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1,013 results for “Acetylation”
Human Dolichyl-Phosphate Alpha-N-Acetyl glucosaminyl transferase (DPAGT1); A Target Enabling Package
<p>The ER integral membrane enzyme dolichyl-phosphate alpha-N-acetyl glucosaminyl phosphotransferase (DPAGT1) catalyses the first step in the synthesis of the oligosaccharide-P-P-dolichol unit which provides the glycans structure for N-glycosylation of proteins. Mutations in DPAGT1 cause two muscle weakness conditions, limb-girdle congenital myasthenic syndrome (CMS) and congenital disorder of glycosylation type 1j (CDG1j). DPAGT1 overexpression has also been implicated in oral cancer. We have produced and solved structures of this integral membrane enzyme, DPAGT1 with the V264G mutation found in a patient with CMS, and complexes with a 50 nM inhibitor, tunicamycin. We have developed enzymatic activity and thermostability assays which have allowed us to assess the activity and stability of DPAGT1 mutants and the effect of small molecules. There are > 20 DPAGT1 associated missense variants in patients with CMS and CDG1j. We have mapped these mutations to the structure, and we will used the assays described here to assess how the activity and stability of DPAGT1 is affected by these missense variants.</p>
Progressive degradation of acetylated wood by the brown rot fungi Coniophora puteana and Rhodonia placenta
<p>This dataset contains measurement data from the following publication: Belt, T.; Awais, M. (2025) Progressive degradation of acetylated wood by the brown rot fungi <em>Coniophora puteana</em> and <em>Rhodonia placenta</em>. Wood Science and Technology 59:13. https://doi.org/10.1007/s00226-024-01620-8. The experimental methods are described in brief below; further details can be found in the publication.</p> <p>Scots pine sapwood samples were acetylated in neat acetic anhydride to 9% or 18% weight percent gain (WPG) or left untreated to act as reference. The samples were exposed to brown rot decay in a stacked-sample decay test conducted in test tubes. Each replicate tube received 6 reference or acetylated samples stacked on top of each other (sample positions 1-6 from top to bottom) over nutrient agar inoculated with <em>Coniophora puteana</em> (N = 7) or <em>Rhodonia placenta</em> (N = 5). The different wood-fungus combinations were incubated for different durations until the visible fungal mycelium reached the top of the topmost block in one replicate tube. The samples were weighed before modification, after modification, at the end of the decay test, and after the decay test to determine their WPG, moisture content at the end of the decay test, and mass loss due to decay. After decay, 15 samples from every wood-fungus combination were selected for acetyl content measurement and FTIR spectroscopy.</p> <p>Acetyl contents were measured on powdered samples by saponification followed by HPLC quantification of the liberated acetic acid. FTIR spectra were measured in the 400-4000 cm<sup>-1</sup> spectral range in triplicate on powdered samples using an ATR accessory. For further analysis, the spectra were cut to 800-1800 cm<sup>-1</sup> range, baseline corrected (third degree polynomial subtraction), smoothed (Savitzky-Golay procedure with a second-order polynomial and a 15-point window), and normalised (unit vector normalisation).</p> <p>The "Mass data and acetyl content.csv" -file gives the sample identifiers (ID, sample type, test fungus, tube number, sample position) and measured mass data of all samples, and the acetyl contents of the selected samples. Masses m<sub>init</sub>, m<sub>mod</sub>, m<sub>wet</sub>, and m<sub>dec</sub> are the initial unmodified dry mass, the modified dry mass, the decaying wet mass, and the decayed dry mass, respectively. Acetyl contents (%) are given on a decayed wood basis.</p> <p>The “Unprocessed FTIR spectra_reference”, “Unprocessed FTIR spectra_9%”, and “Unprocessed FTIR spectra_18%” -files contain the unprocessed FTIR spectra of the reference, 9% WPG and 18% WPG samples (see the "Mass data and acetyl content.csv" -file for sample identifiers). The “Preprocessed FTIR spectra_reference”, “Preprocessed FTIR spectra_9%”, and “Preprocessed FTIR spectra_18%” -files in turn contain the preprocessed FTIR spectra of reference, 9% WPG and 18% WPG samples.</p>
Additional data; Biotechnologically produced chitosans with nonrandom acetylation patterns differ from conventional chitosans in properties and activities
<p>This dataset contains additional data for the research article <em>Biotechnologically produced chitosans with nonrandom acetylation patterns differ from conventional chitosans in properties and activities</em> by Sruthi Sreekumar, Jasper Wattjes, Anna Niehues, Tamara Mengoni, Ana C. Mendes, Edwin R. Morris, Francisco M. Goycoolea, and Bruno M. Moerschbacher.</p> <p>The directory <em>Fig1ab_SuppFig1ab</em> contains data, code, and results of enzymatic mass-spectrometric fingerprinting experiments. The directory <em>cosms</em> contains source code and instructions to create a conda environment in which the code to create Figures 1 A+B and Supplementary Figures 1 A+B can be executed.</p> <p>The directory <em>Fig23456_SuppFig_2567</em> contains Excel Worksheets (.xlsx files) with data underlying Figures 2, 3, 4, 5 and 6, and Supplementary Figures 2, 5, 6 and 7.</p> <p>The directories <em>Fig5b</em> and <em>SuppFig7d</em> contain raw MS data (Bruker .d files) of oligomeric hydrolysis products produced by incubating different chitosans with different chitinolytic enzymes. </p>
Figure 1. Response curves for percent acetyl-coenzyme A in Detecting the effect of ACCase-targeting herbicides on ACCase activity utilizing a malachite green colorimetric functional assay
Figure 1. Response curves for percent acetyl-coenzyme A carboxylase (ACCase) activities of resistant and susceptible Digitaria ciliaris biotypes in response to the increasing concentrations of the ACCase-targeting herbicides, sethoxydim, clethodim,fluazifop-p-butyl, and pinoxaden.The response was modeled based on the log rate of ACCase-targeting herbicides to create equal spacing between rates using least-squares fit regression of ACCase activity to the non-treated check. Means are represented by differing symbols for each biotype, and regression equation models are represented by differing line types for each biotype. Vertical bars represent the standard errors of the means (n = 6). Digitaria ciliaris biotypes: R1 and R2, resistant; S, susceptible. The concentration of ACCase-targeting herbicides required to cause 50% inhibition of ACCase activity (IC50) was calculated from concentration-response curves. CI, confidence interval.
Raw data to: Acetyl-CoA synthetase activity is enzymatically regulated by lysine acetylation using acetyl-CoA or acetyl-phosphate as donor molecule
<p>Initial configuration (PDB) and TIGER2hPE ensemble of all four simulations (R1-4) reported in this study in DCD trajectory format:</p> <ol> <li>AcuA + AcsA + Acetyl-CoA</li> <li>Acua + AcsA + Acetyl-CoA (AcuA:K549 deprotonated)</li> <li>AcuA + AcsA + CoA + AcP (Acetyl-Phosphate)</li> <li>AcuA + AcsA + Desulfo-CoA</li> </ol> <p> </p>
Diffraction data for complex of vancomycin with N-acetyl-D-Ala-D-Ser
<p>Raw diffraction images collected for a single crystal of the glycopeptide antibiotic vancomycin bound to N-acetyl-D-Ala-D-Ser (HDF5 format). Measured at beam line 17-ID-1 (AMX), NSLS-II, in December 2021, using an Eiger 9M detector. Other relevant metadata can be found in the file XDS.INP.</p>
Distinct roles for H4 and H2A.Z acetylation in RNA transcription in African trypanosomes
<p>This repository contains the run scripts for this publication.</p> <p><strong>Complete data download</strong><br> http://resources-molpara.vetmed.lmu.de/Kraus_et_al_2019_sequencing_analysis.tar.gz</p> <p><strong>Contents of the tar.gz archive:</strong><br> upload_sequencing/<br> ├── bin/<br> │ ├── scripts necessary to run the pipeline<br> ├── input/<br> │ ├── input files<br> ├── output/<br> │ ├── output files for ChIP and RNA-seq<br> └── output2/<br> └── output files for ATAC-seq</p> <p><strong>Abstract</strong><br> Despite histone H2A variants and acetylation of histones occurring in almost every eukaryotic organism, it has been difficult to establish direct functional links between canonical histone or H2A variant acetylation, deposition of H2A variants and transcription. To disentangle these complex interdependent processes, we devised a highly sensitive strategy for quantifying histone acetylation levels at specific genomic loci. Taking advantage of the unusual genome organization in <em>Trypanosoma brucei</em>, we identify 58 histone modifications enriched at transcription start sites (TSSs). Furthermore, we find TSS-associated H4 and H2A.Z acetylation to be mediated by two different histone acetyltransferases, HAT2 and HAT1, respectively. Whereas depletion of HAT2 decreases H2A.Z deposition and shifts the site of transcription initiation, depletion of HAT1 does not affect H2A.Z deposition but reduces total mRNA levels by 50%. Thus, specifically reducing H4 or H2A.Z acetylation levels enabled us to reveal distinct roles for these modifications in H2A.Z deposition and RNA transcription.</p>
X-ray diffraction images for DPF3 tandem PHD fingers co-crystallized with an acetylated histone-derived peptide
<p>This submission includes a tar archive of bzipped diffraction images recorded with the ADSC Q315r detector at the Advanced Photon Source of Argonne National Laboratory, Structural Biology Center beam line 19-ID. Relevant meta data can be found in the headers of those diffraction images.</p> <p>Please find below the content of an input file XDS.INP for the program XDS (Kabsch, 2010), which may be used for data reduction. The "NAME_TEMPLATE_OF_DATA_FRAMES=" item inside XDS.INP may need to be edited to point to the location of the downloaded and untarred images.</p> <p>!!! Paste lines below in to a file named XDS.INP</p> <p>DETECTOR=ADSC MINIMUM_VALID_PIXEL_VALUE=1 OVERLOAD= 65000<br /> DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0<br /> DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0<br /> TRUSTED_REGION=0.0 1.05<br /> MAXIMUM_NUMBER_OF_JOBS=10<br /> ORGX= 1582.82 ORGY= 1485.54<br /> DETECTOR_DISTANCE= 150<br /> ROTATION_AXIS= -1.0 0.0 0.0<br /> OSCILLATION_RANGE=1<br /> X-RAY_WAVELENGTH= 1.2821511<br /> INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0<br /> FRACTION_OF_POLARIZATION=0.90<br /> POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0<br /> SPACE_GROUP_NUMBER=20<br /> UNIT_CELL_CONSTANTS= 100.030 121.697 56.554 90.000 90.000 90.000<br /> DATA_RANGE=1 180<br /> BACKGROUND_RANGE=1 6<br /> SPOT_RANGE=1 3<br /> SPOT_RANGE=31 33<br /> MAX_CELL_AXIS_ERROR=0.03<br /> MAX_CELL_ANGLE_ERROR=2.0<br /> TEST_RESOLUTION_RANGE=8.0 3.8<br /> MIN_RFL_Rmeas= 50<br /> MAX_FAC_Rmeas=2.0<br /> VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 6000 30000<br /> INCLUDE_RESOLUTION_RANGE=50.0 1.7<br /> FRIEDEL'S_LAW= FALSE<br /> STARTING_ANGLE= -100 STARTING_FRAME=1<br /> NAME_TEMPLATE_OF_DATA_FRAMES= ../x247398/t1.0???.img</p> <p>!!! End of XDS.INP</p> <p> </p> <p> </p>
Total H3 acetylation in house sparrows
<p class="MsoNormal">Epigenetic mechanisms are increasingly understood to have major impacts across ecology. However, one molecular epigenetic mechanism, DNA methylation, currently dominates the literature. A second mechanism, histone modification, is likely important to ecologically relevant phenotypes and thus warrants investigation, especially because molecular interplay between methylation and histone acetylation can strongly affect gene expression. There are a limited number of histone acetylation studies on non-model organisms, yet those that exist show that it can impact gene expression and phenotypic plasticity. Wild birds provide an excellent system to investigate histone acetylation, as free-living individuals must rapidly adjust to environmental change. Here, we screen histone acetylation in the house sparrow (<em>Passer domesticus</em>); we studied this species because DNA methylation was important in the spread of this bird globally. This species has one of the broadest geographic distributions in the world, and part of this success is related to the way that it uses methylation to its gene expression. Here, we verify that a commercially available assay that was developed for mammals can be used in house sparrows. We detected high variance in histone acetylation among individuals in both liver and spleen tissue. Further, house sparrows with higher epigenetic potential in the <em>TLR-4</em> promoter (i.e., CpG content) had higher histone acetylation in liver. Also, there was a negative correlation between histone acetylation in spleen and <em>TLR-4 </em>expression. In addition to validating a method for measuring histone acetylation in wild songbirds, this study also shows that histone acetylation varies in an ecologically relevant way, adding a new study option for ecological epigenetics.</p>
Increased Drp1 acetylation by lipid overload induces cardiomyocyte death and heart dysfunction
<p>Metabolic syndrome is a cluster of abnormalities characterized by obesity and insulin resistance, which compromise energy metabolism, damage mitochondria, cause cardiomyocyte death, and eventually impair heart contraction and relaxation performance. Despite the increasing prevalence of heart complications in obese and diabetic patients, our knowledge on how obese and diabetes mellitus impair heart function is very limited. In this study, we used animal and cell culture models in rodents or monkeys and generated lipid overload models to mimic obesity conditions. We found that excessive lipid supply decreased nicotinamide adenine dinucleotide (oxidized) levels and increased the acetylation of a fission protein Drp1 at a specific lysine residue (K642). Drp1 acetylation at K642 activated Drp1 through phosphorylation, mitochondrial translocation, and oligomerization. The excessively activated Drp1 had higher GTPase activity, bound with VDAC1 on mitochondria, induced mitochondrial fission, and caused cardiomyocyte death. These findings provide new information regarding how lipid overload regulates redox environment, protein acetylation, and the function of mitochondrial fission protein Drp1 in the heart.</p>
Mass spectrometry of axonemes from Tetrahymena thermophila CU428 and acetylation mutants
<p>Acetylation of α-tubulin at the lysine 40 residue (αK40) by the ATAT1/MEC-17 acetyltransferase influences the properties of microtubules and is a widespread phenomenon in eukaryotic cells. Previous research indicates that microtubules that undergo acetylation at αK40 are more stable and resilient to damage. Notably, αK40 acetylation represents the sole identified post-translational modification site within the microtubule lumen, suggesting its role in regulating the lateral interactions among protofilaments within the microtubule structure. This investigation focuses on evaluating the impact of tubulin acetylation on doublet microtubules present in the cilia of <em>Tetrahymena thermophila</em>, employing mass spectrometry analysis. Cilia samples derived from <em>Tetrahymena</em> wild type, acetylation mutants (K40R and MEC17-Knockout), and non-acetylation mutants (RIB72B-Knockout and RIB72AB-Knockout) underwent comparative mass spectrometry analysis. The results from mass spectrometry revealed a correlation between αK40 acetylation and phosphorylation within the ciliary structures.</p>
Functional miscibility and thermomechanical properties enhancement of substituted phthalic acetylated modified chitin filler in biopolymer composite
<p>The miscibility between hydrophobic and hydrophilic biopolymers has been of significant challenge. This study used a novel simplified chitin modification method to produce phthalic - chitin using phthalic anhydride in a substitution reaction. The FT-IR functional group analysis was used to confirm the substitution reaction. The modified chitin was used as compatibiliser in PLA/starch biocomposite to enhance its properties. The biocomposite was prepared using melt extrusion and compression moulding technique. The biocomposite's morphological, thermomechanical, and water absorption properties were characterised using scanning electron microscope, tensile test, dynamic mechanical analysis, thermogravimetry analysis, differential scanning calorimetry, thickness swelling, and water absorption test. The FT-IR study shows a successful substitution reaction of the amine hydrogen ion present in the chitin as opposed to substituting the hydrogen ion in the hydroxide group. The tensile and impact properties of biocomposite incorporated with modified chitin showed better results compared with other samples. The SEM images showed uniform miscibility of the modified biocomposite. The dynamic mechanical analysis showed improved modulus value with the incorporation of modified chitin. The thermal properties showed improved thermal stability of the modified biocomposite. Furthermore, the percentage of water absorbed by biocomposite with modified chitin is reduced compared to the PLA/starch biocomposite. The produced biodegradable ternary blend can be used as a substitute for plastics in industrial applications.</p>
Vimentin supports cell polarization by enhancing centrosome function and microtubule acetylation
<p>Cell polarity is important for controlling cell shape, motility, and cell division processes. Vimentin intermediate filaments are important for cell migration and cell polarization in mesenchymal cells and assembly of vimentin and microtubule networks is dynamically coordinated, but the precise details of how vimentin mediates cell polarity remain unclear. Here, we characterize the effects of vimentin on the structure and function of the centrosome and the stability of microtubule filaments in wild-type and vimentin-null mouse embryonic fibroblasts (mEFs). We find that vimentin mediates the structure of the pericentrosomal material, promotes centrosome-mediated microtubule regrowth, and increases the level of stable acetylated microtubules in the cell. Loss of vimentin also impairs centrosome repositioning during cell polarization and migration processes that occur during wound closure. Our results suggest that vimentin modulates centrosome structure and function as well as microtubule network stability, which has important implications for how cells establish proper cell polarization and persistent migration.</p>
Chemical perturbations impacting histone acetylation regulate colorectal cancer differentiation
<p>M60.count.Rdata: Rdata that includes the raw count, scaled CPM value and meta data of each sample. (Fig. 1 & 4)</p> <p>DAP.merged.Log2FC.csv: integrated DiffBind results that shows the log2FC and P-value/FDR of peaks. (Fig. 1 & 4)</p> <p>rawdata_scRNA-seq.zip: raw count data of scRNA-seq data from cellranger (labels: A: DMSO, B: MRK60, D: MRK60 + JQAD1). (Fig. 5)</p>
Chromatin regulation by Histone H4 acetylation at Lysine 16 during cell death and differentiation in the myeloid compartment
<p>Histone H4 acetylation at Lysine 16 (H4K16ac) is a key epigenetic mark involved in gene regulation, DNA repair and chromatin remodeling, and though it is known to be essential for embryonic development, its role during adult life is still poorly understood. Here we show that this lysine is massively hyperacetylated in peripheral neutrophils. Genome-wide mapping of H4K16ac in terminally differentiated blood cells, along with functional experiments, supported a role for this histone post-translational modification in the regulation of cell differentiation and apoptosis in the hematopoietic system. Furthermore, in neutrophils, H4K16ac was enriched at specific DNA repeats. These DNA regions presented an accessible chromatin conformation and were associated with the cleavage sites that generate the 50 kb DNA fragments during the first stages of programmed cell death. Our results thus suggest that H4K16ac plays a dual role in myeloid cells as it not only regulates differentiation and apoptosis, but it also exhibits a non-canonical structural role in poising chromatin for cleavage at an early stage of neutrophil cell death.</p> <p> </p>
P300 promotes acetylation of H3K18 during osteogenesis of hAD-MCSs
Open the record for dataset details and reuse information.
Ultra-Accurate Correlation Between Precursor and Fragment Ions in Two-lDimensional Mass Spectrometry: Acetylated vs. Trimethylated Histone Peptides
<p>Two-dimensional mass spectrometry (2D MS) is a method<br> for tandem<br> mass spectrometry in which precursor and fragment ions are correlated<br> by manipulating ion radii rather than by ion isolation. A 2D mass<br> spectrum contains the fragmentation patterns of all analytes in a<br> sample, acquired in parallel. We report ultrahigh-resolution narrowband<br> 2D mass spectra of a mixture of two histone peptides with the same<br> sequence, one of which carries an acetylation and the other a trimethylation<br> (m/z 0.006 difference). We reduced<br> the distance between data points in the precursor ion dimension and<br> compared the accuracy of the precursor-fragment correlation with the<br> resolving power. We manage to perform label-free quantification on<br> the histone peptide mixture and show that precursor and fragment ions<br> can be accurately correlated even though the precursor ions are not<br> resolved. Finally, we show that increasing the resolution of a 2D<br> mass spectrum in the precursor ion dimension too far can lead to a<br> decline in the signal-to-noise ratio.</p>
N-Acetyl Cysteine Plus Behavioral Therapy for Nicotine Dependent Pathological Gamblers
ClinicalTrials.gov study NCT00967005. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Phase 3 Randomized, Double-Blind, Placebo-Controlled Study to Evaluate Sialic Acid in Patients With Glucosamine (UDP-N-acetyl)-2-epimerase Myopathy (GNEM) or Hereditary Inclusion Body Myopathy (HIBM)
ClinicalTrials.gov study NCT02377921. IPD Sharing: Not stated. Countries: 7. Publications: 2.
N-Acetyl-Cysteine (NAC) in Early Phase Schizophrenia Spectrum Psychosis
ClinicalTrials.gov study NCT01354132. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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Annotated Behaviour and Observability Dataset (ABODe)
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