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PubMed2000

Improved safety and titre of murine leukaemia virus (MLV)-based retroviral vectors.

Many retroviral vectors based on murine leukaemia virus (MLV) contain the first 420 nucleotides of the gag gene, as this was reported to increase vector titre by increasing the efficiency of RNA packaging. In this study, deletion of this gag sequence from its original location did not decrease the titre of two retroviral vectors, pBabe puro and MFG-S-. The two vectors could be improved by replacing the gag sequence with a CTE from Mason-Pfizer monkey virus (MPMV). This substitution improved vector titre, while eliminating a region of homology between vector and packaging constructs. Gene Therapy (2000) 7, 300-305.

Animals↗
PubMed2000

RNA export: insights from viral models.

The retroviruses export intron-containing RNA. The complex retroviruses encode a Rev protein that uses a leucine-rich NES to interact with CRM1 and the U snRNA-export pathway. Other viruses encode proteins with a Rev-like NES. The type-D retroviruses contain a CTE that binds the cellular protein TAP to export intron-containing RNA through the mRNA pathway. Intronless viral transcripts contain post-transcriptionally acting RNA elements that may compensate for the lack of an intron. The functions of elements in intronless RNA are not fully understood but may be in export and/or 3'-end processing.

Active Transport, Cell Nucleus↗
PubMed2001

REF proteins mediate the export of spliced and unspliced mRNAs from the nucleus.

The REF family of evolutionarily conserved heterogeneous ribonucleoprotein (hnRNP)-like proteins consists of one central RNP-type RNA binding domain flanked by Arg-Gly-rich regions of variable length. Members of this protein family bind directly to RNA and the mRNA export factor TAP/Mex67p, and it has been suggested that they facilitate the recruitment of TAP/Mex67p to cellular mRNPs. We show that the variable regions are necessary for binding of REFs to RNA and to TAP. Antibodies specific to REFs prevent their interaction with RNA in vitro. After microinjection into Xenopus oocytes, these antibodies inhibit mRNA nuclear export. This inhibition of export is observed whether or not the mRNAs are generated by splicing. The antibodies do not interfere with pre-mRNA splicing or with the nuclear export of constitutive transport element (CTE)-containing RNAs (directly mediated by TAP), so REF proteins must play a critical role in mRNA nuclear export, acting downstream of splicing and upstream of TAP/Mex67p. We also show that recombinant REFs stimulate directly the export of mRNAs that are otherwise exported inefficiently. Together, our data indicate that REFs are directly implicated in the export of mRNAs from the nucleus. More generally, we show that spliced and unspliced mRNAs use common export factors to reach the cytoplasm.

Amino Acid Sequence↗
PubMed1999

Peroxisome proliferator-induced long chain acyl-CoA thioesterases comprise a highly conserved novel multi-gene family involved in lipid metabolism.

Long chain acyl-CoA esters are important intermediates in degradation and synthesis of fatty acids, as well as having important functions in regulation of intermediary metabolism and gene expression. Although the physiological functions for most acyl-CoA thioesterases have not yet been elucidated, previous data suggest that these enzymes may be involved in lipid metabolism by modulation of cellular concentrations of acyl-CoAs and fatty acids. In line with this, we have cloned four highly homologous acyl-CoA thioesterase genes from mouse, showing multiple compartmental localizations. The nomenclature for these genes has tentatively been assigned as CTE-I (cytosolic), MTE-I (mitochondrial), and PTE-Ia and Ib (peroxisomal), based on the identification of putative targeting signals. Although the various isoenzymes show between 67% and 94% identity at amino acid level, each individual enzyme shows a specific tissue expression. Our data suggest that all four genes are located within a very narrow cluster on chromosome 12 in mouse, similar to a sequence cluster on human chromosome 14, which identified four genes homologous to the mouse thioesterase genes. Four related genes were also identified in Caenorhabditis elegans, all containing putative PTS1 targeting signals, suggesting that the ancestral type I thioesterase gene(s) is/are of peroxisomal origin. All four thioesterases are differentially expressed in tissues examined, but all are inducible at mRNA level by treatment with the peroxisome proliferator clofibrate, or during the physiological condition of fasting, both of which conditions cause a perturbation in overall lipid homeostasis. These results strongly support the existence of a novel multi-gene family cluster of mouse acyl-CoA thioesterases, each with a distinct function in lipid metabolism.

Amino Acid Sequence↗
PubMed2001

A role for KH domain proteins (Sam68-like mammalian proteins and quaking proteins) in the post-transcriptional regulation of HIV replication.

Overexpression of Sam68 functionally substitutes for, as well as synergizes with, human immunodeficiency virus type 1 (HIV-1) Rev in RRE (Rev response element)-mediated gene expression and virus replication. In addition, COOH-terminal deletion and/or point mutants of Sam68 exhibit a transdominant negative phenotype for HIV replication. Sam68 is a member of KH domain family that includes SLM-1, SLM-2 (Sam68 like mammalian); and QKI-5, QKI-6, and QKI-7 (mouse quaking) proteins. The objective of this study was to examine the effects of these KH family proteins on RRE- and CTE (constitutive transport element of type-D retrovirus)-mediated transactivation. We now report that SLM-1 and SLM-2 proteins, which are the closest relatives of Sam68, marginally enhanced RRE-mediated transactivation, while QK isoforms that are distant relatives of Sam68 had no effect. Interestingly, these proteins still enhanced the effect of Rev in RRE-mediated gene expression. The increase in chloramphenicol acetyltransferase activity was also reflected at the levels of cytoplasmic RRE-chloramphenicol acetyltransferase mRNAs, indicating that Sam68 and KH proteins may have been involved in the stability or export of unspliced RNA. The increase in Rev activity was sensitive to leptomycin B, but not to olomoucine, indicating that the effect of SLM-1, SLM-2, QKI-5, QKI-6, and QKI-7 is exerted through a CRM-1-dependent mRNA export pathway. Thus, KH family proteins play an important role in the post-transcriptional regulation of HIV.

Adaptor Proteins, Signal Transducing↗
PubMed1983

Evaluation of different cell cultures for the detection of heat-labile enterotoxins of Escherichia coli strains isolated from pigs.

The sensitivity of various cell cultures to heat-labile enterotoxins (LT) and Verocytotoxin (VT) of fifteen E. coli strains isolated from cases of pig colibacillosis in Poland was estimated and compared with the effect of enterotoxins of four standard E. coli strains. Of ten tested cell cultures, only the following were susceptible: CHO, Vero, GMK, and HeLa. Eight strains showed CTE in He La and CHO cells and five of these reacted in Vero cells. The results appear to suggest that some of the tested E. coli strains isolated from pigs produced VT enterotoxin. Morphological changes caused by the above mentioned E. coli toxins in Vero and GMK cells took the form of cell rounding, followed by cell dissolution.

Animals↗
PubMed2005

Viral interactions with the nuclear transport machinery: discovering and disrupting pathways.

Viruses have been invaluable tools for discovering key pathways of nucleocytoplasmic transport. Conversely, disruption of specific nuclear transport pathways, are crucial for the productive life cycle of some viruses. The major cellular mRNA export pathway, which uses TAP (NXF1)/p15(NXT) as receptor, was discovered as a result of TAP interaction with CTE-containing RNAs from Mason-Pfizer Monkey Virus. In addition, CRM1 or exportin 1, which is a transport receptor that mediates nuclear export of proteins, snRNAs, rRNAs and a small subset of mRNAs, was discovered as an interacting partner of the Rev protein of HIV1. Viruses may disrupt the nuclear transport machinery to prevent host antiviral response. VSV Matrix (M) protein inhibits mRNA export by forming a complex with the mRNA export factor Rae1 whereas poliovirus inhibits nuclear import of proteins by probably degrading Nup62 and Nup153. Hence, this review focuses on viruses as tools and as disruptors of nucleocytoplasmic trafficking.

Active Transport, Cell Nucleus↗
PubMed2003

Stimulatory effect of an indirectly attached RNA helicase-recruiting sequence on the suppression of gene expression by antisense oligonucleotides.

Antisense oligonucleotides (ODNs) are powerful tools with which to determine the consequences of the reduced expression of a selected target gene, and they may have important therapeutic applications. Methods for predicting optimum antisense sites are not always effective because various factors, such as RNA-binding proteins, influence the secondary and tertiary structures of RNAs in vivo. To overcome this obstacle, we have attempted to engineer an antisense system that can unravel secondary and tertiary RNA structures. To create such an antisense system, we connected the constitutive transport element (CTE), an RNA motif that has the ability to interact with intracellular RNA helicases, to an antisense sequence so that helicase-binding hybrid antisense ODN would be produced in cells. We postulated that this modification would enhance antisense activity in vivo, with more frequent hybridization of the antisense ODN with its targeting site. Western blotting analysis demonstrated that a hybrid antisense ODN targeted to the bcl-2 gene suppressed the expression of this gene more effectively than did the antisense ODN alone. Our results suggest that the effects of antisense ODNs can be enhanced when their actions are combined with those of RNA helicases.

Gene Expression Regulation↗
PubMed2003

Inhibition of HCV NS3 protease by RNA aptamers in cells.

Non-structural protein 3 (NS3) of hepatitis C virus (HCV) has two distinct activities, protease and helicase, which are essential for HCV proliferation. In previous work, we obtained RNA aptamers (G9-I, II and III) which specifically bound the NS3 protease domain (DeltaNS3), efficiently inhibiting protease activity in vitro. To utilize these aptamers in vivo, we constructed a G9 aptamer expression system in cultured cells, using the cytomegarovirus enhancer + chicken beta-actin globin (CAG) promoter. By conjugating the cis-acting genomic human hepatitis delta virus (HDV) ribozyme and G9-II aptamer, a chimeric HDV ribozyme-G9-II aptamer (HA) was constructed, which was used to produce stable RNA in vivo and to create tandem repeats of the functional unit. To target the transcribed RNA aptamers to the cytoplasm, the minimal mutant of constitutive transport element (CTE), derived from type D retroviruses, was conjugated at the 3' end of HA (HAC). Transcript RNAs from (HA)(n) and (HAC)(n) were processed into the G9-II aptamer unit by the cis-acting HDV ribozyme, both in vitro and in vivo. Efficient protease inhibition activity of HDV ribozyme-G9-II aptamer expression plasmid was demonstrated in HeLa cells. Protease inhibition activity level of tandem chimeric aptamers, (HA)(n) and (HAC)(n), rose with the increase of n from 1 to 4.

Base Sequence↗
PubMed2003

dsRBM1 and a proline-rich domain of RNA helicase A can form a composite binder to recognize a specific dsDNA.

The double-stranded RNA-binding motif (dsRBM) is a widely distributed motif frequently found within proteins with sequence non-specific RNA duplex-binding activity. In addition to the binding of double-stranded RNA, some dsRBMs also participate in complex formation via protein-protein interactions. Interestingly, a lot of proteins containing multiple dsRBMs have only some of their dsRBMs with the expected RNA duplex-binding competency proven, while the functions of the other dsRBMs remain unknown. We show here that the dsRBM1 of RNA helicase A (RHA) can cooperate with a C-terminal domain of proline-rich content to gain novel nucleic acid-binding activities. This integrated nucleic acid-binding module is capable of associating with the consensus sequences of the constitutive transport element (CTE) RNA of type D retrovirus against RNA duplex competitors. Remarkably, binding activity for double-stranded DNA corresponding to the consensus sequences of the cyclic-AMP responsive element also resides within this composite nucleic acid binder. It thus suggests that the dsRBM fold can be used as a platform for the building of a ligand binding module capable of non-RNA macromolecule binding with an accessory sequence, and functional assessment for a newly identified protein containing dsRBM fold should be more cautious.

Amino Acid Motifs↗
PubMed2002

Modulation of beta-secretase gene expression by action of catalytic nucleic acids.

Two sites of the initial translation sequence of beta-secretase (BACE) mRNA were chosen as targets for endogenously delivered hammerhead ribozymes. Ribozyme cassettes coding a catalytic core, flanked by the 5'-tRNA(Val) and the 3'-CTE (constitutive transport element) sequences, were cloned into a pUC119 plasmid and used for transfection of transformed primary human embryonal kidney (HEK293) cells. The ribozymes express in the test cells and inhibit beta-secretase gene biosynthesis on the level of mRNA (up to 95%) and on the level of protein (up to 90%) and thus may be considered as therapeutic inhibitors of beta-secretase activity.

Amyloid Precursor Protein Secretases↗
PubMed2005

Correlation of C-reactive protein with clinical, endoscopic, histologic, and radiographic activity in inflammatory bowel disease.

INTRODUCTION: We sought to examine the relationship between C-reactive protein (CRP) and clinical, endoscopic, histologic, and radiographic activity in inflammatory bowel disease (IBD). METHODS: All IBD patients at our institution between January 2002 and August 2003 who had a CRP, colonoscopy, and either small bowel follow-through (SBFT) or CT enterography (CTE) performed within 14 days were identified. Clinical activity was assessed retrospectively through review of the medical record. Logistic regression was used in Crohn's disease (CD) patients to estimate the odds ratio (OR) with 95% confidence intervals for an elevated CRP. Associations were assessed using Fisher exact test in ulcerative colitis (UC) patients due to small sample size. RESULTS: One-hundred four CD patients (46% males) and 43 UC and indeterminate colitis patients (44% males) were identified. In CD patients, moderate-severe clinical activity (OR, 4.5; 95% CI, 1.1-18.3), active disease at colonoscopy (OR, 3.5; 95% CI, 1.4-8.9), and histologically severe inflammation (OR, 10.6; 95% CI; 1.1-104) were all significantly associated with CRP elevation. Abnormal small bowel radiographic imaging was not significantly associated with CRP elevation. In UC patients, CRP elevation was significantly associated with severe clinical activity, elevation in sedimentation rate, anemia, hypoalbuminemia, and active disease at ileocolonoscopy, but not with histologic inflammation. CONCLUSIONS: CRP elevation in IBD patients is associated with clinical disease activity, endoscopic inflammation, severely active histologic inflammation (in CD patients), and several other biomarkers of inflammation, but not with radiographic activity.

Adolescent↗
PubMed2005

Phylogeny of Wolbachia pipientis based on gltA, groEL and ftsZ gene sequences: clustering of arthropod and nematode symbionts in the F supergroup, and evidence for further diversity in the Wolbachia tree.

Current phylogenies of the intracellular bacteria belonging to the genus Wolbachia identify six major clades (A-F), termed 'supergroups', but the branching order of these supergroups remains unresolved. Supergroups A, B and E include most of the wolbachiae found thus far in arthropods, while supergroups C and D include most of those found in filarial nematodes. Members of supergroup F have been found in arthropods (i.e. termites), and have previously been detected in the nematode Mansonella ozzardi, a causative agent of human filariasis. To resolve the phylogenetic positions of Wolbachia from Mansonella spp., and other novel strains from the flea Ctenocephalides felis and the filarial nematode Dipetalonema gracile, the authors generated new DNA sequences of the Wolbachia genes encoding citrate synthase (gltA), heat-shock protein 60 (groEL), and the cell division protein ftsZ. Phylogenetic analysis confirmed the designation of Wolbachia from Mansonella spp. as a member of the F supergroup. In addition, it was found that divergent lineages from Dip. gracile and Cte. felis lack any clear affiliation with known supergroups, indicating further genetic diversity within the Wolbachia genus. Finally, although the data generated did not permit clear resolution of the root of the global Wolbachia tree, the results suggest that the transfer of Wolbachia spp. from arthropods to nematodes (or vice versa) probably occurred more than once.

Animals↗
PubMed2005

Identification of fatty acid oxidation disorder patients with lowered acyl-CoA thioesterase activity in human skin fibroblasts.

BACKGROUND: Acyl-CoA thioesterases are enzymes that hydrolyze acyl-CoAs to the free fatty acid and coenzyme A (CoASH). These enzymes have been identified in several cellular compartments and are thought to regulate intracellular levels of acyl-CoAs, free fatty acids and CoASH. However, to date no patients deficient in acyl-CoA thioesterases have been identified. DESIGN: Acyl-CoA thioesterase activity was measured in human skin fibroblasts. Western-blot analysis was used to determine Type-II acyl-CoA thioesterase protein levels in patients. RESULTS: Acyl-CoA thioesterase activity was found in human fibroblasts with all saturated acyl-CoAs from C4-CoA to C18-CoA, with highest activity detected with lauroyl-CoA and myristoyl-CoA (C12-CoA and C14-CoA). An antibody that recognizes the major isoforms of Type-II acyl-CoA thioesterases precipitated the majority of acyl-CoA thioesterase activity in fibroblasts, showing that the main thioesterase activity detected in fibroblasts is catalyzed by Type-II thioesterases. Measurement of acyl-CoA thioesterase activity from fibroblasts of 34 patients with putative fatty acid oxidation disorders resulted in the identification of three patients with lowered Type-II acyl-CoA thioesterase activity in fibroblasts. These patients also had lowered expression of Type-II acyl-CoA thioesterase protein in fibroblasts as judged by Western-blot analysis. However, mutation analysis failed to identify any mutation in the coding sequences for the mitochondrial acyl-CoA thioesterase II (MTE-II) or the cytosolic acyl-CoA thioesterase II (CTE-II). CONCLUSIONS: We have described three patients with lowered Type-II acyl-CoA thioesterase protein and activity in human skin fibroblasts, which is the first description of patients with a putative defect in acyl-CoA thioesterases.

Blotting, Western↗
PubMed2004

Diagnosis of flea allergy dermatitis: comparison of intradermal testing with flea allergens and a FcepsilonRI alpha-based IgE assay in response to flea control.

The objective of this study was to evaluate the accuracy of in vivo and in vitro tests in the diagnosis of flea allergy dermatitis in comparison with history, clinical signs and response to flea control. Intradermal testing using four different sources of flea allergens and FcepsilonRIalpha-based immunoglobulin (Ig)E assays were performed in 15 flea-allergic dogs, 15 atopic dogs and 15 dogs infested with fleas but showing no clinical signs of skin disease. Sensitivity, specificity, negative predictive value, positive predictive value and accuracy were calculated for all five tests and results varied greatly. Sensitivity, specificity and overall accuracy were 27, 83 and 64%, respectively, for one extract (Isotec), 67, 90 and 82% for another extract (Greer), 93, 90 and 91% for flea saliva, 40, 90 and 73% for the recombinant Cte f 1 both produced by Heska Corp. and 87, 53 and 64% for a FcepsilonRIalpha-based IgE assay. These results indicate that intradermal testing with flea extracts is more accurate in the diagnosis of flea allergy dermatitis than in vitro tests. Moreover, pure flea saliva used as a reagent for intradermal testing provided the best results in terms of sensitivity, specificity and overall accuracy although the Greer extract, a whole body flea extract, also allowed a good correlation between intradermal testing results and clinical approach to flea allergy dermatitis diagnosis.

Allergens↗
PubMed2004

Hospitalists as teachers.

OBJECTIVE: To compare evaluations of teaching effectiveness among hospitalist, general medicine, and subspecialist attendings on general medicine wards. DESIGN: Cross-sectional. SETTING: A large, inner-city, public teaching hospital. PARTICIPANTS: A total of 423 medical students and house staff evaluating 63 attending physicians. MEASUREMENTS AND MAIN RESULTS: We measured teaching effectiveness with the McGill Clinical Tutor Evaluation (CTE), a validated 25-item survey, and reviewed additional written comments. The response rate was 81%. On a 150-point composite measure, hospitalists' mean score (134.5 [95% confidence interval (CI), 130.2 to 138.8]) exceeded that of subspecialists (126.3 [95% CI, 120.4 to 132.1]), P =.03. General medicine attendings (135.0 [95% CI, 131.2 to 138.8]) were also rated higher than subspecialists, P =.01. Physicians who graduated from medical school in the 1990s received higher scores (136.0 [95% CI, 133.0 to 139.1]) than did more distant graduates (129.1 [95% CI, 125.1 to 133.1]), P =.006. These trends persisted after adjusting for covariates, but only year of graduation remained statistically significant, P =.05. Qualitative analysis of written remarks revealed that trainees valued faculty who were enthusiastic teachers, practiced evidence-based medicine, were involved in patient care, and developed a good rapport with patients and other team members. These characteristics were most often noted for hospitalist and general medicine attendings. CONCLUSIONS: On general medicine wards, medical students and residents considered hospitalists and general medicine attendings to be more effective teachers than subspecialists. This effect may be related to the preferred faculty members exhibiting specific characteristics and behaviors highly valued by trainees, such as enthusiasm for teaching and use of evidence-based medicine.

Adult↗
PubMed1999

The carboxyl terminus of RNA helicase A contains a bidirectional nuclear transport domain.

Human RNA helicase A was recently identified to be a shuttle protein which interacts with the constitutive transport element (CTE) of type D retroviruses. Here we show that a domain of 110 amino acids at the carboxyl terminus of helicase A is both necessary and sufficient for nuclear localization as well as rapid nuclear export of glutathione S-transferase fusion proteins. The import and export activities of this domain overlap but are separable by point mutations. This bidirectional nuclear transport domain (NTD) has no obvious sequence homology to previously identified nuclear import or export signals. However, the Ran-dependent nuclear import of NTD was efficiently competed by excess amounts of the nuclear localization signal (NLS) peptide from simian virus 40 large T antigen, suggesting that import is mediated by the classical NLS pathway. The nuclear export pathway accessed by NTD is insensitive to leptomycin B and thus is distinct from the leucine-rich nuclear export signal pathway mediated by CRM1.

Amino Acid Sequence↗
PubMed2001

Tradeoffs in elastographic imaging.

This paper presents the tradeoffs in elastographic imaging. Elastography is viewed as a new imaging modality and presented in terms of three fundamental concepts that constitute the basis for the elastographic imaging process. These are the tissue elastic deformation process, the statistical analysis of strain estimation and the image characterization. The first concept involves the use of the contrast transfer efficiency (CTE) that describes the mapping of a distribution of local tissue elastic moduli into a distribution of local longitudinal tissue strains. The second concept defines the elastographic system and the relationship between ultrasonic and signal processing parameters. This process is described in terms of a stochastic framework (the strain filter) that provides upper and practical performance bounds and their dependence on the various system parameters. Finally, the output image, the elastogram, is characterized by its image parameters, such as signal-to-noise ratio, contrast-to-noise ratio, dynamic range and resolution. Finite-element simulations are used to generate examples of elastograms that are confirmed by the theoretical prediction tools.

Acoustics↗