title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=810 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Co-occurrence pattern of congeneric tree species provides conflicting evidence for competition relatedness hypothesis link: https://peerj.com/articles/12150 last-modified: 2021-11-02 description: In plants, negative reproductive interaction among closely related species (i.e., reproductive interference) is known to hamper the coexistence of congeneric species while facilitation can increase species persistence. Since reproductive interference in plants may occur through interspecific pollination, the effective range of reproductive interference may reflects the spatial range of interspecific pollination. Therefore, we hypothesized that the coexistence of congeners on a small spatial scale would be less likely to occur by chance but that such coexistence would be likely to occur on a scale larger than interspecific pollination frequently occur. In the present study, we tested this hypothesis using spatially explicit woody plant survey data. Contrary to our prediction, congeneric tree species often coexisted at the finest spatial scale and significant exclusive distribution was not detected. Our results suggest that cooccurrence of congeneric tree species is not structured by reproductive interference, and they indicate the need for further research to explore the factors that mitigate the effects of reproductive interference. creator: Shuntaro Watanabe creator: Yuri Maesako uri: https://doi.org/10.7717/peerj.12150 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Watanabe and Maesako title: Senescence as a trade-off between successful land colonisation and longevity: critical review and analysis of a hypothesis link: https://peerj.com/articles/12286 last-modified: 2021-11-02 description: BackgroundMost common terrestrial animal clades exhibit senescence, suggesting strong adaptive value of this trait. However, there is little support for senescence correlated with specific adaptations. Nevertheless, insects, mammals, and birds, which are the most common terrestrial animal clades that show symptoms of senescence, evolved from clades that predominantly did not show symptoms of senescence. Thus, we aimed to examine senescence in the context of the ecology and life histories of the main clades of animals, including humans, and to formulate hypotheses to explain the causes and origin of senescence in the major clades of terrestrial animals.MethodologyWe reviewed literature from 1950 to 2020 concerning life expectancy, the existence of senescence, and the adaptive characteristics of the major groups of animals. We then proposed a relationship between senescence and environmental factors, considering the biology of these groups of animals. We constructed a model showing the phylogenetic relationships between animal clades in the context of the major stages of evolution, distinguishing between senescent and biologically ‘immortal’ clades of animals. Finally, we synthesised current data on senescence with the most important concepts and theories explaining the origin and mechanisms of senescence. Although this categorisation into different senescent phenotypes may be simplistic, we used this to propose a framework for understanding senescence.ResultsWe found that terrestrial mammals, insects, and birds show senescence, even though they likely evolved from non-senescent ancestors. Moreover, secondarily aquatic animals show lower rate of senescence than their terrestrial counterparts. Based on the possible life histories of these groups and the analysis of the most important factors affecting the transition from a non-senescent to senescent phenotype, we conclude that aging has evolved, not as a direct effect, but as a correlated response of selection on developmental strategies, and that this occurred separately within each clade. Adoption of specific life history strategies could thus have far-reaching effects in terms of senescence and lifespan.ConclusionsOur analysis strongly suggests that senescence may have emerged as a side effect of the evolution of adaptive features that allowed the colonisation of land. Senescence in mammals may be a compromise between land colonisation and longevity. This hypothesis, is supported by palaeobiological and ecological evidence. We hope that the development of new research methodologies and the availability of more data could be used to test this hypothesis and shed greater light on the evolution of senescence. creator: Tomasz Bilinski creator: Aneta Bylak creator: Krzysztof Kukuła creator: Renata Zadrag-Tecza uri: https://doi.org/10.7717/peerj.12286 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Bilinski et al. title: Punicalagin, a pomegranate compound, induces apoptosis and autophagy in acute leukemia link: https://peerj.com/articles/12303 last-modified: 2021-11-02 description: BackgroundPunicalagin is the major phenolic compound found in pomegranate peels. It has several reported medical benefits, including antioxidant, anti-inflammatory, and anticancer properties. The present study investigated the anti-leukemic effects and the molecular mechanism of punicalagin on NB4 and MOLT-4 leukemic cell lines.MethodsLeukemic cells were treated with punicalagin and cell viability was determined using MTS assay. Apoptosis and autophagy were analyzed by flow cytometry using Annexin V-FITC/PI and anti-LC3/FITC antibodies staining, respectively. Apoptotic and autophagic mRNA expression were determined using reverse transcription-quantitative PCR. STITCH bioinformatics tools were used to predict the interaction between punicalagin and its proposed target proteins.ResultsResults indicated that punicalagin decreased NB4 and MOLT-4 cell viability in a dose-dependent manner. Punicalagin, in combination with daunorubicin, exhibited synergistic cytotoxic effects. Punicalagin induced apoptosis through the upregulation of caspase-3/-8/-9, Bax and the downregulation of Bcl-2 expression. Punicalagin also promoted autophagy via the downregulation of mTOR and the upregulation of ULK1 expression. Cyclooxygenase-2 and toll-like receptor 4 were found to be involved in punicalagin-induced cell death in punicalagin-targeted protein interactions.ConclusionsThese results suggest that punicalagin exerts cytotoxic activities by suppressing proliferation and promoting apoptosis and autophagy by activating the caspase cascade, altering Bax and Bcl-2, and regulating autophagy via mTOR/ULK1 signaling. creator: Paweena Subkorn creator: Chosita Norkaew creator: Kamolchanok Deesrisak creator: Dalina Tanyong uri: https://doi.org/10.7717/peerj.12303 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Subkorn et al. title: Adult body size measurement redundancies in Osmia lignaria and Megachile rotundata (Hymenoptera: Megachilidae) link: https://peerj.com/articles/12344 last-modified: 2021-11-02 description: Metrics to assess relative adult bee body size have included both mass and morphometrics, but these metrics may not equally or reliably estimate body size for all bee species and in all situations, due to bee age, diet, and/or environment. Understanding the relationships between different metrics and possible redundancies in the information they afford is important but not always known. Body size measurements provide valuable data for interpreting research outcomes for managed solitary bees, including Osmia lignaria Say and Megachile rotundata F. (Hymenoptera: Megachilidae). Applied studies of these important and readily available U.S. crop pollinators focus on refining commercial management practices, and basic empirical studies in various scientific disciplines (from genomics to ecology) employ them as model systems to study solitary bees. To examine common metrics of body size, we measured head capsule width (HCW), intertegular distance (ITD), and fresh and dry weights of newly emerged adults of both species. Using linear and exponential models, we determined relationships between these body size metrics. For M. rotundata, linear models best described relationships between ITD and all other metrics, and between HCW and fresh and dry weights. For O. lignaria, linear models best fit relationships between all metrics except for fresh weight with both ITD and HCW, which were fitted better with exponential models. For both species, model fits were strongest when males and females were pooled. Depending on the study question, knowing that only one metric may reliably measure body size can simplify evaluations of O. lignaria and M. rotundata responses to artificial or environmental variables. creator: Lindsie M. McCabe creator: Natalie K. Boyle creator: Morgan B. Scalici creator: Theresa L. Pitts-Singer uri: https://doi.org/10.7717/peerj.12344 license: http://www.nationalarchives.gov.uk/doc/open-government-licence/ rights: title: Differential p16 expression levels in the liver, hepatocytes and hepatocellular cell lines link: https://peerj.com/articles/12358 last-modified: 2021-11-02 description: BackgroundOne of the most frequently deleted genes in cancer is CDKN2A encoding p16. This protein is often overexpressed in senescent cells, while its suppression can bypass the oncogene-induced senescence to enable transformation and tumorigenesis. The roles of the protein p16 are recently being expanded from the cell cycle progression regulator to the cellular regulator interacting in several different pathways. Yet data on its liver and liver cells’ expression are inconclusive.MethodsThe expression of the p16 gene in liver and liver cells was determined by RT-qPCR and compared to its protein amounts by western blotting.Resultsp16 is expressed at low levels in the liver and rat hepatocytes. Its expression varies from none to the considerable levels in the examined hepatocellular carcinoma cell lines (FaO and HepG2) and in immortalized mouse hepatocytes. Such significant expression differences of an important cellular regulator warrant the need to closely examine the differences in biochemical pathways correlated with the p16 expression when using hepatocytes and hepatoma liver models. creator: Barbara Kramar creator: Dušan Šuput creator: Irina Milisav uri: https://doi.org/10.7717/peerj.12358 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Kramar et al. title: Spatio-temporal variations of the major meteorological disasters and its response to climate change in Henan Province during the past two millennia link: https://peerj.com/articles/12365 last-modified: 2021-11-02 description: In China, historical documents have recorded large quantities of information related to natural disasters, and these disasters have had long-lasting effects on economic and social activities. Understanding the occurrence of the natural disasters and their spatio-temporal variation characters is crucial for sustainable of our society. Therefore, based on the collection and collation of historical documents, and adopting mathematical statistics, Kriging interpolation, correlation analysis and other methods, we systematically explored the meteorological disasters in Henan Province during the past two millennia in analyzing their spatio-temporal distribution characters and driving forces. The results demonstrate that there were five major types of meteorological disasters in Henan Province, including drought, flood, hails, low temperature and frost and insect pests, which presented obvious spatio-temporal variations and have occurred frequently during the past two millennia. According to the historical documents, the major meteorological disasters occurred 1,929 times in Henan from 221 BCE to 2000 CE. On the whole, the disaster frequency show that the occurrence cycle of the meteorological disasters has obvious changes, which mainly occurred in the middle and late stages during the past two millennia, especially after 1300 CE. Furthermore, we also find that the variation of meteorological disaster events is consistent with the variation of temperature in eastern China and the frequency of meteorological disaster increases in the cold period, but decreases in the warm period. In addition, there are obvious differences in the spatial distribution of the major meteorological disaster, which were mainly distributed in the northwest and southern part region of the Henan Province before 1911 CE. While after 1911 CE, the northern and southeastern parts were the meteorological disaster-prone areas in this region during this period. Spatial correlation analysis of each meteorological disaster before and after 1911 CE points out the droughts disaster frequency-occurring district has transferred in different periods, while the hail and low temperature and frost disasters just have a smaller transferred during these two periods. Conversely, the frequency-occurring districts of floods and insect pest disasters have no obviously transferred in different periods. These results can provide an important scientific basis for governmental decision makers and local people to prevent and mitigate meteorological disaster in the future. creator: Xiang Li creator: Hui Lu creator: Zhaokang Zhang creator: Wei Xing uri: https://doi.org/10.7717/peerj.12365 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: On the enigma of Palaenigma wrangeli (Schmidt), a conulariid with a partly non-mineralized skeleton link: https://peerj.com/articles/12374 last-modified: 2021-11-02 description: Palaenigma wrangeli (Schmidt) is a finger-sized fossil with a tetraradiate conical skeleton; it occurs as a rare component in fossiliferous Upper Ordovician strata of the eastern Baltic Basin and is known exclusively from north Estonia. The systematic affinities and palaeoecology of P. wrangeli remained questionable. Here, the available specimens of P. wrangeli have been reexamined using scanning electron microscopy and x-ray computed tomography (microCT). Additionally, the elemental composition of the skeletal elements has been checked using energy dispersive X-ray spectroscopy. The resulting 2D-, and 3D-scans reveal that P. wrangeli consists of an alternation of distinct calcium phosphate (apatite) lamellae and originally organic-rich inter-layers. The lamellae form four semicircular marginal pillars, which are connected by irregularly spaced transverse diaphragms. Marginally, the diaphragms and pillar lamellae are not connected to each other and thus do not form a closed periderm structure. A non-mineralized or poorly mineralized external periderm existed originally in P. wrangeli but is only rarely and fragmentary preserved. P. wrangeli often co-occurs with conulariids in fossil-rich limestone with mudstone–wackestone lithologies. Based on the new data, P. wrangeli can be best interpreted as a poorly mineralized conulariinid from an original soft bottom habitat. Here the new conulariinid family Palaenigmaidae fam. nov. is proposed as the monotypic taxon for P. wrangeli. creator: Björn Kröger creator: Olev Vinn creator: Ursula Toom creator: Ian J. Corfe creator: Jukka Kuva creator: Michał Zatoń uri: https://doi.org/10.7717/peerj.12374 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kröger et al. title: Integrated bioinformatics analysis reveals dynamic candidate genes and signaling pathways involved in the progression and prognosis of diffuse large B-cell lymphoma link: https://peerj.com/articles/12394 last-modified: 2021-11-02 description: BackgroundDiffuse large B-cell lymphoma (DLBCL) is a highly heterogeneous malignancy with varied outcomes. However, the fundamental mechanisms remain to be fully defined.AimWe aimed to identify core differentially co-expressed hub genes and perturbed pathways relevant to the pathogenesis and prognosis of DLBCL.MethodsWe retrieved the raw gene expression profile and clinical information of GSE12453 from the Gene Expression Omnibus (GEO) database. We used integrated bioinformatics analysis to identify differentially co-expressed genes. The CIBERSORT analysis was also applied to predict tumor-infiltrating immune cells (TIICs) in the GSE12453 dataset. We performed survival and ssGSEA (single-sample Gene Set Enrichment Analysis) (for TIICs) analyses and validated the hub genes using GEPIA2 and an independent GSE31312 dataset.ResultsWe identified 46 differentially co-expressed hub genes in the GSE12453 dataset. Gene expression levels and survival analysis found 15 differentially co-expressed core hub genes. The core genes prognostic values and expression levels were further validated in the GEPIA2 database and GSE31312 dataset to be reliable (p < 0.01). The core genes’ main KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichments were Ribosome and Coronavirus disease-COVID-19. High expressions of the 15 core hub genes had prognostic value in DLBCL. The core genes showed significant predictive accuracy in distinguishing DLBCL cases from non-tumor controls, with the area under the curve (AUC) ranging from 0.992 to 1.00. Finally, CIBERSORT analysis on GSE12453 revealed immune cells, including activated memory CD4+ T cells and M0, M1, and M2-macrophages as the infiltrates in the DLBCL microenvironment.ConclusionOur study found differentially co-expressed core hub genes and relevant pathways involved in ribosome and COVID-19 disease that may be potential targets for prognosis and novel therapeutic intervention in DLBCL. creator: Alice Charwudzi creator: Ye Meng creator: Linhui Hu creator: Chen Ding creator: Lianfang Pu creator: Qian Li creator: Mengling Xu creator: Zhimin Zhai creator: Shudao Xiong uri: https://doi.org/10.7717/peerj.12394 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Charwudzi et al. title: Going rogue: what scientists can learn about Twitter communication from “alt” government accounts link: https://peerj.com/articles/12407 last-modified: 2021-11-02 description: The inauguration of President Trump in the United States led to the active restriction of science communication from federal agencies, resulting in the creation of many unofficial “alt” Twitter accounts to maintain communication. Alt accounts had many followers (e.g., 15 accounts had > 100,000) and received a large amount of media attention, making them ideal for better understanding how differences in messaging can affect public engagement with science on microblogging platforms. We analyzed tweets produced by alt and corresponding official agency accounts to compare the two groups and determine if specific features of a tweet made them more likely to be retweeted or liked to help the average scientist potentially reach a broader audience on Twitter. We found adding links, images, hashtags, and mentions, as well as expressing angry and annoying sentiments all increased retweets and likes. Evidence-based terms such as “peer-review” had high retweet rates but linking directly to peer-reviewed publications decreased attention compared to popular science websites. Word choice and attention did not reflect official or alt account types, indicating topic is more important than source. The number of tweets generated and attention received by alt accounts has decreased since their creation, demonstrating the importance of timeliness in science communication on social media. Together our results show potential pathways for scientists to increase efficacy in Twitter communications. creator: Matthew J. Wilson creator: Elizabeth K. Perkin uri: https://doi.org/10.7717/peerj.12407 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wilson and Perkin title: Characterizing the spatial distribution of coral reefs in the South-Central Coast region of Viet Nam using Planetscope imagery link: https://peerj.com/articles/12413 last-modified: 2021-11-02 description: This study aims to understand the spatial distribution of coral reefs in the central region of Viet Nam. We classified live coral cover in Son Tra Peninsula (ST) and Cu Lao Cham Island (CLC) in the South-Central Coast Region of Viet Nam using the Maximum Likelihood Classifier on 3 m Planetscope imagery. Confusion matrices and the accuracy of the classifier were assessed using field data (1,543 and 1,560 photographs in ST and CLC, respectively). The results showed that the reef’s width ranged from 30 to 300 m across the study site, and we were able to detect live coral cover across a depth gradient of 2 to 6 m below the sea surface. The overall accuracies of the classifier (the Kappa coefficient) were 76.78% (0.76) and 78.08% (0.78) for ST and CLC, respectively. We found that 60.25% of coral reefs in ST were unhealthy and the live coral cover was less than 50%, while 25.75% and 11.46% of those in CLC were in good and excellent conditions, respectively. This study demonstrates the feasibility of utilizing Planetscope imagery to monitor shallow coral reefs of small islands at a high spatial resolution of 3 m. The results of this study provide valuable information for coral reef protection and conservation. creator: Khanh V. Nguyen creator: Vinh C. Duong creator: Kinh T. Kieu creator: Thuong V. Tran creator: Cho-ying Huang creator: Ruth Reef creator: Thien M. Hoang uri: https://doi.org/10.7717/peerj.12413 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Nguyen et al.