Search results | J. Murrey Atkins Library

Title: A subterminal growth zone at arm tip likely underlies life-long indeterminate growth in brittle stars
Author: Janies, Daniel, Machado, Denis Jacob, Reid, Robert, Kofsky, Janice
Date Created: 2022
Subjects--Topical: Genomics, Biology
Description: Background Echinoderms are a phylum of marine invertebrates with close phylogenetic relationships to chordates. Many members of the phylum Echinodermata are capable of extensive post-traumatic regeneration and life-long indeterminate growth. Diffe...

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: 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: 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: Chemoenzymatic preparation of a Campylobacter jejuni lipid-linked heptasaccharide on an azide-linked polyisoprenoid
Author: Reid, Amanda J., Erickson, Katelyn M., Hazel, Joseph M., Troutman, Jerry M.
Date Created: 2023
Subjects--Topical: Biology, Carbohydrates
Description: Complex poly- and oligosaccharides on the surface of bacteria provide a unique fingerprint to different strains of pathogenic and symbiotic microbes that could be exploited for therapeutics or sensors selective for specific glycans. To discover re...

Title: Content and sentiment surveillance (CSI) : A critical component for modeling modern epidemics
Author: Janies, Daniel, Chen, Shi, Zhang, Dongsong
Date Created: 2023
Subjects--Topical: Communicable diseases, Biology
Description: Comprehensive surveillance systems are the key to provide accurate data for effective modeling. Traditional symptom-based case surveillance has been joined with recent genomic, serologic, and environment surveillance to provide more integrated dis...

Title: Convergent shifts in host-associated microbial communities across environmentally elicited phenotypes
Author: Reitzel, Adam M., Carrier, Tyler J.
Date Created: 2018
Subjects--Topical: Evolution (Biology), Biology
Description: Morphological plasticity is a genotype-by-environment interaction that enables organisms to increase fitness across varying environments. Symbioses with diverse microbiota may aid in acclimating to this variation, but whether the associated bacter...

Title: DNA extraction method plays a significant role when defining bacterial community composition in the marine invertebrate Echinometra mathaei
Author: Reitzel, Adam M., Ketchum, Remi, Carrier, Tyler J.
Date Created: 2018
Subjects--Topical: Bacteria, Biology
Description: The microbial assemblages of marine organisms play fundamental biological roles in their eukaryotic hosts. Studies aimed at characterizing this diversity have increased over the last decade and with the availability of high-throughput sequencing, ...

Title: Daily cycle in oxygen consumption by the sea anemone Nematostella vectensis Stephenson
Author: Reitzel, Adam M., Maas, Amy E., Jones, Ian T.
Date Created: 2016
Subjects--Topical: Gene expression, Biology
Description: In bilaterian animals, the circadian clock is intimately involved in regulating energetic metabolism. Although cnidarians exhibit diel behavioral rhythms including cycles in locomotor activity, tentacle extension and spawning, daily cycles in cnid...

Title: Developmental and light-entrained expression of melatonin and its relationship to the circadian clock in the sea anemone Nematostella vectensis
Author: Reitzel, Adam M., Peres, Rafael, Passamaneck, Yale
Date Created: 2014
Subjects--Topical: Gene expression, Biology
Description: Background: The primary hormone of the vertebrate pineal gland, melatonin, has been identified broadly throughout the eukaryotes. While the role for melatonin in cyclic behavior via interactions with the circadian clock has only been reported in v...

Title: Developmental expression of germline- and sex determination-related genes in the ctenophore Mnemiopsis leidyi
Author: Reitzel, Adam M., Pang, Kevin, Martindale, Mark Q.
Date Created: 2016
Subjects--Topical: Evolution (Biology), Biology
Description: Background: An essential developmental pathway in sexually reproducing animals is the specification of germ cells and the differentiation of mature gametes, sperm and oocytes. The germline genes vasa, nanos and piwi are commonly identified in prim...

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: EchinoDB : an update to the web-based application for genomic and transcriptomic data on echinoderms
Author: Janies, Daniel
Date Created: 2022
Subjects--Topical: Genomics, Biology
Description: Background: Here we release a new version of EchinoDB, EchinoDB v2.0 (https://echinodb.uncc.edu). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralog...

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...

Title: Four challenges associated with current mathematical modeling paradigm of infectious diseases and call for a shift
Author: Janies, Daniel, Chen, Shi, Robinson, Patrick, Dulin, Michael
Date Created: 2020
Subjects--Topical: Communicable diseases, Biology
Description: Mathematical models are critical tools to characterize COVID-19 dynamics and take action accordingly. We identified 4 major challenges associated with the current modeling paradigm (SEIR) that hinder the efforts to accurately characterize the emer...

Title: Gene polymorphisms among Plasmodium vivax geographical isolates and the potential as new biomarkers for gametocyte detection
Author: Janies, Daniel, Lo, Eugenia, Ford, Anthony
Date Created: 2022
Subjects--Topical: Genomics, Biology
Description: The unique biological features of Plasmodium vivax not only make it difficult to control but also to eliminate. For the transmission of the malaria parasite from infected human to the vector, gametocytes play a major role. The transmission potenti...

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: 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: Integration of phylogenomics and molecular modeling reveals lineage-specific diversification of toxins in scorpions
Author: Janies, Daniel, Rush, Nathaniel, Witter, Zachary, Williams, John
Date Created: 2018
Subjects--Topical: Genomics, Biology
Description: Scorpions have evolved a variety of toxins with a plethora of biological targets, but characterizing their evolution has been limited by the lack of a comprehensive phylogenetic hypothesis of scorpion relationships grounded in modern, genome-scale...

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...