Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park
New York City parks serve as potential sites of both social and physical climate resilience, but relatively little is known about how microbial organisms and processes contribute to the functioning of these deeply human-impacted ecosystems. We report the sequencing and analysis of 15 shotgun metagenomes, including the reconstruction of 129 high-quality metagenome-assembled genomes, from tidal lagoons and bay water at Bush Terminal Piers Park in Brooklyn, NY sampled from July to September 2024. Our metagenomic database for this site provides an important baseline for ongoing studies of the microbial communities of public parks and waterfront areas in NYC. In particular, we provide rich functional and taxonomic annotations that enable the use of these metagenomes and metagenome-assembled genomes for a wide variety of downstream applications.
Kong et al. (2025) Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park. PeerJ 13:e20081 https://doi.org/10.7717/peerj.20081
Spatially explicit models of density improve estimates of Eastern Bering Sea beluga (Delphinapterus leucas) abundance and distribution from line-transect surveys
We investigate spatially explicit models and ensemble modeling techniques for estimating animal abundance from line-transect survey data. Spatially explicit models are expected to be statistically more efficient, resulting in more precise abundance estimates, than design-based abundance estimators that rely heavily on assumptions about survey design and realization. Ensemble modeling reduces error by averaging among models, and allows for model selection uncertainty to propagate to the abundance estimator. We develop density surface models using Matérn covariance functions and spline-based smooths for a case study, belugas (Delphinapterus leucas) from the Eastern Bering Sea (EBS) stock. EBS belugas are upper trophic level predators in a rapidly changing ecosystem and are a vital nutritional and cultural resource for Alaska Natives. Effective management of this stock requires regular monitoring to derive accurate and unbiased estimates of abundance. Since 1992, aerial line-transect surveys have been the primary means of surveying and estimating abundance of EBS belugas in the region. We compare EBS beluga abundance estimates for 2017 and 2022 that were derived using post-stratified, design-based abundance estimators with analogous estimates the we derive using spatially explicit and ensemble modeling methods. The estimated precision in the abundance estimates from the individual density surface models (DSMs) and the ensemble average of DSMs is higher than for the design-based estimator in both survey years. The design-based models estimated that there were 12,269 belugas in 2017 (coefficient of variation (CV) = 0.118) and 19,811 belugas within a larger study area in 2022 (CV = 0.343). The ensemble spatial models estimate that there were 11,654 belugas in 2017 (CV = 0.118) and 13,313 belugas in 2022 (CV = 0.216). Among the individual spatially explicit models, abundance estimates range from 11,242 to 11,963 (CV = 0.111 to 0.114) in 2017 and 12,023 to 15,593 (CV = 0.172 to 0.198) in 2022. Because spatial models identify spatial patterns in beluga density at finer resolutions than design-based models, we argue that ensembles of spatially explicit density models provide a reasonable path forward for estimating EBS beluga abundance and distribution in a way that is useful to management and conservation efforts.
Spatial and Geographic Information Science
Ferguson et al. (2025) Spatially explicit models of density improve estimates of Eastern Bering Sea beluga (Delphinapterus leucas) abundance and distribution from line-transect surveys. PeerJ 13:e20077 https://doi.org/10.7717/peerj.20077
Morphological, phytochemical, and pharmacological properties of the genus Tamarix in Kazakhstan species: a review
The tree-like plants of the genus Tamarix belong to the Tamaricaceae family and predominantly grow in subtropical areas, steppes, and saline soils. These plants exhibit various pharmacological properties, including antioxidant, antidiabetic, anti-inflammatory, and antimicrobial characteristics. The current flora of Kazakhstan also includes 13 Tamarix species. Despite the diversity of the Tamarix taxon, the species discovered in the region have received limited investigation. Therefore, this review analyzed Kazakhstan and international-related scientific studies concerning the morphological, phytochemical, and pharmacological properties of 13 species within the Tamarix genus. The plants’ biological features and potential applications were also comprehensively analyzed. Consequently, this review significantly contributed to botanical science and practical pharmacology. Conservation and sustainable employment of the Tamarix species for medical purposes could also be developed.
Daulbayeva et al. (2025) Morphological, phytochemical, and pharmacological properties of the genus Tamarix in Kazakhstan species: a review. PeerJ 13:e20059 https://doi.org/10.7717/peerj.20059
Identification and verification of prognostic genes related to zinc homeostasis and zinc transport in breast cancer
Purpose Zinc homeostasis and zinc transporter (ZHT) have been closely associated with the development of various cancers. Therefore, in this study, prognostic genes and their mechanisms related to ZHT in breast cancer (BC) were explored. Patients and methods Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were utilized to identify genes associated with Zinc homeostasis and Zinc transporter-related genes (ZHTGs) in BC. Subsequently, independent prognostic factors and their correlations with clinical features were examined to investigate their association with the prognosis of BC. Finally, we further explored the pathways and immune cells associated with BC prognosis. We also verified gene expression in tissues and cells by quantitative polymerase chain reaction (qPCR). Results In this study, six prognostic genes were identified. Patients were subsequently classified into high-risk and low-risk cohorts based on the median risk score, with the low-risk group presenting superior survival outcomes. Subsequently, riskScore, age, tumor/node/metastasis (T/N/M) stage showed significant associations with the prognosis of BC, and the constructed nomogram demonstrated strong predictive performance. Clinical analysis revealed differences in risk scores among sub-cohorts with different clinical characteristics, such as race (white and others) and T-stage (T1 and T2, T1 and T3). Furthermore, significant disparities were noted in immune cells and immune checkpoints across different risk cohorts. The results of reverse transcription quantitative PCR were basically consistent with the prediction. In addition, the IHC results from the Human Protein Atlas database further validated our prediction. Conclusion We screened six prognosis genes related to ZHT in BC, providing a reference for the prognosis and personalized treatment of BC.
Li et al. (2025) Identification and verification of prognostic genes related to zinc homeostasis and zinc transport in breast cancer. PeerJ 13:e20031 https://doi.org/10.7717/peerj.20031
Unlocking the genomic potential of historical and formalin-fixed specimens: phylogenetic insights from museum-preserved threadfin fishes (Teleostei: Polynemidae)
DNA sequencing continues to revolutionize our understanding of biodiversity, ecology, and evolution. While analyzing sequence data allows us to address countless questions, most of the world’s vertebrate museum specimens have been historically inaccessible for genetic sampling. This is partially due to the absence of modern genetic samples and/or the impact formalin has on DNA during the preservation of specimen vouchers. Recent studies have shown successful extraction of DNA from historic museum specimens using additional chemicals and/or exposing the sample(s) to heat, with these advances enhancing the possibility of capturing genomic information from type specimens, characterizing genetic diversity within species complexes, and incorporating rare samples into phylogenetic analyses. However, questions remain about the reliability of these data and utility of historic DNA in modern phylogenetic analyses. In this study, we use a commercial extraction kit that targets formalin-fixed, paraffin-embedded samples to successfully extract DNA from historic museum specimens of threadfin fishes (Teleostei: Polynemidae). These specimens represent rare, genetically uncharacterized taxa that have yet to be included in a phylogenetic analysis. Low-depth shotgun sequencing is then used to sequence mitochondrial loci from the historic samples. The resulting sequence data are assembled, validated, and incorporated into a newly generated mitochondrial dataset that is simultaneously analyzed with a previously published ultraconserved-element dataset to construct a phylogenetic framework. We then explore new and previously described morphological variation within this new evolutionary framework for threadfins, identifying several shared characters that warrant revision of the generic-level classification. These findings add to the growing body of literature that demonstrates sequencing historical DNA from museum specimens and analyzing these data with complementary datasets of molecular markers from modern genetic samples can provide reliable and comprehensive assessments of biodiversity, ecology, and evolution across fishes and other vertebrates.
Girard et al. (2025) Unlocking the genomic potential of historical and formalin-fixed specimens: phylogenetic insights from museum-preserved threadfin fishes (Teleostei: Polynemidae). PeerJ 13:e20029 https://doi.org/10.7717/peerj.20029
Undernutrition and feeding difficulties among children with disabilities in Zambia: insights for inclusive nutrition strategies
Background Understanding the burden of undernutrition in children with disabilities is crucial for designing inclusive nutrition programs and policies. This study aimed to estimate the prevalence of undernutrition and risk for feeding difficulties and describe common feeding practices among children with disabilities living with families in Zambia and receiving services at selected health centers and community-based rehabilitation centers. Methods We analyzed cross-sectional program data from 483 children aged birth to 10 years with reported special healthcare needs, collected between June 2017 and August 2021 at three health centers and ten community-based rehabilitation centers. Data included demographics, weight, height, mid-upper arm circumference (MUAC), hemoglobin concentrations, risk for feeding difficulties, and reported caregiver feeding practices. Undernutrition was assessed using the World Health Organization z-scores for anthropometric measurements, MUAC cut-off points, and anemia criteria. ANOVA and Pearson’s chi-squared tests were used to compare groups. Results More than half of the children were boys (54.2%) and under 5 years old (59.2%). Cerebral palsy was the most common special healthcare need (63.6%), followed by an unspecified “other” category (18.6%). Undernutrition was prevalent, with 62.8% underweight, 68.1% stunted, 22.6% wasted (using MUAC), and 60.5% anemic. Children with cerebral palsy had consistently lower anthropometric z-scores and higher rates of stunting, wasting, and underweight compared to children with other developmental disabilities or special healthcare needs. A risk for feeding difficulties was identified in 89.5% of the children, with common issues including coughing or choking and prolonged mealtimes. Despite these challenges, most caregivers reported practicing responsive feeding techniques at least some of the time. Conclusion These findings highlight the significant risk of undernutrition and feeding difficulties among children with disabilities, underscoring the urgent need for disability-inclusive, community-based nutrition strategies in Zambia. Stakeholders should use this information to strengthen nutrition programs and policies that uphold the rights of children with disabilities.
Makhoul et al. (2025) Undernutrition and feeding difficulties among children with disabilities in Zambia: insights for inclusive nutrition strategies. PeerJ 13:e20023 https://doi.org/10.7717/peerj.20023
Metabolomic and physiological analysis of bud differentiation in dense apple (Malus×domestica Borkh.) orchards following thinning and reshaping
Background In China, a majority of apple orchards were initially planted under arboriculture. The branch number increases, causing a deterioration of the canopy light conditions as the trees age. This phenomenon blocks bud differentiation, resulting in yield decrease and deterioration of fruit quality. Thinning and reshaping are effective strategies for addressing these issues. However, the impact of thinning and reshaping remains unclear. This study analyzed the physiological and metabolic aspects of flower bud differentiation following thinning and reshaping of an overcrowded orchard. Methods Physiological and metabolomic analyses were conducted on terminal flower bud samples collected during early (T1) and late (T2) bud differentiation following thinning and reshaping alongside controls CK1 and CK2. Results Sucrose, glucose, fructose, and sorbitol contents in T1 and T2 groups were significantly higher than in CK1 and CK2. Metabolomic analysis revealed significant differences: 60 metabolites (32 up-regulated, 28 down-regulated) in T1 vs CK1 and 51 metabolites (26 up-regulated, 25 down-regulated) in T2 vs CK2. KEGG enrichment analysis revealed that the biosynthesis of secondary metabolites was the most enriched pathway, with the crucial compounds associated with flower bud differentiation. There was an accumulation of coumarin (C05851), eriodictyol (C05631), and histidine (C00135) during both the early and late stages of flower bud differentiation, underscoring their promoting role. In T1 vs CK1, 2-isopropylmalic acid (C02504), (+)-catechin (C09727), and trans-ferulic acid (C01494) were significantly up-regulated, highlighting their potential as metabolic activators. Conversely, 3’,5’-dimethoxy-3,5,7,4’-tetrahydroxyflavone (C11620) and 4-hydroxyphenylpyruvic acid (C01179) decreased, implying divergent regulatory mechanisms. Temporal specificity emerged in T2 vs CK2, with significant upregulation of myricetin (C10107) and isopimpinellin (C02162). In contrast, umbelliferone (C09315) and trans-caffeic acid (C01197) exhibited opposing trends. Moreover, jasmonic acid (C08491) and 6-phosphogluconic acid (C00345) increased sharply in T2, while trans-traumatic acid (C16308) declined. Conclusions Thinning and reshaping improved light penetration and increased the accumulation of nutrients and secondary metabolites. Sucrose, glucose, fructose, and sorbitol contents and the relative levels of coumarin, eriodictyol, and histidine increased during early and late flower bud differentiation stages, which suggested their positive roles during these stages. 2-isopropylmalic acid, (+)-catechin, and trans-ferulic acid exhibited metabolic activation potential, while 3’,5’-dimethoxyflavone and 4-hydroxyphenylpyruvic acid were distinctly regulated in T1 vs CK1. Myricetin, isopimpinellin, jasmonic acid, and 6-phosphogluconic acid exhibited activation potential, while trans-traumatic acid was distinctly regulated in T2 vs CK2. Metabolic changes and pathway-specific activation/inhibition patterns underlying flower bud differentiation exhibited a direct-indirect regulatory network in secondary metabolism.
Yang et al. (2025) Metabolomic and physiological analysis of bud differentiation in dense apple (Malus×domestica Borkh.) orchards following thinning and reshaping. PeerJ 13:e20011 https://doi.org/10.7717/peerj.20011
Interprofessional collaboration and associated factors among wound, ostomy, and continence nurses: a cross-sectional study in China
Background Wound, ostomy, and continence (WOC) nurses play a crucial role in providing cost-effective and high-quality care for an increasing number of people with acute and chronic wounds. WOC nursing is a multifaceted, evidence-based specialty practice requiring inter-professional collaboration (IPC). IPC is a core competency that ensures comprehensive and holistic wound management, yet few studies have examined IPC among WOC nurses in China. This study aimed to investigate the level and influencing factors of IPC among WOC nurses in China, providing insights into IPC education and intervention. Methods A cross-sectional study was conducted among 247 WOC nurses recruited from various hospitals from January to February 2025. Participants completed an online questionnaire to assess their IPC competency, readiness for interprofessional learning, and work environment. Multiple linear regression was used to determine influencing factors for IPC competency. Results The mean scores for IPC, readiness for inter-professional learning, and work environment were 134.49 ± 10.99, 81.15 ± 6.00, and 127.1 ± 18.78, respectively. A higher level of inter-professional learning readiness (β = 0.46, P < 0.001), a better work environment (β = 0.39, P < 0.001), and being a WOC team leader (β = 0.12, P = 0.008) were associated with a higher level of IPC competency, collectively explaining 55.1% of the total variance. Conclusion WOC nurses showed a generally good level of IPC, but there is still room for improvement. IPC may be effectively improved through optimizing the work environment, strengthening IPC learning, and empowering nurses with leadership responsibilities.
Shi et al. (2025) Interprofessional collaboration and associated factors among wound, ostomy, and continence nurses: a cross-sectional study in China. PeerJ 13:e20006 https://doi.org/10.7717/peerj.20006
Optimization of anther culture of awnless triticale
Background Compared with traditional breeding methods, anther culture is an effective method for quickly obtaining homozygotes within one generation. The method of cultivating doubled haploid plants derived from the anthers of awnless triticale was studied and optimized. Methods Young awnless triticale spikes were pretreated at 4 °C for 5, 10, 15, 20, or 25 days, respectively, and then the anthers of different treatment days were cultured on cysteine heart blood (CHB) with antibiotics media with four different hormone concentrations, respectively. Results Overall, 15 days was the best low-temperature treatment, and CHB medium containing 1.5 mg/L 2,4-Dichlorophenoxyacetic acid (2,4-D) and 1.5 mg/L Kinetin (KT) was the best hormone concentration treatment. The callus induction rate (CIR) was highest (22.20%) for anthers pretreated for 15-days and inoculated on CHB medium containing 1.5 mg/L 2,4-D and 1.5 mg/L KT. The green plantlet differentiation frequency (DFG) was highest (30.20%) for anthers pretreated for 25-days and inoculated on CHB medium containing 0.5 mg/L 2,4-D+0.5 mg/L KT. Green plantlet production (PRG) was highest (4.58%) for anthers which were pretreated for 10-days and inoculated on CHB medium containing 0.5 mg/L 2,4-D+0.5 mg/L KT. The success rate of chromosome doubling for regenerated green plantlets was 52.8%. Nine of the thirteen DH1 plants (the first generation of double haploid plants) had tip and side awns shorter than 5 mm, implying that they may be used for cultivating awnless triticale. Conclusion Triticale anther culture technology was optimized in this work, enabling the rapid breeding of homozygous varieties of awnless triticale and accelerating the breeding of new varieties of awnless triticale.
Ma et al. (2025) Optimization of anther culture of awnless triticale. PeerJ 13:e19951 https://doi.org/10.7717/peerj.19951
Study on the diagnostic potential and molecular mechanism of hsa_circ_0000831 in oral squamous cell carcinoma
Background Circular RNA (circRNA) are a new class of non-coding RNAs that are involved in the molecular pathology of cancer. This study aims to screen and validate key circRNAs with diagnostic potential in o ral squamous cell carcinoma (OSCC), and explore their possible molecular mechanism. Methods This study first integrated the GSE131182 dataset with clinically obtained OSCC sample data and used the limma package to identify differentially expressed circular RNAs (DEcircRNAs). Subsequently, circRNAs associated with head and neck squamous cell carcinoma were identified using CircNet2.0 and intersected with the differentially expressed circRNAs to determine the key circRNA. The diagnostic value of the key circRNA was evaluated using receiver operating characteristic (ROC) curves, followed by functional validation through in vitro assays including cell counting kit-8 (CCK-8), wound healing, transwell assay, and flow cytometry. Finally, target microRNAs (miRNAs) were predicted using CircNet2.0 and miRDB, a ceRNA network was constructed, and functional enrichment analysis of target genes was performed using Metascape tool. Results A total of 318 and 46 differentially expressed circRNAs (DEcircRNAs) were identified from the GSE131182 dataset and clinical samples, respectively. Through intersection analysis, the key circRNA hsa_circ_0000831 was identified. hsa_circ_0000831 was upregulated in OSCC samples, and ROC curve analysis indicated its high diagnostic performance. In vitro experiments showed that inhibition of hsa_circ_0000831 significantly reduced OSCC cell viability, migration, and invasion, while markedly enhancing apoptosis. ceRNA network analysis predicted that hsa_circ_0000831 targets five miRNAs (including hsa-miR-136-5p, hsa-miR-100-3p, hsa-miR-144-5p, hsa-miR-149-5p and hsa-miR-214-5p), with the associated target genes mainly enriched in cancer-related pathways. Conclusion This work offer s a novel foundation for the early identification of OSCC and provides potential clues for finding new therapeutic targets.
Liu et al. (2025) Study on the diagnostic potential and molecular mechanism of hsa_circ_0000831 in oral squamous cell carcinoma. PeerJ 13:e20082 https://doi.org/10.7717/peerj.20082