Biochemistry &amp; Molecular Biology &ndash; Research Output

2019

Bimolecular Fluorescence Complementation (BiFC) in Tissue Culture and in Developing Tissues of Drosophila to Study Protein-Protein Interactions

Matsui, Y. & Lai, Z., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 75-85 11 p. (Methods in Molecular Biology; vol. 1893).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Drosophila

Fluorescence

Proteins

Artifacts

1 Citation (Scopus)

Biosynthesis of chlorophylls and bacteriochlorophylls in green bacteria

Thweatt, J. L., Canniffe, D. P. & Bryant, D. A., Jan 1 2019, Advances in Botanical Research. Grimm, B. (ed.). Academic Press Inc., p. 35-89 55 p. (Advances in Botanical Research; vol. 90).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

biosynthesis

chlorophyll

bacteria

Acidobacteria

chlorins

CryoEM reconstruction approaches to resolve asymmetric features

Goetschius, D. J., Lee, H. & Hafenstein, S., Jan 1 2019, Advances in Virus Research. Rey, F. A. (ed.). Academic Press Inc., p. 73-91 19 p. (Advances in Virus Research; vol. 105).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Viruses

Capsid

Life Cycle Stages

Genome

Proteins

Information-Theoretic Inference of an Optimal Dictionary of Protein Supersecondary Structures

Konagurthu, A. S., Subramanian, R., Allison, L., Abramson, D., de la Banda, M. G., Stuckey, P. J. & Lesk, A., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 123-131 9 p. (Methods in Molecular Biology; vol. 1958).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Amino Acid Motifs

Data Compression

Protein Folding

Patient Selection

In Vivo Genome-Wide RNA Structure Probing with Structure-seq

Ritchey, L. E., Su, Z., Assmann, S. M. & Bevilacqua, P. C., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 305-341 37 p. (Methods in Molecular Biology; vol. 1933).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Genome

RNA

Glyoxal

Transcriptome

Bacteria

2018

8 Citations (Scopus)

Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a “Plug and Play” Domain

Holliday, G. L., Akiva, E., Meng, E. C., Brown, S. D., Calhoun, S., Pieper, U., Sali, A., Booker, S. J. & Babbitt, P. C., Jan 1 2018, Methods in Enzymology. Bandarian, V. (ed.). Academic Press Inc., p. 1-71 71 p. (Methods in Enzymology; vol. 606).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Atlases

Nucleic Acids

Databases

Enzymes

Metabolism

1 Citation (Scopus)

Biochemical Approaches for Understanding Iron–Sulfur Cluster Regeneration in Escherichia coli Lipoyl Synthase During Catalysis

McCarthy, E. L. & Booker, S. J., Jan 1 2018, Methods in Enzymology. Bandarian, V. (ed.). Academic Press Inc., p. 217-239 23 p. (Methods in Enzymology; vol. 606).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Catalysis

Escherichia coli

Regeneration

S-Adenosylmethionine

Sulfur

Chemical Tools for Studying the Impact of cis/trans Prolyl Isomerization on Signaling: A Case Study on RNA Polymerase II Phosphatase Activity and Specificity

Burkholder, N. T., Medellin, B., Irani, S., Matthews, W., Showalter, S. A. & Zhang, Y. J., Jan 1 2018, Methods in Enzymology. Allen, K. N. (ed.). Academic Press Inc., p. 269-297 29 p. (Methods in Enzymology; vol. 607).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

RNA Polymerase II

Isomerization

Phosphoric Monoester Hydrolases

Proline

Conformations

Predicting Off-Target Effects of Therapeutic Antiviral Ribonucleosides: Inhibition of Mitochondrial RNA Transcription

Arnold, J. J. & Cameron, C. E., Feb 21 2018, Mitochondrial Dysfunction Caused by Drugs and Environmental Toxicants. wiley, Vol. 1-2. p. 407-417 11 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Ribonucleosides

Therapeutic Uses

Transcription

Antiviral Agents

Viruses

2 Citations (Scopus)

The biochemistry and physiology of respiratory-driven reversed methanogenesis

Nazem-Bokaee, H., Yan, Z., Maranas, C. D. & Ferry, J. G., Jun 20 2018, Methane Biocatalysis: Paving the Way to Sustainability. Springer International Publishing, p. 183-197 15 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Respiratory Physiological Phenomena

Biochemistry

Physiology

The Use of ¹³C Direct-Detect NMR to Characterize Flexible and Disordered Proteins

Cook, E. C., Usher, G. A. & Showalter, S. A., Jan 1 2018, Methods in Enzymology. Rhoades, E. (ed.). Academic Press Inc., p. 81-100 20 p. (Methods in Enzymology; vol. 611).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Intrinsically Disordered Proteins

Nuclear magnetic resonance

Nuclear magnetic resonance spectroscopy

Magnetic Resonance Spectroscopy

Proteins

2 Citations (Scopus)

Using Peptide Mimics to Study the Biosynthesis of the Side-Ring System of Nosiheptide

Wang, B., LaMattina, J. W., Badding, E. D., Gadsby, L. K., Grove, T. L. & Booker, S. J., Jan 1 2018, Methods in Enzymology. Bandarian, V. (ed.). Academic Press Inc., p. 241-268 28 p. (Methods in Enzymology; vol. 606).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Biosynthesis

S-Adenosylmethionine

Peptides

Pharmacokinetics

Antimalarials

2017

Anaerobic metabolism of aromatic compounds

Haddock, J. D. & Ferry, J. G., Jan 1 2017, Bioprocessing and Biotreatment of Coal. CRC Press, p. 393-416 24 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

metabolism

degradation

carbon

amino acid

microorganism

18 Citations (Scopus)

A panoply of phototrophs: An Overview of the thermophilic chlorophototrophs of the microbial mats of Alkaline siliceous hot springs in Yellowstone National Park, WY, USA

Tank, M., Thiel, V., Ward, D. M. & Bryant, D. A., Apr 18 2017, Modern Topics in the Phototrophic Prokaryotes: Environmental and Applied Aspects. Springer International Publishing, p. 87-137 51 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Hot Springs

hot springs

microbial mat

autotrophs

Chlorophyll

Biopiracy

Satheeshkumar, P. K. & Narayanan, A., May 10 2017, Status and Strategies for Exploration. Springer Singapore, Vol. 1. p. 185-204 20 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Intellectual Property

Internationality

Intellectual property

Inventors

Nimodipine

DNA analysis

Weedn, V. W., Lee, D. A., Roby, R. K. & Holland, M. M., Jan 1 2017, Handbook of Analytical Therapeutic Drug Monitoring and Toxicology. CRC Press, p. 35-49 15 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

DNA

Textbooks

1 Citation (Scopus)

Mechanism-Based Strategies for Structural Characterization of Radical SAM Reaction Intermediates

Davis, K. M. & Boal, A. K., Jan 1 2017, Methods in Enzymology. Academic Press Inc., p. 331-359 29 p. (Methods in Enzymology; vol. 595).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

S-Adenosylmethionine

Reaction intermediates

Enzymes

Substrate Specificity

Crystal structure

6 Citations (Scopus)

Molecular biology of lignin peroxidases from Phanerochaete chrysosporium

Holzbaur, E. L. F., Andrawis, A. & Tien, M., Jan 1 2017, Molecular Industrial Mycology: Systems and Applications for Filamentous Fungi. CRC Press, p. 197-223 27 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

lignin peroxidase

Phanerochaete

Phanerochaete chrysosporium

Lignin

biodegradation

The role of iron-sulfur clusters in the biosynthesis of the lipoyl cofactor

Lanz, N. D. & Booker, S. J., Aug 21 2017, Characterization, Properties and Applications. Walter de Gruyter GmbH, Vol. 1. p. 327-358 32 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Biosynthesis

Sulfur

Iron

7 Citations (Scopus)

TsrM as a Model for Purifying and Characterizing Cobalamin-Dependent Radical S-Adenosylmethionine Methylases

Blaszczyk, A. J., Wang, R. X. & Booker, S. J., Jan 1 2017, Methods in Enzymology. Academic Press Inc., p. 303-329 27 p. (Methods in Enzymology; vol. 595).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

S-Adenosylmethionine

Vitamin B 12

Enzymes

Proteins

Biosynthesis

2016

2 Citations (Scopus)

A High-Throughput Biological Calorimetry Core: Steps to Startup, Run, and Maintain a Multiuser Facility

Yennawar, N., Fecko, J. A., Showalter, S. A. & Bevilacqua, P. C., Jan 1 2016, Methods in Enzymology. Academic Press Inc., p. 435-460 26 p. (Methods in Enzymology; vol. 567).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Calorimetry

Throughput

Chemical Engineering

Ligands

Bioengineering

3 Citations (Scopus)

Assessing Coupled Protein Folding and Binding Through Temperature-Dependent Isothermal Titration Calorimetry

Sahu, D., Bastidas, M., Lawrence, C. W., Noid, W. G. & Showalter, S. A., Jan 1 2016, Methods in Enzymology. Academic Press Inc., p. 23-45 23 p. (Methods in Enzymology; vol. 567).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Protein folding

Calorimetry

Protein Folding

Titration

Protein Binding

Expression and purification of mitochondrial RNA polymerase and transcription factor a from drosophila melanogaster

Gajewski, J. P., Arnold, J. J., Salminen, T. S., Kaguni, L. S. & Cameron, C. E., Jan 1 2016, Methods in Molecular Biology. Humana Press Inc., p. 199-210 12 p. (Methods in Molecular Biology; vol. 1351).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

DNA-Directed RNA Polymerases

Drosophila melanogaster

Transcription Factors

Mitochondrial Genes

Small Ubiquitin-Related Modifier Proteins

1 Citation (Scopus)

Induction and purification of c. Difficile phage tail-like particles

Hegarty, J. P., Sangster, W., Ashley, R. E., Myers, R., Hafenstein, S. & Stewart, D. B., Jan 1 2016, Methods in Molecular Biology. Humana Press Inc., p. 167-175 9 p. (Methods in Molecular Biology; vol. 1476).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Bacteriophages

Bacteriocins

Viral Genome

Capsid

Infection

Microbial cellulose synthesis

Nagachar, N. & McManus, J., Jan 1 2016, Microbial Factories: Biofuels, Waste treatment: Volume 1. Springer India, p. 203-216 14 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Cellulose

cellulose

synthesis

feedstocks

Carbon

1 Citation (Scopus)

Polymerase mechanism-based method of viral attenuation

Lee, C. A., August, A., Arnold, J. J. & Cameron, C. E., Jan 1 2016, Methods in Molecular Biology. Humana Press Inc., p. 83-104 22 p. (Methods in Molecular Biology; vol. 1349).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Vaccines

Viruses

Lysine

RNA Viruses

Mutation

3 Citations (Scopus)

Preparation, Crystallization, and Structure Determination of Chromatin Enzyme/Nucleosome Complexes

McGinty, R. K., Makde, R. D. & Tan, S., Jan 1 2016, Methods in Enzymology. Academic Press Inc., p. 43-65 23 p. (Methods in Enzymology; vol. 573).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Nucleosomes

Crystallization

Chromatin

Enzymes

Cryoelectron Microscopy

2015

1 Citation (Scopus)

Carbonic Anhydrases of Environmentally and Medically Relevant Anaerobic Prokaryotes

Ferry, J. G., Jan 8 2015, Carbonic Anhydrases as Biocatalysts: From Theory to Medical and Industrial Applications. Elsevier Inc., p. 325-336 12 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Carbonic anhydrase

Carbonic Anhydrases

Carbon Dioxide

Carbon dioxide

Mammals

29 Citations (Scopus)

Mechanisms of 2-oxoglutarate-dependent oxygenases: The hydroxylation paradigm and beyond

Bollinger, Jr., J. M., Chang, W. C., Matthews, M. L., Martinie, R. J., Boal, A. K. & Krebs, C., Jan 1 2015, 2-Oxoglutarate-Dependent Oxygenases. Hausinger, R. P. & Schofield, C. J. (eds.). 3 ed. Royal Society of Chemistry, p. 95-122 28 p. (RSC Metallobiology; vol. 2015-January, no. 3).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Oxygenases

Hydroxylation

Dehydrogenation

Halogenation

Alkenes

Reconstitution of factor-dependent, promoter proximal pausing in Drosophila nuclear extracts

Li, J. & Gilmour, D. S., Feb 9 2015, Bacterial Transcriptional Control: Methods and Protocols. Springer New York, p. 133-152 20 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Drosophila

RNA

RNA Polymerase II

Transcription

Oligonucleotides

1 Citation (Scopus)

Re-routing redox chains for directed photocatalysis

Lubner, C. E., Applegate, A. M. & Golbeck, J. H., Jan 1 2015, Biohydrogen. Walter de Gruyter GmbH, p. 239-264 26 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Photocatalysis

Oxidation-Reduction

Selenium and Cancer Metastasis

Chen, Y. C. & Mastro, A. M., 2015, Betaine: Chemistry, Analysis, Function and Effects. 9 ed. Royal Society of Chemistry, Vol. 2015-January. p. 408-427 20 p. (Food and Nutritional Components in Focus; vol. 2015-January, no. 9).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Selenium

metastasis

selenium

Neoplasm Metastasis

neoplasms

Techniques Analyzing Chromatin Modifications at Specific Single Loci

Chen, X. A., Sun, J. & Wang, Y., Jun 17 2015, Epigenetic Technological Applications. Elsevier Inc., p. 79-100 22 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Histone Code

Chromatin

Histones

DNA

Lysine

2014

1 Citation (Scopus)

Applying UV crosslinking to study RNA-protein interactions in multicomponent ribonucleoprotein complexes

Krasilnikov, A. S., Jan 1 2014, RNA Folding: Methods and Protocols. Humana Press Inc., p. 193-207 15 p. (Methods in Molecular Biology; vol. 1086).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Ribonucleoproteins

RNA

His-His-His-His-His-His

Ribonuclease P

Proteins

2 Citations (Scopus)

Bosnia and Herzegovina: Forensic Archaeology in Support of National and International Organisations Undertaking Criminal Investigations and Identifying the Missing from 1996 to 2013

Hanson, I., Rizviç, A. & Parsons, T. J., Jan 1 2014, Forensic Archaeology: A Global Perspective. Wiley-Blackwell, p. 19-31 13 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Bosnia and Herzegovina

archaeology

war crime

Yugoslavia

prosecution

21 Citations (Scopus)

Experimental approaches for measuring pK_a's in RNA and DNA

Thaplyal, P. & Bevilacqua, P. C., Jan 1 2014, Methods in Enzymology. C ed. Academic Press Inc., p. 189-219 31 p. (Methods in Enzymology; vol. 549, no. C).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

RNA

DNA

Nucleic Acids

Hydroxides

RNA Folding

3 Citations (Scopus)

Finding the epistasis needles in the genome-wide haystack

Ritchie, M. D., Nov 17 2014, Epistasis: Methods and Protocols. Springer New York, p. 19-33 15 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Genome-Wide Association Study

Needles

Genes

Genome

Single Nucleotide Polymorphism

3 Citations (Scopus)

Histone, nucleosome, and chromatin structure

McGinty, R. K. & Tan, S., May 1 2014, Fundamentals of Chromatin. Springer New York, p. 1-28 28 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Nucleosomes

Histones

Chromatin

DNA

Cell Nucleus

Metabolomics

Belton, B. R., Correll, J. B. & Patterson, A. D., Jan 1 2014, Applications of High-Resolution Mass Spectrometry in Drug Discovery and Development. Future Medicine Ltd., p. 106-118 13 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Tissue Extracts

Plasmas

Molecules

Metabolomics

6 Citations (Scopus)

Prioritized Sampling of Bone and Teeth for DNA Analysis in Commingled Cases

Hines, D. Z. C., Vennemeyer, M., Amory, S., Huel, R. L. M., Hanson, I., Katzmarzyk, C. & Parsons, T. J., Jun 17 2014, Commingled Human Remains: Methods in Recovery, Analysis, and Identification. Elsevier Inc., p. 275-305 31 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

genetic test

human being

Yugoslavia

experience

costs

Reducing Dimensionality in the Search for Gene-Gene Interactions

Ritchie, M. D., Jan 1 2014, Between the Lines of Genetic Code: Genetic Interactions in Understanding Disease and Complex Phenotypes. Elsevier Inc., p. 25-37 13 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Genes

Data Mining

Explosions

Sample Size

Data mining

5 Citations (Scopus)

The role of iron-sulfur clusters in the biosynthesis of the lipoyl cofactor

Lanz, N. D. & Booker, S. J., Jan 1 2014, Iron-Sulfur Clusters in Chemistry and Biology. Walter de Gruyter GmbH, p. 211-238 28 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Sulfur

Iron

1 Citation (Scopus)

Using the split-ubiquitin yeast two-hybrid system to test protein-protein interactions of transmembrane proteins

Bashline, L. & Gu, Y., Nov 18 2014, Plant Cell Expansion: Methods and Protocols. Springer New York, p. 143-158 16 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

two hybrid system techniques

Two-Hybrid System Techniques

transmembrane proteins

protein-protein interactions

ubiquitin

2013

5 Citations (Scopus)

Analytical Methodology of POPs

Reiner, E. J., Jobst, K. J., Megson, D., Dorman, Jr., F. L. & Focant, J. F., Dec 1 2013, Environmental Forensics for Persistent Organic Pollutants. Elsevier B.V., p. 59-139 81 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Organic pollutants

Flame Retardants

Environmental Pollutants

Poisons

Flame retardants

12 Citations (Scopus)

An integrated picture of HDV ribozyme catalysis

Golden, B. L., Hammes-Schiffer, S., Carey, P. R. & Bevilacqua, P. C., Jan 1 2013, Biophysics of RNA Folding. Springer New York, p. 135-167 33 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Hepatitis Delta Virus

Catalytic RNA

Catalysis

Viruses

Crystallography

Biomonitoring for POPs

Patterson, D. G. J., Aylward, L. L., Covaci, A. & Franzblau, A., Dec 1 2013, Environmental Forensics for Persistent Organic Pollutants. Elsevier B.V., p. 163-197 35 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Beef

Metabolism

Dust

Clay

Contamination

1 Citation (Scopus)

Electron paramagnetic resonance spectroscopy

Golbeck, J. H. & van der Est, A., Jan 1 2013, Molecular Biophysics for the Life Sciences. Springer New York, p. 175-213 39 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

electron paramagnetic resonance spectroscopy

Electron Spin Resonance Spectroscopy

Paramagnetic resonance

Spectrum Analysis

Spectroscopy

6 Citations (Scopus)

Extraction of hydrophilic metabolites from plasmodium falciparum -infected erythrocytes for metabolomic analysis

Olszewski, K. L. & Llinas, M., Jan 1 2013, Malaria: Methods and Protocols. Humana Press Inc., p. 259-266 8 p. (Methods in Molecular Biology; vol. 923).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Metabolomics

Plasmodium falciparum

Parasites

Erythrocytes

Metabolic Networks and Pathways

1 Citation (Scopus)

Forensic mitochondrial DNA analysis: Current practice and future potential

Holland, M. M., Melton, T. & Holland, C. A., Aug 19 2013, Forensic DNA Analysis: Current Practices and Emerging Technologies. Taylor and Francis, p. 249-278 30 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

genetic test

Mitochondrial DNA

new technology

scientific community

Technology

F_X, F_A, and F_B Iron-Sulfur Clusters in Type I Photosynthetic Reaction Centers

Jagannathan, B. & Golbeck, J. H., Feb 15 2013, Encyclopedia of Biological Chemistry: Second Edition. Elsevier Inc., p. 335-342 8 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Photosynthetic Reaction Center Complex Proteins

Sulfur

Iron

Electrons

Thermodynamics