Category: 4433-40-3

On October 26, 2016, Shen, Weifeng; Han, Wei; Li, Yunong; Meng, Zhiqi; Cai, Leiming; Li, Liang published an article.Computed Properties of 4433-40-3 The title of the article was Development of chemical isotope labeling liquid chromatography mass spectrometry for silkworm hemolymph metabolomics. And the article contained the following:

Silkworm (Bombyx mori) is a very useful target insect for evaluation of endocrine disruptor chems. (EDCs) due to mature breeding techniques, complete endocrine system and broad basic knowledge on developmental biol. Comparative metabolomics of silkworms with and without EDC exposure offers another dimension of studying EDCs. The authors report a workflow on metabolomic profiling of silkworm hemolymph based on high-performance chem. isotope labeling (CIL) liquid chromatog. mass spectrometry (LC-MS) and demonstrate its application in studying the metabolic changes associated with the pesticide dichlorodiphenyltrichloroethane (DDT) exposure in silkworm. Hemolymph samples were taken from mature silkworms after growing on diet that contained DDT at four different concentrations (1, 0.1, 0.01, 0.001 ppm) as well as on diet without DDT as controls. They were subjected to differential 12C-/13C-dansyl labeling of the amine/phenol submetabolome, LC-UV quantification of the total amount of labeled metabolites for sample normalization, and LC-MS detection and relative quantification of individual metabolites in comparative samples. The total concentration of labeled metabolites did not show any significant change between four DDT-treatment groups and one control group. Multivariate statistical anal. of the metabolome data set showed that there was a distinct metabolomic separation between the five groups. Out of the 2044 detected peak pairs, 338 and 1471 metabolites have been putatively identified against the HMDB database and the EML library, resp. 65 metabolites were identified by the dansyl library searching based on the accurate mass and retention time. Among the 65 identified metabolites, 33 pos. metabolites had changes of >1.20-fold or <0.83-fold in one or more groups with p-value of smaller than 0.05. Several useful biomarkers including serine, methionine, tryptophan, asym. dimethylarginine, N-Methyl-D-aspartic and tyrosine were identified. The changes of these biomarkers were likely due to the disruption of the endocrine system of silkworm by DDT. This work illustrates that the method of CIL LC-MS is useful to generate quant. submetabolome profiles from a small volume of silkworm hemolymph with much higher coverage than conventional LC-MS methods, thereby facilitating the discovery of potential metabolite biomarkers related to EDC or other chem. exposure. The experimental process involved the reaction of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione(cas: 4433-40-3).Computed Properties of 4433-40-3

The Article related to isotope labeling hplc mass spectrometry silkworm hemolymph metabolomics, isotope labeling, liquid chromatography, mass spectrometry, metabolomics, pesticide, silkworm, Biochemical Methods: Other (Not Covered At Other Subsections) and other aspects.Computed Properties of 4433-40-3

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On May 31, 2017, Sheng, Xiao-Qi; Wang, Yi-Chao published an article.Quality Control of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione The title of the article was Novel two-step derivation method for the synchronous analysis of inherited metabolic disorders using urine. And the article contained the following:

The aim of the present study was to conduct preliminary clin. screening and monitoring using a novel two-step derivatization process of urine in five categories of inherited metabolic disease (IMD). Urine samples (100 μl, containing 2.5 mmol/l creatinine) were taken from patients with IMDs. The collected urine was then treated using a two-step derivatization method (with oximation and silylation at room temperature), where urea and protein were removed. In the first step of the derivatization, α-ketoacids and α-aldehyde acids were prepared by oximation using novel oximation reagents. The second-step of the derivatization was that residues were silylated for anal. Urine samples were examined using gas chromatog./mass spectrometry (GC/MS) and a retention time-locking technique. The simultaneous anal. and identification of >400 metabolites in >130 types of IMD was possible from the GC/MS results, where the IMDs included phenylketonuria, ornithine trans-carbamylase deficiency, neonatal intrahepatic cholestasis caused by citrin deficiency, β-ureidopropionase deficiency and mitochondrial metabolic disorders. This method was demonstrated to have good repeatability. Considering a-ketoglutarate (α-KG) as an example, the relative standard deviations (RSDs) of the α-KG retention time and peak area were 0.8 and 3.9%, resp., the blank spiked recovery rate was between 89.6 and 99.8%, and the RSD was ≤7.5% (n=5). The method facilitates the anal. of thermally non-stable and semi-volatile metabolites in urine, and greatly expands the range of materials that can be synchronously screened by GC/MS. Furthermore, it provides a comprehensive, effective and reliable biochem. anal. platform for the pathol. research of IMDs. The experimental process involved the reaction of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione(cas: 4433-40-3).Quality Control of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione

The Article related to inherited metabolic disease urine biomarker diagnosis gc ms, biomarker, inherited metabolic disorders, simultaneous, two-step derivatization, urine, Biochemical Methods: Other (Not Covered At Other Subsections) and other aspects.Quality Control of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

Rozalski, Rafal; Gackowski, Daniel; Siomek-Gorecka, Agnieszka; Banaszkiewicz, Zbigniew; Olinski, Ryszard published an article in 2016, the title of the article was Urinary Measurement of Epigenetic DNA Modifications: A Non-Invasive Assessment of the Whole-Body Epigenetic Status in Healthy Subjects and Colorectal Cancer Patients.Reference of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione And the article contains the following content:

Active mechanism of DNA demethylation can be responsible for the activation of previously silenced genes. Products of 5-methylcytosine oxidation are released into the bloodstream and eventually excreted with urine. Therefore, whole-body epigenetic status can be assessed non-invasively on the basis of the urinary excretion of a broad spectrum of epigenetic modifications: 5-hydroxymethylcytosine (5-hmCyt), 5-formylcytosine (5-fCyt), 5-carboxycytosine (5-caCyt), and 5-hydroxymethyluracil (5-hmUra). We have developed a specific and sensitive, isotope-dilution, automated, online, two-dimensional ultra-performance liquid chromatog. system with tandem mass spectrometry (2D UPLC-MS/MS) to measure 5-hmCyt, 5-fCyt, 5-caCyt, and their deoxynucleosides in the same urine sample. Human urine contains all of the modifications except from 5-formyl-2′-deoxycytidine (5-fdC) and 5-carboxy-2′-deoxycytidine (5-cadC). A highly significant difference in the urinary excretion of 5-(hydroxymethyl)-2′-deoxycytidine (5-hmdC) was found between healthy subjects and colorectal cancer patients (3.5 vs. 7.8 nmol mmol-1 creatinine, resp.), as well as strong correlations between the majority of analyzed compounds The experimental process involved the reaction of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione(cas: 4433-40-3).Reference of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione

The Article related to liquid chromatog mass spectrometry epigenetic dna colorectal cancer urine, 2d uplc–ms/ms, dna damage, dna methylation, epigenetics, urine, Biochemical Methods: Other (Not Covered At Other Subsections) and other aspects.Reference of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

Mattelaer, H.-P.; Mattelaer, C.-A.; Papastavrou, N.; Dehaen, W.; Herdewijn, P. published an article in 2017, the title of the article was Oligonucleotide promoted peptide bond formation using a tRNA mimicking approach.Computed Properties of 4433-40-3 And the article contains the following content:

TransferRNA’s role in protein translation is the prime example of an Informational Leaving Group (ILG). A simplified model produced oligophenylalanine with a modified uracil as an ILG in the presence of specific oligonucleotides. Our preliminary studies contribute to the importance of hybrid species in bridging the gap between peptides and nucleic acids. The experimental process involved the reaction of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione(cas: 4433-40-3).Computed Properties of 4433-40-3

The Article related to peptide bond formation informational leaving group oligonucleotide photolysis, oligophenylalanine uracil synthesis hybrid species aminolysis kinetics ph peptidomimetic, Amino Acids, Peptides, and Proteins: Poly(Amino Acids) and Peptides and other aspects.Computed Properties of 4433-40-3

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

Bohacova, Sona; Ludvikova, Lucie; Postova Slavetinska, Lenka; Vanikova, Zuzana; Klan, Petr; Hocek, Michal published an article in 2018, the title of the article was Protected 5-(hydroxymethyl)uracil nucleotides bearing visible-light photo-cleavable groups as building blocks for polymerase synthesis of photo-caged DNA.Name: 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione And the article contains the following content:

Nucleosides, nucleotides and 2′-deoxyribonucleoside triphosphates (dNTPs) containing 5-(hydroxymethyl)uracil protected with photo-cleavable groups (2-nitrobenzyl-, 6-nitropiperonyl or 9-anthrylmethyl) were prepared and tested as building blocks for the polymerase synthesis of photo-caged oligonucleotides and DNA. Photo-deprotection (photo-release) reactions were studied in detail on model nucleoside monophosphates and their photoreaction quantum yields were determined Photo-caged dNTPs were then tested and used as substrates for DNA polymerases in primer extension or PCR. DNA probes containing photo-caged or free 5-hydroxymethyluracil in the recognition sequence of restriction endonucleases were prepared and used for the study of photo-release of caged DNA by UV or visible light at different wavelengths. The nitropiperonyl-protected nucleotide was found to be a superior building block because the corresponding dNTP is a good substrate for DNA polymerases, and the protecting group is efficiently cleavable by irradiation by UV or visible light (up to 425 nm). The experimental process involved the reaction of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione(cas: 4433-40-3).Name: 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione

The Article related to hydroxymethyluracil nucleotide preparation photocleavable polymerase photocaged dna, Carbohydrates: Nucleosides and Nucleotides, Cobalamins, Riboflavin and other aspects.Name: 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On July 31, 2019, Luan, Yunpeng; Li, Yanmei; Yue, Xiaoguan; Cao, Yong; Xiang, Fei; Mao, Dechang; Xiong, Zhi published an article.Quality Control of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione The title of the article was Metabonomics of mice intestine in Codonopsis foetens induced apoptosis of intestine cancer cells. And the article contained the following:

Intestinal cancer is a disease with high morbidity and high mortality in China. Previous studies have shown that Codonopsis foetens can inhibit cellular autophagy and promote the apoptosis of intestine cancer cells. Based on metabolomics method coupled with liquid chromatog.-mass spectrometry (LC-MS) technol., we aimed to analyze intestinal small mol. metabolites in the intestinal cancer model group and the Codonopsis foetens treated group. Principal component anal. (PCA) and Partial Least Squares (PLS-DA) were used to identify the pattern of the data. And the metabolic characteristics of the cancer model group were explored based on the metabolic differences between the groups. Multivariate statistical anal. revealed that metabolites presented with differences included: Acetamide, Phosphoric acid, Hydrogen sulfite, Pyruvic acid, Cytosine, 2-Hydroxypyridine, Phosphoric acid, Uracil, Gamma-Aminobutyric acid, Glycerol alpha-monochlorohydrin, Thiosulfic acid, L-Valine, Cysteamine, Taurine, Creatine, Homocysteine, Hypoxanthine, Se-Methylselenocysteine, 5-Hydroxymethyluracil, Oxoglutaric acid, LysoPC(20:0), LysoPC(22:4(7Z,10Z,13Z,16Z)), LysoPC(18:2(9Z,12Z)), LysoPC(16:1(9Z)), LysoPE(0:0/16:0), LysoPE(0:0/18:2(9Z,12Z)), LysoPE(18:0/0:0), LysoPE(20:1(11Z)/0:0), etc. Combined with metabolic pathway anal., pathways presented with differences included: Citrate cycle (TCA cycle), ABC transporters, 2-Oxocarboxylic acid metabolism, Taurine and hypotaurine metabolism, Butanoate metabolism, Phenylalanine, tyrosine and tryptophan biosynthesis, Biosynthesis of amino acids, Protein digestion and absorption, Aminoacyl-tRNA biosynthesis, C5-Branched dibasic acid metabolism, GABAergic synapse, Proximal tubule bicarbonate reclamation, Mineral absorption, Phenylalanine metabolism The results showed that the proliferation of intestinal cancer cells caused cell metabolism disorders, manifesting as changes in metabolic pathways and resulting in changes in metabolites. The experimental process involved the reaction of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione(cas: 4433-40-3).Quality Control of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione

The Article related to codonopsis metabonomic apoptosis intestine cancer cell, codonopsis foetens, intestinal cancer, metabolic pathway, metabolites, metabonomics, Pharmacology: Effects Of Neoplasm Inhibitors and Cytotoxic Agents and other aspects.Quality Control of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On November 30, 2020, Liu, Yuyang; Hu, Zhangxi; Deng, Yunyan; Shang, Lixia; Gobler, Christopher J.; Tang, Ying Zhong published an article.SDS of cas: 4433-40-3 The title of the article was Dependence of genome size and copy number of rRNA gene on cell volume in dinoflagellates. And the article contained the following:

Dinoflagellates are an ecol. important group of protists in aquatic environment and have evolved many unusual and enigmatic genomic features such as immense genome sizes, high repeated genes, and a large portion of hydroxymethyluracil in DNA. Although previous studies have observed pos. correlations between the large subunit (LSU) rRNA gene copy number and genome size of a variety of eukaryotic organisms (e.g. higher plants and animals), or between cell volume and LSU rRNA gene copy number, and/or between genome size and cell size, which suggests a possible co-evolution among these three features in different lineages of life, it remains an open question regarding the relationships among these three parameters in dinoflagellates. For the first time, we estimated the copy numbers of the LSU rRNA gene, the genome sizes, and cell volumes within a broad range of dinoflagellates (covering 15 species of 11 genera) using single-cell qPCR-based assay (determining LSU rRNA gene copy number), FlowCAM (cell volume measurement), and UV spectrophotometry (genome size estimation). The measured copy number of LSU rRNA gene ranged from 398 ± 184 (Prorocentrum min.) to 152,078 ± 33,555 copies•cell-1 (Alexandrium pacificum), while the genome size and the cell volume ranged from 5.6 ± 0.2 (Karlodinium veneficum) to 853 ± 19.9 pg•cell-1 (Pseliodinium pirum), and from 1,070 ± 225 (Kar. veneficum) to 168,474 ± 124,180 μm3 (Ps. pirum), resp. Together with the three parameters measured in literature, there are significant pos. linear correlations between LSU rRNA gene copy numbers and genome sizes, cell volumes and LSU rRNA gene copy numbers, and between genome sizes and cell volumes via comparisons of multi-model regression analyses, suggesting a dependence of genome size and rRNA gene copy number on the cell volumes of dinoflagellates. Validation of the measurement methods was conducted via comparisons between reported data in the literature and that predicted using the linear equations we obtained, and between genome size measured by flow cytometry (FCM) and UV spectrophotometry (Nanodrop). These results provide insightful understandings of dinoflagellate evolution in terms of the relationships among genomes, gene copy number, and cell volume, and of rRNA gene-based studies in intra-populational and intra-individual genetic diversity, taxonomy, and diversity assessment in the environment of dinoflagellates. The results also provide a dataset useful for reads calibration in environmental metabarcoding studies of dinoflagellates and selection of candidate species for whole genome sequencing. The experimental process involved the reaction of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione(cas: 4433-40-3).SDS of cas: 4433-40-3

The Article related to hydroxymethyluracil genetic diversity aquatic environment alexandrium prorocentrum, cell volume, co-evolution, dinoflagellate, genome size, lsu rrna gene copy number, Placeholder for records without volume info and other aspects.SDS of cas: 4433-40-3

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On April 5, 2022, Zott, Fabian L.; Korotenko, Vasily; Zipse, Hendrik published an article.COA of Formula: C5H6N2O3 The title of the article was The pH-Dependence of the Hydration of 5-Formylcytosine: an Experimental and Theoretical Study. And the article contained the following:

5-Formylcytosine is an important nucleobase in epigenetic regulation, whose hydrate form has been implicated in the formation of 5-carboxycytosine as well as oligonucleotide binding events. The hydrate content of 5-formylcytosine and its uracil derivative has now been quantified using a combination of NMR and mass spectroscopic measurements as well as theor. studies. Small amounts of hydrate can be identified for the protonated form of 5-formylcytosine and for neutral 5-formyluracil. For neutral 5-formylcytosine, however, direct detection of the hydrate was not possible due to its very low abundance. This is in full agreement with theor. estimates The experimental process involved the reaction of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione(cas: 4433-40-3).COA of Formula: C5H6N2O3

The Article related to formylcytosine hydration hydrogen ion concentration, dna methylation, tet enzymes, aldehyde hydrates, computational chemistry, epigenetics, modified nucleic acids, General Biochemistry: Subcellular Processes and other aspects.COA of Formula: C5H6N2O3

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Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

Yang, Hao; Wang, Zhenfei; Shi, Shujun; Yu, Qin; Liu, Meiling; Zhang, Zhelin published an article in 2022, the title of the article was Identification of cerebrospinal fluid metabolites as biomarkers for neurobrucellosis by liquid chromatography-mass spectrometry approach.Computed Properties of 4433-40-3 And the article contains the following content:

Neurobrucellosis is the most morbid form in brucellosis disease. Metabolomics is an emerging method which intends to explore the global alterations of various metabolites in samples. We aimed to identify metabolites in cerebrospinal fluid (CSF) as biomarkers that were potentially unique for neurobrucellosis. CSF samples from 25 neurobrucellosis patients and 25 normal controls (uninfected patients with hydrocephalus) were collected for metabolite detection using liquid chromatog.-mass spectrometry (LC-MS) approach. Inflammatory cytokines in CSF were measured with ELISA (ELISA). The base peak chromatogram in CSF samples showed that small-mol. metabolites were well separated Principal Component Anal. (PCA) anal. exhibited the examined samples were arranged in two main clusters in accordance with their group. Projection to Latent Structures Discriminant Anal. (PLS-DA) revealed there was a noticeable separation between neurobrucellosis and normal groups. Orthogonal Partial Least-Squares-Discriminant Anal. (OPLS-DA) could responsibly illuminate the differences between neurobrucellosis and normal controls. Neurobrucellosis showed a total of 155 differentiated metabolites. Prominent potential biomarkers including 30 metabolites were then selected out, regarded as more capable of distinguishing neurobrucellosis. TNF-α and IL-6 in CSF were remarkably increased in neurobrucellosis. We presented the heatmaps and correlation analyses among the identified 30 potential biomarkers. In conclusion, this study showed that CSF metabolomics based on LC-MS could distinguish neurobrucellosis patients from normal controls. Our data offered perspectives for diagnosis and treatment for neurobrucellosis. The experimental process involved the reaction of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione(cas: 4433-40-3).Computed Properties of 4433-40-3

The Article related to neurobrucellosis cerebrospinal fluid metabolite biomarker lcms, neurobrucellosis, cerebrospinal fluid, liquid chromatography-mass spectrometry, metabolomics, Placeholder for records without volume info and other aspects.Computed Properties of 4433-40-3

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Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On July 31, 2022, Brown, Catherine L. J.; Montina, Tony; Inglis, G. Douglas published an article.Category: pyrimidines The title of the article was Feather pulp: a novel substrate useful for proton nuclear magnetic resonance spectroscopy metabolomics and biomarker discovery. And the article contained the following:

Noninvasive biomarkers of stress that are predictive of poultry health are needed. Feather pulp is highly vascularized and represents a potential source of biomarkers that has not been extensively explored. We investigated the feasibility and use of feather pulp for novel biomarker discovery using 1H-NMR Spectroscopy (NMR)-based metabolomics. To this end, high quality NMR metabolomic spectra were obtained from chicken feather pulp extracted using either ultrafiltration (UF) or Bligh-Dyer methanol-chloroform (BD) methods. In total, 121 and 160 metabolites were identified using the UF and BD extraction methods, resp., with 71 of these common to both methods. The metabolome of feather pulp differed in broiler breeders that were 1-, 23-, and 45-wk-of-age. Moreover, feather pulp was more difficult to obtain from older birds, indicating that age must be considered when targeting feather pulp as a source of biomarkers. The metabolomic profile of feather pulp obtained from 12-day-old broilers administered corticosterone differed from control birds, indicating that the metabolome of feather pulp was sensitive to induced physiol. stress. A comparative examination of feather pulp and serum in broilers revealed that the feather pulp metabolome differed from that of serum but provided more information. The study findings show that metabolite biomarkers in chicken feather pulp may allow producers to effectively monitor stress, and to objectively develop and evaluate on-farm mitigations, including practices that reduce stress and enhance bird health. The experimental process involved the reaction of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione(cas: 4433-40-3).Category: pyrimidines

The Article related to proton nmr spectroscopy metabolomics biomarker, biomarker, broiler chicken, feather pulp, metabolomics, proton nuclear magnetic resonance spectroscopy, Placeholder for records without volume info and other aspects.Category: pyrimidines

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia