Biology Commons^™

Draft Genome Sequence Of Staphylococcus Epidermidis (Winslow And Winslow) Evans (Atcc 14990), Catherine Putonti, Laurynas Kalesinskas, Evan Cudone, Alan J. Wolfe, Kathleen C. Engelbrecht, David W. Koenig

Biology: Faculty Publications and Other Works

Here, we report the draft genome sequence for the type strain Staphylococcus epidermidis (Winslow and Winslow) Evans (ATCC 14990). The assembly consisted of 2,457,519 bp with an observed G+C content of 32.04%. Thirty-seven contigs were produced, including two putative plasmids, with a 296.8× coverage and an N₅₀ of 180,848 bp.

Draft Genome Sequence Of Escherichia Coli K-12 (Atcc 29425), Catherine Putonti, Kathleen C. Engelbrecht, David W. Koenig, Alan J. Wolfe

Biology: Faculty Publications and Other Works

A draft genome sequence for Escherichia coli ATCC 29425 was investigated. The size of the genome was 4,608,319 bp, with an observed G+C content of 50.68%. This assembly consisted of 80 contigs, with an average coverage of 122.2×, including one contig representative of the complete genome for the temperate phage P1.

Draft Genome Sequences Of Two Atcc Staphylococcus Aureus Subsp. Aureus Strains, Catherine Putonti, Laurynas Kalesinskas, Evan Cudone, Kathleen C. Engelbrecht, David W. Koenig, Alan J. Wolfe

Biology: Faculty Publications and Other Works

Draft genome sequences for Staphylococcus aureus subsp. aureus Rosenbach ATCC 14458 and ATCC 27217 strains were investigated. The genome sizes were 2,880,761 bp and 2,759,100 bp, respectively. Strain ATCC 14458 was assembled into 39 contigs, including 3 plasmids, and strain ATCC 27217 was assembled into 25 contigs, including 2 plasmids.

Draft Genome Sequence Of Escherichia Coli K-12 (Atcc 10798), Catherine Putonti, Daniela Dimitrova, Kathleen C. Engelbrecht, David W. Koenig, Alan J. Wolfe

Biology: Faculty Publications and Other Works

Here, we present the draft genome sequence of Escherichia coli ATCC 10798. E. coli ATCC 10798 is a K-12 strain, one of the most well-studied model microorganisms. The size of the genome was 4,685,496 bp, with a G+C content of 50.70%. This assembly consists of 62 contigs and the F plasmid.

Draft Genome Sequence Of Enterococcus Faecalis Atcc Baa-2128, Catherine Putonti, Laurynas Kalesinskas, Evan Cudone, Kathleen C. Engelbrecht, David W. Koenig, Alan J. Wolfe

Biology: Faculty Publications and Other Works

While a part of the native gut microflora, the Gram-positive bacterium Enterococcus faecalis can lead to serious infections elsewhere in the body. The draft genome of E. faecalis strain ATCC BAA-2128, isolated from piglet feces, was examined. This draft genome consists of 42 contigs, 12 of which exhibit homology to annotated plasmids.

Draft Genome Sequence Of Micrococcus Luteus (Schroeter) Cohn (Atcc 12698), Catherine Putonti, Evan Cudone, Laurynas Kalesinskas, Kathleen C. Engelbrecht, David W. Koenig, Alan J. Wolfe

Biology: Faculty Publications and Other Works

The actinobacterium Micrococcus luteus can be found in a wide variety of habitats. Here, we report the 2,411,958-bp draft genome sequence of the type strain M. leuteus (Schroeter) Cohn (ATCC 12698). Characteristic of this taxa, the genome sequence has a high G+C content, 73.14%.

The Double-Edges Role Of Copper In The Fate Of Amyloid Beta In The Presence Of Anti-Oxidants, Hui Ye, Jing Yang, Xueli Zhang, Yiying Zhu, Emily Lenzowski, Yanli Tian, Can Zhang, Markus Hardt, Chunhua Qiao, Rudolph E. Tanzi, Anna Moore, Chongzhao Ran

Biology: Faculty Publications and Other Works

The biological fate of amyloid beta (Aβ) species is a fundamental question in Alzheimer’s disease (AD) pathogenesis. The competition between clearance and aggregation of Aβs is critical for the onset of AD. Copper has been widely considered to be an inducer of harmful crosslinking of Aβs, and an important triggering factor for the onset of AD. In this report, however, we present data to show that copper can also be an inducer of Aβ degradation in the presence of a large excess of well-known intrinsic (such as dopamine) or extrinsic (such as vitamin C) anti-oxidants. The degraded fragments were identified …

Exploring The Diversity Of Bacillus Whole Genome Sequencing Projects Using Peasant, The Prokaryotic Assembly And Annotation Tool, Jonathon Brenner, Laurynas Kalesinskas, Catherine Putonti

Biology: Faculty Publications and Other Works

The persistent decrease in cost and difficulty of whole genome sequencing of microbial organisms has led to a dramatic increase in the number of species and strains characterized from a wide variety of environments. Microbial genome sequencing can now be conducted by small laboratories and as part of undergraduate curriculum. While sequencing is routine in microbiology, assembly, annotation and downstream analyses still require computational resources and expertise, often necessitating familiarity with programming languages. To address this problem, we have created a light-weight, user-friendly tool for the assembly and annotation of microbial sequencing projects. The Prokaryotic Assembly and Annotation Tool, Peasant, …

Ignatian Pedagogy Certificate Final Project, G. Patrick Duffie

Ignatian Pedagogy Educational Resources

No abstract provided.

Two New Genera Of Songbirds Represent Endemic Radiations From The Shola Sky Islands Of The Western Ghats, India, Sushma Reddy, V. V. Robin, C. K. Vishnudas, Pooja Gupta, Frank E. Rheindt, Daniel M. Hooper, Uma Ramakrishnan

Biology: Faculty Publications and Other Works

A long-standing view of Indian biodiversity is that while rich in species, there are few endemics or in-situ radiations within the subcontinent. One exception is the Western Ghats biodiversity hotspot, an isolated mountain range with many endemic species. Understanding the origins of the montane-restricted species is crucial to illuminate both taxonomic and environmental history.

The Role Of Notch-1-Mediated Repression Of Pten On Growth And Cancer Stem Cell Survival In Trastuzumab Resistant, Her2+ Breast Cancer, Andrew Thomas Baker

Dissertations

Trastuzumab targets the ErbB2 (HER2) receptor on breast cancer cells to attenuate HER2 driven tumor formation. Trastuzumab reduces both downstream PI3K/Akt and MAPK pathway signaling as well as the breast cancer stem cell (BCSC) population. BCSCs are hypothesized to be responsible for tumor recurrence, metastasis, as well as drug resistance. Today, resistance to trastuzumab remains a major clinical problem for women diagnosed with HER2+ breast cancer. Attenuation of PI3K/Akt and MAPK pathways may occur through the tumor suppressor, PTEN. Women with HER2+ breast tumors expressing less PTEN and increased PI3K/Akt or MAPK activity have worse overall outcome. Previously we have …

A Review Of Neogene And Quaternary Pikes Of Southeastern Europe And A New Species From The Early Pleistocene Of Nogaisk, Ukraine, Terry C. Grande, Oleksandr M. Kovalchuk, Mark V. H. Wilson

Biology: Faculty Publications and Other Works

The fish genus Esox (Teleostei, Esocidae) has been recorded from thirty late Miocene, Pliocene, and Pleistocene localities where forty-one bone-bearing strata are exposed in the territory of Ukraine, Russian Federation, and Republic of Moldova. From eight localities the genus is reported or described for the first time. A detailed description and morphological analysis of the currently available osteological material demonstrates the presence of four species in the studied area: (i) Esox sibiricus (late Miocene–early Pliocene); (ii) Esox moldavicus (early Pliocene–early Pleistocene); (iii) Esox nogaicus sp. nov. (early Pleistocene, Calabrian); (iv) Esox lucius (early–middle Pleistocene). The Northern Pike (Esox lucius …

Sensitizing Leukemia Stem Cells To Nf-Κb Inhibitor Treatment In Vivo By Inactivation Of Both Tnf And Il-1 Signaling, Peter W. Breslin, Jing Li, Andrew Volk, Jun Zhang, Joseph Cannova, Shaojun Dai, Caiqin Hao, Chenglong Hu, Jiewen Sun, Yan Xu, Wei Wei, Sucha Nand, Jianjun Chen, Ameet Kini, Jiang Zhu, Jiwang Zhang

Biology: Faculty Publications and Other Works

We previously reported that autocrine TNF-α (TNF) is responsible for JNK pathway activation in a subset of acute myeloid leukemia (AML) patient samples, providing a survival/proliferation signaling parallel to NF-κB in AML stem cells (LSCs). In this study, we report that most TNF-expressing AML cells (LCs) also express another pro-inflammatory cytokine, IL1β, which acts in a parallel manner. TNF was produced primarily by LSCs and leukemic progenitors (LPs), whereas IL1β was mainly produced by partially differentiated leukemic blasts (LBs). IL1β also stimulates an NF-κB-independent pro-survival and proliferation signal through activation of the JNK pathway. We determined that co-inhibition of signaling …

Deformation But Not Migration And Rotation – A Model Study On Vesicle Biomechanics In A Uniform Dc Electric Field, Hui Ye, Austen Curcuru

Biology: Faculty Publications and Other Works

Background: Biological cells migrate, deform and rotate in various types of electric fields, which have significant impact on the normal cellular physiology. To investigate electrically-induced deformation, researchers have used artificial giant vesicles that mimic the phospholipid bilayer cell membrane. Containing primarily the neutral molecule phosphatidylcholine, these vesicles deformed under evenly distributed, strong direct current (DC) electric fields. Interestingly, they did not migrate or rotate. A biophysical mechanism underlying the kinematic differences between the biological cells and the vesicles under electric stimulation has not been worked out.

Methods: We modeled the vesicle as a leaky, dielectric sphere and computed …

The Effects Of Treating Multispecies Biofilms With Bacteriophage, Alexandria Francis Cooper

Master's Theses

Biofilms can be found in any environment within proximity to water and are problematic in an assortment of industries. Numerous efforts have been employed to dislodge biofilms including bacteriophages (viruses that infect bacteria). Phage remediation is a promising solution for combatting biofilms that form on catheters in long term use patients. These biofilms often result in catheter-associated urinary tract infections (CAUTIs) and are the most common type of healthcare related infection reported. Additionally, they result in longer hospital stays and increased morbidity. To date, most of the research on the topic focuses on single species biofilms, despite their rarity in …

Discrete Mutations In Colorectal Cancer Correlate With Defined Microbial Communities In The Tumor Microenvironment, Michael B. Burns, Emmanuel Montassier, Juan Abrahante, Timothy K. Starr, Dan Knights, Ran Blekhman

Biology: Faculty Publications and Other Works

Variation in the gut microbiome has been linked to colorectal cancer (CRC), as well as to host genetics. However, we do not know whether genetic mutations in CRC tumors interact with the structure and composition of the microbial communities surrounding the tumors, and if so, whether changes in the microbiome can be used as a predictor for tumor mutational status. Here, we characterized the association between CRC tumor mutational landscape and its proximal microbial communities by performing whole exome sequencing and microbiome profiling in tumors and normal colorectal tissue samples from the same patient. We find a significant association between …

Regulation Of Gonad Morphogenesis In Drosophila Melanogaster By Btb Family Transcription Factors, Diane Silva, Kenneth W. Olsen, Magdalena Bednarz, Andrew Droste, Christopher P. Lenkeit, Jennifer Mierisch, Edwin Chaharbakhshi, Emily R. Temple-Wood

Biology: Faculty Publications and Other Works

During embryogenesis, primordial germ cells (PGCs) and somatic gonadal precursor cells (SGPs) migrate and coalesce to form the early gonad. A failure of the PGCs and SGPs to form a gonad with the proper architecture not only affects germ cell development, but can also lead to infertility. Therefore, it is critical to identify the molecular mechanisms that function within both the PGCs and SGPs to promote gonad morphogenesis. We have characterized the phenotypes of two genes, longitudinals lacking (lola) and ribbon (rib), that are required for the coalescence and compaction of the embryonic gonad in Drosophila melanogaster. rib …

Detritus Quality And Locality Determines Survival And Mass, But Not Export, Of Wood Frogs At Metamorphosis, Joseph Milanovich, Kyle Barrett, John A. Crawford

Biology: Faculty Publications and Other Works

Single-site experiments have demonstrated detritus quality in wetlands can have strongly negative, neutral, and even positive influences on wildlife. However, an examination of the influence of detritus quality across several regions is lacking and can provide information on whether impacts from variation in detritus quality are consistent across species with wide ranges. To address this gap in regional studies we examined effects of emergent and allochthonous detritus of different nutrient qualities on amphibians and assessed a mechanism that may contribute to potential impacts. We used aquatic mesocosms to raise wood frogs (Rana sylvatica) from two regions of the …

Microplastic In Surface Waters Of Urban Rivers: Concentration, Sources, And Associated Bacterial Assemblages, Amanda Rae Mccormick, Timothy Hoellein, Maxwell G. London, Joshua Hittie, John J. Kelly, John W. Scott

Biology: Faculty Publications and Other Works

The ecological dynamics of microplastic (<5 mm) are well documented in marine ecosystems, but the sources, abundance, and ecological role of microplastic in rivers are unknown and likely to be substantial. Microplastic fibers (e.g., synthetic fabrics) and pellets (e.g., abrasives in personal care products) are abundant in wastewater treatment plant (WWTP) effluent, and can serve as a point source of microplastic in rivers. The buoyancy, hydrophobic surface, and long transport distance of microplastic make it a novel substrate for the selection and dispersal of unique microbial assemblages. We measured microplastic concentration and bacterial assemblage composition on microplastic and natural surfaces upstream and downstream of WWTP effluent sites at nine rivers in Illinois, United States. Microplastic concentration was higher downstream of WWTP effluent outfall sites in all but two rivers. Pellets, fibers, and fragments were the dominant microplastic types, and polymers were identified as polypropylene, polyethylene, and polystyrene. Mean microplastic flux was 1,338,757 pieces per day, although the flux was highly variable among nine sites (min = 15,520 per day, max = 4,721,709 per day). High-throughput sequencing of 16S rRNA genes showed bacterial assemblage composition was significantly different among microplastic, seston, and water column substrates. Microplastic bacterial assemblages had lower taxon richness, diversity, and evenness than those on other substrates, and microplastic selected for taxa that may degrade plastic polymers (e.g., Pseudomonas) and those representing common human intestinal pathogens (e.g., Arcobacter). Effluent from WWTPs in rivers is an important component of the global plastic “life cycle,” and microplastic serves as a novel substrate that selects and transports distinct bacterial assemblages in urban rivers. Rates of microplastic deposition, consumption by stream biota, and the metabolic capacity of microplastic biofilms in rivers are unknown and merit further research.

Draft Genome Sequence For A Urinary Isolate Of Nosocomiicoccus Ampullae, Catherine Putonti, Evann E. Hilt, Travis K. Price, Katherine Diebel, Alan J. Wolfe

Biology: Faculty Publications and Other Works

A draft genome sequence for a urinary isolate of Nosocomiicoccus ampullae (UMB0853) was investigated. The size of the genome was 1,578,043 bp, with an observed G+C content of 36.1%. Annotation revealed 10 rRNA sequences, 40 tRNA genes, and 1,532 protein-coding sequences. Genome coverage was 727× and consisted of 32 contigs, with an N₅₀ of 109,831 bp.

Pharmacogenetic Discovery In Calgb (Alliance) 90401 And Mechanistic Validation Of A Vac14 Polymorphism That Increases Risk Of Docetaxel-Induced Neuropathy, Daniel L. Hertz, Kouros Owzar, Sherrie Lessans, Claudia Wing, Chen Jiang, William Kevin Kelly, Jai Patel, Susan Halabi, Yoichi Furukawa, Heather E. Wheeler, Alexander B. Sibley, Cameron Lassiter, Lois Weisman, Dorothy Watson, Stefanie D. Krens, Flora Mulkey, Cynthia L. Renn, Eric J. Small, Phillip G. Febbo, Ivo Shterev, Deanna L. Kroetz, Paula N. Friedman, John F. Mahoney, Michael A. Carducci, Michael J. Kelley, Yusuke Nakamura, Michiaki Kubo, Susan G. Dorsey, M. Eileen Dolan, Michael J. Morris, Howard L. Mcleod

Biology: Faculty Publications and Other Works

Purpose

Discovery of single nucleotide polymorphisms (SNPs) that predict a patient's risk of docetaxel-induced neuropathy would enable treatment individualization to maximize efficacy and avoid unnecessary toxicity. The objectives of this analysis were to discover SNPs associated with docetaxel-induced neuropathy and mechanistically validate these associations in preclinical models of drug-induced neuropathy.

Experimental Design

A genome-wide association study was conducted in metastatic castrate-resistant prostate cancer patients treated with docetaxel, prednisone and randomized to bevacizumab or placebo on CALGB 90401. SNPs were genotyped on the Illumina HumanHap610-Quad platform followed by rigorous quality control. The inference was conducted on the cumulative dose at occurrence …

Genetic And Transcriptional Analysis Of Human Host Response To Healthy Gut Microbiota, Michael B. Burns, Allison L. Richards, Adnan Alazizi, Luis B. Barreiro, Roger Pique-Regi, Ran Blekhman, Francesca Luca

Biology: Faculty Publications and Other Works

Many studies have demonstrated the importance of the gut microbiota in healthy and disease states. However, establishing the causality of host-microbiota interactions in humans is still challenging. Here, we describe a novel experimental system to define the transcriptional response induced by the microbiota for human cells and to shed light on the molecular mechanisms underlying host-gut microbiota interactions. In primary human colonic epithelial cells, we identified over 6,000 genes whose expression changed at various time points following coculturing with the gut microbiota of a healthy individual. Among the differentially expressed genes we found a 1.8-fold enrichment of genes associated with …

Editorial: Linking Ecosystem Function To Microbial Diversity, Anne E. Bernhard, John J. Kelly

Biology: Faculty Publications and Other Works

No abstract provided.

Freshwater Metaviromics And Bacteriophages: A Current Assessment Of The State Of The Art In Relation To Bioinformatic Challenges, Catherine Putonti, Katherine Bruder, Kema Malki, Alexandria Cooper, Emily Sible, Jason W. Shapiro, Siobhan C. Watkins

Biology: Faculty Publications and Other Works

Advances in bioinformatics and sequencing technologies have allowed for the analysis of complex microbial communities at an unprecedented rate. While much focus is often placed on the cellular members of these communities, viruses play a pivotal role, particularly bacteria-infecting viruses (bacteriophages); phages mediate global biogeochemical processes and drive microbial evolution through bacterial grazing and horizontal gene transfer. Despite their importance and ubiquity in nature, very little is known about the diversity and structure of viral communities. Though the need for culture-based methods for viral identification has been somewhat circumvented through metagenomic techniques, the analysis of metaviromic data is marred with …

The Genetic Basis Of Baculum Size And Shape Variation In Mice, Nicholas G. Schultz, Jesse Ingels, Andrew Hillhouse, Keegan Wardwell, Peter L. Chang, James M. Cheverud, Cathleen Lutz, Lu Lu, Robert W. Williams, Matthew D. Dean

Biology: Faculty Publications and Other Works

The rapid divergence of male genitalia is a preeminent evolutionary pattern. This rapid divergence is especially striking in the baculum, a bone that occurs in the penis of many mammalian species. Closely related species often display diverse baculum morphology where no other morphological differences can be discerned. While this fundamental pattern of evolution has been appreciated at the level of gross morphology, nearly nothing is known about the genetic basis of size and shape divergence. Quantifying the genetic basis of baculum size and shape variation has been difficult because these structures generally lack obvious landmarks, so comparing them in three …

Raised Intracellular Calcium Contributes To Ischemia-Induced Depression Of Evoked Synaptic Transmission, Shirin Jalini, Hui Ye, Alexander A. Tonkikh, Milton P. Charlton, Peter L. Carlen

Biology: Faculty Publications and Other Works

Oxygen-glucose deprivation (OGD) leads to depression of evoked synaptic transmission, for which the mechanisms remain unclear. We hypothesized that increased presynaptic [Ca²⁺]_i during transient OGD contributes to the depression of evoked field excitatory postsynaptic potentials (fEPSPs). Additionally, we hypothesized that increased buffering of intracellular calcium would shorten electrophysiological recovery after transient ischemia. Mouse hippocampal slices were exposed to 2 to 8 min of OGD. fEPSPs evoked by Schaffer collateral stimulation were recorded in the stratum radiatum, and whole cell current or voltage clamp recordings were performed in CA1 neurons. Transient ischemia led to increased presynaptic [Ca^{2+ …}

Assessing The Success Of Outreach At Preventing The Movement Of Aquatic Invasive Species In Illinois, Ellen Anne Cole

Master's Theses

Overland transport of recreational boats is the major vector of dispersal for aquatic invasive species among North American waterbodies. These species have large economic and ecosystem impacts, and understanding their movement is essential to understanding the biodiversity and functioning of aquatic ecosystems across the continent. I surveyed Illinois boaters to determine patterns of recreational boat movement and the consistency with which boaters perform actions to prevent the spread of invasive species. Although most boaters perform these actions, a large minority do not and the network for invasive species spread on recreational boats still connects most waterbodies. Next, I interviewed managers …

Chronic Toxicity Of Binary Metal Mixtures Of Cadmium-Zinc And Cadmium-Nickelon Daphnia Magna, Edgar Ramiro Perez

Master's Theses

This study characterizes binary-metal mixture effects of cadmium (Cd2+) + zinc (Zn2+) and Cd2+ + nickel (Ni2+) on Daphnia magna. Although acute studies have shown protective Ni2+ (Traudt et al. 2016) and Zn2+ effects (Meyer et al. 2015) against Cd2+ toxicity, no study has fully characterized a protective effect on D. magna at several endpoints (survival, reproduction, growth, and accumulation) on a chronic study. In this study, the titration design was selected to characterize the 21 day (21-d) chronic effects of the binary-metal mixtures on survival, growth, reproduction, and metal accumulation in D. magna. Using this design, increasing concentrations of …

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 …