title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=696 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Pollen transfer and patterns of reproductive success in pure and mixed populations of nectariferous Platanthera bifolia and P. chlorantha (Orchidaceae) link: https://peerj.com/articles/13362 last-modified: 2022-06-13 description: Plant species evolution is driven by many factors that have different roles in space and time. Using different field and laboratory methods, we studied reproductive patterns and their determinants in pure and mixed P. bifolia and P. chlorantha populations in different habitats. We also considered the probability of hybridisation between these two species and the role of intra-population processes in maintaining species integrity. Generally, we found a high level of reproductive success in both Platantherans. In both species, male (MRS) and female (FRS) reproductive success depended on floral display, and male reproductive success additionally on population structure. The flower traits were only weakly related to reproductive success. Moths’ assemblages varied spatially and temporally, and their diversity and numbers were correlated with MRS in the year, when their abundance was markedly lower. Analysis of patterns of pollen transfer showed that pollen was transported up to 25 m (average 8.2 ± 4.83 m) and showed gene exchange between these two Platanthera species. The germination level of both species was significantly lower than seed viability, although P. bifolia seed germinated with higher frequency than P. chlorantha seeds. We noted differences in viability and germination of seeds developed as an effect of experimental interspecies crossings and those developed from natural pollination. The presence of intermediate ecotypes together with observations of spontaneous interspecies crosses in the field and viability of seeds produced in interspecies crossing suggest that both pre- and postzygotic reproductive barriers are not complete and do not prevent hybrid production. creator: Emilia Brzosko creator: Krzysztof Frąckiel creator: Edyta Jermakowicz creator: Paweł Mirski creator: Beata Ostrowiecka creator: Izabela Tałałaj uri: https://doi.org/10.7717/peerj.13362 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Brzosko et al. title: Factors that influence Cape fur seal predation on Cape gannets at Lambert’s Bay, South Africa link: https://peerj.com/articles/13416 last-modified: 2022-06-13 description: Seabird populations experience predation that can impact their breeding density and breeding success. The Cape gannet Morus capensis is endemic to the Benguela upwelling ecosystem and is classified as Endangered by the IUCN. They are affected by several threats, including predation by the Cape fur seal Arctocephalus pusillus pusillus. Many fledglings succumb to predation during their maiden flight across waters around the island. To curb predation, the selective culling of individual predatory seals was implemented in 2014, 2015, and 2018. Our first study objective was to determine if selective culling of Cape fur seals significantly reduced predation probability on Cape gannets. We tested whether predation probability in 2014, 2015, and 2018 was affected by fish biomass, gannet fledgling numbers, and/or the presence/absence of selective culling. Our second objective was to determine what led to fluctuations in Cape fur seal predation on Cape gannet fledglings between 2007 and 2018. We tested whether fish biomass and the amount of Cape gannet fledglings in the water affected predation probability on the fledglings. Results indicated that selective culling reduced predation within years. We found that with both increased fledgling numbers and increased fish biomass, seal predation probability was reduced. This suggests that a sustainable way to promote the conservation of Cape gannets would be to increase food availability for both the Cape fur seals and Cape gannets. Our findings, collectively with the global trend of the declining Cape gannet population and their endemism, provide reasons advocating for the conservation of the food resources of both the Cape fur seal and the Cape gannet in the Benguela system. creator: Zanri Strydom creator: Lauren J. Waller creator: Mark Brown creator: Hervé Fritz creator: Kevin Shaw creator: Jan A. Venter uri: https://doi.org/10.7717/peerj.13416 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Strydom et al. title: Aggressive signaling among competing species of birds link: https://peerj.com/articles/13431 last-modified: 2022-06-13 description: Aggressive interactions help individuals to gain access to and defend resources, but they can be costly, leading to increased predation risk, injury, or death. Signals involving sounds and color can allow birds to avoid the costs of intraspecific aggressive encounters, but we know less about agonistic signaling between species, where fights can be frequent and just as costly. Here, we review photographic and video evidence of aggressive interactions among species of birds (N = 337 interactions documenting the aggressive signals of 164 different bird species from 120 genera, 50 families, and 24 orders) to document how individuals signal in aggressive encounters among species, and explore whether these visual signals are similar to those used in aggressive encounters with conspecifics. Despite the diversity of birds examined, most aggressively signaling birds displayed weapons (bills, talons, wings) used in fighting and placed these weapons closest to their heterospecific opponent when signaling. Most species oriented their bodies and heads forward with their bills pointing towards their heterospecific opponent, often highlighting their face, throat, mouth, and bill. Many birds also opened their wings and/or tails, increasing their apparent size in displays, consistent with the importance of body size in determining behavioral dominance among species. Aggressive postures were often similar across species and taxonomic families. Exceptions included Accipitridae and Falconidae, which often highlighted their talons in the air, Columbidae, which often highlighted their underwings from the side, and Trochilidae, which often hovered upright in the air and pointed their fanned tail downward. Most species highlighted bright carotenoid-based colors in their signals, but highlighted colors varied across species and often involved multiple colors in combination (e.g., black, white, and carotenoid-based colors). Finally, birds tended to use the same visual signals in aggressive encounters with heterospecifics that they use in aggressive encounters with conspecifics, suggesting that selection from aggressive interactions may act on the same signaling traits regardless of competitor identity. creator: Haley L. Kenyon creator: Paul R. Martin uri: https://doi.org/10.7717/peerj.13431 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Kenyon and Martin title: Effects of turning over intensity on fatty acid metabolites in postharvest leaves of Tieguanyin oolong tea (Camellia sinensis) link: https://peerj.com/articles/13453 last-modified: 2022-06-13 description: Fatty acid derived volatiles (FADVs) are major contributors to the aroma quality of oolong tea (Camellia sinensis). Most of the processing time for oolong tea is taken up by turning over treatments, but the full profile of fatty acid metabolic changes during this process remains unclear. In this study, we detected fatty acids, their derived volatiles, and related genes of Tieguanyin oolong tea using biochemical and molecular biology methods. The results showed that with an increase in turning over intensities, the content of total unsaturated fatty acids continuously dropped and the content of characteristic FADVs, such as hexanoic acid (Z)-3-Hexenly ester and 2-exenal, continued to increase. Lipoxygenase (LOX), a key gene family in the fatty acid metabolic pathway, showed different patterns, and CsLOX1 (TEA025499.1) was considered to be a key gene during the turning over processes. We found that fruit-like aroma (Z)-3-Hexen-1-ol acetate had a strong correlation with the expression levels of eight Camelia sinensis LOX family genes. Tieguanyin had relatively rich pleasant volatile compounds with moderate turning over intensity (five times turning over treatments). This study provides an overall view of how fatty acid metabolites change and affect the quality of oolong tea with different turning over intensities during processing. creator: Zixin Ni creator: Qingyang Wu creator: Ziwei Zhou creator: Yun Yang creator: Qingcai Hu creator: Huili Deng creator: Yucheng Zheng creator: Wanjun Bi creator: Zhenzhang Liu creator: Yun Sun uri: https://doi.org/10.7717/peerj.13453 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ni et al. title: Identification and expression analysis of xyloglucan endotransglucosylase/hydrolase (XTH) family in grapevine (Vitis vinifera L.) link: https://peerj.com/articles/13546 last-modified: 2022-06-13 description: Xyloglucan endotransglucosylases/hydrolases (XTH) are key enzymes in cell wall reformulation. They have the dual functions of catalyzing xyloglucan endotransglucosylase (XET) and xyloglucan endonuclease (XEH) activity and play a crucial role in the responses against abiotic stresses, such as drought, salinity, and freezing. However, a comprehensive analysis of the XTH family and its functions in grapevine (Vitis vinifera L.) has not yet been completed. In this study, 34 XTHs were identified in the whole grapevine genome and then named according to their distribution on chromosomes. Based on a phylogenetic analysis including Arabidopsis XTHs, the VvXTHs were classified into three groups. Cis-element analysis indicated that these family members are related to most abiotic stresses. We further selected 14 VvXTHs from different groups and then examined their transcription levels under drought and salt stress. The results indicated that the transcription levels of selected VvXTHs in the leaves and roots presented the largest changes, suggesting that VvXTHs are likely to take part in the responses to drought and salt stress in grapevines. These results provide useful evidence for the further investigation of VvXTHs function in response to abiotic stresses in grapevine. creator: Tian Qiao creator: Lei Zhang creator: Yanyan Yu creator: Yunning Pang creator: Xinjie Tang creator: Xiao Wang creator: Lijian Li creator: Bo Li creator: Qinghua Sun uri: https://doi.org/10.7717/peerj.13546 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Qiao et al. title: Evaluating a linkage between obesity and the occurrence of dental caries among school going children in Sakaka, Al Jouf, Kingdom of Saudi Arabia link: https://peerj.com/articles/13582 last-modified: 2022-06-13 description: BackgroundObesity and dental caries are global public health problems. There are conflicting reports about the relationship between caries and obesity. The aim of this study was to analyze the type of relationship between the dental caries and obesity among school children in Al-Jouf region of Saudi Arabia.MethodsThis cross-sectional study was conducted among 400 participants aged 6 to 14 years. The study involved measuring caries (dmft/DMFT), assessing body mass index (BMI), and administering a self-completion questionnaire. An independent t-test, one-way ANOVA, and multivariate logistic regression analyses were performed.ResultsOut of 400 participants, 380 agreed to participate in the study. Overall caries prevalence among the participants was 76.1% and mean DMFT and dmft values were 2.8 ± 1.0 and 3.7 ± 1.6. Among the factors associated with mean caries scores, relation between DMFT scores and frequency of consumption of sugar was statistically significant (F = 3.82,0.01). Regression models has identified children with increased BMI values has 3.2 times more risk of getting dental caries in permanent teeth (P = 0.001).ConclusionThere was a positive association between obesity and dental caries in school going Saudi Arabian children. Comprehensive multidisciplinary approach by health professionals is recommended for preventive public health issues related to caries and obesity in teenagers. creator: Osama Khattak creator: Azhar Iqbal creator: Farooq Ahmad Chaudhary creator: Jamaluddin Syed creator: Thani Alsharari creator: Sudhakar Vundavalli creator: Bayan Abdullah Sadiq Aljahdali creator: Ahmed Eidan Abdullah AlZahrani creator: Rakhi Issrani creator: Sherif Elsayed Sultan uri: https://doi.org/10.7717/peerj.13582 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Khattak et al. title: Assessment of job satisfaction, self-efficacy, and the level of professional burnout of primary and secondary school teachers in Poland during the COVID-19 pandemic link: https://peerj.com/articles/13349 last-modified: 2022-06-10 description: BackgroundThe work of teachers during the COVID-19 pandemic created additional challenges and required them to go beyond conventional teaching methods, which in turn required teachers to be more resilient and caused stress and excessive workload. The aim of the study was to assess the level of occupational burnout, the sense of job satisfaction and the self-efficacy of primary and secondary school teachers working during the COVID-19 pandemic in Poland.MethodsThis is a cross-sectional descriptive study conducted among 412 teachers from randomly selected primary and secondary schools in the Podkarpacie region in Poland. The questionnaire contained socio-demographic data of the respondents and three standardized scales: The Scale of Job Satisfaction (SJS), General Self-Efficacy Scale (GSES) and Arbeitsbesorgenes Verhaltens und Erlebenmuster (AVEM). The Shapiro–Wilk, Kruskal–Wallis and Mann–Whitney U-test were used. Statistical analysis was performed with Statistica TIBCO 13.3 and R (version 3.6.1) software.ResultsThe satisfaction with the work of the surveyed teachers was average in the job satisfaction scale. The vast majority of the surveyed teachers presented type B (overburdened risk type) of work-related behavior, and type A (overburdened risk type) in which the probability of burnout is very high. The feeling of self-effectiveness determines the level of job satisfaction and the level of professional burnout among the surveyed teachers. Job satisfaction had a statistically significant impact on the assessment of self-efficacy of the surveyed teachers (p < 0.0001). The types of work-related behavior have a statistically significant impact on the assessment of the teachers’ own effectiveness (p < 0.0001).ConclusionThere is a close relationship between teachers’ level of self- efficacy, job satisfaction and, therefore it may predispose them to the occurrence of burnout syndrome in the future. Support for this professional group is needed. These findings may be important for education policy, teacher’s practice, and subsequent research. Ultimately, the study may provide some suggestions for methodological and educational strategies. creator: Anna Bartosiewicz creator: Edyta Łuszczki creator: Lech Zaręba creator: Maciej Kuchciak creator: Gabriel Bobula creator: Katarzyna Dereń creator: Paweł Król uri: https://doi.org/10.7717/peerj.13349 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Bartosiewicz et al. title: Organ-specific expression of genes involved in iron homeostasis in wheat mutant lines with increased grain iron and zinc content link: https://peerj.com/articles/13515 last-modified: 2022-06-10 description: BackgroundIron deficiency is a well-known nutritional disorder, and the imbalance of trace-elements, specifically iron, is the most common nutrient deficiency of foods across the world, including in Kazakhstan. Wheat has significant nutritional relevance, especially in the provision of iron, however many bread wheat varieties have low iron despite the need for human nourishment. In this study, the expression profiles of wheat homologous genes related to iron homeostasis were investigated. The work resulted in the development of two new M5 mutant lines of spring bread wheat through gamma-irradiation (200 Gy) with higher grain iron and zinc content, lower phytic acid content, and enhanced iron bioavailability compared to the parent variety. Mutant lines were also characterized by higher means of yield associated traits such as grain number per main spike, grain weight per main spike, grain weight per plant, and thousand-grain weight.MethodsThe homologous genes of bread wheat from several groups were selected for gene expression studies exploring the tight control of iron uptake, translocation rate and accumulation in leaves and roots, and comprised the following: (1) S-adenosylmethionine synthase (SAMS), nicotianamine synthase (NAS1), nicotianamine aminotransferase (NAAT), deoxymugineic acid synthetase (DMAS), involved in the synthesis and release of phytosiderophores; (2) transcription factor basic helix-loop-helix (bHLH); (3) transporters of mugineic acid (TOM), involved in long-distance iron transport; (4) yellow stripe-like (YSlA), and the vacuolar transporter (VIT2), involved in intracellular iron transport and storage; and lastly (5) natural resistance-associated macrophage protein (NRAMP) and ferritin (Fer1A).ResultsThe wheat homologous genes TaSAMS, TaNAS1, and TaDMAS, were significantly up-regulated in the roots of both mutant lines by 2.1–4.7-fold compared to the parent variety. The combined over-expression of TaYSlA and TaVIT2 was also revealed in the roots of mutant lines by 1.3–2.7-fold. In one of the mutant lines, genes encoding intracellular iron transport and storage genes TaNRAMP and TaFer1A-D showed significant up-regulation in roots and leaves (by 1.4- and 3.5-fold, respectively). The highest expression was recorded in the transcription factor TabHLH, which was expressed 13.1- and 30.2-fold in the roots of mutant lines. Our research revealed that genotype-dependent and organ-specific gene expression profiles can provide new insights into iron uptake, translocation rate, storage, and regulation in wheat which aid the prioritization of gene targets for iron biofortification and bioavailability. creator: Saule Kenzhebayeva creator: Saule Atabayeva creator: Fatma Sarsu creator: Alfiya Abekova creator: Sabina Shoinbekova creator: Nargul Omirbekova creator: Gulina Doktyrbay creator: Aizhan Beisenova creator: Yuri Shavrukov uri: https://doi.org/10.7717/peerj.13515 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Kenzhebayeva et al. title: The DNA methylation landscape of five pediatric-tumor types link: https://peerj.com/articles/13516 last-modified: 2022-06-10 description: Fewer DNA mutations have been identified in pediatric tumors than in adult tumors, suggesting that alternative tumorigenic mechanisms, including aberrant DNA methylation, may play a prominent role. In one epigenetic process of regulating gene expression, methyl groups are attached at the 5-carbon of the cytosine ring, leading to 5-methylcytosine (5mC). In somatic cells, 5mC occurs mostly in CpG islands, which are often within promoter regions. In Wilms tumors and acute myeloid leukemias, increased levels of epigenetic silencing have been associated with worse patient outcomes. However, to date, researchers have studied methylation primarily in adult tumors and for specific genes—but not on a pan-pediatric cancer scale. We addressed these gaps first by aggregating methylation data from 309 noncancerous samples, establishing baseline expectations for each probe and gene. Even though these samples represent diverse, noncancerous tissue types and population ancestral groups, methylation levels were consistent for most genes. Second, we compared tumor methylation levels against the baseline values for 489 pediatric tumors representing five cancer types: Wilms tumors, clear cell sarcomas of the kidney, rhabdoid tumors, neuroblastomas, and osteosarcomas. Tumor hypomethylation was more common than hypermethylation, and as many as 41.7% of genes were hypomethylated in a given tumor, compared to a maximum of 34.2% for hypermethylated genes. However, in known oncogenes, hypermethylation was more than twice as common as in other genes. We identified 139 probes (31 genes) that were differentially methylated between at least one tumor type and baseline levels, and 32 genes that were differentially methylated across the pediatric tumor types. We evaluated whether genomic events and aberrant methylation were mutually exclusive but did not find evidence of this phenomenon. creator: Alyssa C. Parker creator: Badí I. Quinteros creator: Stephen R. Piccolo uri: https://doi.org/10.7717/peerj.13516 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Parker et al. title: Full-genome sequencing and mutation analysis of SARS-CoV-2 isolated from Makassar, South Sulawesi, Indonesia link: https://peerj.com/articles/13522 last-modified: 2022-06-10 description: IntroductionA global surge in SARS-CoV-2 cases is occurring due to the emergence of new disease variants, and requires continuous adjustment of public health measures. This study aims to continuously monitor and mitigate the impact of SARS-CoV-2 through genomic surveillance, to determine the emergence of variants and their impact on public health.MethodsData were collected from 50 full-genome sequences of SARS-CoV-2 isolates from Makassar, South Sulawesi, Indonesia. Mutation and phylogenetic analysis was performed of SARS-CoV-2 from Makassar, South Sulawesi, Indonesia.ResultsPhylogenetic analysis showed that two samples (4%) were of the B.1.319 lineage, while the others (96%) were of the B.1.466.2 lineage. Mutation analysis of the spike (S) protein region showed that the most common mutation was D614G (found in 100% of the sequenced isolates), followed by N439K (98%) and P681R (76%). Several mutations were also identified in other genomes with a high frequency, including P323L (nsp12), Q57H (ns3-orf3a), and T205I (nucleoprotein).ConclusionOur findings highlight the importance of continuous genomic surveillance to identify new viral mutations and variants with possible impacts on public health. creator: Muhammad Nasrum Massi creator: Rufika Shari Abidin creator: Abd-ElAziem Farouk creator: Handayani Halik creator: Gita Vita Soraya creator: Najdah Hidayah creator: Rizalinda Sjahril creator: Irda Handayani creator: Mohamad Saifudin Hakim creator: Faris Muhammad Gazali creator: Vivi Setiawaty creator: Tri Wibawa uri: https://doi.org/10.7717/peerj.13522 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Massi et al.