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Modeling Cell Line-Specific Recruitment Of Signaling Proteins To The Insulin-Like Growth Factor 1 Receptor, Keesha E. Erickson, Dipak Barua, For Full List Of Authors, See Publisher's Website. Jan 2019

Modeling Cell Line-Specific Recruitment Of Signaling Proteins To The Insulin-Like Growth Factor 1 Receptor, Keesha E. Erickson, Dipak Barua, For Full List Of Authors, See Publisher's Website.

Chemical and Biochemical Engineering Faculty Research & Creative Works

Receptor tyrosine kinases (RTKs) typically contain multiple autophosphorylation sites in their cytoplasmic domains. Once activated, these autophosphorylation sites can recruit downstream signaling proteins containing Src homology 2 (SH2) and phosphotyrosine-binding (PTB) domains, which recognize phosphotyrosine-containing short linear motifs (SLiMs). These domains and SLiMs have polyspecific or promiscuous binding activities. Thus, multiple signaling proteins may compete for binding to a common SLiM and vice versa. To investigate the effects of competition on RTK signaling, we used a rule-based modeling approach to develop and analyze models for ligand-induced recruitment of SH2/PTB domain-containing proteins to autophosphorylation sites in the insulin-like growth factor 1 …


Superelastic And Ph-Responsive Degradable Dendrimer Cryogels Prepared By Cryo-Aza-Michael Addition Reaction, Juan Wang, Hu Yang Dec 2018

Superelastic And Ph-Responsive Degradable Dendrimer Cryogels Prepared By Cryo-Aza-Michael Addition Reaction, Juan Wang, Hu Yang

Chemical and Biochemical Engineering Faculty Research & Creative Works

Dendrimers exhibit super atomistic features by virtue of their well-defined discrete quantized nanoscale structures. Here, we show that hyperbranched amine-terminated polyamidoamine (PAMAM) dendrimer G4.0 reacts with linear polyethylene glycol (PEG) diacrylate (575 g/mol) via the aza-Michael addition reaction at a subzero temperature (-20 °C), namely cryo-aza-Michael addition, to form a macroporous superelastic network, i.e., dendrimer cryogel. Dendrimer cryogels exhibit biologically relevant Young's modulus, high compression elasticity and super resilience at ambient temperature. Furthermore, the dendrimer cryogels exhibit excellent rebound performance and do not show significant stress relaxation under cyclic deformation over a wide temperature range (-80 to 100 °C). The …


The Toxicity Of Nanoparticles Depends On Multiple Molecular And Physicochemical Mechanisms, Yue-Wern Huang, Melissa Cambre, Han-Jung Lee Dec 2017

The Toxicity Of Nanoparticles Depends On Multiple Molecular And Physicochemical Mechanisms, Yue-Wern Huang, Melissa Cambre, Han-Jung Lee

Biological Sciences Faculty Research & Creative Works

Nanotechnology is an emerging discipline that studies matters at the nanoscale level. Eventually, the goal is to manipulate matters at the atomic level to serve mankind. One growing area in nanotechnology is biomedical applications, which involve disease management and the discovery of basic biological principles. In this review, we discuss characteristics of nanomaterials, with an emphasis on transition metal oxide nanoparticles that influence cytotoxicity. Identification of those properties may lead to the design of more efficient and safer nanosized products for various industrial purposes and provide guidance for assessment of human and environmental health risk. We then investigate biochemical and …


No-Boundary Thinking In Bioinformatics, Jason H. Moore, Steven F. Jennings, Casey S. Greene, Lawrence E. Hunter, Andy D. Perkins, Clarlynda Williams-Devane, Donald C. Wunsch, Zhongming Zhao, Xiuzhen Huang Jan 2017

No-Boundary Thinking In Bioinformatics, Jason H. Moore, Steven F. Jennings, Casey S. Greene, Lawrence E. Hunter, Andy D. Perkins, Clarlynda Williams-Devane, Donald C. Wunsch, Zhongming Zhao, Xiuzhen Huang

Electrical and Computer Engineering Faculty Research & Creative Works

The following sections are included:
Bioinformatics is a Mature Discipline
The Golden Era of Bioinformatics Has Begun
No-Boundary Thinking in Bioinformatics
References


Identification Of A Short Cell-Penetrating Peptide From Bovine Lactoferricin For Intracellular Delivery Of Dna In Human A549 Cells, Betty Revon Liu, Yue-Wern Huang, Robert Aronstam, Han-Jung Lee Mar 2016

Identification Of A Short Cell-Penetrating Peptide From Bovine Lactoferricin For Intracellular Delivery Of Dna In Human A549 Cells, Betty Revon Liu, Yue-Wern Huang, Robert Aronstam, Han-Jung Lee

Biological Sciences Faculty Research & Creative Works

Cell-penetrating peptides (CPPs) have been shown to deliver cargos, including protein, DNA, RNA, and nanomaterials, in fully active forms into live cells. Most of the CPP sequences in use today are based on non-native proteins that may be immunogenic. Here we demonstrate that the L5a CPP (RRWQW) from bovine lactoferricin (LFcin), stably and noncovalently complexed with plasmid DNA and prepared at an optimal nitrogen/phosphate ratio of 12, is able to efficiently enter into human lung cancer A549 cells. The L5a CPP delivered a plasmid containing the enhanced green fluorescent protein (EGFP) coding sequence that was subsequently expressed in …


Delivery Of Nucleic Acids And Nanomaterials By Cell-Penetrating Peptides: Opportunities And Challenges, Yue-Wern Huang, Han-Jung Lee, Larry Tolliver, Robert Aronstam Sep 2015

Delivery Of Nucleic Acids And Nanomaterials By Cell-Penetrating Peptides: Opportunities And Challenges, Yue-Wern Huang, Han-Jung Lee, Larry Tolliver, Robert Aronstam

Biological Sciences Faculty Research & Creative Works

Many viral and nonviral systems have been developed to aid delivery of biologically active molecules into cells. Among these, cell-penetrating peptides (CPPs) have received increasing attention in the past two decades for biomedical applications. In this review, we focus on opportunities and challenges associated with CPP delivery of nucleic acids and nanomaterials. We first describe the nature of versatile CPPs and their interactions with various types of cargoes. We then discuss in vivo and in vitro delivery of nucleic acids and nanomaterials by CPPs. Studies on the mechanisms of cellular entry and limitations in the methods used are detailed.


Rapidly Self-Renewing Human Multipotent Marrow Stromal Cells (Hmsc) Express Sialyl Lewis X And Actively Adhere To Arterial Endothelium In A Chick Embryo Model System, Harris E. Mcferrin, Scott D. Olson, Miriam V. Gutschow, Julie A. Semon, Deborah E. Sullivan, Darwin J. Prockop Aug 2014

Rapidly Self-Renewing Human Multipotent Marrow Stromal Cells (Hmsc) Express Sialyl Lewis X And Actively Adhere To Arterial Endothelium In A Chick Embryo Model System, Harris E. Mcferrin, Scott D. Olson, Miriam V. Gutschow, Julie A. Semon, Deborah E. Sullivan, Darwin J. Prockop

Biological Sciences Faculty Research & Creative Works

Background: There have been conflicting observations regarding the receptors utilized by human multipotent mesenchymal bone marrow stromal cells (hMSC) to adhere to endothelial cells (EC). To address the discrepancies, we performed experiments with cells prepared with a standardized, low-density protocol preserving a sub-population of small cells that are rapidly self-renewing.

Methods: Sialyl Lewis X (SLeX) and α4 integrin expression were determined by flow cytometry. Fucosyltransferase expression was determined by quantitative realtime RT-PCR. Cell adhesion assays were carried out with a panel of endothelial cells from arteries, veins and the microvasculature in vitro. In Vivo experiments were performed to determine …


Optimal Aggregation Of Fcεri With A Structurally Defined Trivalent Ligand Overrides Negative Regulation Driven By Phosphatases, Avanika Mahajan, Dipak Barua, Patrick Cutler, Diane S. Lidke, Flor A. Espinoza, Carolyn Pehlke, Rachel Grattan, Yuko Kawakami, Chang-Shung Tung, Andrew R. M. Bradbury, William S. Hlavacek, Bridget S. Wilson Jul 2014

Optimal Aggregation Of Fcεri With A Structurally Defined Trivalent Ligand Overrides Negative Regulation Driven By Phosphatases, Avanika Mahajan, Dipak Barua, Patrick Cutler, Diane S. Lidke, Flor A. Espinoza, Carolyn Pehlke, Rachel Grattan, Yuko Kawakami, Chang-Shung Tung, Andrew R. M. Bradbury, William S. Hlavacek, Bridget S. Wilson

Chemical and Biochemical Engineering Faculty Research & Creative Works

To investigate why responses of mast cells to antigen-induced IgE receptor (FcεRI) aggregation depend nonlinearly on antigen dose, we characterized a new artificial ligand, DF3, through complementary modeling and experimentation. This ligand is a stable trimer of peptides derived from bacteriophage T4 fibritin, each conjugated to a hapten (DNP). We found low and high doses of DF3 at which degranulation of mast cells sensitized with DNP-specific IgE is minimal, but ligand-induced receptor aggregation is comparable to aggregation at an intermediate dose, optimal for degranulation. This finding makes DF3 an ideal reagent for studying the balance of negative and positive signaling …


Recruitment Of The Adaptor Protein Grb2 To Egfr Tetramers, Noga Kozer, Dipak Barua, Christine Henderson, Eduoard C. Nice, Antony W. Burgess, William S. Hlavacek, Andrew H. A. Clayton Apr 2014

Recruitment Of The Adaptor Protein Grb2 To Egfr Tetramers, Noga Kozer, Dipak Barua, Christine Henderson, Eduoard C. Nice, Antony W. Burgess, William S. Hlavacek, Andrew H. A. Clayton

Chemical and Biochemical Engineering Faculty Research & Creative Works

Adaptor protein Grb2 binds phosphotyrosines in the epidermal growth factor (EGF) receptor (EGFR) and thereby links receptor activation to intracellular signaling cascades. Here, we investigated how recruitment of Grb2 to EGFR is affected by the spatial organization and quaternary state of activated EGFR. We used the techniques of image correlation spectroscopy (ICS) and lifetime-detected Förster resonance energy transfer (also known as FLIM-based FRET or FLIM-FRET) to measure ligand-induced receptor clustering and Grb2 binding to activated EGFR in BaF/3 cells. BaF/3 cells were stably transfected with fluorescently labeled forms of Grb2 (Grb2-mRFP) and EGFR (EGFR-eGFP). Following stimulation of the cells with …


Overexpression Of Dcf1 Inhibits Glioma Through Destruction Of Mitochondria And Activation Of Apoptosis Pathway, Yuqiong Xie, Qang Li, Qingbo Yang Jan 2014

Overexpression Of Dcf1 Inhibits Glioma Through Destruction Of Mitochondria And Activation Of Apoptosis Pathway, Yuqiong Xie, Qang Li, Qingbo Yang

Electrical and Computer Engineering Faculty Research & Creative Works

Gliomas are the most common brain tumors affecting the central nervous system and are associated with a high mortality rate. DCF1 is a membrane protein that was previously found to play a role in neural stem cell differentiation. In the present study, we found that overexpression of dcf1 significantly inhibited cell proliferation, migration, and invasion and dramatically promoted apoptosis in the glioblastoma U251 cell line. DCF1 deletion mutations in the functional region showed that the complete structure of DCF1 was necessary for apoptosis. Furthermore, significantly lower tumorigenicity was observed in athymic nude mice by transplanting U251 cells overexpressing dcf1. To …


Specific Intracellular Uptake Of Herceptin-Conjugated Cdse/Zns Quantum Dots Into Breast Cancer Cells, Seung-Jin Han, Pierson Rathinaraj, Soo-Young Park, Young-Kyoo Kim, Joon Hyung Lee, Inn-Kyu Kang, Jong-Sik Moon, Jeffrey G. Winiarz Jan 2014

Specific Intracellular Uptake Of Herceptin-Conjugated Cdse/Zns Quantum Dots Into Breast Cancer Cells, Seung-Jin Han, Pierson Rathinaraj, Soo-Young Park, Young-Kyoo Kim, Joon Hyung Lee, Inn-Kyu Kang, Jong-Sik Moon, Jeffrey G. Winiarz

Chemistry Faculty Research & Creative Works

Herceptin, a typical monoclonal antibody, was immobilized on the surface of CdSe/ZnS core-shell quantum dots (QDs) to enhance their specific interactions with breast cancer cells (SK-BR3). the mean size of the core-shell quantum dots (28 nm), as determined by dynamic light scattering, increased to 86 nm after herceptin immobilization. the in vitro cell culture experiment showed that the keratin forming cancer cells (KB) proliferated well in the presence of herceptin-conjugated QDs (QD-Her, 5 nmol/mL), whereas most of the breast cancer cells (SK-BR3) had died. to clarify the mechanism of cell death, the interaction of SK-BR3 cells with QD-Her was examined …


Modeling The Effect Of Apc Truncation On Destruction Complex Function In Colorectal Cancer Cells, Dipak Barua, William S. Hlavacek Sep 2013

Modeling The Effect Of Apc Truncation On Destruction Complex Function In Colorectal Cancer Cells, Dipak Barua, William S. Hlavacek

Chemical and Biochemical Engineering Faculty Research & Creative Works

In colorectal cancer cells, APC, a tumor suppressor protein, is commonly expressed in truncated form. Truncation of APC is believed to disrupt degradation of β-catenin, which is regulated by a multiprotein complex called the destruction complex. The destruction complex comprises APC, Axin, β-catenin, serine/threonine kinases, and other proteins. The kinases CK1α and GSK-3β, which are recruited by Axin, mediate phosphorylation of β-catenin, which initiates its ubiquitination and proteosomal degradation. The mechanism of regulation of β-catenin degradation by the destruction complex and the role of truncation of APC in colorectal cancer are not entirely understood. Through formulation and analysis of a …


Endocytic Trafficking Of Nanoparticles Delivered By Cell-Penetrating Peptides Comprised Of Nona-Arginine And A Penetration Accelerating Sequence, Betty Revon Liu, Shih-Yen Lo, Chia-Chin Liu, Chia-Lin Chyan, Yue-Wern Huang, Robert Aronstam, Han-Jung Lee Jun 2013

Endocytic Trafficking Of Nanoparticles Delivered By Cell-Penetrating Peptides Comprised Of Nona-Arginine And A Penetration Accelerating Sequence, Betty Revon Liu, Shih-Yen Lo, Chia-Chin Liu, Chia-Lin Chyan, Yue-Wern Huang, Robert Aronstam, Han-Jung Lee

Biological Sciences Faculty Research & Creative Works

Cell-penetrating peptides (CPPs) can traverse cellular membranes and deliver biologically active molecules into cells. In this study, we demonstrate that CPPs comprised of nona-arginine (R9) and a penetration accelerating peptide sequence (Pas) that facilitates escape from endocytic lysosomes, denoted as PR9, greatly enhance the delivery of noncovalently associated quantum dots (QDs) into human A549 cells. Mechanistic studies, intracellular trafficking analysis and a functional gene assay reveal that endocytosis is the main route for intracellular delivery of PR9/QD complexes. Endocytic trafficking of PR9/QD complexes was monitored using both confocal and transmission electron microscopy (TEM). Zeta-potential and size analyses indicate the importance …


Intracellular Delivery Of Nanoparticles And Dnas By Ir9 Cell-Penetrating Peptides, Betty Revon Liu, Ji-Sing Liou, Yue-Wern Huang, Robert Aronstam, Han-Jung Lee May 2013

Intracellular Delivery Of Nanoparticles And Dnas By Ir9 Cell-Penetrating Peptides, Betty Revon Liu, Ji-Sing Liou, Yue-Wern Huang, Robert Aronstam, Han-Jung Lee

Biological Sciences Faculty Research & Creative Works

Cell-penetrating peptides (CPPs) comprised of basic amino residues are able to cross cytoplasmic membranes and are able to deliver biologically active molecules inside cells. However, CPP/cargo entrapment in endosome limits biomedical utility as cargoes are destroyed in the acidic environment. In this study, we demonstrate protein transduction of a novel CPP comprised of an INF7 fusion peptide and nona-arginine (designated IR9). IR9 noncovalently interacts with quantum dots (QDs) and DNAs to form stable IR9/QD and IR9/DNA complexes which are capable of entering human A549 cells. Zeta-potentials were a better predictor of transduction efficiency than gel shift analysis, emphasizing the importance …


Single-Cell Measurements Of Ige-Mediated Fcεri Signaling Using An Integrated Microfluidic Platform, Yanli Liu, Dipak Barua, Peng Liu, Bridget S. Wilson, Janet M. Oliver, William S. Hlavacek, Anup K. Singh Mar 2013

Single-Cell Measurements Of Ige-Mediated Fcεri Signaling Using An Integrated Microfluidic Platform, Yanli Liu, Dipak Barua, Peng Liu, Bridget S. Wilson, Janet M. Oliver, William S. Hlavacek, Anup K. Singh

Chemical and Biochemical Engineering Faculty Research & Creative Works

Heterogeneity in responses of cells to a stimulus, such as a pathogen or allergen, can potentially play an important role in deciding the fate of the responding cell population and the overall systemic response. Measuring heterogeneous responses requires tools capable of interrogating individual cells. Cell signaling studies commonly do not have single-cell resolution because of the limitations of techniques used such as Westerns, ELISAs, mass spectrometry, and DNA microarrays. Microfluidics devices are increasingly being used to overcome these limitations. Here, we report on a microfluidic platform for cell signaling analysis that combines two orthogonal single-cell measurement technologies: on-chip flow cytometry …


Honokiol Blocks Store Operated Calcium Entry In Cho Cells Expressing The M3 Muscarinic Receptor: Honokiol And Muscarinic Signaling, Hsiu-Jen Wang, Alexis Martin, Po-Kuan Chao, Rhett A. Reichard, Adam L. Martin, Yue-Wern Huang, Ming-Huan Chan, Robert Aronstam Feb 2013

Honokiol Blocks Store Operated Calcium Entry In Cho Cells Expressing The M3 Muscarinic Receptor: Honokiol And Muscarinic Signaling, Hsiu-Jen Wang, Alexis Martin, Po-Kuan Chao, Rhett A. Reichard, Adam L. Martin, Yue-Wern Huang, Ming-Huan Chan, Robert Aronstam

Biological Sciences Faculty Research & Creative Works

Background: Honokiol, a cell-permeable phenolic compound derived from the bark of magnolia trees and present in Asian herbal teas, has a unique array of pharmacological actions, including the inhibition of multiple autonomic responses. We determined the effects of honokiol on calcium signaling underlying transmission mediated by human M3 muscarinic receptors expressed in Chinese hamster ovary (CHO) cells. Receptor binding was determined in radiolabelled ligand binding assays; changes in intracellular calcium concentrations were determined using a fura-2 ratiometric imaging protocol; cytotoxicity was determined using a dye reduction assay.

Results: Honokiol had a potent (EC50 ≈ 5 μmol/l) inhibitory effect on store …


Sector Expansion And Elliptical Modeling Of Blue-Gray Ovoids For Basal Cell Carcinoma Discrimination In Dermoscopy Images, Pelin Guvenc, Robert W. Leander, Serkan Kefel, William V. Stoecker, Ryan K. Rader, Kristen A. Hinton, Sherea Monica Stricklin, Harold S. Rabinovitz, Margaret C. Oliviero, Randy Hays Moss Feb 2013

Sector Expansion And Elliptical Modeling Of Blue-Gray Ovoids For Basal Cell Carcinoma Discrimination In Dermoscopy Images, Pelin Guvenc, Robert W. Leander, Serkan Kefel, William V. Stoecker, Ryan K. Rader, Kristen A. Hinton, Sherea Monica Stricklin, Harold S. Rabinovitz, Margaret C. Oliviero, Randy Hays Moss

Chemistry Faculty Research & Creative Works

Background: Blue-gray ovoids (B-GOs), a critical dermoscopic structure for basal cell carcinoma (BCC), offer an opportunity for automatic detection of BCC. Due to variation in size and color, B-GOs can be easily mistaken for similar structures in benign lesions. Analysis of these structures could afford accurate characterization and automatic recognition of B-GOs, furthering the goal of automatic BCC detection. This study utilizes a novel segmentation method to discriminate B-GOs from their benign mimics.

Methods: Contact dermoscopy images of 68 confirmed BCCs with B-GOs were obtained. Another set of 131 contact dermoscopic images of benign lesions possessing B-GO mimics provided a …


Rna Profiles Of Porcine Embryos During Genome Activation Reveal Complex Metabolic Switch Sensitive To In Vitro Conditions, Olga Østrup, Gayla R. Olbricht, Esben Østrup, Poul Hyttel, Philippe Collas, Ryan A. Cabot Jan 2013

Rna Profiles Of Porcine Embryos During Genome Activation Reveal Complex Metabolic Switch Sensitive To In Vitro Conditions, Olga Østrup, Gayla R. Olbricht, Esben Østrup, Poul Hyttel, Philippe Collas, Ryan A. Cabot

Mathematics and Statistics Faculty Research & Creative Works

Fertilization is followed by complex changes in cytoplasmic composition and extensive chromatin reprogramming which results in the abundant activation of totipotent embryonic genome at embryonic genome activation (EGA). While chromatin reprogramming has been widely studied in several species, only a handful of reports characterize changing transcriptome profiles and resulting metabolic changes in cleavage stage embryos. The aims of the current study were to investigate RNA profiles of in vivo developed (ivv) and in vitro produced (ivt) porcine embryos before (2-cell stage) and after (late 4-cell stage) EGA and determine major metabolic changes that regulate totipotency. The period before EGA was …


An Engineered Approach To Stem Cell Culture: Automating The Decision Process For Real-Time Adaptive Subculture Of Stem Cells, Dai Fei Elmer Ker, Lee E. Weiss, Silvina N. Junkers, Mei Chen, Zhaozheng Yin, Mike F. Sandbothe, Seungil Huh, Sungeun Eom, Ryoma Bise, Elvira Osuna-Highley, Takeo Kanade, Phil Gordon Campbell Nov 2011

An Engineered Approach To Stem Cell Culture: Automating The Decision Process For Real-Time Adaptive Subculture Of Stem Cells, Dai Fei Elmer Ker, Lee E. Weiss, Silvina N. Junkers, Mei Chen, Zhaozheng Yin, Mike F. Sandbothe, Seungil Huh, Sungeun Eom, Ryoma Bise, Elvira Osuna-Highley, Takeo Kanade, Phil Gordon Campbell

Computer Science Faculty Research & Creative Works

Current cell culture practices are dependent upon human operators and remain laborious and highly subjective, resulting in large variations and inconsistent outcomes, especially when using visual assessments of cell confluency to determine the appropriate time to subculture cells. Although efforts to automate cell culture with robotic systems are underway, the majority of such systems still require human intervention to determine when to subculture. Thus, it is necessary to accurately and objectively determine the appropriate time for cell passaging. Optimal stem cell culturing that maintains cell pluripotency while maximizing cell yields will be especially important for efficient, cost-effective stem cell-based therapies. …


Nona-Arginine Facilitates Delivery Of Quantum Dots Into Cells Via Multiple Pathways, Yi Xu, Betty Revon Liu, Han Jung Lee, Katie Shannon, Jeffrey G. Winiarz, Tien-Chun Wang, Huey-Jenn Chiang, Yue-Wern Huang Sep 2010

Nona-Arginine Facilitates Delivery Of Quantum Dots Into Cells Via Multiple Pathways, Yi Xu, Betty Revon Liu, Han Jung Lee, Katie Shannon, Jeffrey G. Winiarz, Tien-Chun Wang, Huey-Jenn Chiang, Yue-Wern Huang

Biological Sciences Faculty Research & Creative Works

Semiconductor quantum dots (QDs) have recently been used to deliver and monitor biomolecules, such as drugs and proteins. However, QDs alone have a low efficiency of transport across the plasma membrane. In order to increase the efficiency, we used synthetic nona-arginine (SR9), a cell-penetrating peptide, to facilitate uptake. We found that SR9 increased the cellular uptake of QDs in a noncovalent binding manner between QDs and SR9. Further, we investigated mechanisms of QD/SR9 cellular internalization. Low temperature and metabolic inhibitors markedly inhibited the uptake of QD/SR9, indicating that internalization is an energy-dependent process. Results from both the pathway inhibitors and …


Reverse Engineering Of Oxygen Transport In The Lung: Adaptation To Changing Demands And Resources Through Space-Filling Networks, Chen Hou, Stefan Gheorghiu, Virginia H. Huxley, Peter Pfeifer Aug 2010

Reverse Engineering Of Oxygen Transport In The Lung: Adaptation To Changing Demands And Resources Through Space-Filling Networks, Chen Hou, Stefan Gheorghiu, Virginia H. Huxley, Peter Pfeifer

Biological Sciences Faculty Research & Creative Works

The space-filling fractal network in the human lung creates a remarkable distribution system for gas exchange. Landmark studies have illuminated how the fractal network guarantees minimum energy dissipation, slows air down with minimum hardware, maximizes the gas- exchange surface area, and creates respiratory flexibility between rest and exercise. In this paper, we investigate how the fractal architecture affects oxygen transport and exchange under varying physiological conditions, with respect to performance metrics not previously studied. We present a renormalization treatment of the diffusion-reaction equation which describes how oxygen concentrations drop in the airways as oxygen crosses the alveolar membrane system. The …


Analysis Of Globule Types In Malignant Melanoma, Jin Xu, Kapil Kumar Gupta, William V. Stoecker, Yamini Krishnamurthy, Harold S. Rabinovitz, Austin Bangert, David A. Calcara, Margaret C. Oliviero, Joseph M. Malters, Rhett J. Drugge, R. Joe Stanley, Randy Hays Moss, Mehmed Emre Celebi Nov 2009

Analysis Of Globule Types In Malignant Melanoma, Jin Xu, Kapil Kumar Gupta, William V. Stoecker, Yamini Krishnamurthy, Harold S. Rabinovitz, Austin Bangert, David A. Calcara, Margaret C. Oliviero, Joseph M. Malters, Rhett J. Drugge, R. Joe Stanley, Randy Hays Moss, Mehmed Emre Celebi

Chemistry Faculty Research & Creative Works

Objective: To identify and analyze subtypes of globules based on size, shape, network connectedness, pigmentation, and distribution to determine which globule types and globule distributions are most frequently associated with a diagnosis of malignant melanoma. Design: Retrospective case series of dermoscopy images with globules. Setting: Private dermatology practices. Participants: Patients in dermatology practices. Intervention: Observation only. Main Outcome Measure: Association of globule types with malignant melanoma. Results: The presence of large globules (odds ratio [OR], 5.25) and globules varying in size (4.72) or shape (5.37) had the highest ORs for malignant melanoma among all globule types and combinations studied. Classical …


Identifying Sleep Regulatory Genes Using A Drosophila Model Of Insomnia, Laurent Seugnet, Yasuko Suzuki, Matthew S. Thimgan, Jeffrey Donlea, Sarah I. Gimbel, Laura Gottschalk, Stephen P. Duntley, Paul J. Shaw Jun 2009

Identifying Sleep Regulatory Genes Using A Drosophila Model Of Insomnia, Laurent Seugnet, Yasuko Suzuki, Matthew S. Thimgan, Jeffrey Donlea, Sarah I. Gimbel, Laura Gottschalk, Stephen P. Duntley, Paul J. Shaw

Biological Sciences Faculty Research & Creative Works

Although it is widely accepted that sleep must serve an essential biological function, little is known about molecules that underlie sleep regulation. Given that insomnia is a common sleep disorder that disrupts the ability to initiate and maintain restorative sleep, a better understanding of its molecular underpinning may provide crucial insights into sleep regulatory processes. Thus, we created a line of flies using laboratory selection that share traits with human insomnia. After 60 generations, insomnia-like (ins-l) flies sleep 60 min a day, exhibit difficulty initiating sleep, difficulty maintaining sleep, and show evidence of daytime cognitive impairment. ins-l flies …


Computational Models Of Tandem Src Homology 2 Domain Interactions And Application To Phosphoinositide 3-Kinase, Dipak Barua, James R. Faeder, Jason M. Haugh Mar 2008

Computational Models Of Tandem Src Homology 2 Domain Interactions And Application To Phosphoinositide 3-Kinase, Dipak Barua, James R. Faeder, Jason M. Haugh

Chemical and Biochemical Engineering Faculty Research & Creative Works

Intracellular signal transduction proteins typically utilize multiple interaction domains for proper targeting, and thus a broad diversity of distinct signaling complexes may be assembled. Considering the coordination of only two such domains, as in tandem Src homology 2 (SH2) domain constructs, gives rise to a kinetic scheme that is not adequately described by simple models used routinely to interpret in vitro binding measurements. To analyze the interactions between tandem SH2 domains and bisphosphorylated peptides, we formulated detailed kinetic models and applied them to the phosphoinositide 3-kinase p85 regulatory subunit/platelet-derived growth factor β-receptor system. Data for this system from different in …


Bifidobacteria In Feces And Environmental Waters, Regina Lamendella, Jorge W. Santo Domingo, Catherine A. Kelty, Daniel B. Oerther Feb 2008

Bifidobacteria In Feces And Environmental Waters, Regina Lamendella, Jorge W. Santo Domingo, Catherine A. Kelty, Daniel B. Oerther

Civil, Architectural and Environmental Engineering Faculty Research & Creative Works

Bifidobacteria have been recommended as potential indicators of human fecal pollution in surface waters even though very little is known about their presence in nonhuman fecal sources. The objective of this research was to shed light on the occurrence and molecular diversity of this fecal indicator group in different animals and environmental waters. Genus- and species-specific 16S rRNA gene PCR assays were used to study the presence of bifidobacteria among 269 fecal DNA extracts from 32 different animals. Twelve samples from three wastewater treatment plants and 34 water samples from two fecally impacted watersheds were also tested. The species-specific assays …


Taxol-Stabilized Microtubules Can Position The Cytokinetic Furrow In Mammalian Cells, Katie Shannon, Julie C. Canman, C. Ben Moree, Jennifer S. Tirnauer, Edward D. Salmon Sep 2005

Taxol-Stabilized Microtubules Can Position The Cytokinetic Furrow In Mammalian Cells, Katie Shannon, Julie C. Canman, C. Ben Moree, Jennifer S. Tirnauer, Edward D. Salmon

Biological Sciences Faculty Research & Creative Works

How microtubules act to position the plane of cell division during cytokinesis is a topic of much debate. Recently, we showed that a subpopulation of stable microtubules extends past chromosomes and interacts with the cell cortex at the site of furrowing, suggesting that these stabilized microtubules may stimulate contractility. To test the hypothesis that stable microtubules can position furrows, we used taxol to rapidly suppress microtubule dynamics during various stages of mitosis in PtK1 cells. Cells with stabilized prometaphase or metaphase microtubule arrays were able to initiate furrowing when induced into anaphase by inhibition of the spindle checkpoint. In these …


Melanoma And Seborrheic Keratosis Differentiation Using Texture Features, Srinivas V. Deshabhoina, Scott E. Umbaugh, William V. Stoecker, Randy Hays Moss, Subhashini K. Srinivasan Nov 2003

Melanoma And Seborrheic Keratosis Differentiation Using Texture Features, Srinivas V. Deshabhoina, Scott E. Umbaugh, William V. Stoecker, Randy Hays Moss, Subhashini K. Srinivasan

Chemistry Faculty Research & Creative Works

Purpose: To explore texture features in two-dimensional images to differentiate seborrheic keratosis from melanoma.

Methods: A systematic approach to consistent classification of skin tumors is described. Texture features, based on the second-order histogram, were used to identify the features or a combination of features that could consistently differentiate a malignant skin tumor (melanoma) from a benign one (seborrheic keratosis). Two hundred and seventy-one skin tumor images were separated into training and test sets for accuracy and consistency. Automatic induction was applied to generate classification rules. Data analysis and modeling tools were used to gain further insight into the feature space. …


Mad2 And Bubr1 Function In A Single Checkpoint Pathway That Responds To A Loss Of Tension, Katie Shannon, Julie C. Canman, Edward D. Salmon Oct 2002

Mad2 And Bubr1 Function In A Single Checkpoint Pathway That Responds To A Loss Of Tension, Katie Shannon, Julie C. Canman, Edward D. Salmon

Biological Sciences Faculty Research & Creative Works

The spindle checkpoint monitors microtubule attachment and tension at kinetochores to ensure proper chromosome segregation. Previously, PtK1 cells in hypothermic conditions (23°C) were shown to have a pronounced mitotic delay, despite having normal numbers of kinetochore microtubules. At 23°C, we found that PtK1 cells remained in metaphase for an average of 101 min, compared with 21 min for cells at 37°C. The metaphase delay at 23°C was abrogated by injection of Mad2 inhibitors, showing that Mad2 and the spindle checkpoint were responsible for the prolonged metaphase. Live cell imaging showed that kinetochore Mad2 became undetectable soon after chromosome congression. Measurements …