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Articles 31 - 60 of 745
Full-Text Articles in Biology
Redundant Functions Of Mir156-Targeted Squamosa Promoter Binding Protein-Like Transcription Factors In Promoting Cauline Leaf Identity, Darren Manuela, Liren Du, Qi Zhang, Yifei Liao, Tieqiang Hu, Jim P. Fouracre, Mingli Xu
Redundant Functions Of Mir156-Targeted Squamosa Promoter Binding Protein-Like Transcription Factors In Promoting Cauline Leaf Identity, Darren Manuela, Liren Du, Qi Zhang, Yifei Liao, Tieqiang Hu, Jim P. Fouracre, Mingli Xu
Faculty Publications
No abstract provided.
Evaluating Potential Changes From Nitrogen To Phosphorus Nutrient Limitation Of Phytoplankton Growth In North Inlet Estuary, Catherine Schlenker, James L. Pinckney
Evaluating Potential Changes From Nitrogen To Phosphorus Nutrient Limitation Of Phytoplankton Growth In North Inlet Estuary, Catherine Schlenker, James L. Pinckney
Faculty Publications
In marine systems, molar ratios of the biolimiting inorganic nutrients, nitrogen (N) and phosphorus (P), are assumed to follow the “Redfield ratio” (N:P = 16:1), which is often used to infer nutrient limitation of phytoplankton biomass. Traditionally, estuaries are considered N-limited (N:P < 16) but with higher coastal N-loading, reports of P-limitation (N:P > 16) have increased. In recent decades, nutrient loading in North Inlet Estuary (NIE) has changed such that dissolved inorganic nitrogen (DIN):dissolved inorganic phosphorus (DIP) ratios increased from ca. 7 to 20 (2002–2021). This suggests that primary production in NIE may be transitioning from N-limitation to NP co-limitation or primary P-limitation. Due to high N:P ratios, we hypothesized that …
Human Gut Commensal Alistipes Timonensis Modulates The Host Lipidome And Delivers Anti-Inflammatory Outer Membrane Vesicles To Suppress Colitis In An Il10-Deficient Mouse Model, Ethan Older, Mary K. Mitchell, Andrew Campbell, Xiaoying Lian, Michael Madden, Yuzhen Wang, Lauren E. Van De Wal, Thelma Zaw, Brandon N. Vanderveen, Rodney Tatum, E. Angela Murphy, Yan-Hua Chen, Daping Fang, Melissa Ellermann, Jie Li
Human Gut Commensal Alistipes Timonensis Modulates The Host Lipidome And Delivers Anti-Inflammatory Outer Membrane Vesicles To Suppress Colitis In An Il10-Deficient Mouse Model, Ethan Older, Mary K. Mitchell, Andrew Campbell, Xiaoying Lian, Michael Madden, Yuzhen Wang, Lauren E. Van De Wal, Thelma Zaw, Brandon N. Vanderveen, Rodney Tatum, E. Angela Murphy, Yan-Hua Chen, Daping Fang, Melissa Ellermann, Jie Li
Faculty Publications
Correlative studies have linked human gut microbes to specific health conditions. Alistipes is one such microbial genus negatively linked to inflammatory bowel disease (IBD). However, the protective role of Alistipes in IBD is understudied, and the underlying molecular mechanisms remain unknown. In this study, colonization of Il10-deficient mice with Alistipes timonensis DSM 27924 delays colitis development. Colonization does not significantly alter the gut microbiome composition, but instead shifts the host plasma lipidome, increasing phosphatidic acids while decreasing triglycerides. Outer membrane vesicles (OMVs) derived from Alistipes are detected in the plasma of colonized mice, carrying potentially immunomodulatory metabolites into the …
The Influence Of Geographic Ranges, Climatic Niches And Temperature Fluctuations On Population Variability, Cleber Ten Canten, Lauren Holian, Tad Dallas
The Influence Of Geographic Ranges, Climatic Niches And Temperature Fluctuations On Population Variability, Cleber Ten Canten, Lauren Holian, Tad Dallas
Faculty Publications
The existence of patterns in population dynamics across species geographic ranges and climatic niches is a pervasive idea in ecology. Population variability (i.e. temporal variability in population density) should hypothetically increase near range edges or niche limits because of less suitable environments in these areas, but the occurrence of such patterns remains largely unexplored. Further, fluctuations in temperature could pose demographic constraints on populations and also influence their variability. We used Breeding Bird Survey data to show that the population variability of 97 resident North American birds consistently increases towards their niche limits and in areas with more variable temperatures, …
Cationic Conjugated Polymers With Enhanced Doped-State Planarity For N-Type Organic Thermoelectrics, Jiu-Long Li, Xin-Yu Deng, Jupeng Chen, Peng-Xiang Fu, Shuang-Yan Tian, Yunfei Wang, Xiaodan Gu, Ting Lei
Cationic Conjugated Polymers With Enhanced Doped-State Planarity For N-Type Organic Thermoelectrics, Jiu-Long Li, Xin-Yu Deng, Jupeng Chen, Peng-Xiang Fu, Shuang-Yan Tian, Yunfei Wang, Xiaodan Gu, Ting Lei
Faculty Publications
To date, extensive efforts have been devoted to designing new conjugated polymers with long alkyl or ethylene glycol sidechains. However, these sidechains are insulators, limiting further performance enhancement in doped conjugated polymers. Moreover, the most widely used chlorinated solvents are toxic, limiting the practical applications of many conjugated polymers. Here, we report a water/alcohol processable n-type conjugated polymer P(Py2FT), featuring side chain-free cationic backbones. P(Py2FT) exhibits a high n-type electrical conductivity of up to 28.1 S cm−1 and a high thermoelectric power factor of up to 28.7 μW m−1 K−2, comparable to some conventional …
Whole-Genome Assembly And Annotation Of The Firecracker Penstemon (Penstemon Eatonii), David E. Jarvis, Mikel R. Stevens, Payton Carter, Ying Fei Lin, Kate E. Jaggi, Gabriela Jijon, Teal Kalt, Jouber Calixto, Samantha Standring, Kaitlin Torres, Kayla B. Stephensen, Hayley Mangelson, Noah H. Williams, Carolyn A. Wessinger, Peter J. Maughan, Paul B. Frandsen
Whole-Genome Assembly And Annotation Of The Firecracker Penstemon (Penstemon Eatonii), David E. Jarvis, Mikel R. Stevens, Payton Carter, Ying Fei Lin, Kate E. Jaggi, Gabriela Jijon, Teal Kalt, Jouber Calixto, Samantha Standring, Kaitlin Torres, Kayla B. Stephensen, Hayley Mangelson, Noah H. Williams, Carolyn A. Wessinger, Peter J. Maughan, Paul B. Frandsen
Faculty Publications
The penstemons are ornamental annual flowering plants native to the Intermountain West and Rocky Mountains and commonly used for urban landscaping. Elite commercial penstemons are generally susceptible to abiotic stresses, including drought, root rot, cold, and high salinity. Firecracker penstemon (Penstemon eatonii), however, is much more tolerant to these stresses than most elite cultivars. Importantly, firecracker penstemon has been reported to hybridize with many other penstemons and therefore provides the opportunity to develop more tolerant elite cultivars through strategic crossing. To facilitate the study and utilization of firecracker penstemon, we sequenced and annotated the genome of a P. …
Whole-Genome Assembly And Annotation Of The Firecracker Penstemon (Penstemon Eatonii), David E. Jarvis, Mikel R. Stevens, Payton Carter, Ying Fei Lin, Kate E. Jaggi, Gabriela Jijon, Teal Kalt, Jouber Calixto, Samantha Standring, Kaitlin Torres, Kayla B. Stephensen, Hayley Mangelson, Noah H. Williams, Carolyn A. Wessinger, Peter J. Maughan, Paul B. Frandsen
Whole-Genome Assembly And Annotation Of The Firecracker Penstemon (Penstemon Eatonii), David E. Jarvis, Mikel R. Stevens, Payton Carter, Ying Fei Lin, Kate E. Jaggi, Gabriela Jijon, Teal Kalt, Jouber Calixto, Samantha Standring, Kaitlin Torres, Kayla B. Stephensen, Hayley Mangelson, Noah H. Williams, Carolyn A. Wessinger, Peter J. Maughan, Paul B. Frandsen
Faculty Publications
The penstemons are ornamental annual flowering plants native to the Intermountain West and Rocky Mountains and commonly used for urban landscaping. Elite commercial penstemons are generally susceptible to abiotic stresses, including drought, root rot, cold, and high salinity. Firecracker penstemon (Penstemon eatonii), however, is much more tolerant to these stresses than most elite cultivars. Importantly, firecracker penstemon has been reported to hybridize with many other penstemons and therefore provides the opportunity to develop more tolerant elite cultivars through strategic crossing. To facilitate the study and utilization of firecracker penstemon, we sequenced and annotated the genome of a P. …
Adipocyte-Derived Cchamide-1, Eiger, Growth-Blocking Peptide 3, And Unpaired 2 Regulate Drosophila Melanogaster Oogenesis, Chad Simmons, Isaiah Williams, Tancia Bradshaw, Alissa R. Armstrong
Adipocyte-Derived Cchamide-1, Eiger, Growth-Blocking Peptide 3, And Unpaired 2 Regulate Drosophila Melanogaster Oogenesis, Chad Simmons, Isaiah Williams, Tancia Bradshaw, Alissa R. Armstrong
Faculty Publications
In addition to energy storage, adipose tissue communication to other organs plays a key role in regulating organismal physiology. While the link between adipose tissue dysfunction and pathophysiology, including diabetes, chronic inflammation, and infertility, is clear, the molecular mechanisms that underlie these associations have not been fully described. We use Drosophila melanogaster as a model to better understand how adipose tissue communicates to the ovary. In this study, we utilized D. melanogaster’s robust genetic toolkit to examine the role of five adipokines known to control larval growth during development, CCHamide-1, CCHamide-2, eiger, Growth-blocking peptide 3, and unpaired 2 in regulating …
Adipocyte-Derived Cchamide-1, Eiger, Growth-Blocking Peptide 3, And Unpaired 2 Regulate Drosophila Melanogaster Oogenesis, Chad Simmons, Isaiah H. Williams, Tancia W. Bradshaw, Alissa R. Armstrong
Adipocyte-Derived Cchamide-1, Eiger, Growth-Blocking Peptide 3, And Unpaired 2 Regulate Drosophila Melanogaster Oogenesis, Chad Simmons, Isaiah H. Williams, Tancia W. Bradshaw, Alissa R. Armstrong
Faculty Publications
In addition to energy storage, adipose tissue communication to other organs plays a key role in regulating organismal physiology. While the link between adipose tissue dysfunction and pathophysiology, including diabetes, chronic inflammation, and infertility, is clear, the molecular mechanisms that underlie these associations have not been fully described. We use Drosophila melanogaster as a model to better understand how adipose tissue communicates to the ovary. In this study, we utilized D. melanogaster’s robust genetic toolkit to examine the role of five adipokines known to control larval growth during development, CCHamide-1, CCHamide-2, eiger, Growth-blocking peptide 3, and unpaired 2 in regulating …
Commodity Thermoplastic Elastomer-Enabled Templated Synthesis Of Large-Pore Ordered Mesoporous Materials, Anthony Griffin, Parker Frame, Yizhi Xiang, Zhe Qiang
Commodity Thermoplastic Elastomer-Enabled Templated Synthesis Of Large-Pore Ordered Mesoporous Materials, Anthony Griffin, Parker Frame, Yizhi Xiang, Zhe Qiang
Faculty Publications
Fabrication of ordered mesoporous materials (OMMs) has predominantly relied on templating-based methods. However, these methods are constrained by several limitations, especially the limited pore sizes attainable with commercially available surfactants used as structure-directing agents. To unlock the full potential of the OMMs, it is essential to develop synthetic strategies that facilitate the production of large-pore OMMs using scalable processes and cost-effective precursors. This work demonstrates the use of thermoplastic elastomer (TPE)-derived carbon replicas for synthesizing ordered mesoporous silica (OMS) and metal oxides (OMMOs) via precursor infiltration and template removal. The nanostructural evolution of the resulting inorganic materials was systematically investigated. …
Nucleoredoxin Regulates Wnt Signaling During Pituitary Stem Cell Differentiation, Michelle L. Brinkmeier, Leonard Y M Cheung, Sean P. O'Connell, Diana K. Gutierrez, Eve C. Rhoads, Sally A. Camper, Shannon W. Davis
Nucleoredoxin Regulates Wnt Signaling During Pituitary Stem Cell Differentiation, Michelle L. Brinkmeier, Leonard Y M Cheung, Sean P. O'Connell, Diana K. Gutierrez, Eve C. Rhoads, Sally A. Camper, Shannon W. Davis
Faculty Publications
Nucleoredoxin (Nxn) encodes a multi-functional enzyme with oxidoreductase activity that regulates many different signaling pathways and cellular processes in a redox-dependent manner. Rare NXN mutations are reported in individuals with recessive Robinow syndrome, which involves mesomelic skeletal dysplasia, short stature, craniofacial dysmorphisms, and incompletely penetrant heart and palate defects. Here we report that Nxn is expressed in the ventral diencephalon and developing pituitary gland, and that Nxn deficient mice have pituitary dysmorphology and craniofacial abnormalities that include defects in the skull base and cleft palate. Nxn mutant mice exhibit reduced WNT signaling and reduced differentiation of pituitary stem …
Disruption Of G3bp1 Granules Promotes Mammalian Cns And Pns Axon Regeneration, Pabitra K. Sahoo, Manasi Agrawal, Nicholas Hanovice, Patricia J. Ward, Meghal Desai, Terika P. Smith, Hao Min Sima, Jennifer N. Dulin, Lauren S. Vaughn, Mark H. Tuszynski, Kristy Welshhans, Larry I. Benowitz, Arthur W. English, John D. Houle, Jeffery L. Twiss
Disruption Of G3bp1 Granules Promotes Mammalian Cns And Pns Axon Regeneration, Pabitra K. Sahoo, Manasi Agrawal, Nicholas Hanovice, Patricia J. Ward, Meghal Desai, Terika P. Smith, Hao Min Sima, Jennifer N. Dulin, Lauren S. Vaughn, Mark H. Tuszynski, Kristy Welshhans, Larry I. Benowitz, Arthur W. English, John D. Houle, Jeffery L. Twiss
Faculty Publications
Depletion or inhibition of core stress granule proteins, G3BP1 in mammals and TIAR-2 in Caenorhabditis elegans, increases the growth of spontaneously regenerating axons. Inhibition of G3BP1 by expression of its acidic or “B-domain” accelerates axon regeneration after nerve injury, bringing a potential therapeutic strategy for peripheral nerve repair. Here, we asked whether G3BP1 inhibition is a viable strategy to promote regeneration in injured mammalian central nervous system (CNS) where axons do not regenerate spontaneously. G3BP1 B-domain expression was found to promote axon regeneration in the transected spinal cord provided with a permissive peripheral nerve graft (PNG) as well as in …
Disruption Of G3bp1 Granules Promotes Mammalian Cns And Pns Axon Regeneration, Pabitra K. Sahoo, Manasi Agrawal, Nicholas Hanovice, Patricia J. Ward, Meghal Desai, Terika P. Smith, Haomin Sima, Jennifer N. Dulin, Lauren S. Vaughn, Mark H. Tuszynski, Kristy Welshhans, Larry I. Benowitz, Arthur W. English, John D. Houle, Jeffery L. Twiss
Disruption Of G3bp1 Granules Promotes Mammalian Cns And Pns Axon Regeneration, Pabitra K. Sahoo, Manasi Agrawal, Nicholas Hanovice, Patricia J. Ward, Meghal Desai, Terika P. Smith, Haomin Sima, Jennifer N. Dulin, Lauren S. Vaughn, Mark H. Tuszynski, Kristy Welshhans, Larry I. Benowitz, Arthur W. English, John D. Houle, Jeffery L. Twiss
Faculty Publications
Depletion or inhibition of core stress granule proteins, G3BP1 in mammals and TIAR-2 in Caenorhabditis elegans, increases the growth of spontaneously regenerating axons. Inhibition of G3BP1 by expression of its acidic or “B-domain” accelerates axon regeneration after nerve injury, bringing a potential therapeutic strategy for peripheral nerve repair. Here, we asked whether G3BP1 inhibition is a viable strategy to promote regeneration in injured mammalian central nervous system (CNS) where axons do not regenerate spontaneously. G3BP1 B-domain expression was found to promote axon regeneration in the transected spinal cord provided with a permissive peripheral nerve graft (PNG) as well as …
Population Variability Across Geographical Ranges: Perspectives And Challenges, Cleber Ten Caten, Tad Dallas
Population Variability Across Geographical Ranges: Perspectives And Challenges, Cleber Ten Caten, Tad Dallas
Faculty Publications
Populations fluctuate over time and across geographical space, and understanding how different factors contribute to population variability is a central goal in population ecology. There is a particular interest in identifying trends of population variability within geographical ranges as population densities of species can fluctuate substantially across geographical space. A common assumption is that populations vary more near species geographical range edges because of unsuitable environments and higher vulnerability to environmental variability in these areas. However, empirical data rarely support this expectation, suggesting that population variability is not related to its position within species geographical ranges. We propose that performance …
Is Increased Mutation Driving Genetic Diversity In Dogs Within The Chornobyl Exclusion Zone?, Megan N. Dillon, Allison N. Dickey, Reade B. Roberts, Jennifer A. Betz, Timothy Mousseau, Norman J. Kleiman, Matthew Breen
Is Increased Mutation Driving Genetic Diversity In Dogs Within The Chornobyl Exclusion Zone?, Megan N. Dillon, Allison N. Dickey, Reade B. Roberts, Jennifer A. Betz, Timothy Mousseau, Norman J. Kleiman, Matthew Breen
Faculty Publications
Environmental contamination can have lasting impacts on surrounding communities, though the long-term impacts can be difficult to ascertain. The disaster at the Chornobyl Nuclear Power Plant in 1986 and subsequent remediation efforts resulted in contamination of the local environment with radioactive material, heavy metals, and additional environmental toxicants. Many of these are mutagenic in nature, and the full effect of these exposures on local flora and fauna has yet to be understood. Several hundred free-roaming dogs occupy the contaminated area surrounding the Chornobyl Nuclear Power Plant, and previous studies have highlighted a striking level of genetic differentiation between two geographically …
Is Increased Mutation Driving Genetic Diversity In Dogs Within The Chornobyl Exclusion Zone?, Megan N. Dillon, Allison N. Dickey, Reade B. Roberts, Jennifer A. Betz, Timothy Mousseau, Norman J. Kleiman, Matthew Breen
Is Increased Mutation Driving Genetic Diversity In Dogs Within The Chornobyl Exclusion Zone?, Megan N. Dillon, Allison N. Dickey, Reade B. Roberts, Jennifer A. Betz, Timothy Mousseau, Norman J. Kleiman, Matthew Breen
Faculty Publications
Environmental contamination can have lasting impacts on surrounding communities, though the long-term impacts can be difficult to ascertain. The disaster at the Chornobyl Nuclear Power Plant in 1986 and subsequent remediation efforts resulted in contamination of the local environment with radioactive material, heavy metals, and additional environmental toxicants. Many of these are mutagenic in nature, and the full effect of these exposures on local flora and fauna has yet to be understood. Several hundred free-roaming dogs occupy the contaminated area surrounding the Chornobyl Nuclear Power Plant, and previous studies have highlighted a striking level of genetic differentiation between two geographically …
Progerin Can Induce Dna Damage In The Absence Of Global Changes In Replication Or Cell Proliferation, Liza A. Joudeh, P. Logan Schuck, Nina M. Van, Alannah J. Dicintio, Jason A. Stewart, Alan S. Waldman
Progerin Can Induce Dna Damage In The Absence Of Global Changes In Replication Or Cell Proliferation, Liza A. Joudeh, P. Logan Schuck, Nina M. Van, Alannah J. Dicintio, Jason A. Stewart, Alan S. Waldman
Faculty Publications
Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare genetic condition characterized by features of accelerated aging, and individuals with HGPS seldom live beyond their mid-teens. The syndrome is commonly caused by a point mutation in the LMNA gene which codes for lamin A and its splice variant lamin C, components of the nuclear lamina. The mutation causing HGPS leads to production of a truncated, farnesylated form of lamin A referred to as "progerin." Progerin is also expressed at low levels in healthy individuals and appears to play a role in normal aging. HGPS is associated with an accumulation of genomic DNA …
Mutation In Prkra Results In Cerebellar Abnormality And Reduced Elf2Α Phosphorylation In A Model Of Dyt-Prkra, Samuel B. Burnett, Allison M. Culver, Tricia A. Simon, Taylor Rowson, Kenneth Frederick, Kristina Palmer, Stephen A. Murray, Shannon W. Davis
Mutation In Prkra Results In Cerebellar Abnormality And Reduced Elf2Α Phosphorylation In A Model Of Dyt-Prkra, Samuel B. Burnett, Allison M. Culver, Tricia A. Simon, Taylor Rowson, Kenneth Frederick, Kristina Palmer, Stephen A. Murray, Shannon W. Davis
Faculty Publications
Variants in the PRKRA gene, which encodes PACT, cause the early-onset primary dystonia DYT-PRKRA, a movement disorder associated with disruption of coordinated muscle movements. PACT and its murine homolog RAX activate protein kinase R (PKR; also known as EIF2AK2) by a direct interaction in response to cellular stressors to mediate phosphorylation of the α subunit of eukaryotic translation initiation factor 2 (eIF2α). Mice homozygous for a naturally arisen, recessively inherited frameshift mutation, Prkralear-5J, exhibit progressive dystonia. In the present study, we investigated the biochemical and developmental consequences of the Prkralear-5J mutation. Our results indicated that the …
Neuronal Injury Model Divulges Differences In Dendrite And Axonal Function And Regeneration In Adults, Lauren S. Vaughn, Jinyoung Lee
Neuronal Injury Model Divulges Differences In Dendrite And Axonal Function And Regeneration In Adults, Lauren S. Vaughn, Jinyoung Lee
Faculty Publications
No abstract provided.
Improved Whole-Mount Immunofluorescence Protocol For Consistent And Robust Labeling Of Adult Drosophilamelanogaster Adipose Tissue, Rachael K. Ott, Isaiah H. Williams, Alissa R. Armstrong
Improved Whole-Mount Immunofluorescence Protocol For Consistent And Robust Labeling Of Adult Drosophilamelanogaster Adipose Tissue, Rachael K. Ott, Isaiah H. Williams, Alissa R. Armstrong
Faculty Publications
Energy storage and endocrine functions of the Drosophila fat body make it an excellent model for elucidating mechanisms that underlie physiological and pathophysiological organismal metabolism. Combined with Drosophila's robust genetic and immunofluorescence microscopy toolkits, studies of Drosophila fat body function are ripe for cell biological analysis. Unlike the larval fat body, which is easily removed as a single, cohesive sheet of tissue, isolating intact adult fat body proves to be more challenging, thus hindering consistent immunofluorescence labeling even within a single piece of adipose tissue. Here, we describe an improved approach to handling Drosophila abdomens that ensures full access of …
Research: Why Do It?, Tom Goodwin
Did God Create Viruses?, James Hayward
New Genera And Species Of Caulobacter And Brevundimonas Bacteriophages Provide Insights Into Phage Genome Evolution, Bert Ely, Michael Hils, Aaron Clarke, Maegan Albert, Nadia Holness, Jacob Lenski, Tannaz Mohammadi
New Genera And Species Of Caulobacter And Brevundimonas Bacteriophages Provide Insights Into Phage Genome Evolution, Bert Ely, Michael Hils, Aaron Clarke, Maegan Albert, Nadia Holness, Jacob Lenski, Tannaz Mohammadi
Faculty Publications
Previous studies have identified diverse bacteriophages that infect Caulobacter vibrioides strain CB15 ranging from small RNA phages to four genera of jumbo phages. In this study, we focus on 20 bacteriophages whose genomes range from 40 to 60 kb in length. Genome comparisons indicated that these diverse phages represent six Caulobacter phage genera and one additional genus that includes both Caulobacter and Brevundimonas phages. Within species, comparisons revealed that both single base changes and inserted or deleted genetic material cause the genomes of closely related phages to diverge. Among genera, the basic gene order and the orientation of key genes …
The Cetacean Sanctuary: A Sea Of Unknowns, Jason N. Bruck
The Cetacean Sanctuary: A Sea Of Unknowns, Jason N. Bruck
Faculty Publications
Housing cetaceans in netted sea pens is not new and is common for many accredited managed- care facilities. Hence, the distinction between sanctuary and sea pen is more about the philosophies of those who run these sanctuary facilities, the effects of these philosophies on the animals’ welfare, and how proponents of these sanctuaries fund the care of these animals. Here, I consider what plans exist for cetacean sanctuaries and discuss the caveats and challenges associated with this form of activist-managed captivity. One goal for stakeholders should be to disregard the emotional connotations of the word “sanctuary” …
Ecological Diversification In An Adaptive Radiation Of Plants: The Role Of De Novo Mutation And Introgression, Benjamin Stone, Carolyn A. Wessinger
Ecological Diversification In An Adaptive Radiation Of Plants: The Role Of De Novo Mutation And Introgression, Benjamin Stone, Carolyn A. Wessinger
Faculty Publications
Adaptive radiations are characterized by rapid ecological diversification and speciation events, leading to fuzzy species boundaries between ecologically differentiated species. Adaptive radiations are therefore key systems for understanding how species are formed and maintained, including the role of de novo mutations versus preexisting variation in ecological adaptation and the genome-wide consequences of hybridization events. For example, adaptive introgression, where beneficial alleles are transferred between lineages through hybridization, may fuel diversification in adaptive radiations and facilitate adaptation to new environments. In this study, we employed whole-genome resequencing data to investigate the evolutionary origin of hummingbird-pollinated flowers and to characterize genome-wide patterns …
Multi-Omics Integrative Analysis For Incomplete Data Using Weighted P-Value Adjustment Approaches, Wenda Zhang, Zichen Ma, Yen Yi Ho, Shuyi Yang, Joshua Habiger, Hsin Hsiung Huang, Yufei Huang
Multi-Omics Integrative Analysis For Incomplete Data Using Weighted P-Value Adjustment Approaches, Wenda Zhang, Zichen Ma, Yen Yi Ho, Shuyi Yang, Joshua Habiger, Hsin Hsiung Huang, Yufei Huang
Faculty Publications
The advancements in high-throughput technologies provide exciting opportunities to obtain multi-omics data from the same individuals in a biomedical study, and joint analyses of data from multiple sources offer many benefits. However, the occurrence of missing values is an inevitable issue in multi-omics data because measurements such as mRNA gene expression levels often require invasive tissue sampling from patients. Common approaches for addressing missing measurements include analyses based on observations with complete data or multiple imputation methods. In this paper, we propose a novel integrative multi-omics analytical framework based on p-value weight adjustment in order to incorporate observations with incomplete …
Genome-Wide Search Algorithms For Identifying Dynamic Gene Co-Expression Via Bayesian Variable Selection, Wenda Zhang, Zichen Ma, Lianming Wang, Daping Fan, Yen Yi Ho
Genome-Wide Search Algorithms For Identifying Dynamic Gene Co-Expression Via Bayesian Variable Selection, Wenda Zhang, Zichen Ma, Lianming Wang, Daping Fan, Yen Yi Ho
Faculty Publications
A wealth of gene expression data generated by high-throughput techniques provides exciting opportunities for studying gene-gene interactions systematically. Gene-gene interactions in a biological system are tightly regulated and are often highly dynamic. The interactions can change flexibly under various internal cellular signals or external stimuli. Previous studies have developed statistical methods to examine these dynamic changes in gene-gene interactions. However, due to the massive number of possible gene combinations that need to be considered in a typical genomic dataset, intensive computation is a common challenge for exploring gene-gene interactions. On the other hand, oftentimes only a small proportion of gene …
The Stress Response Of The Seagrass Zostera Noltei And Three Commercial Clam Species To Low Salinity Associated With Heavy Rainfall, Salvador Román, Elsa Vázquez, Marta Román, Rosa M. Viejo, Nicolás Weidberg, Jesús S. Troncoso, Sarah A. Woodin, David S. Wethey, Celia Olabarria
The Stress Response Of The Seagrass Zostera Noltei And Three Commercial Clam Species To Low Salinity Associated With Heavy Rainfall, Salvador Román, Elsa Vázquez, Marta Román, Rosa M. Viejo, Nicolás Weidberg, Jesús S. Troncoso, Sarah A. Woodin, David S. Wethey, Celia Olabarria
Faculty Publications
The maintenance of stocks of estuarine species strongly depends on the ability of the species to cope with environmental stress. In NW Spain, commercial clam beds, which are usually co-occupied by the seagrass Zostera noltei, are often exposed to reduced salinity caused by intense rainfalls. Our goals were to evaluate the effects of low salinity events on both juvenile clams and Z. noltei, including their interactions. A mesocosm experiment was performed to simulate three salinity decreases (35–35, 25–10, and 20–5), and several indicators of clam and seagrass performance were measured after 3 and 6 days of exposure and …
Video Based Estimation Of Surface Currents In A Tidal Inlet, Benjamin Middour, George Voulgaris, Douglas Cahl
Video Based Estimation Of Surface Currents In A Tidal Inlet, Benjamin Middour, George Voulgaris, Douglas Cahl
Faculty Publications
Oceanic surface currents are estimated from analysis of short duration video obtained by a nadir facing camera installed on a bridge over a tidal inlet. Data analyzed consisted of 13 two-minute video clips captured approximately every 40 min over a period of 8 hr, covering a significant portion of the tidal cycle. Surface current speed and direction estimates are obtained from each collected video using (i) a method originally developed for analysis of imagery from drones (CopterCurrents) and (ii) a particle tracking method. The horizontal (u, v) surface current velocity components and total horizontal velocity magnitude, obtained from the two …
Relative Genetic Homogeneity Within A Phenotypically Diverse Group; A Case Of The Lake Tana Labeobarbus (Cyprinidae) Species Flock, Ethiopia, Kebede Beshera
Relative Genetic Homogeneity Within A Phenotypically Diverse Group; A Case Of The Lake Tana Labeobarbus (Cyprinidae) Species Flock, Ethiopia, Kebede Beshera
Faculty Publications
The Lake Tana Labeobarbus species flock represents one of the world’s most famous examples of lacustrine species radiations. Previous studies of this group have resulted in the description of at least 15 species based on their differences in functional morphology and definition of two clades (lacustrine and riverine spawning clades) based on life history traits. A total of 166 fish representing 14 Labeobarbus species were genotyped using 10 lineage-specific hexaploid microsatellite loci. Six of these loci were developed for this study based on DNA sequence contigs derived from a microsatellite-enriched genomic library of Labeobarbus intermedius from Lake Tana; the remaining …