PhyloPrimer: a taxon-specific oligonucleotide design platform
Many environmental and biomedical biomonitoring and detection studies aim to explore the presence of specific organisms or gene functionalities in microbiome samples. In such cases, when the study hypotheses can be answered with the exploration of a small number of genes, a targeted PCR-approach is appropriate. However, due to the complexity of environmental microbial communities, the design of specific primers is challenging and can lead to non-specific results. We designed PhyloPrimer, the first user-friendly platform to semi-automate the design of taxon-specific oligos (i.e., PCR primers) for a gene of interest. The main strength of PhyloPrimer is the ability to retrieve and align GenBank gene sequences matching the user’s input, and to explore their relationships through an online dynamic tree. PhyloPrimer then designs oligos specific to the gene sequences selected from the tree and uses the tree non-selected sequences to look for and maximize oligo differences between targeted and non-targeted sequences, therefore increasing oligo taxon-specificity (positive/negative consensus approach). Designed oligos are then checked for the presence of secondary structure with the nearest-neighbor (NN) calculation and the presence of off-target matches with in silico PCR tests, also processing oligos with degenerate bases. Whilst the main function of PhyloPrimer is the design of taxon-specific oligos (down to the species level), the software can also be used for designing oligos to target a gene without any taxonomic specificity, for designing oligos from preselected sequences and for checking predesigned oligos. We validated the pipeline on four commercially available microbial mock communities using PhyloPrimer to design genus- and species-specific primers for the detection of Streptococcus species in the mock communities. The software performed well on these mock microbial communities and can be found at https://www.cerealsdb.uk.net/cerealgenomics/phyloprimer.
Varliero et al. (2021) PhyloPrimer: a taxon-specific oligonucleotide design platform. PeerJ 9:e11120 https://doi.org/10.7717/peerj.11120
Evidence of integumentary scale diversity in the late Jurassic Sauropod Diplodocus sp. from the Mother’s Day Quarry, Montana
The life appearance of dinosaurs is a hotly debated topic in the world of paleontology, especially when it comes to dinosaur integument. In the case of sauropods, however, the topic is harder to properly discuss due to the limited amount of fossilized skin impressions that have been discovered. Thus far, the fossil record of sauropod integument fossils include titanosaur embryos from Patagonia, possible keratinous diplodocid dorsal spines, track ways with foot impressions, and other isolated skin impressions found in association with sauropod body fossils. Several prominent integument fossils have been found at the Mother’s Day Quarry, located in the Bighorn Basin, Montana. These discoveries may bring new important information about diplodocids, specifically Diplodocus sp. Here we describe newly uncovered fossilized skin that gives evidence of scale diversity in the genus Diplodocus. The scales themselves represent tubercles, and exhibit various shapes including rectangular, ovoid, polygonal, and globular scales. The tubercles are small in size, the biggest of which only reach about 10mm in length. Considering how diverse the scale shapes are in such a small area of skin, it is possible that these distinct scale shapes may represent a transition on the body from one region to another: perhaps from the abdomen to dorsal side, or abdomen to shoulder. Based on analysis of extant integument and scale orientation of crocodilians, it is possible to hypothesize on the location of the integument relative to the body as well as the size and relative maturational status of the individual.
Gallagher et al. (2021) Evidence of integumentary scale diversity in the late Jurassic Sauropod Diplodocus sp. from the Mother’s Day Quarry, Montana. PeerJ 9:e11202 https://doi.org/10.7717/peerj.11202
DNA-based diversity assessment reveals a new coral barnacle, Cantellius alveoporae sp. nov. (Balanomorpha: Pyrgomatidae) exclusively associated with the high latitude coral Alveopora japonica in the waters of southern Korea
In the present study, the Indo-Pacific coral associated barnacle Cantellius euspinulosum (Broch, 1931) was found to have cryptic species in Korea, Taiwan and other regions based on molecular studies. However, the original specimens of C. euspinulosum from Broch have not been previously described or illustrated, making it difficult to assign which cryptic species to the original C. euspinulosum. The original specimen of C. euspinulosum was examined and illustrated here, and the species identity of C. cf. euspinulosum collected from Jejudo Island in the present study and other cryptic species (based on literature illustrations) in the Indo-Pacific were evaluated.C. euspinulosum from Singapore, Java, Mergui Archipelago in Andaman Sea and Nha Trang represented the C. euspinulosum identified by Broch (1931). It is a generalist on Acropora, Favia, Favites, Leptoria, Montipora, Pachyseris and Pocillipora corals and distributed in the Indo-Pacific region. Morphological examination and DNA sequencing (COI, 12S DNA sequences) in the present study showed that C. cf. euspinulosum from Jejudo Island, Korea represents a distinct species, herein named C. alveoporae sp. nov. Cantellius alveroporae sp. nov. is a specialist species that only grows on Alveopora and also present in Palau, and Ogasawara Island in Japan. Cantellius cf. euspinuloum in Taiwan, the Moscos Island, and Australia belong to several other distinct species awaiting further morphological and molecular studies. At least five cryptic species of C. euspinulosum were identified in the present study, including both specialist and generalists.
Kim et al. (2021) DNA-based diversity assessment reveals a new coral barnacle, Cantellius alveoporae sp. nov. (Balanomorpha: Pyrgomatidae) exclusively associated with the high latitude coral Alveopora japonica in the waters of southern Korea. PeerJ 9:e11284 https://doi.org/10.7717/peerj.11284
Identification of QTL for barley grain size
Background Barley grain size is one of the key factors determining storage capacity during grain filling. Large, well-filled grains also have a high malt extract potential. Grain size is a complex quantitative trait and can be easily affected by environmental factors thus the identification of genes controlling the trait and the use of molecular markers linked to the genes in breeding program is the most effective way of improving grain size. Methods Grain sizes of 188 doubled-haploid (DH) lines derived from the cross of a Japanese malting barley variety (Naso Nijo) and a Chinese feed barley variety (TX9425) were obtained from three different sites in two consecutive years. The average data were used for identifying QTL for grain size. Results A total of four significant QTL were identified for grain length (GL) and three for grain width (GW). The two major GL QTL are located at similar positions to the QTL for malt extract on 2H and uzu gene on 3H, respectively. However, the GL QTL on 2H is more likely a different one from the malt extract QTL as most of the candidate genes are located outside the fine mapped QTL region for malt extract. The GL QTL on 3H is closely linked with uzu gene but not due to a pleiotropic effect of uzu. The three QTL for grain width on 1H, 2H and 5H, respectively, were located at same position to those for GL.
Wang et al. (2021) Identification of QTL for barley grain size. PeerJ 9:e11287 https://doi.org/10.7717/peerj.11287
Evaluation of circulating tumor cells as a prognostic biomarker for early recurrence in stage II–III breast cancer patients using CytoSorter® system: a retrospective study
Purpose Circulating tumor cells (CTCs) are known to be associated with late recurrence and poor prognosis in breast cancer (BC). Different CTC enrichment platforms have different CTC cut-off values for poor prognosis. This study aimed to evaluate whether preoperative CTCs could be a prognostic factor for early recurrence of disease in BC patients with resectable tumors, and to ascertain the CTC cut-off value for early recurrence with CytoSorter® CTC system. Methods Thirty-six stage II and III BC patients who had preoperative (pre-op) CTC detection and underwent a mastectomy or lumpectomy for curative intent between January and May 2018 were enrolled in this retrospective study. CTC detection was performed using CytoSorter® CTC system. Correlations of patients’ demographics, clinicopathological characteristics, adjuvant therapies and CTCs with relapse and survival were evaluated. Results CTCs were detected in 32 out of 36 patients before surgery. Nine patients developed relapses during follow-up, and seven of them were distant recurrence. Univariate analysis showed that CTCs were correlated with two-year recurrence free survival (RFS) and distant RFS (D-RFS) (P = 0.013 and 0.029, respectively). Two-year RFS and D-RFS were 85.2% and 88.9%, respectively, for patients with <4 CTCs, while 44.4% and 55.6%, respectively, for patients with ≧4 CTCs. In multivariate analysis, only CTC was shown to be correlated with two-year RFS (HR: 0.219, 95% CI: [0.058–0.82], P = 0.024) and D-RFS (HR: 0.218, 95% CI [0.048–0.977], P = 0.047). Conclusion BC patients with pre-op CTCs ≥4 per four mL of blood have significantly reduced two-year RFS and D-RFS. A pre-op CTC cut-off of four per four mL of blood was found for CytoSorter® to identify BC patients with a higher risk for early recurrence.
Jin et al. (2021) Evaluation of circulating tumor cells as a prognostic biomarker for early recurrence in stage II–III breast cancer patients using CytoSorter® system: a retrospective study. PeerJ 9:e11366 https://doi.org/10.7717/peerj.11366
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