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A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule

Authors: K. Meyer, O. Ostrenko, G. Bourantas, H. Morales-Navarrete, N. Porat-Shliom, F. Segovia-Miranda, H. Nonaka, A. Ghaemi, J. M. Verbavatz, L. Brusch, I. Sbalzarini, Y. Kalaidzidis, R. Weigert, M. Zerial

PubMed ID: 28330614

Date Published: 24th Mar 2017

Projects: Showcase LIAM (Liver Image Analysis Based Model)

Journal: Cell Syst

Citation: Cell Syst. 2017 Mar 15. pii: S2405-4712(17)30052-2. doi: 10.1016/j.cels.2017.02.008.

Scales: Liver lobule

Abstract (Expand)

Bile, the central metabolic product of the liver, is transported by the bile canaliculi network. The impairment of bile flow in cholestatic liver diseases has urged a demand for insights into its ...

Created: 25th Jul 2017 at 13:19

Use of Fibonacci numbers in lipidomics - Enumerating various classes of fatty acids

Authors: S. Schuster, M. Fichtner, S. Sasso

PubMed ID: 28071669

Date Published: 11th Jan 2017

Projects: Showcase Steatosis

Journal: Sci Rep

Citation: Sci Rep. 2017 Jan 10;7:39821. doi: 10.1038/srep39821.

Scales: Cell

Abstract (Expand)

In lipid biochemistry, a fundamental question is how the potential number of fatty acids increases with their chain length. Here, we show that it grows according to the famous Fibonacci numbers when ...

Created: 24th Jun 2017 at 17:16

Establishment of a rat model: Associating liver partition with portal vein ligation for staged hepatectomy

Authors: Weiwei Wei, Tianjiao Zhang, Sara Zafarnia, Andrea Schenk, Chichi Xie, Chunyi Kan, Olaf Dirsch, Utz Settmacher, Uta Dahmen

DOI: 10.1016/j.surg.2015.12.005

Date Published: 1st May 2016

Projects: D4: Regeneration and Liver Size, E3: Horizontal integration on organ scale

Journal: Surgery

Citation: Surgery 159(5) : 1299

Scales: Liver

Abstract (Expand)

BACKGROUND: We adapted the anatomically oriented parenchyma-preserving resection technique for associating liver partition with portal vein ligation (PVL) for staged hepatectomy (ALPPS) in rats and ...

Created: 26th May 2017 at 10:46 Last updated: 26th May 2017 at 10:47

Intrahepatic Size Regulation in a Surgical Model: Liver Resection-Induced Liver Regeneration Counteracts the Local Atrophy following Simultaneous Portal Vein Ligation

Authors: Weiwei Wei, Tianjiao Zhang, Haoshu Fang, Olaf Dirsch, Andrea Schenk, André Homeyer, Felix Gremse, Sara Zafarnia, Utz Settmacher, Uta Dahmen

DOI: 10.1159/000446875

Date Published: 5th Jul 2016

Projects: D4: Regeneration and Liver Size, E3: Horizontal integration on organ scale

Journal: Eur Surg Res

Citation: Eur Surg Res 57(1-2) : 125

Scales: Liver

Abstract (Expand)

Background/Aim: Liver size regulation is based on the balance between hepatic regeneration and atrophy. To achieve a better understanding of intrahepatic size regulation, we explored the size regulation ...

Created: 26th May 2017 at 10:43 Last updated: 26th May 2017 at 10:45

Quantification of Hepatic Vascular and Parenchymal Regeneration in Mice

Authors: Chichi Xie, Lars Ole Schwen, Weiwei Wei, Andrea Schenk, Sara Zafarnia, Felix Gremse, Uta Dahmen

DOI: 10.1371/journal.pone.0160581

Date Published: 5th Aug 2016

Projects: D4: Regeneration and Liver Size, E3: Horizontal integration on organ scale

Journal: PLoS ONE

Citation: PLoS ONE 11(8) : e0160581

Scales: Liver

Abstract (Expand)

Background. Liver regeneration consists of cellular proliferation leading to parenchymal and vascular growth. This study complements previous studies on cellular proliferation and weight recovery by ...

Created: 26th May 2017 at 09:10 Last updated: 26th May 2017 at 09:12

Model-Based Characterization of Inflammatory Gene Expression Patterns of Activated Macrophages

Authors: Julia Rex, Ute Albrecht, Christian Ehlting, Maria Thomas, Ulrich M. Zanger, Oliver Sawodny, Dieter Häussinger, Michael Ederer, Ronny Feuer, Johannes G. Bode

DOI: 10.1371/journal.pcbi.1005018

Date Published: 27th Jul 2016

Projects: B1: Intercellular communication of hepatocytes and macrophages

Journal: PLoS Comput Biol

Citation: PLoS Comput Biol 12(7) : e1005018

Scales: Cell and Intercellular

Abstract (Expand)

Macrophages are cells with remarkable plasticity. They integrate signals from their microenvironment leading to context-dependent polarization into classically (M1) or alternatively (M2) activated ...

Created: 23rd Nov 2016 at 13:29 Last updated: 23rd Nov 2016 at 13:32

Visualization of Vascular and Parenchymal Regeneration after 70% Partial Hepatectomy in Normal Mice

Authors: Chichi Xie, Weiwei Wei, Andrea Schenk, Lars Ole Schwen, Sara Zafarnia, Michael Schwier, Felix Gremse, Isabel Jank, Olaf Dirsch, Uta Dahmen

DOI: 10.3791/53935

Date Published: 2016

Projects: D1: Regulation of Blood Flow and Perfusion in the Liver, D4: Regeneration and Liver Size, E3: Horizontal integration on organ scale, E4: Vertical integration across biological scales

Journal: JoVE

Citation: JoVE (115)

Scales: Liver

Abstract (Expand)

A modified silicone injection procedure was used for visualization of the hepatic vascular tree. This procedure consisted of in-vivo injection of the silicone compound, via a 26 G catheter, into the ...

Created: 14th Sep 2016 at 10:17 Last updated: 14th Sep 2016 at 10:20

Inhibition of bile salt transport by drugs associated with liver injury in primary hepatocytes from human, monkey, dog, rat, and mouse

Authors: J. Zhang, K. He, L. Cai, Y. C. Chen, Y. Yang, Q. Shi, T. F. Woolf, W. Ge, L. Guo, J. Borlak, W. Tong

PubMed ID: 27000539

Date Published: 24th Mar 2016

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: Chem Biol Interact

Citation: Chem Biol Interact. 2016 Mar 19. pii: S0009-2797(16)30089-8. doi: 10.1016/j.cbi.2016.03.019.

Scales: Cell

Abstract (Expand)

Interference of bile salt transport is one of the underlying mechanisms for drug-induced liver injury (DILI). We developed a novel bile salt transport activity assay involving in situ biosynthesis of ...

Created: 18th May 2016 at 10:56

Immunogenomics reveal molecular circuits of diclofenac induced liver injury in mice

Authors: E. H. Lee, J. H. Oh, S. Selvaraj, S. M. Park, M. S. Choi, R. Spanel, S. Yoon, J. Borlak

PubMed ID: 26934552

Date Published: 5th Mar 2016

Projects: A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: Oncotarget

Citation: Oncotarget. 2016 Feb 25. doi: 10.18632/oncotarget.7698.

Scales: Liver

Abstract (Expand)

Diclofenac is a non-steroidal anti-inflammatory drug and its use can be associated with severe adverse reactions, notably myocardial infarction, stroke and drug-induced liver injury (DILI). In pursue ...

Created: 18th May 2016 at 10:52

Mechanistically linked serum miRNAs distinguish between drug induced and fatty liver disease of different grades

Authors: Z. Liu, Y. Wang, J. Borlak, W. Tong

PubMed ID: 27045805

Date Published: 6th Apr 2016

Projects: A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: Sci Rep

Citation: Sci Rep. 2016 Apr 5;6:23709. doi: 10.1038/srep23709.

Scales: Liver

Abstract (Expand)

Hepatic steatosis is characterised by excessive triglyceride accumulation in the form of lipid droplets (LD); however, mechanisms differ in drug induced (DIS) and/or non-alcoholic fatty liver disease ...

Created: 18th May 2016 at 10:50

Zonated Quantification of Steatosis in an Entire Mouse Liver

Authors: Lars Ole Schwen, André Homeyer, Michael Schwier, Uta Dahmen, Olaf Dirsch, Arne Schenk, Lars Kuepfer, Tobias Preusser, Andrea Schenk

DOI: 10.1016/j.compbiomed.2016.04.004

Date Published: 1st Apr 2016

Projects: C1: The role of blood flow in liver lobule function and morphology, D1: Regulation of Blood Flow and Perfusion in the Liver, E3: Horizontal integration on organ scale, E4: Vertical integration across biological scales, Showcase Steatosis

Journal: Computers in Biology and Medicine

Citation: Computers in Biology and Medicine

Scales: Cell, Liver lobule, Liver and Organism

Abstract (Expand)

Many physiological processes and pathological conditions in livers are spatially heterogeneous, forming patterns at the lobular length scale or varying across the organ. Steatosis, a common liver disease ...

Created: 13th Apr 2016 at 15:13 Last updated: 13th Apr 2016 at 15:16

Intrahepatic Vascular Anatomy in Rats and Mice—Variations and Surgical Implications

Authors: Constanze Sänger, Andrea Schenk, Lars Ole Schwen, Lei Wang, Felix Gremse, Sara Zafarnia, Fabian Kiessling, Chichi Xie, Weiwei Wei, Beate Richter, Olaf Dirsch, Uta Dahmen

DOI: 10.1371/journal.pone.0141798

Date Published: 30th Nov 2015

Projects: D1: Regulation of Blood Flow and Perfusion in the Liver, D4: Regeneration and Liver Size, E3: Horizontal integration on organ scale, E4: Vertical integration across biological scales

Journal: PLoS ONE

Citation: PLoS ONE 10(11) : e0141798

Scales: Liver

Abstract (Expand)

Introduction The intra-hepatic vascular anatomy in rodents, its variations and corresponding supplying and draining territories in respect to the lobar structure of the liver have not been described. ...

Created: 13th Jan 2016 at 08:00 Last updated: 13th Jan 2016 at 08:03

The evolution of standards and data management practices in systems biology

Authors: N. J. Stanford, K. Wolstencroft, M. Golebiewski, R. Kania, N. Juty, C. Tomlinson, S. Owen, S. Butcher, H. Hermjakob, N. Le Novere, W. Mueller, J. Snoep, C. Goble

PubMed ID: 26700851

Date Published: 25th Dec 2015

Projects: F1: The data management system, Virtual Liver

Journal: Mol Syst Biol

Citation: Mol Syst Biol. 2015 Dec 23;11(12):851. doi: 10.15252/msb.20156053.

Scales: Not specified

Abstract:

Not specified

Created: 8th Jan 2016 at 09:38

Coordinating Role of RXRα in Downregulating Hepatic Detoxification during Inflammation Revealed by Fuzzy-Logic Modeling

Authors: Roland Keller, Marcus Klein, Maria Thomas, Andreas Dräger, Ute Metzger, Markus F. Templin, Thomas O. Joos, Wolfgang E. Thasler, Andreas Zell, Ulrich M. Zanger

DOI: 10.1371/journal.pcbi.1004431

Date Published: 4th Jan 2016

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Journal: PLoS Comput Biol

Citation: PLoS Comput Biol 12(1) : e1004431

Scales: Cell

Abstract (Expand)

During various inflammatory processes circulating cytokines including IL-6, IL-1β, and TNFα elicit a broad and clinically relevant impairment of hepatic detoxification that is based on the downregulation ...

Created: 7th Jan 2016 at 15:20 Last updated: 7th Jan 2016 at 15:24

Evaluation of multiple mechanism-based toxicity endpoints in primary cultured human hepatocytes for the identification of drugs with clinical hepatotoxicity: Results from 152 marketed drugs with known liver injury profiles

Authors: J. Zhang, U. Doshi, A. Suzuki, C. W. Chang, J. Borlak, A. P. Li, W. Tong

PubMed ID: 26581450

Date Published: 20th Nov 2015

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions

Journal: Chem Biol Interact

Citation: Chem Biol Interact. 2015 Nov 12. pii: S0009-2797(15)30110-1. doi: 10.1016/j.cbi.2015.11.008.

Scales: Cell

Abstract (Expand)

We report here the results of a collaborative research program to develop a robust and reliable in vitro system to allow an accurate definition of the drug-induced liver injury (DILI) potential of new ...

Created: 30th Dec 2015 at 10:41

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study

Authors: J. M. Villaveces, R. C. Jimenez, P. Porras, N. Del-Toro, M. Duesbury, M. Dumousseau, S. Orchard, H. Choi, P. Ping, N. C. Zong, M. Askenazi, B. H. Habermann, H. Hermjakob

PubMed ID: 25652942

Date Published: No date defined

Projects: A1.3: Identification of crucial metabolic processes during hepatocyte pr..., A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.5: The impact of cell polarity on metabolism detoxification and endoc..., C2: Organization of the sinusoidal system and the liver lobule - referen..., C5: Structural changes and functional consequences of the liver lobular/..., C6: Organization and function of the sinusoidal system and the liver lob...

Journal: Database (Oxford)

Citation: Database (Oxford). 2015 Feb 4;2015. pii: bau131. doi: 10.1093/database/bau131. Print 2015.

Scales: Not specified

Abstract (Expand)

The evidence that two molecules interact in a living cell is often inferred from multiple different experiments. Experimental data is captured in multiple repositories, but there is no simple way to ...

Created: 18th Dec 2015 at 12:58

Tools for visualization and analysis of molecular networks, pathways, and -omics data

Authors: J. M. Villaveces, P. Koti, B. H. Habermann

PubMed ID: 26082651

Date Published: 4th Jun 2015

Journal: Adv Appl Bioinform Chem

Citation: Adv Appl Bioinform Chem. 2015 Jun 4;8:11-22. doi: 10.2147/AABC.S63534. eCollection 2015.

Scales: Not specified

Abstract (Expand)

Biological pathways have become the standard way to represent the coordinated reactions and actions of a series of molecules in a cell. A series of interconnected pathways is referred to as a biological ...

Created: 18th Dec 2015 at 12:57

Virtual pathway explorer (viPEr) and pathway enrichment analysis tool (PEANuT): creating and analyzing focus networks to identify cross-talk between molecules and pathways

Authors: M. Garmhausen, F. Hofmann, V. Senderov, M. Thomas, B. A. Kandel, B. H. Habermann

PubMed ID: 26467653

Date Published: 14th Oct 2015

Journal: BMC Genomics

Citation: BMC Genomics. 2015 Oct 14;16(1):790. doi: 10.1186/s12864-015-2017-z.

Scales: Not specified

Abstract (Expand)

BACKGROUND: Interpreting large-scale studies from microarrays or next-generation sequencing for further experimental testing remains one of the major challenges in quantitative biology. Combining ...

Created: 18th Dec 2015 at 12:55

Development of Human Membrane Transporters: Drug Disposition and Pharmacogenetics

Authors: M. G. Mooij, A. T. Nies, C. A. Knibbe, E. Schaeffeler, D. Tibboel, M. Schwab, S. N. de Wildt

PubMed ID: 26410689

Date Published: 28th Sep 2015

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development

Journal: Clin Pharmacokinet

Citation: Clin Pharmacokinet. 2015 Sep 26.

Scales: Not specified

Abstract (Expand)

Membrane transporters play an essential role in the transport of endogenous and exogenous compounds, and consequently they mediate the uptake, distribution, and excretion of many drugs. The clinical ...

Created: 17th Dec 2015 at 11:53

Impact of Genetic Polymorphisms of ABCB1 (MDR1, P-Glycoprotein) on Drug Disposition and Potential Clinical Implications: Update of the Literature

Authors: S. Wolking, E. Schaeffeler, H. Lerche, M. Schwab, A. T. Nies

PubMed ID: 25860377

Date Published: 11th Apr 2015

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development

Journal: Clin Pharmacokinet

Citation: Clin Pharmacokinet. 2015 Jul;54(7):709-35. doi: 10.1007/s40262-015-0267-1.

Scales: Not specified

Abstract (Expand)

ATP-binding cassette transporter B1 (ABCB1; P-glycoprotein; multidrug resistance protein 1) is an adenosine triphosphate (ATP)-dependent efflux transporter located in the plasma membrane of many different ...

Created: 17th Dec 2015 at 11:51

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