How the fear of COVID-19 changed the way we look at human faces
Do we look at persons currently or previously affected by COVID-19 the same way as we do with healthy ones? In this eye-tracking study, we investigated how participants (N = 54) looked at faces of individuals presented as “COVID-19 Free”, “Sick with COVID-19”, or “Recovered from COVID-19”. Results showed that participants tend to look at the eyes of COVID-19-free faces longer than at those of both COVID-19-related faces. Crucially, we also found an increase of visual attention for the mouth of the COVID-19-related faces, possibly due to the threatening characterisation of such area as a transmission vehicle for SARS-CoV-2. Thus, by detailing how people dynamically changed the way of looking at faces as a function of the perceived risk of contagion, we provide the first evidence in the literature about the impact of the pandemic on the most basic level of social interaction.
Federico et al. (2021) How the fear of COVID-19 changed the way we look at human faces. PeerJ 9:e11380 https://doi.org/10.7717/peerj.11380
The role of orthographic neighbourhood effects in lateralized lexical decision: a replication study and meta-analysis
The effect of orthographic neighbourhood size (N) on lexical decision reaction time differs when words are presented in the left or right visual fields. Evidence suggests a facilitatory N effect (i.e., faster reaction times for words with larger neighbourhoods) in the left visual field. However, the N effect in the right visual field remains controversial: it may have a weaker facilitative role or it may even be inhibitory. In a pre-registered online experiment, we replicated the interaction between N and visual field and provided support for an inhibitory N effect in the right visual field. We subsequently conducted a pre-registered systematic review and meta-analysis to synthesise the available evidence and determine the direction of N effects across visual fields. Based on the evidence, it would seem the effect is inhibitory in the right visual field. Furthermore, the size of the N effect is considerably smaller in the right visual field. Both studies revealed considerable heterogeneity between participants and studies, and we consider the implications of this for future work.
Parker et al. (2021) The role of orthographic neighbourhood effects in lateralized lexical decision: a replication study and meta-analysis. PeerJ 9:e11266 https://doi.org/10.7717/peerj.11266
Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma
Background Hepatocellular carcinoma (HCC) is considered to be a malignant tumor with a high incidence and a high mortality. Accurate prognostic models are urgently needed. The present study was aimed at screening the critical genes for prognosis of HCC. Methods The GSE25097, GSE14520, GSE36376 and GSE76427 datasets were obtained from Gene Expression Omnibus (GEO). We used GEO2R to screen differentially expressed genes (DEGs). A protein-protein interaction network of the DEGs was constructed by Cytoscape in order to find hub genes by module analysis. The Metascape was performed to discover biological functions and pathway enrichment of DEGs. MCODE components were calculated to construct a module complex of DEGs. Then, gene set enrichment analysis (GSEA) was used for gene enrichment analysis. ONCOMINE was employed to assess the mRNA expression levels of key genes in HCC, and the survival analysis was conducted using the array from The Cancer Genome Atlas (TCGA) of HCC. Then, the LASSO Cox regression model was performed to establish and identify the prognostic gene signature. We validated the prognostic value of the gene signature in the TCGA cohort. Results We screened out 10 hub genes which were all up-regulated in HCC tissue. They mainly enrich in mitotic cell cycle process. The GSEA results showed that these data sets had good enrichment score and significance in the cell cycle pathway. Each candidate gene may be an indicator of prognostic factors in the development of HCC. However, hub genes expression was weekly associated with overall survival in HCC patients. LASSO Cox regression analysis validated a five-gene signature (including CDC20, CCNB2, NCAPG, ASPM and NUSAP1). These results suggest that five-gene signature model may provide clues for clinical prognostic biomarker of HCC.
Yang et al. (2021) Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma. PeerJ 9:e11273 https://doi.org/10.7717/peerj.11273
Stable isotope compositions of precipitation over Central Asia
Central Asia is one of the driest regions in the world with a unique water cycle and a complex moisture transport process. However, there is little information on the precipitation δ18O content in Central Asia. We compiled a precipitation δ18O database from 47 meteorological stations across Central Asia to reveal its spatial-temporal characteristics. We determined the relationship between precipitation δ18O and environmental variables and investigated the relationship between δ18O and large-scale atmospheric circulation. The Central Asia meteoric water line was established as δ2H = 7.30 δ18O + 3.12 (R2 = 0.95, n = 727, p < 0.01), and precipitation δ18O ranged from +2‰ to −25.4‰ with a mean of −8.7‰. The precipitation δ18O over Central Asia was related to environmental variables. The δ18O had a significant positive correlation with temperature, and the δ18O-temperature gradient ranged from 0.28‰/°C to 0.68‰/°C. However, the dependence of δ18O on precipitation was unclear; a significant precipitation effect was only observed at the Zhangye and Teheran stations, showing δ18O-precipitation gradients of 0.20‰/mm and −0.08‰/mm, respectively. Latitude and altitude were always significantly correlated with annual δ18O, when considering geographical controls on δ18O, with δ18O/LAT and δ18O/ALT gradients of −0.42‰/° and −0.001‰/m, respectively. But both latitude and longitude were significantly correlated with δ18O in winter. The relationship between δ18O and large-scale atmospheric circulation suggested that the moisture in Central Asia is mainly transported by westerly circulation and is indirectly affected by the Indian monsoon. Meanwhile, the East Asian monsoon may affect the precipitation δ18O content in westerly and monsoon transition regions. These results improve our understanding of the precipitation δ18O and moisture transport in Central Asia, as well as the paleoclimatology and hydrology processes in Central Asia.
Yao et al. (2021) Stable isotope compositions of precipitation over Central Asia. PeerJ 9:e11312 https://doi.org/10.7717/peerj.11312
Phenotypic, molecular and pathogenic characterization of Colletotrichum scovillei infecting Capsicum species in Rio de Janeiro, Brazil
Anthracnose is a disease caused by Colletotrichum spp., one of the world’s most damaging sweet and chili pepper pathogens, especially in tropical and subtropical regions. In the state of Rio de Janeiro, anthracnose is one of the main obstacles for pepper crops. However, to date no research has focused on the identification and characterization of the pathogen, which is fundamental to understand the scope of the disease in the state. Thus, the correct identification of the fungal species and pathogenicity studies can provide important support for disease management and control, apart from identifying possible resistance sources for exploitation in peppers breeding programs. In this study, 11 Colletotrichum isolates were collected from peppers with typical symptoms in the Rio de Janeiro state. These isolates were characterized based on morpho-cultural characteristics and sequencing data from five regions (ITS, ACT, CAL, β-TUB and GAPDH), and the genetic variability was estimated by AFLP markers. Simultaneously, microscopy images of the colonization by the fungal species on unripe Capsicum annuum fruits were taken. Pathogenicity was tested and resistance sources were sought by means of infection of ripe and unripe fruits of 50 Capsicum baccatum accessions. The resulting data showed that all isolates belong to Colletotrichum scovillei specie. About the pathogenicity of Capsicum baccatum, differentiated, stage-specific responses, with higher resistance of ripe fruits were recorded. In addition, four possible sources of Colletotrichum scovillei resistance were detected among the tested accessions. The combination of these data can contribute to future studies on the interaction of Colletotrichum scovillei-Capsicum spp., a research line that is still unexploited in the main areas of this anthracnose fungus.
Giacomin et al. (2021) Phenotypic, molecular and pathogenic characterization of Colletotrichum scovillei infecting Capsicum species in Rio de Janeiro, Brazil. PeerJ 9:e10782 https://doi.org/10.7717/peerj.10782
Mediterraneibacter catenae SW178 sp. nov., an intestinal bacterium of feral chicken
A Gram-positive, coccobacillus, white raised and circular with an entire edge colony, and obligately anaerobic bacterium, strain SW178 was isolated from the cecum content of feral chickens in Brookings, South Dakota, USA. The most closely related strain based on 16S rRNA gene sequence analysis of strain SW178 was Mediterraneibacter torques ATCC 27756T (Ruminococcus torques ATCC 27756T) with 96.94% similarity. The genome of strain SW178 is 3.18 Mbp with G+C content of 46.9 mol%. The optimal temperature and pH for growth in modified brain heart infusion (BHI-M) medium were 45 °C and pH 7.5, respectively. The sole carbon sources of the strain were dextrin, L-fucose, D-galacturonic, α-D-glucose, L-rhamnose and D-sorbitol. The primary cellular fatty acids were C14 : 0, C16 : 0 and C16 : 0 dimethyl acetal (DMA). Based on the genotypic and phenotypic comparison, we proposed that strain SW178 belong to the genus Mediterraneibacter in the family Lachnospiraceae as a novel species, in which the name Mediterraneibacter catenae is proposed. The type strain is SW178 (= DSM 109242T = CCOS 1886T).
Wongkuna et al. (2021) Mediterraneibacter catenae SW178 sp. nov., an intestinal bacterium of feral chicken. PeerJ 9:e11050 https://doi.org/10.7717/peerj.11050
Mitogenomics of five Olidiana leafhoppers (Hemiptera: Cicadellidae: Coelidiinae) and their phylogenetic implications
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.
Wang et al. (2021) Mitogenomics of five Olidiana leafhoppers (Hemiptera: Cicadellidae: Coelidiinae) and their phylogenetic implications. PeerJ 9:e11086 https://doi.org/10.7717/peerj.11086
Dysregulation of miR-381-3p and miR-23b-3p in skeletal muscle could be a possible estimator of early post-mortem interval in rats
Background The 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. Methods We 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. Results An 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. Discussion The 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.
Martínez-Rivera et al. (2021) Dysregulation of miR-381-3p and miR-23b-3p in skeletal muscle could be a possible estimator of early post-mortem interval in rats. PeerJ 9:e11102 https://doi.org/10.7717/peerj.11102
Comparative transcriptome and histological analyses provide insights into the skin pigmentation in Minxian black fur sheep (Ovis aries)
Background Minxian 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. Methods Skin 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. Results Small-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.
Shi et al. (2021) Comparative transcriptome and histological analyses provide insights into the skin pigmentation in Minxian black fur sheep (Ovis aries). PeerJ 9:e11122 https://doi.org/10.7717/peerj.11122
Methyl jasmonate enhances ursolic, oleanolic and rosmarinic acid production and sucrose induced biomass accumulation, in hairy roots of Lepechinia caulescens
Background Ursolic (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. Methods Leaves 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. Results High 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. Conclusion This 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.
Vergara-Martínez et al. (2021) Methyl jasmonate enhances ursolic, oleanolic and rosmarinic acid production and sucrose induced biomass accumulation, in hairy roots of Lepechinia caulescens. PeerJ 9:e11279 https://doi.org/10.7717/peerj.11279