Autophagy Patterns and Prognosis in Uveal Melanomas
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MAP1LC3 Antibody Cat
MAP1LC3 Antibody Cat. No.: 7951 MAP1LC3 Antibody Immunohistochemistry of MAP1LC3 in rat brain tissue with MAP1LC3 antibody at 5 μg/ml. Specifications HOST SPECIES: Rabbit SPECIES REACTIVITY: Human, Mouse, Rat HOMOLOGY: Predicted species reactivity based on immunogen sequence: Bovine: (100%) MAP1LC3 antibody was raised against a 12 amino acid peptide near the center of human MAP1LC3A. IMMUNOGEN: The immunogen is located within amino acids 20 - 70 of MAP1LC3. TESTED APPLICATIONS: ELISA, IHC-P, WB September 29, 2021 1 https://www.prosci-inc.com/map1lc3-antibody-7951.html MAP1LC3 antibody can be used for detection of MAP1LC3 by Western blot at 0.5 - 1 μg/ml. Antibody can also be used for Immunohistochemistry starting at 5 μg/mL. APPLICATIONS: Antibody validated: Western Blot in human samples and Immunohistochemistry in rat samples. All other applications and species not yet tested. MAP1LC3 antibody is human, mouse and rat reactive. Multiple isoforms MAP1LC3 are SPECIFICITY: known to exist. MAP1LC3 antibody is predicted to detect MAP1LC3A, MAP1LC3B, and MAP1LC3C. POSITIVE CONTROL: 1) Cat. No. 1303 - Human Brain Tissue Lysate Predicted: 13 kDa PREDICTED MOLECULAR WEIGHT: Observed: 18 kDa Properties PURIFICATION: MAP1LC3 antibody is affinity chromatography purified via peptide column. CLONALITY: Polyclonal ISOTYPE: IgG CONJUGATE: Unconjugated PHYSICAL STATE: Liquid BUFFER: MAP1LC3 antibody is supplied in PBS containing 0.02% sodium azide. CONCENTRATION: 1 mg/mL MAP1LC3 antibody can be stored at 4˚C for three months and -20˚C, stable for up to one STORAGE CONDITIONS: year. Additional Info OFFICIAL SYMBOL: MAP1LC3A MAP1LC3 Antibody: LC3, LC3A, ATG8E, MAP1ALC3, MAP1BLC3Autophagy-related protein ALTERNATE NAMES: LC3 A ACCESSION NO.: NP_115903 PROTEIN GI NO.: 14210522 GENE ID: 84557 USER NOTE: Optimal dilutions for each application to be determined by the researcher. -
De Novo EIF2AK1 and EIF2AK2 Variants Are Associated with Developmental Delay, Leukoencephalopathy, and Neurologic Decompensation
bioRxiv preprint doi: https://doi.org/10.1101/757039; this version posted September 16, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. De novo EIF2AK1 and EIF2AK2 variants are associated with developmental delay, leukoencephalopathy, and neurologic decompensation Dongxue Mao1,2, Chloe M. Reuter3,4, Maura R.Z. Ruzhnikov5,6, Anita E. Beck7, Emily G. Farrow8,9,10, Lisa T. Emrick1,11,12,13, Jill A. Rosenfeld12, Katherine M. Mackenzie5, Laurie Robak2,12,13, Matthew T. Wheeler3,14, Lindsay C. Burrage12,13, Mahim Jain15, Pengfei Liu12, Daniel Calame11,13, Sebastien Küry17,18, Martin Sillesen19, Klaus Schmitz-Abe20, Davide Tonduti21, Luigina Spaccini22, Maria Iascone23, Casie A. Genetti20, Madeline Graf16, Alyssa Tran12, Mercedes Alejandro12, Undiagnosed Diseases Network, Brendan H. Lee12,13, Isabelle Thiffault8,9,24, Pankaj B. Agrawal#,20, Jonathan A. Bernstein#,3,25, Hugo J. Bellen#,2,12,26,27,28, Hsiao- Tuan Chao#,1,2,11,12,13,28,27,29 #Correspondence should be addressed: [email protected] (P.A.), [email protected] (J.A.B.), [email protected] (H.J.B.), [email protected] (H.T.C.) 1Department of Pediatrics, Baylor College of Medicine (BCM), Houston, TX 2Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 3Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA 4Stanford Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, -
Transient Unfolding and Long-Range Interactions in Viral BCL2 M11 Enable Binding to the BECN1 BH3 Domain
biomolecules Article Transient Unfolding and Long-Range Interactions in Viral BCL2 M11 Enable Binding to the BECN1 BH3 Domain Arvind Ramanathan 1,2,*, Akash Parvatikar 3, Srinivas C. Chennubhotla 3,* and Yang Mei 4,† and Sangita C. Sinha 4,* 1 Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA 2 Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA 3 Department of Computational and Systems Biology, University of Pittsburgh, PA 15260, USA; [email protected] 4 Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA; [email protected] * Correspondence: [email protected] (A.R.); [email protected] (S.C.C.); [email protected] (S.C.S.); Tel.: +1-630-252-3805 (A.R.); +1-412-648-7794 (S.C.C.); +1-701-231-5658 (S.C.S.) † Current address: The Wistar Institute, Philadelphia, PA 19104, USA. Received: 27 July 2020; Accepted: 4 September 2020; Published: 11 September 2020 Abstract: Viral BCL2 proteins (vBCL2s) help to sustain chronic infection of host proteins to inhibit apoptosis and autophagy. However, details of conformational changes in vBCL2s that enable binding to BH3Ds remain unknown. Using all-atom, multiple microsecond-long molecular dynamic simulations (totaling 17 µs) of the murine g-herpesvirus 68 vBCL2 (M11), and statistical inference techniques, we show that regions of M11 transiently unfold and refold upon binding of the BH3D. Further, we show that this partial unfolding/refolding within M11 is mediated by a network of hydrophobic interactions, which includes residues that are 10 Å away from the BH3D binding cleft. -
Mitophagy Confers Resistance to Siderophore-Mediated Killing by Pseudomonas Aeruginosa
Mitophagy confers resistance to siderophore-mediated killing by Pseudomonas aeruginosa Natalia V. Kirienkoa,b, Frederick M. Ausubela,b,1, and Gary Ruvkuna,b,1,2 aDepartment of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114; and bDepartment of Genetics, Harvard Medical School, Boston, MA 02115 Contributed by Gary Ruvkun, December 31, 2014 (sent for review December 19, 2014) In the arms race of bacterial pathogenesis, bacteria produce an Results and Discussion array of toxins and virulence factors that disrupt core host Pyoverdin Enters C. elegans and Is Sufficient to Mediate Host Killing. processes. Hosts mitigate the ensuing damage by responding with Despite the presence of rich sources of iron within host cells, immune countermeasures. The iron-binding siderophore pyover- siderophores are generally assumed to scavenge iron from fer- din is a key virulence mediator of the human pathogen Pseudo- riproteins present in the extracellular milieu. However, we hy- monas aeruginosa, but its pathogenic mechanism has not been pothesize that siderophores are capable of harvesting iron from established. Here we demonstrate that pyoverdin enters Caen- intracellular sources and, consequently, function directly as orhabditis elegans and that it is sufficient to mediate host killing. toxins. We exposed worms to a pyoverdin-enriched, cell-free Moreover, we show that iron chelation disrupts mitochondrial ho- bacterial growth media for 24 h to determine whether detectable meostasis and triggers mitophagy both in C. elegans and mamma- levels of pyoverdin could be identified within the host. After lian cells. Finally, we show that mitophagy provides protection exposure, worms were washed extensively, homogenized, and both against the extracellular pathogen P. -
Spermatozoal Gene KO Studies for the Highly Present Paternal Transcripts
Spermatozoal gene KO studies for the highly present paternal Potential maternal interactions Conclusions of the KO studies on the maternal gene transcripts detected by GeneMANIA candidates for interaction with the paternal Fbxo2 Selective cochlear degeneration in mice lacking Cul1, Fbxl2, Fbxl3, Fbxl5, Cul-1 KO causes early embryonic lethality at E6.5 before Fbxo2 Fbxo34, Fbxo5, Itgb1, Rbx1, the onset of gastrulation http://www.jneurosci.org/content/27/19/5163.full Skp1a http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3641602/. Loss of Cul1 results in early embryonic lethality and Another KO study showed the following: Loss of dysregulation of cyclin E F-box only protein 2 (Fbxo2) disrupts levels and http://www.ncbi.nlm.nih.gov/pubmed/10508527?dopt=Abs localization of select NMDA receptor subunits, tract. and promotes aberrant synaptic connectivity http://www.ncbi.nlm.nih.gov/pubmed/25878288. Fbxo5 (or Emi1): Regulates early mitosis. KO studies shown lethal defects in preimplantation embryo A third KO study showed that Fbxo2 regulates development http://mcb.asm.org/content/26/14/5373.full. amyloid precursor protein levels and processing http://www.jbc.org/content/289/10/7038.long#fn- Rbx1/Roc1: Rbx1 disruption results in early embryonic 1. lethality due to proliferation failure http://www.pnas.org/content/106/15/6203.full.pdf & Fbxo2 has been found to be involved in http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732615/. neurons, but it has not been tested for potential decreased fertilization or pregnancy rates. It Skp1a: In vivo interference with Skp1 function leads to shows high expression levels in testis, indicating genetic instability and neoplastic transformation potential other not investigated functions http://www.ncbi.nlm.nih.gov/pubmed/12417738?dopt=Abs http://biogps.org/#goto=genereport&id=230904 tract. -
MAP1LC3A Antibody [E2F7] Cat
MAP1LC3A Antibody [E2F7] Cat. No.: 14-019 MAP1LC3A Antibody [E2F7] Immunohistochemistry of paraffin-embedded mouse Immunohistochemistry of paraffin-embedded human liver brain using MAP1LC3A antibody (14-019) at dilution of using MAP1LC3A antibody (14-019) at dilution of 1:100 (40x 1:100 (40x lens). lens). Immunohistochemistry of paraffin-embedded mouse Immunofluorescence analysis of HeLa cells using MAP1LC3A liver using MAP1LC3A antibody (14-019) at dilution of antibody (14-019). 1:100 (40x lens). Immunofluorescence analysis of PC-12 cells using MAP1LC3A antibody (14-019). Immunofluorescence analysis of HUVEC cells using MAP1LC3A antibody (14-019). September 24, 2021 1 https://www.prosci-inc.com/map1lc3a-antibody-e2f7-14-019.html Specifications HOST SPECIES: Rabbit SPECIES REACTIVITY: Human, Mouse, Rat IMMUNOGEN: Recombinant protein of human MAP1LC3A TESTED APPLICATIONS: IF, IHC, IP, WB WB: ,1:500 - 1:2000 IHC: ,1:50 - 1:200 APPLICATIONS: IF: ,1:50 - 1:200 IP: ,1:20 - 1:50 POSITIVE CONTROL: 1) SHG-44 2) Mouse brain 3) Mouse liver 4) Mouse skeletal muscle PREDICTED MOLECULAR Observed: 14kDa WEIGHT: Properties PURIFICATION: Affinity purification CLONALITY: Monoclonal ISOTYPE: IgG CONJUGATE: Unconjugated PHYSICAL STATE: Liquid BUFFER: PBS with 0.02% sodium azide, 50% glycerol, pH7.3. STORAGE CONDITIONS: Store at -20˚C. Avoid freeze / thaw cycles. Additional Info OFFICIAL SYMBOL: MAP1LC3A MAP1LC3A Antibody: LC3, LC3A, ATG8E, MAP1ALC3, MAP1BLC3Autophagy-related protein ALTERNATE NAMES: LC3 A GENE ID: 84557 USER NOTE: Optimal dilutions for each application to be determined by the researcher. September 24, 2021 2 https://www.prosci-inc.com/map1lc3a-antibody-e2f7-14-019.html Background and References MAP1A and MAP1B are microtubule-associated proteins which mediate the physical interactions between microtubules and components of the cytoskeleton. -
Biology of the Caenorhabditis Elegans Germline Stem Cell System
| WORMBOOK CELL FATE, SIGNALING, AND DEVELOPMENT Biology of the Caenorhabditis elegans Germline Stem Cell System E. Jane Albert Hubbard*,1 and Tim Schedl†,1 *Skirball Institute of Biomolecular Medicine, Departments of Cell Biology and Pathology, New York University School of Medicine, † New York 10016 and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110 ORCID IDs: 0000-0001-5893-7232 (E.J.A.H.); 0000-0003-2148-2996 (T.S.) ABSTRACT Stem cell systems regulate tissue development and maintenance. The germline stem cell system is essential for animal reproduction, controlling both the timing and number of progeny through its influence on gamete production. In this review, we first draw general comparisons to stem cell systems in other organisms, and then present our current understanding of the germline stem cell system in Caenorhabditis elegans. In contrast to stereotypic somatic development and cell number stasis of adult somatic cells in C. elegans, the germline stem cell system has a variable division pattern, and the system differs between larval development, early adult peak reproduction and age-related decline. We discuss the cell and developmental biology of the stem cell system and the Notch regulated genetic network that controls the key decision between the stem cell fate and meiotic development, as it occurs under optimal laboratory conditions in adult and larval stages. We then discuss alterations of the stem cell system in response to environ- mental perturbations and aging. A recurring distinction is between processes that control stem cell fate and those that control cell cycle regulation. C. elegans is a powerful model for understanding germline stem cells and stem cell biology. -
Potential Sperm Contributions to the Murine Zygote Predicted by in Silico Analysis
REPRODUCTIONRESEARCH Potential sperm contributions to the murine zygote predicted by in silico analysis Panagiotis Ntostis1,2, Deborah Carter3, David Iles1, John Huntriss1, Maria Tzetis2 and David Miller1 1Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, West Yorkshire, UK, 2Department of Medical Genetics, St. Sophia’s Children Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Attiki, Greece and 3Leeds Institute of Molecular Medicine, University of Leeds, Leeds, West Yorkshire, UK Correspondence should be addressed to D Miller; Email: [email protected] Abstract Paternal contributions to the zygote are thought to extend beyond delivery of the genome and paternal RNAs have been linked to epigenetic transgenerational inheritance in different species. In addition, sperm–egg fusion activates several downstream processes that contribute to zygote formation, including PLC zeta-mediated egg activation and maternal RNA clearance. Since a third of the preimplantation developmental period in the mouse occurs prior to the first cleavage stage, there is ample time for paternal RNAs or their encoded proteins potentially to interact and participate in early zygotic activities. To investigate this possibility, a bespoke next-generation RNA sequencing pipeline was employed for the first time to characterise and compare transcripts obtained from isolated murine sperm, MII eggs and pre-cleavage stage zygotes. Gene network analysis was then employed to identify potential interactions between paternally and maternally derived factors during the murine egg-to-zygote transition involving RNA clearance, protein clearance and post-transcriptional regulation of gene expression. Our in silico approach looked for factors in sperm, eggs and zygotes that could potentially interact co-operatively and synergisticallyp during zygote formation. -
Beclin-1 Expression Is Retained in High-Grade Serous Ovarian Cancer Yet Is Not Essential for Autophagy Induction in Vitro Rohann J
Western University Scholarship@Western Biochemistry Publications Biochemistry Department 8-2015 Beclin-1 Expression is Retained in High-Grade Serous Ovarian Cancer yet is Not Essential for Autophagy Induction In Vitro Rohann J. M. Correa Western University Yudith Ramos Valdes London Regional Cancer Program Trevor G. Shepherd Western University Gabriel E. DiMattia Western University, [email protected] Follow this and additional works at: https://ir.lib.uwo.ca/biochempub Part of the Biochemistry Commons Citation of this paper: Correa, Rohann J. M.; Valdes, Yudith Ramos; Shepherd, Trevor G.; and DiMattia, Gabriel E., "Beclin-1 Expression is Retained in High- Grade Serous Ovarian Cancer yet is Not Essential for Autophagy Induction In Vitro" (2015). Biochemistry Publications. 166. https://ir.lib.uwo.ca/biochempub/166 Correa et al. Journal of Ovarian Research (2015) 8:52 DOI 10.1186/s13048-015-0182-y RESEARCH Open Access Beclin-1 expression is retained in high-grade serous ovarian cancer yet is not essential for autophagy induction in vitro Rohann J. M. Correa1,2, Yudith Ramos Valdes1, Trevor G. Shepherd1,3,4,5† and Gabriel E. DiMattia1,2,3,4,6*† Abstract Background: Autophagy is a conserved cellular self-digestion mechanism that can either suppress or promote cancer in a context-dependent manner. In ovarian cancer, prevalent mono-allelic deletion of BECN1 (a canonical autophagy-inducer) suggests that autophagy is impaired to promote carcinogenesis and that Beclin-1 is a haploinsufficient tumor suppressor. Nonetheless, autophagy is known to be readily inducible in ovarian cancer cells. We sought to clarify whether Beclin-1 expression is in fact disrupted in ovarian cancer and whether this impacts autophagy regulation. -
The DNA Sequence and Comparative Analysis of Human Chromosome 20
articles The DNA sequence and comparative analysis of human chromosome 20 P. Deloukas, L. H. Matthews, J. Ashurst, J. Burton, J. G. R. Gilbert, M. Jones, G. Stavrides, J. P. Almeida, A. K. Babbage, C. L. Bagguley, J. Bailey, K. F. Barlow, K. N. Bates, L. M. Beard, D. M. Beare, O. P. Beasley, C. P. Bird, S. E. Blakey, A. M. Bridgeman, A. J. Brown, D. Buck, W. Burrill, A. P. Butler, C. Carder, N. P. Carter, J. C. Chapman, M. Clamp, G. Clark, L. N. Clark, S. Y. Clark, C. M. Clee, S. Clegg, V. E. Cobley, R. E. Collier, R. Connor, N. R. Corby, A. Coulson, G. J. Coville, R. Deadman, P. Dhami, M. Dunn, A. G. Ellington, J. A. Frankland, A. Fraser, L. French, P. Garner, D. V. Grafham, C. Grif®ths, M. N. D. Grif®ths, R. Gwilliam, R. E. Hall, S. Hammond, J. L. Harley, P. D. Heath, S. Ho, J. L. Holden, P. J. Howden, E. Huckle, A. R. Hunt, S. E. Hunt, K. Jekosch, C. M. Johnson, D. Johnson, M. P. Kay, A. M. Kimberley, A. King, A. Knights, G. K. Laird, S. Lawlor, M. H. Lehvaslaiho, M. Leversha, C. Lloyd, D. M. Lloyd, J. D. Lovell, V. L. Marsh, S. L. Martin, L. J. McConnachie, K. McLay, A. A. McMurray, S. Milne, D. Mistry, M. J. F. Moore, J. C. Mullikin, T. Nickerson, K. Oliver, A. Parker, R. Patel, T. A. V. Pearce, A. I. Peck, B. J. C. T. Phillimore, S. R. Prathalingam, R. W. Plumb, H. Ramsay, C. M. -
Super-Assembly of ER-Phagy Receptor Atg40 Induces Local ER Remodeling at Contacts with Forming Autophagosomal Membranes
ARTICLE https://doi.org/10.1038/s41467-020-17163-y OPEN Super-assembly of ER-phagy receptor Atg40 induces local ER remodeling at contacts with forming autophagosomal membranes ✉ Keisuke Mochida1,4, Akinori Yamasaki 2,3,4, Kazuaki Matoba 2, Hiromi Kirisako1, Nobuo N. Noda 2 & ✉ Hitoshi Nakatogawa 1 1234567890():,; The endoplasmic reticulum (ER) is selectively degraded by autophagy (ER-phagy) through proteins called ER-phagy receptors. In Saccharomyces cerevisiae, Atg40 acts as an ER-phagy receptor to sequester ER fragments into autophagosomes by binding Atg8 on forming autophagosomal membranes. During ER-phagy, parts of the ER are morphologically rear- ranged, fragmented, and loaded into autophagosomes, but the mechanism remains poorly understood. Here we find that Atg40 molecules assemble in the ER membrane concurrently with autophagosome formation via multivalent interaction with Atg8. Atg8-mediated super- assembly of Atg40 generates highly-curved ER regions, depending on its reticulon-like domain, and supports packing of these regions into autophagosomes. Moreover, tight binding of Atg40 to Atg8 is achieved by a short helix C-terminal to the Atg8-family interacting motif, and this feature is also observed for mammalian ER-phagy receptors. Thus, this study sig- nificantly advances our understanding of the mechanisms of ER-phagy and also provides insights into organelle fragmentation in selective autophagy of other organelles. 1 School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan. 2 Institute of Microbial -
BECN1 (H-300): Sc-11427
SANTA CRUZ BIOTECHNOLOGY, INC. BECN1 (H-300): sc-11427 The Power to Question BACKGROUND APPLICATIONS BECN1 (beclin 1) is a coiled-coil protein that has been implicated as an BECN1 (H-300) is recommended for detection of BECN1 of mouse, rat and inhibitor of tumorigenesis. BECN1, which associates with Bcl-2, plays a human origin by Western Blotting (starting dilution 1:200, dilution range significant role in autophagy. Autophagy is the degradation of cellular pro- 1:100-1:1000), immunoprecipitation [1–2 µg per 100–500 µg of total pro- teins in the lysosomes, and when this pathway is suppressed, cell growth is tein (1 ml of cell lysate)], immunofluorescence and immunohistochemistry deregulated. Autophagy is controlled by the same signal transduction path- (including paraffin-embedded sections) (starting dilution 1:50, dilution way that induces the phosphorylation of the ribosomal protein S6, and both range 1:50-1:500). are mediated via amino acids. BECN1 expression in various carcinoma cell Suitable for use as control antibody for BECN1 siRNA (h): sc-29797, BECN1 lines, such as MCF7, is low, whereas it is ubiquitously expressed in normal siRNA (h2): sc-44286 and BECN1 siRNA (m): sc-29798. breast tissue. In transfected MCF7 cells, BECN1 complements autophagocy- tosis and, subsequently, inhibits cellular proliferation. Additionally, BECN1 Molecular Weight of BECN1: 60 kDa. shares structural similarity to the yeast autophagy gene product, apg6, and Positive Controls: HeLa whole cell lysate: sc-2200, MCF7 whole cell lysate: was one of the first mammalian proteins discovered to mediate autophagy. sc-2206 or NIH/3T3 whole cell lysate: sc-2210.