Physical Sciences and Mathematics Commons^™

Enhancing Digestibility And Ethanol Yield Of Populus Wood Via Expression Of An Engineered Monolignol 4-O-Methyltransferase, Yuanheng Cai, Kewei Zhang, Hoon Kim, Guichuan Hou, Xuebin Zhang, Huijun Yang, Huan Feng, Lisa Miller, John Ralph, Chang-Jun Liu

Huan Feng

Producing cellulosic biofuels and bio-based chemicals from woody biomass is impeded by the presence of lignin polymer in the plant cell wall. Manipulating the monolignol biosynthetic pathway offers a promising approach to improved processability, but often impairs plant growth and development. Here, we show that expressing an engineered 4-O-methyltransferase that chemically modifies the phenolic moiety of lignin monomeric precursors, thus preventing their incorporation into the lignin polymer, substantially alters hybrid aspens’ lignin content and structure. Woody biomass derived from the transgenic aspens shows a 62% increase in the release of simple sugars and up to a 49% increase in the …

Potential Economic Impacts Of Allocating More Land For Bioenergy Biomass Production In Virginia, Thomas O. Ochuodho, Janaki R. R. Alavalapati, Pankaj Lal, Domena A. Agyeman, Bernabas Wolde, Pralhad Burli

Pankaj Lal

The growing attention to renewable energy and rural development has created greater demand for production of biomass feedstock for bioenergy. However, forest growth rates and the amount of land in most existing forests may not be sufficient to sustainably supply the forest biomass required to support existing forest products industries and the expanding bioenergy industry. Additionally, concerns about agricultural land use competition have dampened expansion of biomass production on agricultural land base. One of the ways to meet the growing forest biomass feedstock demand for bioenergy production is by allocating currently marginal non-forested land for growing bioenergy feedstocks. In Virginia, …

The Economic Impacts Of Blackbird (Icteridae) Damage To Sunflower In The Usa, Karina Ernst, Julie Elser, George Linz, Hans Kandel, Jason Holderieath, Samantha Degroot, Steven Shwiff, Stephanie Shwiff

Jason Holderieath

BACKGROUND: Blackbird (Icteridae) damage to ripening sunflower (Helianthus annuus L.) has been a persistent economic issue in the USA for the last five decades. To quantify losses, we surveyed blackbird damage from 2001 to 2013 (excluding 2004) to physiologically mature sunflower in eight states: North Dakota, South Dakota, Texas, Nebraska, Minnesota, Colorado, Kansas, and Vermont.

RESULTS:We pooled data gathered during the most recent 5 years (2009 to 2013) of the survey and found losses averaged $US2.5 million and $US11.3 million for confectionery and oilseed hybrids, respectively. Three states, North Dakota, South Dakota, and Nebraska, had sufficient acreage and bird damage …

United States Midwest Soil And Weather Conditions Influence Anaerobic Potentially Mineralizable Nitrogen, Jason D. Clark, Kristen S. Veum, Fabian G. Fernandez, James J. Camberato, Paul R. Carter, Richard B. Ferguson, David W. Franzen, Daniel E. Kaiser, Newell R. Kitchen, Carrie A.M. Laboski, Emerson D. Nafziger, John E. Sawyer, John F. Shanahan

Jason Clark

Nitrogen provided to crops through mineralization is an important factor in N management guidelines. Understanding of the interactive effects of soil and weather conditions on N mineralization needs to be improved. Relationships between anaerobic potentially mineralizable N (PMN_an) and soil and weather conditions were evaluated under the contrasting climates of eight US Midwestern states. Soil was sampled (0–30 cm) for PMN_an analysis before pre-plant N application (PP_0N) and at the V5 development stage from the pre-plant 0 (V5_0N) and 180 kg N ha⁻¹ (V5_180N) rates and incubated for 7, 14, …

Automated Monitoring Of Behaviour In Zebrafish After Invasive Procedures, Anthony G. Deakin, Jonathan Buckley, Hamzah S. Alzu'bi, Andrew R. Cossins, Joseph W. Spencer, Waleed Al'nuaimy, Iain S. Young, Jack S. Thomson, Lynne U. Sneddon

Lynne Sneddon, PhD

Fish are used in a variety of experimental contexts often in high numbers. To maintain their welfare and ensure valid results during invasive procedures it is vital that we can detect subtle changes in behaviour that may allow us to intervene to provide pain-relief. Therefore, an automated method, the Fish Behaviour Index (FBI), was devised and used for testing the impact of laboratory procedures and efficacy of analgesic drugs in the model species, the zebrafish. Cameras with tracking software were used to visually track and quantify female zebrafish behaviour in real time after a number of laboratory procedures including fin …

Synthesis And Evaluation Of Novel Silica Hydride-Based Stationary Phases For Bioanalytical Applications

Seiichiro Watanabe

Taking The Metabolic Pulse Of The World's Coral Reefs, Tyler Cyronak, Andreas J. Andersson, Chris Langdon, Rebecca Albright, Nicholas R. Bates, Ken Caldeira, Renee Carlton, Jorge E. Corredor, Rob B. Dunbar, Ian Enochs, Jonathan Erez, Bradley D. Eyre, Jean-Pierre Gattuso, Dwight Gledhill, Hajime Kayanne, David I. Kline, David A. Koweek, Coulson Lantz, Boaz Lazar, Derek Manzello, Ashly Mcmahon, Melissa Melendez, Heather N. Page, Isaac R. Santos, Kai G. Schulz, Emily Shaw, Jacob Silverman, Atsushi Suzuki, Lida Teneva, Atsushi Watanabe, Shoji Yamamoto

Tyler Cyronak

Worldwide, coral reef ecosystems are experiencing increasing pressure from a variety of anthropogenic perturbations including ocean warming and acidification, increased sedimentation, eutrophication, and overfishing, which could shift reefs to a condition of net calcium carbonate (CaCO3) dissolution and erosion. Herein, we determine the net calcification potential and the relative balance of net organic carbon metabolism (net community production; NCP) and net inorganic carbon metabolism (net community calcification; NCC) within 23 coral reef locations across the globe. In light of these results, we consider the suitability of using these two metrics developed from total alkalinity (TA) and dissolved inorganic carbon (DIC) …

Temperature-Induced Viral Resistance In Emiliania Huxleyi (Prymnesiophyceae), B. Jacob Kendrick, Giacomo R. Ditullio, Tyler Cyronak, James M. Fulton, Benjamin A. S. Van Mooy, Kay D. Bidle

Tyler Cyronak

Annual Emiliania huxleyi blooms (along with other coccolithophorid species) play important roles in the global carbon and sulfur cycles. E. huxleyi blooms are routinely terminated by large, host-specific dsDNA viruses, (Emiliania huxleyi Viruses; EhVs), making these host-virus interactions a driving force behind their potential impact on global biogeochemical cycles. Given projected increases in sea surface temperature due to climate change, it is imperative to understand the effects of temperature on E. huxleyi’s susceptibility to viral infection and its production of climatically active dimethylated sulfur species (DSS). Here we demonstrate that a 3°C increase in temperature induces EhV-resistant phenotypes …

Nitrous Oxide And Methane Dynamics In A Coral Reef Lagoon Driven By Pore Water Exchange: Insights From Automated High‐Frequency Observations, Chiara O'Reilly, Isaac R. Santos, Tyler Cyronak, Ashly Mcmahon, Damien T. Maher

Tyler Cyronak

Automated cavity ring down spectroscopy was used to make continuous measurements of dissolved methane, nitrous oxide, and carbon dioxide in a coral reef lagoon for 2 weeks (Heron Island, Great Barrier Reef). Radon (²²²Rn) was used to trace the influence of tidally driven pore water exchange on greenhouse gas dynamics. Clear tidal variation was observed for CH₄, which correlated to ²²²Rn in lagoon waters. N2O correlated to ²²²Rn during the day only, which appears to be a response to coupled nitrification‐denitrification in oxic sediments, fueled by nitrate derived from bird guano. The lagoon was …

Permeable Coral Reef Sediment Dissolution Driven By Elevated Pco2 And Pore Water Advection, Tyler Cyronak, Isaac R. Santos, Bradley D. Eyre

Tyler Cyronak

Ocean acidification (OA) is expected to drive the transition of coral reef ecosystems from net calcium carbonate (CaCO₃) precipitating to net dissolving within the next century. Although permeable sediments represent the largest reservoir of CaCO₃ in coral reefs, the dissolution of shallow CaCO₃ sands under future pCO₂ levels has not been measured under natural conditions. In situ, advective chamber incubations under elevated pCO₂ (~800 µatm) shifted the sediments from net precipitating to net dissolving. Pore water advection more than doubled dissolution rates (1.10 g CaCO₃ m⁻² d⁻¹) when compared to …

Hysteresis Between Coral Reef Calcification And The Seawater Aragonite Saturation State, Ashly Mcmahon, Isaac R. Santos, Tyler Cyronak, Bradley D. Eyre

Tyler Cyronak

Some predictions of how ocean acidification (OA) will affect coral reefs assume a linear functional relationship between the ambient seawater aragonite saturation state (Ω_a) and net ecosystem calcification (NEC). We quantified NEC in a healthy coral reef lagoon in the Great Barrier Reef during different times of the day. Our observations revealed a diel hysteresis pattern in the NEC versus Ω_a relationship, with peak NEC rates occurring before the Ω_a peak and relatively steady nighttime NEC in spite of variable Ω_a. Net ecosystem production had stronger correlations with NEC than light, temperature, nutrients, pH, …

Groundwater And Porewater As Major Sources Of Alkalinity To A Fringing Coral Reef Lagoon (Muri Lagoon, Cook Islands), Tyler Cyronak, Isaac R. Santos, Dirk V. Erler, Bradley D. Eyre

Tyler Cyronak

To better predict how ocean acidification will affect coral reefs, it is important to understand how biogeochemical cycles on reefs alter carbonate chemistry over various temporal and spatial scales. This study quantifies the contribution of shallow porewater exchange (as quantified from advective chamber incubations) and fresh groundwater discharge (as traced by ²²²Rn) to total alkalinity (TA) dynamics on a fringing coral reef lagoon along the southern Pacific island of Rarotonga over a tidal and diel cycle. Benthic alkalinity fluxes were affected by the advective circulation of water through permeable sediments, with net daily flux rates of carbonate alkalinity ranging …

Expanding Aquatic Observations Through Recreation, Robert J. W. Brewin, Kieran Hyder, Andreas J. Andersson, Oliver Billson, Philip J. Bresnahan, Thomas G. Brewin, Tyler Cyronak, Giorgio Dall'olmo, Lee De Mora, George Graham, Thomas Jackson, Dionysios E. Raitsos

Tyler Cyronak

Accurate observations of the Earth system are required to understand how our planet is changing and to help manage its resources. The aquatic environment—including lakes, rivers, wetlands, estuaries, coastal and open oceans—is a fundamental component of the Earth system controlling key physical, biological, and chemical processes that allow life to flourish. Yet, this environment is critically undersampled in both time and space. New and cost-effective sampling solutions are urgently needed. Here, we highlight the potential to improve aquatic sampling by tapping into recreation. We draw attention to the vast number of participants that engage in aquatic recreational activities and argue, …

Drivers Of Pco2 Variability In Two Contrasting Coral Reef Lagoons: The Influence Of Submarine Groundwater Discharge, Tyler Cyronak, Isaac R. Santos, Dirk V. Erler, Damien T. Maher, Bradley D. Eyre

Tyler Cyronak

The impact of groundwater on pCO₂ variability was assessed in two coral reef lagoons with distinct drivers of submarine groundwater discharge (SGD). Diel variability of pCO₂ in the two ecosystems was explained by a combination of biological drivers and SGD inputs. In Rarotonga, a South Pacific volcanic island, ²²²Rn‐derived SGD was driven primarily by a steep terrestrial hydraulic gradient, and the water column was influenced by the high pCO₂ (5501 µatm) of the fresh groundwater. In Heron Island, a Great Barrier Reef coral cay, SGD was dominated by seawater recirculation through the sediments …

Enhanced Acidification Of Global Coral Reefs Driven By Regional Biogeochemical Feedbacks, Tyler Cyronak, Kai G. Schulz, Isaac R. Santos, Bradley D. Eyre

Tyler Cyronak

Physical uptake of anthropogenic CO₂ is the dominant driver of ocean acidification (OA) in the open ocean. Due to expected decreases in calcification and increased dissolution of CaCO₃ framework, coral reefs are thought to be highly susceptible to OA. However, biogeochemical processes can influence the pCO₂ and pH of coastal ecosystems on diel and seasonal time scales, potentially modifying the long‐term effects of increasing atmospheric CO₂. By compiling data from the literature and removing the effects of short‐term variability, we show that the average pCO₂ of coral reefs throughout the globe has increased ~3.5‐fold …

Coral Reef Carbonate Chemistry Variability At Different Functional Scales, Yuichiro Takeshita, Tyler Cyronak, Todd R. Martz, Theodor Kindeberg, Andreas J. Andersson

Tyler Cyronak

There is a growing recognition for the need to understand how seawater carbonate chemistry over coral reef environments will change in a high-CO₂ world to better assess the impacts of ocean acidification on these valuable ecosystems. Coral reefs modify overlying water column chemistry through biogeochemical processes such as net community organic carbon production (NCP) and calcification (NCC). However, the relative importance and influence of these processes on seawater carbonate chemistry vary across multiple functional scales (defined here as space, time, and benthic community composition), and have not been fully constrained. Here, we use Bermuda as a case study to …

Comparing Chemistry And Census-Based Estimates Of Net Ecosystem Calcification On A Rim Reef In Bermuda, Travis A. Courtney, Andreas J. Andersson, Nicholas R. Bates, Andrew R. Collins, Tyler Cyronak, Samantha J. De Putron, Bradley D. Eyre, Rebecca Garley, Eric J. Hochberg, Rodney Johnson, Sylvia Musielewicz, Tim J. Noyes, Christopher L. Sabine, Adrienne J. Sutton, Jessy Toncin, Aline Tribollet

Tyler Cyronak

Coral reef net ecosystem calcification (NEC) has decreased for many Caribbean reefs over recent decades primarily due to changes in benthic community composition. Chemistry-based approaches to calculate NEC utilize the drawdown of seawater total alkalinity (TA) combined with residence time to calculate an instantaneous measurement of NEC. Census-based approaches combine annual growth rates with benthic cover and reef structural complexity to estimate NEC occurring over annual timescales. Here, NEC was calculated for Hog Reef in Bermuda using both chemistry and census-based NEC techniques to compare the mass-balance generated by the two methods and identify the dominant biocalcifiers at Hog Reef. …

Antagonistic Effects Of Ocean Acidification And Rising Sea Surface Temperature On The Dissolution Of Coral Reef Carbonate Sediments, Daniel Trnovsky, Laura Stoltenberg, Tyler Cyronak, Bradley D. Eyre

Tyler Cyronak

Increasing atmospheric CO₂ is raising sea surface temperature (SST) and increasing seawater CO₂ concentrations, resulting in a lower oceanic pH (ocean acidification; OA), which is expected to reduce the accretion of coral reef ecosystems. Although sediments comprise most of the calcium carbonate (CaCO₃) within coral reefs, no in situ studies have looked at the combined effects of increased SST and OA on the dissolution of coral reef CaCO₃ sediments. In situ benthic chamber incubations were used to measure dissolution rates in permeable CaCO₃ sands under future OA and SST scenarios in a coral reef …

Closed-Form Probability Distribution Of Number Of Infections At A Given Time In A Stochastic Sis Epidemic Model.Pdf, Michael Otunuga

Olusegun Michael Otunuga

Animal Research, Accountability, Openness And Public Engagement: Report From An International Expert Forum, Elisabeth H. Ormandy, Daniel M. Weary, Katarina Cvek, Mark Fisher, Kathrin Herrmann, Pru Hobson-West, Michael Mcdonald, William Milsom, Margaret Rose, Andrew Rowan, Joanne Zurlo, Marina A.G. Von Keyserlingk

Andrew N. Rowan, DPhil

In November 2013, a group of international experts in animal research policy (n = 11) gathered in Vancouver, Canada, to discuss openness and accountability in animal research. The primary objective was to bring together participants from various jurisdictions (United States, Sweden, Australia, New Zealand, Germany, Canada and the United Kingdom) to share practices regarding the governance of animals used in research, testing and education, with emphasis on the governance process followed, the methods of community engagement, and the balance of openness versus confidentiality. During the forum, participants came to a broad consensus on the need for: (a) evidence-based metrics to …

Predicting Economic Optimal Nitrogen Rate With The Anaerobic Potentially Mineralizable Nitrogen Test, Jason D. Clark, Fabián G. Fernández, Kristen S. Veum, James J. Camberato, Paul R. Carter, Richard B. Ferguson, David W. Franzen, Daniel E. Kaiser, Newell R. Kitchen, Carrie A. M. Laboski, Emerson D. Nafziger, Carl J. Rosen, John E. Sawyer, John F. Shanahan

John E. Sawyer

Estimates of mineralizable N with the anaerobic potentially mineralizable N (PMN_an) test could improve predictions of corn (Zea mays L.) economic optimal N rate (EONR). A study across eight US midwestern states was conducted to quantify the predictability of EONR for single and split N applications by PMN_an. Treatment factors included different soil sample timings (pre-plant and V5 development stage), planting N rates (0 and 180 kg N ha⁻¹), and incubation lengths (7, 14, and 28 d) with and without initial soil NH₄–N included with PMN_an. Soil was sampled …

United States Midwest Soil And Weather Conditions Influence Anaerobic Potentially Mineralizable Nitrogen, Jason D. Clark, Kristen S. Veum, Fabián G. Fernández, James J. Camberato, Paul R. Carter, Richard B. Ferguson, David W. Franzen, Daniel E. Kaiser, Newell R. Kitchen, Carrie A. M. Laboski, Emerson D. Nafziger, Carl J. Rosen, John E. Sawyer, John F. Shanahan

John E. Sawyer

Nitrogen provided to crops through mineralization is an important factor in N management guidelines. Understanding of the interactive effects of soil and weather conditions on N mineralization needs to be improved. Relationships between anaerobic potentially mineralizable N (PMN_an) and soil and weather conditions were evaluated under the contrasting climates of eight US Midwestern states. Soil was sampled (0–30 cm) for PMN_an analysis before pre-plant N application (PP_0N) and at the V5 development stage from the pre-plant 0 (V5_0N) and 180 kg N ha⁻¹ (V5_180N) rates and incubated for 7, 14, …

Wildlife Conservation, Zoos And Animal Protection: A Strategic Analysis, Andrew N. Rowan

Andrew N. Rowan, DPhil

The publication consists of the proceedings of a workshop, sponsored by the Gilman Foundation, and held in April of 1994 at the White Oak Conservation Center in Florida. About thirty participants were invited from zoos, animal protection groups and academic institutions to discuss concepts such as wild, captive and tame; animal well-being in the wild and in zoos; and protecting individuals versus conserving populations. In order to maximize the time engaged in discussion, several individuals were identified to prepare target articles which were distributed to all participants before the meeting. These articles form the main chapters in this book. Other …

The Relationship Of Animal Protection Interests To Animal Damage Management: Historic Paths, Contemporary Concerns And The Uncertain Future, John Hadidian

John Hadidian, PhD

More than a decade ago Schmidt (1989) called for consideration of animal welfare to become a "firstorder" decision rule in wildlife management concerns, including animal damage control. Although there has been movement in that direction, this clearly has not yet come to pass. This paper takes a brief look at the interests we call animal damage management, animal welfare and protection, animal rights, and environmentalism in order to speculate about their shared concerns and the uncertain future before them. Since animal damage and the management of that damage cannot be abstracted from the environmental context in which they occur, this …

“Everyday” Knowledge And A New Paradigm Of Animal Research, David Fraser, Jeffrey M. Spooner, Catherine A. Schuppli

David Fraser, PhD

Commentary on Marino and Allen (2017) The Psychology of Cows

Marine Invertebrates: Communities At Risk, Jennifer A. Mather

Jennifer Mather, PhD

Our definition of the word ‘animal’ centers on vertebrates, yet 99% of the animals on the planet are invertebrates, about which we know little. In addition, although the Census of Marine Life (COML.org) has recently conducted an extensive audit of marine ecosystems, we still do not understand much about the animals of the seas. Surveys of the best-known ecosystems, in which invertebrate populations often play a key role, show that the invertebrate populations are affected by human impact. Coral animals are the foundation of coral reef systems, which are estimated to contain 30% of the species in the ocean. Physical …

Acute Toxicity Testing Without Animals: More Scientific And Less Of A Gamble, Gillian R. Langley

Gill Langley, PhD

In this report, we argue specifically that acute toxicity data should not be sought from animal tests. The underlying principle of such tests on rats and mice is that the results can be effectively extrapolated to humans. In fact, after nearly 80 years of use of these tests, the predictivity of rodent data for human acute toxic effects has been disputed but never proven.

"Being Mindful" And Becoming A "Harmony Worker" During Unsettling Times.Docx

Carroy U "Cuf" Ferguson, Ph.D.

Harvesting Fertilized Rye Cover Crop: Simulated Revenue, Net Energy, And Drainage Nitrogen Loss, R. W. Malone, J. F. Obrycki, Douglas L. Karlen, T. C. Kaspar, D. B. Jaynes, T. B. Parkin, S. H. Lence, G. W. Feyereisen, Q. X. Fang, T. L. Richard, K. Gillette

Douglas L Karlen

Harvesting fertilized rye (Secale cereale L.) cover crop has been suggested as a method to increase producer revenue and biofuel feedstock production, but drainage N loss impacts are currently unknown. Using the tested Root Zone Water Quality Model (RZWQM) across several N rates, spring application of 120 kg N ha^-1 prior to winter rye harvest reduced drainage N loss by 54% compared with no cover crop and by 18% compared with planted rye that was neither fertilized nor harvested. Estimates of producer revenue and net energy were also positive, with 8.3 Mg ha^-1 of harvested rye biomass. …

Impact Of Biochar Amendments On The Quality Of A Typical Midwestern Agricultural Soil, David A. Laird, Pierce Fleming, Dedrick D. Davis, Robert Horton, Baiqun Wang, Douglas L. Karlen

Douglas L Karlen

Biochar, a co-product of thermochemical conversion of lignocellulosic materials into advanced biofuels, may be used as a soil amendment to enhance the sustainability of biomass harvesting. We investigated the impact of biochar amendments (0, 5, 10, and 20 g-biochar kg− 1 soil) on the quality of a Clarion soil (Mesic Typic Hapludolls), collected (0–15 cm) in Boone County, Iowa. Repacked soil columns were incubated for 500 days at 25 °C and 80% relative humidity. On week 12, 5 g of dried and ground swine manure was incorporated into the upper 3 cm of soil for half of the columns. Once …