SIGN INAvailable Projects
ACT Users
Biochemistry
In Silico bioinformatic analysis of duplicated genes in alphaproteobacteria. Students will independently investigate the similarities and differences between multiple copy genes that, by annotation, are predicted to have the same function.
Up to five ArgE paralogs are found in Agrobacterium genomes. ArgE genes have broad substrate specificities that allow catalysis of alternate substrates. Students are assigned a microbial ArgE gene with unknown structure. They construct a homology model with the I-Tasser web server and analyze the binding pocket to construct a hypothesis about that gene's substrate specificity.
Up to three ProC paralogs are found in Agrobacterium genomes. ProC genes have broad substrate specificities that allow catalysis of alternate substrates. Students are assigned a microbial ProC gene with unknown structure. They construct a homology model with the I-Tasser web server and analyze the binding pocket to construct a hypothesis about that gene\\\\\\\\\\\\\\\'s substrate specificity.\\\\\\\\n
Bioinformatics workshop
Up to three ProC paralogs are found in Agrobacterium genomes. ProC genes have considerable sequence diversity for unknown reasons. Students are assigned a microbial ProC gene with unknown structure. They construct a homology model with the I-Tasser web server and analyze the primary and tertiary structures to develop specific functional hypotheses.
The human lipocalin called siderocalin binds iron-siderophore complexes. Siderocalin orthologs grouped by sequence have unknown functions. Students are assigned a eukaryotic siderocalin ortholog with unknown structure. They construct a homology model with the I-Tasser web server and analyze the primary and tertiary structures to develop hypotheses regarding binding and enzymatic activity.
This lab will be a little different than what you’re used to, in large part because what you are called to do for the next six weeks is a little different than what most undergraduate labs call for -- you are being asked to both learn the steps of a “professional” protein preparation and also will use that knowledge to make a batch of protein for research purposes.\\\\\\\\n
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This lab will be a little different than what you’re used to, in large part because what you are called to do for the next six weeks is a little different than what most undergraduate labs call for -- you are being asked to both learn the steps of a “professional” protein preparation and also will use that knowledge to make a batch of protein for research purposes.
In this project a simple BIAcore instrument is used to measure protein-protein binding using surface plasmon resonance (a label-free biophysical technique). This allows students to compare different proteins and determine which bind most tightly and most quickly.
Ecology
In this project, students will asses the degree of animal biodiversity in urban habitats, using both morphological features and DNA barcoding to characterize and classify invertebrate animal species.
Functional Genomics - General
Automated genome annotation indicates the presence of PHB Bioysynthetic genes in Agrobacterium tumefaicens C58, Agrobacterium radiobacter K84, Agrobacterium vitis S4 & Agrobacterium rhizogenes A4. This project will determine if the PHB biosynthetic genes in Agrobacterium species are functional.
Functional Genomics - Arginine
Functional Genomics - Proline
This project will be used for advanced courses who are developing GENI research projects focused on the role and evolution of proline biosynthesis in Agrobacterium. Students in this course will create novel research projects to address this question, and post them on GENI for use by collaborators.
Genetics
This project contains protocols for characterizing a Myxococcus xanthus targeted plasmid insertion mutant using fruiting body development, motility and sporulation efficiency assays.
This project contains the steps and protocols for making a targeted plasmid insertion mutant in the non-pathogenic bacterium Myxococcus xanthus. Targeted plasmid insertions are used to inactivate Myxococcus xanthus genes. To make a targeted plasmid insertion, a fragment of the target gene is generated using PCR, the PCR fragment is cloned into a plasmid that carries an appropriate antibiotic resistance gene, and the plasmid is electroporated into wild-type M. xanthus cells. The plasmid can integrate into the chromosomal copy of the target gene by homologous recombination of the cloned PCR fragment. A single crossover yields kanamycin-resistant electroporants with two incomplete copies of the gene separated by vector DNA. Therefore, the plasmid is likely to inactivate the gene and its corresponding protein product.
Genome Analysis
The M. ruber project is an authentic research project in which students study biological processes in M. ruber that have never been studied in this organism. In this GENI module, students use the GENI-Annotation Collaboration Tool (GENI-ACT) to make function predictions of putative open reading frames in the M. ruber genome.
Genome Finishing
BioInformatics, Homology Modeling, and Protein Structure Analysis of Genes Related to Three Agrobact
In Silico bioinformatic analysis of duplicated genes in alphaproteobacteria. Students will independently investigate the similarities and differences between multiple copy genes that, by annotation, are predicted to have the same function.
Comparative Homology Modeling of ArgE Paralogs and Orthologs
Up to five ArgE paralogs are found in Agrobacterium genomes. ArgE genes have broad substrate specificities that allow catalysis of alternate substrates. Students are assigned a microbial ArgE gene with unknown structure. They construct a homology model with the I-Tasser web server and analyze the binding pocket to construct a hypothesis about that gene's substrate specificity.
Comparative Homology Modeling of ProC Paralogs and Orthologs
Up to three ProC paralogs are found in Agrobacterium genomes. ProC genes have broad substrate specificities that allow catalysis of alternate substrates. Students are assigned a microbial ProC gene with unknown structure. They construct a homology model with the I-Tasser web server and analyze the binding pocket to construct a hypothesis about that gene\\\\\\\\\\\\\\\'s substrate specificity.\\\\\\\\n
Genetic Structure of Siderocalin Paralogs
Bioinformatics workshop
Predicting Structure and Function of ProC Paralogs
Up to three ProC paralogs are found in Agrobacterium genomes. ProC genes have considerable sequence diversity for unknown reasons. Students are assigned a microbial ProC gene with unknown structure. They construct a homology model with the I-Tasser web server and analyze the primary and tertiary structures to develop specific functional hypotheses.
Predicting Structure and Function of Siderocalin Orthologs
The human lipocalin called siderocalin binds iron-siderophore complexes. Siderocalin orthologs grouped by sequence have unknown functions. Students are assigned a eukaryotic siderocalin ortholog with unknown structure. They construct a homology model with the I-Tasser web server and analyze the primary and tertiary structures to develop hypotheses regarding binding and enzymatic activity.
Preparative Protein Production from Cytoplasmic Expression
This lab will be a little different than what you’re used to, in large part because what you are called to do for the next six weeks is a little different than what most undergraduate labs call for -- you are being asked to both learn the steps of a “professional” protein preparation and also will use that knowledge to make a batch of protein for research purposes.\\\\\\\\n
Preparative Protein Production from Inclusion Bodies and Crystallization
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Preparative Protein Production from Periplasmic Expression
This lab will be a little different than what you’re used to, in large part because what you are called to do for the next six weeks is a little different than what most undergraduate labs call for -- you are being asked to both learn the steps of a “professional” protein preparation and also will use that knowledge to make a batch of protein for research purposes.
Protein-Protein Binding by Surface Plasmon Resonance
In this project a simple BIAcore instrument is used to measure protein-protein binding using surface plasmon resonance (a label-free biophysical technique). This allows students to compare different proteins and determine which bind most tightly and most quickly.
Using DNA barcoding to assess animal biodiversity in urban habitats
In this project, students will asses the degree of animal biodiversity in urban habitats, using both morphological features and DNA barcoding to characterize and classify invertebrate animal species.
Functional Genomics of Polyhydroxybutyrate Synthesis Genes in Agrobacterium Species
Automated genome annotation indicates the presence of PHB Bioysynthetic genes in Agrobacterium tumefaicens C58, Agrobacterium radiobacter K84, Agrobacterium vitis S4 & Agrobacterium rhizogenes A4. This project will determine if the PHB biosynthetic genes in Agrobacterium species are functional.
Functional Genomics of Arginine Biosynthesis in A. tumefaciens C58
- Annotation of the A. tumefaciens C58 genome shows two copies of argE. Which of the two copies provides the acetylornithine deacetylase activity to the bacterium? Both? Neither? The focus of this module will be to identify the functional copy of the argE gene.
Functional Genomics of Arginine Biosynthesis in Agrobacterium radiobacter K84
- Annotation of the A. tumefaciens C58 genome shows two copies of argE. Which of the two copies provides the acetylornithine deacetylase activity to the bacterium? Both? Neither? The focus of this module will be to identify the functional copy of the argE gene.
Functional Genomics of Arginine Biosynthesis in Agrobacterium rhizogenes A4
- Annotation of the A. tumefaciens C58 genome shows two copies of argE. Which of the two copies provides the acetylornithine deacetylase activity to the bacterium? Both? Neither? The focus of this module will be to identify the functional copy of the argE gene.
Functional Genomics of Arginine Biosynthesis in Agrobacterium vitis S4
- Annotation of the A. tumefaciens C58 genome shows two copies of argE. Which of the two copies provides the acetylornithine deacetylase activity to the bacterium? Both? Neither? The focus of this module will be to identify the functional copy of the argE gene.
Functional Genomics of Proline Biosynthesis in A. tumefaciens C58
- Annotation of the A. tumefaciens C58 genome shows two copies of proC. Which of the two copies provides the pyrroline-5-carboxylate reducatase activity to the bacterium? Both? Neither? The focus of this module will be to identify the functional copy of the proC gene.
Functional Genomics of Proline Biosynthesis in Agrobacterium radiobacter K84
- Annotation of the A. tumefaciens C58 genome shows two copies of proC. Which of the two copies provides the pyrroline-5-carboxylate reducatase activity to the bacterium? Both? Neither? The focus of this module will be to identify the functional copy of the proC gene.
Functional Genomics of Proline Biosynthesis in Agrobacterium rhizogenes A4
- Annotation of the A. tumefaciens C58 genome shows two copies of proC. Which of the two copies provides the pyrroline-5-carboxylate reducatase activity to the bacterium? Both? Neither? The focus of this module will be to identify the functional copy of the proC gene.
Functional Genomics of Proline Biosynthesis in Agrobacterium vitis S4
- Annotation of the A. tumefaciens C58 genome shows two copies of proC. Which of the two copies provides the pyrroline-5-carboxylate reducatase activity to the bacterium? Both? Neither? The focus of this module will be to identify the functional copy of the proC gene.
Proline biosynthesis in Agrobacterium - project development teams
This project will be used for advanced courses who are developing GENI research projects focused on the role and evolution of proline biosynthesis in Agrobacterium. Students in this course will create novel research projects to address this question, and post them on GENI for use by collaborators.
Characterizing a Myxococcus xanthus Targeted Plasmid Insertion Mutant
This project contains protocols for characterizing a Myxococcus xanthus targeted plasmid insertion mutant using fruiting body development, motility and sporulation efficiency assays.
Generating a Targeted Plasmid Insertion Mutant in Myxococcus xanthus
This project contains the steps and protocols for making a targeted plasmid insertion mutant in the non-pathogenic bacterium Myxococcus xanthus. Targeted plasmid insertions are used to inactivate Myxococcus xanthus genes. To make a targeted plasmid insertion, a fragment of the target gene is generated using PCR, the PCR fragment is cloned into a plasmid that carries an appropriate antibiotic resistance gene, and the plasmid is electroporated into wild-type M. xanthus cells. The plasmid can integrate into the chromosomal copy of the target gene by homologous recombination of the cloned PCR fragment. A single crossover yields kanamycin-resistant electroporants with two incomplete copies of the gene separated by vector DNA. Therefore, the plasmid is likely to inactivate the gene and its corresponding protein product.
Uncovering Novel Genetic Pathways in the Nematode Caenorhabditis elegans
Embryonic development in the nematode (roundworm) Caenorhabditis elegans, is being studied in an effort to understand how different cells acquire their specific fate. In particular, we using RNA interference to identify genetic pathways required for intestine formation.
Meiothermus ruber Genome Analysis Project
The M. ruber project is an authentic research project in which students study biological processes in M. ruber that have never been studied in this organism. In this GENI module, students use the GENI-Annotation Collaboration Tool (GENI-ACT) to make function predictions of putative open reading frames in the M. ruber genome.
Agrobacterium rhizogenes A4 Genome Project: Gap Closure
- Shotgun Sequencing = Gap Filling = Genome Finishing = Annotation = Functional Genomics
- Contigs obtained from initial genome sequencing assembly must be arranged in the correct order and the intervening regions of DNA determined via a process referred to as "gap filling".
Agrobacterium F5R19 Genome Project: Gap Closure
- Shotgun Sequencing = Gap Filling = Genome Finishing = Annotation = Functional Genomics
- Contigs obtained from initial genome sequencing assembly must be arranged in the correct order and the intervening regions of DNA determined via a process referred to as "gap filling".
Azotobacter vinelandii DJ Genome Project: Gap Closure
- Shotgun Sequencing = Gap Filling = Genome Finishing = Annotation = Functional Genomics
- Contigs obtained from initial genome sequencing assembly must be arranged in the correct order and the intervening regions of DNA determined via a process referred to as "gap filling".
GENI v3.6.2