Open Access. Powered by Scholars. Published by Universities.®
- Institution
- Keyword
-
- Cancer genomics (2)
- High-throughput "omics" (2)
- Non-proportional hazards (2)
- Accelerated failure time model (1)
- Addiction (1)
-
- And OxyContin. (1)
- Anthropogenic (1)
- Atherosclerosis (1)
- Biology (1)
- Bogs (1)
- Botanical history (1)
- Censored survival data (1)
- Coefficient of conservatism (1)
- Comparative bioenergetics (1)
- Continuum power regression (1)
- Copper (1)
- Crossing hazards (1)
- Crystallization (1)
- Cyanide-resistant respiration (1)
- Death Rate (1)
- Emma Cole (1)
- Feature selection (1)
- Flora of Grand Rapids (1)
- Floristic ecology (1)
- Floristic quality assessment (1)
- Floristics (1)
- Fluorescence (1)
- Gene therapy (1)
- Generalized F model (1)
- High-dimensional data (1)
Articles 1 - 14 of 14
Full-Text Articles in Biochemistry
Multidrug Resistance Regulators Mara, Soxs, Rob, And Rama Repress Flagellar Gene Expression And Motility In Salmonella Enterica Serovar Typhimurium, Srinivas Thota, Lon Chubiz
Multidrug Resistance Regulators Mara, Soxs, Rob, And Rama Repress Flagellar Gene Expression And Motility In Salmonella Enterica Serovar Typhimurium, Srinivas Thota, Lon Chubiz
Biology Department Faculty Works
Production of flagella is costly and subject to global multilayered regulation, which is reflected in the hierarchical control of flagellar production in many bacterial species. For Salmonella enterica serovar Typhimurium and its relatives, global regulation of flagellar production primarily occurs through the control of flhDC transcription and mRNA translation. In this study, the roles of the homologous multidrug resistance regulators MarA, SoxS, Rob, and RamA (constituting the mar-sox-rob regulon in S. Typhimurium) in regulating flagellar gene expression were explored. Each of these regulators was found to inhibit flagellar gene expression, production of flagella, and motility. To different degrees, repression via …
Dual Activities Of Plant Cgmp-Dependent Protein Kinase And Its Roles In Gibberellin Signaling And Salt Stress., Qingwen Shen, Xinqiao Zhan, Pei Yang, Jing Li, Jie Chen, Bing Tang, Xuemin Wang, Xuemin Wang, Yueyun Hong
Dual Activities Of Plant Cgmp-Dependent Protein Kinase And Its Roles In Gibberellin Signaling And Salt Stress., Qingwen Shen, Xinqiao Zhan, Pei Yang, Jing Li, Jie Chen, Bing Tang, Xuemin Wang, Xuemin Wang, Yueyun Hong
Biology Department Faculty Works
Cyclic GMP (cGMP) is an important regulator in eukaryotes, and cGMP-dependent protein kinase (PKG) plays a key role in perceiving cellular cGMP in diverse physiological processes in animals. However, the molecular identity, property, and function of PKG in plants remain elusive. In this study, we have identified PKG from plants and characterized its role in mediating the gibberellin (GA) response in rice (Oryza sativa). PKGs from plants are structurally unique with an additional type 2C protein phosphatase domain. Rice PKG possesses both protein kinase and phosphatase activities, and cGMP stimulates its kinase activity but inhibits its phosphatase activity. One of …
Quantifying Anthropogenic Indicators And Changes In Dissolved Organic Matter In Coastal Urban Aquatic Ecosystems Exposed To High Tidal Flooding, Gonzalo E. Eyzaguirre
Quantifying Anthropogenic Indicators And Changes In Dissolved Organic Matter In Coastal Urban Aquatic Ecosystems Exposed To High Tidal Flooding, Gonzalo E. Eyzaguirre
Department of Biological Sciences
Sea-level rise is causing an increase in tidal flooding in coastal urban areas. Extreme high tides, also known as king tides, are peak tide moments in which tidal amplitude is increased and shallow groundwater flows from the underlying water table are introduced. During tidal flooding in urban areas, accumulated anthropogenic indicators of different water sources are released from groundwater to surface waters, but how these tidal events affect the contributions of different water sources to urban flood waters is uncertain. We quantified tracers of anthropogenic origin including fluoride, fecal coliform bacteria, as well as dissolved organic carbon (DOC) concentrations and …
Unified Methods For Feature Selection In Large-Scale Genomic Studies With Censored Survival Outcomes, Lauren Spirko-Burns, Karthik Devarajan
Unified Methods For Feature Selection In Large-Scale Genomic Studies With Censored Survival Outcomes, Lauren Spirko-Burns, Karthik Devarajan
COBRA Preprint Series
One of the major goals in large-scale genomic studies is to identify genes with a prognostic impact on time-to-event outcomes which provide insight into the disease's process. With rapid developments in high-throughput genomic technologies in the past two decades, the scientific community is able to monitor the expression levels of tens of thousands of genes and proteins resulting in enormous data sets where the number of genomic features is far greater than the number of subjects. Methods based on univariate Cox regression are often used to select genomic features related to survival outcome; however, the Cox model assumes proportional hazards …
Supervised Dimension Reduction For Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards, Lauren Spirko-Burns, Karthik Devarajan
Supervised Dimension Reduction For Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards, Lauren Spirko-Burns, Karthik Devarajan
COBRA Preprint Series
The past two decades have witnessed significant advances in high-throughput ``omics" technologies such as genomics, proteomics, metabolomics, transcriptomics and radiomics. These technologies have enabled simultaneous measurement of the expression levels of tens of thousands of features from individual patient samples and have generated enormous amounts of data that require analysis and interpretation. One specific area of interest has been in studying the relationship between these features and patient outcomes, such as overall and recurrence-free survival, with the goal of developing a predictive ``omics" profile. Large-scale studies often suffer from the presence of a large fraction of censored observations and potential …
Alternative Nad(P)H Dehydrogenase And Alternative Oxidase: Proposed Physiological Roles In Animals, Allison Mcdonald, Dmytro V. Gospodaryov
Alternative Nad(P)H Dehydrogenase And Alternative Oxidase: Proposed Physiological Roles In Animals, Allison Mcdonald, Dmytro V. Gospodaryov
Biology Faculty Publications
The electron transport systems in mitochondria of many organisms contain alternative respiratory enzymes distinct from those of the canonical respiratory system depicted in textbooks. Two of these enzymes, the alternative NADH dehydrogenase and the alternative oxidase, were of interest to a limited circle of researchers until they were envisioned as gene therapy tools for mitochondrial disease treatment. Recently, these enzymes were discovered in several animals. Here, we analyse the functioning of alternative NADH dehydrogenases and oxidases in different organisms. We propose that both enzymes ensure bioenergetic and metabolic flexibility during environmental transitions or other conditions which may compromise the operation …
Escaping Death: Naloxone's Chemical Nature And Potential To Combat The Opioid Epidemic, Abigale Miller
Escaping Death: Naloxone's Chemical Nature And Potential To Combat The Opioid Epidemic, Abigale Miller
Honors Theses
Naloxone is a life-saving drug with the ability to reverse an opioid overdose. As the opioid epidemic’s death toll rises, we can turn to Naloxone as a tool to combat the crisis. The epidemic, born of corruption, has a wide reach among the people of the United States, with especially firm grasps on middle-aged people, sufferers of chronic pain, white Americans and those living in the eastern portion of the country. Naloxone’s elegant design saves lives by effectively competing for a position on an opioid biding receptor in the brain to almost instantly end an overdose and restore normal breathing. …
Allosteric Mechanism Of The Circadian Protein Vivid Resolved Through Markov State Model And Machine Learning Analysis, Hongyu Zhou, Zheng Dong, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao
Allosteric Mechanism Of The Circadian Protein Vivid Resolved Through Markov State Model And Machine Learning Analysis, Hongyu Zhou, Zheng Dong, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao
Mathematics, Physics, and Computer Science Faculty Articles and Research
The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change. The mechanism by which a blue-light driven covalent bond formation leads to a global conformational change remains unclear, which hinders the further development of VVD as an optogenetic tool. We answered this question through a novel computational platform integrating Markov state models, machine learning methods, and newly developed community analysis algorithms. Applying this new integrative approach, we provided a quantitative evaluation of the contribution from the covalent bond to the protein global conformational change, and proposed an …
Student-Faculty Collaborative Research Grant Report, Megan Bestwick
Student-Faculty Collaborative Research Grant Report, Megan Bestwick
Post-Grant Reports
Mitochondria are essential organelles in most eukaryotic cells because of their role in metabolism and the production of ATP by the oxidative phosphorylation (OXPHOS) pathway, as well as other key cellular processes. Metal cofactors, such as copper (Cu) and iron (Fe), are incorporated into OXPHOS protein complexes of yeast located within the inner membrane of the mitochondria. Misincorporation or modulation of these available metals in mitochondrial enzymes leads to the production of reactive oxygen species (ROS). ROS are reactive molecules containing oxygen such as peroxides, superoxide, and hydroxyl radicals. Yeast are a good model for studying aging and the effect …
Lncegfl7os Regulates Human Angiogenesis By Interacting With Max At The Egfl7/Mir-126 Locus, Quinbo Zhou, Chastain Anderson, Zhan-Peng Huang, Jakub Hanus, Wensheng Zhang, Yu Han
Lncegfl7os Regulates Human Angiogenesis By Interacting With Max At The Egfl7/Mir-126 Locus, Quinbo Zhou, Chastain Anderson, Zhan-Peng Huang, Jakub Hanus, Wensheng Zhang, Yu Han
Faculty and Staff Publications
In an effort to identify human endothelial cell (EC)-enriched lncRNAs,~500 lncRNAswere shown to be highly restricted in primary human ECs. Among them,lncEGFL7OS, located inthe opposite strand of theEGFL7/miR-126gene, is regulated by ETS factors through abidirectional promoter in ECs. It is enriched in highly vascularized human tissues, and upregulatedin the hearts of dilated cardiomyopathy patients. LncEGFL7OS silencing impairs angiogenesis asshown by EC/fibroblast co-culture, in vitro/in vivo and ex vivo human choroid sproutingangiogenesis assays, while lncEGFL7OS overexpression has the opposite function. Mechanistically,lncEGFL7OS is required for MAPK and AKT pathway activation by regulating EGFL7/miR-126expression. MAX protein was identified as a lncEGFL7OS-interacting protein that …
Interaction And Regulation Between Lipid Mediator Phosphatidic Acid And Circadian Clock Regulators, Sang-Chul Kim, Sang-Chul Kim, Dmitri Nusinow, Maria Sorkin, Maria Sorkin, Jose Pruneda-Paz, Xuemin Wang, Xuemin Wang
Interaction And Regulation Between Lipid Mediator Phosphatidic Acid And Circadian Clock Regulators, Sang-Chul Kim, Sang-Chul Kim, Dmitri Nusinow, Maria Sorkin, Maria Sorkin, Jose Pruneda-Paz, Xuemin Wang, Xuemin Wang
Biology Department Faculty Works
Circadian clocks play important roles in regulating cellular metabolism, but the reciprocal effect that metabolism has on the clock is largely unknown in plants. Here we show that the central glycerolipid metabolite and lipid mediator phosphatidic acid (PA) interacts with and modulates the function of the core clock regulators LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED1 (CCA1) in Arabidopsis thaliana. PA reduced the ability of LHY and CCA1 to bind the promoter of their target gene TIMING OF CAB EXPRESSION1. Increased PA accumulation and inhibition of PA-producing enzymes had opposite effects on circadian clock outputs. Diurnal change in levels …
Method Development For Structural Assessment Of Nanolipoprotein Particles With And Without Cross-Linked Lipids, Emma J. Mullen, Wei He, Sean Gilmore, Matthias Frank, Matthew Coleman, Megan Shelby
Method Development For Structural Assessment Of Nanolipoprotein Particles With And Without Cross-Linked Lipids, Emma J. Mullen, Wei He, Sean Gilmore, Matthias Frank, Matthew Coleman, Megan Shelby
STAR Program Research Presentations
Membrane proteins make up approximately 30% of the cellular proteome and account for over 60% of pharmaceutical targets.1 Determining the structures of this class of proteins is critical to our understanding of disease states and will advance rational drug design. But membrane proteins have limited solubility, rarely form large crystals that diffract well, and often misfold outside of a bilayer, hindering crystallographic studies.1 Nanolipoprotein particles (NLPs) have arisen as a platform to readily solubilize membrane proteins while mimicking a native lipid environment. NLPs consist of a discoidal phospholipid bilayer encircled by an apolipoprotein belt. In an effort to optimize and …
Bog Flora In The Grand Rapids, Michigan, Area: A Comparative Study Across Sites And Over Time O 1901 To 2017, Devani Antuma Jolman, Jenna L. Van Donselaar, David P. Warners, Garrett E. Crow
Bog Flora In The Grand Rapids, Michigan, Area: A Comparative Study Across Sites And Over Time O 1901 To 2017, Devani Antuma Jolman, Jenna L. Van Donselaar, David P. Warners, Garrett E. Crow
Faculty and Professional Research
Michigan’s natural landscape includes a diverse assemblage of ecosystems, among the most distinctive of which are peatlands, and more specifically, those known colloquially as “bogs.” When botanist Emma J. Cole published the Grand Rapids Flora in 1901, she included a large number of bog species documented in the greater Grand Rapids area (16 townships in two counties, an area of 585 square miles). Cole’s Flora is still the most comprehensive catalog of vascular plants found in West Michigan. This study is part of an ongoing update of Cole’s work undertaken by the Calvin University Herbarium to relocate and inventory Emma …
Cullin-3 Dependent Deregulation Of Actn1 Represents A New Pathogenic Mechanism In Nemaline Myopathy, Jordan Blondelle, Kavya Tallapaka, Jane T. Seto, Majid Ghassemian, Madison Clark, Jenni M. Laitila, Adam Bournazos, Jeffrey Singer, Stephan Lange
Cullin-3 Dependent Deregulation Of Actn1 Represents A New Pathogenic Mechanism In Nemaline Myopathy, Jordan Blondelle, Kavya Tallapaka, Jane T. Seto, Majid Ghassemian, Madison Clark, Jenni M. Laitila, Adam Bournazos, Jeffrey Singer, Stephan Lange
Biology Faculty Publications and Presentations
Nemaline myopathy is a congenital neuromuscular disorder characterized by muscle weakness, fiber atrophy, and presence of nemaline bodies within myofibers. However, understanding of the underlying pathomechanisms is lacking. Recently, mutations in KBTBD13, KLHL40, and KLHL41, three substrate adaptors for the E3 ubiquitin ligase Cullin-3, have been associated with early-onset nemaline myopathies. We hypothesized that deregulation of Cullin-3 and its muscle protein substrates may be responsible for disease development. Using Cullin-3–knockout mice, we identified accumulation of non-muscle α-actinins (ACTN1 and ACTN4) in muscles of these mice, which we also observed in patients with mutations in KBTBD13. Our …