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Faculty Publications

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Full-Text Articles in Life Sciences

First Data On Aquaculture Of The Tripletail, Lobotes Surinamensis, A Promising Candidate Species For U.S. Marine Aquaculture, Eric Saillant, Nicholas Adams, Jason T. Lemus, James S. Franks, Yonathan Zohar, John Stubblefield, Christopher Manley Jun 2021

First Data On Aquaculture Of The Tripletail, Lobotes Surinamensis, A Promising Candidate Species For U.S. Marine Aquaculture, Eric Saillant, Nicholas Adams, Jason T. Lemus, James S. Franks, Yonathan Zohar, John Stubblefield, Christopher Manley

Faculty Publications

The Tripletail, Lobotes surinamensis, is a warm-water pelagic fish that is increasingly targeted by U.S. anglers. The superior quality of Tripletail flesh coupled with the lack of domestic commercial fisheries stimulated interests to develop aquaculture of this species. In this work, photo-thermal conditioning of captive-held broodstocks promoted maturation in females, but spontaneous spawning was not observed. GnRHa slow-release implants induced ovulation in late vitellogenic females but fertility remained below 10% when GnRHa was administered alone. However, spawns with high fertility (up to 85%) were obtained when a dopamine antagonist was administered in conjunction with GnRHa implants indicating dopamine inhibition …


Genomic Gc Content Drifts Downward In Most Bacterial Genomes, Ely Bert May 2021

Genomic Gc Content Drifts Downward In Most Bacterial Genomes, Ely Bert

Faculty Publications

In every kingdom of life, GC->AT transitions occur more frequently than any other type of mutation due to the spontaneous deamination of cytidine. In eukaryotic genomes, this slow loss of GC base pairs is counteracted by biased gene conversion which increases genomic GC content as part of the recombination process. However, this type of biased gene conversion has not been observed in bacterial genomes, so we hypothesized that GC->AT transitions cause a reduction of genomic GC content in prokaryotic genomes on an evolutionary time scale. To test this hypothesis, we used a phylogenetic approach to analyze triplets of …


Genomic Gc Content Drifts Downward In Most Bacterial Genomes, Bert Ely May 2021

Genomic Gc Content Drifts Downward In Most Bacterial Genomes, Bert Ely

Faculty Publications

In every kingdom of life, GC->AT transitions occur more frequently than any other type of mutation due to the spontaneous deamination of cytidine. In eukaryotic genomes, this slow loss of GC base pairs is counteracted by biased gene conversion which increases genomic GC content as part of the recombination process. However, this type of biased gene conversion has not been observed in bacterial genomes, so we hypothesized that GC->AT transitions cause a reduction of genomic GC content in prokaryotic genomes on an evolutionary time scale. To test this hypothesis, we used a phylogenetic approach to analyze triplets of …


Latewood Ring Width Reveals Ce 1734 Felling Dates For Walker House Timbers In Tupelo, Mississippi, Usa, Thomas W. Patterson, Grant L. Harley, David H. Holt, Raymond T. Doherty, Daniel J. King, Karen J. Heeter, Ashley L. Chavez, Alyssa C. Crowell, Ian M. Stewart May 2021

Latewood Ring Width Reveals Ce 1734 Felling Dates For Walker House Timbers In Tupelo, Mississippi, Usa, Thomas W. Patterson, Grant L. Harley, David H. Holt, Raymond T. Doherty, Daniel J. King, Karen J. Heeter, Ashley L. Chavez, Alyssa C. Crowell, Ian M. Stewart

Faculty Publications

Dendroarchaeology is under-represented in the Gulf Coastal Plain region of the United States (US), and at present, only three published studies have precision dated a collection of 18th–19th-century structures. In this study, we examined the tree-ring data from pine, poplar, and oak timbers used in the Walker House in Tupelo, Mississippi. The Walker House was constructed ca. the mid-1800s with timbers that appeared to be recycled from previous structures. In total, we examined 30 samples (16 pines, 8 oaks, and 6 poplars) from the attic and crawlspace. We cross-dated latewood ring growth from the attic pine samples to the period …


Increased Antimicrobial And Multidrug Resistance Downstream Of Wastewater Treatment Plants In An Urban Watershed, Maitreyee Mukherjee, Edward Laird, Terry J. Gentry, John P. Brooks, Raghupathy Karthikeyan May 2021

Increased Antimicrobial And Multidrug Resistance Downstream Of Wastewater Treatment Plants In An Urban Watershed, Maitreyee Mukherjee, Edward Laird, Terry J. Gentry, John P. Brooks, Raghupathy Karthikeyan

Faculty Publications

Development and spread of antimicrobial resistance (AMR) and multidrug resistance (MDR) through propagation of antibiotic resistance genes (ARG) in various environments is a global emerging public health concern. The role of wastewater treatment plants (WWTPs) as hot spots for the dissemination of AMR and MDR has been widely pointed out by the scientific community. In this study, we collected surface water samples from sites upstream and downstream of two WWTP discharge points in an urban watershed in the Bryan-College Station (BCS), Texas area, over a period of nine months. E. coli isolates were tested for resistance to ampicillin, tetracycline, sulfamethoxazole, …


Host–Guest Interactions In A Metal–Organic Framework Isoreticular Series For Molecular Photocatalytic Co2 Reduction, Philip M. Stanley, Johanna Haimerl, Christopher Thomas, Alexander Urstoeger, Michael Schuster Prof. Dr., Natalia B. Shustova Prof. Dr., Angela Casini Prof. Dr., Bernhard Rieger Prof. Dr., Julien Warnan Dr., Roland A. Fischer Prof. Dr. May 2021

Host–Guest Interactions In A Metal–Organic Framework Isoreticular Series For Molecular Photocatalytic Co2 Reduction, Philip M. Stanley, Johanna Haimerl, Christopher Thomas, Alexander Urstoeger, Michael Schuster Prof. Dr., Natalia B. Shustova Prof. Dr., Angela Casini Prof. Dr., Bernhard Rieger Prof. Dr., Julien Warnan Dr., Roland A. Fischer Prof. Dr.

Faculty Publications

A strategy to improve homogeneous molecular catalyst stability, efficiency, and selectivity is the immobilization on supporting surfaces or within host matrices. Herein, we examine the co-immobilization of a CO2 reduction catalyst [ReBr(CO)3(4,4′-dcbpy)] and a photosensitizer [Ru(bpy)2(5,5′-dcbpy)]Cl2 using the isoreticular series of metal–organic frameworks (MOFs) UiO-66, -67, and -68. Specific host pore size choice enables distinct catalyst and photosensitizer spatial location—either at the outer MOF particle surface or inside the MOF cavities—affecting catalyst stability, electronic communication between reaction center and photosensitizer, and consequently the apparent catalytic rates. These results allow for a rational understanding of an optimized supramolecular layout of catalyst, …


Differences In ​The Proportion Of Children Meeting Behavior Guidelines ​Between Summer ​And School By Socioeconomic Status And Race, Ethan T. Hunt, Lauren Von Klinggraeff, Alexis Jones, Sarah Burkart, Roddrick Dugger, Bridget Armstrong Ph.D., Michael Beets Ph.D., Gabrielle Turner-Mcgrievy Ph.D., Rd, Marco Geraci, Robert Glenn Weaver Med, Phd May 2021

Differences In ​The Proportion Of Children Meeting Behavior Guidelines ​Between Summer ​And School By Socioeconomic Status And Race, Ethan T. Hunt, Lauren Von Klinggraeff, Alexis Jones, Sarah Burkart, Roddrick Dugger, Bridget Armstrong Ph.D., Michael Beets Ph.D., Gabrielle Turner-Mcgrievy Ph.D., Rd, Marco Geraci, Robert Glenn Weaver Med, Phd

Faculty Publications

Objective

Children who fail to meet activity, sleep, and screen-time guidelines are at increased risk for obesity. Further, children who are Black are more likely to have obesity when compared to children who are White, and children from low-income households are at increased risk for obesity when compared to children from higher-income households. The objective of this study was to evaluate the proportion of days meeting obesogenic behavior guidelines during the school year compared to summer vacation by race and free/reduced priced lunch (FRPL) eligibility.

Methods

Mixed-effects linear and logistic regressions estimated the proportion of days participants met activity, sleep, …


Prion-Like C-Terminal Domain Of Tdp-43 And Α-Synuclein Interact Synergistically To Generate Neurotoxic Hybrid Fibrils, Shailendra Dhakal, Courtney E. Wyant, Hannah E. George, Sarah E. Morgan, Vijayaraghavan Rangachari May 2021

Prion-Like C-Terminal Domain Of Tdp-43 And Α-Synuclein Interact Synergistically To Generate Neurotoxic Hybrid Fibrils, Shailendra Dhakal, Courtney E. Wyant, Hannah E. George, Sarah E. Morgan, Vijayaraghavan Rangachari

Faculty Publications

Aberrant aggregation and amyloid formation of tar DNA binding protein (TDP-43) and α-synuclein (αS) underlie frontotemporal dementia (FTD) and Parkinson’s disease (PD), respectively. Amyloid inclusions of TDP-43 and αS are also commonly co-observed in amyotrophic lateral sclerosis (ALS), dementia with Lewy bodies (DLB) and Alzheimer disease (AD). Emerging evidence from cellular and animal models show colocalization of the TDP-43 and αS aggregates, raising the possibility of direct interactions and co-aggregation between the two proteins. In this report, we set out to answer this question by investigating the interactions between αS and prion-like pathogenic C-terminal domain of TDP-43 (TDP-43 PrLD). PrLD …


Beyond Structural Motifs: The Frontier Of Actinide-Containing Metal–Organic Frameworks, Corey R. Martin, Gabrielle A. Leith, Natalia B. Shustova Prof. Dr. May 2021

Beyond Structural Motifs: The Frontier Of Actinide-Containing Metal–Organic Frameworks, Corey R. Martin, Gabrielle A. Leith, Natalia B. Shustova Prof. Dr.

Faculty Publications

In this perspective, we feature recent advances in the field of actinide-containing metal–organic frameworks (An-MOFs) with a main focus on their electronic, catalytic, photophysical, and sorption properties. This discussion deviates from a strictly crystallographic analysis of An-MOFs, reported in several reviews, or synthesis of novel structural motifs, and instead delves into the remarkable potential of An-MOFs for evolving the nuclear waste administration sector. Currently, the An-MOF field is dominated by thorium- and uranium-containing structures, with only a few reports on transuranic frameworks. However, some of the reported properties in the field of An-MOFs foreshadow potential implementation of these materials and …


Beyond Structural Motifs: The Frontier Of Actinide-Containing Metal–Organic Frameworks, Corey R. Martin, Gabrielle A. Leith, Natalia B. Shustova May 2021

Beyond Structural Motifs: The Frontier Of Actinide-Containing Metal–Organic Frameworks, Corey R. Martin, Gabrielle A. Leith, Natalia B. Shustova

Faculty Publications

In this perspective, we feature recent advances in the field of actinide-containing metal-organic frameworks (An-MOFs) with a main focus on their electronic, catalytic, photophysical, and sorption properties. This discussion deviates from a strictly crystallographic analysis of An-MOFs, reported in several reviews, or synthesis of novel structural motifs, and instead delves into the remarkable potential of An-MOFs for evolving the nuclear waste administration sector. Currently, the An-MOF field is dominated by thorium- and uranium-containing structures, with only a few reports on transuranic frameworks. However, some of the reported properties in the field of An-MOFs foreshadow potential implementation of these materials and …


Nanoantibiotics: Functions And Properties At The Nanoscale To Combat Antibiotic Resistance, M. Mustafa Mamun, Adeola Julian Sorinolu, Mariya Munir, Eric P. Vejerano May 2021

Nanoantibiotics: Functions And Properties At The Nanoscale To Combat Antibiotic Resistance, M. Mustafa Mamun, Adeola Julian Sorinolu, Mariya Munir, Eric P. Vejerano

Faculty Publications

One primary mechanism for bacteria developing resistance is frequent exposure to antibiotics. Nanoantibiotics (nAbts) is one of the strategies being explored to counteract the surge of antibiotic resistant bacteria. nAbts are antibiotic molecules encapsulated with engineered nanoparticles (NPs) or artificially synthesized pure antibiotics with a size range of ≤100 nm in at least one dimension. NPs may restore drug efficacy because of their nanoscale functionalities. As carriers and delivery agents, nAbts can reach target sites inside a bacterium by crossing the cell membrane, interfering with cellular components, and damaging metabolic machinery. Nanoscale systems deliver antibiotics at enormous particle number concentrations. …


Environmentally Persistent Free Radicals As Sources Of Pops, Eric P. Vejerano, Jeonghyeon Ahn, Junaid Latif, Mustafa Mamun May 2021

Environmentally Persistent Free Radicals As Sources Of Pops, Eric P. Vejerano, Jeonghyeon Ahn, Junaid Latif, Mustafa Mamun

Faculty Publications

Environmentally persistent free radicals (EPFRs) are a new class organic pollutant sharing some of the attributes of persistent organic pollutants (POPs). This opinion/short review aims to describe the properties of EPFRs that merit their recognition as an additional and potentially significant source of POPs. EPFRs are ubiquitous in diverse environments because of multiple factors: (1) organic precursors from anthropogenic, biogenic, and other natural emission sources are abundant; multiple mechanisms in PM and soils form (2) EPFRs; and (3) EPFRs are stable and persist for a long time, thereby, accumulate in the environment and potentially transported long range. The hazards of …


The Impact Of Aquaculture On The Genetics And Distribution Of The Onuphid Annelid Diopatra Biscayensis, Matthew P. Galaska, David S. Wethey, Andrés Arias, Stanislas F. Dubois, Kenneth M. Halanych, Sarah A. Woodin May 2021

The Impact Of Aquaculture On The Genetics And Distribution Of The Onuphid Annelid Diopatra Biscayensis, Matthew P. Galaska, David S. Wethey, Andrés Arias, Stanislas F. Dubois, Kenneth M. Halanych, Sarah A. Woodin

Faculty Publications

Aim

Evolutionary history of natural populations can be confounded by human intervention such as the case of decorator worm species Diopatra (Onuphidae), which have a history of being transported through anthropogenic activities. Because they build tubes and act as ecosystem engineers, they can have a large impact on the overall ecosystem in which they occur. One conspicuous member, Diopatra biscayensis, which was only described in 2012, has a fragmented distribution that includes the Bay of Biscay and the Normanno-Breton Gulf in the English Channel. This study explores the origin of these worms in the Normanno-Breton region, which has been …


The Impact Of Aquaculture On The Genetics And Distribution Of The Onuphid Annelid Diopatra Biscayensis, Matthew P. Galaska, David S. Wethey, Andrés Arias, Stanislas F. Dubios, Kenneth M. Halanych, Sarah A. Woodin May 2021

The Impact Of Aquaculture On The Genetics And Distribution Of The Onuphid Annelid Diopatra Biscayensis, Matthew P. Galaska, David S. Wethey, Andrés Arias, Stanislas F. Dubios, Kenneth M. Halanych, Sarah A. Woodin

Faculty Publications

Aim

Evolutionary history of natural populations can be confounded by human intervention such as the case of decorator worm species Diopatra (Onuphidae), which have a history of being transported through anthropogenic activities. Because they build tubes and act as ecosystem engineers, they can have a large impact on the overall ecosystem in which they occur. One conspicuous member, Diopatra biscayensis, which was only described in 2012, has a fragmented distribution that includes the Bay of Biscay and the Normanno-Breton Gulf in the English Channel. This study explores the origin of these worms in the Normanno-Breton region, which has been …


Elevated Incidences Of Antimicrobial Resistance And Multidrug Resistance In The Maumee River (Ohio, Usa), A Major Tributary Of Lake Erie, Maitreyee Mukherjee, Leah Marie, Cheyenne Liles, Nadia Mustafa, George Bullerjahn, Terry J. Gentry, John P. Brooks May 2021

Elevated Incidences Of Antimicrobial Resistance And Multidrug Resistance In The Maumee River (Ohio, Usa), A Major Tributary Of Lake Erie, Maitreyee Mukherjee, Leah Marie, Cheyenne Liles, Nadia Mustafa, George Bullerjahn, Terry J. Gentry, John P. Brooks

Faculty Publications

Maumee River, the major tributary in the western basin of Lake Erie, serves as one of major sources of freshwater in the area, supplying potable, recreational, and industrial water. In this study we collected water samples from four sites in the Maumee River Bay between 2016–2017 and E. coli was isolated, enumerated, and analyzed for antimicrobial resistance (AMR) and multidrug resistance (MDR). Strikingly, 95% of the total isolates were found to be resistant to at least one antibiotic. A very high resistance to the drugs cephalothin (95.3%), ampicillin (38.3%), tetracycline (8.8%), gentamicin (8.2%), ciprofloxacin (4.2%), cefoperazone (4%), and sulfamethoxazole (1.5%) …


Insecticidal Rna Interference, Thinking Beyond Long Dsrna, Alex S. Flynt May 2021

Insecticidal Rna Interference, Thinking Beyond Long Dsrna, Alex S. Flynt

Faculty Publications

Over 20 years ago double-stranded RNA (dsRNA) was described as the trigger of RNAi interference (RNAi)-based gene silencing. This paradigm has held since, especially for insect biopesticide technologies where dsRNAs, similar to those described in 1998, are used to inhibit gene expression. In the intervening years, investigation of RNAi pathways has revealed the small RNA effectors of RNAi are diverse and rapidly evolving. The rich biology of insect small RNAs suggests potential to use multiple RNAi modes for manipulating gene expression. By exploiting different RNAi pathways, the menu of options for pest control can be expanded and could lead to …


Recent Advances In Understanding Tick And Rickettsiae Interactions, Shahid Karim, Deepak Kumar, Khemraj Budachetri May 2021

Recent Advances In Understanding Tick And Rickettsiae Interactions, Shahid Karim, Deepak Kumar, Khemraj Budachetri

Faculty Publications

Ticks are haematophagous arthropods with unique molecular mechanisms for digesting host blood meal while acting as vectors for various pathogens of public health significance. The tick's pharmacologically active saliva plays a fundamental role in modulating the host's immune system for several days to weeks, depending on the tick species. The vector tick has also developed sophisticated molecular mechanisms to serve as a competent vector for pathogens, including the spotted fever group (SFG) rickettsiae. Evidence is still inadequate concerning tick–rickettsiae–host interactions and saliva-assisted transmission of the pathogen to the mammalian host. Rickettsia parkeri, of the SFG rickettsia, can cause a …


Comparable Response Of Wild Rodent Gut Microbiome To Anthropogenic Habitat Contamination, Anton Lavrinienko, Ann Hämäläinen, Rasmus Hindstrom, Eugene Tukalenko, Zbyszek Boratynski, Kati Kivisaari, Timothy Mousseau, Phillip C. Watts, Tapio Mappes Apr 2021

Comparable Response Of Wild Rodent Gut Microbiome To Anthropogenic Habitat Contamination, Anton Lavrinienko, Ann Hämäläinen, Rasmus Hindstrom, Eugene Tukalenko, Zbyszek Boratynski, Kati Kivisaari, Timothy Mousseau, Phillip C. Watts, Tapio Mappes

Faculty Publications

Species identity is thought to dominate over environment in shaping wild rodent gut microbiota, but it remains unknown whether the responses of host gut microbiota to shared anthropogenic habitat impacts are species-specific or if the general gut microbiota response is similar across host species. Here, we compare the influence of exposure to radionuclide contamination on the gut microbiota of four wild mouse species: Apodemus flavicollis, A. sylvaticus, A. speciosus and A. argenteus. Building on the evidence that radiation impacts bank vole (Myodes glareolus) gut microbiota, we hypothesized that radiation exposure has a general impact on rodent gut microbiota. Because we …


The Malina Oceanographic Expedition: How Do Changes In Ice Cover, Permafrost And Uv Radiation Impact Biodiversity And Biogeochemical Fluxes In The Arctic Ocean?, Philippe Massicotte, Rainer M.W. Amon, Antoine David, Sergio Balzano, Simon Bélanger, Ronald Benner, Dominique Boeuf, Annick Bricaud, Flavienne Bruyant, Gwenaëlle Chaillou, Malik Chami, Bruno Charrière, Jing Chen, Hervé Claustre, Pierre Coupel, Nicole Delsaut, David Doxaran, Jens Ehn, Cédric Fichot, Marie-Hélène Forget, Et. Al. Apr 2021

The Malina Oceanographic Expedition: How Do Changes In Ice Cover, Permafrost And Uv Radiation Impact Biodiversity And Biogeochemical Fluxes In The Arctic Ocean?, Philippe Massicotte, Rainer M.W. Amon, Antoine David, Sergio Balzano, Simon Bélanger, Ronald Benner, Dominique Boeuf, Annick Bricaud, Flavienne Bruyant, Gwenaëlle Chaillou, Malik Chami, Bruno Charrière, Jing Chen, Hervé Claustre, Pierre Coupel, Nicole Delsaut, David Doxaran, Jens Ehn, Cédric Fichot, Marie-Hélène Forget, Et. Al.

Faculty Publications

The MALINA oceanographic campaign was conducted during summer 2009 to investigate the carbon stocks and the processes controlling the carbon fluxes in the Mackenzie River estuary and the Beaufort Sea. During the campaign, an extensive suite of physical, chemical and biological variables were measured across seven shelf-basin transects (south-north) to capture the meridional gradient between the estuary and the open ocean. Key variables such as temperature, absolute salinity, radiance, irradiance, nutrient concentrations, chlorophyll a concentration, bacteria, phytoplankton and zooplankton abundance and taxonomy, and carbon stocks and fluxes were routinely measured onboard the Canadian research icebreaker CCGS Amundsen and from a …


Root Exudates Alter The Expression Of Diverse Metabolic, Transport, Regulatory, And Stress Response Genes In Rhizosphere Pseudomonas, Olga V. Mavrodi, Janiece R. Mcwilliams, Jacob O. Peter, Anna Berim, Karl A. Hassan, Liam D.H. Elbourne, Melissa K. Letourneau, David R. Gang, Ian T. Paulsen, David M. Weller, Linda S. Thomashow, Alex S. Flynt, Dmitri V. Mavrodi Apr 2021

Root Exudates Alter The Expression Of Diverse Metabolic, Transport, Regulatory, And Stress Response Genes In Rhizosphere Pseudomonas, Olga V. Mavrodi, Janiece R. Mcwilliams, Jacob O. Peter, Anna Berim, Karl A. Hassan, Liam D.H. Elbourne, Melissa K. Letourneau, David R. Gang, Ian T. Paulsen, David M. Weller, Linda S. Thomashow, Alex S. Flynt, Dmitri V. Mavrodi

Faculty Publications

Plants live in association with microorganisms that positively influence plant development, vigor, and fitness in response to pathogens and abiotic stressors. The bulk of the plant microbiome is concentrated belowground at the plant root-soil interface. Plant roots secrete carbon-rich rhizodeposits containing primary and secondary low molecular weight metabolites, lysates, and mucilages. These exudates provide nutrients for soil microorganisms and modulate their affinity to host plants, but molecular details of this process are largely unresolved. We addressed this gap by focusing on the molecular dialog between eight well-characterized beneficial strains of the Pseudomonas fluorescens group and Brachypodium distachyon, a model …


The Msaabcr Operon Regulates Persister Formation By Modulating Energy Metabolism In Staphylococcus Aureus, Shanti Pandey, Gyan S. Sahukhal, Mohamed O. Elasri Apr 2021

The Msaabcr Operon Regulates Persister Formation By Modulating Energy Metabolism In Staphylococcus Aureus, Shanti Pandey, Gyan S. Sahukhal, Mohamed O. Elasri

Faculty Publications

Staphylococcus aureus is a major human pathogen that causes chronic, systemic infections, and the recalcitrance of these infections is mainly due to the presence of persister cells, which are a bacterial subpopulation that exhibits extreme, yet transient, antibiotic tolerance accompanied by a transient halt in growth. However, upon cessation of antibiotic treatment, a resumption in growth of persister cells causes recurrence of infections and treatment failure. Previously, we reported the involvement of msaABCR in several important staphylococcal phenotypes, including the formation of persister cells. Additionally, observations of the regulation of several metabolic genes by the msaABCR operon in transcriptomics and …


The Whole Is Greater Than Its Parts: Ensembling Improves Protein Contact Prediction, Wendy M. Billings, Connor J. Morris, Dennis Della Corte Apr 2021

The Whole Is Greater Than Its Parts: Ensembling Improves Protein Contact Prediction, Wendy M. Billings, Connor J. Morris, Dennis Della Corte

Faculty Publications

The prediction of amino acid contacts from protein sequence is an important problem, as protein contacts are a vital step towards the prediction of folded protein structures. We propose that a powerful concept from deep learning, called ensembling, can increase the accuracy of protein contact predictions by combining the outputs of different neural network models. We show that ensembling the predictions made by different groups at the recent Critical Assessment of Protein Structure Prediction (CASP13) outperforms all individual groups. Further, we show that contacts derived from the distance predictions of three additional deep neural networks—AlphaFold, trRosetta, and ProSPr—can be substantially …


The Supercam Instrument Suite On The Mars 2020 Rover: Science Objectives And Mast-Unit Description, S. Maurice, R. C. Wiens, P. Bernardi, P. Caïs, S. Robinson, T. Nelson, O. Gasnault, J. -M. Reess, M. Deleuze, F. Rull, J. -A. Manrique, S. Abbaki, R. B. Anderson, Y. André, Stanley M. Angel, G. Arana, T. Battault, P. Beck, K. Benzerara, S. Bernard, Et. Al. Apr 2021

The Supercam Instrument Suite On The Mars 2020 Rover: Science Objectives And Mast-Unit Description, S. Maurice, R. C. Wiens, P. Bernardi, P. Caïs, S. Robinson, T. Nelson, O. Gasnault, J. -M. Reess, M. Deleuze, F. Rull, J. -A. Manrique, S. Abbaki, R. B. Anderson, Y. André, Stanley M. Angel, G. Arana, T. Battault, P. Beck, K. Benzerara, S. Bernard, Et. Al.

Faculty Publications

On the NASA 2020 rover mission to Jezero crater, the remote determination of the texture, mineralogy and chemistry of rocks is essential to quickly and thoroughly characterize an area and to optimize the selection of samples for return to Earth. As part of the Perseverance payload, SuperCam is a suite of five techniques that provide critical and complementary observations via Laser-Induced Breakdown Spectroscopy (LIBS), Time-Resolved Raman and Luminescence (TRR/L), visible and near-infrared spectroscopy (VISIR), high-resolution color imaging (RMI), and acoustic recording (MIC). SuperCam operates at remote distances, primarily 2–7 m, while providing data at sub-mm to mm scales. We report …


Broken-Hearted” Carbon Bowl Via Electron Shuttle Reaction: Energetics And Electron Coupling, Gabrielle A. Leith, Allison M. Rice, Brandon J. Yarbrough, Preecha Kittikhunnatham, Abijai Mathur, Nicholas A. Morris, Megan J. Francis, Anna A. Berseneva, Poonam Dhull, Richard D. Adams, M. Victoria Bobo, Aaron A. Vannucci, Mark D. Smith, Sophya Garashchuk, Natalia B. Shustova Apr 2021

Broken-Hearted” Carbon Bowl Via Electron Shuttle Reaction: Energetics And Electron Coupling, Gabrielle A. Leith, Allison M. Rice, Brandon J. Yarbrough, Preecha Kittikhunnatham, Abijai Mathur, Nicholas A. Morris, Megan J. Francis, Anna A. Berseneva, Poonam Dhull, Richard D. Adams, M. Victoria Bobo, Aaron A. Vannucci, Mark D. Smith, Sophya Garashchuk, Natalia B. Shustova

Faculty Publications

Unprecedented one-step CC bond cleavage leading to opening of the buckybowl (π-bowl), that could provide access to carbon-rich structures with previously inaccessible topologies, is reported; highlighting the possibility to implement drastically different synthetic routes to π-bowls in contrast to conventional ones applied for polycyclic aromatic hydrocarbons. Through theoretical modeling, we evaluated the mechanistic pathways feasible for π-bowl planarization and factors that could affect such a transformation including strain and released energies. Through employment of Marcus theory, optical spectroscopy, and crystallographic analysis, we estimated the possibility of charge transfer and electron coupling between “open” corannulene and a strong electron acceptor such …


Protocols For Assessing Transformation Rates Of Nitrous Oxide In The Water Column, Annie Bourbonnais, Claudia Frey, Xin Sun, Laura A. Bristow, Amal Jayakumar, Nathaniel E. Ostrom, Karen L. Casciotti, Bess B. Ward Apr 2021

Protocols For Assessing Transformation Rates Of Nitrous Oxide In The Water Column, Annie Bourbonnais, Claudia Frey, Xin Sun, Laura A. Bristow, Amal Jayakumar, Nathaniel E. Ostrom, Karen L. Casciotti, Bess B. Ward

Faculty Publications

Nitrous oxide (N2O) is a potent greenhouse gas and an ozone destroying substance. Yet, clear step-by-step protocols to measure N2O transformation rates in freshwater and marine environments are still lacking, challenging inter-comparability efforts. Here we present detailed protocols currently used by leading experts in the field to measure water-column N2O production and consumption rates in both marine and other aquatic environments. We present example 15N-tracer incubation experiments in marine environments as well as templates to calculate both N2O production and consumption rates. We discuss important considerations and recommendations regarding (1) precautions to prevent oxygen (O2) contamination during low-oxygen and anoxic …


Genes Related To Redox And Cell Curvature Facilitate Interactions Between Caulobacter Strains And Arabidopsis, Louis Berrios, Bert Ely Apr 2021

Genes Related To Redox And Cell Curvature Facilitate Interactions Between Caulobacter Strains And Arabidopsis, Louis Berrios, Bert Ely

Faculty Publications

Bacteria play an integral role in shaping plant growth and development. However, the genetic factors that facilitate plant-bacteria interactions remain largely unknown. Here, we demonstrated the importance of two bacterial genetic factors that facilitate the interactions between plant-growth-promoting (PGP) bacteria in the genus Caulobacter and the host plant Arabidopsis. Using homologous recombination, we disrupted the cytochrome ubiquinol oxidase (cyo) operon in both C. vibrioides CB13 and C. segnis TK0059 by knocking out the expression of cyoB (critical subunit of the cyo operon) and showed that the mutant strains were unable to enhance the growth of Arabidopsis. In addition, disruption of …


What Is Refractory Organic Matter In The Ocean?, Federico Baltar, Xosé A. Alvarez-Salgado, Javier Arístegui, Ronald Benner, Dennis A. Hansell, Gerhard J. Herndl, Christian Lønborg Apr 2021

What Is Refractory Organic Matter In The Ocean?, Federico Baltar, Xosé A. Alvarez-Salgado, Javier Arístegui, Ronald Benner, Dennis A. Hansell, Gerhard J. Herndl, Christian Lønborg

Faculty Publications

About 20% of the organic carbon produced in the sunlit surface ocean is transported into the ocean’s interior as dissolved, suspended and sinking particles to be mineralized and sequestered as dissolved inorganic carbon (DIC), sedimentary particulate organic carbon (POC) or “refractory” dissolved organic carbon (rDOC). Recently, the physical and biological mechanisms associated with the particle pumps have been revisited, suggesting that accepted fluxes might be severely underestimated (Boyd et al., 2019; Buesseler et al., 2020). Perhaps even more poorly understood are the mechanisms driving rDOC production and its potential accumulation in the ocean. On the basis of …


Activating Mutations In Braf Disrupt The Hypothalamo-Pituitary Axis Leading To Hypopituitarism In Mice And Humans, Angelica Gualtieri, Nikolina Kyprianou, Louise C. Gregory, Maria Lillina Vignola, James G. Nicholson, Rachael Tan, Shin-Ichi Inoue, Valeria Scagliotti, Pedro Casado, James Blackburn, Fernando Abollo-Jimenez, Eugenia Marinelli, Rachael E.J. Besser, Wolfgang Högler, I. Karen Temple, Justin H. Davies, Andrey Gagunashvili, Iain C.A.F. Robinson, Sally A. Camper, Shannon W. Davis, Pedro R. Cutillas, Evelien F. Gevers, Yoko Aoki, Mehul T. Dattani, Carles Gaston-Massuet Apr 2021

Activating Mutations In Braf Disrupt The Hypothalamo-Pituitary Axis Leading To Hypopituitarism In Mice And Humans, Angelica Gualtieri, Nikolina Kyprianou, Louise C. Gregory, Maria Lillina Vignola, James G. Nicholson, Rachael Tan, Shin-Ichi Inoue, Valeria Scagliotti, Pedro Casado, James Blackburn, Fernando Abollo-Jimenez, Eugenia Marinelli, Rachael E.J. Besser, Wolfgang Högler, I. Karen Temple, Justin H. Davies, Andrey Gagunashvili, Iain C.A.F. Robinson, Sally A. Camper, Shannon W. Davis, Pedro R. Cutillas, Evelien F. Gevers, Yoko Aoki, Mehul T. Dattani, Carles Gaston-Massuet

Faculty Publications

Germline mutations in BRAF and other components of the MAPK pathway are associated with the congenital syndromes collectively known as RASopathies. Here, we report the association of Septo-Optic Dysplasia (SOD) including hypopituitarism and Cardio-Facio-Cutaneous (CFC) syndrome in patients harbouring mutations in BRAF. Phosphoproteomic analyses demonstrate that these genetic variants are gain-of-function mutations leading to activation of the MAPK pathway. Activation of the MAPK pathway by conditional expression of the BrafV600E/+ allele, or the knock-in BrafQ241R/+ allele (corresponding to the most frequent human CFC-causing mutation, BRAF p.Q257R), leads to abnormal cell lineage determination and terminal differentiation of …


Non-Steroidal Anti-Inflammatory Drugs On Core Body Temperature During Exercise: A Systematic Review, Dawn M. Emerson, Stephen Cl Chen, Melani R. Kelly, Bryant Parnell, Toni M. Torres-Mcgehee Apr 2021

Non-Steroidal Anti-Inflammatory Drugs On Core Body Temperature During Exercise: A Systematic Review, Dawn M. Emerson, Stephen Cl Chen, Melani R. Kelly, Bryant Parnell, Toni M. Torres-Mcgehee

Faculty Publications

BACKGROUND: Because of their anti-pyretic effects, some individuals prophylactically use non-steroidal anti-inflammatory drugs (NSAIDs) to blunt core temperature (Tc) increases during exercise, thus, potentially improving performance by preventing hyperthermia and/or exertional heat illness. However, NSAIDs induce gastrointestinal damage, alter renal function, and decrease cardiovascular function, which could compromise thermoregulation and increase Tc. The aim of this systematic review was to evaluate the effects of NSAIDs on Tc in exercising, adult humans. METHODS: We conducted searches in MEDLINE, PubMed, Cochrane Reviews, and Google Scholar for literature published up to November 2020. We conducted a quality assessment review using the Physiotherapy Evidence …


What Is Refractory Organic Matter In The Ocean?, Federico Baltar, Xosé A. Alvarez-Salgado, Javier Arístegui, Ronald Benner, Dennis A. Hansell, Gerhard J. Herndl, Christian Lønborg Apr 2021

What Is Refractory Organic Matter In The Ocean?, Federico Baltar, Xosé A. Alvarez-Salgado, Javier Arístegui, Ronald Benner, Dennis A. Hansell, Gerhard J. Herndl, Christian Lønborg

Faculty Publications

About 20% of the organic carbon produced in the sunlit surface ocean is transported into the ocean’s interior as dissolved, suspended and sinking particles to be mineralized and sequestered as dissolved inorganic carbon (DIC), sedimentary particulate organic carbon (POC) or “refractory” dissolved organic carbon (rDOC). Recently, the physical and biological mechanisms associated with the particle pumps have been revisited, suggesting that accepted fluxes might be severely underestimated (Boyd et al., 2019; Buesseler et al., 2020). Perhaps even more poorly understood are the mechanisms driving rDOC production and its potential accumulation in the ocean. On the basis of …