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Ricardo Marti-Arbona
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

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Technical report
Published: 28 May 2020 in Biogenic uranium isotope fractionation
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The U.S. Department of Energy's Office of Scientific and Technical Information

ACS Style

Ricardo Marti-Arbona; Noah Jemison; Robert F. Williams; Hakim Boukhalfa; Chris Michael Yeager; Ning Xu; Velimir Valentinov Vesselinov. Biogenic uranium isotope fractionation. Biogenic uranium isotope fractionation 2020, 1 .

AMA Style

Ricardo Marti-Arbona, Noah Jemison, Robert F. Williams, Hakim Boukhalfa, Chris Michael Yeager, Ning Xu, Velimir Valentinov Vesselinov. Biogenic uranium isotope fractionation. Biogenic uranium isotope fractionation. 2020; ():1.

Chicago/Turabian Style

Ricardo Marti-Arbona; Noah Jemison; Robert F. Williams; Hakim Boukhalfa; Chris Michael Yeager; Ning Xu; Velimir Valentinov Vesselinov. 2020. "Biogenic uranium isotope fractionation." Biogenic uranium isotope fractionation , no. : 1.

Journal article
Published: 04 April 2019 in Toxins
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Mycolactone, the amphiphilic macrolide toxin secreted by Mycobacterium ulcerans, plays a significant role in the pathology and manifestations of Buruli ulcer (BU). Consequently, it follows that the toxin is a suitable target for the development of diagnostics and therapeutics for this disease. Yet, several challenges have deterred such development. For one, the lipophilic nature of the toxin makes it difficult to handle and store and contributes to variability associated with laboratory experimentation and purification yields. In this manuscript, we have attempted to incorporate our understanding of the lipophilicity of mycolactone in order to define the optimal methods for the storage, handling, and purification of this toxin. We present a systematic correlation of variability associated with measurement techniques (thin-layer chromatography (TLC), mass spectrometry (MS), and UV-Vis spectrometry), storage conditions, choice of solvents, as well as the impact of each of these on toxin function as assessed by cellular cytotoxicity. We also compared natural mycolactone extracted from bacterial culture with synthesized toxins in laboratory (solvents, buffers) and physiologically relevant (serum) matrices. Our results point to the greater stability of mycolactone in organic, as well as detergent-containing, solvents, regardless of the container material (plastic, glass, or silanized tubes). They also highlight the presence of toxin in samples that may be undetectable by any one technique, suggesting that each detection approach captures different configurations of the molecule with varying specificity and sensitivity. Most importantly, our results demonstrate for the very first time that amphiphilic mycolactone associates with host lipoproteins in serum, and that this association will likely impact our ability to study, diagnose, and treat Buruli ulcers in patients.

ACS Style

Jessica Z. Kubicek-Sutherland; Dung M. Vu; Aaron S. Anderson; Timothy C. Sanchez; Paul J. Converse; Ricardo Martí-Arbona; Eric L. Nuermberger; Basil I. Swanson; Harshini Mukundan. Understanding the Significance of Biochemistry in the Storage, Handling, Purification, and Sampling of Amphiphilic Mycolactone. Toxins 2019, 11, 202 .

AMA Style

Jessica Z. Kubicek-Sutherland, Dung M. Vu, Aaron S. Anderson, Timothy C. Sanchez, Paul J. Converse, Ricardo Martí-Arbona, Eric L. Nuermberger, Basil I. Swanson, Harshini Mukundan. Understanding the Significance of Biochemistry in the Storage, Handling, Purification, and Sampling of Amphiphilic Mycolactone. Toxins. 2019; 11 (4):202.

Chicago/Turabian Style

Jessica Z. Kubicek-Sutherland; Dung M. Vu; Aaron S. Anderson; Timothy C. Sanchez; Paul J. Converse; Ricardo Martí-Arbona; Eric L. Nuermberger; Basil I. Swanson; Harshini Mukundan. 2019. "Understanding the Significance of Biochemistry in the Storage, Handling, Purification, and Sampling of Amphiphilic Mycolactone." Toxins 11, no. 4: 202.

Journal article
Published: 19 September 2018 in Acta Crystallographica Section F Structural Biology Communications
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Three high-resolution X-ray crystal structures of malate dehydrogenase (MDH; EC 1.1.1.37) from the methylotroph Methylobacterium extorquens AM1 are presented. By comparing the structures of apo MDH, a binary complex of MDH and NAD+, and a ternary complex of MDH and oxaloacetate with ADP-ribose occupying the pyridine nucleotide-binding site, conformational changes associated with the formation of the catalytic complex were characterized. While the substrate-binding site is accessible in the enzyme resting state or NAD+-bound forms, the substrate-bound form exhibits a closed conformation. This conformational change involves the transition of an α-helix to a 310-helix, which causes the adjacent loop to close the active site following coenzyme and substrate binding. In the ternary complex, His284 forms a hydrogen bond to the C2 carbonyl of oxaloacetate, placing it in a position to donate a proton in the formation of (2S)-malate.

ACS Style

Javier M. González; Ricardo Marti-Arbona; Julian C.-H. Chen; Brian Broom-Peltz; Clifford J. Unkefer. Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase. Acta Crystallographica Section F Structural Biology Communications 2018, 74, 610 -616.

AMA Style

Javier M. González, Ricardo Marti-Arbona, Julian C.-H. Chen, Brian Broom-Peltz, Clifford J. Unkefer. Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase. Acta Crystallographica Section F Structural Biology Communications. 2018; 74 (10):610-616.

Chicago/Turabian Style

Javier M. González; Ricardo Marti-Arbona; Julian C.-H. Chen; Brian Broom-Peltz; Clifford J. Unkefer. 2018. "Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase." Acta Crystallographica Section F Structural Biology Communications 74, no. 10: 610-616.

Research communications
Published: 27 January 2017 in Acta Crystallographica Section F Structural Biology Communications
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Malyl-CoA lyase (MCL) is an Mg2+-dependent enzyme that catalyzes the reversible cleavage of (2S)-4-malyl-CoA to yield acetyl-CoA and glyoxylate. MCL enzymes, which are found in a variety of bacteria, are members of the citrate lyase-like family and are involved in the assimilation of one- and two-carbon compounds. Here, the 1.56 Å resolution X-ray crystal structure of MCL fromMethylobacterium extorquensAM1 with bound Mg2+is presented. Structural alignment with the closely relatedRhodobacter sphaeroidesmalyl-CoA lyase complexed with Mg2+, oxalate and CoA allows a detailed analysis of the domain motion of the enzyme caused by substrate binding. Alignment of the structures shows that a simple hinge motion centered on the conserved residues Phe268 and Thr269 moves the C-terminal domain by about 30° relative to the rest of the molecule. This domain motion positions a conserved aspartate residue located in the C-terminal domain in the active site of the adjacent monomer, which may serve as a general acid/base in the catalytic mechanism.

ACS Style

Javier M. González; Ricardo Marti-Arbona; Julian C.-H. Chen; Clifford J. Unkefer. Structure ofMethylobacterium extorquensmalyl-CoA lyase: CoA-substrate binding correlates with domain shift. Acta Crystallographica Section F Structural Biology Communications 2017, 73, 79 -85.

AMA Style

Javier M. González, Ricardo Marti-Arbona, Julian C.-H. Chen, Clifford J. Unkefer. Structure ofMethylobacterium extorquensmalyl-CoA lyase: CoA-substrate binding correlates with domain shift. Acta Crystallographica Section F Structural Biology Communications. 2017; 73 (2):79-85.

Chicago/Turabian Style

Javier M. González; Ricardo Marti-Arbona; Julian C.-H. Chen; Clifford J. Unkefer. 2017. "Structure ofMethylobacterium extorquensmalyl-CoA lyase: CoA-substrate binding correlates with domain shift." Acta Crystallographica Section F Structural Biology Communications 73, no. 2: 79-85.

Journal article
Published: 18 September 2015 in The Protein Journal
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FadR is a versatile global regulator in Escherichia coli that controls fatty acid metabolism and thereby modulates the ability of this bacterium to grow using fatty acids or acetate as the sole carbon source. FadR regulates fatty acid metabolism in response to intra-cellular concentrations of acyl-CoA lipids. The ability of FadR to bind acyl-CoA fatty acids is thus of significant interest for the engineering of biosynthetic pathways for the production of lipid-based biofuels and commodity chemicals. Based on the available crystal structure of E. coli bound to myristoyl-CoA, we predicted amino acid positions within the effector binding pocket that would alter the ability of FadR to bind acyl-CoA fatty acids without affecting DNA binding. We utilized fluorescence polarization to characterize the in vitro binding properties of wild type and mutant FadR. We found that a Leu102Ala mutant enhanced binding of the effector, likely by increasing the size of the binding pocket for the acyl moiety of the molecule. Conversely, the elimination of the guanidine side chain (Arg213Ala and Arg213Met mutants) of the CoA moiety binding site severely diminished the ability of FadR to bind the acyl-CoA effector. These results demonstrate the ability to fine tune FadR binding capacity. The validation of an efficient method to fully characterize all the binding events involved in the specific activity (effector and DNA operator binding) of FadR has allowed us to increase our understanding of the role of specific amino acids in the binding and recognition of acyl-CoA fatty acids and will greatly facilitate efforts aimed at engineering tunable FadR regulators for synthetic biology.

ACS Style

John-Paul Bacik; Chris M. Yeager; Scott N. Twary; Ricardo Marti-Arbona. Modulation of FadR Binding Capacity for Acyl-CoA Fatty Acids Through Structure-Guided Mutagenesis. The Protein Journal 2015, 34, 359 -366.

AMA Style

John-Paul Bacik, Chris M. Yeager, Scott N. Twary, Ricardo Marti-Arbona. Modulation of FadR Binding Capacity for Acyl-CoA Fatty Acids Through Structure-Guided Mutagenesis. The Protein Journal. 2015; 34 (5):359-366.

Chicago/Turabian Style

John-Paul Bacik; Chris M. Yeager; Scott N. Twary; Ricardo Marti-Arbona. 2015. "Modulation of FadR Binding Capacity for Acyl-CoA Fatty Acids Through Structure-Guided Mutagenesis." The Protein Journal 34, no. 5: 359-366.

Research article
Published: 27 July 2015 in ACS Synthetic Biology
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Until recently, engineering strategies for altering gene expression have focused on transcription control using strong inducible promoters or one of several methods to knock down wasteful genes. Recently, synthetic riboregulators have been developed for translational regulation of gene expression. Here, we report a new modular synthetic riboregulator class that has the potential to finely tune protein expression and independently control the concentration of each enzyme in an engineered metabolic pathway. This development is important because the most straightforward approach to altering the flux through a particular metabolic step is to increase or decrease the concentration of the enzyme. Our design includes a cis-repressor at the 5′ end of the mRNA that forms a stem-loop helix, occluding the ribosomal binding sequence and blocking translation. A trans-expressed activating-RNA frees the ribosomal-binding sequence, which turns on translation. The overall architecture of the riboregulators is designed using Watson–Crick base-pairing stability. We describe here a cis-repressor that can completely shut off translation of antibiotic-resistance reporters and a trans-activator that restores translation. We have established that it is possible to use these riboregulators to achieve translational control of gene expression over a wide dynamic range. We have also found that a targeting sequence can be modified to develop riboregulators that can, in principle, independently regulate translation of many genes. In a selection experiment, we demonstrated that by subtly altering the sequence of the trans-activator it is possible to alter the ratio of the repressed and activated states and to achieve intermediate translational control.

ACS Style

Malathy Krishnamurthy; Scott P. Hennelly; Taraka Dale; Shawn R. Starkenburg; Ricardo Martí-Arbona; David T. Fox; Scott N. Twary; Karissa Y. Sanbonmatsu; Clifford J. Unkefer. Tunable Riboregulator Switches for Post-transcriptional Control of Gene Expression. ACS Synthetic Biology 2015, 4, 1326 -1334.

AMA Style

Malathy Krishnamurthy, Scott P. Hennelly, Taraka Dale, Shawn R. Starkenburg, Ricardo Martí-Arbona, David T. Fox, Scott N. Twary, Karissa Y. Sanbonmatsu, Clifford J. Unkefer. Tunable Riboregulator Switches for Post-transcriptional Control of Gene Expression. ACS Synthetic Biology. 2015; 4 (12):1326-1334.

Chicago/Turabian Style

Malathy Krishnamurthy; Scott P. Hennelly; Taraka Dale; Shawn R. Starkenburg; Ricardo Martí-Arbona; David T. Fox; Scott N. Twary; Karissa Y. Sanbonmatsu; Clifford J. Unkefer. 2015. "Tunable Riboregulator Switches for Post-transcriptional Control of Gene Expression." ACS Synthetic Biology 4, no. 12: 1326-1334.

Journal article
Published: 01 January 2014 in BMC Genomics
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The clustering of genes in a pathway and the co-location of functionally related genes is widely recognized in prokaryotes. We used these characteristics to predict the metabolic involvement for a Transcriptional Regulator (TR) of unknown function, identified and confirmed its biological activity.

ACS Style

Ricardo Martí-Arbona; Fangping Mu; Kristy L Nowak-Lovato; Melinda S Wren; Clifford J Unkefer; Pat J Unkefer. Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions. BMC Genomics 2014, 15, 1142 .

AMA Style

Ricardo Martí-Arbona, Fangping Mu, Kristy L Nowak-Lovato, Melinda S Wren, Clifford J Unkefer, Pat J Unkefer. Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions. BMC Genomics. 2014; 15 (1):1142.

Chicago/Turabian Style

Ricardo Martí-Arbona; Fangping Mu; Kristy L Nowak-Lovato; Melinda S Wren; Clifford J Unkefer; Pat J Unkefer. 2014. "Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions." BMC Genomics 15, no. 1: 1142.

Journal article
Published: 28 January 2013 in Journal of Molecular Biology Research
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To study the transcriptional regulation of oxidative tryptophan degradation in Burkholderia , we used comparative genomics that focused on the operon containing the genes annotated as kynA , kynU and kynB . In all sequenced Beta-proteobacteria to-date, including Burkholderia , Ralstonia , Collimonas , and Cupriavidus species, there is a conserved AsnC/Lrp family transcriptional regulator (TR) gene located upstream and in the opposite strand of the operon encoding for the oxidative tryptophan degradation genes. In Burkholderia xenovorans the TR is Bxe_A0736. GST-Bxe_A0736 binds L-kynurenine with greater affinity and specificity than any other amino acid or tryptophan degradation product with a dissociation constant of ~82 ± 11 ?M. DNase I footprinting suggested that Bxe_A0736 protects a set of four degenerate, palindromic sequences within the intergenic region between Bxe_A0735 ( kynB ) and Bxe_A0736. The optimal consensus sequence obtained by analysis for these sites, ATATTCCGAATAT, closely resembles the sequence obtained with a protein binding microarray. Under our fluorescence anisotropy experimental conditions, 1 mM L-kynurenine increased the affinity of Bxe_A0736 for a portion of its promoter region. Our results are consistent with Bxe_A0736 acting as the TR that promotes the transcription of the oxidative tryptophan degradation genes in the presence of L-kynurenine while inhibiting the transcription of its own gene.

ACS Style

Richard S Hall; Scott P Hennelly; Tuhin S Maity; Fangping Mu; John M Dunbar; Clifford J Unkefer; Pat J Unkefer; Ricardo Marti-Arbona. In-vitro Characterization of an L-Kynurenine-Responsive Transcription Regulator of the Oxidative Tryptophan Degradation Pathway in Burkholderia xenovorans. Journal of Molecular Biology Research 2013, 3, p55 .

AMA Style

Richard S Hall, Scott P Hennelly, Tuhin S Maity, Fangping Mu, John M Dunbar, Clifford J Unkefer, Pat J Unkefer, Ricardo Marti-Arbona. In-vitro Characterization of an L-Kynurenine-Responsive Transcription Regulator of the Oxidative Tryptophan Degradation Pathway in Burkholderia xenovorans. Journal of Molecular Biology Research. 2013; 3 (1):p55.

Chicago/Turabian Style

Richard S Hall; Scott P Hennelly; Tuhin S Maity; Fangping Mu; John M Dunbar; Clifford J Unkefer; Pat J Unkefer; Ricardo Marti-Arbona. 2013. "In-vitro Characterization of an L-Kynurenine-Responsive Transcription Regulator of the Oxidative Tryptophan Degradation Pathway in Burkholderia xenovorans." Journal of Molecular Biology Research 3, no. 1: p55.

Journal article
Published: 28 January 2013 in Journal of Molecular Biology Research
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Transcriptional regulators (TRs) are an important and versatile group of proteins, yet very little progress has been achieved towards the discovery and annotation of their biological functions. We have characterized a previously unknown organic hydroperoxide resistance regulator from Burkholderia xenovorans LB400, Bxe_B2842, which is homologous to E. coli’s OhrR. Bxe_B2842 regulates the expression of an organic hydroperoxide resistance protein (OsmC). We utilized frontal affinity chromatography coupled with mass spectrometry (FAC-MS) and electrophoretic mobility gel shift assays (EMSA) to identify and characterize the possible effectors of the regulation by Bxe_B2842. Without an effector, Bxe_B2842 binds a DNA operator sequence (DOS) upstream of osmC . FAC-MS results suggest that 2-aminophenol binds to the protein and is potentially an effector molecule. EMSA analysis shows that 2-aminophenol attenuates the Bxe_B2842’s affinity for its DOS. EMSA analysis also shows that organic peroxides attenuate Bxe_B2842/DOS affinity, suggesting that binding of the TR to its DOS is regulated by the two-cysteine mechanism, common to TRs in this family. Bxe_B2842 is the first OhrR TR to have both oxidative and effector-binding mechanisms of regulation. This paper reveals further mechanistic diversity TR mediated gene regulation and provides insights into methods for function discovery of TRs.

ACS Style

Tinh T. Nguyen; Richard S. Hall; Tuhin Maity; Yolanda E. Valdez; John M. Dunbar; Clifford J. Unkefer; Pat J. Unkefer; Ricardo Marti-Arbona. Identification and In-vivo Characterization of a Novel OhrR Transcriptional Regulator in Burkholderia xenovorans LB400. Journal of Molecular Biology Research 2013, 3, p37 .

AMA Style

Tinh T. Nguyen, Richard S. Hall, Tuhin Maity, Yolanda E. Valdez, John M. Dunbar, Clifford J. Unkefer, Pat J. Unkefer, Ricardo Marti-Arbona. Identification and In-vivo Characterization of a Novel OhrR Transcriptional Regulator in Burkholderia xenovorans LB400. Journal of Molecular Biology Research. 2013; 3 (1):p37.

Chicago/Turabian Style

Tinh T. Nguyen; Richard S. Hall; Tuhin Maity; Yolanda E. Valdez; John M. Dunbar; Clifford J. Unkefer; Pat J. Unkefer; Ricardo Marti-Arbona. 2013. "Identification and In-vivo Characterization of a Novel OhrR Transcriptional Regulator in Burkholderia xenovorans LB400." Journal of Molecular Biology Research 3, no. 1: p37.

Journal article
Published: 28 January 2013 in Journal of Molecular Biology Research
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The search for effectors of novel transcriptional regulators is a challenging task. Here, we present the prediction and validation of an effector for a novel transcriptional regulator (TR). The clustering of genes around the gene coding for Bxe_A0425, a TR in Burkholderia xenovorans LB400 and its closest orthologs, suggests the conservation of a functional operon composed a several open reading frames from which a TR, a transporter, and two oxidoreductases can be easily identified. A search of operons containing these functional components revealed a remarkable resemblance of this system to the evolutionarily convergent and functionally conserved operons found in Escherichia coli , Bacillus subtilis, Staphylococcus xylosus and Pseudomonas aeruginosa . These operons are involved in the uptake and catabolism of choline to create the potent osmo-protectant molecule glycine betaine. We used frontal affinity chromatography coupled to mass spectrometry to screen for the binding of choline and other intermediates of the glycine biosynthesis pathway to the TR Bxe_0425. We then used electrophoretic mobility shift assays to confirm our results. We found that choline was the sole metabolite binding to this TR and identified choline as an effector molecule for Bxe_A0425. These findings suggest that this operon in B. xenovorans is involved in the uptake and catabolism of choline to protect the organism from osmotic stress.

ACS Style

Ricardo Martí-Arbona; Tuhin S. Maity; John M. Dunbar; Clifford J. Unkefer; Pat J. Unkefer. Discovery of a Choline-Responsive Transcriptional Regulator in Burkholderia xenovorans. Journal of Molecular Biology Research 2013, 3, p91 .

AMA Style

Ricardo Martí-Arbona, Tuhin S. Maity, John M. Dunbar, Clifford J. Unkefer, Pat J. Unkefer. Discovery of a Choline-Responsive Transcriptional Regulator in Burkholderia xenovorans. Journal of Molecular Biology Research. 2013; 3 (1):p91.

Chicago/Turabian Style

Ricardo Martí-Arbona; Tuhin S. Maity; John M. Dunbar; Clifford J. Unkefer; Pat J. Unkefer. 2013. "Discovery of a Choline-Responsive Transcriptional Regulator in Burkholderia xenovorans." Journal of Molecular Biology Research 3, no. 1: p91.

Journal article
Published: 01 January 2012 in Journal of Molecular Microbiology and Biotechnology
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We have developed a high-throughput approach using frontal affinity chromatography coupled to mass spectrometry (FAC-MS) for the identification and characterization of the small molecules that modulate transcriptional regulator (TR) binding to TR targets. We tested this approach using the methionine biosynthesis regulator (MetJ). We used effector mixtures containing S-adenosyl-L-methionine (SAM) and S-adenosyl derivatives as potential ligands for MetJ binding. The differences in the elution time of different compounds allowed us to rank the binding affinity of each compound. Consistent with previous results, FAC-MS showed that SAM binds to MetJ with the highest affinity. In addition, adenine and 5'-deoxy-5'-(methylthio)adenosine bind to the effector binding site on MetJ. Our experiments with MetJ demonstrate that FAC-MS is capable of screening complex mixtures of molecules and identifying high-affinity binders to TRs. In addition, FAC-MS experiments can be used to discriminate between specific and nonspecific binding of the effectors as well as to estimate the dissociation constant (K(d)) for effector-TR binding.

ACS Style

Ricardo Marti-Arbona; Munehiro Teshima; Penelope S. Anderson; Kristy L. Nowak-Lovato; Elizabeth Hong-Geller; Clifford J. Unkefer; Pat J. Unkefer. Identification of New Ligands for the Methionine Biosynthesis Transcriptional Regulator (MetJ) by FAC-MS. Journal of Molecular Microbiology and Biotechnology 2012, 22, 205 -214.

AMA Style

Ricardo Marti-Arbona, Munehiro Teshima, Penelope S. Anderson, Kristy L. Nowak-Lovato, Elizabeth Hong-Geller, Clifford J. Unkefer, Pat J. Unkefer. Identification of New Ligands for the Methionine Biosynthesis Transcriptional Regulator (MetJ) by FAC-MS. Journal of Molecular Microbiology and Biotechnology. 2012; 22 (4):205-214.

Chicago/Turabian Style

Ricardo Marti-Arbona; Munehiro Teshima; Penelope S. Anderson; Kristy L. Nowak-Lovato; Elizabeth Hong-Geller; Clifford J. Unkefer; Pat J. Unkefer. 2012. "Identification of New Ligands for the Methionine Biosynthesis Transcriptional Regulator (MetJ) by FAC-MS." Journal of Molecular Microbiology and Biotechnology 22, no. 4: 205-214.