Scientific Reports
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Single-Cell Quantification of mRNA Expression in The Human Brain Abstract RNA analysis at the cellular resolution in the human brain is challenging. Here, we describe an optimised approach for detecting single RNA transcripts in a cell-type specific manner in frozen human brain tissue using multiplexed fluorescent RNAscope probes. We developed a new robust analytical approach for RNAscope quantification. Our method shows that low RNA integrity does not significantly affect RNAscope signal, recapitulates bulk RNA analysis and provides spatial context to transcriptomic analysis of human post-mortem brain at single-cell resolution. In summary, our optimised method allows the usage of frozen human samples from brain banks to perform quantitative RNAscope analysis.
Scientific Reports - Tập 9 Số 1
Segmentation of Heavily Clustered Nuclei from Histopathological Images Abstract Automated cell nucleus segmentation is the key to gain further insight into cell features and functionality which support computer-aided pathology in early diagnosis of diseases such as breast cancer and brain tumour. Despite considerable advances in automated segmentation, it still remains a challenging task to split heavily clustered nuclei due to intensity variations caused by noise and uneven absorption of stains. To address this problem, we propose a novel method applicable to variety of histopathological images stained for different proteins, with high speed, accuracy and level of automation. Our algorithm is initiated by applying a new locally adaptive thresholding method on watershed regions. Followed by a new splitting technique based on multilevel thresholding and the watershed algorithm to separate clustered nuclei. Finalized by a model-based merging step to eliminate oversegmentation and a model-based correction step to improve segmentation results and eliminate small objects. We have applied our method to three image datasets: breast cancer stained for hematoxylin and eosin (H&E), Drosophila Kc167 cells stained for DNA to label nuclei, and mature neurons stained for NeuN. Evaluated results show our method outperforms the state-of-the-art methods in terms of accuracy, precision, F1-measure, and computational time.
Scientific Reports - Tập 9 Số 1
Deregulation of transcription factors controlling intestinal epithelial cell differentiation; a predisposing factor for reduced enteroendocrine cell number in morbidly obese individuals Abstract Morbidly obese patients exhibit impaired secretion of gut hormones that may contribute to the development of obesity. After bariatric surgery there is a dramatic increase in gut hormone release. In this study, gastric and duodenal tissues were endoscopically collected from lean, and morbidly obese subjects before and 3 months after laparoscopic sleeve gastrectomy (LSG). Tissue morphology, abundance of chromogranin A, gut hormones, α-defensin, mucin 2, Na+ /glucose co-transporter 1 (SGLT1) and transcription factors, Hes1, HATH1, NeuroD1, and Ngn3, were determined. In obese patients, the total number of enteroendocrine cells (EEC) and EECs containing gut hormones were significantly reduced in the stomach and duodenum, compared to lean, and returned to normality post-LSG. No changes in villus height/crypt depth were observed. A significant increase in mucin 2 and SGLT1 expression was detected in the obese duodenum. Expression levels of transcription factors required for differentiation of absorptive and secretory cell lineages were altered. We propose that in obesity, there is deregulation in differentiation of intestinal epithelial cell lineages that may influence the levels of released gut hormones. Post-LSG cellular differentiation profile is restored. An understanding of molecular mechanisms controlling epithelial cell differentiation in the obese intestine assists in the development of non-invasive therapeutic strategies.
Scientific Reports - Tập 7 Số 1
Impact of PET data driven respiratory motion correction and BSREM reconstruction of 68Ga-DOTATATE PET/CT for differentiating neuroendocrine tumors (NET) and intrapancreatic accessory spleens (IPAS) Abstract To evaluate whether quantitative PET parameters of motion-corrected 68 Ga-DOTATATE PET/CT can differentiate between intrapancreatic accessory spleens (IPAS) and pancreatic neuroendocrine tumor (pNET). A total of 498 consecutive patients with neuroendocrine tumors (NET) who underwent 68 Ga-DOTATATE PET/CT between March 2017 and July 2019 were retrospectively analyzed. Subjects with accessory spleens (n = 43, thereof 7 IPAS) and pNET (n = 9) were included, resulting in a total of 45 scans. PET images were reconstructed using ordered-subsets expectation maximization (OSEM) and a fully convergent iterative image reconstruction algorithm with β-values of 1000 (BSREM1000 ). A data-driven gating (DDG) technique (MOTIONFREE, GE Healthcare) was applied to extract respiratory triggers and use them for PET motion correction within both reconstructions. PET parameters among different samples were compared using non-parametric tests. Receiver operating characteristics (ROC) analyzed the ability of PET parameters to differentiate IPAS and pNETs. SUVmax was able to distinguish pNET from accessory spleens and IPAs in BSREM1000 reconstructions (p < 0.05). This result was more reliable using DDG-based motion correction (p < 0.003) and was achieved in both OSEM and BSREM1000 reconstructions. For differentiating accessory spleens and pNETs with specificity 100%, the ROC analysis yielded an AUC of 0.742 (sensitivity 56%)/0.765 (sensitivity 56%)/0.846 (sensitivity 62%)/0.840 (sensitivity 63%) for SUVmax 36.7/41.9/36.9/41.7 in OSEM/BSREM1000 /OSEM + DDG/BSREM1000 + DDG, respectively. BSREM1000 + DDG can accurately differentiate pNET from accessory spleen. Both BSREM1000 and DDG lead to a significant SUV increase compared to OSEM and non-motion-corrected data.
Scientific Reports - Tập 11 Số 1
Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum Abstract Genetic linkage maps are indispensable tools in a wide range of genetic and genomic research. With the advancement of genotyping-by-sequencing (GBS) methods, the construction of a high-density linkage maps has become achievable in marine organisms lacking sufficient genomic resources, such as mollusks. In this study, high-density linkage map was constructed for an ecologically and commercially important clam species,Ruditapes philippinarum . For the consensus linkage map, a total of 9658 markers spanning 1926.98 cM were mapped to 18 sex-averaged linkage groups, with an average marker distance of 0.42 cM. Based on the high-density linkage map, ten QTLs for growth-related traits and shell color were detected. The coverage and density of the current map are sufficient for us to effectively detect QTL for segregating traits, and two QTL positions were all coincident with the closest markers. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement ofR. philippinarum and other bivalve molluscan species.
Scientific Reports - Tập 7 Số 1
Linkage mapping of quantitative trait loci for fiber yield and its related traits in the population derived from cultivated ramie and wild B. nivea var. tenacissima Abstract Ramie is an important natural fiber crop, and the fiber yield and its related traits are the most valuable traits in ramie production. However, the genetic basis for these traits is still poorly understood, which has dramatically hindered the breeding of high yield in this fiber crop. Herein, a high-density genetic map with 6,433 markers spanning 2476.5 cM was constructed using a population derived from two parents, cultivated ramie Zhongsizhu 1 (ZSZ1) and its wild progenitor B. nivea var. tenacissima (BNT). The fiber yield (FY) and its four related traits—stem diameter (SD) and length (SL), stem bark weight (BW) and thickness (BT)—were performed for quantitative trait locus (QTL) analysis, resulting in a total of 47 QTLs identified. Forty QTLs were mapped into 12 genomic regions, thus forming 12 QTL clusters. Among 47 QTLs, there were 14 QTLs whose wild allele from BNT was beneficial. Interestingly, all QTLs in Cluster 10 displayed overdominance, indicating that the region of this cluster was likely heterotic loci. In addition, four fiber yield-related genes underwent positive selection were found either to fall into the FY-related QTL regions or to be near to the identified QTLs. The dissection of FY and FY-related traits not only improved our understanding to the genetic basis of these traits, but also provided new insights into the domestication of FY in ramie. The identification of many QTLs and the discovery of beneficial alleles from wild species provided a basis for the improvement of yield traits in ramie breeding.
Scientific Reports - Tập 9 Số 1
Three Dimensional Hybrids of Vertical Graphene-nanosheet Sandwiched by Ag-nanoparticles for Enhanced Surface Selectively Catalytic Reactions Abstract Three dimensional (3D) plasmonic nanostructure is perfect for the surface-enhanced Raman scattering (SERS) and also very suitable for surface catalytic reaction, but how to design and fabricate is still a robust task. Here, we show a 3D plasmonic nanohybrid of vertical graphene-nanosheet sandwiched by Ag-nanoparticles on the silicon nanocone array substrate for enhanced surface catalytic reaction. By SERS detection, we find that this hierarchical nanohybrid structure is highly efficient in the enhancement of catalytic reaction, even at a very low concentration of 10−11 M, which is far better than previous reports by four orders of magnitude. A strong electric field enhancement produced in the 3D framework nanohybrids of graphene nanosheet/Ag-nanoparticles is responsible for this great enhancement of catalytic reaction, due to larger electron collective oscillation in the composite system. Especially the oxygen adsorbed on the graphene and Ag nanoparticles can be excited to triplet excited states and the electrons on the graphene and the nanoparticles can be effectively transferred to the oxygen, which plays very important role in molecular catalytic reactions. Our results demonstrate the contribution of graphene in plasmon-driven catalytic reactions, revealing a co-driven reaction process.This excellent SERS substrate can be used for future plasmon and graphene co-catalytic surface catalytic reactions, graphene-based surface plasmon sensors and so on.
Scientific Reports - Tập 5 Số 1
Transcriptome analysis of human ageing in male skin shows mid-life period of variability and central role of NF-κB Abstract Age is well-known to be a significant factor in both disease pathology and response to treatment, yet the molecular changes that occur with age in humans remain ill-defined. Here, using transcriptome profiling of healthy human male skin, we demonstrate that there is a period of significantly elevated, transcriptome-wide expression changes occurring predominantly in middle age. Both pre and post this period, the transcriptome appears to undergo much smaller, linear changes with increasing age. Functional analysis of the transient changes in middle age suggest a period of heightened metabolic activity and cellular damage associated with NF-kappa-B and TNF signaling pathways. Through meta-analysis we also show the presence of global, tissue independent linear transcriptome changes with age which appear to be regulated by NF-kappa-B. These results suggest that aging in human skin is associated with a critical mid-life period with widespread transcriptome changes, both preceded and proceeded by a relatively steady rate of linear change in the transcriptome. The data provides insight into molecular changes associated with normal aging and will help to better understand the increasingly important pathological changes associated with aging.
Scientific Reports - Tập 6 Số 1
Upregulation of aquaporin expression in the salivary glands of heat-acclimated rats
Scientific Reports - Tập 3 Số 1
Differential expression and regulation of HSP70 gene during growth phase in ruminants in response to heat stress Abstract Heat shock proteins regulate the physiological mechanism of heat stress adaptation at cellular level. The present investigation was carried out to analyse the HSP70 gene regulation in various growth stage in ruminants in peripheral blood mononuclear cells (PBMCs). The relationship between HSP gene expression and thermotolerance in age-specific manner in ruminants has not been analysed. Therefore m-RNA HSP70 expression level was examined in different age groups of Jamunpari goat during hot climatic conditions. The experiment was carried out in 32 animals of Jamunapari goat belonging to the age groups of 3-months, 9-months, 12-months, and adults (2–3 year). Total RNA was isolated from peripheral blood mononuclear cells. The physiological response such as rectal temperature (RT), respiration rate (RR) and heart rate (HR) was used as indicator to heat stress. Temperature Humidity Index (THI) was used as an indicator of severity of environmental stress. The THI range varied from 82.00–92.08 during experimental period. The m-RNA HSP70 expression level at 9-month age of animals was up-regulated and significantly higher than other age groups. It was observed that the level of HSP70 transcripts in PBMCs was highest at 9-month age group, and age-related decline in HSP70 expression was observed in adult age. Based on the physiological response, the contrasting heat-stress phenotypes were recognised as heat stress susceptible (HSS) and heat stress tolerant (HST) individuals and the expression of m-RNA HSP70 was analysed at different ages in response to chronic heat stress. The differential mRNA expression of HSS individuals at 3 and 9-month of age showed the highest fold expression than HST. Age and phenotype had significant effect (p < 0.01) on the crossing point (CP) value. The m-RNA HSP70 gene expression in different age groups was correlated with heat stress tolerance and this could be used as biomarker for breeders to analyse the HSP responsein -vivo in ruminants.
Scientific Reports - Tập 12 Số 1
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