title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=937 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Mitogenomics of five Olidiana leafhoppers (Hemiptera: Cicadellidae: Coelidiinae) and their phylogenetic implications link: https://peerj.com/articles/11086 last-modified: 2021-04-27 description: Similar morphological characteristics and limited molecular data of Olidiana resulted in their unknown phylogenetic statuses and equivocal relationships. To further understand the genus Olidiana, we sequenced and annotated five Olidiana complete mitochondrial genomes (mitogenomes). Our results show that Olidiana mitogenomes range from 15,205 bp to 15,993 bp in length and include 37 typical genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs) and a control region. Their nucleotide composition, codon usage, features of control region, and tRNA secondary structures are similar to other members of Cicadellidae. We constructed the phylogenetic tree of Cicadellidae using the maximum likelihood (ML) and Bayesian inference (BI) methods based on all valid mitogenome sequences. The most topological structure of the obtained phylogenetic tree is consistent. Our results support the monophyletic relationships among 10 subfamilies within Cicadellidae and confirm Iassinae and Coelidiinae to be sister groups with high approval ratings. Interestingly, Olidiana was inferred as a paraphyletic group with strong support via both ML and BI analyses. These complete mitogenomes of five Olidiana species could be useful in further studies for species diagnosis, evolution, and phylogeny research within Cicadellidae. creator: Xianyi Wang creator: Jiajia Wang creator: Ren-Huai Dai uri: https://doi.org/10.7717/peerj.11086 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Dysregulation of miR-381-3p and miR-23b-3p in skeletal muscle could be a possible estimator of early post-mortem interval in rats link: https://peerj.com/articles/11102 last-modified: 2021-04-27 description: BackgroundThe post-mortem interval (PMI) is the time elapsed since the dead of an individual until the body is found, which is relevant for forensic purposes. The miRNAs regulate the expression of some genes; and due to their small size, they can better support degradation, which makes them suitable for forensic analysis. In the present work, we evaluated the gene expression of miR-381-3p, miR-23b-3p, and miR-144-3p in skeletal muscle in a murine model at the early PMI.MethodsWe designed a rat model to evaluate the early PMI under controlled conditions. This model consisted in 25 rats divided into five groups of rats, that correspond to the 0, 3, 6, 12 and 24 hours of PMI. The 0 h-PMI was considered as the control group. Muscle samples were taken from each rat to analyze the expression of miR-381-3p, miR-23b-3p, and miR-144-3p by quantitative RT-PCR. The gene expression of each miRNA was expressed as Fold Change (FC) and compared among groups. To find the targets of these miRNAs and the pathways where they participate, we performed an in-silico analysis. From the gene targets of miR-381-3p identified in the silico analysis, the EPC1 gene was selected for gene expression analysis by quantitative RT-PCR in these samples. Also, to evaluate if miR-381-3p could predict the early PMI, a mixed effects model was calculated using its gene expression.ResultsAn upregulation of miR-381-3p was found at 24 h-PMI compared with the control group of 0 h-PMI and (FC = 1.02 vs. FC = 1.96; p = 0.0079). This was the opposite for miR-23b-3p, which had a down-regulation at 24 h-PMI compared to 0 h-PMI (FC = 1.22 vs. FC = 0.13; p = 0.0079). Moreover, the gene expression of miR-381-3p increased throughout the first 24 h of PMI, contrary to miR-23b-3p. The targets of these two miRNAs, participate in biological pathways related to hypoxia, apoptosis, and RNA metabolism. The gene expression of EPC1 was found downregulated at 3 and 12 h of PMI, whereas it remained unchanged at 6 h and 24 h of PMI. Using a multivariate analysis, it was possible to predict the FC of miR-381-3p of all but 6 h-PMI analyzed PMIs.DiscussionThe present results suggest that miR-23b-3p and miR-381-3p participate at the early PMI, probably regulating the expression of some genes related to the autolysis process as EPC1 gene. Although the miR-381-3p gene expression is a potential estimator of PMI, further studies will be required to obtain better estimates. creator: Vanessa Martínez-Rivera creator: Christian A. Cárdenas-Monroy creator: Oliver Millan-Catalan creator: Jessica González-Corona creator: N. Sofia Huerta-Pacheco creator: Antonio Martínez-Gutiérrez creator: Alexa Villavicencio-Queijeiro creator: Carlos Pedraza-Lara creator: Alfredo Hidalgo-Miranda creator: María Elena Bravo-Gómez creator: Carlos Pérez-Plasencia creator: Mariano Guardado-Estrada uri: https://doi.org/10.7717/peerj.11102 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Martínez-Rivera et al. title: Comparative transcriptome and histological analyses provide insights into the skin pigmentation in Minxian black fur sheep (Ovis aries) link: https://peerj.com/articles/11122 last-modified: 2021-04-27 description: BackgroundMinxian black fur (MBF) sheep are found in the northwestern parts of China. These sheep have developed several special traits. Skin color is a phenotype subject to strong natural selection and diverse skin colors are likely a consequence of differences in gene regulation.MethodsSkin structure, color differences, and gene expression (determined by RNA sequencing) were evaluated the Minxian black fur and Small-tail Han sheep (n = 3 each group), which are both native Chinese sheep breeds.ResultsSmall-tail Han sheep have a thicker skin and dermis than the Minxian black fur sheep (P < 0.01); however, the quantity of melanin granules is greater (P < 0.01) in Minxian black fur sheep with a more extensive distribution in skin tissue and hair follicles. One hundred thirty-three differentially expressed genes were significantly associated with 37 ontological terms and two critical KEGG pathways for pigmentation (“tyrosine metabolism” and “melanogenesis” pathways). Important genes from those pathways with known involvement in pigmentation included OCA2 melanosomal transmembrane protein (OCA2), dopachrome tautomerase (DCT), tyrosinase (TYR) and tyrosinase related protein (TYRP1), melanocortin 1 receptor (MC1R), and premelanosome protein (PMEL). The results from our histological and transcriptome analyses will form a foundation for additional investigation into the genetic basis and regulation of pigmentation in these sheep breeds. creator: Xiaolei Shi creator: Jianping Wu creator: Xia Lang creator: Cailian Wang creator: Yan Bai creator: David Greg Riley creator: Lishan Liu creator: Xiaoming Ma uri: https://doi.org/10.7717/peerj.11122 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Shi et al. title: Methyl jasmonate enhances ursolic, oleanolic and rosmarinic acid production and sucrose induced biomass accumulation, in hairy roots of Lepechinia caulescens link: https://peerj.com/articles/11279 last-modified: 2021-04-27 description: BackgroundUrsolic (UA), oleanolic (OA) and rosmarinic (RA) acids are bioactive metabolites found in Lepechinia caulescens that have generated interest for their health benefits, which include antimicrobial, antioxidant, antimutagenic, gastroprotective, antidiabetic, antihypertensive and anti-inflammatory properties, among others. To date, very few attempts have been made to evaluate the potential for simultaneous production of these bioactive compounds, using a biotechnological approach. Hairy root cultures offer a biotechnology approach that can be used to study the factors affecting the biosynthesis and the production of UA, OA and RA. In the current study, we established hairy root cultures of L. caulescens and evaluated the effect of sucrose on biomass accumulation, and the effect of different concentrations and times of exposure of methyl jasmonate (MeJA), on the accumulation of UA, OA and RA.MethodsLeaves from plants of L. caulescens were inoculated with Agrobacterium rhizogenes strain ATCC 15834. PCR of rolB gene confirmed the transgenic nature of hairy roots. Hairy roots were subcultured in semisolid MSB5 medium, supplemented with 15, 30, 45 or 60 g/L sucrose and after 4 weeks, dry weight was determined. The accumulation of UA, OA and RA of wild plants and hairy roots were determined by HPLC. Finally, the hairy roots were treated with 0, 100, 200 and 300 µM of MeJA and the content of bioactive compounds was analyzed, after 24, 48 and 72 h.ResultsHigh frequency transformation (75%) was achieved, using leaf explants from axenic seedlings, infected with A. rhizogenes. The hairy roots showed an enhanced linear biomass accumulation, in response to the increase in sucrose concentration. The hairy root cultures in MSB5 medium, supplemented with 45 g/L sucrose, were capable to synthesizing UA (0.29 ± 0.00 mg/g DW), OA (0.57 ± 0.00 mg/g DW) and RA (41.66 ± 0.31 mg/g DW), about two, seven and three times more, respectively, than in roots from wild plants. Elicitation time and concentration of MeJA resulted in significant enhancement in the production of UA, OA and RA, with treatments elicited for 24 h, with a concentration of 300 µM of MeJA, exhibiting greatest accumulation.ConclusionThis is the first report on development of hairy root cultures of L. caulescens. Future studies should aim towards further improving triterpenes and polyphenolic compound production in hairy roots of L. caulescens, for use in the pharmaceutical and biotechnological industry. creator: Victor M. Vergara-Martínez creator: Samuel E. Estrada-Soto creator: Susana Valencia-Díaz creator: Karlina Garcia-Sosa creator: Luis Manuel Peña-Rodríguez creator: José de Jesús Arellano-García creator: Irene Perea-Arango uri: https://doi.org/10.7717/peerj.11279 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Vergara-Martínez et al. title: Pre- and post-partum variation in wool cortisol and wool micron in Australian Merino ewe sheep (Ovis aries) link: https://peerj.com/articles/11288 last-modified: 2021-04-27 description: An individual merino sheep’s output of wool production is influenced by synergistic interactions of sheep genetics, climate, farm management, and nutrition available to the whole flock. The price paid to the producer for this wool commodity is determined via numerous tested parameters and /or subjective appraisal of the raw greasy wool. This research investigated the level of variation in wool cortisol (a physiological stress biomarker) and wool micron (MIC) in Merino ewes (Ovis aries), pre-partum and post-lambing (lactation/lambs at foot), using maiden ewe (n = 38) managed in an outdoor paddock in a commercial farm. The key findings of this study are; (1) wool quality indicators showed a significant variation between pre- and post- parturition including significant reduction in MIC and (2) there was a negative correlation between wool cortisol levels and wool micron pre-parturition (rs = − 0.179, p < 0.05). This relationship between wool cortisol and wool micron was positive (rs = + 0.29, p < 0.05) during post-parturition suggesting that ewes with lambs at foot ended up with finer wool (reduction in fibre diameter) but they also maintained high levels of wool cortisol. Furthermore, the comfort factor, curvature, standard deviation and spin fineness of the wool were also significantly reduced post-parturition. The results of this study show that metabolic resources partitioning in ewe associated with pregnancy and lambing can result in a reduction in wool quality indices. The activity of the HPA-axis is attenuated during late gestation and parturition as a maternal adaptation; however, the results of our study show that wool cortisol remained similar between pre- and post- lambing. This result indicates that environmental stressors that may have been operating on farm (e.g., cold winter period) could influence on maternal physiological stress response however the exact level of influence of environment conditions on ewe stress levels and productivity traits (e.g., lambing success and wool quality) warrants further investigation. In conclusion, the use of top-knot wool sampling in combination with wool cortisol analysis provides researchers with a convenient method to quantify wool quality and physiological stress simultaneously under commercial sheep production. creator: Gregory Sawyer creator: Dylan Russell Fox creator: Edward Narayan uri: https://doi.org/10.7717/peerj.11288 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sawyer et al. title: Beneficial effects of an intergenerational exercise intervention on health-related physical and psychosocial outcomes in Swiss preschool children and residential seniors: a clinical trial link: https://peerj.com/articles/11292 last-modified: 2021-04-27 description: BackgroundIntergenerational exercise possesses the potential to becoming an innovative strategy for promoting physical activity in seniors and children. Although this approach has gained attraction within the last decade, controlled trials on physical and psychosocial effects have not been performed yet.MethodsSixty-eight healthy preschool children (age: 4.9 y (SD 0.7)) and 47 residential seniors (age: 81.7 y (7.1)) participated in this five-armed intervention study. All participants were assigned to either an intergenerational (IG), peer (PG) or a control group (CON). Children were tested on gross motor skills (TGMD-2), jump performance and handgrip strength. Social-emotional skills questionnaires (KOMPIK) were assessed by kindergarten teachers. Seniors performed the Short Physical Performance Battery (SPPB), including gait speed. Arterial stiffness parameters were also examined. Questionnaires assessing psychosocial wellbeing were filled in with staff. IG and PG received one comparable exercise session a week lasting 45 minutes for 25-weeks. CON received no intervention. Measurements were performed before and after the intervention.ResultsIn children: IG improved all measured physical parameters. When adjusted for baseline values, large effects were observed in favor of IG compared to CON in TGMD-2 (Cohen’s d=0.78 [0.33;1.24]) and in handgrip strength (d = 1.07 [0.63;1.51]). No relevant differences were found in KOMPIK between groups (−0.38 25 °C, low relative humidity (RH < 60%), and low wind speed (WS < 3 m/s) were favorable for O3 formation and accumulation, and the O3 pollution days (MDA8 O3 > 160 µg/m3) were predominantly observed when the wind was traveling from the easterly and southerly. O3 concentration in urban area of Yulin was higher than that in background. The pollution air masses from Fenwei Plain increase the level and duration of O3 pollution. In order to clarify the formation mechanism and source of O3, online measurements of volatile organic compounds (VOCs) were conducted from 7 July to 10 August in 2019. The average of VOCs concentration was 26 ± 12 ppbv, and large amounts of alkenes followed by aromatics, characteristic pollutants of the coal chemical industry, were detected in the ambient air. To further measure the sensitivity, the observation-based model (OBM) simulation was conducted. Empirical Kinetic Modeling Approach (EKMA) plot and relative incremental reactivity (RIR) value indicated Yulin located on VOCs-limited regime. That implied a slight decrease of NOx may increase O3 concentration. When the emission reduction ratio of anthropogenic VOCs/NOx higher than 1:1, the O3 will decrease. O3 control strategies analysis shows that the O3 targets of 5% and 10% O3 concentration reductions are achievable through precursor control, but more effort is needed to reach the 30% and 40% reduction control targets. creator: Manfei Yin creator: Xin Zhang creator: Yunfeng Li creator: Kai Fan creator: Hong Li creator: Rui Gao creator: Jinjuan Li uri: https://doi.org/10.7717/peerj.11322 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yin et al. title: Comparative transcriptome analysis reveals key insights into male sterility in Salvia miltiorrhiza Bunge link: https://peerj.com/articles/11326 last-modified: 2021-04-27 description: BackgroundLarge-scale heterosis breeding depends upon stable, inherited male sterility lines. We accidentally discovered a male sterility line (SW-S) in the F1progeny of a Salvia miltiorrhiza Bunge from Shandong, China (purple flowers) crossed with a S. miltiorrhiza f. alba from Sichuan, China (white flowers). We sought to provide insights into the pollen development for male sterility in S. miltiorrhiza.MethodsThe phenotypic and cytological features of the SW-S and fertile control SW-F were observed using scanning electron microscopy and paraffin sections to identify the key stage of male sterility. Transcriptome profiles were recorded for anthers at the tetrad stage of SW-S and SW-F using Illumina RNA-Seq.ResultsThe paraffin sections showed that sterility mainly occurred at the tetrad stage of microspore development, during which the tapetum cells in the anther compartment completely fell off and gradually degraded in the sterile line. There was little-to-no callose deposited around the microspore cells. The tetrad microspore was shriveled and had abnormal morphology. Therefore, anthers at the tetrad stage of SW-S and fertile control SW-F were selected for comparative transcriptome analysis. In total, 266,722,270 clean reads were obtained from SW-S and SW-F, which contained 36,534 genes. There were 2,571 differentially expressed genes (DEGs) in SW-S and SW-F, of which 63.5% were downregulated. Gene Ontology (GO) enrichment analysis indicated that the differentially expressed genes were enriched in 56 functional groups (GO terms); of these, all DEGs involved in microgametogenesis and developmental maturation were downregulated in SW-S. These results were confirmed by quantitative RT-PCR. The two GO terms contained 18 DEGs, among which eight DEGs (namely: GPAT3, RHF1A, phosphatidylinositol, PFAS, MYB96, MYB78, Cals5, and LAT52) were related to gamete development. There were 10 DEGs related to development and maturation, among which three genes were directly related to pollen development (namely: ACT3, RPK2, and DRP1C). Therefore, we believe that these genes are directly or indirectly involved in the pollen abortion of SW-S. Our study provides insight into key genes related to sterility traits in S. miltiorrhiza, and the results can be further exploited in functional and mechanism studies. creator: Yan Yu creator: Yuanyuan Jiang creator: Long Wang creator: Yichao Wu creator: Jinqiu Liao creator: Mingzhi Zhong creator: Ruiwu Yang creator: Xingfu Chen creator: Qingmiao Li creator: Li Zhang uri: https://doi.org/10.7717/peerj.11326 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yu et al.