Digital Commons Network^™

Genome-Wide Transcriptional Profiling Of The Cyclic Amp-Dependent Signaling Pathway During Morphogenic Transitions Of Candida Albicans, Yong-Sun Bahn, Matthew Molenda, Janet F. Staab, Courtney A. Lyman, Laura J. Gordon, Paula Sundstrom

Dartmouth Scholarship

Candida albicans is an opportunistic human fungal pathogen that causes systemic candidiasis as well as superficial mucosal candidiasis. In response to the host environment, C. albicans transitions between yeast and hyphal forms. In particular, hyphal growth is important in facilitating adhesion and invasion of host tissues, concomitant with the expression of various hypha-specific virulence factors. In previous work, we showed that the cyclic AMP (cAMP) signaling pathway plays a crucial role in morphogenic transitions and virulence of C. albicans by studying genes encoding adenylate cyclase-associated protein (CAP1) and high-affinity phosphodiesterase (PDE2) (Y. S. Bahn, J. Staab, and P. Sundstrom, Mol. …

A Conserved Cam- And Radial Spoke–Associated Complex Mediates Regulation Of Flagellar Dynein Activity, Erin E. Dymek, Elizabeth F. Smith

Dartmouth Scholarship

For virtually all cilia and eukaryotic flagella, the second messengers calcium and cyclic adenosine monophosphate are implicated in modulating dynein- driven microtubule sliding to regulate beating. Calmodulin (CaM) localizes to the axoneme and is a key calcium sensor involved in regulating motility. Using immunoprecipitation and mass spectrometry, we identify members of a CaM-containing complex that are involved in regulating dynein activity. This complex includes flagellar-associated protein 91 (FAP91), which shares considerable sequence similarity to AAT-1, a protein originally identified in testis as an A-kinase anchor protein (AKAP)- binding protein. FAP91 directly interacts with radial spoke protein 3 (an AKAP), which …

Poly[(Nitrato-KO)Tris((Μ3-1h-1,2,4-Triazolato)Dizinc(Ii)]: A Three-Dimensional Coordination Polymer, Josephy M. Ellsworth, Mark D. Smith, Hans-Conrad Zur Loye

Faculty Publications

In the title compound, [Zn₂(C₂H₂N₃)₃(NO₃)], there are two unique Zn atoms, both with site symmetry m. One forms a ZnN₃O tetrahedron and the other a ZnN₆ octahedron. One and a half 1H-1,2,4-triazolate ligands, with the half-ligand located on a mirror plane, and a disordered nitrate anion complete the asymmetric unit of the structure. The polymeric connectivity is three-dimensional.

Structural Characterization Using The Multiple Scattering Effects In Grazing-Incidence Small-Angle X-Ray Scattering, Byeongdu Lee, Chieh-Tsung Lo, P. Thiyagarajan, Dong R. Lee, Zhongwei Niu, Qian Wang

Faculty Publications

The multiple scattering effects present in grazing-incidence small-angle X-ray scattering (GISAXS) data and interference between them are addressed theoretically as well as experimentally with measurement of a series of patterns at different incident angles, referred to as `incident-angle-resolved GISAXS' (IAR-GISAXS). X-ray reflectivity (XR), GISAXS and IAR-GISAXS of virus particles on Si-substrate supported-polystyrene films have been measured and all the data have been analyzed with appropriate formalisms. It was found that under certain conditions it is possible to extract the correct structural features of the materials from the GISAXS/IAR-GISAXS data using the kinematic SAXS formalisms, without the need to use the …

The Small Rna Repertoire Of Dictyostelium Discoideum And Its Regulation By Components Of The Rnai Pathway, Andrea Hinas, Johan Reimegård, E. Gerhart H. Wagner, Wolfgang Nellen, Victor R. Ambros, Fredrik Soderbum

Dartmouth Scholarship

Small RNAs play crucial roles in regulation of gene expression in many eukaryotes. Here, we report the cloning and characterization of 18–26 nt RNAs in the social amoeba Dictyostelium discoideum . This survey uncovered developmentally regulated microRNA candidates whose biogenesis, at least in one case, is dependent on a Dicer homolog, DrnB. Furthermore, we identified a large number of 21 nt RNAs originating from the DIRS-1 retrotransposon, clusters of which have been suggested to constitute centromeres. Small RNAs from another retrotransposon, Skipper, were significantly up-regulated in strains depleted of the second Dicer-like protein, DrnA, and a putative RNA-dependent RNA polymerase, …

Modification Of Carboplatin By Jurkat Cells, Anthony J. Di Pasqua, Jerry Goodisman, Deborah J. Kerwood, James C. Dabrowiak, Bonnie B. Toms

Chemistry - All Scholarship

Using [¹H,¹⁵N] heteronuclear single quantum coherance (HSQC) NMR and ¹⁵N-labeled carboplatin, 1, we show that Jurkat cells affect the rate of disappearance of the HSQC NMR peak in culture medium for this Pt²⁺ anticancer drug. The decay or disappearance rate constant for 1 in culture medium containing cells is k1=kc[CO32-]+km+kuN, where k_c is the rate constant for reaction of 1 with carbonate in the medium, k_m is the rate constant for reaction of 1 with all other components of the medium, and k_u is the rate constant for reaction of …

Inclusion Of Electrochemically Active Guests By Novel Oxacalixarene Hosts, Daniel Sobransingh, Mahender B. Dewal, Jacob Hiller, Mark D. Smith, Linda S. Shimizu

Faculty Publications

We demonstrate for the first time the utility of oxacalixarenes as hosts and investigate the forces that influence the thermodynamics of binding.

Increased Performance Of Battery Packs By Active Equalization, Jonathan W. Kimball, Brian T. Kuhn, Philip T. Krein

Electrical and Computer Engineering Faculty Research & Creative Works

Battery packs for most applications are series strings of electrochemical cells. Due to manufacturing variations, temperature differences, and aging, the individual cells perform differently. When a complete pack is charged and discharged as a single two-terminal circuit element, some cells are chronically overcharged, undercharged, or overdischarged, all of which act to reduce cell life. The performance and life of the complete pack is limited by the weakest cell. Many methods have been proposed and explored to mitigate this problem. In the present work, a switched-capacitor converter is shown to be a simple and effective method to maintain equal cell or …

Phosphorylation-Induced Conformational Switching Of Cpi-17 Produces A Potent Myosin Phosphatase Inhibitor, Masumi Eto, Toshio Kitazawa, Fumiko Matsuzawa, Sei-Ichi Aikawa, Jason A. Kirkbride, Noriyoshi Isozumi, Yumi Nishimura, David L. Brautigan, Shin-Ya Ohki

Department of Molecular Physiology and Biophysics Faculty Papers

Phosphorylation of endogenous inhibitor proteins specific for type-1 Ser/Thr phosphatase (PP1) provides a mechanism for reciprocal coordination of kinase and phosphatase activities. Phosphorylation of Thr38 in the inhibitor protein CPI-17 transduces G-protein-mediated signaling into a > 1000-fold increase of inhibitory potency toward myosin phosphatase. We show here the solution NMR structure of phospho-T38-CPI-17 with r. m. s. d. of 0.36 ± 0.06 Å for the backbone secondary structure, which reveals how phosphorylation triggers a conformational change and exposes the PP1 inhibitory surface. This active conformation is stabilized by the formation of a hydrophobic core of intercalated side-chains, which is not formed …

Poly[Μ2-Nitrato-(Μ4-Pyrazine-2-Carboxylato)Disilver(I)], Kathryn L. Seward, Joseph M. Ellsworth, Zeeshan M. Khaliq, Hans-Conrad Zur Loye

Faculty Publications

The title compound, [Ag₂(C₅H₃N₂O₂)(NO₃)]_n, is a three-dimensional coordination polymer containing two-dimensional slabs held together by bridging nitrate groups. AgNO₄ and AgNO₅ silver coordination polyhedra arise. Weak argentophilic interactions [AgAg = 3.0686 (7) Å] occur in the crystal structure.

Assays Of Vacuole Fusion Resolve The Stages Of Docking, Lipid Mixing, And Content Mixing, Youngsoo Jun, William Wickner

Dartmouth Scholarship

Membrane fusion entails organelle docking and subsequent mixing of membrane bilayers and luminal compartments. We now present an in vitro assay of fusion, using yeast vacuoles bearing domains of either Fos or Jun fused to complementary halves of beta-lactamase. Upon fusion, these proteins associate to yield beta-lactamase activity. This assay complements the standard fusion assay (activation of pro-Pho8p in protease-deficient vacuoles by proteases from pho8Delta vacuoles). Both the beta-lactamase and pro-Pho8p activation assays of fusion show the same long kinetic delay between SNARE pairing and luminal compartment mixing. Lipid-mixing occurs rapidly after SNARE pairing but well before aqueous compartment mixing. …

Stabilization Of Smar1 Mrna By Pga2 Involves A Stem Loop Structure In The 5' Utr, Lakshminarasimhan Pavritha, Shravanti Rampalli, Surajit Sinha, Kadreppa Sreenath, Richard G. Pestell, Samit Chattopadhyay

Department of Cancer Biology Faculty Papers

Prostaglandins are anticancer agents known to inhibit tumor cell proliferation both in vitro and in vivo by affecting the mRNA stability. Here we report that a MAR-binding protein SMAR1 is a target of Prostaglandin A2 (PGA2) induced growth arrest. We identify a regulatory mechanism leading to stabilization of SMAR1 transcript. Our results show that a minor stem and loop structure present in the 5' UTR of SMAR1 (1-UTR) is critical for nucleoprotein complex formation that leads to SMAR1 stabilization in response to PGA2. This results in an increased SMAR1 transcript and altered protein levels, that in turn causes downregulation of …

Polymorphisms In Nucleotide Excision Repair Genes, Arsenic Exposure, And Non-Melanoma Skin Cancer In New Hampshire, Katie M. Applebaum, Margaret R. Karagas, David J. Hunter, Paul J. Catalano, Steven H. Byler, Steve Morris, Heather H. Nelson

Dartmouth Scholarship

Background:

Arsenic exposure may alter the efficiency of DNA repair. UV damage is specifically repaired by nucleotide excision repair (NER), and common genetic variants in NER may increase risk for non-melanoma skin cancer (NMSC).

Objective:

We tested whether polymorphisms in the NER genes XPA (A23G) and XPD (Asp312Asn and Lys751Gln) modify the association between arsenic and NMSC.

Methods:

Incident cases of basal and squamous cell carcinoma (BCC and SCC, respectively) were identified through a network of dermatologists and pathology laboratories across New Hampshire. Population-based controls were frequency matched to cases on age and sex. Arsenic exposure was assessed in toenail …

A Novel Ensemble Learning Method For De Novo Computational Identification Of Dna Binding Sites, Arijit Chakravarty, Jonathan M. Carlson, Radhika S. Khetani, Robert H H. Gross

Dartmouth Scholarship

Despite the diversity of motif representations and search algorithms, the de novo computational identification of transcription factor binding sites remains constrained by the limited accuracy of existing algorithms and the need for user-specified input parameters that describe the motif being sought.ResultsWe present a novel ensemble learning method, SCOPE, that is based on the assumption that transcription factor binding sites belong to one of three broad classes of motifs: non-degenerate, degenerate and gapped motifs. SCOPE employs a unified scoring metric to combine the results from three motif finding algorithms each aimed at the discovery of one of these classes of motifs. …

A Hybrid First Year Science Course For Engineering Students – Integrating Biology With Chemistry, David Harding, Pauline Schwartz, Jean Nocito-Gobel, Agamemnon Koutsospyros

Civil Engineering Faculty Publications

Biology is playing an increasingly important role in many engineering fields. With the typical engineering program already having a high credit hour requirement, the question becomes, how to best integrate biology concepts into a packed engineering curriculum. A typical biology course is not likely to introduce the important concepts of biology to engineering students. The solution here is to develop a hybrid course that integrates chemistry and biology. In the course, Chemistry with Applications to Biosystems, the concept is to develop a course that integrally links important concepts of chemistry and biology. The course focuses on the areas of biology …

Crystal Structure Of The Vibrio Cholerae Quorum-Sensing Regulatory Protein Hapr, Rukman S. De Silva, Gabriela Kovacikova, Wei Lin, Ronald K. Taylor, Karen Skorupski, F. Jon Kull

Dartmouth Scholarship

Quorum sensing in Vibrio cholerae involves signaling between two-component sensor protein kinases and the response regulator LuxO to control the expression of the master regulator HapR. HapR, in turn, plays a central role in regulating a number of important processes, such as virulence gene expression and biofilm formation. We have determined the crystal structure of HapR to 2.2-Å resolution. Its structure reveals a dimeric, two-domain molecule with an all-helical structure that is strongly conserved with members of the TetR family of transcriptional regulators. The N-terminal DNA-binding domain contains a helix-turn-helix DNA-binding motif and alteration of certain residues in this domain …

P53 Activation By Knockdown Technologies, Mara E. Robu, Jon D. Larson, Aidas Nasevicius, Soraya Beiraghi, Charles Brenner

Dartmouth Scholarship

Morpholino phosphorodiamidate antisense oligonucleotides (MOs) and short interfering RNAs (siRNAs) are commonly used platforms to study gene function by sequence-specific knockdown. Both technologies, however, can elicit undesirable off-target effects. We have used several model genes to study these effects in detail in the zebrafish, Danio rerio. Using the zebrafish embryo as a template, correct and mistargeting effects are readily discernible through direct comparison of MO-injected animals with well-studied mutants. We show here indistinguishable off-targeting effects for both maternal and zygotic mRNAs and for both translational and splice-site targeting MOs. The major off-targeting effect is mediated through p53 activation, as detected …

Interview With Paul Fischer, Professor Of Chemistry, Paul Fischer

Chemistry Department Oral Histories

No abstract provided.

Trans-Snare Complex Assembly And Yeast Vacuole Membrane Fusion, Kevin M. Collins, William T. Wickner

Dartmouth Scholarship

cis-SNARE complexes (anchored in one membrane) are disassembled by Sec17p (α-SNAP) and Sec18p (NSF), permitting the unpaired SNAREs to assemble in trans. We now report a direct assay of trans-SNARE complex formation during yeast vacuole docking. SNARE complex assembly and fusion is promoted by high concentrations of the SNARE Vam7p or Nyv1p or by addition of HOPS (homotypic fusion and vacuole protein sorting), a Ypt7p (Rab)-effector complex with a Sec1/Munc18-family subunit. Inhibitors that target Ypt7p, HOPS, or key regulatory lipids prevent trans-SNARE complex assembly and ensuing fusion. Strikingly, the lipid ligand MED (myristoylated alanine-rich C kinase substrate effector domain) or …

Interview With Emil Slowinski, Dewitt Wallace Professor Of Chemistry, Emil Slowinski

Chemistry Department Oral Histories

No abstract provided.

Metropolitan-Micropolitan Difference In Available Labor Force Characteristics: Three Great Plains Labor Basins, Michael Walker, Brett Zollinger

Sociology Faculty Publications

This study explores differences in labor availability characteristics among those living in metropolitan and micropolitan areas. Data used in this study are from surveys of adults in two adjacent Midwestern states and from three separate labor basins. Primary patterns under examination include wage demands, benefit demands, distance willing to commute for a job, perceived underemployment and entrepreneurial propensity. Bivariate analyses show no relationship between basin size and entrepreneurial propensity nor between basin size and willingness to commute. However, basin size has significant influence on four of the seven dependent variables, even after controlling for many sociodemographic characteristics. In multivariate analyses, …

Electrochemical Detection Of Prostate Carcinoma Biomarkers Using Nanotechnology, Kathryn Leonard

Pell Scholars and Senior Theses

The first chapter of this thesis speaks about prostate specific antigen, carbon nanotubes and horseradish peroxidase. The second chapter discusses the electrochemistry and catalysis of horseradish peroxidase (HRP) and myoglobin (Mb) covalently attached to vertically aligned carbon nanotube arrays used as a tranducer. Cyclic voltammetry results gave quasi-reversible FeIII/FeII voltammetry and electrochemical catalysis involving catalytic reduction of hydrogen peroxide for both the iron-heme enzymes in myoglobin and horseradish peroxidase coupled to the carboxylated ends of the carbon nanotube arrays by amine bioconjugation reactions. Reduction peak currents gave linear relationships with scan-rates, typical of thin layer voltammetry. Results suggest that the …

Computation Of Correlation Functions And Wave Function Projections In The Context Of Quantum Trajectory Dynamics, Sophya Garashchuk

Faculty Publications

The de Broglie-Bohm formulation of the Schrödinger equation implies conservation of the wave function probability density associated with each quantum trajectory in closed systems. This conservation property greatly simplifies numerical implementations of the quantum trajectory dynamics and increases its accuracy. The reconstruction of a wave function, however, becomes expensive or inaccurate as it requires fitting or interpolation procedures. In this paper we present a method of computing wave packet correlation functions and wave function projections, which typically contain all the desired information about dynamics, without the full knowledge of the wave function by making quadratic expansions of the wave function …

Membrane Association And Multimerization Of Tcpt, The Cognate Atpase Ortholog Of The Vibrio Cholerae Toxin-Coregulated-Pilus Biogenesis Apparatus, Shital A. Tripathi, Ronald K. Taylor

Dartmouth Scholarship

The toxin-coregulated pilus (TCP) is one of the major virulence factors of Vibrio cholerae. Biogenesis of this type 4 pilus (Tfp) requires a number of structural components encoded by the tcp operon. TcpT, the cognate putative ATPase, is required for TCP biogenesis and all TCP-mediated functions. We studied the stability and localization of TcpT in cells containing in-frame deletions in each of the tcp genes. TcpT was detectable in each of the biogenesis mutants except the ΔtcpT strain. TcpT was localized to the inner membrane (IM) in a TcpR-dependent manner. TcpR is a predicted bitopic inner membrane protein …

A 368-Base-Pair Cis-Acting Hwp1 Promoter Region, Hcr, Of Candida Albicans Confers Hypha-Specific Gene Regulation And Binds Architectural Transcription Factors Nhp6 And Gcf1p, Samin Kim, Michael J. Wolyniak, Janet F. Staab, Paula Sundstrom

Dartmouth Scholarship

To elucidate the molecular mechanisms controlling the expression of the hypha-specific adhesin gene HWP1 of Candida albicans, its promoter was dissected and analyzed using a green fluorescent protein reporter gene. A 368-bp region, the HWP1 control region (HCR), was critical for activation under hypha-inducing conditions and conferred developmental regulation to a heterologous ENO1 promoter. A more distal region of the promoter served to amplify the level of promoter activation. Using gel mobility shift assays, a 249-bp subregion of HCR, HCRa, was found to bind at least four proteins from crude extracts of yeasts and hyphae with differing binding patterns dependent …

Association Of The Tensin N-Terminal Protein-Tyrosine Phosphatase Domain With The Alpha Isoform Of Protein Phosphatase-1 In Focal Adhesions, Masumi Eto, Jason Kirkbride, Elizabeth Elliott, Su Hao Lo, David L. Brautigan

Department of Molecular Physiology and Biophysics Faculty Papers

Focal adhesions attach cultured cells to the extracellular matrix, and we found endogenous protein phosphatase-1alpha isoform (PP1alpha) localized in adhesions across the entire area of adherent fibroblasts. However, in fibroblasts migrating into a scrape wound or spreading after replating PP1alpha did not appear in adhesions near the leading edge but was recruited into other adhesions coincident in time and space with incorporation of tensin. Endogenous tensin and PP1alpha co-precipitated from cell lysates with isoform-specific PP1 antibodies. Chemical cross-linking of focal adhesion preparations with Lomant's reagent demonstrated molecular proximity of endogenous PP1alpha and tensin, whereas neither focal adhesion kinase nor vinculin …

Trisodium Dicalcium Bismuth Hexaoxide, Irina V. Puzdrjakova, Rene B. Macquart, Mark D. Smith, Hans-Conrad Zur Loye

Faculty Publications

Single crystals of the title compound, Na₃Ca₂BiO₆, were grown from a high-temperature reactive flux solution of Na₂CO₃. Na₃Ca₂BiO₆ crystallizes as an ordered rock-salt structure (space group Fddd), in which the octahedral holes in the oxide array are filled by an ordered 3:2:1 arrangement of Na⁺, Ca²⁺ and Bi⁵⁺ cations. All atoms except for one O atom lie on special positions; site symmetries are as follows: Bi 222, Ca 2, Na 222 and 2, O 2.

Poly[Diaqua(Μ4-3-Fluorophthalato-Κ4O:O:O':O'')Cadmium(Ii)], Diana Rishmawi, Katie Lewis, Mark D. Smith, Leroy Peterson Jr., Hans-Conrad Zur Loye

Faculty Publications

The crystal structure of the title compound, [Cd(C₈H₃FO₄)(H₂O)₂]_n, consists of polymeric sheets formed by the bridging of octahedrally coordinated Cd^II by carboxylate O atoms of the 3-fluorophthalate (3-fpt^2-) ligand. The layers exhibit hydrogen bonding between each of two coordinated water molecules and two O atoms of the ligand. Adjacent sheets are connected through - interactions.

Linking Community Service, Learning, And Enviromental Analytical Chemistry, Joesph A. Gardella Jr., Tammy M. Milillo, Gaurav Sinha, Gunwah Oh, David C. Manns, Eleanor Coffey

Higher Education

In 1994, during a tour of the then-new natural sciences building- a $43 million teaching and research complex fully equipped with the latest in technology and instrumentation for chemistry and geology courses-a member of the Buffalo Public Schools Board of Education asked, "How can the community [that paid for it] have access to this teaching and research equipment?" That question triggered the effort reported here - a program to better link teaching and research to community service.

The Yeast Orthologue Of Grasp65 Forms A Complex With A Coiled-Coil Protein That Contributes To Er To Golgi Traffic, Rudy Behnia, Francis A. Barr, John J. Flanagan, Charles Barlowe, Sean Munro

Dartmouth Scholarship

The mammalian Golgi protein GRASP65 is required in assays that reconstitute cisternal stacking and vesicle tethering. Attached to membranes by an N-terminal myristoyl group, it recruits the coiled-coil protein GM130. The relevance of this system to budding yeasts has been unclear, as they lack an obvious orthologue of GM130, and their only GRASP65 relative (Grh1) lacks a myristoylation site and has even been suggested to act in a mitotic checkpoint. In this study, we show that Grh1 has an N-terminal amphipathic helix that is N-terminally acetylated and mediates association with the cis-Golgi. We find that Grh1 forms a complex with …