Biochemistry, Biophysics, and Structural Biology Commons^™

(1e,3e)-1,4-Bis(4-Methoxyphenyl)Buta1,3-Diene, Gopinathan Narayan, Nigam Rath, Suresh Das

Chemistry & Biochemistry Faculty Works

The title compound, C18H18O2, which exhibits blue emission in the solid state, is an inter­mediate in the preparation of liquid crystals and polymers. The mol­ecule is located on an inversion centre. In the crystal, mol­ecules are arranged in a herringbone motif.

Bilinear Programming And Protein Structure Alignment, J. Cain, D. Kamenetsky, N. Lavine

Mathematical Sciences Technical Reports (MSTR)

Proteins are a primary functional component of organic life, and understanding their function is integral to many areas of research in biochemistry. The three-dimensional structure of a protein largely determines this function. Protein structure alignment compares the structure of a protein with known function to that of a protein with unknown function. A protein’s three-dimensional structure can be transformed through a smooth piecewise-linear sigmoid function to a real symmetric contact matrix that represents the functional significance of certain parts of the protein. We address the protein alignment problem as a minimization of the 2-norm difference of two proteins’ contact matrices. …

An Entrepreneurial Approach To Librarianship, Flora Shrode, Jennifer Duncan, Wendy Holliday

Library Faculty & Staff Publications

Librarians from Utah State University explain recent efforts to encourage subject librarians to take a more holistic view of their roles. We are shifting from a traditional emphasis primarily on collection development and refocusing on natural connections between collections, instruction, liaison, and reference service. The poster provides background about Utah State University’s situation and explains our approach to analyzing local needs and culture to inform development of a new organizational structure. We describe our vision of subject librarianship, the process by which we assessed librarians’ ideas and goals for performing as subject librarians, and the actions we are taking to …

Charge Switch Nucleotides, John G. K. Williams, Gregory R. Bashford, Jiyan Chen, Dan Draney, Nara Narayanan, Bambi L. Reynolds, Pamela Sheaff

Biomedical Imaging and Biosignal Analysis Laboratory

The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charge-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation Without interference from unincorporated NPs and Without illuminating the polymerase-DNA complex.

The 3rd Computational Structural Bioinformatics Workshop, Jing He, Di Wu

Computer Science Faculty Publications

As many other domains in biology, molecular structures have proposed challenging but interesting computational problems. The unique challenge of the 3-dimensional molecular structures comes from the combination of the fundamental concepts of physics, chemistry, biology and geometry, and it is often computationally intensive to search for the correct structure. The Computational Structural Bioinformatics Workshop (CSBW) is a workshop that focuses on the fundamental computational work that is related to 3-dimensional molecular structures. This workshop aims to bring together researchers with expertise in bioinformatics, computational biology, structural biology, data mining, optimization and high performance computing to discuss recent results, new techniques, …

Tracking Profiles Of Genomic Instability In Spontaneous Transformation And Tumorigenesis, Lesley Lawrenson

Wayne State University Dissertations

The dominant paradigm for cancer research focuses on the identification of specific genes for cancer causation and for the discovery of therapeutic targets. Alternatively, the current data emphasize the significance of karyotype heterogeneity in cancer progression over specific gene-based causes of cancer. Variability of a magnitude significant to shift cell populations from homogeneous diploid cells to a mosaic of structural and numerical chromosome alterations reflects the characteristic low-fidelity genome transfer of cancer cell populations. This transition marks the departure from micro-evolutionary gene-level change to macro-evolutionary change that facilitates the generation of many unique karyotypes within a cell population. Considering cancer …

Charge Switch Nucleotides, John G. K. Williams, Gregory R. Bashford, Jiyan Chen, Dan Draney, Nara Narayanan, Bambi Reynolds, Pamela Sheaff

Biomedical Imaging and Biosignal Analysis Laboratory

The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charged-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation Without interference from unincorporated NPs and Without illuminating the polymerase-DNA complex.

Applications Of Variable Number Tandem Repeat Genotyping In The Validation Of An Animal Medical Model And Gene Flow Studies In Threatened Populations Of Reptiles, Candace D. Smith

Graduate Theses and Dissertations

We used variable number tandem repeats (VNTR) to validate the chicken as a human medical model for Pulmonary Arterial Hypertension. We identified seven regions on four chromosomes and interrogated for VNTR markers that significantly associate with Pulmonary Hypertension Syndrome/ascites. In those regions, we identified 7 candidate genes; AGTR1, ACE, p38MAPK, SST, 5HT2B, NET1, and CALM3 for further analysis as significantly contributing QTL for ascites/PHS. We also used variable number tandem repeats to measure gene flow and gather evidence for multiple paternity in a population of Timber rattlesnakes, Crotalus horridus. We were able to verify 1 VNTR that can be used …

Catena-Poly[[(Pyridine-Κn)Copper(Ii)]-Μ3-Pyridine-2,6-Dicarboxylato-Κ3o2:O2′,N,O6:O6′], Manoj Trivedi, Daya Pandey, Nigam Rath

Chemistry & Biochemistry Faculty Works

In the title compound, [Cu(C7H3NO4)(C5H5N)]n, the CuII atom is in a slightly distorted octa­hedral coordination environment. Each CuII atom is bound to two N atoms and one O atom of the pyridine­dicarboxyl­ate (PDA) ligand in a tridentate manner, one N atom of the pyridine mol­ecule and two bridging carboxyl­ate O atoms of adjacent PDA ligands, leading to a linear one-dimensional chain running along the c axis. These chains are further assembled via weak C-H...O and [pi]-[pi] inter­actions into a three-dimensional supra­molecular network structure. The centroid-centroid distance between the [pi]-[pi] inter­acting pyridine rings is 3.9104 (13) Å. The two N atoms …

Resolving The Lateral Component Of Blood Flow Velocity Based On Ultrasound Speckle Size Change With Scan Direction And Speed, Tiantian Xu, Greg R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Conventional blood flow velocity measurement using ultrasound is capable of resolving the axial component (i.e., that aligned with the ultrasound propagation direction) of the blood flow velocity vector. However, these Doppler-based methods are incapable of detecting blood flow in the direction normal to the ultrasound beam. In addition, these methods require repeated pulse-echo interrogation at the same spatial location. In this paper, we introduce a method which estimates the lateral component of blood flow within a single image frame using the observation that the speckle pattern corresponding to the blood reflectors (typically red blood cells) stretches (i.e., is “smeared”) if …

Further Progress On Lateral Flow Estimation Using Speckle Size Variation With Scan Direction, Tiantian Xu, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Conventional blood flow velocity measurement using ultrasound is capable of resolving the axial component (i.e., that aligned with the ultrasound propagation direction) of the blood flow velocity vector. However, these Doppler-based methods are incapable of detecting blood flow in the direction normal to the ultrasound beam. In addition, these methods require repeated pulse-echo interrogation at the same spatial location. In this paper, we report additional data on a new method recently introduced. This method estimates the lateral component of blood flow within a single image frame using the observation that the speckle pattern corresponding to the blood reflectors (typically red …

Single Molecule Diffusion Coefficient Estimation By Image Analysis Of Simulated Ccd Images To Aid High-Throughput Screening, Pengfei Song, Lloyd M. Davis, Greg Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Extension of one-dimensional signal analysis to two-dimensional image analysis could accelerate conventional methods of high-throughput screening in the discovery of new pharmaceutical agents. This work describes a first step taken towards this goal – the evaluation of image-analysis based estimation strategies of the diffusion coefficient of a single molecule transported within a microfabricated flowcell. A computer simulation of single-molecule imaging by a charge-coupled device (CCD) camera is used to determine if it is possible to distinguish three different types of molecules with different diffusion coefficients. The Gaussian fitting algorithm finds the variance of the transverse trajectory, which increases linearly with …

Optimal Thresholds Of Feature Tracking For Blood Velocity And Tissue Motion Estimation, Tiantian Xu, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Feature tracking is an algorithm for estimating blood flow velocity and tissue motion using pulse-echo ultrasound. In contrast to cross-correlation speckle-tracking techniques, feature tracking identifies features at discrete locations and corresponds them from frame to frame. Prior studies have demonstrated that feature-tracking estimates exhibit lower variance than those obtained by the conventional autocorrelation method and require less computational complexity than either speckle tracking or autocorrelation. To date, not much attention has been paid to the process by which trackable features (normally local maxima) are selected from the set of all available features. In the selection process, it is desired to …

A Locus-Based Paradigm For Generating Systems Biological Inferences From Large Scale Functional Genomics Datasets, Ajish Dominic George

Legacy Theses & Dissertations (2009 - 2024)

Genomics data is growing at a exponential rate. The ability to integrate new results with existing knowledge about genomic biology is rapidly becoming the limiting factor as there no universal language with which to describe genomic functional elements. To integrate and compare new and existing genomic data, we define our basic functional unit of a genome to be a locus -- a set of positional coordinates along any genome with an arbitrary amount of functional annotations attached. The locus concept enables addressing genomic elements and annotations at any level of granularity from entire swaths of chromosomes to single base-positions. We …

Molecular Evolution Of Genes Underlying Phenotypic Differences Between Humans And Chimpanzees, Santhoshi Bandla

Legacy Theses & Dissertations (2009 - 2024)

Chimpanzees (Pan troglodytes) and bonobos (P. paniscus) are often used as models to study the genetic and morphological changes on the lineage leading to the modern humans (Homo sapiens). Results of this dissertation suggest that, in comparison to other hominoids, chimpanzees and bonobos are more derived in their relative testes sizes and promiscuous mating systems. Phylogenetic analysis of genes that might underlie increased testes size revealed that, in addition to being a sex-determining gene, SRY displays Pan-specific amino acid replacements that make it a compelling candidate as a testes-size determining gene. Strikingly, SRY and another candidate gene, DMRT3, display patterns …

Molecular Characterisation Of A Bovine-Like Rotavirus Detected From A Giraffe, Emily Mulherin, Jill Bryan, Marijke Beltman, Luke O'Grady, Eugene Pidgeon, Lucie Garon, Andrew Lloyd, John Bainbridge, Helen O'Shea, Paul Whyte, Séamus Fanning

Department of Biological Sciences Publications

Background

Rotavirus (RV), is a member of the Reoviridae family and an important etiological agent of acute viral gastroenteritis in the young. Rotaviruses have a wide host range infecting a broad range of animal species, however little is known about rotavirus infection in exotic animals. In this paper we report the first characterisation of a RV strain from a giraffe calf.

Results

This report describes the identification and detailed molecular characterisation of a rotavirus strain detected from a 14-day-old Giraffe (Giraffa camelopardalis), presenting with acute diarrhea. The RV strain detected from the giraffe was characterized molecularly as G10P[11]. …

Computational Design Of Orthogonal Ribosomes, Lon Chubiz, Christopher Rao

Biology Department Faculty Works

Orthogonal ribosomes (o-ribosomes), also known as specialized ribosomes, are able to selectively translate mRNA not recognized by host ribosomes. As a result, they are powerful tools for investigating translational regulation and probing ribosome structure. To date, efforts directed towards engineering o-ribosomes have involved random mutagenesisbased approaches. As an alternative, we present here a computational method for rationally designing o-ribosomes in bacteria. Working under the assumption that base-pair interactions between the 16S rRNA and mRNA serve as the primary mode for ribosome binding and translational initiation, the algorithm enumerates all possible extended recognition sequences for 16S rRNA and then chooses those …

Tendinopathy Discrimination By Use Of Spatial Frequency Parameters In Ultrasound B-Mode Images, Gregory R. Bashford, Nicholas Tomsen, Shruti Arya, Judith M. Burnfield, Kornelia Kulig

Biomedical Imaging and Biosignal Analysis Laboratory

The structural characteristics of a healthy tendon are related to the anisotropic speckle patterns observed in ultrasonic images. This speckle orientation is disrupted upon damage to the tendon structure as observed in patients with tendinopathy. Quantification of the structural appearance of tendon shows promise in creating a tool for diagnosing, prognosing, or measuring changes in tendon organization over time. The current work describes a first step taken towards this goal—classification of Achilles tendon images into tendinopathy and control categories. Eight spatial frequency parameters were extracted from regions of interest on tendon images, filtered and classified using linear discriminant analysis. Resulting …

Diethyl 2-[(4-Nitro­Phen­Yl)(4-Phenyl-1,2,3-Selenadiazol-5-Yl)Meth­Yl]Malonate, A. Marx, S. Saravanan, S. Muthusubramanian, V. Manivannan, Nigam Rath

Chemistry & Biochemistry Faculty Works

In the title compound, C22H21N3O6Se, the heterocyclic ring makes dihedral angles of 50.03 (11) and 67.75 (11)°, respectively, with the benzene and phenyl rings. The terminal C atoms of the ester groups are disordered over two positions: the site occupancies for the C atoms are 0.62 (3)/0.38 (3) and 0.48 (3)/0.52 (3). In the crystal structure, weak intra- and inter­molecular C-H...O inter­actions are observed.

Dioxidobis(2-Oxo-1,2-Dihydropyridin-3-Olato)­Molybdenum(Vi), Manoj Trivedi, Daya Pandey, Nigam Rath

Chemistry & Biochemistry Faculty Works

In the title compound, [Mo(C5H4NO2)2O2], the MoVI atom exhibits a distorted octa­hedral coordination geometry formed by two terminal oxo ligands and two monoanionic O,O-bidentate pyridinone ligands. The two terminal oxo ligands lie in a cis arrangement, the ketonic O atoms of the pyridinone ligands are coordinated trans to the oxo ligands and the deprotonated hydroxyl O atoms are located trans to each other. The crystal structure contains inter­molecular N-H...O hydrogen bonds, C-H...O contacts and face-to-face [pi]-[pi] stacking inter­actions with an inter­planar separation of 3.25 (1) Å.

4-(4-Chlorophenyl)-5-[1-(4-Chlorophenyl)-2-Methyl-2-Nitropropyl]-1,2,3-Selenadiazole, A. Marx, S. Saravanan, S. Muthusubramanian, V. Manivannan, Nigam Rath

Chemistry & Biochemistry Faculty Works

In the title compound, C18H15Cl2N3O2Se, the selenadiazole ring makes dihedral angles of 49.87 (3) and 55.70 (3)° with the two benzene rings. The dihedral angle between the two benzene rings is 11.90 (5)°. In the crystal structure, intra­molecular C-H...O and C-H...Se inter­actions and inter­molecular C-H...O, C-H...Cl and C-H...N inter­actions are observed.

Novel Functions Of Acyl-Coa Thioesterases And Acyltransferases As Auxiliary Enzymes In Peroxisomal Lipid Metabolism., Mary Hunt, Stefan Alexson

Articles

Peroxisomes are single membrane bound organelles present in almost all eukaryotic cells, and to date have been shown to contain approximately 60 identified enzymes involved in various metabolic pathways, including the oxidation of a variety of lipids. These lipids include very long-chain fatty acids, methyl branched fatty acids, prostaglandins, bile acid precursors, and xenobiotics that are either β-oxidized or α-oxidized in peroxisomes. The recent identification of several acyl-CoA thioesterases and acyltransferases in peroxisomes has revealed their various functions in acting as auxiliary enzymes in α- and β-oxidation in this organelle. To date, 9 functional acyl-CoA thioesterases and acyltransferases have been …

Improved Constrained Global Optimization For Estimating Molecular Structure From Atomic Distances, Terri Marie Grant

Mathematics & Statistics Theses & Dissertations

Determination of molecular structure is commonly posed as a nonlinear optimization problem. The objective functions rely on a vast amount of structural data. As a result, the objective functions are most often nonconvex, nonsmooth, and possess many local minima. Furthermore, introduction of additional structural data into the objective function creates barriers in finding the global minimum, causes additional computational issues associated with evaluating the function, and makes physical constraint enforcement intractable. To combat the computational problems associated with standard nonlinear optimization formulations, Williams et al. (2001) proposed an atom-based optimization, referred to as GNOMAD, which complements a simple interatomic distance …

Direct Comparison Of Feature Tracking And Autocorrelation For Velocity Estimation, Gregory R. Bashford, Derek J. Robinson

Biomedical Imaging and Biosignal Analysis Laboratory

Feature tracking is an algorithm for estimating tissue motion and blood flow using pulse-echo ultrasound. It was proposed as a computationally simpler alternative to other techniques such as autocorrelation and time-domain cross correlation. The advantage of feature tracking is that it selectively extracts easily identifiable parts of the speckle signal (e.g., the local maxima), reducing the amount of information being processed. Studies on feature tracking to date have used stationary, specklegenerating targets to simulate blood flow. Also, feature tracking has not been compared with accepted commercial methods. This study directly compares feature tracking performance with the complex autocorrelation method, which …

Single Molecule Detection Systems And Methods, John G. K. Williams, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

A micofluidic system is provided that includes a substrate, a first microchannel disposed in the substrate for providing a reactant to a reaction zone, a second microchannel disposed in the substrate, the third microchannel providing fluid communication between the first and second microchannels. The system also typically includes first and second electrodes, positioned at opposite ends of the second microchannel, for providing an electric field within the second microchannel. In operation, when the reactant is in the reaction zone, a reaction product is produced having a net electric charge different from the electric of the reactant.

In Vitro Expression And Purification Of Class I Mhc Molecules, Loi Cheng

Honors Scholar Theses

The major histocompatibility complex (MHC) is a gene family responsible for many critical functions of the immune system in most vertebrates. The MHC consists of three classes differentiated by their structure and function, and MHC class I encodes antigen binding proteins as well as chaperone and accessory proteins such as tapasin. The purpose of this project is to reconstitute several human MHC class I molecules in their peptide-filled and peptide-deficient forms, and to purify these proteins for biochemical study. The expressed proteins include wild type and mutant variants of the fusion protein human leukocyte antigen HLA-B*0801-fos, and human beta-2-microglobulin (β2m). …

Analysis Of The Mouse And Human Acyl-Coa Thioesterase (Acot) Gene Clusters Shows That Convergent, Functional Evolution Results In A Reduced Number Of Human Peroxisomal Acots., Mary Hunt, Anna Rautanen, Maria Westin, Thomas Svensson, Stefan Alexson

Articles

The maintenance of cellular levels of free fatty acids and acyl-CoAs, the activated form of free fatty acids, is extremely important as imbalances in lipid metabolism have serious consequences for human health. Acyl-CoA thioesterases (ACOTs) hydrolyze acyl-CoAs to the free fatty acid and CoASH, and thereby have the potential to regulate intracellular levels of these compounds. We have previously identified and characterized a mouse ACOT gene cluster, comprised of six genes that apparently arose by gene duplications, encoding acyl- CoA thioesterases with localizations in cytosol (ACOT1), mitochondria (ACOT2) and peroxisomes (ACOT3-6). However, the corresponding human gene cluster contains only three …

Charge-Switch Nucleotides, John G. K. Williams, Gregory R. Bashford, Jiyan Chen, Dan Draney, Nara Narayanan, Bambi L. Reynolds, Pamela Sheaff

Biomedical Imaging and Biosignal Analysis Laboratory

The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charge-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation Without interference from unincorporated NPs and Without illuminating the polymerase-DNA complex.

Nucleic Acid Sequencing Using Charge-Switch Nucleotides, John G. K. Williams, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charge-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation without interference from unincorporated NPs and without illuminating the polymerase-DNA complex.

Imposed Constraints On The Smith-Waterman Alignment Algorithm For Enhanced Modeling Of A Single-Molecule Dna Sequencer, Patrick G. Humphrey, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

An effort has been underway to develop a system for de novo sequencing of single DNA molecules with very long reads. The system operates by optically detecting the passage of fluorescently tagged DNA bases through a detection zone. A successful system would be revolutionary with respect to speed, read length, cost and minimized laboratory infrastructure. An important part of system development is modeling of the detection process. In particular, predicting the expected error from a set of sequencing parameters is helpful in system design. This paper describes variations on the Smith-Waterman algorithm for subsequence alignment used in a single-molecule detection …