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ABSTRACT:
PROVIDER: PRJNA1233786 | ENA |
REPOSITORIES: ENA
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Project description:Matthew F. Hockin, Kevin M. Cawthern, Michael Kalafatis & Kenneth G. Mann. A model describing the inactivation of factor Va by APC: bond cleavage, fragment dissociation, and product inhibition. Biochemistry 38, 21 (1999).
The inactivation of factor Va is a complex process which includes bond cleavage (at three sites) and dissociation of the A2N.A2C peptides, with intermediate activity in each species. Quantitation of the functional consequences of each step in the reaction has allowed for understanding of the presentation of disease in individuals possessing the factor V polymorphism factor VLEIDEN. APC cleavage of membrane-bound bovine factor Va (Arg306, Arg505, Arg662) leads to the dissociation of fragments of the A2 domain, residues 307-713 (A2N.A2C + A2C-peptide), leaving behind the membrane-bound A1.LC species. Evaluation of the dissociation process by light scattering yields invariant mass loss estimates as a function of APC concentration. The rate constant for A2 fragment dissociation varies with [APC], reaching a maximal value of k = 0.028 s-1, the unimolecular rate constant for A2 domain fragment dissociation. The APC binding site resides in the factor Va light chain (LC) (Kd = 7 nM), suggesting that the membrane-bound LC.A1 product would act to sequester APC. This inhibitory interaction (LC.A1.APC) is demonstrated to exist with either purified factor Va LC or the products of factor Va inactivation. Utilizing these experimental data and the reported rates of bond cleavage, binding constants, and product activity values for factor Va partial inactivation products, a model is developed which describes factor Va inactivation and accounts for the defect in factor VLEIDEN. The model accurately predicts the rates of inactivation of factor Va and factor VaLEIDEN, and the effect of product inhibition. Modeled reaction progress diagrams and activity profiles (from either factor Va or factor VaLEIDEN) are coincident with experimentally derived data, providing a mechanistic and kinetic explanation for all steps in the inactivation of normal factor Va and the pathology associated with factor VLEIDEN.
2024-09-02 | BIOMD0000000365 | BioModels
Project description:Although genetically modified glyphosate resistant soybeans with cp4-epsps gene have been widely planted all over the world, the proteomic characteristics of them are not very clear. In this study, the soybean seeds of a genetically modified (GM) soybean line H06-698 (H) with cp4-epsps gene and its non-transgenic counterpart Mengdou12 (M), which collected from different planting regions in two years, were analyzed with label-free proteomics technique.
2021-05-10 | PXD025908 |
Project description:DNA microarray analysis has been proved to be an effective method in investigating unintended effects in genetically modified (GM) crops. However, unintended effects of GM plants in leaves through DNA microarray analysis has many researches, but research of unintended effects of GM plants of the underground portion has few. In this study, DNA microarray analysis was used to detect DEG in underground portions between transgenic rice HH1 and its non-transgenic control MH63. We used microarrays to study unintended effects in root of transgenic rice Huahui 1.
2013-10-16 | GSE46086 | GEO
Project description:Metagenomic characterization of genetically modified Bacillus contaminations in commercial food enzyme products
| PRJEB53495 | ENA
Project description:Generating sufficient DNA for high-throughput genetic analysis has always been a challenge for clinical settings where the amount of source DNA is limited. Multiple displacement amplification (MDA) has been proposed as a promising candidate for such situations. Previous work with lower-resolution arrays confirmed the utility of single-cell MDA products for large-size (~30 Mb) genome variation screening. We tested the performance of single-cell MDA products on the SNP 6.0 arrays to examine the performance of single-cell MDA in SNP genotyping, copy number polymorphism, de novo copy number variation (CNV) and loss of heterozygosity (LOH) analysis. Our data show that for SNP genotyping, single-cell MDA did not obtain complete genome coverage or high sequence fidelity. For CNV calling, single-cell MDA introduced stochastic amplification artifacts in log2 ratio profiles, reducing the robustness of CNV calling; however, by adjusting smooth window size, it is still possible to analyze large chromosomal aberrations, and homozygous deletions as small as 500 kb can still be identified from the noisy log2 ratio profiles. Our results also suggest that even with a modified protocol (reduction of reaction volume, addition of a molecular crowding reagent, minimization of reaction time), single-cell MDA presented little improvement over the unmodified protocol, but by increasing the number of cells as template to 5M-bM-^@M-^S10 cells, SNP 6.0 array results comparable to those of 10 ng genomic DNA MDA could be obtained. Algorithms like PICNIC improved the CNV calling, suggesting that better algorithms can better utilize single-cell MDA array results. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cell line samples, and multiple displacement samples. Genotyping, Copy number and LOH analysis of Affymetrix SNP 6.0 arrays was performed for 3 samples of unamplified cell line genomic DNA, 2 samples of DNA obtained by multiple displacement amplification from 10ng genomic DNA, 3 single-cell multiple displacement amplification (MDA) products, single cell modified MDA amplification product, 5-cell modified MDA amplification product, 10-cell modified MDA amplification product.
2011-03-25 | E-GEOD-28132 | biostudies-arrayexpress
Project description:DNA microarray analysis has been proved to be an effective method in investigating unintended effects in genetically modified (GM) crops. But the distribution of differentially expressed genes in GM crops remains unclear. So the results of microarray analysis might be invalid for assessment of unintended effects if differentially expressed genes are extremely distributed. We used microarrays to study the distribution pattern of differentially expressed genes in HH1 at different developmental stages and environmental conditions.
2011-10-26 | GSE33204 | GEO
Project description:The nutritional similarities between herbicide-tolerant genetically modified (GM) crops and non-GM counterparts are used as scientific evidence to show GM crops are substantially equivalent and safe and nutritious to non-GM. A previous study demonstrated substantial non-equivalence in ready-to-market soybeans obtained from 31 samples from Iowa, USA and discriminated GM, non-GM conventionally farmed and organic soybean. In the present study, by using high-resolution tandem mass spectrometry (HRMS) coupled with high-throughput proteomics and bioinformatic analyses, the same 31 individual soybean samples were investigated. Our results show that proteomic profiles of GM, conventionally, and organically farmed soybean samples were different. Differentially expressed proteins were found that can be used as markers to separate conventionally and organically farmed soybean seeds. Our data indicate that HRMS coupled with bioinformatic analyses provide a powerful platform to probe the equivalence of GM with non-GM material in food and feeding stuff.
2022-06-08 | MSV000089618 | MassIVE
Project description:There is an ongoing debate on the potential toxicity of genetically modified food. The ability of rodent feeding trials to assess the potential toxicity of these products is highly debated since a 2-year study in rats fed NK603 Roundup-tolerant genetically modified maize, treated or not with Roundup during the cultivation, resulted in anatomorphological and blood/urine biochemical changes indicative of liver and kidney structure and functional pathology. We used microarrays to detail the alterations in gene expression profiles associated with the consumption of a Roundup-tolerant genetically modified maize (NK603) sprayed or unsprayed with a Roundup herbicide from these same animals.
2016-10-01 | GSE73884 | GEO
Project description:There is an ongoing debate on the potential toxicity of genetically modified food. The ability of rodent feeding trials to assess the potential toxicity of these products is highly debated since a 2-year study in rats fed NK603 Roundup-tolerant genetically modified maize, treated or not with Roundup during the cultivation, resulted in anatomorphological and blood/urine biochemical changes indicative of liver and kidney structure and functional pathology. We used microarrays to detail the alterations in gene expression profiles associated with the consumption of a Roundup-tolerant genetically modified maize (NK603) sprayed or unsprayed with a Roundup herbicide from these same animals.
2016-10-01 | GSE73886 | GEO
Project description:Immunoglobulin G (IgG) proteins are known for the huge diversity of the variable domains of their heavy and light chains, aimed at protecting each individual against foreign antigens. The IgG also harbor specific polymorphism concentrated in the CH2 and CH3-CHS constant regions located on the Fc fragment of their heavy chains. But this individual particularity relies only on a few amino acids among which some could make accurate sequence determination a challenge for mass spectrometry-based techniques. The purpose of the study was to bring a molecular validation of proteomic results by the sequencing of encoding DNA fragments. It was performed using ten individual samples (DNA and sera) selected on the basis of their Gm (gamma marker) allotype polymorphism in order to cover the main immunoglobulin heavy gamma (IGHG) gene diversity. Gm allotypes, reflecting part of this diversity, were determined by a serological method. On its side, the IGH locus comprises four functional IGHG genes totalizing 34 alleles and encoding the four IgG subclasses. The genomic study focused on the nucleotide polymorphism of the CH2 and CH3-CHS exons and of the intron. Despite strong sequence identity, four pairs of specific gene amplification primers could be designed. Additional primers were identified to perform the subsequent sequencing. The nucleotide sequences obtained were first assigned to a specific IGHG gene, and then IGHG alleles were deduced using a home-made decision tree reading of the nucleotide sequences. IGHG amino acid (AA) alleles were determined by mass spectrometry. Identical results were found at 95% between alleles identified by proteomics and those deduced from genomics. These results validate the proteomic approach which could be used for diagnostic purposes, namely for a mother-and-child differential IGHG detection in a context of suspicion of congenital infection.
2017-03-13 | PXD005021 | Pride