Increased expression of RUNX1 in clear cell renal cell carcinoma predicts poor prognosis
Background Runt-related transcription factor 1 (RUNX1) was previously reported to play a dual role in promoting or suppressing tumorigenesis in various malignancies. A public dataset from The Cancer Genome Atlas (TCGA) was used to evaluate the role of RUNX1 in clear cell renal cell carcinoma (ccRCC). Methods The Wilcoxon signed-rank test was used to compare the expression of RUNX1 in ccRCC tissues and normal tissues. The Wilcoxon signed-rank test and logistic regression were utilized to investigate the relationship between clinicopathological factors and RUNX1 expression. Additionally, we analysed the differences in prognosis between patients with high and low expression of RUNX1 via the Kaplan–Meier method and Cox regression. Gene set enrichment analysis (GSEA) was performed to explore the mechanisms of RUNX1 in ccRCC. Results The expression of RUNX1 in ccRCC tissues was significantly higher than that in normal tissues. High expression of RUNX1 was significantly associated with gender (p = 0.003), clinical stage (p < 0.001), tissue infiltration (p < 0.001), lymph node metastasis (p = 0.037) and histological grade (p < 0.001). Logistic regression analysis showed that high RUNX1 expression was significantly correlated with gender (OR = 1.71 for male vs. female, p = 0.004), histological grade (OR = 11.61 for grade IV vs. I, p < 0.001), clinical stage (OR = 1.55 for stage III/IV vs. I/II, p = 0.014) and tissue infiltration (OR = 1.54 for positive vs. negative, p = 0.018). Kaplan–Meier survival curves revealed that the prognosis of patients with ccRCC with high RUNX1 expression was worse than that of patients with ccRCC with low RUNX1 expression (p < 0.001). Univariate Cox regression analysis showed that high RUNX1 expression was strongly correlated with poor prognosis (HR = 1.60, 95% CI [1.31–1.97], p < 0.001). In addition, high expression of RUNX1 was an independent prognostic factor for poor overall survival (OS), with an HR of 1.50 (95% CI [1.20–1.87], p < 0.001) in multivariate Cox analysis. GSEA showed that the apoptosis, B cell receptor signalling pathway, calcium signalling pathway, chemokine signalling pathway, JAK/STAT signalling pathway, MAPK signalling pathway, p53 signalling pathway, pathways in cancer, T cell receptor signalling pathway, Toll-like receptor signalling pathway, VEGF signalling pathway, and Wnt signalling pathway were significantly enriched in the RUNX1 high-expression phenotype. In conclusion, RUNX1 can be used as a novel prognostic factor and therapeutic target in ccRCC.
Fu et al. (2019) Increased expression of RUNX1 in clear cell renal cell carcinoma predicts poor prognosis. PeerJ 7:e7854 https://doi.org/10.7717/peerj.7854
Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR
Background In Citrus cultures, three species of Xanthomonas are known to cause distinct diseases. X. citri subsp. citri patothype A, X. fuscans subsp. aurantifolii pathotypes B and C, and X. alfalfae subsp. citrumelonis, are the causative agents of cancrosis A, B, C, and citrus bacterial spots, respectively. Although these species exhibit different levels of virulence and aggressiveness, only limited alternatives are currently available for proper and early detection of these diseases in the fields. The present study aimed to develop a new molecular diagnostic method based on genomic sequences derived from the four species of Xanthomonas. Results Using comparative genomics approaches, primers were synthesized for the identification of the four causative agents of citrus diseases. These primers were validated for their specificity to their target DNA by both conventional and multiplex PCR. Upon evaluation, their sensitivity was found to be 0.02 ng/µl in vitro and 1.5 × 104 CFU ml−1 in infected leaves. Additionally, none of the primers were able to generate amplicons in 19 other genomes of Xanthomonas not associated with Citrus and one species of Xylella, the causal agent of citrus variegated chlorosis (CVC). This denotes strong specificity of the primers for the different species of Xanthomonas investigated in this study. Conclusions We demonstrated that these markers can be used as potential candidates for performing in vivo molecular diagnosis exclusively for citrus-associated Xanthomonas. The bioinformatics pipeline developed in this study to design specific genomic regions is capable of generating specific primers. It is freely available and can be utilized for any other model organism.
Fonseca et al. (2019) Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR. PeerJ 7:e7676 https://doi.org/10.7717/peerj.7676
Suppression of Wolbachia-mediated male-killing in the butterfly Hypolimnas bolina involves a single genomic region
Background Sex ratio distorting agents (maternally inherited symbionts and meiotically-driving sex chromosomes) are common in insects. When these agents rise to high frequencies they create strong population sex ratio bias and selection then favours mutations that act to restore the rare sex. Despite this strong selection pressure, the evolution of mutations that suppress sex ratio distorting elements appears to be constrained in many cases, where sex-biased populations persist for many generations. This scenario has been observed in the butterfly Hypolimnas bolina, where Wolbachia-mediated male killing endured for 800–1,000 generations across multiple populations before the evolution of suppression. Here we test the hypothesis that this evolutionary lag is the result of suppression being a multilocus trait requiring multiple mutations. Methods We developed genetic markers, based on conservation of synteny, for each H. bolina chromosome and verified coverage using recombinational mapping. We then used a Wolbachia-infected mapping family to assess each chromosome for the presence of loci required for male survival, as determined by the presence of markers in all surviving sons. Results Informative markers were obtained for each of the 31 chromosomes in H. bolina. The only marker that cosegregated with suppression was located on chromosome 25. A genomic region necessary for suppression has previously been located on this chromosome. We therefore conclude that a single genomic region of the H. bolina genome is necessary for male-killing suppression. Discussion The evolutionary lag observed in our system is not caused by a need for changes at multiple genomic locations. The findings favour hypotheses in which either multiple mutations are required within a single genomic region, or the suppressor mutation is a singularly rare event.
Reynolds et al. (2019) Suppression of Wolbachia-mediated male-killing in the butterfly Hypolimnas bolina involves a single genomic region. PeerJ 7:e7677 https://doi.org/10.7717/peerj.7677
CD36 identified by weighted gene co-expression network analysis as a hub candidate gene in lupus nephritis
Lupus nephritis (LN) is a severe manifestation of systemic lupus erythematosus (SLE), which often progresses to end-stage renal disease (ESRD) and ultimately leads to death. At present, there are no definitive therapies towards LN, so that illuminating the molecular mechanism behind the disease has become an urgent task for researchers. Bioinformatics has become a widely utilized method for exploring genes related to disease. This study set out to conduct weighted gene co-expression network analysis (WGCNA) and screen the hub gene of LN. We performed WGCNA on the microarray expression profile dataset of GSE104948 from the Gene Expression Omnibus (GEO) database with 18 normal and 21 LN samples of glomerulus. A total of 5,942 genes were divided into 5 co-expression modules, one of which was significantly correlated to LN. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted on the LN-related module, and the module was proved to be associated mainly with the activation of inflammation, immune response, cytokines, and immune cells. Genes in the most significant GO terms were extracted for sub-networks of WGNCA. We evaluated the centrality of genes in the sub-networks by Maximal Clique Centrality (MCC) method and CD36 was ultimately screened out as a hub candidate gene of the pathogenesis of LN. The result was verified by its differentially expressed level between normal and LN in GSE104948 and the other three multi-microarray datasets of GEO. Moreover, we further demonstrated that the expression level of CD36 is related to the WHO Lupus Nephritis Class of LN patients with the help of Nephroseq database. The current study proposed CD36 as a vital candidate gene in LN for the first time and CD36 may perform as a brand-new biomarker or therapeutic target of LN in the future.
Yang et al. (2019) CD36 identified by weighted gene co-expression network analysis as a hub candidate gene in lupus nephritis. PeerJ 7:e7722 https://doi.org/10.7717/peerj.7722
Bioprospection of biocompounds and dietary supplements of microalgae with immunostimulating activity: a comprehensive review
The objective of this review is to analyze the role of microalgal bioprospecting and the application of microalgae as food supplements and immunostimulants in global and regional aquaculture, highlighting the Brazilian Amazon. This study evaluates the primary advantages of the application of the bioactive compounds of these microorganisms, simultaneously identifying the knowledge gaps that hinder their biotechnological and economic exploitation. The methodology used is comparative and descriptive-analytical, considering the hypothesis of the importance of bioprospecting microalgae, the mechanisms of crop development and its biotechnological and sustainable application. In this context, this review describes the primary applications of microalgae in aquaculture during the last decade (2005–2017). The positive effects of food replacement and/or complementation of microalgae on the diets of organisms, such as their influence on the reproduction rates, growth, and development of fish, mollusks and crustaceans are described and analyzed. In addition, the importance of physiological parameters and their association with the associated gene expression of immune responses in organisms supplemented with microalgae was demonstrated. Complementarily, the existence of technical-scientific gaps in a regional panorama was identified, despite the potential of microalgal cultivation in the Brazilian Amazon. In general, factors preventing the most immediate biotechnological applications in the use of microalgae in the region include the absence of applied research in the area. We conclude that the potential of these microorganisms has been relatively well exploited at the international level but not at the Amazon level. In the latter case, the biotechnological potential still depends on a series of crucial steps that involve the identification of species, the understanding of their functional characteristics and their applicability in the biotechnological area, especially in aquaculture.
Silveira Júnior et al. (2019) Bioprospection of biocompounds and dietary supplements of microalgae with immunostimulating activity: a comprehensive review. PeerJ 7:e7685 https://doi.org/10.7717/peerj.7685
Effect of birdsongs and traffic noise on pedestrian walking speed during different seasons
Many studies have explored the effects of auditory and visual stimuli on the perception of an environment. However, there is a lack of investigations examining direct behavioral responses to noise in specific environments. In this study, a behavioral variable, walking speed, was analyzed, as a response to the sounds and visual features of a specific environment. The study examined the effects of birdsongs compared to traffic noise on walking speed in a real outdoor urban environment. It was supposed that the interaction of audition and vision in the perception of an environment may also be shaped by the perceived congruence of the visual and auditory features of the environment. The participants (N = 87 and N = 65), young university students, walked along a 1.8-km urban route. They listened to a soundtrack of crowded city noise or birdsongs, or they walked in the real outdoor environment without listening to any acoustic stimuli. To investigate the effect of the congruence between acoustic and visual stimuli, the experiment was conducted in two different seasons (fall and spring). The results did not show significant differences between the crowded city noise condition and the real outdoor condition. Listening to the soundtrack with birdsongs decreased walking speed, but this effect was significant only in the experiment conducted in spring. These findings can be explained in terms of the congruence between the sounds and the visual environment. The findings raise questions regarding the restorative function of urban greenery during different seasons.
Franěk et al. (2019) Effect of birdsongs and traffic noise on pedestrian walking speed during different seasons. PeerJ 7:e7711 https://doi.org/10.7717/peerj.7711
Bark tissue transcriptome analyses of inverted Populus yunnanensis cuttings reveal the crucial role of plant hormones in response to inversion
Inverted cuttings of Populus yunnanensis exhibit an interesting growth response to inversion. This response is characterized by enlargement of the stem above the shoot site, while the upright stem shows obvious outward growth below the shoot site. In this study, we examined transcriptome changes in bark tissue at four positions on upright and inverted cuttings of P. yunnanensis: position B, the upper portion of the stem; position C, the lower portion of the stem; position D, the bottom of new growth; and position E, the top of new growth. The results revealed major transcriptomic changes in the stem, especially at position B, but little alteration was observed in the bark tissue of the new shoot. The differentially expressed genes (DEGs) were mainly assigned to four pathways: plant hormone signal transduction, plant-pathogen interaction, mitogen-activated protein kinase (MAPK) signaling pathway-plant, and adenosine triphosphate-binding cassette (ABC) transporters. Most of these DEGs were involved in at least two pathways. The levels of many hormones, such as auxin (IAA), cytokinin (CTK), gibberellins (GAs), ethylene (ET), and brassinosteroids (BRs), underwent large changes in the inverted cuttings. A coexpression network showed that the top 20 hub unigenes at position B in the upright and inverted cutting groups were associated mainly with the BR and ET signaling pathways, respectively. Furthermore, brassinosteroid insensitive 1-associated receptor kinase 1 (BAK1) in the BR pathway and both ethylene response (ETR) and constitutive triple response 1 (CTR1) in the ET pathway were important hubs that interfaced with multiple pathways.
Zhou et al. (2019) Bark tissue transcriptome analyses of inverted Populus yunnanensis cuttings reveal the crucial role of plant hormones in response to inversion. PeerJ 7:e7740 https://doi.org/10.7717/peerj.7740
Population genetic structure of Texas horned lizards: implications for reintroduction and captive breeding
The Texas horned lizard (Phrynosoma cornutum) inhabits much of the southern Great Plains of North America. Since the 1950s, this species has been extirpated from much of its eastern range and has suffered declines and local extinctions elsewhere, primarily due to habitat loss. Plans are underway to use captive breeding to produce large numbers of Texas horned lizards for reintroduction into areas that were historically occupied by this species and that currently have suitable habitat. We used mitochondrial markers and nuclear microsatellite markers to determine levels of genetic diversity and population structure in 542 Texas horned lizards sampled from across Texas and some neighboring states to help inform these efforts. Texas horned lizards still retain high genetic diversity in many parts of their current range. We found two highly divergent mitochondrial clades (eastern and western) and three major genetic groupings at nuclear microsatellite loci: a west group corresponding to the western mitochondrial clade and north and south groups within the eastern mitochondrial clade. We also found some evidence for human-mediated movement between these genetic clusters that is probably related to the historical importance of this species in the pet trade and as an iconic symbol of the southwestern United States. We do not know, however, if there are fitness costs associated with admixture (especially for the western and eastern clades) or if there are fitness costs to moving these lizards into habitats that are distinctly different from their ancestral areas. If present, either one or both of these fitness costs would decrease the effectiveness of reintroduction efforts. We therefore recommend that reintroduction efforts should maintain current genetic structure by restricting breeding to be between individuals within their respective genetic clusters, and by reintroducing individuals only into those areas that encompass their respective genetic clusters. This cautionary approach is based on the strong divergence between genetic groupings and their correspondence to different ecoregions.
Williams et al. (2019) Population genetic structure of Texas horned lizards: implications for reintroduction and captive breeding. PeerJ 7:e7746 https://doi.org/10.7717/peerj.7746
Valence makes a stronger contribution than arousal to affective priming
Background Recent data suggest that both word valence and arousal modulate subsequent cognitive processing. However, whether valence or arousal makes a stronger contribution to cognitive processing is less understood. Methods The present study performed three experiments that varied the valence (positive or negative) and arousal (high or low) of prime-target word pairs in a lexical decision-priming task. Affective priming was derived from pure valence (Experiment 1), pure arousal (Experiment 2), or a combination of valence and arousal (Experiment 3). Results By comparing three types of priming effects, we found an effect of valence on affective priming was obvious regardless of whether the relationship of the prime-target varied with valence, arousal, or the combination of valence and arousal. In contrast, an effect of arousal on affective priming only appeared in the condition that based on the arousal relationship of the prime-target pair. Moreover, the valence-driven priming effect, arousal-driven priming effect, and emotional-driven priming effect were modulated by valence type but not by arousal level of word stimuli. Conclusion The present results revealed a pattern of valence and arousal in semantic networks, indicating that the valence information of emotional words tends to be more stable than arousal information within the semantic system, at least in the present lexical decision-priming task.
Yao et al. (2019) Valence makes a stronger contribution than arousal to affective priming. PeerJ 7:e7777 https://doi.org/10.7717/peerj.7777
Thermal biology and swimming performance of Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus)
Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) are two commercially important marine fishes impacted by both overfishing and climate change. Increasing ocean temperatures are affecting the physiology of these species and causing changes in distribution, growth, and maturity. While the physiology of cod has been well investigated, that of haddock has received very little attention. Here, we measured the metabolic response to increasing temperatures, as well as the critical thermal maximum (CTmax), of cod acclimated to 8 and 12 °C and haddock acclimated to 12 °C. We also compared the swimming performance (critical swimming speed, Ucrit) of cod and haddock at 12 °C, as well as the Ucrit of 12 °C-acclimated cod acutely exposed to a higher-than-optimal temperature (16 °C). The CTmax for cod was 21.4 and 23.0 °C for 8- and 12 °C-acclimated fish, respectively, whereas that for the 12 °C-acclimated haddock was 23.9 °C. These values were all significantly different and show that haddock are more tolerant of high temperatures. The aerobic maximum metabolic rate (MMR) of swimming cod remained high at 16 °C, suggesting that maximum oxygen transport capacity was not limited at a temperature above optimal in this species. However, signs of impaired swimming (struggling) were becoming evident at 16 °C. Haddock were found to reach a higher Ucrit than cod at 12 °C (3.02 vs. 2.62 body lengths s−1, respectively), and at a lower MMR. Taken together, these results suggest that haddock perform better than cod in warmer conditions, and that haddock are the superior swimmer amongst the two species.
Norin et al. (2019) Thermal biology and swimming performance of Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus). PeerJ 7:e7784 https://doi.org/10.7717/peerj.7784