Biology Commons^™

Three Fundamental Challenges To The Advancement Of Stemflow Research And Its Integration Into Natural Science, John T. Van Stan Ii, Juan Pinos

Biological, Geological, and Environmental Faculty Publications

Plant canopies divert a portion of precipitation to the base of their stems through "stemflow", a phenomenon that influences the canopy water balance, soil microbial ecology, and intrasystem nutrient cycling. However, a comprehensive integration of stemflow into theoretical and numerical models in natural science remains limited. This perspective examines three unresolved, fundamental questions hindering this integration, spanning the canopy to the soil. First, the precise source area within the canopy that generates stemflow is undefined. Thus, we asked, "whence stemflow?" Current common assumptions equate it to the entire tree canopy, a potentially misleading simplification that could affect our interpretation of …

Hypothesis And Theory: Do Trees "Release The Tension" In Rainwater? Surface Tension Reduction In Throughfall And Stemflow From Urban Trees, Benjamin J. Noren, Nicholas R. Lewis, Kelly Cristina Tonello, Anna Ilek, John T. Van Stan Ii

Biological, Geological, and Environmental Faculty Publications

Knowledge of the processes and impacts associated with the canopy's partitioning of rainfall into stemflow (water that drains to the base of tree stems) and throughfall (water that drips through gaps and from canopy surfaces) has expanded in recent years. However, the effect of canopy interactions on the fundamental physical properties of rainwater as it travels through the canopy to the soil, particularly surface tension, remains understudied. To discuss specific hypotheses within this context and their relevance to ecohydrological theory, the surface tension of rainwater samples was examined directly. Over a period of 9 months, open rainwater, throughfall and stemflow …

Telomere Maintenance In African Trypanosomes, Bibo Li Ph.D.

Biological, Geological, and Environmental Faculty Publications

Telomere maintenance is essential for genome integrity and chromosome stability in eukaryotic cells harboring linear chromosomes, as telomere forms a specialized structure to mask the natural chromosome ends from DNA damage repair machineries and to prevent nucleolytic degradation of the telomeric DNA. In Trypanosoma brucei and several other microbial pathogens, virulence genes involved in antigenic variation, a key pathogenesis mechanism essential for host immune evasion and long-term infections, are located at subtelomeres, and expression and switching of these major surface antigens are regulated by telomere proteins and the telomere structure. Therefore, understanding telomere maintenance mechanisms and how these pathogens achieve …

Meiosis In Budding Yeast, G. Valentin Borner, Andreas Hochwagen, Amy J. Macqueen

Biological, Geological, and Environmental Faculty Publications

Meiosis is a specialized cell division program that is essential for sexual reproduction. The two meiotic divisions reduce chromosome number by half, typically generating haploid genomes that are packaged into gametes. To achieve this ploidy reduction, meiosis relies on highly unusual chromosomal processes including the pairing of homologous chromosomes, assembly of the synaptonemal complex, programmed formation of DNA breaks followed by their processing into crossovers, and the segregation of homologous chromosomes during the first meiotic division. These processes are embedded in a carefully orchestrated cell differentiation program with multiple interdependencies between DNA metabolism, chromosome morphogenesis, and waves of gene expression …

From Myzocytosis To Cytostomal Nutrient Uptake And Transport By Intracellular Plasmodium Species, T. Y. Sam-Yellowe

Biological, Geological, and Environmental Faculty Publications

No abstract provided.

Shower Thoughts: Why Scientists Should Spend More Time In The Rain, John T. Van Stan Ii, Scott T. Allen, Douglas P. Aubrey, Z. Carter Berry, Matthew Biddick, Miriam A.M.J. Coenders-Gerrits, Paolo Giordani, Sybil G. Gotsch, Ethan D. Gutmann, Yakov Kuzyakov, Donát Magyar, Valentina S.A. Mella, Kevin E. Mueller, Alexandra G. Ponette-González, Philipp Porada, Carla E. Rosenfeld, Jack Simmons

Biological, Geological, and Environmental Faculty Publications

Stormwater is a vital resource and dynamic driver of terrestrial ecosystem processes. However, processes controlling interactions during and shortly after storms are often poorly seen and poorly sensed when direct observations are substituted with technological ones. We discuss how human observations complement technological ones and the benefits of scientists spending more time in the storm. Human observation can reveal ephemeral storm-related phenomena such as biogeochemical hot moments, organismal responses, and sedimentary processes that can then be explored in greater resolution using sensors and virtual experiments. Storm-related phenomena trigger lasting, oversized impacts on hydrologic and biogeochemical processes, organismal traits or functions, …

Unlocking Complex Soil Systems As Carbon Sinks: Multi-Pool Management As The Key, Gerrit Angst, Kevin E. Mueller, Michael J. Castellano, Cordula Vogel, Martin Wiesmeier, Carsten W. Mueller

Biological, Geological, and Environmental Faculty Publications

Much research focuses on increasing carbon storage in mineral-associated organic matter (MAOM), in which carbon may persist for centuries to millennia. However, MAOM-targeted management is insufficient because the formation pathways of persistent soil organic matter are diverse and vary with environmental conditions. Effective management must also consider particulate organic matter (POM). In many soils, there is potential for enlarging POM pools, POM can persist over long time scales, and POM can be a direct precursor of MAOM. We present a framework for context-dependent management strategies that recognizes soils as complex systems in which environmental conditions constrain POM and MAOM formation.

Chlorophyll Dynamics From Sentinel-3 Using An Optimized Algorithm For Enhanced Ecological Monitoring In Complex Urban Estuarine Waters, Jonathan Sherman, Maria Tzortziou, Kyle J. Turner, Joaquim Goes, Brice Grunert

Biological, Geological, and Environmental Faculty Publications

Urban estuaries are dynamic environments that hold high ecological and economic value. Yet, their optical complexity hinders accurate satellite retrievals of important biogeochemical variables, such as chlorophyll-a (Chl-a) biomass. Approaches based on a limited number of satellite spectral bands often fail to capture seasonal transitions and sharp spatial gradients in estuarine Chl-a concentrations, inhibiting integration of satellite data into water quality monitoring and conservation programs. We propose a novel approach that utilizes the wide range of spectral information captured by the Ocean and Land Color Instrument (OLCI) to retrieve estuarine Chl-a. To validate our approach, we used measurements in Long …

Molecular Peptide Grafting As A Tool To Create Novel Protein Therapeutics, Anton A. Komar

Biological, Geological, and Environmental Faculty Publications

The study of peptides (synthetic or corresponding to discrete regions of proteins) has facilitated the understanding of protein structure-activity relationships. Short peptides can also be used as powerful therapeutic agents. However, the functional activity of many short peptides is usually substantially lower than that of their parental proteins. This is (as a rule) due to their diminished structural organization, stability, and solubility often leading to an enhanced propensity for aggregation. Several approaches have emerged to overcome these limitations, which are aimed at imposing structural constraints into the backbone and/or sidechains of the therapeutic peptides (such as molecular stapling, peptide backbone …

Hypothalamic Menin Regulates Systemic Aging And Cognitive Decline, Lige Leng, Et. Al, Jingqi Yan, Jie Zhang

Biological, Geological, and Environmental Faculty Publications

Aging is a systemic process, which is a risk factor for impaired physiological functions, and finally death. The molecular mechanisms driving aging process and the associated cognitive decline are not fully understood. The hypothalamus acts as the arbiter that orchestrates systemic aging through neuroinflammatory signaling. Our recent findings revealed that Menin plays important roles in neuroinflammation and brain development. Here, we found that the hypothalamic Menin signaling diminished in aged mice, which correlates with systemic aging and cognitive deficits. Restoring Menin expression in ventromedial nucleus of hypothalamus (VMH) of aged mice extended lifespan, improved learning and memory, and ameliorated aging …

Analysis Of 3.5 Million Sars-Cov-2 Sequences Reveals Unique Mutational Trends With Consistent Nucleotide And Codon Frequencies, Sarah E. Fumagalli, Nigam H. Padhiar, Douglas Meyer, Upendra Katneni, Haim Bar, Michael Dicuccio, Anton A. Komar, Chava Kimchi‑Sarfaty

Biological, Geological, and Environmental Faculty Publications

Background: Since the onset of the SARS-CoV-2 pandemic, bioinformatic analyses have been performed to understand the nucleotide and synonymous codon usage features and mutational patterns of the virus. However, comparatively few have attempted to perform such analyses on a considerably large cohort of viral genomes while organizing the plethora of available sequence data for a month-by-month analysis to observe changes over time. Here, we aimed to perform sequence composition and mutation analysis of SARS-CoV-2, separating sequences by gene, clade, and timepoints, and contrast the mutational profile of SARS-CoV-2 to other comparable RNA viruses.Methods: Using a cleaned, filtered, and pre-aligned dataset …

Rad51-Mediated Interhomolog Recombination During Budding Yeast Meiosis Is Promoted By The Meiotic Recombination Checkpoint And The Conserved Pif1 Helicase, Andrew Ziesel, Qixuan Weng, Jasvinder S. Ahuja, Abhishek Bhattacharya, Raunak Dutta, Evan Cheng, G. Valentin Borner Ph.D., Michael Lichten, Nancy M. Hollingsworth

Biological, Geological, and Environmental Faculty Publications

During meiosis, recombination between homologous chromosomes (homologs) generates crossovers that promote proper segregation at the first meiotic division. Recombination is initiated by Spo11-catalyzed DNA double strand breaks (DSBs). 5' end resection of the DSBs creates 3' single strand tails that two recombinases, Rad51 and Dmc1, bind to form presynaptic filaments that search for homology, mediate strand invasion and generate displacement loops (D-loops). D-loop processing then forms crossover and noncrossover recombinants. Meiotic recombination occurs in two temporally distinct phases. During Phase 1, Rad51 is inhibited and Dmc1 mediates the interhomolog recombination that promotes homolog synapsis. In Phase 2, Rad51 becomes active …

Survival Analysis And Prognostic Factors Of The Carcinoma Of Gallbladder, Zainab Feroz, Priyanka Gautam, Sonia Tiwari, Girish C. Shukla, Munish Kuma

Biological, Geological, and Environmental Faculty Publications

Background: The present study aims to evaluate the survival status of patients with gallbladder cancer (GBC) and explore the prognostic factors for the improvement and preventions.
Methods: The study consists of 176 patients with clinically diagnosed gallbladder cancer; the study was conducted between 2019 and 2021 registered at Kamala Nehru Memorial Cancer Hospital, Prayagraj, India. The survival rates were analyzed by the Kaplan-Meier method; survival rate difference was analyzed by log-rank test, prognosis factors; and hazard ratio for mortality outcomes was estimated using Cox regression method.
Results: The overall median survival time of patients was 5 months with the 1-year, …

Optical Classification Of An Urbanized Estuary Using Hyperspectral Remote Sensing Reflectance, Kyle J. Turner, Maria Tzortziou, Brice K. Grunert, Joaquim Goes, Jonathan Sherman

Biological, Geological, and Environmental Faculty Publications

Optical water classification based on remote sensing reflectance (Rrs(.)) data can provide insight into water components driving optical variability and inform the development and application of bio-optical algorithms in complex aquatic systems. In this study, we use an in situ dataset consisting of hyperspectral Rrs(.) and other biogeochemical and optical parameters collected over nearly five years across a heavily urbanized estuary, the Long Island Sound (LIS), east of New York City, USA, to optically classify LIS waters based on Rrs(.) spectral shape. We investigate the similarities and differences of discrete groupings (k-means clustering) and continuous spectral indexing using the Apparent …

Transcriptomics-Based Network Medicine Approach Identifies Metformin As A Repurposable Drug For Atrial Fibrillation, Jessica C. Lal, Chengsheng Mao, Yadi Zhou, Shamone R. Gore-Panter, Julie H. Rennison, Beth S. Lovano, Et. Al

Biological, Geological, and Environmental Faculty Publications

Effective drugs for atrial fibrillation (AF) are lacking, resulting in significant morbidity and mortality. This study demonstrates that network proximity analysis of differentially expressed genes from atrial tissue to drug tar-gets can help prioritize repurposed drugs for AF. Using enrichment analysis of drug-gene signatures and functional testing in human inducible pluripotent stem cell (iPSC)-derived atrial-like cardiomyocytes, we identify metformin as a top repurposed drug candidate for AF. Using the active compactor, a new design analysis of large-scale longitudinal electronic health record (EHR) data, we determine that metformin use is significantly associated with a reduced risk of AF (odds ratio = …

Circadian Clock Controls Rhythms In Ketogenesis By Interfering With Ppar Alpha Transcriptional Network, Volha Mezhnina, Oghogho P. Ebeigbe, Nikkhil Velingkaar, Allan Poe, Yana I. Sandlers, Roman Kondratov

Biological, Geological, and Environmental Faculty Publications

Ketone bodies are energy-rich metabolites and signaling molecules whose production is mainly regulated by diet. Caloric restriction (CR) is a dietary intervention that improves metabolism and extends longevity across the taxa. We found that CR induced high -amplitude daily rhythms in blood ketone bodies (beta-hydroxybutyrate [beta OHB]) that correlated with liver beta OHB level. Time-restricted feeding, another periodic fasting-based diet, also led to rhythmic beta OHB but with reduced amplitude. CR induced strong circadian rhythms in the expression of fatty acid oxidation and ketogenesis genes in the liver. The transcriptional factor peroxisome-proliferator-activated-receptor alpha (PPAR alpha) and its transcriptional target hepatokine …

Water Availability Dictates How Plant Traits Predict Demographic Rates, Alice E. Stears, Peter B. Adler, Dana M. Blumenthal, Julie A. Kray, Kevin E. Mueller

Biological, Geological, and Environmental Faculty Publications

A major goal in ecology is to make generalizable predictions of organism responses to environmental variation based on their traits. However, straightforward relationships between traits and fitness are rare and likely to vary with environmental context. Characterizing how traits mediate demographic responses to the environment may enhance the predictions of organism responses to global change. We synthesized 15 years of demographic data and species-level traits in a shortgrass steppe to determine whether the effects of leaf and root traits on growth and survival depended on seasonal water availability. We predicted that (1) species with drought-tolerant traits, such as lower leaf …

Aurintricarboxylic Acid Is A Canonical Disruptor Of The Taz-Tead Transcriptional Complex, Kepeng Che, Ajaybabu V. Pobbati, Caleb N. Seavey, Yuriy Fedorov, Anton A. Komar, Ashley Burtscher, Shuang Ma, Brian P. Rubin

Biological, Geological, and Environmental Faculty Publications

Disrupting the formation of the oncogenic YAP/TAZ-TEAD transcriptional complex holds substantial therapeutic potential. However, the three protein interaction interfaces of this complex cannot be easily disrupted using small molecules. Here, we report that the pharmacologically active small molecule aurintricarboxylic acid (ATA) acts as a disruptor of the TAZ-TEAD complex. ATA was identified in a high-throughput screen using a TAZ-TEAD AlphaLISA assay that was tailored to identify disruptors of this transcriptional complex. We further used fluorescence polarization assays both to confirm disruption of the TAZ-TEAD complex and to demonstrate that ATA binds to interface 3. We have previously shown that cell-based …

Regulation Of Antigenic Variation By Trypanosoma Brucei Telomere Proteins Depends On Their Unique Dna Binding Activities, Bibo Li Ph.D., Yanxiang Zhao

Biological, Geological, and Environmental Faculty Publications

Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, Variant Surface Glycoprotein (VSG), to evade the host immune response. Such antigenic variation is a key pathogenesis mechanism that enables T. brucei to establish long-term infections. VSG is expressed exclusively from subtelomere loci in a strictly monoallelic manner, and DNA recombination is an important VSG switching pathway. The integrity of telomere and subtelomere structure, maintained by multiple telomere proteins, is essential for T. brucei viability and for regulating the monoallelic VSG expression and VSG switching. Here we will focus on T. brucei TRF and RAP1, two telomere …

Keeping Balance Between Genetic Stability And Plasticity At The Telomere And Subtelomere Of Trypanosoma Brucei, Bibo Li Ph.D.

Biological, Geological, and Environmental Faculty Publications

Telomeres, the nucleoprotein complexes at chromosome ends, are well-known for their essential roles in genome integrity and chromosome stability. Yet, telomeres and subtelomeres are frequently less stable than chromosome internal regions. Many subtelomeric genes are important for responding to environmental cues, and subtelomeric instability can facilitate organismal adaptation to extracellular changes, which is a common theme in a number of microbial pathogens. In this review, I will focus on the delicate and important balance between stability and plasticity at telomeres and subtelomeres of a kinetoplastid parasite, Trypanosoma brucei, which causes human African trypanosomiasis and undergoes antigenic variation to evade the …

The Ecology Of Rural Roads: Effects, Management, And Research, Alisa W. Coffin, Douglas S. Ouren, Neil D. Bettez, Luís Borda-De-Água, Amy E. Daniels, Clara Grilo, Jochen A.G. Jaeger, Laetitia M. Navarro, Haiganoush K. Preisler, Emily Rauschert

Biological, Geological, and Environmental Faculty Publications

No abstract provided.

Intense Mowing Management Suppresses Invader, But Shifts Competitive Resistance By A Native To Facilitation, David U. Nagy, Emily Rauschert, Ragan M. Callaway, Tamas Henn, Rita Filep, Robert W. Pal

Biological, Geological, and Environmental Faculty Publications

Interactions among native and invasive species may affect management outcomes and goals. We implemented different mowing regimes to control the invasive Solidago gigantea and restore natural diversity, and also examined interactions between Solidago and a European native competitor, Tanacetum vulgare in the context of these regimes. Experimentally planted Tanacetum suppressed Solidago by 79% without management, and a suite of mowing management regimes reduced the density of Solidago by 80–98% when Tanacetum was absent. But, when Tanacetum was added, the density of the invader was not reduced by mowing. Put another way, in mowed plots with Tanacetum, Solidago was twofold to …

Trafficking And Association Of Plasmodium Falciparum Mc-2tm With The Maurer’S Clefts, Raghavendra Yadavalli, John W. Peterson, Judith A. Drazba, Tobili Y. Sam-Yellowe

Biological, Geological, and Environmental Faculty Publications

In this study, we investigated stage specific expression, trafficking, solubility and topology of endogenous PfMC-2TM in P. falciparum (3D7) infected erythrocytes. Following Brefeldin A (BFA) treatment of parasites, PfMC-2TM traffic was evaluated using immunofluorescence with antibodies reactive with PfMC-2TM. PfMC-2TM is sensitive to BFA treatment and permeabilization of infected erythrocytes with streptolysin O (SLO) and saponin, showed that the N and C-termini of PfMC-2TM are exposed to the erythrocyte cytoplasm with the central portion of the protein protected in the MC membranes. PfMC-2TM was expressed as early as 4 h post invasion (hpi), was tightly colocalized with REX-1 and trafficked …

Gene Variants Of Coagulation Related Proteins That Interact With Sars-Cov-2, David Holcomb, Aikaterini Alexaki, Nancy Hernandez, Ryan Hunt, Jacob Kames, Nobuko Hamasaki-Katagiri, Anton A. Komar, Michael Dicuccio, Chava Kimchi-Sarfaty

Biological, Geological, and Environmental Faculty Publications

Increased blood clotting, especially in the lungs, is a common complication of COVID-19. Infectious diseases cause inflammation, which in turn can contribute to increased blood clotting. However, the extent of clot formation that is seen in the lungs of COVID-19 patients suggests that there may be a more direct link. We identified three human proteins that are involved indirectly in the blood clotting cascade and have been shown to interact with proteins of SARS virus, which is closely related to the novel coronavirus. We examined computationally the interaction of these human proteins with the viral proteins. We looked for genetic …

Tbrap1 Has An Unusual Duplex Dna Binding Activity Required For Its Telomere Localization And Vsg Silencing, Marjia Afrin, Amit Kumar Gaurav, Xian Yang, Xuehua Pan, Yanxiang Zhao, Bibo Li Ph.D.

Biological, Geological, and Environmental Faculty Publications

Localization of Repressor Activator Protein 1 (RAP1) to the telomere is essential for its telomeric functions. RAP1 homologs either directly bind the duplex telomere DNA or interact with telomere-binding proteins. We find that Trypanosoma brucei RAP1 relies on a unique double-stranded DNA (dsDNA) binding activity to achieve this goal. T. brucei causes human sleeping sickness and regularly switches its major surface antigen, variant surface glycoprotein (VSG), to evade the host immune response. VSGs are monoallelically expressed from subtelomeres, and TbRAP1 is essential for VSG regulation. We identify dsDNA and single-stranded DNA binding activities in TbRAP1, which require positively charged 737RKRRR741 …

The More We Do, The Less We Gain? Balancing Effort And Efficacy In Managing The Solidago Gigantea Invasion, Dávid U. Nagy, Emily S.J. Rauschert, Tamás Henn, Kevin Cianfaglione, Szilvia Stranczinger, Robert W. Pal

Biological, Geological, and Environmental Faculty Publications

Developing invasive plant management strategies is an important task in modern ecology, conservation biology and land management. Solidago gigantea is considered a problematic invader in Europe and Asia, where it forms dominant stands that can decrease species diversity. There is, therefore, an urgent need for effective management to reduce S. gigantea infestations and their negative impacts. We examined the efficacy of multiple approaches to S. gigantea management in Hungary. In our study, we evaluated the effect of several long-term management techniques such as grazing, mowing and periodic flooding on the invader's density as well as native community diversity. In addition, …

Basal Signalling Through Death Receptor 5 And Caspase 3 Activates P38 Kinase To Regulate Serum Response Factor (Srf)-Mediated Myod Transcription, Jason A. Ross, Brianna Barrett, Victoria Bensimon, Girish Shukla, Crystal M. Weyman

Biological, Geological, and Environmental Faculty Publications

We have previously reported that stable expression of a dominant negative Death Receptor 5 (dnDR5) in skeletal myoblasts results in decreased basal caspase activity and decreased mRNA and protein expression of the muscle regulatory transcription factor MyoD in growth medium (GM), resulting in inhibited differentation when myoblasts are then cultured in differentiation media (DM). Further, this decreased level of MyoD mRNA was not a consequence of altered message stability, but rather correlated with decreased acetylation of histones in the distal regulatory region (DRR) of the MyoD extended promoter known to control MyoD transcription. As serum response factor (SRF) is the …

Trypanosoma Brucei Rap1 Has Essential Functional Domains That Are Required For Different Protein Interactions, Marjia Afrin, Hanadi Kishmiri, Ranjodh Sandhu, M. A.G. Rabbani, Bibo Li

Biological, Geological, and Environmental Faculty Publications

RAP1 is a telomere protein that is well conserved from protozoa to mammals. It plays important roles in chromosome end protection, telomere length control, and gene expression/silencing at both telomeric and nontelomeric loci. Interaction with different partners is an important mechanism by which RAP1 executes its different functions in yeast. The RAP1 ortholog in Trypanosoma brucei is essential for variant surface glycoprotein (VSG) monoallelic expression, an important aspect of antigenic variation, where T. brucei regularly switches its major surface antigen, VSG, to evade the host immune response. Like other RAP1 orthologs, T. brucei RAP1 (TbRAP1) has conserved functional domains, including …

Soil Characteristics Drive Ficaria Verna Abundance And Reproductive Output, Justin P. Kermack, Emily Rauschert

Biological, Geological, and Environmental Faculty Publications

Lesser celandine (Ficaria verna Huds.), an invasive plant from Europe, is becoming widespread in river valleys throughout the northeastern United States and the Pacific Northwest. Its high rate of asexual bulbil and tuber production creates dense infestations threatening native spring ephemerals. Ficaria verna abundance and reproductive output (seeds, bulbils, and tubers) were examined in invaded transects spanning a disturbance gradient away from a river. Site characteristics (photosynthetically active radiation [PAR], soil pH, moisture, texture, and nutrients) were quantified to examine their roles in plant abundance and reproduction. A larger-scale study examined random transects not specifically chosen based on F. …

Shifts In Plant Functional Composition Following Long-Term Drought In Grasslands, Robert J. Griffin‐Nolan, Dana M. Blumenthal, Scott L. Collins, Timothy E. Farkas, Ava M. Hoffman, Kevin E. Mueller, Troy W. Ocheltree, Melinda D. Smith, Kenneth D. Whitney, Alan K. Knapp

Biological, Geological, and Environmental Faculty Publications

1. Plant traits can provide unique insights into plant performance at the community scale. Functional composition, defined by both functional diversity and community-weighted trait means (CWMs), can affect the stability of above-ground net primary production (ANPP) in response to climate extremes. Further complexity arises, however, when functional composition itself responds to environmental change. The duration of climate extremes, such as drought, is expected to increase with rising global temperatures; thus, understanding the impacts of long-term drought on functional composition and the corresponding effect that has on ecosystem function could improve predictions of ecosystem sensitivity to climate change.

2. We experimentally …