Life Sciences Commons^™

Improving Collaborations Between Empiricists And Modelers To Advance Grassland Community Dynamics In Ecosystem Models, Kevin R. Wilcox, Kimberly J. Komatsu, Meghan L. Avolio, Nathan P. Lemoine

Biological Sciences Faculty Research and Publications

No abstract provided.

The Response Of Lianas To 20 Yr Of Nutrient Addition In A Panamanian Forest, Stefan A. Schnitzer, Sergio Estrada Villegas, S. Joseph Wright

Biological Sciences Faculty Research and Publications

Over the past two decades, liana density and basal area have been increasing in many tropical forests, which has profound consequences for forest diversity and functioning. One hypothesis to explain increasing lianas is elevated nutrient deposition in tropical forests resulting from fossil fuels, agricultural fertilizer, and biomass burning. We tested this hypothesis by surveying all lianas ≥1 cm in diameter (n = 3,967) in 32 plots in a fully factorial nitrogen (N), phosphorus (P), and potassium (K) addition experiment in a mature tropical forest in central Panama. We conducted the nutrient-addition experiment from 1998 until present and we first …

Lianas Maintain Insectivorous Bird Abundance And Diversity In A Neotropical Forest, Stefan A. Schnitzer, Nicole L. Michel, Jennifer S. Powers, W. Douglas Robinson

Biological Sciences Faculty Research and Publications

The spatial habitat heterogeneity hypothesis posits that habitat complexity increases the abundance and diversity of species. In tropical forests, lianas add substantial habitat heterogeneity and complexity throughout the vertical forest profile, which may maintain animal abundance and diversity. The effects of lianas on tropical animal communities, however, remain poorly understood. We propose that lianas have a positive effect on animals by enhancing habitat complexity. Lianas may have a particularly strong influence on the forest bird community, providing nesting substrate, protection from predators, and nutrition (food). Understory insectivorous birds, which forage for insects that specialize on lianas, may particularly benefit. Alternatively, …

Challenges Facing Young Scientists In Academia And Industry In The United States From The Lens Of A Millennial Academic, Joseph R. Clark

Biological Sciences Faculty Research and Publications

Rising to the challenge: Pictured from left to right: Salma L. Nuñez, Albert Reyes and Lisandra Santiago-Capeles, Ph.D. The challenges that young scientists face in academia and industry in the United States are discussed. Prof. Joseph Clark provides insight about how social media, funding, diversity, natural disasters, COVID-19 and student loan debt are impacting young scientists. A discussion of strategies to meet these challenges and support young scientists are presented.

Sgx-Mr: Regulating Dataflows For Protecting Access Patterns Of Data-Intensive Sgx Applications, A.K.M. Mubashwir Alam, Sagar Sharma, Keke Chen

Clinical Lab Sciences Faculty Research and Publications

Intel SGX has been a popular trusted execution environment (TEE) for protecting the integrity and confidentiality of applications running on untrusted platforms such as cloud. However, the access patterns of SGX-based programs can still be observed by adversaries, which may leak important information for successful attacks. Researchers have been experimenting with Oblivious RAM (ORAM) to address the privacy of access patterns. ORAM is a powerful low-level primitive that provides application-agnostic protection for any I/O operations, however, at a high cost. We find that some application-specific access patterns, such as sequential block I/O, do not provide additional information to adversaries. Others, …

Multi-Scale 3d Cryo-Correlative Microscopy For Vitrified Cells, Gong-Her Wu, Patrick G. Mitchell, Jesus G. Galaz-Montoya, Corey W. Hecksel, Emily M. Sontag, Vimal Gangadharan, Jeffrey Marshman, David Mankus, Margaret E. Bisher, Abigail K.R. Lytton-Jean, Judith Frydman, Kirk Czymmek, Wah Chiu

Biological Sciences Faculty Research and Publications

Three-dimensional (3D) visualization of vitrified cells can uncover structures of subcellular complexes without chemical fixation or staining. Here, we present a pipeline integrating three imaging modalities to visualize the same specimen at cryogenic temperature at different scales: cryo-fluorescence confocal microscopy, volume cryo-focused ion beam scanning electron microscopy, and transmission cryo-electron tomography. Our proof-of-concept benchmark revealed the 3D distribution of organelles and subcellular structures in whole heat-shocked yeast cells, including the ultrastructure of protein inclusions that recruit fluorescently-labeled chaperone Hsp104. Since our workflow efficiently integrates imaging at three different scales and can be applied to other types of cells, it could …

Biographical Feature: William A. Hinton, M.D., Erik Munson

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.

Comprehensive Molecular Screening In A Cohort Of Young Men Who Have Sex With Men And Transgender Women: Effect Of Additive Rectal Specimen Source Collection And Analyte Testing, Erik Munson, Alyssa Reynoso, Morena Pass, Kathleen Buehler, Daniel Ryan, Antonia Clifford, Ethan Morgan, Brian Mustanski

Clinical Lab Sciences Faculty Research and Publications

Background

This study's purposes were to characterize detection rates of several sexually transmitted infection (STI) agents and describe the effect additional specimen source and analyte screening has on STI detection within a cohort of young men who have sex with men and transgender women.

Methods

Within a 16-month interval, 1966 encounters involved dual urine and rectal swab submissions assessed by commercial transcription-mediated amplification–based assays for Chlamydia trachomatis and Neisseria gonorrhoeae and by off-label transcription-mediated amplification–based Trichomonas vaginalis and Mycoplasma genitalium testing. Identification of STI carriers used algorithms involving Food and Drug Administration–cleared screening methods, laboratory-modified testing for extraurogenital C. trachomatis …

Temporal Variability In Production Is Not Consistently Affected By Global Change Drivers Across Herbaceous-Dominated Ecosystems, Meghan L. Avolio, Kevin R. Wilcox, Kimberly J. Komatsu, Nathan P. Lemoine, William D. Bowman, Scott L. Collins, Alan K. Knapp, Sally E. Koerner, Melinda D. Smith, Sara G. Baer, Katherine Gross, Forest Isbell, Jennie R. Mclaren, Peter B. Reich, Katherine Suding, K. Blake Suttle, David Tilman, Zhuwen Xu, Qiang Yu

Biological Sciences Faculty Research and Publications

Understanding how global change drivers (GCDs) affect aboveground net primary production (ANPP) through time is essential to predicting the reliability and maintenance of ecosystem function and services in the future. While GCDs, such as drought, warming and elevated nutrients, are known to affect mean ANPP, less is known about how they affect inter-annual variability in ANPP. We examined 27 global change experiments located in 11 different herbaceous ecosystems that varied in both abiotic and biotic conditions, to investigate changes in the mean and temporal variability of ANPP (measured as the coefficient of variation) in response to different GCD manipulations, including …

Survivor Microbial Populations In Post-Chlorinated Wastewater Are Strongly Associated With Untreated Hospital Sewage And Include Ceftazidime And Meropenem Resistant Populations, Rachelle E. Beattie, Troy Skwor, Krassimira R. Hristova

Biological Sciences Faculty Research and Publications

Wastewater treatment plant (WWTP) effluent has been implicated in the spread of antibiotic resistant bacteria (ARB), including pathogens, as the WWTP environment contains multiple selective pressures that may increase mutation rates, pathogen survivability, and induce gene transfer between bacteria. In WWTPs receiving hospital sewage, this selective effect may be more pronounced due to increased concentrations of antibiotics, ARB, and clinical pathogens from hospital sewage. To determine the extent to which hospital sewage contributes to the microbial community of disinfected wastewater which is released into the environment, we used 16S rRNA sequencing of hospital sewage, WWTP influent, primary effluent, Post-Chlorinated Effluent, …

Freshwater Sediment Microbial Communities Are Not Resilient To Disturbance From Agricultural Land Runoff, Rachelle E. Beattie, Aditya Bandla, Sanjay Swarup, Krassimira R. Hristova

Biological Sciences Faculty Research and Publications

Microorganisms are critically important for the function of surface water ecosystems but are frequently subjected to anthropogenic disturbances at either acute (pulse) or long-term (press) scales. Response and recovery of microbial community composition and function following pulse disturbance is well-studied in controlled, laboratory scale experiments but is less well-understood in natural environments undergoing continual press disturbance. The objectives of this study were to determine the drivers of sediment microbial compositional and functional changes in freshwaters receiving continual press disturbance from agricultural land runoff and to evaluate the ability of the native microbial community to resist disturbance related changes as a …

Effects Of Low-Level Artificial Light At Night On Kentucky Bluegrass And Introduced Herbivore, Morgan Crump, Cassandra Brown, Robert J. Griffin-Nolan, Lisa Angeloni, Nathan P. Lemoine, Brett Seymoure

Biological Sciences Faculty Research and Publications

Increasing evidence suggests that artificial light at night (ALAN) can negatively impact organisms. However, most studies examine the impacts of ALAN on a single species or under high levels of artificial light that are infrequent or unrealistic in urban environments. We currently have little information on how low levels of artificial light emanating from urban skyglow affect plants and their interactions with herbivores. We examined how low levels of ALAN affect grass and insects, including growth rate, photosynthesis, and stomatal conductance in grass, and foraging behavior and survival in crickets. We compared growth and leaf-level gas exchange of Kentucky Bluegrass …

Comparison Of Cpu And Parabricks Gpu Enabled Bioinformatics Software For High Throughput Clinical Genomic Applications, Stefano Rosati

Master's Theses (2009 -)

In recent years, high performance computing (HPC) has begun to revolutionize the architecture of software and servers to meet the ever-increasing demand for speed & efficiency. One of the ways this change is manifesting is the adoption of graphics processor units (GPUs). Used correctly, GPUS can increase throughput and decrease compute time for certain computational problems. Bioinformatics, an HPC dependent discipline, is no exception. As bioinformatics continues advance clinical care by sequencing patient’s DNA and RNA for diagnosis of diseases, there is an ever-increasing demand for faster data processing to improve clinical sequencing turnaround time. Parabricks, a GPU enabled bioinformatics …

The Role Of System Xc- In Cognition: The Importance Of Neuron-Astrocyte Signaling, Evan Michael Hess

Dissertations (1934 -)

The biological basis of human intelligence is largely a mystery, but likely required evolutionary adaptations to achieve the information processing capacity needed to expand the complexity of cognition among species. The link between evolutionary expansion of signaling complexity in the brain and cognition has largely focused on neuronal mechanisms, in part because information processing has historically been attributed to these cells. However, astrocytes are emerging as a second type of brain cell that is capable of processing information due to their capacity to release glutamate and, thereby, regulate neural circuits. Hence, a modern question is whether astrocytes contributed to the …

Chronic Variable Stress Induces Avolition And Disrupts Corticoaccumbens Encoding Of Approach Cues, Mitchell Spring

Dissertations (1934 -)

Disorders in the ability to process, evaluate, and interact with rewards are hallmarks of a range of mental illnesses. Such disorders are multi-faceted and arise from altered activity throughout diffuse brain regions. Chronic variable stress (CVS) is an oft-used tool for modeling reward-related disorders in preclinical research because it impairs the function of multiple brain regions and causes a range of severe hedonic and motivational deficits. While much research has focused on the former, the latter is poorly characterized. A panel of behavioral tests was used to characterize the effect of CVS exposure on different facets of reward related behaviors …

Can Functional Traits Explain Plant Coexistence? A Case Study With Tropical Lianas And Trees, Felipe N. A. Mello, Sergio Estrada Villegas, David M. Defilippis, Stefan A. Schnitzer

Biological Sciences Faculty Research and Publications

Organisms are adapted to their environment through a suite of anatomical, morphological, and physiological traits. These functional traits are commonly thought to determine an organism’s tolerance to environmental conditions. However, the differences in functional traits among co-occurring species, and whether trait differences mediate competition and coexistence is still poorly understood. Here we review studies comparing functional traits in two co-occurring tropical woody plant guilds, lianas and trees, to understand whether competing plant guilds differ in functional traits and how these differences may help to explain tropical woody plant coexistence. We examined 36 separate studies that compared a total of 140 …

Biographical Feature: Robin Patel, M.D.(C.M.), D(Abmm), F(Aam), Fidsa, Facp, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.

Conserved Zz/Zw Sex Chromosomes In Caribbean Croaking Geckos (Aristelliger: Sphaerodactylidae), Shannon E. Keating, Aaron H. Griffing, Stuart V. Nielsen, Daniel P. Scantlebury, Tony Gamble

Biological Sciences Faculty Research and Publications

Current understanding of sex chromosome evolution is largely dependent on species with highly degenerated, heteromorphic sex chromosomes, but by studying species with recently evolved or morphologically indistinct sex chromosomes we can greatly increase our understanding of sex chromosome origins, degeneration and turnover. Here, we examine sex chromosome evolution and stability in the gecko genus Aristelliger. We used RADseq to identify sex‐specific markers and show that four Aristelliger species, spanning the phylogenetic breadth of the genus, share a conserved ZZ/ZW system syntenic with avian chromosome 2. These conserved sex chromosomes contrast with many other gecko sex chromosome systems by showing …

The Negative Effect Of Lianas On Tree Growth Varies With Tree Species And Season, Alejandro Venegas-Gonzalez, Felipe N. A. Mello, Stefan A. Schnitzer, Ricardo G. Cesar, Mario Tomazello-Filho

Biological Sciences Faculty Research and Publications

Lianas reduce tree growth, reproduction, and survival in tropical forests. Liana competition can be particularly intense in isolated forest fragments, where liana densities are high, and thus, host tree infestation is common. Furthermore, lianas appear to grow particularly well during seasonal drought, when they may compete particularly intensely with trees. Few studies, however, have experimentally quantified the seasonal effects of liana competition on multiple tree species in tropical forests. We used a liana removal experiment in a forest fragment in southeastern Brazil to test whether the effects of lianas on tree growth vary with season and tree species identity. We …

Bk Potassium Currents Contribute Differently To Action Potential Waveform And Firing Rate As Rat Hippocampal Neurons Mature In The First Postnatal Week, Michael Hunsberger, Michelle Mynlieff

Biological Sciences Faculty Research and Publications

The large-conductance calcium-activated potassium (BK) channel is a critical regulator of neuronal action potential firing and follows two distinct trends in early postnatal development: an increase in total expression and a shift from the faster activating STREX isoform to the slower ZERO isoform. We analyzed the functional consequences of developmental trends in BK channel expression in hippocampal neurons isolated from neonatal rats aged 1 to 7 days. Following overnight cultures, action potentials and currents were recorded using whole cell patch-clamp electrophysiology. These neurons undergo a steady increase in excitability during this time, and the effect of blockade of BK channel …

The Actin Cytoskeletal Network Plays A Role In Yeast Prion Transmission And Contributes To Prion Stability, Jane E. Dorweiler, Mitchell J. Oddo, Douglas R. Lyke, Jacob A. Reilly, Brett T. Wisniewski, Emily E. Davis, Abigail M. Kuborn, Stephen J. Merrill, Anita L. Manogaran

Biological Sciences Faculty Research and Publications

Chaperone networks are required for the shearing and generation of transmissible propagons from pre‐existing prion aggregates. However, other cellular networks needed for maintaining yeast prions are largely uncharacterized. Here, we establish a novel role for actin networks in prion maintenance. The [PIN ⁺] prion, also known as [RNQ ⁺], exists as stable variants dependent upon the chaperone machinery for the transmission of propagons to daughter cells during cell division and cytoplasmic transfer. Loss of the Hsp104 molecular chaperone leads to the growth of prion particles until they are too large to be transmitted. Here, we isolated …

The Defining Genomic And Predicted Metabolic Features Of The Acetobacterium Genus, Daniel E. Ross, Christopher Marshall, Djuna Gulliver, Harold D. May, R. Sean Norman

Biological Sciences Faculty Research and Publications

Acetogens are anaerobic bacteria capable of fixing CO₂ or CO to produce acetyl coenzyme A (acetyl-CoA) and ultimately acetate using the Wood-Ljungdahl pathway (WLP). Acetobacterium woodii is the type strain of the Acetobacterium genus and has been critical for understanding the biochemistry and energy conservation in acetogens. Members of the Acetobacterium genus have been isolated from a variety of environments or have had genomes recovered from metagenome data, but no systematic investigation has been done on the unique and various metabolisms of the genus. To gain a better appreciation for the metabolic breadth of the genus, we sequenced the …

Multiple Cold Tolerance Trait Phenotyping Reveals Shared Quantitative Trait Loci In Oryza Sativa, Naoki Shimoyama, Melineeh Johnson, André Beaumont, Michael Schläppi

Biological Sciences Faculty Research and Publications

Background

Developing chilling tolerant accessions of domesticated Asian rice is a potential source of significant crop improvement. The uniquely chilling sensitive nature of the tropically originating Oryza sativa make it the most important cereal crop that can gain significantly from improved tolerance to low temperatures. However, mechanisms underlying this complex trait are not fully understood. Oryza sativa has two subspecies with different levels of chilling tolerance, JAPONICA and INDICA, providing an ideal tool to investigate mechanistic differences in the chilling stress tolerance responses within this important crop species.

Results

The Rice Diversity Panel 1 (RDP1) was used to investigate …

The Structure And Symmetry Of The Radial Spoke Protein Complex In Chlamydomonas Flagella, Emiliya Poghosyan, Ioan Iacovache, Lenka Faltova, Alexander Leitner, Pinfen Yang, Dennis R. Diener, Ruedi Aebersold, Benoit Zuber, Takashi Ishikawa

Biological Sciences Faculty Research and Publications

The radial spoke is a key element in a transducer apparatus controlling the motility of eukaryotic cilia. The transduction biomechanics is a long-standing question in cilia biology. The radial spoke has three regions – a spoke head, a bifurcated neck and a stalk. Although the neck and the stalk are asymmetric, twofold symmetry of the head has remained controversial. In this work we used single particle cryo-electron microscopy (cryo-EM) analysis to generate a 3D structure of the whole radial spoke at unprecedented resolution. We show the head region at 15 Å (1.5 nm) resolution and confirm twofold symmetry. Using distance …

Individual Learning Phenotypes Drive Collective Behavior, Chelsea N. Cook, Natalie J. Lemanski, Thiago Mosqueiro, Cahit Ozturk, Jürgen Gadau, Noa Pinter-Wollman, Brian H. Smith

Biological Sciences Faculty Research and Publications

Individual differences in learning can influence how animals respond to and communicate about their environment, which may nonlinearly shape how a social group accomplishes a collective task. There are few empirical examples of how differences in collective dynamics emerge from variation among individuals in cognition. Here, we use a naturally variable and heritable learning behavior called latent inhibition (LI) to show that interactions among individuals that differ in this cognitive ability drive collective foraging behavior in honey bee colonies. We artificially selected two distinct phenotypes: high-LI bees that ignore previously familiar stimuli in favor of novel ones and low-LI bees …

Moving Targets Of Bacterial Taxonomy Revision: What Are They And Why Should We Care?, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

Due to the increased widespread use of molecular diagnostics, genome sequencing, and microbiome analysis in microbiology, the field has experienced a massive influx of novel taxa and nomenclature revisions. A subset of these changes is relevant to the clinical microbiology laboratory, particularly in the context of appropriate antimicrobial susceptibility testing and epidemiology of emerging infections. However, assimilation of these changes into daily clinical microbiology laboratory operations can be challenging for a variety of reasons. Recent taxonomic revisions to Enterobacteriaceae, as well as the genera Borrelia, Mycoplasma, and Mycobacterium, are reviewed as examples that illustrate discrepancies between resources …

Survival-Related Clustering Of Cancer Patients By Integrating Clinical And Biological Datasets, Xinming Wei

Master's Theses (2009 -)

Subtype-based treatments and drug therapies are essential aspects to be considered in cancer patients' clinical trials to provide appropriate personalized therapies. With the advancement of the next-generation sequencing technology, several computational models, integrating genomic and transcriptomic datasets (i.e., multi-omics) in the prediction of subtype-based classification in cancer patients, were emerged. However, integration of the prognostic features from the clinical data, related to survival risks with the multi-omics datasets in the prediction of different subtypes, is limited and an important research area to be explored. In this study, we proposed a data integration pipeline with the prognostic features from the clinical …

Investigating The Role Of Lin-35 And The Dream Complex In Preserving Fertility Under Stress In C. Elegans, Frances Virginia Compere

Master's Theses (2009 -)

Organisms are subjected to environments that can fluctuate and cause them stress. Therefore, organisms must have the ability to adapt to the stress to survive and propagate. Temperature stress is becoming an increasingly relevant type of stress due to climate change and is known to affect fertility in many types of organisms including the model organism Caenorhabditis elegans. Here we examine the role of LIN-35, the single C. elegans homolog of the tumor suppressor Retinoblastoma (pRB), in fertility under moderate temperature stress. We found that lin-35 mutants lose fertility more drastically under moderate temperature stress than wildtype worms, and that …

Mechanisms Of Atp-Dependent Substrate Reduction In The Nitrogenase-Like Dpor Complex, Elliot Irwin Corless

Dissertations (1934 -)

Iron-Sulfur ([Fe-S]) clusters are the most common transient electron carriers in cells and are necessary for basic metabolism of all life. Bacterial systems use two operons (isc and suf ) for the biogenesis and delivery of [Fe-S] clusters to various proteins. Once delivered, they serve as transient electron carriers necessary for both heterotrophic and autotrophic metabolism and reduction/oxidation chemistry. This work utilizes the hetero-octameric Dark operative Protochlorophyllide Oxido-Reductase (DPOR) complex as a platform to investigate [Fe-S] cluster biogenesis and the concerted action of its multiple [Fe-S] clusters and protein subunits. DPOR catalyzes the penultimate step in bacterial chlorophyll synthesis and …

Characterization Of The Mir-44 Family Of Micrornas In The C. Elegans Germline, Katherine Ann Maniates

Dissertations (1934 -)

While numerous individual miRNAs have been detected in the germline, the functions of most other specific miRNAs remain largely unknown. Functions of miRNAs have been difficult to determine as miRNAs often modestly repress target mRNAs and are suggested to sculpt or fine tune gene expression to allow for the robust expression of cell fates. Analysis of newly generated mir-44 family mutants has identified a group of miRNAs that modulate the pathway of germline sex determination in C. elegans. Mutants produce fewer sperm and display an earlier switch to producing oocytes. In the germline, cell fate decisions are made for germline …