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Articles 1 - 30 of 907
Full-Text Articles in Biology
Characterization Of A Protozoan Phosducin-Like Protein-3 (Phlp-3) Reveals Conserved Redox Activity, Rachel L. Kooistra, Robin David, Ana C. Ruiz, Kyle J. Haselton, Kaitlyn Kiernan, Andrew M. Blagborough, Ligin Solamen, Kenneth W. Olsen, Catherine Putonti, Stefan M. Kanzok
Characterization Of A Protozoan Phosducin-Like Protein-3 (Phlp-3) Reveals Conserved Redox Activity, Rachel L. Kooistra, Robin David, Ana C. Ruiz, Kyle J. Haselton, Kaitlyn Kiernan, Andrew M. Blagborough, Ligin Solamen, Kenneth W. Olsen, Catherine Putonti, Stefan M. Kanzok
Biology: Faculty Publications and Other Works
We recently identified three novel thioredoxin-like genes in the genome of the protozoan parasite Plasmodium that belong to the Phosducin-like family of proteins (PhLP). PhLPs are small cytosolic proteins hypothesized to function in G-protein signaling and protein folding. Although PhLPs are highly conserved in eukaryotes from yeast to mammals, only a few representatives have been experimentally characterized to date. In addition, while PhLPs contain a thioredoxin domain, they lack a CXXC motif, a strong indicator for redox activity, and it is unclear whether members of the PhLP family are enzymatically active. Here, we describe PbPhLP-3 as the first phosducin-like protein …
Enabling Precision Medicine Via Standard Communication Of Hts Provenance, Analysis, And Results, Gil Alterovitz, Dennis Dean, Carole Globe, Michael R. Crusoe, Stiam Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkkayastha, Charles H. King, Dan Taylor, Elaine Johanson, Elaine E. Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K. Vora, Jeremy Goecks, Jianchao Yao, Jonas S. Almeida, Jonathon Keeney, Kanakadurga Addepalli, Konstantinos Krampis, Krista M. Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C. Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder
Enabling Precision Medicine Via Standard Communication Of Hts Provenance, Analysis, And Results, Gil Alterovitz, Dennis Dean, Carole Globe, Michael R. Crusoe, Stiam Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkkayastha, Charles H. King, Dan Taylor, Elaine Johanson, Elaine E. Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K. Vora, Jeremy Goecks, Jianchao Yao, Jonas S. Almeida, Jonathon Keeney, Kanakadurga Addepalli, Konstantinos Krampis, Krista M. Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C. Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder
Publications and Research
A personalized approach based on a patient's or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet-lab procedures to computational methods. The BioCompute framework (https://w3id.org/biocompute/1.3.0) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated …
Characterization Of A Protozoan Phosducin-Like Protein-3 (Phlp-3) Reveals Conserved Redox Activity, Rachel L. Kooistra, Robin David, Ana C. Ruiz, Sean W. Powers, Kyle J. Haselton, Kaitlyn Kiernan, Andrew M. Blagborough, Ligin Solamen, Kenneth W, Olsen, Catherine Putonti, Stefan M. Kanzok
Characterization Of A Protozoan Phosducin-Like Protein-3 (Phlp-3) Reveals Conserved Redox Activity, Rachel L. Kooistra, Robin David, Ana C. Ruiz, Sean W. Powers, Kyle J. Haselton, Kaitlyn Kiernan, Andrew M. Blagborough, Ligin Solamen, Kenneth W, Olsen, Catherine Putonti, Stefan M. Kanzok
Bioinformatics Faculty Publications
We recently identified three novel thioredoxin-like genes in the genome of the protozoan parasite Plasmodium that belong to the Phosducin-like family of proteins (PhLP). PhLPs are small cytosolic proteins hypothesized to function in G-protein signaling and protein folding. Although PhLPs are highly conserved in eukaryotes from yeast to mammals, only a few representatives have been experimentally characterized to date. In addition, while PhLPs contain a thioredoxin domain, they lack a CXXC motif, a strong indicator for redox activity, and it is unclear whether members of the PhLP family are enzymatically active. Here, we describe PbPhLP-3 as the first phosducin-like protein …
Characterization Of A Protozoan Phosducin-Like Protein-3 (Phlp-3) Reveals Conserved Redox Activity, Rachel L. Kooistra, Robin David, Ana C. Ruiz, Sean W. Powers, Kyle J. Haselton, Kaitlyn Kiernan, Andrew M. Blagborough, Ken W. Olsen, Catherine Putonti, Stefan M. Kanzok
Characterization Of A Protozoan Phosducin-Like Protein-3 (Phlp-3) Reveals Conserved Redox Activity, Rachel L. Kooistra, Robin David, Ana C. Ruiz, Sean W. Powers, Kyle J. Haselton, Kaitlyn Kiernan, Andrew M. Blagborough, Ken W. Olsen, Catherine Putonti, Stefan M. Kanzok
Chemistry: Faculty Publications and Other Works
We recently identified three novel thioredoxin-like genes in the genome of the protozoan parasite Plasmodium that belong to the Phosducin-like family of proteins (PhLP). PhLPs are small cytosolic proteins hypothesized to function in G-protein signaling and protein folding. Although PhLPs are highly conserved in eukaryotes from yeast to mammals, only a few representatives have been experimentally characterized to date. In addition, while PhLPs contain a thioredoxin domain, they lack a CXXC motif, a strong indicator for redox activity, and it is unclear whether members of the PhLP family are enzymatically active. Here, we describe PbPhLP-3 as the first phosducin-like protein …
Comparative Transcriptome Analysis Reveals An Efficient Mechanism For Α-Linolenic Acid Synthesis In Tree Peony Seeds, Qingyu Zhang, Rui Yu, Daoyang Sun, Mahbubur Rahman, Lihang Xie, Jiayuan Hu, Lixia He, Aruna Kilaru, Lixin Niu, Yanlong Zhang
Comparative Transcriptome Analysis Reveals An Efficient Mechanism For Α-Linolenic Acid Synthesis In Tree Peony Seeds, Qingyu Zhang, Rui Yu, Daoyang Sun, Mahbubur Rahman, Lihang Xie, Jiayuan Hu, Lixia He, Aruna Kilaru, Lixin Niu, Yanlong Zhang
ETSU Faculty Works
Tree peony (Paeonia section Moutan DC.) species are woody oil crops with high unsaturated fatty acid content, including α-linolenic acid (ALA/18:3; >40% of the total fatty acid). Comparative transcriptome analyses were carried out to uncover the underlying mechanisms responsible for high and low ALA content in the developing seeds of P. rockii and P. lutea, respectively. Expression analysis of acyl lipid metabolism genes revealed upregulation of select genes involved in plastidial fatty acid synthesis, acyl editing, desaturation, and triacylglycerol assembly in seeds of P. rockiirelative to P. lutea. Also, in association with ALA content in seeds, …
Ne Stem 4u Afterschool Intervention Leads To Gains In Stem Content Knowledge For Middle School Youth, Christine E. Cutucache, Taylor Boham, Jamie Luhr, Amie Sommers, Nikolaus Stevenson, Erkko Sointu, Kati Mäkitalo‐Siegl, Sirpa Kärkkäinen, Teemu Valtonen, Neal Grandgenett, William Tapprich
Ne Stem 4u Afterschool Intervention Leads To Gains In Stem Content Knowledge For Middle School Youth, Christine E. Cutucache, Taylor Boham, Jamie Luhr, Amie Sommers, Nikolaus Stevenson, Erkko Sointu, Kati Mäkitalo‐Siegl, Sirpa Kärkkäinen, Teemu Valtonen, Neal Grandgenett, William Tapprich
Biology Faculty Publications
Afterschool interventions in STEM are linked to learning gains during the school day. These opportunities engage and excite students about STEM concepts since they observe a more hands-on, project-oriented approach. Often these opportunities for afterschool interventions are infrequent in nature and leave gaps for students in their maturation and understanding. Herein we describe the first report of an afterschool intervention, named NE STEM 4U, targeting socioeconomically disadvantaged middle school youth via a twice weekly, year-long intervention, studied across two years. We assessed the impact of this program on i.) short-term, individual student gains in STEM content knowledge and ii.) delivery …
Atypical Activation Of The G Protein Gα By The Oncogenic Mutation Q209p, Marcin Maziarz, Anthony Leyme, Arthur Marivin, Alex Luebbers, Prachi P. Patel, Zhe Chen, Stephen R. Sprang, Mikel Garcia-Marcos
Atypical Activation Of The G Protein Gα By The Oncogenic Mutation Q209p, Marcin Maziarz, Anthony Leyme, Arthur Marivin, Alex Luebbers, Prachi P. Patel, Zhe Chen, Stephen R. Sprang, Mikel Garcia-Marcos
Biological Sciences Faculty Publications
The causative role of G protein-coupled receptor (GPCR) pathway mutations in uveal melanoma (UM) has been well-established. Nearly all UMs bear an activating mutation in a GPCR pathway mediated by G proteins of the G family, driving tumor initiation and possibly metastatic progression. Thus, targeting this pathway holds therapeutic promise for managing UM. However, direct targeting of oncogenic Gα mutants, present in ∼90% of UMs, is complicated by the belief that these mutants structurally resemble active Gα WT. This notion is solidly founded on previous studies characterizing Gα mutants in which a conserved catalytic glutamine (Gln-209 in Gα) is replaced …
A Structural And Dynamic Model For The Assembly Of Replication Protein A On Single-Stranded Dna, Luke A. Yates, Ricardo J. Aramayo, Nilisha Pokhrel, Colleen C. Caldwell, Joshua A. Kaplan, Rajika L. Perera, Maria Spies, Edwin Antony, Xiaodong Zhang
A Structural And Dynamic Model For The Assembly Of Replication Protein A On Single-Stranded Dna, Luke A. Yates, Ricardo J. Aramayo, Nilisha Pokhrel, Colleen C. Caldwell, Joshua A. Kaplan, Rajika L. Perera, Maria Spies, Edwin Antony, Xiaodong Zhang
Biological Sciences Faculty Research and Publications
Replication Protein A (RPA), the major eukaryotic single stranded DNA-binding protein, binds to exposed ssDNA to protect it from nucleases, participates in a myriad of nucleic acid transactions and coordinates the recruitment of other important players. RPA is a heterotrimer and coats long stretches of single-stranded DNA (ssDNA). The precise molecular architecture of the RPA subunits and its DNA binding domains (DBDs) during assembly is poorly understood. Using cryo electron microscopy we obtained a 3D reconstruction of the RPA trimerisation core bound with ssDNA (∼55 kDa) at ∼4.7 Å resolution and a dimeric RPA assembly on ssDNA. FRET-based solution studies …
A Generic Pixel-To-Point Comparison For Simulated Large-Scale Ecosystem Properties And Ground-Based Observations: An Example From The Amazon Region, Anja Rammig, Jens Heinke, Florian Hofhansl, Hans Verbeeck, Timothy R. Baker, Bradley O. Christoffersen, Philippe Ciais, Hannes De Deurwaerder, Katrin Fleischer, David Galbraith
A Generic Pixel-To-Point Comparison For Simulated Large-Scale Ecosystem Properties And Ground-Based Observations: An Example From The Amazon Region, Anja Rammig, Jens Heinke, Florian Hofhansl, Hans Verbeeck, Timothy R. Baker, Bradley O. Christoffersen, Philippe Ciais, Hannes De Deurwaerder, Katrin Fleischer, David Galbraith
Biology Faculty Publications and Presentations
Comparing model output and observed data is an important step for assessing model performance and quality of simulation results. However, such comparisons are often hampered by differences in spatial scales between local point observations and large-scale simulations of grid cells or pixels. In this study, we propose a generic approach for a pixel-to-point comparison and provide statistical measures accounting for the uncertainty resulting from landscape variability and measurement errors in ecosystem variables. The basic concept of our approach is to determine the statistical properties of small-scale (within-pixel) variability and observational errors, and to use this information to correct for their …
Repeats Of Unusual Size In Plant Mitochondrial Genomes: Identification, Incidence And Evolution, Emily L. Wynn, Alan C. Christensen
Repeats Of Unusual Size In Plant Mitochondrial Genomes: Identification, Incidence And Evolution, Emily L. Wynn, Alan C. Christensen
School of Biological Sciences: Faculty Publications
Plant mitochondrial genomes have excessive size relative to coding capacity, a low mutation rate in genes and a high rearrangement rate. They also have abundant non-tandem repeats often including pairs of large repeats which cause isomerization of the genome by recombination, and numerous repeats of up to several hundred base pairs that recombine only when the genome is stressed by DNA damaging agents or mutations in DNA repair pathway genes. Early work on mitochondrial genomes led to the suggestion that repeats in the size range from several hundred to a few thousand base pair are underrepresented. The repeats themselves are …
Mrna, Rrna And Dna Quantitative Stable Isotope Probing With H218o Indicates Use Of Old Rrna Among Soil Thaumarchaeota, Katrina Papp, Bruce A. Hungate, Egbert Schwartz
Mrna, Rrna And Dna Quantitative Stable Isotope Probing With H218o Indicates Use Of Old Rrna Among Soil Thaumarchaeota, Katrina Papp, Bruce A. Hungate, Egbert Schwartz
Civil and Environmental Engineering and Construction Faculty Research
RNA is considered to be a short-lived molecule, indicative of cellular metabolic activity, whereas DNA is thoughtto turn over more slowly because living cells do not always grow and divide. To explore differences in the ratesof synthesis of these nucleic acids, we used H218O quantitative stable isotope probing (qSIP) to measure theincorporation of18O into 16S rRNA, the 16S rDNA,amoAmRNA and theamoAgene of soil Thaumarchaeota.Incorporation of18O into the thaumarchaealamoAmRNA pool was faster than into the 16S rRNA pool,suggesting that Thaumarchaea were metabolically active while using rRNA molecules that were likely synthe-tized prior to H218O addition. Assimilation rates of18O into 16S rDNA …
Minimum Information About An Uncultivated Virus Genome (Miuvig), Simon Roux, Evelien M. Adriaenssens, Bas E. Dutilh, Eugene V. Koonin, Andrew M. Kropinski, Mart Krupovic, Jens H. Kuhn, Rob Lavigne, J Rodney Brister, Arvind Varsani, Clara Amid, Ramy K. Aziz, Seth R. Bordenstein, Peer Bork, Mya Breitbart, Guy R. Cochrane, Rebecca A. Daly, Christelle Desnues, Melissa B. Duhaime, Joanne B. Emerson, François Enault, Jed A. Fuhrman, Pascal Hingamp, Philip Hugenholtz, Bonnie L. Hurwitz, Natalie N. Ivanova, Jessica M. Labonté, Kyung-Bum Lee, Rex R. Malmstrom, Manuel Martinez-Garcia, Ilene Karsch Mizrachi, Hiroyuki Ogata, David Páez-Espino, Marie-Agnès Petit, Catherine Putonti, Thomas Rattei, Alejandro Reyes, Francisco Rodriguez-Valera, Karyna Rosario, Lynn Schriml, Frederik Schulz, Grieg F. Steward, Matthew B. Sullivan, Shinichi Sunagawa, Curtis A. Suttle, Ben Temperton, Susannah G. Tringe, Rebecca Vega Thurber, Nicole S. Webster, Katrine L. Whiteson, Steven W. Whilhelm, K Eric Wommack, Tanja Woyke, Kelly C. Wrighton, Pelin Yilmaz, Takashi Yoshida, Mark J. Young, Natalya Yutin, Lisa Zeigler Allen, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh
Minimum Information About An Uncultivated Virus Genome (Miuvig), Simon Roux, Evelien M. Adriaenssens, Bas E. Dutilh, Eugene V. Koonin, Andrew M. Kropinski, Mart Krupovic, Jens H. Kuhn, Rob Lavigne, J Rodney Brister, Arvind Varsani, Clara Amid, Ramy K. Aziz, Seth R. Bordenstein, Peer Bork, Mya Breitbart, Guy R. Cochrane, Rebecca A. Daly, Christelle Desnues, Melissa B. Duhaime, Joanne B. Emerson, François Enault, Jed A. Fuhrman, Pascal Hingamp, Philip Hugenholtz, Bonnie L. Hurwitz, Natalie N. Ivanova, Jessica M. Labonté, Kyung-Bum Lee, Rex R. Malmstrom, Manuel Martinez-Garcia, Ilene Karsch Mizrachi, Hiroyuki Ogata, David Páez-Espino, Marie-Agnès Petit, Catherine Putonti, Thomas Rattei, Alejandro Reyes, Francisco Rodriguez-Valera, Karyna Rosario, Lynn Schriml, Frederik Schulz, Grieg F. Steward, Matthew B. Sullivan, Shinichi Sunagawa, Curtis A. Suttle, Ben Temperton, Susannah G. Tringe, Rebecca Vega Thurber, Nicole S. Webster, Katrine L. Whiteson, Steven W. Whilhelm, K Eric Wommack, Tanja Woyke, Kelly C. Wrighton, Pelin Yilmaz, Takashi Yoshida, Mark J. Young, Natalya Yutin, Lisa Zeigler Allen, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh
Bioinformatics Faculty Publications
We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative …
Life History And Habitat Of The Rare Patch-Nosed Salamander (Urspelerpes Brucei), Carlos D. Camp, Tyler L. Brock, Todd W. Pierson, Joseph Milanovich, John C. Maerz
Life History And Habitat Of The Rare Patch-Nosed Salamander (Urspelerpes Brucei), Carlos D. Camp, Tyler L. Brock, Todd W. Pierson, Joseph Milanovich, John C. Maerz
Biology: Faculty Publications and Other Works
We examined the life history and habitat characteristics for the Patch-nosed Salamander, Urspelerpes brucei. Body-size measurements of individuals captured using litter bags and by hand from 2008 to 2010 indicated that the larval period lasts at least 2 y, salamanders attain reproductive maturity at or shortly after metamorphosis, and adults have very little variation in body size. Occupied streams are characterized by small size, little water, and narrow, steep-walled ravines. Within occupied streams, larval capture rate was significantly and negatively related to mean water depth, underscoring the importance of protecting headwaters. We hypothesize that the only known population of U. …
A Force Sensor That Converts Fluorescence Signal Into Force Measurement Utilizing Short Looped Dna, Golam Mustafa, Cho-Ying Chuang, William A. Roy, Mohamed M. Farhath, Nilisha Pokhrel, Yue Ma, Kazuo Nagawawa, Edwin Antony, Matthew J. Comstock, Soumitra Basu, Hamza Balci
A Force Sensor That Converts Fluorescence Signal Into Force Measurement Utilizing Short Looped Dna, Golam Mustafa, Cho-Ying Chuang, William A. Roy, Mohamed M. Farhath, Nilisha Pokhrel, Yue Ma, Kazuo Nagawawa, Edwin Antony, Matthew J. Comstock, Soumitra Basu, Hamza Balci
Biological Sciences Faculty Research and Publications
A force sensor concept is presented where fluorescence signal is converted into force information via single-molecule Förster resonance energy transfer (smFRET). The basic design of the sensor is a ~100 base pair (bp) long double stranded DNA (dsDNA) that is restricted to a looped conformation by a nucleic acid secondary structure (NAS) that bridges its ends. The looped dsDNA generates a tension across the NAS and unfolds it when the tension is high enough. The FRET efficiency between donor and acceptor (D&A) fluorophores placed across the NAS reports on its folding state. Three dsDNA constructs with different lengths were bridged …
Using Clay Models To Measure Seasonal Predation On Eastern Red-Backed Salamanders, Emma Perry
Using Clay Models To Measure Seasonal Predation On Eastern Red-Backed Salamanders, Emma Perry
Honors Program Theses and Projects
One of the many gaps we have in our knowledge of salamanders is that of predation. Most studies suggest that salamanders are eaten mainly by birds and snakes, but there are still several unanswered questions: What other types of animals tend to prey on salamanders? Is there any difference in predator type during different times of the year? In order to answer these questions, I studied predation on one particular species of salamander, Plethodon cinereus (eastern red-backed salamander). Models of the two primary color morphs of P. cinereus (striped and unstriped) were created using impressionable clay to determine types and …
Miniscule Differences Between Sex Chromosomes In The Giant Genome Of A Salamander, Melissa C. Keinath, Nataliya Y. Timoshevskaya, Vladimir A. Timoshevskiy, S. Randal Voss, Jeramiah J. Smith
Miniscule Differences Between Sex Chromosomes In The Giant Genome Of A Salamander, Melissa C. Keinath, Nataliya Y. Timoshevskaya, Vladimir A. Timoshevskiy, S. Randal Voss, Jeramiah J. Smith
Biology Faculty Publications
In the Mexican axolotl (Ambystoma mexicanum), sex is determined by a single Mendelian factor, yet its sex chromosomes do not exhibit morphological differentiation typical of many vertebrate taxa that possess a single sex-determining locus. As sex chromosomes are theorized to differentiate rapidly, species with undifferentiated sex chromosomes provide the opportunity to reconstruct early events in sex chromosome evolution. Whole genome sequencing of 48 salamanders, targeted chromosome sequencing and in situ hybridization were used to identify the homomorphic sex chromosome that carries an A. mexicanum sex-determining factor and sequences that are present only on the W chromosome. Altogether, …
Gene Flow Mediates The Role Of Sex Chromosome Meiotic Drive During Complex Speciation, Colin D. Meiklejohn, Emily L. Landeen, Kathleen E. Gordon, Thomas Rzatkiewicz, Sarah B. Kingan, Anthony J. Geneva, Jeffrey P. Vedanayagam, Christina A. Muirhead, Daniel Garrigan, Daven C. Presgraves, David L. Stern
Gene Flow Mediates The Role Of Sex Chromosome Meiotic Drive During Complex Speciation, Colin D. Meiklejohn, Emily L. Landeen, Kathleen E. Gordon, Thomas Rzatkiewicz, Sarah B. Kingan, Anthony J. Geneva, Jeffrey P. Vedanayagam, Christina A. Muirhead, Daniel Garrigan, Daven C. Presgraves, David L. Stern
School of Biological Sciences: Faculty Publications
During speciation, sex chromosomes often accumulate interspecific genetic incompatibilities faster than the rest of the genome. The drive theory posits that sex chromosomes are susceptible to recurrent bouts of meiotic drive and suppression, causing the evolutionary build- up of divergent cryptic sex-linked drive systems and, incidentally, genetic incompatibilities. To assess the role of drive during speciation, we combine high-resolution genetic mapping of X-linked hybrid male sterility with population genomics analyses of divergence and recent gene flow between the fruitfly species, Drosophila mauritiana and D. simulans. Our findings reveal a high density of genetic incompatibilities and a corresponding dearth of gene …
Effect Of Temperature Change On Synaptic Transmission At Crayfish Neuromuscular Junctions, Yuechen Zhu, Leo De Castro, Robin L. Cooper
Effect Of Temperature Change On Synaptic Transmission At Crayfish Neuromuscular Junctions, Yuechen Zhu, Leo De Castro, Robin L. Cooper
Biology Faculty Publications
Ectothermic animals in areas characterised by seasonal changes are susceptible to extreme fluctuations in temperature. To survive through varied temperatures, ectotherms have developed unique strategies. This study focuses on synaptic transmission function at cold temperatures, as it is a vital component of ectothermic animals' survival. For determining how synaptic transmission is influenced by an acute change in temperature (20°C to 10°C within a minute) and chronic cold (10°C), the crayfish (Procambarus clarkii) neuromuscular junction (NMJ) was used as a model. To simulate chronic cold conditions, crayfish were acclimated to 15°C for 1 week and then to 10°C for …
Cryo-Em Structures Of Eastern Equine Encephalitis Virus Reveal Mechanisms Of Virus Disassembly And Antibody Neutralization, Saif Hasan, Chengqun Sun, Arthur S. Kim, Yasunori Watanabe, Chun-Liang Chen, Thomas Klose, Geeta Buda, Max Crispin, Michael S. Diamond, William B. Klimstra, Michael G. Rossmann
Cryo-Em Structures Of Eastern Equine Encephalitis Virus Reveal Mechanisms Of Virus Disassembly And Antibody Neutralization, Saif Hasan, Chengqun Sun, Arthur S. Kim, Yasunori Watanabe, Chun-Liang Chen, Thomas Klose, Geeta Buda, Max Crispin, Michael S. Diamond, William B. Klimstra, Michael G. Rossmann
Department of Biological Sciences Faculty Publications
Alphaviruses are enveloped pathogens that cause arthritis and encephalitis. Here, we report a 4.4-Å cryoelectron microscopy (cryo-EM) structure of eastern equine encephalitis virus (EEEV), an alphavirus that causes fatal encephalitis in humans. Our analysis provides insights into viral entry into host cells. The envelope protein E2 showed a binding site for the cellular attachment factor heparan sulfate. The presence of a cryptic E2 glycan suggests how EEEV escapes surveillance by lectin-expressing myeloid lineage cells, which are sentinels of the immune system. A mechanism for nucleocapsid core release and disassembly upon viral entry was inferred based on pH changes and capsid …
Molecular Machinery Of Auxin Synthesis,Secretion, And Perception In The Unicellular Chlorophyte Alga Chlorella Sorokiniana Utex 1230, Maya Khasin, Rebecca E. Cahoon, Kenneth Nickerson, Wayne R. Riekhof
Molecular Machinery Of Auxin Synthesis,Secretion, And Perception In The Unicellular Chlorophyte Alga Chlorella Sorokiniana Utex 1230, Maya Khasin, Rebecca E. Cahoon, Kenneth Nickerson, Wayne R. Riekhof
School of Biological Sciences: Faculty Publications
Indole-3-acetic acid is a ubiquitous small molecule found in all domains of life. It is the predominant and most active auxin in seed plants, where it coordinates a variety of complex growth and development processes. The potential origin of auxin signaling in algae remains a matter of some controversy. In order to clarify the evolutionary context of algal auxin signaling, we undertook a genomic survey to assess whether auxin acts as a signaling molecule in the emerging model chlorophyte Chlorella sorokiniana UTEX 1230. C. sorokiniana produces the auxin indole-3-acetic acid (IAA), which was present in both the cell pellet and …
A High-Fat Diet Alters Genome-Wide Dna Methylation And Gene Expression In Sm/J Mice, Madeline R. Keleher, Rabab Zaidi, Lauren Hicks, Shyam Shah, Xiaoyun Xing, Daofeng Li, Ting Wang, James M. Cheverud
A High-Fat Diet Alters Genome-Wide Dna Methylation And Gene Expression In Sm/J Mice, Madeline R. Keleher, Rabab Zaidi, Lauren Hicks, Shyam Shah, Xiaoyun Xing, Daofeng Li, Ting Wang, James M. Cheverud
Biology: Faculty Publications and Other Works
Background: While the genetics of obesity has been well defined, the epigenetics of obesity is poorly understood. Here, we used a genome-wide approach to identify genes with differences in both DNA methylation and expression associated with a high-fat diet in mice. Results: We weaned genetically identical Small (SM/J) mice onto a high-fat or low-fat diet and measured their weights weekly, tested their glucose and insulin tolerance, assessed serum biomarkers, and weighed their organs at necropsy. We measured liver gene expression with RNA-seq (using 21 total libraries, each pooled with 2 mice of the same sex and diet) and DNA methylation …
The Impact Of Online Homework, Time On Homework, Gender, And Metacognition In Improving Student Achievement In Undergraduate Biology Courses, Donald Bishop Cook Jr
The Impact Of Online Homework, Time On Homework, Gender, And Metacognition In Improving Student Achievement In Undergraduate Biology Courses, Donald Bishop Cook Jr
Doctoral Dissertations and Projects
This study sought to address a gap in the literature to determine whether a relationship exists between use of online homework and student achievement in undergraduate biology courses. Previous studies have examined other STEM courses, but few have considered biology. The purpose of the study was to determine whether homework grades in online homework systems can predict student achievement in introductory undergraduate biology courses. This study utilized a correlational analysis by multiple regression using archival data to determine whether final course grades in undergraduate biology courses can be predicted by grades on online homework, time spent on online homework, gender, …
The Genomic Landscape Of Molecular Responses To Natural Drought Stress In Panicum Hallii., John T. Lovell, Jerry Jenkins, David B. Lowry, Sujan Mamidi, Avinash Sreedasyam, Xiaoyu Weng, Kerrie Barry, Jason Bonnette, Brandon Campitelli, Chris Daum, Sean P. Gordon, Billie A. Gould, Albina Khasanova, Anna Lipzen, Alice Macqueen, Juan Diego Palacio-Mejía, Christopher Plott, Eugene V. Shakirov, Shengqiang Shu, Yuko Yoshinaga, Matt Zane, Dave Kudrna, Jason D. Talag, Daniel Rokhsar, Jane Grimwood, Jeremy Schmutz, Thomas E. Juenger
The Genomic Landscape Of Molecular Responses To Natural Drought Stress In Panicum Hallii., John T. Lovell, Jerry Jenkins, David B. Lowry, Sujan Mamidi, Avinash Sreedasyam, Xiaoyu Weng, Kerrie Barry, Jason Bonnette, Brandon Campitelli, Chris Daum, Sean P. Gordon, Billie A. Gould, Albina Khasanova, Anna Lipzen, Alice Macqueen, Juan Diego Palacio-Mejía, Christopher Plott, Eugene V. Shakirov, Shengqiang Shu, Yuko Yoshinaga, Matt Zane, Dave Kudrna, Jason D. Talag, Daniel Rokhsar, Jane Grimwood, Jeremy Schmutz, Thomas E. Juenger
Biological Sciences Faculty Research
Environmental stress is a major driver of ecological community dynamics and agricultural productivity. This is especially true for soil water availability, because drought is the greatest abiotic inhibitor of worldwide crop yields. Here, we test the genetic basis of drought responses in the genetic model for C4 perennial grasses, Panicum hallii, through population genomics, field-scale gene-expression (eQTL) analysis, and comparison of two complete genomes. While gene expression networks are dominated by local cis-regulatory elements, we observe three genomic hotspots of unlinked trans-regulatory loci. These regulatory hubs are four times more drought responsive than the genome-wide average. Additionally, cis- and trans-regulatory …
Canvass: A Crowd-Sourced, Natural-Product Screening Library For Exploring Biological Space, Sara E. Kearney, Gergely ZahoráNszky-KőHalmi, Kyle R. Brimacombe, Mark J. Henderson, Caitlin Lynch, Tongan Zhao, Kanny K. Wan, Zina Itkin, Christopher Dillon, Min Shen, Dorian M. Cheff, Tobie D. Lee, Danielle Bougie, Ken Cheng, Nathan P. Coussens, Dorjbal Dorjsuren, Richard T. Eastman, Ruili Huang, Michael J. Iannotti, Surendra Karavadhi, Carleen Klumpp-Thomas, Jacob S. Roth, Srilatha Sakamuru, Wei Sun, Steven A. Titus, Adam Yasgar, Ya-Qin Zhang, Jinghua Zhao, Rodrigo B. Andrade, M. Kevin Brown, Robert B. Grossman
Canvass: A Crowd-Sourced, Natural-Product Screening Library For Exploring Biological Space, Sara E. Kearney, Gergely ZahoráNszky-KőHalmi, Kyle R. Brimacombe, Mark J. Henderson, Caitlin Lynch, Tongan Zhao, Kanny K. Wan, Zina Itkin, Christopher Dillon, Min Shen, Dorian M. Cheff, Tobie D. Lee, Danielle Bougie, Ken Cheng, Nathan P. Coussens, Dorjbal Dorjsuren, Richard T. Eastman, Ruili Huang, Michael J. Iannotti, Surendra Karavadhi, Carleen Klumpp-Thomas, Jacob S. Roth, Srilatha Sakamuru, Wei Sun, Steven A. Titus, Adam Yasgar, Ya-Qin Zhang, Jinghua Zhao, Rodrigo B. Andrade, M. Kevin Brown, Robert B. Grossman
Chemistry Faculty Publications
Natural products and their derivatives continue to be wellsprings of nascent therapeutic potential. However, many laboratories have limited resources for biological evaluation, leaving their previously isolated or synthesized compounds largely or completely untested. To address this issue, the Canvass library of natural products was assembled, in collaboration with academic and industry researchers, for quantitative high-throughput screening (qHTS) across a diverse set of cell-based and biochemical assays. Characterization of the library in terms of physicochemical properties, structural diversity, and similarity to compounds in publicly available libraries indicates that the Canvass library contains many structural elements in common with approved drugs. The …
Priming Of Grasping Muscles When Viewing A Safety Handle Is Diminished With Age, David A.E. Bolton, Sarah E. Schwartz, Manhoud Mansour, Garrett Rydalch, Douglas W. Mcdannald
Priming Of Grasping Muscles When Viewing A Safety Handle Is Diminished With Age, David A.E. Bolton, Sarah E. Schwartz, Manhoud Mansour, Garrett Rydalch, Douglas W. Mcdannald
Kinesiology and Health Science Faculty Publications
Merely viewing objects within reachable space can activate motor cortical networks and potentiate movement. This holds potential value for smooth interaction with objects in our surroundings, and could offer an advantage for quickly generating targeted hand movements (e.g. grasping a support rail to maintain stability). The present study investigated if viewing a wall-mounted safety handle resulted in automatic activation of motor cortical networks, and if this effect changes with age. Twenty-five young adults (18–30 years) and seventeen older adults (65+ years) were included in this study. Single-pulse, transcranial magnetic stimulation was applied over the motor cortical hand representation of young …
Reducing Protected Lands In A Hotspot Of Bee Biodiversity: Bees Of Grand Staircase-Escalante National Monument, Joseph S. Wilson, Matt Kelly, Olivia Messinger Carril
Reducing Protected Lands In A Hotspot Of Bee Biodiversity: Bees Of Grand Staircase-Escalante National Monument, Joseph S. Wilson, Matt Kelly, Olivia Messinger Carril
Biology Faculty Publications
Grand Staircase-Escalante National Monument is a federally protected area found in central southern Utah. Designated in 1996 by President William J. Clinton, it was recently reduced in size by President Donald J. Trump in a proclamation that turned the one large monument into three smaller ones. A long-term, standardized study of the bees had been conducted from 2000–2003, revealing 660 species. The bee communities of the area are characterized by being spatially heterogeneous; most of the bees occur in isolated areas, with only a few being both abundant and widespread. Here we examine what affect the recent resizing of the …
Florida's Pillar Coral (Dendrogyra Cylindrus): The Roles Of The Holobiont Partners In Bleaching, Recovery, And Disease Processes, Cynthia Fairbank Lewis
Florida's Pillar Coral (Dendrogyra Cylindrus): The Roles Of The Holobiont Partners In Bleaching, Recovery, And Disease Processes, Cynthia Fairbank Lewis
FIU Electronic Theses and Dissertations
The iconic pillar coral, Dendrogyra cylindrus, is one of five Caribbean species listed in 2014 under the US Federal Endangered Species Act because of its extreme low abundance and continued decline in US waters. Until recently, little was known about the demographics or genetic diversity of Florida’s D. cylindrus population. This study represents the first time two holobiont partners (coral animal and associated photosynthetic algal endosymbionts) have been closely examined, spatially and temporally, in this little-studied species. The aim was to explore the influences of coral animal genotypes, mutualistic photosynthetic algal strains, and hyperthermal stress on bleaching and …
Long-Term Experimental Hybridisation Results In The Evolution Of A New Sex Chromosome In Swordtail Fish, Paolo Franchini, Julia C. Jones, Peiwen Xiong, Susanne Kneitz, Zachariah Gompert, Wesley C. Warren, Ronald B. Walter, Axel Meyer, Manfred Schartl
Long-Term Experimental Hybridisation Results In The Evolution Of A New Sex Chromosome In Swordtail Fish, Paolo Franchini, Julia C. Jones, Peiwen Xiong, Susanne Kneitz, Zachariah Gompert, Wesley C. Warren, Ronald B. Walter, Axel Meyer, Manfred Schartl
Biology Faculty Publications
The remarkable diversity of sex determination mechanisms known in fish may be fuelled by exceptionally high rates of sex chromosome turnovers or transitions. However, the evolutionary causes and genomic mechanisms underlying this variation and instability are yet to be understood. Here we report on an over 30-year evolutionary experiment in which we tested the genomic consequences of hybridisation and selection between two Xiphophorus fish species with different sex chromosome systems. We find that introgression and imposing selection for pigmentation phenotypes results in the retention of an unexpectedly large maternally derived genomic region. During the hybridisation process, the sex-determining region of …
Polyol-Producing Lactic Acid Bacteria Isolated From Sourdough And Their Application To Reduce Sugar In A Quinoa-Based Milk Substitute, Stephanie Jeske, Emanuele Zannini, Kieran M. Lynch, Aidan Coffey, Elke K. Arendt
Polyol-Producing Lactic Acid Bacteria Isolated From Sourdough And Their Application To Reduce Sugar In A Quinoa-Based Milk Substitute, Stephanie Jeske, Emanuele Zannini, Kieran M. Lynch, Aidan Coffey, Elke K. Arendt
Department of Biological Sciences Publications
The interest for plant-based dairy substitutes is expanding rapidly and consumers are opting for nutritious and healthy dairy alternatives. The reduction of sugar using different exogenous enzymes in combination with lactic acid fermentation in a quinoa-based milk substitute was explored in this study. Different amylolytic enzymes were used to release sugar from the raw material, which were further metabolised to mannitol, due to fermentation with two heterofermentative lactic acid bacteria. Using these two biotechnological techniques enables the reduction of sugar, while also preserving some of the sweetness. Leuconostoc citreum TR116, and Lactobacillus brevis TR055 were isolated from sourdough. Both strains …
Evidence For Divergent Patterns Of Local Selection Driving Venom Variation In Mojave Rattlesnakes (Crotalus Scutulatus), Jason L. Strickland, Cara F. Smith, Andrew J. Mason, Drew R. Schield, Miguel Borja, Gamaliel Castañeda-Gaytán, Carol L. Spencer, Lydia L. Smith, Ann Trápaga, Nassima M. Bouzid, Gustavo Campillo-García, Oscar A. Flores-Villela, Daniel Antonio-Rangel, Stephen P. Mackessy, Todd A. Castoe, Darin R. Rokyta, Christopher L. Parkinson
Evidence For Divergent Patterns Of Local Selection Driving Venom Variation In Mojave Rattlesnakes (Crotalus Scutulatus), Jason L. Strickland, Cara F. Smith, Andrew J. Mason, Drew R. Schield, Miguel Borja, Gamaliel Castañeda-Gaytán, Carol L. Spencer, Lydia L. Smith, Ann Trápaga, Nassima M. Bouzid, Gustavo Campillo-García, Oscar A. Flores-Villela, Daniel Antonio-Rangel, Stephen P. Mackessy, Todd A. Castoe, Darin R. Rokyta, Christopher L. Parkinson
Publications
Snake venoms represent an enriched system for investigating the evolutionary processes that lead to complex and dynamic trophic adaptations. It has long been hypothesized that natural selection may drive geographic variation in venom composition, yet previous studies have lacked the population genetic context to examine these patterns. We leverage range-wide sampling of Mojave Rattlesnakes (Crotalus scutulatus) and use a combination of venom, morphological, phylogenetic, population genetic, and environmental data to characterize the striking dichotomy of neurotoxic (Type A) and hemorrhagic (Type B) venoms throughout the range of this species. We find that three of the four previously identified …