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Articles 1 - 30 of 49
Full-Text Articles in Physical Sciences and Mathematics
Importance Of Refractory Ligands And Their Photodegradation For Iron Oceanic Inventories And Cycling, Christel Hassler, Damien Cabanes, Sonia Blanco-Ameijeiras, Sylvia G. Sander, Ronald Benner
Importance Of Refractory Ligands And Their Photodegradation For Iron Oceanic Inventories And Cycling, Christel Hassler, Damien Cabanes, Sonia Blanco-Ameijeiras, Sylvia G. Sander, Ronald Benner
Faculty Publications
Iron is an essential micronutrient that limits primary production in up to 40% of the surface ocean and influences carbon dioxide uptake and climate change. Dissolved iron is mostly associated with loosely characterised organic molecules, called ligands, which define key aspects of the iron cycle such as its residence time, distribution and bioavailability to plankton. Models based on in situ ligand distributions and the behaviour of purified compounds include long-lived ligands in the deep ocean, bioreactive ligands in the surface ocean and photochemical processes as important components of the iron cycle. Herein, we further characterise biologically refractory ligands in dissolved …
Δscope: A New Method To Quantify 3d Biological Structures And Identify Differences In Zebrafish Forebrain Development, Morgan S. Schwartz, Jake Schnabl, Mackenzie P.H. Litz, Benjamin Baumer, Michael Barresi
Δscope: A New Method To Quantify 3d Biological Structures And Identify Differences In Zebrafish Forebrain Development, Morgan S. Schwartz, Jake Schnabl, Mackenzie P.H. Litz, Benjamin Baumer, Michael Barresi
Biological Sciences: Faculty Publications
Research in the life sciences has traditionally relied on the analysis of clear morphological phenotypes, which are often revealed using increasingly powerful microscopy techniques analyzed as maximum intensity projections (MIPs). However, as biology turns towards the analysis of more subtle phenotypes, MIPs and qualitative approaches are failing to adequately describe these phenotypes. To address these limitations and quantitatively analyze the three-dimensional (3D) spatial relationships of biological structures, we developed the computational method and program called ∆SCOPE (Changes in Spatial Cylindrical Coordinate Orientation using PCA Examination). Our approach uses the fluorescent signal distribution within a 3D data set and reorients the …
Spatial And Temporal Variation Of Offshore Wind Power And Its Values Along The Central California Coast, Yi-Hui Wang, Ryan K. Walter, Crow White, Matthew D. Kehrli, Stephen F. Hamilton, Patrick H. Soper, Benjamin I. Ruttenberg
Spatial And Temporal Variation Of Offshore Wind Power And Its Values Along The Central California Coast, Yi-Hui Wang, Ryan K. Walter, Crow White, Matthew D. Kehrli, Stephen F. Hamilton, Patrick H. Soper, Benjamin I. Ruttenberg
Physics
The analysis of the spatiotemporal variability of wind power remains limited during the planning stage of an offshore wind farm. This study provides a framework to investigate how offshore wind power varies along the Central California Coast over diurnal and seasonal time scales, which is critical for reliability and functionality of the grid system. We find that offshore wind power in this region peaks during evening hours across all seasons and maximizes in spring and summer. The timing of peak offshore wind power production better aligns with that of peak demand across California than solar and land-based wind power production, …
Microwave Solventless Synthesis Of Meso-Tetrakis (Pentafluorophenyl)Poprphyrin (Tppf20) And Tris(Pentafluorophenyl))Corrole [Chemistry], Sunaina Singh
Microwave Solventless Synthesis Of Meso-Tetrakis (Pentafluorophenyl)Poprphyrin (Tppf20) And Tris(Pentafluorophenyl))Corrole [Chemistry], Sunaina Singh
Open Educational Resources
Organic chemistry is a two-semester course (Organic Chemistry I, SCC 251 and Organic Chemistry II, SCC 252) required for majors in Biology. The SCC 251 course has been designated for the Integrative Learning Core Competency as well the Digital Communication Ability. This course emphasizes the synthesis, structure, reactivity, and mechanisms of reaction of organic compounds. Laboratory stresses various organic synthetic and analytic techniques (distillation, extraction, chromatography and spectroscopy).
This lab provided an opportunity for students to go deeper with the chemistry content by correlating to the concepts they learned in General Chemistry courses such as Valence shell electron pair repulsion …
Titration Of A Newtown Creek Environmental Water Sample To Determine The Amount Of Chloride Ions [Chemistry], Kevin Mark
Titration Of A Newtown Creek Environmental Water Sample To Determine The Amount Of Chloride Ions [Chemistry], Kevin Mark
Open Educational Resources
Main Course Learning Objectives:
The General Chemistry 1 (SCC 201) course has multiple course learning objectives, which articulate key introductory chemistry concepts that all STEM students should possess. In particular, the Newtown Creek titration experiment aligns with SCC 201 learning objectives of:
- Demonstrate an appreciation of the role of chemistry in various aspects of life
- Perform basic laboratory skills such as the proper execution of titration techniques
- Describe and explain the fundamental chemistry concept of solution concentration
- Analyze and represent experimental data in tables and graphs, interpret experimental results and write laboratory reports
In the SCC 201 laboratory, students are …
Potential Restoration Methods Of Native Fish In The Clinch And Powell Rivers, Hartley Thacker
Potential Restoration Methods Of Native Fish In The Clinch And Powell Rivers, Hartley Thacker
Fall Showcase for Research and Creative Inquiry
This proposal uses citizen science to attempt to restore native fish populations in southwestern Virginia and the Tennessee River Valley.
Reorganization Of Surviving Mammal Communities After The End-Pleistocene Megafaunal Extinction, Anikó B. Tóth, S. Kathleen Lyons, W. Andrew Barr, Anna K. Behrensmeyer, Jessica L. Blois, René Bobe, Matt Davis, Andrew Du, Jussi T. Eronen, J. Tyler Faith, Danielle Fraser, Nicholas J. Gotelli, Gary R. Graves, Advait M. Jukar, Joshua H. Miller, Silvia Pineda-Munoz, Laura C. Soul, Amelia Villaseñor, John Alroy
Reorganization Of Surviving Mammal Communities After The End-Pleistocene Megafaunal Extinction, Anikó B. Tóth, S. Kathleen Lyons, W. Andrew Barr, Anna K. Behrensmeyer, Jessica L. Blois, René Bobe, Matt Davis, Andrew Du, Jussi T. Eronen, J. Tyler Faith, Danielle Fraser, Nicholas J. Gotelli, Gary R. Graves, Advait M. Jukar, Joshua H. Miller, Silvia Pineda-Munoz, Laura C. Soul, Amelia Villaseñor, John Alroy
School of Biological Sciences: Faculty Publications
Large mammals are at high risk of extinction globally. To understand the consequences of their demise for community assembly, we tracked community structure through the end- Pleistocene megafaunal extinction in North America.We decomposed the effects of biotic and abiotic factors by analyzing co-occurrence within the mutual ranges of species pairs. Although shifting climate drove an increase in niche overlap, co-occurrence decreased, signaling shifts in biotic interactions. Furthermore, the effect of abiotic factors on cooccurrence remained constant over time while the effect of biotic factors decreased. Biotic factors apparently played a key role in continental-scale community assembly before the extinctions. Specifically, …
Shifts In Plant Functional Composition Following Long-Term Drought In Grasslands, Robert J. Griffin‐Nolan, Dana M. Blumenthal, Scott L. Collins, Timothy E. Farkas, Ava M. Hoffman, Kevin E. Mueller, Troy W. Ocheltree, Melinda D. Smith, Kenneth D. Whitney, Alan K. Knapp
Shifts In Plant Functional Composition Following Long-Term Drought In Grasslands, Robert J. Griffin‐Nolan, Dana M. Blumenthal, Scott L. Collins, Timothy E. Farkas, Ava M. Hoffman, Kevin E. Mueller, Troy W. Ocheltree, Melinda D. Smith, Kenneth D. Whitney, Alan K. Knapp
Biological, Geological, and Environmental Faculty Publications
1. Plant traits can provide unique insights into plant performance at the community scale. Functional composition, defined by both functional diversity and community-weighted trait means (CWMs), can affect the stability of above-ground net primary production (ANPP) in response to climate extremes. Further complexity arises, however, when functional composition itself responds to environmental change. The duration of climate extremes, such as drought, is expected to increase with rising global temperatures; thus, understanding the impacts of long-term drought on functional composition and the corresponding effect that has on ecosystem function could improve predictions of ecosystem sensitivity to climate change.
2. We experimentally …
A Comparison Of The Trojan Y Chromosome Strategy To Harvesting Models For Eradication Of Non-Native Species, Jingjing Lyu, Pamela J. Schofield, Kristen M. Reaver, Matthew Beauregard, Rana D. Parshad
A Comparison Of The Trojan Y Chromosome Strategy To Harvesting Models For Eradication Of Non-Native Species, Jingjing Lyu, Pamela J. Schofield, Kristen M. Reaver, Matthew Beauregard, Rana D. Parshad
Faculty Publications
The Trojan Y Chromosome Strategy (TYC) is a promising eradication method for biological control of non-native species. The strategy works by manipulating the sex ratio of a population through the introduction of supermales that guarantee male offspring. In the current manuscript, we compare the TYC method with a pure harvesting strategy. We also analyze a hybrid harvesting model that mirrors the TYC strategy. The dynamic analysis leads to results on stability of solutions and bifurcations of the model. Several conclusions about the different strategies are established via optimal control methods. In particular, the results affirm that either a pure harvesting …
Neuro And Hepatic Toxicological Profile Of (S)-2,4-Diaminobutanoic Acid In Embryonic, Adolescent And Adult Zebrafish, Rosa-Maria Ferraiuolo, Daniel Meister, Dominique Leckie, Jonathan Franke, Lisa A. Porter, John F. Trant
Neuro And Hepatic Toxicological Profile Of (S)-2,4-Diaminobutanoic Acid In Embryonic, Adolescent And Adult Zebrafish, Rosa-Maria Ferraiuolo, Daniel Meister, Dominique Leckie, Jonathan Franke, Lisa A. Porter, John F. Trant
Chemistry and Biochemistry Publications
(S)-2,4-Diaminobutanoic acid (DABA) is a noncanonical amino acid often co-produced by cyanobacteria along with β-N-methylamino-l-alanine (BMAA) in algal blooms. Although BMAA is a well-established neurotoxin, the toxicity of DABA remains unclear. As part of our development of biocompatible materials, we wish to make use of DABA as both a building block and as the end-product of enzymatically-induced depolymerization; however, if it is toxic at very low concentrations, this would not be possible. We examined the toxicity of DABA using both in vivo embryonic and adult zebrafish models. At higher sub-lethal concentrations (700 µM), the fish demonstrated early …
Expanding Beyond Carnivores To Improve Livestock Protection And Conservation, Shari L. Rodriguez, Christie Sampson
Expanding Beyond Carnivores To Improve Livestock Protection And Conservation, Shari L. Rodriguez, Christie Sampson
Publications
Promoting human–wildlife coexistence is critical to the long-term conservation of many wild animal species that come into conflict with humans. Loss of livestock to carnivore species (e.g., lions, tigers, wolves) is a well-documented occurrence and the focus of mitigation strategies around the world. One area that has received little research is the impact of noncarnivores on livestock. Both African and Asian elephant species are known to cause livestock injuries and deaths. Livestock owners within elephant ranges perceive elephants as a risk to their livestock, which may reduce their tolerance towards elephants and jeopardize conservation efforts in the area. Though feral …
Adaptive Responses Of Animals To Climate Change Are Most Likely Insufficient, Viktoriia Radchuk, Thomas Reed, Céline Teplitsky, Martijn Van De Pol, Anne Charmantier, Christopher Hassall, Peter Adamík, Frank Adriaensen, Markus P. Ahola, Karl S. Berg
Adaptive Responses Of Animals To Climate Change Are Most Likely Insufficient, Viktoriia Radchuk, Thomas Reed, Céline Teplitsky, Martijn Van De Pol, Anne Charmantier, Christopher Hassall, Peter Adamík, Frank Adriaensen, Markus P. Ahola, Karl S. Berg
Biology Faculty Publications and Presentations
Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e. whether observed trait changes are adaptive. Here we reviewed 10,090 abstracts and extracted data from 71 studies reported in 58 relevant publications, to assess quantitatively whether phenotypic trait changes associated with climate change are adaptive in animals. A meta-analysis focussing on birds, the taxon best represented in our dataset, suggests that global warming has not systematically affected morphological traits, but has advanced phenological traits. We demonstrate that these advances are adaptive …
Large And Small Data Blow-Up Solutions In The Trojan Y Chromosome Model, Rana D. Parshad, Matthew Beauregard, Eric M. Takyi, Thomas Griffin, Landrey Bobo
Large And Small Data Blow-Up Solutions In The Trojan Y Chromosome Model, Rana D. Parshad, Matthew Beauregard, Eric M. Takyi, Thomas Griffin, Landrey Bobo
Faculty Publications
The Trojan Y Chromosome Strategy (TYC) is an extremely well investigated biological control method for controlling invasive populations with an XX-XY sex determinism. In [35, 36] various dynamical properties of the system are analyzed, including well posedness, boundedness of solutions, and conditions for extinction or recovery. These results are derived under the assumption of positive solutions. In the current manuscript, we show that if the introduction rate of trojan fish is zero, under certain large data assumptions, negative solutions are possible for the male population, which in turn can lead to finite time blow-up in the female and male populations. …
Coral Reef Change Detection In Remote Pacific Islands Using Support Vector Machine Classifiers, Justin J. Gapper, Hesham El-Askary, Erik Linstead, Thomas Piechota
Coral Reef Change Detection In Remote Pacific Islands Using Support Vector Machine Classifiers, Justin J. Gapper, Hesham El-Askary, Erik Linstead, Thomas Piechota
Mathematics, Physics, and Computer Science Faculty Articles and Research
Despite the abundance of research on coral reef change detection, few studies have been conducted to assess the spatial generalization principles of a live coral cover classifier trained using remote sensing data from multiple locations. The aim of this study is to develop a machine learning classifier for coral dominated benthic cover-type class (CDBCTC) based on ground truth observations and Landsat images, evaluate the performance of this classifier when tested against new data, then deploy the classifier to perform CDBCTC change analysis of multiple locations. The proposed framework includes image calibration, support vector machine (SVM) training and tuning, statistical assessment …
Draft Genome Sequences Of Three Monokaryotic Isolates Of The White-Rot Basidiomycete Fungus Dichomitus Squalens, Sara Casado López, Mao Peng, Paul Daly, Bill Andreopoulos, Jasmyn Pangilinan, Anna Lipzen, Robert Riley, Steven Ahrendt, Vivian Ng, Kerrie Barry, Chris Daum, Igor Grigoriev, Kristiina Hildén, Miia Mäkelä, Ronald De Vries
Draft Genome Sequences Of Three Monokaryotic Isolates Of The White-Rot Basidiomycete Fungus Dichomitus Squalens, Sara Casado López, Mao Peng, Paul Daly, Bill Andreopoulos, Jasmyn Pangilinan, Anna Lipzen, Robert Riley, Steven Ahrendt, Vivian Ng, Kerrie Barry, Chris Daum, Igor Grigoriev, Kristiina Hildén, Miia Mäkelä, Ronald De Vries
Faculty Publications, Computer Science
Here, we report the draft genome sequences of three isolates of the wood-decaying white-rot basidiomycete fungus Dichomitus squalens. The genomes of these monokaryons were sequenced to provide more information on the intraspecies genomic diversity of this fungus and were compared to the previously sequenced genome of D. squalens LYAD-421 SS1.
Predicting Habitat Choice After Rapid Environmental Change, Philip H. Crowley, Pete C. Trimmer, Orr Spiegel, Sean M. Ehlman, William S. Cuello, Andrew Sih
Predicting Habitat Choice After Rapid Environmental Change, Philip H. Crowley, Pete C. Trimmer, Orr Spiegel, Sean M. Ehlman, William S. Cuello, Andrew Sih
Biology Faculty Publications
Decisions made while searching for settlement sites (e.g., nesting, oviposition) often have major fitness implications. Despite numerous case studies, we lack theory to explain why some species are thriving while others are making poor habitat choices after environmental change. We develop a model to predict (1) which kinds of environmental change have larger, negative effects on fitness, (2) how evolutionary history affects susceptibility to environmental change, and (3) how much lost fitness can be recovered via readjustment after environmental change. We model the common scenario where animals search an otherwise inhospitable matrix, encountering habitats of varying quality and settling when …
Trans-Cinnamic Acid-Induced Leaf Expansion Involves An Auxin-Independent Component, Jasmina Kurepa, Jan A. Smalle
Trans-Cinnamic Acid-Induced Leaf Expansion Involves An Auxin-Independent Component, Jasmina Kurepa, Jan A. Smalle
Plant and Soil Sciences Faculty Publications
The phenylpropanoid pathway, the source of a large array of compounds with diverse functions, starts with the synthesis of trans-cinnamic acid (t-CA) that is converted by cinnamate-4-hydroxylase (C4H) into p-coumaric acid. We have recently shown that in Arabidopsis, exogenous t-CA promotes leaf growth by increasing cell expansion and that this response requires auxin signaling. We have also shown that cell expansion is increased in C4H loss-of-function mutants. Here we provide further evidence that leaf growth is enhanced by either t-CA or a t-CA derivative that accumulates upstream of C4H. We also show that …
Reduced-Impact Logging For Climate Change Mitigation (Ril-C) Can Halve Selective Logging Emissions From Tropical Forests, Anand Roopsind
Reduced-Impact Logging For Climate Change Mitigation (Ril-C) Can Halve Selective Logging Emissions From Tropical Forests, Anand Roopsind
Biology Faculty Publications and Presentations
Selective logging causes at least half of the emissions from tropical forest degradation. Reduced-impact logging for climate (RIL-C) is proposed as a way to maintain timber production while minimizing forest damage. Here we synthesize data from 61 coordinated field-based surveys of logging impacts in seven countries across the tropics. We estimate that tropical selective logging emitted 834 Tg CO2 in 2015, 6% of total tropical greenhouse gas emissions. Felling, hauling, and skidding caused 59%, 31%, and 10% of these emissions, respectively. We suggest that RIL-C incentive programs consider a feasible target carbon impact factor of 2.3 Mg emitted per …
Effects Of Increased Precipitation On The Life History Of Spring- And Autumn-Germinated Plants Of The Cold Desert Annual Erodium Oxyrhynchum (Geraniaceae), Yanfeng Chen, Xiang Shi, Lingwei Zhang, Jerry M. Baskin, Carol C. Baskin, Huiliang Liu, Daoyuan Zhang
Effects Of Increased Precipitation On The Life History Of Spring- And Autumn-Germinated Plants Of The Cold Desert Annual Erodium Oxyrhynchum (Geraniaceae), Yanfeng Chen, Xiang Shi, Lingwei Zhang, Jerry M. Baskin, Carol C. Baskin, Huiliang Liu, Daoyuan Zhang
Biology Faculty Publications
Future increased precipitation in cold desert ecosystems may impact annual/ephemeral plant species that germinate in both spring and autumn. Our primary aim was to compare the life history characteristics of plants from spring-germinating (SG) and autumn-germinating (AG) seeds of Erodium oxyrhynchum. Plants in field plots with simulated increases in precipitation of 0, 30 and 50 % in spring and summer were monitored to determine seedling survival, phenology, plant size, seed production and biomass accumulation and allocation. Germination characteristics were determined in the laboratory for seeds produced by plants in all increased precipitation treatments. Increased precipitation in spring significantly improved survival …
The Effects Of Organic And Inorganic Nanoparticles On Bacterial Deactivation, Lauren Cooper
The Effects Of Organic And Inorganic Nanoparticles On Bacterial Deactivation, Lauren Cooper
Mahurin Honors College Capstone Experience/Thesis Projects
Antibacterial resistance is one of the greatest problems in modern medicine, as healthcare professionals are experiencing more and more difficulty in providing effective care. As such, alternative methods of treatment are needed in order to overcome this issue. One recently proposed method of alternative treatment is photodynamic therapy. Photodynamic therapy is a light-based method of treatment that utilizes (1) a photosensitizing agent, (2) light, (3) produced oxygen species. When the photosensitizing agent is injected into an infected region of interest and then irradiated with a certain wavelength of light, the agent is photoactivated and begins to produce harmful forms of …
Putting The I In Science, Naomi Kirkvold
Putting The I In Science, Naomi Kirkvold
Honors Expanded Learning Clubs
This club gets kids interested in science in ways that they may not have experienced in a classroom by doing weekly experiments.
Optimal Control Theory And Estimation Of Parameters In A Differential Equation Model For Patients With Lupus, Peter Agaba
Optimal Control Theory And Estimation Of Parameters In A Differential Equation Model For Patients With Lupus, Peter Agaba
Masters Theses & Specialist Projects
System Lupus Erythematosus (SLE) is a chronic inflammatory autoimmune disorder that affects many parts of the body including skin, joints, kidneys, brains and other organs. Lupus Nephritis (LN) is a disease caused by SLE. Given the complexity of LN, we establish an optimal treatment strategy based on a previously developed mathematical model.For our thesis work, the model variables are: Immune Complexes (I), Pro-inflammatory mediators (P), Damaged tissue (D), and Anti-inflammatory mediators (A). The analysis in this research project focuses on analyzing therapeutic strategies to control damage using both parameter estimation techniques (integration of data to quantify any uncertainties associated with …
Ultra-Strong Long-Chain Polyamide Elastomers With Programmable Supramolecular Interactions And Oriented Crystalline Microstructures, Lingzhi Song, Tianyu Zhu, Liang Yuan, Jiangjun Zhou, Yaqiong Zhang, Zhongkai Wang, Chuanbing Tang
Ultra-Strong Long-Chain Polyamide Elastomers With Programmable Supramolecular Interactions And Oriented Crystalline Microstructures, Lingzhi Song, Tianyu Zhu, Liang Yuan, Jiangjun Zhou, Yaqiong Zhang, Zhongkai Wang, Chuanbing Tang
Faculty Publications
Polyamides are one of the most important polymers. Long-chain aliphatic polyamides could bridge the gap between traditional polyamides and polyethylenes. Here we report an approach to preparing sustainable ultra-strong elastomers from biomass-derived long-chain polyamides by thiol-ene addition copolymerization with diamide diene monomers. The pendant polar hydroxyl and non-polar butyrate groups between amides allow controlled programming of supramolecular hydrogen bonding and facile tuning of crystallization of polymer chains. The presence of thioether groups on the main chain can further induce metal–ligand coordination (cuprous-thioether). Unidirectional step-cycle tensile deformation has been applied to these polyamides and significantly enhances tensile strength to over 210 …
How Acidic Sediments And Seawater Affect Interactive Effects Of Predation On Survival, Growth, And Recruitment Of Wild And Cultured Soft-Shell Clams, Mya Arenaria L., Along A Tidal Gradient At Two Intertidal Sites In Eastern Maine, Brian F. Beal, William Otto
How Acidic Sediments And Seawater Affect Interactive Effects Of Predation On Survival, Growth, And Recruitment Of Wild And Cultured Soft-Shell Clams, Mya Arenaria L., Along A Tidal Gradient At Two Intertidal Sites In Eastern Maine, Brian F. Beal, William Otto
Miscellaneous Publications
No abstract provided.
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 …
The Accelerating Influence Of Humans On Mammalian Macroecological Patterns Over The Late Quaternary, Felisa A. Smith, Rosemary E. Elliott Smith, S. Kathleen Lyons, Jonathan L. Payne, Amelia Villaseñor
The Accelerating Influence Of Humans On Mammalian Macroecological Patterns Over The Late Quaternary, Felisa A. Smith, Rosemary E. Elliott Smith, S. Kathleen Lyons, Jonathan L. Payne, Amelia Villaseñor
School of Biological Sciences: Faculty Publications
The transition of hominins to a largely meat-based diet ~1.8 million years ago led to the exploitation of other mammals for food and resources. As hominins, particularly archaic and modern humans, became increasingly abundant and dispersed across the globe, a temporally and spatially transgressive extinction of large-bodied mammals followed; the degree of selectivity was unprecedented in the Cenozoic fossil record. Today, most remaining large-bodied mammal species are confined to Africa, where they coevolved with hominins. Here, using a comprehensive global dataset of mammal distribution, life history and ecology, we examine the consequences of “body size downgrading” of mammals over the …
Restoration Of Aberrant Mtor Signaling By Intranasal Rapamycin Reduces Oxidative Damage: Focus On Hne-Modified Proteins In A Mouse Model Of Down Syndrome, Fabio Di Domenico, Antonella Tramutola, Eugenio Barone, Chiara Lanzillotta, Olivia Defever, Andrea Arena, Ilaria Zuliani, Cesira Foppoli, Federica Iavarone, Federica Vincenzoni, Massimo Castagnola, D. Allan Butterfield, Marzia Perluigi
Restoration Of Aberrant Mtor Signaling By Intranasal Rapamycin Reduces Oxidative Damage: Focus On Hne-Modified Proteins In A Mouse Model Of Down Syndrome, Fabio Di Domenico, Antonella Tramutola, Eugenio Barone, Chiara Lanzillotta, Olivia Defever, Andrea Arena, Ilaria Zuliani, Cesira Foppoli, Federica Iavarone, Federica Vincenzoni, Massimo Castagnola, D. Allan Butterfield, Marzia Perluigi
Chemistry Faculty Publications
Increasing evidences support the notion that the impairment of intracellular degradative machinery is responsible for the accumulation of oxidized/misfolded proteins that ultimately results in the deposition of protein aggregates. These events are key pathological aspects of “protein misfolding diseases”, including Alzheimer disease (AD). Interestingly, Down syndrome (DS) neuropathology shares many features with AD, such as the deposition of both amyloid plaques and neurofibrillary tangles. Studies from our group and others demonstrated, in DS brain, the dysfunction of both proteasome and autophagy degradative systems, coupled with increased oxidative damage. Further, we observed the aberrant increase of mTOR signaling and of its …
Seasonal Origins Of Soil Water Used By Trees, Scott T. Allen, James W. Kirchner, Sabine Braun, Rolf T. W. Siegwolf, Gregory R. Goldsmith
Seasonal Origins Of Soil Water Used By Trees, Scott T. Allen, James W. Kirchner, Sabine Braun, Rolf T. W. Siegwolf, Gregory R. Goldsmith
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Rain recharges soil water storages and either percolates downward into aquifers and streams or is returned to the atmosphere through evapotranspiration. Although it is commonly assumed that summer rainfall recharges plant-available water during the growing season, the seasonal origins of water used by plants have not been systematically explored. We characterize the seasonal origins of waters in soils and trees by comparing their midsummer isotopic signatures (δ2H) to seasonal isotopic cycles in precipitation, using a new seasonal origin index. Across 182 Swiss forest sites, xylem water isotopic signatures show that summer rain was not the predominant water source …
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 …