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ATACSeq fastq files associated with the manuscript entitled 'Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion'
<p>This next-generation sequencing dataset is associated with the research manuscript entitled ‘<em>Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion</em>’ (https://www.biorxiv.org/content/10.1101/754002v2).</p> <p>The zipped folder ‘<strong>Zenodo_Saxena_etal_2021_ATACSeq_FastqFiles</strong>’ contains raw/unprocessed ATACSeq Fatsq read files for postnatal day 5 (P5) mouse (Mus) and jerboa (Jac) cartilage samples (Metatarsal = MT; Radius/Ulna = RU).</p> <p>> The <strong>Jac_P5</strong> subfolder contains paired-end reads (R1 and R2) for three jerboa metatarsals (MT1-3) and radius/ulna (RU1-3) biological replicates.</p> <p>> The <strong>Mus_P5</strong> subfolder contains paired-end reads (R1 and R2) for two mouse metatarsals (MT1-2) and radius/ulna (RU1-2) biological replicates.</p>
Supplementary data for: Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression
<p><strong>Supplementary Note 1:</strong></p> <ul> <li>S1 Text: Oncogenomic comparisons between SB candidate Trunk driver genes and their direct orthologs in human Cancer Gene Census; Pyrosequencing analysis of SB-driven keratinocyte cancer models; References.</li> </ul> <p><strong>Supplementary Figures 1-11:</strong></p> <ul> <li>S1 Fig: Overview of genetic crosses to generate SB|Trp53|Onc3 mouse model.</li> <li>S2 Fig: SB insertion patterns in activated and inactivated drivers.</li> <li>S3 Fig: Evaluating the reproducibility of SBCapSeq results from bulk cuSCC and normal skin specimens.</li> <li>S4 Fig. Hierarchical two-dimensional clustering of recurrent events in cuKA and cuSCC.</li> <li>S5 Fig. Curated biological pathways and processes enriched within SB-induced cuSCC.</li> <li>S7 Fig: ZMIZ1 metagene within the TCGA Head & Neck Squamous Cell Carcinoma (hnSCC) RNA-seq dataset.</li> <li>S8 Fig: Clonally selected SB insertions affect trunk driver proto-oncogene expression in SB-cuSCC genomes.</li> <li>S9 Fig: Clonally selected SB insertions affect trunk driver genes by inactivating expression in SB-cuSCC genomes.</li> <li>S10 Fig: CREBBP knockdown does not alter proliferation rate in cuSCC cell lines.</li> <li>S11 Fig: Gross photographs of cuSCC xenograft masses collected at necropsy showing robust TurboGFP expression.</li> <li>S12 Fig: SB T2/Onc3 TG.12740 allele donor position mapping and exclusion for SB Driver Analysis.</li> </ul> <p><strong>Supplementary Tables 1-20:</strong></p> <ul> <li>S1 Table: Tumor incidence and subgroup classifications by cohort.</li> <li>S2 Table: Specimen metafile data for projects sequenced using SBCapSeq protocol with Ion Torrent Proton sequencer.</li> <li>S3 Table: Discovery and progression SB Driver Analysis for cuSCC60_SBC.</li> <li>S4 Table: Trunk SB Driver Analysis for cuSCC60_SBC.</li> <li>S5 Table: Discovery and progression SB Driver Analysis for cuKA11_SBC.</li> <li>S6 Table: Trunk SB Driver Analysis for cuKA11_SBC.</li> <li>S7 Table: Discovery and progression SB Driver Analysis for cuSK32_SBC.</li> <li>S8 Table: SBCapSeq read depth and analysis for 4 cuSCC genomes selected for multi-region resequencing because they had intermixing of cuSCC and cuKA histologies.</li> <li>S9 Table: Enrichr gene set pathway enrichment analysis of cuSCC drivers.</li> <li>S10 Table: Summary of 7 cuSCC transcriptomes selected for whole transcriptome RNAseq analysis.</li> <li>S11 Table: BED file of SBfusion insertions in 7 cuSCC genomes by whole transcriptome RNAseq analysis.</li> <li>S12 Table: Venn diagram for overlap of genes with SBfusion reads detected by whole transcriptome RNAseq analysis and cuSCC60_SBC discovery driver.</li> <li>S13 Table: Venn diagram for overlap of genes with SBfusion reads detected by whole transcriptome RNAseq analysis and all cuSCC drivers.</li> <li>S14 Table: Transcripts per million (TPM) normalized whole transcriptome RNAseq values per gene from RNA isolated from cuSCC genomes with and without Zmiz1 insertions.</li> <li>S15 Table: Fragments Per Kilobase of Transcripts per Million (FPKM) normalized whole transcriptome RNAseq values per gene transcript from RNA isolated from cuSCC genomes with and without Zmiz1 insertions.</li> <li>S16 Table: Normalized microarray values per gene from RNA isolated from cuSCC genomes with and without <em>Zmiz1</em> insertions.</li> <li>S17 Table: Normalized microarray values per probe from RNA isolated from cuSCC genomes with and without <em>Zmiz1</em> insertions.</li> <li>S18 Table: All 289 genes with differential expression analysis from microarray data from RNA isolated from cuSCC genomes with and without Zmiz1 insertions with P<0.0001 and q<0.05.</li> <li>S19 Table: Lentiviral vectors containing shRNAs used in this study.</li> <li>S20 Table: TaqMan probes used in this study.</li> </ul> <p><strong>Supplementary Datasets 1-5:</strong></p> <ul> <li>S1 Data: BED file of SB insertions for cuSCC60_SBC.</li> <li>S2 Data: BED file of SB insertions for cuKA11_SBC.</li> <li>S3 Data: BED file of SB insertions for cuSK32_SBC</li> <li>S4 Data: BED file of SB insertions for 4 cuSCC genomes selected for multi-region resequencing because they had intermixing of cuSCC and cuKA histologies.</li> <li>S5 Data: Numerical data for graphs pertaining to Figure Panels Fig1A; Fig5A–E; Fig6A–B,D; Fig7C–G; Fig8A–B,D–F; Fig9A–I in the paper on the publicly availble <em>PLOS Genetics</em> Web site.</li> </ul>
Figures 20–24. Partially identified Geometridae Sterrhinae. 20–22 in A preliminary catalogue of the moths (Lepidoptera except Papilionoidea) of Tobago, West Indies
Figures 20–24. Partially identified Geometridae Sterrhinae. 20–22, Idaea sp. near triangulata (Warren); 23–24, Scopula sp. 20, ♂, Speyside, MVL, 14–17 May 1982 (M.J.W. Cock) [MJWC]. 21, ♀, Charlotteville, at light, 15–19 Jun 1998 (Roger Hammond & Piers Meynell) [MJWC]. 22, ♀, Morne Bleu, Textel Installation, at light, 6 Dec 1980 (M.J.W. Cock) [MJWC]. 23, ♂, Crown Point, at light, 9 Jan 1982 (M.J.W. Cock) [MJWC]. 24, ♀, Speyside, MVL, 14–17 May 1982 (M.J.W. Cock) [MJWC]
Figures 32–34. Partially identified Tobago Erebidae. 32 in A preliminary catalogue of the moths (Lepidoptera except Papilionoidea) of Tobago, West Indies
Figures 32–34. Partially identified Tobago Erebidae. 32, Metria sp. ♂, Trinidad, Mt. St. Benedict, Pax Guest House, 600 ft., at light, 10–16 Jul 1996 (M.J.W. Cock) [MJWC]. 33, Ophisma sp. nr. variata Schaus, ♀, Tobago, Speyside, MVL, 14–17 May 1982 (M.J.W. Cock) [MJWC]. 34, Hemicephalis sp. nr. laronia (Druce) ♂ Trinidad, Curepe, MVL, 13 Sep 1978 (M.J.W. Cock) [MJWC].
Global ubiquitylation analysis of mitochondria in primary neurons identifies endogenous Parkin targets following activation of PINK1
<p> How activation of PINK1 and Parkin leads to elimination of damaged mitochondria by mitophagy is largely based on cell lines with few studies in neurons. Herein we have undertaken proteomic analysis of mitochondria from mouse neurons to identify ubiquitylated substrates of endogenous Parkin. Comparative analysis with human iNeuron datasets revealed a subset of 49 PINK1 activation-dependent diGLY sites in 22 proteins conserved across mouse and human systems. We employ reconstitution assays to demonstrate direct ubiquitylation by Parkin in vitro. We also identified a subset of cytoplasmic proteins recruited to mitochondria that undergo PINK1 and Parkin independent ubiquitylation indicating the presence of alternate ubiquitin E3 ligase pathways that are activated by mitochondrial depolarisation in neurons. Finally we have developed an online resource to search for ubiquitin sites and enzymes in mitochondria of neurons, MitoNUb. These findings will aid future studies to understand Parkin activation in neuronal subtypes.</p> <p> </p> <p><strong>FILE DECRIPTIONS</strong></p> <p><strong>Figure 1C: Immunoblots for PINK1 signaling in PINK1 WT and KO mouse cortical neurons.</strong></p> <p>Scans of X-ray film:</p> <ul> <li>GAPDH shown in <strong>Figure1C_GAPDH.tif</strong></li> <li>Parkin shown in <strong>Figure1C_Parkin.tif</strong></li> <li>Phospho-Ser65 Parkin shown in <strong>Figure1C_ParkinPSer65.tif</strong></li> <li>PINK1 shown in <strong>Figure1C_PINK1.tif </strong>(immunoprecipitation)</li> <li>Rab8A shown in <strong>Figure1C_Rab8A.tif</strong></li> <li>Phospho-Ser111 Rab8A shown in <strong>Figure1C_Rab8APSer111.tif</strong></li> <li>Ubiquitin shown in <strong>Figure1C_ S10A_Ubiquitin.tif </strong>(same blot used for Figure_S10A, Halo-multiDSK pull-down)</li> <li>Phospho-Ser65 Ubiquitin shown in <strong>Figure1C_S10A_UbiquitinPSer65.tif </strong>(same blot used for Figure_S10A, Halo-multiDSK pull-down)</li> </ul> <p> </p> <p><strong>Figure 4A: Immunoblots for time-course of Parkin-dependent substrates in C57BL/6J neurons.</strong></p> <p>Scans of X-ray film:</p> <ul> <li>CISD1 shown in <strong>Figure4A_CISD1.tif </strong>(Halo-multiDSK pull-down) <ul> <li><strong> Figure4A_INPUT_CISD1.tif</strong> (INPUT)</li> </ul> </li> <li>CPT1α shown in <strong>Figure4A_ CPT1</strong><strong>a</strong><strong>.tif</strong> (Halo-multiDSK pull-down) <ul> <li><strong> Figure4A_INPUT_CPT1</strong><strong>a</strong><strong>.tif</strong> (INPUT)</li> </ul> </li> <li>Ubiquitin shown in <strong>Figure4A_Ubiquitin.tif </strong>(Halo-multiDSK pull-down) <ul> <li><strong> Figure4A_INPUT_Ubiquitin.tif</strong> (INPUT)</li> </ul> </li> <li>Phospho-Ser65 Ubiquitin shown in <strong>Figure4_UbiquitinPSer65.tif </strong>(Halo-multiDSK pull-down)</li> <li>GAPDH Shown in <strong>Figure4A_INPUT_GAPDH.tif </strong>(INPUT)</li> </ul> <p><strong>Figure 4B: Immunoblots for validation of Parkin-dependent substrates in PARKIN WT and KO neurons.</strong></p> <p>Scans of X-ray film:</p> <ul> <li>CISD1 shown in <strong>Figure4B_CISD1.tif </strong>(Halo-multiDSK pull-down) <ul> <li>(bottom blot)<strong> Figure4B_INPUT_CPT1a_CISD1.tif</strong> (INPUT)</li> </ul> </li> <li>CPT1α shown in <strong>Figure4B_ CPT1a.tif</strong> (Halo-multiDSK pull-down) <ul> <li>(top blot)<strong> Figure4B_INPUT_CPT1a_CISD1.tif</strong> ( (INPUT)</li> </ul> </li> <li>Ubiquitin shown in <strong>Figure4B_Ubiquitin.tif </strong>(Halo-multiDSK pull-down) <ul> <li><strong> Figure4B_INPUT_Ubiquitin.tif</strong> (INPUT)</li> </ul> </li> <li>Phospho-Ser65 Ubiquitin shown in <strong>Figure4B_UbiquitinPSer65.tif </strong>(Halo-multiDSK pull-down)</li> <li>GAPDH Shown in <strong>Figure4B_INPUT_GAPDH.tif </strong>(INPUT)</li> </ul> <p> </p> <p><strong>Figure 5A: Immunoblots for <em>in vitro</em> reconstitution assay in PINK1 WT and KO mouse embryonic fibroblasts.</strong></p> <p>Scans of X-ray film:</p> <ul> <li>CISD1shown in <strong>Figure5A_CISD1.tif</strong></li> <li>CPT1α shown in <strong>Figure5A_ CPT1a.tif</strong></li> <li>CYB5B shown in <strong>Figure5A_CYB5B.tif</strong></li> <li>HK1 shown in <strong>Figure5A_HK1.tif</strong></li> <li>MFN2 shown in <strong>Figure5A_MFN2.tif</strong></li> <li>VDAC shown in <strong>Figure5A_VDAC.tif</strong></li> <li>Phospho-Ser65 Parkin shown in <strong>Figure5A_ParkinPSer65.tif</strong></li> <li>Parkin shown in <strong>Figure5A_Parkin.tif</strong></li> <li>Ubiquitin shown in <strong>Figure5A_Ubiquitin.tif</strong></li> <li>Phospho-Ser65 Ubiquitin shown in <strong>Figure5A_UbiquitinPSer65.tif </strong></li> </ul> <p> </p> <p><strong>Figure 5B: Immunoblots for validation of Parkin-dependent substrates in<em> in vitro </em>studies.</strong></p> <p>Scans of Western blots (LI-COR):</p> <ul> <li>CPT1α shown in <strong>Figure5B_ CPT1 </strong><strong>α_800nm</strong><strong>.tif</strong></li> <li>Flag-Ub (CPT1α) shown in <strong>Figure5B_ CPT1 </strong><strong>α_Flag_800nm</strong><strong>.tif</strong></li> <li>His (CPT1α) shown in <strong>Figure5B_ CPT1 </strong><strong>α_His_800nm</strong><strong>.tif</strong></li> </ul> <p> </p> <ul> <li>Miro1 shown in <strong>Figure5B_Miro1_800nm.tif</strong></li> <li>Flag-Ub (Miro1) shown in <strong>Figure5B_ Miro1</strong><strong>_Flag_800nm</strong><strong>.tif</strong></li> <li>His (Miro1) shown in <strong>Figure5B_ Miro1</strong><strong>_His_800nm</strong><strong>.tif</strong></li> </ul> <p> </p> <p><strong>Figure 5C: Immunoblots for time-course of CPT1</strong><strong>α</strong><strong> ubiquitylation in<em> in vitro </em>studies.</strong></p> <p>Scans of Western blots (LI-COR):</p> <ul> <li>CPT1α shown in top blot: <strong>Figure5C_Flag_CPT1</strong><strong>α_800nm</strong><strong>.tif</strong></li> <li>Flag-Ub shown in bottom blot: <strong>Figure5C_Flag_CPT1</strong><strong>α_800nm</strong><strong>.tif</strong></li> <li>His shown in <strong>Figure5C_ CPT1 </strong><strong>α_His_800nm</strong><strong>.tif</strong></li> </ul> <p> </p> <p><strong>Figure S3A: Immunoblots for PINK1 signaling in C57BL/6J neurons.</strong></p> <p>Scans of X-ray film:</p> <ul> <li>GAPDH shown in <strong>FigureS3A_GAPDH.tif</strong></li> <li>Parkin shown in <strong>FigureS3A_Parkin.tif</strong></li> <li>Phospho-Ser65 Parkin shown in <strong>FigureS3A_ParkinPSer65.tif</strong></li> <li>PINK1 shown in <strong>FigureS3A_PINK1.tif </strong>(immunoprecipitation)</li> <li>Rab8A shown in <strong>FigureS3A_Rab8A.tif</strong></li> <li>Phospho-Ser111 Rab8A shown in <strong>FigureS3A_Rab8APSer111.tif</strong></li> <li>Ubiquitin shown in <strong>FigureS3A_Ubiquitin.tif </strong>(same blot used for Figure_4A, Halo-multiDSK pull-down)</li> <li>Phospho-Ser65 Ubiquitin shown in <strong>FigureS3A_UbiquitinPSer65.tif </strong>(same blot used for Figure_4A, Halo-multiDSK pull-down)</li> <li>Phospho-Ser111 Rab8A and Phospho-Ser65 Parkin also shown in <strong>FigureS3A_ParkinPSer65_Rab8APSer111.tif</strong></li> </ul> <p> </p> <p><strong>Figure S3B: Immunoblots for comparison of Halo-multiDSK and Halo-TUBE in C57BL/6J neurons.</strong></p> <ul> <li>Ubiquitin shown in <strong>FigureS9_S3_Ubiquitin.tif </strong>(same blot used for Figure_S9)</li> <li>Phospho-Ser65 Ubiquitin shown in <strong>FigureS9_S3_UbiquitinPSer65.tif </strong>(same blot used for Figure_S9)</li> </ul> <p> </p> <p><strong>Figure S3C: Immunoblots for PINK1 signaling in Parkin WT and KO mouse cortical neurons.</strong></p> <p>Scans of X-ray film:</p> <ul> <li>GAPDH shown in <strong>FigureS3C_GAPDH.tif</strong></li> <li>Parkin shown in <strong>FigureS3C_Parkin.tif</strong></li> <li>Phospho-Ser65 Parkin shown in <strong>FigureS3C_ParkinPSer65.tif</strong></li> <li>PINK1 shown in <strong>FigureS3C_PINK1.tif </strong>(immunoprecipitation)</li> <li>Rab8A shown in <strong>FigureS3C_Rab8A.tif</strong></li> <li>Phospho-Ser111 Rab8A shown in <strong>FigureS3C_Rab8APSer111.tif</strong></li> <li>Ubiquitin shown in <strong>FigureS3C_ Ubiquitin.tif </strong>(same blot used for Figure_4B, Halo-multiDSK pull-down)</li> <li>Phospho-Ser65 Ubiquitin shown in <strong>FigureS3C_ UbiquitinPSer65.tif </strong>(same blot used for Figure_4B, Halo-multiDSK pull-down)</li> </ul> <p> </p> <p><strong>Figure S4: Immunoblots for PINK-Parkin signaling in VPS35 D620N mouse cortical neurons.</strong></p> <p>Scans of X-ray film:</p> <ul> <li>GAPDH shown in <strong>FigureS4_GAPDH.tif</strong></li> <li>Parkin shown in <strong>FigureS4_Parkin.tif</strong></li> <li>Phospho-Ser65 Parkin shown in <strong>FigureS4_ParkinPSer65.tif</strong></li> <li>Rab8A shown in <strong>FigureS4_Rab8A.tif</strong></li> <li>Phospho-Ser111 Rab8A shown in <strong>FigureS4_Rab8APSer111.tif</strong></li> <li>CISD1 shown in <strong>FigureS4_ CISD1.tif </strong>(Halo-UBQLN1 pull-down)</li> <li>Phospho-Ser65 Ubiquitin shown in <strong>FigureS4_ UbiquitinPSer65.tif</strong> (Halo-UBQLN1 pull-down)</li> <li>VPS35 shown in <strong>FigureS4_VPS35.tif</strong></li> </ul> <p>Scan of Memcode shown in <strong>FigureS4_Memcode.tif</strong></p> <p> </p> <p><strong>Figure S6: Immunoblots for biochemical analysis in C56BL/6J mouse cortical neurons.</strong></p> <p>Scans of X-ray film:</p> <ul> <li>GAPDH shown in <strong>FigureS6_GAPDH.tif</strong></li> <li>Phospho-Ser65 Ubiquitin shown in <strong>FigureS6_ UbiquitinPSer65.tif </strong></li> </ul> <p> </p> <p><strong>Figure S8: Immunoblots for biochemical analysis in PINK1 WT and KO mouse cortical neurons.</strong></p> <p>Scans of X-ray film:</p> <ul> <li>GAPDH shown in <strong>FigureS8_GAPDH.tif</strong></li> <li>Phospho-Ser65 Ubiquitin shown in <strong>FigureS8_ UbiquitinPSer65.tif</strong></li> </ul> <p> </p> <p><strong>Figure S9: Immunoblots for biochemical analysis of ubiquitylated target in C56BL/6J mouse cortical neurons.</strong></p> <p>Membrane-enriched lysate subjected to ubiquitin capture using UBQLN1(TUBE), multiDSK and mutant multiDSK pull-down (Illustration of sample loading in figures FigureS9_ACSL6,_MFN2, _UbiquitinPSer65, _NAV1.7).</p> <p>Scans of X-ray film:</p> <ul> <li>Ubiquitin shown in <strong>FigureS9_S3_Ubiquitin.tif </strong>(same blot used for Figure_S3B)</li> <li>Phospho-Ser65 Ubiquitin shown in <strong>FigureS9_S3_UbiquitinPSer65.tif </strong>(same blot used for Figure_S3B)</li> <li>ABCD3 shown in <strong>FigureS9_ABCD3.tif</strong></li> <li>ACSL1shown in <strong>FigureS9_ ACSL1.tif</strong></li> <li>ACSL6 shown in <strong>FigureS9_ACSL6.tif</strong></li> <li>AGPAT5 shown in <strong>FigureS9_AGPAT5.tif</strong></li> <li>ARHGAP33 shown in <strong>FigureS9_ARHGAP33.tif</strong></li> <li>ATAD1 shown in <strong>FigureS9_ATAD1.tif</strong></li> <li>CAD shown in <strong>FigureS9_ CAD.tif</strong></li> <li>CAMK2A shown in <strong>FigureS9_CAMK2A.tif</strong></li> <li>CAMK2B shown in <strong>FigureS9_CAMK2B.tif</strong></li> <li>CDK16 shown in <strong>FigureS9_CDK16.tif</strong></li> <li>CISD1shown in <strong>FigureS9_CISD1.tif</strong></li> <li>CNN3 shown in<strong> FigureS9_CNN3.tif</strong></li> <li>CPT1α shown in <strong>FigureS9_ CPT1A.tif</strong></li> <li>CYB5B shown in <strong>FigureS9_CYB5B.tif</strong></li> <li>CYB5R3 shown in <strong>FigureS9_CYB5R3.tif</strong></li> <li>DCAKD shown in <strong>FigureS9_DCAKD.tif</strong></li> <li>DCAMKL2 shown in <strong>FigureS9_DCAMKL2.tif</strong></li> <li>FAM213A shown in <strong>FigureS9_FAM213A.tif</strong></li> <li>FBXO41 shown in <strong>FigureS9_FBXO41.tif</strong></li> <li>GK shown in <strong>FigureS9_GK.tif</strong></li> <li>HK1 shown in <strong>FigureS9_HK1.tif</strong></li> <li>HSDL1 shown in <strong>FigureS9_HSDL1.tif</strong></li> <li>MAO-A shown in <strong>FigureS9_MAOA.tif</strong></li> <li>MAO-B shown in <strong>FigureS9_MAOB.tif</strong></li> <li>MAPRE2 shown in <strong>FigureS9_MAPRE2.tif</strong></li> <li>MARC2 shown in <strong>FigureS9_MARC2.tif</strong></li> <li>MFN1 shown in <strong>FigureS9_MFN1.tif</strong></li> <li>MFN2 shown in <strong>FigureS9_MFN2.tif</strong></li> <li>NAV1.7 shown in <strong>FigureS9_NAV1.7.tif</strong></li> <li>P23 shown in <strong>FigureS9_p23.tif</strong></li> <li>PRKCG shown in <strong>FigureS9_PRKCG.tif</strong></li> <li>RAB5C shown in <strong>FigureS9_Rab5c.tif</strong></li> <li>RHOT2 shown in <strong>FigureS9_RHOT2.tif</strong></li> <li>RIMS4 shown in <strong>FigureS9_RIMS4.tif</strong></li> <li>RUFY3 shown in <strong>FigureS9_RUFY3.tif</strong></li> <li>SH3BP4 shown in <strong>FigureS9_SH3BP4.tif</strong></li> <li>SNX3 shown in <strong>FigureS9_SNX3.tif</strong></li> <li>TDRKH shown in <strong>FigureS9_TDRKH.tif</strong></li> <li>TOMM70 shown in <strong>FigureS9_TOMM70.tif</strong></li> </ul> <p> </p> <p><strong>Figure S10A: Immunoblots for validation of Parkin-dependent substrates in PINK1 WT and KO neurons.</strong></p> <p>Scans of X-ray film:</p> <ul> <li>CISD1 shown in <strong>Figure S10A _CISD1.tif </strong>(Halo-multiDSK pull-down) <ul> <li><strong> Figure S10A _INPUT_CISD1.tif </strong>(INPUT)</li> </ul> </li> <li>CPT1α shown in <strong>Figure S10A _ CPT1A.tif</strong> (Halo-multiDSK pull-down) <ul> <li><strong> Figure S10A _INPUT_ CPT1A.tif</strong> (INPUT)</li> </ul> </li> <li>Ubiquitin shown in <strong>Figure1C_ S10A _Ubiquitin.tif </strong>(same blot used for FigureS1C, Halo-multiDSK pull-down) <ul> <li><strong> Figure S10A _INPUT_Ubiquitin.tif</strong> (INPUT)</li> </ul> </li> <li>Phospho-Ser65 Ubiquitin shown in <strong>Figure1C_ S10A_UbiquitinPSer65.tif </strong>(same blot used for FigureS1C, Halo-multiDSK pull-down)</li> <li>GAPDH Shown in <strong>Figure S10A _INPUT_GAPDH.tif </strong>(INPUT)</li> </ul> <p> </p> <p><strong>Figure S10B: Immunoblots for time-course of Parkin-dependent substrates in SH-SY5Y cells.</strong></p> <p>Scans of X-ray film:</p> <ul> <li>CISD1 shown in <strong>Figure S10B _CISD1.tif </strong>(Halo-multiDSK pull-down)</li> <li>CPT1α shown in <strong>Figure S10B _ CPT1A.tif</strong> (Halo-multiDSK pull-down)</li> <li>Ubiquitin shown in <strong>Figure S10B _Ubiquitin.tif </strong>(Halo-multiDSK pull-down)</li> <li>Phospho-Ser65 Ubiquitin shown in <strong>Figure S10B _UbiquitinPSer65.tif </strong>(Halo-multiDSK pull-down)</li> <li>GAPDH Shown in <strong>Figure S10B _GAPDH.tif </strong></li> <li>Parkin shown in <strong>FigureS10B_Parkin.tif</strong></li> <li>Phospho-Ser65 Parkin shown in <strong>FigureS10B_ParkinPSer65.tif</strong></li> <li>PINK1 shown in <strong>FigureS10B_PINK1.tif</strong></li> <li>OPA1 shown in <strong>FigureS10B_OPA1.tif</strong></li> </ul> <p> </p> <p><strong>Figure S11: Immunoblots for <em>in vitro</em> reconstitution assay in HeLa cells.</strong></p> <p>Scans of X-ray film:</p> <ul> <li>CISD1shown in <strong>FigureS11_CISD1.tif</strong></li> <li>CPT1α shown in <strong>FigureS11_ CPT1</strong><strong>a</strong><strong>.tif</strong></li> <li>CYB5B shown in <strong>FigureS11_CYB5B.tif</strong></li> <li>HK1 shown in <strong>FigureS11_HK1.tif</strong></li> <li>MFN2 shown in <strong>FigureS11_MFN2.tif</strong></li> <li>VDAC shown in <strong>FigureS11_VDAC.tif</strong></li> <li>Phospho-Ser65 Parkin shown in <strong>FigureS11_ParkinPSer65.tif</strong></li> <li>Parkin shown in <strong>FigureS11_Parkin.tif</strong></li> <li>Ubiquitin shown in <strong>FigureS11_Ubiquitin .tif</strong></li> <li>Phospho-Ser65 Ubiquitin shown in <strong>FigureS11_UbiquitinPSer65 .tif</strong></li> </ul> <p> </p> <p><strong>FigureS12A: Purification of CPT1</strong><strong>α protein.</strong></p> <ul> <li><strong>FigureS12A_</strong><strong> Akta_Purifier_Curves.txt</strong>.</li> </ul> <p> Tab delimited text of data from the AKTA system, plotted in figure S12A. Columns are laid out as volume/measured parameter for each parameter from the Akta. The columns plotted in figure S12A were mAU (columns A and B in excel) and fractions (columns M and N in excel).</p> <ul> <li><strong>Figure_S12A_Coomassie_Gel.tif</strong>. </li> </ul> <p>Coomassie stained gels of fractions from the AKTA system in figure S12A.</p> <p>Top: Left hand Coomassie gel, figure S12A</p> <p>Bottom: Right hand Coomassie gel, figure S12A</p> <p> </p> <p><strong>FigureS12B-C: Purification of recombinant Parkin targets </strong></p> <p>Blots shown in the paper are highlighted in bold.</p> <ul> <li><strong>FigureS12B_Ub_Targets_High_800nm.tif</strong></li> </ul> <p>Coomassie stained gels of the parkin targets alongside a BSA curve.</p> <p>Left: Lane: 1: Mwt Marker, 2: Fam213A, 3: MAO-B, 4: CAMK2α, <strong>5: MAO-A (figure S12B)</strong>, 6: GST-MAPRE2, 7: MBP-CYB5R3, 8: MBP-CYB5B, 9: MBP-CYB5B, 10: SNX3, 11: His-SUMO-MAO-B, 12: GST-MAO-B, 13: 0.03125 ug BSA, 14: 0.0625 ug BSA, 15: 0.125 ug BSA, 16: 0.25 ug BSA, 17: 0.5 ug BSA, 18: 1 ug BSA</p> <p>Right: Lane: 1: Mwt Marker, 2: GST-MAO-A, 3: GST-FAM213A, <strong>4: MBP-CAMK2</strong><strong>α</strong><strong> (figure S12B)</strong>, 5: GST-TDRKH, 6: MBP-CPT1α, 7: MBP-CYB5B, 8: CAMK2β, 9:, 10: His-SUMO-MAO-B, 11: GST-MAO-B, 12: 0.03125 ug BSA, 13: 0.0625 ug BSA, 14: 0.125 ug BSA, 15: 0.25 ug BSA, 16: 0.5 ug BSA, 17: 1 ug BSA</p> <p> </p> <ul> <li><strong>Figure_S12B_Ub_Targets_Low_800nm.tif</strong></li> </ul> <p>Coomassie stained gels of the parkin targets alongside a BSA curve.</p> <p>Lane: 1: Mwt Marker, <strong>2: GST-Miro1 (figure S12B</strong>), 3: His-SUMO-Fam213A, 4: His-SUMO-MAPRE2, 5: His-SUMO-MAO-A, 6: His-SUMO-MAO-B, 7: His-SUMO-SNX26, 8: His-SNX3, 9: His-MAPRE2, 10: GST-FAM213A, 11: His-SUMO-CAMK2α, 12: His-SUMO-CAMK2β, 13: GST-FAM213A, 14: 0.03125 ug BSA, 15: 0.0625 ug BSA, 16: 0.125 ug BSA, 17: 0.25 ug BSA, 18: 0.5 ug BSA, 19: 1 ug BSA</p> <p> </p> <ul> <li><strong>Figure_S12C_Ub_Targets_800nm.tif</strong></li> </ul> <p>Coomassie stained gels of the parkin targets in duplicate alongside a BSA curve.</p> <p>Top: Lane: 1: Mwt Marker, <strong>2+3: ACSL1 45-end (Figure S12C)</strong>, <strong>4+5: SNX3 (Figure S12C),</strong> 6+7: MFN1, 8+9: MFN2, 10+11: 0.125 ug BSA, 12+13: 0.25 ug BSA, 14+15: 0.5 ug BSA, 16+17: 1 ug BSA</p> <p>Middle: Lane: 1: Mwt Marker, 2+3: CAMK2α, <strong>4+5: CAMK2</strong><strong>β</strong><strong> (Figure S12C)</strong>, 6+7: MAO-A, <strong>8+9: MAO-B (Figure S12C)</strong>, 10+11: 0.125 ug BSA, 12+13: 0.25 ug BSA, 14+15: 0.5 ug BSA, 16+17: 1 ug BSA</p> <p>Bottom: Lane: 1: Mwt Marker, 2+3: SRCIN, 4+5: His-MAPRE2, 6+7: <strong>FAM213A (Figure S12C)</strong>, 8+9: CISD1, 10+11: 0.125 ug BSA, 12+13: 0.25 ug BSA, 14+15: 0.5 ug BSA, 16+17: 1 ug BSA</p> <p> </p> <p><strong>FigureS13-S14: Immunoblots for validation of Parkin-dependent substrates in<em> in vitro </em>studies.</strong></p> <p>Blots shown in the paper are highlighted in bold.</p> <p>Scans of X-ray film:</p> <ul> <li><strong>FigureS13A-B_S14C-D_a6His_Film.tif</strong></li> </ul> <p>Gel loading: lanes: 1+2: – PINK1, 3+4: WT PINK1, 5+6: KD PINK1</p> <p>Membranes from left to right:</p> <p>Top: 1: <strong>FAM213A (Figure S13B</strong>), 2: <strong>MAO-B (Figure S13A</strong>), 3: MAPRE2, 4: <strong>CAMK2</strong><strong>β</strong><strong> (Figure S14D)</strong></p> <p>Top: 1: <strong>CAMK2</strong><strong>α</strong><strong> (Figure S14C)</strong>, 2: Miro1, 3: <strong>MAO-A (Figure S13A)</strong></p> <p> </p> <ul> <li><strong>FigureS13A-B_S14C-D_aFLAG_Film.tif</strong></li> </ul> <p>Gel loading: lanes: 1+2: – PINK1, 3+4: WT PINK1, 5+6: KD PINK1</p> <p>Membranes from left to right:</p> <p>Top: 1: <strong>FAM213A (Figure S13B)</strong>, 2: MAPRE2, 3: <strong>MAO-A (Figure S13A)</strong></p> <p>Top: 1: <strong>MAO-B (Figure S13A)</strong>, 2: <strong>CAMK2</strong><strong>α</strong><strong> (Figure S14C),</strong> 3: <strong>CAMK2</strong><strong>β</strong><strong> (Figure S14D)</strong>, 4: Miro1 </p> <p> </p> <ul> <li><strong>FigureS13A-B_S14C-D_aTarget_05m00s_Film.tif</strong></li> </ul> <p>Gel loading: lanes: 1+2: – PINK1, 3+4: WT PINK1, 5+6: KD PINK1</p> <p>Membranes from left to right:</p> <p>Top: 1: FAM213A, 2: MAPRE2, 3: MAO-A</p> <p>Top: 1: MAO-B, 2<strong>: CAMK2</strong><strong>α</strong><strong> (Figure S14C)</strong>, 3: <strong>CAMK2</strong><strong>β</strong><strong> (Figure S14D</strong>), 4: Miro1 </p> <p> </p> <ul> <li><strong>FigureS13A-B_S14C-D_aTarget_06m00s_Film.tif</strong></li> </ul> <p>Gel loading: lanes: 1+2: – PINK1, 3+4: WT PINK1, 5+6: KD PINK1</p> <p>Membranes from left to right:</p> <p>Top: 1: <strong>FAM213A (Figure S13B)</strong>, 2: MAPRE2, 3: <strong>MAO-A (Figure S13A)</strong></p> <p>Top: 1: <strong>MAO-B (Figure S13A)</strong>, 2: CAMK2α, 3: CAMK2β, 4: Miro1 </p> <p> </p> <p><strong>FigureS13C: Immunoblots for validation of Parkin-dependent substrates in<em> in vitro </em>studies.</strong></p> <p>Scans of Western blots (LI-COR):</p> <ul> <li>ACSL1 shown in <strong>FigureS13C_ACSL1_800nm.tif</strong></li> <li>Flag-Ub (ACSL1) shown in <strong>Figure_S13C_ACSL1_Flag_800nm.tif</strong></li> <li>His (ACSL1) shown in <strong>Figure_S13C_ACSL1_His_800nm.tif</strong></li> </ul> <p> </p> <p><strong>FigureS14B: Immunoblots for validation of Parkin-dependent substrates in<em> in vitro </em>studies.</strong></p> <p>Blots shown in the paper are highlighted in bold.</p> <p>Scans of Western blots (LI-COR):</p> <ul> <li>SNX3 shown in <strong>FigureS14B_SNX3_800nm.tif</strong></li> </ul> <p>Gel loading: lanes: 1+2: – PINK1, 3+4: WT PINK1, 5+6: KD PINK1</p> <p>Membranes, left to right: <strong>SNX3 (Figure S14B</strong>), FAM213A, Miro1, Miro1</p> <ul> <li>Flag-Ub (SNX3) shown in <strong>Figure_S14B_Flag_SNX3_800nm.tif</strong></li> </ul> <p>Gel loading: lanes: 1+2: – PINK1, 3+4:WT PINK1, 5+6: KD PINK1</p> <p>Membranes, left to right: Miro1, FAM213A, Miro1, <strong>SNX3 (Figure S14B)</strong></p> <ul> <li>His (SNX3) shown in <strong>Figure_S14B_His_SNX3_700nm.tif</strong></li> </ul> <p>Gel loading: lanes: 1+2: – PINK1, 3+4: WT PINK1, 5+6: KD PINK1</p> <p>Membranes, left to right: CPT1α, MFN1, <strong>SNX3 (Figure S14B)</strong>, FAM213A</p> <p> </p> <p><strong>FigureS1: Immunocytochemistry of mouse cortical neurons.</strong></p> <ul> <li><strong>FigureS1_TILE_maximun intensity projection.tif</strong></li> </ul> <p>Original acquisition: MAP2 neuronal marker (green-488); GFAP astrocytic marker (red-594); Hoechst nuclear marker (blue 361/497). </p> <ul> <li><strong>FigureS1MGB (RGB).tif</strong></li> </ul> <p>Modified from FigureS1_TILE_maximun intensity projection.tif: MAP2 (green); GFAP (magenta); Hoechst (blue).</p> <p> </p> <p><strong>Table for Fig1DE.xlsx</strong></p> <p>Numerical data for the charts shown in Figure1D and Figure1E.</p> <p> </p> <p><strong>Table for FigS1A.xlsx</strong></p> <p> Numerical data for quantification of Map2 and GFAP in mouse cortical neurons shown in FigureS1A.</p> <p> </p> <p><strong>Table for FigS1B (Cortical neurons_DIA_Report).xlsx</strong></p> <p> Numerical data for DIA proteomic analysis of AO and DMSO treated cortical neurons shown in FigureS1B.</p> <p> </p> <p><strong>Table for FigS2B_C_Oxygraph.xlsx</strong></p> <p>Numerical data for the charts shown in FigureS2B and FigureS2C.</p> <p> </p> <p><strong>Table for Fig3A.xlsx</strong></p> <p>Numerical data for total protein abundance in PINK1 WT and KO shown in Figure3A.</p> <p> </p> <p><strong>Table for Fig3B.xlsx</strong></p> <p>Numerical data of abundance of phosphorylated-Ser65 or Ser57 shown in Figure3B.</p>
Figure 3 in Use of morphological and molecular data to identify three new sibling species of the genus Munida Leach, 1820 (Crustacea, Decapoda, Galatheidae) from New Caledonia
Figure 3. Munida pectinata sp. nov., ovigerous female 6.9 mm, holotype from stn 1727 (NORFOLK 1). (A) Carapace, dorsal view; (B) sternal plastron; (C) ventral view of cephalic region, showing antennular and antennal peduncles; (D) right third maxilliped, lateral view; (E) right cheliped, dorsal view; (F) right first walking leg, lateral view; (G) dactylus of right first walking leg, lateral view.
Figure 2 in Use of morphological and molecular data to identify three new sibling species of the genus Munida Leach, 1820 (Crustacea, Decapoda, Galatheidae) from New Caledonia
Figure 2. Munida simulatrix sp. nov., male 7.7 mm, holotype from stn 1721 (NORFOLK 1). (A) Carapace, dorsal view; (B) sternal plastron; (C) ventral view of cephalic region, showing antennular and antennal peduncles; (D) right third maxilliped, lateral view; (E) right cheliped, dorsal view; (F) right first walking leg, lateral view; (G) dactylus of right first walking leg, lateral view.
Figure 1 in Use of morphological and molecular data to identify three new sibling species of the genus Munida Leach, 1820 (Crustacea, Decapoda, Galatheidae) from New Caledonia
Figure 1. Munida parile sp. nov., ovigerous female 3.7 mm, holotype from stn 1701 (NORFOLK 1). (A) Carapace, dorsal view; (B) sternal plastron; (C) ventral view of cephalic region, showing antennular and antennal peduncles; (D) left third maxilliped, lateral view; (E) right cheliped, dorsal view; (F) left first walking leg, lateral view; (G) dactylus of left first walking leg, lateral view.
Fig. 4 in DNA barcoding applied: identifying the larva of Merodon avidus (Diptera: Syrphidae)
Fig. 4. SEM micrographs of the anal segment of Merodon avidus Rossi, 1790 larva (La): A – anal segment; B – lappet; C – posterior respiratory process; D – inter-spiracular setae. Abbreviations: cs – central scars; is – inter-spiracular setae; lp – lappets; prp – posterior respiratory process; so – spiracular openings.
Fig. 2 in DNA barcoding applied: identifying the larva of Merodon avidus (Diptera: Syrphidae)
Fig. 2. Light micrographs of Merodon avidus Rossi, 1790 larva: A – larva in ventral view (La); B – head (Lc); C – thorax (La); D – primordia of pupal spiracles (Lc); E – lappets (Lc); F – posterior respiratory process (La). Abbreviations: am – antenno-maxillary organs; as – anterior spiracles; lp – lappets; mh – mouth hooks; prp – posterior respiratory process; pps – primordia of pupal spiracles.
Fig. 3 in DNA barcoding applied: identifying the larva of Merodon avidus (Diptera: Syrphidae)
Fig. 3. SEM micrographs of Merodon avidus Rossi, 1790 larva (La): A – mandibles; B – head; C – antenno-maxillary organs; D – anterior spiracle; E – larva in ventral view; F – locomotory organ. Abbreviations: ac – antennal cone; am – antenno-maxillary organs; an – antenna; lo – locomotory organs; mh – mouth hooks; mp – maxillary palp.
Fig. 11 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 11. Haplotype network of Ngirhaphium sivasothii. Thailand: Krabi, Phangnga, Satun; Singapore: Sarimbun, Pulau Tekong, Pulau Ubin, Labrador, Semakau Island, and Sungei Buloh.
Fig. 10 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 10. Haplotype network of Ngirhaphium murphyi. Singapore: Pulau Ubin, Mandai Sungei Buloh; Thailand: Satun and Krabi.
Fig. 12 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 12. Compilation of male terminalia of Ngirhaphium in lateral view. A, Ngirhaphium sivasothii left side with ventral surstylus removed; cerci dorsally; B, Ngirhaphium murphyi left side with ventral surstylus removed; cerci and dorsal surstyli dorsally; C, Ngirhaphium caeruleum left side with ventral surstylus removed; cerci and dorsal surstyli dorsally; D, Ngirhaphium meieri, new species left side with ventral surstylus removed; E, Ngirhaphium chutamasae left side with ventral surstylus removed; F, Ngirhaphium thaicum, new species right side. Scale = 0.1 mm.
Fig. 8 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 8. Ngirhaphium meieri, new species, holotype male terminalia: A, Lateral view of genital capsule with left ventral surstylus removed; B, Cerci dorsally; C. Left ventral surstylus; D, Ventral view of genital capsule. Abbreviations: ae = aedeagus; c = cercus; ds = dorsal surstylus; hy = hypandrium; sp = sperm pump; vs = ventral surstylus. Scale = 0.1 mm.
Fig. 5 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 5. Ngirhaphium thaicum, new species male terminalia (27_009) A, epandrium left side; B, cerci dorsal view; C, left surstylus inside view. Scale = 0.1 mm.
Fig. 2 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 2. Ngirhaphium caeruleum-complex. View of inside of the dorsal surstylus of the left side and the fused dorsal and ventral surstyli of the right side. Scale = 0.1mm. A, green caeruleum from Tutong, Brunei (ZRCBDP0066395) at 1.6 % from the Semakau population; B, green caeruleum from Pulau Tekong, Singapore (ZRCBDP0001462) at 0.6% from the Semakau population; C, green caeruleum from Pulau Ubin, Singapore (ZRC_BDP_0084430) at 0.6% from the Semakau population; D, blue caeruleum from the type locality on Semakau Island, Singapore (ZRCBDP0118762); E, green thaicum, new species from Surat Thani, Thailand (24-018) at 4.2% from the Semakau population; F, green thaicum, new species from Cambodia (JP3C_Ngi-cambodiensis_Misc002) within the variability of the southern Thailand populations.
Fig. 1 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 1. Haplotype network of the Ngirhaphium caeruleum-complex. Brunei: Berambang, Tutong, Labu; Singapore: Pulau Ubin, Pulau Tekong, Semakau Island; Thailand: Chumphon, Surat Thani, and Cambodia.
Fig. 11 in The Use of Molecular Phylogenetic and Morphological Tools to Identify Cryptic and Paraphyletic Species: Examples from the Diminutive Long-fingered Bats (Chiroptera: Miniopteridae: Miniopterus) on Madagascar
Fig. 11. Projections of factor 1 (x-axis) and factor 2 (y-axis) in principal component analysis of A, cranial measurements and B, dental measurements of different diminutive species of Miniopterus from Madagascar, all of which were previously considered to be M. manavi, as well as M. petersoni. Loadings of variables on each axis are shown in table 6.
Fig. 10 in The Use of Molecular Phylogenetic and Morphological Tools to Identify Cryptic and Paraphyletic Species: Examples from the Diminutive Long-fingered Bats (Chiroptera: Miniopteridae: Miniopterus) on Madagascar
Fig. 10. Lateral views of skulls and mandibles of Miniopterus spp. from Madagascar: (above, from left to right) M. manavi (FMNH 194074) from the Grotte de Fandanana, near Fandriana; M. griveaudi (FMNH 169712) from near the Andrafiabe Cave, Ankarana; holotype of M. aelleni (FMNH 173067), from the Canyon d'Antsiroandoa, Ankarana; (below, left) holotype of M. brachytragos (FMNH 175840), from the Forêt d'Ambovonomby, Parc National de Namoroka, Forêt d'Ambovonomby; and (below, right) holotype of M. mahafaliensis (FMNH 173197), from near Mitoho Cave, Parc National de Tsimanampetsotsa. (Photograph taken by J. Weinstein, Field Museum image number Z94488_03d.)
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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