Punicalagin, a pomegranate compound, induces apoptosis and autophagy in acute leukemia
Background Punicalagin 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. Methods Leukemic 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. Results Results 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. Conclusions These 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.
Subkorn et al. (2021) Punicalagin, a pomegranate compound, induces apoptosis and autophagy in acute leukemia. PeerJ 9:e12303 https://doi.org/10.7717/peerj.12303
Adult body size measurement redundancies in Osmia lignaria and Megachile rotundata (Hymenoptera: Megachilidae)
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.
McCabe et al. (2021) Adult body size measurement redundancies in Osmia lignaria and Megachile rotundata (Hymenoptera: Megachilidae). PeerJ 9:e12344 https://doi.org/10.7717/peerj.12344
Differential p16 expression levels in the liver, hepatocytes and hepatocellular cell lines
Background One 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. Methods The expression of the p16 gene in liver and liver cells was determined by RT-qPCR and compared to its protein amounts by western blotting. Results p16 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.
Kramar et al. (2021) Differential p16 expression levels in the liver, hepatocytes and hepatocellular cell lines. PeerJ 9:e12358 https://doi.org/10.7717/peerj.12358
Spatio-temporal variations of the major meteorological disasters and its response to climate change in Henan Province during the past two millennia
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.
Spatial and Geographic Information Science
Li et al. (2021) Spatio-temporal variations of the major meteorological disasters and its response to climate change in Henan Province during the past two millennia. PeerJ 9:e12365 https://doi.org/10.7717/peerj.12365
On the enigma of Palaenigma wrangeli (Schmidt), a conulariid with a partly non-mineralized skeleton
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.
Kröger et al. (2021) On the enigma of Palaenigma wrangeli (Schmidt), a conulariid with a partly non-mineralized skeleton. PeerJ 9:e12374 https://doi.org/10.7717/peerj.12374
Integrated bioinformatics analysis reveals dynamic candidate genes and signaling pathways involved in the progression and prognosis of diffuse large B-cell lymphoma
Background Diffuse large B-cell lymphoma (DLBCL) is a highly heterogeneous malignancy with varied outcomes. However, the fundamental mechanisms remain to be fully defined. Aim We aimed to identify core differentially co-expressed hub genes and perturbed pathways relevant to the pathogenesis and prognosis of DLBCL. Methods We 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. Results We 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. Conclusion Our 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.
Charwudzi et al. (2021) Integrated bioinformatics analysis reveals dynamic candidate genes and signaling pathways involved in the progression and prognosis of diffuse large B-cell lymphoma. PeerJ 9:e12394 https://doi.org/10.7717/peerj.12394
Going rogue: what scientists can learn about Twitter communication from “alt” government accounts
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.
Wilson et al. (2021) Going rogue: what scientists can learn about Twitter communication from “alt” government accounts. PeerJ 9:e12407 https://doi.org/10.7717/peerj.12407
Characterizing the spatial distribution of coral reefs in the South-Central Coast region of Viet Nam using Planetscope imagery
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.
Nguyen et al. (2021) Characterizing the spatial distribution of coral reefs in the South-Central Coast region of Viet Nam using Planetscope imagery. PeerJ 9:e12413 https://doi.org/10.7717/peerj.12413
Comparing size selectivity and exploitation pattern of diamond-mesh codends for Southern velvet shrimp (Metapenaeopsis palmensis) in shrimp trawl fishery of the South China Sea
In this study, size selectivity and exploitation pattern of six diamond-mesh codends with different mesh sizes, ranging from 25 to 54 mm, for Southern velvet shrimp (Metapenaeopsis palmensis) were tested and compared in a shrimp trawl fishery of the South China Sea (SCS). We used a codend with a mesh size of 25 mm (D25) as a starting point, which is the minimum mesh size (MMS) currently regulated in the studied area. Four different fishing population scenarios were applied to quantify and compare how mesh sizes of codends used would impact the size selectivity and exploitation pattern for the target shrimp species. The results demonstrated that the D25 codend was not proper for protecting juvenile shrimp at the studied area. By applying this legal codend, L50 (50% retention length) of the target shrimp species was below its minimum conservation reference size (MCRS, 7.0 cm total length), the retention probability of shrimp with a length of MCRS was above 95% CI [91–99] and more than 43% of undersized shrimp was retained. To mitigate the bycatch issue of undersized shrimp, increasing the mesh size in the diamond mesh codend is a simple and effective option. However, the loss of catch efficiency for marketable shrimp is a major concern while increasing the mesh size. A good compromise between releasing undersized shrimp and maintaining the legal individuals is manifested by using the codend with 35 mm mesh size (D35). Our study will be beneficial for the management of shrimp trawl fisheries in the SCS.
Yang et al. (2021) Comparing size selectivity and exploitation pattern of diamond-mesh codends for Southern velvet shrimp (Metapenaeopsis palmensis) in shrimp trawl fishery of the South China Sea. PeerJ 9:e12436 https://doi.org/10.7717/peerj.12436
Parallel power posterior analyses for fast computation of marginal likelihoods in phylogenetics
In Bayesian phylogenetic inference, marginal likelihoods can be estimated using several different methods, including the path-sampling or stepping-stone-sampling algorithms. Both algorithms are computationally demanding because they require a series of power posterior Markov chain Monte Carlo (MCMC) simulations. Here we introduce a general parallelization strategy that distributes the power posterior MCMC simulations and the likelihood computations over available CPUs. Our parallelization strategy can easily be applied to any statistical model despite our primary focus on molecular substitution models in this study. Using two phylogenetic example datasets, we demonstrate that the runtime of the marginal likelihood estimation can be reduced significantly even if only two CPUs are available (an average performance increase of 1.96x). The performance increase is nearly linear with the number of available CPUs. We record a performance increase of 13.3x for cluster nodes with 16 CPUs, representing a substantial reduction to the runtime of marginal likelihood estimations. Hence, our parallelization strategy enables the estimation of marginal likelihoods to complete in a feasible amount of time which previously needed days, weeks or even months. The methods described here are implemented in our open-source software RevBayes which is available from http://www.RevBayes.com.
Höhna et al. (2021) Parallel power posterior analyses for fast computation of marginal likelihoods in phylogenetics. PeerJ 9:e12438 https://doi.org/10.7717/peerj.12438