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Selection and validation of reference genes for gene expression studies in Klebsiella pneumoniae using Reverse Transcription Quantitative real-time PCR.
Gomes, AÉI, Stuchi, LP, Siqueira, NMG, Henrique, JB, Vicentini, R, Ribeiro, ML, Darrieux, M, Ferraz, LFC
Scientific reports. 2018;(1):9001
Abstract
For reliable results, Reverse Transcription Quantitative real-time Polymerase Chain Reaction (RT-qPCR) analyses depend on stably expressed reference genes for data normalization purposes. Klebsiella pneumoniae is an opportunistic Gram-negative bacterium that has become a serious threat worldwide. Unfortunately, there is no consensus for an ideal reference gene for RT-qPCR data normalization on K. pneumoniae. In this study, the expression profile of eleven candidate reference genes was assessed in K. pneumoniae cells submitted to various experimental conditions, and the expression stability of these candidate genes was evaluated using statistical algorithms BestKeeper, NormFinder, geNorm, Delta CT and RefFinder. The statistical analyses ranked recA, rho, proC and rpoD as the most suitable reference genes for accurate RT-qPCR data normalization in K. pneumoniae. The reliability of the proposed reference genes was validated by normalizing the relative expression of iron-regulated genes in K. pneumoniae cells submitted to iron-replete and iron-limited conditions. This work emphasizes that the stable expression of any potential reference candidate gene must be validated in each physiological condition or experimental treatment under study.
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Anti-Inflammatory and Tissue Regenerative Effects of Topical Treatment with Ozonated Olive Oil/Vitamin E Acetate in Balanitis Xerotica Obliterans.
Currò, M, Russo, T, Ferlazzo, N, Caccamo, D, Antonuccio, P, Arena, S, Parisi, S, Perrone, P, Ientile, R, Romeo, C, et al
Molecules (Basel, Switzerland). 2018;(3)
Abstract
Balanitis xerotica obliterans (BXO) is a chronic inflammatory skin disorder, considered the male genital variant of lichen sclerosus. Anti-inflammatory drugs are commonly used in BXO. We evaluated the effects of an innovative formulation of ozonated olive oil with vitamin E acetate (OZOILE®) on the inflammatory status and tissue remodeling in male children with BXO. The mRNA transcripts of proteins involved either in inflammation or in dynamics of tissue regeneration were analyzed by quantitative real-time PCR, in foreskins affected by BXO removed from patients untreated or treated with OZOILE® cream for 7 days before circumcision. We found a significant reduction in mRNA levels of IL-1β, TNF-α, INF-γ, transglutaminase 2 and NOS2 in foreskins treated with OZOILE® in comparison to untreated ones (p < 0.001). No significant differences were observed in NF-κB activation in the specimens obtained from treated and untreated patients. Hence, OZOILE® treatment up-regulated hypoxia-inducible factor (HIF)-1alpha, vascular endothelial growth factor (VEGF) and E-cadherin gene expression (p < 0.001). The treatment with OZOILE® showed effective results in children affected by BXO by reducing the inflammatory process and stimulating mechanisms for tissue regeneration of the foreskin. A randomized clinical trial on a large number of children affected by BXO might be useful to verify the efficacy of topical treatment with OZOILE®.
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Celiac disease biomarkers identified by transcriptome analysis of small intestinal biopsies.
Bragde, H, Jansson, U, Fredrikson, M, Grodzinsky, E, Söderman, J
Cellular and molecular life sciences : CMLS. 2018;(23):4385-4401
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Abstract
Establishing a celiac disease (CD) diagnosis can be difficult, such as when CD-specific antibody levels are just above cutoff or when small intestinal biopsies show low-grade injuries. To investigate the biological pathways involved in CD and select potential biomarkers to aid in CD diagnosis, RNA sequencing of duodenal biopsies from subjects with either confirmed Active CD (n = 20) or without any signs of CD (n = 20) was performed. Gene enrichment and pathway analysis highlighted contexts, such as immune response, microbial infection, phagocytosis, intestinal barrier function, metabolism, and transportation. Twenty-nine potential CD biomarkers were selected based on differential expression and biological context. The biomarkers were validated by real-time polymerase chain reaction of eight RNA sequencing study subjects, and further investigated using an independent study group (n = 43) consisting of subjects not affected by CD, with a clear diagnosis of CD on either a gluten-containing or a gluten-free diet, or with low-grade intestinal injury. Selected biomarkers were able to classify subjects with clear CD/non-CD status, and a subset of the biomarkers (CXCL10, GBP5, IFI27, IFNG, and UBD) showed differential expression in biopsies from subjects with no or low-grade intestinal injury that received a CD diagnosis based on biopsies taken at a later time point. A large number of pathways are involved in CD pathogenesis, and gene expression is affected in CD mucosa already in low-grade intestinal injuries. RNA sequencing of low-grade intestinal injuries might discover pathways and biomarkers involved in early stages of CD pathogenesis.
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Differential Gene Expression in Prostate Tissue According to Ejaculation Frequency.
Sinnott, JA, Brumberg, K, Wilson, KM, Ebot, EM, Giovannucci, EL, Mucci, LA, Rider, JR
European urology. 2018;(5):545-548
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Abstract
UNLABELLED In a prospective study of 31 925 men with 18 yr of follow-up, higher ejaculation frequency (EF) throughout adulthood was associated with lower rates of prostate cancer. To further explore this association, we evaluated whole transcriptome gene expression in the prostate tissue from study participants who developed prostate cancer between 1992 and 2004 (n=157 tumor tissue, n=85 adjacent normal). We tested for trends in gene expression according to the level of EF as self-reported in 1992 for ages 20-29 yr, 40-49 yr, and the year prior to the questionnaire, 1991. There were no associations between EF and gene expression in areas of tumor after accounting for multiple testing. In contrast, in the adjacent normal tissue, 409 genes and six pathways were differentially expressed at a false discovery rate ≤0.2 across categories of EF in 1991. These results suggest that ejaculation affects the expression of genes in the normal prostate tissue. The identified genes and pathways provide potential biological links between EF and prostate tumorigenesis. PATIENT SUMMARY To explore previous findings that men who ejaculate more frequently have lower risk of prostate cancer, we evaluated molecular alterations in the prostate tissue according to each man's frequency of ejaculation prior to diagnosis. We identified biological processes that could link ejaculation frequency and prostate cancer.
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A key structural gene, AaLDOX, is involved in anthocyanin biosynthesis in all red-fleshed kiwifruit (Actinidia arguta) based on transcriptome analysis.
Li, Y, Fang, J, Qi, X, Lin, M, Zhong, Y, Sun, L
Gene. 2018;:31-41
Abstract
Study on kiwifruit (Actinidia chinensis and A. deliciosa) color mainly concentrated in green and yellow-fleshed cultivars, less about molecular mechanism of red-fleshed trait formation, rarely in all red-fleshed fruit. Using 'Tianyuanhong' and 'Yongfengyihao' ('TY', a kind of all red-fleshed cultivar, from Actinidia arguta; 'YF', a kind of all green-fleshed cultivar, also from Actinidia arguta) as experimental material, we performed RNA-seq to obtain 202,742 unigenes with an average length of 603bp and N50 of 873bp via transcriptome data analysis. Of these unigenes, 72,508 (35.76%) were annotated and 997 were assigned to secondary metabolic pathways, of which 104 unigenes were involved in flavonoid and anthocyanin biosynthesis. According to the parameter log2fold-change and p-adjusted, 12 differentially expressed structural genes were selected for performing expression profiles and cluster analysis. Physiological traits including color ration, hue angle, and anthocyanin content were also investigated. From the results, we concluded AaLDOX (genes encoding leucoanthocyanidin dioxygenase) maybe the key gene controlling anthocyanin biosynthesis in flesh of 'TY' kiwifruit, which promoted accumulation of anthocyanin, finally leading to the red flesh coloration.
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Identification of genes related to proliferative diabetic retinopathy through RWR algorithm based on protein-protein interaction network.
Zhang, J, Suo, Y, Liu, M, Xu, X
Biochimica et biophysica acta. Molecular basis of disease. 2018;(6 Pt B):2369-2375
Abstract
Proliferative diabetic retinopathy (PDR) is one of the most common complications of diabetes and can lead to blindness. Proteomic studies have provided insight into the pathogenesis of PDR and a series of PDR-related genes has been identified but are far from fully characterized because the experimental methods are expensive and time consuming. In our previous study, we successfully identified 35 candidate PDR-related genes through the shortest-path algorithm. In the current study, we developed a computational method using the random walk with restart (RWR) algorithm and the protein-protein interaction (PPI) network to identify potential PDR-related genes. After some possible genes were obtained by the RWR algorithm, a three-stage filtration strategy, which includes the permutation test, interaction test and enrichment test, was applied to exclude potential false positives caused by the structure of PPI network, the poor interaction strength, and the limited similarity on gene ontology (GO) terms and biological pathways. As a result, 36 candidate genes were discovered by the method which was different from the 35 genes reported in our previous study. A literature review showed that 21 of these 36 genes are supported by previous experiments. These findings suggest the robustness and complementary effects of both our efforts using different computational methods, thus providing an alternative method to study PDR pathogenesis.
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Experimental design for single-cell RNA sequencing.
Baran-Gale, J, Chandra, T, Kirschner, K
Briefings in functional genomics. 2018;(4):233-239
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Abstract
Single-cell RNA sequencing (scRNA-seq) has opened new avenues for the characterization of heterogeneity in a large variety of cellular systems. As this is a relatively new technique, the field is fast evolving. Here, we discuss general considerations in experimental design and the two most popular approaches, plate-based Smart-Seq2 and microdroplet-based scRNA-seq at the example of 10x Chromium. We discuss advantages and disadvantages of both methods and point out major factors to consider in designing successful experiments.
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Comparative Genomics and Transcriptome Profiling in Primary Aldosteronism.
Aristizabal Prada, ET, Castellano, I, Sušnik, E, Yang, Y, Meyer, LS, Tetti, M, Beuschlein, F, Reincke, M, Williams, TA
International journal of molecular sciences. 2018;(4)
Abstract
Primary aldosteronism is the most common form of endocrine hypertension with a prevalence of 6% in the general population with hypertension. The genetic basis of the four familial forms of primary aldosteronism (familial hyperaldosteronism FH types I-IV) and the majority of sporadic unilateral aldosterone-producing adenomas has now been resolved. Familial forms of hyperaldosteronism are, however, rare. The sporadic forms of the disease prevail and these are usually caused by either a unilateral aldosterone-producing adenoma or bilateral adrenal hyperplasia. Aldosterone-producing adenomas frequently carry a causative somatic mutation in either of a number of genes with the KCNJ5 gene, encoding an inwardly rectifying potassium channel, a recurrent target harboring mutations at a prevalence of more than 40% worldwide. Other than genetic variations, gene expression profiling of aldosterone-producing adenomas has shed light on the genes and intracellular signalling pathways that may play a role in the pathogenesis and pathophysiology of these tumors.
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Comparative Transcriptome Analysis Reveals the Mechanism Underlying 3,5-Dibromo-4-Hydroxybenzoate Catabolism via a New Oxidative Decarboxylation Pathway.
Chen, K, Mu, Y, Jian, S, Zang, X, Chen, Q, Jia, W, Ke, Z, Gao, Y, Jiang, J
Applied and environmental microbiology. 2018;(6)
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Abstract
The compound 3,5-dibromo-4-hydroxybenzoate (DBHB) is both anthropogenically released into and naturally produced in the environment, and its environmental fate is of great concern. Aerobic and anaerobic reductive dehalogenations are the only two reported pathways for DBHB catabolism. In this study, a new oxidative decarboxylation pathway for DBHB catabolism was identified in a DBHB-utilizing strain, Pigmentiphaga sp. strain H8. The genetic determinants underlying this pathway were elucidated based on comparative transcriptome analysis and subsequent experimental validation. A gene cluster comprising orf420 to orf426, with transcripts that were about 33- to 4,400-fold upregulated in DBHB-induced cells compared with those in uninduced cells, was suspected to be involved in DBHB catabolism. The gene odcA (orf420), which is essential for the initial catabolism of DBHB, encodes a novel NAD(P)H-dependent flavin monooxygenase that mediates the oxidative decarboxylation of DBHB to 2,6-dibromohydroquinone (2,6-DBHQ). The substrate specificity of the purified OdcA indicated that the 4-hydroxyl group and its ortho-halogen(s) are important for hydroxylation of the C-1 site carboxyl group by OdcA. 2,6-DBHQ is then ring cleaved by the dioxygenase OdcB (Orf425) to 2-bromomaleylacetate, which is finally transformed to β-ketoadipate by the maleylacetate reductase OdcC (Orf426). These results provide a better understanding of the molecular mechanism underlying the catabolic diversity of halogenated para-hydroxybenzoates.IMPORTANCE Halogenated hydroxybenzoates (HBs), which are widely used synthetic precursors for chemical products and common metabolic intermediates from halogenated aromatics, exert considerable adverse effects on human health and ecological security. Microbial catabolism plays key roles in the dissipation of halogenated HBs in the environment. In this study, the discovery of a new catabolic pathway for 3,5-dibromo-4-hydroxybenzoate (DBHB) and clarification of the genetic determinants underlying the pathway broaden our knowledge of the catabolic diversity of halogenated HBs in microorganisms. Furthermore, the NAD(P)H-dependent flavin monooxygenase OdcA identified in Pigmentiphaga sp. strain H8 represents a novel 1-monooxygenase for halogenated para-HBs found in prokaryotes and enhances our knowledge of the decarboxylative hydroxylation of (halogenated) para-HBs.
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Full-length transcriptome sequences of ephemeral plant Arabidopsis pumila provides insight into gene expression dynamics during continuous salt stress.
Yang, L, Jin, Y, Huang, W, Sun, Q, Liu, F, Huang, X
BMC genomics. 2018;(1):717
Abstract
BACKGROUND Arabidopsis pumila is native to the desert region of northwest China and it is extraordinarily well adapted to the local semi-desert saline soil, thus providing a candidate plant system for environmental adaptation and salt-tolerance gene mining. However, understanding of the salt-adaptation mechanism of this species is limited because of genomic sequences scarcity. In the present study, the transcriptome profiles of A. pumila leaf tissues treated with 250 mM NaCl for 0, 0.5, 3, 6, 12, 24 and 48 h were analyzed using a combination of second-generation sequencing (SGS) and third-generation single-molecule real-time (SMRT) sequencing. RESULTS Correction of SMRT long reads by SGS short reads resulted in 59,328 transcripts. We found 8075 differentially expressed genes (DEGs) between salt-stressed tissues and controls, of which 483 were transcription factors and 1157 were transport proteins. Most DEGs were activated within 6 h of salt stress and their expression stabilized after 48 h; the number of DEGs was greatest within 12 h of salt stress. Gene annotation and functional analyses revealed that expression of genes associated with the osmotic and ionic phases rapidly and coordinately changed during the continuous salt stress in this species, and salt stress-related categories were highly enriched among these DEGs, including oxidation-reduction, transmembrane transport, transcription factor activity and ion channel activity. Orphan, MYB, HB, bHLH, C3H, PHD, bZIP, ARF and NAC TFs were most enriched in DEGs; ABCB1, CLC-A, CPK30, KEA2, KUP9, NHX1, SOS1, VHA-A and VP1 TPs were extensively up-regulated in salt-stressed samples, suggesting that they play important roles in slat tolerance. Importantly, further experimental studies identified a mitogen-activated protein kinase (MAPK) gene MAPKKK18 as continuously up-regulated throughout salt stress, suggesting its crucial role in salt tolerance. The expression patterns of the salt-responsive 24 genes resulted from quantitative real-time PCR were basically consistent with their transcript abundance changes identified by RNA-Seq. CONCLUSION The full-length transcripts generated in this study provide a more accurate depiction of gene transcription of A. pumila. We identified potential genes involved in salt tolerance of A. pumila. These data present a genetic resource and facilitate better understanding of salt-adaptation mechanism for ephemeral plants.