Scientific Reports

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ISSN / EISSN : 20452322 / 20452322
Current Publisher: Springer Nature (10.1038)
Total articles ≅ 90,412
Google Scholar h5-index: 151
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A. Borrero-Palacios, A. Cebrián, M. T. Gómez Del Pulgar, R. García-Carbonero, P. Garcia-Alfonso, E. Aranda, E. Elez, R. López-López, A. Cervantes, M. Valladares, et al.
Published: 17 May 2019
Scientific Reports, Volume 9; doi:10.1038/s41598-019-43809-z

Wei Hu, Zhongxia Wang, Shan Zhang, Xian Lu, Junyi Wu, Kuanyong Yu, Anlai Ji, Wei Lu, Zhong Wang, Junhua Wu, et al.
Published: 17 May 2019
Scientific Reports, Volume 9; doi:10.1038/s41598-019-44048-y

Abstract:IQ motif-containing GTPase-activating protein 1 (IQGAP1) is a scaffold protein that participates in several cellular functions, including cytoskeletal regulation, cell adhesion, gene transcription and cell polarization. IQGAP1 has been implicated in the tumorigenesis and progression of several human cancers. However, the role of IQGAP1 in pancreatic ductal adenocarcinoma (PDAC) is still unknown. We found that IQGAP1 expression was an independent prognostic factor for PDAC. IQGAP1 upregulation significantly promoted cell proliferation, migration, invasion and epithelial-mesenchymal transition (EMT), whereas IQGAP1 downregulation impaired its oncogenic functions. Overexpression of IQGAP1 increased the protein level of Dishevelled2 (DVL2) and enhanced canonical Wnt signaling as evidenced by increased DVL2 level, β-catenin transcriptional activity, β-catenin nuclear translocation and expression of the direct target genes of β-catenin (cyclin D1 and c-myc). In contrast, knockdown of IQGAP1 decreased the level of DVL2 and attenuated Wnt/β-catenin signaling. In vivo results revealed that IQGAP1 promoted tumor growth and metastasis. Co-immunoprecipitation studies demonstrated that IQGAP1 interacted with both DVL2 and β-catenin. Moreover, knockdown of DVL2 reversed IQGAP1-induced EMT. Our findings thus confirmed that IQGAP1 could be used as a potential target for PDAC treatment.
Y. F. Shen, X. X. Dong, X. T. Song, N. Jia
Published: 17 May 2019
Scientific Reports, Volume 9; doi:10.1038/s41598-019-44105-6

Abstract:Ultrahigh strength and good ductility are obtained for two low-alloy transformation-induced-plasticity steels fabricated by the quenching and partitioning (Q&P) processing, respectively. Compared to 0.19 wt.% C steel in which γ → α′-martensite transformation is the dominant mechanism under deformation, the relatively high C content of austenite in 0.47 wt.% C steel is responsible for the transformation from γ to ε-martensite, suggesting that the transformation is not solely determined by the stacking fault energy. The study shows that during the Q&P process, strong and ductile steels with specific transformation procedures can be obtained by adjusting volume fraction and carbon content of the retained austenite.
Aurycéia J. Guimarães-Costa, Fabíola S. Machado, Rory R. S. Oliveira, Vinícius Silva-Costa, Marcelo C. Andrade, Tommaso Giarrizzo, Ulrich Saint-Paul, Iracilda Sampaio, Horacio Schneider
Published: 17 May 2019
Scientific Reports, Volume 9; doi:10.1038/s41598-019-43930-z

Abstract:Deltas are dynamic and productive systems of enormous ecological significance, encompassing unique and biologically diverse wetland habitats. Here, we present the first data on the molecular diversity of the fish fauna of the Parnaíba Delta, the largest deltaic formation of the Americas. Partial sequences (626 bp) of the mitochondrial COI gene (Cytochrome c oxidase subunit I) were used to barcode 402 individuals, representing 128 species, belonging to 98 genera, 57 families, 17 orders and two classes. The most abundant orders were the Perciformes, Siluriformes, Gobiiformes, and Pleuronectiformes. The Neighbor-Joining (NJ), Bayesian Inference (BI), and BIN analyses produced 103 molecular clusters, while the Automatic Barcode Gap Discovery (ABGD) and Maximum Likelihood (ML) approaches revealed 102 clusters. The mean conspecific, congeneric and confamilial genetic distances were 0.33%, 14.37%, and 18.60%, respectively. Intraspecific divergence ranged from 0.0% to 1.4%, and all species presented barcode gaps, with the exception of two clusters of Cathorops spixii (OTU 96 and OTU 103), which were separated by a low interspecific distance (1.2%), which overlaps the maximum intraspecific genetic distance (1.4%). The barcode data provide new insights into the fish diversity of the Parnaíba Delta, which will be important for the development of further research on this fauna.
Gun Woo Kim, Young-Sang Kim, Soo Hyun Lee, Seung Geon Park, Duk Hwan Kim, Joo Young Cho, Ki Baik Hahm, Sung Pyo Hong, Jun-Hwan Yoo
Published: 17 May 2019
Scientific Reports, Volume 9; doi:10.1038/s41598-019-44014-8

Abstract:Interval colorectal cancers detected after colonoscopy are known to be highly associated with proximal colorectal neoplasms (CRNs). This cross-sectional study investigated whether periodontitis could be a risk factor for proximal CRNs in healthy individuals. A total of 2504 subjects who received a colonoscopy and dental exam were enrolled in this study. We divided the subjects into the periodontitis group (n = 216) and the control group (n = 2288). The periodontitis group was defined as subjects who had one or more teeth with a probing pocket depth (PPD) ≥4 mm. The prevalence of proximal CRNs was significantly higher in the periodontitis group (25.0%) than in the control group (12.3%) (P < 0.001). Independent risk factors for proximal CRNs in the multivariate analysis were periodontitis, smoking, age, waist circumference, and triglycerides, and those for proximal advanced CRNs were periodontitis, age, and family history of CRC. However, periodontitis was not a risk factor for overall CRNs and advanced CRNs. Periodontitis was associated with an increased risk of proximal CRNs (odds ratio [OR], 1.525; 95% confidence intervals [95% CI], 1.071–2.172) and proximal advanced CRNs (OR, 2.671; 95% CI, 1.088–6.560). Periodontitis might be associated with proximal CRNs and proximal advanced CRNs.
Pierre-Louis Stenger, Jérémie Vidal-Dupiol, Céline Reisser, Serge Planes, Chin-Long Ky
Published: 17 May 2019
Scientific Reports, Volume 9; doi:10.1038/s41598-019-43777-4

Abstract:The bivalve Pinctada margaritifera has the capacity to produce the most varied and colourful pearls in the world. Colour expression in the inner shell is under combined genetic and environmental control and is correlated with the colour of pearls produced when the same individual is used as a graft donor. One major limitation when studying colour phenotypes is grader subjectivity, which leads to inconsistent colour qualification and quantification. Through the use of HSV (Hue Saturation Value) colour space, we created an R package named ‘ImaginR’ to characterise inner shell colour variations in P. margaritifera. Using a machine-learning protocol with a training dataset, ImaginR was able to reassign individual oysters and pearls to predefined human-based phenotype categories. We then tested the package on samples obtained in an experiment testing the effects of donor conditioning depth on the colour of the donor inner shell and colour of the pearls harvested from recipients following grafting and 20 months of culture in situ. These analyses successfully detected donor shell colour modifications due to depth-related plasticity and the maintenance of these modifications through to the harvested pearls. Besides its potential interest for standardization in the pearl industry, this new method is relevant to other research projects using biological models.
Marie-Ange Palomares, Cyril Dalmasso, Eric Bonnet, Céline Derbois, Solène Brohard-Julien, Christophe Ambroise, Christophe Battail, Jean-François Deleuze, Robert Olaso
Published: 17 May 2019
Scientific Reports, Volume 9; doi:10.1038/s41598-019-43983-0

Abstract:High-throughput RNA-sequencing has become the gold standard method for whole-transcriptome gene expression analysis, and is widely used in numerous applications to study cell and tissue transcriptomes. It is also being increasingly used in a number of clinical applications, including expression profiling for diagnostics and alternative transcript detection. However, despite its many advantages, RNA sequencing can be challenging in some situations, for instance in cases of low input amounts or degraded RNA samples. Several protocols have been proposed to overcome these challenges, and many are available as commercial kits. In this study, we systematically test three recent commercial technologies for RNA-seq library preparation (TruSeq, SMARTer and SMARTer Ultra-Low) on human biological reference materials, using standard (1 mg), low (100 ng and 10 ng) and ultra-low (<1 ng) input amounts, and for mRNA and total RNA, stranded and unstranded. The results are analyzed using read quality and alignment metrics, gene detection and differential gene expression metrics. Overall, we show that the TruSeq kit performs well with an input amount of 100 ng, while the SMARTer kit shows decreased performance for inputs of 100 and 10 ng, and the SMARTer Ultra-Low kit performs relatively well for input amounts <1 ng. All the results are discussed in detail, and we provide guidelines for biologists for the selection of an RNA-seq library preparation kit.
Oleksandr A. Savchuk, Oscar F. Silvestre, Ricardo M. R. Adão, Jana B. Nieder
Published: 17 May 2019
Scientific Reports, Volume 9; doi:10.1038/s41598-019-44023-7

Abstract:Nanothermometry methods with intracellular sensitivities have the potential to make important contributions to fundamental cell biology and medical fields, as temperature is a relevant physical parameter for molecular reactions to occur inside the cells and changes of local temperature are well identified therapeutic strategies. Here we show how the GFP can be used to assess temperature-based on a novel fluorescence peak fraction method. Further, we use standard GFP transfection reagents to assess temperature intracellularly in HeLa cells expressing GFP in the mitochondria. High thermal resolution and sensitivity of around 0.26% °C−1 and 2.5% °C−1, were achieved for wt-GFP in solution and emGFP-Mito within the cell, respectively. We demonstrate that the GFP-based nanothermometer is suited to directly follow the temperature changes induced by a chemical uncoupler reagent that acts on the mitochondria. The spatial resolution allows distinguishing local heating variations within the different cellular compartments. Our discovery may lead to establishing intracellular nanothermometry as a standard method applicable to the wide range of live cells able to express GFP.
Emma L. Hesketh, Christian Tiede, Hope Adamson, Thomas L. Adams, Matthew J. Byrne, Yulia Meshcheriakova, Inga Kruse, Michael J. McPherson, George P. Lomonossoff, Darren C. Tomlinson, et al.
Published: 17 May 2019
Scientific Reports, Volume 9; doi:10.1038/s41598-019-43945-6

Abstract:Plant viruses can cause devastating losses to agriculture and are therefore a major threat to food security. The rapid identification of virally-infected crops allowing containment is essential to limit such threats, but plant viral diseases can be extremely challenging to diagnose. An ideal method for plant virus diagnosis would be a device which can be implemented easily in the field. Such devices require a binding reagent that is specific for the virus of interest. We chose to investigate the use of Affimer reagents, artificial binding proteins and a model plant virus Cowpea Mosaic virus (CPMV) empty virus like particles (eVLPs). CPMV-eVLP mimic the morphology of wild-type (WT) CPMV but lack any infectious genomic material and so do not have biocontainment issues. We have produced and purified an Affimer reagent selected for its ability to bind to CPMV-eVLP and have shown that the selected Affimer also specifically binds to WT CPMV. We have produced a 3.4 Å structure of WT CPMV bound to the Affimer using cryo-electron microscopy. Finally, we have shown that this Affimer is capable of reliably detecting the virus in crude extracts of CPMV-infected leaves and can therefore form the basis for the future development of diagnostic tests.