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Full-Text Articles in Life Sciences

Formulation Of Hybrid Knowledge-Based/Molecular Mechanics Potentials For Protein Structure Refinement And A Novel Graph Theoretical Protein Structure Comparison And Analysis Technique, Aaron Maus Aug 2019

Formulation Of Hybrid Knowledge-Based/Molecular Mechanics Potentials For Protein Structure Refinement And A Novel Graph Theoretical Protein Structure Comparison And Analysis Technique, Aaron Maus

University of New Orleans Theses and Dissertations

Proteins are the fundamental machinery that enables the functions of life. It is critical to understand them not just for basic biology, but also to enable medical advances. The field of protein structure prediction is concerned with developing computational techniques to predict protein structure and function from a protein’s amino acid sequence, encoded for directly in DNA, alone. Despite much progress since the first computational models in the late 1960’s, techniques for the prediction of protein structure still cannot reliably produce structures of high enough accuracy to enable desired applications such as rational drug design. Protein structure refinement ...


Designing Computational Biology Workflows With Perl - Part 2, Esma Yildirim May 2019

Designing Computational Biology Workflows With Perl - Part 2, Esma Yildirim

Open Educational Resources

This material briefly reintroduces the DNA double Helix structure, explains SNP and INDEL mutations in genes and describes FASTA, FASTQ, BAM and VCF file formats. It also explains the index creation, alignment, sorting, marking duplicates and variant calling steps of a simple preprocessing workflow and how to write a Perl script to automate the execution of these steps on a Virtual Machine Image.


Designing Computational Biology Workflows With Perl - Part 1, Esma Yildirim May 2019

Designing Computational Biology Workflows With Perl - Part 1, Esma Yildirim

Open Educational Resources

This material introduces Linux File System structures and demonstrates how to use commands to communicate with the operating system through a Terminal program. Basic program structures and system() function of Perl are discussed. A brief introduction to gene-sequencing terminology and file formats are given.


Designing Computational Biology Workflows With Perl - Part 1, Esma Yildirim May 2019

Designing Computational Biology Workflows With Perl - Part 1, Esma Yildirim

Open Educational Resources

This material introduces the AWS console interface, describes how to create an instance on AWS with the VMI provided, connect to that machine instance using the SSH protocol. Once connected, it requires the students to write a script to enter the data folder, which includes gene-sequencing input files and print the first five line of each file remotely. The same exercise can be applied if the VMI is installed on a local machine using virtualization software (e.g. Oracle VirtualBox). In this case, the Terminal program of the VMI can be used to do the exercise.


Designing Computational Biology Workflows With Perl - Part 2, Esma Yildirim May 2019

Designing Computational Biology Workflows With Perl - Part 2, Esma Yildirim

Open Educational Resources

This material introduces the AWS console interface, describes how to create an instance on AWS with the VMI provided and connect to that machine instance using the SSH protocol. Once connected, it requires the students to write a script to automate the tasks to create VCF files from two different sample genomes belonging to E.coli microorganisms by using the FASTA and FASTQ files in the input folder of the virtual machine. The same exercise can be applied if the VMI is installed on a local machine using virtualization software (e.g. Oracle VirtualBox). In this case, the Terminal program ...


Designing Computational Biology Workflows With Perl - Part 1 & 2, Esma Yildirim May 2019

Designing Computational Biology Workflows With Perl - Part 1 & 2, Esma Yildirim

Open Educational Resources

This manual guides the instructor to combine the partial files of the virtual machine image and construct sequencer.ova file. It is accompanied by the partial files of the virtual machine image.


Mrub_3018 Is Orthologous To E. Coli B2759 (Casb), Kyle Parker, Dr. Lori Scott Feb 2019

Mrub_3018 Is Orthologous To E. Coli B2759 (Casb), Kyle Parker, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We studied the biological activity of the Mrub_3018 gene, which we hypothesize is orthologous to E. coli gene B2759. We predicted that Mrub_3018(DNA coordinates 3057916… 3058524) encodes the protein CasB. CasB is a protein in the CRISPR CASCADE that will function as a structural protein. When the rest of the proteins form an “S” formation CasB will connect the front and back of the “S” creating a back bone for the structure. It will help bind ...


Mrub_3015 Is Orthologous To The B2757 Gene Found In Escherichia Coli Coding For Casd, Ramona Collins, Dr. Lori Scott Feb 2019

Mrub_3015 Is Orthologous To The B2757 Gene Found In Escherichia Coli Coding For Casd, Ramona Collins, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of the gene Mrub_3015, which we hypothesize is a component of the CRISPR-Cas prokaryotic defense system. We predict that Mrub_3015 (DNA coordinates 3055550...3056245) encodes the the CRISPR-associated protein cas5, which is integral in maintaining the crRNA-DNA structure, keeping the complex from base pairing with the target phage DNA. Our hypothesis is supported by identical hits for Mrub_3015 and b2527 to the KEGG, Pfam, TIGRfam, CDD and PDB databases as well as ...


Effects Of Temperature On Crispr/Cas System, Eddie Beckom, Dr. Lori Scott Jan 2019

Effects Of Temperature On Crispr/Cas System, Eddie Beckom, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the effect of temperature on the complexity of CRISPR/Cas systems in bacterial organisms across temperature classifications. We predict that temperature extremes would result in CRISPR/Cas systems with multiple operons, repeating cas genes, and complex systems. CRISPR/Cas systems can be classified into three types with a number of subtypes based on the CRISPR-associated genes, cas genes, present in a given organism. Our hypothesis is supported by the presence of multiple operons in thermophilic ...


Mrub_3014 Is Orthologous To B2756, Samir Abdelkarim, Dr. Lori Scott Jan 2019

Mrub_3014 Is Orthologous To B2756, Samir Abdelkarim, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of the gene Mrub_3014, which we hypothesize is a component of the CRISPR-Cas prokaryotic defense system. We predict that Mrub_3014 (DNA coordinates 3054943..3055575) encodes CRISPR-associated protein Cse3/case which function as an endonuclease. Our hypothesis is supported by identical hits for Mrub_3014 and b2756 to the KEGG, Pfam, TIGRfam, CDD and PDB databases, as well as a low E-value for a pairwise NCBI BLAST comparison. Both protein products are predicted to ...


M. Ruber Mrub_3013 Is Orthologous To E. Coli B2755, Laura Butcher, Dr. Lori Scott Jan 2019

M. Ruber Mrub_3013 Is Orthologous To E. Coli B2755, Laura Butcher, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of gene Mrub_3013, which we hypothesize is orthologous to b2755 in E. coli K12 MG1655 (a.k.a. Cas1). We investigated the biological function of a gene with the M. ruber locus tag of Mrub_3013, which we hypothesize is a component of the CRISPR-Cas prokaryotic defense system in M. ruber. We predict that Mrub_3013 (DNA coordinates 3,053,978-3,054,940) encodes the protein Cas1 which as part of the CRISPR-Cas system ...


An Investigation Into The Relationship Between Mrub_3013, Mrub_1477, And Mrub_0224: Are They Paralogs?, Melette Devore, Dr. Lori Scott Jan 2019

An Investigation Into The Relationship Between Mrub_3013, Mrub_1477, And Mrub_0224: Are They Paralogs?, Melette Devore, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of mrub_3013 and the nature of its relationship with mrub_1477 and mrub_0224. We hypothesized that mrub_3013 is orthologous to b2755 in E. coli K12 MG1655 (a.k.a. cas1). We predict that mrub_3013 encodes the enzyme Cas1, which is involved in spacer acquisition in the CRISPR-Cas prokaryotic defense system. Our hypothesis is supported by identical hits for b2755, mrub_3013, mrub_1477, and mrub_0224 from the CDD and Pfam databases and highly similar hits ...


Mrub_3020, A Paralog Of Mrub_1489, Is Orthologous To E. Coli Casc (Locus Tag B2761), Alfred Dei-Ampeh, Dr. Lori Scott Jan 2019

Mrub_3020, A Paralog Of Mrub_1489, Is Orthologous To E. Coli Casc (Locus Tag B2761), Alfred Dei-Ampeh, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological functions of two genes: mrub_3020 and mrub_1489. We make two hypotheses in this investigation: a) mrub_3020 is orthologous to the gene b2761 in E. coli K12 MG1655 (a.k.a. casC); b) mrub_1489 is a paralog of mrub_3020. We also predict that the two genes encode unique proteins: mrub_3020 with DNA coordinates 3060491…3063190 encodes a CRISPR – associated helicase (Cas3) that supports the Cascade complex of the CRISPR – Cas adaptive immune system by ...


Evaluating Predixcan’S Ability To Predict Differential Expression Between Alcoholics And Non-Alcoholics, John E. Drake Jr Jan 2019

Evaluating Predixcan’S Ability To Predict Differential Expression Between Alcoholics And Non-Alcoholics, John E. Drake Jr

Theses and Dissertations

PrediXcan is a recent software for the imputation of gene expression from genotype data alone. Using an overlapping set of transcriptome datasets from postmortem brain tissues of donors with alcohol use disorder and neurotypical controls, which were generated by two different platforms (e.g., Arraystar and Affymetrix), and an additional unrelated transcriptome dataset from lung tissue, we sought to evaluate PrediXcan’s ability to impute gene expression and identify differentially expressed genes. From the Arraystar platform, 1.3% of matched genes between the measured and imputed expression had a Pearson correlation ≥ 0.5. Our attempt to replicate this finding using ...


Algorithms For Synteny-Based Phylostratigraphy And Gene Origin Classification, Zebulun Arendsee Jan 2019

Algorithms For Synteny-Based Phylostratigraphy And Gene Origin Classification, Zebulun Arendsee

Graduate Theses and Dissertations

With every newly sequenced species we discover hundreds of novel protein coding genes. Many of these "orphan" genes have been experimentally proven to have dramatic functions in development, sexual dimorphism, pathogen resistance, and social traits like symbiosis. Whereas in the past, researchers viewed genes as the product of continuous variation acting on ancient material, we now know that novel genes may arise de novo from non-genic sequence. Thus evolutionary experimentation is not limited to tweaking existing genes or their regulatory patterns. Any orphan genes that arose in the distant past, should appear today as lineage-specific genes (or gene families). The ...


Saccharomyces Genome Database & Uniprot Bioinformatics Analysis, Ray A. Enke Dec 2018

Saccharomyces Genome Database & Uniprot Bioinformatics Analysis, Ray A. Enke

Ray Enke Ph.D.

This in class activity introduces basic bioinformatics analysis using the Saccharomyces Genome Database (SGD) and the UniProt Database. The yeast URA3 gene is studied in this activity, however, any other yeast gene can be substituted. This activity is designed for novice instructors and students for implementation into core biology lecture or lab courses.