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Environmental Cost Vs. Health Benefit Of Radioisotope Usage In Medicine, Nicholas Whiting 2019 Rowan University

Environmental Cost Vs. Health Benefit Of Radioisotope Usage In Medicine, Nicholas Whiting

Open Educational Resources

This module is developed for implementation in a class that discusses the use of radioisotopes in a biomedical setting. The inspiration is a class I teach (Advanced Biomedical Instrumentation), which covers the use of radioisotopes as tracers in biomedical imaging (scintigraphy, SPECT, PET, etc.). The goal of the module is to go further in depth regarding the environmental impact of the use of radioisotopes (from their generation to their disposal—keeping track of any radioactive byproducts), and compare that to the potential for benefits in the quality and/or quantity of a patient’s life (does using the radioisotopes allow ...


Hyaluronan At The Brain-Environment Interface, Donald M. Thevalingam 2019 The Graduate Center, City University of New York

Hyaluronan At The Brain-Environment Interface, Donald M. Thevalingam

All Dissertations, Theses, and Capstone Projects

Hyaluronan (HA; Hyaluronic Acid), a primary scaffolding component of the brain extracellular matrix, serves as an integral structural component to the brain extracellular space (ECS). The fossorial African naked mole-rat (Heterocephalus glaber; NM-R), a mammal which lives in a low-oxygen environment and is capable of tolerating hypoxia and hypercapnia, has been shown to synthesize and sustain a unique high-molecular-mass variant of hyaluronan macromolecule (HMM-HA). This body of work highlights HA’s role in mediating the interplay between brain ECM composition, ECS structure, and cell viability.

Here we employ the NM-R as a unique animal model to observe the role of ...


Minimalistic Peptide-Based Supramolecular Systems Relevant To The Chemical Origin Of Life, Daniela Kroiss 2019 The Graduate Center, City University of New York

Minimalistic Peptide-Based Supramolecular Systems Relevant To The Chemical Origin Of Life, Daniela Kroiss

All Dissertations, Theses, and Capstone Projects

All forms of life are based on biopolymers, which are made up of a selection of simple building blocks, such as amino acids, nucleotides, fatty acids and sugars. Their individual properties govern their interactions, giving rise to complex supramolecular structures with highly specialized functionality, including ligand recognition, catalysis and compartmentalization. In this thesis, we aim to answer the question whether short peptides could have acted as precursors of modern proteins during prebiotic evolution. Using a combination of experimental and computational techniques, we screened a large molecular search space for peptide sequences that are capable of forming supramolecular complexes with adenosine ...


Monocyte Mri Relaxation Rates Are Regulated By Extracellular Iron And Hepcidin, Praveen S.B Dassanayake 2019 The University of Western Ontario

Monocyte Mri Relaxation Rates Are Regulated By Extracellular Iron And Hepcidin, Praveen S.B Dassanayake

Electronic Thesis and Dissertation Repository

Monocytes are an important immune cell type in chronic inflammatory conditions like atherosclerosis and heart failure. The increase in number of monocytes released to the peripheral blood circulation, the differentiation of monocytes to macrophages, and the presence of different macrophage subpopulations during pro- and anti-inflammatory stages of tissue injury may provide markers for monitoring inflammation. In particular, changes in monocyte iron metabolism during an inflammatory response may increase the possibility of tracking these immune cells non-invasively using magnetic resonance imaging (MRI). When secretion of the polypeptide hormone hepcidin is stimulated during inflammation, it binds the iron export protein ferroportin (FPN ...


Parallel Multipole Expansion Algorithms And Their Biology Applications, Jiahui Chen 2019 Southern Methodist University

Parallel Multipole Expansion Algorithms And Their Biology Applications, Jiahui Chen

Mathematics Theses and Dissertations

N-body pairwise interactions are ubiquitous in scientific areas such as astrophysics, fluids mechanics, electrical engineering, molecular biology, etc. Computing these interactions using direct sum of an O(N) cost is expensive, whereas multipole expansion methods, such as the fast multipole method (FMM) or treecode, can reduce the cost to O(N) or O(N log N). This thesis focuses on developing numerical algorithms of Cartesian FMM and treecode, as well as using these algorithms to directly or implicitly solve biological problems involving pairwise interactions. This thesis consists of the following topics. 1) A cyclic parallel scheme is developed to handle ...


Nonnative Structure In A Peptide Model Of The Unfolded State Of Sod1: Implications For Als-Linked Aggregation, Noah R. Cohen, Jill A. Zitzewitz, Osman Bilsel, C. Robert Matthews 2019 University of Massachusetts Medical School

Nonnative Structure In A Peptide Model Of The Unfolded State Of Sod1: Implications For Als-Linked Aggregation, Noah R. Cohen, Jill A. Zitzewitz, Osman Bilsel, C. Robert Matthews

Open Access Articles

Dozens of mutations throughout the sequence of the gene encoding superoxide dismutase 1 (SOD1) have been linked to toxic protein aggregation in the neurodegenerative disease amyotrophic lateral sclerosis (ALS). A parsimonious explanation for numerous genotypes resulting in a common phenotype would be mutation-induced perturbation of the folding free-energy surface that increases the populations of high-energy states prone to aggregation. The absence of intermediates in the folding of monomeric SOD1 suggests that the unfolded ensemble is a potential source of aggregation. To test this hypothesis, here we dissected SOD1 into a set of peptides end-labeled with FRET probes to model the ...


High-Resolution Cryo-Em Structures Of Outbreak Strain Human Norovirus Shells Reveal Size Variations, James Jung, Timothy Grant, Dennis R. Thomas, Chris W. Diehnelt, Nikolaus Grigorieff, Leemor Joshua-Tor 2019 Cold Spring Harbor Laboratory

High-Resolution Cryo-Em Structures Of Outbreak Strain Human Norovirus Shells Reveal Size Variations, James Jung, Timothy Grant, Dennis R. Thomas, Chris W. Diehnelt, Nikolaus Grigorieff, Leemor Joshua-Tor

Open Access Articles

Noroviruses are a leading cause of foodborne illnesses worldwide. Although GII.4 strains have been responsible for most norovirus outbreaks, the assembled virus shell structures have been available in detail for only a single strain (GI.1). We present high-resolution (2.6- to 4.1-A) cryoelectron microscopy (cryo-EM) structures of GII.4, GII.2, GI.7, and GI.1 human norovirus outbreak strain virus-like particles (VLPs). Although norovirus VLPs have been thought to exist in a single-sized assembly, our structures reveal polymorphism between and within genogroups, with small, medium, and large particle sizes observed. Using asymmetric reconstruction, we were able ...


Unfolded States Under Folding Conditions Accommodate Sequence-Specific Conformational Preferences With Random Coil-Like Dimensions, Ivan Peran, Alex S. Holehouse, Isaac S. Carrico, Rohit V. Pappu, Osman Bilsel, Daniel P. Raleigh 2019 Stony Brook University

Unfolded States Under Folding Conditions Accommodate Sequence-Specific Conformational Preferences With Random Coil-Like Dimensions, Ivan Peran, Alex S. Holehouse, Isaac S. Carrico, Rohit V. Pappu, Osman Bilsel, Daniel P. Raleigh

Open Access Articles

Proteins are marginally stable molecules that fluctuate between folded and unfolded states. Here, we provide a high-resolution description of unfolded states under refolding conditions for the N-terminal domain of the L9 protein (NTL9). We use a combination of time-resolved Forster resonance energy transfer (FRET) based on multiple pairs of minimally perturbing labels, time-resolved small-angle X-ray scattering (SAXS), all-atom simulations, and polymer theory. Upon dilution from high denaturant, the unfolded state undergoes rapid contraction. Although this contraction occurs before the folding transition, the unfolded state remains considerably more expanded than the folded state and accommodates a range of local and nonlocal ...


Modulation Of Biological Responses To 2 Ns Electrical Stimuli By Field Reversal, Esin B. Sözer, P. Thomas Vernier 2019 Old Dominion University

Modulation Of Biological Responses To 2 Ns Electrical Stimuli By Field Reversal, Esin B. Sözer, P. Thomas Vernier

Bioelectrics Publications

Nanosecond bipolar pulse cancellation, a recently discovered Phenomenon, is modulation of the effects of a unipolar electric pulse exposure by a second pulse of opposite polarity. This attenuation of biological response by reversal of the electric field direction has been reported with pulse durations from 60 ns to 900 ns for a wide range of endpoints, and it is not observed with conventional electroporation pulses of much longer duration (> 100 mu s) where pulses are additive regardless of polarity. The most plausible proposed mechanisms involve the field-driven migration of ions to and from the membrane interface (accelerated membrane discharge). Here ...


An Order-To-Disorder Structural Switch Activates The Foxm1 Transcription Factor, Aimee H. Marceau, Caileen M. Brison, Santrupti Nerli, Heather E. Arsenault, Andrew C. McShan, Eefei Chen, Hsiau-Wei Lee, Jennifer A. Benanti, Nikolaos G. Sgourakis, Seth M. Rubin 2019 University of California, Santa Cruz

An Order-To-Disorder Structural Switch Activates The Foxm1 Transcription Factor, Aimee H. Marceau, Caileen M. Brison, Santrupti Nerli, Heather E. Arsenault, Andrew C. Mcshan, Eefei Chen, Hsiau-Wei Lee, Jennifer A. Benanti, Nikolaos G. Sgourakis, Seth M. Rubin

Open Access Articles

Intrinsically disordered transcription factor transactivation domains (TADs) function through structural plasticity, adopting ordered conformations when bound to transcriptional co-regulators. Many transcription factors contain a negative regulatory domain (NRD) that suppresses recruitment of transcriptional machinery through autoregulation of the TAD. We report the solution structure of an autoinhibited NRD-TAD complex within FoxM1, a critical activator of mitotic gene expression. We observe that while both the FoxM1 NRD and TAD are primarily intrinsically disordered domains, they associate and adopt a structured conformation. We identify how Plk1 and Cdk kinases cooperate to phosphorylate FoxM1, which releases the TAD into a disordered conformation that ...


Stochastic Modeling Of Neuronal Transport In Various Cellular Geometries, Abhishek Choudhary Mr., Peter Kramer 2019 Rensselaer Polytechnic Institute

Stochastic Modeling Of Neuronal Transport In Various Cellular Geometries, Abhishek Choudhary Mr., Peter Kramer

Biology and Medicine Through Mathematics Conference

No abstract provided.


Modeling Mechanisms Behind Force Generation By Actin Polymerization, Seyed Fowad Motahari 2019 Washington University in St. Louis

Modeling Mechanisms Behind Force Generation By Actin Polymerization, Seyed Fowad Motahari

Arts & Sciences Electronic Theses and Dissertations

Actin polymerization is the primary mechanism for overcoming the large turgor pressure that opposes endocytosis in yeast. While generation of pushing forces by actin polymerization is fairly well understood, it is not clear how actin polymerization produces pulling forces. In order to understand this process, it is necessary to simulate polymerization of filaments having various types of interactions with the membrane. Since existing methodologies in the literature do not treat such problems correctly, we develop a thermodynamically consistent methodology for treating polymerization of filaments having arbitrary interaction potentials with the membrane. Then I perform stochastic simulations for a system of ...


Assessing The Potential Impact Of Nanotechnology On The Purification Of Water, Noor Khan 2019 Collin College

Assessing The Potential Impact Of Nanotechnology On The Purification Of Water, Noor Khan

Quest

Independent Research Paper

Research in progress for PHYS 2426: University Physics II

Faculty Mentor: Raji Kannampuzha, Ph.D.

The following paper represents research work done by students in a University Physics 2426 class, the second half of a two-semester introductory course in physics. It is a calculus-based physics course, intended primarily for physics, chemistry, math, and engineering majors. Students are introduced to the concept of academic research by learning to ask research-focused questions and then use the library resources to pursue outside research to find answers. For this assignment, students are asked to investigate a physical science, biological science, or ...


Incorporation Of Egfr And Ron Receptors Into Nanodiscs, Cristina Flores-Cadengo 2019 University of New Mexico

Incorporation Of Egfr And Ron Receptors Into Nanodiscs, Cristina Flores-Cadengo

Biomedical Engineering ETDs

Understanding the structure-function relationship of membrane receptors is essential to comprehend the crosstalk between key signaling pathways. Aberrant trans-activation between receptors can lead to tumorigenesis. Two of these receptors known to be involved in cancer development are receptor tyrosine kinases (RTKs), RON (Recepteur d'Origine Nantais) and EGFR (Epidermal Growth Factor Receptor). There has been evidence of heterodimerization and crosstalk between these two receptors based on co-immunoprecipitation, however the structural requirements behind these interactions remain unknown. Structural studies could provide insights into these RTKs’ modes of dimerization and structure-function relationship. However, structural studies of full-length membrane proteins are often difficult ...


Aptamers For Diagnostics With Applications For Infectious Diseases, Muslum Ilgu, Rezzan Fazlioglu, Meric Ozturk, Yasemin Ozsurekci, Marit Nilsen-Hamilton 2019 Middle East Technical University

Aptamers For Diagnostics With Applications For Infectious Diseases, Muslum Ilgu, Rezzan Fazlioglu, Meric Ozturk, Yasemin Ozsurekci, Marit Nilsen-Hamilton

Biochemistry, Biophysics and Molecular Biology Publications

Aptamers are in vitro selected oligonucleotides (DNA, RNA, oligos with modified nucleotides) that can have high affinity and specificity for a broad range of potential targets with high affinity and specificity. Here we focus on their applications as biosensors in the diagnostic field, although they can also be used as therapeutic agents. A small number of peptide aptamers have also been identified. In analytical settings, aptamers have the potential to extend the limit of current techniques as they offer many advantages over antibodies and can be used for real-time biomarker detection, cancer clinical testing, and detection of infectious microorganisms and ...


An Automated Bayesian Pipeline For Rapid Analysis Of Single-Molecule Binding Data, Carlas Smith, Karina Jouravleva, Maximiliaan Huisman, Samson M. Jolly, Phillip D. Zamore, David Grünwald 2019 University of Massachusetts Medical School

An Automated Bayesian Pipeline For Rapid Analysis Of Single-Molecule Binding Data, Carlas Smith, Karina Jouravleva, Maximiliaan Huisman, Samson M. Jolly, Phillip D. Zamore, David Grünwald

David Grünwald

Single-molecule binding assays enable the study of how molecular machines assemble and function. Current algorithms can identify and locate individual molecules, but require tedious manual validation of each spot. Moreover, no solution for high-throughput analysis of single-molecule binding data exists. Here, we describe an automated pipeline to analyze single-molecule data over a wide range of experimental conditions. In addition, our method enables state estimation on multivariate Gaussian signals. We validate our approach using simulated data, and benchmark the pipeline by measuring the binding properties of the well-studied, DNA-guided DNA endonuclease, TtAgo, an Argonaute protein from the Eubacterium Thermus thermophilus. We ...


Bisthioether Stapled Peptides Targeting Polycomb Repressive Complex 2 Gene Repression, Gan Zhang 2019 The Graduate Center, City University of New York

Bisthioether Stapled Peptides Targeting Polycomb Repressive Complex 2 Gene Repression, Gan Zhang

All Dissertations, Theses, and Capstone Projects

Interactions between proteins play a key role in nearly all cellular process, and therefore, disruption of such interactions may lead to many different types of cellular dysfunctions. Hence, pathologic protein-protein interactions (PPIs) constitute highly attractive drug targets and hold great potential for developing novel therapeutic agents for the treatment of incurable human diseases. Unfortunately, the identification of PPI inhibitors is an extremely challenging task, since traditionally used small molecule ligands are mostly unable to cover and anchor on the extensive flat surfaces that define those binary protein complexes. In contrast, large biomolecules such as proteins or peptides are ideal fits ...


Analyzing Neuronal Dendritic Trees With Convolutional Neural Networks, Olivier Trottier, Jonathon Howard 2019 Yale University

Analyzing Neuronal Dendritic Trees With Convolutional Neural Networks, Olivier Trottier, Jonathon Howard

Yale Day of Data

In the biological sciences, image analysis software are used to detect, segment or classify a variety of features encountered in living matter. However, the algorithms that accomplish these tasks are often designed for a specific dataset, making them hardly portable to accomplish the same tasks on images of different biological structures. Recently, convolutional neural networks have been used to perform complex image analysis on a multitude of datasets. While applications of these networks abound in the technology industry and computer science, use cases are not as common in the academic sciences. Motivated by the generalizability of neural networks, we aim ...


A Three State Model Can Explain The Dynamics Of Class Iv Drosophila Dendritic Tips, Sabyasachi Sutradhar 2019 Yale University

A Three State Model Can Explain The Dynamics Of Class Iv Drosophila Dendritic Tips, Sabyasachi Sutradhar

Yale Day of Data

No abstract provided.


An Automated Bayesian Pipeline For Rapid Analysis Of Single-Molecule Binding Data, Carlas Smith, Karina Jouravleva, Maximiliaan Huisman, Samson M. Jolly, Phillip D. Zamore, David Grünwald 2019 University of Massachusetts Medical School

An Automated Bayesian Pipeline For Rapid Analysis Of Single-Molecule Binding Data, Carlas Smith, Karina Jouravleva, Maximiliaan Huisman, Samson M. Jolly, Phillip D. Zamore, David Grünwald

Open Access Articles

Single-molecule binding assays enable the study of how molecular machines assemble and function. Current algorithms can identify and locate individual molecules, but require tedious manual validation of each spot. Moreover, no solution for high-throughput analysis of single-molecule binding data exists. Here, we describe an automated pipeline to analyze single-molecule data over a wide range of experimental conditions. In addition, our method enables state estimation on multivariate Gaussian signals. We validate our approach using simulated data, and benchmark the pipeline by measuring the binding properties of the well-studied, DNA-guided DNA endonuclease, TtAgo, an Argonaute protein from the Eubacterium Thermus thermophilus. We ...


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