Perceived physical activity during stay-at-home COVID-19 pandemic lockdown March–April 2020 in Polish adults
Background Lockdowns amid the COVID-19 pandemic drastically reduced the possibility of undertaking physical activity (PA) in gyms, swimming pools, or work-related PA, e.g., active commuting. However, the stay-at-home order could have reduced PA the most, i.e., the ban of unnecessary outdoor activities. It affected free walking, running, skiing, active tourism, etc. It is, therefore, crucial to estimate how the stay-at-home order affected PA. We estimated how the stay-at-home order affected perceived PA and sedentary behavior compared to the pre-pandemic time in Poland. Methods We used a self-reported International Physical Activity Questionnaire—Long Form (IPAQ-LF) to estimate the time (minutes per day) of vigorous and moderate PA and walking and sitting time. Results We gathered data from 320 Polish participants. Bayesian approaches, including t-test and Bayesian correlations, were used to find differences and correlations between PA before and during the stay-at-home lockdown. Our data supported the hypotheses that vigorous PA, as well as walking, declined during the lockdown. Surprisingly, our data did not support the hypothesis that moderate physical activity was reduced. We found that moderate PA during lockdown increased compared to the pre-lockdown PA. As hypothesized, our data strongly evinced that sitting time inclined during the lockdown. PA decline was not correlated with the available living space. People who had access to gardens did not demonstrate a higher PA level than those without. Discussion Walking and sitting time have drastically changed during the stay-at-home lockdown, decreasing and increasing, respectively. Given results from studies focusing on lockdowns without the stay-at-home restriction, it may be assumed that letting people go outside is crucial in keeping them more active and less sedentary. Authorities should take into account the effect the stay-at-home order may have on PA and sedentary behavior and as a result, on health. Stay-at-home orders should be the last considered restriction, given its detrimental consequences.
Czyż et al. (2022) Perceived physical activity during stay-at-home COVID-19 pandemic lockdown March–April 2020 in Polish adults. PeerJ 10:e12779 https://doi.org/10.7717/peerj.12779
Almost all known sauropod necks are incomplete and distorted
Sauropods are familiar dinosaurs, immediately recognisable by their great size and long necks. However, their necks are much less well known than is often assumed. Surprisingly few complete necks have been described in the literature, and even important specimens such as the Carnegie Diplodocus and Apatosaurus, and the giant Berlin brachiosaur, in fact have imperfectly known necks. In older specimens, missing bone is often difficult to spot due to over-enthusiastic restoration. Worse still, even those vertebrae that are complete are often badly distorted—for example, in consecutive cervicals of the Carnegie Diplodocus CM 84, the aspect ratio of the posterior articular facet of the centrum varies so dramatically that C14 appears 35% broader proportionally than C13. And even in specimens where the cervicodorsal sequence is preserved, it is often difficult or impossible to confidently identify which vertebra is the first dorsal. Widespread incompleteness and distortion are both inevitable due to sauropod anatomy: large size made it almost impossible for whole individuals to be preserved because sediment cannot be deposited quickly enough to cover a giant carcass on land; and distortion of presacral vertebrae is common due to their lightweight hollow construction. This ubiquitous incompleteness and unpredictable distortion compromise attempts to mechanically analyze necks, for example to determine habitual neck posture and range of motion by modelling articulations between vertebrae.
Taylor (2022) Almost all known sauropod necks are incomplete and distorted. PeerJ 10:e12810 https://doi.org/10.7717/peerj.12810
Impervious surface and local abiotic conditions influence arthropod communities within urban greenspaces
The abundance of arthropods is declining globally, and human-modification of natural habitat is a primary driver of these declines. Arthropod declines are concerning because arthropods mediate critical ecosystem functions, and sustained declines may lead to cascading trophic effects. There is growing evidence that properly managed urban environments can provide refugium to arthropods, but few cities have examined arthropods within urban greenspaces to evaluate their management efforts. In this study, we surveyed arthropod communities within a medium-sized, growing city. We investigated arthropod communities (abundance, richness, diversity, community composition) within 16 urban greenspaces across metropolitan Grand Rapids, Michigan (USA). We focused our efforts on urban gardens and pocket prairies, and measured environmental variables at each site. We collected 5,468 individual arthropods that spanned 14 taxonomic orders and 66 morphospecies. The results showed that community composition was influenced by impervious surface, white flower abundance, and humidity. Total arthropod abundance and diversity were positively associated with humidity. For specific orders, Hymenoptera (bees, ants, wasps) abundance was negatively associated with temperature, and positively associated with site perimeter-area ratio. Hemiptera (true bugs) were negatively associated with impervious surface and positively associated with humidity. These findings show that impervious surfaces impact arthropod communities, but many of the observed changes were driven by local abiotic conditions like temperature and humidity. This suggests that management decisions within urban greenspaces are important in determining the structure of arthropod communities. Future studies on arthropods in cities should determine whether manipulating the abiotic conditions of urban greenspaces influences the composition of arthropod communities. These results should inform city planners and homeowners of the need to properly manage urban greenspaces in cities to maintain diverse arthropod assemblages.
Maher et al. (2022) Impervious surface and local abiotic conditions influence arthropod communities within urban greenspaces. PeerJ 10:e12818 https://doi.org/10.7717/peerj.12818
Characterization of transcriptional landscape in bone marrow-derived mesenchymal stromal cells treated with aspirin by RNA-seq
Introduction Aspirin is a common antipyretic, analgesic, and anti-inflammatory drug, which has been reported to extend life in animal models and application in the treatment of aging-related diseases. However, it remains unclear about the effects of aspirin on bone marrow-derived mesenchymal stromal cells (BM-MSCs). Here, we aimed to analyze the influence of aspirin on senescence and young BM-MSCs. Methods BM-MSCs were serially passaged to construct a replicative senescence model. SA-β-gal staining, PCR, western blot, and RNA-sequencing were performed on BM-MSCs with or without aspirin treatment, to examine aspirin’s impact on bone marrow-derived mesenchymal stem cells. Results SA-β-gal staining, PCR, and western blot revealed that aspirin could alleviate the cellular expression of senescence-related indicators of BM-MSCs, including a decrease of SA-β-gal-positive cells and staining intensity, and downregulation of p16, p21, and p53 expression after aspirin treatment. RNA-sequencing results shown in the biological processes related to aging, aspirin could influence cellular immune response and lipid metabolism. Conclusion The efficacy of aspirin for retarding senescence of BM-MSCs was demonstrated. Our study indicated that the mechanisms of this delay might involve influencing immune response and lipid metabolism.
Liu et al. (2022) Characterization of transcriptional landscape in bone marrow-derived mesenchymal stromal cells treated with aspirin by RNA-seq. PeerJ 10:e12819 https://doi.org/10.7717/peerj.12819
Retrogene survival is not impacted by linkage relationships
In retrogene evolution, the out-of-the-X pattern is the retroduplication of X-linked housekeeping genes to autosomes, hypothesized to be driven by meiotic sex chromosome inactivation during spermatogenesis. This pattern suggests that some retrogene survival is driven by selection on X-linkage. We asked if selection on linkage constitutes an important evolutionary force in retrogene survival, including for autosomal parents. Specifically, is there a correlation between retrogene survival and changes in linkage with parental gene networks? To answer this question, we compiled data on retrogenes in both Homo sapiens and Drosophila melanogaster and using Monte Carlo methods, we tested whether retrogenes exhibit significantly different linkage relationships than expected under a null assumption of uniform distribution in the genome. Overall, after excluding genes involved in the out-of-the-X pattern, no general pattern was found associating genetic linkage and retrogene survival. This demonstrates that selection on linkage may not represent an overarching force in retrogene survival. However, it remains possible that this type of selection still influences the survival of specific retrogenes.
Lo et al. (2022) Retrogene survival is not impacted by linkage relationships. PeerJ 10:e12822 https://doi.org/10.7717/peerj.12822
Identification and validation of an epithelial mesenchymal transition-related gene pairs signature for prediction of overall survival in patients with skin cutaneous melanoma
Background We aimed to construct a novel epithelial-mesenchymal transition (EMT)-related gene pairs (ERGPs) signature to predict overall survival (OS) in skin cutaneous melanoma (CM) patients. Methods Expression data of the relevant genes, corresponding clinicopathological parameters, and follow-up data were obtained from The Cancer Genome Atlas database. Univariate Cox regression analysis was utilized to identify ERGPs significantly associated with OS, and LASSO analysis was used to identify the genes used for the construction of the ERGPs signature. The optimal cutoff value determined by the receiver operating characteristic curve was used to classify patients into high-risk and low-risk groups. Survival curves were generated using the Kaplan–Meier method, and differences between the two groups were estimated using the log-rank test. The independent external datasets GSE65904 and GSE19234 were used to verify the performance of the ERGPs signature using the area under the curve (AUC) values. In addition, we also integrated clinicopathological parameters and risk scores to develop a nomogram that can individually predict the prognosis of patients with CM. Results A total of 104 ERGPs related to OS were obtained, of which 21 ERGPs were selected for the construction of the signature. All CM patients were stratified into high-and low-risk groups based on an optimal risk score cutoff value of 0.281. According to the Kaplan–Meier analysis, the mortality rate in the low-risk group was lower than that in the high-risk group in the TCGA cohort (P < 0.001), GSE65904 cohort (P = 0.006), and GSE19234 cohort (P = 0.002). Multivariate Cox regression analysis indicated that our ERGP signature was an independent risk factor for OS in CM patients in the three cohorts (for TCGA: HR, 2.560; 95% CI [1.907–3.436]; P < 0.001; for GSE65904: HR = 2.235, 95% CI [1.492–3.347], P < 0.001; for GSE19234: HR = 2.458, 95% CI [1.065–5.669], P = 0.035). The AUC value for predicting the 5-year survival rate of patients with CM of our developed model was higher than that of two previously established prognostic signatures. Both the calibration curve and the C-index (0.752, 95% CI [0.678–0.826]) indicated that the developed nomogram was highly accurate. Most importantly, the decision curve analysis results showed that the nomogram had a higher net benefit than that of the American Joint Committee on Cancer stage system. Conclusion Our study established an ERGPs signature that could be potentially used in a clinical setting as a genetic biomarker for risk stratification of CM patients. In addition, the ERGPs signature could also predict which CM patients will benefit from PD-1 and PD-L1 inhibitors.
Shi et al. (2022) Identification and validation of an epithelial mesenchymal transition-related gene pairs signature for prediction of overall survival in patients with skin cutaneous melanoma. PeerJ 10:e12646 https://doi.org/10.7717/peerj.12646
Antimicrobial peptides properties beyond growth inhibition and bacterial killing
Antimicrobial peptides (AMPs) are versatile molecules with broad antimicrobial activity produced by representatives of the three domains of life. Also, there are derivatives of AMPs and artificial short peptides that can inhibit microbial growth. Beyond killing microbes, AMPs at grow sub-inhibitory concentrations also exhibit anti-virulence activity against critical pathogenic bacteria, including ESKAPE pathogens. Anti-virulence therapies are an alternative to antibiotics since they do not directly affect viability and growth, and they are considered less likely to generate resistance. Bacterial biofilms significantly increase antibiotic resistance and are linked to establishing chronic infections. Various AMPs can kill biofilm cells and eradicate infections in animal models. However, some can inhibit biofilm formation and promote dispersal at sub-growth inhibitory concentrations. These examples are discussed here, along with those of peptides that inhibit the expression of traits controlled by quorum sensing, such as the production of exoproteases, phenazines, surfactants, toxins, among others. In addition, specific targets that are determinants of virulence include secretion systems (type II, III, and VI) responsible for releasing effector proteins toxic to eukaryotic cells. This review summarizes the current knowledge on the anti-virulence properties of AMPs and the future directions of their research.
Castillo-Juárez et al. (2022) Antimicrobial peptides properties beyond growth inhibition and bacterial killing. PeerJ 10:e12667 https://doi.org/10.7717/peerj.12667
Chondrochelia Guţu, 2016 (Crustacea, Peracarida, Tanaidacea, Leptocheliidae) from North America: new species, redescription and distribution using morphological and molecular data
Until now, four species of the genus Chondrochelia Guţu, 2016 have been recorded from America. Using morphological and molecular data, we were able to recognize and describe two new species, Chondrochelia caribensis sp. nov. from the Mexican Caribbean and Chondrochelia winfieldi sp. nov. from the Gulf of Mexico. We found significant genetic divergence values between species based on the nucleotide sequences of cytochrome oxidase subunit I to support the morphological data. Also, the range of distribution of two species: Chondrochelia mexicana (Jarquín-González, García-Madrigal & Carrera-Parra, 2015) and Chondrochelia ortizi (Jarquín-González, 2016), were expanded within their described geographic regions. In contrast, the supposed distribution of the Brazilian C. dubia in the Mexican Caribbean and the Gulf of Mexico was rejected. Additionally, Chondrochelia algicola (Harger, 1878) was redescribed based upon type material. Minute details and ornamentation of some structures of three species were examined using SEM.
© 2022 Jarquín-González and Carrera-Parra
Jarquín-González et al. (2022) Chondrochelia Guţu, 2016 (Crustacea, Peracarida, Tanaidacea, Leptocheliidae) from North America: new species, redescription and distribution using morphological and molecular data. PeerJ 10:e12773 https://doi.org/10.7717/peerj.12773
Measuring mass: variation among 3,161 species of Canadian Coleoptera and the prospects of a mass registry for all insects
Although biomass values are critical for diverse ecological and evolutionary analyses, they are unavailable for most insect species. Museum specimens have the potential to address this gap, but the variation introduced by sampling and preservation methods is uncertain. This study quantifies species-level variation in the body mass of Canadian Coleoptera based on the analysis of 3,744 specimens representing 3,161 Barcode Index Number (BIN) clusters. Employing the BIN system as a proxy for species allows the inclusion of groups where the taxonomic impediment prevents the assignment of specimens to a Linnaean species. By validating the reproducibility of measurements and evaluating the error introduced by operational complexities such as curatorial practice and the loss of body parts, this study demonstrates that museum specimens can speed the assembly of a mass registry. The results further indicate that congeneric species of Coleoptera generally have limited variation in mass, so a genus-level identification allows prediction of the body mass of species that have not been weighed or measured. Building on the present results, the construction of a mass registry for all insects is feasible.
Hu et al. (2022) Measuring mass: variation among 3,161 species of Canadian Coleoptera and the prospects of a mass registry for all insects. PeerJ 10:e12799 https://doi.org/10.7717/peerj.12799
Effectiveness of interactive teaching intervention on medical students’ knowledge and attitudes toward stem cells, their therapeutic uses, and potential research applications
Background Stem cell science is rapidly developing with the potential to alleviate many non-treatable diseases. Medical students, as future physicians, should be equipped with the proper knowledge and attitude regarding this hopeful field. Interactive teaching, whereby the teachers actively involve the students in the learning process, is a promising approach to improve their interest, knowledge, and team spirit. This study aims to evaluate the effectiveness of an interactive teaching intervention on medical students’ knowledge and attitudes about stem cell research and therapy. Methods A pre-post test study design was employed. A six-session interactive teaching course was conducted for a duration of six weeks as an intervention. Pre- and post-intervention surveys were used. The differences in the mean scores of students’ knowledge and attitudes were examined using paired t-test, while gender differences were examined using an independent t-test. Results Out of 71 sixth-year medical students from different nationalities invited to participate in this study, the interactive teaching course was initiated by 58 students resulting in a participation rate of 81.7%. Out of 58 students, 48 (82.8%) completed the entire course. The mean age (standard deviation) of students was 24 (1.2) years, and 32 (66.7%) were males. The results showed poor knowledge about stem cells among the medical students in the pre-intervention phase. Total scores of stem cell-related knowledge and attitudes significantly improved post-intervention. Gender differences in knowledge and attitudes scores were not statistically significant post-intervention. Conclusions Integrating stem cell science into medical curricula coupled with interactive learning approaches effectively increased students’ knowledge about recent advances in stem cell research and therapy and improved attitudes toward stem cell research and applications.
Abdulrazeq et al. (2022) Effectiveness of interactive teaching intervention on medical students’ knowledge and attitudes toward stem cells, their therapeutic uses, and potential research applications. PeerJ 10:e12824 https://doi.org/10.7717/peerj.12824