Spatial temporal distribution of COVID-19 risk during the early phase of the pandemic in Malawi
Background COVID-19 has been one of the greatest challenges the world has faced since the second world war. This study aimed at investigating the distribution of COVID-19 in both space and time in Malawi. Methods The study used publicly available data of COVID-19 cases for the period from 2 April 2020 to 28 October 2020. Semiparametric spatial temporal models were fitted to the number of monthly confirmed cases as an outcome data, with time and district as independent variables, where district was the spatial unit, while accounting for sociodemographic factors. Results The study found significant effects of location and time, with the two interacting. The spatial distribution of COVID-19 risk showed major cities being at greater risk than rural areas. Over time, the COVID-19 risk was increasing then decreasing in most districts with the rural districts being consistently at lower risk. High proportion of elderly people was positively associated with COVID-19 risk (β = 1.272, 95% CI [0.171, 2.370]) than low proportion of elderly people. There was negative association between poverty incidence and COVID-19 risk (β = −0.100, 95% CI [−0.136, −0.065]). Conclusion Future or present strategies to limit the spread of COVID-19 should target major cities and the focus should be on time periods that had shown high risk. Furthermore, the focus should be on elderly and rich people.
Spatial and Geographic Information Science
Ngwira et al. (2021) Spatial temporal distribution of COVID-19 risk during the early phase of the pandemic in Malawi. PeerJ 9:e11003 https://doi.org/10.7717/peerj.11003
Low compositions of human toll-like receptor 7/8-stimulating RNA motifs in the MERS-CoV, SARS-CoV and SARS-CoV-2 genomes imply a substantial ability to evade human innate immunity
Background The innate immune system especially Toll-like receptor (TLR) 7/8 and the interferon pathway, constitutes an important first line of defense against single-stranded RNA viruses. However, large-scale, systematic comparisons of the TLR 7/8-stimulating potential of genomic RNAs of single-stranded RNA viruses are rare. In this study, a computational method to evaluate the human TLR 7/8-stimulating ability of single-stranded RNA virus genomes based on their human TLR 7/8-stimulating trimer compositions was used to analyze 1,002 human coronavirus genomes. Results The human TLR 7/8-stimulating potential of coronavirus genomic (positive strand) RNAs followed the order of NL63-CoV > HKU1-CoV >229E-CoV ≅ OC63-CoV > SARS-CoV-2 > MERS-CoV > SARS-CoV. These results suggest that among these coronaviruses, MERS-CoV, SARS-CoV and SARS-CoV-2 may have a higher ability to evade the human TLR 7/8-mediated innate immune response. Analysis with a logistic regression equation derived from human coronavirus data revealed that most of the 1,762 coronavirus genomic (positive strand) RNAs isolated from bats, camels, cats, civets, dogs and birds exhibited weak human TLR 7/8-stimulating potential equivalent to that of the MERS-CoV, SARS-CoV and SARS-CoV-2 genomic RNAs. Conclusions Prediction of the human TLR 7/8-stimulating potential of viral genomic RNAs may be useful for surveillance of emerging coronaviruses from nonhuman mammalian hosts.
Yang et al. (2021) Low compositions of human toll-like receptor 7/8-stimulating RNA motifs in the MERS-CoV, SARS-CoV and SARS-CoV-2 genomes imply a substantial ability to evade human innate immunity. PeerJ 9:e11008 https://doi.org/10.7717/peerj.11008
Comparison between cultured and wild Pacific white shrimp (Penaeus vannamei) vitellogenesis: next-generation sequencing and relative expression of genes directly and indirectly related to reproduction
Shrimp fisheries are among the most important fisheries worldwide, and shrimp culture has increased considerably in recent years. Most current studies on reproduction-related genes have been conducted on cultured shrimp. However, gene expression is intimately linked to physiological and environmental conditions, and therefore an organism’s growth environment has a great influence on reproduction. Thus, gene expression profiling, should be applied in fisheries studies. Here, we identified the expression patterns of 76 reproduction-related genes in P. vannamei via the analysis of pooled transcriptomes from a time-series experiment encompassing a full circadian cycle. The expression patterns of genes associated both directly (Vtg, ODP, and ProR) and indirectly (FAMet, CruA1, and CruC1) with reproduction were evaluated, as these genes could be used as molecular markers of previtellogenic and vitellogenic maturation stages. The evaluated genes were prominently upregulated during vitellogenic stages, with specific expression patterns depending on the organism’s environment, diet, and season. Vtg, ProR, ODP, and FaMet could serve as molecular markers for both wild and cultured organisms.
Montes-Dominguez et al. (2021) Comparison between cultured and wild Pacific white shrimp (Penaeus vannamei) vitellogenesis: next-generation sequencing and relative expression of genes directly and indirectly related to reproduction. PeerJ 9:e10694 https://doi.org/10.7717/peerj.10694
Fat mass prediction equations and reference ranges for Saudi Arabian Children aged 8–12 years using machine technique method
Background The number of children with obesity has increased in Saudi Arabia, which is a significant public health concern. Early diagnosis of childhood obesity and screening of the prevalence is needed using a simple in situ method. This study aims to generate statistical equations to predict body fat percentage (BF%) for Saudi children by employing machine learning technology and to establish gender and age-specific body fat reference range. Methods Data was combined from two cross-sectional studies conducted in Saudi Arabia for 1,292 boys and girls aged 8–12 years. Body fat was measured in both studies using bio-electrical impedance analysis devices. Height and weight were measured and body mass index was calculated and classified according to CDC 2,000 charts. A total of 603 girls and 374 boys were randomly selected for the learning phase, and 153 girls and 93 boys were employed in the validation set. Analyses of different machine learning methods showed that an accurate, sensitive model could be created. Two regression models were trained and fitted with the construction samples and validated. Gradient boosting algorithm was employed to achieve a better estimation and produce the equations, then the root means squared error (RMSE) equation was performed to decrease the error. Body fat reference ranges were derived for children aged 8–12 years. Results For the gradient boosting models, the predicted fat percentage values were more aligned with the true value than those in regression models. Gradient boosting achieved better performance than the regression equation as it combined multiple simple models into a single composite model to take advantage of that weak classifier. The developed predictive model archived RMSE of 3.12 for girls and 2.48 boys. BF% and Fat mass index charts were presented in which cut-offs for 5th, 75th and 95th centiles are used to define ‘under-fat’, ‘normal’, ‘overfat’ and ‘subject with obesity’. Conclusion Machine learning models could represent a significant advancement for investigators studying adiposity-related issues in children. These models and newly developed centile charts could be useful tools for the estimation and classification of BF%.
Alkutbe et al. (2021) Fat mass prediction equations and reference ranges for Saudi Arabian Children aged 8–12 years using machine technique method. PeerJ 9:e10734 https://doi.org/10.7717/peerj.10734
Contact toxicity of three insecticides for use in tier I pesticide risk assessments with Megachile rotundata (Hymenoptera: Megachilidae)
The current pesticide risk assessment paradigm may not adequately protect solitary bees as it focuses primarily on the honey bee (Apis mellifera). The alfalfa leafcutting bee (Megachile rotundata) is a potential surrogate species for use in pesticide risk assessment for solitary bees in North America. However, the toxicity of potential toxic reference standards to M. rotundata will need to be determined before pesticide risk assessment tests (tier I trials) can be implemented. Therefore, we assessed the acute topical toxicity and generated LD50 values for three insecticides: dimethoate (62.08 ng a.i./bee), permethrin (50.01 ng a.i./bee), and imidacloprid (12.82 ng a.i/bee). The variation in the mass of individual bees had a significant but small effect on these toxicity estimates. Overall, the toxicity of these insecticides to M. rotundata were within the 10-fold safety factor currently used with A. mellifera toxicity estimates from tier I trials to estimate risk to other bee species. Therefore, tier I pesticide risk assessments with solitary bees may not be necessary, and efforts could be directed to developing more realistic, higher-tier pesticide risk assessment trials for solitary bees.
Ansell et al. (2021) Contact toxicity of three insecticides for use in tier I pesticide risk assessments with Megachile rotundata (Hymenoptera: Megachilidae). PeerJ 9:e10744 https://doi.org/10.7717/peerj.10744
Psychometric properties of the Multi-group Ethnic Identity Measure (MEIM) in a sample of Iranian young adults
Background This study examines the factor structure, reliability and test-retest validity of the 12-item Iranian version of the Multigroup Ethnic Identity Measure (MEIM). Additionally, the MEIM’s concurrent validity was tested by investigating the association between ethnic identity and subjective well-being. Method The scale was translated into Persian language and was administered to 426 students (193 female) at a major public university in Tehran along with the Positive Affect Negative Affect Schedule, and the Satisfaction with Life Scale. Results The confirmatory factor analysis supported the two-factor first-order commitment, and exploration (consisting of 12 items), and the second-order unidimensional factor structure of general ethnic identity. Moreover, we found evidence for good internal consistency, test re-test reliability, and concurrent validity. Conclusion The MEIM Persian version was found to be a valid and reliable measure to examine ethnic identity in this Iranian student population, for both males and females. These results support the utility of the Persian version of the MEIM for its use in Middle-Eastern contexts.
Habibi et al. (2021) Psychometric properties of the Multi-group Ethnic Identity Measure (MEIM) in a sample of Iranian young adults. PeerJ 9:e10752 https://doi.org/10.7717/peerj.10752
Evaluation of key miRNAs during early pregnancy in Kazakh horse using RNA sequencing
Background miRNA has an important role in cell differentiation, biological development, and physiology. Milk production is an important quantitative trait in livestock and miRNA plays a role in the amount of milk produced. Methods The role of regulatory miRNAs involved in equine milk production is not fully understood. We constructed two miRNA libraries for Kazakh horse milk production from higher-producing (H group) and lower-producing (L group) individuals, and used RNA-Seq technology to identify the differentially expressed miRNAs between the two milk phenotypes of Kazakh horses. Results A total of 341 known and 333 novel miRNAs were detected from the H and L groups, respectively. Eighty-three differentially expressed miRNAs were identified between the H and L group s, of which 32 were known miRNAs (27 were up-regulated, five were down-regulated) and 51 were novel miRNAs (nine were up-regulated, 42 were down-regulated). A total of 2,415 genes were identified. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that these genes were annotated to mammary gland development, mammary gland morphogenesis, tissue development and PI3K-Akt signaling pathways, insulin signaling pathway and TGF-beta signaling pathway, among others. Five miRNAs (miR-199a-3p, miR143, miR145, miR221, miR486-5p) were identified as affecting horse milk production and these five miRNAs were validated using qRT-PCR. Conclusions We described a methodology for the transcriptome-wide profiling of miRNAs in milk, which may help the design of new intervention strategies to improve the milk yield of Kazakh horses.
Liu et al. (2021) Evaluation of key miRNAs during early pregnancy in Kazakh horse using RNA sequencing. PeerJ 9:e10796 https://doi.org/10.7717/peerj.10796
Behavioral dominance interactions between Nicrophorus orbicollis and N. tomentosus burying beetles (Coleoptera: Silphidae)
Asymmetric interference competition, where one species is behaviorally dominant over another, appears widespread in nature with the potential to structure ecological communities through trade-offs between competitive dominance and environmental tolerance. The details of how species interact and the factors that contribute to behavioral dominance, however, are poorly known for most species, yet such details are important for understanding when and why trade-offs occur. Here, we examine behavioral interactions between two species of burying beetles (Coleoptera: Silphidae) that compete for limited breeding resources (i.e., small vertebrate carcasses) in nature, to identify behaviors involved in interference competition and to test if large body size, species identity, or time of arrival best predict behavioral dominance among species. To test these ideas, we placed same-sex individuals of Nicrophorus orbicollis (early to mid-summer breeder) and N. tomentosus (late summer to fall breeder) into an enclosure together with a 25–30 g mouse carcass (Mus musculus). We then video-recorded all behaviors, including neutral and aggressive interactions, for 13 h per trial (N = 14 trials). For each interaction, we assigned a winner based on which beetle retained its position instead of fleeing or retained possession of the carcass; the overall behavioral dominant was determined as the individual that won the most interactions over the length of the trial. We found that large body size was the best predictor of behavioral dominance. In most interactions, N. orbicollis was larger and dominant over N. tomentosus; however, when N. tomentosus was larger they outcompeted smaller N. orbicollis, illustrating the importance of body size in aggressive contests. The order of arrival to the carcass (priority effects) did not predict behavioral dominance. The larger size and abundance of N. orbicollis in nature suggest a competitive asymmetry between the species, supporting the idea that N. orbicollis constrains the ability of N. tomentosus to breed earlier in the summer.
Schrempf et al. (2021) Behavioral dominance interactions between Nicrophorus orbicollis and N. tomentosus burying beetles (Coleoptera: Silphidae). PeerJ 9:e10797 https://doi.org/10.7717/peerj.10797
The long non-coding RNA MEG3 plays critical roles in the pathogenesis of cholesterol gallstone
Background Cholesterol gallstone (CG) is the most common gallstone disease, which is induced by biliary cholesterol supersaturation. The purpose of this study is to investigate the pathogenesis of CG. Methods Sixteen mice were equally and randomly divided into model group and normal control group. The model group was fed with lithogenic diets to induce CG, and then gallbladder bile lipid analysis was performed. After RNA-seq library was constructed, differentially expressed mRNAs (DE-mRNAs) and differentially expressed lncRNAs (DE-lncRNAs) between model group and normal control group were analyzed by DESeq2 package. Using the cluster Profiler package, enrichment analysis for the DE-mRNAs was carried out. Based on Cytoscape software, the protein-protein interaction (PPI) network and competing endogenous RNA (ceRNA) network were built. Using quantitative real-time reverse transcription-PCR (qRT-PCR) analysis, the key RNAs were validated. Results The mouse model of CG was suc cessfully established, and then 181 DE-mRNAs and 33 DE-lncRNAs between model and normal groups were obtained. Moreover, KDM4A was selected as a hub node in the PPI network, and lncRNA MEG3 was considered as a key lncRNA in the regulatory network. Additionally, the miR-107-5p/miR-149-3p/miR-346-3-MEG3 regulatory pairs and MEG3-PABPC4/CEP131/NUMB1 co-expression pairs existed in the regulatory network. The qRT-PCR analysis showed that KDM4A expression was increased, and the expressions of MEG3, PABPC4, CEP131, and NUMB1 were downregulated. Conclusion These RNAs might be related to the pathogenesis of CG.
Qian et al. (2021) The long non-coding RNA MEG3 plays critical roles in the pathogenesis of cholesterol gallstone. PeerJ 9:e10803 https://doi.org/10.7717/peerj.10803
Characterization of the GRAS gene family reveals their contribution to the high adaptability of wheat
GRAS transcription factors play important roles in many processes of plant development as well as abiotic and biotic stress responses. However, little is known about this gene family in bread wheat (Triticum aestivum), one of the most important crops worldwide. The completion of a quality draft genome allows genome-wide detection and evolutionary analysis of the GRAS gene family in wheat. In this study, 188 TaGRAS genes were detected and divided into 12 subfamilies based on phylogenetic analyses: DELLA, DLT, HAM, LISCL, SCL3, SCL4/7, SCR, SHR, PAT1, Os19, Os4 and LAS. Tandem and segmental duplications are the main contributors to the expansion of TaGRAS, which may contribute to the adaptation of wheat to various environmental conditions. A high rate of homoeolog retention during hexaploidization was detected, suggesting the nonredundancy and biological importance of TaGRAS homoeologs. Systematic analyses of TaGRAS indicated the conserved expression pattern and function of the same subfamily during evolution. In addition, we detected five genes belonging to the LISCL subfamily induced by both biotic and abiotic stresses and they may be potential targets for further research through gene editing. Using degradome and ChIP-seq data, we identified the targets of miR171 and histone modifications and further analyzed the contribution of epigenetic modification to the subfunctionalization of TaGRAS. This study laid a foundation for further functional elucidation of TaGRAS genes.
Liu et al. (2021) Characterization of the GRAS gene family reveals their contribution to the high adaptability of wheat. PeerJ 9:e10811 https://doi.org/10.7717/peerj.10811