title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=804 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Enhanced soluble sugar content in tomato fruit using CRISPR/Cas9-mediated SlINVINH1 and SlVPE5 gene editing link: https://peerj.com/articles/12478 last-modified: 2021-11-09 description: 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. creator: Baike Wang creator: Ning Li creator: Shaoyong Huang creator: Jiahui Hu creator: Qiang Wang creator: Yaping Tang creator: Tao Yang creator: Patiguli Asmutola creator: Juan Wang creator: Qinghui Yu uri: https://doi.org/10.7717/peerj.12478 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wang et al. title: Identification of keygenes, miRNAs and miRNA-mRNA regulatory pathways for chemotherapy resistance in ovarian cancer link: https://peerj.com/articles/12353 last-modified: 2021-11-08 description: BackgroundChemotherapy 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.MethodsOne 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.ResultsA 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.ConclusionsThe 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. creator: Wenwen Wang creator: Wenwen Zhang creator: Yuanjing Hu uri: https://doi.org/10.7717/peerj.12353 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wang et al. title: Horsenettle (Solanum carolinense) fruit bacterial communities are not variable across fine spatial scales link: https://peerj.com/articles/12359 last-modified: 2021-11-08 description: 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. creator: Ariel R. Heminger creator: Lisa K. Belden creator: Jacob N. Barney creator: Brian D. Badgley creator: David C. Haak uri: https://doi.org/10.7717/peerj.12359 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Heminger et al. title: Returning to the roots: resolution, reproducibility, and robusticity in the phylogenetic inference of Dissorophidae (Amphibia: Temnospondyli) link: https://peerj.com/articles/12423 last-modified: 2021-11-08 description: 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. creator: Bryan M. Gee uri: https://doi.org/10.7717/peerj.12423 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Gee title: Incidence and clinicopathological features of colorectal cancer among multi-ethnic patients in Kuala Lumpur, Malaysia: a hospital-based retrospective analysis over two decades link: https://peerj.com/articles/12425 last-modified: 2021-11-08 description: BackgroundThe 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).MethodsA 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.ResultsAfter 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%).ConclusionThe 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. creator: Khairul Najmi Muhammad Nawawi creator: Norfilza M. Mokhtar creator: Zhiqin Wong creator: Zairul Azwan Mohd Azman creator: Deborah Chia Hsin Chew creator: Rasyidah Rehir creator: Jocelyn Leong creator: Fuad Ismail creator: Isa Mohamed Rose creator: Yazmin Yaacob creator: Hamzaini Abdul Hamid creator: Ismail Sagap creator: Raja Affendi Raja Ali uri: https://doi.org/10.7717/peerj.12425 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Muhammad Nawawi et al. title: Abundant CpG-sequences in human genomes inhibit KIR3DL2-expressing NK cells link: https://peerj.com/articles/12258 last-modified: 2021-11-05 description: 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. creator: Jason Pugh creator: Lisbeth Guethlein creator: Peter Parham uri: https://doi.org/10.7717/peerj.12258 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Pugh et al. title: Dissection of full-length transcriptome and metabolome of Dichocarpum (Ranunculaceae): implications in evolution of specialized metabolism of Ranunculales medicinal plants link: https://peerj.com/articles/12428 last-modified: 2021-11-05 description: 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. creator: Da-Cheng Hao creator: Pei Li creator: Pei-Gen Xiao creator: Chun-Nian He uri: https://doi.org/10.7717/peerj.12428 license: https://creativecommons.org/licenses/by-nc/4.0/ rights: ©2021 Hao et al. title: Evolutionary history of the vertebrate Piwi gene family link: https://peerj.com/articles/12451 last-modified: 2021-11-05 description: 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. creator: Javier Gutierrez creator: Roy Platt creator: Juan C. Opazo creator: David A. Ray creator: Federico Hoffmann creator: Michael Vandewege uri: https://doi.org/10.7717/peerj.12451 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Gutierrez et al. title: Phage strategies facilitate bacterial coexistence under environmental variability link: https://peerj.com/articles/12194 last-modified: 2021-11-04 description: Bacterial communities are often exposed to temporal variations in resource availability, which exceed bacterial generation times and thereby affect bacterial coexistence. Bacterial population dynamics are also shaped by bacteriophages, which are a main cause of bacterial mortality. Several strategies are proposed in the literature to describe infections by phages, such as “Killing the Winner”, “Piggyback the loser” (PtL) or “Piggyback the Winner” (PtW). The two temperate phage strategies PtL and PtW are defined by a change from lytic to lysogenic infection when the host density changes, from high to low or from low to high, respectively. To date, the occurrence of different phage strategies and their response to environmental variability is poorly understood. In our study, we developed a microbial trophic network model using ordinary differential equations (ODEs) and performed ‘in silico’ experiments. To model the switch from the lysogenic to the lytic cycle, we modified the lysis rate of infected bacteria and their growth was turned on or off using a density-dependent switching point. We addressed whether and how the different phage strategies facilitate bacteria coexistence competing for limiting resources. We also studied the impact of a fluctuating resource inflow to evaluate the response of the different phage strategies to environmental variability. Our results show that the viral shunt (i.e. nutrient release after bacterial lysis) leads to an enrichment of the system. This enrichment enables bacterial coexistence at lower resource concentrations. We were able to show that an established, purely lytic model leads to stable bacterial coexistence despite fluctuating resources. Both temperate phage models differ in their coexistence patterns. The model of PtW yields stable bacterial coexistence at a limited range of resource supply and is most sensitive to resource fluctuations. Interestingly, the purely lytic phage strategy and PtW both result in stable bacteria coexistence at oligotrophic conditions. The PtL model facilitates stable bacterial coexistence over a large range of stable and fluctuating resource inflow. An increase in bacterial growth rate results in a higher resilience to resource variability for the PtL and the lytic infection model. We propose that both temperate phage strategies represent different mechanisms of phages coping with environmental variability. Our study demonstrates how phage strategies can maintain bacterial coexistence in constant and fluctuating environments. creator: Esther Voigt creator: Björn C. Rall creator: Antonis Chatzinotas creator: Ulrich Brose creator: Benjamin Rosenbaum uri: https://doi.org/10.7717/peerj.12194 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Voigt et al. title: Courtship behavior and identification of a sex pheromone in Ibalia leucospoides (Hymenoptera: Ibaliidae), a larval parasitoid of Sirex noctilio (Hymenoptera: Siricidae) link: https://peerj.com/articles/12266 last-modified: 2021-11-04 description: BackgroundIbalia leucospoides (Hymenoptera: Ibaliidae) is a larval parasitoid that has been widely introduced as a biological control agent for the invasive woodwasp,Sirex noctilio (Hymenoptera: Siricidae) in the Southern Hemisphere. In this study, the courtship behavior and identificaion of sex pheromones are described for I. leucospoides under laboratory conditions.MethodsFor courtship behavior, both sexes were observed in a wire mesh observation cylinder (75 cm length ×10 cm diameter) for 15 minutes. The female body washes were analyzed using Gas Chromatography- Electroantennographic Detection (GC-EAD). Then the EAD-active compounds were tentatively identified using GC-Mass Spectrometry (GC-MS) and examined in olfactometer assays.ResultsThe courtship behavior included rhythmic lateral movements, mounting, head-nodding cycles in males, and wing-fanning in females. GC-EAD analysis of female body washes with male antennae revealed seven compounds which elicited antennal responses, four of which are straight-chain alkanes (C23, C25, C26, and C27). The identities of these alkanes were confirmed by matching the retention times, mass spectra, and male antennal activity to those of commercially obtained chemicals. In olfactometer assays, a blend of the four straight-chain alkanes was attractive to I. leucospoides males, and there was no response to blends that lacked any of these four compounds. Female body wash was no more attractive than the four-component blend. The ratios of EAD-active components differ between hydrocarbon profiles from males and females.ConclusionThis study is the first investigation of cuticular hydrocarbons in the family Ibaliidae. It provides evidence that the ubiquitous alkanes (C23, C25, C26, and C27) in sex-specific ratios attract I. leucospoides males. creator: Hajar Faal creator: Peter J. Silk creator: Peter D. Mayo creator: Stephen A. Teale uri: https://doi.org/10.7717/peerj.12266 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Faal et al.