Open Access. Powered by Scholars. Published by Universities.®

Life Sciences Commons

Open Access. Powered by Scholars. Published by Universities.®

Articles 1 - 30 of 101

Full-Text Articles in Life Sciences

Cullin-4 Regulates Wingless And Jnk Signaling-Mediated Cell Death In The Drosophila Eye., Meghana Tare, Ankita Sarkar, Shimpi Bedi, Madhuri Kango-Singh, Amit Singh Dec 2016

Cullin-4 Regulates Wingless And Jnk Signaling-Mediated Cell Death In The Drosophila Eye., Meghana Tare, Ankita Sarkar, Shimpi Bedi, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

In all multicellular organisms, the fundamental processes of cell proliferation and cell death are crucial for growth regulation during organogenesis. Strict regulation of cell death is important to maintain tissue homeostasis by affecting processes like regulation of cell number, and elimination of unwanted/unfit cells. The developing Drosophila eye is a versatile model to study patterning and growth, where complex signaling pathways regulate growth and cell survival. However, the molecular mechanisms underlying regulation of these processes is not fully understood. In a gain-of-function screen, we found that misexpression of cullin-4 (cul-4), an ubiquitin ligase, can rescue reduced eye mutant phenotypes. Previously, …


Murine Models Of Splenic Marginal Zone Lymphoma: A Role For Cav1?, Chelsey L. Patten, Christine E. Cutucache Dec 2016

Murine Models Of Splenic Marginal Zone Lymphoma: A Role For Cav1?, Chelsey L. Patten, Christine E. Cutucache

Biology Faculty Publications

Dozens of murine models of indolent and aggressive B-cell lymphomas have been generated to-date. These include those manifesting chronic lymphocytic leukemia (CLL), diffuse large B-cell lymphoma (DLBCL) as well as xenografts of mantle cell lymphoma (MCL). These models have led to an improved understanding of disease etiology, B-cell biology, immunomodulation, and the importance of the tumor microenvironment. Despite these efforts in CLL, DLBCL, and MCL, considerably little progress toward a model of splenic marginal zone lymphoma (SMZL) has been accomplished. Herein, we describe the similarities and differences between CLL, MCL, and SMZL, and highlight effective murine models that mimic disease …


Animating And Exploring Phylogenies With Fibre Plots, William D. Pearse Nov 2016

Animating And Exploring Phylogenies With Fibre Plots, William D. Pearse

Biology Faculty Publications

Despite the progress that has been made in many other aspects of data visualisation, phylogenies are still represented in much the same way as they first were by Darwin. In this brief essay, I give a short review of what I consider to be some recent major advances, and outline a new kind of phylogenetic visualisation. This new graphic, the fibre plot, uses the metaphor of sections through a tree to describe change in a phylogeny. I suggest it is a useful tool in gaining an rapid overview of the timing and scale of diversification in large phylogenies.


Photography-Based Taxonomy Is Inadequate, Unnecessary, And Potentially Harmful For Biological Sciences, Luis M. P. Ceríaco, Eliécer E. Gutiérrez, Alain Dubois, Rafael O. De Sá, Et Al. Nov 2016

Photography-Based Taxonomy Is Inadequate, Unnecessary, And Potentially Harmful For Biological Sciences, Luis M. P. Ceríaco, Eliécer E. Gutiérrez, Alain Dubois, Rafael O. De Sá, Et Al.

Biology Faculty Publications

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per …


Importance Of Heat And Pressure For Solubilization Of Recombinant Spider Silk Proteins In Aqueous Solution, Justin A. Jones, Thomas I. Harris, Paula F. Oliveira, Brianne E. Bell, Abdulrahman Alhabib, Randolph V. Lewis Nov 2016

Importance Of Heat And Pressure For Solubilization Of Recombinant Spider Silk Proteins In Aqueous Solution, Justin A. Jones, Thomas I. Harris, Paula F. Oliveira, Brianne E. Bell, Abdulrahman Alhabib, Randolph V. Lewis

Biology Faculty Publications

The production of recombinant spider silk proteins continues to be a key area of interest for a number of research groups. Several key obstacles exist in their production as well as in their formulation into useable products. The original reported method to solubilize recombinant spider silk proteins (rSSp) in an aqueous solution involved using microwaves to quickly generate heat and pressure inside of a sealed vial containing rSSp and water. Fibers produced from this system are remarkable in their mechanical ability and demonstrate the ability to be stretched and recover 100 times. The microwave method dissolves the rSSPs with dissolution …


Photography-Based Taxonomy Is Inadequate, Unnecessary, And Potentially Harmful For Biological Sciences, Luis M P Ceríaco, Eliécer E. Gutiérrez, Alain Dubois, Hendrik Freitag, 537 Co-Authors Nov 2016

Photography-Based Taxonomy Is Inadequate, Unnecessary, And Potentially Harmful For Biological Sciences, Luis M P Ceríaco, Eliécer E. Gutiérrez, Alain Dubois, Hendrik Freitag, 537 Co-Authors

Biology Faculty Publications

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per …


Assessment Of Olfactory Function In Maptassociated Neurodegenerative Disease Reveals Odor-Identification Irreproducibility As A Non-Disease-Specific, General Characteristic Of Olfactory Dysfunction, Katerina Markopoulou, Bruce A. Chase, Piotr Robowski, Audrey Strongosky, Ewa Narożańska, Emilia J. Sitek, Mariusz Berdynski, Maria Barcikowska, Matt C. Baker, Jarosøaw Søawek, Christine Klein, Katja Hückelheim, Meike Kasten, Zbigniew K. Wszolek Nov 2016

Assessment Of Olfactory Function In Maptassociated Neurodegenerative Disease Reveals Odor-Identification Irreproducibility As A Non-Disease-Specific, General Characteristic Of Olfactory Dysfunction, Katerina Markopoulou, Bruce A. Chase, Piotr Robowski, Audrey Strongosky, Ewa Narożańska, Emilia J. Sitek, Mariusz Berdynski, Maria Barcikowska, Matt C. Baker, Jarosøaw Søawek, Christine Klein, Katja Hückelheim, Meike Kasten, Zbigniew K. Wszolek

Biology Faculty Publications

Olfactory dysfunction is associated with normal aging, multiple neurodegenerative disorders, including Parkinson’s disease, Lewy body disease and Alzheimer’s disease, and other diseases such as diabetes, sleep apnea and the autoimmune disease myasthenia gravis. The wide spectrum of neurodegenerative disorders associated with olfactory dysfunction suggests different, potentially overlapping, underlying pathophysiologies. Studying olfactory dysfunction in presymptomatic carriers of mutations known to cause familial parkinsonism provides unique opportunities to understand the role of genetic factors, delineate the salient characteristics of the onset of olfactory dysfunction, and understand when it starts relative to motor and cognitive symptoms. We evaluated olfactory dysfunction in 28 carriers …


Transcriptomic Comparison Of Invasive Bigheaded Carps (Hypophthalmichthys Nobilis And Hypophthalmichthys Molitrix) And Their Hybrids, Jun Wang, James T. Lamer, Sarah Gaughan, Michael Wachholtz, Chenghui Wang, Guoquing Lu Oct 2016

Transcriptomic Comparison Of Invasive Bigheaded Carps (Hypophthalmichthys Nobilis And Hypophthalmichthys Molitrix) And Their Hybrids, Jun Wang, James T. Lamer, Sarah Gaughan, Michael Wachholtz, Chenghui Wang, Guoquing Lu

Biology Faculty Publications

Bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix), collectively called bigheaded carps, are invasive species in the Mississippi River Basin (MRB). Interspecific hybridization between bigheaded carps has been considered rare within their native rivers in China; however, it is prevalent in the MRB. We conducted de novo transcriptome analysis of pure and hybrid bigheaded carps and obtained 40,759 to 51,706 transcripts for pure, F1 hybrid, and backcross bigheaded carps. The search against protein databases resulted in 20,336–28,133 annotated transcripts (over 50% of the transcriptome) with over 13,000 transcripts mapped to 23 Gene Ontology biological processes and 127 KEGG metabolic …


Better Late Than Never: Effective Air-Borne Hearing Of Toads Delayed By Late Maturation Of The Tympanic Middle Ear Structures, Molly C. Womack, Jakob Christensen-Dalsgaard, Kim L. Hoke Oct 2016

Better Late Than Never: Effective Air-Borne Hearing Of Toads Delayed By Late Maturation Of The Tympanic Middle Ear Structures, Molly C. Womack, Jakob Christensen-Dalsgaard, Kim L. Hoke

Biology Faculty Publications

Most vertebrates have evolved a tympanic middle ear that enables effective hearing of airborne sound on land. Although inner ears develop during the tadpole stages of toads, tympanic middle ear structures are not complete until months after metamorphosis, potentially limiting the sensitivity of post-metamorphic juveniles to sounds in their environment. We tested the hearing of five species of toads to determine how delayed ear development impairs airborne auditory sensitivity. We performed auditory brainstem recordings to test the hearing of the toads and used micro-computed tomography and histology to relate the development of ear structures to hearing ability. We found a …


Beryllium Nitrate Inhibits Fibroblast Migration To Disrupt Epimorphic Regeneration, Adam B. Cook, Ashley W. Seifert Oct 2016

Beryllium Nitrate Inhibits Fibroblast Migration To Disrupt Epimorphic Regeneration, Adam B. Cook, Ashley W. Seifert

Biology Faculty Publications

Epimorphic regeneration proceeds with or without formation of a blastema, as observed for the limb and skin, respectively. Inhibition of epimorphic regeneration provides a means to interrogate the cellular and molecular mechanisms that regulate it. In this study, we show that exposing amputated limbs to beryllium nitrate disrupts blastema formation and causes severe patterning defects in limb regeneration. In contrast, exposing full-thickness skin wounds to beryllium only causes a delay in skin regeneration. By transplanting full-thickness skin from ubiquitous GFP-expressing axolotls to wild-type hosts, we demonstrate that beryllium inhibits fibroblast migration during limb and skin regeneration in vivo. Moreover, …


Correlation Analysis Of Enzyme Activities And Deconstruction Of Ammonia-Pretreated Switchgrass By Bacterial-Fungal Communities, Abhiney Jain, H. Sandra Pelle, J. Michael Henson Oct 2016

Correlation Analysis Of Enzyme Activities And Deconstruction Of Ammonia-Pretreated Switchgrass By Bacterial-Fungal Communities, Abhiney Jain, H. Sandra Pelle, J. Michael Henson

Biology Faculty Publications

The mixed microbial communities that occur naturally on lignocellulosic feedstocks can provide feedstock-specific enzyme mixtures to saccharify lignocelluloses. Bacterial-fungal communities were enriched from switchgrass bales to deconstruct ammonia-pretreated switchgrass (DSG). Correlation analysis was carried out to elucidate the relationship between microbial decomposition of DSG by these communities, enzymatic activities produced and enzymatic saccharification of DSG using these enzyme mixtures. Results of the analysis showed that β glucosidase activities and xylosidase activities limited the extent of microbial deconstruction and enzymatic saccharification of DSG. The results also underlined the importance of ligninase activity for the enzymatic saccharification of pretreated lignocellulosic feedstock. The …


Convergence In Nitrogen Deposition And Cryptic Isotopic Variation Across Urban And Agricultural Valleys In Northern Utah, Steven J. Hall, E. M. Ogata, Samantha R. Weintraub, Michelle A. Baker, James R. Ehleringer, C I. Czimczik, David R. Bowling Sep 2016

Convergence In Nitrogen Deposition And Cryptic Isotopic Variation Across Urban And Agricultural Valleys In Northern Utah, Steven J. Hall, E. M. Ogata, Samantha R. Weintraub, Michelle A. Baker, James R. Ehleringer, C I. Czimczik, David R. Bowling

Biology Faculty Publications

The extent to which atmospheric nitrogen (N) deposition reflects land use differences and biogenic versus fossil fuel reactive N sources remains unclear yet represents a critical uncertainty in ecosystem N budgets. We compared N concentrations and isotopes in precipitation-event bulk (wet + dry) deposition across nearby valleys in northern Utah with contrasting land use (highly urban versus intensive agriculture/low-density urban). We predicted greater nitrate (NO3−) versus ammonium (NH4+) and higher δ15N of NO3− and NH4+ in urban valley sites. Contrary to expectations, annual N deposition (3.5–5.1 kg N ha−1 yr−1) and inorganic N concentrations were similar within and between valleys. …


Secondary Structure Adopted By The Gly-Gly-X Repetitive Regions Of Dragline Spider Silk, Geoffrey M. Gray, Arjan Van Der Vaart, Chengchen Guo, Justin A. Jones, David Onofrei, Brian R. Cherry, Randolph V. Lewis, Jeffery L. Yarger, Gregory P. Holland Sep 2016

Secondary Structure Adopted By The Gly-Gly-X Repetitive Regions Of Dragline Spider Silk, Geoffrey M. Gray, Arjan Van Der Vaart, Chengchen Guo, Justin A. Jones, David Onofrei, Brian R. Cherry, Randolph V. Lewis, Jeffery L. Yarger, Gregory P. Holland

Biology Faculty Publications

Solid-state NMR and molecular dynamics (MD) simulations are presented to help elucidate the molecular secondary structure of poly(Gly-Gly-X), which is one of the most common structural repetitive motifs found in orb-weaving dragline spider silk proteins. The combination of NMR and computational experiments provides insight into the molecular secondary structure of poly(Gly-Gly-X) segments and provides further support that these regions are disordered and primarily non-β-sheet. Furthermore, the combination of NMR and MD simulations illustrate the possibility for several secondary structural elements in the poly(Gly-Gly-X) regions of dragline silks, including β-turns, 310-helicies, and coil structures with a negligible population of α-helix observed.


Review Of Experimental Compounds Demonstrating Anti-Toxoplasma Activity, Madalyn M. Mcfarland, Sydney J. Zach, Xiaofang Wang, Lakshmi-Prasad Potluri, Andrew J. Neville, Jonathan L. Vennerstrom, Paul H. Davis Sep 2016

Review Of Experimental Compounds Demonstrating Anti-Toxoplasma Activity, Madalyn M. Mcfarland, Sydney J. Zach, Xiaofang Wang, Lakshmi-Prasad Potluri, Andrew J. Neville, Jonathan L. Vennerstrom, Paul H. Davis

Biology Faculty Publications

Toxoplasma gondii is a ubiquitous apicomplexan parasite capable of infecting humans and other animals. Current treatment options for T. gondii infection are limited and most have drawbacks, including high toxicity and low tolerability. Additionally, no FDA-approved treatments are available for pregnant women, a high-risk population due to transplacental infection. Therefore, the development of novel treatment options is needed. To aid this effort, this review highlights experimental compounds that, at a minimum, demonstrate inhibition of in vitro growth of T. gondii. When available, host cell toxicity and in vivo data are also discussed. The purpose of this review is to facilitate …


Burrowing Through The Heterogeneity: Review Of Mouse Models Of Ptcl-Nos, Christine E. Cutucache, Tyler Herek Aug 2016

Burrowing Through The Heterogeneity: Review Of Mouse Models Of Ptcl-Nos, Christine E. Cutucache, Tyler Herek

Biology Faculty Publications

Currently, there are 19 different peripheral T-cell lymphoma (PTCL) entities recognized by the World Health Organization; however, ~70% of PTCL diagnoses fall within one of three subtypes [i.e., peripheral T-cell lymphoma not otherwise specified (PTCL-NOS), anaplastic large-cell lymphoma, and angioimmunoblastic T-cell lymphoma]. PTCL-NOS is a grouping of extra-thymic neoplasms that represent a challenging and heterogeneous subset of non-Hodgkin’s lymphomas. Research into peripheral T-cell lymphomas has been cumbersome as the lack of defining cytogenetic, histological, and molecular features has stymied diagnosis and treatment of these diseases. Similarly, the lacks of genetically manipulated murine models that faithfully recapitulate disease characteristics were absent …


App Regulates Microglial Phenotype In A Mouse Model Of Alzheimer's Disease, Gunjan D. Manocha, Angela M. Floden, Keiko Rausch, Joshua A. Kulas, Brett A. Mcgregor, Lalida Rojanathammanee, Kelley R. Puig, Kendra L. Puig, Sanjib Karki, Michael R. Nichols, Diane C. Darland, James E. Porter, Colin K. Combs Aug 2016

App Regulates Microglial Phenotype In A Mouse Model Of Alzheimer's Disease, Gunjan D. Manocha, Angela M. Floden, Keiko Rausch, Joshua A. Kulas, Brett A. Mcgregor, Lalida Rojanathammanee, Kelley R. Puig, Kendra L. Puig, Sanjib Karki, Michael R. Nichols, Diane C. Darland, James E. Porter, Colin K. Combs

Biology Faculty Publications

Prior work suggests that amyloid precursor protein (APP) can function as a proinflammatory receptor on immune cells, such as monocytes and microglia. Therefore, we hypothesized that APP serves this function in microglia during Alzheimer's disease. Although fibrillar amyloid β (Aβ)-stimulated cytokine secretion from both wild-type and APP knock-out (mAPP−/−) microglial cultures, oligomeric Aβ was unable to stimulate increased secretion from mAPP−/− cells. This was consistent with an ability of oligomeric Aβ to bind APP. Similarly, intracerebroventricular infusions of oligomeric Aβ produced less microgliosis in mAPP−/− mice compared with wild-type mice. The mAPP−/− mice crossed to an APP/PS1 transgenic mouse line …


External Morphology Of The Eggs Of Asplanchnopus Multiceps (Schrank, 1793) (Rotifera): Solving The 150-Year-Old Case Of Mistaken Identity, Elizabeth S. Wurdak Aug 2016

External Morphology Of The Eggs Of Asplanchnopus Multiceps (Schrank, 1793) (Rotifera): Solving The 150-Year-Old Case Of Mistaken Identity, Elizabeth S. Wurdak

Biology Faculty Publications

This report calls into question the practice of passing along illustrations and anatomical descriptions from the literature without scrutiny. An error made by Leydig (Zeischrift für wissenschaftliche Zoologie 6:1–120, 1854) in characterizing the egg of Asplanchnopus multiceps was perpetuated in authoritative publications (Hyman, The Invertebrates: Acanthocephala, Aschelminthes, and Entoprocta. The pseudocoelomate Bilateria, McGraw-Hill Book Company, New York, 1951; Voigt, Rotatoria: Die Rädertiere Mitteleuropas, Gebrüder Borntraeger, Berlin-Nikolassee, 1957; Ruttner-Kolisko, Plankton rotifers, biology and taxonomy supplementary edition of Die Binnengewässer 26, Stuttgart, 1974; Koste, Rotatoria: Die Rädertiere Mitteleuropas begründet von Max Voigt. Monogononta 2. Auflage neubearbeitet von Walter Koste, Gebrüder Borntraeger, Berlin, …


Human Observers Differ In Ability To Perceive Insect Diversity, Joseph S. Wilson, Joshua P. Jahner, Matthew L. Forister Aug 2016

Human Observers Differ In Ability To Perceive Insect Diversity, Joseph S. Wilson, Joshua P. Jahner, Matthew L. Forister

Biology Faculty Publications

Human perception of biological variation is an important and understudied issue in the conservation and management of natural resources. Here, we took a novel approach by asking 1152 participants, primarily college biology students, to score examples of insect mimicry by the number of distinct kinds of animals they saw. Latent class analysis successfully separated participants based on their accuracy of perception as well as demographic information and opinions about biodiversity. Contrary to expectations, factors such as childhood experience (growing up in urban, suburban or rural areas) did not affect the ability to see biodiversity as much as political views (location …


Physiological Perturbation Reveals Modularity Of Eyespot Development In The Painted Lady Butterfly, Vanessa Cardui, Heidi Connahs, Turk Rhen, Rebecca Simmons Aug 2016

Physiological Perturbation Reveals Modularity Of Eyespot Development In The Painted Lady Butterfly, Vanessa Cardui, Heidi Connahs, Turk Rhen, Rebecca Simmons

Biology Faculty Publications

Butterfly eyespots are complex morphological traits that can vary in size, shape and color composition even on the same wing surface. Homology among eyespots suggests they share a common developmental basis and function as an integrated unit in response to selection. Despite strong evidence of genetic integration, eyespots can also exhibit modularity or plasticity, indicating an underlying flexibility in pattern development. The extent to which particular eyespots or eyespot color elements exhibit modularity or integration is poorly understood, particularly following exposure to novel conditions. We used perturbation experiments to explore phenotypic correlations among different eyespots and their color elements on …


Molecular Cloning And Expression Of Chitin Deacetylase 1 Gene From The Gills Of Penaeus Monodon (Black Tiger Shrimp), Katreena P. Sarmiento, Vivian A. Panes, Mudjekeewis D. Santos Aug 2016

Molecular Cloning And Expression Of Chitin Deacetylase 1 Gene From The Gills Of Penaeus Monodon (Black Tiger Shrimp), Katreena P. Sarmiento, Vivian A. Panes, Mudjekeewis D. Santos

Biology Faculty Publications

Chitin deacetylases have been identified and studied in several fungi and insects but not in crustaceans. These glycoproteins function in catalyzing the conversion of chitin to chitosan by the hydrolysis of N-acetamido bonds of chitin. Here, for the first time, the full length cDNA of chitin deacetylase (CDA) gene from crustaceans was fully cloned using a partial fragment obtained from a transcriptome database of the gills of black tiger shrimp Penaeus monodon that survived White Spot Syndrome Virus (WSSV) infection employing Rapid Amplification of cDNA Ends (RACE) PCR. The shrimp CDA, named PmCDA1, was further characterized by in silico …


A Review On The Invasion Ecology Of Amur Honeysuckle (Lonicera Maackii, Caprifoliaceae), A Case Study Of Ecological Impacts At Multiple Scales, Rachel E. Mcneish, Ryan W. Mcewan Aug 2016

A Review On The Invasion Ecology Of Amur Honeysuckle (Lonicera Maackii, Caprifoliaceae), A Case Study Of Ecological Impacts At Multiple Scales, Rachel E. Mcneish, Ryan W. Mcewan

Biology Faculty Publications

Invasive species are of global importance because of their impacts on ecological communities, habitat structure, native community dynamics, and ecosystem processes and function. Scientists and conservation managers are increasingly focusing on the biological impacts of invasive species and on devising management practices that emphasize the health of ecosystems based on measured biological processes. Amur honeysuckle (Lonicera maackii (Rupr.) Herder) is a highly successful invasive shrub in forests of eastern North America. The scientific literature surrounding this species has grown in the past several decades as researchers have investigated L. maackii impacts across multiple ecological scales. In this review we …


Thirty Years Of Compositional Change In An Old-Growth Temperate Forest: The Role Of Topographic Gradients In Oak-Maple Dynamics, Julia I. Chapman, Ryan W. Mcewan Jul 2016

Thirty Years Of Compositional Change In An Old-Growth Temperate Forest: The Role Of Topographic Gradients In Oak-Maple Dynamics, Julia I. Chapman, Ryan W. Mcewan

Biology Faculty Publications

Ecological communities are structured in response to spatial and temporal variation of numerous factors, including edaphic conditions, biotic interactions, climatic patterns and disturbance regimes. Widespread anthropogenic factors such as timber harvesting can create long-lasting impacts, obscuring the relationship between community structure and environmental conditions. Minimally impacted systems such as old-growth forests can serve as a useful ecological baseline for predicting long-term compositional shifts. We utilized decadal tree species sampling data (1979–2010) divided into three strata (understory, midstory, overstory) to examine temporal changes in relative abundances and spatial distributions of dominant taxa, as well as overall shifts in community composition, in …


Model-Based Clustering With Certainty Estimation: Implication For Clade Assignment Of Influenza Viruses, Shunpu Zhang, Zhong Li, Kevin Beland, Guoquing Lu Jul 2016

Model-Based Clustering With Certainty Estimation: Implication For Clade Assignment Of Influenza Viruses, Shunpu Zhang, Zhong Li, Kevin Beland, Guoquing Lu

Biology Faculty Publications

Background

Clustering is a common technique used by molecular biologists to group homologous sequences and study evolution. There remain issues such as how to cluster molecular sequences accurately and in particular how to evaluate the certainty of clustering results.

Results

We presented a model-based clustering method to analyze molecular sequences, described a subset bootstrap scheme to evaluate a certainty of the clusters, and showed an intuitive way using 3D visualization to examine clusters. We applied the above approach to analyze influenza viral hemagglutinin (HA) sequences. Nine clusters were estimated for high pathogenic H5N1 avian influenza, which agree with previous findings. …


System-Aware Smart Network Management For Nano-Enriched Water Quality Monitoring, Bassem Mokhtar, Mohamed Azab, Nader Shehata, Mohamed Rizk Jul 2016

System-Aware Smart Network Management For Nano-Enriched Water Quality Monitoring, Bassem Mokhtar, Mohamed Azab, Nader Shehata, Mohamed Rizk

Biology Faculty Publications

This paper presents a comprehensive water quality monitoring system that employs a smart network management, nano-enriched sensing framework, and intelligent and efficient data analysis and forwarding protocols for smart and system-aware decision making. The presented system comprises two main subsystems, a data sensing and forwarding subsystem (DSFS), and Operation Management Subsystem (OMS). The OMS operates based on real-time learned patterns and rules of system operations projected from the DSFS to manage the entire network of sensors. The main tasks of OMS are to enable real-time data visualization, managed system control, and secure system operation. The DSFS employs a Hybrid Intelligence …


Pheromone Lure And Trap Color Affects Bycatch In Agricultural Landscapes Of Utah, Lori R. Spears, Chris Looney, Harold Ikerd, Jonathan B. Koch, Terry L. Griswold, James P. Strange, Ricardo A. Ramirez Jul 2016

Pheromone Lure And Trap Color Affects Bycatch In Agricultural Landscapes Of Utah, Lori R. Spears, Chris Looney, Harold Ikerd, Jonathan B. Koch, Terry L. Griswold, James P. Strange, Ricardo A. Ramirez

Biology Faculty Publications

Aerial traps, using combinations of color and attractive lures, are a critical tool for detecting and managing insect pest populations. Yet, despite improvements in trap efficacy, collection of nontarget species (“bycatch”) plagues many insect pest surveys. Bycatch can influence survey effectiveness by reducing the available space for target species and increasing trap screening time, especially in areas where thousands of insects are captured as bycatch in a given season. Additionally, bycatch may negatively impact local nontarget insect populations, including beneficial predators and pollinators. Here, we tested the effect of pheromone lures on bycatch rates of Coccinellidae (Coleoptera), Apoidea (Hymenoptera), and …


Cellular And Molecular Features Of Developmentally Programmed Genome Rearrangement In A Vertebrate (Sea Lamprey: Petromyzon Marinus), Vladimir A. Timoshevskiy, Joseph R. Herdy, Melissa C. Keinath, Jeramiah J. Smith Jun 2016

Cellular And Molecular Features Of Developmentally Programmed Genome Rearrangement In A Vertebrate (Sea Lamprey: Petromyzon Marinus), Vladimir A. Timoshevskiy, Joseph R. Herdy, Melissa C. Keinath, Jeramiah J. Smith

Biology Faculty Publications

The sea lamprey (Petromyzon marinus) represents one of the few vertebrate species known to undergo large-scale programmatic elimination of genomic DNA over the course of its normal development. Programmed genome rearrangements (PGRs) result in the reproducible loss of ~20% of the genome from somatic cell lineages during early embryogenesis. Studies of PGR hold the potential to provide novel insights related to the maintenance of genome stability during the cell cycle and coordination between mechanisms responsible for the accurate distribution of chromosomes into daughter cells, yet little is known regarding the mechanistic basis or cellular context of PGR in …


Sine-Wave Electrical Stimulation Initiates A Voltage-Gated Potassium Channel-Dependent Soft Tissue Response Characterized By Induction Of Hemocyte Recruitment And Collagen Deposition, Brandon M. Franklin, Eleni Maroudas, Jeffrey L. Osborn Jun 2016

Sine-Wave Electrical Stimulation Initiates A Voltage-Gated Potassium Channel-Dependent Soft Tissue Response Characterized By Induction Of Hemocyte Recruitment And Collagen Deposition, Brandon M. Franklin, Eleni Maroudas, Jeffrey L. Osborn

Biology Faculty Publications

Soft tissue repair is a complex process that requires specific communication between multiple cell types to orchestrate effective restoration of physiological functions. Macrophages play a critical role in this wound healing process beginning at the onset of tissue injury. Understanding the signaling mechanisms involved in macrophage recruitment to the wound site is an essential step for developing more effective clinical therapies. Macrophages are known to respond to electrical fields, but the underlying cellular mechanisms mediating this response is unknown. This study demonstrated that low‐amplitude sine‐wave electrical stimulation (ES) initiates a soft tissue response in the absence of injury in Procambarus …


Loss Of Cell Adhesion Increases Tumorigenic Potential Of Polarity Deficient Scribble Mutant Cells, Indrayani Waghmare, Madhuri Kango-Singh Jun 2016

Loss Of Cell Adhesion Increases Tumorigenic Potential Of Polarity Deficient Scribble Mutant Cells, Indrayani Waghmare, Madhuri Kango-Singh

Biology Faculty Publications

Epithelial polarity genes are important for maintaining tissue architecture, and regulating growth. The Drosophila neoplastic tumor suppressor gene scribble (scrib) belongs to the basolateral polarity complex. Loss of scrib results in disruption of its growth regulatory functions, and downregulation or mislocalization of Scrib is correlated to tumor growth. Somatic scribble mutant cells (scrib-) surrounded by wild-type cells undergo apoptosis, which can be prevented by introduction of secondary mutations that provide a growth advantage. Using genetic tools in Drosophila, we analyzed the phenotypic effects of loss of scrib in different growth promoting backgrounds. We investigated if a central …


Digital Fragment Analysis Of Short Tandem Repeats By High‐Throughput Amplicon Sequencing, Brian J. Darby, Shay F. Erickson, Samuel D. Hervey, Susan N. Ellis-Felege Jun 2016

Digital Fragment Analysis Of Short Tandem Repeats By High‐Throughput Amplicon Sequencing, Brian J. Darby, Shay F. Erickson, Samuel D. Hervey, Susan N. Ellis-Felege

Biology Faculty Publications

High‐throughput sequencing has been proposed as a method to genotype microsatellites and overcome the four main technical drawbacks of capillary electrophoresis: amplification artifacts, imprecise sizing, length homoplasy, and limited multiplex capability. The objective of this project was to test a high‐throughput amplicon sequencing approach to fragment analysis of short tandem repeats and characterize its advantages and disadvantages against traditional capillary electrophoresis. We amplified and sequenced 12 muskrat microsatellite loci from 180 muskrat specimens and analyzed the sequencing data for precision of allele calling, propensity for amplification or sequencing artifacts, and for evidence of length homoplasy. Of the 294 total alleles, …


Collybolide Is A Novel Biased Agonist Of Κ-Opioid Receptors With Potent Antipruritic Activity, Achla Gupta, Ivone Gomes, Erin N. Bobeck, Amanda K. Fakira, Nicholas P. Massaro, Indrajeet Sharma, Adrien Cavé, Heidi E. Hamm, Joseph Parello, Lakshmi A. Devi May 2016

Collybolide Is A Novel Biased Agonist Of Κ-Opioid Receptors With Potent Antipruritic Activity, Achla Gupta, Ivone Gomes, Erin N. Bobeck, Amanda K. Fakira, Nicholas P. Massaro, Indrajeet Sharma, Adrien Cavé, Heidi E. Hamm, Joseph Parello, Lakshmi A. Devi

Biology Faculty Publications

Among the opioid receptors, the κ-opioid receptor (κOR) has been gaining considerable attention as a potential therapeutic target for the treatment of complex CNS disorders including depression, visceral pain, and cocaine addiction. With an interest in discovering novel ligands targeting κOR, we searched natural products for unusual scaffolds and identified collybolide (Colly), a nonnitrogenous sesquiterpene from the mushroom Collybia maculata. This compound has a furyl-δ-lactone core similar to that of Salvinorin A (Sal A), another natural product from the plant Salvia divinorum. Characterization of the molecular pharmacological properties reveals that Colly, like Sal A, is a highly potent and selective …