Life Sciences Commons^™

Motif-Cluster: A Spatial Clustering Package For Repetitive Motif Binding Patterns, Mengyuan Zhou

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Previous efforts in using genome-wide analysis of transcription factor binding sites (TFBSs) have overlooked the importance of ranking potential significant regulatory regions, especially those with repetitive binding within a local region. Identifying these homogenous binding sites is critical because they have the potential to amplify the binding affinity and regulation activity of transcription factors, impacting gene expression and cellular functions. To address this issue, we developed an open-source tool Motif-Cluster that prioritizes and visualizes transcription factor regulatory regions by incorporating the idea of local motif clusters. Motif-Cluster can rank the significant transcription factor regulatory regions without the need for experimental …

Sequence-Based Bioinformatics Approaches To Predict Virus-Host Relationships In Archaea And Eukaryotes, Yingshan Li

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Viral metagenomics is independent of lab culturing and capable of investigating viromes of virtually any given environmental niches. While numerous sequences of viral genomes have been assembled from metagenomic studies over the past years, the natural hosts for the majority of these viral contigs have not been determined. Different computational approaches have been developed to predict hosts of bacteria phages. Nevertheless, little progress has been made in the virus-host prediction, especially for viruses that infect eukaryotes and archaea. In this study, by analyzing all documented viruses with known eukaryotic and archaeal hosts, we assessed the predictive power of four computational …

A Pipeline To Generate Deep Learning Surrogates Of Genome-Scale Metabolic Models, Achilles Rasquinha

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Genome-Scale Metabolic Models (GEMMs) are powerful reconstructions of biological systems that help metabolic engineers understand and predict growth conditions subjected to various environmental factors around the cellular metabolism of an organism in observation, purely in silico. Applications of metabolic engineering range from perturbation analysis and drug-target discovery to predicting growth rates of biotechnologically important metabolites and reaction objectives within dierent single-cell and multi-cellular organism types. GEMMs use mathematical frameworks for quantitative estimations of flux distributions within metabolic networks. The reasons behind why an organism activates, stuns, or fluctuates between alternative pathways for growth and survival, however, remain relatively unknown. GEMMs …

Comparative Analyses Of De Novo Transcriptome Assembly Pipelines For Diploid Wheat, Natasha Pavlovikj

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Gene expression and transcriptome analysis are currently one of the main focuses of research for a great number of scientists. However, the assembly of raw sequence data to obtain a draft transcriptome of an organism is a complex multi-stage process usually composed of pre-processing, assembling, and post-processing. Each of these stages includes multiple steps such as data cleaning, error correction and assembly validation. Different combinations of steps, as well as different computational methods for the same step, generate transcriptome assemblies with different accuracy. Thus, using a combination that generates more accurate assemblies is crucial for any novel biological discoveries. Implementing …

Ubjective Information And Survival In A Simulated Biological System, Tyler S. Barker, Massimiliano Pierobon, Peter J. Thomas

School of Computing: Faculty Publications

Information transmission and storage have gained traction as unifying concepts to characterize biological systems and their chances of survival and evolution at multiple scales. Despite the potential for an information-based mathematical framework to offer new insights into life processes and ways to interact with and control them, the main legacy is that of Shannon’s, where a purely syntactic characterization of information scores systems on the basis of their maximum information efficiency. The latter metrics seem not entirely suitable for biological systems, where transmission and storage of different pieces of information (carrying different semantics) can result in different chances of survival. …

Hyperseed: An End-To-End Method To Process Hyperspectral Images Of Seeds, Tian Gao, Anil Kumar Nalini Chandran, Puneet Paul, Harkamal Walia, Hongfeng Yu

School of Computing: Faculty Publications

High-throughput, nondestructive, and precise measurement of seeds is critical for the evaluation of seed quality and the improvement of agricultural productions. To this end, we have developed a novel end-to-end platform named HyperSeed to provide hyperspectral information for seeds. As a test case, the hyperspectral images of rice seeds are obtained from a high-performance line-scan image spectrograph covering the spectral range from 600 to 1700 nm. The acquired images are processed via a graphical user interface (GUI)-based open-source software for background removal and seed segmentation. The output is generated in the form of a hyperspectral cube and curve for each …

Introduction To The R-Package: Usdampr, Elliott James Dennis, Bowen Chen

Extension Farm and Ranch Management News

Why the Need for the Package? In the 1990’s, concern over growing packer concentration and a hog industry market shock resulted in discontent among producers and packers. As a result, the United States Congress passed the Livestock Mandatory Reporting Act of 1999 (1999 Act) [Pub. L. 106-78, Title IX] which is required to be reauthorized every five years. See here for a full history of the Livestock Mandatory Reporting Background.

Market reports were publicly issued in the form of .txt files with varying frequency from April 2000 to April 2020. Current and historical data were also housed in a USDA-AMS …

Repositories For Taxonomic Data: Where We Are And What Is Missing, Aurélian Miralles, Teddy Bruy, Katherine Wolcott, Mark D. Scherz, Dominik Begerow, Bank Beszteri, Michael Bonkowski, Janine Felden, Birgit Gemeinholzer, Frank Glaw, Frank Oliver Glöckner, Oliver Hawlitschek, Ivaylo Kostadinov, Tim W. Nattkemper, Christian Printzen, Jasmin Renz, Nataliya Rybalka, Marc Stadler, Tanja Weibulat, Thomas Wilke, Susanne S. Renner, Miguel Vences

Harold W. Manter Laboratory: Library Materials

Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000–20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4,113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use …

"Flagella Base Model" And "Flagellin Monomer", Brandon Lasalle, Rebecca Roston

3-D Printed Model Structural Files

"Flagella Base Model" and "Flagellin monomer"

Description: This is a teaching model of the proteins that make a bacterial flagella. All models are depicted in space-fill. The Flagellin monomer and the Flagella base can slot together to show protein quaternary structure and filamentous protein assembly.

Printable models are already uploaded to Shapeways.com in the MacroMolecules shop under the names "Flagella Base Model" and "Flagellin monomer".

This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Processed Versatile Plastic (Strong & Flexible Plastic).

Model designer: Brandon Lasalle Authors: Brandon Lasalle and Rebecca Roston …

A Data-Driven Approach For Detecting Stress In Plants Using Hyperspectral Imagery, Suraj Gampa

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

A phenotype is an observable characteristic of an individual and is a function of its genotype and its growth environment. Individuals with different genotypes are impacted differently by exposure to the same environment. Therefore, phenotypes are often used to understand morphological and physiological changes in plants as a function of genotype and biotic and abiotic stress conditions. Phenotypes that measure the level of stress can help mitigate the adverse impacts on the growth cycle of the plant. Image-based plant phenotyping has the potential for early stress detection by means of computing responsive phenotypes in a non-intrusive manner. A large number …

Amino Acid Pop-Set: Model File Name: Amino-Acid-Wgrp-Pop_Sc3.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model for protein primary structure. It consists of four amino acids (tryptophan, proline, arginine, and glycine) depicted in stick and space-fill representations, five peptide bonds depicted in space-fill, and an N-terminus and a C-terminus depicted in space-fill. It is designed so that students can make various peptides to explore the amount of space of the electron clouds of the amino acids and bonds, and explore the psi and phi angles for the peptides. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Amino acid pop-set”. This model has …

Lipoprotein Signal Peptidase Ii: Model File Name: 5dir-Lipoii-Reps_Sc1-5.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of lipoprotein signal peptidase II (PDB: 5DIR). It is designed with different regions of the protein depicted in space-filling, ribbon, stick, and backbone-only representations to explore protein secondary structure and illustrate how much space the protein takes up. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Lipoprotein signal peptidase II” and is intended to accompany the “Crambin”, “Cytochrome c” and “3 water molecules” models. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in …

3 Water Molecules: Model File Name: 3hoh-Final.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of 3 water molecules depicted in space-fill. It is designed to the same scale as the “Lipoprotein signal peptidase II”, “Crambin”, and “Cytochrome c” models to illustrate the amount of space taken up by proteins. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “3 water molecules” and is intended to accompany the “Lipoprotein signal peptidase II”, “Crambin”, and “Cytochrome c” models. This model has been printed successfully using these parameters on Shapeways’ laser sintering …

Crambin: Model File Name: 2fd7-Crambin-Stick_Sc1-5.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of cytochrome c (PDB: 2FD7). It is designed in a stick representation to explore protein secondary structure and how much space the protein takes up. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Crambin” and is intended to accompany the “Lipoprotein signal peptidase II”, “Cytochrome c”, and “3 water molecules” models. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Processed Versatile Plastic (Strong & Flexible Plastic).

Cytochrome C: Model File Name: 1b7v-Cytc-Stick_Sc1-5.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of cytochrome c (PDB: 1B7V). It is designed in a stick representation to explore protein secondary structure and how much space the protein takes up. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Cytochrome c” and is intended to accompany the “Lipoprotein signal peptidase II”, “Crambin”, and “3 water molecules” models. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Processed Versatile Plastic (Strong & Flexible Plastic).

Human Hexokinase I - Allosteric Regulation: Model File Name: 1dgk-Editb22-Allostery_Sc06.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of human Hexokinase I in a surface representation with small molecules ADP and G6P included (PDB: 1DGK). It is designed to be hollow with a lever to mimic allosteric regulation. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Human Hexokinase I - Allosteric regulation model”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Processed Versatile Plastic (Strong & Flexible Plastic).

Recta: Regulon Identification Based On Comparative Genomics And Transcriptomics Analysis, Xin Chen, Anjun Ma, Adam Mcdermaid, Hanyuan Zhang, Chao Liu, Huansheng Cao, Qin Ma

School of Computing: Faculty Publications

Regulons, which serve as co-regulated gene groups contributing to the transcriptional regulation of microbial genomes, have the potential to aid in understanding of underlying regulatory mechanisms. In this study, we designed a novel computational pipeline, regulon identification based on comparative genomics and transcriptomics analysis (RECTA), for regulon prediction related to the gene regulatory network under certain conditions. To demonstrate the effectiveness of this tool, we implemented RECTA on Lactococcus lactis MG1363 data to elucidate acid-response regulons. A total of 51 regulons were identified, 14 of which have computational-verified significance. Among these 14 regulons, five of them were computationally predicted to …

Model File Name: 1ehz-Trna(Thick).Stl, Michelle Howell, Karin Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1ehz-tRNA(thick).stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of Phe-tRNA in a thick stick-representation (PDB: 1ehz), designed to go with a teaching module comparing DNA and RNA basic structures and functions. The printable model is already uploaded to Shapeways.com under the name “tRNA-Phe small”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following materials: Strong & Flexible Plastic and Elasto Plastic.

Model File Name: 1lmb-Dbd-Tfmono.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1lmb-DBD-TFmono.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of the DNA binding domain of a Lambda repressor transcription factor monomer that accompanies the full color DNA helix (PDB: 1lmb). It is in a cartoon ribbon representation with key amino acid residues in stick representation to highlight interactions with the DNA. This model is designed to accompany a teaching module illustrating transcription factor-DNA binding. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Lambda TF DBD”. This model has been printed …

Model File Name: 1ehz-Trna(Thin-Big).X3d, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1ehz-tRNA(thin-big).x3d

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of Phe-tRNA in a large, but thin stick-representation (PDB: 1ehz), designed to go with a teaching module comparing DNA and RNA basic structures and functions. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Full color Phe-tRNA (1ehz)”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Strong & Flexible Plastic.

Model File Name: 1lmb-Dnalong_Fordimer-Test6b.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1lmb-DNAlong_fordimer-test6b.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of the 19-bp segment of DNA to which Lambda repressor transcription factor interacts (PDB: 1lmb). It is in a stick representation and has been designed with sites to add magnets to illustrate binding interactions with the transcription factor. Sphere magnets with a 1/8” diameter can be purchased separately from K&J Magnets. The model can interact with the dimer form of the transcription factor. This model is designed to accompany a teaching module illustrating transcription factor-DNA binding. The printable model …

Model File Name: 1lmb-Tfdimer-Mags-Joints-Jnd-Sc1-8-Parts-V4b.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1lmb-TFdimer-mags-joints-jnd-sc1-8-parts-v4b.stl

Additional files: 1lmb-Lys-Ser-extras-v4b.stl and 1lmb-TFdimer-Leu-v4b.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a ribbon and stick representation of the transcription factor lambda repressor (PDB: 1lmb). Key amino acid residues are in stick representation to illustrate the interactions between the repressor and the DNA to which it binds. Some of these residues have been designed with sites to add magnets to illustrate these interactions. Sphere magnets with a 1/8” diameter can be purchased separately from K&J Magnets. Some of the residues can be interchanged with other …

Model File Name: Dna-294bp-Magnet-Supercoil.Stl, Michelle Howell, Karin V. Van Dijk, Kalika Mahato, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNA-294bp-magnet-supercoil.stl

Authors: Michelle E Howell, Karin van Dijk, Kalika Mahato, Rebecca L Roston

This is a teaching model of a long, thin representation of double stranded DNA (294 bp). The DNA model has small sites on the ends where the user can glue magnets to mimic circular DNA, and to aid in manipulating the model. Disc magnets with a diameter of 1/8” or 1/10” and thickness of 1/16” can be purchased online from K&J Magnetics and glued into the magnet sites. The model is designed to go with a teaching module on DNA supercoiling. The model can …

Model File Name: Dna-294bp-Handle-Supercoil.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNA-294bp-handle-supercoil.stl

Authors: Michelle E Howell, Karin van Dijk, Kalika Mahato, Rebecca L Roston

This is a teaching model of a long, thin representation of double stranded DNA (294 bp). The DNA model has small handles on the ends to aid in holding and manipulating the model. The model is designed to go with a teaching module on DNA supercoiling. The model can be accompanied by Nucleosome and H1 histone models to demonstrate DNA packaging in the cell. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “294bp DNA (handles)”. …

Model File Name: Dna-420bp-Handle-Supercoil.Stl, Michelle Howell, Karin V. Van Dijk, Kalika Mahato, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNA-420bp-handle-supercoil.stl

Authors: Michelle E Howell, Karin van Dijk, Kalika Mahato, Rebecca L Roston

This is a teaching model of a long, thin representation of double stranded DNA (420 bp). The DNA model has small handles on the ends to aid in holding and manipulating the model. The model is designed to go with a teaching module on DNA supercoiling. The model can be accompanied by Nucleosome and H1 histone models to demonstrate DNA packaging in the cell. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “420bp DNA (handles)”. …

Model File Name: Dnalong-3pc-Lego.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNAlong-3pc-Lego.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a stick representation of the DNA to which the transcription factor lambda repressor binds (PDB: 1lmb). This model can be adapted to accompany a teaching module illustrating transcription factor-DNA binding. The model has been designed in 3 parts that can be joined together by Lego®-style junctions. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Lego DNA with GCbp”. This model has been printed successfully using these parameters on Shapeways’ laser …

Model File Name: Dna-420bp-Magnet-Supercoil.Stl, Michelle Howell, Karin V. Van Dijk, Kalika Mahato, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNA-420bp-magnet-supercoil.stl

Authors: Michelle E Howell, Karin van Dijk, Kalika Mahato, Rebecca L Roston

This is a teaching model of a long, thin representation of double stranded DNA (420 bp). The DNA model has small sites on the ends where the user can glue magnets to mimic circular DNA, and to aid in manipulating the model. Disc magnets with a diameter of 1/8” or 1/10” and thickness of 1/16” can be purchased online from K&J Magnetics and glued into the magnet sites. The model is designed to go with a teaching module on DNA supercoiling. The model can …

Model File Name: H1-Protein.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: H1-protein.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a crude representation of an H1-protein intended to accompany the nucleosome and a long, thin double stranded DNA helix model in order to illustrate DNA packaging and supercoiling. This model is designed to go with a teaching module on DNA supercoiling. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Histone H1 protein”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following materials: Strong …

Model File Name: Dna-Short-Helix.X3d, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNA-short-helix.x3d

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a DNA helix in which the atoms are colored by heteroatom (PDB: 1lmb). This model is designed to go with a teaching module comparing DNA and RNA basic structures and functions, and with one that studies transcription factor-DNA binding. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “DNA helix - polynucleotide molecule”. This model has been printed successfully using these parameters on Shapeways’ binder jetting printer in the Coated Full …

Model File Name: Ssdna.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: ssDNA.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a single stranded piece of DNA in stick representation (PDB: 1ehz). This model is designed to go with a teaching module comparing DNA and RNA basic structures and functions. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “ssDNA”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the Elasto Plastic material.