Diagenode

Cell Lysis

204 publications found.

Folic acid administration inhibits amyloid β-peptide accumulation in APP/PS1 transgenic mice.
Published: August, 2015

Abstract: Alzheimer's disease (AD) is associated with malnutrition, altered one-carbon metabolism and increased hippocampal amyloid-β peptide (Aβ) accumulation. Aberrant DNA methylation may be an epigenetic mechanism that underlies AD pathogenesis...
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GCDCA down-regulates gene expression by increasing Sp1 binding to the NOS-3 promoter in an oxidative stress dependent manner.
Published: July, 2015

Abstract: During the course of cholestatic liver diseases, the toxic effect of bile acids accumulation has been related to the decreased expression of endothelial nitric oxide synthase (NOS-3) and cellular oxidative stress increase. In the present study, we...
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The N-terminal Set-β Protein Isoform Induces Neuronal Death.
Published: May, 2015

Abstract: Set-β protein plays different roles in neurons, but the diversity of Set-β neuronal isoforms and their functions have not been characterized. The expression and subcellular localization of Set-β are altered in Alzheimer disease, cleavage of Set-β ...
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Control of brain patterning by Engrailed paracrine transfer: a new function of the Pbx interaction domain.
Published: May, 2015

Abstract: Homeoproteins of the Engrailed family are involved in the patterning of mesencephalic boundaries through a mechanism classically ascribed to their transcriptional functions. In light of recent reports on the paracrine activity of homeoproteins, in...
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The Novel Gene CRNDE Encodes a Nuclear Peptide (CRNDEP) Which Is Overexpressed in Highly Proliferating Tissues.
Published: May, 2015

Abstract: CRNDE, recently described as the lncRNA-coding gene, is overexpressed at RNA level in human malignancies. Its role in gametogenesis, cellular differentiation and pluripotency has been suggested as well. Herein, we aimed to verify our hypothesis th...
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Aerobic glycolysis tunes YAP/TAZ transcriptional activity.
Published: May, 2015

Abstract: Increased glucose metabolism and reprogramming toward aerobic glycolysis are a hallmark of cancer cells, meeting their metabolic needs for sustained cell proliferation. Metabolic reprogramming is usually considered as a downstream consequence of t...
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Antisense RNA Controls LRP1 Sense Transcript Expression through Interaction with a Chromatin-Associated Protein, HMGB2.
Published: May, 2015

Abstract: Long non-coding RNAs (lncRNAs), including natural antisense transcripts (NATs), are expressed more extensively than previously anticipated and have widespread roles in regulating gene expression. Nevertheless, the molecular mechanisms of action of...
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Widespread Proteome Remodeling and Aggregation in Aging C. elegans.
Published: May, 2015

Abstract: Aging has been associated with a progressive decline of proteostasis, but how this process affects proteome composition remains largely unexplored. Here, we profiled more than 5,000 proteins along the lifespan of the nematode C. elegans. We find t...
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Non-coding RNA Generated following Lariat Debranching Mediates Targeting of AID to DNA.
Published: May, 2015

Abstract: Transcription through immunoglobulin switch (S) regions is essential for class switch recombination (CSR), but no molecular function of the transcripts has been described. Likewise, recruitment of activation-induced cytidine deaminase (AID) to S r...
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Impact of oxidative stress defense on bacterial survival and morphological change in Campylobacter jejuni under aerobic conditions.
Published: April, 2015

Abstract: Campylobacter jejuni, a microaerophilic foodborne pathogen, inescapably faces high oxygen tension during its transmission to humans. Thus, the ability of C. jejuni to survive under oxygen-rich conditions may significantly impact C. jejuni viabilit...
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Zinc regulates a switch between primary and alternative S18 ribosomal proteins in Mycobacterium tuberculosis.
Published: April, 2015

Abstract: The Mycobacterium tuberculosis genome encodes five putative 'alternative' ribosomal proteins whose expression is repressed at high Zn(2+) concentration. Each alternative protein has a primary homologue that is predicted to bind Zn(2+) . We hypothe...
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Regulation of protein quality control by UBE4B and LSD1 through p53-mediated transcription.
Published: April, 2015

Abstract: Protein quality control is essential for clearing misfolded and aggregated proteins from the cell, and its failure is associated with many neurodegenerative disorders. Here, we identify two genes, ufd-2 and spr-5, that when inactivated, synergisti...
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STAT3 and HIF1alpha Signalling Drives Oncogenic Cellular Phenotypes in Malignant Peripheral Nerve Sheath Tumors (MPNSTs).
Published: April, 2015

Abstract: Therapeutic options are limited for Neurofibromatosis type 1 (NF1) associated malignant peripheral nerve sheath tumours(MPNSTs) and clinical trials using drug agents have so far been unsuccessful. This lack of clinical success is likely attributed...
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The Integrator complex controls the termination of transcription at diverse classes of gene targets.
Published: March, 2015

Abstract: Complexes containing INTS3 and either NABP1 or NABP2 were initially characterized in DNA damage responses, but their biochemical function remained unknown. Using affinity purifications and HIV Integration targeting-sequencing (HIT-Seq), we find th...
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Genipin as a novel chemical activator of EBV lytic cycle.
Published: February, 2015

Abstract: Epstein-Barr virus (EBV) is a ubiquitous gammaherpesvirus that causes acute infection and establishes life-long latency. EBV causes several human cancers, including Burkitt's lymphoma, nasopharyngeal and gastric carcinoma. Antiviral agents can be ...
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Pharmacologically relevant doses of valproate upregulate CD20 expression in three diffuse large B-cell lymphoma patients in vivo
Published: January, 2015

Abstract: Background Epigenetic code modifications by histone deacetylase inhibitors (HDACi) have been proposed as potential new therapies for lymphoid malignancies. Diffuse large B-cell lymphoma (DLBCL) is the most common type of aggressive lymphoma for ...
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Alternative splicing regulates the expression of G9A and SUV39H2 methyltransferases, and dramatically changes SUV39H2 functions.
Published: January, 2015

Abstract: Alternative splicing is the main source of proteome diversity. Here, we have investigated how alternative splicing affects the function of two human histone methyltransferases (HMTase): G9A and SUV39H2. We show that exon 10 in G9A and exon 3 in SU...
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Htt CAG repeat expansion confers pleiotropic gains of mutant huntingtin function in chromatin regulation
Published: January, 2015

Abstract: The CAG repeat expansion in the Huntington's disease gene HTT extends a polyglutamine tract in mutant huntingtin that enhances its ability to facilitate polycomb repressive complex 2 (PRC2). To gain insight into this dominant gain of function, we ...
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Phosphorylation of TET proteins is regulated via O-GlcNAcylation by the glycosyltransferase OGT.
Published: January, 2015

Abstract: TET proteins oxidize 5-methylcytosine (mC) to 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC) and 5-carboxylcytosine (caC) and thus provide a possible means for active DNA demethylation in mammals. Although their catalytic mechanism is well c...
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Retromer vesicles interact with RNA granules in haploid male germ cells.
Published: December, 2014

Abstract: Spermatozoa are produced during spermatogenesis as a result of mitotic proliferation, meiosis and cellular differentiation. Postmeiotic spermatids are exceptional cells given their haploid genome and remarkable sperm-specific structural transforma...
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Nuclear envelope remodelling during human spermiogenesis involves somatic B-type lamins and a spermatid-specific B3 lamin isoform.
Published: December, 2014

Abstract: The nuclear lamina (NL) is a filamentous protein meshwork, composed essentially of lamins, situated between the inner nuclear membrane and the chromatin. There is mounting evidence that the NL plays a role in spermatid differentiation during sperm...
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RAN-Binding Protein 9 is Involved in Alternative Splicing and is Critical for Male Germ Cell Development and Male Fertility.
Published: December, 2014

Abstract: As a member of the large Ran-binding protein family, Ran-binding protein 9 (RANBP9) has been suggested to play a critical role in diverse cellular functions in somatic cell lineages in vitro, and this is further supported by the neonatal lethality...
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Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization.
Published: December, 2014

Abstract: DNA glycosylases from the Fpg/Nei structural superfamily are base excision repair enzymes involved in the removal of a wide variety of mutagen and potentially lethal oxidized purines and pyrimidines. Although involved in genome stability, the rece...
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O-GlcNAcylation Prevents Aggregation of the Polycomb Group Repressor Polyhomeotic.
Published: November, 2014

Abstract: The glycosyltransferase Ogt adds O-linked N-Acetylglucosamine (O-GlcNAc) moieties to nuclear and cytosolic proteins. Drosophila embryos lacking Ogt protein arrest development with a remarkably specific Polycomb phenotype, arising from the failure ...
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Cell cycle-linked MeCP2 phosphorylation modulates adult neurogenesis involving the Notch signalling pathway.
Published: November, 2014

Abstract: Neuronal activity regulates the phosphorylation states at multiple sites on MeCP2 in postmitotic neurons. The precise control of the phosphorylation status of MeCP2 in neurons is critical for the normal development and function of the mammalian br...
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Neuropeptide Y promotes adipogenesis in chicken adipose cells in vitro.
Published: November, 2014

Abstract: Neuropeptide Y is an evolutionarily conserved neurotransmitter that stimulates food intake in higher vertebrate species and promotes adipogenesis in mammals. The objective of this study was to determine if NPY also enhances adipogenesis in birds, ...
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Global quantitative proteomics reveals novel factors in the ecdysone signaling pathway in Drosophila melanogaster.
Published: November, 2014

Abstract: The ecdysone signaling pathway plays a major role in various developmental transitions in insects. Recent advances in the understanding of ecdysone action have relied to a large extent on the application of molecular genetic tools in Drosophila. H...
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Protein arginine methyltransferase 5 is a key regulator of the MYCN oncoprotein in neuroblastoma cells.
Published: November, 2014

Abstract: Approximately half of poor prognosis neuroblastomas (NBs) are characterized by pathognomonic MYCN gene amplification and MYCN over-expression. Here we present data showing that short-interfering RNA mediated depletion of the protein arginine methy...
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Structure-guided mutational analysis reveals the functional requirements for product specificity of DOT1 enzymes.
Published: November, 2014

Abstract: DOT1 enzymes are conserved methyltransferases that catalyse the methylation of lysine 79 on histone H3 (H3K79). Most eukaryotes contain one DOT1 enzyme, whereas African trypanosomes have two homologues, DOT1A and DOT1B, with different enzymatic ac...
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Serine Deprivation Enhances Anti-neoplastic Activity of Biguanides.
Published: November, 2014

Abstract: Metformin, a biguanide widely used in the treatment of type II diabetes, clearly exhibits anti-neoplastic activity in experimental models and has been reported to reduce cancer incidence in diabetics. . There are ongoing clinical trials to evaluat...
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Ultrasensitive proteome analysis using paramagnetic bead technology.
Published: October, 2014

Abstract: In order to obtain a systems-level understanding of a complex biological system, detailed proteome information is essential. Despite great progress in proteomics technologies, thorough interrogation of the proteome from quantity-limited biological...
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Enantioselective regulation of lactate racemization by LarR in Lactobacillus plantarum.
Published: October, 2014

Abstract: Lactobacillus plantarum is a lactic acid bacterium that produces a racemic mixture of L- and D-lactate from sugar fermentation. The inter-conversion of lactate isomers is performed by a lactate racemase (Lar) that is transcriptionally controlled b...
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Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile.
Published: October, 2014

Abstract: The gastrointestinal tracts of mammals are colonized by hundreds of microbial species that contribute to health, including colonization resistance against intestinal pathogens. Many antibiotics destroy intestinal microbial communities and increase...
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In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9.
Published: October, 2014

Abstract: Probing gene function in the mammalian brain can be greatly assisted with methods to manipulate the genome of neurons in vivo. The clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated endonuclease (Cas)9 from Streptococc...
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Transforming Growth Factor β1 (TGF-β1) Enhances Expression of Profibrotic Genes through a Novel Signaling Cascade and MicroRNAs in Renal Mesangial Cells.
Published: October, 2014

Abstract: Increased expression of transforming growth factor-β1 (TGF-β1) in glomerular mesangial cells (MC) augments extracellular matrix accumulation and hypertrophy during the progression of diabetic nephropathy (DN), a debilitating renal complication of ...
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Inactivation of Phaeodactylum tricornutum urease gene using transcription activator-like effector nuclease-based targeted mutagenesis.
Published: October, 2014

Abstract: Diatoms are unicellular photosynthetic algae with promise for green production of fuels and other chemicals. Recent genome-editing techniques have greatly improved the potential of many eukaryotic genetic systems, including diatoms, to enable know...
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Cellular uptake behaviour, photothermal therapy performance, and cytotoxicity of gold nanorods with various coatings.
Published: October, 2014

Abstract: With the development of Au nanorods for a number of biomedical applications, understanding their cellular responses has become increasingly important. In this study, we systematically evaluated the cellular uptake behaviour and cytotoxicity of Au ...
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PaperClip: rapid multi-part DNA assembly from existing libraries.
Published: September, 2014

Abstract: Assembly of DNA 'parts' to create larger constructs is an essential enabling technique for bioengineering and synthetic biology. Here we describe a simple method, PaperClip, which allows flexible assembly of multiple DNA parts from currently exist...
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Somatic mutations in DROSHA and DICER1 impair microRNA biogenesis through distinct mechanisms in Wilms tumours.
Published: September, 2014

Abstract: Wilms tumour is the most common childhood kidney cancer. Here we report the whole-exome sequencing of 44 Wilms tumours, identifying missense mutations in the microRNA (miRNA)-processing enzymes DROSHA and DICER1, and novel mutations in MYCN, SMARC...
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Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors.
Published: September, 2014

Abstract: Cell type-specific master transcription factors (TFs) play vital roles in defining cell identity and function. However, the roles ubiquitous factors play in the specification of cell identity remain underappreciated. Here we show that the ubiquito...
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Pregnane X receptor activation and silencing promote steatosis of human hepatic cells by distinct lipogenic mechanisms.
Published: September, 2014

Abstract: In addition to its well-characterized role in the regulation of drug metabolism and transport by xenobiotics, pregnane X receptor (PXR) critically impacts on lipid homeostasis. In mice, both ligand-dependent activation and knockout of PXR were pre...
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A dynamic CTCF chromatin binding landscape promotes DNA hydroxymethylation and transcriptional induction of adipocyte differentiation.
Published: September, 2014

Abstract: CCCTC-binding factor (CTCF) is a ubiquitously expressed multifunctional transcription factor characterized by chromatin binding patterns often described as largely invariant. In this context, how CTCF chromatin recruitment and functionalities are ...
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Transgenic analysis of the Leishmania MAP kinase MPK10 reveals an auto-inhibitory mechanism crucial for stage-regulated activity and parasite viability.
Published: September, 2014

Abstract: Protozoan pathogens of the genus Leishmania have evolved unique signaling mechanisms that can sense changes in the host environment and trigger adaptive stage differentiation essential for host cell infection. The signaling mechanisms underlying p...
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Histone methylation has distinct dynamics from histone acetylation in cell cycle re-entry from quiescence.
Published: August, 2014

Abstract: Cell growth is attuned to nutrient availability to sustain homeostatic biosynthetic processes. In unfavorable environments, cells enter a non-proliferative state termed quiescence, but rapidly return to the cell cycle once conditions support energ...
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Dynamics of carbon concentrating mechanism induction and protein re-localisation during the dark to light transition in synchronised Chlamydomonas.
Published: August, 2014

Abstract: In the model green alga Chlamydomonas reinhardtii, a carbon concentrating mechanism (CCM) is induced under low CO2 in the light and comprises: active inorganic carbon transport components, carbonic anhydrases and aggregation of Rubisco in the chlo...
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Identification and Validation of Genetic Variants that Influence Transcription Factor and Cell Signaling Protein Levels.
Published: August, 2014

Abstract: Many genetic variants associated with human disease have been found to be associated with alterations in mRNA expression. Although it is commonly assumed that mRNA expression changes will lead to consequent changes in protein levels, methodologica...
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Lipid peroxidation product 4-hydroxy-2-nonenal modulates base excision repair in human cells.
Published: July, 2014

Abstract: Oxidative-stress-driven lipid peroxidation (LPO) is involved in the pathogenesis of several human diseases, including cancer. LPO products react with cellular proteins changing their properties, and with DNA bases to form mutagenic etheno-DNA addu...
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Screening and identification of small molecule inhibitors of ErbB2-induced invasion
Published: July, 2014

Abstract: ERBB2 amplification and overexpression are strongly associated with invasive cancer with high recurrence and poor prognosis. Enhanced ErbB2 signaling induces cysteine cathepsin B and L expression leading to their higher proteolytic activity (zFRas...
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Synergistic apoptosis in head and neck squamous cell carcinoma cells by co-inhibition of insulin-like growth factor-1 receptor signaling and compensatory signaling pathways.
Published: July, 2014

Abstract: Background: In head and neck squamous cell carcinoma (HNSCC), resistance to single agent targeted therapy may be overcome by co-targeting of compensatory signaling pathways. Methods: A targeted drug screen with 120 combinations was used on 9 HNSCC...
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The telomerase inhibitor Gno1p/PINX1 activates the helicase Prp43p during ribosome biogenesis.
Published: July, 2014

Abstract: We provide evidence that a central player in ribosome synthesis, the ribonucleic acid helicase Prp43p, can be activated by yeast Gno1p and its human ortholog, the telomerase inhibitor PINX1. Gno1p and PINX1 expressed in yeast interact with Prp43p ...
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The Leishmania donovani chaperone cyclophilin 40 is essential for intracellular infection independent of its stage-specific phosphorylation status.
Published: July, 2014

Abstract: During its life cycle, the protozoan pathogen Leishmania donovani is exposed to contrasting environments inside insect vector and vertebrate host, to which the parasite must adapt for extra- and intracellular survival. Combining null mutant analys...
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Functional Conservation of the Pre-Sensor One Beta-Finger Hairpin (PS1-hp) Structures in Mini-Chromosome Maintenance Proteins of Saccharomyces cerevisiae and Archaea.
Published: July, 2014

Abstract: Mini-chromosome maintenance (MCM) proteins form complexes that are required for DNA replication and are highly conserved throughout evolution. The replicative helicase of eukaryotic organisms is composed of the six paralogs MCM2-7, which form a he...
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3β,5α,6β-Cholestanetriol and 25-hydroxycholesterol accumulate in ATP-binding cassette transporter G1 (ABCG1)-deficiency.
Published: July, 2014

Abstract: OBJECTIVE: Oxysterols are oxidized derivatives of sterols that have cytotoxic effects and are potent regulators of diverse cellular functions. Efficient oxysterol removal by the sub-family G member 1 of the ATP-binding cassette transporters (ABCG1...
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Proteomics-Based Identification of Differentially Abundant Proteins from Human Keratinocytes Exposed to Arsenic Trioxide
Published: June, 2014

Abstract: Introduction: Arsenic i s a widely distributed environmental toxicant that can cause multi-tissue pathologies. Proteomic assays allow for the identification of biological processes modulated by arsenic in diverse tissue types. Method: The altered ...
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Otx2 and Oct4 Drive Early Enhancer Activation during Embryonic Stem Cell Transition from Naive Pluripotency.
Published: June, 2014

Abstract: Embryonic stem cells (ESCs) are unique in that they have the capacity to differentiate into all of the cell types in the body. We know a lot about the complex transcriptional control circuits that maintain the naive pluripotent state under self-re...
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Listeria monocytogenes induces IFNβ expression through an IFI16-, cGAS- and STING-dependent pathway.
Published: June, 2014

Abstract: Listeria monocytogenes is a gram-positive facultative intracellular bacterium, which replicates in the cytoplasm of myeloid cells. Interferon β (IFNβ) has been reported to play an important role in the mechanisms underlying Listeria disease. Altho...
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RPLP1, a Crucial Ribosomal Protein for Embryonic Development of the Nervous System.
Published: June, 2014

Abstract: Ribosomal proteins are pivotal to development and tissue homeostasis. RP Large P1 (Rplp1) overexpression is associated with tumorigenesis. However, the physiological function of Rplp1 in mammalian development remains unknown. In this study, we dis...
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ZNF143 is regulated through alternative 3'UTR isoforms.
Published: June, 2014

Abstract: ZNF143 is a ubiquitously expressed transcription factor conserved in all vertebrates, regulating genes involved in primary metabolism and cell growth. It is therefore crucial to tightly maintain the adequate level of this factor in the cell. Altho...
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Cell cycle transition from S-phase to G1 in Caulobacter is mediated by ancestral virulence regulators.
Published: June, 2014

Abstract: Zinc-finger domain transcriptional regulators regulate a myriad of functions in eukaryotes. Interestingly, ancestral versions (MucR) from Alpha-proteobacteria control bacterial virulence/symbiosis. Whether virulence regulators can also control cel...
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Protein Phosphatase 2A (PP2A) Regulates Low Density Lipoprotein Uptake through Regulating Sterol Response Element-binding Protein-2 (SREBP-2) DNA Binding.
Published: June, 2014

Abstract: LDL-cholesterol (LDL-C) uptake by Ldlr is regulated at the transcriptional level by the cleavage-dependent activation of membrane-associated sterol response element-binding protein (SREBP-2). Activated SREBP-2 translocates to the nucleus, where it...
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A Histone Deacetylase Complex Mediates Biofilm Dispersal and Drug Resistance in Candida albicans.
Published: June, 2014

Abstract: UNLABELLED: Biofilms are resilient, surface-associated communities of cells with specialized properties (e.g., resistance to drugs and mechanical forces) that are distinct from those of suspension (planktonic) cultures. Biofilm formation by the op...
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PARG is dispensable for recovery from transient replicative stress but required to prevent detrimental accumulation of poly(ADP-ribose) upon prolonged replicative stress.
Published: June, 2014

Abstract: Poly(ADP-ribosyl)ation is involved in numerous bio-logical processes including DNA repair, transcription and cell death. Cellular levels of poly(ADP-ribose) (PAR) are regulated by PAR polymerases (PARPs) and the degrading enzyme PAR glycohydrolase...
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CETP inhibitors downregulate hepatic LDL receptor and PCSK9 expression in vitro and in vivo through a SREBP2 dependent mechanism.
Published: June, 2014

Abstract: BACKGROUND: CETP inhibitors block the transfer of cholesteryl ester from HDL-C to VLDL-C and LDL-C, thereby raising HDL-C and lowering LDL-C. In this study, we explored the effect of CETP inhibitors on hepatic LDL receptor (LDLR) and PCSK9 express...
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Regulating Set-β's Subcellular Localization Toggles Its Function between Inhibiting and Promoting Axon Growth and Regeneration.
Published: May, 2014

Abstract: The failure of the CNS neurons to regenerate axons after injury or stroke is a major clinical problem. Transcriptional regulators like Set-β are well positioned to regulate intrinsic axon regeneration capacity, which declines developmentally in ma...
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Expanding the chemical diversity of natural esters by engineering a polyketide-derived pathway into Escherichia coli.
Published: May, 2014

Abstract: Microbial fatty acid (FA)-derived molecules have emerged as promising alternatives to petroleum-based chemicals for reducing dependence on fossil hydrocarbons. However, native FA biosynthetic pathways often yield limited structural diversity, and ...
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The plant metacaspase AtMC1 in pathogen-triggered programmed cell death and aging: functional linkage with autophagy.
Published: May, 2014

Abstract: Autophagy is a major nutrient recycling mechanism in plants. However, its functional connection with programmed cell death (PCD) is a topic of active debate and remains not well understood. Our previous studies established the plant metacaspase At...
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Unraveling vitamin B12-responsive gene regulation in algae.
Published: May, 2014

Abstract: Photosynthetic microalgae play a vital role in primary productivity and biogeochemical cycling in both marine and freshwater systems across the globe. However, the growth of these cosmopolitan organisms depends on the bioavailability of nutrients ...
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The ETS family member GABPα modulates androgen receptor signalling and mediates an aggressive phenotype in prostate cancer.
Published: April, 2014

Abstract: In prostate cancer (PC), the androgen receptor (AR) is a key transcription factor at all disease stages, including the advanced stage of castrate-resistant prostate cancer (CRPC). In the present study, we show that GABPα, an ETS factor that is up-...
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Targeting vertebrate intron-encoded box C/D 2'-O-methylation guide RNAs into the Cajal body.
Published: April, 2014

Abstract: Post-transcriptional pseudouridylation and 2'-O-methylation of splicesomal small nuclear ribonucleic acids (snRNAs) is mediated by box H/ACA and box C/D small Cajal body (CB)-specific ribonucleoproteins (scaRNPs), respectively. The WD-repeat prote...
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Protein quantitative trait Loci identify novel candidates modulating cellular response to chemotherapy.
Published: April, 2014

Abstract: Annotating and interpreting the results of genome-wide association studies (GWAS) remains challenging. Assigning function to genetic variants as expression quantitative trait loci is an expanding and useful approach, but focuses exclusively on mRN...
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The antineoplastic effect of carnosine is accompanied by induction of PDK4 and can be mimicked by L-histidine.
Published: April, 2014

Abstract: Carnosine (β-alanyl-L-histidine) is a naturally occurring dipeptide that shows antineoplastic effects in cell culture as well as in animal experiments. Since its mode of action and the targets at the molecular level have not yet been elucidated, w...
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Identification of protein partners in mycobacteria using a single-step affinity purification method.
Published: March, 2014

Abstract: Tuberculosis is a leading cause of death in developing countries. Efforts are being made to both prevent its spread and improve curability rates. Understanding the biology of the bacteria causing the disease, Mycobacterium tuberculosis (M. tubercu...
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PI3K-p110-alpha-subtype signalling mediates survival, proliferation and neurogenesis of cortical progenitor cells via activation of mTORC2.
Published: March, 2014

Abstract: Development of the cerebral cortex is controlled by growth factors among which transforming growth factor beta (TGFβ) and insulin-like growth factor 1 (IGF1) have a central role. The TGFβ- and IGF1-pathways cross-talk and share signalling molecule...
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Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells.
Published: March, 2014

Abstract: Mass spectrometry (MS)-based proteomics typically employs multistep sample-preparation workflows that are subject to sample contamination and loss. We report an in-StageTip method for performing sample processing, from cell lysis through elution o...
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Characterization of two different Asf1 histone chaperones with distinct cellular localizations and functions in Trypanosoma brucei.
Published: March, 2014

Abstract: The anti-silencing function protein 1 (Asf1) is a chaperone that forms a complex with histones H3 and H4 facilitating dimer deposition and removal from chromatin. Most eukaryotes possess two different Asf1 chaperones but their specific functions a...
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CDK phosphorylation of SLD-2 is required for replication initiation and germline development in C. elegans.
Published: February, 2014

Abstract: Cyclin-dependent kinase (CDK) plays a vital role in proliferation control across eukaryotes. Despite this, how CDK mediates cell cycle and developmental transitions in metazoa is poorly understood. In this paper, we identify orthologues of Sld2, a...
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DSSylation, a novel protein modification targets proteins induced by oxidative stress, and facilitates their degradation in cells.
Published: February, 2014

Abstract: Timely removal of oxidatively damaged proteins is critical for cells exposed to oxidative stresses; however, cellular mechanism for clearing oxidized proteins is not clear. Our study reveals a novel type of protein modification that may play a rol...
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An Easy, Convenient Cell and Tissue Extraction Protocol for Nuclear Magnetic Resonance Metabolomics.
Published: January, 2014

Abstract: INTRODUCTION: As a complement to the classic metabolomics biofluid studies, the visualisation of the metabolites contained in cells or tissues could be a very powerful tool to understand how the local metabolism and biochemical pathways could be a...
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Analyzing the functions and structure of the human lipodystrophy protein seipin.
Published: January, 2014

Abstract: Disruption of the gene BSCL2, which encodes the protein seipin, causes severe generalized lipodystrophy in humans with a near complete absence of adipose tissue. Moreover, cell culture studies have demonstrated that seipin plays a critical cell-au...
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Prmt7 is dispensable in tissue culture models for adipogenic differentiation
Published: December, 2013

Abstract: Protein arginine methylation is a common posttranslational modification that has been implicated in numerous biological processes including gene expression. The mammalian genome encodes nine protein arginine methyltransferases (Prmts) that catalyz...
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ZRF1 controls the retinoic acid pathway and regulates leukemogenic potential in acute myeloid leukemia.
Published: December, 2013

Abstract: Acute myeloid leukemia (AML) is frequently linked to epigenetic abnormalities and deregulation of gene transcription, which lead to aberrant cell proliferation and accumulation of undifferentiated precursors. ZRF1, a recently characterized epigene...
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BORIS/CTCFL is an RNA-binding protein that associates with polysomes.
Published: November, 2013

Abstract: BACKGROUND: BORIS (CTCFL), a paralogue of the multifunctional and ubiquitously expressed transcription factor CTCF, is best known for its role in transcriptional regulation. In the nucleus, BORIS is particularly enriched in the nucleolus, a crucia...
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Transcriptome surveillance by selective termination of noncoding RNA synthesis.
Published: November, 2013

Abstract: Pervasive transcription of eukaryotic genomes stems to a large extent from bidirectional promoters that synthesize mRNA and divergent noncoding RNA (ncRNA). Here, we show that ncRNA transcription in the yeast S. cerevisiae is globally restricted b...
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Adenovirus precursor pVII protein stability is regulated by its propeptide sequence.
Published: November, 2013

Abstract: Adenovirus encodes for the pVII protein, which interacts and modulates virus DNA structure in the infected cells. The pVII protein is synthesized as the precursor protein and undergoes proteolytic processing by viral proteinase Avp, leading to rel...
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Mouse BAZ1A (ACF1) is dispensable for double-strand break repair but is essential for averting improper gene expression during spermatogenesis.
Published: November, 2013

Abstract: ATP-dependent chromatin remodelers control DNA access for transcription, recombination, and other processes. Acf1 (also known as BAZ1A in mammals) is a defining subunit of the conserved ISWI-family chromatin remodelers ACF and CHRAC, first purifie...
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The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana.
Published: October, 2013

Abstract: How alternative splicing (AS) is regulated in plants has not yet been elucidated. Previously, we have shown that the nuclear cap-binding protein complex (AtCBC) is involved in AS in Arabidopsis thaliana. Here we show that both subunits of AtCBC (A...
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Sequestration by IFIT1 impairs translation of 2'O-unmethylated capped RNA.
Published: October, 2013

Abstract: Viruses that generate capped RNA lacking 2'O methylation on the first ribose are severely affected by the antiviral activity of Type I interferons. We used proteome-wide affinity purification coupled to mass spectrometry to identify human and mous...
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Verification of Intraovum Transmission of a Microsporidium of Vertebrates: Pseudoloma neurophilia Infecting the Zebrafish, Danio rerio.
Published: September, 2013

Abstract: Direct transmission from parents to offspring, referred to as vertical transmission, occurs within essentially all major groups of pathogens. Several microsporidia (Phylum Microsporidia) that infect arthropods employ this mode of transmission, and...
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A new strategy for gene targeting and functional proteomics using the DT40 cell line.
Published: September, 2013

Abstract: DT40 cells derived from chicken B lymphocytes exhibit exceptionally high homologous recombination rates. Therefore, they can be used as a convenient tool and model for gene targeting experiments. However, lack of efficient cloning strategies, prot...
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Mutant IDH1 promotes leukemogenesis in vivo and can be specifically targeted in human AML.
Published: August, 2013

Abstract: Mutations in the metabolic enzymes isocitrate dehydrogenase 1 (IDH1) and 2 (IDH2) are frequently found in glioma, acute myeloid leukemia (AML), melanoma, thyroid cancer and chondrosarcoma patients. Mutant IDH produces 2-hydroxyglutarate (2HG), whi...
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Systematic Identification of Proteins Binding to Chromatin-Embedded Ubiquitylated H2B Reveals Recruitment of SWI/SNF to Regulate Transcription.
Published: August, 2013

Abstract: Chromatin posttranslational modifications (PTMs), including monoubiquitylation of histone H2B on lysine 120 (H2Bub1), play a major role in regulating genome functions. To elucidate the molecular mechanisms of H2Bub1 activity, a chromatin template ...
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The 26S proteasome drives trinucleotide repeat expansions.
Published: July, 2013

Abstract: Trinucleotide repeat (TNR) expansion is the causative mutation for at least 17 inherited neurological diseases. An important question in the field is which proteins drive the expansion process. This study reports that the multi-functional protein ...
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Stepwise activation of the ATR signaling pathway upon increasing replication stress impacts fragile site integrity.
Published: July, 2013

Abstract: Breaks at common fragile sites (CFS) are a recognized source of genome instability in pre-neoplastic lesions, but how such checkpoint-proficient cells escape surveillance and continue cycling is unknown. Here we show, in lymphocytes and fibroblast...
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Stalled RNAP-II molecules bound to non-coding rDNA spacers are required for normal nucleolus architecture.
Published: July, 2013

Abstract: The correct distribution of nuclear domains is critical for the maintenance of normal cellular processes such as transcription and replication, which are regulated depending on their location and surroundings. The most well-characterized nuclear d...
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Epigenetic regulation of microRNA expression in renal cell carcinoma.
Published: June, 2013

Abstract: The underlying mechanisms of microRNA deregulation in cancer cells include epigenetic modifications, which play a crucial role in carcinogenesis. We demonstrate that numerous microRNAs are induced in renal cell carcinoma cell lines after treatment...
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Myc binds the pluripotency factor Utf1 through the basic-helix-loop-helix leucine zipper domain.
Published: June, 2013

Abstract: In order to elucidate the function of Myc in the maintenance of pluripotency and self-renewal in mouse embryonic stem cells (mESCs), we screened for novel ESC-specific interactors of Myc by mass spectrometry. Undifferentiated embryonic cell transc...
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The histone deacetylase inhibitor SAHA acts in synergism with fenretinide and doxorubicin to control growth of rhabdoid tumor cells.
Published: June, 2013

Abstract: BACKGROUND: Rhabdoid tumors are highly aggressive malignancies affecting infants and very young children. In many instances these tumors are resistant to conventional type chemotherapy necessitating alternative approaches. METHODS: Proliferation a...
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Choroid-plexus-derived Otx2 homeoprotein constrains adult cortical plasticity.
Published: June, 2013

Abstract: Brain plasticity is often restricted to critical periods in early life. Here, we show that a key regulator of this process in the visual cortex, Otx2 homeoprotein, is synthesized and secreted globally from the choroid plexus. Consequently, Otx2 is...
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N-linked glycosylation supports cross-talk between receptor tyrosine kinases and androgen receptor.
Published: May, 2013

Abstract: Prostate cancer is the second most common cause of cancer-associated deaths in men and signalling via a transcription factor called androgen receptor (AR) is an important driver of the disease. Androgen treatment is known to affect the expression ...
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Use of red autofluorescence for monitoring prodiginine biosynthesis.
Published: May, 2013

Abstract: Prodigiosin-like pigments or prodiginines (PdGs) are promising drugs owing to their reported antitumor, antibiotic, and immunosuppressive activities. These natural compounds are produced by several bacteria, including Streptomyces coelicolor and S...
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The complete targeted profile of the organic acid intermediates of the citric acid cycle using a single stable isotope dilution analysis, sodium borodeuteride reduction and selected ion monitoring GC/MS
Published: April, 2013

Abstract: The quantitative profiling of the organic acid intermediates of the citric acid cycle (CAC) presents a challenge due to the lack of commercially available internal standards for all of the organic acid intermediates. We developed an analytical met...
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Multiple mechanisms of action of pyridoxine in primary hyperoxaluria type 1.
Published: April, 2013

Abstract: Primary hyperoxaluria type 1 (PH1) is a rare hereditary calcium oxalate kidney stone disease caused by a deficiency of the liver-specific pyridoxal-phosphate-dependent peroxisomal enzyme alanine:glyoxylate aminotransferase (AGT). About one third o...
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Retinoic acid represses invasion and stem cell phenotype by induction of the metastasis suppressors RARRES1 and LXN.
Published: April, 2013

Abstract: The mouse haematopoietic stem cell (SC) regulator Latexin (LXN) is the only known homologue of the retinoic acid receptor responder 1 (RARRES1) gene. Both genes lie adjacent on chromosome 3 and differ mostly by the presence of a transmembrane doma...
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CPEB1 coordinates alternative 3'-UTR formation with translational regulation.
Published: March, 2013

Abstract: More than half of mammalian genes generate multiple messenger RNA isoforms that differ in their 3' untranslated regions (3' UTRs) and therefore in regulatory sequences, often associated with cell proliferation and cancer; however, the mechanisms c...
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Endogenous purification reveals GREB1 as a key estrogen receptor regulatory factor.
Published: February, 2013

Abstract: Estrogen receptor-α (ER) is the driving transcription factor in most breast cancers, and its associated proteins can influence drug response, but direct methods for identifying interacting proteins have been limited. We purified endogenous ER usin...
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Mechanism of competence activation by the ComRS signaling system in streptococci.
Published: January, 2013

Abstract: In many streptococci, competence for natural DNA transformation is regulated by the Rgg-type regulator ComR and the pheromone ComS, which is sensed intracellularly. We compared the ComRS systems of four model streptococcal species using in vitro a...
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Caspase-dependent cleavage of the mono-ADP-ribosyltransferase ARTD10 interferes with its pro-apoptotic function.
Published: January, 2013

Abstract: ADP-ribosylation is a posttranslational modification regulating various physiological processes, including DNA damage repair, gene transcription, and signal transduction. Intracellular ADP-ribosyltransferases (ARTDs or PARPs) modify their substrat...
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Comprehensive histone phosphorylation analysis and identification of pf14-3-3 protein as a histone h3 phosphorylation reader in malaria parasites.
Published: January, 2013

Abstract: The important role of histone posttranslational modifications, particularly methylation and acetylation, in Plasmodium falciparum gene regulation has been established. However, the role of histone phosphorylation remains understudied. Here, we inv...
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AMPK Is a Negative Regulator of the Warburg Effect and Suppresses Tumor Growth In Vivo.
Published: December, 2012

Abstract: AMPK is a metabolic sensor that helps maintain cellular energy homeostasis. Despite evidence linking AMPK with tumor suppressor functions, the role of AMPK in tumorigenesis and tumor metabolism is unknown. Here we show that AMPK negatively regulat...
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The Potential for Isocitrate Dehydrogenase Mutations to Produce 2-Hydroxyglutarate Depends on Allele Specificity and Subcellular Compartmentalization.
Published: December, 2012

Abstract: Monoallelic point mutations in cytosolic isocitrate dehydrogenase 1 (IDH1) and its mitochondrial homolog IDH2 can lead to elevated levels of 2-hydroxyglutarate (2HG) in multiple cancers. Here we report that cellular 2HG production from cytosolic I...
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A Genome-Wide RNAi Screen Reveals MAP Kinase Phosphatases as Key ERK Pathway Regulators during Embryonic Stem Cell Differentiation.
Published: December, 2012

Abstract: Embryonic stem cells and induced pluripotent stem cells represent potentially important therapeutic agents in regenerative medicine. Complex interlinked transcriptional and signaling networks control the fate of these cells towards maintenance of ...
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Control of somatic tissue differentiation by the long non-coding RNA TINCR.
Published: December, 2012

Abstract: Several of the thousands of human long non-coding RNAs (lncRNAs) have been functionally characterized; however, potential roles for lncRNAs in somatic tissue differentiation remain poorly understood. Here we show that a 3.7-kilobase lncRNA, termin...
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Bone morphogenetic protein-7 regulates Snail signaling in carbon tetrachloride-induced fibrosis in the rat liver.
Published: December, 2012

Abstract: The aim of this study was to explore the molecular mechanism of the bone morphogenetic protein-7 (BMP-7) downregulation of Snail-mediated E-cadherin repression and mesenchymal-epithelial transition (MET) induction, since little is presently known ...
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Ubiquitin-dependent regulation of phospho-AKT dynamics by the ubiquitin E3 ligase, NEDD4-1, in the IGF-1 response.
Published: November, 2012

Abstract: AKT is a critical effector kinase downstream of the PI3K pathway that regulates a plethora of cellular processes including cell growth, death, differentiation and migration. Mechanisms underlying activated phospho-AKT (pAKT) translocation to its a...
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Dual Role of Dextran Sulfate 5000 Da as Anti-Apoptotic and Pro-Autophagy Agent.
Published: November, 2012

Abstract: Dextran sulfate 5,000 Da (DS), a sulfated polysaccharide, has been used in recombinant mammalian cell cultures to prevent cell aggregation, thereby increasing cell viability. Previous studies using Chinese hamster ovary (CHO) suspension cultures h...
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BTB-ZF factors recruit the E3 ligase cullin 3 to regulate lymphoid effector programs.
Published: November, 2012

Abstract: The differentiation of several T- and B-cell effector programs in the immune system is directed by signature transcription factors that induce rapid epigenetic remodelling. Here we report that promyelocytic leukaemia zinc finger (PLZF), the BTB-zi...
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Alterations in Cellular Energy Metabolism Associated with the Antiproliferative Effects of the ATM Inhibitor KU-55933 and with Metformin.
Published: November, 2012

Abstract: KU-55933 is a specific inhibitor of the kinase activity of the protein encoded by Ataxia telangiectasia mutated (ATM), an important tumor suppressor gene with key roles in DNA repair. Unexpectedly for an inhibitor of a tumor suppressor gene, KU-55...
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Systematic identification of functional residues in mammalian histone H2AX.
Published: October, 2012

Abstract: The histone variant H2AX is a principal component of chromatin involved in the detection, signaling and repair of DNA double-strand breaks (DSBs). H2AX is thought to operate primarily through its C-terminal S139 phosphorylation, which mediates the...
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The H3K27 Demethylase JMJD3 Is Required for Maintenance of the Embryonic Respiratory Neuronal Network, Neonatal Breathing, and Survival.
Published: October, 2012

Abstract: JMJD3 (KDM6B) antagonizes Polycomb silencing by demethylating lysine 27 on histone H3. The interplay of methyltransferases and demethylases at this residue is thought to underlie critical cell fate transitions, and the dynamics of H3K27me3 during ...
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Periodontitis in established rheumatoid arthritis patients: a cross-sectional clinical, microbiological and serological study.
Published: October, 2012

Abstract: ABSTRACT: INTRODUCTION: The association between rheumatoid arthritis (RA) and periodontitis is suggested to be linked to the periodontal pathogen Porphyromonas gingivalis. Colonization of P. gingivalis in the oral cavity of RA patients has been sc...
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A Quantitative Proteomic Workflow for Characterization of Frozen Clinical Biopsies: Laser Capture Microdissection Coupled with Label-Free Mass Spectrometry
Published: September, 2012

Abstract: This paper describes a simple, highly efficient and robust proteomic workflow for routine liquid-chromatography tandem mass spectrometry analysis of Laser Microdissection Pressure Catapulting (LMPC) isolates. Highly efficient protein recovery was ...
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PML promotes MHC class II gene expression by stabilizing the class II transactivator.
Published: September, 2012

Abstract: Promyelocytic leukemia (PML) nuclear bodies selectively associate with transcriptionally active genomic regions, including the gene-rich major histocompatibility (MHC) locus. In this paper, we have explored potential links between PML and interfer...
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Salinomycin Induces Autophagy in Colon and Breast Cancer Cells with Concomitant Generation of Reactive Oxygen Species
Published: September, 2012

Abstract: Background Salinomycin is a polyether ionophore antibiotic that has recently been shown to induce cell death in human cancer cells displaying multiple mechanisms of drug resistance. The underlying mechanisms leading to cell death after salinomyci...
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PARP activation regulates the RNA-binding protein NONO in the DNA damage response to DNA double-strand breaks.
Published: August, 2012

Abstract: After the generation of DNA double-strand breaks (DSBs), poly(ADP-ribose) polymerase-1 (PARP-1) is one of the first proteins to be recruited and activated through its binding to the free DNA ends. Upon activation, PARP-1 uses NAD(+) to generate la...
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Prdm3 and Prdm16 are H3K9me1 Methyltransferases Required for Mammalian Heterochromatin Integrity.
Published: August, 2012

Abstract: Heterochromatin serves important functions, protecting genome integrity and stabilizing gene expression programs. Although the Suv39h methyltransferases (KMTs) are known to ensure pericentric H3K9me3 methylation, the mechanisms that initiate and m...
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Serine 192 in the tiny RS repeat of the adenoviral L4-33K splicing enhancer protein is essential for function and reorganization of the protein to the periphery of viral replication centers.
Published: August, 2012

Abstract: The adenovirus L4-33K protein is a key regulator involved in the temporal shift from early to late pattern of mRNA expression from the adenovirus major late transcription unit. L4-33K is a virus-encoded alternative splicing factor, which enhances ...
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Zinc finger transcription factor zDC is a negative regulator required to prevent activation of classical dendritic cells in the steady state.
Published: August, 2012

Abstract: Classical dendritic cells (cDCs) process and present antigens to T cells. Under steady-state conditions, antigen presentation by cDCs induces tolerance. In contrast, during infection or inflammation, cDCs become activated, express higher levels of...
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FM19G11 Favors Spinal Cord Injury Regeneration and Stem Cell Self-Renewal by Mitochondrial Uncoupling and Glucose Metabolism Induction.
Published: August, 2012

Abstract: Spinal cord injury is a major cause of paralysis with no currently effective therapies. Induction of self-renewal and proliferation of endogenous regenerative machinery with non-invasive and non-toxic therapies could constitute a real hope and an ...
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Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data.
Published: July, 2012

Abstract: The Photo-Activatable Ribonucleoside-enhanced CrossLinking and ImmunoPrecipitation (PAR-CLIP) method was recently developed for global identification of RNAs interacting with proteins. The strength of this versatile method results from induction o...
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Expression of endogenous retroviruses is negatively regulated by the pluripotency marker Rex1/Zfp42.
Published: July, 2012

Abstract: Rex1/Zfp42 is a Yy1-related zinc-finger protein whose expression is frequently used to identify pluripotent stem cells. We show that depletion of Rex1 levels notably affected self-renewal of mouse embryonic stem (ES) cells in clonal assays, in the...
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Role of SUMOylation in full antiestrogenicity.
Published: July, 2012

Abstract: The selective estrogen receptor downregulator (SERD) fulvestrant can be used as second line treatment in patients relapsing after treatment with tamoxifen, a selective estrogen receptor modulator (SERM). Unlike tamoxifen, SERDs are devoid of parti...
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Up-regulation of 2-oxoglutarate dehydrogenase as a stress response.
Published: July, 2012

Abstract: 2-Oxoglutarate dehydrogenase multienzyme complex (OGDHC) operates at a metabolic cross-road, mediating Ca(2+)- and ADP-dependent signals in mitochondria. Here, we test our hypothesis that OGDHC plays a major role in the neurotransmitter metabolism...
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The linker histone plays a dual role during gametogenesis in S. cerevisiae.
Published: May, 2012

Abstract: The differentiation of gametes involves dramatic changes to chromatin, affecting transcription, meiosis, and cell morphology. Sporulation in S. cerevisiae shares many chromatin features with spermatogenesis, including a ten-fold compaction of the ...
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Characterization of glomerular diseases using proteomic analysis of laser capture microdissected glomeruli.
Published: May, 2012

Abstract: The application of molecular techniques to characterize clinical kidney biopsies has the potential to provide insights into glomerular diseases that cannot be revealed by traditional renal pathology. The present work is a proof-of-concept approach...
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Antiproliferative Effects of DNA Methyltransferase 3B Depletion Are Not Associated with DNA Demethylation.
Published: May, 2012

Abstract: Silencing of genes by hypermethylation contributes to cancer progression and has been shown to occur with increased frequency at specific genomic loci. However, the precise mechanisms underlying the establishment and maintenance of aberrant methyl...
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Alterations of glucose metabolism in Escherichia coli mutants defective in respiratory-chain enzymes.
Published: April, 2012

Abstract: The effects of reduced efficiency of proton-motive force (pmf) generation on glucose metabolism were investigated in Escherichia coli respiratory-chain mutants. The respiratory chain of E. coli consists of two NADH dehydrogenases and three termina...
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A novel reporter system for bacterial and mammalian cells based on the non-ribosomal peptide indigoidine.
Published: April, 2012

Abstract: The biosynthesis of non-ribosomal peptides, many of which have pharmaceutical activities, is an evolutionary privilege of microorganisms. Capitalizing on the universal set of the Streptomyces lavendulae non-ribosomal peptide synthase BpsA and the ...
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Characterization of endolysin from a Salmonella Typhimurium-infecting bacteriophage SPN1S.
Published: April, 2012

Abstract: The full genome sequence of bacteriophage SPN1S, which infects Salmonella, contains genes that encode homologues of holin, endolysin and Rz/Rz1-like accessory proteins, which are 4 phage lysis proteins. The ability of these proteins to lyse Escher...
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Rev-erbα and Rev-erbβ coordinately protect the circadian clock and normal metabolic function.
Published: April, 2012

Abstract: The nuclear receptor Rev-erbα regulates circadian rhythm and metabolism, but its effects are modest and it has been considered to be a secondary regulator of the cell-autonomous clock. Here we report that depletion of Rev-erbα together with closel...
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A synthetic biology approach to self-regulatory recombinant protein production in Escherichia coli.
Published: March, 2012

Abstract: ABSTRACT: BACKGROUND: Recombinant protein production is a process of great industrial interest, with products that range from pharmaceuticals to biofuels. Since high level production of recombinant protein imposes significant stress in the host or...
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Mammalian HCA66 protein is required for both ribosome synthesis and centriole duplication.
Published: March, 2012

Abstract: Ribosome production, one of the most energy-consuming biosynthetic activities in living cells, is adjusted to growth conditions and coordinated with the cell cycle. Connections between ribosome synthesis and cell cycle progression have been descri...
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Proteome analysis of Acetobacter pasteurianus during acetic acid fermentation.
Published: March, 2012

Abstract: Acetic acid bacteria (AAB) are Gram-negative, strictly aerobic microorganisms that show a unique resistance to ethanol (EtOH) and acetic acid (AcH). Members of the Acetobacter and Gluconacetobacter genera are capable of transforming EtOH into AcH ...
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Mutually exclusive binding of telomerase RNA and DNA by ku alters telomerase recruitment model.
Published: March, 2012

Abstract: In Saccharomyces cerevisiae, the Ku heterodimer contributes to telomere maintenance as a component of telomeric chromatin and as an accessory subunit of telomerase. How Ku binding to double-stranded DNA (dsDNA) and to telomerase RNA (TLC1) promote...
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Two Cellular Protein Kinases, DNA-PK and PKA, Phosphorylate the Adenoviral L4-33K Protein and Have Opposite Effects on L1 Alternative RNA Splicing
Published: February, 2012

Abstract: Accumulation of the complex set of alternatively processed mRNA from the adenovirus major late transcription unit (MLTU) is subjected to a temporal regulation involving both changes in poly (A) site choice and alternative 39 splice site usage. We ...
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Polychlorinated biphenyls affect histone modification pattern in early development of rats: a role for androgen receptor-dependent modulation?
Published: February, 2012

Abstract: BACKGROUND: The epigenome represents an important target of environmental pollution. Early-life exposure to polychlorinated biphenyls (PCBs) modifies sex steroid enzymes and receptor transcription patterns. Steroid receptors, such as androgen rece...
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Improvement of the redox balance increases L-valine production by Corynebacterium glutamicum under oxygen deprivation conditions.
Published: February, 2012

Abstract: Production of L-valine under oxygen deprivation conditions by Corynebacterium glutamicum lacking the lactate dehydrogenase gene ldhA and overexpressing the L-valine biosynthesis genes ilvBNCDE was repressed. This was attributed to imbalanced cofac...
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cAMP response element-binding protein is a primary hub of activity-driven neuronal gene expression.
Published: December, 2011

Abstract: Long-lasting forms of neuronal plasticity require de novo gene expression, but relatively little is known about the events that occur genome-wide in response to activity in a neuronal network. Here, we unveil the gene expression programs initiated...
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Notch1 binds and induces degradation of Snail in hepatocellular carcinoma.
Published: November, 2011

Abstract: BACKGROUND: Hepatocellular carcinoma (HCC) is a common, highly invasive malignant tumor associated with a high mortality rate. We previously reported that the aberrant expression of Snail via activation of reactive oxygen species contributes to th...
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Expression profile of the sphingosine kinase signalling system in the lung of patients with chronic obstructive pulmonary disease.
Published: November, 2011

Abstract: AIMS: Chronic obstructive pulmonary disease (COPD) is a leading cause of death worldwide. Despite its importance, treatment methods are limited and restricted to symptomatic care, highlighting the urgent need for new treatment options. Tissue dama...
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The oxidized thiol proteome in fission yeast--optimization of an ICAT-based method to identify H2O2-oxidized proteins.
Published: October, 2011

Abstract: Major intracellular disulfide formation is prevented in the cytosol by potent reducing systems. However, protein thiols can be oxidized as a consequence of redox-mediated physiological reactions or due to the unwanted toxicity of reactive oxygen s...
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A Protein Epitope Signature Tag (PrEST) Library Allows SILAC-based Absolute Quantification and Multiplexed Determination of Protein Copy Numbers in Cell Lines
Published: September, 2011

Abstract: Mass spectrometry-based proteomics increasingly relies on relative or absolute quantification. In relative quantification, stable isotope based methods often allow mixing at early stages of sample preparation, whereas for absolute quantification t...
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Improved quantitative and qualitative production of single-domain intrabodies mediated by the co-expression of Erv1p sulfhydryl oxidase.
Published: September, 2011

Abstract: Camelidae single domain antibodies (VHHs) have structural and binding features that render them suitable alternatives to conventional IgG antibodies. VHHs are usually easier to produce as recombinant proteins than other antibody fragments. However...
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A cytoplasmic negative regulator isoform of ATF7 impairs ATF7 and ATF2 phosphorylation and transcriptional activity.
Published: August, 2011

Abstract: Alternative splicing and post-translational modifications are processes that give rise to the complexity of the proteome. The nuclear ATF7 and ATF2 (activating transcription factor) are structurally homologous leucine zipper transcription factors ...
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Reversible epigenetic fingerprint-mediated glutathione-S-transferase P1 gene silencing in human leukemia cell lines.
Published: June, 2011

Abstract: Glutathione-S-transferase P1 (GSTP1) gene is commonly silenced by CpG island promoter hypermethylation in prostate, breast, and liver cancers. However, mechanisms leading to GSTP1 repression by promoter hypermethylation in leukemia and its relatio...
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RNF20 inhibits TFIIS-facilitated transcriptional elongation to suppress pro-oncogenic gene expression.
Published: May, 2011

Abstract: hBRE1/RNF20 is the major E3 ubiquitin ligase for histone H2B. RNF20 depletion causes a global reduction of monoubiquitylated H2B (H2Bub) levels and augments the expression of growth-promoting, pro-oncogenic genes. Those genes reside preferentially...
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Requirement for Dot1l in murine postnatal hematopoiesis and leukemogenesis by MLL translocation.
Published: May, 2011

Abstract: Disruptor of telomeric silencing 1-like (Dot1l) is a histone 3 lysine 79 methyltransferase. Studies of constitutive Dot1l knockout mice show that Dot1l is essential for embryonic development and prenatal hematopoiesis. DOT1L also interacts with tr...
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Recombineering, transfection, Western, IP and ChIP methods for protein tagging via gene targeting or BAC transgenesis.
Published: April, 2011

Abstract: Protein tagging offers many advantages for proteomic and regulomic research. Ideally, protein tagging is equivalent to having a high affinity antibody for every chosen protein. However, these advantages are compromised if the tagged protein is ove...
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Prolyl hydroxylase 3 (PHD3) is essential for hypoxic regulation of neutrophilic inflammation in humans and mice.
Published: March, 2011

Abstract: The regulation of neutrophil lifespan by induction of apoptosis is critical for maintaining an effective host response and preventing excessive inflammation. The hypoxia-inducible factor (HIF) oxygen-sensing pathway has a major effect on the susce...
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A critical role for the protein phosphatase 2A B'α regulatory subunit in dephosphorylation of sphingosine kinase 1.
Published: March, 2011

Abstract: Sphingosine kinase 1 (SK1) is an important regulator of cellular signalling that has gained recent attention as a potential target for anti-cancer therapies. SK1 activity, subcellular localization and oncogenic function are regulated by phosphoryl...
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Recombineering BAC transgenes for protein tagging.
Published: February, 2011

Abstract: Protein tagging offers many advantages for proteomic and regulomic research, particularly due to the use of generic and highly sensitive methods that can be applied with reasonable throughput. Ideally, protein tagging is equivalent to having a hig...
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Integrative features of the yeast phosphoproteome and protein-protein interaction map.
Published: January, 2011

Abstract: Following recent advances in high-throughput mass spectrometry (MS)-based proteomics, the numbers of identified phosphoproteins and their phosphosites have greatly increased in a wide variety of organisms. Although a critical role of phosphorylati...
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Identification and characterisation of a novel adhesin Ifp in Yersinia pseudotuberculosis.
Published: January, 2011

Abstract: BACKGROUND: In order to identify new virulence determinants in Y. pseudotuberculosis a comparison between its genome and that of Yersinia pestis was undertaken. This reveals dozens of pseudogenes in Y. pestis, which are still putatively functional...
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Phosphatidylinositol 3-kinase (PI3K) signaling via glycogen synthase kinase-3 (Gsk-3) regulates DNA methylation of imprinted loci.
Published: December, 2010

Abstract: Glycogen synthase kinase-3 (Gsk-3) isoforms, Gsk-3α and Gsk-3β, are constitutively active, largely inhibitory kinases involved in signal transduction. Underscoring their biological significance, altered Gsk-3 activity has been implicated in diabet...
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Transcription factor IIS impacts UV-inhibited transcription.
Published: November, 2010

Abstract: Inhibition of transcription elongation can cause severe developmental and neurological abnormalities notably manifested by the rare recessive progeroid disorder Cockayne syndrome (CS). DNA alterations can cause permanent blocks to an elongating RN...
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Effects of atypical antipsychotics and haloperidol on PC12 cells: only aripiprazole phosphorylates AMP-activated protein kinase.
Published: October, 2010

Abstract: By converting changes in intracellular energy status to changes in cell membrane polarization, ATP-sensitive K(+) (K(ATP)) channels in hypothalamic appetite-regulating neurons play a critical role in linking neuronal electrochemical function, meta...
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Demonstrating polymorphic miRNA-mediated gene regulation in vivo: application to the g+6223G->A mutation of Texel sheep.
Published: September, 2010

Abstract: We herein describe the development of a biochemical method to evaluate the effect of single nucleotide polymorphisms (SNPs) in target genes on their regulation by microRNAs in vivo. The method is based on the detection of allelic imbalance in RNAs...
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Iron regulatory proteins secure mitochondrial iron sufficiency and function.
Published: August, 2010

Abstract: Mitochondria supply cells with ATP, heme, and iron sulfur clusters (ISC), and mitochondrial energy metabolism involves both heme- and ISC-dependent enzymes. Here, we show that mitochondrial iron supply and function require iron regulatory proteins...
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Roles of COMM-domain-containing 1 in stability and recruitment of the copper-transporting ATPase in a mouse hepatoma cell line.
Published: July, 2010

Abstract: A novel function of COMMD1 {COMM [copper metabolism MURR1 (mouse U2af1-rs1 region 1)]-domain-containing 1}, a protein relevant to canine copper toxicosis, was examined in the mouse hepatoma cell line Hepa 1-6 with multi-disciplinary techniques con...
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Accumulation of piRNAs in the chromatoid bodies purified by a novel isolation protocol.
Published: May, 2010

Abstract: Haploid male germ cells are featured by an intriguing cytoplasmic cloud-like structure that has been named as chromatoid body (CB) on the basis of its staining properties and appearance under a microscope. Notwithstanding its early discovery in th...
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Novel snail1 target proteins in human colon cancer identified by proteomic analysis.
Published: January, 2010

Abstract: BACKGROUND: The transcription factor Snail1 induces epithelial-to-mesenchymal transition (EMT), a process responsible for the acquisition of invasiveness during tumorigenesis. Several transcriptomic studies have reported Snail1-regulated genes in ...
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Cag3 is a novel essential component of the Helicobacter pylori Cag type IV secretion system outer membrane subcomplex.
Published: December, 2009

Abstract: Helicobacter pylori strains harboring the cag pathogenicity island (PAI) have been associated with more severe gastric disease in infected humans. The cag PAI encodes a type IV secretion (T4S) system required for CagA translocation into host cells...
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Simultaneous quantitative analysis of N-acylethanolamides in clinical samples.
Published: December, 2009

Abstract: A simple and rapid analytical method is described for the simultaneous quantitative analysis of three different N-acylethanolamides in human biological samples: anandamide (AEA), oleoylethanolamide (OEA), and palmitoylethanolamide (PEA). The metho...
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INTS3 controls the hSSB1-mediated DNA damage response.
Published: October, 2009

Abstract: Human SSB1 (single-stranded binding protein 1 [hSSB1]) was recently identified as a part of the ataxia telangiectasia mutated (ATM) signaling pathway. To investigate hSSB1 function, we performed tandem affinity purifications of hSSB1 mutants mimic...
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Functional connection between deimination and deacetylation of histones.
Published: September, 2009

Abstract: Histone methylation plays key roles in regulating chromatin structure and function. The recent identification of enzymes that antagonize or remove histone methylation offers new opportunities to appreciate histone methylation plasticity in the reg...
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Growth promotion and cell binding ability of bovine lactoferrin to Bifidobacterium longum.
Published: August, 2009

Abstract: Lactoferrin, a major whey protein of human milk, is considered as growth promoter for bifidobacteria, the predominant microorganisms of human intestine. In the present study, in vitro growth promotion and cell binding ability of bovine lactoferrin...
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Snail2 cooperates with Snail1 in the repression of vitamin D receptor in colon cancer.
Published: August, 2009

Abstract: Vitamin D receptor (VDR) mediates the antitumoral action of the active vitamin D metabolite 1alpha,25-dihydroxyvitamin D(3) (1,25(OH)(2)D(3)). VDR expression is lost during colon cancer progression causing unresponsiveness to 1,25(OH)(2)D(3) and i...
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Phosphorylation of histone H3 Thr-45 is linked to apoptosis.
Published: June, 2009

Abstract: Numerous post-translational modifications have been identified in histones. Most of these occur within the histone tails, but a few have been identified within the histone core sequences. Histone core post-translational modifications have the pote...
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Copper accumulation and compartmentalization in mouse fibroblast lacking metallothionein and copper chaperone, Atox1.
Published: June, 2009

Abstract: Copper (Cu) is the active center of some enzymes because of its redox-active property, although that property could have harmful effects. Because of this, cells have strict regulation/detoxification systems for this metal. In this study, multi-dis...
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Rapid antibody selection by mRNA display on a microfluidic chip.
Published: May, 2009

Abstract: In vitro antibody-display technologies are powerful approaches for isolating monoclonal antibodies from recombinant antibody libraries. However, these display techniques require several rounds of affinity selection which is time-consuming. Here, w...
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Conversion of cholic acid and chenodeoxycholic acid into their 7-oxo derivatives by Bacteroides intestinalis AM-1 isolated from human feces.
Published: April, 2009

Abstract: Secondary bile acid-producing bacteria were isolated from human feces to improve our appreciation of the functional diversity and redundancy of the intestinal microbiota. In total, 619 bacterial colonies were isolated using a nutrient-poor agar me...
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Genome-wide regulon and crystal structure of BlaI (Rv1846c) from Mycobacterium tuberculosis.
Published: March, 2009

Abstract: Comparative genomics with Staphylococcus aureus suggested the existence of a regulatory system governing beta-lactamase (BlaC) production in Mycobacterium tuberculosis. The crystal structure of Rv1846c, a winged helix regulator of previously unkno...
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Monodispersity of recombinant Cre recombinase correlates with its effectiveness in vivo.
Published: January, 2009

Abstract: BACKGROUND: Cre recombinase is a common reagent used for the in vivo on/off switching of the expression of target genes flanked by loxP sites. In particular, recombinant TAT-Cre fusion constructs purified from bacteria have been used to promote th...
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Multi-walled carbon nanotubes injure the plasma membrane of macrophages.
Published: October, 2008

Abstract: Carbon nanotubes (CNTs) are emerging nanotechnology materials which are likely to be mass-produced in the near future. However, prior to mass-production, certain health-related concerns should first be addressed. For example, when inhaled, the thi...
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Glutaredoxin modulates platelet-derived growth factor-dependent cell signaling by regulating the redox status of low molecular weight protein-tyrosine phosphatase.
Published: September, 2006

Abstract: Glutaredoxin (GRX) is a glutathione-disulfide oxidoreductase involved in various cellular functions, including the redox-dependent regulation of certain integral proteins. Here we demonstrated that overexpression of GRX suppressed the proliferatio...
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Effects of various growth conditions in a chemostat on expression of virulence factors in Porphyromonas gingivalis.
Published: May, 2006

Abstract: Porphyromonas gingivalis, one of the gram-negative organisms associated with periodontal disease, possesses potential virulence factors, including fimbriae, proteases, and major outer membrane proteins (OMPs). In this study, P. gingivalis ATCC 332...
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The hemoglobin receptor protein of porphyromonas gingivalis inhibits receptor activator NF-kappaB ligand-induced osteoclastogenesis from bone marrow macrophages.
Published: May, 2006

Abstract: Extracellular proteinaceous factors of Porphyromonas gingivalis, a periodontal pathogen, that influence receptor activator of nuclear factor-kappaB (NF-kappaB) ligand (RANKL)-induced osteoclastogenesis from bone marrow macrophages were investigate...
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Cell lysis directed by sigmaE in early stationary phase and effect of induction of the rpoE gene on global gene expression in Escherichia coli.
Published: August, 2005

Abstract: It has been shown that Escherichia coli cells with increased expression of the rpoE gene encoding sigma(E) exhibit enhanced cell lysis in early stationary phase. Further analysis of the lysis phenomenon was performed using a transient expression s...
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Identification of a novel adhesion molecule involved in the virulence of Legionella pneumophila.
Published: July, 2005

Abstract: Legionella pneumophila is an intracellular bacterium, and its successful parasitism in host cells involves two reciprocal phases: transmission and intracellular replication. In this study, we sought genes that are involved in virulence by screenin...
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Missense mutations in the gp91-phox gene encoding cytochrome b558 in patients with cytochrome b positive and negative X-linked chronic granulomatous disease.
Published: March, 1999

Abstract: Chronic granulomatous disease (CGD) is a disorder of host defense due to genetic defects of the superoxide (O2-) generating NADPH oxidase in phagocytes. A membrane-bound cytochrome b558, a heterodimer consisting of gp91-phox and p22-phox, is a cri...
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Gel-based and gel-free proteomic analysis of Nicotiana tabacum trichomes identifies proteins involved in secondary metabolism and in the (a)biotic stress response

Abstract: Nicotiana tabacum leaves are covered by trichomes involved in the secretion of large amounts of secondary metabolites, some of which play a major role in plant defense. However, little is known about the metabolic pathways that operate in these st...
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Atypical Regulation of Virulence-Associated Functions by a Diffusible Signal Factor in Xanthomonas oryzae pv. oryzae

Abstract: In Xanthomonas oryzae pv. oryzae, the bacterial blight pathogen of rice, a secreted fatty acid signaling molecule known as diffusible signal factor (DSF) is required for virulence and growth on low-iron medium. To identify other virulence-associat...
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Cell type-specific affinity purification of nuclei for chromatin profiling in whole animals.

Abstract: Analyzing cell differentiation during development in a complex organism requires the analysis of expression and chromatin profiles in individual cell types. Our laboratory has developed a simple and generally applicable strategy to purify specific...
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Step-by-step preparation of proteins for mass spectrometric analysis.

Abstract: Nowadays, identification of proteins from biological samples by mass spectrometry is widely used. In principle there are two scenarios. Proteins are pre-fractionated in some way, e.g. by gel electrophoresis or are analyzed as complex mixture (shot...
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Difference in Legionella pneumophila growth permissiveness between J774.1 murine macrophage-like JA-4 cells and lipopolysaccharide (LPS)-resistant mutant cells, LPS1916, after stimulation with LPS.

Abstract: To elucidate the role of the oxidative burst in macrophage resistance to Legionella infection, we examined a murine macrophage-like cell line, J774.1, for permissiveness to Legionella growth, using a mutant that has a selective defect in the oxida...
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Isolation of integrin-based adhesion complexes.

Abstract: The integration of cells with their extracellular environment is facilitated by cell surface adhesion receptors, such as integrins, which play important roles in both normal development and the onset of pathologies. Engagement of integrins with th...
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Continuous binding of the PAF molecule to its receptor is necessary for the long-term aggregation of platelets.

Abstract: Human and rabbit platelets fully aggregated by platelet-activating factor (PAF) underwent slow disaggregation but were rapidly disaggregated by the PAF receptor antagonists WEB-2086, Y-24180, SM-12502, and CV-3988. Whereas the 1-alkyl-2-[3H]acetyl...
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FoxK2 is required for cellular proliferation and survival

Abstract: FoxK2 is a forkhead transcription factor expressed ubiquitously in the developing murine central nervous system. Here we investigated the role of FoxK2 in vitro and focused on proliferation and cellular survival. Knockdown of FoxK2 results in a de...
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Big answers from small worlds: a user's guide for protist microcosms as a model system in ecology and evolution

Abstract: Laboratory microcosm experiments using protists as model organisms have a long tradition and are widely used to investigate general concepts in population biology, community ecology and evolutionary biology. Many variables of interest are meas...
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Loss of Sirt1 Promotes Prostatic Intraepithelial Neoplasia, Reduces Mitophagy, and Delays Park2 Translocation to Mitochondria

Abstract: Prostatic intraepithelial neoplasia is a precursor to prostate cancer. Herein, deletion of the NAD+-dependent histone deacetylase Sirt1 induced histological features of prostatic intraepithelial neoplasia at 7 months of age; these features were as...
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Intracellular MMP-2 Activity in Skeletal Muscle Is Associated With Type II Fibers.

Abstract: Matrix metalloproteinase 2 (MMP-2) is a proteolytic enzyme implicated in motility, differentiation, and regeneration of skeletal muscle fibers through processing of extracellular substrates. Although MMP-2 has been found to be localized intracellu...
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A method for measuring fatty acid oxidation in C. elegans

Abstract: The nematode C. elegans has during the past decade proven to be a valuable model organism to identify and examine molecular mechanisms regulating lipid storage and metabolism. While the primary approach has been to identify genes and pathways conf...
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Effect of hypoxia on the expression of αB-crystallin in head and neck squamous cell carcinoma.

Abstract: BACKGROUND: The presence of hypoxia in head and neck squamous cell carcinoma (HNSCC) is associated with therapeutic resistance and increased risk of metastasis formation. αB-crystallin (HspB5) is a small heat shock protein, which is also associate...
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