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PubMed2006

Indoor air modification interventions for prolonged non-specific cough in children.

BACKGROUND: Non-specific cough has been defined as non-productive cough in the absence of identifiable respiratory disease or known aetiology and is common in childhood. These children are treated with a variety of therapies, including non-pharmacological treatments. There is a wide variety and a growing market for these non-pharmacological treatments that include air-modification modalities. OBJECTIVES: To determine the efficacy of air-modification modalities, (ionisers, vaporisers, humidifiers, air filters, regular vacuuming), in treating children with non-specific cough. SEARCH STRATEGY: The Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, OLDMEDLINE and EMBASE databases were searched by the Cochrane Airways Group. The latest searches were performed in November 2005. SELECTION CRITERIA: All randomised controlled trials comparing air-modification modalities with a placebo treatment, for any duration. DATA COLLECTION AND ANALYSIS: Results of searches were reviewed against pre-determined criteria for inclusion. Five papers were considered for inclusion but no eligible trials were identified and thus no data was available for analysis. MAIN RESULTS: No randomised controlled trials that examined the efficacy of air-modification modalities in the management of prolonged, non-specific cough in children were found. AUTHORS' CONCLUSIONS: Based on the evidence currently available, a recommendation can not be given for air-modification interventions in the treatment of prolonged, non-specific cough in children.

Air Pollution, Indoor↗
PubMed1993

Effects of annular cranial vault modification on the cranial base and face.

Artificial modification of the cranial vault was practiced by a number of prehistoric and protohistoric populations, frequently during an infant's first year of life. We test the hypothesis that, in addition to its direct effects on the cranial vault, annular cranial vault modification has a significant indirect effect on cranial base and facial morphology. Two skeletal series from the Pacific Northwest Coast, which include both nonmodified and modified crania, were used: the Kwakiutl (62 nonmodified, 45 modified) and Nootka (28 nonmodified, 20 modified). Three-dimensional coordinates of 53 landmarks were obtained using a diagraph, and 36 landmarks were used to define nine finite elements in the cranial vault, cranial base, and face. Finite element scaling was used to compare average nonmodified and average modified crania, and the significance of the results were evaluated using a bootstrap test. Annular modification of the cranial vault produces significant effects on the morphology of the cranial base and face. Annular modification in the Kwakiutl resulted in restrictions of the cranial vault in the medial-lateral and superior-inferior dimensions and an increase in anterior-posterior growth. Similar dimensional changes are observed in the cranial base. The Kwakiutl face is increased anterior-posteriorly and reduced anterior-laterally to posterior-medially. Similar effects of modification are observed in the Nootka cranial vault and cranial base, though not in the face. These results demonstrate the developmental interdependence of the cranial vault, cranial base, and face.

Cephalometry↗
PubMed2005

Protein posttranslational modifications: the chemistry of proteome diversifications.

The diversity of distinct covalent forms of proteins (the proteome) greatly exceeds the number of proteins predicted by DNA coding capacities owing to directed posttranslational modifications. Enzymes dedicated to such protein modifications include 500 human protein kinases, 150 protein phosphatases, and 500 proteases. The major types of protein covalent modifications, such as phosphorylation, acetylation, glycosylation, methylation, and ubiquitylation, can be classified according to the type of amino acid side chain modified, the category of the modifying enzyme, and the extent of reversibility. Chemical events such as protein splicing, green fluorescent protein maturation, and proteasome autoactivations also represent posttranslational modifications. An understanding of the scope and pattern of the many posttranslational modifications in eukaryotic cells provides insight into the function and dynamics of proteome compositions.

Animals↗
PubMed2004

Transglutaminase-mediated modification of glutamine and lysine residues in native bovine beta-lactoglobulin.

Bovine beta-lactoglobulin (BLG) is a major component in whey and its physical properties are important for the texture of many dairy-based foods. Modification of proteins with transglutaminase from Streptoverticillium mobaraense (MTGase) can be used to alter their physical properties. MTGase-mediated modification of native BLG was until now, however, not effective. Here we report a method that allows for the enzymatic modification of native BLG with MTGase. Lysines 8, 77, and 141 were modified with alpha-N-carbobenzyloxy-glutamine-glycine and glutamines 35, 59, 68,and 155 were modified with 6-aminohexanoic acid under nonreducing and nondenaturing conditions. MTGase-mediated BLG crosslinking is hampered by the low reactivity of the lysines and enzymatic deamidation of the glutamines prevails. Modification of BLG with poly-lysine yields a BLG derivative with increased affinity for the water-air interface and stronger surface tension lowering capacities than normal BLG. Hence, this modification method offers the opportunity to change the functional properties of BLG and to prepare novel protein foods.

Amino Acid Sequence↗
PubMed1994

Native electrophoresis to monitor chemical modifications of human interleukin-3.

Native electrophoresis on the Pharmacia PhastSystem using a new buffer system is used to monitor chemical modifications of human interleukin-3. The method is faster, more gentle and more convenient than amino acid analysis. Micrograms of protein suffice in contrast with milligrams required in spectrophotometric methods. As compared to generally used native electrophoresis, the combination of a changed conductivity, lower pH and the low density matrix results in a much better separation and detection of both the reaction products containing a high charge and the reaction products containing a low charge. This enables monitoring of extensive modifications as well as mild modifications. Our method also provides indications for denaturation of the protein. It has proven to be highly reproducible for at least 10 different modification reactions. Information can be obtained about the presence of the various distinct forms of the modified molecule, for instance leading to the average number of groups on the molecule. It also detects modifications not detectable with generally used native electrophoresis.

Circular Dichroism↗
PubMed1998

The identification of peptide modifications derived from gel-separated proteins using electrospray triple quadrupole and ion trap analyses.

Microspray tandem mass spectrometry (MS/MS) in combination with database search routines has become a powerful tool for the identification of proteins from femtomole amounts of material following gel electrophoresis and in-gel digestion procedures. However, artifactual modification of susceptible residues can arise during gel electrophoresis, leading to unexpected peptide mass shifts during mass analysis. Consequently, collision-induced dissociation (CID) spectra generated from these derivatized peptides can defy direct interpretation by automated database search routines and remain unidentified. Here, we evaluate the MS/MS spectra of peptides carrying oxidized derivatives of tryptophane and methionine residues, and various modifications of cysteine. We demonstrate that certain of these modifications generate characteristic fragmentation patterns or "fingerprints", during CID analysis, the knowledge of which can facilitate the interpretation of the spectra. We will show that these signature fragment ions are predominantly produced during the CID analysis of singly charged ions although they can be observed in the MS/MS spectra of the doubly charged species as well. In other cases, the CID spectrum lacks a characteristic fingerprint and the modification remains silent. However, CID spectra of related peptides, differing only by their modifications, are similar and all or part of the fragment ion spectra will have shifted by a discreet mass, which facilitates the identification of the modified residue. At the same time, the comparison of related spectra can prevent misinterpretations such as the assignment of a residue mass to the wrong amino acid or a neutral loss fragment ion to a gamma- or b-ion.

Amino Acid Sequence↗
PubMed1997

Lifestyle modification in the pharmacologic treatment of obesity: a pilot investigation of a potential primary care approach.

This study examined a new method of providing brief, individual lifestyle modification to obese individuals treated by pharmacotherapy. Twenty-six women with a mean (+/- SD) age of 47.0 +/- 7.2 years, weight of 97.6 +/- 13.0 kg, and body mass index of 36.5 +/- 5.0 kg/m2 were prescribed 60 mg/d of fenfluramine and 15 mg/d of phentermine for one year. In addition, half of the women were randomly assigned to traditional group behavior modification, conducted by a nutritionist, which included 32 75-minute sessions during the year. The other half were provided lifestyle modification by a physician during 10 15-20 minute structured visits. All participants received identical treatment manuals and comparable assignments for behavior change. At the end of one year, patients in the physician group achieved the same highly successful weight losses as those treated by group behavior modification (13.9 +/- 9.6 kg vs. 15.4 +/- 7.9 kg, respectively). Treatment was associated with highly significant improvements in lipids and lipoproteins, as well as in mood and several measures of appetite. Weight loss the first four weeks, as well as patient completion of daily food records during the first 18 weeks, correlated positively with weight loss at weeks 18, 26, and 52. Results of this study await replication using larger samples but strongly suggest that effective lifestyle modification can be provided during brief, structured physician visits. The findings are discussed in terms of their implications for the treatment of obesity in primary care practice.

Adult↗
PubMed2004

Application of mass spectrometry to the identification and quantification of histone post-translational modifications.

The core histones are the primary protein component of chromatin, which is responsible for the packaging of eukaryotic DNA. The NH(2)-terminal tail domains of the core histones are the sites of numerous post-translational modifications that have been shown to play an important role in the regulation of chromatin structure. In this study, we discuss the recent application of modern analytical techniques to the study of histone modifications. Through the use of mass spectrometry, a large number of new sites of histone modification have been identified, many of which reside outside of the NH(2)-terminal tail domains. In addition, techniques have been developed that allow mass spectrometry to be effective for the quantitation of histone post-translational modifications. Hence, the use of mass spectrometry promises to dramatically alter our view of histone post-translational modifications.

Animals↗
PubMed2005

Histone H4 post-translational modifications in chordate mitotic and endoreduplicative cell cycles.

Histone post-translational modifications mark distinct structural and functional chromatin states but little is known of their involvement in the progression of different cell cycle types across phylogeny. We compared temporal and spatial dynamics of histone H4 post-translational modifications during both mitotic and endoreduplicative cycles of the urochordate, Oikopleura dioica, and proliferating mammalian cells. Endocycling cells showed no signs of chromosome condensation or entry into mitosis. They exhibited an evolution of replication patterns indicative of reduced chromatin compartmentalization relative to proliferating mammalian cells. In the latter cells, published cell cycle profiles of histone H4 acetylated at lysine 16 (H4AcK16) or dimethylated at lysine 20 (H4Me2K20) are disputed. Our results, using different, widely used H4AcK16 antibodies, revealed significant antibody-specific discrepancies in spatial and temporal cell cycle regulation of this modification, with repercussions for interpretation of previous immunofluorescence and immunoprecipitation data based on these reagents. On the other hand, three different antibodies to H4Me2K20 revealed similar cell cycle profiles of this modification that were conserved throughout the mitotic cell cycle in urochordate and mammalian cells, with accumulation at mitosis and a decrease during S-phase. H4Me2K20 also cycled in endocycles, indicating that dynamics of this modification are not strictly constrained by the mitotic phase of the cell cycle and suggesting additional roles during G- and S-phase progression. This article contains Supplementary Material available at http://www.mrw.interscience.wiley.com/suppmat/0730-2312/suppmat/2005/95/spada.html.

Acetylation↗
PubMed2025

Multiomics Reveal Associations Between CpG Methylation, Histone Modifications and Transcription in a Species That has Lost DNMT3, the Colorado Potato Beetle.

Insects display exceptional phenotypic plasticity, which can be mediated by epigenetic modifications, including CpG methylation and histone modifications. In vertebrates, both are interlinked and CpG methylation is associated with gene repression. However, little is known about these regulatory systems in invertebrates, where CpG methylation is mainly restricted to gene bodies of transcriptionally active genes. A widely conserved mechanism involves the co-transcriptional deposition of H3K36 trimethylation and the targeted methylation of unmethylated CpGs by the de novo DNA methyltransferase DNMT3. However, DNMT3 has been lost multiple times in invertebrate lineages raising the question of how the links between CpG methylation, histone modifications and gene expression are affected by its loss. Here, we report the epigenetic landscape of Leptinotarsa decemlineata, a beetle species that has lost DNMT3 but retained CpG methylation. We combine RNA-seq, enzymatic methyl-seq and CUT&Tag to study gene expression, CpG methylation and patterns of H3K36me3 and H3K27ac histone modifications on a genome-wide scale. Despite the loss of DNMT3, H3K36me3 mirrors CpG methylation patterns. Together, they give rise to signature profiles for expressed and not expressed genes. H3K27ac patterns show a prominent peak at the transcription start site that is predictive of expressed genes irrespective of their methylation status. Our study provides new insights into the evolutionary flexibility of epigenetic modification systems that urge caution when generalizing across species.

Animals↗
PubMed1990

Effects of monomethoxypoly(ethylene glycol) modification of ribonuclease on antibody recognition, substrate accessibility and conformational stability.

The effects of modification of bovine pancreatic ribonuclease A by monomethoxypoly(ethylene glycol) (MPEG) were examined for changes in recognition by antiRNase antibodies, enzymatic activity against low and high molecular weight substrates and conformational stability to temperature elevation. Modified forms of RNase were prepared containing an average of 4, 9, and 11 mol of MPEG/mol protein, by amino group modification. These were analysed by binding to RNase antibodies crosslinked to solid phase-immobilized protein A. The affinity column was incorporated into a high performance liquid chromatograph and the RNase species were studied by both zonal and frontal analytical affinity chromatography. An antibody dissociation constant of 7.6 x 10(-8) M was found for unmodified RNase, as compared to values of 1.3 x 10(-7) and 1.2 x 10(-6) M for RNase with 4 and 9 covalently bound MPEG chains, respectively. Modification also led to progressive loss of enzymatic activity against RNA, down to 3% for the most highly modified enzyme. In contrast, enzymatic activity against cytidine-2',3'-cyclic monophosphate was suppressed to a maximum of only 33% at the highest modification level, and the stability to temperature, as followed by circular dichroism, was reduced only partially, from 67 degrees C for native protein to 57 degrees C for RNase with 11 mol equivalents MPEG incorporated. The above differential effects on enzymatic activity, antibody binding and temperature effects are consistent with the view that MPEG modification has relatively small effects on conformational stability and small molecule accessibility, but more dramatic effects on large molecule (substrate as well as antibody) accessibility.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2007

Detection and identification of arginine modifications on methylglyoxal-modified ribonuclease by mass spectrometric analysis.

Analysis of the broad range of trace chemical modifications of proteins in biological samples is a significant challenge for modern mass spectrometry. Modification at lysine and arginine residues, in particular, causes resistance to digestion by trypsin, producing large tryptic peptides that are not readily sequenced by mass spectrometry. In this work, we describe the analysis of ribonuclease (RNase) modified by methylglyoxal (MGO) under physiological conditions. For detection of modifications, we use comparative analysis of the single combined spectra extracted from the full-scan MS data of the tryptic digests from native and modified proteins. This approach revealed 11 ions unique to MGO-modified RNase, including a 32-amino acid peptide containing a modified Arg-85 residue. Sequential digestion of MGO-modified RNase by endoproteinase Glu-C and trypsin was required to obtain peptides that were amenable to sequencing analysis. Arg-39 was identified as the main site of modification (35% modification) on MGO-modified Rnase, and the dihydroxyimidazolidine and hydroimidazolone derivatives were the main adducts formed, with minor amounts of the tetrahydropyrimidine and argpyrimidine derivatives. For identification of these products, we used variations in source voltage and collision energy to obtain the dehydration and decarboxylation products of the tetrahydropyrimidine-containing peptides and dehydration of the dihydroxyimidazoline-containing peptides. The resultant spectra were dependent on the cone voltage and collision energy, and analysis of spectra at various settings permitted structural assignments. These studies illustrate the usefulness of single combined mass spectra extracted from full-scan data and variations in source and collision cell voltages for detection and structural characterization of chemical adducts on proteins.

Amino Acid Sequence↗
PubMed2003

Analysis of post-translational modification and characterization of the domain structure of dynamin A from Dictyostelium discoideum.

The post-translational modifications of the 96 kDa protein dynamin A from Dictyostelium discoideum were analyzed using Q-TOF mass spectrometry. The accurate molecular mass of the intact protein revealed a covalent modification causing an additional mass of 42 Da. The modification could be identified as N-terminal acetylation by tandem mass spectrometry. Extracted ion chromatograms for the a(1) and b(1) ion of the tryptic T1 peptide were used to detect the acetylated peptide within 54 nanoelectrospray ionization tandem mass spectra. Owing to the accurate molecular mass of the intact protein, additional covalent modifications could be excluded. In addition to the covalent modification, the domain structure of dynamin A was determined by applying a combination of limited proteolysis, sodium dodecylsulfate polyacrylamide gel electrophoresis, automated tandem mass spectrometry and protein database searching.

Acetylation↗
PubMed2003

Hypoxia-induced modification of the inositol triphosphate receptor in neuronal nuclei of newborn piglets: role of nitric oxide.

Previous studies have shown that hypoxia results in increased Ca2+ influx in neuronal nuclei and generation of nitric oxide (NO) free radicals in the cerebral cortical tissue of newborn piglets. The present study tests the hypothesis that hypoxia results in modification of the inositol triphosphate (IP3) receptor characteristics in neuronal nuclei and that the hypoxia-induced modification of the IP3 receptor is NO mediated. Studies were performed in piglets, 3-5 days old, divided into normoxic (n = 5), hypoxic (n = 5), and NO synthase (NOS) inhibitor N-nitro-L-arginine (NNLA)-treated hypoxic (n = 5) groups. The NNLA-treated hypoxic group received an infusion of NNLA (40 mg/kg) over 1 hr prior to hypoxic exposure. The hypoxia was induced by lowering the FiO2 to 0.05-0.07 for 1 hr. Brain tissue hypoxia was documented biochemically by determining ATP and phosphocreatine (PCr) levels. Neuronal nuclei were isolated from the cerebral cortical tissue, and IP3 receptor binding was performed in a medium containing 50 mM HEPES (pH 8.0), 2 mM EDTA, 3H-IP3 (7.5-100 nM), and 100 microg nuclear protein. Nonspecific binding was determined in the presence of 10 microM unlabelled IP3. The IP3 receptor characteristics Bmax (number of receptor sites) and Kd (dissociation constant) were determined. In normoxic, hypoxic, and NNLA-hypoxic groups, ATP levels were 4.46 +/- 0.35, 1.52 +/- 0.10 (P <.05 vs. normoxic), and 1.96 +/- 0.33 micromoles/g brain, respectively (P <.05 vs. normoxic). PCr levels were 3.75 +/- 0.35, 0.87 +/- 0.09 (P <.05 vs. normoxic), and 1.31 +/- 0.10 micromoles/g brain, respectively (P <.05 vs. normoxic). IP3 receptor binding characteristics in normoxic nuclear membranes showed that the Bmax value was 150.0 +/- 14.1 pmoles/mg protein compared with 239.3 +/- 13.6 pmoles/mg protein in the hypoxic group (P <.05). In the NNLA-treated hypoxic group, the Bmax value was 159.0 +/- 42.6 pmoles/mg protein (P <.05 vs. hypoxic a, P = NS vs. normoxic). Similarly, the Kd was 25.2 +/- 0.28 nM in the normoxic group, 44.6 +/- 5.4 nM in the hypoxic group (P <.05), and 28.1 +/- 6.4 nM in the NNLA-treated hypoxic group. (P <.05 vs. hypoxic and P = NS vs. normoxic). The results show that hypoxia results in increased Bmax and Kd values for the IP3 receptor. Furthermore, the data demonstrate that administration of NNLA prior to hypoxia prevents the hypoxia-induced modification of the IP3 receptor in neuronal nuclei of newborn piglets. Because NNLA inhibits NOS and prevents generation of NO, we conclude that the mechanism of hypoxia-induced modification of the neuronal nuclear membrane IP3 receptor is NO mediated. We propose that NO-mediated modification of the IP3 receptor during hypoxia may lead to increased intranuclear Ca2+, resulting in altered transcription of apoptotic genes and activation of cascades of hypoxia-induced programmed neuronal death.

Adenosine Triphosphate↗
PubMed2026

Epitranscriptomic Regulation of ALDOA by SHMT2-Mediated m6A Modification Drives Gastric Cancer Malignancy.

Gastric cancer (GC) remains a leading cause of cancer-related mortality worldwide, with limited therapeutic advancements despite progress in early detection. Serine hydroxymethyltransferase 2 (SHMT2), a key metabolic enzyme, and fructose-1,6-bisphosphate aldolase A (ALDOA), a glycolytic enzyme, are implicated in tumor progression. However, the molecular mechanisms linking SHMT2 and ALDOA in GC remain unclear. This study investigates how SHMT2 regulates ALDOA expression via m6A RNA modification to drive GC malignancy. Bioinformatic analyses (TCGA, LinkedOmics, and SRAMP) were used to assess SHMT2 expression in GC patients and identify its correlated genes. In vitro experiments (CCK-8, EdU, Transwell, and wound healing) evaluated the effects of SHMT2 overexpression or knockdown on GC cell proliferation, migration, invasion, and glycolysis. m6A modification of ALDOA was analyzed via MeRIP-PCR and dual-luciferase assays, while RNA stability was assessed using actinomycin D treatment. Xenograft models validated SHMT2's role in vivo. SHMT2 was upregulated in GC tissues and cell lines, correlating with advanced tumor stages and poor prognosis. SHMT2 knockdown suppressed GC cell viability, migration, invasion, and glycolysis, while overexpression enhanced these traits. Mechanistically, SHMT2 increased S-adenosylmethionine levels, promoting ALDOA m6A modification, likely mediated through the predicted site 1 (position 291). This modification stabilized ALDOA mRNA via IGF2BP1 recognition, an m6A reader. ALDOA overexpression reversed the tumor-suppressive effects of SHMT2 knockdown. In vivo, SHMT2 depletion reduced tumor growth and Ki67 expression in xenograft models. In conclusion, SHMT2 drives GC progression by enhancing ALDOA expression through m6A modification and IGF2BP1-mediated stabilization. Targeting the SHMT2-ALDOA axis represents a promising therapeutic strategy for gastric cancer.

Humans↗
PubMed2004

Molecular modification of Penaeus monodon sperm in female thelycum and its consequent responses.

Using Penaeus monodon as the model, we demonstrated the molecular changes and the mechanism of thelycal-dependent sperm modification resulting in an enhanced acrosome reaction (AR) response. Attention was paid to the modification of the sperm plasma membrane which was mediated through an adsorption or removal of sperm peripheral and integral membrane proteins as indicated by the different profiles of these proteins in spermatophore (S) and thelycal (T) sperm. In vitro adsorption of Alexa-488 conjugated T proteins onto the entire S-sperm surface confirmed protein transfer in a time-dependent manner. Specific anchoring of 83 and 140 kDa proteins to sperm peripheral proteins as well as 53/55 and 60 kDa proteins to sperm lipids was demonstrated. Apart from membrane modification, a substantial increase in protein tyrosine phosphorylation was shown to be closely associated with T-dependent sperm modification event. The physiological significance of this sperm modification in enhancing sperm AR response, which required at least 3 days of T residence in order for the sperm to gain a complete AR response, was also elucidated.

Acrosome Reaction↗
PubMed2002

Home environmental modification strategies used by caregivers of elders.

Although several definitions and categorizations of home environmental modification strategies exist, previous researchers have not addressed whether the conceptualizations developed by clinicians and researchers match the way families think about how they modify the home environment in order to provide care to frail elders. The aim of the analysis reported here was to describe, from the family's perspective, the home environmental modification strategies that they use. Twenty-four caregivers of community-dwelling elders with a variety of impairments were interviewed. Seventeen families provided guided tours of the elder's home and allowed selected observation of some caregiving activities. Forty-four modification strategies were identified and categorized into one of seven home environmental modification purposes: organizing the home, supplementing the elder's function, structuring the elder's day, protecting the elder, working around limitations or deficits in the home environment, enriching the home environment, and transitioning to a new home setting. More research is needed on the processes families use to generate and refine the home environmental modification strategies identified in this study.

Activities of Daily Living↗
PubMed2004

A combination of different mass spectroscopic techniques for the analysis of dynamic changes of histone modifications.

The N-terminal tails of the histones are subject to many enzyme-mediated post-translational modifications, such as lysine acetylation, lysine and arginine methylation, serine phosphorylation, poly-ADP ribosylation and the attachment of the small peptide ubiquitin. These modifications, singly or in combination, are thought to generate an epigenetic code that specifies different patterns of gene activity. We present a detailed study on the mapping of histone post-translational modifications using a combination of matrix-assisted laser desorption/ionization-time of flight and electrospray ionization tandem mass spectrometry analysis of peptides generated by protease cleavage of individual histones isolated from different developmental stages. Due to their high content in basic amino acid residues and in order to be able to quantitatively compare two different samples we developed a chemical derivatization protocol. This strategy enabled us to determine the primary sequence of the peptides and to unambiguously assign specific modifications. This method is generally applicable to histone samples from various sources and can be used to study changes of modification patterns during early embryonic development or tissue differentiation and regeneration.

Amino Acid Sequence↗