title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=939 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Effect of extreme temperature changes on phenolic, flavonoid contents and antioxidant activity of tomato seedlings (Solanum lycopersicum L.) link: https://peerj.com/articles/11193 last-modified: 2021-05-12 description: BackgroundClimatic changes are the most important abiotic factor affecting plant growth, crop quality and nutritional value. Plants exposed to thermal stress respond by accumulation of secondary metabolites/molecules (SMs). Tomato (Solanum lycopersicum) is a cosmopolitan crop, eaten by most of the world’s people because it is highly nutritious plant. It is cultivated in more than 16 thousand hectares in Saudi Arabia and thus is influenced by extreme climatic changes.ObjectiveIn the current study, the phytochemical effect of thermal stress was investigated in seedlings of S. lycopersicum. Such information will be very helpful in developing more tolerant tomato cultivars in a climate change scenario.MethodsSeedlings of S. lycopersicum were subjected to heat shock; HS1 and HS2 (45 and 50 °C) and cold shock; CS (4 °C) in comparison to control; Con (25 °C). Phenolic compounds, flavonoids, total phenolic content (TPC), total flavonoid content (TFC) and antioxidant activity were estimated under the four temperature treatments.ResultsUsing 23 standards (17 phenolic and six flavonoids), HPLC resulted in the estimation of 16, 20, 15 and 18 compounds for Con, CS, HS1 and HS2, respectively. Differences in the amounts of total phenolics, and total flavonoids were strongly correlated to thermal stress. CS plants exhibited the highest number of signals and the highest absolute quantities of total phenolics, flavonoids and sum of both. The major peaks of phenolics were (Chlorogenic acid, Resvertol), (Vanillic acid, Benzoic acid, Quinol), (Vanillic acid, Benzoic acid) and (Vanillic acid, Benzoic acid) for Con, CS, HS1 and HS2, respectively. The major peaks of flavonoids were (Quercetin, Myricetin), (Quercetin, Rutin), (Quercetin, Rutin, Catechin) and (Quercetin) for Con, CS, HS1 and HS2, respectively. CS plants contain the highest amounts of Benzoic acid (8010.37 mg/kg FW) and Quercetin (2319.48 mg/kg FW). The highest TPC (131 mg GAE/100 g FW) and TFC (61 mg QE/100 g FW) were determined in the case of CS plants. In terms of IC50s, the CS plants showed the highest antioxidant activities (lowest values) in both of DPPH (467.73 µM TE/100 g FW) and ABTS (8.97 µM TE/100 g FW) assays.ConclusionsOur findings supported that the complexity and quantity of phenolics and flavonoids in tomato’s extract are strongly related to thermal stress. Additionally, the CS plants demonstrated more desirable phytochemical profile over the other treatments. CS plants exhibited higher number, absolute amounts of SMs, higher TPC and TFC than those of Con, HS1 and HS2 plants. Additionally, CS plants showed higher antioxidant activity than that of both HS1 and HS2 plants. Such results are very useful in justifying mechanism of tolerance in tomato plant to thermal stress in the context of climate change. Additional research has turned on to reveal molecular response of tomato to such thermal stress. creator: Haifa A.S. Alhaithloul creator: Fatma H. Galal creator: AlaaEddeen M. Seufi uri: https://doi.org/10.7717/peerj.11193 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Alhaithloul et al. title: Response of Escherichia coli minimal ter operon to UVC and auto-aggregation: pilot study link: https://peerj.com/articles/11197 last-modified: 2021-05-12 description: AimThe study of minimal ter operon as a determinant of tellurium resistance (TeR) is important for the purpose of confirming the relationship of these genes to the pathogenicity of microorganisms. The ter operon is widespread among bacterial species and pathogens, implicated also in phage inhibition, oxidative stress and colicin resistance. So far, there is no experimental evidence for the role of the Escherichia coli (E. coli) minimal ter operon in ultraviolet C (UVC) resistance, biofilm formation and auto-aggregation. To identify connection with UVC resistance of the minimal ter operon, matched pairs of Ter-positive and -negative E. coli cells were stressed and differences in survival and whole genome sequence analysis were performed. This study was aimed also to identify differences in phenotype of cells induced by environmental stress.MethodsIn the current study, a minimal ter operon(terBCDEΔF) originating from the uropathogenic strain E. coli KL53 was used. Clonogenic assay was the method of choice to determine cell reproductive death after treatment with UVC irradiation at certain time intervals. Bacterial suspensions were irradiated with 254 nm UVC-light (germicidal lamp in biological safety cabinet) in vitro. UVC irradiance output was 2.5 mW/cm2 (calculated at the UVC device aperture) and plate-lamp distance of 60 cm. DNA damage analysis was performed using shotgun sequencing on Illumina MiSeq platform. Biofilm formation was measured by a crystal violet retention assay. Auto-aggregation assay was performed according to the Ghane, Babaeekhou & Ketabi (2020).ResultsA large fraction of Ter-positive E. coli cells survived treatment with 120-s UVC light (300 mJ/cm2) compared to matched Ter-negative cells; ∼5-fold higher resistance of Ter-positive cells to UVC dose (p = 0.0007). Moreover, UVC surviving Ter-positive cells showed smaller mutation rate as Ter-negative cells. The study demonstrated that a 1200-s exposure to UVC (3,000 mJ/cm2) was sufficient for 100% inhibition of growth for all the Ter-positive and -negative E. coli cells. The Ter-positive strain exhibited of 26% higher auto-aggregation activities and was able to inhibit biofilm formation over than Ter- negative strain (**** P < 0.0001).ConclusionOur study shows that Ter-positive cells display lower sensitivity to UVC radiation, corresponding to a presence in minimal ter operon. In addition, our study suggests that also auto-aggregation ability is related to minimal ter operon. The role of the minimal ter operon (terBCDEΔF) in resistance behavior of E. coli under environmental stress is evident. creator: Lenka Jánošíková creator: Lenka Pálková creator: Dušan Šalát creator: Andrej Klepanec creator: Katarina Soltys uri: https://doi.org/10.7717/peerj.11197 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Jánošíková et al. title: Brain-derived neurotrophic factor increases cell number of neural progenitor cells derived from human induced pluripotent stem cells link: https://peerj.com/articles/11388 last-modified: 2021-05-12 description: BackgroundSeveral pieces of evidence from in vitro studies showed that brain-derived neurotrophic factor (BDNF) promotes proliferation and differentiation of neural stem/progenitor cells (NSCs) into neurons. Moreover, the JAK2 pathway was proposed to be associated with mouse NSC proliferation. BDNF could activate the STAT-3 pathway and induce proliferation in mouse NSCs. However, its effects on proliferation are not fully understood and JAK/STAT pathway was proposed to play a role in this activity.MethodsIn the present study, the effects of BDNF on cell proliferation and neurite outgrowth of Alzheimer’s disease (AD) induced pluripotent stem cells (iPSCs)-derived human neural progenitor cells (hNPCs) were examined. Moreover, a specific signal transduction pathway important in cell proliferation was investigated using a JAK2 inhibitor (AG490) to clarify the role of that pathway.ResultsThe proliferative effect of BDNF was remarkably observed as an increase in Ki-67 positive cells. The cell number of hNPCs was significantly increased after BDNF treatment represented by cellular metabolic activity of the cells measured by MTT assay. This noticeable effect was statistically shown at 20 ng/ml of BDNF treatment. BDNF, however, did not promote neurite outgrowth but increased neuronal cell number. It was found that AG490 suppressed hNPCs proliferation. However, this inhibitor partially decreased BDNF-induced hNPCs proliferation. These results demonstrated the potential role of BDNF for the amelioration of AD through the increase of AD-derived hNPCs number. creator: Panetha Pansri creator: Phetcharat Phanthong creator: Nopparat Suthprasertporn creator: Yindee Kitiyanant creator: Alisa Tubsuwan creator: Andras Dinnyes creator: Julianna Kobolak creator: Narisorn Kitiyanant uri: https://doi.org/10.7717/peerj.11388 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2021 Pansri et al. title: Genome-wide identification of the Tubby-Like Protein (TLPs) family in medicinal model plant Salvia miltiorrhiza link: https://peerj.com/articles/11403 last-modified: 2021-05-12 description: Tubby-Like Proteins (TLPs) are important transcription factors with many functions and are found in both animals and plants. In plants, TLPs are thought to be involved in the abiotic stress response. To reveal the potential function of TLPs in the medicinal model plant Salvia miltiorrhiza, we identified 12 S. miltiorrhiza TLPs (SmTLPs) and conducted a comprehensive analysis. We examined SmTLP gene structure, protein structure, phylogenetics, and expression analysis. Our results show that all SmTLPs, except SmTLP11, have a complete typical Tub domain. Promoter analysis revealed that most SmTLPs are involved in hormone and abiotic stress responses. Expression analysis revealed that the 12 SmTLPs could be divided into three categories: those specifically expressed in roots, those specifically expressed in stems, and those specifically expressed in leaves. Additional studies have shown that SmTLP10 may play an important role in the plant cold resistance, while SmTLP12 may be involved in the S. miltiorrhiza ABA metabolic pathway. Our study represents the first comprehensive investigation of TLPs in S. miltiorrhiza. These data may provide useful clues for future studies and may support the hypotheses regarding the role of TLPs in plant abiotic stress process. All in all, we may provide a reference for improving S. miltiorrhiza quality using genetic engineering technology. creator: Kai Wang creator: Yating Cheng creator: Li Yi creator: Hailang He creator: Shaofeng Zhan creator: Peng Yang uri: https://doi.org/10.7717/peerj.11403 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Comparative transcriptome profiling of a resistant vs susceptible bread wheat (Triticum aestivum L.) cultivar in response to water deficit and cold stress link: https://peerj.com/articles/11428 last-modified: 2021-05-12 description: Bread wheat (Triticum aestivum L.) is one of the most important agricultural plants wearing abiotic stresses, such as water deficit and cold, that cause its productivity reduction. Since resistance to abiotic factors is a multigenic trait, therefore modern genome-wide approaches can help to involve various genetic material in breeding. One technique is full transcriptome analysis that reveals groups of stress response genes serving marker-assisted selection markers. Comparing transcriptome profiles of the same genetic material under several stresses is essential and makes the whole picture. Here, we addressed this by studying the transcriptomic response to water deficit and cold stress for two evolutionarily distant bread wheat varieties: stress-resistant cv. Saratovskaya 29 (S29) and stress-sensitive cv. Yanetzkis Probat (YP). For the first time, transcriptomes for these cultivars grown under abiotic stress conditions were obtained using Illumina based MACE technology. We identified groups of genes involved in response to cold and water deficiency stresses, including responses to each stress factor and both factors simultaneously that may be candidates for resistance genes. We discovered a core group of genes that have a similar pattern of stress-induced expression changes. The particular expression pattern was revealed not only for the studied varieties but also for the published transcriptomic data on cv. Jing 411 and cv. Fielder. Comparative transcriptome profiling of cv. S29 and cv. YP in response to water deficit and cold stress confirmed the hypothesis that stress-induced expression change is unequal within a homeologous gene group. As a rule, at least one changed significantly while the others had a relatively lower expression. Also, we found several SNPs distributed throughout the genomes of cv. S29 and cv. YP and distinguished the studied varieties from each other and the reference cv. Chinese Spring. Our results provide new data for genomics-assisted breeding of stress-tolerant wheat cultivars. creator: Dmitrii K. Konstantinov creator: Ulyana S. Zubairova creator: Anton A. Ermakov creator: Alexey V. Doroshkov uri: https://doi.org/10.7717/peerj.11428 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Konstantinov et al. title: Psychometric properties of the Swedish version of the satisfaction with life scale in a sample of individuals with mental illness link: https://peerj.com/articles/11432 last-modified: 2021-05-12 description: BackgroundHealth assessment among individuals with mental health problems often involves measures of ill-being (e.g., anxiety, depression). Health is, however, defined as a state of physical, mental and social well-being and not merely the absence of disease (WHO, 1948, 2001). Hence, in order to address mental illness during the 21st century, we need to develop methods for the prevention, identification and treatment of mental illness; but also, for the promotion, identification, and maintenance of well-being. In this context, over three decades of subjective well-being research have resulted in the development of measures of positive aspects of human life, such as the Satisfaction with Life Scale (Diener et al., 1985). Our aim was to investigate the psychometric properties of the Satisfaction with Life Scale in a Swedish population of individuals with mental illness using both Classical Test Theory (CTT) and Item Response Theory (IRT).MethodA total of 264 participants (age mean = 43.46, SD = 13.31) diagnosed with different types of mental illness answered to the Swedish version of the Satisfaction with Life Scale (five items, 7-point scale: 1 = strongly disagree, 7 = strongly agree).ResultsWe found positive and significant relationships between the five items of the scale (r ranging from 0.37 to 0.75), good reliability (Cronbach’s alpha = 0.86), and that the one-factor solution had best goodness of fit (loadings between 0.52–0.88, p < 0.001). Additionally, there were no significant differences in comparative fit indexes regarding gender and occupation status. All items had high discrimination values (between 1.95–3.81), but item 5 (“If I could live my life over, I would change almost nothing”); which had a moderate discrimination value (1.17) and the highest estimated difficulty on response 7 (3.06). Moreover, item 2 (“The conditions of my life are excellent”) had less discrimination and redundant difficulty with both item 1 (“In most ways my life is close to my ideal”; 2.03) on response 7 and with item 3 (“I am satisfied with my life”; –1.21) on response 1. The five items together provided good information, with especial good reliability and small standard error within −1.00 up to about 2.00 and the highest amount of test information at 0.00 of the level of life satisfaction within this population.ConclusionsConsistent with previous research, the scale had good reliability and provided good information across most of the latent trait range. In addition, within this population, sociodemographic factors such as gender and occupation status do not influence how individuals respond to the items in the scale. However, the items couldn’t measure extreme levels of low/high life satisfaction. We suggest replication of these findings, the test of additional items, and the modification of items 2 and 5 in order to use the scale among individuals with mental illness. creator: Danilo Garcia creator: Ali Al Nima creator: Maryam Kazemitabar creator: Clara Amato creator: Franco Lucchese creator: Marko Mihailovic creator: Nobuhiko Kijima uri: https://doi.org/10.7717/peerj.11432 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Garcia et al. title: Analysis of multi-omics differences in left-side and right-side colon cancer link: https://peerj.com/articles/11433 last-modified: 2021-05-12 description: BackgroundColon cancer is one of the most common tumors in the digestive tract. Studies of left-side colon cancer (LCC) and right-side colon cancer (RCC) show that these two subtypes have different prognoses, outcomes, and clinical responses to chemotherapy. Therefore, a better understanding of the importance of the clinical classifications of the anatomic subtypes of colon cancer is needed.MethodsWe collected colon cancer patients’ transcriptome data, clinical information, and somatic mutation data from the Cancer Genome Atlas (TCGA) database portal. The transcriptome data were taken from 390 colon cancer patients (172 LCC samples and 218 RCC samples); the somatic mutation data included 142 LCC samples and 187 RCC samples. We compared the expression and prognostic differences of LCC and RCC by conducting a multi-omics analysis of each using the clinical characteristics, immune microenvironment, transcriptomic differences, and mutation differences. The prognostic signatures was validated using the internal testing set, complete set, and external testing set (GSE39582). We also verified the independent prognostic value of the signature.ResultsThe results of our clinical characteristic analysis showed that RCC had a significantly worse prognosis than LCC. The analysis of the immune microenvironment showed that immune infiltration was more common in RCC than LCC. The results of differential gene analysis showed that there were 360 differentially expressed genes, with 142 upregulated genes in LCC and 218 upregulated genes in RCC. The mutation frequency of RCC was generally higher than that of LCC. BRAF and KRAS gene mutations were the dominant genes mutations in RCC, and they had a strong mutual exclusion with APC, while APC gene mutation was the dominant gene mutation in LCC. This suggests that the molecular mechanisms of RCC and LCC differed. The 4-mRNA and 6-mRNA in the prognostic signatures of LCC and RCC, respectively, were highly predictive and may be used as independent prognostic factors.ConclusionThe clinical classification of the anatomic subtypes of colon cancer is of great significance for early diagnosis and prognostic risk assessment. Our study provides directions for individualized treatment of left and right colon cancer. creator: Yanyi Huang creator: Jinzhong Duanmu creator: Yushu Liu creator: Mengyun Yan creator: Taiyuan Li creator: Qunguang Jiang uri: https://doi.org/10.7717/peerj.11433 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Huang et al. title: O-GlcNAcylation is a key regulator of multiple cellular metabolic pathways link: https://peerj.com/articles/11443 last-modified: 2021-05-12 description: O-GlcNAcylation modifies proteins in serine or threonine residues in the nucleus, cytoplasm, and mitochondria. It regulates a variety of cellular biological processes and abnormal O-GlcNAcylation is associated with diabetes, cancer, cardiovascular disease, and neurodegenerative diseases. Recent evidence has suggested that O-GlcNAcylation acts as a nutrient sensor and signal integrator to regulate metabolic signaling, and that dysregulation of its metabolism may be an important indicator of pathogenesis in disease. Here, we review the literature focusing on O-GlcNAcylation regulation in major metabolic processes, such as glucose metabolism, mitochondrial oxidation, lipid metabolism, and amino acid metabolism. We discuss its role in physiological processes, such as cellular nutrient sensing and homeostasis maintenance. O-GlcNAcylation acts as a key regulator in multiple metabolic processes and pathways. Our review will provide a better understanding of how O-GlcNAcylation coordinates metabolism and integrates molecular networks. creator: Hongshuo Zhang creator: Zhen Li creator: Yufei Wang creator: Ying Kong uri: https://doi.org/10.7717/peerj.11443 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zhang et al. title: First days at sea: depicting migration patterns of juvenile seabirds in highly impacted seascapes link: https://peerj.com/articles/11054 last-modified: 2021-05-11 description: Increasing human activities have detrimental consequences on marine ecosystems and their impact can have cumulative effects. Within marine ecosystems, seabirds respond to ecosystem variability and face multiple human pressures, especially threatened species. In long-lived species, juveniles and immatures could represent up to 50% of the total population, but their migratory movements remain largely unknown. Here, we depict the migratory patterns of juvenile Balearic shearwaters Puffinus mauretanicus, the most threatened European seabird, using miniaturised satellite transmitters. At the end of the 2012 breeding season, five tagged juveniles left the breeding colonies of Eivissa Island (western Mediterranean) the first week of July. They moved westwards to reach the Atlantic Ocean between 3 and 13 days afterwards. Juveniles showed a two-phase migratory pattern: they first travelled slower close to the breeding colonies, and then moved towards their wintering areas in the Atlantic Ocean by rapid directional movements. Environmental cues (e.g.,marine productivity, water mass distribution, frontal systems) might have a prominent role in driving the migratory patterns of juvenile Balearic shearwaters, moving from warm and poor marine areas in the Mediterranean Sea to cooler and rich non-breeding grounds in the Atlantic Ocean. Based on observational findings, we observed certain spatial overlap of juvenile Balearic shearwaters with areas of high human impact, but the relationship between flying travel speed and both fishing effort and cumulative human impacts were not statistically significant. These results suggest that more research is needed to assess whether the movement patterns of migrating juveniles are affected by human activities. Therefore, understanding the at-sea spatial ecology of juveniles should be a priority for research and conservation due to the importance of this population component in long-lived species, as well as assessing their vulnerability to multiple anthropogenic pressures. creator: Maite Louzao creator: Karine Delord creator: David García creator: Isabel Afán creator: José Manuel Arcos creator: Henri Weimerskirch uri: https://doi.org/10.7717/peerj.11054 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Louzao et al. title: Variation in the sacroiliac joint in Felidae link: https://peerj.com/articles/11116 last-modified: 2021-05-11 description: Felidae species show a great diversity in their diet, foraging and hunting strategies, from small to large prey. Whether they belong to solitary or group hunters, the behavior of cats to subdue resisting small or large prey presents crucial differences. It is assumed that pack hunting reduces the per capita risk of each individual. We hypothesize that the sacroiliac articulation plays a key role in stabilizing the predator while subduing and killing prey. Using CT-scan from 59 felid coxal bones, we calculated the angle between both iliac articular surfaces. Correlation of this inter-iliac angle with body size was calculated and ecological stressors were evaluated on inter-iliac angle. Body size significantly influences inter-iliac angle with small cats having a wider angle than big cats. Arboreal species have a significantly larger angle compared to cursorial felids with the smallest value, and to scansorial and terrestrial species with intermediate angles. Felids hunting large prey have a smaller angle than felids hunting small and mixed prey. Within the Panthera lineage, pack hunters (lions) have a larger angle than all other species using solitary hunting strategy. According to the inter-iliac angle, two main groups of felids are determined: (i) predators with an angle of around 40° include small cats (i.e., Felis silvestris, Leopardus wiedii, Leptailurus serval, Lynx Canadensis, L. rufus; median = 43.45°), the only pack-hunting species (i.e., Panthera leo; median = 37.90°), and arboreal cats (i.e., L. wiedii, Neofelis nebulosa; median = 49.05°), (ii) predators with an angle of around 30° include solitary-hunting big cats (i.e., Acinonyx jubatus, P. onca, P. pardus, P. tigris, P. uncia; median = 31.80°). We suggest different pressures of selection to interpret these results. The tightening of the iliac wings around the sacrum probably enhances big cats’ ability for high speed and large prey control. In contrast, pack hunting in lions reduced the selective pressure for large prey. creator: Jean-Pierre Pallandre creator: Franck Lavenne creator: Eric Pellé creator: Grégory Breton creator: Mélina Ribaud creator: Vincent Bels uri: https://doi.org/10.7717/peerj.11116 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Pallandre et al.