PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “variable methylation”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 181 records · Page 10Linked to original sources
PubMed1982

Poisoning by Gyromitra : a possible mechanism.

"Gyromitra" are considered to be edible mushrooms although their potential toxicity has been long known. They have caused numerous accidents, sometimes lethal. Historical accounts of poisoning are reported and the authors describe the main characteristics : inconstant toxicity, influence of repetitive ingestions and variable individual sensitivity. Knowing the "gyromitrin" (N-methyl-N-formyl-acetyl-hydrazone) can be converted into methyl-hydrazine, the authors suggest a relation between individual sensitivity to the mushrooms and variation of every body's ability to carry out such a conversion. Several metabolites of gyromitrin can produce enzyme activation ith subsequent synthesis of methylhydrazine. The cumulative activating role of consecutive ingestions is emphasized.

Acetaldehyde↗
PubMed2026

The role of circulating tumor DNA (ctDNA) to detect minimal residual disease in locally advanced gastroesophageal carcinoma: the BUTTERFLY study.

BACKGROUND: Despite advances in perioperative and neoadjuvant strategies, patients with locally advanced gastroesophageal cancers remain at high risk of recurrence after curative intent treatment. No validated biomarkers are available to detect minimal residual disease (MRD) or to guide post-operative risk-adapted management. Circulating tumor DNA (ctDNA) has emerged as a noninvasive tool for disease monitoring; single-parameter or tumor-informed assays, however, may lack sensitivity in low-tumor burden settings. Multimodal, tumor-agnostic approaches may overcome these limitations. METHODS: The BUTTERFLY study is a prospective, multicenter observational study enrolling patients with stage II-III gastric, gastroesophageal junction, or esophageal cancer treated with perioperative chemotherapy or neoadjuvant chemoradiotherapy followed by surgery. It evaluates the diagnostic performance and prognostic value of an academic, tumor-agnostic, multimodal ctDNA assay for MRD detection and prognostic stratification. Serial plasma samples are collected from baseline through post-operative follow-up and at relapse. Cell-free DNA is analyzed using the Agnostic Liquid Biopsy Multimodal Advancement (ALMA) platform, integrating tumor fraction estimation, somatic copy number alterations, fragmentomic features, single-nucleotide variants, and whole-genome methylation profiling. Multimodal features are combined with clinical variables using machine learning-based models to enhance MRD detection and relapse risk stratification. The primary endpoint includes sensitivity and specificity of ALMA-defined ctDNA/MRD status at the 4-8 weeks after surgery landmark, whereas secondary endpoints assess diagnostic performance at other time points and associations between ctDNA status and dynamics with disease-free survival, overall survival, treatment response, and lead time to recurrence. FUTURE PERSPECTIVES: If validated, this tumor-agnostic, multimodal ctDNA approach may enable earlier molecular relapse detection and support personalized post-operative management strategies.

circulating tumor DNA (ctDNA)↗
PubMed1994

Three-dimensional molecular shape analysis-quantitative structure-activity relationship of a series of cholecystokinin-A receptor antagonists.

The three-dimensional molecular shape analysis-quantitative structure-activity relationship (3D-MSA-QSAR) technique has been applied to develop correlations between the calculated physicochemical properties and the in vitro activities of a series of 3-(acylamino)-5-phenyl-2H-1,4-benzodiazepine cholecystokinin-A (CCK-A) antagonists. 3D-MSA-QSARs were developed for varying subsets of 53 analogs (J. Med. Chem. 1988, 31, 2235-2246). An active conformation is hypothesized for these compounds using the loss in biological activity-loss in conformational stability principle. After placing all compounds in the active conformation and performing pairwise molecular shape analysis, it was determined that not any one analog serves as the best shape reference compound. Nonidentical volumes of allowed receptor space are mapped out by different antagonists. A shape reference compound that consists of selected overlapped structures expands the definition of the accessible receptor space. This type of mutant improves the predicted activity of analogs over the value predicted if only one compound is chosen as the reference. Molecular shape, as represented by common overlap steric volume and nonoverlap steric volume, is the major factor contributing to the affinity of this class of compounds. Intramolecular conformational stability, as measured by the difference in energy of the active conformation and the global minimum energy conformation, is also important. It is further concluded from the 3D-MSA-QSAR models that part of the binding pocket for the 3-amido substituent has a preference for lipophilicity. The method used in this study of fragmenting the antagonist into spheres of varying radii and measuring lipophilicity isolates the substructure with highest probability of interacting with the receptor. Two indicator variables marking the presence of an N-methyl group and an o-fluoro atom on the 5'-phenyl substituent of the benzodiazepine ring structure also contribute significantly to the 3D-MSA-QSAR models. The 3D-MSA-QSAR results have led to the proposal of a 3D pharmacophore model for the benzodiazepine CCK-A antagonists.

Animals↗
PubMed1998

2-Substituted aminopyrido[2,3-d]pyrimidin-7(8H)-ones. structure-activity relationships against selected tyrosine kinases and in vitro and in vivo anticancer activity.

While engaged in therapeutic intervention against a number of proliferative diseases, we have discovered the 2-aminopyrido[2, 3-d]pyrimidin-7(8H)-ones as a novel class of potent, broadly active tyrosine kinase (TK) inhibitors. An efficient route was developed that enabled the synthesis of a wide variety of analogues with substitution on several positions of the template. From the lead structure 2, a series of analogues bearing variable substituents at the C-2 position and methyl or ethyl at N-8 was made. Compounds of this series were competitive with ATP and displayed submicromolar to low nanomolar potency against a panel of TKs, including receptor (platelet-derived growth factor, PDGFr; fibroblast growth factor, FGFr; epidermal growth factor, EGFr) and nonreceptor (c-Src) classes. One of the more thoroughly evaluated members was 63 with IC50 values of 0.079 microM (PDGFr), 0.043 microM (bFGFr), 0.044 microM (EGFr), and 0.009 microM (c-Src). In cellular studies, 63 inhibited PDGF-mediated receptor autophosphorylation in a number of cell lines at IC50 values of 0.026-0.002 microM and proliferation of two PDGF-dependent lines at 0.3 microM. It also caused inhibition of soft agar colony formation in three cell lines that overexpress the c-Src TK, with IC50 values of 0.33-1.8 microM. In in vivo studies against a panel of seven xenograft tumor models with known and/or inferred dependence on the EGFr, PDGFr, and c-Src TKs, compound 63 produced a tumor growth delay of 10.6 days against the relatively refractory SK-OV-3 ovarian xenograft and also displayed activity against the HT-29 tumor. In rat oral bioavailability studies, compound 63 plasma concentrations declined in a biexponential manner, and systemic plasma clearance was high relative to liver blood flow. Finally, in rat metabolism studies, HPLC chromatography identified two metabolites of 63, which were proved by mass spectrometry and synthesis to be the primary amine (58) and N-oxide (66). Because of the excellent potency of 63 against selected TKs, in vitro and in vivo studies are underway for this compound in additional tumor models dependent upon PDGFr, FGFr, and c-Src to assess its potential for advancement to clinical trials.

3T3 Cells↗
PubMed1998

Seven new microcystins possessing two L-glutamic acid units, isolated from Anabaena sp. strain 186.

Electrospray ionization mass spectrometry has been applied to the structure assignment of seven new microcystins (1-7), obtained from cultured Anabaena sp. strain 186. The seven new microcystins contain the dehydroalanine (Dha) or L-Ser unit instead of the N-methyldehydroalanine unit and the L-Glu and/or its delta-methyl ester [E(OMe)] units at the two variable L-amino acid units, and the structures were assigned as [Dha7]microcystin-E(OMe)E(OMe) (1), [D-Asp3,Dha7]microcystin-E(OMe)E(OMe) (2), [L-Ser7]microcystin-E(OMe)E(OMe) (3), [D-Asp3,L-Ser7]microcystin-E(OMe)E(OMe) (4), [Dha7]microcystin-EE(OMe) (5), [D-Asp3,Dha7]microcystin-EE(OMe) (6), and [L-Ser7]microcystin-EE(OMe) (7). These microcystins are the first examples containing dicarboxylic amino acids at the two variable L-amino acid units in microcystins.

Anabaena↗
PubMed1988

Characterization of Vibrio metschnikovii and Vibrio gazogenes by DNA-DNA hybridization and phenotype.

Vibrio metschnikovii and Vibrio gazogenes are two new Vibrio species that have been little studied. Thirteen strains of V. metschnikovii were highly related to the type strain, NCTC 8443, by DNA-DNA hybridization. Relatedness values were 83 to 90% at 60 degrees C and 75 to 84% at the more stringent 75 degrees C. Divergence values ranged from 0.7 to 1.9. Strains of V. metschnikovii were oxidase negative and did not reduce nitrate to nitrite. The other phenotypic characteristics agreed with published data. Twenty-three strains of V. gazogenes were isolated from salt marshes and marshy areas on the coast of North and South Carolina. A new medium, marine agar supplemented with an additional 2.5% agar, reduced the problem of swarming by marine Vibrio species and enhanced the isolation of V. gazogenes and other organisms. By DNA-DNA hybridization, 22 of 23 strains were 76% or more related to the type strain of V. gazogenes, ATCC 29988. However, four DNA hybridization subgroups were defined on the basis of divergence values and/or phenotype. Strains of DNA group 1 were more highly related to each other, and this group contained the type strain and six other strains. Strains of DNA group 2 were more highly related to each other, and this group contained reference strain ATCC 43942 and 14 other strains. Strains of DNA group 1 did not ferment melibiose or D-sorbitol (one strain was sorbitol positive), but strains of DNA group 2 fermented both sugars. A revised phenotypic description of V. gazogenes based on 24 strains was written on the basis of reactions (within 2 days of incubation) at 25 degrees C in media supplemented with Na+, K+, and Mg2+. Positive results (100% positive unless indicated) included motility; gas production during fermentation (96% at 2 days, 100% at 3 to 7 days); growth in nutrient broth with the addition of 1% NaCl (88%), 2% NaCl, 3.5% NaCl, 6% NaCl, 8% NaCl, and 10% NaCl (92%); dry red or orange colonies on marine agar; and fermentation of L-arabinose, cellobiose, D-galactose (88%), D-glucose, lactose (88%), maltose, D-mannitol (96%), D-mannose, salicin, sucrose, trehalose, and D-xylose. Negative results included oxidase; nitrate reduction to nitrite (4% positive); indole production; lysine decarboxylase; ornithine decarboxylase; arginine dihydrolase; swarming; growth on TCBS agar; growth in nutrient broth with 0% NaCl, 0.1% NaCl, 0.2% NaCl, 0.3% NaCl, and 0.4% NaCl (8% positive); and fermentation of adonitol, D-arabitol, dulcitol, erythritol, D-galacturonate, i-inositol, alpha-methyl-D-glucoside, raffinose, and L-rhamnose. Variable results were found for the Voges-Proskauer reaction (62% positive), growth in nutrient broth plus 0.5% NaCl (29%) and 12% NaCL (42%), and fermentation of melibiose (71%) and D-sorbitol (71%).

DNA, Bacterial↗
PubMed1995

[Fragile X syndrome: clinical and molecular genetics correlations].

The fragile X form of mental retardation is presently recognized as the most frequent hereditable cause of mental impairment. The estimated frequency among males is 1 in 1250, and 1 in 2000 among females. Beside mental impairment and behavioural disturbance with hyperactivity and autistic features, the patients are characterized by morphological anomalies, such as an oblong face, broad, rectangular chin, large protruding ears and macro-orchidism. A less severe clinical expression can be found among females heterozygotes of the disorder, manifesting mainly as learning disability. The disorder is associated with the expression of a fragile site at Xq27.3 under conditions of folate depletion in the chromosome culture medium. The molecular mechanism is based on the expansion of a trinucleotide repeat [CCG]n in the promoter region of the FMR1 gene resulting in methylation of the gene. The trinucleotide repeat shows variable lengths of 6 to 53 repeats in the general population, 60 to 200 repeats in carriers of a premutation and over 200 repeats in patients with fragile X syndrome.

Adult↗
PubMed1996

Reactivity of purified complement component 3b with bovine neutrophils and modulation of complement receptor 1.

OBJECTIVE: To study binding of purified complement component C3b to bovine blood and mammary neutrophils (PMN) after various treatments and determine their ability to modulate receptor numbers. DESIGN: Cell isolation, activation, and flow cytometric studies. ANIMALS: Healthy lactating Holstein cattle. PROCEDURE: Complement component C3b (18,300 kd) was isolated from bovine serum by column chromatography, and flow cytometric assays using fluorescein isothiocyanate-labeled C3b were developed to evaluate binding to PMN complement receptor 1. Multiple substances were tested to determine their overall effect on C3b binding to PMN. Blood and milk PMN were isolated by differential centrifugation and exposed to optimal concentrations of recombinant human C5a, formyl-methyl leucyl phenylalanine, recombinant bovine interferon-gamma, variable concentrations of phorbol myristate acetate (0.01 to 100 ng), calcium ionophore A23187, serum-opsonized zymosan, zymosan-activated serum (ZAS), zymosan-activated plasma (ZAP), and hydrocortisone acetate (25 and 70 ng). Additionally, mammary and blood PMN were preincubated in skim milk and whey. RESULTS: Variable concentrations of phorbol myristate acetate caused a dose-dependent increase in percentage of PMN binding C3b, and increased the amount of C3b bound per cell. Significant increases were observed after PMN treatment with calcium ionophore, serum opsonized zymosan, ZAS, and ZAP; conversely, incubation of PMN with hydrocortisone acetate resulted in reduced overall binding of C3b. Mammary PMN consistently bound more C3b, which was attributed to their activation during migration into the mammary gland. Binding of C3b was inhibited by skim milk. Activation of blood PMN with PMA, ZAS, and ZAP elicited larger responses than those observed for mammary PMN. CONCLUSIONS: Modulation of complement receptors on bovine PMN is possible. Additionally, significant difference between the level of binding of C3b to blood and milk PMN, with milk PMN having higher binding, may be attributable to migration of PMN into the mammary gland, causing increased receptor expression. CLINICAL RELEVANCE: Contribution to a greater understanding of the role of complement in bovine immunologic systems, leading to testing for in vivo enhancement of bovine immune responses to invading pathogens.

Animals↗
PubMed1996

Superficial versus deep: options in venous drainage of the radial forearm free flap.

We performed a fresh cadaver dissection study of the superficial venous system (cephalic vein and its branches) and the deep venous system (venae comitantes) of the radial forearm to assess the suitability of each system for venous anastomosis during free tissue transfer. We used methyl methacrylate to evaluate vessel diameters and anatomic variability of both venous systems. Colored radiopaque injectate allowed us to combine anatomic dissection with tissue radiographs. We discovered the cephalic vein to invariably be of larger caliber than the venae comitantes. Ensuring capture of the cephalic vein in the flap necessitated additional dorsoradial subcutaneous dissection beyond the boundaries of the skin flap in four of ten specimens. The vessel diameters of the venae comitantes in four cadavers were less than 2 mm. Proximal confluence of the two venae comitantes, and communication between the deep and superficial venous systems were encountered in only four cases. In these cases, had an anastomotic site been chosen proximal to such a communication to ensure greater vessel caliber, pedicle length probably would have made free tissue transfer unwieldy. We recommend mapping the course of the cephalic vein before flap elevation and maintaining a wide proximal subcutaneous pedicle to capture the best possible superficial drainage system. If the superficial venous system has been damaged (as by previous intravenous catheterization), one may not necessarily be able to rely on the vessel caliber of the deep venae comitantes for microvenous anastomosis.

Brachial Artery↗
PubMed1989

Multifactorial hamster respiratory carcinogenesis with interdependent effects of cannula-induced mucosal wounding, saline, ferric oxide, benzo[a]pyrene and N-methyl-N-nitrosourea.

The carcinogenic response induced in the respiratory tract of Syrian golden hamsters by repeated intratracheal instillations of benzo[a]pyrene (BP) adsorbed to ferric oxide (Fe2O3) particles suspended in saline, is shown to result from the interactions of these factors and cannula-induced tracheal wounding. Previous acute studies of intratracheal cannulation (ITC) versus intralaryngeal cannulation (ILC) showed that tracheal cell proliferation increased significantly in ITC-induced mucosal wounds. Only mild increases in intrapulmonary cell proliferation were produced by Fe2O3-saline given by ILC or ITC (Keenan et al., Cancer Res., 49: 1521-1527, 1989). The present chronic studies included the following variables: a single instillation by ILC of N-methyl-N-nitrosourea (MNU) at 5 weeks of age; 15 weekly treatments (beginning at 7 weeks of age) by ILC or ITC alone, or with instillations of saline, or Fe2O3-saline, or BP-Fe2O3-saline; and appropriate controls. Repeated ITC-induced tracheal wounds caused persistent tracheal epithelial hyperplasia, metaplasia and/or atrophy and submucosal fibroplasia during the observation period of 22 to 78 weeks of age (the time of terminal sacrifice). Tracheal cancers (in situ or invasive carcinomas) were seen only in those hamsters which had received repeated ITC and one or both carcinogens. The cancer latency was shortest and the incidence of tracheal (50%) and main-stem bronchial (21%) cancers highest in hamsters given MNU and repeated ITC with BP-Fe2O3-saline. Hamsters given carcinogens by ILC (which induced laryngeal but not tracheal wounds) developed proliferative lesions and cancers of the larynx but no tracheobronchial cancers. These data show the singular importance of repeated ITC-induced intratracheal wounding as an enhancing factor in this respiratory carcinogenesis model. The findings suggest that the mechanism of tumor enhancement involves not only changes in target epithelial cell proliferation, but also alterations in normal epithelial-mesenchymal interactions during tracheal regeneration from repeated chronic submucosal inflammation and mesenchymal repair. In the present experimental model, a single dose of MNU at 5 weeks of age, repeated instilled doses of BP, and tracheal mucosal wounding were each found to be important determinants of the carcinogenic response. Additional effects were observed for instilled Fe2O3 particles, and possibly saline. Interplay of all these factors, as well as of genetic, nutritional, and infectious factors, are considered in relation to risk assessment and prevention.

Animals↗
PubMed1995

CpG methylation represses the activity of the rat prolactin promoter in rat GH3 pituitary cell lines.

In the present report, we have investigated the role of DNA methylation on the binding and trans-acting properties of transcription factors involved in the regulation of the rat prolactin (rPRL) gene, specifically Pit-1. To this aim we took advantage of a model system composed of three GH3 rat pituitary tumor cell lines that greatly differed in the extent of rPRL gene methylation and in the level of rPRL gene expression. Northern blot analyses indicated that identical species of Pit-1 mRNA were present to similar extent in the three GH3 cell lines. Electrophoretic mobility shift assays further demonstrated that Pit-1 was present in nuclear extracts and displayed equal affinities to bind the 1P responsive element encompassing the -65 to -38 region of the rPRL promoter, whatever the GH3 cell line tested. These data suggested that differential expression of the rPRL gene among cell lines did not result from variable amounts of Pit-1. By combining in vitro methylation and transient transfection experiments with a rPRL promoter-driven CAT construct, we showed that extensive methylation at CpG sites abolished the expression of the reporter gene. Furthermore, in vivo competition assays demonstrated that CpG methylation inhibited gene expression by preventing the binding of transcription factors We propose that related mechanisms linked to DNA methylation might alter the activity of the endogenous PRL gene in the low expressing cell line.

Animals↗
PubMed1996

Variability in biological exposure indices using physiologically based pharmacokinetic modeling and Monte Carlo simulation.

By using physiologically based pharmacokinetic (PBPK) modeling coupled with Monte Carlo simulation, the interindividual variability in the concentrations of chemicals in a worker's exhaled breath and urine were estimated and compared with existing biological exposure indices (BEIs). The PBPK model simulated an exposure regimen similar to a typical workday, while exposure concentrations were set to equal the ambient threshold limit values (TLVs) of six industrial solvents (benzene, chloroform, carbon tetrachloride, methylene chloride, methyl chloroform, and trichloroethylene). Based on model predictions incorporating interindividual variability, the percentage of population protected was derived using TLVs as the basis for worker protection. Results showed that current BEIs may not protect the majority or all of the workers in an occupational setting. For instance, current end-expired air indices for benzene and methyl chloroform protect 95% and less than 10% of the worker population, respectively. Urinary metabolite concentrations for benzene, methyl chloroform, and trichloroethylene were also estimated. The current BEI recommendation for phenol metabolite concentration at the end-of-shift sampling interval was estimated to protect 68% of the worker population, while trichloroacetic acid (TCAA) and trichloroethanol (TCOH) concentrations for methyl chloroform exposure were estimated to protect 54% and 97%, respectively. The recommended concentration of TCAA in urine as a determinant of trichloroethylene exposure protects an estimated 84% of the workers. Although many of the existing BEIs considered appear to protect a majority of the worker population, an inconsistent proportion of the population is protected. The information presented in this study may provide a new approach for administrative decisions establishing BEIs and allow uniform application of biological monitoring among different chemicals.

Humans↗
PubMed1978

Metabolism of 3, 4-dihydroxyphenylalanine, its metabolites and analogues in vivo in the rat: urinary excretion pattern.

The metabolism and interrelationships of orally and intraperitoneally administered L-dopa, related amino acids and their metabolites have been studied 2. Amino acids were decarboxylated. N-Methyldopa formed dopamine but not epinine. D-Dopa was absorbed from the intestine and metabolized by a series of reactions which resulted in greater decarboxylation than was observed after L-dopa. Transamination was a minor pathway. 3. m-Hydroxylated phenylpyruvic acids were poorly reduced, but vanilpyruvic acid was reduced fairly readily. Lactic acids were largely unchanged. Lactic and pyruvic acids formed phenylethylamines and their metabolites. Small amounts of phenylpyruvic acids may be decarboxylated to phenylacetic acids. 4. Glycine conjugates were formed from phenylacetic acids, a partially reversible change 3,4-Dihydroxyphenylacetic acid was metabolized to homovanillic and m-hydroxyphenylacetic acids, especially when given orally. Little 3-hydroxy-4-methoxyphenylacetic acid was oxidized to 3,4-dihydroxyphenylacetic acid but some increase in m-hydroxyphenylacetic acid excretion was observed. 5. 2-Phenylethanol analogues were largely converted to the corresponding acids. 3,4-Dihydroxyphenylethanol was partially m-O-methylated before oxidation. 6. beta-Phenylethylamine analogues were oxidized mainly to phenylacetic acids. but a variable amount of analogous phenylethanol was also formed, especially from m-tyramine. Dopamine was O-methylated, a process not readily reversible. It was also p-dehydroxylated following oral and intraperitoneal administration but not after oral neomycin; biliary excretion of amines may be involved in this sequence of events. N-Methylated amines were oxidized less readily than the parent amine. 7. Differences in route of administration resulted in quantitative changes in degradation pathways, an effect deriving, to some extent, from p-dehydroxylation and O-methylation in the gut.

Alcohols↗
PubMed1989

Effects of phencyclidine and other N-methyl-D-aspartate antagonists on the schedule-controlled behavior of rats.

The behavioral effects of phencyclidine (PCP) were compared with those of several compounds known to antagonize the actions of N-methyl-D-aspartate using two patterns of schedule-controlled responding in rats. Rates of variable interval responding suppressed by punishment were increased greatly by the benzodiazepine chlorodiazepoxide and showed small increases after MK-801 [(+)-5-methyl-10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5,10-imine] . However, no consistent increases in response rates were produced by PCP, by the stereoisomers of N-allylnormetazocine (NANM: SKF 10,047) or by the anti-ischemic drug, ifenprodil. Small doses of PCP did increase rates of unpublished variable interval responding, as did a low dose of MK-801. Timing behavior maintained by a differential reinforcement of low rate schedule was disrupted by all the compounds studied. Response rates were increased by at least one dose of PCP, MK-801, (+)-NANM and 3-(2-carboxypiperazine-4-yl)propyl-1-phosphonic acid. The effect of MK-801, however, was considerably greater than that of the other compounds. Ifenprodil and (-)-NANM did not increase rates of responding but, at high doses, produced decreases in reinforcement frequency indicating that efficient timing behavior had been disrupted. These results show that although PCP, MK-801 and (+)-NANM produce generally similar behavioral effects, there may also be some differences between the compounds, notably a more consistent effect of MK-801 on punished responding. These behavioral effects may be related to antagonism of N-methyl-D-aspartate but ifenprodil, which is also an N-methyl-D-aspartate antagonist, does not show a similar behavioral profile.

Animals↗
PubMed1989

Solution structure of a tRNA with a large variable region: yeast tRNASer.

Different chemical reagents were used to study the tertiary structure of yeast tRNASer, a tRNA with a large variable region: ethylnitrosourea, which alkylates the phosphate groups; dimethylsulphate, which methylates N-7 of guanosine and N-3 of cytosine; and diethylpyrocarbonate, which modifies N-7 of adenine. The non-reactivity of N-3 of cytidine 47:1, 47:6, 47:7 and 47:8 and the reactivity of cytidine 47:3 confirms the existence of a variable stem of four base-pairs and a short variable loop of three residues. For the N-7 positions in purines, accessible residues are G1, G10, Gm18, G19, G30, I34, G35, A36, i6A37, G45, G47, G47:5, G47:9 and G73. The protection of N-7 atoms of residues G9, G15, A21, A22 and G47:9 reflects the tertiary folding. Strong phosphate protection was observed for P8 to P11, P20:1 to P22, P48 to P50 and for P59 and P60. A model was built on a PS300 graphic system on the basis of these data and its stereochemistry refined. While trying to keep most tertiary interactions, we adapted the tertiary folding of the known structures of tRNAAsp and tRNAPhe to the present sequence and solution data. The resulting model has the variable arm not far from the plane of the common L-shaped structure. A generalization of this model to other tRNAs with large variable regions is discussed.

Adenine↗
PubMed1993

Selective antagonism of native and cloned kainate and NMDA receptors by polyamine-containing toxins.

Antagonism of rat excitatory amino acid receptors by a synthetic analog [philanthotoxin-343 (PhTX-343)] of a polyamine amide, wasp toxin (philanthotoxin-433) and a structurally related spider toxin, argiotoxin-636 (ArgTX-636), was examined in Xenopus oocytes injected with rat brain RNA or RNA transcribed from the excitatory amino acid receptor clones GluR1, GluR2 and NMDAR1. Antagonism of both kainate- and N-methyl-D-aspartate (NMDA)-elicited responses by PhTX-343 and ArgTX-636 was reversible, noncompetitive and partly voltage-dependent. Dose-inhibition curves were constructed using EC50 concentrations of kainate (100 microM) and N-methyl-D-aspartate (33 microM) in the presence of variable concentrations of ArgTX-636 and PhTX-343. In oocytes injected with rat brain RNA, IC50s for antagonism of kainate-induced currents were similar, i.e., 0.07 microM and 0.12 microM for ArgTX-636 and PhTX-343, respectively, whereas IC50s for antagonism of NMDA-induced currents were dissimilar, i.e., 0.04 microM for ArgTX-636 and 2.5 microM for PhTX-343. In oocytes expressing NMDAR1, IC50s were similar to those for the antagonism of NMDA-induced currents of oocytes injected with rat brain RNA. PhTX-343 and ArgTX-636 were more or less equally potent (IC50s were 2.8 microM and 3.4 microM, respectively) antagonists of the response of GluR1 to 100 microM kainate. However, GluR1 was approximately 50 times less sensitive to the toxins than non-N-methyl-D-aspartate receptors expressed in oocytes injected with rat brain RNA. Receptors co-expressed from GluR1 + GluR2 were virtually insensitive to PhTX-343 (IC50 = 270 microM) and to ArgTX-343 (IC50 approximately 300 microM).

Animals↗
PubMed2025

Methylation-based droplet digital polymerase chain reaction shows high concordance with chronic lymphocytic leukemia IGHV somatic mutation status.

OBJECTIVE: Somatic hypermutation at immunoglobulin heavy chain variable (IGHV) genes, an established prognostic and predictive biomarker for chronic lymphocytic leukemia (CLL), is assessed by gene sequencing. We developed a single methylation-specific droplet digital polymerase chain reaction (methyl-ddPCR) to predict IGHV status in patients with CLL. METHODS: The CLL methylation array and IGHV data from the International Cancer Genome Consortium (ICGC) were used for biomarker discovery. Top-ranked candidate regions were manually screened for PCR primer and probe binding sites. A single methyl-ddPCR was evaluated on an internal cohort of CLLs with mutated (M), unmutated (U), and inconclusive IGHV results originally determined by next-generation sequencing (NGS). RESULTS: Analysis of ICGC data identified array probe cg23844018 as a candidate for the PCR. The corresponding CpG site showed high methylation levels in U-CLL and lower levels in M-CLL. On the internal cohort, a single optimal cutoff correctly classified 104 of 115 U- and M-CLLs (90.4%; area under the curve = 0.96). The PCR data correlated with some prognostic fluorescence in situ hybridization and CLL subset groupings. Limited analysis suggests that the PCR may be able to stratify some patients with CLL who have inconclusive results on IGHV NGS testing. CONCLUSIONS: The methyl-ddPCR showed high concordance with CLL IGHV status in an internal cohort.

Humans↗