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PubMed1990

The expression pattern of an insulin-like growth factor (IGF)-binding protein gene is distinct from IGF-II in the midgestational rat embryo.

Insulin-like growth factor-II (IGF-II), the predominant form of IGF in fetal and neonatal serum and tissues, is found in vivo complexed with IGF-binding proteins. One of these binding proteins, IGFBP-2, is present at high levels in fetal rat plasma and binds both IGF-I and IGF-II with high affinity. We here have used in situ hybridization to compare the distribution of IGFBP-2 mRNA with that of IGF-II mRNA in embryonic day 13.5-15 rat embryos. The spatial patterns of IGF-II and IGFBP-2 expression in the fetal trunk were distinct and, in general, nonoverlapping. Most mesoderm derivatives that express IGF-II at high levels contained little, if any, IGFBP-2 mRNA. Instead, IGFBP-2 mRNA was expressed at high levels in many cell types derived from ectoderm and endoderm. The expression of IGFBP-2 mRNA in the central nervous system (CNS) during this developmental period was examined in particular detail. The three most prominent sites of IGFBP-2 expression in the CNS were comprised of cells with nonneuronal phenotypes: 1) the epithelium of the choroid plexus, a tissue that produces cerebrospinal fluid; 2) the floor plate, an area that can guide axonal outgrowth from commissural neurons of the spinal cord in vitro; and 3) the infundibulum, the progenitor of the posterior pituitary that is believed to influence differentiation of the adjacent intermediate pituitary.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1997

A practical guide to the use of interferons in the management of hepatitis virus infections.

The recommended interferon dosage for patients with chronic hepatitis and typical hepatitis B virus (HBV) infection is 10 MU 3 times weekly for 4 to 6 months; with such a regimen sustained alanine aminotransferase (ALT) normalisation, liver histology improvement, clearance of HBV DNA and seroconversion from hepatitis B e antigen (HBeAg) to anti-HBe are obtained in about 40% of treated patients. Patients with elevated disease activity (high ALT values, active chronic hepatitis, low HBV DNA levels) tend to respond better to therapy; Oriental patients and immunocompromised patients are not ideal candidates for interferon. Patients with chronic hepatitis B and the HBeAg-negative variant should be given intermediate dosages (6 to 9 MU thrice weekly) of interferon for prolonged periods (12 months); however, even with this approach, the relapse rate is high (> 60%) during the follow-up. In chronic hepatitis D virus (HDV) infection, therapy with 9 to 10 MU of interferon 3 times weekly for 12 months induces a transient remission in disease (ALT normalisation, HDV RNA clearance) in more than 50% of treated patients, but a sustained response is found in less than 20% of patients. In such disease, baseline predictive factors of long term response are still unknown. In chronic hepatitis C, treatment with 3 to 5 MU of interferon given 3 times weekly for 6 to 12 months induces a sustained remission in no more than 30% of treated patients. Probable predictive factors of long term response are: low viraemia, genotype other than 1, absence of cirrhosis, low intrahepatic iron content, low nucleotide diversity of the envelope 2 gene of the hepatitis C virus. Prolonged (> 12 months) therapeutic courses seem to enhance the sustained response rate; in nonresponders/relapsers, combined therapy (interferon plus indomethacin, interferon plus ketoprofen, interferon plus ribavirin) is promising but randomised controlled trials are needed in order to establish the real efficacy and safety of such therapeutic regimens.

Hepatitis B↗
PubMed2000

Massive idiosyncratic exon skipping corrects the nonsense mutation in dystrophic mouse muscle and produces functional revertant fibers by clonal expansion.

Conventionally, nonsense mutations within a gene preclude synthesis of a full-length functional protein. Obviation of such a blockage is seen in the mdx mouse, where despite a nonsense mutation in exon 23 of the dystrophin gene, occasional so-called revertant muscle fibers are seen to contain near-normal levels of its protein product. Here, we show that reversion of dystrophin expression in mdx mice muscle involves unprecedented massive loss of up to 30 exons. We detected several alternatively processed transcripts that could account for some of the revertant dystrophins and could not detect genomic deletion from the region commonly skipped in revertant dystrophin. This, together with exon skipping in two noncontiguous regions, favors aberrant splicing as the mechanism for the restoration of dystrophin, but is hard to reconcile with the clonal idiosyncrasy of revertant dystrophins. Revertant dystrophins retain functional domains and mediate plasmalemmal assembly of the dystrophin-associated glycoprotein complex. Physiological function of revertant fibers is demonstrated by the clonal growth of revertant clusters with age, suggesting that revertant dystrophin could be used as a guide to the construction of dystrophin expression vectors for individual gene therapy. The dystrophin gene in the mdx mouse provides a favored system for study of exon skipping associated with nonsense mutations.

Aging↗
PubMed2005

Natural mutations in a 2'-5' oligoadenylate synthetase transgene revealed residues essential for enzyme activity.

Unlike other RNA polymerases, 2'-5' oligoadenylate synthetases, a family of interferon-induced enzymes, catalyze the formation of 2'-5', not 3'-5', phosphodiester bonds. Moreover, to be active, these proteins require double-stranded RNA as a cofactor. We have been identifying the specific residues of these proteins that impart their novel properties. Here, we report the identity of three such residues that underwent natural mutations in a transgenic mouse line. When deliberately introduced into recombinant proteins, each of these mutations rendered the protein enzymatically inactive. In an effort to understand the roles of these residues in enzyme activity, new mutants carrying other residues in one of these three sites were generated. Detailed characterization of the properties of the mutant proteins revealed that Lys 404 is needed for proper binding of the acceptor substrate, Pro 500 provides structural flexibility to the protein, and Ser 471 is probably required for its proper folding. This study illustrates the power of using natural mutations in transgenes as guides for studying structure-function relationships of proteins.

2',5'-Oligoadenylate Synthetase↗
PubMed1999

Human endothelium: endovascular biopsy and molecular analysis.

PURPOSE: To develop a safe and reproducible method for harvesting viable vascular endothelium to analyze gene expression at sites of vascular lesions. MATERIALS AND METHODS: Coaxial curved stainless-steel guide wires were used to obtain samples of endothelial cells from large arteries and veins in 29 patients undergoing routine endovascular procedures. Three immunocytochemical markers were used to identify cells as endothelial. Cellular viability was evaluated in terms of cell membrane integrity, energy-dependent uptake of acetylated low-density lipoprotein, and cellular response to lipopolysaccharide. Single-cell reverse transcription polymerase chain reaction (PCR) and immunocytochemistry were used to study endothelial gene expression. RESULTS: Cells with endothelial morphology and immunoreactivity for von Willebrand factor, thrombomodulin, and angiotensin-converting enzyme were consistently obtained from iliac and carotid arteries and large veins (average yield [+/- standard error] from 26 iliac arteries, 262 endothelial cells +/- 45, 20%-30% of which were viable). These cells displayed induction of E-selection messenger RNA at PCR after exposure to lipopolysaccharide. Expression of vascular cell adhesion molecule 1 transcripts in endothelial cells increased with patient age (P < .01), whereas expression of intercellular adhesion molecule 1 did not. CONCLUSION: Viable endothelium can be obtained during routine angiography. Immunocytochemical and reverse transcription PCR analyses of these cells allowed determination of transcripts and proteins expressed by endothelium at sites of vascular lesions. Such information could aid in understanding mechanisms of vascular diseases and in clinical decision making.

Adolescent↗
PubMed2000

Genetic mosaic analysis based on Cre recombinase and navigated laser capture microdissection.

Defining molecular interactions that occur at the interface between "normal" and "abnormal" cell populations represents an important but often underexplored aspect of the pathogenesis of diseases with focal origins. Here, we illustrate an approach for conducting such analyses based on mosaic patterns of Cre recombinase expression in the adult mouse intestinal epithelium. Transgenic mice were generated that express Cre in the stem cell niche of crypts located in specified regions of their intestine. Some of these mice were engineered to allow for doxycycline-inducible Cre expression. Recombination in all pedigrees was mosaic: Cre-expressing crypts that supported recombination in all of their active multipotent stem cells were located adjacent to "control" crypts that did not express Cre at detectable levels. Cre-mediated recombination of a floxed LacZ reporter provided direct evidence that adult small-intestinal crypts contain more than one active multipotent stem cell, and that these cells can be retained in both small-intestinal and colonic crypts for at least 80 d. A method was developed to recover epithelial cells from crypts with or without recombination for subsequent gene expression profiling. Stained sections of intestine were used to create electronic image templates to guide laser capture microdissection (LCM) of adjacent frozen sections. This navigated form of LCM overcomes problems with mRNA degradation encountered when cells are marked directly by immunohistochemical methods. Combining Cre-engineered genetic mosaic mice with navigated-LCM will allow biology and pathobiology to be explored at the junction between normal and perturbed cellular cohorts.

Animals↗
PubMed2000

Drug resistance. An updated, user-friendly guide to genotype interpretation.

Genotypic antiretroviral resistance testing (GART) has been shown to be of value in selecting antiretroviral therapy. Unfortunately, GART reports often are difficult to interpret and, at times, can be misleading. Published lists of "primary" resistance mutations often do not include the combinations of "secondary" mutations, which also limit the efficacy of antiretroviral agents. This article tries to rectify this situation by introducing a general approach to genotype interpretation and by providing more "user-friendly" tables of key single mutations and key mutation combinations.

Drug Resistance, Microbial↗
PubMed2003

Central administration of the neurotensin receptor antagonist SR48692 attenuates vacuous chewing movements in a rodent model of tardive dyskinesia.

Tardive dyskinesia is a movement disorder that develops in 20-30% of patients treated with chronic neuroleptics. Whilst the pathogenesis of tardive dyskinesia remains unclear, altered expression of neuropeptides in the basal ganglia has been implicated in its emergence. The peptide neurotensin is expressed in both dopamine D1 receptor-bearing neurons of the direct striatonigral pathway and dopamine D2 receptor-bearing neurons of the indirect striatopallidal pathway. Increased levels of striatal neurotensin messenger RNA (mRNA) are reported following chronic neuroleptic therapy. Chronic treatment with the typical antipsychotic haloperidol elicits neurotensin immunoreactivity in a large number of striatopallidal and a modest number of striatonigral projection neurons, whilst treatment with the potent dopamine releaser, methamphetamine, induces intense neurotensin immunoreactivity in striatonigral projection neurons. In order to determine whether increased levels of striatal neurotensin mRNA in the direct striatonigral or the indirect striatopallidal pathway play a more influential role in the development of tardive dyskinesia, we explored the effects of a specific neurotensin antagonist in a rodent model (vacuous chewing movements [VCMs] induced by chronic neuroleptics). Three groups of animals received injections of fluphenazine decanoate (25 mg/kg) or its vehicle sesame oil every 3 weeks for at least 18 weeks. They were then surgically implanted with bilateral guide cannulae aimed at the striatum, the substantia nigra pars reticulata, or the globus pallidus respectively. After recovery, animals were infused with 2-[(1-(7-chloro-4-quinolinyl)-5-(2,6-imethoxyphenyl)pyrazol-3-yl)carbonylamino]tricyclo(3.3.1.1.(3.7))decan-2-carboxylic acid (SR48692; 0.25, 0.50, and 1.0 nmol/microl), or its vehicle (10% dimethyl sulfoxide [DMSO] in saline) and observed for 60 min. Intra-striatal, intra-nigral or intra-pallidal infusion of SR48692 attenuated neuroleptic-induced VCMs. These findings lend further support to a role for neurotensin in the development of VCMs but do not clarify which pathway plays a more important role. Thus, treatments that reduce or prevent the effects of increased neurotensin expression and release may be useful in the management of tardive dyskinesia.

Animals↗
PubMed2005

Coevolution theory of the genetic code at age thirty.

The coevolution theory of the genetic code, which postulates that prebiotic synthesis was an inadequate source of all twenty protein amino acids, and therefore some of them had to be derived from the coevolving pathways of amino acid biosynthesis, has been assessed in the light of the discoveries of the past three decades. Its four fundamental tenets regarding the essentiality of amino acid biosynthesis, role of pretran synthesis, biosynthetic imprint on codon allocations and mutability of the encoded amino acids are proven by the new knowledge. Of the factors that guided the evolutionary selection of the universal code, the relative contributions of Amino Acid Biosynthesis: Error Minimization: Stereochemical Interaction are estimated to first approximation as 40,000,000:400:1, which suggests that amino acid biosynthesis represents the dominant factor shaping the code. The utility of the coevolution theory is demonstrated by its opening up experimental expansions of the code and providing a basis for locating the root of life.

Amino Acids↗
PubMed1975

The origin of the genetic code.

A new approach to the origin of the genetic code is proposed based on some regularities in the nucleotide distribution pattern of the code. The relative amounts of various amino acids in primitive proteins were possibly different from those in organisms living today. The primordial ratio was supposed to shift to the modern one guided by the action of primitive nucleotides. Each primitive tRNA had a discriminator site and, distinguished from it, an anticodon site. It also postulated that primordially each amino acid could correspond to a wide variety of codons. During the course of the evolutionary change, a selective mechanism worked among the protobionts so that less frequent nucleotides became associated with more abundant amino acids in the primordial conditions,thus finally leading to the present codon catalogue.

Amino Acids↗
PubMed2025

UMI-nea: a fast, robust tool for reference-free UMI deduplication and accurate quantification.

MOTIVATION: One of the key applications of Unique Molecular Identifiers (UMIs) in high-throughput sequencing is to correct for PCR amplification bias and removal of PCR duplicates, thereby improving quantification in DNA-seq and RNA-seq applications. Accurately grouping error-bearing UMIs that originate from the same input molecule through a UMI deduplication method is a critical step in this process. However, many existing UMI deduplication tools rely on simple Hamming distance comparisons or suboptimal clustering algorithms, often resulting in erroneous UMI groupings, particularly in error-prone long-read sequencing or ultra-high-depth short-read sequencing. RESULTS: We introduce UMI-nea, a tool that utilizes Levenshtein distance comparisons and a novel clustering approach to optimize multithreading workflows. Compared against three other indel-aware UMI deduplication tools, UMI-nea achieves more accurate UMI groupings with efficient run time. It demonstrates robust performance across diverse sequencing platforms, depths, and UMI lengths. Additionally, UMI-nea incorporates a data-guided adaptive UMI filter, further enhancing quantification accuracy. AVAILABILITY AND IMPLEMENTATION: UMI-nea is available on github https://github.com/Qiaseq-research/UMI-nea.git or Zenodo https://doi.org/10.5281/zenodo.16745758. Sequencing data are stored at https://qiagenpublic.blob.core.windows.net/umi-nea-datasets/.

High-Throughput Nucleotide Sequencing↗
PubMed2026

CARM1 in human cancer: a multifunctional epigenetic node driving tumor plasticity and therapeutic vulnerability.

Coactivator-associated arginine methyltransferase 1 (CARM1/PRMT4) is a signal-responsive epigenetic regulator that couples oncogenic and stress signals to chromatin, transcription, RNA processing, metabolism, and genome maintenance. Its effects arise from both asymmetric arginine methylation of histone and non-histone substrates and methyltransferase-independent scaffolding activities. This review critically synthesizes the structural basis, substrate networks, methylarginine readers, and cancer-contextual functions of CARM1. We propose that its apparently opposing oncogenic and tumor-suppressive activities are determined by lineage-specific substrates, regulatory post-translational modifications, cofactor and chromatin availability, and stage- or microenvironment-dependent stress signals. We further evaluate CARM1-directed therapy using an evidence-graded framework. Catalytic inhibitors such as TP-064 and EZM2302 differ in binding mode and substrate coverage, whereas emerging degraders can remove scaffolding functions but remain constrained by delivery, E3-ligase heterogeneity, pharmacokinetics, and therapeutic-window uncertainties. Biomarker-guided synthetic-lethal and immunotherapy combinations may therefore offer the most tractable route to clinical translation. This framework positions CARM1 as a context-conditioned signal-to-chromatin translator rather than a uniformly druggable oncogene.

Humans↗
PubMed2003

Molecular recognition properties of IGS-mediated reactions catalyzed by a Pneumocystis carinii group I intron.

We report the development, analysis and use of a new combinatorial approach to analyze the substrate sequence dependence of the suicide inhibition, cyclization, and reverse cyclization reactions catalyzed by a group I intron from the opportunistic pathogen Pneumocystis carinii. We demonstrate that the sequence specificity of these Internal Guide Sequence (IGS)-mediated reactions is not high. In addition, the sequence specificity of suicide inhibition decreases with increasing MgCl(2) concentration, reverse cyclization is substantially more sequence specific than suicide inhibition, and multiple reverse cyclization products occur, in part due to the formation of multiple cyclization intermediates. Thermodynamic analysis reveals that a base pair at position -4 of the resultant 5' exon-IGS (P1) helix is crucial for tertiary docking of the P1 helix into the catalytic core of the ribozyme in the suicide inhibition reaction. In contrast to results reported with a Tetrahymena ribozyme, altering the sequence of the IGS of the P.carinii ribozyme can result in a marked reduction in tertiary stability of docking the resultant P1 helix into the catalytic core of the ribozyme. Finally, results indicate that RNA targeting strategies which exploit tertiary interactions could have low specificity due to the tolerance of mismatched base pairs.

Base Sequence↗
PubMed2006

Testing the importance of p27 degradation by the SCFskp2 pathway in murine models of lung and colon cancer.

Decreased expression of the CDK inhibitor p27kip1 in human tumors directly correlates with increased resistance to chemotherapies, increased rates of metastasis, and an overall increased rate of patient mortality. It is thought that decreased p27 expression in tumors is caused by increased proteasomal turnover, in particular activation of the pathway governed by the SCFskp2 E3 ubiquitin protein ligase. We have directly tested the importance of the SCFskp-mediated degradation of p27 in tumorigenesis by analyzing the tumor susceptibility of mice that express a form of p27 that cannot be ubiquitinated and degraded by this pathway (p27T187A). In mouse models of both lung and colon cancer down-regulation of p27 promotes tumorigenesis. However, we found that preventing p27 degradation by the SCFskp2 pathway had no impact on tumor incidence or overall survival in either tumor model. Our study unveiled a previously unrecognized role for the control of p27 mRNA abundance in the development of non-small cell lung cancers. In the colon cancer model, the frequency of intestinal adenomas was similarly unaffected by the p27T187A mutation, but, unexpectedly, we found that it inhibited progression of intestinal adenomas to carcinomas. These studies may guide the choice of clinical settings in which pharmacologic inhibitors of the Skp2 pathway might be of therapeutic value.

Animals↗
PubMed2004

Netrin 1-mediated chemoattraction regulates the migratory pathway of LHRH neurons.

Luteinizing hormone-releasing hormone (LHRH) neurons migrate from the vomeronasal organ (VNO) to the forebrain in all mammals studied. In mice, the direction of LHRH neuron migration is dependent upon axons that originate in the VNO, but bypass the olfactory bulb and project caudally into the basal forebrain. Thus, factors that guide this unique subset of vomeronasal axons that comprise the caudal vomeronasal nerve (cVNN) are candidates for regulating the migration of LHRH neurons. We previously showed that deleted in colorectal cancer (DCC) is expressed by neurons that migrate out of the VNO during development [Schwarting et al. (2001) J. Neurosci., 21, 911-919]. We examined LHRH neuron migration in Dcc-/- mice and found that trajectories of the cVNN and positions of LHRH neurons are abnormal. Here we extend these studies to show that cVNN trajectories and LHRH cell migration in netrin 1 (Ntn1) mutant mice are also abnormal. Substantially reduced numbers of LHRH neurons are found in the basal forebrain and many LHRH neurons migrate into the cerebral cortex of Ntn1 knockout mice. In contrast, migration of LHRH cells is normal in Unc5h3rcm mutant mice. These results are consistent with the idea that the chemoattraction of DCC+ vomeronasal axons by a gradient of netrin 1 protein in the ventral forebrain guides the cVNN, which, in turn, determines the direction of LHRH neuron migration in the forebrain. Loss of function through a genetic deletion in either Dcc or Ntn1 results in the migration of many LHRH neurons to inappropriate destinations.

Animals↗
PubMed2005

Surveillance for HIV-1 incidence using tests for recent infection in resource-constrained countries.

Over the past few years, several assays have been developed for the purpose of estimating HIV-1 incidence from cross-sectional population surveys. The tests detect features of the evolving virological or immunological response to HIV-1 infection that distinguish recent from established infection. Surveillance programmes that collect specimens from population surveys for HIV-1 prevalence can apply some of these tests to the same specimen sets to estimate incidence. We describe these tests and discuss the principle and strategy for implementation of a testing programme for recent infection in surveillance settings. Test-specific prerequisites, such as calibration, validation, and quality assurance, and other test-specific performance characteristics that may influence interpretation, epidemiological considerations that may guide application, and practical operational considerations for implementation in surveillance settings are considered. When properly and judiciously applied, the capacity to estimate incidence from existing programmes that conduct surveillance for prevalent HIV-1 infection will enhance the capacity for more precise and timely analysis of the dynamics of the epidemic and the effectiveness of public health interventions.

AIDS Serodiagnosis↗
PubMed2005

A prospective study comparing cytomegalovirus antigenemia, DNAemia and RNAemia tests in guiding pre-emptive therapy in thoracic organ transplant recipients.

We evaluated the usefulness of DNAemia and mRNAemia tests in guiding the pre-emptive therapy against cytomegalovirus (CMV) infections in thoracic organ transplant recipients using antigenemia test as the reference. Seven lung (LTR) and 14 heart (HTR) transplant recipients were prospectively monitored for CMV by antigenemia, DNAemia (Cobas Amplicor PCR Monitor) and pp67-mRNAemia (NASBA) tests. However, only the antigenemia test guided pre-emptive therapy with cut-off levels of >or=2 and >or=5-10 pp65-positive leukocytes/50 000 leukocytes in the LTRs and HTRs, respectively. CMV DNAemia was detected in 26/28 (93%) and RNAemia in 17/28 (61%) of the CMV antigenemias requiring antiviral therapy (P = 0.01). Optimal DNAemia levels (sensitivity/specificity) estimated from receiver-operating characteristic curve to achieve maximal sum of sensitivity and specificity were 400 (75.9/92.7%), 850 (91.3/91.3%) and 1250 (100/91.5%) copies/ml for the antigenemia of 2, 5 and 10 pp65-positive leukocytes, respectively. The sensitivities of nucleic acid sequence-based amplification (NASBA) were 25.9%, 43.5% and 56.3% in detecting the same cut-off levels of antigenemia. In thoracic organ transplant recipients, the Cobas PCR assay is comparable with the antigenemia test in guiding pre-emptive therapy against CMV infections when threshold levels of over 5 pp65-antigen-positive leukocytes are used as the reference. In contrast, the low sensitivity of NASBA limits its usefulness in the guidance of pre-emptive therapy.

Adolescent↗
PubMed1997

Screening for bioactive compounds targeting the cellular signal transduction pathway using an RT-PCR-based bioassay system.

A novel bioassay system based on RT-PCR has been established to search for biologically active compounds which can modulate the expression of genes encoding important regulatory proteins. Changes in target mRNA level in the treated cell cultures were quantitatively determined by competitive PCR using internal standard DNA. The compounds discovered using this bioassay will be useful tools to elucidate the mechanisms of cellular signaling guiding the expression of the target genes. As the first application of the new bioassay strategy, the expression of the interleukin-2 gene in Jurkat cells, a human T cell line, was investigated. Screening of several crude drugs used in traditional Chinese medicines demonstrated that the aqueous acetone extract of Coptidis Rhizoma enhanced the expression of the interleukin-2 gene by about 5-fold as compared to the control.

Cell Line↗