17 results on '"Christopher W. Johnson"'
Search Results
2. Improving growth of Cupriavidus necator H16 on formate using adaptive laboratory evolution-informed engineering
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Christopher H. Calvey, Violeta Sànchez i Nogué, Aleena M. White, Colin M. Kneucker, Sean P. Woodworth, Hannah M. Alt, Carrie A. Eckert, and Christopher W. Johnson
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Bioengineering ,Applied Microbiology and Biotechnology ,Biotechnology - Abstract
Conversion of CO
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- 2023
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3. Straining to find the permeability
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Bryan Euser, Christopher W. Johnson, Robert A. Guyer, Esteban Rougier, Carly M. Donahue, George D. Guthrie, Antonio Munjiza, and Paul A. Johnson
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Geophysics ,Space and Planetary Science ,Geochemistry and Petrology ,Earth and Planetary Sciences (miscellaneous) - Published
- 2023
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4. Gene amplification, laboratory evolution, and biosensor screening reveal MucK as a terephthalic acid transporter in Acinetobacter baylyi ADP1
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Ramesh K. Jha, Molly Gaddis, Emily A. McIntyre, Ellen L. Neidle, Felicia Bratti, William E. Michener, Christopher W. Johnson, Ryan E. Bermel, Taraka Dale, Isabel Pardo, and Gregg T. Beckham
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Operon ,Phthalic Acids ,Repressor ,Heterologous ,Bioengineering ,Biosensing Techniques ,Applied Microbiology and Biotechnology ,Metabolic engineering ,03 medical and health sciences ,Rhodococcus ,Gene ,030304 developmental biology ,0303 health sciences ,Acinetobacter ,integumentary system ,biology ,030306 microbiology ,Chemistry ,Gene Amplification ,biology.organism_classification ,Major facilitator superfamily ,Biochemistry ,Heterologous expression ,Laboratories ,Bacteria ,Biotechnology - Abstract
Microbial terephthalic acid (TPA) catabolic pathways are conserved among the few bacteria known to turnover this xenobiotic aromatic compound. However, to date there are few reported cases in which this pathway has been successfully expressed in heterologous hosts to impart efficient utilization of TPA as a sole carbon source. In this work, we aimed to engineer TPA conversion in Acinetobacter baylyi ADP1 via the heterologous expression of catabolic and transporter genes from a native TPA-utilizing bacterium. Specifically, we obtained ADP1-derived strains capable of growing on TPA as the sole carbon source using chromosomal insertion and targeted amplification of the tph catabolic operon from Comamonas sp. E6. Adaptive laboratory evolution was then used to improve growth on this substrate. TPA consumption rates of the evolved strains, which retained multiple copies of the tph genes, were ~0.2 g/L/h (or ~1 g TPA/g cells/h), similar to that of Comamonas sp. E6 and almost 2-fold higher than that of Rhodococcus jostii RHA1, another native TPA-utilizing strain. To evaluate TPA transport in the evolved ADP1 strains, we engineered a TPA biosensor consisting of the transcription factor TphR and a fluorescent reporter. In combination with whole-genome sequencing, the TPA biosensor revealed that transport of TPA was not mediated by the heterologous proteins from Comamonas sp. E6. Instead, the endogenous ADP1 muconate transporter MucK, a member of the major facilitator superfamily, was responsible for TPA transport in several evolved strains in which MucK variants were found to enhance TPA uptake. Furthermore, the IclR-type transcriptional regulator DcaS was identified as a repressor of mucK expression. Overall, this work presents an unexpected function of a native protein identified through gene amplification, adaptive laboratory evolution, and a combination of screening methods. This study also provides a TPA biosensor for application in ADP1 and identifies transporter variants for use in metabolic engineering applications focused on plastic upcycling of polyesters.
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- 2020
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5. Dynamic and single cell characterization of a CRISPR-interference toolset in Pseudomonas putida KT2440 for β-ketoadipate production from p-coumarate
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Jacob A. Fenster, Allison Z. Werner, Jian Wei Tay, Matthew Gillen, Leo Schirokauer, Nicholas C. Hill, Audrey Watson, Kelsey J. Ramirez, Christopher W. Johnson, Gregg T. Beckham, Jeffrey C. Cameron, and Carrie A. Eckert
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Endocrinology, Diabetes and Metabolism ,Biomedical Engineering - Published
- 2022
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6. Corrigendum to 'Engineering glucose metabolism for enhanced muconic acid production in Pseudomonas putida KT2440' [Metab. Eng. 59 (2020) 64–75]
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Gayle J. Bentley, Niju Narayanan, Ramesh K. Jha, Davinia Salvachúa, Joshua R. Elmore, George L. Peabody, Brenna A. Black, Kelsey Ramirez, Annette De Capite, William E. Michener, Allison Z. Werner, Dawn M. Klingeman, Heidi S. Schindel, Robert Nelson, Lindsey Foust, Adam M. Guss, Taraka Dale, Christopher W. Johnson, and Gregg T. Beckham
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Bioengineering ,Applied Microbiology and Biotechnology ,Biotechnology - Published
- 2022
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7. Innovative Chemicals and Materials from Bacterial Aromatic Catabolic Pathways
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Peter C. St. John, Nicholas S. Cleveland, Graham Dominick, Priyanka Singh, William E. Michener, Davinia Salvachúa, Xiunan Yi, Brenna A. Black, Derek R. Vardon, Kelsey J. Ramirez, Chelsea R. Martinez, Adam M. Guss, A. Nolan Wilson, Gregg T. Beckham, Nicholas J. Grundl, Todd A. VanderWall, Nicholas A. Rorrer, Christopher W. Johnson, Payal Khanna, Joshua R. Elmore, Darren J. Peterson, Mary J. Biddy, and Yannick J. Bomble
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Muconic acid ,biology ,Catabolism ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,biology.organism_classification ,01 natural sciences ,Decomposition ,Combinatorial chemistry ,Pseudomonas putida ,0104 chemical sciences ,Metabolic pathway ,chemistry.chemical_compound ,General Energy ,Petrochemical ,chemistry ,Bioreactor ,Molecule ,0210 nano-technology - Abstract
Summary To drive innovation in chemical and material applications beyond what has been afforded by the mature petrochemical industry, new molecules that possess diverse chemical functionality are needed. One source of such molecules lies in the varied metabolic pathways that soil microbes utilize to catabolize aromatic compounds generated during plant decomposition. Here, we have engineered Pseudomonas putida KT2440 to convert these aromatic compounds to 15 catabolic intermediates that exhibit substantial chemical diversity. Bioreactor cultivations, analytical methods, and bench-scale separations were developed to enable production (up to 58 g/L), detection, and purification of each target molecule. We further engineered strains for production of a subset of these molecules from glucose, achieving a 41% molar yield of muconic acid. Finally, we produce materials from three compounds to illustrate the potential for realizing performance-advantaged properties relative to petroleum-derived analogs.
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- 2019
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8. Production of β-ketoadipic acid from glucose in Pseudomonas putida KT2440 for use in performance-advantaged nylons
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Nicholas A. Rorrer, Sandra F. Notonier, Brandon C. Knott, Brenna A. Black, Avantika Singh, Scott R. Nicholson, Christopher P. Kinchin, Graham P. Schmidt, Alberta C. Carpenter, Kelsey J. Ramirez, Christopher W. Johnson, Davinia Salvachúa, Michael F. Crowley, and Gregg T. Beckham
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General Energy ,General Engineering ,General Physics and Astronomy ,General Materials Science ,General Chemistry - Published
- 2022
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9. A protocatechuate biosensor for Pseudomonas putida KT2440 via promoter and protein evolution
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Christopher W. Johnson, Payal Khanna, Jeremy M. Bingen, Taraka Dale, Gregg T. Beckham, Theresa L. Kern, Ramesh K. Jha, Daniel S. Trettel, and Charlie E. M. Strauss
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0301 basic medicine ,lcsh:Biotechnology ,Endocrinology, Diabetes and Metabolism ,Allosteric regulation ,ved/biology.organism_classification_rank.species ,Biomedical Engineering ,macromolecular substances ,Computational biology ,010402 general chemistry ,medicine.disease_cause ,01 natural sciences ,Protein evolution ,03 medical and health sciences ,Synthetic biology ,lcsh:TP248.13-248.65 ,medicine ,Model organism ,lcsh:QH301-705.5 ,Escherichia coli ,biology ,Chemistry ,ved/biology ,technology, industry, and agriculture ,Limiting ,biology.organism_classification ,Pseudomonas putida ,0104 chemical sciences ,030104 developmental biology ,lcsh:Biology (General) ,Biosensor - Abstract
Robust fluorescence-based biosensors are emerging as critical tools for high-throughput strain improvement in synthetic biology. Many biosensors are developed in model organisms where sophisticated synthetic biology tools are also well established. However, industrial biochemical production often employs microbes with phenotypes that are advantageous for a target process, and biosensors may fail to directly transition outside the host in which they are developed. In particular, losses in sensitivity and dynamic range of sensing often occur, limiting the application of a biosensor across hosts. Here we demonstrate the optimization of an Escherichia coli-based biosensor in a robust microbial strain for the catabolism of aromatic compounds, Pseudomonas putida KT2440, through a generalizable approach of modulating interactions at the protein-DNA interface in the promoter and the protein-protein dimer interface. The high-throughput biosensor optimization approach demonstrated here is readily applicable towards other allosteric regulators. Keywords: Whole cell biosensor, Aromatic catabolism, Transcription factor, PcaU, Shikimate
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- 2018
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10. Conversion and assimilation of furfural and 5-(hydroxymethyl)furfural by Pseudomonas putida KT2440
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Mary Ann Franden, Gregg T. Beckham, Michael T. Guarnieri, and Christopher W. Johnson
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0301 basic medicine ,integumentary system ,biology ,lcsh:Biotechnology ,Endocrinology, Diabetes and Metabolism ,Cupriavidus basilensis ,Biomedical Engineering ,biology.organism_classification ,Furfural ,Article ,Pseudomonas putida ,Hydrolysate ,Furfuryl alcohol ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,lcsh:Biology (General) ,chemistry ,Biochemistry ,lcsh:TP248.13-248.65 ,Organic chemistry ,Hydroxymethyl ,Energy source ,Sugar ,lcsh:QH301-705.5 - Abstract
The sugar dehydration products, furfural and 5-(hydroxymethyl)furfural (HMF), are commonly formed during high-temperature processing of lignocellulose, most often in thermochemical pretreatment, liquefaction, or pyrolysis. Typically, these two aldehydes are considered major inhibitors in microbial conversion processes. Many microbes can convert these compounds to their less toxic, dead-end alcohol counterparts, furfuryl alcohol and 5-(hydroxymethyl)furfuryl alcohol. Recently, the genes responsible for aerobic catabolism of furfural and HMF were discovered in Cupriavidus basilensis HMF14 to enable complete conversion of these compounds to the TCA cycle intermediate, 2-oxo-glutarate. In this work, we engineer the robust soil microbe, Pseudomonas putida KT2440, to utilize furfural and HMF as sole carbon and energy sources via complete genomic integration of the 12 kB hmf gene cluster previously reported from Burkholderia phytofirmans. The common intermediate, 2-furoic acid, is shown to be a bottleneck for both furfural and HMF metabolism. When cultured on biomass hydrolysate containing representative amounts of furfural and HMF from dilute-acid pretreatment, the engineered strain outperforms the wild type microbe in terms of reduced lag time and enhanced growth rates due to catabolism of furfural and HMF. Overall, this study demonstrates that an approach for biological conversion of furfural and HMF, relative to the typical production of dead-end alcohols, enables both enhanced carbon conversion and substantially improves tolerance to hydrolysate inhibitors. This approach should find general utility both in emerging aerobic processes for the production of fuels and chemicals from biomass-derived sugars and in the biological conversion of high-temperature biomass streams from liquefaction or pyrolysis where furfural and HMF are much more abundant than in biomass hydrolysates from pretreatment., Highlights • HMF and furfural are common microbial inhibitors in biomass conversion. • HMF and furfural gene cluster was isolated from Burkholderia phytofirmans.. • We heterologously express the HMF/furfural gene cluster in Pseudomonas putida.. • Expression enables cultivation on HMF and furfural as a sole carbon source. • Expression also enables enhanced conversion on lignocellulosic hydrolysate.
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- 2017
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11. Aromatic catabolic pathway selection for optimal production of pyruvate and lactate from lignin
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Gregg T. Beckham and Christopher W. Johnson
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chemistry.chemical_classification ,Catechol ,biology ,Pseudomonas putida ,Bioengineering ,biology.organism_classification ,Lignin ,Applied Microbiology and Biotechnology ,Sphingobium ,Citric acid cycle ,chemistry.chemical_compound ,Enzyme ,chemistry ,Biochemistry ,Metabolic Engineering ,Dioxygenase ,Yield (chemistry) ,Pyruvic Acid ,Lactic Acid ,Biotechnology - Abstract
Lignin represents an untapped feedstock for the production of fuels and chemicals, but its intrinsic heterogeneity makes lignin valorization a significant challenge. In nature, many aerobic organisms degrade lignin-derived aromatic molecules through conserved central intermediates including catechol and protocatechuate. Harnessing this microbial approach offers potential for lignin upgrading in modern biorefineries, but significant technical development is needed to achieve this end. Catechol and protocatechuate are subjected to aromatic ring cleavage by dioxygenase enzymes that, depending on the position, ortho or meta relative to adjacent hydroxyl groups, result in different products that are metabolized through parallel pathways for entry into the TCA cycle. These degradation pathways differ in the combination of succinate, acetyl-CoA, and pyruvate produced, the reducing equivalents regenerated, and the amount of carbon emitted as CO2-factors that will ultimately impact the yield of the targeted product. As shown here, the ring-cleavage pathways can be interchanged with one another, and such substitutions have a predictable and substantial impact on product yield. We demonstrate that replacement of the catechol ortho degradation pathway endogenous to Pseudomonas putida KT2440 with an exogenous meta-cleavage pathway from P. putida mt-2 increases yields of pyruvate produced from aromatic molecules in engineered strains. Even more dramatically, replacing the endogenous protocatechuate ortho pathway with a meta-cleavage pathway from Sphingobium sp. SYK-6 results in a nearly five-fold increase in pyruvate production. We further demonstrate the aerobic conversion of pyruvate to l-lactate with a yield of 41.1 ± 2.6% (wt/wt). Overall, this study illustrates how aromatic degradation pathways can be tuned to optimize the yield of a desired product in biological lignin upgrading.
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- 2015
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12. Kisspeptin Neurons in the Arcuate Nucleus of the Hypothalamus Orchestrate Circadian Rhythms and Metabolism
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Richard D. Palmiter, Stephanie L Padilla, Horacio O. de la Iglesia, Jazmine G. Perez, Miriam Ben-Hamo, Raymond E A Sanchez, Ivana L. Bussi, and Christopher W. Johnson
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0301 basic medicine ,Circadian clock ,Biology ,Article ,General Biochemistry, Genetics and Molecular Biology ,Body Temperature ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Kisspeptin ,Arcuate nucleus ,Biological neural network ,Animals ,Circadian rhythm ,Neurons ,Kisspeptins ,Suprachiasmatic nucleus ,Arcuate Nucleus of Hypothalamus ,Feeding Behavior ,Circadian Rhythm ,030104 developmental biology ,nervous system ,Hypothalamus ,Female ,Wakefulness ,Sleep ,General Agricultural and Biological Sciences ,Neuroscience ,Locomotion ,030217 neurology & neurosurgery - Abstract
Summary Successful reproduction in female mammals is precisely timed and must be able to withstand the metabolic demand of pregnancy and lactation. We show that kisspeptin-expressing neurons in the arcuate hypothalamus (Kiss1ARH) of female mice control the daily timing of food intake, along with the circadian regulation of locomotor activity, sleep, and core body temperature. Toxin-induced silencing of Kiss1ARH neurons shifts wakefulness and food consumption to the light phase and induces weight gain. Toxin-silenced mice are less physically active and have attenuated temperature rhythms. Because the rhythm of the master clock in the suprachiasmatic nucleus (SCN) appears to be intact, we hypothesize that Kiss1ARH neurons signal to neurons downstream of the master clock to modulate the output of the SCN. We conclude that, in addition to their well-established role in regulating fertility, Kiss1ARH neurons are a critical component of the hypothalamic circadian oscillator network that times overt rhythms of physiology and behavior.
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- 2019
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13. Evidence for the involvement of the NADPH Oxidase enzyme complex in the optimal accumulation of Platelet-activating factor in the human cell line PLB-985
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Mary C. Dinauer, Christopher W. Johnson, Tejindervir S. Hiran, Jeffrey B. Travers, and Keith L. Clay
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Cell type ,Enzyme complex ,Receptors, Peptide ,Physiology ,Inflammation ,Biology ,Biochemistry ,Gas Chromatography-Mass Spectrometry ,Cell Line ,chemistry.chemical_compound ,Superoxides ,NADPH oxidase complex ,medicine ,Humans ,Platelet Activating Factor ,Receptors, Immunologic ,Calcimycin ,Pharmacology ,NADPH oxidase ,Ionophores ,Platelet-activating factor ,NADPH Oxidases ,Cell Biology ,Glycerylphosphorylcholine ,Receptors, Formyl Peptide ,Respiratory burst ,N-Formylmethionine Leucyl-Phenylalanine ,chemistry ,Leukemia, Myeloid ,Cell culture ,Phosphatidylcholines ,biology.protein ,Tetradecanoylphorbol Acetate ,Calcium ,lipids (amino acids, peptides, and proteins) ,medicine.symptom - Abstract
Platelet-activating factor (PAF) is an early product of the inflammatory environment, influencing development and resolution of inflammation. Its production is greater in neutrophils and macrophages, which predominantly synthesize 1-alkyl sn-2 acetyl glycerophosphocholine (GPC) than in non-granulocytes (B cells and endothelial cells), which lack a respiratory burst and synthesize 1-acyl sn-2 acetyl GPC as their major PAF species. This study investigated whether the respiratory burst was responsible for the quantitative and qualitative differences in sn-2 acetyl GPC species generation by neutrophils and macrophages versus those cells lacking the NADPH oxidase complex. The myeloid cell line PLB-985 (capable of differentiation into neutrophils) was used to test this hypothesis, since these cells had previously been generated with a non-functional respiratory burst (X-CGD PLB-985). Differentiated PLB-985 cells underwent a large respiratory burst in response to PMA (phorbol ester), and smaller respiratory bursts in response to A23187 (calcium ionophore), and the bacterial polypeptide fMLP (receptor mediated activation). Concurrently, treated cells were assessed for production of 1-hexadecyl and 1-palmitoyl sn-2 acetyl GPC species by gas chromatography/mass spectrometry. Neither cell type generated these lipid species in response to PMA, but both cell types generated equal levels of sn-2 acetyl GPC in response to A23187, with five times more 1-hexadecyl than 1-palmitoyl species. Upon fMLP activation, X-CGD PLB-985 cells produced significantly less 1-hexadecyl and 1-palmitoyl sn-2 acetyl GPC in comparison to the wild-type PLB-985 cells. These findings suggest phagocytic oxidant production by NADPH oxidase is not essential for sn-2 acetyl GPC generation, but appears important for optimal production of PAF in response to some stimuli.
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- 2001
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14. Corrigendum to 'Extended-release naltrexone opioid treatment at jail reentry (XOR)' [Contemp. Clin. Trials 49 (2016) 57–64]
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John Rotrosen, Nadina Santana-Correa, Keith Goldfeld, Eugene M. Laska, Neil Leibowitz, Mara Flannery, Marc N. Gourevitch, Babak Tofighi, Christopher W. Johnson, Ryan McDonald, Joshua D. Lee, and Wanda Bonilla
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Opioid ,Extended release naltrexone ,business.industry ,Medicine ,Pharmacology (medical) ,General Medicine ,Reentry ,Pharmacology ,business ,Article ,medicine.drug - Published
- 2016
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15. Corrigendum to 'Vgll2a is required for neural crest cell survival during zebrafish craniofacial development' [Dev. Biol. 357 (2011) 269–281]
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Vida Senkus Melvin, Christopher W. Johnson, Weiguo Feng, Laura Hernandez-Lagunas, Kristin Bruk Artinger, and Trevor Williams
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biology ,Neural crest ,Cell Biology ,Anatomy ,Craniofacial ,biology.organism_classification ,Molecular Biology ,Zebrafish ,Developmental Biology - Abstract
Corrigendum to “Vgll2a is required for neural crest cell survival during zebrafish craniofacial development” [Dev. Biol. 357 (2011) 269–281] Christopher W. Johnson , Laura Hernandez-Lagunas , Weiguo Feng , Vida Senkus Melvin , Trevor Williams , Kristin Bruk Artinger a,⁎ a Department of Craniofacial Biology, University of Colorado Denver, School of Dental Medicine, Aurora, CO 80045, USA b Molecular Biology Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
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- 2012
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16. Vgl-2a is Required for Neural Crest Cell Survival During Zebrafish Craniofacial Development
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Kristin Bruk Artinger, Trevor Williams, Weiguo Feng, and Christopher W. Johnson
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Neural crest ,Cell Biology ,Craniofacial ,Biology ,biology.organism_classification ,Molecular Biology ,Zebrafish ,Neuroscience ,Developmental Biology - Published
- 2010
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17. Erratum to ‘Prognostic indicators for long term outcome following radical retropubic prostatectomy for prostate cancer involving the seminal vesicles’[Urol Oncol 22 (2004) 107–111]
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Laurent Salomon, Samuel H. Eaton, Mitchell C. Benson, Aristotelis G. Anastasiadis, Christopher W. Johnson, Carl A. Olsson, Erik T. Goluboff, and James M. McKiernan
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medicine.medical_specialty ,Prostate cancer ,Oncology ,business.industry ,Urology ,medicine.medical_treatment ,Medicine ,business ,medicine.disease ,Radical retropubic prostatectomy - Published
- 2004
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