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 1,045 records · Page 58Linked to original sources
PubMedDate not supplied

A generalized Hebbian rule for activity-dependent synaptic modifications.

In this paper our previous model of activity-dependent synaptic modification is extended and applied to a model neuron with active dendrites and is used in computer simulations to examine in detail the dependence of synaptic modifications on the interval between the onset of excitatory postsynaptic potentials (EPSPs) and postsynaptic action potentials (APs). The EPSP amplitude is increased when the action potentials occur within 20 ms after EPSPs and is reduced when the action potentials occur within 20 ms before EPSPs. Furthermore, the absolute value of changes in the EPSP amplitude tends to increase as the interval between APs and EPSPs decreases. A learning rule for synaptic modifications described in this paper may, hence, further generalize the Hebbian rule which requires conjunctive presynaptic and postsynaptic activity for synaptic modification to occur. Functional roles for such a generalized Hebbian rule are also considered.

Action Potentials↗
PubMed2003

Development and validation of a knowledge test for health professionals regarding lifestyle modification.

OBJECTIVES: We wanted to develop and validate a test that assesses the knowledge and practices of health professionals (HPs) with regard to the role of nutrition, physical activity, and smoking cessation (lifestyle modification) in chronic diseases of lifestyle. METHODS: A descriptive cross-sectional validation study was carried out. The validation design consisted of two phases, namely 1) test planning and development and 2) test evaluation. The study sample consisted of five groups of HPs: dietitians, dietetic interns, general practitioners, medical students, and nurses. The overall response rate was 58%, resulting in a sample size of 186 participants. A test was designed to evaluate the knowledge and practices of HPs. The test was first evaluated by an expert group to ensure content, construct, and face validity. Thereafter, the questionnaire was tested on five groups of HPs to test for criterion validity. Internal consistency was evaluated by Cronbach's alpha. RESULTS: An expert panel ensured content, construct, and face validity of the test. Groups with the most training and exposure to nutrition (dietitians and dietetic interns) had the highest group mean score, ranging from 61% to 88%, whereas those with limited nutrition training (general practitioners, medical students, and nurses) had significantly lower scores, ranging from 26% to 80%. This result demonstrated criterion validity. Internal consistency of the overall test demonstrated a Cronbach's alpha of 0.99. Most HPs identified the mass media as their main source of information on lifestyle modification. These HPs also identified lack of time, lack of patient compliance, and lack of knowledge as barriers that prevent them from providing counseling on lifestyle modification. CONCLUSIONS: The results of this study showed that this test instrument identifies groups of health professionals with adequate training (knowledge) in lifestyle modification and those who require further training (knowledge).

Chronic Disease↗
PubMed2000

Chemical changes of polymeric surfaces after modification with multi-source cluster deposition.

A new process for surface modification of polymers with multi-source cluster deposition apparatus has been reported in our previous work. The apparatus simultaneously supplies reactant of ammonium sulfamate and activator of energetic Ar(+) ion. In this work chemical changes are analyzed on the basis of XPS spectra and the relations of contact angle and platelet adhesion with chemical changes are discussed. Polymer film, setting on a turning holder, was irradiated by Ar(+) ions during bombardment with ammonium sulfamate clusters. The Ar(+) ion source served for activation of polymer surface and a cluster ion source supplied ammonium sulfamate molecules to react with activated surface. After thorough washing with deionized sterile water, the modified surfaces were evaluated in terms of contact angle of water, elemental composition and binding state on XPS and platelet adhesion with platelet rich plasma (PRP). The modification of polysulfone decreased the contact angle of water on surfaces from 82.6 down to 34.5 degrees. The adhesion number of platelets were decreased to one-tenth of the original surface. Ammonium, amine, sulfate and thiophene combinations were formed on the modified surfaces. The primary studies showed successful modification of polysulfone with ammonium sulfamate by assistance of Ar(+) ion irradiation. The polar groups like N-sulfate were formed on surfaces and contribute to the decrease of surface contact angle and adhesion number of platelets. Since the same process can also be applied to other polymeric materials with various substrates, combining with the features of no solvent and no topographic changes, this method might be developed in a promising way for modification of polymers.

Journal Article↗
PubMed2002

Genome-wide histone modifications: gaining specificity by preventing promiscuity.

More than 20 residues within the four core histone proteins of the nucleosome are potential sites of post-translational modifications, such as methylation, acetylation, ubiquitination and phosphorylation. It has been hypothesized that specific patterns of these modifications on the nucleosome facilitate recruitment of non-histone proteins to chromatin. When such modifications are restricted to particular regions of the genome, they seem to play an important role in creating specific chromatin domains. However, more recent results suggest that some histone modifications, particularly those that exist on a genome-wide scale, act to reduce nonspecific binding by chromatin proteins involved in silencing. This decrease of promiscuous binding ensures that the silent chromatin proteins are not titrated away from their normal locations on chromosomes. We suggest that preventing such promiscuous binding of chromatin proteins is an important part of generating specificity to create chromatin domains and overall chromosome organization.

Animals↗
PubMed2002

Nanotransducers in cellular redox signaling: modification of thiols by reactive oxygen and nitrogen species.

The control of signal transduction involves post-translational modification of proteins at key amino acids. Cysteine residues are important in the control of 'redox' cell-signaling pathways, as thiol chemistry offers the possibility of modification by structurally diverse species, including those derived from oxidized lipids, peroxides or nitric oxide. An important and provocative study of the modification of thiols in the transcription factor OxyR recently extended this hypothesis. The findings offer the enticing possibility that the cell can distinguish between different degrees of oxidant and nitrosative exposure by modification at a single site on a signaling molecule.

Animals↗
PubMed1998

Modification of Unicryl composition for rapid polymerization at low temperature without alteration of immunocytochemical sensitivity.

We introduced a slight modification of Unicryl for fast polymerization at low temperature (in the range-20 degree C to-35 degree C) without modification of both physical properties and immunocytochemical yield. An UV initiator benzoin ethyl ether (BEE) is added at 0.05% concentration in neat resin during infiltration and final polymerization at-35 degree C. Immunogold labeling of amylase of mouse pancreas embedded in standard conditions recommended by the manufacturer or with our modification were compared by counting colloidal gold particles over zymogen granules using MACS, a specialized software dedicated to this operation. We noticed that addition of 0.05% BEE in Unicryl reduces the curing time to 16 h, which can be extended up to a maximum of 48 h at-35 degree C without noticeable modification of ultrastructural morphology, physical properties and immunocytochemical yield.

Acrylic Resins↗
PubMed2006

Results of chimney modification technique in ureterointestinal anastomosis of Hautmann ileal neobladder in bladder cancer.

BACKGROUND: To evaluate the surgical technique and functional outcome of a new application of the chimney modification to the popular Hautmann ileal neobladder. This modification used 3-5 cm chimney tubularized ileal segment for the bilateral ureterointestinal anastomosis. METHODS: Between December 2000 and July 2004, 15 patients (14 men, 1 woman) with invasive bladder cancer underwent radical cystectomy and Hautmann neobladder with chimney modification at Siriraj Hospital, Bangkok. Mean age was 61.7 years (range, 43-72 years). Perioperative morbidity, early and late urinary diversion-related complications, other surgical complications, follow-up results of ureterointestinal anastomosis, renal function and metabolic disorders were evaluated. Patients were interviewed about their continence, voiding function and potency. RESULTS: At a mean follow-up of 29.5 months, two patients had died of cancer progression. Of the 15 patients, nine (60%) had 10 early complications. Eight complications were related to the neobladder and two were not. Three (20%) patients had three late complications. Two complications were neobladder-related and one was not. There was no perioperative mortality. There was no ureteroileal anastomosis stricture in this series. Neobladder-ureteral reflux was demonstrated in eight of 22 ureteral units in 11 patients in whom cystography was performed. All patients had normal upper urinary tract without evidence of urinary obstruction. All 14 men (93% of study sample) had spontaneous urination, normal renal function and no metabolic acidosis. Good and satisfactory continence in the day and night were 93% and 73%, respectively. All male patients experienced impotence postoperatively. Only one sought treatment and was successfully treated with sildenafil. The one woman in this study required intermittent catheterization to empty the neobladder completely. She also had renal insufficiency with serum creatinine of 2.2 mg/dL and hyperchloraemic metabolic acidosis. CONCLUSION: New chimney modification in Hautmann ileal neobladder is simple and safe. Complications are acceptable. Follow-up results of renal and voiding functions are satisfactory. This operation can maintain good quality of life for patients with bladder cancer undergoing radical cystectomy.

Adult↗
PubMed2003

Study of protein modification by 4-hydroxy-2-nonenal and other short chain aldehydes analyzed by electrospray ionization tandem mass spectrometry.

A convenient way to study lipid oxidation products-modified proteins by means of suitable model systems has been investigated. As a model peptide, the oxidized B chain of insulin has been chemically modified by either 4-hydroxy-2-nonenal (HNE) or hexanal and the extent, sites, and structure of modifications were assessed by electrospray mass spectrometry. A reduction step, using either NaCNBH(3) or NaBH(4), was also studied to stabilize the alkylated compounds. From the data gathered, it appeared that NaCNBH(3), when added at the beginning of incubation, dramatically influenced the HNE-induced modifications in terms of the addition mechanism (Schiff base formation instead of Michael addition) but also of the amino acid residues modified (N-terminal amino acid instead of histidine residues). However, by reducing the HNE-adducted species at the end of the reaction with NaBH(4), the fragment ions obtained in the product ion scan experiments become more stable and thus, easier to interpret in terms of origin and mechanism involved. With regard to hexanal induced modifications, we have observed that hexanal addition under reductive conditions led to an extensive modification of the peptide backbone. Moreover, as confirmed by "in-source" collision followed by collision induced dissociation (CID) experiments on selected precursor ions (pseudo-MS(3) experiments), N,N-di-alkylations were first observed on the N-terminal residue and further on Lys(29) residue. On the other hand, compared to the native peptide, no significant changes in MS/MS fragmentation patterns (b and y ions series) were observed whatever the basic site modified by the aldehyde-addition.

Aldehydes↗
PubMed1998

SUMO-1 modification of IkappaBalpha inhibits NF-kappaB activation.

Activation of NF-kappaB is achieved by ubiquitination and proteasome-mediated degradation of IkappaBalpha. We have detected modified IkappaBalpha, conjugated to the small ubiquitin-like protein SUMO-1, which is resistant to signal-induced degradation. In the presence of an E1 SUMO-1-activating enzyme, Ubch9 conjugated SUMO-1 to IkappaBalpha primarily on K21, which is also utilized for ubiquitin modification. Thus, SUMO-1-modified IkappaBalpha cannot be ubiquitinated and is resistant to proteasome-mediated degradation. As a result, overexpression of SUMO-1 inhibits signal-induced activation of NF-kappaB-dependent transcription. Unlike ubiquitin modification, which requires phosphorylation of S32 and S36, SUMO-1 modification of IkappaBalpha is inhibited by phosphorylation. Thus, while ubiquitination targets proteins for rapid degradation, SUMO-1 modification acts antagonistically to generate proteins resistant to degradation.

Amino Acid Sequence↗
PubMed2001

Proteomics: posttranslational modifications, immune responses and current analytical tools.

The publication of the human genome sequence enables most of the still unknown protein sequences to be added to the current databases. A sequence alone does not, however, give information about the possible expression level of the corresponding protein, neither does it inform about the possible posttranslational modifications, like phosphorylation, glycosylation or changes in individual amino acids. Thus, the human proteome project, a large scale analysis of the functions of gene products, will have an enormous impact on our understanding of the biochemistry of proteins, processes and pathways they are involved in. The diversity in proteins is considerably expanded by various posttranslational modifications. These also pose problems to the investigators, but their careful analysis often pays back because they can reveal important properties in proteins or peptides--like an increased antigenicity leading to (auto)immune responses or an active form of a signaling protein. Immune tolerance usually exists towards self-proteins, but in specific cases it may be broken by posttranslational modifications in the proteins. Novel mass spectrometric, affinity and display techniques offer valuable tools for the large-scale analysis of proteomes. In the present paper we discuss their use for the detection of posttranslational modifications, functional interactions and possible disease-associated abnormalities in proteins.

Electrophoresis, Gel, Two-Dimensional↗
PubMed2003

Modification of the alkaline Comet assay to allow simultaneous evaluation of mitomycin C-induced DNA cross-link damage and repair of specific DNA sequences in RT4 cells.

The alkaline Comet assay is a simple, sensitive method for measuring the extent of DNA strand breaks in individual cells. Several modifications to the original assay have been developed to increase its applications. One such modification allows the measurement of DNA cross-links by assessing the relative reduction in DNA migration induced by a strand-breaking agent. Another modification includes the application of fluorescent in situ hybridisation (FISH) to investigate the localisation of specific gene domains within a cell. Although several studies have used these approaches separately, no report to date has combined these two versions of the Comet assay. The current study describes the modification of the Comet assay, to allow both measurement of mitomycin C (MMC)-induced cross-links and the subsequent application of FISH to study repair in the TP53 gene region. RT4 human bladder cancer cells were treated with 0, 5, 50 and 200 microg/ml MMC to study dose response, whilst for cross-link repair studies, they were treated with 50 microg/ml MMC and allowed to repair for up to 24 h. A clear dose response to MMC was displayed, demonstrable by a marked reduction in DNA migration, whilst repair studies showed that MMC-induced cross-links take at least 24 h to repair fully in RT4 cells. For Comet-FISH experiments, the number and location of TP53 hybridisation spots was also recorded for each cell. In dose response experiments, the number of spots per cell, and per Comet tail, decreased as MMC dose increased. In repair experiments, the number of spots, particularly in the Comet tail, increased as repair time increased. Furthermore, our results suggest that repair of the TP53 gene region is most rapid within the first 4 h following MMC treatment. We conclude that the novel experimental protocol presented here has considerable potential in evaluating DNA damage and sequence-related repair responses to cross-linking agents.

Cell Line, Tumor↗
PubMed2003

Modifications of arginines and their role in autoimmunity.

Posttranslational modifications of proteins often perform a key role in the biological functioning of proteins. Some of these modifications also change the immunogenicity of proteins and peptides and create 'self'-antigens which might induce autoimmune responses. In particular modifications of arginines within a defined protein context can lead to a specific B-cell immune response. This review discusses the generation of such modifications and their relevance for autoimmunity.

Animals↗
PubMed1995

The cultural basis of prosodic modifications to infants and children: a response to Fernald's universalist theory.

Fernald and her colleagues have argued for the universality of prosodic modifications in speech addressed to infants (e.g. Fernald, 1987; Fernald, Taeschner, Dunn, Papousek, de Boysson-Bardies & Fukui, 1989). An alternative proposal in Bernstein-Ratner & Pye (1984) and Pye (1986) argues that speech modifications to children are the result of a set of conventions that may vary from culture to culture. This note presents arguments against Fernald and in support of the cultural account of prosodic modifications to infants and children. First, in response to criticisms in Fernald et al., data are presented which defend the conclusion in Bernstein-Ratner & Pye that Quiché mothers show less prosodic modification to children than do mothers in other cultures studied to date. Second, data used to support the universal position in Fernald (1987) on adult identification of infant affective states are reinterpreted and shown to be equally interpretable as the result of a set of culturally transmitted rules.

Adult↗
PubMed2002

A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA.

Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, as well as in some archaea. In Saccharomyces cerevisiae every sequenced tRNA has at least one such modification, and all but one have two or more. We have used a biochemical genomics approach to identify the gene encoding dihydrouridine synthase 1 (Dus1, ORF YML080w), using yeast pre-tRNA(Phe) as a substrate. Dus1 is a member of a widespread family of conserved proteins, three other members of which are found in yeast: YNR015w, YLR405w, and YLR401c. We show that one of these proteins, Dus2, encoded by ORF YNR015w, has activity with two other substrates: yeast pre-tRNA(Tyr) and pre-tRNA(Leu). Both Dus1 and Dus2 are active as a single subunit protein expressed and purified from Escherichia coli, and the activity of both is stimulated in the presence of flavin adenine dinucleotide. Dus1 modifies yeast pre-tRNA(Phe) in vitro at U17, one of the two positions that are known to bear this modification in vivo. Yeast extract from a dus1-A strain is completely defective in modification of yeast pre-tRNAPhe, and RNA isolated from dus1-delta and dus2-delta strains is significantly depleted in dihydrouridine content.

Amino Acid Sequence↗
PubMed2002

Residue-specific mass signatures for the efficient detection of protein modifications by mass spectrometry.

Currently available mass spectrometric (MS) techniques lack specificity in identifying protein modifications because molecular mass is the only parameter used to characterize these changes. Consequently, the suspected modified peptides are subjected to tandem MS/MS sequencing that may demand more time and sample. We report the use of stable isotope-enriched amino acids as residue-specific "mass signatures" for the rapid and sensitive detection of protein modifications directly from the peptide mass map (PMM) without enrichment of the modified peptides. These mass signatures are easily recognized through their characteristic spectral patterns and provide fingerprints for peptides containing the same content of specific amino acid residue(s) in a PMM. Without the need for tandem MS/MS sequencing, a peptide and its modified form(s) can readily be identified through their identical fingerprints, regardless of the nature of modifications. In this report, we demonstrate this strategy for the detection of methionine oxidation and protein phosphorylation. More interestingly, the phosphorylation of a histone protein, H2A.X, obtained from human skin fibroblast cells, was effectively identified in response to low-dose radiation. In general, this strategy of residue-specific mass tagging should be applicable to other posttranslational modifications.

Fibroblasts↗
PubMed2004

Prediction of posttranslational modifications using intact-protein mass spectrometric data.

We present a Web-based application that uses whole-protein masses determined by mass spectrometry to identify putative co- and posttranslational proteolytic cleavages and chemical modifications. The protein cleavage and modification engine (PROCLAME) requires as input an intact mass measurement and a precursor identification based on peptide mass fingerprinting or tandem mass spectrometry. This approach predicts mass-modifying events using a depth-first tree search, bounded by a set of rules controlled by a custom-built fuzzy logic engine, to explore a large number of possible combinations of modifications accounting for the experimental mass. Candidates are saved during a search if they are within a user-specified instrument mass accuracy; the total number of possible candidates searched is based on a specified fuzzy cutoff score. Candidates are scored and ranked using a simple probabilistic model. There is generally not enough information in an intact mass measurement to determine a single unique protein characterization; however, the program provides utility by expediting the identification of sets of putative events consistent with the mass data and ranking them for further investigation. This approach uses a simple, intuitive rule base and lends itself to discovery of unannotated posttranslational events. We have assessed the program with both in silico-generated test data and with published data from an analysis of large ribosomal subunit proteins, both from the yeast S. cerevisiae. Results indicate a high degree of sensitivity and specificity in characterizing proteins whose masses resulted from reasonable proteolysis and covalent modification scenarios. The application is available on the web at http://proclame.unc.edu.

Computational Biology↗
PubMed2005

Protein pI shifts due to posttranslational modifications in the separation and characterization of proteins.

Proteins from breast cancer cell lines are characterized using a 2-D liquid separation technique in which protein pI is used as the first-dimension separation parameter. To effect this protein pI separation, chromatofocusing(CF) is employed whereby a pH gradient is generated on-column using a weak anion exchange medium with the intact proteins fractionated and collected every 0.2 pH unit. It is demonstrated that the pI for expressed intact proteins as generated by CF is an important parameter for identification and characterization of the actual protein modifications occurring in the cancer cell. For most proteins, the experimentally determined pI is very close to that predicted by the databases. In other cases, however, where the pI is observed to be shifted from the expected value, it is shown that this shift is often correlated to protein modifications. The modifications that cause such shifts include truncations and deletions often observed in cancer cells or phosphorylations that can shift the pI by several pH units. It is also shown that the effects of phosphorylation on the observed shift can vary depending upon the protein and the amount of phosphorylation. Moreover, large changes in the pI are often observed for proteins with a pI above 7.0 upon phosphorylation, whereas little change is observed for proteins with a pI of approximately 5.0. The expressed protein's pI value thus becomes an important parameter together with the intact MW value, peptide map, and MS/MS results for identification of the presence and type of posttranslational modifications occurring in the cancer cell.

Amino Acid Sequence↗
PubMed2005

Characterization of a novel modification to monoclonal antibodies: thioether cross-link of heavy and light chains.

A novel, nonreducible thioether bridge between the light and heavy chains of different IgG1 monoclonal antibodies has been characterized. An additional band with an apparent molecular weight of 92 kDa was detected when monoclonal antibodies were analyzed by reducing capillary gel electrophoresis (rCGE) and reducing SDS-PAGE. To further investigate this observation, an early-eluting peak in the size exclusion chromatogram of a reduced and alkylated monoclonal antibody was collected and characterized by liquid chromatography, mass spectrometry, and gel electrophoresis. The reduced and alkylated Mab was shown to be a cross-linked adduct with a molecular weight of 75 kDa. In the adduct, the heavy and light chains of the antibody were cross-linked by a nonreducible thioether bond between Cys-223 of the heavy chain and the C-terminal Cys residue of the light chain. The thioether bond modification was confirmed in the Fab fragment of a monoclonal antibody by LC-MS and nonreduced Lys-C peptide mapping with tandem mass spectrometry. The data show that the disulfide bond modification occurred under nonreducing conditions and was not an artifact of sample preparation for the rCGE analysis. The thioether bond modification was observed in several IgG1 monoclonal antibody products. Structural characterization of this novel modification is important in understanding the mechanism of thioether bond formation.

Amino Acid Sequence↗