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Basic & Clinical Pharmacology &... Feb 2010The present in vivo study investigated the genotoxicity of four dental resin monomers: triethyleneglycoldimethacrylate (TEGDMA), hydroxyethylmethacrylate (HEMA),... (Comparative Study)
Comparative Study
The present in vivo study investigated the genotoxicity of four dental resin monomers: triethyleneglycoldimethacrylate (TEGDMA), hydroxyethylmethacrylate (HEMA), urethanedimethacrylate (UDMA) and bisphenol A-glycidylmethacrylate (BisGMA). The Somatic Mutation and Recombination Test (SMART) in Drosophila melanogaster was applied to analyse their genotoxicity expressed as homologous mitotic recombination, point and chromosomal mutation. SMART detects the loss of heterozygosity of marker genes expressed phenotypically on the fly's wings. This fruit fly has an extensive genetic homology to mammalians, which makes it a suitable model organism for genotoxic investigations. The present findings provide evidence that the mechanistic basis underlying the genotoxicity of UDMA and TEGDMA is related to homologous recombination and gene/chromosomal mutation. A genotoxic pattern can correspondingly be discerned for both UDMA and TEGDMA: their genotoxicity is attributed respectively to 49% and 44% of mitotic recombination, as well as 51% and 56% of mutational events, including point and chromosomal alterations. The monomer UDMA is 1.6 times more active than TEGDMA to induce mutant clones per treatment unit. BisGMA and HEMA had no statistically significant effect on total spot frequencies - suggesting no genotoxic action in the SMART assay. The clinical significance of these observations has to be interpreted for data obtained in other bioassays.
Topics: Animals; DNA Damage; Drosophila melanogaster; Mitosis; Mutagenicity Tests; Mutagens; Mutation; Point Mutation; Resins, Synthetic
PubMed: 20041880
DOI: 10.1111/j.1742-7843.2009.00479.x -
International Journal of Epidemiology Apr 2014Recent advances in the genetics of neurodevelopmental disorder (NDD) have demonstrated that rare mutations play a role not only in Mendelian syndromes, but in complex,... (Review)
Review
Recent advances in the genetics of neurodevelopmental disorder (NDD) have demonstrated that rare mutations play a role not only in Mendelian syndromes, but in complex, common forms of NDDs as well. Strikingly, both common polymorphisms and rare variations in a single gene or genetic locus have been found to carry risk for conditions previously considered to be clinically and aetiologically distinct. Recent developments in the methods and tools available for studying complex NDDs have led to systematic and reliable genome-wide variant discovery. Both common as well as rare, and structural as well as sequence, genetic variations have been identified as contributing to NDDs. There are multiple examples in which the identical variant had been found to contribute to a wide range of formerly distinct diagnoses, including autism, schizophrenia, epilepsy, intellectual disability and language disorders. These include variations in chromosomal structure at 16p11.2, rare de novo point mutations at the gene SCN2A, and common single nucleotide polymorphisms (SNPs) mapping near loci encoding the genes ITIH3, AS3MT, CACNA1C and CACNB2. These selected examples point to the challenges to current diagnostic approaches. Widely used categorical schema have been adequate to provide an entré into molecular mechanisms of NDDs, but there is a need to develop an alternative, more biologically-relevant nosology. Thus recent advances in gene discovery in the area of NDDs are leading to a re-conceptualization of diagnostic boundaries. Findings suggest that epidemiological samples may provide important new insights into the genetics and diagnosis of NDDs and that other areas of medicine may provide useful models for developing a new diagnostic nosology, one that simultaneously integrates categorical diagnoses, biomarkers and dimensional variables.
Topics: Child; Developmental Disabilities; Diagnostic and Statistical Manual of Mental Disorders; Genetic Markers; Genomics; Humans; Intellectual Disability; Phenotype; Point Mutation
PubMed: 24618187
DOI: 10.1093/ije/dyu037 -
Plant Biotechnology Journal Aug 2017Application of nitrogen fertilizer in the past 50 years has resulted in significant increases in crop yields. However, loss of nitrogen from crop fields has been...
Application of nitrogen fertilizer in the past 50 years has resulted in significant increases in crop yields. However, loss of nitrogen from crop fields has been associated with negative impacts on the environment. Developing maize hybrids with improved nitrogen use efficiency is a cost-effective strategy for increasing yield sustainably. We report that a dominant male-sterile mutant Ms44 encodes a lipid transfer protein which is expressed specifically in the tapetum. A single amino acid change from alanine to threonine at the signal peptide cleavage site of the Ms44 protein abolished protein processing and impeded the secretion of protein from tapetal cells into the locule, resulting in dominant male sterility. While the total nitrogen (N) content in plants was not changed, Ms44 male-sterile plants reduced tassel growth and improved ear growth by partitioning more nitrogen to the ear, resulting in a 9.6% increase in kernel number. Hybrids carrying the Ms44 allele demonstrated a 4%-8.5% yield advantage when N is limiting, 1.7% yield advantage under drought and 0.9% yield advantage under optimal growth conditions relative to the yield of wild type. Furthermore, we have developed an Ms44 maintainer line for fertility restoration, male-sterile inbred seed increase and hybrid seed production. This study reveals that protein secretion from the tapetum into the locule is critical for pollen development and demonstrates that a reduction in competition between tassel and ear by male sterility improves grain yield under low-nitrogen conditions in maize.
Topics: Nitrogen; Plant Infertility; Plant Proteins; Point Mutation; Polymorphism, Single Nucleotide; Zea mays
PubMed: 28055137
DOI: 10.1111/pbi.12689 -
PloS One 2013Somatic mutation calling from next-generation sequencing data remains a challenge due to the difficulties of distinguishing true somatic events from artifacts arising...
Somatic mutation calling from next-generation sequencing data remains a challenge due to the difficulties of distinguishing true somatic events from artifacts arising from PCR, sequencing errors or mis-mapping. Tumor cellularity or purity, sub-clonality and copy number changes also confound the identification of true somatic events against a background of germline variants. We have developed a heuristic strategy and software (http://www.qcmg.org/bioinformatics/qsnp/) for somatic mutation calling in samples with low tumor content and we show the superior sensitivity and precision of our approach using a previously sequenced cell line, a series of tumor/normal admixtures, and 3,253 putative somatic SNVs verified on an orthogonal platform.
Topics: Computational Biology; DNA Copy Number Variations; High-Throughput Nucleotide Sequencing; Humans; Mutation; Neoplasms; Point Mutation; Polymerase Chain Reaction; Software
PubMed: 24250782
DOI: 10.1371/journal.pone.0074380 -
STAR Protocols Jun 2020Infections caused by drug-resistant have posed a serious threat to global public health. However, genetic manipulation methods, the primary way to study pathogenesis...
Infections caused by drug-resistant have posed a serious threat to global public health. However, genetic manipulation methods, the primary way to study pathogenesis and drug-resistance mechanisms, remain time consuming and inefficient. Here, we provide a detailed protocol for genetic manipulation, including gene deletion, insertion, and point mutation in using the platform. For complete details on the use and execution of this protocol, please refer to Wang et al. (2019).
Topics: Acinetobacter baumannii; CRISPR-Cas Systems; Cytidine; Electroporation; Gene Editing; Point Mutation
PubMed: 33111078
DOI: 10.1016/j.xpro.2020.100025 -
Molecules (Basel, Switzerland) Nov 2022Cocoonase is folded in the form of a zymogen precursor protein (prococoonase) with the assistance of the propeptide region. To investigate the role of the propeptide...
Cocoonase is folded in the form of a zymogen precursor protein (prococoonase) with the assistance of the propeptide region. To investigate the role of the propeptide sequence on the disulfide-coupled folding of cocoonase and prococoonase, the amino acid residues at the degradation sites during the refolding and auto-processing reactions were determined by mass spectrometric analyses and were mutated to suppress the numerous degradation reactions that occur during the reactions. In addition, the Lys residue at the propeptide region was also mutated to estimate whether the entire sequence is absolutely required for the activation of cocoonase. Finally, a degradation-suppressed [K8D,K63G,K131G,K133A]-proCCN protein was prepared and was found to refold readily without significant degradation. The results of an enzyme assay using casein or Bz-Arg-OEt suggested that the mutations had no significant effect on either the enzyme activity or the protein conformation. Thus, we, herein, provide the non-degradative cocoonase protein to investigate the propeptide-mediated protein folding of the molecule. We also examined the catalytic residues using the degradation-suppressed cocoonase. The point mutations at the putative catalytic residues in cocoonase resulted in the loss of catalytic activity without any secondary structural changes, indicating that the mutated residues play a role in the catalytic activity of this enzyme.
Topics: Amino Acid Sequence; Protein Folding; Protein Precursors; Point Mutation; Mutation
PubMed: 36432163
DOI: 10.3390/molecules27228063 -
Genome Biology and Evolution Feb 2017Transposable elements (TEs) are selfish, autonomously replicating DNA sequences that constitute a major component of eukaryotic genomes and contribute to genome...
Transposable elements (TEs) are selfish, autonomously replicating DNA sequences that constitute a major component of eukaryotic genomes and contribute to genome evolution through their movement and amplification. Many fungal genomes, including the anther-smut fungi in the basidiomycete genus Microbotryum, have genome defense mechanisms, such as repeat-induced point mutation (RIP), which hypermutate repetitive DNA and limit TE activity. Little is known about how hypermutation affects the tempo of TE activity and their sequence evolution. Here we report the identification of a massive burst-like expansion of Gypsy-like retrotransposons in a strain of Microbotryum. This TE expansion evidently occurred in the face of RIP-like hypermutation activity. By examining the fitness of individual TE insertion variants, we found that RIP-like mutations impair TE fitness and limit proliferation. Our results provide evidence for a punctuated pattern of TE expansion in a fungal genome, similar to that observed in animals and plants. While targeted hypermutation is often thought of as an effective protection against mobile element activity, our findings suggest that active TEs can persist and undergo selection while they proliferate in genomes that have RIP-like defenses.
Topics: Basidiomycota; DNA Repeat Expansion; Mutation Rate; Point Mutation; Recombinant Proteins; Transcription Factors
PubMed: 28164239
DOI: 10.1093/gbe/evx011 -
Bioinformatics (Oxford, England) Oct 2016Mutations in human genome are mainly through single nucleotide polymorphism, some of which can affect stability and function of proteins, causing human diseases. Several...
MOTIVATION
Mutations in human genome are mainly through single nucleotide polymorphism, some of which can affect stability and function of proteins, causing human diseases. Several methods have been proposed to predict the effect of mutations on protein stability; but most require features from experimental structure. Given the fast progress in protein structure prediction, this work explores the possibility to improve the mutation-induced stability change prediction using low-resolution structure modeling.
RESULTS
We developed a new method (STRUM) for predicting stability change caused by single-point mutations. Starting from wild-type sequences, 3D models are constructed by the iterative threading assembly refinement (I-TASSER) simulations, where physics- and knowledge-based energy functions are derived on the I-TASSER models and used to train STRUM models through gradient boosting regression. STRUM was assessed by 5-fold cross validation on 3421 experimentally determined mutations from 150 proteins. The Pearson correlation coefficient (PCC) between predicted and measured changes of Gibbs free-energy gap, ΔΔG, upon mutation reaches 0.79 with a root-mean-square error 1.2 kcal/mol in the mutation-based cross-validations. The PCC reduces if separating training and test mutations from non-homologous proteins, which reflects inherent correlations in the current mutation sample. Nevertheless, the results significantly outperform other state-of-the-art methods, including those built on experimental protein structures. Detailed analyses show that the most sensitive features in STRUM are the physics-based energy terms on I-TASSER models and the conservation scores from multiple-threading template alignments. However, the ΔΔG prediction accuracy has only a marginal dependence on the accuracy of protein structure models as long as the global fold is correct. These data demonstrate the feasibility to use low-resolution structure modeling for high-accuracy stability change prediction upon point mutations.
AVAILABILITY AND IMPLEMENTATION
http://zhanglab.ccmb.med.umich.edu/STRUM/ CONTACT: [email protected] and [email protected]
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Algorithms; Humans; Models, Molecular; Point Mutation; Protein Stability; Proteins; Software; Structure-Activity Relationship
PubMed: 27318206
DOI: 10.1093/bioinformatics/btw361 -
Nature Communications Mar 2024This paper presents an innovative approach for predicting the relative populations of protein conformations using AlphaFold 2, an AI-powered method that has...
This paper presents an innovative approach for predicting the relative populations of protein conformations using AlphaFold 2, an AI-powered method that has revolutionized biology by enabling the accurate prediction of protein structures. While AlphaFold 2 has shown exceptional accuracy and speed, it is designed to predict proteins' ground state conformations and is limited in its ability to predict conformational landscapes. Here, we demonstrate how AlphaFold 2 can directly predict the relative populations of different protein conformations by subsampling multiple sequence alignments. We tested our method against nuclear magnetic resonance experiments on two proteins with drastically different amounts of available sequence data, Abl1 kinase and the granulocyte-macrophage colony-stimulating factor, and predicted changes in their relative state populations with more than 80% accuracy. Our subsampling approach worked best when used to qualitatively predict the effects of mutations or evolution on the conformational landscape and well-populated states of proteins. It thus offers a fast and cost-effective way to predict the relative populations of protein conformations at even single-point mutation resolution, making it a useful tool for pharmacology, analysis of experimental results, and predicting evolution.
Topics: Protein Conformation; Mutation; Point Mutation; Sequence Alignment
PubMed: 38538622
DOI: 10.1038/s41467-024-46715-9 -
Plant Physiology Jul 2017A forward genetic screen is one of the best methods for revealing the function of genes. In plants, this technique is highly efficient, as it is relatively easy to grow...
A forward genetic screen is one of the best methods for revealing the function of genes. In plants, this technique is highly efficient, as it is relatively easy to grow and screen hundreds or thousands of individuals. The cost efficiency and ease of data production afforded by next-generation sequencing have created new opportunities for rapid mapping of induced mutations. Current mapping tools are often not user friendly, are complicated, or require extensive preparation steps. To simplify the process of mapping new mutations, we developed a pipeline that takes next-generation sequencing fastq files as input, calls on several well-established and freely available genome-analysis tools, and outputs the most likely causal DNA changes. The pipeline has been validated in (Arabidopsis) and can be readily applied to other species, with the possibility of mapping either dominant or recessive mutations.
Topics: Alleles; Arabidopsis; Chromosome Mapping; Chromosomes, Plant; Point Mutation; Seedlings
PubMed: 28546435
DOI: 10.1104/pp.17.00415