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PubMed2004

Different restriction and modification phenotypes in ruminal lactate-utilizing bacteria.

Analysis of restriction and modification activities in lactate-utilizing bacteria belonging to the Megasphaera elsdenii and Mitsuokella multiacida species revealed the presence of GATC-specific, MboI isospecific, restriction-modification (R-M) systems in all strains tested. While restriction endonucleases isolated from M. elsdenii strains were found to be sensitive to Dam methylation, enzymes from M. multiacida cleaved DNA irrespective of Dam methylation. The comparison of type II R-M systems specificities in three closely related lactate-utilizing ruminal bacterial species indicated complete lack of restriction and/or modification enzymes previously characterized from Selenomonas ruminantium in tested M. elsdenii and M. multiacida strains. R-M systems are believed to represent the main defense tool against phage infection. Based on the results of our experiments it could be assumed that M. elsdenii and M. multiacida use the different strategy for bacteriophage protection compared to S. ruminantium.

Animals↗
PubMed2004

A randomized, 48-week, placebo-controlled trial of intensive lifestyle modification and/or metformin therapy in overweight women with polycystic ovary syndrome: a pilot study.

OBJECTIVE: To obtain data from a pilot randomized trial on the effect of metformin therapy and lifestyle modification on ovulation and androgen concentrations in women with polycystic ovary syndrome (PCOS). DESIGN: Prospective, randomized, placebo-controlled pilot trial. SETTING: Academic medical center. PATIENT(S): Thirty-eight overweight or obese women with PCOS. INTERVENTION(S): All subjects were randomized to one of four 48-week interventions: metformin 850 mg two times per day, lifestyle modification plus metformin 850 mg two times per day, lifestyle modification plus placebo, or placebo alone. MAIN OUTCOME MEASURE(S): Recruitment, dropout, and compliance with a long-term lifestyle intervention in PCOS; preliminary estimates of treatment effect on ovulation, as measured by weekly urinary pregnanediol glucuronide, and on total T and free androgen index. RESULT(S): It was necessary to screen seven women to have one subject randomized. The dropout rate was 39%, with the majority of dropouts occurring within the first 24 weeks. Mean body mass index was >39 mg/kg(2). Modest weight reduction was found in all treatment groups, with the most significant reduction occurring with the combination of metformin and lifestyle intervention. Significant androgen reduction occurred in the combination group only. Ovulation rates did not differ significantly between groups. However, when data were analyzed by presence or absence of weight reduction in subjects, independent of treatment group, the estimated odds ratio for weight loss was 9.0 (95% confidence interval 1.2-64.7) with respect to regular ovulation. If weight loss occurred during metformin therapy, the odds ratio for regular ovulation was 16.2 (95% confidence interval 4.4-60.2). CONCLUSION(S): Key methodologic issues for a large-scale, randomized trial of lifestyle intervention in PCOS include minimizing early dropout from the lifestyle intervention and including a range of body mass index that is not skewed toward severe obesity. Weight reduction might play the most significant role in restoration of ovulation in obese women with PCOS.

Adipose Tissue↗
PubMed2004

Reactive oxygen species derived from the mitochondrial respiratory chain are not responsible for the basal levels of oxidative base modifications observed in nuclear DNA of Mammalian cells.

The mitochondrial electron transport chain (ETC) is the most important source of reactive oxygen species (ROS) in mammalian cells. To assess its relevance to the endogenous generation of oxidative DNA damage in the nucleus, we have compared the background (steady-state) levels of oxidative DNA base modifications sensitive to the repair glycosylase Fpg (mostly 7,8-dihydro-8-oxoguanine) in wild-type HeLa cells and HeLa rho0 cells. The latter are depleted of mitochondrial DNA and therefore are unable to produce ROS in the ETC. Although the levels of ROS measured by flow cytometry and redox-sensitive probes in rho0 cells were only 10-15% those of wild-type cells, steady-state levels of oxidative DNA base modifications were the same as in wild-type cells. Mitochondrial generation of ROS was then stimulated in HeLa wild-type cells using inhibitors interfering with the ETC. Although mitochondrial ROS production was raised up to 6-fold, none of the substances nor their combinations induced additional oxidative base modifications in the nuclear DNA. This was also true for glutathione-depleted cells. The results indicate that the contribution of mitochondria to the endogenously generated background levels of oxidative damage in the nuclear DNA is negligible.

Animals↗
PubMed2005

Protein-protein interactions and posttranslational modifications in mammalian base excision repair.

Base excision repair (BER) averts the cytotoxic and mutagenic effects of most endogenously produced DNA damage, including lesions that arise spontaneously due to the intrinsic instability of DNA or modifications that are formed from reactions with intracellular chemicals, such as reactive oxygen species and alkylating agents. Defects in the BER process have been associated with cancer susceptibility and neurodegenerative disorders. In its most simplistic form, BER can be fully reconstituted with a minimum of four human proteins and is completed in just five sequential steps: (i) excision of an inappropriate base by a DNA glycosylase (e.g., uracil DNA glycosylase); (ii) incision of the DNA backbone immediately adjacent to the resulting abasic site by apurinic/apyrimidimic endonuclease 1; (iii) removal of the 5'-abasic terminal fragment, and (iv) repair synthesis to fill the gap by DNA polymerase beta; and (v) ligation to seal the remaining nick by DNA ligase 1 or a complex of DNA ligase 3 and X-ray repair cross-complementing 1. However, BER can involve the participation of other proteins as well, such as alternative DNA polymerases or one of several nonessential "auxiliary" factors. In addition, BER operates most efficiently when specific protein-protein coordination occurs. Furthermore, several BER protein activities have been shown to be regulated by posttranslational modification, and some of the physical protein interactions link BER to other DNA transaction pathways. In this review, we summarize the current state of the emerging complexities of mammalian BER, focusing on the growing number of reported protein-protein interactions and posttranslational modifications.

Animals↗
PubMed2005

Carbonyl modification in rat liver histones: decrease with age and increase by dietary restriction.

We studied carbonylation, a form of oxidative modification of proteins, of histones in rat livers. Histones H1, H2B/H2A, and H3 were significantly carbonylated but the modification was almost undetectable in H4. Contrary to the generally accepted view of increased protein carbonylation with age, the modification of histones was significantly lower in old (30-month-old) than in young (5-month-old) animals. Dietary restriction of older animals for 2 months resulted in increase in carbonylation comparable to that at the young level. These findings may have physiological implications in chromatin structure/function in aging and beneficial effects of DR by influencing transcription, replication, and/or repair activities.

Aging↗
PubMed2006

Mass spectrometry of protein modifications by reactive oxygen and nitrogen species.

The modification of proteins by reactive oxygen and nitrogen species plays an important role in various biologic processes involving protein activation and inactivation, protein translocation and turnover during signal transduction, stress response, proliferation, and apoptosis. Recent advances in protein and peptide separation and mass spectrometry provide increasingly sophisticated tools for the quantitative analysis of such protein modifications, which are absolutely necessary for their correlation with biologic phenomena. The present review focuses specifically on the qualitative and quantitative mass spectrometric analysis of the most common protein modifications caused by reactive oxygen and nitrogen species in vivo and in vitro and details a case study on a membrane protein the sarco/endoplasmic reticulum Ca-ATPase (SERCA).

Amino Acids↗
PubMed2005

DNA methylation and histone modifications: teaming up to silence genes.

DNA methylation, histone deacetylation, and methylation of histone H3 at lysine 9 are the three best-characterized covalent modifications associated with a repressed chromatin state. Recent advances highlight an essential, intricate web of interactions among these processes, generating a self-reinforcing, self-perpetuating cycle of epigenetic events that lead to long-term transcriptional repression. Histone deacetylation and methylation at lysine 9 of H3 might also contribute to the establishment of DNA methylation patterns, a long-standing mystery in epigenetics. What's more, recent clues suggest a potential link between CpG methylation and other histone modifications. A complex picture is emerging in which DNA methylation and histone modifications work hand-in-hand as parts of an epigenetic program that integrates gene-silencing networks within the cell.

Animals↗
PubMed2006

Histone modifications: signalling receptors and potential elements of a heritable epigenetic code.

The genetic code epitomises simplicity, near universality and absolute predictive power. By contrast, epigenetic information, in the form of histone modifications, is characterised by complexity, diversity and an overall tendency to respond to changes in genomic function rather than to predict them. Perhaps the transient changes in histone modifications involved in intranuclear signalling and ongoing chromatin functions mask stable, predictive modifications that lie beneath. The current rapid progress in unravelling the diversity and complexity of epigenetic information might eventually reveal an underlying histone or epigenetic code. But whether it does or not, it will certainly provide unprecedented opportunities, both for understanding how the genome responds to environmental and metabolic change and for manipulating its activities for experimental and therapeutic benefit.

Chromatin↗
PubMed2005

Noise and sleep disturbance factors before and after implementation of a behavioural modification programme.

The purpose of this study was to examine sleep disturbance factors documented by the personnel and recorded noise level during two weeks before (measurement one M1) and after (measurement two M2) the implementation of a behavioural modification programme. The behavioural modification programme included non-disturbance periods on a neurointensive care unit (NICU) in a University hospital. Sleep disturbance factors were identified as general and specific nursing care, and medical treatment documented over fourteen 24-h periods. Minimum, maximum and peak mean noise levels in dBA were recorded continuously during fourteen 24-h periods by a decibel meter. The behavioural modified programme included changing nursing and medical routines and the introduction of afternoon and night non-disturbance periods. The most disturbing documented factors at both M1 and M2 were general nursing care activities. Noise levels showed great variation at both M1 and M2. At M2 minimum and maximum noise levels varied when compared to M1. Implementation of a behavioural modification programme and non-disturbance periods co-ordinated routines resulted in reduced sleep disturbance factors and partly reduced noise levels on the NICU. Changes of the physical care/working environment, preparations before non-disturbance periods, regular evaluations of routines and education are needed to improve sleep on NICUs.

Adolescent↗
PubMed2006

Studies on the hydrothermal modifications of new cocoyam (Xanthosoma sagittifolium) starch.

Native new cocoyam starch (nNCS) was subjected to annealing (aNCS) and heat moisture treatment at 18% moisture level (h18NCS), 21% moisture level (h21NCS), 24% moisture level (h24NCS) and 27% moisture level (h27NCS) as hydrothermal treatments. Scanning electron and light microscopy revealed round and polygonal shapes with sizes ranging from 15 to 40 microm for native and modified starches. nNCS showed "A" pattern X-ray diffraction and no significant differences were observed in the X-ray pattern of the modified starches. Swelling power and solubility reduced following heat moisture treatment. At all pH studied (2-12), unmodified new cocoyam starch exhibited higher swelling capacity and solubility than the modified derivatives. Hydrothermal modifications improved water absorption capacity but reduced oil absorption capacity. Pasting temperature of native starch shifted to higher values following annealing and heat moisture treatment. Hot paste viscosity (Hv), viscosity after 30 min holding at 95 degrees C (Hv30) and cold paste viscosity (Cv) reduced after annealing and heat moisture treatment. The result also indicates that hydrothermal treatments reduced the tendency for setback. As the number of days of storage of starch paste increased from 1 to 10, light transmittance of all the starches reduced but marked reduction of light transmittance was observed in native starch. DSC studies revealed increase in gelatinization temperature following annealing and heat moisture treatment. Starch hydrothermal modifications reduced retrogradation as enthalpies of regelatinization reduced following modifications. The regelatinization peak in the second day scanning shifted to lower temperature than the gelatinization peak in first run heating DSC curve for all samples. The regelatinization peak also became larger and shifted to higher temperature range when the storage days increased from 2 to 7.

Calorimetry, Differential Scanning↗
PubMed2005

Histone modifications associated with somatic hypermutation.

A number of modified histones, including acetylated H3 and H4 and phosphorylated H2AX (gammaH2AX), are associated with V(D)J recombination and class switch recombination (CSR). In contrast, little is known concerning the chromatin modifications associated with somatic hypermutation (SHM) in vivo. Here, we report that several modifications--including histone acetylation and H3-lysine 4 methylation--fail to demarcate an actively hypermutating immunoglobulin (Ig) locus or to correlate spatially with SHM within Ig loci. Furthermore, no obvious association between SHM and gammaH2AX could be detected. Instead, we find that the phosphorylated form of histone H2B (H2B(Ser14P)) correlates tightly with SHM and CSR. Phosphorylation of H2B within Ig variable and switch regions requires AID and may be mediated by the histone kinase Mst1. These findings indicate that SHM and CSR trigger distinct DNA damage responses and identify a novel histone modification pattern for SHM consisting of H2B(Ser14P) in the absence of gammaH2AX.

Acetylation↗
PubMed2004

Modification of Cytochrome c by 4-hydroxy- 2-nonenal: evidence for histidine, lysine, and arginine-aldehyde adducts.

4-Hydroxy-2-nonenal (4HNE), a major secondary product of lipid peroxidation, has been associated with a number of disease states involving oxidative stress. Despite the recognized importance of post-translational modification of proteins by products such as 4HNE, little is known of the modification of cytochrome c by this reagent and its analysis by mass spectrometry. The purpose of this study was to investigate the chemical interaction of 4HNE and cytochrome c, a protein essential to cellular respiration, under in vitro conditions. Isoelectric focusing of native and 4HNE-modified cytochrome c using immobilized pH gradient (IpG) strips showed a decrease in the pI of the 4HNE-modified protein suggesting modification of charged amino acids. Reaction of 4HNE with cytochrome c resulted in increases in molecular weight consistent with the addition of four 4HNE residues as determined by matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS). Samples of both native and 4HNE-modified cytochrome c were enzymatically digested and subjected to peptide mass fingerprinting using MALDI-TOF MS. Analysis of these samples using LC-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) provided sequence information that was used to determine specific residues to which the aldehyde adducted. Taken together, the data indicated that H33, K87, and R38 were modified by 4HNE. Mapping these results onto the X-ray crystal structure of native cytochrome c suggest that 4HNE adduction to cytochrome c could have significant effects on tertiary structure, electron transport, and ultimately, mitochondrial dysfunction.

Aldehydes↗
PubMed2006

The antigenic determinants on HIV p24 for CD4+ T cell inhibiting antibodies as determined by limited proteolysis, chemical modification, and mass spectrometry.

In the last decade, mass spectrometry has been employed by more and more researchers for identifying the proteins in a macromolecular complex as well as for defining the surfaces of their binding interfaces. This characterization of protein-protein interfaces usually involves at least one of several different methodologies in addition to the actual mass spectrometry. For example, limited proteolysis is often used as a first step in defining regions of a protein that are protected from proteolysis when the protein of interest is part of a macromolecular complex. Other techniques used in conjunction with mass spectrometry for determining regions of a protein involved in protein-protein interactions include chemical modification, such as covalent cross-linking, acetylation of lysines, hydrogen-deuterium exchange, or other forms of modification. In this report, both limited proteolysis and chemical modification were combined with several mass spectrometric techniques in efforts to define the protein surface on the HIV core protein, p24, recognized by two different monoclonal human antibodies that were isolated from HIV+ patients. One of these antibodies, 1571, strongly inhibits the CD4+ T cell proliferative response to a known epitope (PEVIPMFSALSEGATP), while the other antibody, 241-D, does not inhibit as strongly. The epitopes for both of these antibodies were determined to be discontinuous and localized to the N-terminus of p24. Interestingly, the epitope recognized by the strongly inhibiting antibody, 1571, completely overlaps the T cell epitope PEVIPMFSALSEGATP, while the antibody 241-D binds to a region adjacent to the region of p24 recognized by the antibody 1571. These results suggest that, possibly due to epitope competition, antibodies produced during HIV infection can negatively affect CD4+ T cell-mediated immunity against the virus.

Amino Acid Sequence↗
PubMed2005

Modification of MSW fly ash by anionic chelating surfactant.

This paper elucidates a study on the re-utilization and stabilization of municipal solid waste (MSW) fly ash in producing a high value-added product by the surface modification of anionic chelating surfactant on the particles. After modification, MSW fly ash can be expected using as a filler of ultra-high molecular weight polymers. The effects of anionic chelating surfactants (ACS) on surface modification of MSW fly ash and fixing capacity for heavy metals were explored. Meanwhile, the interaction mechanism between surfactants and MSW fly ash was suggested. The results showed that anionic chelating surfactants can be used to effectively modify MSW fly ash particles and achieve a high active ratio. At the same time, they also exhibited a strong fixing capacity for heavy metals. Of the two modified MSW fly ash, ED3A-modified MSW fly ash has a much higher active ratio than MAP-modified MSW fly ash at over 95%, although its fixing capacity for heavy metals was a shade lower than MAP-modified MSW fly ash.

Anions↗
PubMed2006

Surface modification of nanometer size TiO2 with salicylic acid for photocatalytic degradation of 4-nitrophenol.

The efficiency of photocatalytic reactions was limited by the wide band-gap of TiO(2) and the high degree of electron-hole recombination inherent in photocatalytic process, as well as by the limited adsorption capability of photocatalysts. In order to increase the overall efficiency, the surface of nanometer size TiO(2) was simply and fast modified by chemical adsorption in saturated solution of salicylic acid. A stable, light yellow surface complex was formed quickly, which has obvious absorption in the region from 320 to 420 nm. Through surface modification, the adsorption efficiency of 4-nitrophenol by TiO(2) was enhanced from 42 to 84%. The photocatalytic efficiency was tested on the degradation of 4-nitrophenol. The influences of catalyst and its dosage, pH value, and 4-nitrophenol concentration on the degradation were investigated. Under such photodegradation conditions as initial pH 4.0, 4-nitrophenol 5 mg l(-1), catalyst 100 mg, and irradiation time 160 min with 160 W high-pressure mercury lamp, the degradation efficiency of 4-nitrophenol by TiO(2) was increased from 39.5 to 79.3% after surface modification, and furthermore, the degradation efficiency could be enhanced to 91.1% if the concentration of 4-nitrophenol was not more than 1 mg l(-1). Compared with the pure TiO(2), surface modification led not only to improve the surface coverage of 4-nitrophenol, but also to increase the light utilization. Both of these factors were crucial for the photocatalytic activity of heterogeneous photocatalysis, especially for photodegradation of aromatic pollutants.

Adsorption↗
PubMed2006

Activated carbon with excellent chromium(VI) adsorption performance prepared by acid-base surface modification.

In the present work, activated carbon (AC) with excellent Cr(VI) adsorption performance especially at low concentrations was prepared by an acid-base surface modification method. Raw activated carbon (AC(0)) was first oxidized in boiling HNO(3) (AC(1)), then treated with a mixture of NaOH and NaCl (AC(2)). Batch equilibrium and continuous column adsorption were conducted to evaluate the adsorption performance. Boehm titration, elemental analysis, and N(2)/77K adsorption isotherm methods were used to characterize the surface properties and pore structure of modified ACs. The results revealed that the modified AC exhibited excellent Cr(VI) adsorption performance in terms of adsorption capacity and adsorption rate: AC(2)>AC(1)>AC(0). Modification caused S(BET) to decrease and the total number of surface oxygen acidic groups to increase. HNO(3) oxidization produced positive acid groups, and subsequently NaOH treatment replaced H(+) of surface acid groups by Na(+), and the acidity of AC decreased. The main cause of higher Cr(VI) adsorption capacity and rate for AC(2) was the presence of more oxygen surface acidic groups and suitable surface acidity. HNO(3)-NaOH modification shows potential for the preparation of high quality AC for the effective removal of low concentrations of Cr(VI).

Adsorption↗
PubMed2005

Effects of supercoiling on the sequence-specific photo-modification of DNA by a vanadium(V)-peroxo complex.

Sequence-specific photo-modification of DNA has been demonstrated, for the first time, in a vanadium(V)-peroxo complex, NH4[VO(O2)2(5,6-Me2phen)] (where 5,6-Me2phen = 5,6-dimethyl-1,10-phenanthroline). Using molecular cloning technique, a consensus sequence motif of 5'-G(A/G)TA(T/C)C was identified associated with the two specific photo-modification sites, 5'-ATC and 5'-TACC found on a plasmid DNA, pBluescript, by a modified Sanger sequencing technique. DNA supercoiling was shown to be a critical prerequisite for this observed sequence-specific photo-modification activity.

Base Sequence↗
PubMed2003

Naturally-occurring modification restricts the anticodon domain conformational space of tRNA(Phe).

Post-transcriptional modifications contribute chemistry and structure to RNAs. Modifications of tRNA at nucleoside 37, 3'-adjacent to the anticodon, are particularly interesting because they facilitate codon recognition and negate translational frame-shifting. To assess if the functional contribution of a position 37-modified nucleoside defines a specific structure or restricts conformational flexibility, structures of the yeast tRNA(Phe) anticodon stem and loop (ASL(Phe)) with naturally occurring modified nucleosides differing only at position 37, ASL(Phe)-(Cm(32),Gm(34),m(5)C(40)), and ASL(Phe)-(Cm(32),Gm(34),m(1)G(37),m(5)C(40)), were determined by NMR spectroscopy and restrained molecular dynamics. The ASL structures had similarly resolved stems (RMSD approximately 0.6A) of five canonical base-pairs in standard A-form RNA. The "NOE walk" was evident on the 5' and 3' sides of the stems of both RNAs, and extended to the adjacent loop nucleosides. The NOESY cross-peaks involving U(33) H2' and characteristic of tRNA's anticodon domain U-turn were present but weak, whereas those involving the U(33) H1' proton were absent from the spectra of both ASLs. However, ASL(Phe)-(Cm(32),Gm(34),m(1)G(37),m(5)C(40)) exhibited the downfield shifted 31P resonance of U(33)pGm(34) indicative of U-turns; ASL(Phe)-(Cm(32),Gm(34),m(5)C(40)) did not. An unusual "backwards" NOE between Gm(34) and A(35) (Gm(34)/H8 to A(35)/H1') was observed in both molecules. The RNAs exhibited a protonated A(+)(38) resulting in the final structures having C(32).A(+)(38) intra-loop base-pairs, with that of ASL(Phe)-(Cm(32),Gm(34),m(1)G(37),m(5)C(40)) being especially well defined. A single family of low-energy structures of ASL(Phe)-(Cm(32),Gm(34), m(1)G(37),m(5)C(40)) (loop RMSD 0.98A) exhibited a significantly restricted conformational space for the anticodon loop in comparison to that of ASL(Phe)-(Cm(32),Gm(34),m(5)C(40)) (loop RMSD 2.58A). In addition, the ASL(Phe)-(Cm(32),Gm(34),m(1)G(37),m(5)C(40)) average structure had a greater degree of similarity to that of the yeast tRNA(Phe) crystal structure. A comparison of the resulting structures indicates that modification of position 37 affects the accuracy of decoding and the maintenance of the mRNA reading frame by restricting anticodon loop conformational space.

Anticodon↗