Biochemistry and Molecular Biology

Publications 1975 2018

2018

2,3,7,8-Tetrachlorodibenzo-p-dioxin dose-dependently increases bone mass and decreases marrow adiposity in juvenile mice

Fader, K. A., Nault, R., Raehtz, S., McCabe, L. R. & Zacharewski, T. R. Jun 1 2018 In : Toxicology and Applied Pharmacology. 348, p. 85-98 14 p.

Research output: Contribution to journalArticle

Adiposity
Bone
Aryl Hydrocarbon Receptors
Bone Marrow
Bone and Bones
3 Citations

A biosensor-based framework to measure latent proteostasis capacity

Wood, R. J., Ormsby, A. R., Radwan, M., Cox, D., Sharma, A., Vöpel, T., Ebbinghaus, S., Oliveberg, M., Reid, G. E., Dickson, A. & Hatters, D. M. Dec 1 2018 In : Nature Communications. 9, 1, 287

Research output: Contribution to journalArticle

homeostasis
gene expression
Protein Folding
heat shock
flow cytometry

A failsafe for sensing chromatid tension in mitosis with the histone H3 tail in saccharomyces cerevisiae

Buehl, C. J., Deng, X., Luo, J., Buranasudja, V., Hazbun, T. & Kuo, M. H. Feb 1 2018 In : Genetics. 208, 2, p. 565-578 14 p.

Research output: Contribution to journalArticle

Chromatids
Mitosis
Histones
Saccharomyces cerevisiae
Centromere

A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data

Bipolar Disorders Working Group of the Psychiatric Genomics Consortium May 1 2018 In : PLoS Computational Biology. 14, 5, e1006105

Research output: Contribution to journalArticle

Biclustering
Genome-Wide Association Study
Gene expression
Gene Expression
gene expression

Amazing Diversity in Biochemical Roles of Fe(II)/2-Oxoglutarate Oxygenases

Herr, C. Q. & Hausinger, R. P. Jan 1 2018 (Accepted/In press) In : Trends in Biochemical Sciences.

Research output: Contribution to journalArticle

Oxygenases
Efflorescence
Cracks
Thermionic emission
Messenger RNA

A Structural Model of the Urease Activation Complex Derived from Ion Mobility-Mass Spectrometry and Integrative Modeling

Eschweiler, J. D., Farrugia, M. A., Dixit, S. M., Hausinger, R. P. & Ruotolo, B. T. Apr 3 2018 In : Structure. 26, 4, p. 599-606.e3

Research output: Contribution to journalArticle

Urease
Structural Models
Mass Spectrometry
Apoproteins
Ions

AttrActin’ Attention to Early Mouse Development

Frum, T. & Ralston, A. Apr 19 2018 In : Cell. 173, 3, p. 544-545 2 p.

Research output: Contribution to journalShort survey

Time-Lapse Imaging
Actins
Embryonic Structures
Imaging techniques

Automated inference of chemical discriminants of biological activity

Raschka, S., Scott, A. M., Huertas, M., Li, W. & Kuhn, L. A. Jan 1 2018 Methods in Molecular Biology. Humana Press Inc., p. 307-338 32 p. (Methods in Molecular Biology; vol. 1762)

Research output: Chapter in Book/Report/Conference proceedingChapter

Synthetic Chemistry Techniques
Decision Trees
Quantitative Structure-Activity Relationship
Biological Assay
Vertebrates
3 Citations

Bacterial microcompartments

Kerfeld, C. A., Aussignargues, C., Zarzycki, J., Cai, F. & Sutter, M. May 1 2018 In : Nature Reviews Microbiology. 16, 5, p. 277-290 14 p.

Research output: Contribution to journalArticle

Synthetic Biology
Bacteria
Carbon Cycle
Carbon Dioxide
Organelles

Breaking symmetry in viral icosahedral capsids as seen through the lenses of X-ray crystallography and cryo-electron microscopy

Parent, K. N., Schrad, J. R. & Cingolani, G. Feb 7 2018 In : Viruses. 10, 2, 67

Research output: Contribution to journalReview article

Cryoelectron Microscopy
Capsid
X Ray Crystallography
Lenses
Product Packaging
Camptotheca
Camptotheca acuminata
Flavonoids
Alkaloids
methyltransferases

Capturing and Interconverting Embryonic Cell Fates in a Dish

Watts, J., Lokken, A., Moauro, A. & Ralston, A. Jan 1 2018 (Accepted/In press) In : Current Topics in Developmental Biology.

Research output: Contribution to journalArticle

Stem Cells
Embryonic Stem Cells
Embryonic Structures
Pluripotent Stem Cells
Endoderm

Challenges and opportunities in connecting simulations with experiments via molecular dynamics of cellular environments

Feig, M., Nawrocki, G., Yu, I., Wang, P. H. & Sugita, Y. Jun 27 2018 In : Journal of Physics: Conference Series. 1036, 1, 012010

Research output: Contribution to journalConference article

Molecular dynamics
molecular dynamics
simulation
Experiments
artificial intelligence
1 Citations

Coexpression analysis identifies two oxidoreductases involved in the biosynthesis of the monoterpene acid moiety of natural pyrethrin insecticides in Tanacetum cinerariifolium

Xu, H., Moghe, G. D., Wiegert-Rininger, K., Schilmiller, A. L., Barry, C. S., Last, R. L. & Pichersky, E. Jan 1 2018 In : Plant Physiology. 176, 1, p. 524-537 14 p.

Research output: Contribution to journalArticle

Chrysanthemum cinerariifolium
Tanacetum cinerariifolium
Pyrethrins
Monoterpenes
oxidoreductases
Aryl Hydrocarbon Receptors
Pyruvate Kinase
Liver
Protein Isoforms
Muscles
6 Citations

Conserved dynamics of chloroplast cytoskeletal FtsZ proteins across photosynthetic lineages

Terbush, A. D., MacCready, J. S., Chen, C., Ducat, D. C. & Osteryoung, K. W. Jan 1 2018 In : Plant Physiology. 176, 1, p. 295-306 12 p.

Research output: Contribution to journalArticle

Chloroplasts
chloroplasts
Temperature
temperature
proteins
Photosystem I Protein Complex
photosystem I
Photosynthesis
funding
Publications
Iron-Regulatory Proteins
Hepcidins
Aryl Hydrocarbon Receptors
Production control
Heme

Critical roles of Shugoshin and histones as tension sensors during mitosis

Buehl, C. J. & Kuo, M. H. May 23 2018 (Accepted/In press) In : Current Genetics. p. 1-5 5 p.

Research output: Contribution to journalArticle

Mitosis
Histones
Chromatin
Personnel Selection
Proteins

Direct activation of a phospholipase by cyclic GMP-AMP in El Tor Vibrio cholerae

Severin, G. B., Ramliden, M. S., Hawver, L. A., Wang, K., Pell, M. E., Kieninger, A. K., Khataokar, A., O’Hara, B. J., Behrmann, L. V., Neiditch, M. B., Benning, C., Waters, C. M. & Ng, W. L. Jun 26 2018 In : Proceedings of the National Academy of Sciences of the United States of America. 115, 26, p. E6048-E6055

Research output: Contribution to journalArticle

Vibrio cholerae
Phospholipases
Vibrio
Second Messenger Systems
GMP synthase (glutamine-hydrolyzing)

Distinct transcriptomic and exomic abnormalities within myelodysplastic syndrome marrow cells

Im, H., Rao, V., Sridhar, K., Bentley, J., Mishra, T., Chen, R., Hall, J., Graber, A., Zhang, Y., Li, X., Mias, G. I., Snyder, M. P. & Greenberg, P. L. Apr 5 2018 (Accepted/In press) In : Leukemia and Lymphoma. p. 1-11 11 p.

Research output: Contribution to journalArticle

Myelodysplastic Syndromes
Bone Marrow
Transcriptome
High-Throughput Nucleotide Sequencing
Acute Myeloid Leukemia

Editorial

Blumwald, E., Grotewold, E., Okita, T., Jiang, L. & Wendehenne, D. Jan 1 2018 In : Plant Science. 266, 1 p.

Research output: Contribution to journalEditorial

1 Citations

Enabling the hypothesis-driven prioritization of ligand candidates in big databases: Screenlamp and its application to GPCR inhibitor discovery for invasive species control

Raschka, S., Scott, A. M., Liu, N., Gunturu, S., Huertas, M., Li, W. & Kuhn, L. A. Jan 30 2018 (Accepted/In press) In : Journal of Computer-Aided Molecular Design. p. 1-19 19 p.

Research output: Contribution to journalArticle

Introduced Species
Computer-Aided Design
Structure-Activity Relationship
G-Protein-Coupled Receptors
inhibitors
1 Citations

Engineered Lignin in Poplar Biomass Facilitates Cu-Catalyzed Alkaline-Oxidative Pretreatment

Bhalla, A., Bansal, N., Pattathil, S., Li, M., Shen, W., Particka, C. A., Karlen, S. D., Phongpreecha, T., Semaan, R. R., Gonzales-Vigil, E., Ralph, J., Mansfield, S. D., Ding, S. Y., Hodge, D. B. & Hegg, E. L. Mar 5 2018 In : ACS Sustainable Chemistry and Engineering. 6, 3, p. 1932-1941 10 p.

Research output: Contribution to journalArticle

copper compound
Copper compounds
hierarchical system
Hierarchical systems
Delignification
3 Citations

Engineering nanoreactors using bacterial microcompartment architectures

Plegaria, J. S. & Kerfeld, C. A. Jun 1 2018 In : Current Opinion in Biotechnology. 51, p. 1-7 7 p.

Research output: Contribution to journalReview article

Nanoreactors
Enzymes
Proteins
Carbon Cycle
Bacterial Genes
Strontium titanates
Adders
Straw
Sugars
straw

Enhancing oil production and harvest by combining the marine alga Nannochloropsis oceanica and the oleaginous fungus Mortierella elongata

Du, Z. Y., Alvaro, J., Hyden, B., Zienkiewicz, K., Benning, N., Zienkiewicz, A., Bonito, G. & Benning, C. Jun 22 2018 In : Biotechnology for Biofuels. 11, 1, 174

Research output: Contribution to journalArticle

Mortierella
Algae
Fungi
flocculation
oil production
Pseudomonas chlororaphis
nitrous oxide
denitrification
isotopes
isotope
1 Citations

Expanding the Substrate Specificity of Thermoanaerobacter pseudoethanolicus Secondary Alcohol Dehydrogenase by a Dual Site Mutation

Musa, M. M., Bsharat, O., Karume, I., Vieille, C., Takahashi, M. & Hamdan, S. M. Feb 14 2018 In : European Journal of Organic Chemistry. 2018, 6, p. 798-805 8 p.

Research output: Contribution to journalArticle

dehydrogenases
mutations
alcohols
Ketones
ketones

Exposure Assessment of Acetamide in Milk, Beef, and Coffee Using Xanthydrol Derivatization and Gas Chromatography/Mass Spectrometry

Vismeh, R., Haddad, D., Moore, J., Nielson, C., Bals, B., Campbell, T., Julian, A., Teymouri, F., Jones, A. D. & Bringi, V. Jan 10 2018 In : Journal of Agricultural and Food Chemistry. 66, 1, p. 298-305 8 p.

Research output: Contribution to journalArticle

acetamides
Beef
Coffee
exposure assessment
derivatization
1 Citations

Extended Zinc AMBER Force Field (EZAFF)

Yu, Z., Li, P. & Merz, K. M. Jan 9 2018 In : Journal of Chemical Theory and Computation. 14, 1, p. 242-254 13 p.

Research output: Contribution to journalArticle

field theory (physics)
Zinc
zinc
Molecular mechanics
Organometallic Compounds

Fluorescence and Excited-State Conformational Dynamics of the Orange Carotenoid Protein

Gurchiek, J. K., Bao, H., Domínguez-Martín, M. A., McGovern, S. E., Marquardt, C. E., Roscioli, J. D., Ghosh, S., Kerfeld, C. A. & Beck, W. F. Feb 15 2018 In : Journal of Physical Chemistry B. 122, 6, p. 1792-1800 9 p.

Research output: Contribution to journalArticle

carotenoids
Carotenoids
Excited states
Fluorescence
proteins

Folding-Degradation Relationship of a Membrane Protein Mediated by the Universally Conserved ATP-Dependent Protease FtsH

Yang, Y., Guo, R., Gaffney, K., Kim, M., Muhammednazaar, S., Tian, W., Wang, B., Liang, J. & Hong, H. Apr 4 2018 In : Journal of the American Chemical Society. 140, 13, p. 4656-4665 10 p.

Research output: Contribution to journalArticle

ATP-Dependent Proteases
Adenosinetriphosphate
Membrane Proteins
Proteolysis
Proteins

Free-Energy-Based Protein Design: Re-Engineering Cellular Retinoic Acid Binding Protein II Assisted by the Moveable-Type Approach

Zhong, H. A., Santos, E. M., Vasileiou, C., Zheng, Z., Geiger, J. H., Borhan, B. & Merz, K. M. Mar 14 2018 In : Journal of the American Chemical Society. 140, 10, p. 3483-3486 4 p.

Research output: Contribution to journalArticle

Tretinoin
Free energy
Proteins
Protein Engineering
Acids

Functions of triacylglycerols during plant development and stress

Yang, Y. & Benning, C. Feb 1 2018 In : Current Opinion in Biotechnology. 49, p. 191-198 8 p.

Research output: Contribution to journalReview article

Plant Development
Triglycerides
Tissue
Pollination
Plant Oils
1 Citations

Galactoglycerolipid lipase PGD1 is involved in thylakoid membrane remodeling in response to adverse environmental conditions in chlamydomonas

Du, Z. Y., Lucker, B. F., Zienkiewicz, K., Miller, T. E., Zienkiewicz, A., Sears, B. B., Kramer, D. M. & Benning, C. Feb 1 2018 In : Plant Cell. 30, 2, p. 447-465 19 p.

Research output: Contribution to journalArticle

Chlamydomonas
Thylakoids
Plastids
Lipase
thylakoids
1 Citations

Genes affecting progression of bacteriophage P22 infection in Salmonella identified by transposon and single gene deletion screens

Bohm, K., Porwollik, S., Chu, W., Dover, J. A., Gilcrease, E. B., Casjens, S. R., Mcclelland, M. & Parent, K. N. Jan 1 2018 (Accepted/In press) In : Molecular Microbiology.

Research output: Contribution to journalArticle

Bacteriophage P22
Salmonella Infections
Gene Deletion
Genes
Bacteriophages
3 Citations

Genetic basis of photosynthetic responses to cold in two locally adapted populations of Arabidopsis thaliana

Oakley, C. G., Savage, L., Lotz, S., Larson, G. R., Thomashow, M. F., Kramer, D. M. & Schemske, D. W. Jan 23 2018 In : Journal of Experimental Botany. 69, 3, p. 699-709 11 p.

Research output: Contribution to journalArticle

photostability
Quantitative Trait Loci
Photosynthesis
Arabidopsis
quantitative trait loci
1 Citations

Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments

Scott, K. M. , Williams, J. , Porter, C. M. B. , Russel, S. , Harmer, T. L. , Paul, J. H. , Antonen, K. M. , Bridges, M. K. , Camper, G. J. , Campla, C. K. , Casella, L. G. , Chase, E. , Conrad, J. W. , Cruz, M. C. , Dunlap, D. S. , Duran, L. , Fahsbender, E. M. , Goldsmith, D. B. , Keeley, R. F. , Kondoff, M. R. & 30 others Kussy, B. I., Lane, M. K., Lawler, S., Leigh, B. A., Lewis, C., Lostal, L. M., Marking, D., Mancera, P. A., Mcclenthan, E. C., Mcintyre, E. A., Mine, J. A., Modi, S., Moore, B. D., Morgan, W. A., Nelson, K. M., Nguyen, K. N., Ogburn, N., Parrino, D. G., Pedapudi, A. D., Pelham, R. P., Preece, A. M., Rampersad, E. A., Richardson, J. C., Rodgers, C. M., Schaffer, B. L., Sheridan, N. E., Solone, M. R., Staley, Z. R., Tabuchi, M. & Kerfeld, C. A. Jan 1 2018 (Accepted/In press) In : Environmental microbiology.

Research output: Contribution to journalArticle

Hydrogenovibrio
Piscirickettsiaceae
Thiomicrospira
Chemoautotrophic Growth
ferredoxin hydrogenase

High-Performance Data Analysis on the Big Trajectory Data of Cellular Scale All-atom Molecular Dynamics Simulations

Yu, I., Feig, M. & Sugita, Y. Jun 27 2018 In : Journal of Physics: Conference Series. 1036, 1, 012009

Research output: Contribution to journalConference article

trajectories
molecular dynamics
atoms
crowding
cytoplasm

Homeostasis of second messenger cyclic-di-AMP is critical for cyanobacterial fitness and acclimation to abiotic stress

Agostoni, M., Logan-Jackson, A. R., Heinz, E. R., Severin, G. B., Bruger, E. L., Waters, C. M. & Montgomery, B. L. May 29 2018 In : Frontiers in Microbiology. 9, MAY, 1121

Research output: Contribution to journalArticle

Acclimatization
Cyanobacteria
Second Messenger Systems
Cyclic AMP
Homeostasis
2 Citations

Identification of an algal xylan synthase indicates that there is functional orthology between algal and plant cell wall biosynthesis

Jensen, J. K., Busse-Wicher, M., Poulsen, C. P., Fangel, J. U., Smith, P. J., Yang, J. Y., Peña, M. J., Dinesen, M. H., Martens, H. J., Melkonian, M., Wong, G. K. S., Moremen, K. W., Wilkerson, C. G., Scheller, H. V., Dupree, P., Ulvskov, P., Urbanowicz, B. R. & Harholt, J. Jan 1 2018 (Accepted/In press) In : New Phytologist.

Research output: Contribution to journalArticle

xylan
algae
Plant Cells
Cell Wall
cell walls

Imaging vacuolar anthocyanins with fluorescence lifetime microscopy (FLIM)

Chanoca, A., Burkel, B., Grotewold, E., Eliceiri, K. W. & Otegui, M. S. Jan 1 2018 Methods in Molecular Biology. Humana Press Inc., p. 131-141 11 p. (Methods in Molecular Biology; vol. 1789)

Research output: Chapter in Book/Report/Conference proceedingChapter

Anthocyanins
Fluorescence Microscopy
Fluorescence
Optical Imaging
Plant Cells
3 Citations

Impact of Ultrathin C60 on Perovskite Photovoltaic Devices

Liu, D., Wang, Q., Traverse, C. J., Yang, C., Young, M., Kuttipillai, P. S., Lunt, S. Y., Hamann, T. W. & Lunt, R. R. Jan 23 2018 In : ACS Nano. 12, 1, p. 876-883 8 p.

Research output: Contribution to journalArticle

Fullerenes
Perovskite
fullerenes
solar cells
Photocurrents
14 Citations

Improvements to the APBS biomolecular solvation software suite

Jurrus, E. , Engel, D. , Star, K. , Monson, K. , Brandi, J. , Felberg, L. E. , Brookes, D. H. , Wilson, L. , Chen, J. , Liles, K. , Chun, M. , Li, P. , Gohara, D. W. , Dolinsky, T. , Konecny, R. , Koes, D. R. , Nielsen, J. E. , Head-Gordon, T. , Geng, W. , Krasny, R. & 4 others Wei, G. W., Holst, M. J., McCammon, J. A. & Baker, N. A. Jan 1 2018 In : Protein science : a publication of the Protein Society. 27, 1, p. 112-128 17 p.

Research output: Contribution to journalArticle

Solvation
Static Electricity
Electrostatics
Software
Insulator Elements
1 Citations

Incorporating population-level genetic variability within laboratory models in toxicology: From the individual to the population

Dornbos, P. & LaPres, J. J. Feb 15 2018 In : Toxicology. 395, p. 1-8 8 p.

Research output: Contribution to journalReview article

Population Genetics
Toxicology
Population
Risk assessment
Decision Making
1 Citations

In silico analysis of the regulation of the photosynthetic electron transport Chain in C3 plants

Morales, A., Yin, X., Harbinson, J., Driever, S. M., Molenaar, J., Kramer, D. M. & Struik, P. C. Feb 1 2018 In : Plant Physiology. 176, 2, p. 1247-1261 15 p.

Research output: Contribution to journalArticle

C3 plants
electron transport chain
Electron Transport
Computer Simulation
electron transfer

Integrated experimental and technoeconomic evaluation of two-stage Cu-catalyzed alkaline-oxidative pretreatment of hybrid poplar

Bhalla, A., Fasahati, P., Particka, C. A., Assad, A. E., Stoklosa, R. J., Bansal, N., Semaan, R., Saffron, C. M., Hodge, D. B. & Hegg, E. L. May 17 2018 In : Biotechnology for Biofuels. 11, 1, 143

Research output: Contribution to journalArticle

Hydrolysis
Temperature
Ethanol
Costs and Cost Analysis
Water
6 Citations
Protein Binding
Affine transformation
Learning systems
Homology
Machine Learning
3 Citations

In the grass species Brachypodium distachyon, the production of mixed-linkage (1,3;1,4)-β-glucan (MLG) occurs in the Golgi apparatus

Kim, S. J., Zemelis-Durfee, S., Jensen, J. K., Wilkerson, C. G., Keegstra, K. & Brandizzi, F. Mar 1 2018 In : Plant Journal. 93, 6, p. 1062-1075 14 p.

Research output: Contribution to journalArticle

Brachypodium
Plant cell culture
Brachypodium distachyon
brefeldin A
Brefeldin A