Expression Analysis on Archival Material Revisited: Isolation and Quantification of RNA Extracted From FFPE Samples.
AuthorsDeben C, Zwaenepoel K, Boeckx C, Wouters A, Pauwels P, Peeters M, Lardon F, Baay M, Deschoolmeester V,
JournalDiagn Mol Pathol
PubMed ID23370428
'BACKGROUND:: Formalin-fixed paraffin-embedded (FFPE) tissue is the most readily available source of RNA for the gene expression studies. The main disadvantage is the poor quality of isolated RNA. Our group recently compared 5 commercially available RNA isolation kits and concluded that the RNeasy FFPE kit from Qiagen was the most ... More
Analysis of in vivo expressed genes in Mannheimia haemolytica A1.
AuthorsLo RY, Sathiamoorthy S, Shewen PE
JournalFEMS Microbiol Lett
PubMed ID16984402
'The expression of Mannheimia haemolytica A1 genes during in vivo growth was examined by reverse transcriptase-polymerase chain reaction (RT-PCR) using total RNA extracted directly from M. haemolytica A1 recovered from pneumonic lungs of cattle. Primers specific for three groups of genes were used. Group 1 includes virulence-related genes: lktC, tbpB, ... More
High transcript level of fatty acid-binding protein 11 but not of very low-density lipoprotein receptor is correlated to ovarian follicle atresia in a teleost fish (Solea senegalensis).
AuthorsAgulleiro MJ, André M, Morais S, Cerdà J, Babin PJ,
JournalBiol Reprod
PubMed ID17554079
'Transcripts encoding a fatty acid-binding protein (FABP), Fabp11, and two isoforms of very low-density lipoprotein receptor (Vldlr; vitellogenin receptor) were characterized from the ovary of Senegalese sole (Solea senegalensis). Phylogenetic analyses of vertebrate FABPs demonstrated that Senegalese sole Fabp11, as zebrafish (Danio rerio) homologous sequences, is part of a newly ... More
Comparative expression analysis of rpf-like genes of Mycobacterium tuberculosis H37Rv under different physiological stress and growth conditions.
AuthorsGupta RK, Srivastava BS, Srivastava R,
JournalMicrobiology
PubMed ID20522500
'Mycobacterium tuberculosis H37Rv possesses five resuscitation-promoting factors, RpfA-E, which are required for the resuscitation of dormancy in mycobacteria induced by prolonged incubation of the culture in stationary phase. This study explores the transcriptional profile of all the rpf-like genes of M. tuberculosis H37Rv in the exponential phase, stationary phase, non-culturable ... More
Bioreactor environment-sensitive sentinel genes as novel metrics for cell culture scale-down comparability.
AuthorsKondragunta B, Joshi BH, Han J, Brorson KA, Puri RK, Moreira AR, Rao G,
JournalBiotechnol Prog
PubMed ID22848039
Scale-down of bioreactors is currently done based on matching one or more measurable parameters such as k(L) a and P/V, which could result in insufficient process comparability. Currently, there is a lack of genomic translational studies in cell culture scale-down, which could help delineate measurable cellular attributes for improved scale-down. ... More
Differential expression of microRNAs between eutopic and ectopic endometrium in ovarian endometriosis.
AuthorsFiligheddu N, Gregnanin I, Porporato PE, Surico D, Perego B, Galli L, Patrignani C, Graziani A, Surico N,
JournalJ Biomed Biotechnol
PubMed ID20300586
Endometriosis, defined as the presence of endometrial tissue outside the uterus, is a common gynecological disease with poorly understood pathogenesis. MicroRNAs are members of a class of small noncoding RNA molecules that have a critical role in posttranscriptional regulation of gene expression by repression of target mRNAs translation. We assessed ... More
Evaluation of methodologies for microRNA biomarker detection by next generation sequencing.
AuthorsCoenen-Stass AML, Magen I, Brooks T, Ben-Dov IZ, Greensmith L, Hornstein E, Fratta P
JournalRNA Biol
PubMed ID30223713
'In recent years, microRNAs (miRNAs) in tissues and biofluids have emerged as a new class of promising biomarkers for numerous diseases. Blood-based biomarkers are particularly desirable since serum or plasma is easily accessible and can be sampled repeatedly. To comprehensively explore the biomarker potential of miRNAs, sensitive, accurate and cost-efficient ... More
Anti-Inflammatory Effects of 5a,8a-Epidioxycholest-6-en-3ß-ol, a Steroidal Endoperoxide Isolated from Aplysia depilans, Based on Bioguided Fractionation and NMR Analysis.
'Sea hares of Aplysia genus are recognized as a source of a diverse range of metabolites. 5a,8a-Endoperoxides belong to a group of oxidized sterols commonly found in marine organisms and display several bioactivities, including antimicrobial, anti-tumor, and immunomodulatory properties. Herein we report the isolation of 5a,8a-epidioxycholest-6-en-3ß-ol (EnP(5,8)) from Aplysia depilans ... More
RNA-Seq differential expression analysis: An extended review and a software tool.
AuthorsCosta-Silva J, Domingues D, Lopes FM
JournalPLoS One
PubMed ID29267363
'The correct identification of differentially expressed genes (DEGs) between specific conditions is a key in the understanding phenotypic variation. High-throughput transcriptome sequencing (RNA-Seq) has become the main option for these studies. Thus, the number of methods and softwares for differential expression analysis from RNA-Seq data also increased rapidly. However, there ... More
Transcriptomic study of Herpes simplex virus type-1 using full-length sequencing techniques.
AuthorsBoldogkoi Z, Szucs A, Balázs Z, Sharon D, Snyder M, Tombácz D
JournalSci Data
PubMed ID30480662
Herpes simplex virus type-1 (HSV-1) is a human pathogenic member of the Alphaherpesvirinae subfamily of herpesviruses. The HSV-1 genome is a large double-stranded DNA specifying about 85 protein coding genes. The latest surveys have demonstrated that the HSV-1 transcriptome is much more complex than it had been thought before. Here, ... More
Total RNA extraction from tissues for microRNA and target gene expression analysis: not all kits are created equal.
microRNAs (miRNAs) are short non-coding RNAs that fine-tune gene expression. The aberrant expression of miRNAs is associated with many diseases and they have both therapeutic and biomarker potential. However, our understanding of their usefulness is dependent on the tools we have to study them. Previous studies have identified the need ... More
Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments.
AuthorsTian L, Dong X, Freytag S, Lê Cao KA, Su S, JalalAbadi A, Amann-Zalcenstein D, Weber TS, Seidi A, Jabbari JS, Naik SH, Ritchie ME
JournalNat Methods
PubMed ID31133762
Single cell RNA-sequencing (scRNA-seq) technology has undergone rapid development in recent years, leading to an explosion in the number of tailored data analysis methods. However, the current lack of gold-standard benchmark datasets makes it difficult for researchers to systematically compare the performance of the many methods available. Here, we generated ... More
Growth rate and myofibroblast differentiation of desmoid fibroblast-like cells are modulated by TGF-ß signaling.
AuthorsEnzo MV, Cattelan P, Rastrelli M, Tosi A, Rossi CR, Hladnik U, Segat D
JournalHistochem Cell Biol
PubMed ID30173360
Desmoid-like fibromatosis (DF) is a rare myofibroblastic benign tumor, often associated with local and repeated injuries, spontaneous regression and stabilization of disease progression suggesting the involvement of altered Wnt/ß-catenin signaling activation and/or aberrant response of the DF cells to external environmental stimuli. The aim of this study was to investigate ... More
A Designed Small Molecule Inhibitor of a Non-Coding RNA Sensitizes HER2 Negative Cancers to Herceptin.
AuthorsCostales MG, Hoch DG, Abegg D, Childs-Disney JL, Velagapudi SP, Adibekian A, Disney MD
JournalJ Am Chem Soc
PubMed ID30726072
A small molecule (1) with overlapping affinity for two microRNA (miRNA) precursors was used to inform design of a dimeric compound (2) selective for one of the miRNAs. In particular, 2 selectively targets the microRNA(miR)-515 hairpin precursor to inhibit production of miR-515 that represses sphingosine kinase 1 (SK1), a key ... More
A novel long noncoding RNA FAF inhibits apoptosis via upregulating FGF9 through PI3K/AKT signaling pathway in ischemia-hypoxia cardiomyocytes.
AuthorsShi HJ, Wang MW, Sun JT, Wang H, Li YF, Chen BR, Fan Y, Wang SB, Wang ZM, Wang QM, Wang LS
JournalJ Cell Physiol
PubMed ID31093967
Long noncoding RNAs (lncRNAs) have been increasingly considered to play an important role in the pathological process of various cardiovascular diseases, which often bind to the proximal promoters of the protein-coding gene to regulate the protein expression. However, the functions and mechanisms of lncRNAs in cardiomyocytes have not been fully ... More
Benzoquinones from Cyperus spp. trigger IRE1a-independent and PERK-dependent ER stress in human stomach cancer cells and are novel proteasome inhibitors.
The roots and tubers of several species of the Cyperus genus are used in several parts of the world as foodstuffs and beverages. The genus is rich in several classes of quinones, however their biological properties have not been studied before. ... More
Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes.
AuthorsSberro H, Fremin BJ, Zlitni S, Edfors F, Greenfield N, Snyder MP, Pavlopoulos GA, Kyrpides NC, Bhatt AS
JournalCell
PubMed ID31402174
Small proteins are traditionally overlooked due to computational and experimental difficulties in detecting them. To systematically identify small proteins, we carried out a comparative genomics study on 1,773 human-associated metagenomes from four different body sites. We describe >4,000 conserved protein families, the majority of which are novel; ~30% of these ... More
Porcine Circovirus Type 2 Induces Single Immunoglobulin Interleukin-1 Related Receptor (SIGIRR) Downregulation to Promote Interleukin-1ß Upregulation in Porcine Alveolar Macrophage.
AuthorsYang S, Liu B, Yin S, Shang Y, Zhang X, Khan MUZ, Liu X, Cai J
JournalViruses
PubMed ID31684202
Multisystemic inflammation in pigs affected by porcine circovirus type 2 (PCV2) indicates the disordered expression of inflammatory cytokines. However, the PCV2-induced expression profile of inflammation cytokines and its regulating mechanism remain poorly understood. In this study, inflammatory cytokines and receptors in porcine alveolar macrophages (PAMs) after PCV2 infection were profiled ... More
Circulating RNA Transcriptome of Pregnant Women with TSH Just Above the Trimester-Specific Reference and its Correlation with the Hypertensive Phenotype.
AuthorsHirata AHL, Rocha LAJ, da Silva VA, de Almeida RJ, Bacigalupo LDS, Varela P, Martins L, Pesquero JB, Dellê H, Camacho CP
JournalSci Rep
PubMed ID32296081
During gestation, a woman's body undergoes physiological changes that alter thyroid function. Pregnant women with hypothyroidism may exhibit gestational complications, including hypertension and preeclampsia. We investigated differentially expressed genes (DEGs) in circulating RNAs from pregnant women with TSH levels just above the normal range to determine the impact of a ... More