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Precision Subclassification Of Type 2 Diabetes: A Systematic Review, Shivani Misra, Shivani Misra, Robert Wagner, Bige Ozkan, Martin Schön, Magdalena Sevilla-Gonzalez, Katsiaryna Prystupa, Caroline C. Wang, Raymond J. Kreienkamp, Sara J. Cromer, Mary R. Rooney, Daisy Duan, Anne Cathrine Baun Thuesen, Amelia S. Wallace, Aaron Leong, Aaron J. Deutsch, Mette K. Andersen, Liana K. Billings, Liana K. Billings, Robert H. Eckel, Wayne Huey Herng Sheu, Torben Hansen, Norbert Stefan, Mark O. Goodarzi, Debashree Ray, Elizabeth Selvin, Jose C. Florez, Paul W. Franks, Stephen S. Rich, Tina Vilsbøll, Kimberly K. Vesco, Miriam S. Udler, Tiinamaija Tuomi, Arianne Sweeting Dec 2023

Precision Subclassification Of Type 2 Diabetes: A Systematic Review, Shivani Misra, Shivani Misra, Robert Wagner, Bige Ozkan, Martin Schön, Magdalena Sevilla-Gonzalez, Katsiaryna Prystupa, Caroline C. Wang, Raymond J. Kreienkamp, Sara J. Cromer, Mary R. Rooney, Daisy Duan, Anne Cathrine Baun Thuesen, Amelia S. Wallace, Aaron Leong, Aaron J. Deutsch, Mette K. Andersen, Liana K. Billings, Liana K. Billings, Robert H. Eckel, Wayne Huey Herng Sheu, Torben Hansen, Norbert Stefan, Mark O. Goodarzi, Debashree Ray, Elizabeth Selvin, Jose C. Florez, Paul W. Franks, Stephen S. Rich, Tina Vilsbøll, Kimberly K. Vesco, Miriam S. Udler, Tiinamaija Tuomi, Arianne Sweeting

Clinical Research Faculty Publications

Background: Heterogeneity in type 2 diabetes presentation and progression suggests that precision medicine interventions could improve clinical outcomes. We undertook a systematic review to determine whether strategies to subclassify type 2 diabetes were associated with high quality evidence, reproducible results and improved outcomes for patients. Methods: We searched PubMed and Embase for publications that used ‘simple subclassification’ approaches using simple categorisation of clinical characteristics, or ‘complex subclassification’ approaches which used machine learning or ‘omics approaches in people with established type 2 diabetes. We excluded other diabetes subtypes and those predicting incident type 2 diabetes. We assessed quality, reproducibility and clinical …

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Impact Of Individual And Environmental Factors On Dietary Or Lifestyle Interventions To Prevent Type 2 Diabetes Development: A Systematic Review, Dhanasekaran Bodhini, Robert W. Morton, Vanessa Santhakumar, Mariam Nakabuye, Hugo Pomares-Millan, Hugo Pomares-Millan, Christoffer Clemmensen, Stephanie L. Fitzpatrick, Marta Guasch-Ferre, James S. Pankow, Mathias Ried-Larsen, Paul W. Franks, Stephen S. Rich, Robert Wagner, Tina Vilsbøll, Kimberly K. Vesco, Miriam S. Udler, Tiinamaija Tuomi, Arianne Sweeting, Emily K. Sims, Jennifer L. Sherr, Robert K. Semple, Rebecca M. Reynolds, Maria J. Redondo, Leanne M. Redman, Richard E. Pratley, Rodica Pop-Busui, Toni I. Pollin, Wei Perng, Ewan R. Pearson, Susan E. Ozanne, Katharine R. Owen, Richard Oram, Rinki Murphy Dec 2023

Impact Of Individual And Environmental Factors On Dietary Or Lifestyle Interventions To Prevent Type 2 Diabetes Development: A Systematic Review, Dhanasekaran Bodhini, Robert W. Morton, Vanessa Santhakumar, Mariam Nakabuye, Hugo Pomares-Millan, Hugo Pomares-Millan, Christoffer Clemmensen, Stephanie L. Fitzpatrick, Marta Guasch-Ferre, James S. Pankow, Mathias Ried-Larsen, Paul W. Franks, Stephen S. Rich, Robert Wagner, Tina Vilsbøll, Kimberly K. Vesco, Miriam S. Udler, Tiinamaija Tuomi, Arianne Sweeting, Emily K. Sims, Jennifer L. Sherr, Robert K. Semple, Rebecca M. Reynolds, Maria J. Redondo, Leanne M. Redman, Richard E. Pratley, Rodica Pop-Busui, Toni I. Pollin, Wei Perng, Ewan R. Pearson, Susan E. Ozanne, Katharine R. Owen, Richard Oram, Rinki Murphy

Clinical Research Faculty Publications

Background: The variability in the effectiveness of type 2 diabetes (T2D) preventive interventions highlights the potential to identify the factors that determine treatment responses and those that would benefit the most from a given intervention. We conducted a systematic review to synthesize the evidence to support whether sociodemographic, clinical, behavioral, and molecular factors modify the efficacy of dietary or lifestyle interventions to prevent T2D. Methods: We searched MEDLINE, Embase, and Cochrane databases for studies reporting on the effect of a lifestyle, dietary pattern, or dietary supplement interventions on the incidence of T2D and reporting the results stratified by any effect …

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Treatment Effect Heterogeneity Following Type 2 Diabetes Treatment With Glp1-Receptor Agonists And Sglt2-Inhibitors: A Systematic Review, Katherine G. Young, Eram Haider Mcinnes, Robert J. Massey, Anna R. Kahkoska, Scott J. Pilla, Sridharan Raghavan, Maggie A. Stanislawski, Deirdre K. Tobias, Andrew P. Mcgovern, Andrew P. Mcgovern, Adem Y. Dawed, Angus G. Jones, Ewan R. Pearson, Ewan R. Pearson, John M. Dennis, John M. Dennis, Paul W. Franks, Stephen S. Rich, Robert Wagner, Tina Vilsbøll, Kimberly K. Vesco, Miriam S. Udler, Tiinamaija Tuomi, Arianne Sweeting, Emily K. Sims, Jennifer L. Sherr, Robert K. Semple, Rebecca M. Reynolds, Maria J. Redondo, Leanne M. Redman, Richard E. Pratley, Rodica Pop-Busui, Toni I. Pollin, Wei Perng Dec 2023

Treatment Effect Heterogeneity Following Type 2 Diabetes Treatment With Glp1-Receptor Agonists And Sglt2-Inhibitors: A Systematic Review, Katherine G. Young, Eram Haider Mcinnes, Robert J. Massey, Anna R. Kahkoska, Scott J. Pilla, Sridharan Raghavan, Maggie A. Stanislawski, Deirdre K. Tobias, Andrew P. Mcgovern, Andrew P. Mcgovern, Adem Y. Dawed, Angus G. Jones, Ewan R. Pearson, Ewan R. Pearson, John M. Dennis, John M. Dennis, Paul W. Franks, Stephen S. Rich, Robert Wagner, Tina Vilsbøll, Kimberly K. Vesco, Miriam S. Udler, Tiinamaija Tuomi, Arianne Sweeting, Emily K. Sims, Jennifer L. Sherr, Robert K. Semple, Rebecca M. Reynolds, Maria J. Redondo, Leanne M. Redman, Richard E. Pratley, Rodica Pop-Busui, Toni I. Pollin, Wei Perng

Clinical Research Faculty Publications

Background: A precision medicine approach in type 2 diabetes requires the identification of clinical and biological features that are reproducibly associated with differences in clinical outcomes with specific anti-hyperglycaemic therapies. Robust evidence of such treatment effect heterogeneity could support more individualized clinical decisions on optimal type 2 diabetes therapy. Methods: We performed a pre-registered systematic review of meta-analysis studies, randomized control trials, and observational studies evaluating clinical and biological features associated with heterogenous treatment effects for SGLT2-inhibitor and GLP1-receptor agonist therapies, considering glycaemic, cardiovascular, and renal outcomes. After screening 5,686 studies, we included 101 studies of SGLT2-inhibitors and 75 studies …

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Disease-Modifying Therapies And Features Linked To Treatment Response In Type 1 Diabetes Prevention: A Systematic Review, Jamie L. Felton, Kurt J. Griffin, Kurt J. Griffin, Richard A. Oram, Richard A. Oram, Cate Speake, S. Alice Long, Suna Onengut-Gumuscu, Stephen S. Rich, Stephen S. Rich, Gabriela S.F. Monaco, Carmella Evans-Molina, Linda A. Dimeglio, Heba M. Ismail, Andrea K. Steck, Dana Dabelea, Randi K. Johnson, Marzhan Urazbayeva, Stephen Gitelman, John M. Wentworth, Maria J. Redondo, Emily K. Sims, Emily K. Sims, Paul W. Franks, Robert Wagner, Tina Vilsbøll, Kimberly K. Vesco, Miriam S. Udler, Tiinamaija Tuomi, Arianne Sweeting, Jennifer L. Sherr, Robert K. Semple, Rebecca M. Reynolds, Leanne M. Redman Dec 2023

Disease-Modifying Therapies And Features Linked To Treatment Response In Type 1 Diabetes Prevention: A Systematic Review, Jamie L. Felton, Kurt J. Griffin, Kurt J. Griffin, Richard A. Oram, Richard A. Oram, Cate Speake, S. Alice Long, Suna Onengut-Gumuscu, Stephen S. Rich, Stephen S. Rich, Gabriela S.F. Monaco, Carmella Evans-Molina, Linda A. Dimeglio, Heba M. Ismail, Andrea K. Steck, Dana Dabelea, Randi K. Johnson, Marzhan Urazbayeva, Stephen Gitelman, John M. Wentworth, Maria J. Redondo, Emily K. Sims, Emily K. Sims, Paul W. Franks, Robert Wagner, Tina Vilsbøll, Kimberly K. Vesco, Miriam S. Udler, Tiinamaija Tuomi, Arianne Sweeting, Jennifer L. Sherr, Robert K. Semple, Rebecca M. Reynolds, Leanne M. Redman

Clinical Research Faculty Publications

Background: Type 1 diabetes (T1D) results from immune-mediated destruction of insulin-producing beta cells. Prevention efforts have focused on immune modulation and supporting beta cell health before or around diagnosis; however, heterogeneity in disease progression and therapy response has limited translation to clinical practice, highlighting the need for precision medicine approaches to T1D disease modification. Methods: To understand the state of knowledge in this area, we performed a systematic review of randomized-controlled trials with ≥50 participants cataloged in PubMed or Embase from the past 25 years testing T1D disease-modifying therapies and/or identifying features linked to treatment response, analyzing bias using a …

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The Partner-An Underutilized Facilitator To Support Healthy Gestational Weight Gain, Joshua R. Sparks, Suzanne Phelan, Kimberly L. Drews, Leanne M. Redman Dec 2023

The Partner-An Underutilized Facilitator To Support Healthy Gestational Weight Gain, Joshua R. Sparks, Suzanne Phelan, Kimberly L. Drews, Leanne M. Redman

Clinical Research Faculty Publications

No abstract provided.

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Deep Learning-Based Polygenic Risk Analysis For Alzheimer’S Disease Prediction, Xiaopu Zhou, Yu Chen, Fanny C.F. Ip, Yuanbing Jiang, Han Cao, Ge Lv, Huan Zhong, Jiahang Chen, Tao Ye, Yuewen Chen, Yulin Zhang, Shuangshuang Ma, Ronnie M.N. Lo, Estella P.S. Tong, Ansgar J. Furst, Joy L. Taylor, Jerome A. Yesavage, Gail Li, Eric C. Petrie, Elaine R. Peskind, Sandra Harding, J. Jay Fruehling, Dino Massoglia, Olga James, Konstantinos Arfanakis, Debra Fleischman, Karl Friedl, Shannon Finley, Jacqueline Hayes, Rosemary Morrison, Melissa Davis, Jordan Grafman, Thomas Neylan, Balebail Ashok Raj Dec 2023

Deep Learning-Based Polygenic Risk Analysis For Alzheimer’S Disease Prediction, Xiaopu Zhou, Yu Chen, Fanny C.F. Ip, Yuanbing Jiang, Han Cao, Ge Lv, Huan Zhong, Jiahang Chen, Tao Ye, Yuewen Chen, Yulin Zhang, Shuangshuang Ma, Ronnie M.N. Lo, Estella P.S. Tong, Ansgar J. Furst, Joy L. Taylor, Jerome A. Yesavage, Gail Li, Eric C. Petrie, Elaine R. Peskind, Sandra Harding, J. Jay Fruehling, Dino Massoglia, Olga James, Konstantinos Arfanakis, Debra Fleischman, Karl Friedl, Shannon Finley, Jacqueline Hayes, Rosemary Morrison, Melissa Davis, Jordan Grafman, Thomas Neylan, Balebail Ashok Raj

Clinical Research Faculty Publications

Background: The polygenic nature of Alzheimer’s disease (AD) suggests that multiple variants jointly contribute to disease susceptibility. As an individual’s genetic variants are constant throughout life, evaluating the combined effects of multiple disease-associated genetic risks enables reliable AD risk prediction. Because of the complexity of genomic data, current statistical analyses cannot comprehensively capture the polygenic risk of AD, resulting in unsatisfactory disease risk prediction. However, deep learning methods, which capture nonlinearity within high-dimensional genomic data, may enable more accurate disease risk prediction and improve our understanding of AD etiology. Accordingly, we developed deep learning neural network models for modeling AD …

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Prognostic Relevance Of Gait-Related Cognitive Functions For Dementia Conversion In Amnestic Mild Cognitive Impairment, Cosimo Tuena, Sara Maestri, Silvia Serino, Elisa Pedroli, Marco Stramba-Badiale, Giuseppe Riva, Lisa C. Silbert, Betty Lind, Rachel Crissey, Jeffrey A. Kaye, Raina Carter, Sara Dolen, Joseph Quinn, Lon S. Schneider, Sonia Pawluczyk, Mauricio Becerra, Liberty Teodoro, Karen Dagerman, Bryan M. Spann, James Brewer, Adam Fleisher, Helen Vanderswag, Jaimie Ziolkowski, Judith L. Heidebrink, Lisa Zbizek-Nulph, Joanne L. Lord, Colleen S. Albers, Ronald Petersen, Sara S. Mason, David Knopman, Kris Johnson, Javier Villanueva-Meyer, Valory Pavlik, Nathaniel Pacini Dec 2023

Prognostic Relevance Of Gait-Related Cognitive Functions For Dementia Conversion In Amnestic Mild Cognitive Impairment, Cosimo Tuena, Sara Maestri, Silvia Serino, Elisa Pedroli, Marco Stramba-Badiale, Giuseppe Riva, Lisa C. Silbert, Betty Lind, Rachel Crissey, Jeffrey A. Kaye, Raina Carter, Sara Dolen, Joseph Quinn, Lon S. Schneider, Sonia Pawluczyk, Mauricio Becerra, Liberty Teodoro, Karen Dagerman, Bryan M. Spann, James Brewer, Adam Fleisher, Helen Vanderswag, Jaimie Ziolkowski, Judith L. Heidebrink, Lisa Zbizek-Nulph, Joanne L. Lord, Colleen S. Albers, Ronald Petersen, Sara S. Mason, David Knopman, Kris Johnson, Javier Villanueva-Meyer, Valory Pavlik, Nathaniel Pacini

Clinical Research Faculty Publications

Background: Increasing research suggests that gait abnormalities can be a risk factor for Alzheimer’s Disease (AD). Notably, there is growing evidence highlighting this risk factor in individuals with amnestic Mild Cognitive Impairment (aMCI), however further studies are needed. The aim of this study is to analyze cognitive tests results and brain-related measures over time in aMCI and examine how the presence of gait abnormalities (neurological or orthopedic) or normal gait affects these trends. Additionally, we sought to assess the significance of gait and gait-related measures as prognostic indicators for the progression from aMCI to AD dementia, comparing those who converted …

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Global Dataset Of Soil Organic Carbon In Tidal Marshes, Tania L. Maxwell, André S. Rovai, Maria Fernanda Adame, Janine B. Adams, José Álvarez-Rogel, William E.N. Austin, Kim Beasy, Francesco Boscutti, Michael E. Böttcher, Tjeerd J. Bouma, Richard H. Bulmer, Annette Burden, Shannon A. Burke, Saritta Camacho, Doongar R. Chaudhary, Gail L. Chmura, Margareth Copertino, Grace M. Cott, Christopher Craft, John Day, Carmen B. De Los Santos, Lionel Denis, Weixin Ding, Joanna C. Ellison, Carolyn J. Ewers Lewis, Luise Giani, Maria Gispert, Swanne Gontharet, José A. González-Pérez, M. Nazaret González-Alcaraz, Connor Gorham, Anna Elizabeth L. Graversen, Anthony Grey Dec 2023

Global Dataset Of Soil Organic Carbon In Tidal Marshes, Tania L. Maxwell, André S. Rovai, Maria Fernanda Adame, Janine B. Adams, José Álvarez-Rogel, William E.N. Austin, Kim Beasy, Francesco Boscutti, Michael E. Böttcher, Tjeerd J. Bouma, Richard H. Bulmer, Annette Burden, Shannon A. Burke, Saritta Camacho, Doongar R. Chaudhary, Gail L. Chmura, Margareth Copertino, Grace M. Cott, Christopher Craft, John Day, Carmen B. De Los Santos, Lionel Denis, Weixin Ding, Joanna C. Ellison, Carolyn J. Ewers Lewis, Luise Giani, Maria Gispert, Swanne Gontharet, José A. González-Pérez, M. Nazaret González-Alcaraz, Connor Gorham, Anna Elizabeth L. Graversen, Anthony Grey

Faculty Publications

Tidal marshes store large amounts of organic carbon in their soils. Field data quantifying soil organic carbon (SOC) stocks provide an important resource for researchers, natural resource managers, and policy-makers working towards the protection, restoration, and valuation of these ecosystems. We collated a global dataset of tidal marsh soil organic carbon (MarSOC) from 99 studies that includes location, soil depth, site name, dry bulk density, SOC, and/or soil organic matter (SOM). The MarSOC dataset includes 17,454 data points from 2,329 unique locations, and 29 countries. We generated a general transfer function for the conversion of SOM to SOC. Using this …

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Enviromic-Based Kernels May Optimize Resource Allocation With Multi-Trait Multi-Environment Genomic Prediction For Tropical Maize, Raysa Gevartosky, Humberto Fanelli Carvalho, Germano Costa-Neto, Osval A. Montesinos-López, José Crossa, Roberto Fritsche-Neto Dec 2023

Enviromic-Based Kernels May Optimize Resource Allocation With Multi-Trait Multi-Environment Genomic Prediction For Tropical Maize, Raysa Gevartosky, Humberto Fanelli Carvalho, Germano Costa-Neto, Osval A. Montesinos-López, José Crossa, Roberto Fritsche-Neto

Faculty Publications

Background: Success in any genomic prediction platform is directly dependent on establishing a representative training set. This is a complex task, even in single-trait single-environment conditions and tends to be even more intricated wherein additional information from envirotyping and correlated traits are considered. Here, we aimed to design optimized training sets focused on genomic prediction, considering multi-trait multi-environment trials, and how those methods may increase accuracy reducing phenotyping costs. For that, we considered single-trait multi-environment trials and multi-trait multi-environment trials for three traits: grain yield, plant height, and ear height, two datasets, and two cross-validation schemes. Next, two strategies for …

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Dna Methylation Is Differentially Associated With Glycemic Outcomes By Different Types Of Weight-Loss Interventions: An Epigenome-Wide Association Study, Xiaoxiao Wen, Helena Palma-Gudiel, Guanhong Miao, Mingjing Chen, Zhiguang Huo, Hao Peng, Stephen Anton, Gang Hu, Ricky Brock, Phillip J. Brantley, Jinying Zhao Dec 2023

Dna Methylation Is Differentially Associated With Glycemic Outcomes By Different Types Of Weight-Loss Interventions: An Epigenome-Wide Association Study, Xiaoxiao Wen, Helena Palma-Gudiel, Guanhong Miao, Mingjing Chen, Zhiguang Huo, Hao Peng, Stephen Anton, Gang Hu, Ricky Brock, Phillip J. Brantley, Jinying Zhao

Population and Public Health Science Faculty Publications

Background: Alterations in DNA methylation (DNAm) have been reported to be a mechanism by which bariatric surgeries resulted in considerable metabolic improvements. Previous studies have mostly focused on change in DNAm following weight-loss interventions, yet whether DNAm prior to intervention can explain the variability in glycemic outcomes has not been investigated. Here, we aim to examine whether baseline DNAm is differentially associated with glycemic outcomes induced by different types of weight-loss interventions. Methods: Participants were 75 adults with severe obesity who underwent non-surgical intensive medical intervention (IMI), adjustable gastric band (BAND) or Roux-en-Y gastric bypass (RYGB) (n = 25 each). …

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Calorie Restriction Modulates The Transcription Of Genes Related To Stress Response And Longevity In Human Muscle: The Calerie Study, Jayanta Kumar Das, Nirad Banskota, Julián Candia, Michael E. Griswold, Melissa Orenduff, Rafael De Cabo, David L. Corcoran, Sai Krupa Das, Supriyo De, Kim Marie Huffman, Virginia B. Kraus, William E. Kraus, Corby K Martin, Susan B. Racette, Leanne M. Redman, Birgit Schilling, Daniel W Belsky, Luigi Ferrucci Dec 2023

Calorie Restriction Modulates The Transcription Of Genes Related To Stress Response And Longevity In Human Muscle: The Calerie Study, Jayanta Kumar Das, Nirad Banskota, Julián Candia, Michael E. Griswold, Melissa Orenduff, Rafael De Cabo, David L. Corcoran, Sai Krupa Das, Supriyo De, Kim Marie Huffman, Virginia B. Kraus, William E. Kraus, Corby K Martin, Susan B. Racette, Leanne M. Redman, Birgit Schilling, Daniel W Belsky, Luigi Ferrucci

Clinical Research Faculty Publications

The lifespan extension induced by 40% caloric restriction (CR) in rodents is accompanied by postponement of disease, preservation of function, and increased stress resistance. Whether CR elicits the same physiological and molecular responses in humans remains mostly unexplored. In the CALERIE study, 12% CR for 2 years in healthy humans induced minor losses of muscle mass (leg lean mass) without changes of muscle strength, but mechanisms for muscle quality preservation remained unclear. We performed high-depth RNA-Seq (387–618 million paired reads) on human vastus lateralis muscle biopsies collected from the CALERIE participants at baseline, 12- and 24-month follow-up from the 90 …

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Single-Cell Analysis In Hypersaline Brines Predicts A Water-Activity Limit Of Microbial Anabolic Activity, Emily R. Paris, Nestor Arandia-Gorostidi, Benjamin Klempay, Jeff S. Bowman, Alexandra Pontefract, Claire E. Elbon, Jennifer B. Glass, Ellery D. Ingall, Peter T. Doran, Sanjoy M. Som, Britney E. Schmidt, Anne E. Dekas Dec 2023

Single-Cell Analysis In Hypersaline Brines Predicts A Water-Activity Limit Of Microbial Anabolic Activity, Emily R. Paris, Nestor Arandia-Gorostidi, Benjamin Klempay, Jeff S. Bowman, Alexandra Pontefract, Claire E. Elbon, Jennifer B. Glass, Ellery D. Ingall, Peter T. Doran, Sanjoy M. Som, Britney E. Schmidt, Anne E. Dekas

Faculty Publications

Hypersaline brines provide excellent opportunities to study extreme microbial life. Here, we investigated anabolic activity in nearly 6000 individual cells from solar saltern sites with water activities (aw) ranging from 0.982 to 0.409 (seawater to extreme brine). Average anabolic activity decreased exponentially with aw, with nuanced trends evident at the single-cell level: The proportion of active cells remained high (>50%) even after NaCl saturation, and subsets of cells spiked in activity as aw decreased. Intracommunity heterogeneity in activity increased as seawater transitioned to brine, suggesting increased phenotypic heterogeneity with increased physiological stress. No microbial activity was detected in the …

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Light-Driven And Nutrient-Driven Displacements Of Subsurface Chlorophyll Maximum Depth In Subtropical Gyres, Xiaogang Xing, Peng Xiu, Edward A. Laws, Guo Yang, Xin Liu, Fei Chai Nov 2023

Light-Driven And Nutrient-Driven Displacements Of Subsurface Chlorophyll Maximum Depth In Subtropical Gyres, Xiaogang Xing, Peng Xiu, Edward A. Laws, Guo Yang, Xin Liu, Fei Chai

Faculty Publications

The mechanism that determines the dynamics of subsurface chlorophyll maximum depth (zSCM) has long been debated. Although a coupling between zSCM and the top of nitracline (znit) has been widely observed in the open ocean, a co-location of zSCM and an isolume depth (ziso) has often been reported in oligotrophic waters. In this study, based on continuous observations of ten BGC-Argo floats, we found that the seasonal displacement of zSCM in all subtropical gyres was driven mainly by light, but zSCM displayed a nutrient-driven pattern occasionally when znit became shallower than ziso. We therefore proposed a “two-group competition framework”: zSCM …

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Bearded Or Smooth? Awns Improve Yield When Wheat Experiences Heat Stress During Grain Fill In The Southeastern United States, Noah Dewitt, Jeanette Lyerly, Mohammed Guedira, James B. Holland, J. Paul Murphy, Brian P. Ward, Richard E. Boyles, Mohamed Mergoum, Md Ali Babar, Ehsan Shakiba, Russel Sutton, Amir Ibrahim, Vijay Tiwari, Nicholas Santantonio, David A. Van Sanford, Kimberly Howell, Jared H. Smith, Stephen A. Harrison, Gina Brown-Guedira Nov 2023

Bearded Or Smooth? Awns Improve Yield When Wheat Experiences Heat Stress During Grain Fill In The Southeastern United States, Noah Dewitt, Jeanette Lyerly, Mohammed Guedira, James B. Holland, J. Paul Murphy, Brian P. Ward, Richard E. Boyles, Mohamed Mergoum, Md Ali Babar, Ehsan Shakiba, Russel Sutton, Amir Ibrahim, Vijay Tiwari, Nicholas Santantonio, David A. Van Sanford, Kimberly Howell, Jared H. Smith, Stephen A. Harrison, Gina Brown-Guedira

Faculty Publications

The presence or absence of awns-whether wheat heads are 'bearded' or 'smooth' - is the most visible phenotype distinguishing wheat cultivars. Previous studies suggest that awns may improve yields in heat or water-stressed environments, but the exact contribution of awns to yield differences remains unclear. Here we leverage historical phenotypic, genotypic, and climate data for wheat (Triticum aestivum) to estimate the yield effects of awns under different environmental conditions over a 12-year period in the southeastern USA. Lines were classified as awned or awnless based on sequence data, and observed heading dates were used to associate grain fill periods of …

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An Intersection Of Science & Art: Vitrification Approaches And Open-Fabricated Tools For The Biomedical Model Sea Hare, Aplysia Californica, Allyssa M. Oune Nov 2023

An Intersection Of Science & Art: Vitrification Approaches And Open-Fabricated Tools For The Biomedical Model Sea Hare, Aplysia Californica, Allyssa M. Oune

LSU Master's Theses

The California sea hare (Aplysia californica) is an important biomedical model for molecular neurobiology, electrophysiology, learning, and memory due to their well-mapped and large neurons and well-characterized learning capabilities. The National Resource for Aplysia (NRA, University of Miami) maintains large stocks of live animals and relies on regular shipments of wild-caught individuals to maintain genetic diversity. This is labor and cost-intensive, and environmental changes could alter the availability of wild animals increasing the need to preserve this genetic resource. One solution is vitrification, ultra-fast cooling which produces an amorphous glass that minimizes damage to cells. Aplysia californica presents …

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Improving Cellphone-Based Bio-Imaging Technique For Fluorescence Detection, Erteza T. Efaz Nov 2023

Improving Cellphone-Based Bio-Imaging Technique For Fluorescence Detection, Erteza T. Efaz

LSU Master's Theses

The research presented in this thesis focuses on the design, development, and evaluation of a fluorescence detection system. The system is implemented primarily as an Android application, Auto Camera, which leverages smartphone cameras to capture and analyze fluorescent images. The application provides a user-friendly interface with some configurable features like exposure time, ISO speed, and storage limit; as well as defining detection thresholds and setting acquisition intervals. This study begins with the architectural framework of the Android application, which is written in Java using Android Studio. The API compatibility is set to version 33, and users are prompted to grant …

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Optimizing Virulence And Understanding The Endophytic Colonization Of Metarhizium Spp. In Sweetpotato For The Control Of Cylas Formicarius Elegantulus (Summers), Santosh Bhandari Nov 2023

Optimizing Virulence And Understanding The Endophytic Colonization Of Metarhizium Spp. In Sweetpotato For The Control Of Cylas Formicarius Elegantulus (Summers), Santosh Bhandari

LSU Master's Theses

In the United States, control of the sweetpotato weevil [SPW, Cylas formicarius elegantulus (Summers)] occurs through quarantine and regular use of chemical insecticides. However, an overreliance on chemical control may lead to resistance. Entomopathogenic fungi have potential to act as an alternative to chemical control. In this study, we assessed four different strains of Metarhizium isolated from soil collected in Louisiana (Mp-K048, Ma-K056, Mr-K082, and Mr-K101) and compared them to a well-known licensed strain (Mb-ARSEF 1095) for virulence against C. formicarius elegantulus. Results suggested that Mp-K048, Ma-K056, and Mr-K082 …

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A Study Of Tissue-Specific Rho Signaling Activation During Tubular Organ Formation In Drosophila, Charlotte Jean-Louise Adams Nov 2023

A Study Of Tissue-Specific Rho Signaling Activation During Tubular Organ Formation In Drosophila, Charlotte Jean-Louise Adams

LSU Master's Theses

Several organs within the human body are tubular in structure. In the event of a malfunction in the development of these tubular structures, maladies like spina bifida, anencephaly, and several other defects can arise. To understand the mechanisms of tubular organ formation, we use the Drosophila embryonic salivary gland (SG) as a model. During embryogenesis, SG cells undergo a series of cell shape changes, like apical constriction, to accommodate the developing gland. Apical constriction is regulated in part by the signal of the secreted ligand Folded gastrulation (Fog) and its G protein-coupled receptor (GPCR) at the cell membrane, which leads …

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Mirna As Systemic Mediators For Environmentally Persistent Free Radical-Induced Cardiovascular Dysfunction, Ankit Aryal Nov 2023

Mirna As Systemic Mediators For Environmentally Persistent Free Radical-Induced Cardiovascular Dysfunction, Ankit Aryal

LSU Doctoral Dissertations

Air pollution is consistently linked with elevations in cardiovascular disease (CVD) and its mortality. Particulate matter (PM) is a pivotal factor in air pollution-associated CVD. PM containing environmentally persistent free radicals (EPFR) forms from the incomplete combustion of organic wastes. These products adhere to particulate matter carrying redox-active transition metals on its surface. To enable systematic research of the health impacts of EPFR, our colleagues developed a combustion method to produce EPFR-containing PM that closely resemble urban PM and validated their use for typical laboratory settings. We exposed mice to laboratory generated EPFR through whole-body inhalation and investigated their dose-dependent …

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A Dance Of Resistance: The Puerto Rican Bomba As A Means To Challenge Intersections Of Discrimination On The Island, Daniel Loving Nov 2023

A Dance Of Resistance: The Puerto Rican Bomba As A Means To Challenge Intersections Of Discrimination On The Island, Daniel Loving

LSU Master's Theses

This thesis examines the Puerto Rican Bomba as a multifaceted cultural and political phenomenon, focusing on its pivotal role in challenging and subverting the enduring issues of racial and gender discrimination on the Island. Drawing from an interdisciplinary framework that encompasses cultural studies, anthropology, history, performance and film studies, this research elucidates the complex interplay between Bomba's rhythmic and choreographic elements, its historical evolution, and its contemporary significance in the context of Puerto Rico's sociopolitical landscape. By analyzing Bomba's historical roots in African and indigenous traditions, its adaptation during colonial and post-colonial eras, and its ongoing relevance in the struggle …

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Understanding The Impacts Of Molecular And Macromolecular Crowding Agents On Protein-Polymer Complex Coacervates, Shanta Biswas, Alison L. Hecht, Sadie A. Noble, Qingqiu Huang, Richard E. Gillilan, Amy Y. Xu Nov 2023

Understanding The Impacts Of Molecular And Macromolecular Crowding Agents On Protein-Polymer Complex Coacervates, Shanta Biswas, Alison L. Hecht, Sadie A. Noble, Qingqiu Huang, Richard E. Gillilan, Amy Y. Xu

Faculty Publications

Complex coacervation refers to the liquid-liquid phase separation (LLPS) process occurring between charged macromolecules. The study of complex coacervation is of great interest due to its implications in the formation of membraneless organelles (MLOs) in living cells. However, the impacts of the crowded intracellular environment on the behavior and interactions of biomolecules involved in MLO formation are not fully understood. To address this knowledge gap, we investigated the effects of crowding on a model protein-polymer complex coacervate system. Specifically, we examined the influence of sucrose as a molecular crowder and polyethylene glycol (PEG) as a macromolecular crowder. Our results reveal …

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The Structures And Functions Of Offices Of Academic Affairs: A Case Study, Ryan Thomas Landry Nov 2023

The Structures And Functions Of Offices Of Academic Affairs: A Case Study, Ryan Thomas Landry

LSU Doctoral Dissertations

This study sought to describe how offices of academic affairs (administrative offices supporting provosts) at public, research-intensive universities in the United States are structured and what kind of work these offices do. There is a dearth of scholarly literature on the topic, indicative of an overall lack of knowledge about these organizations. From a practical standpoint, I intended for this study to contribute to the body of knowledge of higher education administration with hopes that it provides helpful insights to administrators as they consider organizational design. Using the theoretical framework of modern organization theory, I employed an embedded case study …

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Efficient Chemical-Free Degradation Of Waterborne Micropollutants With An Immobilized Dual-Porous Tio2 Photocatalyst, Daniel E. Willis, Ella C. Sheets, Mary R. Worbington, Madhusudan Kamat, Sarah K. Glass, Ma Cayla J. Caso, Tochukwu Ofoegbuna, Liz M. Diaz, Caleb Osei-Appau, Samuel D. Snow, Kevin M. Mcpeak Nov 2023

Efficient Chemical-Free Degradation Of Waterborne Micropollutants With An Immobilized Dual-Porous Tio2 Photocatalyst, Daniel E. Willis, Ella C. Sheets, Mary R. Worbington, Madhusudan Kamat, Sarah K. Glass, Ma Cayla J. Caso, Tochukwu Ofoegbuna, Liz M. Diaz, Caleb Osei-Appau, Samuel D. Snow, Kevin M. Mcpeak

Faculty Publications

Photocatalytic advanced oxidation processes (AOPs) promise a chemical-free route to energy-efficient degradation of waterborne micropollutants if long-standing mass transfer and light management issues can be overcome. Herein, we developed a dual-porous photocatalytic system consisting of a mesoporous (i.e., 2-50 nm pores) TiO2 (P25) photocatalyst supported on macroporous (i.e., >50 nm pores) fused quartz fibers (P25/QF). Our reusable photocatalytic AOP reduces chemical consumption and exhibits excellent energy efficiency, demonstrated by degrading various pharmaceutical compounds (acetaminophen, sulfamethoxazole, and carbamazepine) in natural waters with electrical energy per order (EEO) values of 4.07, 0.96, and 1.35 kWh/m3, respectively. Compared to the conventional H2O2/UVC AOP, …

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Uavs And Deep Neural Networks: An Alternative Approach To Monitoring Waterfowl At The Site Level, Zachary J. Loken Nov 2023

Uavs And Deep Neural Networks: An Alternative Approach To Monitoring Waterfowl At The Site Level, Zachary J. Loken

LSU Master's Theses

Understanding how waterfowl respond to habitat restoration and management activities is crucial for evaluating and refining conservation delivery programs. However, site-specific waterfowl monitoring is challenging, especially in heavily forested systems such as the Mississippi Alluvial Valley (MAV)—a primary wintering region for ducks in North America. I hypothesized that using uncrewed aerial vehicles (UAVs) coupled with deep learning-based methods for object detection would provide an efficient and effective means for surveying non-breeding waterfowl on difficult-to-access restored wetland sites. Accordingly, during the winters of 2021 and 2022, I surveyed wetland restoration easements in the MAV using a UAV equipped with a dual …

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Using Machine Learning To Measure Changes In Immunity Due To Climate Change In The Fall Armyworm, Spodoptera Frugiperda, Nathaniel T. Haulk Nov 2023

Using Machine Learning To Measure Changes In Immunity Due To Climate Change In The Fall Armyworm, Spodoptera Frugiperda, Nathaniel T. Haulk

LSU Master's Theses

Object detection is a recent development that allows for the detection of multiple objects in photographs. Numerous machine learning algorithms have been developed for object detection. Here we sought to determine which algorithm performed best when relating to an organism's health and immunological response. The fall armyworm (Spodoptera frugiperda) is a major agricultural pest causing millions of dollars in damage to farmlands across the globe. With their recent spread into Africa and Asia, the need for understanding how best to control population outbreaks via biocontrol has increased. While viruses are a major biocontrol agent for controlling insect pests, we …

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Shifting Taxonomic And Functional Community Composition Of Rivers Under Land Use Change, Kai Chen, Stephen R. Midway, Brandon K. Peoples, Beixin Wang, Julian D. Olden Nov 2023

Shifting Taxonomic And Functional Community Composition Of Rivers Under Land Use Change, Kai Chen, Stephen R. Midway, Brandon K. Peoples, Beixin Wang, Julian D. Olden

Faculty Publications

Land use intensification has led to conspicuous changes in plant and animal communities across the world. Shifts in trait-based functional composition have recently been hypothesized to manifest at lower levels of environmental change when compared to species-based taxonomic composition; however, little is known about the commonalities in these responses across taxonomic groups and geographic regions. We investigated this hypothesis by testing for taxonomic and geographic similarities in the composition of riverine fish and insect communities across gradients of land use in major hydrological regions of the conterminous United States. We analyzed an extensive data set representing 556 species and 33 …

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The Future Of Cyanobacteria Toxicity In Estuaries Undergoing Pulsed Nutrient Inputs: A Case Study From Coastal Louisiana, Sibel Bargu, Matthew Hiatt, Kanchan Maiti, Paul Miller, John R. White Nov 2023

The Future Of Cyanobacteria Toxicity In Estuaries Undergoing Pulsed Nutrient Inputs: A Case Study From Coastal Louisiana, Sibel Bargu, Matthew Hiatt, Kanchan Maiti, Paul Miller, John R. White

Faculty Publications

Harmful cyanobacteria blooms (cyanoHABs) are a global phenomenon, especially in calm, warm, and nutrient-rich freshwater and estuarine systems. These blooms can produce various potent toxins responsible for animal poisoning and human health problems. Nutrient-rich freshwater pulsed into estuaries affects turbidity, water temperature, salinity, and nutrient concentrations and ratios at irregular intervals, creating a highly dynamic habitat. However, the underlying processes that lead to the selective development of cyanoHABs for certain species and the fate of their toxins are still uncertain. This paper draws upon the rich body of research available for one such system, the Lake Pontchartrain Estuary, Louisiana, to …

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Limnological Response Of Las Curias Reservoir, San Juan, Puerto Rico: Successful Management Of The Invasive Aquatic Fern, Salvinia Molesta, Xavier A. García-López, Jorge R. Ortiz-Zayas, Rodrigo Díaz, Aurelio Castro-Jiménez, Charles F. Wahl Nov 2023

Limnological Response Of Las Curias Reservoir, San Juan, Puerto Rico: Successful Management Of The Invasive Aquatic Fern, Salvinia Molesta, Xavier A. García-López, Jorge R. Ortiz-Zayas, Rodrigo Díaz, Aurelio Castro-Jiménez, Charles F. Wahl

Faculty Publications

The anthropogenic deterioration of aquatic ecosystems affects water resources due to agricultural malpractices, pollution from domestic septic tanks, recreational activities, and poor watershed management, among other factors. This study examines the management of Las Curias Reservoir, San Juan, Puerto Rico, after the 2016 arrival of the invasive aquatic fern Salvinia molesta. In September 2019, a community-led initiative introduced the Cyrtobagous salviniae weevil, an effective biological control agent for S. molesta, and commenced a mechanical removal campaign using an aquatic harvester. Limnological sampling (September 2019 to September 2022) and drone flights were employed to measure physicochemical and floating plant cover changes, …

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A Phoenix Glimmers Within The Ashes: Generalized Defensive Traits Suggest Hope For Plants Under Attack By Invasive Pests, Todd D. Johnson, Justin G.A. Whitehill Nov 2023

A Phoenix Glimmers Within The Ashes: Generalized Defensive Traits Suggest Hope For Plants Under Attack By Invasive Pests, Todd D. Johnson, Justin G.A. Whitehill

Faculty Publications

No abstract provided.

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A Membrane Protein Of The Rice Pathogen Burkholderia Glumae Required For Oxalic Acid Secretion And Quorum Sensing, Asif Iqbal, George Nwokocha, Vijay Tiwari, Inderjit K. Barphagha, Anne Grove, Jong Hyun Ham, William T. Doerrler Nov 2023

A Membrane Protein Of The Rice Pathogen Burkholderia Glumae Required For Oxalic Acid Secretion And Quorum Sensing, Asif Iqbal, George Nwokocha, Vijay Tiwari, Inderjit K. Barphagha, Anne Grove, Jong Hyun Ham, William T. Doerrler

Faculty Publications

Bacterial panicle blight is caused by Burkholderia glumae and results in damage to rice crops worldwide. Virulence of B. glumae requires quorum sensing (QS)-dependent synthesis and export of toxoflavin, responsible for much of the damage to rice. The DedA family is a conserved membrane protein family found in all bacterial species. B. glumae possesses a member of the DedA family, named DbcA, which we previously showed is required for toxoflavin secretion and virulence in a rice model of infection. B. glumae secretes oxalic acid as a “common good” in a QS-dependent manner to combat toxic alkalinization of the growth medium …

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