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PubMed1990

Interactions among modifiers of retrotransposon-induced alleles of the white locus of Drosophila melanogaster.

Mutations in five loci that modify the phenotype of whiteapricot (wa), caused by the retrotransposon, copia, were examined in two-way combinations to determine whether their effects were additive or epistatic. All two-way combinations of mutations in these five loci, mottler of white (mw), suppressor of forked (su(f], suppressor of white apricot (su(wa], Enhancer of whiteapricot, (E(wa] and Darkener of apricot (Doa), are additive in their effects on wa, implying that each second-site modifier locus affects a different process. Three other copia-induced mutations, HwUa, whd81b25 and ctns were also examined for responsiveness to mutations in these modifier loci. None clearly responded. Mutations associated with B104 insertions, including Gl, vgni, ctn and wric were also examined for responsiveness to mw mutations, which have specificity for this element as well. Both vgni and wric respond to mutations in mw. The former interaction demonstrates that mw is capable of interacting with B104 elements in loci other than white. The significance of the results with respect to the nature of second-site modifier loci is discussed.

Alleles↗
PubMed1993

Dosage dependent modifiers of white alleles in Drosophila melanogaster.

As part of a study to identify dosage-sensitive modifiers of the white eye colour locus and the retrotransposon, copia, a segmental aneuploid screen was conducted. It surveys the autosomal complement of the genome for dosage dependent modifiers of white, including ones effective upon retrotransposon insertion-induced alleles. Several regions were found which, when present as a segmental trisomy, affected one or more of the alleles tested in a strong and consistent fashion. Two of these regions have been identified as containing previously described modifiers, Darkener-of-apricot and Inverse regulator-a. The remainder identify new white allele modifiers. Selected segmental monosomics were also tested where possible for regions exhibiting a trisomic effect. At least three regions were found to have a dosage-dependent effect in one, two and three copies.

Alleles↗
PubMed1995

Genotype-specific modifiers of transgene methylation and expression in the zebrafish, Danio rerio.

Previous reports involving mammalian systems, particularly mice, have demonstrated the existence of cis- and trans-acting modifiers of transgene methylation. These modifiers are thought to be important in dominance modification, genome imprinting and cellular expression mosaicism. Their potential role in the penetrance and severity of many complex human diseases could be of even greater significance. In the present investigation we demonstrate that modifiers that act in a similar fashion to those identified in mice also exist in a non-mammalian vertebrate, the zebrafish Danio rerio. We also provide evidence that the transgene methylation pattern may be influenced by the sex of the individual and environmental modulators such as temperature and sodium butyrate. These data support the theory that this type of dominance modification is mechanistically similar to position effect variegation in Drosophila. Furthermore, these data suggest evolutionary conservation of the modifiers, at least within vertebrates, and imply that they and their actions are important in normal vertebrate development.

5-Methylcytosine↗
PubMed1995

The Cardinal Needs Schedule--a modified version of the MRC Needs for Care Assessment Schedule.

This paper describes a modified version of the MRC Needs for Care Schedule (the Cardinal Needs Schedule), for measuring needs for psychiatric and social care amongst patients with severe psychiatric disorders. The modified schedule has three new features: (i) it is quick and easy to use; (ii) it takes systematic account of the views of patients and their carers; (iii) it defines and identifies need in a way that is concise and easy to interpret. The paper describes why the three new features were considered necessary, and then gives an overview of the structure of the Cardinal Needs Schedule, together with a description of how the three new features were developed. During a study of social services care management the practicality of the modified schedule was investigated and further data were obtained on the reliability and validity of the standardized approach to measuring need, in domains not previously investigated. Because of its speed and simplicity, the Cardinal Needs Schedule offers a new choice to researchers who wish to use a standardized and practical assessment of need in evaluative studies of community care. Examples of the usage of the modified schedule are given in an Appendix.

Activities of Daily Living↗
PubMed1991

Modified repetition in poems elicited from young children.

Attempts were made to elicit poems from 133 children between the ages of 2;3 and 6;11. Seventy-eight of the children produced 606 poems between them. Forty-five per cent of the poems contained the syntactic device of modified repetition: a substitution exercise where a grammatical frame is repeated and the substitution occurs in part of the grammatical frame. This was so despite the fact that modified repetition was not present in the examples that were used to elicit poems from the children. The frequency and types of modified repetition used by the children did not vary much with age. The question of whether children's use of modified repetition in their rhythmical poems has the function of helping them to practise grammatical forms, or whether it is simply one reflection of a general human tendency towards the use of pattern in language, is discussed.

Child↗
PubMed2006

Initial clinical experience in transcatheter closure of large patent arterial ducts in infants using the modified and angled Amplatzler duct occluder.

OBJECTIVE: To establish the feasibility and efficacy of closing large patent arterial duct in infants, using the modified and angled variants of the Amplatzer duct occluder. BACKGROUND: Closure of large patent arterial ducts by inserting devices in sick and underweight infants, particularly those weighing around 5 kilograms, remains a challenge. Bigger devices require larger delivery sheaths and may cause obstruction either to the aorta or left pulmonary artery. Negotiating a large device is difficult or impossible, as the sheath gets kinked. Because of these problems, such underweight infants with large ducts who are failing to thrive, and in left ventricular failure with associated lesions, are typically referred for surgery, often leading to higher morbidity and mortality. METHODS: We attempted to close such large patent arterial ducts using the new Amplatzer occluder, modified with single layer of polyester, and the angled occluder, with no polyester material, inserted through a specially braided kink-resistant sheath. RESULTS: Closure was achieved in 10 infants, with mean age of 8.2 months, mean weight of 5.5 kilograms, the lowest weighing 3.9 kilograms. The mean size of the patent ducts was 6.3 millimetres, with the largest measuring 8.6 millimetres. We implanted 6 modified and 4 angled occluders. In one patient, suffering from hydronephrosis, a 14/12 angled device embolized and was retrieved, but the patient died. In the remaining patients, all ducts were closed completely, with no obstruction to either the aorta or left pulmonary artery. On follow up, all showed excellent clinical improvement. CONCLUSION: Complete closure of very large patent arterial ducts is now possible, even in very sick and underweight infants, using the large but low profile custom-made angled or modified versions of the Amplatzer occluder.

Balloon Occlusion↗
PubMed1992

Controlling solvent strength and selectivity in micellar liquid chromatography: role of organic modifiers and micelles.

Simultaneous enhancement in elution strength and selectivity which has been previously observed in micellar liquid chromatography (MLC) for a variety of compounds is further investigated. The reasons behind the occurrence of this unique phenomenon are studied, and the influence of micelles and organic solvents on elution strength and selectivity is discussed. A model is developed which explains the dependence of the solvation ability of organic solvents in MLC (represented by the solvent strength parameter, S, of solutes) and the degree of solute interactions with micelles. Whenever the difference in solvent strength parameter values of two solutes in micellar eluents, dS, is positive, maximum selectivity is observed at the weakest eluent strength. When dS less than 0, there exists an inverse relationship between retention and solvent strength parameter so that selectivity monotonically increases with volume fraction of organic solvent in micellar eluents. It is shown that usually there is no direct relationship between the solvent strength parameter in MLC and retention. As a result, selectivity enhancement due to an increase in the concentration of organic modifier (i.e. solvent strength) occurs frequently in MLC. Interestingly, for cases where selectivity decreases with an increase in organic modifier, simultaneous enhancement of selectivity and solvent strength can be observed by increasing micelle concentration. In a sense, the concentrations of organic modifier and micelles complement one another in improving selectivity at higher elution strengths. As a result of this unique phenomenon better separations in shorter analysis times can be observed. The mutual effects of micelles and organic modifier on one another would also require a simultaneous optimization of these two parameters.

1-Butanol↗
PubMed1994

Sequence-specific gene detection with a gold electrode modified with DNA probes and an electrochemically active dye.

A synthesized 20-mer DNA probe complementary to a part of an oncogene v-myc region having a mercaptohexyl group at the 5'-phosphate end was immobilized on a gold electrode by chemisorption. The immobilized DNA was detected voltammetrically using Hoechst 33258 with a DNA minor groove binder and an electrochemically active dye. The modified electrode was immersed into a 100 mumol/L Hoechst 33258 solution and washed with a phosphate buffer (pH 7.0). The anodic peak current (ipa) of Hoechst 33258 on the modified electrode was higher than that on a bare gold electrode (128 and 75 nA, respectively). It was considered that Hoechst 33258 was concentrated on the electrode surface due to its association with DNA. When the modified electrode was hybridized in a solution of a model targeted gene (10(-7) g/mL), single-stranded pVM623 containing the PstI fragment of a 1.5-kilobase pair of oncogene v-myc, the ipa was 192 nA. On the other hand, the ipa was 128 nA when the modified electrode was reacted in a solution of single-stranded pUC119 without a region complementary to v-myc in pVM623. The ipa was related to the concentration of the targeted DNA in the hybridization reaction. The use of Hoechst 33258 resulted in a sequence-specific detection of the targeted DNA quantitatively ranging from 10(-7) to 10(-13) g/mL in a buffer solution.

Base Sequence↗
PubMed1995

Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database.

A method to correlate uninterpreted tandem mass spectra of modified peptides, produced under low-energy (10-50 eV) collision conditions, with amino acid sequences in a protein database has been developed. The fragmentation patterns observed in the tandem mass spectra of peptides containing covalent modifications is used to directly search and fit linear amino acid sequences in the database. Specific information relevant to sites of modification is not contained in the character-based sequence information of the databases. The search method considers each putative modification site as both modified and unmodified in one pass through the database and simultaneously considers up to three different sites of modification. The search method will identify the correct sequence if the tandem mass spectrum did not represent a modified peptide. This approach is demonstrated with peptides containing modifications such as S-carboxymethylated cysteine, oxidized methionine, phosphoserine, phosphothreonine, or phosphotyrosine. In addition, a scanning approach is used in which neutral loss scans are used to initiate the acquisition of product ion MS/MS spectra of doubly charged phosphorylated peptides during a single chromatographic run for data analysis with the database-searching algorithm. The approach described in this paper provides a convenient method to match the nascent tandem mass spectra of modified peptides to sequences in a protein database and thereby identify previously unknown sites of modification.

Algorithms↗
PubMed1995

Analysis of modified oligonucleotides by matrix-assisted laser desorption/ionization Fourier transform mass spectrometry.

Matrix-assisted laser desorption/ionization (MALDI) Fourier transform ion cyclotron resonance mass spectrometry (FTMS) has been applied to the structural characterization of modified oligodeoxyribonucleotide 4-, 6-, and 11-mers. Each oligonucleotide contained one modified base, either an O6-methyl-substituted guanine, an N6-(10R)-trans-opened benzo[a]pyrenediol epoxide adduct of adenine, or an N2-(R)-styrene oxide adduct of guanine. 3-Hydroxypicolinic acid was used as the MALDI matrix for molecular weight and purity determinations, while either 2,5-dihydroxybenzoic acid (DHBA) or an anthranilic/nicotinic acid (AA/NA) mixture was used to induce fragmentation for the production of structurally significant fragment ions. For the 4- and 6-mers, the oligonucleotide sequence could be obtained from the direct AA/NA or DHBA spectra. Sequence information was also obtained by inserting a time delay between the laser desorption event and ion detection to permit metastable decomposition. For the 11-mers, high-mass sequence ions were not detected. Although similar sequence ions were observed in both the positive and the negative ion mass spectra, more fragmentation was generally observed in the positive ion mode. In the positive ion mode, modified base fragment ions were observed when DHBA was used, and these fragments were examined using accurate mass measurements, collisionally induced dissociations, and ion-molecule reactions to characterize the modified base. MALDI-FTMS signals from one sample application can be used for the measurement of hundreds of spectra. The direct MALDI-FT mass spectra show matrix-dependent, structurally informative fragments, and CID experiments can be implemented using low-picomole sample quantities.

Base Sequence↗
PubMed2003

Scanning tunneling microscopy with chemically modified gold tips: in situ reestablishment of chemical contrast.

A method was developed for the reestablishment of chemical contrast in STM images obtained with chemically modified gold tips. Such tips display selective chemical contrast, which allows the selective imaging of specific species on the sample surface. Chemically modified STM tips can be fabricated by forming a self-assembled monolayer (SAM) on an electrochemically etched gold tip. One difficulty with this method thus far has been the relatively short lifetime of SAM-treated tips. The method described here utilizes the brief application of a high bias voltage between the sample and the tip to cause SAM molecules to reoccupy the tip apex, thereby allowing the tips to display selective chemical contrast in imaging. These treatments consist of applying a +1.9-V sample bias for 0.5-10 min under tunneling conditions. The usable lifetime of SAM-modified tips could be increased by more than 2 orders of magnitude, from hours to at least a month, dramatically increasing the efficiency of using SAM-modified gold tips. SAM molecules can also be removed from the tip apex by application of a negative sample bias (-2.0 V for 0.5-10 min) making it possible to alternate between conventional STM images and STM images with chemically enhanced contrasts.

Journal Article↗
PubMed2003

Modified carbon surfaces as "organic electrodes" that exhibit conductance switching.

Glassy carbon (GC) surfaces modified with monolayers of biphenyl and nitrobiphenyl molecules were examined as voltammetric electrodes for ferrocene, benzoquinone, and tetracyanoquinodimethane electrochemistry in acetonitrile. The modified electrodes exhibited slower electron transfer than unmodified GC, by factors that varied with the monolayer and redox system. However, after a negative potential excursion to approximately -2.0 V versus Ag+/Ag, the modified electrodes exhibited much faster electron-transfer kinetics, approaching those observed on unmodified GC. The effect is attributed to an apparently irreversible structural change in the biphenyl or nitrobiphenyl monolayer, which increases the rate of electron tunneling. The transition to the "ON" state is associated with electron injection into the monolayer similar to that observed in previous spectroscopic investigations and causes a significant decrease in the calculated HOMO-LUMO gap for the monolayer molecule. Once the monolayer is switched ON, it supports rapid electron exchange with outer-sphere redox systems, but not with dopamine, which requires adsorption to the GC surface. The increase in electron-transfer rate with electron injection is consistent with an increase in electron tunneling rate through the monolayer, caused by a significant decrease in tunneling barrier height. The ON electrode can reduce biphenyl- or nitrobiphenyldiazonium reagent in solution to permit formation of a second modification layer of biphenyl or nitrobiphenyl molecules. This "double derivatization" procedure was used to prepare tetraphenyl- and nitrotetraphenyl-modified electrodes, which exhibit significantly slower electron transfer than their biphenyl and nitrobiphenyl counterparts. A "switching" electrode may have useful properties for electroanalytical applications and possibly in electrocatalysis. In addition, the ON state represents an "organic electrode" in which electron transfer occurs at an interface between an organic conductor and a solution rather than an interface between a solution and a metal or carbon electrode.

Journal Article↗
PubMed2003

Voltammetric procedure for examining DNA-modified surfaces: quantitation, cationic binding activity, and electron-transfer kinetics.

To examine DNA-modified surfaces, we have developed a simple, convenient, and reliable procedure based on the voltammetric response of multiply charged transition metal cations (such as [Ru(NH3)6]3+) bound electrostatically to the DNA probes. At micromolar concentrations of the redox molecules in the electrolyte, the reduction and oxidation waves resulting from the immobilized cations on DNA-modified electrodes are well defined, stable, and reproducible. The surface densities of both single- and double-stranded oligonucleotides were accurately determined by integration of the peak for reduction of [Ru(NH3)6]3+ to [Ru(NH3)6]2+. In addition, the binding constant and electron-transfer rate constant of [Ru(NH3)6]3+ on DNA-modified electrodes were evaluated with the help of classical models. The present research provides not only an applicable and simple protocol for the quantitation of DNA probes on chips but also a versatile and powerful tool for the investigation of the binding activity and electron-transfer kinetics of cationic analytes on DNA-modified surfaces.

Cations↗
PubMed2004

Electrochemical coding of single-nucleotide polymorphisms by monobase-modified gold nanoparticles.

Rapidly increasing information about the human genome requires a fast and simple method for the detection of single-nucleotide polymorphisms (SNPs). To date, the conventional SNP detection technologies have been unable to identify all possible SNPs and needed further development in cost, speed, and sensitivity. Here we describe a novel method to discriminate and code all possible combinations. SNPs were coded by monitoring the changes in the electrochemical signal of the monobase-modified colloidal gold (Au) nanoparticles. First, a chitosan layer was formed on the alkanethiol self-assembled monolayer-modified Au nanoparticle. The monobases were then attached onto the chitosan-coated Au nanoparticles through their 5' phosphate group via the formation of a phosphoramidate bond with the free amino groups of chitosan. The size of the surface-modified Au nanoparticle was found to be 8.46 +/- 1.53 nm by using atomic force microscopy. If there is a SNP in DNA and the mismatched bases are complementary to the monobase, Au nanoparticles accumulate on the electrode surface in the presence of DNA polymerase I (Klenow fragment), thus resulting in a significant change in the Au oxide wave. In this report, monobase-modified Au nanoparticles show not only the presence of a SNP, but also identify which bases are involved within the pair. Especially, the identification of a transversion SNP, which contains a couple of the same pyrimidine or purine bases, is greatly simplified. A model study was performed by using a synthetic 21-base DNA probe related to tumor necrosis factor (TNF-alpha) along with its all possible mutant combinations. This versatile nanoparticle-based electrochemical protocol is a promising candidate for coding all mutational changes.

Base Sequence↗
PubMed2004

Use of polymer-modified MALDI-MS probes to improve analyses of protein digests and DNA.

The use of sample probe surfaces patterned with 200-microm-diameter spots of hydrophilic, charged polymers significantly enhances the analysis of protein digests and DNA by MALDI-MS. Selective adsorption on these polymer-modified surfaces allows collection of specific proteolytic peptides, while subsequent rinsing of the deposited sample removes contaminants. In the case of partially digested myoglobin, the mass spectrum obtained using a sample probe modified with polyanionic functionalities permits detection of 22 proteolytic fragments, while analysis using a stainless steel MALDI sample probe gives only 11 detectable fragments. Similarly, during the analysis of bovine serum albumin digests, the use of several different surface-modified MALDI sample probes increases sequence coverage from 61.3 to 74.5%. Detection of phosphorylated peptides can be quite challenging during analyses of phosphoprotein digests by MALDI-MS because these anionic proteolytic fragments have low ionization efficiencies. However, MALDI signals from the phosphorylated proteolytic fragments sometimes increase dramatically when using a sample probe surface modified by a polycation (polyethylenimine or poly(acrylic acid) complexed with Fe(3+)). The signal enhancement apparently occurs because the positive surface selectively binds the phosphorylated peptides. The use of patterned, polycationic surfaces also shows great promise for selective adsorption and decontamination of DNA samples; a simple water rinse diminishes or eliminates the formation of multi-ion adducts, thereby improving mass resolution during subsequent analysis by MALDI-MS.

Acrylic Resins↗
PubMed2004

Top-down characterization of nucleic acids modified by structural probes using high-resolution tandem mass spectrometry and automated data interpretation.

A top-down approach based on sustained off-resonance irradiation collision-induced dissociation (SORI-CID) has been implemented on an electrospray ionization (ESI) Fourier transform mass spectrometer (FTMS) to characterize nucleic acid substrates modified by structural probes. Solvent accessibility reagents, such as dimethyl sulfate (DMS), 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMCT), and beta-ethoxy-alpha-ketobutyraldehyde (kethoxal, KT) are widely employed to reveal the position of single- vs double-stranded regions and obtain the footprint of bound proteins onto nucleic acids structures. Established methods require end-labeling of the nucleic acid constructs, probe-specific chemistry to produce strand cleavage at the modified nucleotides, and analysis by polyacrylamide gel electrophoresis to determine the position of the susceptible sites. However, these labor-intensive procedures can be avoided when mass spectrometry is used to identify the probe-induced modifications from their characteristic mass signatures. In particular, ESI-FTMS can be directly employed to monitor the conditions of probe application to avoid excessive alkylation, which could induce unwanted distortion or defolding of the substrate of interest. The sequence position of the covalent modifications can be subsequently obtained from classic tandem techniques, which allow for the analysis of individual target adducts present in complex reaction mixtures with no need for separation techniques. Selection and activation by SORI-CID has been employed to reveal the position of adducts in nucleic acid substrates in excess of 6 kDa. The stability of the different covalent modifications under SORI-CID conditions was investigated. Multiple stages of isolation and activation were employed in MS(n)() experiments to obtain the desired sequence information whenever the adduct stability was not particularly favorable, and SORI-CID induced the facile loss of the modified base. A new program called MS2Links was developed for the automated reduction and interpretation of fragmentation data obtained from modified nucleic acids. Based on an algorithm that searches for plausible isotopic patterns, the data reduction module is capable of discriminating legitimate signals from noise spikes of comparable intensity. The fragment identification module calculates the monoisotopic mass of ion products expected from a certain sequence and user-defined covalent modifications, which are finally matched with the signals selected by the data reduction program. Considering that MS2Links can generate similar fragment libraries for peptides and their covalent conjugates with other peptides or nucleic acids, this program provides an integrated platform for the structural investigation of protein-nucleic acid complexes based on cross-linking strategies and top-down ESI-FTMS.

Aldehydes↗
PubMed2006

Global identification of O-GlcNAc-modified proteins.

The O-linked N-acetylglucosamine (O-GlcNAc) modification of serine/threonine residues is an abundant posttranslational modification present in cytosolic and nuclear proteins. The functions and subproteome of O-GlcNAc modification remain largely undefined. Here we report the application of the tagging-via-substrate (TAS) approach for global identification of O-GlcNAc-modified proteins. The TAS method utilizes an O-GlcNAc azide analogue for metabolic labeling of O-GlcNAc-modified proteins, which can be chemoselectively conjugated for detection and enrichment of the proteins for proteomics studies. Our study led to the identification of 199 putative O-GlcNAc-modified proteins from HeLa cells, among which 23 were confirmed using reciprocal immunoprecipitation. Functional classification shows that proteins with diverse functions are modified by O-GlcNAc, implying that O-GlcNAc might be involved in the regulation of multiple cellular pathways.

Acetylglucosamine↗
PubMed2006

Direct DNA hybridization at disposable graphite electrodes modified with carbon nanotubes.

The performance of glassy carbon (GCE) and graphite pencil electrodes (PGE) modified with multiwalled carbon nanotubes (CNTs) are compared, based on the direct electrochemical detection of nucleic acids. This is accomplished by monitoring the differential pulse voltammetry changes of the guanine signal. CNT-modified PGE compares favorably to that of the commonly used CNT-modified GCE owing to the intrinsic improved performance of the supporting PGE. The better intrinsic characteristics of the PGE are related to its composite structure and higher level of porosity compared to GCE. The performance characteristics of the direct DNA hybridization on the disposable CNT-modified PGE are studied in terms of optimum analytical conditions such as probe concentration, target concentration, hybridization time, and selectivity. The new DNA biosensor described here has shown some important advantages such being inexpensive, sensitive, selective, and able to generate reproducible results using a simple and direct electrochemical protocol.

DNA↗