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Gene Expression Research

11:34 EST 21st November 2018 | BioPortfolio

Increased expression of lncRNA SNHG12 predicts a poor prognosis of nasopharyngeal carcinoma and regulates cell proliferation and metastasis by modulating Notch signal pathway.

Small nucleolar RNA host gene 12 (SNHG12) has been shown to be a long noncoding RNA (lncRNA) that facilitates the progression of a number of malignancies. However, the expression pattern and biological function of SNHG12 in nasopharyngeal carcinoma (NPC) have not been investigated.

Transcriptional Regulation of the Huntingtin Gene.

Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by a CAG trinucleotide expansion in the HTT gene, which encodes for an abnormal polyglutamine tract in the huntingtin protein (HTT). This review examines the known mechanisms of HTT gene regulation. We discuss HTT expression patterns, features of the HTT promoter, regulatory regions of the HTT promoter with functi...

Co-expression of IL-15 enhances anti-neuroblastoma effectivity of a tyrosine hydroxylase-directed DNA vaccination in mice.

Long-term survival of high-risk neuroblastoma (NB) patients still remains under 50%. Here, we report the generation, in vitro characterization and anti-tumor effectivity of a new bicistronic xenogenic DNA vaccine encoding tyrosine hydroxylase (TH) that is highly expressed in NB tumors, and the immune stimulating cytokine interleukin 15 (IL-15) that induces cytotoxic but not regulatory T cells. The...

FOXO1 regulates uterine epithelial integrity and progesterone receptor expression critical for embryo implantation.

Successful embryo implantation requires a receptive endometrium. Poor uterine receptivity can account for implantation failure in women who experience recurrent pregnancy loss or multiple rounds of unsuccessful in vitro fertilization cycles. Here, we demonstrate that the transcription factor Forkhead Box O1 (FOXO1) is a critical regulator of endometrial receptivity in vivo. Uterine ablation of Fox...

Macrophage activation by IFN-γ triggers restriction of phagosomal copper from intracellular pathogens.

Copper toxicity and copper limitation can both be effective host defense mechanisms against pathogens. Tolerance of high copper by fungi makes toxicity as a defense mechanism largely ineffective against fungal pathogens. A forward genetic screen for Histoplasma capsulatum mutant yeasts unable to replicate within macrophages showed the Ctr3 copper transporter is required for intramacrophage prolife...

Genetic Neural Networks: An artificial neural network architecture for capturing gene expression relationships.

Gene expression prediction is one of the grand challenges in computational biology. The availability of transcriptomics data combined with recent advances in artificial neural networks provide an unprecedented opportunity to create predictive models of gene expression with far reaching applications.

Bioinformatics methodologies for coeliac disease and its comorbidities.

Coeliac disease (CD) is a complex, multifactorial pathology caused by different factors, such as nutrition, immunological response and genetic factors. Many autoimmune diseases are comorbidities for CD, and a comprehensive and integrated analysis with bioinformatics approaches can help in evaluating the interconnections among all the selected pathologies. We first performed a detailed survey of ge...

iCatch: a new strategy for capturing large DNA fragments using homing endonucleases.

Natural genetic materials contain many biosynthetic gene clusters encoding potentially valuable natural products, many of which can be used directly without codon optimization or other manipulations. With the development of synthetic biology, several DNA assembly standards have been proposed, conveniently facilitating the reuse of natural materials. Among these standards, the iBrick assembly stand...

DiPhiSeq: Robust comparison of expression levels on RNA-Seq data with large sample sizes.

In the analysis of RNA-Seq data, detecting differentially expressed (DE) genes has been a hot research area in recent years and many methods have been proposed. DE genes show different average expression levels in different sample groups, and thus can be important biological markers. While generally very successful, these methods need to be further tailored and improved for cancerous data, which o...

VIGS - empowering genetics in non-model organisms.

Virus-induced gene silencing (VIGS) is an RNA interference-based technology used to transiently knock-down target gene expression, utilizing modified plant viral genomes. VIGS can be adapted to many angiosperm species that cover large phylogenetic distances, allowing the analysis of gene functions in species recalcitrant to stable genetic transformation. With a vast amount of sequence information ...

The influence of Farmatan® and Flimabend® on the mucosal immunity of broiler chicken1.

The aim of the present study was to monitor selected parameters of mucosal immunity in jejunum and ileum (immunoglobulin A [IgA], mucin 2 [MUC-2], and pro-inflammatory cytokines) in commercial broiler farm chicken after treatment with flubendazole (Flimabend®) and natural extract from chestnut wood (Farmatan®). A total of 24 forty-day-old Kalimero-Super Master hybrid chickens were divided into 4...

Small molecule inhibition of dipeptidyl peptidase-4 enhances bone marrow progenitor cell function and angiogenesis in diabetic wounds.

In diabetes, stromal cell-derived factor-1 (SDF-1) expression and progenitor cell recruitment are reduced. Dipeptidyl peptidase-4 (DPP-4) inhibits SDF-1 expression and progenitor cell recruitment. Here we examined the impact of the DPP-4 inhibitor, MK0626, on progenitor cell kinetics in the context of wound healing. Wildtype (WT) murine fibroblasts cultured under high-glucose to reproduce a diabet...

Class A scavenger receptors mediate extracellular dsRNA sensing, leading to downstream antiviral gene expression in a novel American toad cell line, BufoTad.

Viral double-stranded (ds)RNA is a potent pathogen-associated molecular pattern (PAMP), capable of inducing a strong antiviral state within the cell, protecting the cell from virus infection. In mammals and fish, sensing extracellular dsRNA is mediated by cell-surface class A scavenger receptors (SR-As). Currently, very little is known about SR-A's in amphibians, including: sequence, expression pa...

Gene expression profiling of two epilepsy models reveals the ECM/integrin signaling pathway is involved in epiletogenesis.

The molecular mechanisms underlying the development of epilepsy, i.e., epileptogenesis, are due to altered expression of a series of genes. Global expression profiling of temporal lobe epilepsy is confounded by a number of factors, including the variability among animal species, animal models, and tissue sampling time-points. In this study, we pooled two microarray datasets of the most used piloca...

Clustered miR-2, miR-13a, miR-13b and miR-71 coordinately target Notch gene to regulate oogenesis of the migratory locust Locusta migratoria.

MicroRNAs (miRNAs), ∼22-nt small noncoding RNAs with a crucial role in various biological processes of organisms, are usually clustered in the genome. However, little is known about the miRNA clusters involved in insect reproduction. By small RNA sequencing and quantification followed by qRT-PCR, we found that the expression of invertebrate-specific miR-2/13/71 cluster including miR-2, miR-13a, ...

Cloning and effects of fasting on the brain expression levels of appetite-regulators and reproductive hormones in glass catfish (Kryptopterus vitreolus).

The regulation of feeding is a complex process that involves coordination between various signals. Feeding hormones can be described as orexigenic (stimulate food intake, e.g. orexin and neuropeptide Y - NPY) or anorexigenic (inhibit food intake, e.g. cocaine and amphetamine regulated transcript - CART). Reproduction and energy homeostasis are closely linked, as factors that affect appetite have a...

Independent association of whole blood miR-328 expression and polymorphism at 3'UTR of the PAX6 gene with myopia.

This study aimed to find associations between miR-328 expression in whole blood, polymorphism at 3'UTR of the PAX6 gene (paired box homeotic gene 6) and myopia.

Genome-wide identification and expression analysis of glycine-rich RNA-binding protein family in sweet potato wild relative Ipomoea trifida.

Glycine-rich RNA-binding proteins (GRPs) contain RNA recognition motif (RRM) and glycine-rich domains at the N- or C-terminus, respectively, and they participate in varied physiological and biochemical processes, as well as environmental stresses. Sweet potato from the genus Ipomoea is one of the most important crops. However, the role of the GRP gene family in Ipomoea plant species has not been r...

Identification of microRNAs in granulosa cells from patients with different levels of ovarian reserve function and the potential regulatory function of miR-23a in granulosa cell apoptosis.

This study aimed to determine the microRNA (miRNA) profiles in granulosa cells (GCs) from the follicular fluid (FF) of patients with varying levels of ovarian reserve function. We included 45 women undergoing in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI) treatment. After collecting GCs from each patient, total RNA was extracted from 12 samples. Using Illumina/deep-sequen...

Identification and expression analysis of a novel miRNA derived from ERV-E1 LTR in Equus caballus.

Horses (Equus caballus) have been domesticated and bred to enhance speed, strength, and agility. Members of the Equus caballus Endogenous Retrovirus (EqERV) family affect several of these abilities in horses. EqERV elements have been integrated in the horse genome during evolution and generate repeat elements such as long terminal repeats (LTRs). LTR sequences are involved in retrovirus replicatio...

Multiple transcription factors mediating the expressional regulation of myosin heavy chain gene involved in the indeterminate muscle growth of fish.

Torafugu myosin heavy chain gene, MYH, is specifically expressed in neonatal slow and fast muscle fibers, suggesting its functional role in indeterminate muscle growth in fish. However, the transcriptional regulatory mechanisms of MYH involved in indeterminate muscle growth in fish remained unknown. We previously isolated a 2100 bp 5'- flanking sequence of torafugu MYH that showed sufficient promo...

Genome-wide characterization of the cellulose synthase gene superfamily in Solanum lycopersicum.

The cellulose synthase gene superfamily, which includes the cellulose synthase (CesA) and cellulose synthase-like (Csl) gene families, plays a vital role in the biosynthesis of cellulose and hemicellulose in plants. However, these genes have not been extensively studied in tomato (Solanum lycopersicum), a model for Solanaceae plants and for fleshy fruit development. Here, we identified and systema...

A targeted next-generation gene panel reveals a novel heterozygous nonsense variant in TP63 gene in Arrhythmogenic Cardiomyopathy patients.

Arrhythmogenic Cardiomyopathy (ACM) is associated with arrhythmias and risk of sudden death. Mutations in genes encoding proteins of cardiac intercalated discs account for about 60% of ACM cases, but the remaining 40% is still genetically elusive.

Inhibition of Lithium Sensitive Orai1/ STIM1 Expression and Store Operated Ca2+ Entry in Chorea-Acanthocytosis Neurons by NF-κB Inhibitor Wogonin.

The neurodegenerative disease Chorea-Acanthocytosis (ChAc) is caused by loss-of-function-mutations of the chorein-encoding gene VPS13A. In ChAc neurons transcript levels and protein abundance of Ca2+ release activated channel moiety (CRAC) Orai1 as well as its regulator STIM1/2 are decreased, resulting in blunted store operated Ca2+-entry (SOCE) and enhanced suicidal cell death. SOCE is up-regulat...

The enhancer RNA lnc-SLC4A1-1 epigenetically regulates unexplained recurrent pregnancy loss (URPL) by activating CXCL8 and NF-kB pathway.

Enhancer RNAs (eRNAs) are a group of lncRNAs transcribed from enhancers, whose regulatory effects on gene expression are an emerging area of interest. However, the role of eRNAs in regulating trophoblast cells and unexplained recurrent pregnancy loss (URPL) remains elusive.

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