Digital Commons Network^™

Finding Function In The Unknown, Kelly Boyd, Emma Highland, Amanda Misch, Amber Hu, Sushma Reddy, Catherine Putonti

Bioinformatics Faculty Publications

Through high-throughput RNA sequencing (RNAseq), transcriptomes for a single cell, tissue, or organism(s) can be ascertained at a high resolution. While a number of bioinformatic tools have been developed for transcriptome analyses, significant challenges exist for studies of non-model organisms. Without a reference sequence available, raw reads must first be assembled de novo followed by the tedious task of BLAST searches and data mining for functional information. We have created a pipeline, PyRanger, to automate this process. The pipeline includes functionality to assess a single transcriptome and also facilitate comparative transcriptomic studies.

A Polyglot Approach To Bioinformatics Data Integration: A Phylogenetic Analysis Of Hiv-1, Steven Reisman, Thomas Hatzopoulos, Konstantin Laufer, George K. Thiruvathukal, Catherine Putonti

Bioinformatics Faculty Publications

As sequencing technologies continue to drop in price and increase in throughput, new challenges emerge for the management and accessibility of genomic sequence data. We have developed a pipeline for facilitating the storage, retrieval, and subsequent analysis of molecular data, integrating both sequence and metadata. Taking a polyglot approach involving multiple languages, libraries, and persistence mechanisms, sequence data can be aggregated from publicly available and local repositories. Data are exposed in the form of a RESTful web service, formatted for easy querying, and retrieved for downstream analyses. As a proof of concept, we have developed a resource for annotated HIV-1 …

Bacteriophages Isolated From Lake Michigan Demonstrate Broad Host-Range Across Several Bacterial Phyla, Kema Malki, Alex Kula, Katherine Bruder, Emily Sible, Thomas Hatzopoulos, Stephanie Steidel, Siobhan C. Watkins, Catherine Putonti

Biology: Faculty Publications and Other Works

BACKGROUND:

The study of bacteriophages continues to generate key information about microbial interactions in the environment. Many phenotypic characteristics of bacteriophages cannot be examined by sequencing alone, further highlighting the necessity for isolation and examination of phages from environmental samples. While much of our current knowledge base has been generated by the study of marine phages, freshwater viruses are understudied in comparison. Our group has previously conducted metagenomics-based studies samples collected from Lake Michigan - the data presented in this study relate to four phages that were extracted from the same samples.

FINDINGS:

Four phages were extracted from Lake Michigan …

Injury In Aged Animals Robustly Activates Quiescent Olfactory Neural Stem Cells, Jessica H. Brann, Deandra Ellis, Benson Ku, Eleonora Spinazzi, Stuart Firestein

Biology: Faculty Publications and Other Works

While the capacity of the olfactory epithelium (OE) to generate sensory neurons continues into middle age in mice, it is presumed that this regenerative potential is present throughout all developmental stages. However, little experimental evidence exists to support the idea that this regenerative capacity remains in late adulthood, and questions about the functionality of neurons born at these late stages remain unanswered. Here, we extend our previous work in the VNO to investigate basal rates of proliferation in the OE, as well as after olfactory bulbectomy, a commonly used surgical lesion. In addition, we show that the neural stem cell …

A Gene-Based Association Method For Mapping Traits Using Reference Transcriptome Data, Eric R. Gamazon, Heather Wheeler, Kaanan P. Shah, Sahar V. Mozaffari, Keston Aquino-Michaels, Robert J. Carroll, Anne E. Eyler, Joshua C. Denny, Gtex Consortium, Dan L. Nicolae, Nancy J. Cox, Hae Kyung Im

Bioinformatics Faculty Publications

Genome-wide association studies (GWAS) have identified thousands of variants robustly associated with complex traits. However, the biological mechanisms underlying these associations are, in general, not well understood. We propose a gene-based association method called PrediXcan that directly tests the molecular mechanisms through which genetic variation affects phenotype. The approach estimates the component of gene expression determined by an individual’s genetic profile and correlates ‘imputed’ gene expression with the phenotype under investigation to identify genes involved in the etiology of the phenotype. Genetically regulated gene expression is estimated using whole-genome tissue-dependent prediction models trained with reference transcriptome data sets. PrediXcan enjoys …

An Analytical Method For Detecting Toxic Metal Cations Using Cyclotriveratrylene Derivative Capped Gold Nanoparticles, Zachary R. Osner, Richard C. Holz, Daniel P. Becker Ph.D.

Chemistry: Faculty Publications and Other Works

Cyclotriveratrylene-oxime (CTV-oxime) derivatives that terminate with a dithiolate linker were synthesized enabling the supramolecular scaffold to adhere to gold nanoparticles (AuNPs) with the bowl-shaped cavity of the CTV scaffold exposed for utilization in host–guest chemistry. Exposure of these CTV functionalized AuNPs to varying concentrations of di- and trivalent metal cations resulted in the formation of large CTV-AuNP polymeric clusters and an accompanying a shift in the plasmon resonance. These interactions between the CTV-AuNPs and the metal cations in solution provides proof-of-concept that supramolecular functionalized AuNPs can be used as a simple and straightforward, on-site detection system for toxic metal cations …

Metal-Free Tandem Beckmann–Electrophilic Aromatic Substitution Cascade Affording Diaryl Imines, Ketones, Amines, And Quinazolines, Samuel Sarsah, Marlon R. Lutz Jr., Kailyn Chichi Bobb, Daniel Becker

Chemistry: Faculty Publications and Other Works

A cascade reaction sequence involving a Beckmann rearrangement on benzophenone oxime followed by an electrophilic aromatic substitution (EAS) on the intermediate nitrilium ion affords N-phenyl diaryl imines that may then be hydrolyzed to ketones, or reduced to the corresponding amines. Reaction with benzonitrile afforded 2,4-diphenylquinazoline through a Beckmann–Ritter–EAS cascade.

Specific Intensity Direct Current (Dc) Electric Field Improves Neural Stem Cell Migration And Enhances Differentiation Towards Βiii-Tubulin+ Neurons, Huiping Zhao, Amanda Steiger, Mitch Nohner, Hui Ye

Biology: Faculty Publications and Other Works

Control of stem cell migration and differentiation is vital for efficient stem cell therapy. Literature reporting electric field–guided migration and differentiation is emerging. However, it is unknown if a field that causes cell migration is also capable of guiding cell differentiation— and the mechanisms for these processes remain unclear. Here, we report that a 115 V/m direct current (DC) electric field can induce directional migration of neural precursor cells (NPCs). Whole cell patching revealed that the cell membrane depolarized in the electric field, and buffering of extracellular calcium via EGTA prevented cell migration under these conditions. Immunocytochemical staining indicated that …

Using Whole-Genome Sequences Of The Lg/J And Sm/J Inbred Mouse Strains To Prioritize Quantitative Trait Genes And Nucleotides, Igor Nikolskiy, Donald F. Conrad, Sung Chun, Justin C. Fay, James M. Cheverud, Heather A. Lawson

Biology: Faculty Publications and Other Works

Background

The laboratory mouse is the most commonly used model for studying variation in complex traits relevant to human disease. Here we present the whole-genome sequences of two inbred strains, LG/J and SM/J, which are frequently used to study variation in complex traits as diverse as aging, bone-growth, adiposity, maternal behavior, and methamphetamine sensitivity.

Results

We identified small nucleotide variants (SNVs) and structural variants (SVs) in the LG/J and SM/J strains relative to the reference genome and discovered novel variants in these two strains by comparing their sequences to other mouse genomes. We find that 39% of the LG/J and …

Comparing Acute Effects Of A Nano-Tio2 Pigment On Cosmopolitan Freshwater Phototrophic Microbes Using High-Throughput Screening, Binh Chu, Christopher G. Peterson, Tiezheng Tong, Kimberly A. Gray, Jean-François Gaillard, John Kelly

Biology: Faculty Publications and Other Works

Production of titanium-dioxide nanomaterials (nano-TiO2) is increasing, leading to potential risks associated with unintended release of these materials into aquatic ecosystems. We investigated the acute effects of nano-TiO2 on metabolic activity and viability of algae and cyanobacteria using high-throughput screening. The responses of three diatoms (Surirella angusta, Cocconeis placentula, Achnanthidium lanceolatum), one green alga (Scenedesmus quadricauda), and three cyanobacteria (Microcystis aeruginosa, Gloeocapsasp., Synechococcus cedrorum) to short-term exposure (15 to 60 min) to a common nano-TiO2 pigment (PW6; average crystallite size 81.5 nm) with simulated solar illumination were assessed. Five concentrations of nano-TiO2 (0.5, 2.5, 5, 10, and 25 mg L-1) …

Vesicle Biomechanics In A Time-Varying Magnetic Field, Hui Ye, Austen Curcuru

Biology: Faculty Publications and Other Works

Background Cells exhibit distortion when exposed to a strong electric field, suggesting that the field imposes control over cellular biomechanics. Closed pure lipid bilayer membranes (vesicles) have been widely used for the experimental and theoretical studies of cellular biomechanics under this electrodeformation. An alternative method used to generate an electric field is by electromagnetic induction with a time-varying magnetic field. References reporting the magnetic control of cellular mechanics have recently emerged. However, theoretical analysis of the cellular mechanics under a time-varying magnetic field is inadequate. We developed an analytical theory to investigate the biomechanics of a modeled vesicle under a …

Hash-Map-Eradicator: Filtering Non-Target Sequences From Next Generation Sequencing Reads, Jonathon Brenner, Catherine Putonti

Bioinformatics Faculty Publications

Contemporary DNA sequencing technologies are continuously increasing throughput at ever decreasing costs. Moreover, due to recent advances in sequencing technology new platforms are emerging. As such computational challenges persist. The average read length possible has taken a giant leap forward with the PacBio and Nanopore solutions. Regardless of the platform used, impurities within the DNA preparation of the sample - be it from unintentional contaminants or pervasive symbiots - remains an issue. We have developed a new tool, HAsh-MaP-ERadicator (HAMPER), for the detection and removal of non-target, contaminating DNA sequences. Integrating hash-based and mapping-based strategies, HAMPER is both memory and …

Assessment Of A Metaviromic Dataset Generated From Nearshore Lake Michigan, Siobhan C. Watkins, Neil Kuehnle, C Anthony Ruggeri, Kema Malki, Katherine Bruder, Jinan Elayyan, Kristina Damisch, Naushin Vahora, Paul O'Malley, Brianne Ruggles-Sage, Zachary Romer, Catherine Putonti

Bioinformatics Faculty Publications

Bacteriophages are powerful ecosystem engineers. They drive bacterial mortality rates and genetic diversity, and affect microbially mediated biogeochemical processes on a global scale. This has been demonstrated in marine environments; however, phage communities have been less studied in freshwaters, despite representing a potentially more diverse environment. Lake Michigan is one of the largest bodies of freshwater on the planet, yet to date the diversity of its phages has yet to be examined. Here, we present a composite survey of viral ecology in the nearshore waters of Lake Michigan. Sequence analysis was performed using a web server previously used to analyse …

Survey Of Viral Populations Within Lake Michigan Nearshore Waters At Four Chicago Area Beaches, Emily Sible, Alexandria Cooper, Kema Malki, Katherine Bruder, Siobhan C. Watkins, Yuriy Fofanov, Catherine Putonti

Bioinformatics Faculty Publications

In comparison to the oceans, freshwater environments represent a more diverse community of microorganisms, exhibiting comparatively high levels of variability both temporally and spatially Maranger and Bird, Microb. Ecol. 31 (1996) 141–151. This level of variability is likely to extend to the world of viruses as well, in particular bacteria-infecting viruses (bacteriophages). Phages are known to influence bacterial diversity, and therefore key processes, in environmental niches across the globe Clokie et al., Bacteriophage 1 (2011) 31–45; Jacquet et al., Adv. Ocean Limn. 1 (2010) 97–141; Wilhelm and Suttle, Bioscience 49 (1999) 781–788; Bratback et al., Microb. Ecol. 28 (1994) 209–221. …

The Genetic Architecture Of Fluctuating Asymmetry Of Mandible Size And Shape In A Population Of Mice: Another Look, James M. Cheverud, Larry J. Leamy, Christian Peter Klingenberg, Emma Sherratt, Jason B. Wolf

Biology: Faculty Publications and Other Works

Fluctuating asymmetry (FA), typically measured by variation in the differences between right and left sides of bilateral traits, is commonly used to assess developmental instability (DI) in populations. A previous quantitative trait locus (QTL) investigation using an F2 intercross mouse population found little evidence of individual loci affecting FA in mandible size, but an abundance of epistatic interactions between loci. Here we extend this work by testing whether these patterns replicate in an F3 population derived from the same intercross. Using a large number of molecular markers genotyped in over 1200 mice, we uncovered significant interactions between loci (QTLs) affecting …

Survey Of Microbial Populations Within Lake Michigan Nearshore Waters At Two Chicago Public Beaches, Kema Malki, Katherine Bruder, Catherine Putonti

Bioinformatics Faculty Publications

Lake Michigan is a critical resource for the residents of Chicago, providing drinking water to its 9+ million area residents. Along Chicago׳s 26 miles of public beaches the populous urban environment and this freshwater environment meet. While city-led monitoring initiatives investigate pathogenic bacteria in these nearshore waters, very little is known about other microbial species present. We collected surface water samples from two Chicago public beaches – Montrose Beach and 57th Street Beach – every ten days from June 5 through August 4, 2013 as well as once in early Fall (October 4, 2013). Sixteen bacterial communities in total were …

The Brain Geography Mini-Course: A Neuroscience Outreach Effort, Mark Albert

Computer Science: Faculty Publications and Other Works

The way we experience the world - how we go between sensing, thinking, and acting - is in some ways no more of a mystery than understanding how a computer works. Brains are quite complicated and we may never understand the details, but what we know in general can be very interesting. In this mini-course, we will learn how we think. When we see, hear, smell, touch, taste, remember, rehearse, fear something, understand or produce language, move our bodies...specific parts of the brain are used. Students will get a rough introduction to each part and how they interact. This will …

Assessment Of Microbial Populations Within Chicago Area Nearshore Waters And Interfaces With River Systems, Emily Sible, Alexandria Cooper, Kema Malki, Katherine Bruder, Thomas Hatzopoulos, Siobhan C. Watkins, Catherine Putonti

Bioinformatics Faculty Publications

The Chicago area locks separate and control water flow between the freshwaters of Lake Michigan and the network of Illinois waterways. Under extreme storm conditions, however, the locks are opened and storm waters, untreated waste, and runoff are released directly into the lake. These combined sewer overflow (CSO) events introduce microbes, viruses, and nutrients such as nitrogen and phosphorous into nearshore waters which likely affect the native species. We collected surface water samples from four Chicago area beaches – Gillson Park, Montrose Beach, 57th Street Beach, and Calumet Beach – every two weeks from May 13 through August 5, 2014. …

Identification Of Eqtls For Hepatic Xbp1s And Socs3 Gene Expression In Mice Fed A High-Fat, High Caloric Diet, James M. Cheverud, Sarina Pasricha, Jane Kenney-Hunt, Kristy Anderson, Naderah Jafari, Rabea A. Hall, Frank Lammert, Richard M. Green

Biology: Faculty Publications and Other Works

Nonalcoholic fatty liver disease (NAFLD) is a highly prevalent form of human hepatic disease and feeding mice a high-fat, high-caloric (HFHC) diet is a standard model of NAFLD. To better understand the genetic basis of NAFLD, we conducted an expression quantitative trait locus (eQTL) analysis of mice fed a HFHC diet. Two-hundred sixty-five (A/J × C57BL/6J) F₂ male mice were fed a HFHC diet for 8 wk. eQTL analysis was utilized to identify genomic regions that regulate hepatic gene expression of Xbp1s and Socs3. We identified two overlapping loci for Xbp1s and Socs3 on Chr 1 (164.0–185.4 Mb …

Effective Use Of Trails For Assessing Terrestrial Salamander Abundance And Detection: A Case Study At Great Smoky Mountains National Park, Joseph Milanovich, Daniel J. Hocking, William E. Peterman, John A. Crawford

Biology: Faculty Publications and Other Works

The conservation and management of wildlife species is contingent on estimating distribution and abundance. Sampling of wildlife requires repeated visits to accurately determine species occurrence and to quantify abundance across temporal and spatial scales. The use of trails to sample wildlife populations is increasing and offers opportunities to potentially sample more frequently, with increased ease of access, and less disturbance to habitats, which can be important in sensitive natural areas. We examined capture dataof terrestrial salamanders within Great Smoky Mountains National Park to determine if detection and abundance estimates from trail and non-trail transects were significantly different. Across two, 3-week …