parameters: pH ranges from 3.05 to 11.09, total dissolved solids (TDS) from 25.38 to 1,635.21 mg/L, Mn from below detection limits to 19.93 mg/L, COD from below detection limits to 8.57 mg/L, and TH from 9.47 to 905.78 mg/L. A notable proportion of samples breach the Class III groundwater quality standards, with 38% for Mn, 39% for COD, and 15% for NH4+. The Piper diagram analysis categorizes the primary groundwater type as HCO3− -Ca, with a secondary Cl-Ca-Mg type. Through the EWQI assessment, while the overall water quality is deemed acceptable, we identify 56 sites with EWQI values indicative of poor to very poor quality, predominantly influenced by Mn and NH4+. The irrigation risk assessment highlights extensive areas unsuitable for irrigation, particularly within the Ganjiang River basin. Health risk assessments utilizing a deterministic model reveal significant non-carcinogenic risks from F− and NO3− in groundwater, especially for children. However, our Monte Carlo simulation indicates that the probabilities of F− and NO3− posing non-carcinogenic health risks are virtually zero, suggesting that the deterministic assessment may have overestimated the health risks. This study provides critical insights into the groundwater quality and health risks in the Poyang Lake basin and underscores the necessity for targeted water management strategies to mitigate pollution sources and safeguard public health.
Environmental Contamination and Remediation
Chu et al. (2025) Unveiling water quality and health risks from groundwater chemicals in Poyang Lake basin of China: a sophisticated analysis. PeerJ 13:e19937 https://doi.org/10.7717/peerj.19937