Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “modification”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 1,009 records · Page 56Linked to original sources

Chromatin modifications in the germinal vesicle (GV) of mammalian oocytes.

The nucleus of eukaryotic cells is organized into functionally specialized compartments that are essential for the control of gene expression, chromosome architecture and cellular differentiation. The mouse oocyte nucleus or germinal vesicle (GV) exhibits a unique chromatin configuration that is subject to dynamic modifications during oogenesis. This process of 'epigenetic maturation' is critical to confer the female gamete with meiotic as well as developmental competence. In spite of its biological significance, little is known concerning the cellular and molecular mechanisms regulating large-scale chromatin structure in mammalian oocytes. Here, recent findings that provide mechanistic insight into the complex relationship between large-scale chromatin structure and global transcriptional repression in pre-ovulatory oocytes will be discussed. Post-translational modifications of histone proteins such as acetylation and methylation are crucial for heterochromatin formation and thus play a key role in remodeling the oocyte genome. This strategy involves multiple and hierarchical chromatin modifications that regulate nuclear dynamics in response to a developmentally programmed signal(s), presumably of paracrine origin, before the resumption of meiosis. Models for the experimental manipulation of large-scale chromatin structure in vivo and in vitro will be instrumental to determine the key cellular pathways and oocyte-derived factors involved in genome-wide chromatin modifications. Importantly, analysis of the functional differentiation of chromatin structure in the oocyte genome with high resolution and in real time will have wide-ranging implications to understand the role of nuclear organization in meiosis, the events of nuclear reprogramming and the spatio-temporal regulation of gene expression during development and differentiation.

Animals↗

Genome-wide analysis of histone modifications by ChIP-on-chip.

Post-translational modifications to histone proteins regulate the packaging of genomic DNA into chromatin, gene activity and other functions of the genome. They are understood to play key roles in embryonic development and disease pathogenesis. Recent advances in technology have made it possible to analyze chromatin structure genome-wide in mammalian cells. Global patterns of histone modifications can be observed using a technique called ChIP-on-chip, which combines the specificity of chromatin immunoprecipitation with the unbiased, high-throughput capabilities of microarrays. The resulting maps provide insight into the functions of, and relationships between, different modifications. Here, we provide validated ChIP-on-chip methods for analyzing histone modification patterns at genome-scale in mammalian cells.

Animals↗

The development of a monoclonal antibody specific for a 2(')-C-allyl modification of uridine, and its use in the localization of ribozymes in vivo.

Ribozymes are catalytically active RNA molecules that cleave other RNA molecules in a sequence-specific fashion, with significant turnover. The successful design and synthesis of ribozymes with modifications to increase their stability in biological fluids, while maintaining catalytic activity, has been instrumental in moving this technology from the laboratory into clinical trials. With the entry of ribozymes into the clinical setting, the need has arisen for reagents and/or assays to detect these drugs in tissues. We have developed a monoclonal antibody to the 2(')-deoxy-2(')-C-allyl uridine modification present in our synthetic hammerhead ribozymes. The monoclonal antibody, termed CA1USR, is a murine IgG1(k), whose epitope appears to involve both the 2(')-C-allyl modification, and the uridine base. Use of CA1USR for immunohistochemical detection of ribozymes in the tissues of mice which were administered two structurally different ribozymes has demonstrated its utility as a reagent for in vivo localization of ribozymes containing the 2(')-C-allyl uridine modification.

Allyl Compounds↗

Electromyographic effects of ergonomic modifications in selected meatpacking tasks.

This project evaluated the feasibility of a new method of collection of electromyographic (EMG) data during working conditions in industry, and quantified the effects of specific job modifications on the EMG activity of selected upper extremity muscle groups. Average root mean square (RMS) surface EMG activity, calibrated to force equivalent units, was collected on 20 workers from three pork processing tasks before and after ergonomic modifications to their tasks. Significant reductions in muscle effort were detected in the biceps and/or wrist and finger flexors after modification for two of the three tasks. This EMG measurement technique can be used to objectively validate reduced muscle effort with ergonomic modifications.

Adult↗

Enzymatic and chemical modifications of lipoprotein(a) selectively alter its lysine-binding functions.

The pathogenicity of lipoprotein(a) [Lp(a)] as a risk factor for cardiovascular disease may depend upon its lysine binding sites (LBS) which impart unique functions to Lp(a) not shared with low density lipoprotein. Biologically relevant modifications of Lp(a) were tested for alterations of LBS activity using two previously described functional assays, a LBS-Lp(a) immunoassay and a lysine-Sepharose bead assay. In the LBS-Lp(a) immunoassay, minimal changes in the LBS activity of Lp(a) were observed after modification with lipoprotein lipase, sphingomyelinase, or phospholipase C. In contrast, a significant (p<0.003) increase in the LBS activity of Lp(a) occurred after phospholipase A2 (PLA2) treatment, and this increase was confirmed using the lysine-Sepharose bead assay. The increase depended upon the release of fatty acids from Lp(a) by PLA2. A decrease in the LBS activity of Lp(a) occurred after oxidation of Lp(a) with 2,2'-azobis(2-amidinopropane) dihydrochloride (AAPH) (44% decrease), but CuSO4 oxidation increased LBS activity (210%). N-acetylcysteine (NAC) treatment of Lp(a) decreased (48%) LBS activity while homocysteine treatment had no (89%) effect. Thus, modification of phospholipids and protein moieties can alter the LBS-activity of Lp(a). Such enzymatic and chemical modifications may contribute to the variability in LBS function of Lp(a) seen within the population.

Acetylcysteine↗

Structural implications of the chemical modification of Cys(10) on actin.

Cys(10) is located in subdomain 1 of actin, which has an important role in the interaction of actin with myosin- and actin-binding proteins. Cys(10) was modified with fluorescence probes N-(iodoacetyl)N'-(5-sulfo-1-naphthyl)ethylene diamine (IAEDANS), 7-diethylamino-3-(4'-maleimidylphenyl)-4-methylcoumarin (CPM), or monobromo bimane (MBB) by the method of, J. Biol. Chem. 266:5508-5513). The specificity of Cys(10) modification was verified by showing that the 33-kDa subtilisin fragment of actin (residues 48-375), which contains all of the actin thiols but Cys(10), is not fluorescent. Cys(10) modification exposed a new site on actin to subtilisin cleavage. Edman degradation revealed this site to be between Ala(19) and Gly(20). The modification slightly increased the rate of epsilonATP-ATP exchange and decreased the rates of G-actin ATPase and polymerization. The activation of S1 ATPase by Cys(10)-modified F-actin showed small probe-dependent changes in the values of V(max) and K(M). The sliding speed of actin filaments in the in vitro motility assay remained unchanged upon modification of Cys(10). These results indicate that although the labeling of Cys(10) perturbs the structure of subdomain 1, the modified actin remains fully functional. The binding of S1 to actin filaments decreases the accessibility of Cys(10) probes to acrylamide and nitromethane quenchers. Because Cys(10) does not participate directly in either actin polymerization or S1 binding, our results indicate that actin-actin and actin-myosin interactions induce dynamic, allosteric changes in actin structure.

Actins↗

Cooperativity in F-actin: chemical modifications of actin monomers affect the functional interactions of myosin with unmodified monomers in the same actin filament.

We have chemically modified a fraction of the monomers in actin filaments, and then measured the effects on the functional interaction of myosin with unmodified monomers within the same filament. Two modifications were used: (a) covalent attachment of various amounts of myosin subfragment-1 (S1) with the bifunctional reagent disuccinimidyl suberate and (b) copolymerization of unmodified actin monomers with monomers cross-linked internally with 1-ethyl-3-(dimethylaminopropyl)-carbodiimide. Each of these modifications abolished the interaction of the modified monomers with myosin, so the remaining interactions were exclusively with unmodified monomers. The two modifications had similar effects on the interaction of actin with myosin in solution: decreased affinity of myosin heads for unmodified actin monomers, without a change in the Vmax of actin-activated myosin ATPase activity. However, modification (b) produced much greater inhibition of actin sliding on a myosin-coated surface, as measured by an in vitro motility assay. These results provide insight into the functional consequences of cooperative interactions within the actin filament.

Actins↗

Trimethyloxonium modification of batrachotoxin-activated Na channels alters functionally important protein residues.

The extracellular side of single batrachotoxin-activated voltage-dependent Na channels isolated from rat skeletal muscle membranes incorporated into neutral planar lipid bilayers were treated in situ with the carboxyl methylating reagent, trimethyloxonium (TMO). These experiments were designed to determine whether TMO alters Na channel function by a general through-space electrostatic mechanism or by methylating specific carboxyl groups essential to channel function. TMO modification reduced single-channel conductance by decreasing the maximal turnover rate. Modification increased channel selectivity for sodium ions relative to potassium ions as measured under biionic conditions. TMO modification increased the mu-conotoxin (muCTX) off-rate by three orders of magnitude. Modification did not alter the muCTX on-rate at low ionic strength or Na channel voltage-dependent gating characteristics. These data demonstrate that TMO does not act via a general electrostatic mechanism. Instead, TMO targets protein residues specifically involved in ion conduction, ion selectivity, and muCTX binding. These data support the hypothesis that muCTX blocks open-channel current by physically obstructing the ion channel pore.

Animals↗

Charge immobilization caused by modification of internal cysteines in squid Na channels.

We studied the effects of modification of native cysteines present in squid giant axon Na channels with methanethiosulfonates. We find that intracellular, but not extracellular, perfusion of axons with positively charged [(2-trimethylammonium)-ethyl]methanethiosulfonate (MTSET), or 3(triethylammonium)propyl]methanethiosulfonate (MTS-PTrEA) irreversibly reduces sodium ionic (INa) and gating (Ig) currents. The rate of modification of Na channels was dependent on the concentration of the modifying agent and the transmembrane voltage. Hyperpolarized membrane potentials (e.g., -110 mV) protected the channels from modification by MTS-PTrEA. In addition to reducing the amplitudes of INa and Ig, MTS-PTrEA also altered their kinetics such that the remaining INa did not appear to inactivate, whereas Ig was made sharper and declined to baseline more quickly. The shape and amplitude of Ig after modification of channels with MTS-PTrEA appeared to be "charge-immobilized," as if the modified channels were inactivated. MTS-PTrEA did not affect INa or Ig when inactivation was removed by internal perfusion of the axon with pronase. In addition, we find that the steady-state inactivation curve of modified Na channels is made much shallower and is markedly shifted to hyperpolarized potentials. The rates of activation, deactivation, or open-state inactivation were not altered in MTS-PTrEA-modified channels. The uncharged sulfhydryl reagent methymethanethiosulfonate (MMTS) did not affect either INa or Ig, but prevented the irreversible effects of MTS-PTrEA or MTSET on Na channels. It is proposed that the positively charged methanethiosulfonates MTS-PTrEA and MTSET modify a native internal cysteine(s) in squid Na channels, and by doing so promote inactivation from closed states, resulting in charge immobilization and reduction of INa.

Anesthetics, Local↗

Effects of SH1 and SH2 modifications on myosin: similarities and differences.

The properties of myosin modified at the SH2 group (Cys-697) were studied and compared with the previously reported properties of myosin modified at the SH1 group (Cys-707). 4-[N-[(iodoacetoxy)ethyl]-N methylamino]-7-nitrobenz-2-oxa-1, 3-diazole (IANBD) was used for selective modification of the SH2 group on myosin. SH2-labeled heavy meromyosin (SH2-HMM), similar to SH1-labeled HMM (SH1-HMM), did not propel actin filaments in the in vitro motility assays. SH1- and SH2-HMM produced similar amounts of load in the mixtures with unmodified HMM; the sliding speed of actin filaments gradually decreased with an increase in the fraction of either one of the modified HMMs in the mixture. In analogy to SH1-labeled myosin subfragment 1 (SH1-S1), SH2-labeled S1 (SH2-S1) activated regulated actin in the in vitro motility assays. SH2 modification inhibited Mg-ATPase of S1 and its activation by actin. The weak binding of S1 to actin was unaffected whereas the strong binding was weakened by SH2 modification. Overall, our results demonstrate similar behavior of SH1- and SH2-modified myosin heads in the in vitro motility assays despite some differences in their enzymatic properties. The effects of these modifications are ascribed to the location of the SH1-SH2 helix relative to other functional centers of S1.

Actins↗

Lipid hydroperoxide modification of proteins during myocardial ischaemia.

OBJECTIVE: Lipid hydroperoxides (LOOH) are lipid peroxidation products formed during oxidative stress. A component of their cytotoxicity is mediated by the direct modification of proteins. OBJECTIVES: (i) To assess whether ischaemia and reperfusion in the isolated rat heart generates LOOH-protein (ii) to characterise the extent, time-course and subcellular localization of any protein adducts formed. METHODS: Using a well-characterised antibody which binds to LOOH-modified proteins and densitometry of Western blots, we quantified the amounts of LOOH-protein in control aerobically perfused rat hearts and those subjected to ischaemia with and without reperfusion. RESULTS: Hearts (n=3/4 group), analysed after various periods (0, 5, 10, 20 and 30 min) of zero-flow global ischaemia, exhibited a time-dependent increase in the LOOH-mediated modification of a number of proteins. In hearts subjected to 30 min of ischaemia and then reperfused for various times (0, 5, 10, 20, 30 or 60 min) no changes in LOOH-protein content achieved during the proceeding ischaemic episode were detected. Reperfusion after short periods of ischaemia (5 or 10 min) also did not result in reperfusion-induced LOOH-protein formation. Administration of mercaptopropionylglycine (1 mM) to hearts for 5 min before the onset of 30 min ischaemia efficiently attenuated the formation of LOOH-protein, maintaining the modified proteins at control levels. These Western immunoblot results were confirmed by additional in situ immunofluorescent studies which showed marked LOOH-protein immunostaining in ischaemic tissue around the sarcolemmal membrane. CONCLUSIONS: We conclude that the modification of proteins (particularly those associated with sarcolemmal membranes) by LOOH during ischaemia may contribute to the pathophysiology of ischaemic injury. In addition, these modifications may be initiators of oxidant-induced signal transduction pathways. These findings are consistent with an oxidant stress occurring during ischaemia which is not exacerbated or reduced during the first 60 min of reperfusion.

Animals↗

O-GlcNAc turns twenty: functional implications for post-translational modification of nuclear and cytosolic proteins with a sugar.

O-linked beta-N-acetylglucosamine (O-GlcNAc) is a dynamic nucleocytoplasmic post-translational modification more analogous to phosphorylation than to classical complex O-glycosylation. A large number of nuclear and cytosolic proteins are modified by O-GlcNAc. Proteins modified by O-GlcNAc include transcription factors, signaling components, and metabolic enzymes. While the modification has been known for almost 20 years, functions for the monosaccharide modification are just now emerging. In this review, we will focus on the cycling enzymes and emerging roles for this post-translational modification in regulating signal transduction and transcription. Finally, we will discuss future directions and the working model of O-GlcNAc serving as a nutrient sensor.

Acetylglucosamine↗

Chemical modification of glucose oxidase: possible formation of molten globule-like intermediate structure.

Chemical modification of lysine residues in glucose oxidase was carried out using citraconic anhydride. Modification brought about changes in the kinetic properties of the enzyme as evident by substantial lowering of V(max) and K(m). Enhancement of tryptophan fluorescence was observed with a dramatic change in its pH dependence due to modification. Near- and far-UV circular dichroism spectra of the native and modified forms suggested formation of molten globule-like structures, further supported by 8-anilino-1-naphthalenesulfonic acid fluorescence which indicated higher exposure of hydrophobic residues as a result of chemical modification.

Anilino Naphthalenesulfonates↗

Effect of the human serum paraoxonase 55 and 192 genetic polymorphisms on the protection by high density lipoprotein against low density lipoprotein oxidative modification.

Human serum paraoxonase (PON1) associated with high density lipoprotein (HDL) has been postulated to have a role in protecting low density lipoprotein (LDL) against oxidative modification, which has led to the proposal that PON1 is an anti-atherogenic, anti-inflammatory enzyme. PON1 has two genetically determined polymorphic sites giving rise to amino-acid substitutions at positions 55 (L-->M) and 192 (R-->Q) and therefore 4 potential alloenzymes. We have examined the effects of these molecular polymorphisms on the ability of HDL to protect LDL from oxidative modification. HDL protected LDL from oxidative modification, whatever the combination of PON1 alloenzymes present in it. However, HDL from QQ/MM homozygotes was most effective at protecting LDL while HDL from RR/LL homozygotes was least effective. Thus after 6 h of co-incubation of HDL and LDL with Cu2+ PON1-QQ HDL retained 57 +/- 6.3% of its original ability to protect LDL from oxidative modification, while PON1-QR HDL retained less at 25.1 +/- 4.5% (P < 0.01) and PON1-RR HDL retained only 0.75 +/- 0.40% (P < 0.005). In similar experiments HDL from LL and LM genotypes retained 21.8 +/- 7.5% and 29.5 +/- 6.6% (P = NS), respectively, of their protective ability, whereas PON1-MM HDL maintained 49.5 +/- 5.3% (P < 0.01). PON1 polymorphisms may affect the ability of HDL to impede the development of atherosclerosis and to prevent inflammation.

Adult↗

Evaluation of urinary continence and voiding function: early results in men with neo-urethral modification of the Hautmann orthotopic neobladder.

PURPOSE: At our institution we use the Hautmann orthotopic bladder replacement with a chimney and neo-urethral modification. A neo-urethral tube allows tension-free intestino-urethral anastomosis, thus providing application of this procedure for patients who may otherwise not qualify due to the inability of the small bowel to reach the urethra. However, this neo-urethral tube may also enhance continence by providing significant intra-abdominal urethral length. Conversely, such a modification may be associated with a higher degree of urinary retention. Early evaluation and reporting on the results of this procedure appear warranted. MATERIALS AND METHODS: From April 1996 to March 2000, 14 consecutive male patients underwent cystoprostatectomy and urinary reconstruction with Hautmann repair using chimney and neo-urethral modifications. We performed a retrospective analysis of urinary function and continence with data obtained from patient questionnaires completed preoperatively and at each postoperative office visit. The examining physician chart notes were reviewed for information about urinary retention. The American Urological Association symptom score and voiding bother index were used to assess urinary function and bother, respectively. Urinary continence was defined as the complete absence of any form of urinary leakage protection. RESULTS: Of the 14 patients 12 were completely continent day and night, with a median followup of 17 months. There were 2 patients who wore pads less than 7 months after surgery. Improvement of urinary continence appeared to continue up to 12 months postoperatively. Despite this encouraging effect, when our data were compared to the published literature, we noted a somewhat increased incidence of patients requiring clean intermittent catheterization to manage significant post-void urinary residuals. We had no patients with urethro-intestinal strictures who required clean intermittent catheterization. CONCLUSIONS: The neo-urethral tube modification appears to have a significant and favorable impact on urinary continence while seeming to be associated with a trend towards an increased rate of chronic urinary retention. Longer followup will be required to determine whether this higher rate of chronic urinary retention will remain stable or change with time.

Aged↗

Age-related chemical modification of the skeletal muscle sarcoplasmic reticulum Ca-ATPase of the rat.

Much emphasis has been placed on the description of age-related changes in skeletal muscle physiology. The present paper summarizes the chemical characterization of age-related post-translational modifications of the rat skeletal muscle sarcoplasmic reticulum (SR) Ca-ATPase isoforms SERCA1 and SERCA2a obtained from 5- and 28-month-old male Fischer 344 rats. Whereas the SERCA1 isoform shows an age-dependent loss of Cys and Arg, the SERCA2a isoform displays a loss of Cys but also a significant accumulation of 3-nitrotyrosine. The in vitro exposure of SR vesicles particularly rich in SERCA1 (>90%) from 5-month-old rats to low levels of peroxyl radicals yielded SR vesicles with physical properties of the SR Ca-ATPase identical to those observed for the SR Ca-ATPase obtained from 28-month-old rats. The peroxyl radical-modified SR Ca-ATPase showed a loss of Cys and Arg but also of Ser and Met, indicating that peroxyl radicals, though a good model oxidant to generate 'aged' SR vesicles, may not be the only oxidant responsible for the chemical modification of the SR Ca-ATPase in vivo. In fact, efficient thiol modification of the SERCA1 was also observed after the exposure to peroxynitrite. Peroxynitrite selectively nitrated the tyrosine residues of the SERCA2a isoform even in the presence of an excess of SERCA1. Thus, peroxynitrite may be responsible for the age-dependent modification of the SR Ca-ATPase in vivo.

Aging↗

Mapping histone modifications by nucleosome immunoprecipitation.

Studies of histone modification patterns and their role in gene regulation have led to the proposal that there is a "histone code." We have developed a method for nucleosome immunoprecipitation that can precisely identify the specific nucleosomes that carry a posttranslational modification of interest. The process involves the isolation and micrococcal nuclease digestion of minichromosomes to generate nucleosome core particles. These are then used in immunoprecipitation reactions with an antibody directed against the histone modification of interest. Subsequently, nucleosome core particle DNA is purified and end labeled. The original locations of the nucleosomes in the immunoprecipitate can be determined at low resolution (using a modified Southern blot hybridization procedure) or at maximal resolution (using the monomer extension method). Using the latter method, the positions of specific nucleosomes that carry the posttranslational modification of interest can be identified precisely. This method is sensitive, provides maximal resolution, and is inexpensive. The approach described here may serve as a paradigm for the study of histone-modifying patterns.

Animals↗

O-GlcNAc modification is an endogenous inhibitor of the proteasome.

The ubiquitin proteasome system classically selects its substrates for degradation by tagging them with ubiquitin. Here, we describe another means of controlling proteasome function in a global manner. The 26S proteasome can be inhibited by modification with the enzyme, O-GlcNAc transferase (OGT). This reversible modification of the proteasome inhibits the proteolysis of the transcription factor Sp1 and a hydrophobic peptide through inhibition of the ATPase activity of 26S proteasomes. The Rpt2 ATPase in the mammalian proteasome 19S cap is modified by O-GlcNAc in vitro and in vivo and as its modification increases, proteasome function decreases. This mechanism may couple proteasomes to the general metabolic state of the cell. The O-GlcNAc modification of proteasomes may allow the organism to respond to its metabolic needs by controlling the availability of amino acids and regulatory proteins.

Adenosine Triphosphatases↗