Physical activity and socio-economic status of single and married urban adults: a cross-sectional study
Background Changing family models have resulted in a large increase in the number of single-person households. This phenomenon has certain implications for society and the economy as single people often exhibit different behaviours, including their engagement in health-related physical activity, than those who are married and living with partners. However, the results of studies on determinants of physical activity in people of different marital status have been inconclusive. The aim of this study was to identify associations between physical activity and socioeconomic status in single and married urban adults. Methods The study material consisted of 4,460 persons (1,828 single and 2,632 married and living with partners). A cross-sectional study was conducted in Wroclaw (Poland). A diagnostic survey-direct interview method was used. Two research tools were applied: the International Physical Activity Questionnaire Short Form (IPAQ-SF) and the Socioeconomic Status Questionnaire (S-ESQ). The level of respondents’ physical activity was assessed following WHO recommendations. The descriptive statistics included the number and frequency of categories of dependent and independent variables as well as measures of association between them, i.e., crude and adjusted odds ratios. Results The odds ratio of meeting the WHO physical activity recommendations was almost 70% higher in single than in married respondents (OR = 1.67; CI [1.46–2.19]), and slightly more than 40% higher after adjusting for sex, age and education (aOR = 1.42; CI [1.21–1.67]). In both groups socioeconomic the respondents’ status revealed a significant and slightly different association with their levels of physical activity. Occupational status and financial savings significantly affected the level of physical activity in single respondents, while net disposable income was a significant modifier of physical activity levels in respondents who were married or lived with their partners. Conclusions Assessment of the levels and determinants of physical activity among people of different marital status should be continued and extended to other subpopulations. This will allow effective preventive and therapeutic measures to be taken for groups most at risk of hypokinesia. Programs aimed at improving physical activity accounting for the socioeconomic status and marital status of their beneficiaries are particularly important.
Puciato et al. (2021) Physical activity and socio-economic status of single and married urban adults: a cross-sectional study. PeerJ 9:e12466 https://doi.org/10.7717/peerj.12466
Fine-scale plasticity in nest placement can compensate for poor quality junipers as nesting trees for gray vireos
Understanding the interactions between behavior and habitat characteristics can have important implications for species of conservation concern. Gray vireos (Vireo vicinior) are one example of a species of conservation concern that is understudied in terms of nest survival probabilities and the habitat characteristics that influence them. Our objective was to determine if habitat features such as juniper density, juniper foliage density, or tree height influence nest survival probabilities, and if gray vireo nest placement can mitigate habitat risks. Based on previous work, we expected daily nest survival probabilities to be associated with nest height and surrounding vegetation. We monitored 89 nests in central New Mexico from 2016–2018 to estimate daily nest survival probabilities. We compared variation in nest placement, nest tree characteristics, and surrounding vegetation between failed and successful nests using logistic exposure models and Akaike Information Criteria. Daily and cumulative nest survival probability were 0.983 (95% CI [0.973–0.989]) and 0.575 (95% CI [0.444–0.702]), respectively. Top models predicting nest survival included a negative interaction between nest-tree foliage density and the distance of the nest from the edge of the nesting tree. This suggests that gray vireos can mitigate risks associated with low nest concealment by nesting closer to the interior of the nesting tree.
Harris et al. (2021) Fine-scale plasticity in nest placement can compensate for poor quality junipers as nesting trees for gray vireos. PeerJ 9:e12477 https://doi.org/10.7717/peerj.12477
Enhanced soluble sugar content in tomato fruit using CRISPR/Cas9-mediated SlINVINH1 and SlVPE5 gene editing
Soluble sugar is known to improve the sweetness and increase tomato sauce yield. Studies have focused on improving the content of soluble sugar in tomato fruits, usually by promoting functional genes. We studied two genes (SlINVINH1 and SlVPE5) that inhibited the accumulation of soluble sugar in tomato fruits and obtained two genes’ knocked-out lines (CRISPR-invinh1 or CRISPR-vpe5) using CRISPR/Cas9. Aggregated lines with CRISPR-invinh1 and CRISPR-vpe5 were gained by hybridization and self-pollination. Compared to wild-type lines, the glucose, fructose, and total soluble solid (TSS) contents of CRISPR-invinh1 and CRISPR-vpe5 increased significantly. Glucose, fructose, and TSS levels further improved simultaneously with CRISPR-invinh1 and CRISPR-vpe5 than with single gene knock-out lines. This indicates that these genes have a synergistic effect and will increase the soluble sugar content. Thus, the knock-out SlINVINH1 and SlVPE5 may provide a practical basis for improving the sweetness of tomato fruits and their processing quality.
Wang et al. (2021) Enhanced soluble sugar content in tomato fruit using CRISPR/Cas9-mediated SlINVINH1 and SlVPE5 gene editing. PeerJ 9:e12478 https://doi.org/10.7717/peerj.12478
Identification of keygenes, miRNAs and miRNA-mRNA regulatory pathways for chemotherapy resistance in ovarian cancer
Background Chemotherapy resistance, especially platinum resistance, is the main cause of poor prognosis of ovarian cancer. It is of great urgency to find molecular markers and mechanism related to platinum resistance in ovarian cancer. Methods One mRNA dataset (GSE28739) and one miRNA dataset (GSE25202) were acquired from Gene Expression Omnibus (GEO) database. The GEO2R tool was used to screen out differentially expressed genes (DEGs) and differentially expressed miRNAs (DE-miRNAs) between platinum-resistant and platinum-sensitive ovarian cancer patients. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for DEGs were performed using the DAVID to present the most visibly enriched pathways. Protein–protein interaction (PPI) of these DEGs was constructed based on the information of the STRING database. Hub genes related to platinum resistance were visualized by Cytoscape software. Then, we chose seven interested hub genes to further validate using qRT-PCR in A2780 ovarian cancer cell lines. And, at last, the TF-miRNA-target genes regulatory network was predicted and constructed using miRNet software. Results A total of 63 upregulated DEGs, 124 downregulated DEGs, four upregulated miRNAs and six downregulated miRNAs were identified. From the PPI network, the top 10 hub genes were identified, which were associated with platinum resistance. Our further qRT-PCR showed that seven hub genes (BUB1, KIF2C, NUP43, NDC80, NUF2, CCNB2 and CENPN) were differentially expressed in platinum-resistant ovarian cancer cells. Furthermore, the upstream transcription factors (TF) for upregulated DE-miRNAs were SMAD4, NFKB1, SMAD3, TP53 and HNF4A. Three overlapping downstream target genes (KIF2C, STAT3 and BUB1) were identified by miRNet, which was regulated by hsa-miR-494. Conclusions The TF-miRNA–mRNA regulatory pairs, that is TF (SMAD4, NFKB1 and SMAD3)-miR-494-target genes (KIF2C, STAT3 and BUB1), were established. In conclusion, the present study is of great significance to find the key genes of platinum resistance in ovarian cancer. Further study is needed to identify the mechanism of these genes in ovarian cancer.
Wang et al. (2021) Identification of keygenes, miRNAs and miRNA-mRNA regulatory pathways for chemotherapy resistance in ovarian cancer. PeerJ 9:e12353 https://doi.org/10.7717/peerj.12353
Horsenettle (Solanum carolinense) fruit bacterial communities are not variable across fine spatial scales
Fruit house microbial communities that are unique from the rest of the plant. While symbiotic microbial communities complete important functions for their hosts, the fruit microbiome is often understudied compared to other plant organs. Fruits are reproductive tissues that house, protect, and facilitate the dispersal of seeds, and thus they are directly tied to plant fitness. Fruit microbial communities may, therefore, also impact plant fitness. In this study, we assessed how bacterial communities associated with fruit of Solanum carolinense, a native herbaceous perennial weed, vary at fine spatial scales (<0.5 km). A majority of the studies conducted on plant microbial communities have been done at large spatial scales and have observed microbial community variation across these large spatial scales. However, both the environment and pollinators play a role in shaping plant microbial communities and likely have impacts on the plant microbiome at fine scales. We collected fruit samples from eight sampling locations, ranging from 2 to 450 m apart, and assessed the fruit bacterial communities using 16S rRNA gene amplicon sequencing. Overall, we found no differences in observed richness or microbial community composition among sampling locations. Bacterial community structure of fruits collected near one another were not more different than those that were farther apart at the scales we examined. These fine spatial scales are important to obligate out-crossing plant species such as S. carolinense because they are ecologically relevant to pollinators. Thus, our results could imply that pollinators serve to homogenize fruit bacterial communities across these smaller scales.
Heminger et al. (2021) Horsenettle (Solanum carolinense) fruit bacterial communities are not variable across fine spatial scales. PeerJ 9:e12359 https://doi.org/10.7717/peerj.12359
Returning to the roots: resolution, reproducibility, and robusticity in the phylogenetic inference of Dissorophidae (Amphibia: Temnospondyli)
The phylogenetic relationships of most Paleozoic tetrapod clades remain poorly resolved, which is variably attributed to a lack of study, the limitations of inference from phenotypic data, and constant revision of best practices. While refinement of phylogenetic methods continues to be important, any phylogenetic analysis is inherently constrained by the underlying dataset that it analyzes. Therefore, it becomes equally important to assess the accuracy of these datasets, especially when a select few are repeatedly propagated. While repeat analyses of these datasets may appear to constitute a working consensus, they are not in fact independent, and it becomes especially important to evaluate the accuracy of these datasets in order to assess whether a seeming consensus is robust. Here I address the phylogeny of the Dissorophidae, a speciose clade of Paleozoic temnospondyls. This group is an ideal case study among temnospondyls for exploring phylogenetic methods and datasets because it has been extensively studied (eight phylogenetic studies to date) but with most (six studies) using a single matrix that has been propagated with very little modification. In spite of the conserved nature of the matrix, dissorophid studies have produced anything but a conserved topology. Therefore, I analyzed an independently designed matrix, which recovered less resolution and some disparate nodes compared to previous studies. In order to reconcile these differences, I carefully examined previous matrices and analyses. While some differences are a matter of personal preference (e.g., analytical software), others relate to discrepancies with respect to what are currently considered as best practices. The most concerning discovery was the identification of pervasive dubious scorings that extend back to the origins of the widely propagated matrix. These include scores for skeletal features that are entirely unknown in a given taxon (e.g., postcrania in Cacops woehri) and characters for which there appear to be unstated working assumptions to scoring that are incompatible with the character definitions (e.g., scoring of taxa with incomplete skulls for characters based on skull length). Correction of these scores and other pervasive errors recovered a distinctly less resolved topology than previous studies, more in agreement with my own matrix. This suggests that previous analyses may have been compromised, and that the only real consensus of dissorophid phylogeny is the lack of one.
Gee (2021) Returning to the roots: resolution, reproducibility, and robusticity in the phylogenetic inference of Dissorophidae (Amphibia: Temnospondyli). PeerJ 9:e12423 https://doi.org/10.7717/peerj.12423
Incidence and clinicopathological features of colorectal cancer among multi-ethnic patients in Kuala Lumpur, Malaysia: a hospital-based retrospective analysis over two decades
Background The incidence rate of colorectal cancer (CRC) in Asian countries is increasing. Furthermore, recent studies have shown a concerning rise in the incidence of CRC among younger patients aged less than 50 years. This study aimed to analyze the incidence trends and clinicopathological features in patients with early-onset CRC (EOCRC) and later-onset CRC (at age ≥ 50 years). Methods A retrospective analysis was performed on 946 patients with CRC diagnosed from 1997 to 2017 at Universiti Kebangsaan Malaysia Medical Centre. The time trend was assessed by dividing the two decades into four 5-year periods. The mean age-standardized and age-specific incidence rates were calculated by using the 5-year cumulative population of Kuala Lumpur and World Health Organization standard population. The mean incidence was expressed per 100,000 person-years. Results After a stable (all age groups) CRC incidence rate during the first decade (3.00 per 100,000 and 3.85 per 100,000), it sharply increased to 6.12 per 100,000 in the 2008–2012 period before decreasing to 4.54 per 100,000 in the 2013–2017 period. The CRC incidence trend in later-onset CRC showed a decrease in the 2013–2017 period. Contrariwise, for age groups of 40–44 and 45–49 years, the trends showed an increase in the latter 15 years of the study period (40–44 years: 1.44 to 1.92 to 2.3 per 100,000; 45–49 years: 2.87 to 2.94 to 4.01 per 100,000). Malays’ EOCRC incidence rate increased from 2008–2012 to 2013–2017 for both the age groups 40–44 years (1.46 to 2.89 per 100,000) and 45–49 years (2.73 to 6.51 per 100,000). Nearly one-fifth of EOCRC cases were diagnosed at an advanced stage (Dukes D: 19.9%), and the majority of them had rectal cancer (72.8%). Conclusion The incidence of EOCRC increased over the period 1997–2017; the patients were predominantly Malays, diagnosed at a later stage, and with cancer commonly localized in the rectal region. All the relevant stakeholders need to work on the management and prevention of CRC in Malaysia.
Muhammad Nawawi et al. (2021) Incidence and clinicopathological features of colorectal cancer among multi-ethnic patients in Kuala Lumpur, Malaysia: a hospital-based retrospective analysis over two decades. PeerJ 9:e12425 https://doi.org/10.7717/peerj.12425
Abundant CpG-sequences in human genomes inhibit KIR3DL2-expressing NK cells
Killer Immunoglobulin-like Receptors (KIR) comprise a diverse, highly polymorphic family of cell-surface glycoproteins that are principally expressed by Natural Killer (NK) cells. These innate immune lymphocytes fulfill vital functions in human reproduction and immune responses to viral infection. KIR3DL2 is an inhibitory NK cell receptor that recognizes a common epitope of the HLA-A3 and HLA-A11 class I glycoproteins of the major histocompatibility complex. KIR3DL2 also binds exogenous DNA containing the CpG motif. This interaction causes internalization of the KIR-DNA. Exogenous CpG-DNA typically activates NK cells, but the specificity of KIR3DL2-DNA binding and internalization is unclear. We hypothesized that KIR3DL2 binds exogenous DNA in a sequence-specific manner that differentiates pathogen DNA from self-DNA. In testing this hypothesis, we surveyed octameric CpG-DNA sequences in the human genome, and in reference genomes of all bacteria, fungi, viruses, and parasites, with focus on medically relevant species. Among all pathogens, the nucleotides flanking CpG motifs in the genomes of parasitic worms that infect humans are most divergent from those in the human genome. We cultured KIR3DL2+NKL cells with the commonest CpG-DNA sequences in either human or pathogen genomes. DNA uptake was negatively correlated with the most common CpG-DNA sequences in the human genome. These CpG-DNA sequences induced inhibitory signaling in KIR3DL2+NKL cells. In contrast, KIR3DL2+NKL cells lysed more malignant targets and produced more IFNγ after culture with CpG-DNA sequences prevalent in parasitic worms. By applying functional immunology to evolutionary genomics, we conclude that KIR3DL2 allows NK cells to differentiate self-DNA from pathogen DNA.
Pugh et al. (2021) Abundant CpG-sequences in human genomes inhibit KIR3DL2-expressing NK cells. PeerJ 9:e12258 https://doi.org/10.7717/peerj.12258
Dissection of full-length transcriptome and metabolome of Dichocarpum (Ranunculaceae): implications in evolution of specialized metabolism of Ranunculales medicinal plants
Several main families of Ranunculales are rich in alkaloids and other medicinal compounds; many species of these families are used in traditional and folk medicine. Dichocarpum is a representative medicinal genus of Ranunculaceae, but the genetic basis of its metabolic phenotype has not been investigated, which hinders its sustainable conservation and utilization. We use the third-generation high-throughput sequencing and metabolomic techniques to decipher the full-length transcriptomes and metabolomes of five Dichocarpum species endemic in China, and 71,598 non-redundant full-length transcripts were obtained, many of which are involved in defense, stress response and immunity, especially those participating in the biosynthesis of specialized metabolites such as benzylisoquinoline alkaloids (BIAs). Twenty-seven orthologs extracted from trancriptome datasets were concatenated to reconstruct the phylogenetic tree, which was verified by the clustering analysis based on the metabolomic profile and agreed with the Pearson correlation between gene expression patterns of Dichocarpum species. The phylogenomic analysis of phytometabolite biosynthesis genes, e.g., (S)-norcoclaurine synthase, methyltransferases, cytochrome p450 monooxygenases, berberine bridge enzyme and (S)-tetrahydroprotoberberine oxidase, revealed the evolutionary trajectories leading to the chemodiversity, especially that of protoberberine type, aporphine type and bis-BIA abundant in Dichocarpum and related genera. The biosynthesis pathways of these BIAs are proposed based on full-length transcriptomes and metabolomes of Dichocarpum. Within Ranunculales, the gene duplications are common, and a unique whole genome duplication is possible in Dichocarpum. The extensive correlations between metabolite content and gene expression support the co-evolution of various genes essential for the production of different specialized metabolites. Our study provides insights into the transcriptomic and metabolomic landscapes of Dichocarpum, which will assist further studies on genomics and application of Ranunculales plants.
Hao et al. (2021) Dissection of full-length transcriptome and metabolome of Dichocarpum (Ranunculaceae): implications in evolution of specialized metabolism of Ranunculales medicinal plants. PeerJ 9:e12428 https://doi.org/10.7717/peerj.12428
Evolutionary history of the vertebrate Piwi gene family
PIWIs are regulatory proteins that belong to the Argonaute family. Piwis are primarily expressed in gonads and protect the germline against the mobilization and propagation of transposable elements (TEs) through transcriptional gene silencing. Vertebrate genomes encode up to four Piwi genes: Piwil1, Piwil2, Piwil3 and Piwil4, but their duplication history is unresolved. We leveraged phylogenetics, synteny and expression analyses to address this void. Our phylogenetic analysis suggests Piwil1 and Piwil2 were retained in all vertebrate members. Piwil4 was the result of Piwil1 duplication in the ancestor of gnathostomes, but was independently lost in ray-finned fishes and birds. Further, Piwil3 was derived from a tandem Piwil1 duplication in the common ancestor of marsupial and placental mammals, but was secondarily lost in Atlantogenata (Xenarthra and Afrotheria) and some rodents. The evolutionary rate of Piwil3 is considerably faster than any Piwi among all lineages, but an explanation is lacking. Our expression analyses suggest Piwi expression has mostly been constrained to gonads throughout vertebrate evolution. Vertebrate evolution is marked by two early rounds of whole genome duplication and many multigene families are linked to these events. However, our analyses suggest Piwi expansion was independent of whole genome duplications.
Gutierrez et al. (2021) Evolutionary history of the vertebrate Piwi gene family. PeerJ 9:e12451 https://doi.org/10.7717/peerj.12451