Insights Into Halophilic Microbial Adaptation: Analysis Of Integrons And Associated Genomic Structures And Characterization Of A Nitrilase In Hypersaline Environments, 2021 American University in Cairo
Insights Into Halophilic Microbial Adaptation: Analysis Of Integrons And Associated Genomic Structures And Characterization Of A Nitrilase In Hypersaline Environments, Sarah Sonbol
Theses and Dissertations
Hypersaline environments are extreme habitats that can be exploited as biotechnological resources. Here, we characterized a nitrilase (NitraS-ATII) isolated from Atlantis II Deep brine pool. It showed higher thermal stability and heavy metal tolerance compared to a closely related nitrilase.
We also studied integrons in halophiles and hypersaline environments. Integrons are genetic platforms in which an integron integrase (IntI) mediates the excision and integration of gene cassettes at specific recombination sites. In order to search for integrons in halophiles and hypersaline metagenomes, we used a PCR-based approach, in addition to different bioinformatics tools, mainly IntegronFinder.
We found that integrons and ...
Automated Parsing Of Flexible Molecular Systems Using Principal Component Analysis And K-Means Clustering Techniques, Matthew J. Nwerem
Computational and Data Sciences (MS) Theses
Computational investigation of molecular structures and reactions of biological and pharmaceutical interests remains a grand scientific challenge due to the size and conformational flexibility of these systems. The work requires parsing and analyzing thousands of conformations in each molecular state for meaningful chemical information and subjecting the ensemble to costly quantum chemical calculations. The current status quo typically involves a manual process where the investigator must look at each conformation, separating each into structural families. This process is time-intensive and tedious, making this process infeasible in some cases, and limiting the ability of theoreticians to study these systems. However, the ...
Bridging The 12-6-4 Model And The Fluctuating Charge Model, 2021 Loyola University Chicago
Bridging The 12-6-4 Model And The Fluctuating Charge Model, Pengfei Li
Chemistry: Faculty Publications and Other Works
Metal ions play important roles in various biological systems. Molecular dynamics (MD) using classical force field has become a popular research tool to study biological systems at the atomic level. However, meaningful MD simulations require reliable models and parameters. Previously we showed that the 12-6 Lennard-Jones nonbonded model for ions could not reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values simultaneously when ion has a charge of +2 or higher. We discussed that this deficiency arises from the overlook of the ion-induced dipole interaction in the 12-6 model, and this term is proportional to 1/r ...
A Two-Step Actin Polymerization Mechanism Drives Dendrite Branching, 2021 Stanford University
A Two-Step Actin Polymerization Mechanism Drives Dendrite Branching, Rebecca Shi, Daniel A. Kramer, Baoyu Chen, Kang Shen
Biochemistry, Biophysics and Molecular Biology Publications
Background: Dendrite morphogenesis plays an essential role in establishing the connectivity and receptive fields of neurons during the development of the nervous system. To generate the diverse morphologies of branched dendrites, neurons use external cues and cell surface receptors to coordinate intracellular cytoskeletal organization; however, the molecular mechanisms of how this signaling forms branched dendrites are not fully understood.
Methods: We performed in vivo time-lapse imaging of the PVD neuron in C. elegans in several mutants of actin regulatory proteins, such as the WAVE Regulatory Complex (WRC) and UNC-34 (homolog of Enabled/Vasodilator-stimulated phosphoprotein (Ena/VASP)). We examined the direct ...
Medical Schools Ignore The Nature Of Consciousness At Great Cost, 2021 independent scholar
Medical Schools Ignore The Nature Of Consciousness At Great Cost, Anoop Kumar
Journal of Wellness
The essential question of the relationship between consciousness and matter is ignored in medical school curricula, leading to a machine-like view of the human being that contributes to physician burnout and intellectual dissatisfaction. The evidence suggesting that the brain may not be the seat of consciousness is generally ignored to preserve the worldview of the primacy of matter. By investigating new frameworks detailing the nature of consciousness at different levels of hierarchy, we can bring intellectual rigor to a once opaque subject that supports a fundamental reality about our experience: We are human beings, not only human bodies.
Tp-5801 In Vitro Kinase Screen Data, 2021 Brigham Young University
Tp-5801 In Vitro Kinase Screen Data, Joshua Andersen
In vitro kinase screen data for TP-5801 to accompany Chan and Egbert et al., Nature Communications, 2021 (in press)
Link Between Muscle And Whole-Body Energetic Responses To Exercise, 2021 University of Massachusetts Amherst
Link Between Muscle And Whole-Body Energetic Responses To Exercise, Christopher M.T. Hayden
Substantial evidence exists regarding how skeletal muscles use energy and how this affects muscular performance. What remains unclear is how characteristics of muscle energetics affect whole-body energetics during daily living, and what effects this may have on mobility. The goal of this study was to determine the associations between muscle and whole-body energetics including the relationships between: 1) muscle PCr depletion (∆PCr) in response to light intensity isotonic contractions and the oxygen deficit at the onset of a 30-min treadmill walk (30MTW), and, 2) muscle oxidative capacity and excess post-exercise oxygen consumption (EPOC; 30MTW), respiratory exchange ratio (RER; 30MTW), and ...
Ahr Expression On Rorc-Expressing Immune Cells Is Essential For I3c-Mediated Protection Against Colitis, 2021 University of South Carolina
Ahr Expression On Rorc-Expressing Immune Cells Is Essential For I3c-Mediated Protection Against Colitis, Michal C. Williams
Colitis is an inflammatory bowel disorder (IBD) whose etiology is attributed to modification in the luminal microbiota and dysregulation in the immune response. Indole is a signaling molecule which is naturally produced by gut luminal microbiota. Indole-3- carbinol (I3C) is a compound commonly found in vegetables and a ligand for the aryl hydrocarbon receptor (AhR). Previous studies have detected decreased expression and activation on the AhR receptor in colitis patients, thought to possibly alter gut microbiota metabolism, subsequently promoting colitis. 1 AhR, expressed in a variety of immune and epithelial cells, contributes to gut homeostasis by affecting vital mediators such ...
College Of Natural Sciences Newsletter, July 2021, 2021 South Dakota State University
College Of Natural Sciences Newsletter, July 2021, College Of Natural Sciences
College of Natural Sciences Newsletters and Reports
Volume 2, Issue 7.
Page 1 Dean's Message
Page 2 Celebrating Three Years
Page 3 Summer School Travel
Page 4 Media Coverage of CNS
Page 5 Chemistry Teachers Visit
Page 5 Remembering Dr. Warren Hein
Page 6 Research Spotlights: Undergraduate Summer Experiences
Page 7 Open PRAIRIE Data; Grants Awarded in CNS
Isolation And Characterization Of Ethyl Acetate Fraction From Abroma Augusta L As An Anti-Inflammatory Agent, 2021 Department of Chemistry, Faculty of Science and Technology, Universitas Jambi, Jambi 36361, Indonesia
Isolation And Characterization Of Ethyl Acetate Fraction From Abroma Augusta L As An Anti-Inflammatory Agent, Madyawati Latief, Indra Lasmana Tarigan, Muhaimin Muhaimin, Hilda Amanda, Nike Desvi Yulianti
Makara Journal of Science
Abroma augusta is a bush plant that lives on the edge of the river. This plant is commonly used as an anti-inflammatory drug for joints and broken bones. It contains several secondary metabolites, such as alkaloids, triterpenoids, steroids, and flavonoids, which exhibit anti-inflammatory activity. UV-visible (UV-Vis) spectrophotometry of isolate 1.3 indicated absorption at a maximum wavelength of 282 nm. The wavelength suggested that the electron transition π–π* is the absorption of UV spectra typical for triterpenoid compounds that have chromophores in the form of non-conjugated double bonds. FT-IR spectrophotometer characterization data from isolate 1.3 revealed the presence ...
Hierarchical Harmonization Of Atom-Resolved Metabolic Reactions Across Metabolic Databases, 2021 University of Kentucky
Hierarchical Harmonization Of Atom-Resolved Metabolic Reactions Across Metabolic Databases, Huan Jin, Hunter N. B. Moseley
Molecular and Cellular Biochemistry Faculty Publications
Metabolic models have been proven to be useful tools in system biology and have been successfully applied to various research fields in a wide range of organisms. A relatively complete metabolic network is a prerequisite for deriving reliable metabolic models. The first step in constructing metabolic network is to harmonize compounds and reactions across different metabolic databases. However, effectively integrating data from various sources still remains a big challenge. Incomplete and inconsistent atomistic details in compound representations across databases is a very important limiting factor. Here, we optimized a subgraph isomorphism detection algorithm to validate generic compound pairs. Moreover, we ...
Novel Approaches Towards Improved Purity In High Yield Transcription Reactions, 2021 University of Massachusetts Amherst
Novel Approaches Towards Improved Purity In High Yield Transcription Reactions, Elvan Cavac
High yields of RNA (e.g., mRNA, gRNA, lncRNA) are routinely prepared following a two-step approach: high yield in vitro transcription using T7 RNA polymerase, followed by extensive purification using gel or chromatic methods. In high yield transcription reactions, as RNA accumulates in solution, T7 RNA polymerase rebinds and extends the encoded RNA (using the RNA as a template), resulting in a product pool contaminated with longer than desired, (partially) double stranded impurities. Current purification methods often fail to fully eliminate these impurities which, if present in therapeutics, can stimulate the innate immune response with potentially fatal consequences. This study ...
Effect Of Clinical Isolate Or Cleavage Site Mutations In The Sars-Cov-2 Spike Protein On Protein Stability, Cleavage, And Cell-Cell Fusion, Chelsea T. Barrett, Hadley E. Neal, Kearstin Edmonds, Carole L. Moncman, Rachel Thompson, Jean M. Branttie, Kerri Beth Boggs, Cheng-Yu Wu, Daisy W. Leung, Rebecca E. Dutch
Molecular and Cellular Biochemistry Faculty Publications
The trimeric severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S) is the sole viral protein responsible for both viral binding to a host cell and the membrane fusion event needed for cell entry. In addition to facilitating fusion needed for viral entry, S can also drive cell-cell fusion, a pathogenic effect observed in the lungs of SARS-CoV-2-infected patients. While several studies have investigated S requirements involved in viral particle entry, examination of S stability and factors involved in S cell-cell fusion remain limited. A furin cleavage site at the border between the S1 and S2 subunits (S1/S2 ...
Characterization And Modulatory Influence Of Pyruvate Kinase Muscle Isoforms 1 And 2 Within The Murine Pluripotent Continuum, 2021 The University of Western Ontario
Characterization And Modulatory Influence Of Pyruvate Kinase Muscle Isoforms 1 And 2 Within The Murine Pluripotent Continuum, Joshua G. Dierolf
Electronic Thesis and Dissertation Repository
Mouse embryonic stem cells (mESCs) and mouse epiblast stem cells (mEpiSCs) represent opposite ends of a pluripotency continuum, respectively referred to as naïve and primed pluripotent states. A third, recently discovered intermediate state has been described as the ‘formative state’. Metabolism has been traditionally regarded as a by-product of cell fate; however, recent evidence now supports metabolism as promoting stem cell fate. Pyruvate kinase muscle isoforms 1 and 2 (PKM1 and PKM2) catalyze the final, rate limiting step of glycolysis generating adenosine triphosphate (ATP) and pyruvate; however, the precise role(s) of these isozymes in naïve, formative, and primed pluripotency ...
Algebraic Graph-Assisted Bidirectional Transformers For Molecular Property Prediction, 2021 Peking University, China
Algebraic Graph-Assisted Bidirectional Transformers For Molecular Property Prediction, Dong Chen, Kaifu Gao, Duc Duy Nguyen, Xin Chen, Yi Jiang, Guo-Wei Wei, Feng Pan
Mathematics Faculty Publications
The ability of molecular property prediction is of great significance to drug discovery, human health, and environmental protection. Despite considerable efforts, quantitative prediction of various molecular properties remains a challenge. Although some machine learning models, such as bidirectional encoder from transformer, can incorporate massive unlabeled molecular data into molecular representations via a self-supervised learning strategy, it neglects three-dimensional (3D) stereochemical information. Algebraic graph, specifically, element-specific multiscale weighted colored algebraic graph, embeds complementary 3D molecular information into graph invariants. We propose an algebraic graph-assisted bidirectional transformer (AGBT) framework by fusing representations generated by algebraic graph and bidirectional transformer, as well as ...
Synphilin-1 And Its Effects On Pathogenesis Of Parkinson’S Disease, 2021 University of Connecticut
Synphilin-1 And Its Effects On Pathogenesis Of Parkinson’S Disease, Mirghani Mohamed
Honors Scholar Theses
Parkinson's Disease (PD) is a progressive neurodegenerative and movement disorder primarily caused by the degradation of dopaminergic neurons. Known markers of neurodegeneration in PD are Lewy Bodies, which are fibrillar aggregates that are found in the brains of PD patients. Lewy Bodies can accumulate from specific mutations in the SNCA gene that codes for alpha-synuclein, a protein enriched in presynaptic neurons. A mutated SNCA gene can cause conformational aggregates of alpha-synuclein to form toxic species mediating neuronal death. Research into alpha-synuclein has led to the discovery of a binding partner known as synphilin-1 that is also found in protein ...
Physical Models Of Living Systems New Chapter: Single Particle Reconstruction In Cryo-Electron Microscopy, 2021 University of Pennsylvania
Physical Models Of Living Systems New Chapter: Single Particle Reconstruction In Cryo-Electron Microscopy, Philip C. Nelson
Department of Physics Papers
This chapter extends Part III of the book Physical Models of Living Systems (WH Freeman 2015). This preliminary version is made freely available as-is in the hope that it will be useful.
Quantification Of Antisense Oligonucleotides By Splint Ligation And Quantitative Polymerase Chain Reaction [Preprint], 2021 University of Massachusetts Medical School
Quantification Of Antisense Oligonucleotides By Splint Ligation And Quantitative Polymerase Chain Reaction [Preprint], Minwook Shin, Pranathi Meda Krishnamurthy, Jonathan K. Watts
University of Massachusetts Medical School Faculty Publications
Reliable detection and quantification of antisense oligonucleotides (ASOs) in experimental and clinical specimens is essential to understand the biological function of novel oligonucleotide-based therapeutics. In this study, we describe a method to detect and quantify ASOs in biological samples, whereby the ASO acts as a splint to direct the ligation of complementary probes and quantitative real-time PCR was used to monitor ligation products. Low levels of 2′-O-MOE gapmer ASO in serum, liver, kidney, lung, heart, muscle, and brain tissues can be detected over a 6-log linear range for detection using this method. This method allows quantification of various ...
Synthesis And Evaluation Of C-10 Nitrogenated Aporphine Alkaloids At Serotonin And Dopamine Receptors, 2021 The Graduate Center, City University of New York
Synthesis And Evaluation Of C-10 Nitrogenated Aporphine Alkaloids At Serotonin And Dopamine Receptors, Anupam Karki
Dissertations, Theses, and Capstone Projects
Aporphine alkaloids, belonging to the isoquinoline class of compounds, have been investigated as a potential source of ligands for Central Nervous System (CNS) receptors. Previous research indicates that the aporphine scaffold may be manipulated to synthesize selective ligands for serotonin and dopamine receptors. Novel aporphine alkaloids containing C10 nitrogen substitutions were synthesized, and their affinities were evaluated at serotonin (5-HT1A, 5-HT1B, 5-HT2A, 5-HT7A) receptors and dopamine (D1, D2, D3, D4, and D5) receptors. Two series of racemic aporphine compounds with C10 nitrogenous functionalities were synthesized and analyzed at the aforementioned receptors. The first series of aporphine alkaloids contain C10 nitro ...
College Of Natural Sciences Newsletter, June 2021, 2021 South Dakota State University
College Of Natural Sciences Newsletter, June 2021, College Of Natural Sciences
College of Natural Sciences Newsletters and Reports
Volume 2, Issue 6.
Page 1 Dean's Message
Page 2-6 Remembering the Life of Dr. Pengra and Celebrating His legacy for Entire Generations to Come.