Journal of Cell Science Supplementary information. Arl8b +/- Arl8b -/- Inset B. electron density. genotype

Size: px
Start display at page:

Download "Journal of Cell Science Supplementary information. Arl8b +/- Arl8b -/- Inset B. electron density. genotype"

Transcription

1 J. Cell Sci. : doi:.4/jcs.59: Supplementary information E9. A Arl8b /- Arl8b -/- Arl8b Arl8b non-specific band Gapdh Tbp E7.5 HE Inset B D Control al am hf C E Arl8b -/- al am hf E8.5 F low middle high G genotype electron density high middle low Arl8b /... Arl8b -/ Fig. S. Arl8b / mutant phenotypes. (A) RT-PCR analysis of Arl8b mrna in E9. embryos. (B E) HE-stained transverse cryosections of E7.5 embryos. The insets in (B) and (C) are magnified in (D) and (E), respectively. Bars, μm. (F) Examples of high-, middle-, and low-electron density vesicles in the Arl8b / VYSE. Vesicles were classified into three groups on the basis of their electron densities: vesicles with suprathreshold intensity across their whole area were classified as high-density, those with subthreshold intensity across their whole area as low-density, and others as middle-density. Bar, 5. μm. (G) The numbers of vesicles per 5 cells were scored for wild-type and Arl8b / VYSE (n = ).

2 J. Cell Sci. : doi:.4/jcs.59: Supplementary information Visceral Yolk Sac (E9.5) Glycine Ala Alanine Isoleucine Ile BCAA Val Valine Serine Threonine 5 Ser Thr 4 Leucine Lysine Arginine His Histidine Methionine Tyr Phe Tyrosine Phenylalanine Tryptophan 4 5 Trp BAA AAA 8 6 Pro Proline Gln Glutamine Glutamic acid Asn Asparagine Aspartic acid : Arl8b flox/ or Arl8b flox/flox : Ttr-Cre; Arl8b flox/ : Ttr-Cre; Arl8b flox/flox Fig. S. Alterations of amino acid level in the VYS of the Ttr-Cre;Arl8b flox/flox embryo. Relative amounts of amino acids in the VYS of the E9.5 embryo. BCAA, BAA, and AAA represent branched-chain amino acids, basic amino acids, and aromatic amino acids, respectively. The scale of the vertical axis in each panel is given in arbitrary units. P<.5, P<., P<..

3 J. Cell Sci. : doi:.4/jcs.59: Supplementary information Embryo Glycolysis 5 5 Glucose Glucose-6-phosphate 5 glucose 6-phosphate dehydrogenase Pentose phosphate pathway 6-Phosphogluconoδ-lactone 6-Phosphogluconate Ribulose 5-phosphate 5 ribulose phosphate -epimerase ribose 5-phosphate isomerase phosphoglucose isomerase Fructose-6-phosphate 5 transketolase Xylulose 5-phosphate Ribose 5-phosphate 5 Fructose 6-phosphate Glyceraldehyde -phosphate fructose,6-bisphosphatase phosphofructokinase- Fructose-,6-diphosphate Erythrose 4-phosphate Sedoheptulose 7-phosphate Dihydroxyacetone phosphate (DHAP) TPI Aldolase, Diphospho glycerate DHAPGA--P : Arl8b flox/ or Arl8b flox/flox : Ttr-Cre; Arl8b flox/ : Ttr-Cre; Arl8b flox/flox 6 4 Glyceraldehyde -phosphate (GA--P) Gapdh, Di-phospho glycerate Glycine PGK -Phosphoglycerate 5 5 -Phospho-D-glycerate Fig. S. Metabolite levels of glycolysis and pentose phosphate pathway in the embryo proper. Relative amounts of metabolites of glycolysis and pentose phosphate pathway in the embryo proper of the E9.5 embryo. The scale of the vertical axis in each panel is given in arbitrary units. P< PGM Lactate ENO Phosphoenolpyruvate LDH PK Pyruvate TCA Cycle

4 J. Cell Sci. : doi:.4/jcs.59: Supplementary information Embryo Ketone-Bodies β-hydroxybutyrate Malate Mevalonate Acetoacetate Acetyl-CoA Oxaloacetate 6 4 CoASH Glucose Pyruvate Citrate 5 4 Pantothenate cis-aconitate 4 Fumarate 5 5 TCA cycle 4 Iso-citrate Succinate : Arl8b flox/ or Arl8b flox/flox : Ttr-Cre; Arl8b flox/ : Ttr-Cre; Arl8b flox/flox Succinyl-CoA α-ketoglutarate 5 5 Glu AAs N-Acetyl-L-glutamic acid Fig. S4. Metabolite levels of TCA cycle in the embryo proper. Relative amounts of metabolites of TCA cycle in the embryo proper of the E9.5 embryo. The scale of the vertical axis in each panel is given in arbitrary units. P<

5 J. Cell Sci. : doi:.4/jcs.59: Supplementary information Visceral Yolk Sac Glycolysis 6 4 Glucose Glucose-6-phosphate 4 glucose 6-phosphate dehydrogenase Pentose phosphate pathway 6-Phosphogluconoδ-lactone 6-Phosphogluconate 5 5 Ribulose 5-phosphate ribulose phosphate -epimerase ribose 5-phosphate isomerase phosphoglucose isomerase Fructose-6-phosphate 4 transketolase Xylulose 5-phosphate Ribose 5-phosphate Fructose 6-phosphate Glyceraldehyde -phosphate fructose,6-bisphosphatase Dihydroxyacetone phosphate (DHAP) phosphofructokinase- Fructose-,6-diphosphate 5, Di-phospho glycerate PGK, Diphospho glycerate -Phosphoglycerate TPI : Arl8b flox/ or Arl8b flox/flox : Ttr-Cre; Arl8b flox/ : Ttr-Cre; Arl8b flox/flox Aldolase DHAPGA--P Glyceraldehyde -phosphate (GA--P) Glycine Gapdh Erythrose 4-phosphate -Phospho-D-glycerate Fig. S5. Metabolite levels of glycolysis and pentose phosphate pathway in the VYS. Relative amounts of metabolites of glycolysis and pentose phosphate pathway in the VYS of the E9.5 embryo. The scale of the vertical axis in each panel is given in arbitrary units. P<.5, P< PGM Lactate Sedoheptulose 7-phosphate ENO Phosphoenolpyruvate LDH PK Pyruvate TCA Cycle

6 J. Cell Sci. : doi:.4/jcs.59: Supplementary information Visceral Yolk Sac Ketone-Bodies β-hydroxybutyrate 5 4 Mevalonate Acetoacetate Acetyl-CoA Glucose Pyruvate 5 5 CoASH Pantothenate Oxaloacetate 5 Malate Citrate 5 5 cis-aconitate Fumarate TCA cycle 5 4 Iso-citrate 5 5 Succinate : Arl8b flox/ or Arl8b flox/flox : Ttr-Cre; Arl8b flox/ : Ttr-Cre; Arl8b flox/flox Succinyl-CoA α-ketoglutarate 5 5 Glu AAs N-Acetyl-L-glutamic acid 5 Fig. S6. Metabolite levels of TCA cycle in the VYS. Relative amounts of metabolites of TCA cycle in the VYS of the E9.5 embryo. The scale of the vertical axis in each panel is given in arbitrary units. P<.5. 5

7 J. Cell Sci. : doi:.4/jcs.59: Supplementary information Table S. Primers used for construction of a conditional knockout targeting vector. Short arm forward 5 - CCA GCT GGG GCT CGA ATA AGC AGC CCT GTC CCA GTC - Short arm reverse 5 - CGG CCG CCA CCT CGA GAA TTC TCA ATT TGT CCT CTT TTT GGC - Middle arm forward Middle arm reverse Long arm forward 5 - ACG AAG TTA TGT CGA GTG CAT TTT ATT AGC CCT ATT AG GGG GGA TGT GGT CGA TCA GAA CTC TAA TTC TAG TGC TAT GGA TCC GCG GCC TCT CCG GCC TTG CTT CCT GTG - Long arm reverse 5 - ATG GCC ATA GCG GCC GCA AGC AGG CAG GTC TAG AGT TG - Table S. Primers used for RT-PCR analysis. Arl8b forward 5 - GTG GGG GGG GTA GGG - Arl8b reverse 5 - GTG ACG TTG CCT TTA GTT ACT TTC C - Gapdh forward 5 - CAT GGC CTT CCG TGT TCC TA - Gapdh reverse 5 - GCG GCA CGT CAG ATC CA - Tbp forward 5 - ACC CTT CAC CAA TGA CTC CTA TG - Tbp reverse 5 - TGA CTG CAG CAA ATC GCT TGG -

8 J. Cell Sci. : doi:.4/jcs.59: Supplementary information Table S. The working dilutions of antibodies used in this study. Antibodies Manufacturers or Ref. Clone or Cat.# Dilution or concentration anti-lamp DSHB D4B /5 for IF anti-albumin Abcam ab658 / for IB anti-cathepsin L R&D AF55. µg/ml for IB anti-actin Merck Millipore MAB5 /5 for IB anti-arl8 Okai et al., 4 N/A /5 for IF, / for IB Anti-Gapdh Merck Millipore MAB74 / for IB IF: Immunofluorescence staining, IB: Immunoblotting, N/A: not applicable Table S4. MRM conditions for each amino acid. Compounds Q m/z Q m/z Collision Energy L-Met Serine Asparagine Aspartic acid Glycine Glutamine Threonine Cysteine Alanine Glutamic acid Lysine Histidine Proline Arginine Valine Methionine Tyrosine Isoleucine Leucine Phenylalanine Tryptophan

Supplementary Table 3. 3 UTR primer sequences. Primer sequences used to amplify and clone the 3 UTR of each indicated gene are listed.

Supplementary Table 3. 3 UTR primer sequences. Primer sequences used to amplify and clone the 3 UTR of each indicated gene are listed. Supplemental Figure 1. DLKI-DIO3 mirna/mrna complementarity. Complementarity between the indicated DLK1-DIO3 cluster mirnas and the UTR of SOX2, SOX9, HIF1A, ZEB1, ZEB2, STAT3 and CDH1with mirsvr and PhastCons

More information

a) Primary cultures derived from the pancreas of an 11-week-old Pdx1-Cre; K-MADM-p53

a) Primary cultures derived from the pancreas of an 11-week-old Pdx1-Cre; K-MADM-p53 1 2 3 4 5 6 7 8 9 10 Supplementary Figure 1. Induction of p53 LOH by MADM. a) Primary cultures derived from the pancreas of an 11-week-old Pdx1-Cre; K-MADM-p53 mouse revealed increased p53 KO/KO (green,

More information

c Tuj1(-) apoptotic live 1 DIV 2 DIV 1 DIV 2 DIV Tuj1(+) Tuj1/GFP/DAPI Tuj1 DAPI GFP

c Tuj1(-) apoptotic live 1 DIV 2 DIV 1 DIV 2 DIV Tuj1(+) Tuj1/GFP/DAPI Tuj1 DAPI GFP Supplementary Figure 1 Establishment of the gain- and loss-of-function experiments and cell survival assays. a Relative expression of mature mir-484 30 20 10 0 **** **** NCP mir- 484P NCP mir- 484P b Relative

More information

Lezione 10. Sommario. Bioinformatica. Lezione 10: Sintesi proteica Synthesis of proteins Central dogma: DNA makes RNA makes proteins Genetic code

Lezione 10. Sommario. Bioinformatica. Lezione 10: Sintesi proteica Synthesis of proteins Central dogma: DNA makes RNA makes proteins Genetic code Lezione 10 Bioinformatica Mauro Ceccanti e Alberto Paoluzzi Lezione 10: Sintesi proteica Synthesis of proteins Dip. Informatica e Automazione Università Roma Tre Dip. Medicina Clinica Università La Sapienza

More information

BIOLOGY 621 Identification of the Snorks

BIOLOGY 621 Identification of the Snorks Name: Date: Block: BIOLOGY 621 Identification of the Snorks INTRODUCTION: In this simulation activity, you will examine the DNA sequence of a fictitious organism - the Snork. Snorks were discovered on

More information

Supplemental Data. Shin et al. Plant Cell. (2012) /tpc YFP N

Supplemental Data. Shin et al. Plant Cell. (2012) /tpc YFP N MYC YFP N PIF5 YFP C N-TIC TIC Supplemental Data. Shin et al. Plant Cell. ()..5/tpc..95 Supplemental Figure. TIC interacts with MYC in the nucleus. Bimolecular fluorescence complementation assay using

More information

www.lessonplansinc.com Topic: Protein Synthesis - Sentence Activity Summary: Students will simulate transcription and translation by building a sentence/polypeptide from words/amino acids. Goals & Objectives:

More information

Supplementary Figure 1. ROS induces rapid Sod1 nuclear localization in a dosagedependent manner. WT yeast cells (SZy1051) were treated with 4NQO at

Supplementary Figure 1. ROS induces rapid Sod1 nuclear localization in a dosagedependent manner. WT yeast cells (SZy1051) were treated with 4NQO at Supplementary Figure 1. ROS induces rapid Sod1 nuclear localization in a dosagedependent manner. WT yeast cells (SZy1051) were treated with 4NQO at different concentrations for 30 min and analyzed for

More information

Supplementary Document

Supplementary Document Supplementary Document 1. Supplementary Table legends 2. Supplementary Figure legends 3. Supplementary Tables 4. Supplementary Figures 5. Supplementary References 1. Supplementary Table legends Suppl.

More information

CD31 5'-AGA GAC GGT CTT GTC GCA GT-3' 5 ' -TAC TGG GCT TCG AGA GCA GT-3'

CD31 5'-AGA GAC GGT CTT GTC GCA GT-3' 5 ' -TAC TGG GCT TCG AGA GCA GT-3' Table S1. The primer sets used for real-time RT-PCR analysis. Gene Forward Reverse VEGF PDGFB TGF-β MCP-1 5'-GTT GCA GCA TGA ATC TGA GG-3' 5'-GGA GAC TCT TCG AGG AGC ACT T-3' 5'-GAA TCA GGC ATC GAG AGA

More information

Supplementary Figure 1 a

Supplementary Figure 1 a Supplementary Figure a Normalized expression/tbp (A.U.).6... Trip-br transcripts Trans Trans Trans b..5. Trip-br Ctrl LPS Normalized expression/tbp (A.U.) c Trip-br transcripts. adipocytes.... Trans Trans

More information

Supplementary Appendix

Supplementary Appendix Supplementary Appendix This appendix has been provided by the authors to give readers additional information about their work. Supplement to: Sherman SI, Wirth LJ, Droz J-P, et al. Motesanib diphosphate

More information

Supplementary Figures

Supplementary Figures Supplementary Figures Supplementary Figure 1. H3F3B expression in lung cancer. a. Comparison of H3F3B expression in relapsed and non-relapsed lung cancer patients. b. Prognosis of two groups of lung cancer

More information

Figure S1. Analysis of genomic and cdna sequences of the targeted regions in WT-KI and

Figure S1. Analysis of genomic and cdna sequences of the targeted regions in WT-KI and Figure S1. Analysis of genomic and sequences of the targeted regions in and indicated mutant KI cells, with WT and corresponding mutant sequences underlined. (A) cells; (B) K21E-KI cells; (C) D33A-KI cells;

More information

Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1

Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1 Supplementary Figure 1 U1 inhibition causes a shift of RNA-seq reads from exons to introns. (a) Evidence for the high purity of 4-shU-labeled RNAs used for RNA-seq. HeLa cells transfected with control

More information

Toluidin-Staining of mast cells Ear tissue was fixed with Carnoy (60% ethanol, 30% chloroform, 10% acetic acid) overnight at 4 C, afterwards

Toluidin-Staining of mast cells Ear tissue was fixed with Carnoy (60% ethanol, 30% chloroform, 10% acetic acid) overnight at 4 C, afterwards Toluidin-Staining of mast cells Ear tissue was fixed with Carnoy (60% ethanol, 30% chloroform, 10% acetic acid) overnight at 4 C, afterwards incubated in 100 % ethanol overnight at 4 C and embedded in

More information

Abbreviations: P- paraffin-embedded section; C, cryosection; Bio-SA, biotin-streptavidin-conjugated fluorescein amplification.

Abbreviations: P- paraffin-embedded section; C, cryosection; Bio-SA, biotin-streptavidin-conjugated fluorescein amplification. Supplementary Table 1. Sequence of primers for real time PCR. Gene Forward primer Reverse primer S25 5 -GTG GTC CAC ACT ACT CTC TGA GTT TC-3 5 - GAC TTT CCG GCA TCC TTC TTC-3 Mafa cds 5 -CTT CAG CAA GGA

More information

Supplementary Materials

Supplementary Materials Supplementary Materials 1 Supplementary Table 1. List of primers used for quantitative PCR analysis. Gene name Gene symbol Accession IDs Sequence range Product Primer sequences size (bp) β-actin Actb gi

More information

Table S1. Oligonucleotides used for the in-house RT-PCR assays targeting the M, H7 or N9. Assay (s) Target Name Sequence (5 3 ) Comments

Table S1. Oligonucleotides used for the in-house RT-PCR assays targeting the M, H7 or N9. Assay (s) Target Name Sequence (5 3 ) Comments SUPPLEMENTAL INFORMATION 2 3 Table S. Oligonucleotides used for the in-house RT-PCR assays targeting the M, H7 or N9 genes. Assay (s) Target Name Sequence (5 3 ) Comments CDC M InfA Forward (NS), CDC M

More information

Supplementary Figure 1 MicroRNA expression in human synovial fibroblasts from different locations. MicroRNA, which were identified by RNAseq as most

Supplementary Figure 1 MicroRNA expression in human synovial fibroblasts from different locations. MicroRNA, which were identified by RNAseq as most Supplementary Figure 1 MicroRNA expression in human synovial fibroblasts from different locations. MicroRNA, which were identified by RNAseq as most differentially expressed between human synovial fibroblasts

More information

Citation for published version (APA): Oosterveer, M. H. (2009). Control of metabolic flux by nutrient sensors Groningen: s.n.

Citation for published version (APA): Oosterveer, M. H. (2009). Control of metabolic flux by nutrient sensors Groningen: s.n. University of Groningen Control of metabolic flux by nutrient sensors Oosterveer, Maaike IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it.

More information

Supplementary Table 2. Conserved regulatory elements in the promoters of CD36.

Supplementary Table 2. Conserved regulatory elements in the promoters of CD36. Supplementary Table 1. RT-qPCR primers for CD3, PPARg and CEBP. Assay Forward Primer Reverse Primer 1A CAT TTG TGG CCT TGT GCT CTT TGA TGA GTC ACA GAA AGA ATC AAT TC 1B AGG AAA TGA ACT GAT GAG TCA CAG

More information

SUPPLEMENTARY DATA. Supplementary Table 1. Primer sequences for qrt-pcr

SUPPLEMENTARY DATA. Supplementary Table 1. Primer sequences for qrt-pcr Supplementary Table 1. Primer sequences for qrt-pcr Gene PRDM16 UCP1 PGC1α Dio2 Elovl3 Cidea Cox8b PPARγ AP2 mttfam CyCs Nampt NRF1 16s-rRNA Hexokinase 2, intron 9 β-actin Primer Sequences 5'-CCA CCA GCG

More information

Supplementary Figure 1

Supplementary Figure 1 Supplementary Figure 1 Supplementary Figure 1. Lats1/2 deleted ihbs and ihps showed decreased transcripts of hepatocyte related genes (a and b) Western blots (a) and recombination PCR (b) of control and

More information

Amino Acids. Amino Acids. Fundamentals. While their name implies that amino acids are compounds that contain an NH. 3 and CO NH 3

Amino Acids. Amino Acids. Fundamentals. While their name implies that amino acids are compounds that contain an NH. 3 and CO NH 3 Fundamentals While their name implies that amino acids are compounds that contain an 2 group and a 2 group, these groups are actually present as 3 and 2 respectively. They are classified as α, β, γ, etc..

More information

Nature Immunology: doi: /ni.3836

Nature Immunology: doi: /ni.3836 Supplementary Figure 1 Recombinant LIGHT-VTP induces pericyte contractility and endothelial cell activation. (a) Western blot showing purification steps for full length murine LIGHT-VTP (CGKRK) protein:

More information

Supplementary Figure 1a

Supplementary Figure 1a Supplementary Figure 1a Hours: E-cadherin TGF-β On TGF-β Off 0 12 24 36 48 24 48 72 Vimentin βactin Fig. S1a. Treatment of AML12 cells with TGF-β induces EMT. Treatment of AML12 cells with TGF-β results

More information

Culture Density (OD600) 0.1. Culture Density (OD600) Culture Density (OD600) Culture Density (OD600) Culture Density (OD600)

Culture Density (OD600) 0.1. Culture Density (OD600) Culture Density (OD600) Culture Density (OD600) Culture Density (OD600) A. B. C. D. E. PA JSRI JSRI 2 PA DSAM DSAM 2 DSAM 3 PA LNAP LNAP 2 LNAP 3 PAO Fcor Fcor 2 Fcor 3 PAO Wtho Wtho 2 Wtho 3 Wtho 4 DTSB Low Iron 2 4 6 8 2 4 6 8 2 22 DTSB Low Iron 2 4 6 8 2 4 6 8 2 22 DTSB

More information

Nucleotide Sequence of the Australian Bluetongue Virus Serotype 1 RNA Segment 10

Nucleotide Sequence of the Australian Bluetongue Virus Serotype 1 RNA Segment 10 J. gen. Virol. (1988), 69, 945-949. Printed in Great Britain 945 Key words: BTV/genome segment lo/nucleotide sequence Nucleotide Sequence of the Australian Bluetongue Virus Serotype 1 RNA Segment 10 By

More information

Detection of 549 new HLA alleles in potential stem cell donors from the United States, Poland and Germany

Detection of 549 new HLA alleles in potential stem cell donors from the United States, Poland and Germany HLA ISSN 2059-2302 BRIEF COMMUNICATION Detection of 549 new HLA alleles in potential stem cell donors from the United States, Poland and Germany C. J. Hernández-Frederick 1, N. Cereb 2,A.S.Giani 1, J.

More information

A smart acid nanosystem for ultrasensitive. live cell mrna imaging by the target-triggered intracellular self-assembly

A smart acid nanosystem for ultrasensitive. live cell mrna imaging by the target-triggered intracellular self-assembly Electronic Supplementary Material (ESI) for Chemical Science. This journal is The Royal Society of Chemistry 2017 A smart ZnO@polydopamine-nucleic acid nanosystem for ultrasensitive live cell mrna imaging

More information

Integration Solutions

Integration Solutions Integration Solutions (1) a) With no active glycosyltransferase of either type, an ii individual would not be able to add any sugars to the O form of the lipopolysaccharide. Thus, the only lipopolysaccharide

More information

Astaxanthin prevents and reverses diet-induced insulin resistance and. steatohepatitis in mice: A comparison with vitamin E

Astaxanthin prevents and reverses diet-induced insulin resistance and. steatohepatitis in mice: A comparison with vitamin E Supplementary Information Astaxanthin prevents and reverses diet-induced insulin resistance and steatohepatitis in mice: A comparison with vitamin E Yinhua Ni, 1,2 Mayumi Nagashimada, 1 Fen Zhuge, 1 Lili

More information

Cross-talk between mineralocorticoid and angiotensin II signaling for cardiac

Cross-talk between mineralocorticoid and angiotensin II signaling for cardiac ONLINE SUPPLEMENT TO Crosstalk between mineralocorticoid and angiotensin II signaling for cardiac remodeling An Di ZHANG,,3, Aurelie NGUYEN DINH CAT*,,3, Christelle SOUKASEUM *,,3, Brigitte ESCOUBET, 4,

More information

Supplemental Information. Cancer-Associated Fibroblasts Neutralize. the Anti-tumor Effect of CSF1 Receptor Blockade

Supplemental Information. Cancer-Associated Fibroblasts Neutralize. the Anti-tumor Effect of CSF1 Receptor Blockade Cancer Cell, Volume 32 Supplemental Information Cancer-Associated Fibroblasts Neutralize the Anti-tumor Effect of CSF1 Receptor Blockade by Inducing PMN-MDSC Infiltration of Tumors Vinit Kumar, Laxminarasimha

More information

Supplemental Information. Th17 Lymphocytes Induce Neuronal. Cell Death in a Human ipsc-based. Model of Parkinson's Disease

Supplemental Information. Th17 Lymphocytes Induce Neuronal. Cell Death in a Human ipsc-based. Model of Parkinson's Disease Cell Stem Cell, Volume 23 Supplemental Information Th17 Lymphocytes Induce Neuronal Cell Death in a Human ipsc-based Model of Parkinson's Disease Annika Sommer, Franz Maxreiter, Florian Krach, Tanja Fadler,

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION doi: 10.1038/nature05883 SUPPLEMENTARY INFORMATION Supplemental Figure 1 Prostaglandin agonists and antagonists alter runx1/cmyb expression. a-e, Embryos were exposed to (b) PGE2 and (c) PGI2 (20μM) and

More information

1. Describe the relationship of dietary protein and the health of major body systems.

1. Describe the relationship of dietary protein and the health of major body systems. Food Explorations Lab I: The Building Blocks STUDENT LAB INVESTIGATIONS Name: Lab Overview In this investigation, you will be constructing animal and plant proteins using beads to represent the amino acids.

More information

Supplementary Figure 1

Supplementary Figure 1 Supplementary Figure 1 3 3 3 1 1 Bregma -1.6mm 3 : Bregma Ref) Http://www.mbl.org/atlas165/atlas165_start.html Bregma -.18mm Supplementary Figure 1 Schematic representation of the utilized brain slice

More information

SUPPORTING INFORMATION

SUPPORTING INFORMATION SUPPORTING INFORMATION Biology is different in small volumes: endogenous signals shape phenotype of primary hepatocytes cultured in microfluidic channels Amranul Haque, Pantea Gheibi, Yandong Gao, Elena

More information

Advanced Subsidiary Unit 1: Lifestyle, Transport, Genes and Health

Advanced Subsidiary Unit 1: Lifestyle, Transport, Genes and Health Write your name here Surname Other names Edexcel GCE Centre Number Candidate Number Biology Advanced Subsidiary Unit 1: Lifestyle, Transport, Genes and Health Thursday 8 January 2009 Morning Time: 1 hour

More information

A basic helix loop helix transcription factor controls cell growth

A basic helix loop helix transcription factor controls cell growth A basic helix loop helix transcription factor controls cell growth and size in root hairs Keke Yi 1,2, Benoît Menand 1,3, Elizabeth Bell 1, Liam Dolan 1,4 Supplementary note Low soil phosphate availability

More information

Supplementary Information. Bamboo shoot fiber prevents obesity in mice by. modulating the gut microbiota

Supplementary Information. Bamboo shoot fiber prevents obesity in mice by. modulating the gut microbiota Supplementary Information Bamboo shoot fiber prevents obesity in mice by modulating the gut microbiota Xiufen Li 1,2, Juan Guo 1, Kailong Ji 1,2, and Ping Zhang 1,* 1 Key Laboratory of Tropical Plant Resources

More information

Supporting Information. Mutational analysis of a phenazine biosynthetic gene cluster in

Supporting Information. Mutational analysis of a phenazine biosynthetic gene cluster in Supporting Information for Mutational analysis of a phenazine biosynthetic gene cluster in Streptomyces anulatus 9663 Orwah Saleh 1, Katrin Flinspach 1, Lucia Westrich 1, Andreas Kulik 2, Bertolt Gust

More information

Supplementary Materials and Methods

Supplementary Materials and Methods DD2 suppresses tumorigenicity of ovarian cancer cells by limiting cancer stem cell population Chunhua Han et al. Supplementary Materials and Methods Analysis of publicly available datasets: To analyze

More information

Supporting Information

Supporting Information Supporting Information Malapeira et al. 10.1073/pnas.1217022110 SI Materials and Methods Plant Material and Growth Conditions. A. thaliana seedlings were stratified at 4 C in the dark for 3 d on Murashige

More information

Description of Supplementary Files. File Name: Supplementary Information Description: Supplementary Figures and Supplementary Tables

Description of Supplementary Files. File Name: Supplementary Information Description: Supplementary Figures and Supplementary Tables Description of Supplementary Files File Name: Supplementary Information Description: Supplementary Figures and Supplementary Tables Supplementary Figure 1: (A), HCT116 IDH1-WT and IDH1-R132H cells were

More information

Integrative Metabolism: Significance

Integrative Metabolism: Significance Integrative Metabolism: Significance Energy Containing Nutrients Carbohydrates Fats Proteins Catabolism Energy Depleted End Products H 2 O NH 3 ADP + Pi NAD + NADP + FAD + Pi NADH+H + NADPH+H + FADH2 Cell

More information

Phylogenetic analysis of human and chicken importins. Only five of six importins were studied because

Phylogenetic analysis of human and chicken importins. Only five of six importins were studied because Supplementary Figure S1 Phylogenetic analysis of human and chicken importins. Only five of six importins were studied because importin-α6 was shown to be testis-specific. Human and chicken importin protein

More information

Formylpeptide receptor2 contributes to colon epithelial homeostasis, inflammation, and tumorigenesis

Formylpeptide receptor2 contributes to colon epithelial homeostasis, inflammation, and tumorigenesis Supplementary Data Formylpeptide receptor2 contributes to colon epithelial homeostasis, inflammation, and tumorigenesis Keqiang Chen, Mingyong Liu, Ying Liu, Teizo Yoshimura, Wei Shen, Yingying Le, Scott

More information

Amino acids-incorporated nanoflowers with an

Amino acids-incorporated nanoflowers with an Amino acids-incorporated nanoflowers with an intrinsic peroxidase-like activity Zhuo-Fu Wu 1,2,+, Zhi Wang 1,+, Ye Zhang 3, Ya-Li Ma 3, Cheng-Yan He 4, Heng Li 1, Lei Chen 1, Qi-Sheng Huo 3, Lei Wang 1,*

More information

Biology 12 January 2004 Provincial Examination

Biology 12 January 2004 Provincial Examination Biology 12 January 2004 Provincial Examination ANSWER KEY / SCORING GUIDE CURRICULUM: Organizers 1. Cell Biology 2. Cell Processes and Applications 3. Human Biology Sub-Organizers A, B, C, D E, F, G, H

More information

Nomenclature What is in a name? My name Joseˊ Jimenez = Bill Dana John L.C. Savony = Frank Fontaine

Nomenclature What is in a name? My name Joseˊ Jimenez = Bill Dana John L.C. Savony = Frank Fontaine Nomenclature What is in a name? My name Joseˊ Jimenez = Bill Dana John L.C. Savony = Frank Fontaine Three categories of Amyloid Terms 1. Amyloidologists, Amyloid Centers, Researchers official nomenclature

More information

Supplementary Information

Supplementary Information Supplementary Information Remodeling of heterochromatin structure slows neuropathological progression and prolongs survival in an animal model of Huntington s disease Junghee Lee, Yu Jin Hwang, Yunha Kim,

More information

Protein sequence alignment using binary string

Protein sequence alignment using binary string Available online at www.scholarsresearchlibrary.com Scholars Research Library Der Pharmacia Lettre, 2015, 7 (5):220-225 (http://scholarsresearchlibrary.com/archive.html) ISSN 0975-5071 USA CODEN: DPLEB4

More information

9/6/2011. Amino Acids. C α. Nonpolar, aliphatic R groups

9/6/2011. Amino Acids. C α. Nonpolar, aliphatic R groups Amino Acids Side chains (R groups) vary in: size shape charge hydrogen-bonding capacity hydrophobic character chemical reactivity C α Nonpolar, aliphatic R groups Glycine (Gly, G) Alanine (Ala, A) Valine

More information

LAB#23: Biochemical Evidence of Evolution Name: Period Date :

LAB#23: Biochemical Evidence of Evolution Name: Period Date : LAB#23: Biochemical Evidence of Name: Period Date : Laboratory Experience #23 Bridge Worth 80 Lab Minutes If two organisms have similar portions of DNA (genes), these organisms will probably make similar

More information

Beta Thalassemia Sami Khuri Department of Computer Science San José State University Spring 2015

Beta Thalassemia Sami Khuri Department of Computer Science San José State University Spring 2015 Bioinformatics in Medical Product Development SMPD 287 Three Beta Thalassemia Sami Khuri Department of Computer Science San José State University Hemoglobin Outline Anatomy of a gene Hemoglobinopathies

More information

BHP 2-7 and Nthy-ori 3-1 cells were grown in RPMI1640 medium (Hyclone) supplemented with 10% fetal bovine serum (Gibco), 2mM L-glutamine, and 100 U/mL

BHP 2-7 and Nthy-ori 3-1 cells were grown in RPMI1640 medium (Hyclone) supplemented with 10% fetal bovine serum (Gibco), 2mM L-glutamine, and 100 U/mL 1 2 3 4 Materials and Methods Cell culture BHP 2-7 and Nthy-ori 3-1 cells were grown in RPMI1640 medium (Hyclone) 5 supplemented with 10% fetal bovine serum (Gibco), 2mM L-glutamine, and 100 U/mL 6 penicillin-streptomycin.

More information

Supplementary Figure 1

Supplementary Figure 1 Metastatic melanoma Primary melanoma Healthy human skin Supplementary Figure 1 CD22 IgG4 Supplementary Figure 1: Immunohisochemical analysis of CD22+ (left) and IgG4 (right), cells (shown in red and indicated

More information

Supplementary information

Supplementary information Supplementary information Unique polypharmacology nuclear receptor modulator blocks inflammatory signaling pathways Mi Ra Chang 1, Anthony Ciesla 1, Timothy S. Strutzenberg 1, Scott J. Novick 1, Yuanjun

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION doi:10.1038/nature10743 Supplementary Figures and Legends Supplementary Figure 1. CYP17A1 (red boxes) lies at the intersection of steroid hormone biosynthetic pathways. CYP17A1

More information

Short polymer. Dehydration removes a water molecule, forming a new bond. Longer polymer (a) Dehydration reaction in the synthesis of a polymer

Short polymer. Dehydration removes a water molecule, forming a new bond. Longer polymer (a) Dehydration reaction in the synthesis of a polymer HO 1 2 3 H HO H Short polymer Dehydration removes a water molecule, forming a new bond Unlinked monomer H 2 O HO 1 2 3 4 H Longer polymer (a) Dehydration reaction in the synthesis of a polymer HO 1 2 3

More information

Biomolecules: amino acids

Biomolecules: amino acids Biomolecules: amino acids Amino acids Amino acids are the building blocks of proteins They are also part of hormones, neurotransmitters and metabolic intermediates There are 20 different amino acids in

More information

SUPPLEMENTAL METHODS Cell culture RNA extraction and analysis Immunohistochemical analysis and laser capture microdissection (LCM)

SUPPLEMENTAL METHODS Cell culture RNA extraction and analysis Immunohistochemical analysis and laser capture microdissection (LCM) SUPPLEMENTAL METHODS Cell culture Human peripheral blood mononuclear cells were isolated from healthy donors by Ficoll density gradient centrifugation. Monocyte differentiation to resting macrophages ()

More information

Citation for published version (APA): Hofstra, R. M. W. (1995). The RET gene and its associated diseases s.n.

Citation for published version (APA): Hofstra, R. M. W. (1995). The RET gene and its associated diseases s.n. University of Groningen The RET gene and its associated diseases Hofstra, Robert Martinus Wouter IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION BASELINE ISCHAEMIA a b Phd2 +/- c d Collateral growth and maintenance SMC recruitment SMC proliferation Phd2 +/- NF- B off NF- B on NF- B on NF- B on Endothelial cell Smooth muscle cell Pro-arteriogenic

More information

Loyer, et al. microrna-21 contributes to NASH Suppl 1/15

Loyer, et al. microrna-21 contributes to NASH Suppl 1/15 Loyer, et al. microrna-21 contributes to NASH Suppl 1/15 SUPPLEMENTARY MATERIAL: Liver MicroRNA-21 is Overexpressed in Non Alcoholic Steatohepatitis and Contributes to the Disease in Experimental Models

More information

ice-cold 70% ethanol with gentle vortexing, incubated at -20 C for 4 hours, and washed with PBS.

ice-cold 70% ethanol with gentle vortexing, incubated at -20 C for 4 hours, and washed with PBS. Cell cycle analysis For cell cycle analysis, single cell suspensions of E12.5 fetal liver cells were suspended in 4 ml ice-cold 7% ethanol with gentle vortexing, incubated at -2 C for 4 hours, and washed

More information

Baseline clinical characteristics for the 81 CMML patients Routine diagnostic testing and statistical analyses... 3

Baseline clinical characteristics for the 81 CMML patients Routine diagnostic testing and statistical analyses... 3 Next-Generation Sequencing Technology Reveals a Characteristic Pattern of Molecular Mutations in 72.8% of Chronic Myelomonocytic Leukemia (CMML) by Detecting Frequent Alterations in TET2, CBL, RAS, and

More information

Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis SUPPLEMENTARY INFORMATION

Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis SUPPLEMENTARY INFORMATION Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis Pooja Arora 1, Aneesh Goyal 2, Vivek T atarajan 1, Eerappa Rajakumara 2, Priyanka Verma 1, Radhika Gupta 3,

More information

Mutation Screening and Association Studies of the Human UCP 3 Gene in Normoglycemic and NIDDM Morbidly Obese Patients

Mutation Screening and Association Studies of the Human UCP 3 Gene in Normoglycemic and NIDDM Morbidly Obese Patients Mutation Screening and Association Studies of the Human UCP 3 Gene in Normoglycemic and NIDDM Morbidly Obese Patients Shuichi OTABE, Karine CLEMENT, Séverine DUBOIS, Frederic LEPRETRE, Veronique PELLOUX,

More information

AMINO ACID METABOLISM. Sri Widia A Jusman Dept. of Biochemistry & Molecular Biology FMUI

AMINO ACID METABOLISM. Sri Widia A Jusman Dept. of Biochemistry & Molecular Biology FMUI AMINO ACID METABOLISM Sri Widia A Jusman Dept. of Biochemistry & Molecular Biology FMUI Amino acids derived from dietary protein absorbed from intestine through blood taken up by tissues used for biosynthesis

More information

Isolate Sexual Idiomorph Species

Isolate Sexual Idiomorph Species SUPLEMENTARY TABLE 1. Isolate identification, sexual idiomorph and species of each isolate used for MAT locus distribution in Paracoccidioides species. Isolate Sexual Idiomorph Species Pb01 MAT1-1 P. lutzii

More information

Quantitative analysis of hydrophilic metabolite using ion-paring chromatography with a high-speed triple quadrupole mass spectrometer

Quantitative analysis of hydrophilic metabolite using ion-paring chromatography with a high-speed triple quadrupole mass spectrometer Quantitative analysis of hydrophilic metabolite using ion-paring chromatography with a high-speed triple ASMS 2012 ThP11-251 Zanariah Hashim 1 ; Yudai Dempo1; Tairo Ogura 2 ; Ichiro Hirano 2 ; Junko Iida

More information

E.coli Core Model: Metabolic Core

E.coli Core Model: Metabolic Core 1 E.coli Core Model: Metabolic Core 2 LEARNING OBJECTIVES Each student should be able to: Describe the glycolysis pathway in the core model. Describe the TCA cycle in the core model. Explain gluconeogenesis.

More information

Page 8/6: The cell. Where to start: Proteins (control a cell) (start/end products)

Page 8/6: The cell. Where to start: Proteins (control a cell) (start/end products) Page 8/6: The cell Where to start: Proteins (control a cell) (start/end products) Page 11/10: Structural hierarchy Proteins Phenotype of organism 3 Dimensional structure Function by interaction THE PROTEIN

More information

Amino acid metabolism II

Amino acid metabolism II Amino acid metabolism II Fates of amino acid carbon skeleton degradation to common intermediates pyruvate, intermediates of citric acid cycle, acetyl-coa Glucogenic AA precursors of glucose - degradation

More information

Objective: You will be able to explain how the subcomponents of

Objective: You will be able to explain how the subcomponents of Objective: You will be able to explain how the subcomponents of nucleic acids determine the properties of that polymer. Do Now: Read the first two paragraphs from enduring understanding 4.A Essential knowledge:

More information

*To whom correspondence should be addressed. This PDF file includes:

*To whom correspondence should be addressed.   This PDF file includes: www.sciencemag.org/cgi/content/full/science.1212182/dc1 Supporting Online Material for Partial Retraction to Detection of an Infectious Retrovirus, XMRV, in Blood Cells of Patients with Chronic Fatigue

More information

Fate of Dietary Protein

Fate of Dietary Protein Fate of Dietary Protein Dietary protein Stomach: l, pepsin Denatured and partially hydrolyzed protein (large polypeptides) small intestine: proteases Amino acids and dipeptides intestinal lining: proteases

More information

SUPPLEMENTARY RESULTS

SUPPLEMENTARY RESULTS SUPPLEMENTARY RESULTS Supplementary Table 1. hfpr1- Flpln-CHO hfpr2-flpln-cho pec 50 E max (%) Log( /K A) Log( /K A) N pec 50 E max (%) Log( /K A) Log( /K A) n ERK1/2 phosphorylation fmlp 9.0±0.6 80±7

More information

Four Classes of Biological Macromolecules. Biological Macromolecules. Lipids

Four Classes of Biological Macromolecules. Biological Macromolecules. Lipids Biological Macromolecules Much larger than other par4cles found in cells Made up of smaller subunits Found in all cells Great diversity of func4ons Four Classes of Biological Macromolecules Lipids Polysaccharides

More information

Amino Acid Metabolism

Amino Acid Metabolism Amino Acid Metabolism Fate of Dietary Protein Dietary protein Stomach: l, pepsin Denatured and partially hydrolyzed protein (large polypeptides) small intestine: proteases Amino acids and dipeptides intestinal

More information

Relationship of the APOA5/A4/C3/A1 gene cluster and APOB gene polymorphisms with dyslipidemia

Relationship of the APOA5/A4/C3/A1 gene cluster and APOB gene polymorphisms with dyslipidemia elationship of the APOA5/A4/C3/A1 gene cluster and APOB gene polymorphisms with dyslipidemia H.J. Ou 1, G. Huang 2, W. Liu 3, X.L. Ma 2, Y. Wei 4, T. Zhou 5 and Z.M. Pan 3 1 Department of Neurology, The

More information

CS612 - Algorithms in Bioinformatics

CS612 - Algorithms in Bioinformatics Spring 2016 Protein Structure February 7, 2016 Introduction to Protein Structure A protein is a linear chain of organic molecular building blocks called amino acids. Introduction to Protein Structure Amine

More information

PATIENTS AND METHODS. Subjects

PATIENTS AND METHODS. Subjects PATIENTS AND METHODS Subjects Twenty-nine morbidly obese subjects involved in a gastric surgery program were enrolled in the study between October 25 and March 21. Bariatric surgery was performed in patients

More information

Plasmids Western blot analysis and immunostaining Flow Cytometry Cell surface biotinylation RNA isolation and cdna synthesis

Plasmids Western blot analysis and immunostaining Flow Cytometry Cell surface biotinylation RNA isolation and cdna synthesis Plasmids psuper-retro-s100a10 shrna1 was constructed by cloning the dsdna oligo 5 -GAT CCC CGT GGG CTT CCA GAG CTT CTT TCA AGA GAA GAA GCT CTG GAA GCC CAC TTT TTA-3 and 5 -AGC TTA AAA AGT GGG CTT CCA GAG

More information

CIRCRESAHA/2004/098145/R1 - ONLINE 1. Validation by Semi-quantitative Real-Time Reverse Transcription PCR

CIRCRESAHA/2004/098145/R1 - ONLINE 1. Validation by Semi-quantitative Real-Time Reverse Transcription PCR CIRCRESAHA/2004/098145/R1 - ONLINE 1 Expanded Materials and Methods Validation by Semi-quantitative Real-Time Reverse Transcription PCR Expression patterns of 13 genes (Online Table 2), selected with respect

More information

Beta Thalassemia Case Study Introduction to Bioinformatics

Beta Thalassemia Case Study Introduction to Bioinformatics Beta Thalassemia Case Study Sami Khuri Department of Computer Science San José State University San José, California, USA sami.khuri@sjsu.edu www.cs.sjsu.edu/faculty/khuri Outline v Hemoglobin v Alpha

More information

Metabolism of amino acids. Vladimíra Kvasnicová

Metabolism of amino acids. Vladimíra Kvasnicová Metabolism of amino acids Vladimíra Kvasnicová Classification of proteinogenic AAs -metabolic point of view 1) biosynthesis in a human body nonessential (are synthesized) essential (must be present in

More information

Nitrogen Metabolism. Overview

Nitrogen Metabolism. Overview Nitrogen Metabolism Pratt and Cornely Chapter 18 Overview Nitrogen assimilation Amino acid biosynthesis Nonessential aa Essential aa Nucleotide biosynthesis Amino Acid Catabolism Urea Cycle Juicy Steak

More information

Pathway overview. Glucose + 2NAD + + 2ADP +2Pi 2NADH + 2pyruvate + 2ATP + 2H 2 O + 4H +

Pathway overview. Glucose + 2NAD + + 2ADP +2Pi 2NADH + 2pyruvate + 2ATP + 2H 2 O + 4H + Glycolysis Glycolysis The conversion of glucose to pyruvate to yield 2ATP molecules 10 enzymatic steps Chemical interconversion steps Mechanisms of enzyme conversion and intermediates Energetics of conversions

More information

Resistance to Tetracycline Antibiotics by Wangrong Yang, Ian F. Moore, Kalinka P. Koteva, Donald W. Hughes, David C. Bareich and Gerard D. Wright.

Resistance to Tetracycline Antibiotics by Wangrong Yang, Ian F. Moore, Kalinka P. Koteva, Donald W. Hughes, David C. Bareich and Gerard D. Wright. Supplementary Data for TetX is a Flavin-Dependent Monooxygenase Conferring Resistance to Tetracycline Antibiotics by Wangrong Yang, Ian F. Moore, Kalinka P. Koteva, Donald W. Hughes, David C. Bareich and

More information

Amino Acid Metabolism

Amino Acid Metabolism Amino Acid Metabolism Last Week Most of the Animal Kingdom = Lazy - Most higher organisms in the animal kindom don t bother to make all of the amino acids. - Instead, we eat things that make the essential

More information

Supplementary Figure 1

Supplementary Figure 1 Supplementary Figure 1 Supplementary Figure 1: Cryopreservation alters CD62L expression by CD4 T cells. Freshly isolated (left) or cryopreserved PBMCs (right) were stained with the mix of antibodies described

More information

TetR repressor-based bioreporters for the detection of doxycycline using Escherichia

TetR repressor-based bioreporters for the detection of doxycycline using Escherichia Supplementary materials TetR repressor-based bioreporters for the detection of doxycycline using Escherichia coli and Acinetobacter oleivorans Hyerim Hong and Woojun Park * Department of Environmental

More information

McAlpine PERK-GSK3 regulates foam cell formation. Supplemental Material. Supplementary Table I. Sequences of real time PCR primers.

McAlpine PERK-GSK3 regulates foam cell formation. Supplemental Material. Supplementary Table I. Sequences of real time PCR primers. Mclpine PERK-GSK3 regulates foam cell formation Supplemental Material Supplementary Table I. Sequences of real time PCR primers. Primer Name Primer Sequences (5-3 ) Product Size (bp) GRP78 (human) Fwd:

More information

Biological systems interact, and these systems and their interactions possess complex properties. STOP at enduring understanding 4A

Biological systems interact, and these systems and their interactions possess complex properties. STOP at enduring understanding 4A Biological systems interact, and these systems and their interactions possess complex properties. STOP at enduring understanding 4A Homework Watch the Bozeman video called, Biological Molecules Objective:

More information

Biochemistry 423 Final Examination NAME:

Biochemistry 423 Final Examination NAME: Biochemistry 423 Final Examination NAME: 1 Circle the single BEST answer (3 points each) 1. At equilibrium the free energy of a reaction G A. depends only on the temperature B. is positive C. is 0 D. is

More information