Search results | J. Murrey Atkins Library

Title: Rigidity emerges during antibody evolution in three distinct antibody systems: evidence from QSFR analysis of fab fragments
Author: Jacobs, Donald J., Li, Tong, Livesay, Dennis R.
Date Created: 2015
Subjects--Topical: Immunoglobulins, Biology
Description: The effects of somatic mutations that transform polyspecific germline (GL) antibodies to affinity mature (AM) antibodies with monospecificity are compared among three GL-AM Fab pairs. In particular, changes in conformational flexibility are assess...

Title: Variations within class-a beta-lactamase physiochemical properties reflect evolutionary and environmental patterns, but not antibiotic specificity
Author: Jacobs, Donald J., Verma, Deeptak, Livesay, Dennis R.
Date Created: 2013
Subjects--Topical: Biology, Bacteria
Description: The bacterial enzyme beta-lactamase hydrolyzes the beta-lactam ring of penicillin and chemically related antibiotics, rendering them ineffective. Due to rampant antibiotic overuse, the enzyme is evolving new resistance activities at an alarming ra...

Title: Calculating ensemble averaged descriptions of protein rigidity without sampling
Author: Jacobs, Donald J., Gonzalez, Luis C., Wang, Hui, Livesay, Dennis R.
Date Created: 2012
Subjects--Topical: Biology, Proteins
Description: Previous works have demonstrated that protein rigidity is related to thermodynamic stability, especially under conditions that favor formation of native structure. Mechanical network rigidity properties of a single conformation are efficiently cal...

Title: JEDi: Java essential dynamics inspector - a molecular trajectory analysis toolkit
Author: Jacobs, Donald J., Avery, Chris
Date Created: 2021
Subjects--Topical: Biology, Proteins
Description: Background Principal component analysis (PCA) is commonly applied to the atomic trajectories of biopolymers to extract essential dynamics that describe biologically relevant motions. Although application of PCA is straightforward, specialized soft...

Title: Characterizing the diversity of heat shock proteins in Nematostella vectensis and Saccharomyces cerevisiae
Author: Alexander, William, Reitzel, Adam M., Truman, Andrew
Date Created: 2022
Subjects--Topical: Heat shock proteins, Biology
Description: Heat shock proteins (HSPs) are a highly conserved family of proteins critical to both environmental stress response and cellular function under normal conditions. More specifically HSPs are chaperone proteins that work to refold other misfolded pr...

Title: JED: a Java essential dynamics program for comparative analysis of protein trajectories
Author: Jacobs, Donald J., Ramaprasad, Azhagiya Singam Ettayapuram, David, Charles C.
Date Created: 2017
Subjects--Topical: Biology, Proteins
Description: Background: Essential Dynamics (ED) is a common application of principal component analysis (PCA) to extract biologically relevant motions from atomic trajectories of proteins. Covariance and correlation based PCA are two common approaches to dete...

Title: Redistribution of flexibility in stabilizing antibody fragment mutants follows Le Chatelier's principle
Author: Jacobs, Donald J., Li, Tong, Livesay, Dennis R.
Date Created: 2014
Subjects--Topical: Immunoglobulins, Biology
Description: Le Chatelier's principle is the cornerstone of our understanding of chemical equilibria. When a system at equilibrium undergoes a change in concentration or thermodynamic state (i.e., temperature, pressure, etc.), La Chatelier's principle states t...

Title: Quantifying reproductive behavior in the sea anemone Nematostella vectensis
Author: Alexander, William, Justin, Hannah, Reitzel, Adam M.
Date Created: 2022
Subjects--Topical: Cnidaria, Biology, Developmental biology, Marine biology, Sea anemones
Description: The Starlet Sea Anemone Nematostella vectensis (Nv) exists widely in coastal estuarine environments across North America. Nv has become a popular cnidarian model organism with a growing number of applications, including evolutionary developmental ...

Title: Genetic variation at aryl hydrocarbon receptor (AHR) loci in populations of Atlantic killifish (Fundulus heteroclitus) inhabiting polluted and reference habitats
Author: Reitzel, Adam M., Karchner, Sibel I., Franks, Diana G.
Date Created: 2014
Subjects--Topical: Gene expression, Biology
Description: Background: The non-migratory killifish Fundulus heteroclitus inhabits clean and polluted environments interspersed throughout its range along the Atlantic coast of North America. Several populations of this species have successfully adapted to en...

Title: Diel patterning in the bacterial community associated with the sea anemone Nematostella vectensis
Author: Reitzel, Adam M., Leach, Whitney B., Carrier, Tyler J.
Date Created: 2019
Subjects--Topical: Gene expression, Biology
Description: Microbes can play an important role in the physiology of animals by providing essential nutrients, inducing immune pathways, and influencing the specific species that compose the microbiome through competitive or facilitatory interactions. The com...

Title: Origin of the animal circadian clock : diurnal and light-entrained gene expression in the sponge amphimedon queenslandica
Author: Reitzel, Adam M., Jindrich, Katia, Roper, Kathrein E.
Date Created: 2017
Subjects--Topical: Evolution (Biology), Biology
Description: The circadian clock is a molecular network that coordinates organismal behavior and physiology with daily environmental changes in the day-night cycle. In eumetazoans (bilaterians + cnidarians), this network appears to be largely conserved, yet di...

Title: Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi : a new view of ctenophore photocytes
Author: Reitzel, Adam M., Schnitzler, Christine E.
Date Created: 2012
Subjects--Topical: Bioluminescence, Biology
Description: Background: Calcium-activated photoproteins are luciferase variants found in photocyte cells of bioluminescent jellyfish (Phylum Cnidaria) and comb jellies (Phylum Ctenophora). The complete genomic sequence from the ctenophore Mnemiopsis leidyi, a...

Title: Microbial diversity and activity in the Nematostella vectensis holobiont : insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression
Author: Reitzel, Adam M., Har, Jia Y., Helbig, Tim
Date Created: 2015
Subjects--Topical: Gene expression, Biology
Description: We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt mar...

Title: Linear mitochondrial genome in Anthozoa (Cnidaria) : a case study in Ceriantharia
Author: Reitzel, Adam M., Stampar, Sergio N., Macrander, Jason
Date Created: 2019
Subjects--Topical: Gene expression, Biology
Description: Sequences and structural attributes of mitochondrial genomes have played a critical role in the clarification of relationships among Cnidaria, a key phylum of early-diverging animals. Among the major lineages of Cnidaria, Ceriantharia (tube anemon...

Title: Tracking a serial killer : integrating phylogenetic relationships, epidemiology, and geography for two invasive meningococcal disease outbreaks
Author: Janies, Daniel, Galac, Madeline R., Kilianski, Andrew
Date Created: 2018
Subjects--Topical: Communicable diseases, Biology
Description: Background While overall rates of meningococcal disease have been declining in the United States for the past several decades, New York City (NYC) has experienced two serogroup C meningococcal disease outbreaks in 2005-2006 and in 2010-2013. The o...

Title: Active Notch signaling is required for arm regeneration in a brittle star
Author: Janies, Daniel, Machado, Denis Jacob, Reid, Robert
Date Created: 2020
Subjects--Topical: Genomics, Biology
Description: Cell signaling pathways play key roles in coordinating cellular events in development. The Notch signaling pathway is highly conserved across all multicellular animals and is known to coordinate a multitude of diverse cellular events, including pr...

Title: Phylogeny of echinoderm hemoglobins
Author: Janies, Daniel, Linchangco, Gregorio V., Jr.
Date Created: 2015
Subjects--Topical: Genomics, Biology
Description: Background Recent genomic information has revealed that neuroglobin and cytoglobin are the two principal lineages of vertebrate hemoglobins, with the latter encompassing the familiar myoglobin and alpha-globin/beta-globin tetramer hemoglobin, and ...

Title: The first complete mitochondrial genome of the sand dollar Sinaechinocyamus mai (Echinoidea: Clypeasteroida)
Author: Janies, Daniel, Machado, Denis Jacob
Date Created: 2020
Subjects--Topical: Genomics, Biology
Description: Morphologic and molecular data often lead to different hypotheses of phylogenetic relationships. Such incongruence has been found in the echinoderm class Echinoidea. In particular, the phylogenetic status of the order Clypeasteroida is not well re...

Title: Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms
Author: Janies, Daniel, Clouse, Ronald M., Linchangco, Gregorio V., Jr.
Date Created: 2015
Subjects--Topical: Genomics, Biology
Description: Tissue inhibitors of metalloproteinases (TIMPs) help regulate the extracellular matrix (ECM) in animals, mostly by inhibiting matrix metalloproteinases (MMPs). They are important activators of mutable collagenous tissue (MCT), which have been exte...

Title: EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms
Author: Janies, Daniel, Witter, Zachary, Linchangco, Gregorio V., Jr.
Date Created: 2016
Subjects--Topical: Genomics, Biology
Description: Background: One of our goals for the echinoderm tree of life project (http://echinotol.org) is to identify orthologs suitable for phylogenetic analysis from next-generation transcriptome data. The current dataset is the largest assembled for echin...