Physical Sciences and Mathematics | Open Access Articles

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 …

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The Role Of Blowing Snow In The Activation Of Bromine Over First-Year Antarctic Sea Ice, R. M. Lieb-Lappen, R. W. Obbard

Dartmouth Scholarship

It is well known that during polar springtime halide sea salt ions, in particular Br^-, are photochemically activated into reactive halogen species (e.g., Br and BrO), where they break down tropospheric ozone. This research investigated the role of blowing snow in transporting salts from the sea ice/snow surface into reactive bromine species in the air. At two different locations over first-year ice in the Ross Sea, Antarctica, collection baskets captured blowing snow at different heights. In addition, sea ice cores and surface snow samples were collected throughout the month-long campaign. Over this time, sea ice and surface snow …

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Regulating Signal Enhancement With Coordination-Coupled Deprotonation Of A Hydrazone Switch, Justin T. Foy, Debdas Ray, Ivan Aprahamian

Dartmouth Scholarship

Proton relay plays an important role in many biocatalytic pathways. In order to mimic such processes in the context of molecular switches, we developed coordination-coupled deprotonation (CCD) driven signaling and signal enhancement sequences. This was accomplished by using the zinc(ii)-initiated CCD of a hydrazone switch to instigate an acid catalyzed imine bond hydrolysis that separates a quencher from a fluorophore thus leading to emission amplification. Because CCD is a reversible process, we were able to show that the catalysis can be regulated and turned “on” and “off” using a metalation/demetalation cycle.

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Gene And Protein Sequence Optimization For High-Level Production Of Fully Active And Aglycosylated Lysostaphin In Pichia Pastoris, Hongliang Zhao, Kristina Blazanovic, Yoonjoo Choi, Chris Bailey-Kellogg, Karl E. Griswold

Dartmouth Scholarship

Lysostaphin represents a promising therapeutic agent for the treatment of staphylococcal infections, in particular those of methicillin-resistant Staphylococcus aureus (MRSA). However, conventional expression systems for the enzyme suffer from various limitations, and there remains a need for an efficient and cost-effective production process to facilitate clinical translation and the development of nonmedical applications. While Pichia pastoris is widely used for high-level production of recombinant proteins, there are two major barriers to the production of lysostaphin in this industrially relevant host: lack of expression from the wild-type lysostaphin gene and aberrant glycosylation of the wild-type protein sequence. The first barrier can …

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Relationship Between Altitude And Lithium In Groundwater In The United States Of America: Results Of A 1992–2003 Study, Rebekah S. Huber, Namkug Kim, Carl E. Renshaw, Perry F. Renshaw, Douglas Kondo

Dartmouth Scholarship

Therapeutic dosages of lithium are known to reduce suicide rates, which has led to investigations of confounding environmental risk factors for suicide such as lithium in groundwater. It has been speculated that this might play a role in the potential relationship between suicide and altitude. A recent study in Austria involving geospatial analysis of lithium in groundwater and suicide found lower levels of lithium at higher altitudes. Since there is no reason to suspect this correlation is universal given variation in geology, the current study set out to investigate the relationship between altitude and lithium in groundwater in the United …

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Kinetic Fractionation Of Gases By Deep Air Convection In Polar Firn, K. Kawamura, J. P. Severinghaus, M. R. Albert, Z. R. Courville

Dartmouth Scholarship

A previously unrecognized type of gas fractiona- tion occurs in firn air columns subjected to intense convec- tion. It is a form of kinetic fractionation that depends on the fact that different gases have different molecular diffusivi- ties. Convective mixing continually disturbs diffusive equi- librium, and gases diffuse back toward diffusive equilibrium under the influence of gravity and thermal gradients. In near- surface firn where convection and diffusion compete as gas transport mechanisms, slow-diffusing gases such as krypton (Kr) and xenon (Xe) are more heavily impacted by convec- tion than fast diffusing gases such as nitrogen (N2) and ar- gon …

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Surficial Redistribution Of Fallout 131iodine In A Small Temperate Catchment, Joshua D. Landis, Nathan T. Hamm, Carl E. Renshaw, W. Brian Dade, Francis J. Magilligan, John D. Gartner

Dartmouth Scholarship

Isotopes of iodine play significant environmental roles, including a limiting micronutrient (¹²⁷I), an acute radiotoxin (¹³¹I), and a geochemical tracer (¹²⁹I). But the cycling of iodine through terrestrial ecosystems is poorly understood, due to its complex environmental chemistry and low natural abundance. To better understand iodine transport and fate in a terrestrial ecosystem, we traced fallout ¹³¹iodine throughout a small temperate catchment following contamination by the 11 March 2011 failure of the Fukushima Daiichi nuclear power facility. We find that radioiodine fallout is actively and efficiently scavenged by the soil system, where it …

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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 …

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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.

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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 …

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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 …

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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 …

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Regulation And Localization Of Endogenous Human Tristetraprolin, Anna-Marie Fairhurst, John E. Connolly, Katharine A Hintz, Nicolas J Goulding

Dartmouth Scholarship

Tumor necrosis factor (TNF) has been implicated in the development and pathogenicity of infectious diseases and autoimmune disorders, such as septic shock and arthritis. The zinc-finger protein tristetraprolin (TTP) has been identified as a major regulator of TNF biosynthesis. To define its intracellular location and examine its regulation of TNF, a quantitive intracellular staining assay specific for TTP was developed. We establish for the first time that in peripheral blood leukocytes, express

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Full-Text Articles in Physical Sciences and Mathematics

Dartmouth Scholarship

The Role Of Blowing Snow In The Activation Of Bromine Over First-Year Antarctic Sea Ice, R. M. Lieb-Lappen, R. W. Obbard

Dartmouth Scholarship

Regulating Signal Enhancement With Coordination-Coupled Deprotonation Of A Hydrazone Switch, Justin T. Foy, Debdas Ray, Ivan Aprahamian

Dartmouth Scholarship

Gene And Protein Sequence Optimization For High-Level Production Of Fully Active And Aglycosylated Lysostaphin In Pichia Pastoris, Hongliang Zhao, Kristina Blazanovic, Yoonjoo Choi, Chris Bailey-Kellogg, Karl E. Griswold

Dartmouth Scholarship

Relationship Between Altitude And Lithium In Groundwater In The United States Of America: Results Of A 1992–2003 Study, Rebekah S. Huber, Namkug Kim, Carl E. Renshaw, Perry F. Renshaw, Douglas Kondo

Dartmouth Scholarship

Kinetic Fractionation Of Gases By Deep Air Convection In Polar Firn, K. Kawamura, J. P. Severinghaus, M. R. Albert, Z. R. Courville

Dartmouth Scholarship

Surficial Redistribution Of Fallout 131iodine In A Small Temperate Catchment, Joshua D. Landis, Nathan T. Hamm, Carl E. Renshaw, W. Brian Dade, Francis J. Magilligan, John D. Gartner

Dartmouth Scholarship

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

Dartmouth Scholarship

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

Dartmouth Scholarship

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

Dartmouth Scholarship

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

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

Regulation And Localization Of Endogenous Human Tristetraprolin, Anna-Marie Fairhurst, John E. Connolly, Katharine A Hintz, Nicolas J Goulding

Dartmouth Scholarship