Genome-wide identification and expression analysis of the Dof gene family under drought stress in tea (Camellia sinensis)
Background DNA-binding one zinc finger (Dof) proteins are plant-specific transcription factors important for seed development, hormone regulation, and defense against abiotic stress. Although drought stress is a key determinant of plant physiology and metabolic homeostasis, the role of Dof genes in different degrees of PEG6000-induced drought stress has received little attention. Methods Tea plants (Camellia sinensis) were exposed to mild, moderate and severe drought stress. The Tea Genome and Plant TFDB databases were used to identify Dof gene family members in the tea plant. Clustal W2.1, MEGA6.0, ScanProsite, SMART, ExPASy, GSDS, MEME and STRING were used to build a phylogenetic tree, predict the molecular masses and isoelectric points of the Dof proteins, and construct a predicted protein-protein interaction network between the CsDof TFs and proteins in the A. thaliana database. The expression patterns of Dof genes in different tissues were analyzed, and qRT-PCR was used to measure the expression of Dof genes under different degrees of drought stress in tea. Results We identified 16 Dof genes in tea (C. sinensis cv. Huangjinya) using whole-genome analysis. Through comparative analysis of tea and Arabidopsis thaliana, we divided the Dof genes into four families (A, B, C, and D). We identified 15 motifs in the amino acid sequences of the CsDof proteins. Gene sequences and motif structures were highly conserved among families, especially in the B1 and C2 subfamilies. The protein-protein interaction network indicated that multiple CsDof proteins may be involved in the response to drought stress. Real-time PCR was used to examine the tissue-specific expression patterns of the CsDof genes and to measure their responses to different levels of PEG6000-induced drought stress in mature leaves. Most CsDof genes responded to drought stress. These results provide information on the Dof gene family in tea, offer new insights into the function of CsDof genes in a perennial species, and lay the foundation for further analysis of their functions.
Yu et al. (2020) Genome-wide identification and expression analysis of the Dof gene family under drought stress in tea (Camellia sinensis). PeerJ 8:e9269 https://doi.org/10.7717/peerj.9269
DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics
Restriction site Associated DNA Sequencing (RAD-Seq) is a technique characterized by the sequencing of specific loci along the genome that is widely employed in the field of evolutionary biology since it allows to exploit variants (mainly Single Nucleotide Polymorphism—SNPs) information from entire populations at a reduced cost. Common RAD dedicated tools, such as STACKS or IPyRAD, are based on all-vs-all read alignments, which require consequent time and computing resources. We present an original method, DiscoSnp-RAD, that avoids this pitfall since variants are detected by exploiting specific parts of the assembly graph built from the reads, hence preventing all-vs-all read alignments. We tested the implementation on simulated datasets of increasing size, up to 1,000 samples, and on real RAD-Seq data from 259 specimens of Chiastocheta flies, morphologically assigned to seven species. All individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within-species genetic structure linked to the geographic distribution. Furthermore, our results show that DiscoSnp-RAD is significantly faster than state-of-the-art tools. The overall results show that DiscoSnp-RAD is suitable to identify variants from RAD-Seq data, it does not require time-consuming parameterization steps and it stands out from other tools due to its completely different principle, making it substantially faster, in particular on large datasets.
Gauthier et al. (2020) DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics. PeerJ 8:e9291 https://doi.org/10.7717/peerj.9291
Succession of bacterial communities on carrion is independent of vertebrate scavengers
The decomposition of carrion is carried out by a suite of macro- and micro-organisms who interact with each other in a variety of ecological contexts. The ultimate result of carrion decomposition is the recycling of carbon and nutrients from the carrion back into the ecosystem. Exploring these ecological interactions among animals and microbes is a critical aspect of understanding the nutrient cycling of an ecosystem. Here we investigate the potential impacts that vertebrate scavenging may have on the microbial community of carrion. In this study, we placed seven juvenile domestic cow carcasses in the Grassy Mountain region of Utah, USA and collected tissue samples at periodic intervals. Using high-depth environmental sequencing of the 16S rRNA gene and camera trap data, we documented the microbial community shifts associated with decomposition and with vertebrate scavenger visitation. The remarkable scarcity of animals at our study site enabled us to examine natural carrion decomposition in the near absence of animal scavengers. Our results indicate that the microbial communities of carcasses that experienced large amounts of scavenging activity were not significantly different than those carcasses that observed very little scavenging activity. Rather, the microbial community shifts reflected changes in the stage of decomposition similar to other studies documenting the successional changes of carrion microbial communities. Our study suggests that microbial community succession on carrion follows consistent patterns that are largely unaffected by vertebrate scavenging.
Dangerfield et al. (2020) Succession of bacterial communities on carrion is independent of vertebrate scavengers. PeerJ 8:e9307 https://doi.org/10.7717/peerj.9307
Mining of candidate genes involved in the biosynthesis of dextrorotatory borneol in Cinnamomum burmannii by transcriptomic analysis on three chemotypes
Background Dextrorotatory borneol (D-borneol), a cyclic monoterpene, is widely used in traditional Chinese medicine as an efficient topical analgesic drug. Fresh leaves of Cinnamomum trees, e.g., C. burmannii and C. camphor, are the main sources from which D-borneol is extracted by steam distillation, yet with low yields. Insufficient supply of D-borneol has hampered its clinical use and production of patent remedies for a long time. Biological synthesis of D-borneol offers an additional approach; however, mechanisms of D-borneol biosynthesis remain mostly unresolved. Hence, it is important and necessary to elucidate the biosynthetic pathway of D-borneol. Results Comparative analysis on the gene expression patterns of different D-borneol production C. burmannii samples facilitates elucidation on the underlying biosynthetic pathway of D-borneol. Herein, we collected three different chemotypes of C. burmannii, which harbor different contents of D-borneol.A total of 100,218 unigenes with an N50 of 1,128 bp were assembled de novo using Trinity from a total of 21.21 Gb clean bases. We used BLASTx analysis against several public databases to annotate 45,485 unigenes (45.38%) to at least one database, among which 82 unigenes were assigned to terpenoid biosynthesis pathways by KEGG annotation. In addition, we defined 8,860 unigenes as differentially expressed genes (DEGs), among which 13 DEGs were associated with terpenoid biosynthesis pathways. One 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and two monoterpene synthase, designated as CbDXS9, CbTPS2 and CbTPS3, were up-regulated in the high-borneol group compared to the low-borneol and borneol-free groups, and might be vital to biosynthesis of D-borneol in C. burmannii. In addition, we identified one WRKY, two BHLH, one AP2/ERF and three MYB candidate genes, which exhibited the same expression patterns as CbTPS2 and CbTPS3, suggesting that these transcription factors might potentially regulate D-borneol biosynthesis. Finally, quantitative real-time PCR was conducted to detect the actual expression level of those candidate genes related to the D-borneol biosynthesis pathway, and the result showed that the expression patterns of the candidate genes related to D-borneol biosynthesis were basically consistent with those revealed by transcriptome analysis. Conclusions We used transcriptome sequencing to analyze three different chemotypes of C. burmannii, identifying three candidate structural genes (one DXS, two monoterpene synthases) and seven potential transcription factor candidates (one WRKY, two BHLH, one AP2/ERF and three MYB) involved in D-borneol biosynthesis. These results provide new insight into our understanding of the production and accumulation of D-borneol in C. burmannii.
Yang et al. (2020) Mining of candidate genes involved in the biosynthesis of dextrorotatory borneol in Cinnamomum burmannii by transcriptomic analysis on three chemotypes. PeerJ 8:e9311 https://doi.org/10.7717/peerj.9311
Plasma membrane proteomic analysis by TMT-PRM provides insight into mechanisms of aluminum resistance in tamba black soybean roots tips
Aluminum (Al) toxicity in acid soil is a worldwide agricultural problem that inhibits crop growth and productivity. However, the signal pathways associated with Al tolerance in plants remain largely unclear. In this study, tandem mass tag (TMT)-based quantitative proteomic methods were used to identify the differentially expressed plasma membrane (PM) proteins in Tamba black soybean (TBS) root tips under Al stress. Data are available via ProteomeXchange with identifier PXD017160. In addition, parallel reaction monitoring (PRM) was used to verify the protein quantitative data. The results showed that 907 PM proteins were identified in Al-treated plants. Among them, compared to untreated plants, 90 proteins were differentially expressed (DEPs) with 46 up-regulated and 44 down-regulated (fold change > 1.3 or < 0.77, p < 0.05). Functional enrichment based on GO, KEGG and protein domain revealed that the DEPs were associated with membrane trafficking and transporters, modifying cell wall composition, defense response and signal transduction. In conclusion, our results highlight the involvement of GmMATE13, GmMATE75, GmMATE87 and H+-ATPase in Al-induced citrate secretion in PM of TBS roots, and ABC transporters and Ca2+ have been implicated in internal detoxification and signaling of Al, respectively. Importantly, our data provides six receptor-like protein kinases (RLKs) as candidate proteins for further investigating Al signal transmembrane mechanisms.
Wei et al. (2020) Plasma membrane proteomic analysis by TMT-PRM provides insight into mechanisms of aluminum resistance in tamba black soybean roots tips. PeerJ 8:e9312 https://doi.org/10.7717/peerj.9312
Non-linear responses of net ecosystem productivity to gradient warming in a paddy field in Northeast China
Global warming has a known impact on ecosystems but there is a lack of understanding about its impact on ecosystem processes. Net ecosystem productivity (NEP) and its components play a key part in the global carbon cycle. Analysing the impact of global warming on NEP will improve our understanding of how warming affects ecosystems. In our study, conducted in 2018, five warming treatments were manipulated (0 W, 500 W, 1000 W, 1500 W, and 3000 W) using three repetitions of far infrared open warming over a paddy field in Northeast China. NEP and its two related components, gross primary productivity (GPP) and ecosystem respiration (ER), were measured using the static chamber-infrared gas analyser method to explore the effects of different warming magnitudes on NEP. Results showed that measurement dates, warming treatments, and their interactions significantly affected NEP, ER, and GPP. Warming significantly increased NEP and its components but they showed a non-linear response to different warming magnitudes. The maximum increases in NEP and its components occurred at 1500 W warming. NEP is closely related to its components and the non-linear response of NEP may have primarily resulted from that of GPP. Gradient warming non-linearly increased GPP in the paddy field studied in Northeast China, resulting in the non-linear response of NEP. This study provides a basis for predicting the responses of carbon cycles in future climate events.
Sun et al. (2020) Non-linear responses of net ecosystem productivity to gradient warming in a paddy field in Northeast China. PeerJ 8:e9327 https://doi.org/10.7717/peerj.9327
Host transcriptome-guided drug repurposing for COVID-19 treatment: a meta-analysis based approach
Background Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been declared a pandemic by the World Health Organization, and the identification of effective therapeutic strategy is a need of the hour to combat SARS-CoV-2 infection. In this scenario, the drug repurposing approach is widely used for the rapid identification of potential drugs against SARS-CoV-2, considering viral and host factors. Methods We adopted a host transcriptome-based drug repurposing strategy utilizing the publicly available high throughput gene expression data on SARS-CoV-2 and other respiratory infection viruses. Based on the consistency in expression status of host factors in different cell types and previous evidence reported in the literature, pro-viral factors of SARS-CoV-2 identified and subject to drug repurposing analysis based on DrugBank and Connectivity Map (CMap) using the web tool, CLUE. Results The upregulated pro-viral factors such as TYMP, PTGS2, C1S, CFB, IFI44, XAF1, CXCL2, and CXCL3 were identified in early infection models of SARS-CoV-2. By further analysis of the drug-perturbed expression profiles in the connectivity map, 27 drugs that can reverse the expression of pro-viral factors were identified, and importantly, twelve of them reported to have anti-viral activity. The direct inhibition of the PTGS2 gene product can be considered as another therapeutic strategy for SARS-CoV-2 infection and could suggest six approved PTGS2 inhibitor drugs for the treatment of COVID-19. The computational study could propose candidate repurposable drugs against COVID-19, and further experimental studies are required for validation.
Loganathan et al. (2020) Host transcriptome-guided drug repurposing for COVID-19 treatment: a meta-analysis based approach. PeerJ 8:e9357 https://doi.org/10.7717/peerj.9357
Relationship between the average slope in the active commuting to and from school and fitness in adolescents: the mediator role of fatness
Active commuting to and from school (ACS) has been recognized as a potential tool to improve physical fitness. Thus, this study aims to test the relationships between the average slope in the ACS and physical fitness, as well as to verify the mediator role of fatness in the relationship between average slope and physical fitness. A total of 257 participants, 137 boys and 120 girls, from 22 schools belonged to first and second High School grades participated in this study. Based on self-reported measure and Google Earth, participants were grouped into the active commuter (number of trips was ≥5, and the time of the trip was ≥15 min), mixed commuter (number of weekly trips was <5, and the time spent on the trip was <15 min) and passive commuter groups (those who reported traveling regularly by car, motorcycle, or bus). Specifically, in the active commuter group, a positive association between the average slope in the ACS with fatness was found, which in turn was positively related to strength lower limbs and cardiorrespiratory fitness. The average slope was not significantly associated with physical fitness indicators. Furtheremore, fatness did not mediate the relathionship between average slope and physical fitness. This research concluded positive associations between average slope and the body fat in the ACS. The tendency of findings signal that the average slope should be taken into account along with the distance, time and frequency of the active commuting.
Sánchez Miguel et al. (2020) Relationship between the average slope in the active commuting to and from school and fitness in adolescents: the mediator role of fatness. PeerJ 8:e8824 https://doi.org/10.7717/peerj.8824
Plastome of the mycoheterotrophic eudicot Exacum paucisquama (Gentianaceae) exhibits extensive gene loss and a highly expanded inverted repeat region
Mycoheterotrophic plants are highly specialized species able to acquire organic carbon from symbiotic fungi, with relaxed dependence on photosynthesis for carbon fixation. The relaxation of the functional constraint of photosynthesis and thereby the relaxed selective pressure on functional photosynthetic genes usually lead to substantial gene loss and a highly degraded plastid genome in heterotrophs. In this study, we sequenced and analyzed the plastome of the eudicot Exacum paucisquama, providing the first plastid genome of a mycoheterotroph in the family Gentianaceae to date. The E. paucisquama plastome was 44,028 bp in length, which is much smaller than the plastomes of autotrophic eudicots. Although the E. paucisquama plastome had a quadripartite structure, a distinct boundary shift was observed in comparison with the plastomes of other eudicots. We detected extensive gene loss and only 21 putative functional genes (15 protein-coding genes, four rRNA genes and two tRNA genes). Our results provide valuable information for comparative evolutionary analyses of plastomes of heterotrophic species belonging to different phylogenetic groups.
Li et al. (2020) Plastome of the mycoheterotrophic eudicot Exacum paucisquama (Gentianaceae) exhibits extensive gene loss and a highly expanded inverted repeat region. PeerJ 8:e9157 https://doi.org/10.7717/peerj.9157
Validation of a general subjective well-being factor using Classical Test Theory
Background Subjective Well-Being (SWB) is usually conceptualized in terms of an affective (i.e., judgements of biological emotional reactions and experiences) and a cognitive component (i.e., judgements of life satisfaction in relation to a psychological self-imposed ideal). Recently, researchers have suggested that judgements of harmony in life can replace or at least complement the cognitive component of SWB. Here, however, we go beyond that suggestion and propose that harmony in life should be seen as SWB’s social component since it is the sense of balance between the individual and the world around her—a process that comprises acceptance, adaptation, and balance. By adding judgements of one’s social interactions (i.e., harmony in life) to judgments of one’s life satisfaction (psycho) and judgements of one’s emotional reactions (bio), we propose a tentatively biopsychosocial model of SWB. As a first step, we used different factorial models in order to determine if both a general factor and specific sub-factors contribute to the biopsychosocial model of SWB. Method A total of 527 participants responded to the Positive Affect Negative Affect Schedule (PANAS; 20 items), the Satisfaction with Life Scale (SWLS; five items), and the Harmony in life Scale (HILS; five items). We conducted exploratory and confirmatory factor analyses to validate the biopsychosocial model of subjective well-being and a general factor (SWBS). Results The 20 PANAS items reflected a mixture of general latent structure saturation and specific latent structure saturation, but contributed to their respective specific latent factor (PA: 48%; NA: 49%) more than to the general latent SWBS factor (positive affect: 25%; negative affect: 32%). The five SWLS items contributed to a larger degree to the general SWBS factor (72%) than to life satisfaction itself (22%), while the five HILS items contributed to even a larger degree to the general SWBS factor (98%) than to harmony in life (0%). The bifactor model was the best model compared with all other models we tested (χ2 = 1,660.78, df = 375, p < 0.001); Satorra Bentler χ2 = 1,265.80, df = 375, p < 0.001; CFI = 0.92; Tucker–Lewis Index = 0.91; RMSEA = 0.067. This model of a general SWBS factor explained about 64% of the total variance in the model, while specific SWBS components together explained 15% of the total variance. Conclusion Our study suggests SWB as a general factor in a multidimensional biopsychosocial model. Indeed, as much as 64% of the variance of SWB was explained by this general factor. The SWB components, however, contributed to a different degree to each corresponding factor in the model. For instance, while the affective and cognitive components seem to be their own constructs and also part of the general SWB factor, the social component tested here contributed 0% to its own variance but 98% to the general factor.
Nima et al. (2020) Validation of a general subjective well-being factor using Classical Test Theory. PeerJ 8:e9193 https://doi.org/10.7717/peerj.9193