TY - JOUR. T1 - RNA-binding protein HuR interacts with thrombomodulin 5′untranslated region and represses internal ribosome entry site-mediated translation under IL-1β treatment. AU - Yeh, Chiu Hung. AU - Hung, Liang Y.. AU - Hsu, Chin. AU - Le, Shu Y.. AU - Lee, Pin T.. AU - Liao, Wan L.. AU - Lin, Yi Tseng. AU - Chang, Wen Chang. AU - Tseng, Joseph T.. PY - 2008/9. Y1 - 2008/9. N2 - Reduction in host-activated protein C levels and resultant microvascular thrombosis highlight the important functional role of protein C anticoagulant system in the pathogenesis of sepsis and septic shock. Thrombomodulin (TM) is a critical factor to activate protein C in mediating the anticoagulation and anti-inflammation effects. However, TM protein content is decreased in inflammation and sepsis, and the mechanism is still not well defined. In this report, we identified that the TM 5′ untranslated region (UTR) bearing the internal ribosome entry site (IRES) element controls TM protein expression. Using RNA ...
An assay based on the competitive polymerase chain reaction (PCR) was developed to quantify Glomus mosseae, an arbuscular mycorrhizal (AM) fungus, within plant roots. Using previously designed G. mosseae specific primers, a heterologous internal standard was constructed by amplifying Pseudomonas DNA under low stringency annealing conditions. Go-amplification of G. mosseae and internal standard DNA within leek root extracts provided accurate quantification of target DNA. Colonization of leek roots by G. mosseae was monitored in a comparative study by competitive PCR and microscopy, a conventional method of quantification. These two methods gave closely parallel data for G. mosseae colonization from three different inoculum levels over a 6 week period Results indicate that competitive PCR is a sensitive and accurate method of quantification. The major advantage of competitive PCR over microscopy is that it can quantify specific AM fungi. ...
TY - JOUR. T1 - Differential mRNA expression of prostaglandin receptor subtypes in macrophage activation. AU - Hubbard, Neil. AU - Lee, S. H.. AU - Lim, D.. AU - Erickson, Kent L. PY - 2001. Y1 - 2001. N2 - Assessing the regulation of macrophage receptors for prostaglandin (PGE2) is essential to understanding the control which that potent lipid mediator has in modulating macrophage activities. The purpose of this study was to assess the differential mRNA expression of PGE2 receptor subtypes (EP) during macrophage exposure to activating and transducing agents. RAW 264.7 macrophages constitutively expressed mRNA for EP2, EP3 and EP4 receptor subtypes. Messenger RNA for EP4 was expressed at a much higher level when compared to EP2 in unstimulated macrophages as assessed by kinetic quantitative RT-PCR. When macrophages were stimulated with LPS, EP2 mRNA levels were 12-fold higher when compared to unstimulated macrophages, while EP4 mRNA remained unchanged. Conversely, mRNA levels of both EP2 and EP4 ...
Looking for online definition of cystic fibrosis transmembrane conductance regulator gene in the Medical Dictionary? cystic fibrosis transmembrane conductance regulator gene explanation free. What is cystic fibrosis transmembrane conductance regulator gene? Meaning of cystic fibrosis transmembrane conductance regulator gene medical term. What does cystic fibrosis transmembrane conductance regulator gene mean?
Avian encephalomyelitis virus (AEV) is a picornavirus that affects young chickens, quails, pheasants and turkeys. Translation initiation on picornavirus mRNA is cap independent and occurs through a mechanism known as internal initiation, which depends on Internal Ribosome Entry Site (IRES) element within the 5 untranslated region (UTR) of the viral RNA. AEV has been assigned within the Hepatovirus genus and shares protein sequence similarity with hepatitis A virus (HAV). I have demonstrated that the 494 nucleotide 5 UTR of the AEV genome contains an internal ribosome entry site (IRES) element. However, in contrast to the HAV IRES, the AEV IRES functions efficiently in the presence of cleaved eEF4G, suggesting functional differences exist. Characterization of the AEV IRES element revealed that there are remarkable structural and functional similarities between the AEV, flavivirus [especially hepatitis C virus (HCV)] and newly discovered type 4 picornaviras IRES elements, including porcine ...
Looking for online definition of putative RNA-binding protein 11 in the Medical Dictionary? putative RNA-binding protein 11 explanation free. What is putative RNA-binding protein 11? Meaning of putative RNA-binding protein 11 medical term. What does putative RNA-binding protein 11 mean?
TY - JOUR. T1 - Partial nucleotide sequence of the Murray Valley encephalitis virus genome. Comparison of the encoded polypeptides with yellow fever virus structural and non-structural proteins. AU - Dalgarno, Lynn. AU - Trent, Dennis W.. AU - Strauss, James H.. AU - Rice, Charles M.. PY - 1986/2/5. Y1 - 1986/2/5. N2 - The sequence of 5400 bases corresponding to the 5′-terminal half of the Murray Valley encephalitis virus genome has been determined. The genome contains a 5′ non-coding region of about 97 nucleotides, followed by a single continuous open reading frame that encodes the structural proteins followed by the non-structural proteins. Amino acid sequence homology between the Murray Valley encephalitis and yellow fever (Rice et al., 1985) polyproteins is 42% over the region sequenced. The start points of the various Murray Valley encephalitis virus-coded proteins have been assigned on the basis of this homology and a consistent set of potential proteolytic cleavage sites identified, ...
BACKGROUND Sequence type 131 (ST131) is a predominant lineage among extraintestinal pathogenic Escherichia coli. It plays a major role in the worldwide dissemination of extended-spectrum β-lactamase (ESBL)-producing E. coli. The ST131 pandemic is mainly the result of clonal expansion of the single well-adapted subclone H30-Rx, which is acquired in hospitals more frequently than other ESBL-producing E. coli clones. AIM To develop a rapid method using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify ST131 for infection control purposes. METHODS Peak biomarkers of ST131 were identified from the mass spectrum profiles of 109 E. coli isolates (including 50 ST131 isolates). FINDINGS The models accurately identified ST131 isolates from mass spectrum profiles obtained with and without protein extraction. CONCLUSIONS The rapid identification of ST131 isolates with MALDI-TOF MS can be easily implemented in the laboratory, and could help to target
Proprotein convertase furin is responsible for the processing of a wide variety of precursors consisted of signal peptide, propeptide and mature peptide in mammal. Many precursors processed by furin have important physiological functions and can be recombinantly expressed in Pichia pastoris expression system for research, pharmaceutical and vaccine applications. However, it is not clear whether the furin cleavage sites between the propeptide and mature peptide can be properly processed in P. pastoris, bringing uncertainty for proper expression of the coding DNA sequences of furin precursors containing the propeptides and mature peptides. In this study, we evaluated the ability of P. pastoris to process furin cleavage sites and how to improve the cleavage efficiencies of furin cleavage sites in P. pastoris. The results showed that P. pastoris can process furin cleavage sites but the cleavage efficiencies are not high. Arg residue at position P1 or P4 in furin cleavage sites significantly affect cleavage
Evolution of a species specific determinant essay, buy custom Evolution of a species specific determinant essay paper cheap, Evolution of a species specific determinant essay paper sample, Evolution of a species specific determinant essay sample service online
Genetic susceptibility to autoimmunity is frequently associated with specific MHC alleles. Diabetogenic MHC class II molecules, such as human HLA-DQ8 and mouse I-Ag7, typically have a small, uncharged amino acid residue at position 57 of their β chain (β57); this results in the absence of a salt bridge between β57 and Argα76, which is adjacent to the P9 pocket of the peptide-binding groove. However, the influence of Argα76 on the selection of the TCR repertoire remains unknown, particularly when the MHC molecule binds a peptide with a neutral amino acid residue at position P9. Here, we have shown that diabetogenic MHC class II molecules bound to a peptide with a neutral P9 residue primarily selected and expanded cells expressing TCRs bearing a negatively charged residue in the first segment of their complementarity determining region 3β. The crystal structure of one such TCR in complex with I-Ag7 bound to a peptide containing a neutral P9 residue revealed that a network of favorable ...
We describe the effect of nearest-neighbor sequence context on mismatch-dependent activation of hMSH2-hMSH6. Examination of the intrinsic sequences that occur around symmetric mismatched nucleotides suggests little if any effect of non-nearest-neighbor base pairs on hMSH2-hMSH6 mismatch recognition and ATPase activation (20), although longer-range effects have been reported (22). Although a sequence context effect is not novel in MMR (21), the underlying mechanism is unknown. Our studies have suggested that when a significant nearest-neighbor sequence context effect is manifest, 2 × 3′-purines enhanced, and 2 × 3′-pyrimidines reduced hMSH2-hMSH6 ATPase activation (kcat). A similar trend is observed for mismatch binding (KD), whereas an inverse effect was observed for the Tm of unbound mismatched oligonucleotides. Importantly, the KD and Tm do not accurately account for hMSH2-hMSH6 ATPase activation. Interestingly, the effect of sequence context on KD appears associated with alteration of ...
10) A base other than U at position 5 of the sense strand.(11) A base other than A at position 11 of the sense strand.(12) A base other than an A at position 1 of the sense strand.(13) A base other than an A at position 2 of the sense strand.(14) An A base at position 4 of the sense strand.(15) An A base at position 5 of the sense strand.(16) An A base at position 6 of the sense strand.(17) An A base at position 7 of the sense strand.(18) An A base at position 8 of the sense strand.(19) A base other than an A at position 9 of the sense strand.(20) A base other than an A at position 10 of the sense strand.(21) A base other than an A at position 11 of the sense strand.(22) A base other than an A at position 12 of the sense strand.(23) An A base at position 13 of the sense strand.(24) A base other than an A at position 14 of the sense strand.(25) An A base at position 15 of the sense strand(26) An A base at position 16 of the sense strand.(27) An A base at position 17 of the sense strand.(28) An A ...
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Promoter Methylation and Relative mRNA Expression of the p16 Gene in Cervical Cancer in North Indians Cervical cancer;p16 methylation;p16 mRNA expression;North Indian population; Background: Cervical carcinoma is one of the main causes of mortality in women worldwide as well as in India. It occurs as a result of various molecular events that develop from the combined influences of an individuals genetic predisposition and external agents such as smoking and menstrual hygiene, for example. However, infection with human papillomavirus (HPV) is the established major risk factor. The aim of the current study was to investigate p16 CpG island methylation and establish any correlation with mRNA expression in north Indian population. Materials and Methods: We analyzed 196 woman volunteer out of which 98 were cases and 98 healthy controls. For the analysis of methylation pattern, DNA extracted from blood samples was modified with a bisulfate kit and used as template for methylation specific PCR (MSP).
The chicken ovalbumin upstream promoter transcription factors (COUP-TFs) are members from the steroid/thyroid hormone receptor superfamily and function in transcriptional regulation of a multitude of genes. of the ovalbumin gene (Bagchi et al., 1987; Pastorcic et al., 1986; Wang et Procyanidin B3 inhibitor Mouse monoclonal to Human Albumin al., 1987). It was found to bind an element (COUP) between C90 and C70 within the ovalbumin promoter that is much like thyroid and estrogen response elements (Pastorcic et al., 1986). The COUP-TF has also been shown to bind cis-elements involved in positive transcription rules in the rat insulin II (Hwung et al., 1988; Hwung et al., 1988b), chicken VLDL II (Wijnholds et Procyanidin B3 inhibitor al., 1988), and human being apolipoprotein AI and CIII genes (Ladias and Karathanasis, 1991). It was also reported to bind to bad regulatory elements in the proopiomelanocortin (Drouin et al., 1989a; Drouin et al., 1989b) and HIV-1 (Cooney et al., 1991) promoters. The ...
RATIONALE: Regulatory DNA elements in the human genome play important roles in determining the transcriptional abundance and spatiotemporal gene expression during embryonic heart development and somatic cell reprogramming. It is not well known how chromatin marks in regulatory DNA elements are modulated to establish cell type-specific gene expression in the human heart. OBJECTIVE: We aimed to decipher the cell type-specific epigenetic signatures in regulatory DNA elements and how they modulate heart-specific gene expression. METHODS AND RESULTS: We profiled genome-wide transcriptional activity and a variety of epigenetic marks in the regulatory DNA elements using massive RNA-seq (n=12) and ChIP-seq (chromatin immunoprecipitation combined with high-throughput sequencing; n=84) in human endothelial cells (CD31(+)CD144(+)), cardiac progenitor cells (Sca-1(+)), fibroblasts (DDR2(+)), and their respective induced pluripotent stem cells. We uncovered 2 classes of regulatory DNA elements: class I was ...
The endogenous opioid enkephalin neuropeptides are mediators of pain perception and have been implicated in human addictions. The preproenkephalin gene and its mRNA have also provided many examples of tissue- and species-specific variations in mRNA structure produced through a variety of transcriptional and post-transcriptional mechanisms. Resultant differences in mRNA structure, in several cases, have impact on translation of enkephalin prepropeptide. The reports and discussion presented herein describe studies of the preproenkephalin gene and mRNA structure in the guinea pig, an animal that may have specific advantages for modeling the human endogenous opioid system. A guinea pig brain cDNA library was constructed and screened for clones of preproenkephalin and preprodynorphin, which were then sequenced. These studies confirmed the predicted mRNA structure that had been previously proposed based on homology with gene sequences and other methods. Multiple transcription initiation sites for each ...
The expression of mRNA for the epidermal growth factor (EGF) receptor, EGF and transforming growth factor alpha (TGF-alpha) was determined in 76 malignant, six borderline and 15 benign primary ovarian tumours using the reverse transcriptase-polymerase chain reaction and related to clinical and pathological parameters. Of the malignant tumours, 70% (53/76) expressed EGF receptor mRNA, 31% (23/75) expressed EGF mRNA and 35% (26/75) expressed TGF-alpha mRNA. For the borderline tumours, four of six (67%) expressed EGF receptor mRNA, 1/6 (17%) expressed TGF-alpha mRNA and none expressed EGF mRNA. Finally, 33% (5/15) of the benign tumours expressed EGF receptor mRNA, whereas 40% (6/15) expressed EGF mRNA and 7% (1/15) expressed TGF-alpha mRNA. The presence of the EGF receptor in malignant tumours was associated with that of TGF-alpha (P = 0.0015) but not with EGF (P = 1.00), whereas there was no relationship between the presence of EGF and TGF-alpha (P = 1.00). EGF receptor mRNA expression was significantly
An accurate method based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has been developed for quantitative analysis of calcitonin and insulin in different commercially available pharmaceutical products. Tryptic peptides derived from these polypeptides were chemically modified at their C-terminal lysine-residues with 2-methoxy-4,5-dihydro-imidazole (light tagging) as standard and deuterated 2-methoxy-4,5-dihydro-imidazole (heavy tagging) as internal standard (IS). The heavy modified tryptic peptides (4D-Lys tag), differed by four atomic mass units from the corresponding light labelled counterparts (4H-Lys tag). The normalized peak areas (the ratio between the light and heavy tagged peptides) were used to construct a standard curve to determine the concentration of the analytes. The concentrations of calcitonin and insulin content of the analyzed pharmaceutical products were accurately determined, and less than 5% error was obtained between the ...
article{1fdd16d8-cade-46c6-b3bf-0719173f035c, abstract = {Both brain-derived neurotrophic factor (BDNF) and the serotonin receptor 2A (5-HT2A) have been related to depression pathology. Specific 5-HT2A receptor changes seen in BDNF conditional mutant mice suggest that BDNF regulates the 5-HT2A receptor level. Here we show a direct effect of BDNF on 5-HT2A receptor protein levels in primary hippocampal neuronal and mature hippocampal organotypic cultures exposed to different BDNF concentrations for either 1, 3, 5 or 7 days. In vivo effects of BDNF on hippocampal 5-HT2A receptor levels were further corroborated in (BDNF +/-) mice with reduced BDNF levels. In primary neuronal cultures, 7 days exposure to 25 and 50 ng/mL BDNF resulted in downregulation of 5-HT2A, but not of 5-HT1A, receptor protein levels. The BDNF-associated downregulation of 5-HT2A receptor levels was also observed in mature hippocampal organotypic cultures, excluding confounding effects of BDNF on immature tissue. BDNF +/- mice ...
In this paper, the taxonomy of the genus Arthrobacter is discussed, from its first description in 1947 to the present state. Emphasis is given to intrageneric phylogeny and chemotaxonomic characteristics, concentrating on quinone systems, peptidoglycan compositions and polar lipid profiles. Internal groups within the genus Arthrobacter indicated from homogeneous chemotaxonomic traits and corresponding to phylogenetic grouping and/or high 16S rRNA gene sequence similarities are highlighted. Furthermore, polar lipid profiles and quinone systems of selected species are shown, filling some gaps concerning these chemotaxonomic traits. Based on phylogenetic groupings, 16S rRNA gene sequence similarities and homogeneity in peptidoglycan types, quinone systems and polar lipid profiles, a description of the genus Arthrobacter sensu lato and an emended description of Arthrobacter roseus are provided. Furthermore, reclassifications of selected species of the genus Arthrobacter into novel genera are proposed,
Integrins control the cell attachment to the extracellular matrix and play an important role in mediating cell proliferation, migration and survival. A number of important cancer-associated integrin genes can be regulated by microRNAs (miRNAs) that bind to their target sites in the 3 untranslated regions. We examined the effect of single-nucleotide polymorphisms (SNPs) in predicted miRNA target sites of six integrin genes (ITGA3, ITGA6, ITGAv, ITGB3, ITGB4 and ITGB5) on breast cancer (BC) risk and clinical outcome. Six SNPs were genotyped in 749 Swedish incident BC cases with detailed clinical data and up to 15 years of follow-up together with 1493 matched controls. We evaluated associations between genotypes and BC risk and clinical tumour characteristics. Survival probabilities were compared between different subgroups. As a novel finding, several SNPs seemed to associate with the hormone receptor status. The strongest association was observed between the A allele of the SNP rs743554 in the ...
92118DNAArtificial SequenceA synthetic DNA fragment 1aaggagcgat cgccatgn 18210DNAArtificial SequenceA synthetic DNA fragment, wherein nnn is the first codon which is 3 to the start codon followed by the remainder of an open reading frame 2cgccatgnnn 10312DNAArtificial SequenceA synthetic DNA fragment 3nnnnnngtct tc 12410DNAArtificial SequenceA synthetic DNA fragment 4nnnngaagag 10513DNAArtificial SequenceA synthetic DNA fragment 5gcagcnnnnn nnn 13611DNAArtificial SequenceA synthetic DNA fragment 6nnnnngagac g 11711DNAArtificial SequenceA synthetic DNA fragment 7gccnnnnngg c 11814DNAArtificial SequenceA synthetic DNA fragment 8ggatgnnnnn nnnn 14911DNAArtificial SequenceA synthetic DNA fragment 9nnnnngagac c 111010DNAArtificial SequenceA synthetic DNA fragment 10gacgcnnnnn 101111DNAArtificial SequenceA synthetic DNA fragment 11ccnnnnnnng g 111211DNAArtificial SequenceA synthetic DNA fragment 12gcnnnnnnng c 111310DNAArtificial SequenceA synthetic DNA fragment 13nnnnngagac 101411DNAArtificial ...
GO Terms Descrition:, periodic partitioning by pair rule gene, central nervous system development, RNA polymerase II distal enhancer sequence-specific DNA binding, positive regulation of transcription from RNA polymerase II promoter, trunk segmentation, cell fate specification, RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription, regulation of transcription from RNA polymerase II promoter, blastoderm segmentation, negative regulation of transcription from RNA polymerase II promoter, regulation of transcription, DNA-templated, sequence-specific DNA binding transcription factor activity, nucleus, sequence-specific DNA binding, gonadal mesoderm development, segmentation, posterior head segmentation, germ cell migration ...
The 72 kDa IE1 protein of human cytomegalovirus (HCMV) is one of a few viral regulatory proteins expressed immediately after infection of a host cell. Although it is now well-established that IE1 is a potent transcriptional activator of the human immunodeficiency virus (HIV) long terminal repeat (LTR), the identity of the nucleotide sequence responsive to IE1 remains elusive and the molecular mechanism of this interaction is not well-understood. We have constructed various LTR mutants and tested them for their ability to be activated by IE1 using transient transfection assays. Mutations in the NF-κB sites, of either a few changes in the nucleotide sequence or a deletion of the entire region, abrogated IE1-driven transactivation. Deletion of the Tat-responsive element (TAR) had no significant effect on reporter expression. Mutations in the Sp1 sites or the TATA box significantly lowered LTR activity, but this is probably due to an effect on the general transcription system, as these elements are also
http://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0006-4971&volume=&spage=&epage=&date=2013&atitle=Single+nucleotide+variation+in+the+TP53+3%27+untranslated+region+in+diffuse+large+B-cell+lymphoma+treated+with+rituximab-CHOP:+a+report+from+the+International+DLBCL+Rituximab-CHOP+Consortium+ ...
Hepatitis C virus (HCV) protein synthesis is mediated by a highly conserved internal ribosome entry site (IRES), mostly located at the 5′ untranslatable region (UTR) of the viral genome. The translation mechanism is different from that used by cellular cap-mRNAs, making IRESs an attractive target site for new antiviral drugs. The present work characterizes a chimeric RNA molecule (HH363-50) composed of two inhibitors: a hammerhead ribozyme targeting position 363 of the HCV genome and an aptamer directed towards the essential stem-loop structure in domain IV of the IRES region (which contains the translation start codon). The inhibitor RNA interferes with the formation of a translationally active complex, stalling its progression at the level of 80S particle formation. This action is likely related to the effective and specific blocking of HCV IRES-dependent translation achieved in Huh-7 cells. The inhibitor HH363-50 also reduces HCV RNA levels in a subgenomic replicon system. The present findings
Abstract: The development of cancer is a consequence of mutations that lead to dysfunctional cell processes such as unrestrained cell proliferation resistance to apoptosis and improper regulation of cell processes such as translation. Cell proliferation and apoptosis are linked to specific gene expression events regulated by protein synthesis which begins with the binding of various eukaryotic initiation factors (eIF) to mRNA and ribosomes to initiate translation. eIF4G-1 catalyzes two types of translation initiation. Cap-dependent translation requires eIF4E to bind a 5-methylated mRNA cap and eIF4G-1. This in turn facilitates recruitment and promotes translation of cell cycle and growth-related proteins. Cap-independent translation initiates internally through internal ribosome entry sites (IRES) in the 5 UTR of mRNA and promotes translation of apoptotic mRNAs such as Apaf-1. Previous studies found that eight variants of eIF4G-1 mRNA exist and five protein isoforms can be resolved by ...
Project Abstract = miRNAs were found to be key regulators in proliferation, differentiation, apoptosis, hematopoesis and oncogenesis. Different cell types have unique and dynamic miRNA expression profiles that could be used to discriminate between those cell types and even between cellular stages. The iGEM Team Heidelberg 2010 will create miRNA binding site patterns enabling the control of any target gene of choice according to the cellular miRNA expression profile. Therefore, we will apply evolutionary methods for creating large miRNA binding site pattern libraries and we will develop two new and powerful methods for miRNA binding site pattern library screening. In parallel, computational modeling will be used for getting information on natural binding site pattern structure in order to enable rational design of complex binding site patterns recognizing certain cellular miRNA expression profiles in the future. ---- ,br /> Sponsors ,br /> ,br /> [[Image:febit_logo.jpg,150px,left]] ...
The genetic continuity of the potato spindle tuber viroid (PSTVd) genome was analysed after infection of tomato plants with cloned cDNAs of parental strains. During the six weeks of the experiment, several new sequence variants appeared. The sequence variants detected in the progeny population induced sequence-specific disease symptoms. The PSTVd genome therefore follows the pattern expected for typical pseudo-strains propagating in plants as a population of similar sequences. Assessing further the replicon continuity, a PSTVd cDNA mutant with a deletion in the central conserved region was constructed and proven to be non-infectious. Surprisingly, in a sub-population of potato transformants expressing the same deleted PSTVd RNA an infectious viroid was detected. This suggests specific transcript conversion followed by recovery of the full-length pathogen genome ...
TY - JOUR. T1 - Extensive Replication of a Retroviral Replicating Vector Can Expand the A Bulge in the Encephalomyocarditis Virus Internal Ribosome Entry Site and Change Translation Efficiency of the Downstream Transgene. AU - Lin, Amy H.. AU - Liu, Yanzheng. AU - Burrascano, Cynthia. AU - Cunanan, Kathrina. AU - Logg, Christopher R.. AU - Robbins, Joan M.. AU - Kasahara, Noriyuki. AU - Gruber, Harry. AU - Ibañez, Carlos. AU - Jolly, Douglas J.. PY - 2016/4/1. Y1 - 2016/4/1. N2 - We have developed retroviral replicating vectors (RRV) derived from Moloney murine gammaretrovirus with an amphotropic envelope and an encephalomyocarditis virus (EMCV) internal ribosome entry site (IRES)-transgene cassette downstream of the env gene. During long-term (180 days) replication of the vector in animals, a bulge of 7 adenosine residues (As) in the J-K bifurcation domain sometimes serially added As. Therefore, vectors with 4-12 As in the A bulge in the J-K bifurcation domain were generated, and the impact ...
An miRNA-Mediated Therapy for SCA6 Blocks IRES-Driven Translation of the CACNA1A Second Cistron Researchers identified miR-3191-5p as a microRNA (miRNA) that targeted CACNA1A internal ribosomal entry site (IRES) and preferentially inhibited the CACNA1A IRES-driven translation of α1ACT in an Argonaute 4-dependent manner. They found that eukaryotic initiation factors (eIFs), eIF4AII and eIF4GII, interacted with the CACNA1A IRES to enhance α1ACT translation. [Sci Transl Med] Abstract Neurons Differentiated from Transplanted Stem Cells Respond Functionally to Acoustic Stimuli in the Awake Monkey Brain Researchers examined whether neurons differentiated from transplanted stem cells can integrate into the host neural network and function in awake animals, a goal of transplanted stem cell therapy in the brain. [Cell Rep] Full Article , Graphical Abstract Cardiac Chemical Exchange Saturation Transfer MR Imaging Tracking of Cell Survival or Rejection in Mouse Models of Cell Therapy One million C2C12 ...
BRCA1 is a breast cancer susceptibility gene that is down-regulated in a significant proportion of sporadic breast cancers. BRCA1 is posttranscriptionally regulated by RNA-binding proteins, the identities of which are unknown. HuR is an RNA binding protein implicated in posttranscriptional regulation of many genes and is overexpressed in sporadic breast cancer. To investigate the possibility that these two molecules are functionally linked in breast cancer, we performed bioinformatic analysis of the BRCA1 3 untranslated region (UTR), RNA-protein assays with the HuR protein and the BRCA1 3UTR, and immunohistochemical analysis of a cohort of breast tumors using antibodies against BRCA1 and HuR. Here, we describe the identification of two predicted HuR-binding sites in the BRCA1 3UTR, one of which binds specifically to HuR. We also show that this interaction is disrupted by single nucleotide substitutions in the BRCA1 3UTR and that endogenous HuR protein associates with BRCA1 transcripts in ...
Our research focuses on the characterization and modeling of post-transcriptional regulatory networks involved in the coordination of gene expression programs in vertebrates, using a combination of cell and molecular biology studies with genomics and bioinformatics approaches. We are particularly interested in regulatory events determined by small non-coding RNAs and the interaction of RNA binding proteins with mRNA untranslated sequence elements (UTRs)and how they can be targeted to influence on gene expression outputs for therapeutic applications. ...
TNFAIP2 is a crucial gene involved in apoptosis. Single nucleotide polymorphisms (SNPs) in its miRNA binding sites could modulate functions of the miRNA-target genes and thus risk of cancers. In this study, we investigated associations between potentially functional SNPs in the miRNA binding sites of the 3UTR of TNFAIP2 and gastric cancer risk in a US population.We conducted a case-control study of 301 gastric cancer patients and 313 cancer-free controls frequency-matched by age, sex and ethnicity. We genotyped four selected TNFAIP2 SNPs (rs8126 T,C, rs710100 G,A, rs1052912 G,A and rs1052823 G,T) and used the logistic regression analysis to assess associations of these SNPs with cancer risk.The rs8126 CC genotype was associated with a significantly elevated risk of gastric cancer (adjusted OR = 2.00, 95% CI = 1.09-3.64 and P = 0.024), compared with the combined rs8126 TT+TC genotypes, particularly in current drinkers. However, none of other TNFAIP2 SNPs was associated with risk of gastric ...
Alternative polyadenylation (APA) can for example occur when a protein-coding gene has several polyadenylation (polyA) signals in its last exon, resulting in messenger RNAs (mRNAs) with different 3′ untranslated region (UTR) lengths. Different 3′UTR lengths can give different microRNA (miRNA) regulation such that shortened transcripts have increased expression. The APA process is part of human cells natural regulatory processes, but APA also seems to play an important role in many human diseases. Although altered APA in disease can have many causes, we reasoned that mutations in DNA elements that are important for the polyA process, such as the polyA signal and the downstream GU-rich region, can be one important mechanism. To test this hypothesis, we identified single nucleotide polymorphisms (SNPs) that can create or disrupt APA signals (APA-SNPs). By using a data-integrative approach, we show that APA-SNPs can affect 3′UTR length, miRNA regulation, and mRNA expression-both between ...
K17002 MIR17; microRNA 17 K17003 MIR18A; microRNA 18a K17005 MIR19; microRNA 19 K17005 MIR19; microRNA 19 K17006 MIR20A; microRNA 20a K17008 MIR92A; microRNA 92a K01110 PTEN; phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN [EC:3.1.3.16 3.1.3.48 3.1.3.67] K17010 MIR221; microRNA 221 K17011 MIR222; microRNA 222 K06624 CDKN1B; cyclin-dependent kinase inhibitor 1B K16866 TIMP3; metalloproteinase inhibitor 3 K16980 MIRLET7; microRNA let-7 K16980 MIRLET7; microRNA let-7 K16980 MIRLET7; microRNA let-7 K16980 MIRLET7; microRNA let-7 K16980 MIRLET7; microRNA let-7 K17397 MIRLET7C; microRNA let-7c K07827 KRAS; GTPase KRas K07827 KRAS; GTPase KRas K07827 KRAS; GTPase KRas K07827 KRAS; GTPase KRas K02091 CDK6; cyclin-dependent kinase 6 [EC:2.7.11.22] K06645 CDC25A; M-phase inducer phosphatase 1 [EC:3.1.3.48] K05866 CDC25B; M-phase inducer phosphatase 2 [EC:3.1.3.48] K05867 CDC25C; M-phase inducer phosphatase 3 [EC:3.1.3.48] K09283 HMGA2; high mobility ...
Coxsackie B4 Virus are enteroviruses that belong to the Picornaviridae family. These viruses can be found worldwide. They are positive-sense, single-stranded, non-enveloped RNA viruses with icosahedral geometry. Coxsackieviruses have two groups, A and B, each associated with different diseases. Coxsackievirus group A is known for causing hand-foot-and-mouth diseases while Group B, which contains six serotypes, can cause a varying range of symptoms like gastrointestinal distress myocarditis. Coxsackievirus B4 has a cell tropism for natural killer cells and pancreatic islet cells. Infection can lead to beta-cell apoptosis which increases the risk of insulitis. Coxsackievirus B4 is one of the six serotypes found in Group B and is a positive sense, single-stranded, non-enveloped RNA virus. Its genome is linear and is 7,293 nucleotides in length with both a 5 and 3 untranslated region and encodes its own 3 poly-A tail. The 5 untranslated region contains an internal ribosomal entry site (Type I ...
TY - JOUR. T1 - Gene expression variability as a unifying element of the pluripotency network. AU - Mason, Elizabeth A.. AU - Mar, Jessica C.. AU - Laslett, Andrew L.. AU - Pera, Martin F.. AU - Quackenbush, John. AU - Wolvetang, Ernst. AU - Wells, Christine A.. PY - 2014/8/12. Y1 - 2014/8/12. N2 - Heterogeneity is a hallmark of stem cell populations, in part due to the molecular differences between cells undergoing self-renewal and those poised to differentiate. We examined phenotypic and molecular heterogeneity in pluripotent stem cell populations, using public gene expression data sets. A high degree of concordance was observed between global gene expression variability and the reported heterogeneity of different human pluripotent lines. Network analysis demonstrated that low-variability genes were the most highly connected, suggesting that these are the most stable elements of the gene regulatory network and are under the highest regulatory constraints. Known drivers of pluripotency were ...
The p38 mitogen-activated protein kinase (MAPK) pathway plays an important role in the post-transcriptional regulation of inflammatory genes. p38 has been found to regulate both the translation and the stability of inflammatory mRNAs. The mRNAs regulated by p38 share common AU-rich elements (ARE) present in their 3-untranslated regions. AREs act as mRNA instability determinants but also confer stabilisation of the mRNA by the p38 pathway. In recent years, AREs have shown to be binding sites for numerous proteins including HuR, TTP, AUF1, AUF2, FBP1, FBP2 (KSRP), TIA-1, and TIAR. However, it is unclear which protein is responsible for mRNA stabilisation by p38. This review gives an overview of the major ARE-binding proteins and discusses reasons for and against their involvement in p38-mediated mRNA stabilisation.
Foot-and-mouth disease (FMD) is a highly contagious disease of domestic and wild ruminants that is caused by FMD virus (FMDV). FMD outbreaks have occurred in livestock-containing regions worldwide. Apigenin, which is a flavonoid naturally existing in plant, possesses various pharmacological effects, including anti-inflammatory, anticancer, antioxidant and antiviral activities. Results show that apigenin can inhibit FMDV-mediated cytopathogenic effect and FMDV replication in vitro. Further studies demonstrate the following: (i) apigenin inhibits FMDV infection at the viral post-entry stage; (ii) apigenin does not exhibit direct extracellular virucidal activity; and (iii) apigenin interferes with the translational activity of FMDV driven by internal ribosome entry site. Studies on applying apigein in vivo are required for drug development and further identification of potential drug targets against FDMV infection.
Title:MicroRNA Regulation and Role in Stem Cell Maintenance, Cardiac Differentiation and Hypertrophy. VOLUME: 13 ISSUE: 5. Author(s):K.T. Kuppusamy, H. Sperber and H. Ruohola- Baker. Affiliation:Department of Biochemistry, University of Washington, UW Medicine at South Lake Union, 815 Mercer Street, Seattle, WA 98109, USA.. Keywords:Cardiomyocyte maturation, hESC, human, microRNA, mouse, regulation, stem cells.. Abstract:There are currently 1527 known microRNAs (miRNAs) in human, each of which may regulate hundreds or thousands of target genes. miRNA expression levels vary between cell types; for example, miR- 302 and miR-290 families are highly enriched in embryonic stem cells, while miR-1 is a muscle specific miRNA. miRNA biosynthesis and function are highly regulated and this regulation may be cell type specific. The processing enzymes and factors that recognize features in sequence and secondary structure of the miRNA play key roles in regulating the production of mature miRNA. Mature miRNA ...
In molecular genetics, the three prime untranslated region (3-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codon. An mRNA molecule is transcribed from the DNA sequence and is later translated into protein. Several regions of the mRNA molecule are not translated into protein including the 5 cap, 5 untranslated region, 3 untranslated region, and the poly(A) tail. The 3-UTR often contains regulatory regions that post-transcriptionally influence gene expression. Regulatory regions within the 3-untranslated region can influence polyadenylation, translation efficiency, localization, and stability of the mRNA. The 3-UTR contains both binding sites for regulatory proteins as well as microRNAs (miRNAs). By binding to specific sites within the 3-UTR, miRNAs can decrease gene expression of various mRNAs by either inhibiting translation or directly causing degradation of the transcript. The 3-UTR also has silencer regions which bind to repressor ...
Gap junctions allow intercellular communication. Their structural subunits are four-transmembrane proteins named connexins (Cxs), which can be post-transcriptionally regulated by developmental and cellular signalling cues. Cx translation and mRNA stability is regulated by miRNAs and RNA-binding proteins (RBPs) such as human antigen R (HuR). In addition, several Cxs have also been suggested to contain 5′ internal ribosome entry site (IRES) elements that are thought to allow cap-independent translation in situations such as mitosis, stress and senescence. Furthermore, several recent reports have documented internal translation of Cx mRNAs that result in N-terminally truncated protein isoforms that may have unique gap junction-independent functions [Ul-Hussain et al. (2008) BMC Mol. Biol. 9, 52; Smyth and Shaw (2013) Cell Rep. 5, 611-618; Salat-Canela et al. (2014) Cell Commun. Signal. 12, 31; Ul-Hussain et al. (2014) J. Biol. Chem. 289, 20979-20990]. This review covers the emerging field of the ...
The mouse Tcp10 genes are transcribed exclusively in male germ cells and display multiple 5 and 3 untranslated variations generated by alternative splicing and polyadenylation signal usage. To investigate the possible role of untranslated sequences in the regulation of these genes, chimeric expression constructs with or without endogenous 5 and 3 untranslated sequences were generated and used to make transgenic mice. Analysis of these animals showed that the untranslated sequences have no effect on the transcription or translation of an attached lacZ reporter gene, thereby implying these sequences are dispensible. However, the endogenous pattern of polyadenylation site usage was altered when Tcp10 3 untranslated sequences were linked to lacZ, indicating that internal coding sequence can influence recognition of polyadenylation signals in testis. The characteristics of alternative splicing and polyadenylation signal variability reflects a common theme of promiscuity in testicular gene
Regulatory RNA regions within a transcript, particularly in the 5′ untranslated region (5′UTR), have been shown in a variety of organisms to control the expression levels of these mRNAs in response to various metabolites or environmental conditions. Considering the unique tolerance of Zymomonas mobilis to ethanol and the growing interest in engineering microbial strains with enhanced tolerance to industrial inhibitors, we searched natural cis-regulatory regions in this microorganism using transcriptomic data and bioinformatics analysis. Potential regulatory 5′UTRs were identified and filtered based on length, gene function, relative gene counts, and conservation in other organisms. An in vivo fluorescence-based screening system was developed to confirm the responsiveness of 36 5′UTR candidates to ethanol, acetate, and xylose stresses. UTR_ZMO0347 (5′UTR of gene ZMO0347 encoding the RNA binding protein Hfq) was found to down-regulate downstream gene expression under ethanol stress. Genomic
An example of underestimating the probability of frequent word occurrences is apparent in a recent study by Rigoutsos et al [16]. They reported that certain DNA words, termed pyknons, appear frequently in human gene-related sequences andin noncoding regions, in restricted configurations, and presented many arguments for the pyknon s functionality. By relying on a Bernoulli model, they reasoned that 16-mers should appear in a random genome sequence more than forty times with a probability ,10-32. Such a word frequency, however, is not as extraordinary if we take into account the universal shape of genomic spectra. A DPL distribution fitted to the human genome spectrum yields a P-value of 0.001 (see Supplementary Material).This latter translates to about four million 16-mers that are expected to occur at least forty times in a random genome-sized sequence. Strikingly, at least 460 thousand frequent words appear already in the repeat-masked sequence as accidental constituents of the fitted ...
Naturally Occurring Human Genetic Variation in the 3′-Untranslated Region of the Secretory Protein Chromogranin A Is Associated With Autonomic Blood Pressure Regulation and Hypertension in a Sex-Dependent Fashion Academic Article ...
Advances in single-cell technologies have revealed vast differences between cells once thought to be in the same category, calling into question how we define cell type in the first place ...