title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=673 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Individual-level specialisation and interspecific resource partitioning in bees revealed by pollen DNA metabarcoding link: https://peerj.com/articles/13671 last-modified: 2022-08-05 description: It is increasingly recognised that intraspecific variation in traits, such as morphology, behaviour, or diet is both ubiquitous and ecologically important. While many species of predators and herbivores are known to display high levels of between-individual diet variation, there is a lack of studies on pollinators. It is important to fill in this gap because individual-level specialisation of flower-visiting insects is expected to affect their efficiency as pollinators with consequences for plant reproduction. Accordingly, the aim of our study was to quantify the level of individual-level specialisation and foraging preferences, as well as interspecific resource partitioning, in three co-occurring species of bees of the genus Ceratina (Hymenoptera: Apidae: Xylocopinae), C. chalybea, C. nigrolabiata, and C. cucurbitina. We conducted a field experiment where we provided artificial nesting opportunities for the bees and combined a short-term mark-recapture study with the dissection of the bees’ nests to obtain repeated samples from individual foraging females and complete pollen provisions from their nests. We used DNA metabarcoding based on the ITS2 locus to identify the composition of the pollen samples. We found that the composition of pollen carried on the bodies of female bees and stored in the brood provisions in their nests significantly differed among the three co-occurring species. At the intraspecific level, individual females consistently differed in their level of specialisation and in the composition of pollen carried on their bodies and stored in their nests. We also demonstrate that higher generalisation at the species level stemmed from larger among-individual variation in diets, as observed in other types of consumers, such as predators. Our study thus reveals how specialisation and foraging preferences of bees change from the scale of individual foraging bouts to complete pollen provisions accumulated in their nests over many days. Such a multi-scale view of foraging behaviour is necessary to improve our understanding of the functioning of plant-flower visitor communities. creator: Jan Klečka creator: Michael Mikát creator: Pavla Koloušková creator: Jiří Hadrava creator: Jakub Straka uri: https://doi.org/10.7717/peerj.13671 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Klečka et al. title: Influence of beamlet width on dynamic IMRT plan quality in nasopharyngeal carcinoma link: https://peerj.com/articles/13748 last-modified: 2022-08-05 description: ObjectiveThis study aimed to identify the effects of beamlet width on dynamic intensity-modulated radiation therapy (IMRT) for nasopharyngeal carcinoma (NPC) and determine the optimal parameters for the most effective radiotherapy plan.MethodsThis study evaluated 20 patients with NPC were selected for dynamic IMRT. Only the beamlet width in the optimization parameters was changed (set to 2, 4, 6, 8, and 10 mm that were named BL02, BL04, BL06, BL08, and BL10, respectively) to optimize the results of the five groups of plans. Using the plan quality scoring system, the dose results of the planning target volumes (PTVs) and organs at risks (OARs) were analyzed objectively and comprehensively. The lower the quality score, the better the quality of the plan. The efficiency and accuracy of plan execution were evaluated using monitor units (MUs) and plan delivery time (PDT).ResultsThe BL04 mm group had the lowest quality score for the targets and OARs (0.087), while the BL10 mm group had the highest total score (1.249). The BL04 mm group had the highest MUs (837 MUs) and longest PDT (358 s). However, the MUs range of each group plan was below 100 MUs, and the PDT range was within 30 s. In the BL02, BL04, BL06, BL08, and BL10 plans, <5 MUs segments accounted for 33%, 16%, 24%, 33%, and 40% of total segments, respectively, with which the lowest was in the BL04 mm group.ConclusionSmaller beamlet widths have not only reduced OARs dose while maintaining high dose coverage to the PTVs, but also lead to more MUs that would produce greater PDT. Considering the quality and efficiency of dynamic IMRT, the beamlet width value of the Monaco treatment planning system set to 4 mm would be optimal for NPC. creator: Manya Wu creator: Jinhui Jin creator: Zhenghuan Li creator: Fantu Kong creator: Yadi He creator: Lijiang Liu creator: Wei Yang creator: Xiangying Xu uri: https://doi.org/10.7717/peerj.13748 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wu et al. title: Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing link: https://peerj.com/articles/13790 last-modified: 2022-08-05 description: DNA barcoding is critical to conservation and biodiversity research, yet public reference databases are incomplete. Existing barcode databases are biased toward cytochrome oxidase subunit I (COI) and frequently lack associated voucher specimens or geospatial metadata, which can hinder reliable species assignments. The emergence of metabarcoding approaches such as environmental DNA (eDNA) has necessitated multiple marker techniques combined with barcode reference databases backed by voucher specimens. Reference barcodes have traditionally been generated by Sanger sequencing, however sequencing multiple markers is costly for large numbers of specimens, requires multiple separate PCR reactions, and limits resulting sequences to targeted regions. High-throughput sequencing techniques such as genome skimming enable assembly of complete mitogenomes, which contain the most commonly used barcoding loci (e.g., COI, 12S, 16S), as well as nuclear ribosomal repeat regions (e.g., ITS1&2, 18S). We evaluated the feasibility of genome skimming to generate barcode references databases for marine fishes by assembling complete mitogenomes and nuclear ribosomal repeats. We tested genome skimming across a taxonomically diverse selection of 12 marine fish species from the collections of the National Museum of Natural History, Smithsonian Institution. We generated two sequencing libraries per species to test the impact of shearing method (enzymatic or mechanical), extraction method (kit-based or automated), and input DNA concentration. We produced complete mitogenomes for all non-chondrichthyans (11/12 species) and assembled nuclear ribosomal repeats (18S-ITS1-5.8S-ITS2-28S) for all taxa. The quality and completeness of mitogenome assemblies was not impacted by shearing method, extraction method or input DNA concentration. Our results reaffirm that genome skimming is an efficient and (at scale) cost-effective method to generate all mitochondrial and common nuclear DNA barcoding loci for multiple species simultaneously, which has great potential to scale for future projects and facilitate completing barcode reference databases for marine fishes. creator: Mykle L. Hoban creator: Jonathan Whitney creator: Allen G. Collins creator: Christopher Meyer creator: Katherine R. Murphy creator: Abigail J. Reft creator: Katherine E. Bemis uri: https://doi.org/10.7717/peerj.13790 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Hoban et al. title: Epigenetic modification mechanism of histone demethylase KDM1A in regulating cardiomyocyte apoptosis after myocardial ischemia-reperfusion injury link: https://peerj.com/articles/13823 last-modified: 2022-08-05 description: Hypoxia and reoxygenation (H/R) play a prevalent role in heart-related diseases. Histone demethylases are involved in myocardial injury. In this study, the mechanism of the lysine-specific histone demethylase 1A (KDM1A/LSD1) on cardiomyocyte apoptosis after myocardial ischemia-reperfusion injury (MIRI) was investigated. Firstly, HL-1 cells were treated with H/R to establish the MIRI models. The expressions of KDM1A and Sex Determining Region Y-Box Transcription Factor 9 (SOX9) in H/R-treated HL-1 cells were examined. The cell viability, markers of myocardial injury (LDH, AST, and CK-MB) and apoptosis (Bax and Bcl-2), and Caspase-3 and Caspase-9 protein activities were detected, respectively. We found that H/R treatment promoted cardiomyocyte apoptosis and downregulated KDM1A, and overexpressing KDM1A reduced apoptosis in H/R-treated cardiomyocytes. Subsequently, tri-methylation of lysine 4 on histone H3 (H3K4me3) level on the SOX9 promoter region was detected. We found that KDM1A repressed SOX9 transcription by reducing H3K4me3. Then, HL-1 cells were treated with CPI-455 and plasmid pcDNA3.1-SOX9 and had joint experiments with pcDNA3.1-KDM1A. We disclosed that upregulating H3K4me3 or overexpressing SOX9 reversed the inhibitory effect of overexpressing KDM1A on apoptosis of H/R-treated cardiomyocytes. In conclusion, KDM1A inhibited SOX9 transcription by reducing the H3K4me3 on the SOX9 promoter region and thus inhibited H/R-induced apoptosis of cardiomyocytes. creator: Lin He creator: Yanbo Wang creator: Jin Luo uri: https://doi.org/10.7717/peerj.13823 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 He et al. title: Gender differences in demographic and clinical characteristics in patients with HBV-related liver diseases in China link: https://peerj.com/articles/13828 last-modified: 2022-08-05 description: BackgroundThe gender differences in demographic and clinical characteristics were examined in patients with hepatitis B virus (HBV)-related liver diseases.MethodsOverall, 634 patients (44.7 ± 13.8 years) were consecutively included. Data of demographic and clinical characteristics were collected during an assessment interview. Comparisons between male and female patients in terms of demographic and clinical data were carried out using univariate analyses. The independent associations between the demographic and clinical variables and gender were examined with either logistic regression or analysis of covariance as appropriate.ResultsThe study sample consisted of 452 male and 182 female patients. Multiple logistic regression analyses revealed that being employed (OR = 3.4), personal monthly income <3,000 yuan (OR = 0.3), being current alcohol users (OR = 6.4), Cirrhosis (OR = 5.9), Hepatocellular Carcinoma (HCC) (OR = 8.5) and having less severe insomnia (OR = 0.6) were independently associated with male gender. The analysis of covariance revealed that after controlling for other potential confounding variables, later onset of HBV-related diseases (F = 4.5, p = 0.03) and older age (F = 6.7, p = 0.009) were independently associated with male gender.ConclusionsGiven the significant clinical differences in male and female patients with HBV-related liver diseases, more attention should be given to gender-specific treatment and prevention for this population. creator: Mei Liu creator: Lu Li creator: Jing Zhao creator: Gabor S. Ungvari creator: Chee H. Ng creator: Zhongping Duan creator: Su-Jun Zheng creator: Yu-Tao Xiang uri: https://doi.org/10.7717/peerj.13828 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: In silico testing of flavonoids as potential inhibitors of protease and helicase domains of dengue and Zika viruses link: https://peerj.com/articles/13650 last-modified: 2022-08-04 description: BackgroundDengue and Zika are two major vector-borne diseases. Dengue causes up to 25,000 deaths and nearly a 100 million cases worldwide per year, while the incidence of Zika has increased in recent years. Although Zika has been associated to fetal microcephaly and Guillain-Barré syndrome both it and dengue have common clinical symptoms such as severe headache, retroocular pain, muscle and join pain, nausea, vomiting, and rash. Currently, vaccines have been designed and antivirals have been identified for these diseases but there still need for more options for treatment. Our group previously obtained some fractions from medicinal plants that blocked dengue virus (DENV) infection in vitro. In the present work, we explored the possible targets by molecular docking a group of molecules contained in the plant fractions against DENV and Zika virus (ZIKV) NS3-helicase (NS3-hel) and NS3-protease (NS3-pro) structures. Finally, the best ligands were evaluated by molecular dynamic simulations.MethodsTo establish if these molecules could act as wide spectrum inhibitors, we used structures from four DENV serotypes and from ZIKV. ADFR 1.2 rc1 software was used for docking analysis; subsequently molecular dynamics analysis was carried out using AMBER20.ResultsDocking suggested that 3,5-dicaffeoylquinic acid (DCA01), quercetin 3-rutinoside (QNR05) and quercetin 3,7-diglucoside (QND10) can tightly bind to both NS3-hel and NS3-pro. However, after a molecular dynamics analysis, tight binding was not maintained for NS3-hel. In contrast, NS3-pro from two dengue serotypes, DENV3 and DENV4, retained both QNR05 and QND10 which converged near the catalytic site. After the molecular dynamics analysis, both ligands presented a stable trajectory over time, in contrast to DCA01. These findings allowed us to work on the design of a molecule called MOD10, using the QND10 skeleton to improve the interaction in the active site of the NS3-pro domain, which was verified through molecular dynamics simulation, turning out to be better than QNR05 and QND10, both in interaction and in the trajectory.DiscussionOur results suggests that NS3-hel RNA empty binding site is not a good target for drug design as the binding site located through docking is too big. However, our results indicate that QNR05 and QND10 could block NS3-pro activity in DENV and ZIKV. In the interaction with these molecules, the sub-pocket-2 remained unoccupied in NS3-pro, leaving opportunity for improvement and drug design using the quercetin scaffold. The analysis of the NS3-pro in complex with MOD10 show a molecule that exerts contact with sub-pockets S1, S1’, S2 and S3, increasing its affinity and apparent stability on NS3-pro. creator: Omar Cruz-Arreola creator: Abdu Orduña-Diaz creator: Fabiola Domínguez creator: Julio Reyes-Leyva creator: Verónica Vallejo-Ruiz creator: Lenin Domínguez-Ramírez creator: Gerardo Santos-López uri: https://doi.org/10.7717/peerj.13650 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cruz-Arreola et al. title: Randomized feasibility trial of the Scleroderma Patient-centered Intervention Network hand exercise program (SPIN-HAND) link: https://peerj.com/articles/13471 last-modified: 2022-08-04 description: PurposeThe Scleroderma Patient-centered Intervention Network (SPIN) online hand exercise program (SPIN-HAND), is an online self-help program of hand exercises designed to improve hand function for people with scleroderma. The objective of this feasibility trial was to evaluate aspects of feasibility for conducting a full-scale randomized controlled trial of the SPIN-HAND program.Materials and MethodsThe feasibility trial was embedded in the SPIN cohort and utilized the cohort multiple randomized controlled trial (cmRCT) design. In the cmRCT design, at the time of cohort enrollment, cohort participants consent to be assessed for trial eligibility and randomized prior to being informed about trials conducted using the cohort. When trials were conducted in the cohort, participants randomized to the intervention were informed and consented to access the intervention. Participants randomized to control were not informed that they have not received an intervention. All participants eligible and randomized to participate in the trial were included in analyses on an intent-to-treat basis. Cohort participants with a Cochin Hand Function Scale score ≥ 3/90 and an interest in using an online hand-exercise intervention were randomized (1:1 ratio) to be offered as usual care plus the SPIN-HAND Program or usual care for 3 months. User satisfaction was assessed with semi-structured interviews.ResultsOf the 40 randomized participants, 24 were allocated to SPIN-HAND and 16 to usual care. Of 24 participants randomized to be offered SPIN-HAND, 15 (63%) consented to use the program. Usage of SPIN-HAND content among the 15 participants who consented to use the program was low; only five (33%) logged in more than twice. Participants found the content relevant and easy to understand (satisfaction rating 8.5/10, N = 6). Automated eligibility and randomization procedures via the SPIN Cohort platform functioned properly. The required technical support was minimal.ConclusionsTrial methodology functioned as designed, and the SPIN-HAND Program was feasibly delivered; however, the acceptance of the offer and use of program content among accepters were low. Adjustments to information provided to potential participants will be implemented in the full-scale SPIN-HAND trial to attempt to increase offer acceptance. creator: Linda Kwakkenbos creator: Marie-Eve Carrier creator: Joep Welling creator: Kimberly A. Turner creator: Julie Cumin creator: Mia Pépin creator: Cornelia van den Ende creator: Anne A. Schouffoer creator: Marie Hudson creator: Ward van Breda creator: Maureen Sauve creator: Maureen D. Mayes creator: Vanessa L. Malcarne creator: Warren R. Nielson creator: Christelle Nguyen creator: Isabelle Boutron creator: François Rannou creator: Brett D. Thombs creator: Luc Mouthon uri: https://doi.org/10.7717/peerj.13471 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Kwakkenbos et al. title: Molecular identification and first demographic insights of sharks based on artisanal fisheries bycatch in the Pacific Coast of Colombia: implications for conservation link: https://peerj.com/articles/13478 last-modified: 2022-08-04 description: The Pacific coast of Colombia is characterized by mangrove ecosystems which play a crucial role as possible nurseries for juvenile sharks. However, trophic food webs from coastal ecosystems are heavily disturbed by increased fishing pressure, which affects numerous shark species. In this region of the Eastern Tropical Pacific (ETP), fisheries’ data from coastal areas are scarce and unspecific, as most sharks from artisanal fisheries are landed decapitated and finless, making their morphological identification difficult. For the establishment and implementation of effective regional conservation and management policies, information on the diversity and population dynamics of shark species is crucial. We therefore sequenced the mitochondrial NADH2 gene of 696 samples taken from fishermen’s landings of shark’s bycatch along the Colombian north Pacific coast. We were able to identify 14 species of sharks, two of the most abundant species were Sphyrna lewini and Carcharhinus falciformis, both evaluated on IUCN the Red List of Threatened species (Critically Endangered and Vulnerable) and CITES regulated. We found low genetic diversity in the sampled area increasing the concern for both species in the region, even more considering that the majority of individuals were juveniles. Our results showed the importance of genetic markers for first population genetic insights as a complementary tool during the decision-making process in management plans. For this specific region, strategies such as the delimitation of conservation priority areas or the regulation of fishing gears could help improve the sustainability of shark populations in the Colombian Pacific. creator: Melany Villate-Moreno creator: Juan Camilo Cubillos-M creator: Herwig Stibor creator: Andrew J. Crawford creator: Nicolas Straube uri: https://doi.org/10.7717/peerj.13478 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Villate-Moreno et al. title: Factors limiting reproductive success in urban Greylag Geese (Anser anser) link: https://peerj.com/articles/13685 last-modified: 2022-08-04 description: In the late eighties, Greylag Geese (Anser anser) started to colonise an urban area previously void of geese in southwestern Germany. Between 2004 and 2020, in a period of steady population increase with subsequent population stagnation, we analysed two measures of reproductive success: (1) the relation between freshly hatched to fledged young for each brood and (2) the probability of a hatchling to survive to fledging. We were able to show that the dispersal of pairs from the nesting site to a different brood rearing area resulted in higher reproductive success. However, the increasing population size of Greylag Geese and the number of breeding pairs of recently immigrated Egyptian Geese (Alopochen aegyptiaca) had a negative impact on reproductive success, indicating density dependence. Our results show that newly established populations in urban settings do not grow indefinitely, which is an important fact that should be taken into account by wildlife managers. creator: Sabrina Mai creator: Jean-Louis Berthoud creator: Holger Haag creator: Friederike Woog uri: https://doi.org/10.7717/peerj.13685 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Mai et al. title: The COVID-19 infodemic in Brazil: trends in Google search data link: https://peerj.com/articles/13747 last-modified: 2022-08-04 description: BackgroundSince the beginning of the new coronavirus pandemic, there has been much information about the disease and the virus has been in the spotlight, shared and commented upon on the Internet. However, much of this information is infodemics and can interfere with the advancement of the disease and that way that populations act. Thus, Brazil is a country that requires attention, as despite the fact that in almost two years of pandemic it has shown a devastating numbers of deaths and number of cases, and generates false, distorted and malicious news about the pandemic. This work intends to understand the attitudes of the Brazilian population using infodemic queries from the Google Trends search tool and social and income variables.MethodsData from infodemic research carried out on Google Trends, between January 1, 2020 and June 30, 2021, with socioeconomic data, such as income and education, were unified in a single database: standardization and exploratory and multivalued techniques based on grouping were used in the study.ResultsIn the analysis of the search trend of infodemic terms, it is clear that the categories of Prevention and Beliefs should stand out in Brazil, where there is a diverse culture. It is followed by the COVID-19 Treatment category, with treatments that were not those recommended by the authorities. Income transfer programs and information on socioeconomic variables did not have much impact on infodemic surveys, but it was observed that states where President Bolsonaro has more supporters had researched more infodemic information.ConclusionsIn a country as geographically large as Brazil, it is important that political authorities go to great lengths to disseminate reliable information and monitor the infodemic in the media and on the internet. It was concluded that the denial of the pandemic and the influence of political leaders influenced the search for infodemic information, contributing to a disorganization in the control of the disease and prevention measures. creator: Maria da Penha Harb creator: Lena Veiga e Silva creator: Nandamudi Vijaykumar creator: Marcelino Silva da Silva creator: Carlos Renato Lisboa Frances uri: https://doi.org/10.7717/peerj.13747 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Harb et al.