Life Sciences Institute

Research Output 1969 2017

2017

A few words of introduction from your new diabetes editorial board

Myers, M. G., D'Alessio, D. A., Gannon, M. A., Seeley, R. J., Burant, C. F., Doria, A., Grant, M. B., Herman, W. H., Herold, K. C., Horowitz, J. F., Lin, J. D., Lumeng, C. N. K., MacDougald, O. A., Pietropaolo, M., Pop-Busui, R., Satin, L., Stoffers, D. A. & White, M. F. Jan 1 2017 In : Diabetes. 66, 1, p. 3-4 2 p.

Research output: Contribution to journalComment/debate

A pathway of targeted autophagy is induced by DNA damage in budding yeast

Eapen, V. V., Waterman, D. P., Bernard, A., Schiffmann, N., Sayas, E., Kamber, R., Lemos, B., Memisoglu, G., Ang, J., Mazella, A., Chuartzman, S. G., Loewith, R. J., Schuldiner, M., Denic, V., Klionsky, D. J. & Haber, J. E. Feb 14 2017 In : Proceedings of the National Academy of Sciences of the United States of America. 114, 7, p. E1158-E1167

Research output: Contribution to journalArticle

Saccharomycetales
Autophagy
DNA Damage
Mutagens
Proteins

A Receptor on Acid

Chen, Q. & Tesmer, J. J. G. Jan 26 2017 In : Cell. 168, 3, p. 339-341 3 p.

Research output: Contribution to journalShort survey

Hallucinogens
Lysergic Acid Diethylamide
Hallucinations
Serotonin
Acids

Autophagic membrane delivery through ATG9

Feng, Y. & Klionsky, D. J. Jan 10 2017 In : Cell Research.

Research output: Contribution to journalArticle

Autophagy
Membranes
trans-Golgi Network
Starvation
Phosphotransferases
1 Citations
Autophagy
Medicine
Nobel Prize
Explosions
Secretory Pathway

Blame it on Southern, but it's a western blot

Klionsky, D. J. Jan 2 2017 In : Autophagy. 13, 1, p. 1-2 2 p.

Research output: Contribution to journalEditorial

Southern Blotting
Western Blotting
Molecular Biology
Genome
Polymerase Chain Reaction

Comparative analysis of satellite DNA in the drosophila melanogaster species complex

Jagannathan, M., Warsinger-Pepe, N., Watase, G. J. & Yamashita, Y. M. 2017 In : G3: Genes, Genomes, Genetics. 7, 2, p. 693-704 12 p.

Research output: Contribution to journalArticle

Satellite DNA
Drosophila melanogaster
Genome
Genetic Techniques
Heterochromatin

Conserved function of the long noncoding RNA Blnc1 in brown adipocyte differentiation

Mi, L., Zhao, X. Y., Li, S., Yang, G. & Lin, J. D. Jan 1 2017 In : Molecular Metabolism. 6, 1, p. 101-110 10 p.

Research output: Contribution to journalArticle

Long Noncoding RNA
Ribonucleoproteins
RNA
Gene Expression
Genes

Does relevancy matter?

Klionsky, D. J. 2017 In : Biochemistry and Molecular Biology Education.

Research output: Contribution to journalArticle

Evaluation of the asymmetric division of Drosophila male germline stem cells

Inaba, M. & Yamashita, Y. M. 2017 Methods in Molecular Biology. Humana Press Inc., Vol. 1463, p. 49-62 14 p. (Methods in Molecular Biology; vol. 1463)

Research output: Chapter in Book/Report/Conference proceedingChapter

Asymmetric Cell Division
Drosophila
Stem Cells
Homeostasis

PHB2/prohibitin 2: An inner membrane mitophagy receptor

Lahiri, V. & Klionsky, D. J. Mar 1 2017 In : Cell Research. 27, 3, p. 311-312 2 p.

Research output: Contribution to journalReview article

Mitochondria
Mitochondrial Degradation

PRDM9 interactions with other proteins provide a link between recombination hotspots and the chromosomal axis in meiosis

Parvanov, E. D., Tian, H., Billings, T., Saxl, R. L., Spruce, C., Aithal, R., Krejci, L., Paigen, K., Petkov, P. M. & Yamashita, Y. Feb 1 2017 In : Molecular Biology of the Cell. 28, 3, p. 488-499 12 p.

Research output: Contribution to journalArticle

Meiosis
Genetic Recombination
Proteins
Spermatocytes
DNA

Preferential hydrolysis of truncated oxidized glycerophospholipids by lysosomal phospholipase A2

Abe, A., Hiraoka, M., Ohguro, H., Tesmer, J. J. & Shayman, J. A. 2017 In : Journal of Lipid Research. 58, 2, p. 339-349 11 p.

Research output: Contribution to journalArticle

Glycerophospholipids
Phospholipases A2
Hydrolysis
Phosphorylcholine
Phosphatidylcholines

Safety and immunogenicity of mammalian cell derived and Modified Vaccinia Ankara vectored African swine fever subunit antigens in swine

Lopera-Madrid, J., Osorio, J. E., He, Y., Xiang, Z., Adams, L. G., Laughlin, R. C., Mwangi, W., Subramanya, S., Neilan, J., Brake, D., Burrage, T. G., Brown, W. C., Clavijo, A. & Bounpheng, M. A. Mar 1 2017 In : Veterinary Immunology and Immunopathology. 185, p. 20-33 14 p.

Research output: Contribution to journalArticle

African Swine Fever
Vaccinia
Swine
Safety
Antigens

Snail/Slug-YAP/TAZ complexes cooperatively regulate mesenchymal stem cell function and bone formation

Tang, Y. & Weiss, S. J. Feb 9 2017 In : Cell Cycle. p. 1-7 7 p.

Research output: Contribution to journalArticle

Gastropoda
Snails
Mesenchymal Stromal Cells
Osteogenesis
Epithelial-Mesenchymal Transition

spict, a cyst cell-specific gene, regulates starvation-induced spermatogonial cell death in the Drosophila testis

Chiang, A. C. Y., Yang, H. & Yamashita, Y. M. Jan 10 2017 In : Scientific Reports. 7, 40245

Research output: Contribution to journalArticle

Starvation
Drosophila
Testis
Cysts
Cell Death

The molecular mechanism of Atg13 function in autophagy induction: What is hidden behind the data?

Popelka, H. & Klionsky, D. J. Mar 4 2017 In : Autophagy. p. 1-3 3 p.

Research output: Contribution to journalArticle

Autophagy
Yeasts
Proteins
Class III Phosphatidylinositol 3-Kinases
Crystallography

Xenophagy: A battlefield between host and microbe, and a possible avenue for cancer treatment

Mao, K. & Klionsky, D. J. Feb 1 2017 In : Autophagy. 13, 2, p. 223-224 2 p.

Research output: Contribution to journalEditorial

Autophagy
Eukaryota
Neoplasms
Mitochondrial Degradation
Antiviral Agents
2016
6 Citations

2.8-Å Cryo-EM Structure of the Large Ribosomal Subunit from the Eukaryotic Parasite Leishmania

Shalev-Benami, M., Zhang, Y., Matzov, D., Halfon, Y., Zackay, A., Rozenberg, H., Zimmerman, E., Bashan, A., Jaffe, C. L., Yonath, A. & Skiniotis, G. Mar 13 2016 In : Cell Reports.

Research output: Contribution to journalArticle

Eukaryotic Large Ribosome Subunits
Large Ribosome Subunits
Leishmania
Parasites
Leishmania donovani

Aberrant mTORC1 activation kills tubular cells by inactivating miR148b-3p

Inoki, K. Dec 1 2016 In : Kidney International. 90, 6, p. 1146-1148 3 p.

Research output: Contribution to journalComment/debate

Sirolimus
Cell Death
Kidney
Endoplasmic Reticulum Stress
Tumor Necrosis Factor-alpha

Alternative autophagy, brefeldin A and viral trafficking pathways

Grose, C. & Klionsky, D. J. Aug 11 2016 In : Autophagy. p. 1-2 2 p.

Research output: Contribution to journalArticle

Brefeldin A
Autophagy
Membranes
DNA Viruses
RNA Viruses
4 Citations

A mitochondrial DNA hypomorph of cytochrome oxidase specifically impairs male fertility in Drosophila melanogaster

Patel, M. R., Miriyala, G. K., Littleton, A. J., Yang, H., Trinh, K., Young, J. M., Kennedy, S. R., Yamashita, Y. M., Pallanck, L. J. & Malik, H. S. Aug 2 2016 In : eLife. 5, AUGUST, e16923

Research output: Contribution to journalArticle

Electron Transport Complex IV
Drosophila melanogaster
Mitochondrial DNA
Fertility
Mutation

A novel PINK1- and PARK2-dependent protective neuroimmune pathway in lethal sepsis

Kang, R., Zeng, L., Xie, Y., Yan, Z., Zhou, B., Cao, L., Klionsky, D. J., Tracey, K. J., Li, J., Wang, H., Billiar, T. R., Jiang, J. & Tang, D. Dec 1 2016 In : Autophagy. 12, 12, p. 2374-2385 12 p.

Research output: Contribution to journalArticle

Sepsis
HMGB1 Protein
Critical Care
Messenger RNA
Glycyrrhizic Acid
9 Citations

An overview of macroautophagy in yeast

Wen, X. & Klionsky, D. J. May 8 2016 In : Journal of Molecular Biology. 428, 9, p. 1681-1699 19 p.

Research output: Contribution to journalReview article

Yeasts
Cell Physiological Phenomena
Recycling
Biogenesis
Starvation
1 Citations

An oxygen-insensitive Hif-3α isoform inhibits Wnt signaling by destabilizing the nuclear β-catenin complex

Zhang, P., Bai, Y., Lu, L., Li, Y. & Duan, C. Jan 14 2016 In : eLife. 5, JANUARY2016, e08996

Research output: Contribution to journalArticle

beta Catenin
Protein Isoforms
Oxygen
Anoxia
Response Elements

An unconventional pathway for mitochondrial protein degradation

Yao, Z. & Klionsky, D. J. Nov 1 2016 In : Autophagy. 12, 11, p. 1971-1972 2 p.

Research output: Contribution to journalEditorial

Mitochondrial Proteins
Proteolysis
Mitochondria
Mitochondrial Degradation
Cell Aging
1 Citations

Architecture and Nucleotide-Dependent Conformational Changes of the Rvb1-Rvb2 AAA+ Complex Revealed by Cryoelectron Microscopy

Ewens, C. A., Su, M., Zhao, L., Nano, N., Houry, W. A. & Southworth, D. R. May 3 2016 In : Structure. 24, 5, p. 657-666 10 p.

Research output: Contribution to journalArticle

Cryoelectron Microscopy
Nucleotides
Adenosine Triphosphate
Hydrolysis
Small Nucleolar Ribonucleoproteins

A role of autophagy in spinocerebellar ataxia—Rare exception or general principle?

Burmeister, M., Lee, J. H., Schulman, B. A., Yapici, Z., Tolun, A., Juhasz, G., Li, J. Z. & Klionsky, D. J. Jul 2 2016 In : Autophagy. p. 1-2 2 p.

Research output: Contribution to journalArticle

Spinocerebellar Ataxias
Autophagy

Autolysosome biogenesis and developmental senescence are regulated by both Spns1 and v-ATPase

Sasaki, T., Lian, S., Khan, A., Llop, J. R., Samuelson, A. V., Chen, W., Klionsky, D. J. & Kishi, S. Dec 15 2016 In : Autophagy. p. 1-18 18 p.

Research output: Contribution to journalArticle

Biogenesis
Adenosine Triphosphatases
Drosophila
Genes
Clustered Regularly Interspaced Short Palindromic Repeats
2 Citations

Autophagy core machinery: overcoming spatial barriers in neurons

Ariosa, A. R. & Klionsky, D. J. Nov 1 2016 In : Journal of Molecular Medicine. 94, 11, p. 1217-1227 11 p.

Research output: Contribution to journalReview article

Autophagy
Proteins
Poisons
Vacuoles
Lysosomes
1 Citations
Autophagy
Stem Cells
Cell Physiological Phenomena
Recycling

Autophagy-mediated catabolism of visual transduction proteins prevents retinal degeneration

Yao, J., Jia, L., Feathers, K., Lin, C., Khan, N. W., Klionsky, D. J., Ferguson, T. A. & Zacks, D. N. Dec 1 2016 In : Autophagy. 12, 12, p. 2439-2450 12 p.

Research output: Contribution to journalArticle

Retinal Degeneration
Autophagy
Proteins
Transducin
Retinal Rod Photoreceptor Cells

Autophagy promotes cell motility by driving focal adhesion turnover

Xu, Z. & Klionsky, D. J. Oct 2 2016 In : Autophagy. p. 1-2 2 p.

Research output: Contribution to journalArticle

Focal Adhesions
Autophagy
Cell Movement
Proteins
Traction
1 Citations

Autophagy regulates cytoplasmic remodeling during cell reprogramming in a zebrafish model of muscle regeneration

Saera-Vila, A., Kish, P. E., Louie, K. W., Grzegorski, S. J., Klionsky, D. J. & Kahana, A. Oct 2 2016 In : Autophagy. 12, 10, p. 1864-1875 12 p.

Research output: Contribution to journalArticle

Autophagy
Zebrafish
Regeneration
Muscles
Cellular Reprogramming

Buried Hydrogen Bond Interactions Contribute to the High Potency of Complement Factor D Inhibitors

Yang, C. Y., Phillips, J. G., Stuckey, J. A., Bai, L., Sun, H., Delproposto, J., Brown, W. C. & Chinnaswamy, K. Dec 8 2016 In : ACS Medicinal Chemistry Letters. 7, 12, p. 1092-1096 5 p.

Research output: Contribution to journalArticle

Complement Factor D
Hydrogen
Amides
Alternative Complement Pathway
Interferometry
2 Citations

Can i solve my structure by SAD phasing? Anomalous signal in SAD phasing

Terwilliger, T. C., Bunkóczi, G., Hung, L. W., Zwart, P. H., Smith, J. L., Akey, D. L. & Adams, P. D. 2016 In : Acta Crystallographica Section D: Structural Biology. 72, 3, p. 346-358 13 p.

Research output: Contribution to journalArticle

Signal-To-Noise Ratio
Research Design
Datasets
2 Citations

Can i solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal

Terwilliger, T. C., Bunkóczi, G., Hung, L. W., Zwart, P. H., Smith, J. L., Akey, D. L. & Adams, P. D. 2016 In : Acta Crystallographica Section D: Structural Biology. 72, 3, p. 359-374 16 p.

Research output: Contribution to journalArticle

Datasets
Signal-To-Noise Ratio

Conformational sampling and binding site assessment of suppression of tumorigenicity 2 ectodomain

Yang, C. Y., Delproposto, J., Chinnaswamy, K., Brown, W. C., Wang, S., Stuckey, J. A. & Wang, X. Jan 6 2016 In : PLoS One. 11, 1, e0146522

Research output: Contribution to journalArticle

Binding Sites
Interleukin-1 Receptors
Structural Models
Graft vs Host Disease
Molecular Dynamics Simulation
5 Citations

CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma

Carlson, H. A., Smith, R. D., Damm-Ganamet, K. L., Stuckey, J. A., Ahmed, A., Convery, M. A., Somers, D. O., Kranz, M., Elkins, P. A., Cui, G., Peishoff, C. E., Lambert, M. H. & Dunbar, J. B. Jun 27 2016 In : Journal of Chemical Information and Modeling. 56, 6, p. 1063-1077 15 p.

Research output: Contribution to journalArticle

participant
Ligands
structure
method
Proteins
3 Citations

CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge

Smith, R. D., Damm-Ganamet, K. L., Dunbar, J. B., Ahmed, A., Chinnaswamy, K., Delproposto, J. E., Kubish, G. M., Tinberg, C. E., Khare, S. D., Dou, J., Doyle, L., Stuckey, J. A., Baker, D. & Carlson, H. A. Jun 27 2016 In : Journal of Chemical Information and Modeling. 56, 6, p. 1022-1031 10 p.

Research output: Contribution to journalArticle

measurement method
Proteins
activity structure
score
resources
1 Citations

Demystifying Mechanosensitive Piezo Ion Channels

Xu, X. Z. S. May 11 2016 In : Neuroscience Bulletin. p. 1-3 3 p.

Research output: Contribution to journalArticle

Proprioception
Touch
Molecular Structure
Ion Channels
Hearing
2 Citations

Deprotonations in the Reaction of Flavin-Dependent Thymidylate Synthase

Stull, F. W., Bernard, S. M., Sapra, A., Smith, J. L., Zuiderweg, E. R. P. & Palfey, B. A. Jun 14 2016 In : Biochemistry. 55, 23, p. 3261-3269 9 p.

Research output: Contribution to journalArticle

Thymidylate Synthase
Deoxyuridine
Deoxyuracil Nucleotides
NADP
Thymidine
4 Citations

Developing a set of guidelines for your research field: A practical approach

Klionsky, D. J. Mar 1 2016 In : Molecular Biology of the Cell. 27, 5, p. 733-738 6 p.

Research output: Contribution to journalReview article

Autophagy
1 Citations

DHX9/RHA Binding to the PBS-Segment of the Genomic RNA during HIV-1 Assembly Bolsters Virion Infectivity

Boeras, I., Song, Z., Moran, A., Franklin, J., Brown, W. C., Johnson, M., Boris-Lawrie, K. & Heng, X. Jun 5 2016 In : Journal of Molecular Biology. 428, 11, p. 2418-2429 12 p.

Research output: Contribution to journalArticle

RNA Helicases
Virion
HIV-1
Binding Sites
RNA
4 Citations

Discovery of cahuitamycins as biofilm inhibitors derived from a convergent biosynthetic pathway

Park, S. R., Tripathi, A., Wu, J., Schultz, P. J., Yim, I., McQuade, T. J., Yu, F., Arevang, C. J., Mensah, A. Y., Tamayo-Castillo, G., Xi, C. & Sherman, D. H. Feb 16 2016 In : Nature Communications. 7, 10710

Research output: Contribution to journalArticle

Biofilms
Acinetobacter baumannii
Streptomyces
Microbial Drug Resistance
Biological Products
2 Citations

Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast

Booth, G. T., Wang, I. X., Cheung, V. G. & Lis, J. T. Jun 1 2016 In : Genome Research. 26, 6, p. 799-811 13 p.

Research output: Contribution to journalArticle

Peptide Elongation Factors
Saccharomycetales
Schizosaccharomyces
RNA Polymerase II
Transcription Initiation Site

Domain Organization and Active Site Architecture of a Polyketide Synthase C-methyltransferase

Skiba, M. A., Sikkema, A. P., Fiers, W. D., Gerwick, W. H., Sherman, D. H., Aldrich, C. C. & Smith, J. L. Dec 16 2016 In : ACS Chemical Biology. 11, 12, p. 3319-3327 9 p.

Research output: Contribution to journalArticle

Polyketide Synthases
Methyltransferases
Catalytic Domain
Acyl Carrier Protein
Polyketides

Downregulation of autophagy through CUL3-KLHL20-mediated turnover of the ULK1 and PIK3C3/VPS34 complexes

Feng, Y. & Klionsky, D. J. Jul 2 2016 In : Autophagy. p. 1-2 2 p.

Research output: Contribution to journalArticle

Autophagy
Down-Regulation
Ligases
Ubiquitin

Editorial: Molecular regulation and therapeutic potential of thermogenic fat cells

Wu, J. Mar 29 2016 In : Frontiers in Endocrinology. 7, MAR, 26

Research output: Contribution to journalEditorial