Biochemistry, Biophysics, and Structural Biology Commons^™

A Parallel G Quadruplex-Binding Protein Regulates The Boundaries Of Dna Elimination Events Of Tetrahymena Thermophila, Christine M. Carle, Hani S. Zaher, Douglas L. Chalker

Biology Faculty Research

Guanine (G)-rich DNA readily forms four-stranded quadruplexes in vitro, but evidence for their participation in genome regulation is limited. We have identified a quadruplex-binding protein, Lia3, that controls the boundaries of germline-limited, internal eliminated sequences (IESs) of Tetrahymena thermophila. Differentiation of this ciliate’s somatic genome requires excision of thousands of IESs, targeted for removal by small-RNA-directed heterochromatin formation. In cells lacking LIA3 (ΔLIA3), the excision of IESs bounded by specific G-rich polypurine tracts was impaired and imprecise, whereas the removal of IESs without such controlling sequences was unaffected. We found that oligonucleotides containing these polypurine tracts formed …

Data Publication With The Structural Biology Data Grid Supports Live Analysis, Peter A. Meyer, Stephanie Socias, Jason Key, Elizabeth Ransey, Emily C. Tjon, Alejandro Buschiazzo, Ming Lei, Chris Botka, James Withrow, David Neau, Kanagalaghatta Rajashankar, Karen S. Anderson, Chung-I Chang, Walter J. Chazin, Kevin D. Corbett, Michael S. Cosgrove, Sean Crosson, Sirano Dhe-Paganon, Enrico Di Cera, Catherine L. Drennan, Michael J. Eck, Brandt F. Eichman, Qing R. Fan, Adrian R. Ferre-D’Amare, J. Christopher Fromme, K. Christopher Garcia, Rachelle Gaudet, Peng Gong, Stephen C. Harrison, Ekaterina E. Heldwein, Zongchao Jia, Robert J. Keenan, Andrew C. Kruse, Marc Kvansaku, Jason S. Mclellan

Dartmouth Scholarship

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the …

Drought Responsive Gene Expression Regulatory Divergence Between Upland And Lowland Ecotypes Of A Perennial C4 Grass, John T. Lovell, Scott Schwartz, David B. Lowry, Eugene V. Shakirov, Jason E. Bonnette, Xiaoyu Weng, Mei Wang, Jenifer Johnson, Avinash Sreedasyam, Christopher Plott, Jerry Jenkins, Jeremy Schmutz, Thomas E. Juenger

Biological Sciences Faculty Research

Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C₄ grass, Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. …

Hoxd Expression In The Fin-Fold Compartment Of Basal Gnathostomes And Implications For Paired Appendage Evolution, Frank J. Tulenko, Gaius J. Augustus, James L. Massey, Seth E. Sims

Faculty Articles

The role of Homeobox transcription factors during fin and limb development have been the focus of recent work investigating the evolutionary origin of limb-specific morphologies. Here we characterize the expression of HoxD genes, as well as the cluster-associated genes Evx2 and LNP, in the paddlefish Polyodon spathula, a basal ray-finned fish. Our results demonstrate a collinear pattern of nesting in early fin buds that includes HoxD14, a gene previously thought to be isolated from global Hoxregulation. We also show that in both Polyodon and the catsharkScyliorhinus canicula (a representative chondrichthyan) late phaseHoxD transcripts are present in cells of the fin-fold …

Analysis Of Lung Microbiota In Bronchoalveolar Lavage, Protected Brush And Sputum Samples From Subjects With Mild-To-Moderate Cystic Fibrosis Lung Disease, Deborah A. Hogan, Sven D. Willger, Emily L. Dolben, Thomas H. Hampton, Bruce A. Stanton, Hilary G. Morrison, Mitchell L. Sogin, Julianna Czum, Alix Ashare, Michael Tunney

Dartmouth Scholarship

Individuals with cystic fibrosis (CF) often acquire chronic lung infections that lead to irrevers- ible damage. We sought to examine regional variation in the microbial communities in the lungs of individuals with mild-to-moderate CF lung disease, to examine the relationship between the local microbiota and local damage, and to determine the relationships between microbiota in samples taken directly from the lung and the microbiota in spontaneously expectorated sputum. In this initial study, nine stable, adult CF patients with an FEV1>50% underwent regional sampling of different lobes of the right lung by bronchoalveolar lavage (BAL) and protected brush (PB) sampling …

Analysis Of Johne's Disease Elisa Status And Associated Performance Parameters In Irish Dairy Cows, A. E. Kennedy, N. Byrne, A. B. Garcia, Jim O'Mahony, R. G. Sayers

Department of Biological Sciences Publications

Background

Infection with Mycobacterium avium subspecies paratuberculosis (MAP) has been associated with reductions in milk production in dairy cows and sub optimal fertility. The aim of this study was to highlight the production losses associated with testing MAP ELISA positive in Irish dairy cows. Secondary objectives included investigation of risk factors associated with testing MAP ELISA positive. A survey of management practices on study farms was also conducted, with examination of associations between management practices and herd MAP status.

Blood samples were collected from 4188 breeding animals on 22 farms. Samples were ELISA tested using the ID Screen Paratuberculosis Indirect …

The Glucose Metabolite Methylglyoxal Inhibits Expression Of The Glucose Transport Genes By Inactivating The Cell Surface Glucose Sensors Rgt2 And Snf3 In Yeast, Adhiraj Roy, Salman Hashmi, Zerui Li, Angela Dement, Kyu Hong Cho, Jeong-Ho Kim

Biochemistry and Molecular Medicine Faculty Publications

Methylglyoxal (MG) is a cytotoxic by-product of glycolysis. MG has inhibitory effect on the growth of cells ranging from microorganisms to higher eukaryotes, but its molecular targets are largely unknown. The yeast cell-surface glucose sensors Rgt2 and Snf3 function as glucose receptors that sense extracellular glucose and generate a signal for induction of expression of genes encoding glucose transporters (HXTs). Here we provide evidence that these glucose sensors are primary targets of MG in yeast. MG inhibits the growth of glucose-fermenting yeast cells by inducing endocytosis and degradation of the glucose sensors. However, the glucose sensors with mutations …

Uplc–Qtof–Ms And Nmr Analyses Of Graviola (Annona Muricata) Leaves, Ingrid De Moraes, Paulo Ribeiro, Flávio Schmidt, Kirley Canuto, Guilherme Zocolo, Edy De Brito, Rensheng Luo, Kristy Richards, Kevin Tran, Robert Smith

Chemistry & Biochemistry Faculty Works

No abstract provided.

Structure–Function Relationships Of Fullerene Esters In Polymer Solar Cells: Unexpected Structural Effects On Lifetime And Efficiency, Michael Tro, Alexis Sarabia, Kyle J. Bandaccari, David Oparko, Emma Lewis, Maxwell J. Giammona, Justin Isaac, Parisa Tajalli-Tehrani Valverde, Grace E. Chesmore, Thorsteinn Adalsteinsson, Richard P. Barber Jr., Brian J. Mcnelis

Physics

We report both transport measurements and spectroscopic data of polymer/fullerene blend photovoltaics using a small library of fullerene esters to correlate device properties with a range of functionality and structural diversity of the ester substituent. We observe that minor structural changes can lead to significant and surprising differences in device efficiency and lifetime. For example we have found that isomeric R-groups in the fullerene ester-based devices we have studied have dramatically different efficiencies. The characteristic lifetimes derived from both transport and spectroscopic measurements are generally comparable; however, some more rapid effects in specific fullerene esters are not observed spectroscopically. It …

Automated Discrimination Of Dicentric And Monocentric Chromosomes By Machine Learning-Based Image Processing., Yanxin Li, Joan H Knoll, Ruth C Wilkins, Farrah N Flegal, Peter K Rogan

Biochemistry Publications

Dose from radiation exposure can be estimated from dicentric chromosome (DC) frequencies in metaphase cells of peripheral blood lymphocytes. We automated DC detection by extracting features in Giemsa-stained metaphase chromosome images and classifying objects by machine learning (ML). DC detection involves (i) intensity thresholded segmentation of metaphase objects, (ii) chromosome separation by watershed transformation and elimination of inseparable chromosome clusters, fragments and staining debris using a morphological decision tree filter, (iii) determination of chromosome width and centreline, (iv) derivation of centromere candidates, and (v) distinction of DCs from monocentric chromosomes (MC) by ML. Centromere candidates are inferred from 14 image …

Development And Application Of New Solid-State Models For Low-Energy Vibrations, Lattice Defects, Entropies Of Mixing, And Magnetic Properties, Jacob M. Schliesser

Theses and Dissertations

Low-temperature heat capacity data contain information on the physical properties of materials, and new models continue to be developed to aid in the analysis and interpretation of heat capacity data into physically meaningful properties. This work presents the development of two such models and their application to real material systems. Equations describing low-energy vibrational modes with a gap in the density of states (DOS) have been derived and tested on several material systems with known gaps in the DOS, and the origins of such gaps in the DOS are presented. Lattice vacancies have been shown to produce a two-level system …

Transcriptional Profile Of Immediate Response To Ionizing Radiation Exposure, Eric C. Rouchka, Robert M. Flight, Brigitte H. Fasciotto, Rosendo Estrada, John W. Eaton, Phani K. Patibandla, Sabine J. Waigel, Dazhuo Li, John K. Kirtley, Palaniappan Sethu, Robert S. Keynton

Molecular and Cellular Biochemistry Faculty Publications

Astronauts participating in long duration space missions are likely to be exposed to ionizing radiation associated with highly energetic and charged heavy particles. Previously proposed gene biomarkers for radiation exposure include phosphorylated H2A Histone Family, Member X (γH2AX), Tumor Protein 53 (TP53), and Cyclin-Dependent Kinase Inhibitor 1A (CDKN1A). However, transcripts of these genes may not be the most suitable biomarkers for radiation exposure due to a lack of sensitivity or specificity. As part of a larger effort to develop lab-on-a-chip methods for detecting radiation exposure events using blood samples, we designed a dose–course microarray study in order to determine coding …

Biological Nanomotors With A Revolution, Linear, Or Rotation Motion Mechanism, Peixuan Guo, Hiroyuki Noji, Christopher M. Yengo, Zhengyi Zhao, Ian Grainge

Nanobiotechnology Center Faculty Publications

The ubiquitous biological nanomotors were classified into two categories in the past: linear and rotation motors. In 2013, a third type of biomotor, revolution without rotation (http://rnanano.osu.edu/movie.html), was discovered and found to be widespread among bacteria, eukaryotic viruses, and double-stranded DNA (dsDNA) bacteriophages. This review focuses on recent findings about various aspects of motors, including chirality, stoichiometry, channel size, entropy, conformational change, and energy usage rate, in a variety of well-studied motors, including F_oF₁ ATPase, helicases, viral dsDNA-packaging motors, bacterial chromosome translocases, myosin, kinesin, and dynein. In particular, dsDNA translocases are used to illustrate how …

Spectral Pre And Post Processing For Infrared And Raman Spectroscopy Of Biological Tissues And Cells, Hugh Byrne, Peter Knief, Mark Keating, Franck Bonnier

Articles

Vibrational Spectroscopy, both infrared absorption and Raman spectroscopy, have attracted increasing attention for biomedical applications, from in vivo and ex vivo disease diagnostics and screening, to in vitro screening of therapeutics. There remain, however, many challenges related to the accuracy of analysis of physically and chemically inhomogeneous samples, across heterogeneous sample sets. Data preprocessing is required to deal with variations in instrumental responses and intrinsic spectral backgrounds and distortions in order to extract reliable spectral data. Data postprocessing is required to extract the most reliable information from the sample sets, based on often very subtle changes in spectra associated with …

Analysis Of Enzyme-Responsive Peptide Surfaces By Raman Spectroscopy, Jugal Kishore Sahoo, Narayana M.S. Sirimuthu, Anne Canning, Mischa Zelzer, Duncan Graham, Rein V. Ulijn

Advanced Science Research Center

We report on the use of Raman spectroscopy as a tool to characterize model peptide functionalised surfaces. By taking advantage of Raman reporters built into the peptide sequence, the enzymatic hydrolysis of these peptides could be determined.

Alternative Regulation Of Myc In Lung Cancer, Patrick N. Backman

Open Access Theses

Lung cancer is the leading cause of cancer deaths in the United States, accounting for 27% of all cancer induced deaths1. In an attempt to create a effective targeted therapy for the treatment of lung cancer, a strategy used to treat an activated KrasG12D/+;p53 R172H/+ transgenic lung cancer mouse model was to deliver a known tumor suppressive microRNA (miRNA) to stop tumor growth. The tumor suppressive miRNA let-7 was lentivirally delivered in the form of its primary transcript, pri-let-7a-1, and resulted in increased lung size and inflammation compared to lungs exposed to a control lentivirus. It was identified …

Identification Of Plant Extracts That Inhibit The Formation Of Diabetes-Linked Iapp Amyloid, Ana Lucia Fuentes, Kathleen Hennessy, Jacob Pascual, Nicole Pepe, In Wang, Cynthia Chaggan, Jessica Martinez, Evelyn Rivera, Paola Cota, Christina Cunha, Luiza A. Nogaj, David A. Moffet

Chemistry and Biochemistry Faculty Works

The extracts of 27 vegetables, spices and herbs were screened for their functional ability to inhibit the aggregation of islet amyloid polypeptide (IAPP, amylin) into toxic amyloid aggregates. The aggregation of IAPP has been directly linked to the death of pancreatic β-islet cells in type 2 diabetes. Inhibiting the aggregation of IAPP is believed to have the potential to slow, if not prevent entirely, the progression of this disease. As vegetables, spices and herbs are known to possess many different positive health effects, the extracts of 27 plants (abundant within the United States and spanning several plant families) were screened …

Retigabine Holds Kv7 Channels Open And Stabilizes The Resting Potential, Aaron Corbin-Leftwich, Sayeed M. Mossadeq, Junghoon Ha, Iwona Ruchala, Audrey Han Ngoc Le, Carlos A. Villalba-Galea

School of Pharmacy Faculty Articles

The anticonvulsant Retigabine is a KV7 channel agonist used to treat hyperexcitability disorders in humans. Retigabine shifts the voltage dependence for activation of the heteromeric KV7.2/KV7.3 channel to more negative potentials, thus facilitating activation. Although the molecular mechanism underlying Retigabine's action remains unknown, previous studies have identified the pore region of KV7 channels as the drug's target. This suggested that the Retigabine-induced shift in voltage dependence likely derives from the stabilization of the pore domain in an open (conducting) conformation. Testing this idea, we show that the heteromeric KV7.2/KV7.3 channel has at least two open states, which we named O1 …

14-3-3Ζ Regulation Of Metastasis Through Mediation Of Liprin-Α And Liprin-Β, Rachel Hynes

Theses and Dissertations

Cancer is a set of varied and diverse diseases that share common characteristics, such as active proliferation, increased replicative potential, and tissue invasion or metastasis. One protein, 14-3-3ζ, is shown to be upregulated in a number of different cancers and also correlates with poor patient prognosis, recurrence, and mortality. This protein comes from a family of adapter proteins known for their scaffolding ability, pro- and anti-oncogenic capabilities, and affinity for phosphorylated substrates. It has been shown previously to participate in cancer progression, subversion of apoptosis, and to increase chemoresistance. Herein we will discuss the ability of 14-3-3ζ to promote distant-site …

Methods For Detecting Microbial Methane Production And Consumption By Gas Chromatography, Jared T. Aldridge, Jennie L. Catlett, Megan L. Smith, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Methane is an energy-dense fuel but is also a greenhouse gas 25 times more detrimental to the environment than CO2. Methane can be produced abiotically by serpentinization, chemically by Sabatier or Fisher-Tropsh chemistry, or biotically by microbes (Berndt et al., 1996; Horita and Berndt, 1999; Dry, 2002; Wolfe, 1982; Thauer, 1998; Metcalf et al., 2002). Methanogens are anaerobic archaea that grow by producing methane gas as a metabolic byproduct (Wolfe, 1982; Thauer, 1998). Our lab has developed and optimized three different gas chromatograph-utilizing assays to characterize methanogen metabolism (Catlett et al., 2015). Here we describe the end point and kinetic …