PoLiMeR - Polymers in the Liver: Metabolism and Regulation

In biomedical text mining, named entity recognition (NER) is an important task used to extract information from biomedical articles. Improving the NER’s performance will directly have a positive impact on extracting relations between those entities. In recent years, deep learning has become the main research direction of NER due to the development of effective models. Language transformer models like e.g. BERT are frequently used because they enable the specialisation of models by domain-specific ...

Following on in silico and in vitro work, the effect of MCAD deficiency on CoA metabolism was investigated. Using a recently published HILIC-MS/MS method, free and acylated CoA species could be measured simultaneously in HepG2 MCAD-KO cells. The levels of CoA biosynthesis intermediates and total CoA was also characterised by HPLC in liver samples from MCAD-KO mice exposed to energetic stress (fasting adn cold). qPCR was applied to investigate changes in the CoA metabolism that might constitute ...

Biomedical pre-trained language models (BioPLMs) have been achieving state-of-the-art results for various biomedical text mining tasks. However, prevailing fine-tuning approaches naively train BioPLMs on targeted datasets without considering the class distributions. This is problematic, especially with dealing with imbalanced biomedical gold-standard datasets for named entity recognition (NER). Regardless of the high-performing SOTA fine-tuned NER models, they are biased towards other (O) tags ...

The spatio-temporal model that allows investigating the structure of glycogen in three dimensions . The model is based on a stochastic process that simulates the key enzymatic steps. The model is designed to track the position of all glucose units in time together with the activities of the enzymatic reactions. The four main reactions involved in synthesis and degradation (catalysed by Glycogen Synthase - GYS, Glycogen Branching Enzyme - GBE, Glycogen Phosphorylase – GLP - and Glycogen Debranching ...

Validation of model's ability to predict oxygen consumption flux as measured usign permeabilised cells in an Oroboros Oxygraph. Generates Fig. 2A in the associated publication.

Download "Model_notebooks.rar", unzip, and run: "2, generate-model-Oroboros-validation-[needs(1)]-20221109.nb" and "4, Fig2A-Oroboros-simulation-data-[needs-(1-2-and-3)]-20221109.nb" after running "1, generate-model-20221109.nb"

Validation of model's ability to predict whole-body ketogeneic flux as extracted form Fletcher et al. (2019). Generates Fig. 2B in the associated publication.

Download "Model_notebooks.rar", unzip, and run: "2, generate-model-Oroboros-validation-[needs(1)]-20221109.nb" and "5, Fig2B-ketogenesis-validation-[needs-(1)]-20221109.nb" after running "1, generate-model-20221109.nb"

Testing the model's ability to predict palmitoyl-CoA and octanoyl-CoA dehydrogenation in human liver lysate, with and without anti-MCAD and anti-VLCAD antibodies. Generates Fig. 2 C and D in the associated publication. Data from Aoyama et al. (1995).

Downoad and unzip "Model_notebooks.rar" and run "6, Fig2C+D-ACAD-partitioning-validation-[needs-(1)]-20221109.nb" after running "1, generate-model-20221109.nb".

Minireviews about each enzyme in the mitochindrial beta-oxidation model on which the final parameter choices (fixed-parameter model) and parameter sampling distributions (ensemble) were based.

The behaviour of a published MCAD-KO HepG2 cell line was compared to that of a wild-type HepG2 cell line in terms of the changes in acyl-CoA and acylcarnitine levels (measured by HILIC-MS/MS) and gene expression pertaining to CoA metabolism (characterised by qPCR). Additionally, the incorporation of label from stable isotope-labelled pantothenate (vitamine B5) was over 24 hours of exposure to an energetic stressor was also investigated.

MCAD-KO mice (C57BL/6J background) were exposed to three different conditions: "fed", "fasting", and "fasting + cold". In this study we determined the concentration of various CoA biosynthetic intermediates (including CoA) and the expression of CoA metabolic genes in liver tissue samples from these groups of mice.

Prediction of patient urinary acylcarnitine under metabolic decompensation. Generates Fig. 3, Table 1, and Table S2 in the associated publication.

Download and unzip "Model_notebooks.rar" and run "7, Fig3+4+S1+S3-ACADDs-[needs-(1)]-20221109.nb" after running "1, generate-model-20221109.nb"

Based on odendaal1, a control model is made and compared to model deficient for short-chain acyl-CoA dehydrogenase (SCADD, 0%), medium-chain acyl-CoA dehydrogenase (MCADD, 0%), and very long-chain acyl-CoA dehydrogenase (VLCADD, 10%). With and withou metabolite partitioning, and with a fixed mitohondrial free CoASH. Generates Figures 3, 4, S1, S2, and S3 in the related paper.

Download "Model_notebooks.rar", unzip, and run: "7, Fig3+4+S1+S3-ACADDs-[needs-(1)]-20221109.nb" and "14, ...

Calculation of control and response coefficients. Generates Fig. 5, Fig. S4, and Table S2 in the associated publication.

Download "Model_notebooks.rar", unzip, and run: "8, Fig5-control-coefficients-[needs-(1)]-20221109.nb", "9, TableS2-response-coefficients-[needs-(1)]-20230302.nb", and "15, FigS4-control-coefficients-low-AcetylCoA-[needs-(1)]-20221109.nb" after running "1, generate-model-20221109.nb"

Incrementally increase the activity of some target rescue enzymes from 20% of default expression to 200% of default expression in a control and MCADD model to see if flux and CoASH concentration are rescued. Generates Fig. 6, S5, and S6.

Download "Model_notebooks.rar", unzip, and run "11, Fig6+S5-rescues-[needs-(1-and-10)]-20221109.nb", "10, Fig6B-inset-rescues-(low-acetylCoA)-[needs-(1)]-20221109.nb", and "16, FigS6-rescues-20221109-fixed-[needs-(1)]-CoASH.nb" after running "1, generate-model-20221109.nb" ...

Creation of personalised models of control, symptomatic MCADD, asymptomatic MCADD, and early diagnosis MCADD individuals using fibroblast proteomics to adjust model Vmaxes. Generates Fig. 7 and S7.

Download and unzip "Model_notebooks.rar" and run "13, Fig7-personalised-models-[needs-(1-and-12)]-20221109.nb" after running "1, generate-model-20221109.nb" and "12, Fig7-S7-preprocessing-[needs-(1)-]-20221109.nb".

The expression of various genes related to the CoA metabolism as measured by qPCR.

Incorporation of stable isotope from pantothenate into total and free CoA pools.

Protein measurement used to normalised the oxygen consumption flux measured on an Oroboros oxygraph.

Measured in an Oroboros oxygraph.

Proteomics from MCADD and control individuals' fibroblasts.

Transcriptome analysis suggests a compensatory role of the cofactors coenzyme A and NAD+ in medium-chain acyl-CoA dehydrogenase knockout mice. During fasting, mitochondrial fatty-acid β-oxidation (mFAO) is essential for the generation of glucose by the liver. Children with a loss-of-function deficiency in the mFAO enzyme medium-chain acyl-Coenzyme A dehydrogenase (MCAD) are at serious risk of life-threatening low blood glucose levels during fasting in combination with intercurrent disease. However, ...

We performed network analysis to investigate the dysregulated biological processes in the disease progression and revealed the molecular mechanism underlying NAFLD C57BL/6J mice were fed a standard mouse chow diet and housed in a 12‐h light–dark cycle. From the age of 8 weeks, the mice were then divided into two groups of 5 mice fed with chow diet, 4 mice fed with high-sucrose diet for 3 weeks, respectively. At the age of 11 weeks, we performed a genome-wide transcriptomic analysis on tissue ...

In this study, we used publically available dataset from gene expression omnibus (GEO):

Transcriptomic analysis of liver biopsies that cover the spectrum of nonalcoholic fatty liver disease reveals genes that are progressively regulated over the course of the disease. This study demonstrates that progressive changes in expression of these genes can be used to approximate the histological grade of a liver biopsy. Furthermore, the relative progression profiles of these disease-responsive genes are ...

In this study, we used publically available dataset from gene expression omnibus (GEO):

The pathophysiological mechanisms that drive non-alcoholic fatty liver disease (NAFLD) progression remain poorly understood. This multicenter study characterized the transcriptional changes that occur as liver disease progresses. 216 snap frozen liver biopsies, comprising 206 NAFLD cases with different fibrosis stages and 10 controls were studied. Samples underwent high-throughput RNA sequencing. This study ...

Unzip model notebooks and keep in the same folder. Notebook "0, generate_model.nb" needs to be run before the others can be, as the model needs to be exported as Excel files before they cvan be used to make the figures.

This folder contains the python code for developing weighted loss trainer (WeLT) with all the expiremnatal work. Here is the link for our public [GitHub repository] (https://github.com/mobashgr/WELT.git).

Adjusted model to test the model's ability to oxygen consumption rate by permeabilised HepG2 cells in an Oroboros oxygraph. Data from Fletcher et al. (2019).

Adjusted model to test the model's ability to predict palmitoyl-CoA and octanoyl-CoA dehydrogenation in human liver lysate, with and without anti-MCAD and anti-VLCAD antibodies. Data from Aoyama et al. (1995).

Human mitochondrial fatty acid oxidation of saturated, even chain acyl-Coas beginning at C16. See Model description for detail.

Unzip model notebooks and keep in the same folder. Notebook names state which notebooks need to be run before them in order for them to word, e.g. "[needs-(1)]" indicates that the notebook numbered 1 must be run and its exported output generated before the given notebook can work. This has to do with the model being generated in only one notebook to avoid duplication.

Standard Operating Procedure describes the labeling of eukaryotic RNA with aminoallyl labeled nucleotides via first strand cDNA synthesis followed by a coupling of the aminoallyl groups to either Cyanine 3 or 5 (Cy 3/Cy5) fluorescent molecules (published by The Institute For Genomic Research

This guidlines has been developed by Rita Volkers from Wageningen University for IBISBA project, as example to use

FAIRDOM: hands-on basic training

Medium-/short-chain hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35)

Medium-chain ketoacyl-CoA thiolase (EC 2.3.1.16)

Mitochondrial trifunctional protein (UniProt: P40939)

Acyl-CoA thioesterases (EC 3.1.2.1. and EC 3.1.2.2)

L-carnitine as conserved moiety

CoA as conserved moiety

Acetyl-CoA in the mitochondrion as constant metabolite

NADH and NAD+ (Nicotinamide adinine dinucleotide) as constant values.

Oxidised and reduced electron transferring flavoprotein as constant values.

Volume per mg mitochondrial protein of mitochondrion and cytosol.

Carnitine palmitoyltransferase 1 (EC 2.3.1.21)

The theory, calculations, and conditions that went into estimating the Keqs.

Carnitine acylcarnitine translocase (UniProt: O43772)

Carnitine palmitoyltransferase 2 (EC 2.3.1.21)

Carnitine acetyltransferase (EC 2.3.1.7)

Short-chain acyl-CoA dehydrogenase (EC 1.3.99.2)

Medium-chain acyl-CoA dehydrogenase (EC 1.3.99.3)

Very long-chain acyl-CoA dehydrogenase (EC 1.3.8.9)

Crotonase / Enoyl-CoA hydratase (EC 4.2.1.17)

A short description of the experiments conducted to decide on HepG2 cells as the appropriate line for the generation of an MCAD knockout. IHH, Hep3B, HepG2, and HUH-7 cells were all consdered.