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Synaptic Clustering Of Psd-95 Is Regulated By C-Abl Through Tyrosine Phosphorylation, Karen Perez de Arce, Lorena Varela-Nallar, Olivia Farias, Alejandra Cifuentes, Paulina Bull, Brian A. Couch, Anthony J. Koleske, Nibaldo C. Inestrosa, Alejandra R. Alvarez 2010 Pontificia Universidad Católica de Chile

Synaptic Clustering Of Psd-95 Is Regulated By C-Abl Through Tyrosine Phosphorylation, Karen Perez De Arce, Lorena Varela-Nallar, Olivia Farias, Alejandra Cifuentes, Paulina Bull, Brian A. Couch, Anthony J. Koleske, Nibaldo C. Inestrosa, Alejandra R. Alvarez

Faculty Publications in the Biological Sciences

The c-Abl tyrosine kinase is present in mouse brain synapses, but its precise synaptic function is unknown. We found that c-Abl levels in the rat hippocampus increase postnatally, with expression peaking at the first postnatal week. In 14 d in vitro hippocampal neuron cultures, c-Abl localizes primarily to the postsynaptic compartment, in which it colocalizes with the postsynaptic scaffold protein postsynaptic density protein-95 (PSD-95) in apposition to presynaptic markers. c-Abl associates with PSD-95, and chemical or genetic inhibition of c-Abl kinase activity reduces PSD-95 tyrosine phosphorylation, leading to reduced PSD-95 clustering and reduced synapses in treated neurons. c-Abl can phosphorylate ...


Agmatidine, A Modified Cytidine In The Anticodon Of Archaeal TrnaIle, Base Pairs With Adenosine But Not With Guanosine, Debabrata Mandal, Caroline Köhrer, Dan Su, Susan P. Russell, Kady Krivos, Colette M. Castleberry, Paul H. Blum, Patrick A. Limbach, Dieter Söll, Uttam L. RajBhandary 2010 Massachusetts Institute of Technology

Agmatidine, A Modified Cytidine In The Anticodon Of Archaeal TrnaIle, Base Pairs With Adenosine But Not With Guanosine, Debabrata Mandal, Caroline Köhrer, Dan Su, Susan P. Russell, Kady Krivos, Colette M. Castleberry, Paul H. Blum, Patrick A. Limbach, Dieter Söll, Uttam L. Rajbhandary

Faculty Publications in the Biological Sciences

Modification of the cytidine in the first anticodon position of the AUA decoding tRNAIle (tRNAIle 2 ) of bacteria and archaea is essential for this tRNA to read the isoleucine codon AUA and to differentiate between AUA and the methionine codon AUG. To identify the modified cytidine in archaea, we have purified this tRNA species from Haloarcula marismortui, established its codon reading properties, used liquid chromatography–mass spectrometry (LC-MS) to map RNase A and T1 digestion products onto the tRNA, and used LC-MS/MS to sequence the oligonucleotides in RNase A digests. These analyses revealed that the modification of ...


Isolation And Characterization Of Bacteria Resistant To Metallic Copper Surfaces, Christophe Espírito Santo, Paula Vasconcelos Morais, Gregor Grass 2010 Instituto do Mar (IMAR-CMA)

Isolation And Characterization Of Bacteria Resistant To Metallic Copper Surfaces, Christophe Espírito Santo, Paula Vasconcelos Morais, Gregor Grass

Faculty Publications in the Biological Sciences

Metallic copper alloys have recently attracted attention as a new antimicrobial weapon for areas where surface hygiene is paramount. Currently it is not understood on a molecular level how metallic copper kills microbes, but previous studies have demonstrated that a wide variety of bacteria, including Escherichia coli, Staphylococcus aureus, and Clostridium difficile, are inactivated within minutes or a few hours of exposure. In this study, we show that bacteria isolated from copper alloy coins comprise strains that are especially resistant against the toxic properties exerted by dry metallic copper surfaces. The most resistant of 294 isolates were Gram-positive staphylococci and ...


Activity And Toxicity Of Farnesol Towards Candida Albicans Are Dependent On Growth Conditions, Melanie L. Langford, Sahar Hasim, Kenneth W. Nickerson, Audrey L. Atkin 2010 University of Nebraska-Lincoln

Activity And Toxicity Of Farnesol Towards Candida Albicans Are Dependent On Growth Conditions, Melanie L. Langford, Sahar Hasim, Kenneth W. Nickerson, Audrey L. Atkin

Faculty Publications in the Biological Sciences

Farnesol interacts with Candida albicans as both a quorum-sensing molecule and toxic agent, but confusion abounds regarding which conditions promote these distinct responses. Farnesol sensitivity was measured when inoculum cell history and size, temperature, and growth media were altered. Parameters for farnesol tolerance/ sensitivity were defined, validating previous studies and identifying new variables, such as energy availability. This study clearly defines what farnesol concentrations are lethal to C. albicans, based on environmental conditions.


Cordyceps Mushroom: A Potent Anticancer Nutraceutical, Md. Asaduzzaman Khan, Mousumi Tania, Dianzheng Zhang, Hanchun Chen 2010 Philadelphia College of Osteopathic Medicine

Cordyceps Mushroom: A Potent Anticancer Nutraceutical, Md. Asaduzzaman Khan, Mousumi Tania, Dianzheng Zhang, Hanchun Chen

PCOM Scholarly Papers

The Cordyceps mushrooms have a long history as medicinal fungi. In Traditional Chinese Medicine, Cordyceps have been used to treat several conditions including cancers for thousand of years. Extracts from both mycelium and fruiting bodies of C. sinensis, C. militaris and other Cordyceps species showed significant anticancer activities by various mechanisms such as, modulating immune system and inducing cell apoptosis. Some polysaccharide components and cordycepin (3' -deoxyadenosine) have been isolated from C. sinensis and C. militaris, which acted as potent anticancer components. This review article aims to further elucidate the importance of Cordyceps mushrooms by summarizing the findings of some ...


Effect Of Resistant Starch On Microbial Content Of The Intestinal Tract, Reshani Nisansala Senevirathne 2010 Louisiana State University and Agricultural and Mechanical College

Effect Of Resistant Starch On Microbial Content Of The Intestinal Tract, Reshani Nisansala Senevirathne

LSU Doctoral Dissertations

Resistant starch (RS) increases beneficial gastro-intestinal bacterial populations simultaneously increasing short-chain fatty acids (SCFA) such as butyrate. Butyrate acts as energy source for epithelial cells of colonic mucosa which stimulates intestinal cell proliferation and has been implicated as important in reducing obesity, diabetes and cancer. The Lactobacillus spp, Bifidobacterium spp, Bacteroides thetaiotaomicron, Clostridium cluster IV and Clostridium cluster XIV are mainly involved in the production of butyrate by fermenting RS in the large intestine. With age there is a decline in these gut bacteria, but in the present study RS and diet restriction both enhanced the bacteria involved in butyrate ...


Choosing A Genome Browser For A Model Organism Database: Surveying The Maize Community, Taner Z. Sen, Lisa C. Harper, Mary L. Schaeffer, Carson M. Andorf, Trent E. Seigfried, Darwin A. Campbell, Carolyn J. Lawrence 2010 Iowa State University

Choosing A Genome Browser For A Model Organism Database: Surveying The Maize Community, Taner Z. Sen, Lisa C. Harper, Mary L. Schaeffer, Carson M. Andorf, Trent E. Seigfried, Darwin A. Campbell, Carolyn J. Lawrence

Genetics, Development and Cell Biology Publications

As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resource, personnel at MaizeGDB surveyed researchers’ needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation of a browser with quick interface and intuitive tools would meet most researchers’ needs. Here, we document the survey’s outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing ...


Moesin1 And Ve-Cadherin Are Required In Endothelial Cells During In Vivo Tubulogenesis, Ying Wang, Mark S. Kaiser, Jon D. Larson, Aidas Nasevicius, Karl J. Clark, Shannon A. Wadman, Sharon E. Roberg-Perez, Stephen C. Ekker, Perry B. Hackett, Maura McGrail, Jeffrey J. Essner 2010 Iowa State University

Moesin1 And Ve-Cadherin Are Required In Endothelial Cells During In Vivo Tubulogenesis, Ying Wang, Mark S. Kaiser, Jon D. Larson, Aidas Nasevicius, Karl J. Clark, Shannon A. Wadman, Sharon E. Roberg-Perez, Stephen C. Ekker, Perry B. Hackett, Maura Mcgrail, Jeffrey J. Essner

Genetics, Development and Cell Biology Publications

Endothelial tubulogenesis is a crucial step in the formation of functional blood vessels during angiogenesis and vasculogenesis. Here, we use in vivo imaging of living zebrafish embryos expressing fluorescent fusion proteins of β-Actin, α-Catenin, and the ERM family member Moesin1 (Moesin a), to define a novel cord hollowing process that occurs during the initial stages of tubulogenesis in intersegmental vessels (ISVs) in the embryo. We show that the primary lumen elongates along cell junctions between at least two endothelial cells during embryonic angiogenesis. Moesin1-EGFP is enriched around structures that resemble intracellular vacuoles, which fuse with the luminal membrane during expansion ...


Metnetge: Interactive Views Of Biological Networks And Ontologies, Jia Ming, Suh-Yeon Choi, Dirk Reiners, Eve S. Wurtele, Julie A. Dickerson 2010 Iowa State University

Metnetge: Interactive Views Of Biological Networks And Ontologies, Jia Ming, Suh-Yeon Choi, Dirk Reiners, Eve S. Wurtele, Julie A. Dickerson

Genetics, Development and Cell Biology Publications

Background

Linking high-throughput experimental data with biological networks is a key step for understanding complex biological systems. Currently, visualization tools for large metabolic networks often result in a dense web of connections that is difficult to interpret biologically. The MetNetGE application organizes and visualizes biological networks in a meaningful way to improve performance and biological interpretability.

Results

MetNetGE is an interactive visualization tool based on the Google Earth platform. MetNetGE features novel visualization techniques for pathway and ontology information display. Instead of simply showing hundreds of pathways in a complex graph, MetNetGE gives an overview of the network using the ...


Zifit (Zinc Finger Targeter): An Updated Zinc Finger Engineering Tool, Jeffry D. Sander, Morgan L. Maeder, Deepak Reyon, Daniel F. Voytas, J. Keith Joung, Drena Dobbs 2010 Massachusetts General Hospital

Zifit (Zinc Finger Targeter): An Updated Zinc Finger Engineering Tool, Jeffry D. Sander, Morgan L. Maeder, Deepak Reyon, Daniel F. Voytas, J. Keith Joung, Drena Dobbs

Genetics, Development and Cell Biology Publications

ZiFiT (Zinc Finger Targeter) is a simple and intuitive web-based tool that provides an interface to identify potential binding sites for engineered zinc finger proteins (ZFPs) in user-supplied DNA sequences. In this updated version, ZiFiT identifies potential sites for ZFPs made by both the modular assembly and OPEN engineering methods. In addition, ZiFiT now integrates additional tools and resources including scoring schemes for modular assembly, an interface with the Zinc Finger Database (ZiFDB) of engineered ZFPs, and direct querying of NCBI BLAST servers for identifying potential off-target sites within a host genome. Taken together, these features facilitate design of ZFPs ...


Struct-Nb: Predicting Protein-Rna Binding Sites Using Structural Features, Fadi Towfic, Cornelia Caragea, David C. Gemperline, Drena Dobbs, Vasant Honavar 2010 Iowa State University

Struct-Nb: Predicting Protein-Rna Binding Sites Using Structural Features, Fadi Towfic, Cornelia Caragea, David C. Gemperline, Drena Dobbs, Vasant Honavar

Genetics, Development and Cell Biology Publications

We explore whether protein-RNA interfaces differ from non-interfaces in terms of their structural features and whether structural features vary according to the type of the bound RNA (e.g., mRNA, siRNA, etc.), using a non-redundant dataset of 147 protein chains extracted from protein-RNA complexes in the Protein Data Bank. Furthermore, we use machine learning algorithms for training classifiers to predict protein-RNA interfaces using information derived from the sequence and structural features. We develop the Struct-NB classifier that takes into account structural information. We compare the performance of Naïve Bayes and Gaussian Naïve Bayes with that of Struct-NB classifiers on the ...


Predicting Success Of Oligomerized Pool Engineering (Open) For Zinc Finger Target Site Sequences, Jeffry D. Sander, Deepak Reyon, Morgan L. Maeder, Jonathan E. Foley, Stacey Thibodeau-Beganny, Xiaohong Li, Maureen R. Regan, Elizabeth J. Dahlborg, Matthew J. Goodwin, Fengli Fu, Daniel F. Voytas, J Keith Joung, Drena Dobbs 2010 Iowa State University

Predicting Success Of Oligomerized Pool Engineering (Open) For Zinc Finger Target Site Sequences, Jeffry D. Sander, Deepak Reyon, Morgan L. Maeder, Jonathan E. Foley, Stacey Thibodeau-Beganny, Xiaohong Li, Maureen R. Regan, Elizabeth J. Dahlborg, Matthew J. Goodwin, Fengli Fu, Daniel F. Voytas, J Keith Joung, Drena Dobbs

Genetics, Development and Cell Biology Publications

Background: Precise and efficient methods for gene targeting are critical for detailed functional analysis of genomes and regulatory networks and for potentially improving the efficacy and safety of gene therapies. Oligomerized Pool ENgineering (OPEN) is a recently developed method for engineering C2H2 zinc finger proteins (ZFPs) designed to bind specific DNA sequences with high affinity and specificity in vivo. Because generation of ZFPs using OPEN requires considerable effort, a computational method for identifying the sites in any given gene that are most likely to be successfully targeted by this method is desirable.

Results: Analysis of the base composition of experimentally ...


Tor Is A Negative Regulator Of Autophagy In Arabidopsis Thaliana, Yimo Liu, Diane C. Bassham 2010 Iowa State University

Tor Is A Negative Regulator Of Autophagy In Arabidopsis Thaliana, Yimo Liu, Diane C. Bassham

Genetics, Development and Cell Biology Publications

Background: Autophagy is a protein degradation process by which cells recycle cytoplasmic contents under stress conditions or during senescence; a basal level of housekeeping autophagy also occurs under non-stressed conditions. Although a number of genes that function in autophagy (ATG genes) have been identified in plants, the upstream components that regulate the plant autophagy pathway are still obscure. Target of rapamycin (TOR) is a negative regulator of autophagy in both yeast and animals, and homologs of TOR in plants control plant growth and protein synthesis. However, a role for TOR in regulation of autophagy in plants has not been demonstrated ...


Apoptosis: Lack Of Oxygen Aids Cell Survival, Jo Anne Powell-Coffman, Clark R. Coffman 2010 Iowa State University

Apoptosis: Lack Of Oxygen Aids Cell Survival, Jo Anne Powell-Coffman, Clark R. Coffman

Genetics, Development and Cell Biology Publications

In worms, neurons respond to low levels of environmental oxygen in a way that protects distant tissues from stress-induced cell death. The molecules that mediate this cell-cell signalling may be targets for cancer treatment.


Regional Management Units For Marine Turtles: A Novel Framework For Prioritizing Conservation And Research Across Multiple Scales, Bryan P. Wallace, John A. Musick 2010 et al

Regional Management Units For Marine Turtles: A Novel Framework For Prioritizing Conservation And Research Across Multiple Scales, Bryan P. Wallace, John A. Musick

VIMS Articles

Background: Resolving threats to widely distributed marine megafauna requires definition of the geographic distributions of both the threats as well as the population unit(s) of interest. In turn, because individual threats can operate on varying spatial scales, their impacts can affect different segments of a population of the same species. Therefore, integration of multiple tools and techniques - including site-based monitoring, genetic analyses, mark-recapture studies and telemetry - can facilitate robust definitions of population segments at multiple biological and spatial scales to address different management and research challenges. Methodology/Principal Findings: To address these issues for marine turtles, we collated all ...


A Molecular Genetic Investigation Of The Population Structure Of Atlantic Menhaden (Brevoortia Tyrannus), Abigail J. Lynch, Jan R. McDowell, John E. Graves 2010 Virginia Institute of Marine Science

A Molecular Genetic Investigation Of The Population Structure Of Atlantic Menhaden (Brevoortia Tyrannus), Abigail J. Lynch, Jan R. Mcdowell, John E. Graves

VIMS Articles

Atlantic menhaden (Brevoortia tyrannus), through landings, support one of the largest commercial fisheries in the United States. Recent consolidation of the once coast-wide reduction fishery to waters within and around Chesapeake Bay has raised concerns over the possibility of the loss of unique genetic variation resulting from concentrated fishing pressure. To address this question, we surveyed variation at the mitochondrial cytochrome c oxidase subunit I (COI) gene region and seven nuclear microsatellite loci to evaluate stock structure of Atlantic menhaden. Samples were collected from up to three cohorts of Atlantic menhaden at four geographic locations along the U.S. Atlantic ...


The Effects Of Anoxic Conditions On Thermal Tolerance And Stress Protein Levels In Four Local Bivalves, Rachel Allee 2010 Western Washington University

The Effects Of Anoxic Conditions On Thermal Tolerance And Stress Protein Levels In Four Local Bivalves, Rachel Allee

WWU Graduate School Collection

Areas of oxygen depletion in the world's oceans have been on the rise, with the main culprits being anthropogenic causes such as eutrophication and pollution. Coastal marine areas, such as estuaries, are some of the more impacted ecosystems and they have been the focus of recent studies. This study focused on the effects of anoxia and the interactions it has with thermal tolerance in four local intertidal bivalves: Nuttallia obscurata, Venerupis phillipinarum, Leukoma staminea, and Mytilus trossulus. Nuttallia obscurata is a recent invader on which little physiological research has been conducted. Both V. phillipinarum and L. staminea are commercially ...


Predicting Cyanobacteria Blooms In 50 Lakes Of Northwest Washington, Chandra T. (Chandra Terezina) Llewellyn 2010 Western Washington University

Predicting Cyanobacteria Blooms In 50 Lakes Of Northwest Washington, Chandra T. (Chandra Terezina) Llewellyn

WWU Graduate School Collection

Eutrophication is one of the foremost problems affecting our freshwater resources. Excessive nutrient loading impacts freshwater lakes by altering ecosystem processes and degrading water quality, often resulting in human-induced eutrophication. Worldwide, cyanobacteria blooms occur in many anthropogenically eutrophic lakes. Such blooms are of increasing concern in the Pacific Northwest because they negatively affect lake system and function. A major concern is their unpredictable production of toxins, which can be deadly to animals, including humans. Therefore, an improved understanding of the incidence and persistence of cyanobacteria blooms is a critical aspect of protecting our water supply. The goal of this thesis ...


Meta!Blast: A Serious Game To Explore The Complexities Of Structural And Metabolic Cell Biology, Eve S. Wurtele, Diane C. Bassham, Julie Dickerson, David J. Kabala, William Schneller, Mark Stenerson, Achyuthan Vasanth 2010 Iowa State University

Meta!Blast: A Serious Game To Explore The Complexities Of Structural And Metabolic Cell Biology, Eve S. Wurtele, Diane C. Bassham, Julie Dickerson, David J. Kabala, William Schneller, Mark Stenerson, Achyuthan Vasanth

Genetics, Development and Cell Biology Presentations, Posters and Proceedings

Knowledge of cellular structure and function has increased dramatically with the advent of modern molecular and computational technologies. Helping students to understand cellular dynamics is a major challenge to educators. To address this challenge, we have developed the Kabala Engine, an open source engine based on OpenSG (http://www.opensg.org) and VRJuggler (http://www.vrjuggler.org). This engine is designed to enable biologists, and indeed any domain expert — chemists, artists, psychologists — to create virtual interactive worlds for teaching or research. As a proof-of-concept, we have used this engine to create Meta!Blast, a virtual plant cell containing a prototype ...


Metapopulation Dynamics Of Mid-Continent Lesser Snow Geese: Implications For Management, Lise M. Aubry, Robert F. Rockwell, David N. Koons 2010 Utah State University

Metapopulation Dynamics Of Mid-Continent Lesser Snow Geese: Implications For Management, Lise M. Aubry, Robert F. Rockwell, David N. Koons

Human–Wildlife Interactions

The rapid increase in abundance of lesser snow goose (LSG; Chen caerulescens caerulescens) numbers and their devastating effects on arctic and subarctic habitats has inspired much research on the use of population models for defining appropriate management policies. We use the not yet considered metapopulation approach to examine the elasticity of mid-continent LSG population dynamics to changes in underlying vital rates to determine whether management efforts aimed at decreasing burgeoning numbers should be reevaluated. After considering a variety of geographic scenarios in the metapopulation model, we found that changes in survival would still have a larger impact on population dynamics ...


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