Life Sciences Commons^™

Her2 Targeted Molecular Mr Imaging Using A De Novo Designed Protein Contrast Agent, Jingjuan Qiao, Shunyi Li, Lixia Wei, Jie Jiang, Robert Long, Hui Mao, Ling Wei, Liya Wang, Hua Yang, Hans E. Grossniklaus, Zhi-Ren Liu, Jenny J. Yang

Chemistry Faculty Publications

The application of magnetic resonance imaging (MRI) to non-invasively assess disease biomarkers has been hampered by the lack of desired contrast agents with high relaxivity, targeting capability, and optimized pharmacokinetics. We have developed a novel MR imaging probe targeting to HER2, a biomarker for various cancer types and a drug target for anti-cancer therapies. This multimodal HER20targeted MR imaging probe integrates a de novo designed protein contrast agent with a high affinity HER2 affibody and a near IR fluorescent dye. Our probe can differentially monitor tumors with different expression levels of HER2 in both human cell lines and xenograft mice …

Cellulose- And Xylan-Degrading Thermophilic Anaerobic Bacteria From Biocompost, M. V. Sizova, J. A. Izquierdo, N. S. Panikov, L. R. Lynd

Dartmouth Scholarship

Nine thermophilic cellulolytic clostridial isolates and four other noncellulolytic bacterial isolates were isolated from self-heated biocompost via preliminary enrichment culture on microcrystalline cellulose. All cellulolytic isolates grew vigorously on cellulose, with the formation of either ethanol and acetate or acetate and formate as principal fermentation products as well as lactate and glycerol as minor products. In addition, two out of nine cellulolytic strains were able to utilize xylan and pretreated wood with roughly the same efficiency as for cellulose. The major products of xylan fermentation were acetate and formate, with minor contributions of lactate and ethanol. Phylogenetic analyses of 16S …

The Australian Methane Budget: Interpreting Surface And Train-Borne Measurements Using A Chemistry Transport Model, A Fraser, C C. Miller, Paul Palmer, Nicholas M. Deutscher, Nicholas B. Jones, David W. Griffith

Faculty of Science - Papers (Archive)

We investigate the Australian methane budget from 2005-2008 using the GEOS-Chem 3D chemistry transport model, focusing on the relative contribution of emissions from different sectors and the influence of long-range transport. To evaluate the model, we use in situ surface measurements of methane, methane dry air column average (XCH 4) from ground-based Fourier transform spectrometers (FTSs), and train-borne surface concentration measurements from an in situ FTS along the north-south continental transect. We use gravity anomaly data from Gravity Recovery and Climate Experiment to describe the spatial and temporal distribution of wetland emissions and scale it to a prior emission estimate, …

Advanced Statistical Methods For Biochemical And Forensic Applications Of Raman Spectroscopy, Vitali Sikirzhytski

Legacy Theses & Dissertations (2009 - 2024)

This work is dedicated to the development and application of advanced statistical methods for biochemical and forensic applications of Raman spectroscopy. We developed a new concept of multidimensional Raman signatures for forensic identification of body fluid traces, which was successfully applied to the study of dried blood, semen, saliva, sweat and vaginal fluid stains. Several alternative advanced chemometric techniques were also successfully tested for the problems of pure body fluids discrimination and mixture analysis. Studies of body fluid mixtures with low blood and semen concentrations indicated that the detection limit of a minor contributor was as low as a few …

10th Annual Senior Research Symposium Of The Department Of Biological Sciences, Chemistry And Biochemistry, Messiah College

School of Science, Engineering & Health (SEH) Symposium

No abstract provided.

A Framework For Automated Enrichment Of Functionally Significant Inverted Repeats In Whole Genomes, Cyriac Kandoth, Fikret ErçAl, Ronald L. Frank

Computer Science Faculty Research & Creative Works

Background: RNA transcripts from genomic sequences showing dyad symmetry typically adopt hairpin-like, cloverleaf, or similar structures that act as recognition sites for proteins. Such structures often are the precursors of non-coding RNA (ncRNA) sequences like microRNA (miRNA) and small-interfering RNA (siRNA) that have recently garnered more functional significance than in the past. Genomic DNA contains hundreds of thousands of such inverted repeats (IRs) with varying degrees of symmetry. But by collecting statistically significant information from a known set of ncRNA, we can sort these IRs into those that are likely to be functional.

Results: A novel method was developed to …

Chemistry Of Hydrogen Oxide Radicals (Hox) In The Arctic Troposphere In Spring, J Mao, D J. Jacob, M J. Evans, J R. Olson, X Ren, W H. Brune, T M. St. Clair, J D. Crounse, K M. Spencer, M R. Beaver, P O. Wennberg, M J. Cubison, J L. Jimenez, A Fried, P Weibring, J G. Walega, S R. Hall, A J. Weinheimer, R C. Cohen, G Chen, J H. Crawford, C Mcnaughton, A D. Clarke, L Jaegle, Jenny A. Fisher, R M. Yantosca, P Le Sager, C C. Carouge

Faculty of Science - Papers (Archive)

We use observations from the April 2008 NASA ARCTAS aircraft campaign to the North American Arctic, interpreted with a global 3-D chemical transport model (GEOS-Chem), to better understand the sources and cycling of hydrogen oxide radicals (HO_x≡H+OH+peroxy radicals) and their reservoirs (HO_y≡HO_x+peroxides) in the springtime Arctic atmosphere. We find that a standard gas-phase chemical mechanism overestimates the observed HO₂ and H₂O₂ concentrations. Computation of HO_x and HO_y gas-phase chemical budgets on the basis of the aircraft observations also indicates a large missing sink for both. We hypothesize that …

Protein Chemistry Of Amyloid Fibrils And Chaperones: Implications For Amyloid Formation And Disease, Justin J. Yerbury, Janet R. Kumita

Faculty of Science - Papers (Archive)

Understanding the mechanisms by which amyloid fibrils are formed, both in vivo and in vitro, is vital for developing methods to treat and prevent debilitating deposition diseases such as Alzheimer's disease, Parkinson's disease, type II diabetes and systemic amyloidoses. In recent years, computer modelling and biophysical studies have broadened our understanding of the biochemical mechanisms underpinning protein aggregation. As a result, it is now believed that the ability to form fibrils is an intrinsic property of polypeptide chains and not isolated to disease-related proteins or peptides. Molecular chaperones are a diverse group of functionally related proteins well known for their …

Chemistry In Second Life, Andrew Lang, Jean-Claude Bradley

College of Science and Engineering Faculty Research and Scholarship

This review will focus on the current level on chemistry research, education, and visualization possible within the multi-user virtual environment of Second Life. We discuss how Second Life has been used as a platform for the interactive and collaborative visualization of data from molecules and proteins to spectra and experimental data. We then review how these visualizations can be scripted for immersive educational activities and real-life collaborative research. We also discuss the benefits of the social networking affordances of Second Life for both chemists and chemistry students.

Validation Of Ozone Measurements From The Atmospheric Chemistry Experiment (Ace), Nicholas B. Jones, David W. Griffith, M Wolff, E Mahieu, G Bodeker, I Boyd, M De Maziere, P Demoulin, T Blumenstock, Y. Murayama, A. Kagawa, J Jin, Christopher Mcelroy, J Hannigan, M Coffey, M Hopfner, H W. Fischer, T Kerzenmacher, I Kramer, J Mellqvist, R Sussmann, K Strong, J R. Taylor, K Mizutani, Y Kasai, J Urban, D Murtagh, E Dupuy, V Catoire, S Chabrillat, P Baron, C Brogniez, G L. Manney, C Piccolo, C Randall, C Robert, C Senten, C Tetard, N J. Livesey, A Kleinbohl, S Godin-Beekmann, T Borsdorff, James Drummond, C De Clercq, J C. Lambert, U Cortesi, K W. Jucks, C Boone, H Oelhaf, M Schneider, T Steck, K A. Walker, P Bernath, T Von Clarmann, R Hughes, C Vigouroux, J Kuttippurath, A Bracher, J Mcconnell, C Mclinden, H Kullmann, L Froidevaux, J Dodion, F Vanhellemont, J P. Burrows, J Kar, F Goutail, D G. Dufour, J M. Zawodny, F Nichitiu, J-P Pommereau, C Nowlan, D Fussen, J Zou, A R Klekociuk, G Forbes, H Bovensmann, R M Bevilacqua, C Haley, S Ceccherini, S D Mcleod, P Gerard, R Skelton, B Firanski, A E Bourassa, D A Degenstein, J Davies, T Christensen, J Granville, A Parrish, C Roth, J W. Waters, C Von Savigny, A Standberg, M Mchugh, A M. Thompson, E J Llewellyn, P Von Der Gathen, M B. Tully, J C. Witte, C Roth, B T. Marshall, K B. Strawbridge, E Kyrola, M P. Mccormick, D P J Swart, N D Lloyd, D W. Tarasick, S V. Petelina, L W. Thomason, A Jones, I S. Mcdermid

Faculty of Science - Papers (Archive)

This paper presents extensive bias determination analyses of ozone observations from the Atmospheric Chemistry Experiment (ACE) satellite instruments: the ACE Fourier Transform Spectrometer (ACE-FTS) and the Measurement of Aerosol Extinction in the Stratosphere and Troposphere Retrieved by Occultation (ACE-MAESTRO) instrument. Here we compare the latest ozone data products from ACE-FTS and ACE-MAESTRO with coincident observations from nearly 20 satellite-borne, airborne, balloonborne and ground-based instruments, by analysing volume mixing ratio profiles and partial column densities. The ACEFTS version 2.2 Ozone Update product reports more ozone than most correlative measurements from the upper troposphere to the lower mesosphere. At altitude levels from …

Photocycloaddition Of Allenes, Crystal Ward

Theses and Dissertations

For the past ten years the Fleming research group has been involved in the research of allene compounds. We have explored the synthesis of allenes as well as several reactions involving allenes, such as oxidation and nitrene addition. Recently, we have explored the synthesis and photochemistry of allenic alcohols tethered to silicon. There are literature examples using allenes in synthesis, but very few examples exist using allenes in photochemical cycloaddition reactions. We have found that a diisopropylallenyloxy(cinnamyloxy)silane derivative undergoes [2+2] photochemical cycloaddition to produce a cyclobutylsilane product when irradiated for 60-75 minutes.

Validation Of Hno3, C1ono2, And N2o5 From The Atmospheric Chemistry Experiment Fourier Transform Spectrometer (Ace-Fts), M A. Wolff, T Kerzenmacher, K Strong, K A. Walker, M Toohey, E Dupuy, P F. Bernath, C Boone, S Brohede, V Catoire, T Von Clarmann, M Coffey, W Daffer, M De Maziere, P Duchatelet, N Glatthor, David W. Griffith, J Hannigan, F Hase, M Hopfner, N Huret, Nicholas B. Jones, K W. Jucks, A. Kagawa, Y Kasai, I Kramer, H Kullmann, J Kuttippurath, E Mahieu, G L. Manney, Christopher Mcelroy, C Mclinden, Y Mebarki, S Mikuteit, D Murtagh, C Piccolo, P Raspollini, M Ridolfi, R Ruhnke, M Santee, C Senten, D Smale, C Tetard, J Urban, S Wood

Faculty of Science - Papers (Archive)

The Atmospheric Chemistry Experiment (ACE) satellite was launched on 12 August 2003. Its two instruments measure vertical profiles of over 30 atmospheric trace gases by analyzing solar occultation spectra in the ultraviolet/visible and infrared wavelength regions. The reservoir gases HNO₃, ClONO₂, and N₂O₅ are three of the key species provided by the primary instrument, the ACE Fourier Transform Spectrometer (ACE-FTS). This paper describes the ACE-FTS version 2.2 data products, including the N₂O₅ update, for the three species and presents validation comparisons with available observations. We have compared volume mixing ratio …

Validation Of No2 And No From The Atmospheric Chemistry Experiment (Ace), Nicholas B. Jones, David W. Griffith, M Wolff, L Llewellyn, T Blumenstock, Christopher Mcelroy, M Hopfner, T Kerzenmacher, I Kramer, K Strong, Cassandra Haley, J R. Taylor, Thorsten Warneke, D Murtagh, E Dupuy, V Catoire, N Huret, C Brogniez, G L. Manney, C Piccolo, C Randall, C Tetard, M Lopez-Puertas, James Drummond, C Boone, B Funke, M Schneider, S Mikuteit, G P. Stiller, K A. Walker, P Bernath, O Schrems, P Raspollini, C Mclinden, S Brohede, M Toohey, M Ridolfi, J Dodion, F Vanhellemont, R L. Batchelor, J P. Burrows, J Kar, L K. Amekudzi, S Melo, F Goutail, C Bramstedt, D G. Dufour, M Silicani, J M. Zawodny, A Richter, G Berthet, F Nichitiu, J-P Pommereau, C Nowlan, D Fussen, J Zou, Irwin S. Pakula, Justus Notholt

Faculty of Science - Papers (Archive)

Vertical profiles of NO2 and NO have been obtained from solar occultation measurements by the Atmospheric Chemistry Experiment (ACE), using an infrared Fourier Transform Spectrometer (ACE-FTS) and (for NO2) an ultraviolet-visible-near-infrared spectrometer, MAESTRO (Measurement of Aerosol Extinction in the Stratosphere and Troposphere Retrieved by Occultation). In this paper, the quality of the ACE-FTS version 2.2 NO2 and NO and the MAESTRO version 1.2 NO2 data are assessed using other solar occultation measurements

(HALOE, SAGE II, SAGEIII, POAMIII, SCIAMACHY), stellar occultation measurements (GOMOS), limb measurements (MIPAS, OSIRIS), nadir measurements (SCIAMACHY), balloon-borne measurements (SPIRALE, SAOZ) and ground-based measurements (UV-VIS, FTIR). Time differences …

Dna-Templated Nanomaterials, Hector Alejandro Becerril-Garcia

Theses and Dissertations

Nanomaterials display interesting physical and chemical properties depending on their shape, size and composition. Self assembly is an intriguing route to producing nanomaterials with controllable compositions and morphologies. DNA has been used to guide the self assembly of materials, resulting in: (1) metal nanowires; (2) metal or semiconductor nanorods; (3) carbon nanotubes; and (4) semiconductor, metal or biological nanoparticles. My work expands the range of DNA templated nanomaterials and develops novel ways of using DNA to pattern nanostructures on surfaces. I have performed the first synthesis of silver nanorods on single stranded DNA, an attractive material for localizing DNA coupled …

Photoreductive Dissolution Of Ferrihydrite By Methanesulfinic Acid: Evidence Of A Direct Link Between Dimethylsulfide And Iron-Bioavailability, Anne M. Johansen, Jennifer M. Key

All Faculty Scholarship for the College of the Sciences

Within open‐ocean regions where excess macronutrients are present, phytoplankton growth is limited by the bioavailability of iron supplied to these areas primarily within atmospheric aerosols of crustal origin. However, processes that control the abundance of biologically accessible iron in these aerosols are largely unknown. Here we show that dissolution of ferrihydrite, a surrogate iron(oxy)hydroxide phase found in atmospheric waters, is enhanced in the presence of methanesulfinic acid (MSIA, CH₃SO₂H, a dimethylsulfide (DMS) oxidation intermediate) in laboratory irradiation experiments with aqueous suspensions that simulate marine aerosol particles. The increased release of soluble Fe(II) is attributed to a …

Bounded Search For De Novo Identification Of Degenerate Cis-Regulatory Elements, Jonathan M. Carlson, Arijit Chakravarty, Radhika S. Khetani, Robert H. Gross

Dartmouth Scholarship

The identification of statistically overrepresented sequences in the upstream regions of coregulated genes should theoretically permit the identification of potential cis-regulatory elements. However, in practice many cis-regulatory elements are highly degenerate, precluding the use of an exhaustive word-counting strategy for their identification. While numerous methods exist for inferring base distributions using a position weight matrix, recent studies suggest that the independence assumptions inherent in the model, as well as the inability to reach a global optimum, limit this approach.

Abstracts Of Papers, 84th Annual Meeting Of The Virginia Academy Of Science

Virginia Journal of Science

Full abstracts of papers for the 84th Annual Meeting of the Virginia Academy of Science, May 25-26, 2006, Virginia Polytechnic Institute and State University, Blacksburg, VA

Principal Component Analysis For Predicting Transcription-Factor Binding Motifs From Array-Derived Data, Yunlong Liu, Matthew P Vincenti, Hiroki Yokota

Dartmouth Scholarship

The responses to interleukin 1 (IL-1) in human chondrocytes constitute a complex regulatory mechanism, where multiple transcription factors interact combinatorially to transcription-factor binding motifs (TFBMs). In order to select a critical set of TFBMs from genomic DNA information and an array-derived data, an efficient algorithm to solve a combinatorial optimization problem is required. Although computational approaches based on evolutionary algorithms are commonly employed, an analytical algorithm would be useful to predict TFBMs at nearly no computational cost and evaluate varying modelling conditions. Singular value decomposition (SVD) is a powerful method to derive primary components of a given matrix. Applying SVD …

Crystal Structure Of The Gtpase Domain Of Rat Dynamin 1, Thomas F. Reubold, Susanne Eschenburg, Andreas Becker, Marilyn Leonard, Sandra L. Schmid, Richard B. Vallee, F. Jon Kull, Dietmar J. Manstein

Dartmouth Scholarship

Here, we present the 1.9-A crystal structure of the nucleotide-free GTPase domain of dynamin 1 from Rattus norvegicus. The structure corresponds to an extended form of the canonical GTPase fold observed in Ras proteins. Both nucleotide-binding switch motifs are well resolved, adopting conformations that closely resemble a GTP-bound state not previously observed for nucleotide-free GTPases. Two highly conserved arginines, Arg-66 and Arg-67, greatly restrict the mobility of switch I and are ideally positioned to relay information about the nucleotide state to other parts of the protein. Our results support a model in which switch I residue Arg-59 gates GTP binding …

Simulations Of Nanopore Formation And Phosphatidylserine Externalization In Lipid Membranes Subjected To A High-Intensity, Ultrashort Electric Pulse, Q. Hu, R. P. Joshi, K. H. Schoenbach

Bioelectrics Publications

A combined MD simulator and time dependent Laplace solver are used to analyze the electrically driven phosphatidylserine externalization process in cells. Time dependent details of nanopore formation at cell membranes in response to a high-intensity (100kV∕cm), ultrashort (10ns) electric pulse are also probed. Our results show that nanosized pores could typically be formed within about 5ns. These predictions are in very good agreement with recent experimental data. It is also demonstrated that defect formation and PS externalization in membranes should begin on the anode side. Finally, the simulations confirm that PS externalization is a nanopore facilitated event, rather than the …

Examination Of Technologies For Student-Generated Work In A Peer-Led, Peer-Review Instructional Environment, Brian P. Coppola, Alan L. Kiste

Chemistry and Biochemistry

There is a growing literature demonstrating the effectiveness of using computer environments to assist students’ in visualizing science and mathematics concepts. However, with many of these computerized learning environments, students do not have the option of manipulating the environment. Instead, they are presented with pre-made visualizations. Enabling students to display their understanding through multiple representational forms is more interesting. In our peer-led, peer-review environment, students generate a complex, literature-based, multimedia text on which their final examination is based. However, there are great time and personnel costs in this design. Collaborating with SRI Inc., we are addressing these demands via the …

A Subgroup Algorithm To Identify Cross-Rotation Peaks Consistent With Non-Crystallographic Symmetry, Ryan H. Lilien, Chris Bailey-Kellogg, Amy C. Anderson, Bruce R. Donald

Dartmouth Scholarship

Molecular replacement (MR) often plays a prominent role in determining initial phase angles for structure determination by X-ray crystallography. In this paper, an efficient quaternion-based algorithm is presented for analyzing peaks from a cross-rotation function in order to identify model orientations consistent with proper non-crystallographic symmetry (NCS) and to generate proper NCS-consistent orientations missing from the list of cross-rotation peaks. The algorithm, CRANS, analyzes the rotation differences between each pair of cross-rotation peaks to identify finite subgroups. Sets of rotation differences satisfying the subgroup axioms correspond to orientations compatible with the correct proper NCS. The CRANS algorithm was first …

The Enzymatic Oxidation Of Aldehydes By Xanthine Oxidase, Duane Beal Gregory

All Master's Theses

As early as sixty years ago, the existence of an enzyme from mammalian tissues which catalyzed the oxidation of xanthine and hypoxanthine was recognized. The name given the enzyme was derived from its earliest recognized action, hence xanthine oxidase. Although little is known about the biological functions of the enzyme, the high affinity shown for xanthine and hypoxanthine may indicate that these are the most significant substrates biologically.

The Alcohols, Charles E. Baker

Manuscript Thesis Collection

A study of Alcohols and the human body's reactions to them.