1 Role of the IKK complex during liver regeneration Analysis of the differential role of IKKβ/IKK2 and IKKγ/Nemo during liver regeneration Von der Fakultät für Mathematik, Informatik und Naturwissenschaften der RWTH Aachen University zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigte Dissertation vorgelegt von Master of Science Yann Malato aus Bordeaux (Frankreich) Berichter: Universitätsprofessor Dr. med. Christian Trautwein Universitätsprofessor Dipl. Ing. Dr. Werner Baumgartner Tag der mündlichen Prüfung: 24. November 2009 Diese Dissertation ist auf den Internetseiten der Hochschulbibliothek online verfügbar.
2 "Check your heart, free your soul, never give up" Mike Muir
3 Teile dieser Arbeit wurden bereits vorab veröffentlicht oder zur Publikation eingereicht: Y. Malato, N. Beraza, N. Gassler, M. Al-Masaoudi, C. Liedtke, C. Trautwein activation of progenitor cells triggers the repopulation of conditional nemo KO livers during liver regeneration in mice Journal of Hepatology, April 2009 (Vol. 50, Page S310) Poster n th Annual Meeting of the European Association for the Study of the Liver (EASL), Copenhagen, Denmark. Y. Malato, L. E. Sander, C. Liedtke, M. Al-Masaoudi, F. Tacke, C. Trautwein, N. Beraza Hepatocyte-specific inhibitor-of-kappab-kinase deletion triggers the innate immune response and promotes earlier cell proliferation during liver regeneration Hepatology Jun;47(6): Y. Malato, N. Beraza, L.E. Sander, M. Almasaoudi, C. Liedtke, C. Trautwein Hepatocyte specific IKK2 deletion causes imbalanced NF-κB activation after partial hepatectomy and leads to an earlier resolution of liver damage Journal of Hepatology, April 2008 (Vol. 48, Page S58) Oral Presentation n rd Annual Meeting of the European Association for the Study of the Liver (EASL), Milan, Italy. Y. Malato, N. Beraza, L.E. Sander, M. Almasaoudi, C. Liedtke, C. Trautwein Enhanced innate immune response and accelerated liver regeneration in hepatocytespecific IKK2 deleted mice Hepatology 46, November Oral presentation n th Annual Meeting of the American Association for the Study of Liver Diseases (AASLD), Boston, MA, USA.
4 Y. Malato, N. Beraza, M. Pasparakis, C. Trautwein IKK2 hepatocyte specific deletion alters cell cycle progression after partial hepatectomy Journal of Hepatology, April 2007 (Vol. 46, Page S21) Oral presentation n 44 42nd Annual Meeting of the European Association for the Study of the Liver (EASL), Barcelona, Spain.
5 Table of Contents I Table of Contents 1. INTRODUCTION PHYSIOLOGY AND CENTRAL FUNCTION OF THE LIVER LIVER REGENERATION NF-ΚB, IKK2, NEMO AND LIVER REGENERATION THE CELL CYCLE INVOLVEMENT OF THE INNATE IMMUNE RESPONSE DURING LIVER REGENERATION REACTIVE OXYGEN SPECIES KNOCKOUT TECHNOLOGY AND TRANSGENIC MICE Generation of conditional IKK2 knockout mice Generation of conditional Nemo knockout mice AIM OF THE STUDY MATERIAL AND METHODS CHEMICALS Radiochemicals INSTRUMENTS AND EQUIPMENT CONSUMABLES General material Material for animal experimentation Material for cell culture and flow cytometry ELISA and MACS kits Antibodies Non-labeled primary antibodies Labeled primary antibodies Secondary antibodies Enzymes ANALYTICAL CHEMICALS, REAGENTS AND KITS ANIMALS Animal breeding Partial hepatectomy Blood taking Systemic IKK2 inhibition Oval cell expansion (DDC diet)... 28
6 Table of Contents II Antioxidant treatment (BHA diet) Oxidative stress induction (PEITC injection) Isolation of primary hepatocytes Cell isolation and flow cytometry RNA ISOLATION Isolation of RNA from liver tissue Isolation of RNA from cell culture Determination of RNA concentration Reverse Transcription (RT-PCR) Real-Time PCR ISOLATION AND CHARACTERIZATION OF PROTEINS Protein extraction from liver tissue and primary hepatocytes Quantification of proteins by Bradford Assay c-jun-n-terminal-kinase activity assay Zymography GENOTYPING Buffer PCR protocols and programs PRIMERS LIST Genotyping primers (5 -> 3 ) Real-Time PCR primers GENERAL PROTOCOL FOR IMMUNOFLUORESCENCE BrdU and Histone H3 staining CK19 staining TUNEL assay DHE staining IMMUNOHISTOCHEMISTRY ANALYSIS Image analysis Flow cytometry analysis Statistical analysis RESULTS PART I IKK2 HEPATOCYTE-SPECIFIC DELETION MODIFIES IΚB-α PHOSPHORYLATION AND NF-ΚB ACTIVATION AFTER PH LACK OF HEPATOCYTE IKK2 PROMOTES EARLIER CELL CYCLE ENTRY AFTER PH 47
7 Table of Contents III 3.3. EARLIER S-PHASE PROGRESSION AND HEPATOCYTE PROLIFERATION IN IKK2 ΔHEPA MICE AFTER PH PROLONGED MITOTIC PHASE IN IKK2 ΔHEPA MICE AFTER PH STRONGER CXCL1 AND ACUTE PHASE GENE EXPRESSION IN IKK2 ΔHEPA MICE AFTER PH IKK2 ΔHEPA MICE SHOW ENHANCED RECRUITMENT OF INFLAMMATORY CELLS AFTER PH SYSTEMIC IKK2 INHIBITION WITH AS DOES NOT AFFECT HEPATOCYTE PROLIFERATION AFTER PH RESULTS PART II NEMO ΔHEPA MICE DIE MASSIVELY AFTER PARTIAL HEPATECTOMY HEPATOCYTE SPECIFIC DELETION OF NEMO MODIFIES THE PROLIFERATIVE RESPONSE AFTER PARTIAL HEPATECTOMY PARTIAL HEPATECTOMY LEADS TO A STRONG OVAL CELL RESPONSE IN NEMO ΔHEPA MICE IMPAIRED PRIMING PHASE IN NEMO ΔHEPA MICE OXIDATIVE STRESS-INDUCED DNA DAMAGE IN NEMO ΔHEPA MICE INCREASED LIVER DAMAGE IN NEMO ΔHEPA MICE AFTER PARTIAL HEPATECTOMY LIVER PHENOTYPE IN NEMO ΔHEPA MICE AT LATE TIME POINTS AFTER PARTIAL HEPATECTOMY PARTIAL HEPATECTOMY LEADS TO COUNTER SELECTION OF CRE NEGATIVE OVAL CELLS ,5-DICARBETHOXY-1,4-DIHYDROCOLLIDINE DIET MODEL (DDC) IN NEMO ΔHEPA MICE HIGHER LIVER DAMAGE IN NEMO ΔHEPA DDC FED MICE PRE-OVAL CELL EXPANSION IMPROVES THE SURVIVAL OF NEMO ΔHEPA MICE AFTER PARTIAL HEPATECTOMY MODULATING OXIDATIVE STRESS IN MICE OXIDATIVE STRESS LEVEL DETERMINES THE OUTCOME OF NEMO ΔHEPA MICE AFTER PARTIAL HEPATECTOMY THE CELLULAR REDOX HOMEOSTASIS IS ALTERED IN NEMO ΔHEPA MICE OXIDATIVE STRESS TRIGGERS LIVER REGENERATION AND OVAL CELL EXPANSION SURVIVAL OF NEMO ΔHEPA MICE AFTER PARTIAL HEPATECTOMY DEPENDS ON OVAL CELL ACTIVATION AND THE OXIDATIVE STRESS STATUS IN THE LIVER... 98
8 Table of Contents IV 5. DISCUSSION HEPATOCYTE-SPECIFIC IKK2 DELETION TRIGGERS THE INNATE IMMUNE RESPONSE AND PROMOTES EARLIER CELL PROLIFERATION DURING LIVER REGENERATION MOLECULAR DISSECTION OF NEMO-DEPENDENT PATHWAYS IN HEPATOCYTES DURING LIVER REGENERATION IL-6, STAT3 and hepatoprotection Stem Cells and liver regeneration NF-κB, oxidative stress and liver regeneration Oxidative stress modulation, cancer and liver surgery NF-κB modulation during liver regeneration REFERENCES SUMMARY... V 8. RESUME... VI 9. ABBREVIATIONS... VIII 10. EIDESSTATTLICHE ERKLÄRUNG... XIV 11. ACKNOWLEDGEMENT... XVI 12. LEBENSLAUF... XVIII
9 Introduction 1 1. Introduction Having stolen the secret of fire from the gods of Olympus, Prometheus drew down on himself the anger of Zeus, the ruler of gods and men. Zeus punished Prometheus by chaining him to Mount Caucasus where he was tormented by an eagle. The eagle preyed on Prometheus liver, which was renewed as fast as it was devoured. Adapted from Bulfinch s Mythology 1.1. Physiology and central function of the liver The liver is the largest glandular organ of the mammalian body. It plays a central role in metabolic homeostasis and it serves as the primary regulatory site for energy metabolism, synthesizes essential proteins, enzymes and co-factors for digestion and regulation of metabolic functions. Essential functions are formation and secretion of bile acid, regulation of ammonia, iron and bicarbonate homeostasis and synthesis of most plasma proteins. Additionally, the liver has an important role as the major detoxifying organ, eliminating a variety of endogenous and exogenous compounds. Finally, providing important immunologic function, the liver is the central organ for phagocytosis of macromolecules and microorganisms such as bacteria. As the first line of defence against ingested toxins and many infectious agents, the liver has evolutionarily conserved responses including the ability to regenerate and to protect itself against injury. Due to the extensive functions, the ultrastructure of the liver consists of various cell populations of complex organisation. The most abundant cell type by mass and number are hepatocytes constituting 80% of the lobular parenchyma and form the largest cell population in the liver. The hepatocyte is a polarized epithelial cell consisting of three different specialized membrane domains: the basolateral (sinusoidal), a specialized bile canalicular and the intercellular domain, containing tight junctions, gap junctions and desmosomes. In dependence on age, metabolic load, location of the cell and regenerative activity hepatocytes vary in shape and size. The typical shape of hepatocytes is an irregular polyhedral with a size ranging from 20 to 30 µm (Motta 1977; Motta 1984). The nucleus of the hepatocyte constitutes 5 to 10 percent of cell volume, is spherical in shape and contains one or more prominent nucleoli. Twenty-five percent of hepatocytes are
10 Introduction 2 binucleate. The nuclear size is correlated with nuclear ploidy; approximately 15% of hepatocytes are tetraploid (Gupta 2000). Hepatocytes develop from a primitive precursor cell called hepatoblast derived from endodermal outgrowth of the hepatic diverticulum, which gives rise to hepatocytes and parenchymal cells. Characteristic for the hepatoblast is the synthesis of α-fetoprotein (AFP) starting in the human liver as early as day 19. In contrast, expression of the most prominent liver-specific secreted protein albumin starts later. The induction of albumin increases in parallel with the decrease of AFP gene expression. As the most typical marker for early stages of liver development the expression of AFP stops almost completely after birth (Sala-Trepat, Dever et al. 1979; Hatano, Nakata et al. 1992). The liver also consists of nonparenchymal cells, like resident immune cells including Kupffer cells, NK and NKT cells, T-lymphocytes and the population of mesenchymal cells, providing stellate cells, liver myofibroblasts and specialized cells like sinusoidal endothelial cells and cholangiocytes. In addition to these common cells, a last population of cells can be found in damaged livers only, the progenitors cells of the liver also called oval cells (Fausto 2004) Liver regeneration The healthy liver is a quiescent organ in terms of proliferation with a very low cell-turnover. However, after injury caused by surgical resection, chemicals or viral infections the liver can restore its mass and cell function due to hepatocyte proliferation. As a general rule, replication of existing hepatocytes is the quickest and most efficient way to generate hepatocytes for liver regeneration and repair. Oval cells usually replicate and differentiate into hepatocytes only when the replication of mature hepatocytes is delayed or entirely blocked (Wang, Foster et al. 2003). The most common method to study liver regeneration in rodents is partial hepatectomy (PH) of two-thirds (70%) of the liver as described by Higgins and Anderson (1931). This model allows the analysis of cell proliferation in vivo and enhances the understanding of regulating Cyclins and Cdks and the arrangement of protein complexes. Although the adult liver contains cells with "stem-cell" properties, regeneration is accomplished by replication of mature hepatocytes. The hepatocyte is a unique cell that is highly differentiated but remains capable of replication. After PH, the remaining
11 Introduction 3 hepatocytes leave their quiescent state (G 0 ), enter the cell cycle and proliferate, followed by the non-parenchymal cells (NPC). During this regenerative process, cells maintain their major morphologic features, have an active urea cycle, continue to metabolize drugs and synthesize albumin. In general terms, the replicative response of quiescent hepatocytes after partial hepatectomy involves multiple steps, each requiring different sets of controls and circuits. These steps start by DNA binding of transcription factors such as NF-κB or STAT3 and the rapid activation of proto-oncogenes and other genes that encode proteins of diverse functions (immediate early genes). Initiation of the regenerative response depends on IL-6 and TNFα, priming quiescent hepatocytes for progressing G0/G1 transition of the cell cycle (Diehl 2000; Streetz, Luedde et al. 2000). These initial events sensitize hepatocytes to growth factors that subsequently drive quiescent cells to G1 phase of the cell cycle. Progression of primed/competent hepatocytes through G1 and subsequent replicative cycling is depending on hepatocyte growth factor (HGF) and transforming growth factor-alpha (TGF-α) signaling. Through this regenerative capacity the liver is able to restore its liver mass in rodents within approximately 7-10 days after surgery within 10% of the original hepatic mass before hepatectomy (Fausto 2000; Fausto, Campbell et al. 2006). This extraordinary capacity for compensatory growth in response to conditions induced by toxic injury and physical or infectious cell loss is a tightly regulated process of both hypertrophy (increase in cell size) and hyperplasia (increase in the number of cells). Involving different liver cell populations liver regeneration is regulated by the interplay between growth factors, cytokines, extracellular matrix components and other regulators (Michalopoulos and DeFrances 1997; Fausto 2000; Fausto, Campbell et al. 2006) NF-κB, IKK2, Nemo and liver regeneration NF-κB plays a major role during liver regeneration and gets activated directly after PH. NF-κB nuclear translocation can be found already 30 minutes after PH and its activation lasts until 4-5 hours after PH (FitzGerald, Webber et al. 1995). The relevance of NF-κB has been highlighted by previous studies showing impairment of DNA synthesis in TNFR1 knockout mice which exhibit lack of STAT3 and NF-κB
12 Introduction 4 activation (Yamada, Kirillova et al. 1997). Also adenovirus mediated NF-κB inhibition during liver regeneration after partial hepatectomy resulted in increased liver apoptosis and dysregulation of cell cycle progression (Iimuro, Nishiura et al. 1998) suggesting a role of NF-κB in protecting the liver from TNF induced apoptosis (Beg and Baltimore 1996) during liver regeneration. NF-κB comprises a family of transcription factors (Annexe 1) which are kept in the cytoplasm by binding to its inhibitor IκB. NF-κB can be activated by two distinct mechanisms: the classical pathway and the alternative pathway. Most of our current knowledge relies on the classical pathway. This pathway is triggered by bacterial and viral infections, as well as pro-inflammatory cytokines, all of which activate the IKK complex. The IKK complex consists of two catalytic subunits with kinase activity; IKK1 (IKKα) and IKK2 (IKKβ) and a third regulatory subunit, IKKγ also called Nemo. The IKK complex phosphorylates IκBs (inhibitors of NF-κB) thereby targeting them for proteasomal degradation and liberating NF-κB dimers that are composed of either REL-A (also known as p65), c-rel or p50 subunits to enter the nucleus and mediate transcription of target genes (Hayden and Ghosh 2004) (Annexe 2).
13 Introduction 5 Annexe 1. The NF-κB and IKK Protein Families Members of the NF-κB and IKK proteins are shown. The number of amino acids in each human protein is indicated on the right. Posttranslational modifications that influence IKK activity or transcriptional activation are indicated with P, U, or Ac for phosphorylation, ubiquitination, or acetylation, respectively. Inhibitory events and phosphorylation and ubiquitination sites on p100 and p105 proteins that mediate proteasomal degradation are indicated with red Ps and Us, respectively (Hayden and Ghosh 2008). RHD, Rel homology domain; TAD, transactivation domain; LZ, leucine zipper domain; GRR, glycine-rich region; HLH, helix-loop-helix domain; Z, zinc finger domain; CC1/2, coiled-coil domains; NBD, Nemo-binding domain; MOD/UBD, minimal oligomerization domain and ubiquitin-binding domain; and DD, death domain (Hayden and Ghosh 2008).
14 Introduction 6 Annexe 2. Crystallographic structure p50 (left) and p65/rel A (right) This reaction mostly depends on the classical pathway involving IKK2, the subunit with the strongest catalytic activity, which phosphorylates IκB (Ghosh and Karin 2002) and Nemo, the regulatory subunit. The alternative NF-κB-activation pathway involves the upstream kinase NF-κB-inducing kinase (NIK) which activates IKK-α homodimers, independently of either IKK2 or Nemo leading to the phosphorylation and processing of p100, in response to certain members of the TNF family (Bonizzi and Karin 2004) (Hayden and Ghosh 2004). The two pathways switch on different gene sets and therefore mediate different immune functions (Bonizzi and Karin 2004). (Annexe 3)
15 Introduction 7 Annexe 3. Signaling pathways that lead to the activation of different nuclear factor-b transcription factors and the biological consequences of these pathways. a. Two pathways can activate nuclear factor-κb (NF-κB). The classical pathway is triggered by proinflammatory stimuli and genotoxic stress, including the following: cytokines, such as tumor-necrosis factor (TNF) and interleukin-1 (IL-1); bacterial cell-wall components, such as lipopolysaccharide; viruses; and DNA-damaging agents. This leads to the IKK-β (inhibitor of NF-κB (IκB) kinase-β)- dependent and Nemo-dependent phosphorylation of IκBs, which results in their proteasomal degradation, and to the subsequent liberation of NF-κB dimers (which are mostly p50 REL-A dimers). The alternative pathway is triggered by certain TNF-family members and leads, in an IKK-β independent and Nemo-independent manner, to the phosphorylation of p100 by IKK-α and the degradation of its carboxy-terminal half by the proteasome. This results in nuclear translocation of p52 REL-B dimers. b. Activation of the classical pathway (which involves p50 REL-A dimers) leads to increased transcription of genes that can be divided into three functional classes, all of which contribute to tumor promotion and progression. BCL-XL, B-cell lymphoma XL; BFL1, a B-cell-lymphoma-2-related protein; ciaps, cellular inhibitors of apoptosis; COX2, cyclooxygenase-2; GADD45β, growth arrest and DNAdamage inducible 45β; inos, inducible nitric-oxide synthase; SOD2, superoxide dismutase 2. (Karin and Greten 2005).
16 Introduction 8 The IKK complex subunits are not redundant. While IKK1 KO mice show limb and skeletal defects (Hu, Baud et al. 1999), IKK2 KO mice die embryonically due to massive liver apoptosis (Li, Chu et al. 1999). Nemo KO mice also die in utero although embryonic fibroblast from these mice exhibit a complete lack of NF-κB activation in response to TNF while MEFs from IKK2 slightly respond to the cytokine (Rudolph, Yeh et al. 2000). In this line of evidence our group has recently described striking differences, when these mice are challenged by different mechanisms of liver injury. While hepatocyte-specific IKK2 KO mice (IKK2 Δhepa ) show NF-κB activation and no liver damage after TNF injection (Luedde, Assmus et al. 2005), hepatocytespecific Nemo knockout mice (Nemo Δhepa ) present massive liver apoptosis and a complete lack of NF-κB activation (Beraza, Ludde et al. 2007). After Ischemia/reperfusion (I/R)-induced liver injury, IKK2 Δhepa mice present less inflammation, apoptosis and necrosis compared to wildtype (WT) littermates which show high NF-kB activation that is significantly diminished in KO animals (Luedde, Assmus et al. 2005). In contrast, Nemo Δhepa mice die shortly after I/R-injury due to massive liver apoptosis showing high non-parenchymal cells-dependent NF-κB and TNF activation even during the ischemic phase, which predisposes the liver to reperfusion-induced liver injury (Beraza, Ludde et al. 2007). During the past years, multiple studies with genetically modified animals have been performed in order to clarify the implication of different molecules and signaling pathways during liver regeneration (Yamada, Kirillova et al. 1997), (Hayashi, Nagaki et al. 2005), (Nakamura, Nonaka et al. 2004). However, deletion of a single gene frequently does not result in a complete inhibition of liver regeneration but can be linked to a dysregulation in cell cycle progression (Fausto, Campbell et al. 2006). This observation is probably best explained by the redundancy in signaling pathways between the different cytokines, growth or transcription factors activated during liver regeneration. However, since both TNF and NF-κB are key players during liver regeneration and based on the striking differences between IKK2 Δhepa and Nemo Δhepa KO mice, the current interest of this thesis is to use these mice to better define the mechanisms that are involved in activating NF-κB during liver regeneration after PH.
17 Introduction The cell cycle Regulation and precise control of the cell cycle is central to normal proliferation and differentiation. The cell cycle is divided in two events: mitosis and cytokinesis (Norbury and Nurse 1992). Replication of the DNA in each chromosome, followed by acurate separation is accomplished during M (mitotic) phase (nuclear division) of the cell cycle (Norbury and Nurse 1992). The interphase, situated between two M phases, is divided into three phases of the cell cycle: during S phase (S = synthesis) the nuclear DNA is replicated. The two remaining phases of the cell cycle occur between M and S phases and are designated as gap phases and constitute checkpoints for the cell (Jacobs 1992). The interval between the completion of M phase and beginning of S phase is G1 phase (G = gap), while G2 phase is the interval between end of S phase and beginning of the M phase. Checkpoints of the cell cycle are in late G1 phase (restriction point), at the end of G2 phase (G2/M checkpoint) or during mitosis (mitotic spindle checkpoint). Gaps during the interphase are fronting long-term mitotic inactivation of the cell during the G0 phase (Lea, Orr et al. 2003),(Cooper 2003). Transition through cell cycle is tightly controlled by a number of cellular proteins, called Cyclin-dependent kinases (Cdks). They are regulated by their regulatory subunits termed Cyclins and Cdk inhibitors. Typically, protein levels of Cyclins peak during cell cycle in a cyclic manner. The process of DNA synthesis is initiated and regulated by four families of regulatory Cyclins (Cyclin D, E, A and B) combined with a limited number of Cdks (Cdk4/6, Cdk2 and Cdk1). The D family of Cyclins transduces mitogenic signals through their activation of Cdk4 and Cdk6 allowing activation of the next two complexes (Draetta 1994; Sherr 1994; Kato 1999), through synthesis of Cyclin E1, E2 and Cyclin A. The E type Cyclins bind to Cdk2 and initiate DNA replication (Draetta 1994) (Reed, Wittenberg et al. 1991; Dulic, Lees et al. 1992; Lees, Faha et al. 1992). Cyclin A also binds to Cdk2 and is important for progression through S phase though they also bind Cdk1 in the later S phase and during G2 phase (Murphy, Stinnakre et al. 1997), (Liu, Lucibello et al. 1998). Finally, entrance into mitosis involves activation of Cdk1 by the Cyclin B family members
18 Introduction 10 Annexe 4. Schematic representation of cell cycle control. Progression through the mitotic cycle involves the successive formation, activation and subsequent inactivation of Cyclin-dependent protein kinases (Cdks). The kinases bind sequentially to a series of Cyclins, which are responsible for differential activation of the kinase during the cell cycle. The G1 to S transition is thought to be controlled by Cdks containing D-type Cyclins that phosphorylate the retinoblastoma protein, releasing E2F transcription factors. E2F are involved in the transcription of genes needed for the G1 to S transition. The G2 to M transition is controlled by Cdk complexes containing A and B Cyclins. Cdk complexes are kept in inactive state by phosphorylation by the Wee1 kinase, and by interaction with inhibiting proteins (CKIs) (Andrietta, Eloy et al. 2001).
19 Introduction Involvement of the innate immune response during liver regeneration Activation of the innate immune system through TLR and other patternrecognition molecules (PRRs) play a key role in host defence against invading pathogens (Akira, Uematsu et al. 2006). Recent studies have highlighted the crucial contribution of these mechanisms to the inflammatory response after PH (Strey, Markiewski et al. 2003; Seki, Tsutsui et al. 2005; Campbell, Riehle et al. 2006). During the priming phase of liver regeneration, Kupffer cells get activated and secrete pro-inflammatory cytokines, most prominently Tumour Necrosis Factor alpha (TNF), Interleukin-6 (IL-6) and Interleukin-1 beta (IL-1β) which can initiate the Acute Phase Response (APR) in hepatocytes (Trautwein, Boker et al. 1994; Gabay and Kushner 1999; Fausto, Campbell et al. 2006). Serum Amyloid A (SAA), C-reactive protein and the complement system are proteins involved in this physiological response to restore liver homeostasis (Trautwein, Boker et al. 1994; Gabay and Kushner 1999; Yoo and Desiderio 2003). Pro-inflammatory cytokine secretion from Kupffer cells during liver injury requires NF-κB activation and triggers a cascade leading to influx of inflammatory cells (Schwabe, Seki et al. 2006). LPS, IL-1β or TNF can induce production of chemotactic cytokines (chemokines) such as Chemokine (C-X-C motif) ligand 1 (CXCL-1, GRO1, or KC). These chemokines belong to the ELR + CXC family which differ from ELR - CXC chemokines both structurally, due to the presence of 3-aa sequence (Glu-Leu-Arg; ELR) and functionally, as they can exert antagonistic effects (Charo and Ransohoff 2006). ELR + CXC chemokines contribute to wound healing and resolution of inflammatory events by stimulating polymorphonuclear cell (PMN) recruitment to the site of injury (Charo and Ransohoff 2006). Furthermore, they have protective and pro-regenerative properties as shown during acetaminophen-induced liver injury (Hogaboam, Bone- Larson et al. 1999) Reactive Oxygen Species ROS are chemically reactive molecules that have essential biological functions. They regulate many signal transduction pathways by directly reacting and modifying the structure of proteins, transcription factors and genes to modulate their
20 Introduction 12 functions. ROS are involved in signaling cell growth and differentiation, regulating the activity of enzymes (such as ribonucleotide reductase), mediating inflammation by stimulating cytokine production, and eliminating pathogens and foreign particles. A moderate increase in ROS can promote cell proliferation and differentiation (Balaban, Nemoto et al. 2005; Nishikawa 2008). In contrary, excessive amounts of ROS can cause oxidative damage to lipids, proteins and DNA because oxygen free radicals are highly reactive with biological molecules. The free radical reaction could cause oxidative modification of these biomolecules and alter their functions. A mild increase in the level of ROS may result in transient cellular alteration, whereas a severe increase of ROS in cells causes irreversible oxidative damage, leading to cell death. Therefore, maintaining ROS homeostasis is crucial for normal cell growth and survival. Cells control ROS levels by balancing ROS generation with their elimination by ROS-scavenging systems such as superoxide dismutases (SOD1, SOD2 and SOD3), glutathione peroxidase, peroxiredoxins, glutaredoxin, thioredoxin and catalase. An increase in ROS reflects a disruption of redox homeostasis due to either an elevation of ROS production or to a decline of ROS-scavenging capacity, a condition known as oxidative stress. ROS can be found either in the environment, for example, as pollutants, tobacco smoke, iron salts and radiation, or it can be generated inside cells. Cells produce ROS through multiple mechanisms. A major source of ROS is produced in the mitochondria. Electron leakage from the mitochondrial respiratory chain may react with molecular oxygen, resulting in the formation of superoxide, which can subsequently be converted to other ROS. In phagocytes and some cancer cells, ROS can be produced through a reaction catalysed by NADPH oxidase complexes. ROS can also be produced as a byproduct of certain biochemical reactions, such as β- oxidation in peroxisomes, prostaglandin synthesis and detoxification reactions by cytochrome P450.
21 Introduction 13 Annexe 5. Schematic illustration of cellular redox homeostasis. Major sites of cellular reactive oxygen species (ROS) generation (indicated in red) include the mitochondrial electron transport chain (Mito-ETC), the endoplasmic reticulum (ER) system and the NADPH oxidase (NOX) complex. Superoxide (O 2 ) is the main initial free radical species, which can be converted to other reactive species. In the mitochondria, superoxide is generated by the capture of electrons escaping from the electron transport chain by molecular oxygen. Superoxide can be rapidly converted to H 2 O 2 by superoxide dismutases (SOD, yellow), which can be reused to generate superoxide radicals or converted to water by catalase. In the presence of transition metals (such as Fe2+), H 2 O 2 can be converted to hydroxyl radicals (HO ), which are highly reactive and can cause damage to lipids, proteins and DNA. Nitric oxide (NO ) is a reactive radical produced from arginine by nitric oxide synthase (NOS). Nitric oxide has a very short half-life and can react with superoxide to form peroxynitrite (ONOO ), a non-radical species that is capable of modifying the structure and function of proteins. To prevent the harmful effects of ROS, cells regulate ROS levels by maintaining the balance between ROS generation and elimination Major ROS-scavenging enzymes are shown in green. GPX, glutathione peroxidase; GR, glutathione reductase; GRXo, glutaredoxin (oxidized); GRXr, glutaredoxin (reduced); GSHr, glutathione (reduced); GSSG, glutathione (oxidized); TRXo, thioredoxin (oxidized); TRXr, thioredoxin (reduced); XO, xanthine oxidase. (Trachootham, Alexandre et al. 2009).
Anti-ATF6 α antibody, mouse monoclonal (1-7) 73-500 50 ug ATF6 (activating transcription factor 6) is an endoplasmic reticulum (ER) membrane-bound transcription factor activated in response to ER stress.
Protocol for Western Blotting Materials Materials used on Day 3 Protease inhibitor stock: 1 μg/μl pepstatin A in DMSO 200 μm leupeptin in OG Buffer 200 mm PMSF: Freshly made. Ex) 34.8 mg PMSF in 1 ml isopropanol
Chromatin Immunoprecipitation (ChIP) Day 1 A) DNA shearing 1. Samples Dissect tissue (One Mouse OBs) of interest and transfer to an eppendorf containing 0.5 ml of dissecting media (on ice) or PBS but without
x TABLE OF CONTENT ACKNOWLEDGEMENTS ENGLISH ABSTRACT THAI ABSTRACT LIST OF TABLES LIST OF FIGURES ABBREVIATIONS iii iv vii xv xvi xviii CHAPTER I: INTRODUCTION 1.1 Statement of problems 1 1.2 Literature
TRI Reagent For processing tissues, cells cultured in monolayer or cell pellets Catalog Number T9424 Store at room temperature. TECHNICAL BULLETIN Product Description TRI Reagent is a quick and convenient
Protocol for GenomePlex Whole Genome Amplification from Formalin-Fixed Parrafin-Embedded (FFPE) tissue Application Guide... 2 I. Description... 2 II. Product Components... 2 III. Materials to be Supplied
i 1 INTRODUCTION 1.1 Human Hepatitis B virus (HBV) 1 1.1.1 Pathogenesis of Hepatitis B 1 1.1.2 Genome organization of HBV 3 1.1.3 Structure of HBV virion 5 1.1.4 HBV life cycle 5 1.1.5 Experimental models
RevertAid Premium First Strand cdna Synthesis Kit #K1651, #K1652 CERTIFICATE OF ANALYSIS #K1651 Lot QUALITY CONTROL RT-PCR using 100 fg of control GAPDH RNA and GAPDH control primers generated a prominent
292PR 01 G-Biosciences 1-800-628-7730 1-314-991-6034 firstname.lastname@example.org A Geno Technology, Inc. (USA) brand name Classic Immunoprecipitation Utilizes Protein A/G Agarose for Antibody Binding (Cat.
Western Blot Analysis with Cell Samples Grown in Channel-µ-Slides Polyacrylamide gel electrophoresis (PAGE) and subsequent analyses are common tools in biochemistry and molecular biology. This Application
Genomic DNA Extraction Kit INSTRUCTION MANUAL Table of Contents Introduction 3 Kit Components 3 Storage Conditions 4 Recommended Equipment and Reagents 4 Introduction to the Protocol 4 General Overview
HiPer RT-PCR Teaching Kit Product Code: HTBM024 Number of experiments that can be performed: 5 Duration of Experiment: Protocol: 4 hours Agarose Gel Electrophoresis: 45 minutes Storage Instructions: The
User Manual CelluLyser Lysis and cdna Synthesis Kit Version 1.4 Oct 2012 From cells to cdna in one tube CelluLyser Lysis and cdna Synthesis Kit Table of contents Introduction 4 Contents 5 Storage 5 Additionally
Running protein gels and detection of proteins 1. Protein concentration determination using the BIO RAD reagent This assay uses a colour change reaction to give a direct measurement of protein concentration.
ab185916 Hi-Fi cdna Synthesis Kit Instructions for Use For cdna synthesis from various RNA samples This product is for research use only and is not intended for diagnostic use. Version 1 Last Updated 1
In vitro analysis of pri-mirna processing by Drosha-DGCR8 complex (Narry Kim s lab) 1-1. Preparation of radiolabeled pri-mirna transcript The RNA substrate for a cropping reaction can be prepared by in
Optimal Conditions for F(ab ) 2 Antibody Fragment Production from Mouse IgG2a Ryan S. Stowers, 1 Jacqueline A. Callihan, 2 James D. Bryers 2 1 Department of Bioengineering, Clemson University, Clemson,
All in One First Strand cdna Synthesis Kit For reliable first strand cdna synthesis from all RNA sources Cat. No. AORT 0020 Cat. No. AORT 0050 (20 synthesis reactions) (50 synthesis reactions) User Manual
Supplemental Material: Western blot: SDS gel electrophoresis was performed using a 4% by 20% gradient gel 8. Quantification of Western blots was performed using Image J Processing and Analysis (NIH). Quantitative
TECHNICAL BULLETIN Reverse Transcription System Instruc ons for use of Product A3500 Revised 1/14 TB099 Reverse Transcription System All technical literature is available on the Internet at: www.promega.com/protocols/
BIOTECHNOLOGY Levels: 11-12 Units of Credit: 1.0 CIP Code: 51.1201 Prerequisite: Biology or Chemistry Skill Certificates: #708 COURSE DESCRIPTION is an exploratory course designed to create an awareness
Understanding the immune response to bacterial infections A Ph.D. (SCIENCE) DISSERTATION SUBMITTED TO JADAVPUR UNIVERSITY SUSHIL KUMAR PATHAK DEPARTMENT OF CHEMISTRY BOSE INSTITUTE 2008 CONTENTS Page SUMMARY
Microbiology Laboratory: MOLECULAR IDENTIFICATION OF UNKNOWN BACTERIA Classical Microbiology courses are typically structured to introduce the identification of bacterial species using a series of biochemical
Chromatin Immunoprecipitation A) Prepare a yeast culture (see the Galactose Induction Protocol for details). 1) Start a small culture (e.g. 2 ml) in YEPD or selective media from a single colony. 2) Spin
竞 争 性 分 析 Epitope Mapping 实 验 方 法 ABSTRACT The simplest way to determine whether two monoclonal antibodies bind to distinct sites on a protein antigen is to carry out a competition assay. The assay can
Title: Mapping T cell epitopes in PCV2 capsid protein - NPB #08-159 Investigator: Institution: Carol Wyatt Kansas State University Date Submitted: 12-11-09 Industry summary: Effective circovirus vaccines
PR110 G-Biosciences 1-800-628-7730 1-314-991-6034 email@example.com A Geno Technology, Inc. (USA) brand name Dot Blot Analysis Teacher s Guidebook (Cat. # BE 502) think proteins! think G-Biosciences
Islet Viability Assessment by Single Cell Flow Cytometry Page 1 of 8 Purpose: To comprehensively assess the viability of the islet cell preparation prior to transplantation. Tissue Samples: A sample containing
BUFFERS and MEDIAS Coomassie Blue Staining Solution 2 g Coomassie Blue 2 L Methanol or Ethanol * 1.6 L 400 ml Glacial acetic acid *If you will be microwaving the gel in staining solution for rapid staining
Adaptive Immunity Chapter 17: Adaptive (specific) Immunity Bio 139 Dr. Amy Rogers Host defenses that are specific to a particular infectious agent Can be innate or genetic for humans as a group: most microbes
HIS-Select Nickel Affinity Gel Catalog Number P6611 Storage Temperature 2 8 C TECHNICAL BULLETIN Product Description HIS-Select Nickel Affinity Gel is an immobilized metalion affinity chromatography (IMAC)
Western Blotting Sive Lab Protocol March 2007 Prepare samples: For zebrafish embryos: Option 1: Take live embryos and put into 1.5 ml tube with E3. Centrifuge gently for 1-2 minutes -yolk lipids will rise
Benchtop Mitochondria Isolation Protocol Note: Specific protocols are available for the following products: MS850 Mitochondria Isolation Kit for Rodent Tissue MS851 Mitochondria Isolation Kit for Rodent
QIAGEN Supplementary Protocol Isolation of Peripheral Blood Mononuclear Cells (PBMC) and Purification of Total RNA from PBMC Using the RNeasy Micro or Mini Kit This protocol describes how to isolate PBMC
Western Blotting: Mini-gels Materials a Protein Extraction Buffer (for callus or kernel), Solution Stock Final Volume Tris-HCl ph 80 1 M 200 mm 20 ml NaCl 4 M 100 mm 25 ml Sucrose 2 M 400 mm 20 ml EDTA
Western Blot Protocol (updated on 05/20/14) Required Solutions 10x PBS (1L) 80 g NaCl 2 g KCl 14.4 g Na 2 HPO 4 or 22 g Na 2 HPO 4 7H 2 O 2.4 g KH 2 PO 4 or 2 g KH 2 PO4 Adjust ph to 7.4 Autoclave PBST
ab185915 Protein Sumoylation Assay Ultra Kit Instructions for Use For the measuring in vivo protein sumoylation in various samples This product is for research use only and is not intended for diagnostic
Notch 1 -dependent regulation of cell fate in colorectal cancer Referees: PD Dr. Tobias Dick Prof. Dr. Wilfried Roth http://d-nb.info/1057851272 CONTENTS Summary 1 Zusammenfassung 2 1 INTRODUCTION 3 1.1
ELISA BIO 110 Lab 1 Immunity and Disease Introduction The principal role of the mammalian immune response is to contain infectious disease agents. This response is mediated by several cellular and molecular
User Manual Ordering information: (for detailed kit content see Table 2) EdU Flow Cytometry Kits for 50 assays: Product number EdU Used fluorescent dye BCK-FC488-50 10 mg 6-FAM Azide BCK-FC555-50 10 mg
Chapter 9 Biotechnology and Recombinant DNA Biotechnology and Recombinant DNA Q&A Interferons are species specific, so that interferons to be used in humans must be produced in human cells. Can you think
Western Blotting All steps are carried out at room temperature unless otherwise indicated. Recipes for all solutions highlighted bold are included at the end of the protocol. SDS-PAGE 1. Construct an SDS-PAGE
Revision No.: ZJ0002 Issue Date: Aug 7 th, 2008 HBV Quantitative Real Time PCR Kit Cat. No.: HD-0002-01 For Use with LightCycler 1.0/LightCycler2.0/LightCycler480 (Roche) Real Time PCR Systems (Pls ignore
1.0 Purpose: 1.1 The characterisation of of main leukocyte subsets in peripheral blood cells from mice by flow cytometry. Reliable values of frequencies of leukocyte clusters are very much dependent on
THE IMMUNE SYSTEM 1 ANATOMY OF THE IMMUNE SYSTEM 2 We all get sick sometimes...but then we get better. What happens when we get sick? Why do we get better? The immune system is localized in several parts
is a is a state of the art transfection reagent, specifically designed for the transfer of sirna and mirna into a variety of eukaryotic cell types. is a state of the art transfection reagent, specifically
Page 1 of 8 Mouse IFN-gamma ELISpot Kit Without Plates With Plates With Sterile Plates Quantity Catalog Nos. 862.031.001 862.031.001P 862.031.001S 1 x 96 tests 862.031.005 862.031.005P 862.031.005S 5 x
SUPPLEMENTAL DATA MATERIALS AND METHODS Peptide synthesis, radiolabelling and radiochemical analysis Solid phase synthesis of peptides was carried out on using ABI 433A peptide synthesizer, on a preloaded
DNA Isolation Kit for Cells and Tissues for 10 isolations of 00 mg each for tissue or 5 x 10 7 cultured cells Cat. No. 11 81 770 001 Principle Starting material Application Time required Results Benefits
HARVESTING AND CRYOPRESERVATION OF HUMAN EMBRYONIC STEM CELLS (hescs) OBJECTIVE: can be cryopreserved in a liquid nitrogen (LN 2 ) freezer for long-term storage. This Standard Operating Procedure (SOP)
DNA Fingerprinting Unless they are identical twins, individuals have unique DNA DNA fingerprinting The name used for the unambiguous identifying technique that takes advantage of differences in DNA sequence
User Manual Mir-X mirna First-Strand Synthesis Kit User Manual United States/Canada 800.662.2566 Asia Pacific +1.650.919.7300 Europe +33.(0)1.3904.6880 Japan +81.(0)77.543.6116 Clontech Laboratories, Inc.
Creatine Kinase Activity Colorimetric Assay Kit ABE5487 100 assays; Store at -20 C I. Introduction: Creatine Kinase (CK) also known as creatine phosphokinase (CPK) and ATP: creatine N- phosphotransferase
Common Course Topics Biology 1406: Cell and Molecular Biology 1. Introduction to biology --the scientific study of organisms --properties of life --assumptions, methods and limitations of science --underlying
Common Course Topics Biology 1414: Introduction to Biotechnology I Assumptions Students may be enrolled in this course for several reasons; they are enrolled in the Biotechnology Program, they need a science
Unit 2 Metabolism and Survival Summary 1 Metabolism pathways and their control (a) Introduction to metabolic pathways This involves integrated and controlled pathways of enzymecatalysed reactions within
HighPure Maxi Plasmid Kit For purification of high pure plasmid DNA with high yields www.tiangen.com PP120109 HighPure Maxi Plasmid Kit Kit Contents Storage Cat.no. DP116 Contents RNaseA (100 mg/ml) Buffer
Plant Genomic DNA Extraction using CTAB Introduction The search for a more efficient means of extracting DNA of both higher quality and yield has lead to the development of a variety of protocols, however
icell Skeletal Myoblasts Application Protocol Introduction Modulating Glucose Uptake in Skeletal Myotubes: Insulin Induction with Bioluminescent Glucose Uptake Analysis The skeletal muscle is one of the
PROTOCOL Immunostaining for Flow Cytometry 1850 Millrace Drive, Suite 3A Eugene, Oregon 97403 Rev.0 Background The combination of single cell analysis using flow cytometry and the specificity of antibody-based
Chapter 5: Organization and Expression of Immunoglobulin Genes I. Genetic Model Compatible with Ig Structure A. Two models for Ab structure diversity 1. Germ-line theory: maintained that the genome contributed
RNA Cloning Method Flowchart Extract total RNA containing small RNAs. Check quality on denaturing gel with EtBr staining 5' End label RNA markers 18.113 (18mer) and 44.12 (24mer) with Kinase and 32P-gamma-ATP.
Theoretical and practical approaches of Hepatocyte primary culture Workshop 14-16 February 2006 Lecture (2) Disaggregation & purification of target cells Coarse organizer Dr. Abo bakr Mohamed Eltayeb General
Concept 1 - Thinking Practice 1. If the following molecules were to undergo a dehydration synthesis reaction, what molecules would result? Circle the parts of each amino acid that will interact and draw
6 Characterization of Casein and Bovine Serum Albumin (BSA) Objectives: A) To separate a mixture of casein and bovine serum albumin B) to characterize these proteins based on their solubilities as a function
Fighting the Battles: Conducting a Clinical Assay 6 Vocabulary: In Vitro: studies in biology that are conducted using components of an organism that have been isolated from their usual biological surroundings
Biotechnology and Recombinant DNA (Chapter 9) Lecture Materials for Amy Warenda Czura, Ph.D. Suffolk County Community College Primary Source for figures and content: Eastern Campus Tortora, G.J. Microbiology
CUSTOM ANTIBODIES Highly competitive pricing without compromising quality. Rat monoclonal antibodies for the study of gene expression and proteomics in mice and in mouse models of human diseases available.
Protein Trafficking/Targeting (8.1) Lecture 8 Protein Trafficking/Targeting Protein targeting is necessary for proteins that are destined to work outside the cytoplasm. Protein targeting is more complex
Chapter 18 Regulation of Gene Expression 18.1. Gene Regulation Is Necessary By switching genes off when they are not needed, cells can prevent resources from being wasted. There should be natural selection
DESCRIPTION Biotechnology is designed to create an awareness of career possibilities in the field of biotechnology. Students are introduced to diagnostic and therapeutic laboratory procedures that support