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Validation of ESA CCI SM active v06.1 vs ISMN 20210131 global
QA4SM validation of soil moisture data: ESA CCI SM active v06.1 vs ISMN 20210131 global. URL: https://qa4sm.eu/result/4fc5718a-db09-4748-953d-341f5127485e/. Produced on QA4SM (https://qa4sm.eu)
Magnetic Proxy for Solar Activity
<p>Proxies for solar activity are often used to extend solar irradiance measurements in time or forecast future variability. We calculate images of the solar photospheric magnetic field from a flux transport simulation and create a multicomponent proxy for solar activity.</p>
Longitudinal structural MRI and behavioural data for mice prenatally exposed to maternal immune activation either early or late in gestation
<p>Prenatal maternal immune activation (MIA) is a risk factor for neurodevelopmental disorders. How the gestational timing of MIA-exposure differentially impacts downstream development remains unclear. The data presented here includes longitudinal structural magnetic resonance imaging (MRI) data from weaning to adulthood, and behavioural testing in adolescence and adulthood on C57BL/6 mice exposed to MIA induced by the viral mimetic, polyinosinic:polycytidylic acid (poly I:C) either early (gestational day [GD]9) or late (GD17) in gestation. </p> <p>The data published here was collected and analyzed for the following publication, where more details can be found (Guma et al., 2021 https://doi.org/10.1016/j.biopsych.2021.03.017). Briefly, we found that early MIA-exposure was associated with accelerated brain volume increases in adolescence/early-adulthood that normalized in later adulthood, in regions including the striatum, hippocampus, and cingulate cortex. Similarly, alterations in anxiety-like, stereotypic, and sensorimotor gating behaviours observed in adolescence normalized in adulthood. In contrast, MIA-exposure in late gestation had less impact on anatomical and behavioural profiles. </p> <p>In addition to the univariate analyses described above, we also undertook a multivariate analysis (partial least squares) to relate imaging and behavioural variables for the time of greatest alteration, i.e. adolescence/early adulthood. We further explored the molecular underpinnings of region-specific alterations in early MIA-exposed mice in adolescence using RNA sequencing (data for differentially expressed genes in the anterior cingulate cortex, dorsal hippocampus, and ventral hippocampus are available via the original publication https://doi.org/10.1016/j.biopsych.2021.03.017 for a separate cohort of adolescent mice prenatally exposed to MIA or vehicle at GD9). </p> <p>In this dataset, you will find a total of <strong>376 preprocessed structural MRIs</strong> (in MINC format) acquired at postnatal day ~21, ~38, ~60, and ~90 in mice exposed to poly I:C or vehicle control (0.9% sterile saline) at GD9 or 17. These are T1-weighted, manganese enhanced (50mg/kg 24 hours pre-scan), structural images at 100 micron isotropic resolution acquired on a 7 Tesla Bruker Biospec 70/30; matrix size of 180 x 160 x 90; 14.5 minutes, 2 averages, using 5% isoflurane for induction, 1.5% for maintenance of anesthesia during the scan. T1-weighted scans were preprocessed by stripping native coordinates, flipping left-right to maintain fidelity, denoising, correcting inhomogeneities in the bias field using the N4 algorithm, and registering in LSQ6 alignment (i.e. 6 degrees of freedom are allowed for imagine alignment: translations and rotations along x, y, and z dimensions). The demographics information for each animal is included in the <strong>demographics.csv</strong> file. </p> <p>Behavioural tests were performed following the postnatal day 38 and 90 scans in all animals with a 2 day rest period. These include: open field test, marble burying test, three chambered social approach, and prepulse inhibition. The attentional set shifting task was also performed following the final behavioural test in the postnatal day 90 wave of behaviours. The data for all of these tests is presented in its own individual .csv spreadsheet and includes data for both the timepoints evaluated.</p> <p>Included in this data set are the structural MRIs in MINC format, the behavioural .csv data, and a <strong>readme.txt</strong> file providing further detail on the data structure and content, and on how to interpret the data column titles. DICOMS are also available for the structural MRI data, as are the raw (not-preprocessed) MINC files, available upon request to the authors. </p> <p>Finally, the authors would like to acknowledge the funding bodies that supported the completion of this work including the Canadian Institute for Health Research, the Fonds de Recherche du Québec en Santé, and the Healthy Brains for Healthy Lives at McGill University.</p>
COESO: funding entities of citizen science activities on social sciences and humanities topics
<p>This database has been compiled by the Ibercivis team working in COESO together with contributions from other members of the COESO Consortium and representatives of the COESO Advisory Board, in addition to those who contributed information through the surveys and interviews.</p>
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 2 in A not so natural history of the tarantula Brachypelma vagans: Interaction with human activity
Figure 2. Preferred orientations of the burrows for Brachypelma vagans. (A) For all sites (n5110); (B) for backyards (BY1 and BY2, n550) and for football field (FG and FC, n560).
Figure 3 in A not so natural history of the tarantula Brachypelma vagans: Interaction with human activity
Figure 3. Mean diameters of the burrow entrances of Brachypelma vagans. (A) Between backyards (BY: BY1 and BY2) and football field (FB: FC and FG); (B) among individuals. ANOVA test: **P,0.01; Fisher LSD, interclass group at 1% level.
Figure 1 in A not so natural history of the tarantula Brachypelma vagans: Interaction with human activity
Figure 1. Density of Brachypelma vagans in different vegetation/land use classes representing a gradient of human activity. F: mean of MF and SF. Site class codes are referred to in the Methods section.
Figure 1 in Food habits and daily activity patterns of the North African ocellated lizard Timon pater from northeastern Algeria
Figure 1. Mean monthly temperature (°C, bars) and rainfall (mm, line) at the study area in north-eastern Algeria.
Figure 3 in Food habits and daily activity patterns of the North African ocellated lizard Timon pater from northeastern Algeria
Figure 3. Daily activity patterns of Timon pater at the study area, expressed as the mean number of individuals seen at each daytime interval along several independent 1000-m-long transects.
Figure 2 in Food habits and daily activity patterns of the North African ocellated lizard Timon pater from northeastern Algeria
Figure 2. Monthly variation in the number of faecal pellets collected (A) (total sample, n5164) and in the mean volume of each pellet (B) (total sample, n5139) of Timon pater at the study area.
Fig. 3 in Motoric activity of the receptaculum seminis and ductus receptaculi in females of the house cricket Acheta domesticus (L., 1758) (Insecta: Orthoptera)
Fig. 3: (a) Comparison of mean values of contraction frequencies of the receptacular complexes between the different physiological groups. Double asterisks indicate highly significant differences between neighboring columns (p <0.01). (b) Effect of variable cation concentrations in the Ringer's solution on the contraction frequency of the receptacular complexes. Double asterisks mark highly significant deviation from the standard value (left column) measured for virgins.
Fig. 1 in Motoric activity of the receptaculum seminis and ductus receptaculi in females of the house cricket Acheta domesticus (L., 1758) (Insecta: Orthoptera)
Fig. 1: Position, morphology and histology of the receptacular complex in crickets. Whilst the receptaculum seminis is characterized by uniform histological organization, the ductus receptaculi can be subdivided in at least three regions with different cellular structures and arrangements (ESSLER et al 1992, STURM 2005, 2007, 2008).
Fig. 2 in Motoric activity of the receptaculum seminis and ductus receptaculi in females of the house cricket Acheta domesticus (L., 1758) (Insecta: Orthoptera)
Fig. 2: Graphs depicting the motoric activity of the receptacular complex (mean + standard deviation) measured in 5-minutes intervals among female house crickets belonging to different physiological states: (a) virgins, (b) mated females, (c) females during oviposition, (d) females after oviposition.
Fig. 6 in Activity pattern and resource use of two Callosciurus species in different habitats in northeastern Thailand
Fig. 6. Proportion of food items consumed by (a) Callosciurus finlaysonii (n = 143) and (b) C. caniceps (n = 35).
Fig. 2 in Activity pattern and resource use of two Callosciurus species in different habitats in northeastern Thailand
Fig. 2. Frequencies of detection of active (a) Callosciurus finlaysonii and (b) C. caniceps in each survey time. Data are displayed as mean ± SD. Different letters in the figure indicate a significant difference (Steel-Dwass test; P <0.05).
Fig. 1 in Activity pattern and resource use of two Callosciurus species in different habitats in northeastern Thailand
Fig. 1. Location of the study site in the headquarters (HQ) of the Sakaerat Environmental Research Station and census routes. Upper figure shows the location of Sakaerat Biosphere Reserve and the bottom figure shows an enlarged view of the HQ. Solid lines show the census route of the present study, broken lines show paved survey route of the previous study (Kobayashi et al., 2019b), broken line shows non-paved survey route of the previous study (Kobayashi et al., 2019b) in natural forests (DDF: dry dipterocarp forest in light grey; DEF: dry evergreen forest in dark grey). Dotted areas in the bottom figure are relatively open spaces with few trees, white square is the nursery, and striped squares are buildings.
Fig. 2 in The first recorded activity pattern for the Sunda stink-badger Mydaus javanensis (Mammalia: Carnivora: Mephitidae) using camera traps
Fig. 2. Daily activity patterns of Sunda stink-badger within Lots 5 and 7 of the Lower Kinabatangan Wildlife Sanctuary, Sabah, Borneo. The grey areas represent an extension of the activity pattern to depict its circular nature, and 'carpet' marks along the x-axis represent individual photographic events. Vertical dashed red lines indicate either the end or beginning of the diurnal phase of the diel (0700–1659 hours). Vertical blue lines indicate either the end or beginning of the nocturnal phase of the diel (1900–0459 hours). Regions between red and blue lines represent the crepuscular regions of the diel (0500–0659 hours and 1700–1859 hours).
Fig. A3 in The first recorded activity pattern for the Sunda stink-badger Mydaus javanensis (Mammalia: Carnivora: Mephitidae) using camera traps
Fig. A3. Co-occurrence of Sunda stink-badger Mydaus javanensis and Malay civet Viverra tangalunga photo-captured in the Lower Kinabatangan Wildlife Sanctuary, Sabah, Malaysian Borneo on 13 June 2013.
Fig. A2 in The first recorded activity pattern for the Sunda stink-badger Mydaus javanensis (Mammalia: Carnivora: Mephitidae) using camera traps
Fig. A2. Kernel density modelled activity patterns for the Sunda stink-badger during different periods; overlap between activity patterns is indicated by the shaded regions. Vertical dashed red lines indicate either the end or beginning of the diurnal phase of the diel (0700–1659h). Vertical blue lines indicate either the end or beginning of the nocturnal phase of the diel (1900–0459h). Regions between red and blue lines represent the crepuscular regions of the diel (0500–0659h and 1700–1859h). 'Carpet' marks along the x-axis represent individual photographic events, and are colour co-ordinated to their respective activity pattern. Top (a): Overlap in kernel density modelled activity pattern in the wet season (November–February) compared to the dry season (March–October). Middle (b): Overlap in kernel density modelled activity pattern on full moon nights compared to new moon nights. Bottom (c): Overlap in kernel density modelled activity pattern on 'bright' nights (full moon, waxing gibbous, and waning gibbous) compared to 'dim' nights (new moon, new crescent, and old crescent).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.