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School of Biological Sciences: Faculty Publications

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Full-Text Articles in Biology

Identification Of Benzothiophene-Derived Inhibitors Of Flaviviruses By Targeting Rna-Dependent Rna Polymerase, Leah Liu Wang, Shazeed-Ul Karim, Aidan Hand, Ryan Brunkhorst, Mackenna Petersen, Sarah Altam, Yi Liu, Luwen Zhang, Fengwei Bai, Shi-Hua Xiang Jan 2025

Identification Of Benzothiophene-Derived Inhibitors Of Flaviviruses By Targeting Rna-Dependent Rna Polymerase, Leah Liu Wang, Shazeed-Ul Karim, Aidan Hand, Ryan Brunkhorst, Mackenna Petersen, Sarah Altam, Yi Liu, Luwen Zhang, Fengwei Bai, Shi-Hua Xiang

School of Biological Sciences: Faculty Publications

Flaviviruses such as Dengue, West Nile, and Zika viruses are mosquito-borne RNA viruses that can cause serious diseases in humans. To develop effective drugs for treating these viruses’ infections, we create a new approach for developing common or shared drugs that may work for several different viral species of flaviviruses. It is based on the conserved RNA-dependent RNA polymerase (RdRp), which is the key enzyme for viral replication. We built up a common structure of RdRps (POLcon) from their consensus sequence. A conserved Triple-D structural motif was identified at the active site of POLcon that has been used for virtual …


Models Of Classroom Assessment For Course-Based Research Experiences, Howard Hughes Medical Institute Dec 2024

Models Of Classroom Assessment For Course-Based Research Experiences, Howard Hughes Medical Institute

School of Biological Sciences: Faculty Publications

Course-based research pedagogy involves positioning students as contributors to authentic research projects as part of an engaging educational experience that promotes their learning and persistence in science. To develop a model for assessing and grading students engaged in this type of learning experience, the assessment aims and practices of a community of experienced course-based research instructors were collected and analyzed. This approach defines four aims of course-based research assessment – 1) Assessing Laboratory Work and Scientific Thinking; 2) Evaluating Mastery of Concepts, Quantitative Thinking and Skills; 3) Appraising Forms of Scientific Communication; and 4) Metacognition of Learning – along with …


The Prognostic Significance Of Androgen Receptor Expression In Gliomas, Chi Zhang, Nan Zhao, Rubayat Khan, Ming-Yang Hung, Chi Zhang, Shuo Wang, Tony J.C. Wang, Chi Lin Sep 2024

The Prognostic Significance Of Androgen Receptor Expression In Gliomas, Chi Zhang, Nan Zhao, Rubayat Khan, Ming-Yang Hung, Chi Zhang, Shuo Wang, Tony J.C. Wang, Chi Lin

School of Biological Sciences: Faculty Publications

Androgen receptor (AR) overexpression has been identified in gliomas and its stem cells, suggesting that AR plays an important role in tumor carcinogenesis. The prognostic significance of AR overexpression in gliomas remains unknown. AR mRNA expression in gliomas and relevant clinical data were obtained from The Cancer Genome Atlas and Chinese Glioma Genome Atlas databases. AR expression levels were compared across gliomas of different histopathologic grades and molecular subtypes. Kaplan–Meier analyses in patients with different AR expression levels were investigated for the potential prognostic values of AR. Compared with normal brain tissue, gliomas show significantly higher AR mRNA expression ( …


Immunity And Protective Efficacy Of A Plant-Based Tobacco Mosaic Virus-Like Nanoparticle Vaccine Against Influenza A Virus In Mice, Adthakorn Madapong, Erika M. Petro-Turnquist, Richard J. Webby, Allison A. Mccormick, Eric A. Weaver Sep 2024

Immunity And Protective Efficacy Of A Plant-Based Tobacco Mosaic Virus-Like Nanoparticle Vaccine Against Influenza A Virus In Mice, Adthakorn Madapong, Erika M. Petro-Turnquist, Richard J. Webby, Allison A. Mccormick, Eric A. Weaver

School of Biological Sciences: Faculty Publications

Background: The rapid production of influenza vaccines is crucial to meet increasing pandemic response demands. Here, we developed plant-made vaccines comprising centralized consensus influenza hemagglutinin (HA-con) proteins (H1 and H3 subtypes) conjugated to a modified plant virus, tobacco mosaic virus (TMV) nanoparticle (TMV-HA-con). Methods: We compared immune responses and protective efficacy against historical H1 or H3 influenza A virus infections among TMV-HA-con, HA-con protein combined with AddaVax™ adjuvant, and whole-inactivated virus vaccine (Fluzone®). Results: Immunogenicity studies demonstrated robust IgG, IgM, and IgA responses in the TMV-HA-con and HA-con protein vaccinated groups, with relatively low induction of interferon (IFN)-γ+ T-cell …


Immunological Feedback Loops Generate Parasite Persistence Thresholds That Explain Variation In Infection Duration, Clayton E. Cressler, Daniel C.G. Metz, David A. Chang Van Oordt, Andrea L. Graham Aug 2024

Immunological Feedback Loops Generate Parasite Persistence Thresholds That Explain Variation In Infection Duration, Clayton E. Cressler, Daniel C.G. Metz, David A. Chang Van Oordt, Andrea L. Graham

School of Biological Sciences: Faculty Publications

Infection duration affects individual host fitness and between-host transmission. Whether an infection is cleared or becomes chronic depends on the complex interaction between host immune responses and parasite growth. Empirical and theoretical studies have suggested that there are critical thresholds of parasite dose that can determine clearance versus chronicity, driven by the ability of the parasite to manipulate host immunity. However, the mammalian immune response is characterized by strong positive and negative feedback loops that could generate duration thresholds even in the absence of direct immunomodulation. Here, we derive and analyse a simple model for the interaction between T-cell subpopulations …


Lymphoid Tissues Contribute To Plasma Viral Clonotypes Early After Antiretroviral Therapy Interruption In Siv-Infected Rhesus Macaques, Antonio Solis-Leal, Nongthombam Boby, Suvadip Mallick, Yilun Cheng, Fei Wu, Grey De La Torre, Jason Dufour, Xavier Alvarez, Vinay Shivanna, Yaozhong Liu, Christine M. Fennessey, Jeffrey D. Lifson, Qingsheng Li, Brandon F. Keele, Binhua Ling Jul 2024

Lymphoid Tissues Contribute To Plasma Viral Clonotypes Early After Antiretroviral Therapy Interruption In Siv-Infected Rhesus Macaques, Antonio Solis-Leal, Nongthombam Boby, Suvadip Mallick, Yilun Cheng, Fei Wu, Grey De La Torre, Jason Dufour, Xavier Alvarez, Vinay Shivanna, Yaozhong Liu, Christine M. Fennessey, Jeffrey D. Lifson, Qingsheng Li, Brandon F. Keele, Binhua Ling

School of Biological Sciences: Faculty Publications

The rebound-competent viral reservoir, composed of a virus that is able to persist during antiretroviral therapy (ART) and mediate reactivation of systemic viral replication and rebound viremia after ART interruption (ATI), remains the biggest obstacle to treating HIV infection. A better understanding of the cellular and tissue origins and the dynamics of viral populations that initiate rebound upon ATI could help develop therapeutic strategies for reducing the rebound-competent viral reservoir. In this study, barcoded simian immunodeficiency virus (SIV), SIVmac239M, was used to infect rhesus macaques to enable monitoring of viral barcode clonotypes contributing to virus detectable in plasma after ATI. …


Winter Gps Tagging Reveals Home Ranges During The Breeding Season For A Borealnesting Migrant Songbird, The Goldencrowned Sparrow, Autumn R. Iverson, Diana L. Humple, Renée L. Cromier, Thomas P. Hahn, Theadora A. Block, Daizaburo Shizuka, Bruce E. Lyon, Alexis S. Chaine, Emily J. Hudson, Elisha M. Hull Jun 2024

Winter Gps Tagging Reveals Home Ranges During The Breeding Season For A Borealnesting Migrant Songbird, The Goldencrowned Sparrow, Autumn R. Iverson, Diana L. Humple, Renée L. Cromier, Thomas P. Hahn, Theadora A. Block, Daizaburo Shizuka, Bruce E. Lyon, Alexis S. Chaine, Emily J. Hudson, Elisha M. Hull

School of Biological Sciences: Faculty Publications

Determining space use for species is fundamental to understanding their ecology, and tracking animals can reveal insights into their spatial ecology on home ranges and territories. Recent technological advances have led to GPS-tracking devices light enough for birds as small as ~30 g, creating novel opportunities to remotely monitor fine-scale movements and space use for these smaller species. We tested whether miniaturized GPS tags can allow us to understand space use of migratory birds away from their capture sites and sought to understand both pre-breeding space use as well as territory and habitat use on the breeding grounds. We used …


Open Resources For Biology Education (Orbe): A Resource Collection, Sanah Ahmed, Tiffany Adjei-Opong, Ashley B. Heim, Keenan Noyes, Kelly Schmid, Brian A. Couch, Mackenzie R. Stetzer, Lillian G. Senn, Erin Vinson, Michelle K. Smith, Kira Treibergs May 2024

Open Resources For Biology Education (Orbe): A Resource Collection, Sanah Ahmed, Tiffany Adjei-Opong, Ashley B. Heim, Keenan Noyes, Kelly Schmid, Brian A. Couch, Mackenzie R. Stetzer, Lillian G. Senn, Erin Vinson, Michelle K. Smith, Kira Treibergs

School of Biological Sciences: Faculty Publications

In undergraduate life sciences education, open educational resources (OERs) increase accessibility and retention for students, reduce costs, and save instructors time and effort. Despite increasing awareness and utilization of these resources, OERs are not centrally located, and many undergraduate instructors describe challenges in locating relevant materials for use in their classes. To address this challenge, we have designed a resource collection (referred to as Open Resources for Biology Education, ORBE) with 89 unique resources that are primarily relevant to undergraduate life sciences education. To identify the resources in ORBE, we asked undergraduate life sciences instructors to list what OERs they …


Undergraduate Biology Lecture Courses Predominantly Test Facts About Science Rather Than Scientific Practices, Crystal Uminski, Sara M. Burbach, Brian A. Couch Mar 2024

Undergraduate Biology Lecture Courses Predominantly Test Facts About Science Rather Than Scientific Practices, Crystal Uminski, Sara M. Burbach, Brian A. Couch

School of Biological Sciences: Faculty Publications

Scientific practices are the skills used to develop scientific knowledge and are essential for careers in science. Despite calls from education and government agencies to cultivate scientific practices, there remains little evidence of how often students are asked to apply them in undergraduate courses. We analyzed exams from biology courses at 100 institutions across the United States and found that only 7% of exam questions addressed a scientific practice and that 32% of biology exams did not test any scientific practices. The low occurrence of scientific practices on exams signals that undergraduate courses may not be integrating foundational scientific skills …


Viral Epitope Scanning Reveals Correlation Between Seasonal Hcovs And Sars-Cov-2 Antibody Responses Among Cancer And Non-Cancer Patients, Salum J. Lidenge, Dicle Yalcin, Sydney J. Bennett, Owen Ngalamika, Brenda B. Kweyamba, Chacha J. Mwita, For Yue Tso, Julius Mwaiselage, John T. West, Charles Wood Mar 2024

Viral Epitope Scanning Reveals Correlation Between Seasonal Hcovs And Sars-Cov-2 Antibody Responses Among Cancer And Non-Cancer Patients, Salum J. Lidenge, Dicle Yalcin, Sydney J. Bennett, Owen Ngalamika, Brenda B. Kweyamba, Chacha J. Mwita, For Yue Tso, Julius Mwaiselage, John T. West, Charles Wood

School of Biological Sciences: Faculty Publications

Seasonal coronaviruses (HCoVs) are known to contribute to cross-reactive antibody (Ab) responses against SARS-CoV-2. While these responses are predictable due to the high homology between SARS-CoV-2 and other CoVs, the impact of these responses on susceptibility to SARS-CoV-2 infection in cancer patients is unclear. To investigate the influence of prior HCoV infection on anti- SARS-CoV-2 Ab responses among COVID-19 asymptomatic individuals with cancer and controls without cancers, we utilized the VirScan technology in which phage immunoprecipitation and sequencing (PhIP-seq) of longitudinal plasma samples was performed to investigate high-resolution (i.e., epitope level) humoral CoV responses. Despite testing positive for anti-SARS-CoV-2 Ab …


Microclimate, An Important Part Of Ecology And Biogeography, Julia Kemppinen, Jonas J. Lembrechts Mar 2024

Microclimate, An Important Part Of Ecology And Biogeography, Julia Kemppinen, Jonas J. Lembrechts

School of Biological Sciences: Faculty Publications

Brief introduction: What are microclimates and why are they important? Microclimate science has developed into a global discipline. Microclimate science is increasingly used to understand and mitigate climate and biodiversity shifts. Here, we provide an overview of the current status of microclimate ecology and biogeography in terrestrial ecosystems, and where this field is heading next.

Microclimate investigations in ecology and biogeography: We highlight the latest research on interactions between microclimates and organisms, including how microclimates influence individuals, and through them populations, communities and entire ecosystems and their processes. We also briefly discuss recent research on how organisms shape microclimates from …


The Spliceosome-Associated Protein Cwc15 Promotes Mirna Biogenesis In Arabidopsis, Bangjun Zhou, Huihui Yu, Yong Xue, Mu Li, Chi Zhang, Bin Yu Feb 2024

The Spliceosome-Associated Protein Cwc15 Promotes Mirna Biogenesis In Arabidopsis, Bangjun Zhou, Huihui Yu, Yong Xue, Mu Li, Chi Zhang, Bin Yu

School of Biological Sciences: Faculty Publications

MicroRNAs (miRNAs) play a key role in regulating gene expression and their biogenesis is precisely controlled through modulating the activity of microprocessor. Here, we report that CWC15, a spliceosome-associated protein, acts as a positive regulator of miRNA biogenesis. CWC15 binds the promoters of genes encoding miRNAs (MIRs), promotes their activity, and increases the occupancy ofDNA-dependent RNA polymerases atMIR promoters, suggesting that CWC15 positively regulates the transcription of primary miRNA transcripts (pri-miRNAs). In addition, CWC15 interacts with Serrate (SE) and HYL1, two key components of microprocessor, and is required for efficient primiRNA processing and the HYL1-pri-miRNA interaction. Moreover, CWC15 interacts with …


Antibody Profiling And Predictive Modeling Discriminate Between Kaposi Sarcoma And Asymptomatic Kshv Infection, Sydney J. Bennett, Dicle Yalcin, Sara R. Privatt, Owen Ngalamika, Salum J. Lidenge, John T. West, Charles Wood Feb 2024

Antibody Profiling And Predictive Modeling Discriminate Between Kaposi Sarcoma And Asymptomatic Kshv Infection, Sydney J. Bennett, Dicle Yalcin, Sara R. Privatt, Owen Ngalamika, Salum J. Lidenge, John T. West, Charles Wood

School of Biological Sciences: Faculty Publications

Protein-level immunodominance patterns against Kaposi sarcoma-associated herpesvirus (KSHV), the aetiologic agent of Kaposi sarcoma (KS), have been revealed from serological probing of whole protein arrays, however, the epitopes that underlie these patterns have not been defined. We recently demonstrated the utility of phage display in high-resolution linear epitope mapping of the KSHV latency-associated nuclear antigen (LANA/ORF73). Here, a VirScan phage immunoprecipitation and sequencing approach, employing a library of 1,988 KSHV proteome-derived peptides, was used to quantify the breadth and magnitude of responses of 59 sub-Saharan African KS patients and 22 KSHV-infected asymptomatic individuals (ASY), and ultimately to support an application …


Hybridization And Gene Expression: Beyond Differentially Expressed Genes, Anna Runemark, Emily C. Moore, Erica L. Larson Feb 2024

Hybridization And Gene Expression: Beyond Differentially Expressed Genes, Anna Runemark, Emily C. Moore, Erica L. Larson

School of Biological Sciences: Faculty Publications

Gene expression has a key role in reproductive isolation, and studies of hybrid gene expression have identified mechanisms causing hybrid sterility. Here, we review the evidence for altered gene expression following hybridization and outline the mechanisms shown to contribute to altered gene expression in hybrids. Transgressive gene expression, transcending that of both parental species, is pervasive in early generation sterile hybrids, but also frequently observed in viable, fertile hybrids. We highlight studies showing that hybridization can result in transgressive gene expression, also in established hybrid lineages or species. Such extreme patterns of gene expression in stabilized hybrid taxa suggest that …


Foraging Rates From Metabarcoding: Predators Have Reduced Functional Responses In Wild, Diverse Prey Communities, Stella F. Uiterwaal, John Delong Feb 2024

Foraging Rates From Metabarcoding: Predators Have Reduced Functional Responses In Wild, Diverse Prey Communities, Stella F. Uiterwaal, John Delong

School of Biological Sciences: Faculty Publications

Functional responses describe foraging rates across prey densities and underlie many fundamental ecological processes. Most functional response knowledge comes from simplified lab experiments, but we do not know whether these experiments accurately represent foraging in nature. In addition, the difficulty of conducting multispecies functional response experiments means that it is unclear whether interaction strengths are weakened in the presence of multiple prey types. We developed a novel method to estimate wild predators' foraging rates from metabarcoding data and use this method to present functional responses for wild wolf spiders foraging on 27 prey families. These field functional responses were considerably …


Trade-Offs In Rooting Strategy Dimensions Along An Edaphic Gradient In A Grassland Ecosystem, Yuguo Yang, Sabrina E. Russo Jan 2024

Trade-Offs In Rooting Strategy Dimensions Along An Edaphic Gradient In A Grassland Ecosystem, Yuguo Yang, Sabrina E. Russo

School of Biological Sciences: Faculty Publications

  1. Roots are essential to the diversity and functioning of plant communities, but trade-offs in rooting strategies are still poorly understood.
  2. We evaluated existing frameworks of rooting strategy trade-offs and tested their underlying assumptions, guided by the hypothesis that community-level rooting strategies are best described by a combination of variation in organ-level traits, plant-level root:shoot allocation and symbiosis-level mycorrhizal dependency. We tested this hypothesis using data on plant community structure, above-and below-ground biomass, eight root traits including mycorrhizal colonisation and soil properties from an edaphic gradient driven by elevation and water availability in sandhills prairie, Nebraska, USA.
  3. We found multidimensional trade-offs …


Vibroscape Analysis Reveals Acoustic Niche Overlap And Plastic Alteration Of Vibratory Courtship Signals In Ground-Dwelling Wolf Spiders, Noori Choi, Pat Miller, Eileen A. Hebets Jan 2024

Vibroscape Analysis Reveals Acoustic Niche Overlap And Plastic Alteration Of Vibratory Courtship Signals In Ground-Dwelling Wolf Spiders, Noori Choi, Pat Miller, Eileen A. Hebets

School of Biological Sciences: Faculty Publications

To expand the scope of soundscape ecology to encompass substrate-borne vibrations (i.e. vibroscapes), we analyzed the vibroscape of a deciduous forest floor using contact microphone arrays followed by automated processing of large audio datasets. We then focused on vibratory signaling of ground-dwelling Schizocosa wolf spiders to test for (i) acoustic niche partitioning and (ii) plastic behavioral responses that might reduce the risk of signal interference from substrate-borne noise and conspecific/heterospecific signaling. Two closely related species - S. stridulans and S. uetzi - showed high acoustic niche overlap across space, time, and dominant frequency. Both species show plastic behavioral …


Biogeographic Affiliation And Centers Of Richness As Predictors Of Elevational Range-Size Patterns For Malesian Flora, Melissa Whitman, Sabrina E. Russo Jan 2024

Biogeographic Affiliation And Centers Of Richness As Predictors Of Elevational Range-Size Patterns For Malesian Flora, Melissa Whitman, Sabrina E. Russo

School of Biological Sciences: Faculty Publications

Our goal was to interrogate the idea that “mountain passes are higher in the tropics” by investigating ecological and biogeographic drivers of elevational range-sizes patterns among equatorial flora. We used herbarium records for 60 species-rich plant families, representing 18 535 species total, to estimate distributions over a 4500 m elevational gradient. For each family, we estimated the change in average range-sizes with increasing elevation (i.e. Rapoport's rule, abbreviated as ERR) and quantified 15 metrics of familial richness distribution, evolutionary age, and biogeographic affiliation. We visualized covariation across families using phylogenetic principal components analysis (pPCA). We then evaluated how family-level ERR …


Nutrient And Microbiome-Mediated Plant–Soil Feedback In Domesticated And Wild Andropogoneae: Implications For Agroecosystems, Amanda Quattrone, Yuguo Yang, Pooja Yadav, Karrie A. Weber, Sabrina E. Russo Dec 2023

Nutrient And Microbiome-Mediated Plant–Soil Feedback In Domesticated And Wild Andropogoneae: Implications For Agroecosystems, Amanda Quattrone, Yuguo Yang, Pooja Yadav, Karrie A. Weber, Sabrina E. Russo

School of Biological Sciences: Faculty Publications

Plants influence the abiotic and biotic environment of the rhizosphere, affecting plant performance through plant–soil feedback (PSF). We compared the strength of nutrient and microbemediated PSF and its implications for plant performance in domesticated and wild grasses with a fully crossed greenhouse PSF experiment using four inbred maize genotypes (Zea mays ssp. mays b58, B73- wt, B73-rth3, and HP301), teosinte (Z. mays ssp. parviglumis), and two wild prairie grasses (Andropogon gerardii and Tripsacum dactyloides) to condition soils for three feedback species (maize B73-wt, teosinte, Andropogon gerardii). We found evidence of negative …


Social Connections Across Migration: Do Golden- Crowned Sparrows (Zonotrichia Atricapilla) That Socialize In Winter Also Breed Together?, Theadora A. Block, Bruce E. Lyon, Zachary Milakonis, Alexis S. Chaine, Daizaburo Shizuka Dec 2023

Social Connections Across Migration: Do Golden- Crowned Sparrows (Zonotrichia Atricapilla) That Socialize In Winter Also Breed Together?, Theadora A. Block, Bruce E. Lyon, Zachary Milakonis, Alexis S. Chaine, Daizaburo Shizuka

School of Biological Sciences: Faculty Publications

Many birds that are territorial in the breeding season live in groups during the nonbreeding season, thereby gaining benefits such as protection from predators and increased access to resources. However, how the social connections in group life change across seasons in migratory animals is mostly unknown. We ask whether winter social connections continue during the breeding season in a migratory songbird. Golden-crowned Sparrows (Zonotrichia atricapilla) have distinct, stable winter communities that include both site and group fidelity across years: birds almost always rejoin the same social community each year after migration. If these birds have social connectivity across …


Enzyme Kinetics Of Deoxyuridine Triphosphatase From Western Corn Rootworm, Carlos Riera‑Ruiz, Hideaki Moriyama Nov 2023

Enzyme Kinetics Of Deoxyuridine Triphosphatase From Western Corn Rootworm, Carlos Riera‑Ruiz, Hideaki Moriyama

School of Biological Sciences: Faculty Publications

Objective The Western corn rootworm (WCR), Diabrotica virgifera virgifera, is a highly adaptable insect pest that has evolved resistance to a variety of control strategies, including insecticides. Therefore, it is interesting to examine how housekeeping proteins in WCR have been changed under WCR-controlling strategies. In this study, we focused on one of such proteins in WCR, a ubiquitous enzyme 5’-triphosphate nucleotidohydrolase (dUTPase). In the thymidine synthetic pathway, dUTPase hydrolyzes deoxyuridine triphosphate (dUTP) and supplies the substrate, deoxyuridine monophosphate, for the thymidylate synthase (TS). It decreases the cellular content of uracil, reducing uracil misincorporation into DNA. Suppressing the dUTPase activity, …


Enzyme Kinetics Of Deoxyuridine Triphosphatase From Western Corn Rootworm, Carlos Riera‑Ruiz, Hideaki Moriyama Nov 2023

Enzyme Kinetics Of Deoxyuridine Triphosphatase From Western Corn Rootworm, Carlos Riera‑Ruiz, Hideaki Moriyama

School of Biological Sciences: Faculty Publications

Objective The Western corn rootworm (WCR), Diabrotica virgifera virgifera, is a highly adaptable insect pest that has evolved resistance to a variety of control strategies, including insecticides. Therefore, it is interesting to examine how housekeeping proteins in WCR have been changed under WCR-controlling strategies. In this study, we focused on one of such proteins in WCR, a ubiquitous enzyme 5’-triphosphate nucleotidohydrolase (dUTPase). In the thymidine synthetic pathway, dUTPase hydrolyzes deoxyuridine triphosphate (dUTP) and supplies the substrate, deoxyuridine monophosphate, for the thymidylate synthase (TS). It decreases the cellular content of uracil, reducing uracil misincorporation into DNA. Suppressing the dUTPase activity, …


Genome Sequences Of Six Cluster Ct And Two Cluster Dj Bacteriophages That Infect Gordonia Rubripertincta, Xavier F. Rodriguez, Daniel C. Williams, Catherine P. Chia Oct 2023

Genome Sequences Of Six Cluster Ct And Two Cluster Dj Bacteriophages That Infect Gordonia Rubripertincta, Xavier F. Rodriguez, Daniel C. Williams, Catherine P. Chia

School of Biological Sciences: Faculty Publications

We report the genome sequences of eight bacteriophages isolated using Gordonia rubripertincta NRRL B-16540-SEA. Based on gene content similarity to phages in the Actinobacteriophage database, six of the phages are assigned to phage cluster CT while two are assigned to cluster DJ.


To What Extent Do Physiological Tolerances Determine Elevational Range Limits Of Mammals?, Jay F. Storz, Graham R. Scott Oct 2023

To What Extent Do Physiological Tolerances Determine Elevational Range Limits Of Mammals?, Jay F. Storz, Graham R. Scott

School of Biological Sciences: Faculty Publications

A key question in biology concerns the extent to which distributional range limits of species are determined by intrinsic limits of physiological tolerance. Here, we use common-garden data for wild rodents to assess whether species with higher elevational range limits typically have higher thermogenic capacities in comparison to closely related lowland species. Among South American leaf-eared mice (genus Phyllotis), mean thermogenic performance is higher in species with higher elevational range limits, but there is little among-species variation in the magnitude of plasticity in this trait. In the North American rodent genus Peromyscus, highland deer mice (Peromyscus maniculatus …


Temperature And Predators As Interactive Drivers Of Community Properties, John P. Delong, Kyle E. Coblentz, Stella F. Uiterwaal, Chika Akwani, Miranda E. Salsbery Oct 2023

Temperature And Predators As Interactive Drivers Of Community Properties, John P. Delong, Kyle E. Coblentz, Stella F. Uiterwaal, Chika Akwani, Miranda E. Salsbery

School of Biological Sciences: Faculty Publications

The effects of warming on ecological communities emerge from a range of potentially asymmetric impacts on individual physiology and development. Understanding these responses, however, is limited by our ability to connect mechanisms or emergent patterns across the many processes that drive variation in demography. Further complicating this understanding is the gain or loss of predators to many communities, which may interact with changes in temperature to drive community change. Here we conducted a factorial warming and predation experiment to test generalized predictions about responses to warming. We used microcosms with a range of protists, rotifers, and a gastrotrich, with and …


Temperature And Predators As Interactive Drivers Of Community Properties, John Delong, Kyle E. Coblentz, Stella F. Uiterwaal, Chika Akwani, Miranda E. Salsbery Oct 2023

Temperature And Predators As Interactive Drivers Of Community Properties, John Delong, Kyle E. Coblentz, Stella F. Uiterwaal, Chika Akwani, Miranda E. Salsbery

School of Biological Sciences: Faculty Publications

The effects of warming on ecological communities emerge from a range of potentially asymmetric impacts on individual physiology and development. Understanding these responses, however, is limited by our ability to connect mechanisms or emergent patterns across the many processes that drive variation in demography. Further complicating this understanding is the gain or loss of predators to many communities, which may interact with changes in temperature to drive community change. Here we conducted a factorial warming and predation experiment to test generalized predictions about responses to warming. We used microcosms with a range of protists, rotifers, and a gastrotrich, with and …


Effects Of Large Mammal Exclusion On Seedling Communities Depend On Plant Species Traits And Landscape Protection In Human-Modified Costa Rican Forests, Nohemi Huanca-Nuñez, University Of Connecticut, University Of The Sunshine Coast, Sabrina E. Russo Oct 2023

Effects Of Large Mammal Exclusion On Seedling Communities Depend On Plant Species Traits And Landscape Protection In Human-Modified Costa Rican Forests, Nohemi Huanca-Nuñez, University Of Connecticut, University Of The Sunshine Coast, Sabrina E. Russo

School of Biological Sciences: Faculty Publications

  1. Large terrestrial herbivorous mammals (LTH-mammals) influence plant community structure by affecting seedling establishment in mature tropical forests. Many of these LTH-mammals frequent secondary forests, but their effects on seedling establishment in them are understudied, hindering our understanding of how LTH-mammals influence forest regeneration in human-modified landscapes.
  2. We tested the hypothesis that the strength of LTH-mammals' effects on seedling establishment depends on landscape protection, forest successional stage and plant species' traits using a manipulative field experiment in six 1-ha sites with varying successional age and landscape protection. In each site, we established 40 seedling plot-pairs, with one plot excluding LTH-mammals and …


Effects Of Large Mammal Exclusion On Seedling Communities Depend On Plant Species Traits And Landscape Protection In Human-Modified Costa Rican Forests, Nohemi Huanca-Nuñez, Robin L. Chazdon, Sabrina E. Russo Oct 2023

Effects Of Large Mammal Exclusion On Seedling Communities Depend On Plant Species Traits And Landscape Protection In Human-Modified Costa Rican Forests, Nohemi Huanca-Nuñez, Robin L. Chazdon, Sabrina E. Russo

School of Biological Sciences: Faculty Publications

  1. Large terrestrial herbivorous mammals (LTH-mammals) influence plant community structure by affecting seedling establishment in mature tropical forests. Many of these LTH-mammals frequent secondary forests, but their effects on seedling establishment in them are understudied, hindering our understanding of how LTH-mammals influence forest regeneration in human-modified landscapes.

  2. We tested the hypothesis that the strength of LTH-mammals' effects on seedling establishment depends on landscape protection, forest successional stage and plant species' traits using a manipulative field experiment in six 1-ha sites with varying successional age and landscape protection. In each site, we established 40 seedling plot-pairs, with one plot excluding LTH-mammals and …


Genome Sequences Of Six Cluster Ct And Two Cluster Dj Bacteriophages That Infect Gordonia Rubripertincta, Xavier F. Rodriguez, Daniel C. Williams, Catherine P. Chia Sep 2023

Genome Sequences Of Six Cluster Ct And Two Cluster Dj Bacteriophages That Infect Gordonia Rubripertincta, Xavier F. Rodriguez, Daniel C. Williams, Catherine P. Chia

School of Biological Sciences: Faculty Publications

We report the genome sequences of eight bacteriophages isolated using Gordonia rubripertincta NRRL B-16540-SEA. Based on gene content similarity to phages in the Actinobacteriophage database, six of the phages are assigned to phage cluster CT while two are assigned to cluster DJ.


Comparative Polar And Lipid Plasma Metabolomics Differentiate Kshv Infection And Disease States, Sara R. Privatt, Camila Pereira Braga, Alicia Johnson, Salum J. Lidenge, Luke Berry, John R. Ngowi, Owen Ngalamika, Andrew G. Chapple, Julius Mwaiselage, Charles Wood, John T. West, Jiri Adamec Aug 2023

Comparative Polar And Lipid Plasma Metabolomics Differentiate Kshv Infection And Disease States, Sara R. Privatt, Camila Pereira Braga, Alicia Johnson, Salum J. Lidenge, Luke Berry, John R. Ngowi, Owen Ngalamika, Andrew G. Chapple, Julius Mwaiselage, Charles Wood, John T. West, Jiri Adamec

School of Biological Sciences: Faculty Publications

Background Kaposi sarcoma (KS) is a neoplastic disease etiologically associated with infection by the Kaposi sarcoma-associated herpesvirus (KSHV). KS manifests primarily as cutaneous lesions in individuals due to either age (classical KS), HIV infection (epidemic KS), or tissue rejection preventatives in transplantation (iatrogenic KS) but can also occur in individuals, predominantly in sub-Saharan Africa (SSA), lacking any obvious immune suppression (endemic KS). The high endemicity of KSHV and human immunodeficiency virus-1 (HIV) co-infection in Africa results in KS being one of the top 5 cancers there. As with most viral cancers, infection with KSHV alone is insufficient to induce tumorigenesis. …