title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=588 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A cross-sectional survey of avian influenza knowledge among poultry farmworkers in Indonesia link: https://peerj.com/articles/14600 last-modified: 2023-01-16 description: BackgroundAvian influenza (AI) poses a serious threat to global public health, especially the highly pathogenic form. Awareness and protective behavior among the public, particularly the high-risk populations, are essential for prevention and control. This study aimed to ascertain the level of AI knowledge among Indonesia’s poultry farmworkers.MethodsThis was a cross-sectional study conducted online. A predesigned standardized questionnaire, containing six demographic questions and 14 questions on AI knowledge, was used. The questionnaire was distributed via WhatsApp and email platforms. Volunteers (respondents) included 119 men and 81 women, aged 18–50 years, who work on poultry farms in Indonesia. Data were analyzed using the chi-squared and Fisher exact tests.ResultsThe study’s findings revealed that more than two-thirds (67.0%) of the respondents had heard about AI. Their primary sources of information were health workers (36.0%) and media, especially television (34.0%). The majority of the participants (91.3%) had good knowledge about AI as a contagious infection, transmissible from birds to other birds, animals, or humans. A total of 76.8% of the respondents believed that poultry workers and veterinarians were at high risk of contracting AI infection.ConclusionsThe study concluded that poultry workers had good knowledge about AI infection, transmission, and risk variables. Health workers and television were the main sources of information on AI. The level of AI knowledge was high among the respondents. creator: Saifur Rehman creator: Aamir Shehzad creator: Lisa Dyah Andriyani creator: Mustofa Helmi Effendi creator: Zain Ul Abadeen creator: Muhammad Ilyas Khan creator: Muhammad Bilal uri: https://doi.org/10.7717/peerj.14600 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Rehman et al. title: Transcription analyses of differentially expressed mRNAs, lncRNAs, circRNAs, and miRNAs in the growth plate of rats with glucocorticoid-induced growth retardation link: https://peerj.com/articles/14603 last-modified: 2023-01-16 description: BackgroundGlucocorticoids (GCs) are commonly used to treat autoimmune diseases and malignancies in children and adolescents. Growth retardation is a common adverse effect of GC treatment in pediatric patients. Accumulating evidence indicates that non-coding RNAs (ncRNAs) are involved in the pathogenesis of glucocorticoid-induced growth retardation (GIGR), but the roles of specific ncRNAs in growth remain largely unknown.MethodsIn this study, 2-week-old male Sprague-Dawley rats had been treated with 2 mg/kg/d of dexamethasone for 7 or 14 days, after which the growth plate tissues were collected for high-throughput RNA sequencing to identify differentially expressed mRNAs, lncRNAs, circRNAs, and miRNAs in GIGR rats.ResultsTranscriptomic analysis identified 1,718 mRNAs, 896 lncRNAs, 60 circRNAs, and 72 miRNAs with different expression levels in the 7d group. In the 14d group, 1,515 mRNAs, 880 lncRNAs, 46 circRNAs, and 55 miRNAs with differential expression were identified. Four mRNAs and four miRNAs that may be closely associated with the development of GIGR were further validated by real-time quantitative fluorescence PCR. Function enrichment analysis indicated that the PI3K-Akt signaling pathway, NF-kappa B signaling pathway, and TGF-β signaling pathway participated in the development of the GIGR. Moreover, the constructed ceRNA networks suggested that several miRNAs (including miR-140-3p and miR-127-3p) might play an important role in the pathogenesis of GIGR.ConclusionsThese results provide new insights and important clues for exploring the molecular mechanisms underlying GIGR. creator: Mingyue Yin creator: Junqi Wang creator: Juanjuan Zhang creator: Wei Wang creator: Wenli Lu creator: Fei Xu creator: Xiaoyu Ma creator: Sheng Lyu creator: Lifen Chen creator: Lidan Zhang creator: Zhiya Dong creator: Yuan Xiao uri: https://doi.org/10.7717/peerj.14603 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yin et al. title: High and low dose of luzindole or 4-phenyl-2-propionamidotetralin (4-P-PDOT) reverse bovine granulosa cell response to melatonin link: https://peerj.com/articles/14612 last-modified: 2023-01-16 description: BackgroundCommunication between oocytes and granulosa cells ultimately dictate follicle development or atresia. Melatonin is also involved in follicle development. This study aimed to investigate the effects of melatonin and its receptor antagonists on hormone secretion, as well as gene expression related to hormone synthesis, TGF-β superfamily, and follicle development in bovine granulosa cells, and assess the effects of melatonin in the presence of 4-P-PDOT and luzindole.MethodsBovine ovaries were collected from a local abattoir and follicular fluid (follicle diameter 5–8 mm) was collected for granulosa cell isolation and culture. Granulosa cells and culture medium were collected 48 h after treatment with melatonin at high dose concentrations (10−5 M) and low dose concentrations (10−9 M) in the absence/presence of 4-P-PDOT and luzindole (10−5 M or 10−9 M). Furthermore, the expression level of genes related to hormonal synthesis (CYP11A1, CYP19A1, StAR, and RUNX2), TGF-β superfamily (BMP6, INHA, INHBA, INHBB, and TGFBR3), and development (EGFR, DNMT1A, and FSHR) were detected in each experimental group by real-time quantitative PCR. In addition, the level of hormones in culture medium were detected using ELISA.ResultsBoth 10−5 M and 10−9 M melatonin doses promoted the secretion of inhibin A and progesterone without affecting the production of inhibin B and estradiol. In addition, both promoted the gene expression of INHA, StAR, RUNX2, TGFBR3, EGFR, and DNMT1A, and inhibited the expression of BMP6, INHBB, CYP11A1, CYP19A1, and FSHR. When combined with different doses of 4-P-PDOT and luzindole, they exhibited different effects on the secretion of inhibin B, estradiol, inhibin A, and progesterone, and the expression of CYP19A1, RUNX2, BMP6, INHBB, EGFR, and DNMT1A induced by melatonin.ConclusionHigh and low dose melatonin receptor antagonists exhibited different effects in regulating hormone secretion and the expression of various genes in response to melatonin. Therefore, concentration effects must be considered when using luzindole or 4-P-PDOT. creator: Wenju Liu creator: Zhihao Chen creator: Rui Li creator: Menghao Zheng creator: Xunsheng Pang creator: Aiyou Wen creator: Bing Yang creator: Shujuan Wang uri: https://doi.org/10.7717/peerj.14612 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liu et al. title: Comparative studies of two AA10 family lytic polysaccharide monooxygenases from Bacillus thuringiensis link: https://peerj.com/articles/14670 last-modified: 2023-01-16 description: Bacillus thuringiensis, known to be one of the most important biocontrol microorganisms, contains three AA10 family lytic polysaccharide monooxygenases (LPMOs) in its genome. In previous reports, two of them, BtLPMO10A and BtLPMO10B, have been preliminarily characterized. However, some important biochemical features and substrate preference, as well as their potential applications in chitin degradation, still deserve further investigation. Results from present study showed that both BtLPMO10A and BtLPMO10B exhibit similar catalytic domains as well as highly conserved substrate-binding planes. However, unlike BtLPMO10A, which has comparable binding ability to both crystalline and amorphous form of chitins, BtLPMO10B exhibited much stronger binding ability to colloidal chitin, which mainly attribute to its carbohydrate-binding module-5 (CBM5). Interestingly, the relative high binding ability of BtLPMO10B to colloidal chitin does not lead to high catalytic activity of the enzyme. In contrast, the enzyme exhibited higher activity on β-chitin. Further experiments showed that the binding of BtLPMO10B to colloidal chitin was mainly non-productive, indicating a complicated role for CBM5 in LPMO activity. Furthermore, synergistic experiments demonstrated that both LPMOs boosted the activity of the chitinase, and the higher efficiency of BtLPMO10A can be overridden by BtLPMO10B. creator: Huiyan Zhang creator: Haichuan Zhou creator: Yong Zhao creator: Tang Li creator: Heng Yin uri: https://doi.org/10.7717/peerj.14670 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Inter-rater and intra-rater reliability of isotonic exercise monitoring device for measuring active knee extension link: https://peerj.com/articles/14672 last-modified: 2023-01-16 description: BackgroundThe goal of this study was to assess the reliability of electromyography and range of motion measurements obtained using a knee exercise monitoring system. This device was developed to collect data on knee exercise activities.MethodsTwenty healthy individuals performed isotonic quadriceps exercises in this study. The vastus medialis surface electromyography (sEMG) and range of motion (ROM) of the knee were recorded during the exercise using the isotonic knee exercise monitoring device, the Mobi6-6b, and a video camera system. Each subject underwent a second measuring session at least 24 h after the first session. To determine reliability, the intraclass correlation coefficients (ICCs) and standard error of measurement (SEM) at the 95% confidence interval were calculated, and a Bland–Altman analysis was performed.ResultsFor inter-rater reliability, the ICCs of the mean absolute value (MAV) and root mean square (RMS) of sEMG were 0.73 (0.49, 0.86) and 0.79 (0.61, 0.89), respectively. ROM had an ICC of 0.93 (0.02, 0.98). The intra-rater reliability of the MAV of the sEMG was 0.89 (0.71, 0.96) and the intra-rater reliability of RMS of the sEMG was 0.88 (0.70, 0.95). The ROM between days had an intra-rater reliability of 0.82 (0.54, 0.93). The Bland–Altman analysis demonstrated no systematic bias in the MAV and RMS of sEMG, but revealed a small, systematic bias in ROM (−0.8311 degrees).ConclusionFor sEMG and range of motion measures, the isotonic knee exercise monitoring equipment revealed moderate to excellent inter- and intra-rater agreement. However, the confidence interval of ROM inter-rater reliability was quite large, indicating a small agreement bias; hence, the isotonic knee exercise monitor may not be suitable for measuring ROM. This isotonic knee exercise monitor could detect and collect information on a patient’s exercise activity for the benefit of healthcare providers. creator: Chonnanid Limsakul creator: Kiattisak Sengchuai creator: Rakkrit Duangsoithong creator: Nattha Jindapetch creator: Jermphiphut Jaruenpunyasak uri: https://doi.org/10.7717/peerj.14672 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Limsakul et al. title: Stories told by corals, algae, and sea-urchins in a Mesoamerican coral reef: degradation trumps succession link: https://peerj.com/articles/14680 last-modified: 2023-01-16 description: Understanding the mechanisms that allow the permanence of coral reefs and the constancy of their characteristics is necessary to alleviate the effects of chronic environmental changes. After a disturbance, healthy coral reefs display trajectories that allow regaining coral cover and the establishment of framework building corals. Through a comparative approach, in a patch reef partially affected by a ship grounding, we analyzed the successional trajectories in affected and unaffected sectors. Fleshy algae (which do not promote the recruitment of corals) dominated the reef surface irrespective of the impact of the ship grounding incident. Acropora species had near-zero contributions to community structure, whereas non-framework building corals like Porites sp. had a slightly higher recruitment. Cover of coral and calcareous crustose algae decreased over time, and neither the latter nor adult coral colonies had any effect on the occurrence probabilities of small corals. Sea urchin (Diadema antillarum) densities were generally low, and thus unlikely to contribute to reverting algal dominance. The successional trajectories of the community in the impacted and non-impacted sectors of the coral patch reef agree with the inhibition successional model, leading to the development of a degraded state dominated by fleshy algae. It is probable that the stability and resilience of this degraded state are high due to the ability of fleshy algae to monopolize space, along with low coral recovery potential. creator: Isael Victoria-Salazar creator: Edgar J. González creator: Jorge A. Meave creator: Miguel-Ángel Ruiz-Zárate creator: Héctor A. Hernández-Arana uri: https://doi.org/10.7717/peerj.14680 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Victoria-Salazar et al. title: Molecular marker development and genetic diversity exploration in Medicago polymorpha link: https://peerj.com/articles/14698 last-modified: 2023-01-16 description: Medicago polymorpha L. (bur clover), an invasive plant species of the genus Medicago, has been traditionally used in China as an edible vegetable crop because of its high nutritive value. However, few molecular markers for M. polymorpha have been identified. Using the recently published high-quality reference genome of M. polymorpha, we performed a specific-locus amplified fragment sequencing (SLAF-seq) analysis of 10 M. polymorpha accessions to identify molecular markers and explore genetic diversity. A total of 52,237 high-quality single nucleotide polymorphisms (SNPs) were developed. These SNPs were mostly distributed on pseudochromosome 3, least distributed on pseudochromosome 7, and relatively evenly distributed on five other pseudochromosomes of M. polymorpha. Phenotypic analysis showed that there was a great difference in phenotypic traits among different M. polymorpha accessions. Moreover, clustering all M. polymorpha accessions based on their phenotypic traits revealed three groups. Both phylogenetic analysis and principal component analysis (PCA) of all M. polymorpha accessions based on SNP markers consistently indicated that all M. polymorpha accessions could be divided into three distinct groups (I, II, and III). Subsequent genetic diversity analysis for the 10 M. polymorpha accessions validated the effectiveness of the M. polymorpha germplasm molecular markers in China. Additionally, SSR mining analysis was also performed to identify polymorphic SSR motifs, which could provide valuable candidate markers for the further breeding of M. polymorpha. Since M. polymorpha genetics have not been actively studied, the molecular markers generated from our research will be useful for further research on M. polymorpha resource utilization and marker-assisted breeding. creator: Hailong Ren creator: Zhenwu Wei creator: Bo Zhou creator: Xiang Chen creator: Qiang Gao creator: Zhibin Zhang uri: https://doi.org/10.7717/peerj.14698 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Ren et al. title: Change and stasis of distinct sediment microbiomes across Port Everglades Inlet (PEI) and the adjacent coral reefs link: https://peerj.com/articles/14288 last-modified: 2023-01-13 description: Deep water ports are human built coastal structures that by definition welcome ship traffic and disturbance. Evidence is accumulating that enhanced port activities such as dredging or deepening have negatively affected nearby natural habitats. Port Everglades Inlet (PEI) is a large active South Florida cargo port for over two million people and lies adjacent to coral reefs, dwindling mangroves, and recreational beaches. In this study, the microbial communities of PEI and adjacent reef sediments were characterized to serve as indicators for change due to dredging and assess anthropogenic influence on these sensitive ecosystems by sequencing the V4 region of 16S rRNA ahead of a large-scale port deepening event. For the first time, this study established baseline bacterial community characterizations and their patterns of diversity prior to and after a maintenance dredging event. PEI samples were collected for two consecutive years 2020 (Phase I, before maintenance dredging) and 2021 (Phase II, after maintenance dredging) from PEI sediments and adjacent coral reef sediments. In spite of their proximity and tidal connections through the PEI, reef and PEI sediment microbial communities were distinct. Changes in microbial diversity within the intracoastal waterway (ICW), a route for community exchange or transfers, were the greatest after maintenance dredging occurred. Microbial diversity in reef sediments also changed after dredging, indicating potential influence from resuspended sediments due to an associated increase in trace metals and decrease in cyanobacterial diversity. Sediments were identified as a possible source of human and coral pathogens, although dredging did not affect the relative abundances of these indicator microorganisms. This study highlighted the utility and relative ease of applying current molecular ecology methods to address macroscale questions with environmental management ramifications. creator: Lauren E. Krausfeldt creator: Jose Victor Lopez creator: Catherine Margaret Bilodeau creator: Hyo Won Lee creator: Shelby L. Casali uri: https://doi.org/10.7717/peerj.14288 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Krausfeldt et al. title: Systematics and diversification of the Ichthyomyini (Cricetidae, Sigmodontinae) revisited: evidence from molecular, morphological, and combined approaches link: https://peerj.com/articles/14319 last-modified: 2023-01-13 description: Ichthyomyini, a morphologically distinctive group of Neotropical cricetid rodents, lacks an integrative study of its systematics and biogeography. Since this tribe is a crucial element of the Sigmodontinae, the most speciose subfamily of the Cricetidae, we conducted a study that includes most of its recognized diversity (five genera and 19 species distributed from southern Mexico to northern Bolivia). For this report we analyzed a combined matrix composed of four molecular markers (RBP3, GHR, RAG1, Cytb) and 56 morphological traits, the latter including 15 external, 14 cranial, 19 dental, five soft-anatomical and three postcranial features. A variety of results were obtained, some of which are inconsistent with the currently accepted classification and understanding of the tribe. Ichthyomyini is retrieved as monophyletic, and it is divided into two main clades that are here recognized as subtribes: one to contain the genus Anotomys and the other composed by the remaining genera. Neusticomys (as currently recognized) was found to consist of two well supported clades, one of which corresponds to the original concept of Daptomys. Accordingly, we propose the resurrection of the latter as a valid genus to include several species from low to middle elevations and restrict Neusticomys to several highland forms. Numerous other revisions are necessary to reconcile the alpha taxonomy of ichthyomyines with our phylogenetic results, including placement of the Cajas Plateau water rat (formerly Chibchanomys orcesi) in the genus Neusticomys (sensu stricto), and the recognition of at least two new species (one in Neusticomys, one in Daptomys). Additional work is necessary to confirm other unanticipated results, such as the non-monophyletic nature of Rheomys and the presence of a possible new genus and species from Peru. Our results also suggest that ichthyomyines are one of the main Andean radiations of sigmodontine cricetids, with an evolutionary history dating to the Late Miocene and subsequent cladogenesis during the Pleistocene. creator: Jorge Salazar-Bravo creator: Nicolás Tinoco creator: Horacio Zeballos creator: Jorge Brito creator: Daniela Arenas-Viveros creator: David Marín-C creator: José Daniel Ramírez-Fernández creator: Alexandre R. Percequillo creator: Thomas E. Lee, Jr. creator: Sergio Solari creator: Javier Colmenares-Pinzon creator: Carlos Nivelo creator: Bernal Rodríguez Herrera creator: William Merino creator: Cesar E. Medina creator: Oscar Murillo-García creator: Ulyses F.J. Pardiñas uri: https://doi.org/10.7717/peerj.14319 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Salazar-Bravo et al. title: Immunoexpression of stem cell markers SOX-2, NANOG AND OCT4 in ameloblastoma link: https://peerj.com/articles/14349 last-modified: 2023-01-13 description: BackgroundAmeloblastoma (AME) is characterized by a locally invasive growth pattern. In an attempt to justify the aggressiveness of neoplasms, the investigation of the role of stem cells has gained prominence. The SOX-2, NANOG and OCT4 proteins are important stem cell biomarkers.MethodologyTo verify the expression of these proteins in tissue samples of AME, dentigerous cyst (DC) and dental follicle (DF), immunohistochemistry was performed and indirect immunofluorescence were performed on the human AME (AME-hTERT) cell line.ResultsRevealed expression of SOX-2, NANOG and OCT4 in the tissue samples and AME-hTERT lineage. Greater immunostaining of the studied proteins was observed in AME compared to DC and DF (p < 0.001).ConclusionsThe presence of biomarkers indicates a probable role of stem cells in the genesis and progression of AME. creator: Karolyny Martins Balbinot creator: Felippe José Almeida Loureiro creator: Giordanna Pereira Chemelo creator: Ricardo Alves Mesquita creator: Aline Maria Pereira Cruz Ramos creator: Rommel Thiago Jucá Ramos creator: Artur Luiz da Costa da Silva creator: Sílvio Augusto Fernandes de Menezes creator: Maria Sueli da Silva Kataoka creator: Sergio de Melo Alves Junior creator: João de Jesus Viana Pinheiro uri: https://doi.org/10.7717/peerj.14349 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Martins Balbinot et al.