Life Sciences Commons^™

Molecular Phylogeny Implemented In An Introductory Plant Classification Course, Chao Cai, Jo Ann Banks

Libraries Faculty and Staff Presentations

Plant classification is one of the core components in undergraduate programs related to plant sciences. Traditionally plant classification courses primarily introduce morphology-based taxonomy because of practical needs in the field. However, the publication of new plant classification systems by Angiosperm Phylogeny Group (APG) using molecular phylogeny methods leads to the trends of using molecular evidence (DNA barcode) for plant identification. In our introductory plant classification course, we included a two-week module (lectures and labs) to introduce key concepts and fundamental skills in molecular phylogeny. Week 1 included concepts of evolutionary tree thinking, data mining in NCBI using BLAST search, and …

Genome Analysis Of Multiple Mycobacteriophage, Emily Kerstiens, Kari Clase, Yi Li, Gillian Smith, Sarah Bell

The Summer Undergraduate Research Fellowship (SURF) Symposium

Bacteriophage are viruses that infect and kill bacteria. They can be used as treatments for antibiotic resistant bacterial infections, but more knowledge is needed about phage and how they interact with bacteria in order to develop safe and effective phage therapy treatments. This study examines the genomes of eighteen mycobacteriophage that were isolated from the environment on and surrounding Purdue University. Phage genomes were annotated using several bioinformatics software, including DNA Master, GeneMark, and PECAAN. Evidence was examined to determine the correct location within the genome and the potential function. Approximately two thousand genes were annotated in this study. A …

Investigations On The Vampire Moth Genus Calyptra Ochsenheimer, Incorporating Taxonomy, Life History, And Bioinformatics (Lepidoptera: Erebidae: Calpinae), Julia L. Snyder

Open Access Theses

The seventeen species and two subspecies described in the genus Calyptra are known to be obligate fruit piercers, with some species being of economic importance. Males within the genus have not only been observed piercing their fruit hosts, but have also been documented to occasionally feed on mammalian blood. The genetic and ecological mechanisms contributing to host preference for either plant or vertebrate hosts in this lineage are unknown. Thus, the focus of this study was to investigate the chemosensory systems between and among Calyptra species exhibiting differential feeding strategies. Before investigating the chemosensory systems within Calyptra, the taxonomy …

Dynamic Regulation Of Dna Demethylation And Rna-Directed Dna Methylation In Arabidopsis, Kai Tang

Open Access Dissertations

DNA methylation is an important epigenetic mark present in many eukaryotes, and is involved in many crucial biological processes, such as gene imprinting, regulation of gene expression, and genome stability. Proper genomic DNA methylation patterns are achieved through the concerted action of DNA methylation and demethylation pathways. In the model plant species Arabidopsis thaliana, ROS1 (REPRESSOR OF SILENCING 1) is one of the DNA demethylases and the key component in the demethylation pathway. Dysfunction of ROS1 leads to increase in DNA methylation level at thousands of genomic loci. However, the features of ROS1 targets are not well understood. In the …

The Application Of The Hadoop Software Framework In Bioinformatics Programs, Dan Wang

Open Access Dissertations

The project described in this dissertation proposal attempted to improve the efficiency and scalability performance as well as the usability and user experience of three Bioinformatics applications - DNA/peptide sequence similarity comparison, digital DNA library subtraction, and DNA/peptide sequence de-duplication - by 1) adopting the Hadoop MapReduce algorithms and distributed file system and 2) implementing the fully automated Hadoop programs into a user friendly graphical user interface (GUI). In addition, the researcher was also interested in investigating the advantages and limitations of applying the Hadoop software framework as a general methodology in parallelizing Bioinformatics programs.

After considering the original calculation …

Graphical User Interface On Analysis Of Mechanics And Dynamics Of Biopolymers In Living Cells, Peter D. Russel, Shubham Agrawal, Taeyoon Kim, Abdel-Rahman Hassan

The Summer Undergraduate Research Fellowship (SURF) Symposium

The mechanical properties of cells depend on the qualities of filamentous-actin (f-actin for short), among other cytoskeletal polymers. The ability to quickly determine f-actin qualities in a sample will help cellular biologists with cytoskeletal protein research. The goal of this project is to create a Matlab program which would allow researchers to determine, with limited manual input, the average filament length and persistence lengths of selected filaments. Through the graphical user interface, the user loads the image stack and can optimize the tracking result by altering several expectations of the program such as the expected contrast between the filament and …

Analysis Of Mechanics And Dynamics Of Biopolymers In Living Cells, Shubham Agrawal, Peter D. Russel, Abdel-Rahman Hassan, Taeyoon Kim

The Summer Undergraduate Research Fellowship (SURF) Symposium

F-actin polymers in the cytoskeleton provide mechanical strength and deformability to cells. Thus, understanding their dynamic responses to intracellular and extracellular cues is of critical importance for studying the biological and mechanical behaviors of cells. Unfortunately, to date, no computer software can provide researchers with adequate means to measure these responses since in vivo F-actin cytoskeleton is quite dynamic and complex unlike in vitro actin networks. We aim at developing a tool which would allow researchers to semi-automatically analyze time-lapse microscope images of these F-actin polymers and thus evaluate the length and stochastic dynamics of F-actins (filament elongation, shrinkage and …