Marc Facciotti - Academia.edu (original) (raw)
Papers by Marc Facciotti
Microbiology Resource Announcements
Halophile-specific enzymes have wide-ranging industrial and commercial applications. Despite thei... more Halophile-specific enzymes have wide-ranging industrial and commercial applications. Despite their importance, there is a paucity of available halophile whole-genome sequences. Here, we report the draft genome sequences of 16 diverse salt-tolerant strains of bacteria and archaea isolated from a variety of high-salt environments.
While numerous effective peak finders have been developed for eukaryotic systems, we have found t... more While numerous effective peak finders have been developed for eukaryotic systems, we have found that the approaches used can be error prone when run on high coverage bacterial and archaeal ChIP-Seq datasets. We have developed Pique, an easy to use ChIP-Seq peak finding application for bacterial and archaeal ChIP-Seq experiments. The software is cross-platform and Open Source, and based on only freely licensed dependencies. Output is provided in standardized file formats, and may be easily imported by the Gaggle Genome Browser (Bare et al. 2010) for manual curation and data exploration, or into statistical and graphics software such as R (R Core Team 2013) for further analysis. The software is available under the BSD-3 license, and tutorial and test data are included with the documentation. http://github.com/ryneches/pique.
Viruses
Chloroviruses (family Phycodnaviridae) are dsDNA viruses found throughout the world’s inland wate... more Chloroviruses (family Phycodnaviridae) are dsDNA viruses found throughout the world’s inland waters. The open reading frames in the genomes of 41 sequenced chloroviruses (330 ± 40 kbp each) representing three virus types were analyzed for evidence of evolutionarily conserved local genomic “contexts”, the organization of biological information into units of a scale larger than a gene. Despite a general loss of synteny between virus types, we informatically detected a highly conserved genomic context defined by groups of three or more genes that we have termed “gene gangs”. Unlike previously described local genomic contexts, the definition of gene gangs requires only that member genes be consistently co-localized and are not constrained by strand, regulatory sites, or intervening sequences (and therefore represent a new type of conserved structural genomic element). An analysis of functional annotations and transcriptomic data suggests that some of the gene gangs may organize genes in...
Evidence-based teaching is a highly complex skill, requiring repeated cycles of deliberate practi... more Evidence-based teaching is a highly complex skill, requiring repeated cycles of deliberate practice and feedback to master. Despite existing well characterized frameworks for practice-based training in K-12 teacher education, the major principles of these frameworks have not yet been transferred to instructor development in higher educational contexts, including training of graduate teaching assistants (GTAs). We sought to determine whether a practice-based training program could help GTAs learn and use evidence-based teaching methods in their classrooms. We implemented a weekly training program for introductory biology GTAs, which included structured drills of techniques selected to enhance student practice, logic-development, and accountability and reduce apprehension. GTAs received regular performance feedback based on classroom observations. To quantify use of target techniques and levels of student participation, we collected and coded 160 hours of video footage. We found that,...
ACS Chemical Biology
The rapidly growing appreciation of enzymes' catalytic and substrate promiscuity may lead... more The rapidly growing appreciation of enzymes' catalytic and substrate promiscuity may lead to their expanded use in the fields of chemical synthesis and industrial biotechnology. Here, we explore the substrate promiscuity of enoyl-acyl carrier protein reductases (commonly known as FabI) and how that promiscuity is a function of inherent reactivity and the geometric demands of the enzyme's active site. We demonstrate that these enzymes catalyze the reduction of a wide range of substrates, particularly α,β-unsaturated aldehydes. In addition, we demonstrate that a combination of quantum mechanical hydride affinity calculations and molecular docking can be used to rapidly categorize compounds that FabI can use as substrates. The results here provide new insight into the determinants of catalysis for FabI and set the stage for the development of a new assay for drug discovery, organic synthesis, and novel biocatalysts.
Journal of Investigative Medicine, 2009
Following is a portion of the proceedings of the panel and audience discussion from the AFMR-Tran... more Following is a portion of the proceedings of the panel and audience discussion from the AFMR-Translational Medical Research Development Workshop at EB08.
Journal of Investigative Medicine, 2009
The rise of interdisciplinary research programs in recent years has spawned numerous questions re... more The rise of interdisciplinary research programs in recent years has spawned numerous questions regarding the best way to organize interdisciplinary programs and how to best train new interdisciplinary scientists in ways that will catalyze novel discoveries in biology. Systems biology, a relatively new branch of science, can be considered in many respects a poster child for modern interdisciplinary science. It not only requires that people from different traditional disciplines work closely together but it also requires the development of unique training environments to educate the next generation of systems biologists. The unique scientific and training challenges associated with the development of systems biology are certainly faced across the spectrum of interdisciplinary endeavors. Therefore, it is useful for scientists interested in building interdisciplinary research programs to consider the merits of successful systems biology initiatives. Institute for Systems Biology is one such example, and in the following, several key aspects of Institute for Systems Biology that make it both a unique and successful interdisciplinary science and training center are discussed.
Microbiology, 2015
Mercury is a heavy metal and toxic to all forms of life. Metal exposure can invoke a response to ... more Mercury is a heavy metal and toxic to all forms of life. Metal exposure can invoke a response to improve survival. In archaea, several components of a mercury response system have been identified but it is not known if metal transport is a member of this system. To identify such missing components, a peptide tagged MerR transcription factor was used to localize enriched chromosome regions by chromosome immunoprecipitation combined with DNA sequence analysis (ChIP-Seq). Such regions could serve as secondary regulatory binding sites to control the expression of additional genes associated with mercury detoxification. Among the 31 highly enriched loci a subset of 5 were pursued as potential candidates based on their current annotations. qRT-PCR analysis of these regions with and without mercury treatment in wild-type and mutant strains lacking merR indicated significant regulatory responses under these conditions. Of these, a Family 5 extracellular solute-binding protein and the MarR transcription factor shown previously to control responses to oxidation were most strongly affected. Inactivation of the solute binding protein by gene disruption increased the resistance of mutant cells to mercury challenge. ICP-MS analysis of the mutant cell line following metal challenge indicated there was less intracellular mercury compared to the isogenic wild type strain. Together, these regulated genes comprise new members of the archaeal MerR regulon and reveal a cascade of transcriptional control not previously demonstrated in this model organism.
Scientific reports, Jan 29, 2015
A limiting factor in synthetic gene circuit design is the number of independent control elements ... more A limiting factor in synthetic gene circuit design is the number of independent control elements that can be combined together in a single system. Here, we present RiboTALEs, a new class of inducible repressors that combine the specificity of TALEs with the ability of riboswitches to recognize exogenous signals and differentially control protein abundance. We demonstrate the capacity of RiboTALEs, constructed through different combinations of TALE proteins and riboswitches, to rapidly and reproducibly control the expression of downstream targets with a dynamic range of 243.7 ± 17.6-fold, which is adequate for many biotechnological applications.
Nature biotechnology, 1999
The engineering of crops for selected fatty acid production is one of the major goals of plant bi... more The engineering of crops for selected fatty acid production is one of the major goals of plant biotechnology. The Garm FatA1, an acyl-acyl carrier protein (ACP) thioesterase isolated from Garcinia mangostana, generates an elevated stearate (18:0) phenotype in transgenic Brassica plants. By site-directed mutagenesis, we generated seven mutants that showed up to a 13-fold increase in specific enzyme activity toward 18:0-ACP in vitro. The seed-specific expression of mutant S111A/V193A in Brassica plants results in transgenic plants that accumulate 55-68% more stearate than plants expressing the wild-type enzyme. Our results demonstrate that a thioesterase can be engineered to increase specific activity and that its improved function demonstrated in vitro is retained in vivo.
Springer Series in Chemical Physics, 2003
The outcome of a photochemical reaction in the condensed phase depends on the nature of the react... more The outcome of a photochemical reaction in the condensed phase depends on the nature of the reacting chromophore and its environment, which may for instance be a liquid, glass or a protein. In liquids, solvation dynamics has been well characterized, primarily through the use of time-resolved fluorescence and photon echo techniques, combined with molecular dynamics (MD) simulations [1]. Two solvation components are often observed: a fast inertial response, occurring on a timescale less than 100 fs, followed by a slower, diffusive ...
Genome biology, 2006
We present a method (the Inferelator) for deriving genome-wide transcriptional regulatory interac... more We present a method (the Inferelator) for deriving genome-wide transcriptional regulatory interactions, and apply the method to predict a large portion of the regulatory network of the archaeon Halobacterium NRC-1. The Inferelator uses regression and variable selection to identify transcriptional influences on genes based on the integration of genome annotation and expression data. The learned network successfully predicted Halobacterium's global expression under novel perturbations with predictive power similar to that seen over training data. Several specific regulatory predictions were experimentally tested and verified.
Microbiology Resource Announcements
Halophile-specific enzymes have wide-ranging industrial and commercial applications. Despite thei... more Halophile-specific enzymes have wide-ranging industrial and commercial applications. Despite their importance, there is a paucity of available halophile whole-genome sequences. Here, we report the draft genome sequences of 16 diverse salt-tolerant strains of bacteria and archaea isolated from a variety of high-salt environments.
While numerous effective peak finders have been developed for eukaryotic systems, we have found t... more While numerous effective peak finders have been developed for eukaryotic systems, we have found that the approaches used can be error prone when run on high coverage bacterial and archaeal ChIP-Seq datasets. We have developed Pique, an easy to use ChIP-Seq peak finding application for bacterial and archaeal ChIP-Seq experiments. The software is cross-platform and Open Source, and based on only freely licensed dependencies. Output is provided in standardized file formats, and may be easily imported by the Gaggle Genome Browser (Bare et al. 2010) for manual curation and data exploration, or into statistical and graphics software such as R (R Core Team 2013) for further analysis. The software is available under the BSD-3 license, and tutorial and test data are included with the documentation. http://github.com/ryneches/pique.
Viruses
Chloroviruses (family Phycodnaviridae) are dsDNA viruses found throughout the world’s inland wate... more Chloroviruses (family Phycodnaviridae) are dsDNA viruses found throughout the world’s inland waters. The open reading frames in the genomes of 41 sequenced chloroviruses (330 ± 40 kbp each) representing three virus types were analyzed for evidence of evolutionarily conserved local genomic “contexts”, the organization of biological information into units of a scale larger than a gene. Despite a general loss of synteny between virus types, we informatically detected a highly conserved genomic context defined by groups of three or more genes that we have termed “gene gangs”. Unlike previously described local genomic contexts, the definition of gene gangs requires only that member genes be consistently co-localized and are not constrained by strand, regulatory sites, or intervening sequences (and therefore represent a new type of conserved structural genomic element). An analysis of functional annotations and transcriptomic data suggests that some of the gene gangs may organize genes in...
Evidence-based teaching is a highly complex skill, requiring repeated cycles of deliberate practi... more Evidence-based teaching is a highly complex skill, requiring repeated cycles of deliberate practice and feedback to master. Despite existing well characterized frameworks for practice-based training in K-12 teacher education, the major principles of these frameworks have not yet been transferred to instructor development in higher educational contexts, including training of graduate teaching assistants (GTAs). We sought to determine whether a practice-based training program could help GTAs learn and use evidence-based teaching methods in their classrooms. We implemented a weekly training program for introductory biology GTAs, which included structured drills of techniques selected to enhance student practice, logic-development, and accountability and reduce apprehension. GTAs received regular performance feedback based on classroom observations. To quantify use of target techniques and levels of student participation, we collected and coded 160 hours of video footage. We found that,...
ACS Chemical Biology
The rapidly growing appreciation of enzymes' catalytic and substrate promiscuity may lead... more The rapidly growing appreciation of enzymes' catalytic and substrate promiscuity may lead to their expanded use in the fields of chemical synthesis and industrial biotechnology. Here, we explore the substrate promiscuity of enoyl-acyl carrier protein reductases (commonly known as FabI) and how that promiscuity is a function of inherent reactivity and the geometric demands of the enzyme's active site. We demonstrate that these enzymes catalyze the reduction of a wide range of substrates, particularly α,β-unsaturated aldehydes. In addition, we demonstrate that a combination of quantum mechanical hydride affinity calculations and molecular docking can be used to rapidly categorize compounds that FabI can use as substrates. The results here provide new insight into the determinants of catalysis for FabI and set the stage for the development of a new assay for drug discovery, organic synthesis, and novel biocatalysts.
Journal of Investigative Medicine, 2009
Following is a portion of the proceedings of the panel and audience discussion from the AFMR-Tran... more Following is a portion of the proceedings of the panel and audience discussion from the AFMR-Translational Medical Research Development Workshop at EB08.
Journal of Investigative Medicine, 2009
The rise of interdisciplinary research programs in recent years has spawned numerous questions re... more The rise of interdisciplinary research programs in recent years has spawned numerous questions regarding the best way to organize interdisciplinary programs and how to best train new interdisciplinary scientists in ways that will catalyze novel discoveries in biology. Systems biology, a relatively new branch of science, can be considered in many respects a poster child for modern interdisciplinary science. It not only requires that people from different traditional disciplines work closely together but it also requires the development of unique training environments to educate the next generation of systems biologists. The unique scientific and training challenges associated with the development of systems biology are certainly faced across the spectrum of interdisciplinary endeavors. Therefore, it is useful for scientists interested in building interdisciplinary research programs to consider the merits of successful systems biology initiatives. Institute for Systems Biology is one such example, and in the following, several key aspects of Institute for Systems Biology that make it both a unique and successful interdisciplinary science and training center are discussed.
Microbiology, 2015
Mercury is a heavy metal and toxic to all forms of life. Metal exposure can invoke a response to ... more Mercury is a heavy metal and toxic to all forms of life. Metal exposure can invoke a response to improve survival. In archaea, several components of a mercury response system have been identified but it is not known if metal transport is a member of this system. To identify such missing components, a peptide tagged MerR transcription factor was used to localize enriched chromosome regions by chromosome immunoprecipitation combined with DNA sequence analysis (ChIP-Seq). Such regions could serve as secondary regulatory binding sites to control the expression of additional genes associated with mercury detoxification. Among the 31 highly enriched loci a subset of 5 were pursued as potential candidates based on their current annotations. qRT-PCR analysis of these regions with and without mercury treatment in wild-type and mutant strains lacking merR indicated significant regulatory responses under these conditions. Of these, a Family 5 extracellular solute-binding protein and the MarR transcription factor shown previously to control responses to oxidation were most strongly affected. Inactivation of the solute binding protein by gene disruption increased the resistance of mutant cells to mercury challenge. ICP-MS analysis of the mutant cell line following metal challenge indicated there was less intracellular mercury compared to the isogenic wild type strain. Together, these regulated genes comprise new members of the archaeal MerR regulon and reveal a cascade of transcriptional control not previously demonstrated in this model organism.
Scientific reports, Jan 29, 2015
A limiting factor in synthetic gene circuit design is the number of independent control elements ... more A limiting factor in synthetic gene circuit design is the number of independent control elements that can be combined together in a single system. Here, we present RiboTALEs, a new class of inducible repressors that combine the specificity of TALEs with the ability of riboswitches to recognize exogenous signals and differentially control protein abundance. We demonstrate the capacity of RiboTALEs, constructed through different combinations of TALE proteins and riboswitches, to rapidly and reproducibly control the expression of downstream targets with a dynamic range of 243.7 ± 17.6-fold, which is adequate for many biotechnological applications.
Nature biotechnology, 1999
The engineering of crops for selected fatty acid production is one of the major goals of plant bi... more The engineering of crops for selected fatty acid production is one of the major goals of plant biotechnology. The Garm FatA1, an acyl-acyl carrier protein (ACP) thioesterase isolated from Garcinia mangostana, generates an elevated stearate (18:0) phenotype in transgenic Brassica plants. By site-directed mutagenesis, we generated seven mutants that showed up to a 13-fold increase in specific enzyme activity toward 18:0-ACP in vitro. The seed-specific expression of mutant S111A/V193A in Brassica plants results in transgenic plants that accumulate 55-68% more stearate than plants expressing the wild-type enzyme. Our results demonstrate that a thioesterase can be engineered to increase specific activity and that its improved function demonstrated in vitro is retained in vivo.
Springer Series in Chemical Physics, 2003
The outcome of a photochemical reaction in the condensed phase depends on the nature of the react... more The outcome of a photochemical reaction in the condensed phase depends on the nature of the reacting chromophore and its environment, which may for instance be a liquid, glass or a protein. In liquids, solvation dynamics has been well characterized, primarily through the use of time-resolved fluorescence and photon echo techniques, combined with molecular dynamics (MD) simulations [1]. Two solvation components are often observed: a fast inertial response, occurring on a timescale less than 100 fs, followed by a slower, diffusive ...
Genome biology, 2006
We present a method (the Inferelator) for deriving genome-wide transcriptional regulatory interac... more We present a method (the Inferelator) for deriving genome-wide transcriptional regulatory interactions, and apply the method to predict a large portion of the regulatory network of the archaeon Halobacterium NRC-1. The Inferelator uses regression and variable selection to identify transcriptional influences on genes based on the integration of genome annotation and expression data. The learned network successfully predicted Halobacterium's global expression under novel perturbations with predictive power similar to that seen over training data. Several specific regulatory predictions were experimentally tested and verified.