scholarly journals Deep metabolic profiling assessment of tissue extraction protocols for three model organisms

2021 ◽  
Author(s):  
Hagen M. Gegner ◽  
Nils Mechtel ◽  
Elena Heidenreich ◽  
Angela Wirth ◽  
Fabiola Garcia Cortizo ◽  
...  
Keyword(s):  
Metabolic Profiling ◽  
Human Studies ◽  
Model Organisms ◽  
Butyl Ether ◽  
Data Set ◽  
Tertiary Butyl ◽  
Analytical Technique ◽  
New Associations ◽  
Extraction Protocol ◽  
Shiny App

Metabolic profiling harbors the potential to better understand various disease entities such as cancer, diabetes, Alzheimer's, Parkinson's disease or COVID-19. Deciphering these intricate pathways in human studies requires large sample sizes as a means of reducing variability. While such broad human studies have discovered new associations between a given disease and certain affected metabolites, i.e. biomarkers, they often provide limited functional insights. To design more standardized experiments, reduce variability in the measurements and better resolve the functional component of such dynamic metabolic profiles, model organisms are frequently used. Standardized rearing conditions and uniform sampling strategies are prerequisites towards a successful metabolomic study. However, further aspects such as the choice of extraction protocol and analytical technique can influence the outcome drastically. Here, we employed a highly standardized metabolic profiling assay analyzing 630 metabolites across three commonly used model organisms (Drosophila, mouse and Zebrafish) to find the optimal extraction protocols for various matrices. Focusing on parameters such as metabolite coverage, metabolite yield and variance between replicates we compared seven extraction protocols. We found that the application of a combination of 75% ethanol and methyl tertiary-butyl ether (MTBE), while not producing the broadest coverage and highest yields, was the most reproducible extraction protocol. We were able to determine up to 530 metabolites in mouse kidney samples, 509 in mouse liver, 422 in Zebrafish and 388 in Drosophila and discovered a core overlap of 261 metabolites in these four matrices. To enable other scientists to search for the most suitable extraction protocol in their experimental context and interact with this comprehensive data, we have integrated our data set in the open-source shiny app MetaboExtract. This will enable scientists to search for their metabolite or metabolite class of interest, compare it across the different tested extraction protocols and sample types as well as find reference concentrations.

APPLICATION OF IR SPECTROSCOPY IN THE STUDY OF MINERAL OIL

2017 ◽  
pp. 91-95
Author(s):  
E. I. Grushova ◽  
A. .. Al Razuqi ◽  
E. S. Chaiko ◽  
O. A. Miloserdova
Keyword(s):  
Ir Spectroscopy ◽  
Group Composition ◽  
Mineral Oil ◽  
Vacuum Distillate ◽  
Methyl Tertiary Butyl Ether ◽  
Butyl Ether ◽  
Tertiary Butyl ◽  
Mineral Oils ◽  
Modifying Additive

IR spectroscopy investigated structural and group composition of base mineral oils isolated from the vacuum distillate by selective purification of N-methylpyrrolidone and the low temperature dewaxing in the presence of a solvent. The role of the latter was carried out by the systems acetone - toluene, acetone - methyl tertiary butyl ether, methyl ethyl ketone - toluene, acetone - toluene - modifying additive. It was shown that the chemical composition of the group of base oils and slack waxes is defined as the nature of the solvent to the dewaxing, and oils sequence of purification steps.

scholarly journals BREC: an R package/Shiny app for automatically identifying heterochromatin boundaries and estimating local recombination rates along chromosomes

2021 ◽  
Vol 22 (S6) ◽  
Author(s):  
Yasmine Mansour ◽  
Annie Chateau ◽  
Anna-Sophie Fiston-Lavier
Keyword(s):  
Data Quality ◽  
Data Science ◽  
Fruit Fly ◽  
R Package ◽  
Model Organisms ◽  
Data Quality Control ◽  
Recombination Rates ◽  
Functional Dynamics ◽  
Shiny App ◽  
User Friendly

Abstract Background Meiotic recombination is a vital biological process playing an essential role in genome's structural and functional dynamics. Genomes exhibit highly various recombination profiles along chromosomes associated with several chromatin states. However, eu-heterochromatin boundaries are not available nor easily provided for non-model organisms, especially for newly sequenced ones. Hence, we miss accurate local recombination rates necessary to address evolutionary questions. Results Here, we propose an automated computational tool, based on the Marey maps method, allowing to identify heterochromatin boundaries along chromosomes and estimating local recombination rates. Our method, called BREC (heterochromatin Boundaries and RECombination rate estimates) is non-genome-specific, running even on non-model genomes as long as genetic and physical maps are available. BREC is based on pure statistics and is data-driven, implying that good input data quality remains a strong requirement. Therefore, a data pre-processing module (data quality control and cleaning) is provided. Experiments show that BREC handles different markers' density and distribution issues. Conclusions BREC's heterochromatin boundaries have been validated with cytological equivalents experimentally generated on the fruit fly Drosophila melanogaster genome, for which BREC returns congruent corresponding values. Also, BREC's recombination rates have been compared with previously reported estimates. Based on the promising results, we believe our tool has the potential to help bring data science into the service of genome biology and evolution. We introduce BREC within an R-package and a Shiny web-based user-friendly application yielding a fast, easy-to-use, and broadly accessible resource. The BREC R-package is available at the GitHub repository https://github.com/GenomeStructureOrganization.

The Effect of Adding Oxygenated Compounds to Gasoline on Automotive Exhaust Emissions

2002 ◽  
Vol 125 (1) ◽  
pp. 344-350 ◽  
Author(s):  
S. G. Poulopoulos ◽  
C. J. Philippopoulos
Keyword(s):  
Octane Number ◽  
Combustion Engine ◽  
Methyl Tertiary Butyl Ether ◽  
Butyl Ether ◽  
Tertiary Butyl ◽  
Research Octane Number ◽  
Oxygenated Compounds ◽  
Reid Vapor Pressure ◽  
Three Way Catalyst ◽  
Unregulated Emissions

In the present work, the effect of adding ethanol or methyl tertiary butyl ether (MTBE) to gasoline on the regulated and unregulated emissions from an internal combustion engine with a typical three-way catalyst was studied. The addition of ethanol to fuel (10% w/w) increased both the research octane number and the Reid vapor pressure of the fuel, whereas adding 11% w/w MTBE caused an increase only in the research octane number of the fuel. When the fuel contained MTBE, less hydrocarbons, carbon monoxide, and acetaldehyde were emitted in the tailpipe. The increased emissions of acetaldehyde and ethanol were the main disadvantages of using ethanol.

scholarly journals Can We Protect Everybody from Drinking Water Contaminants?

2002 ◽  
Vol 21 (5) ◽  
pp. 389-395 ◽  
Author(s):  
Robert A. Howd
Keyword(s):  
Drinking Water ◽  
The Elderly ◽  
Butyl Ether ◽  
Water Contaminants ◽  
Tertiary Butyl ◽  
Health Goals ◽  
Fuel Tanks ◽  
Beneficial Uses ◽  
Alkyl Benzenes

Dozens of chemicals, both natural and manmade, are often found in drinking water. Some, such as the natural contaminants uranium and arsenic, are well-known toxicants with a large toxicology database. Other chemicals, such as methyl tertiary-butyl ether (MTBE) from leaking fuel tanks, we learn about as we go along. For still others, such as the alkyl benzenes, there are very little available data, and few prospects of obtaining more. In some cases, chemicals are purposely added to drinking water for beneficial purposes (e.g., chlorine, fluoride, alum), which may cause a countervailing hazard. Removing all potentially toxic chemicals from the water is virtually impossible and is precluded for beneficial uses and for economic reasons. Determination of safe levels of chemicals in drinking water merges the available toxicity data with exposure and human effect assumptions into detailed hazard assessments. This process should incorporate as much conservatism as is needed to allow for uncertainty in the toxicity and exposure estimates. Possible sensitive subpopulations such as unborn children, infants, the elderly, and those with common diseases such as impaired kidney function must also be considered. However, the range of sensitivity and the variability of toxicity and exposure parameters can never be fully documented. In addition, the validity of the low-dose extrapolations, and whether the toxic effect found in animals occurs at all in humans, is never clear. This publication discusses how these competing needs and uncertainties intersect in the development of Public Health Goals for uranium, fluoride, arsenic, perchlorate, and other highly debated chemicals.

Remediation of MTBE-contaminated groundwater by integrated circulation wells and advanced oxidation technologies

2017 ◽  
Vol 18 (2) ◽  
pp. 399-407 ◽  
Author(s):  
Bassam Tawabini ◽  
Mohammed Makkawi
Keyword(s):  
Groundwater Remediation ◽  
Treatment Time ◽  
Shallow Groundwater ◽  
Advanced Oxidation ◽  
Shallow Aquifer ◽  
Contaminated Groundwater ◽  
Butyl Ether ◽  
Tertiary Butyl ◽  
Industrial Facilities ◽  
Environmental Threats

Abstract The proximity of shallow groundwater systems to sources of contamination usually exposes them to severe environmental threats. Hazardous pollutants that leak from gas stations, landfills, and industrial facilities may eventually reach the underneath shallow groundwater aquifers, posing risks to human health and the environment. Cleaning contaminated groundwater sources has always been a challenge to the local authorities. This is even more challenging when dealing with difficult pollutants such as methyl tertiary butyl ether (MTBE) due its high solubility in water, poor biodegradability, and poor adsorption onto solids. This study aims to assess the efficiency of a pilot groundwater remediation system to treat a shallow aquifer contaminated with MTBE. The in-house designed and fabricated pilot system combines the technology of circulation wells and UV-based advanced oxidation technology for the breakdown and removal of MTBE from water. An ultraviolet/hydrogen peroxide (UV/H2O2) process was used in this study to remove MTBE from water. The concentration of MTBE was reduced from approximately 1,400 μg/L to as low as 34 μg/L within 30 minutes, with a treatment efficiency of about 98%. The study also assesses the effects of the UV intensity and the treatment time needed to remove the target pollutant.

Methyl tertiary-butyl ether mode of action for cancer endpoints in rodents

2007 ◽  
Vol 47 (2) ◽  
pp. 156-165 ◽  
Author(s):  
George Cruzan ◽  
Susan J. Borghoff ◽  
Ann de Peyster ◽  
Gordon C. Hard ◽  
Michael McClain ◽  
...  
Keyword(s):  
Mode Of Action ◽  
Methyl Tertiary Butyl Ether ◽  
Butyl Ether ◽  
Tertiary Butyl

Simulation of Methyl Tertiary Butyl Ether Production in Catalytic Distillation

2012 ◽  
Vol 263-266 ◽  
pp. 444-447
Author(s):  
Jin Nan Chen ◽  
Yu Chun Zhang ◽  
Xing Yong Sun
Keyword(s):  
Relative Error ◽  
Conversion Rate ◽  
Model Development ◽  
Methyl Tertiary Butyl Ether ◽  
Reflux Ratio ◽  
Distillation Process ◽  
Butyl Ether ◽  
Catalytic Distillation ◽  
Design Data ◽  
Tertiary Butyl

The software of the catalytic distillation process of methyl tertiary butyl ether was developed by using Process Simulation System Platform. The isobutylene conversion rate was calculated by using the catalytic distillation software. The relative error of isobutylene conversion rate between the simulation results and the design data from the China Petroleum Hohhot Petrochemical Co. was less than 5%. The relative error satisfies industrial design requirements. At present, enterprise workers use this software to learn how to operate the catalytic distillation process. The catalytic distillation software is further used to study the influence of reaction temperature and reflux ratio on the isobutylene conversion rate which can be used for future empirical model development and control studies.

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