Life Sciences Commons^™

Future Directions In The Molecular Breeding Of Forage And Turf, G. C. Spangenberg, J. W. Forster, D. Edwards, U. John, A. Mouradov, M. Emmerling, J. Batley, S. Felitti, N. O. I. Cogan, K. F. Smith, M. P. Dobrowolski

IGC Proceedings (1997-2023)

Key points

1. Molecular breeding of forage and turf plants and their endosymbionts has entered the post-genomic era with a large amount of structural genomics information and genomic resources available for key forage and turf species and relevant model systems.
2. A primary future challenge is the conversion of this information into useful functional knowledge for the development of molecular breeding technologies and products that address a range of high impact outcome scenarios in forage and turf.
3. High-throughput approaches for spatial and temporal analysis, from genome to phenome, and the respective data integration in a systems biology context will be critical for …

A Computational Pipeline For The Development Of Comparative Anchor Tagged Sequence (Cats) Markers, J. Schauser, J. Fredslund, L. Heegaard Madsen, Niels Sandal, Jens Stougaard

IGC Proceedings (1997-2023)

Key points:

1. Molecular markers that allow the transfer of map information from one species to another are vital in comparative genetics.
2. To identify potential anchor marker sequences more efficiently, we have established a bioinformatic pipeline that combines multi-species EST- and genome- sequence data.
3. Taking advantage of information from a few related species, comparative EST sequence analysis identifies evolutionary conserved sequences in less well-characterised species in the same family.
4. Alignment of evolutionary conserved EST sequences with corresponding genomic sequences defines sets of PCR primer sites flanking introns.
5. Markers identified by this procedure will be readily transferable to other species since they …

Gene Annotation Of The Hypothetical Protein-Coding Genes Of Yersinia Pestis, Bethany Wilkinson, Celestino Velasquez

Research Symposium

Technological advances within the past two decades have allowed researchers the capacity to sequence and analyze any genome. However, while many organisms have had their genomes sequenced, hardly any have been manually interpreted to propose the organism’s hypothetical protein-coding genes’ functions. The primary amino acid sequences of the organism’s genes can be used to offer functions for the organism’s proteins. Online programs such as BLAST, T-COFFEE, MUSCLE, TMHMM, SignalP, Phobius, and PSORTb, identify several properties such as conserved domains, protein families, protein conformations, signal peptides, and transmembrane regions of the sequences. These elements can be examined to provide insight into …

Gene Annotation Of The Hypothetical Protein-Coding Genes Of Coxiella Burnetii, Jason Salvato, Celestino Velasquez

Research Symposium

Genetic information of organisms and microorganisms has become readily accessible due to advances in genomic sequencing and bioinformatic technology. Despite these advances, there are numerous organisms with genome sequences that have yet to be annotated. Many of these genome sequences require manual annotation, which can uncover hypothetical protein-coding genes. Through the use of publicly available online bioinformatics tools, such as BLAST, T- COFFEE, TMHMM, SignalP, Phobius, and PSORTb, the functions of hypothetical protein- coding genes can be predicted from primary amino acid sequences. Two clusters of properties that aid in determining and predicting the hypothetical genes involve sequence similarity and …

Using Active Learning To Build A Foundation For Bioinformatics Training., Stacey E. Wahl Ph.D., Amy L. Olex Ms

Transforming Libraries for Graduate Students

As Health Sciences Libraries evolve, the support they offer graduate students has evolved to incorporate many aspects of the research life cycle. At Tompkins-McCaw Library for the Health Sciences, we have partnered with the Wright Center for Clinical and Translational Research to offer training workshops for graduate students who are interested in using bioinformatics to plan, analyze, or execute scientific experiments. We offer two series: 1) an 8-week, 1-hour per week seminar series providing a general overview of available techniques and 2) a week-long intensive, two hours per session, series on utilizing free databases from the National Center for Biotechnology …

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 …

Mutations In Braf Are Associated With Higher Levels Of Immune Infiltrates In Microsatellite-Stable Colon Cancer, Jake Rubin, Eduard Porta Parto

GW Research Days 2016 - 2020

While BRAF is among the most well-established oncogenes in human cancers, more recently it has garnered attention for its role in suppressing antitumor immunity, especially in melanoma. Because tumor-infiltrating lymphocyte (TIL) density is strongly prognostic in colorectal cancer (CRC)⁷, we decided to investigate the connection between TIL density and the BRAF-activating V600E mutation in CRC.

We used ESTIMATE to quantify immune infiltrate in samples from the TCGA colon adenocarcinoma (COAD) dataset (n = 216). This is an algorithm that uses the gene-expression signature of 141 immune-related genes to infer the presence of immune cells in the tumor infiltrate. …

Confirmation Of The Function Of Mrub1080 As Γ-Glutamyl Kinase (Prob) In Meiothermus Ruber, Cale J. Mccormick, Dr. Lori Scott

Celebration of Learning

This project is part of the Meiothermus ruber genome analysis project, which uses wet lab procedures and computational analysis to gather evidence of orthologous genes between Escherichia coli and Meiothermus ruber. In previous work, bioinformatics evidence supported the hypothesis that the gene Mrub1080 was an ortholog of E. coli proB. We investigated the biological function of Meiothermus ruber genes proB and proBA using the complementation assay. However, functional analysis proved inconclusive. For this particular research project, we confirmed that weakly complementing E. coli proB- null strains actually contained the desired M. ruber proB and proBA genes (inserted into a pKt1 …

Can Collection Specimen Data Reveal Temporal Shifts Due To Climate Change?, Julie Maurer

Scholars Week

Climate change is altering the distribution, behavior, and migration patterns of many species. Typically, these responses are documented studies in which standardized methods are used to collect population or behavioral data over several years. Multi-decade studies are rare and few predate the recent dramatic increase in global temperatures, limiting our ability to understand long-term consequences of climate change. Natural history (NH) collections offer a potential solution; they hold a wealth of species occurrence documentation spanning from decades to centuries. However, because the sampling of natural history collectors is spatially and temporally haphazard, it remains unclear whether NH data is useful …

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 …

Artificial Intelligence – I: Dna Innovate: Visualizing Dna Sequences, M. Shahzad, Nazish Alia, Sadaf Mahmood

International Conference on Information and Communication Technologies

Exploring DNA sequences is really important in the context of bioinformatics, as it maintains every function of our body - being the building block. Bioinformaticians have unfolded numerous features of this sequence and it is probable that still there are more features to discover within DNA sequence. To get the desired information from DNA sequence quickly, depends largely on its presentation. It is desirable to investigate the sequence in visual or textual form, as needed. In this paper, we put forward a software tool which can be helpful in exploring DNA features and observing it in different representations (simultaneously or …