title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=280 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Estimates of the vitality and performances of Apis mellifera mellifera and hybrid honey bee colonies in Siberia: a 13-year study link: https://peerj.com/articles/17354 last-modified: 2024-07-12 description: Honeybees display a great range of biological, behavioral, and economic traits, depending on their genetic origin and environmental factors. The high diversity of honeybees is the result of natural selection of specific phenotypes adapted to the local environment. Of particular interest is adaptation of local and non-local bee colonies to environmental conditions. To study the importance of genotype-environment interactions on the viability and productivity of local and non-local bee colonies, we analyzed the long-term dynamics of the main traits in dark forest bees (Apis mellifera mellifera) and hybrid colonies. From 2010 to 2022, a total of 64 colonies living in an apiary in Siberia, Russia, were monitored and tested to assess their biological, behavioral, and economic traits in a temperate continental climate. We detected significant correlations between the studied biological and behavioral indicators of the bee colony such as colony strength, overwintering ability, infection of colonies with diseases, hygienic behavior, and others. No relationships between the biological and economic (honey productivity) traits of bee colonies are shown. The overall result of our study is that local dark forest bee, A.m.mellifera, showed higher values for all analyzed traits than hybrid colonies. Compared to hybrids, dark forest bee colonies showed more gentleness, productivity, and survivorship. The results from our study indicate a specific local adaptation of the A.m.mellifera subspecies in a temperate continental climate. Siberia represents a unique region for the conservation of the dark forest bee. The creation of conservation areas is one way to protect local bee populations, well adapted to local environmental conditions, from uncontrolled importation of bee breeds from different regions. creator: Nadezhda V. Ostroverkhova creator: Svetlana A. Rosseykina creator: Ilona A. Yaltonskaya creator: Michail S. Filinov uri: https://doi.org/10.7717/peerj.17354 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ostroverkhova et al. title: Molecular identification of Trichobilharzia species in recreational waters in North-Eastern Poland link: https://peerj.com/articles/17598 last-modified: 2024-07-12 description: BackgroundIn Europe, avian schistosomes of the genus Trichobilharzia are the most common etiological agents involved in human cercarial dermatitis (swimmer’s itch). Manifested by a skin rash, the condition is caused by an allergic reaction to cercariae of nonhuman schistosomes. Humans are an accidental host in this parasite’s life cycle, while water snails are the intermediate, and waterfowl are the final hosts. The study aimed to conduct a molecular and phylogenetic analysis of Trichobilharzia species occurring in recreational waters in North-Eastern Poland.MethodologyThe study area covered three water bodies (Lake Skanda, Lake Ukiel, and Lake Tyrsko) over the summer of 2021. In total, 747 pulmonate freshwater snails (Radix spp., Lymnaea stagnalis) were collected. Each snail was subjected to 1–2 h of light stimulation to induce cercarial expulsion. The phylogenetic analyses of furcocercariae were based on the partial sequence of the ITS region (ITS1, 5.8S rDNA, ITS2 and 28SrDNA). For Radix spp. phylogenetic analyses were based on the ITS-2 region.ResultsThe prevalence of the Trichobilharzia species infection in snails was 0.5%. Two out of 478 (0.4%) L. stagnaliswere found to be infected with Trichobilharzia szidati. Moreover, two out of 269 (0.7%) snails of the genus Radix were positive for schistosome cercariae. Both snails were identified as Radix auricularia. One of them was infected with Trichobilharzia franki and the other with Trichobilharzia sp.ConclusionsMolecular identification of avian schistosome species, both at the intermediate and definitive hosts level, constitutes an important source of information on a potential threat and prognosis of local swimmer’s itch occurrence, and helps to determine species diversity in a particular area. creator: Joanna Korycińska creator: Jana Bulantová creator: Petr Horák creator: Ewa Dzika uri: https://doi.org/10.7717/peerj.17598 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Korycińska et al. title: Two new Cortinarius species in subgenus Leprocybe from Southwest China link: https://peerj.com/articles/17599 last-modified: 2024-07-12 description: Two new Cortinarius species in subgenus Leprocybe, Cortinarius hengduanensis and C. yadingensis, are proposed based on a combination of morphological and molecular evidence. Cortinarius hengduanensis has distinct olive tinged basidiomata, a squamulose pileus, and small, subglobose to broadly ellipsoid basidiospores, the ITS sequence differs from that of C. flavifolium by at least 28 substitutions and independent positions. Cortinarius yadingensis has a squamulose pileus and subglobose to broadly ellipsoid coarsely verrucose basidiospores, the ITS sequence has at least 11 substitutions and index position deviations from the other members of the Leprocybe section. Both new species were found in mixed forests of southwest China. creator: Peng Hong creator: Ke Wang creator: Zhuo Du creator: Ming-Jun Zhao creator: Meng-Le Xie creator: Di Liu creator: Tie-Zheng Wei uri: https://doi.org/10.7717/peerj.17599 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hong et al. title: In field use of water samples for genomic surveillance of infectious spleen and kidney necrosis virus (ISKNV) infecting tilapia fish in Lake Volta, Ghana link: https://peerj.com/articles/17605 last-modified: 2024-07-12 description: Viral outbreaks are a constant threat to aquaculture, limiting production for better global food security. A lack of diagnostic testing and monitoring in resource-limited areas hinders the capacity to respond rapidly to disease outbreaks and to prevent viral pathogens becoming endemic in fisheries productive waters. Recent developments in diagnostic testing for emerging viruses, however, offers a solution for rapid in situ monitoring of viral outbreaks. Genomic epidemiology has furthermore proven highly effective in detecting viral mutations involved in pathogenesis and assisting in resolving chains of transmission. Here, we demonstrate the application of an in-field epidemiological tool kit to track viral outbreaks in aquaculture on farms with reduced access to diagnostic labs, and with non-destructive sampling. Inspired by the “lab in a suitcase” approach used for genomic surveillance of human viral pathogens and wastewater monitoring of COVID19, we evaluated the feasibility of real-time genome sequencing surveillance of the fish pathogen, Infectious spleen and kidney necrosis virus (ISKNV) in Lake Volta. Viral fractions from water samples collected from cages holding Nile tilapia (Oreochromis niloticus) with suspected ongoing ISKNV infections were concentrated and used as a template for whole genome sequencing, using a previously developed tiled PCR method for ISKNV. Mutations in ISKNV in samples collected from the water surrounding the cages matched those collected from infected caged fish, illustrating that water samples can be used for detecting predominant ISKNV variants in an ongoing outbreak. This approach allows for the detection of ISKNV and tracking of the dynamics of variant frequencies, and may thus assist in guiding control measures for the rapid isolation and quarantine of infected farms and facilities. creator: Shayma Alathari creator: Andrew Joseph creator: Luis M. Bolaños creator: David J. Studholme creator: Aaron R. Jeffries creator: Patrick Appenteng creator: Kwaku A. Duodu creator: Eric B. Sawyerr creator: Richard Paley creator: Charles R. Tyler creator: Ben Temperton uri: https://doi.org/10.7717/peerj.17605 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Alathari et al. title: Effect of carbon nanoparticles on the growth and photosynthetic property of Ficus tikoua Bur. plant link: https://peerj.com/articles/17652 last-modified: 2024-07-12 description: The application of nanomaterials in different plants exerts varying effects, both positive and negative. This study aimed to investigate the influence of carbon nanoparticles (CNPs) on the growth and development of Ficus tikoua Bur. plant. The morphological characteristics, photosynthetic parameters, and chlorophyll content of F. tikoua Bur. plants were evaluated under four different concentrations of CNPs. Results indicated a decreasing trend in several agronomic traits, such as leaf area, branching number, and green leaf number and most photosynthetic parameters with increasing CNPs concentration. Total chlorophyll and chlorophyll b contents were also significantly reduced in CNPs-exposed plants compared to the control. Notably, variations in plant tolerance to CNPs were observed based on morphological and physiological parameters. A critical concentration of 50 g/kg was identified as potentially inducing plant toxicity, warranting further investigation into the effects of lower CNPs concentrations to determine optimal application levels. creator: Nian Chen creator: Xiaojian Tian creator: Mingli Yang creator: Jiajun Xu creator: Tinghong Tan creator: Jiyue Wang uri: https://doi.org/10.7717/peerj.17652 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Chen et al. title: Global changes of miRNA expression indicates an increased reprogramming efficiency of induced mammary epithelial cells by repression of miR-222-3p in fibroblasts link: https://peerj.com/articles/17657 last-modified: 2024-07-12 description: BackgroundOur previous studies have successfully reported the reprogramming of fibroblasts into induced mammary epithelial cells (iMECs). However, the regulatory relationships and functional roles of MicroRNAs (miRNAs) in the progression of fibroblasts achieving the cell fate of iMECs are insufficiently understood.MethodsFirst, we performed pre-and post-induction miRNAs sequencing analysis by using high-throughput sequencing. Following that, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment studies were used to determine the primary roles of the significantly distinct miRNAs and targeted genes. Finally, the effect of miR-222-3p on iMECs fate reprogramming in vitro by transfecting.ResultsAs a result goat ear fibroblasts (GEFs) reprogramming into iMECs activates a regulatory program, involving 79 differentially expressed miRNAs. Besides, the programming process involved changes in multiple signaling pathways such as adherens junction, TGF-β signaling pathway, GnRH secretion and the prolactin signaling pathway, etc. Furthermore, it was discovered that the expression of miR-222-3p downregulation by miR-222-3p inhibitor significantly increase the reprogramming efficiency and promoted lipid accumulation of iMECs. creator: Mingxing Liu creator: Siyi Liu creator: Liangshan Qin creator: Danwei Lv creator: Guodong Wang creator: Quanhui Liu creator: Ben Huang creator: Dandan Zhang uri: https://doi.org/10.7717/peerj.17657 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: Phylogenetic and population genetic analyses of Thrips tabaci Lindeman (Thysanoptera: Thripidae) on Allium host in India link: https://peerj.com/articles/17679 last-modified: 2024-07-12 description: BackgroundOnion thrips (Thrips tabaci) is a complex of cryptic species with subtle morphological differences and distinct genetic backgrounds; thus, species identification using traditional methods remains challenging. The existence of different haplotypes and genotypes within a species can significantly influence various aspects of its biology, including host preference, reproductive capacity, resistance to pesticides, and vector competence for plant viruses. Understanding the genetic diversity and population structure of cryptic species within T. tabaci will not only aid in the development of more effective control strategies tailored to specific genetic variants but also in monitoring population dynamics, tracking invasive species, and implementing quarantine measures to prevent the spread of economically damaging thrips biotypes.MethodsThis study aims to explore intraspecies genetic diversity and molecular evolutionary relationships of the mitochondrial cytochrome oxidase gene subunit I (mtCOI) in T. tabaci populations from India. To capture diversity within the Indian T. tabaci populations, amplicon sequencing was performed for the thrips mtCOI gene from eight diverse localities in India. A total of 48 sequences retrieved for the mtCOI gene from the NCBI Nucleotide database were analysed.ResultsMultiple insertions and deletions were detected at various genomic positions across the populations from different localities, with the highest variation observed in the 300–400 genome position range. Molecular diversity analyses identified 30 haplotypes within the population, with certain subpopulations exhibiting higher gene flow. Analysis of single nucleotide polymorphism patterns within the mtCOI gene across diverse Indian locales revealed significant intrapopulation genetic heterogeneity and its potential repercussions on gene functionality. Elevated F statistics (Fst) values in the northern–western subpopulations suggested high genetic variability, particularly evident in haplotype networks originating mainly from the northern region, notably Delhi. While most populations displayed stable and ancient evolutionary histories, thrips populations from northern, western, and north-eastern regions indicated rapid growth. creator: Tushar Gawai creator: Sharwari Sadawarte creator: Kiran Khandagale creator: Anusha Raj creator: Abhijeet Kulkarni creator: Durgesh Kumar Jaiswal creator: Avinash B. Ade creator: Suresh Gawande uri: https://doi.org/10.7717/peerj.17679 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Gawai et al. title: Evaluation of phytochemical profile, and antioxidant, antidiabetic activities of indigenous Thai fruits link: https://peerj.com/articles/17681 last-modified: 2024-07-12 description: BackgroundThis research aims to explore the phenolics identification, phenolics quantification, antioxidant and potential biofunctional properties of lesser-known Thai fruits and their potency to treat type 2 diabetes mellitus (T2DM). Including, Antidesma puncticulatum, Dillenia indica, Diospyros decandra, Elaeagnus latifolia, Flacourtia indica, Garcinia dulcis, Lepisanthes fruticose, Mimusops elengi, Muntingia calabura, Phyllanthus reticulatus, Streblus asper, Syzygium cumini, Syzygium malaccense, Willughbeia edulis and Schleichera oleosa were analyzed by their phenolic and flavonoid content. These fruits have received limited scientific attention, prompting an investigation into their health benefits, particularly their relevance to diabetes management.MethodsThe study utilized methanolic crude extracts to measure phenolic and flavonoid levels. Additionally, UHPLC-DAD was utilized to identify and quantify phenolics. The methanolic extracts were assessed for antioxidant and antidiabetic abilities, including α-glucosidase and α-amylase inhibition.Results and ConclusionThe study highlighted S. cumini as a rich source of phenolic (980.42 ± 0.89 mg GAE/g and flavonoid (3.55 ± 0.02 mg QE/g) compounds with strong antioxidant activity (IC50 by DPPH; 3.00 ± 0.01 µg/ml, IC50 by ABTS; 40 ± 0.01 µg/ml, FRAP; 898.63 ± 0.02 mg TE/ml). Additionally, S. cumini exhibited promising antidiabetic effects (S. cumini IC50; 0.13 ± 0.01 mg/ml for α-glucosidase inhibition, 3.91 ± 0.05 mg/ml for α-amylase inhibition), compared to Acarbose (IC50; 0.86 ± 0.01 mg/ml for α-glucosidase inhibition, 0.39 ± 0.05 mg/ml for α-amylase inhibition). Remarkably, compounds like catechins, gallic acid, kaempferol, and ellagic acid were identified in various quantities.This study suggests that these fruits, packed with phenolics, hold the potential to be included in an anti-diabetic diet and even pharmaceutical applications due to their health-promoting properties. creator: Jirayupan Prakulanon creator: Sutsawat Duangsrisai creator: Srunya Vajrodaya creator: Thanawat Thongchin uri: https://doi.org/10.7717/peerj.17681 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Prakulanon et al. title: Estimation of reference evapotranspiration using some class-A pan evaporimeter pan coefficient estimation models in Mediterranean–Southeastern Anatolian transitional zone conditions of Turkey link: https://peerj.com/articles/17685 last-modified: 2024-07-12 description: BackgroundReference evapotranspiration (ETo), which is used as the basic data in many studies within the scope of hydrology, meteorology, irrigation and soil sciences, can be estimated by using the evaporation (Epan) measured from the class-A pan evaporimeter. However, this method requires reliable pan coefficients (Kp). Many empirical models are used to estimate Kp coefficients. The reliability of these models varies depending on climatic and environmental conditions. Therefore, they need to be tested in the local conditions where they will be used. In this study, conducted in Kahramanmaraş, which has a semi-arid Mediterranean climate in Turkey during the July–October periods of 2020 and 2021, aimed to determine the usability levels of six Kp models in estimating daily and monthly average ETo.MethodsThe Kp coefficients estimated by the models were multiplied with the daily Epan values, and the daily average ETo values were estimated on the basis of the model. The daily Epan values were measured using an ultrasonic sensor sensitive to the water surface placed on the class-A pan evaporimeter. The ultrasonic sensor was managed by a programmable logic controller (PLC). To enable the sensor to be managed by PLC, a software was prepared using the CODESYS programming language and uploaded to the PLC. The daily average ETo values determined by the FAO-56 Penman–Monteith equation were accepted as actual values. The ETo values estimated by the Kp models were compared with the actual ETo values using the mean absolute error (MAE), mean absolute percentage error (MAPE), root mean square error (RMSE) and determination coefficient (R2) statistical approaches.ResultsThe Wahed & Snyder outperformed the other models in estimating daily (MAE = 0.78 mm day−1, MAPE = 14.40%, RMSE = 0.97 mm day−1, R2 = 0.82) and monthly (MAE = 0.32 mm day−1, MAPE = 5.88%, RMSE = 0.32 mm day−1, R2 = 0.99) average ETo. FAO-56 showed the nearest performance to Wahed & Snyder. The Snyder model presented the worst performance in estimating daily (MAE = 2.09 mm day−1, MAPE = 37.53%, RMSE = 2.36 mm day−1, R2 = 0.82) and monthly (MAE = 1.83 mm day−1, MAPE = 31.82%, RMSE = 1.87 mm day−1, R2 = 0.99) average ETo. It has been concluded that none of the six Kp models can be used to estimate the daily ETo in Kahramanmaraş located in the Mediterranean–Southeastern Anatolian transitional zone, and only Wahed & Snyder and FAO-56 can be used to estimate the monthly ETo without calibration. creator: Selçuk Usta uri: https://doi.org/10.7717/peerj.17685 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Usta title: Whole-brain radiation therapy plus simultaneous integrated boost for brain metastases from breast cancers link: https://peerj.com/articles/17696 last-modified: 2024-07-12 description: BackgroundThe effect of whole-brain radiation therapy (WBRT) plus simultaneous integrated boost (SIB) in brain metastasis from breast cancers has not been demonstrated.MethodIn this single-center retrospective study, we reviewed consecutive breast cancer patients who developed brain metastasis and were treated with hypofractionated radiation therapy plus WBRT using intensity-modulated radiation therapy (IMRT)-SIB approaches. We analyzed clinical outcomes, prognostic factors and patterns of treatment failure.ResultA total of 27 patients were eligible for analysis. Four (14.8%) patients achieved clinical complete response and 14 (51.9%) had partial response of brain lesions. The other nine patients were not evaluated for brain tumor response. The median brain progression-free survival was 8.60 (95% CI [6.43–13.33]) months and the median overall survival was 16.8 (95% CI [13.3–27.7]) months. Three patients had in-field failure, five had out-field failure and two had in-field and out-field failure.ConclusionWBRT plus SIB led to improved tumor control and clinical outcome in breast cancer patients with brain metastasis. creator: Hongyan Zhang creator: Qiuji Wu creator: Li Li creator: Linwei Wang creator: Yahua Zhong uri: https://doi.org/10.7717/peerj.17696 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al.