Biology Commons^™

Social Networks In The Single Cell, Moira Rodriguez, Ana Martinez-Hottovy, Alan C. Christensen

School of Biological Sciences: Faculty Publications

Plant mitochondrial DNA (mtDNA) can become damaged in many ways. A major repair mechanism is homologous recombination, which requires an undamaged DNA template. Presumably, this template comes from a different mitochondrion in the same cell. Plant mitochondria undergo fission and fusion to form transient networks which could allow the exchange of genetic information. To test this hypothesis, Chustecki et al. (2022) used msh1 mutants with defective DNA repair, and showed that mitochondrial interactions increased, revealing a link between the physical and genetic behavior of mitochondria.

Towards An Integrative View Of Virus Phenotypes, John P. Delong, Maitham A. Al-Sammak, Zeina Al-Ameeli, David Dunigan, Kyle F. Edwards, Jeffry J. Fuhrmann, Jason P. Gleghorn, Hanqun Li, Kona Haramoto, Amelia O. Harrison, Marcia F. Marston, Ryan M. Moore, Shawn W. Polson, Barbra D. Ferrell, Miranda E. Salsbery, Christopher R. Schvarcz, Jasmine Shirazi, Grieg F. Steward, James L. Van Etten, K. Eric Wommack

School of Biological Sciences: Faculty Publications

Understanding how phenotypes emerge from genotypes is a foundational goal in biology. As challenging as this task is when considering cellular life, it is further complicated in the case of viruses. During replication, a virus as a discrete entity (the virion) disappears and manifests itself as a metabolic amalgam between the virus and the host (the virocell). Identifying traits that unambiguously constitute a virus’s phenotype is straightforward for the virion, less so for the virocell. Here, we present a framework for categorizing virus phenotypes that encompasses both virion and virocell stages and considers functional and performance traits of viruses in …

Aspergillus Nidulans Septa Are Indispensable For Surviving Cell Wall Stress, Ryland N. Spence, Walker Huso, Harley Edwards, Alexander Doan, Samantha Reese, Steven D. Harris, Ranjan Srivastava, Mark R. Marten

School of Biological Sciences: Faculty Publications

Septation in filamentous fungi is a normal part of development, which involves the formation of cross-hyphal bulkheads, typically containing pores, allowing cytoplasmic streaming between compartments. Based on previous findings regarding septa and cell wall stress, we hypothesized that septa are critical for survival during cell wall stress. To test this hypothesis, we used known Aspergillus nidulans septation-deficient mutants (ΔsepH, Δbud3, Δbud4, and Δrho4) and six antifungal compounds. Three of these compounds (micafungin, Congo red, and calcofluor white) are known cell wall stressors which activate the cell wall integrity signaling pathway (CWIS), while the three others (cycloheximide, miconazole, and 2,3-butanedione monoxime) …

The Centennial Of The Pecking Order: Current State And Future Prospects For The Study Of Dominance Hierarchies, Eli D. Strauss, James P. Curley, Daizaburo Shizuka, Elizabeth A. Hobson

School of Biological Sciences: Faculty Publications

A century ago, foundational work by Thorleif Schjelderup-Ebbe described a ‘pecking order’ in chicken societies, where individuals could be ordered according to their ability to exert their influence over their group-mates. Now known as dominance hierarchies, these structures have been shown to influence a plethora of individual characteristics and outcomes, situating dominance research as a pillar of the study of modern social ecology and evolution. Here, we first review some of the major questions that have been answered about dominance hierarchies in the last 100 years.Next,we introduce the contributions to this theme issue and summarize howthey provide ongoing insight in …

2019ncovr – A Comprehensive Genomic Resource For Sars-Cov-2 Variant Surveillance And Covid-19 Control, Guoquing Lu, Etsuko N. Moriyama

School of Biological Sciences: Faculty Publications

No abstract provided.

The Dynamics Of Dominance: Open Questions, Challenges And Solutions, Eli D. Strauss, Daizaburo Shizuka

School of Biological Sciences: Faculty Publications

Although social hierarchies are recognized as dynamic systems, they are typically treated as static entities for practical reasons. Here, we ask what we can learn from a dynamical view of dominance, and provide a research agenda for the next decades. We identify five broad questions at the individual, dyadic and group levels, exploring the causes and consequences of individual changes in rank, the dynamics underlying dyadic dominance relationships, and the origins and impacts of social instability. Although challenges remain, we propose avenues for overcoming them. We suggest distinguishing between different types of social mobility to provide conceptual clarity about hierarchy …

Domarchive: A Century Of Published Dominance Data, Eli D. Strauss, Alex R. Decasien, Gabriela Galindo, Elizabeth A. Hobson, Daizaburo Shizuka, James P. Curley

School of Biological Sciences: Faculty Publications

Dominance behaviours have been collected for many groups of animals since 1922 and serve as a foundation for research on social behaviour and social structure. Despite a wealth of data from the last century of research on dominance hierarchies, these data are only rarely used for comparative insight. Here, we aim to facilitate comparative studies of the structure and function of dominance hierarchies by compiling published dominance interaction datasets from the last 100 years of work. This compiled archive includes 436 datasets from 190 studies of 367 unique groups (mean group size 13.8, s.d. = 13.4) of 135 different species, …

Engineered Clostridium Botulinum Toxin Adapted To Deliver Molecules Into Selected Cells, Benjamin J. Pavlik, Paul Blum, Kevin Van Cott

School of Biological Sciences: Faculty Publications

An engineered payload - delivery system includes a target cell binding unit, covalently bound to a pore forming unit, and a payload portion adapted with a region capable of non-covalently binding to the pore forming unit. The pore forming unit is derived from a particular sub-serotype of Clostridium toxin, while the payload region is derived from a different sub-serotype of Clostridium toxin. The disclosed chimeric protein-based composition is capable of specifically delivering payload to neural cells.

Human Microglia Extensively Reconstitute In Humanized-Blt Mice With Human Interleukin-34 Transgene And Support Hiv-1 Brain Infection, Jianshui Zhang, Saroj Chandra Lohani, Yilun Cheng, Tao Wang, Lili Guo, Woong-Ki Kim, Santhi Gorantla, Qingsheng Li

School of Biological Sciences: Faculty Publications

Humanized bone marrow-liver-thymic (hu-BLT) mice develop a functional immune system in periphery, nevertheless, have a limited reconstitution of human myeloid cells, especially microglia, in CNS. Further, whether bone marrow derived hematopoietic stem and progenitor cells (HSPCs) can enter the brain and differentiate into microglia in adults remains controversial. To close these gaps, in this study we unambiguously demonstrated that human microglia in CNS were extensively reconstituted in adult NOG mice with human interleukin-34 transgene (hIL34 Tg) from circulating CD34+ HSPCs, nonetheless not in hu-BLT NOG mice, providing strong evidence that human CD34+ HSPCs can enter adult brain and differentiate into …

Forkhead-Associated Domain 2 Links Light Signal To Mirna Biogenesis, Lu Gan, Bin Yu

School of Biological Sciences: Faculty Publications

MicroRNAs (miRNAs) are one of the most important regulators of gene expression. Their biogenesis starts with the transcription of primary miRNA transcripts (pri-miRNAs). In plants, the RNase III enzyme DICER-LIKER 1 (DCL1), together with its partner, the double-stranded RNA-binding protein HYPONASTIC LEAVES 1 (HYL1), and the zinc-finger protein SERRATE (SE), process the imperfect miRNA-residing stem loop of primiRNAs to release the miRNA/miRNA* duplexes in the nucleus, which are then methylated by HUA1 ENHANCER 1 (Rogers and Chen, 2013; Song et al., 2019). Then, most miRNAs are sorted into AGONAUTE 1 to mediate mRNA-cleavage or translation inhibition based on sequence complementarity …

Evidence That Toxin Resistance In Poison Birds And Frogs Is Not Rooted In Sodium Channel Mutations And May Rely On “Toxin Sponge” Proteins, Fayal Abderemane-Ali, Nathan D. Rossen, Megan E. Kobiela, Robert A. Craig Ii, Catherine E. Garrison, Zhou Chen, Claire M. Colleran, Lauren A. O'Connell, J Du Bois, John P. Dumbacher, Daniel L. Minor Jr

School of Biological Sciences: Faculty Publications

Many poisonous organisms carry small-molecule toxins that alter voltage-gated sodium channel (Na_V) function. Among these, batrachotoxin (BTX) from Pitohui poison birds and Phyllobates poison frogs stands out because of its lethality and unusual effects on Na_V function. How these toxin-bearing organisms avoid autointoxication remains poorly understood. In poison frogs, a NaV DIVS6 pore-forming helix N-to-T mutation has been proposed as the BTX resistance mechanism. Here, we show that this variant is absent from Pitohui and poison frog NaVs, incurs a strong cost compromising channel function, and fails to produce BTX-resistant channels in poison frog NaVs. We also …

Hybrid Sterility, Genetic Conflict And Complex Speciation: Lessons From The Drosophila Simulans Clade Species, Daven C. Presgraves, Colin D. Meiklejohn

School of Biological Sciences: Faculty Publications

The three fruit fly species of the Drosophila simulans clade— D. simulans, D. mauritiana, and D. sechellia— have served as important models in speciation genetics for over 40 years. These species are reproductively isolated by geography, ecology, sexual signals, postmating-prezygotic interactions, and postzygotic genetic incompatibilities. All pairwise crosses between these species conform to Haldane’s rule, producing fertile F1 hybrid females and sterile F1 hybrid males. The close phylogenetic proximity of the D. simulans clade species to the model organism, D. melanogaster, has empowered genetic analyses of their species differences, including reproductive incompatibilities. But perhaps no phenotype has been subject to …

The Brain Transcriptome Of The Wolf Spider, Schizocosa Ocreata, Daniel Stribling, Peter L. Chang, Justin E. Dalton, Christopher A. Conow, Malcolm Rosenthal, Eileen Hebets, Rita M. Graze, Michelle N. Arbeitman

School of Biological Sciences: Faculty Publications

Objectives: Arachnids have fascinating and unique biology, particularly for questions on sex differences and behavior, creating the potential for development of powerful emerging models in this group. Recent advances in genomic techniques have paved the way for a significant increase in the breadth of genomic studies in non-model organisms. One growing area of research is comparative transcriptomics. When phylogenetic relationships to model organisms are known, comparative genomic studies provide context for analysis of homologous genes and pathways. The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a …

The Sensitivity Of Neotoma To Climate Change And Biodiversity Loss Over The Late Quaternary, Catalina P. Tomé, S. Kathleen Lyons, Seth D. Newsome, Felisa A. Smith

School of Biological Sciences: Faculty Publications

The late Quaternary in North America was marked by highly variable climate and considerable biodiversity loss including a megafaunal extinction event at the terminal Pleistocene. Here, we focus on changes in body size and diet in Neotoma (woodrats) in response to these ecological perturbations using the fossil record from the Edwards Plateau (Texas) across the past 20,000 years. Body mass was estimated using measurements of fossil teeth and diet was quantified using stable isotope analysis of carbon and nitrogen from fossil bone collagen. Prior to ca. 7,000 cal yr BP, maximum mass was positively correlated to precipitation and negatively correlated …

Trait-Based Variation In The Foraging Performance Of Individuals, John P. Delong, Stella F. Uiterwaal, Anthony I. Dell

School of Biological Sciences: Faculty Publications

Although average, species-level interaction strength plays a key role in driving population dynamics and community structure, predator-prey interactions occur among individuals. As a result, individual variation in foraging rates may play an important role in determining the effects of predator-prey interactions on communities. Such variation in foraging rates stems from individual variation in traits that influence the mechanistic components of the functional response, such as movements that determine encounters and behaviors such as decisions to attack. However, we still have little information about individual-level variation in functional responses or the traits that give rise to such variation. Here we combine …

Longitudinal Study Of Pogonomyrmex Occidentalis (Hymenoptera: Formicideae), Western Harvester Ant, Colony Survival In Western Nebraska, Kathleen H. Keeler

School of Biological Sciences: Faculty Publications

I observed individual western harvester ant (Pogonomyrmex occidentalis) colonies, marked between 1977 and 1994, to live a mean of 15.65 years (n = 112). The longest-lived colony lived 42 years.

Androgen Receptor, Although Not A Specific Marker For, Is A Novel Target To Suppress Glioma Stem Cells As A Therapeutic Strategy For Glioblastoma, Nan Zhao, Fei Wang, Shaheen Ahmed, Kan Liu, Chi Zhang, Sahara J. Cathcart, Dominick J. Dimaio, Michael Punsoni, Bingjie Guan, Ping Zhou, Shuo Wang, Surinder K. Batra, Tatiana Bronich, Tom K. Hei, Chi Lin, Chi Zhang

School of Biological Sciences: Faculty Publications

Targeting androgen receptor (AR) has been shown to be promising in treating glioblastoma (GBM) in cell culture and flank implant models but the mechanisms remain unclear. AR antagonists including enzalutamide are available for treating prostate cancer patients in clinic and can pass the blood–brain barrier, thus are potentially good candidates for GBM treatment but have not been tested in GBM orthotopically. Our current studies confirmed that in patients, a majority of GBM tumors overexpress AR in both genders. Enzalutamide inhibited the proliferation of GBM cells both in vitro and in vivo. Although confocal microscopy demonstrated that AR is expressed but …

Interplay Between Mirnas And Lncrnas: Mode Of Action And Biological Roles In Plant Development And Stress Adaptation, Xianxiang Meng, Aixia Li, Bin Yu, Shengjun Li

School of Biological Sciences: Faculty Publications

Plants employ sophisticated mechanisms to control developmental processes and to cope with environmental changes at transcriptional and post-transcriptional levels. MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs), two classes of endogenous noncoding RNAs, are key regulators of gene expression in plants. Recent studies have identified the interplay between miRNAs and lncRNAs as a novel regulatory layer of gene expression in plants. On one hand, miRNAs target lncRNAs for the production of phased small interfering RNAs (phasiRNAs). On the other hand, lncRNAs serve as origin of miRNAs or regulate the accumulation or activity of miRNAs at transcription and post-transcriptional levels. Theses lncRNA …

Seed Rain–Successional Feedbacks In Wet Tropical Forests, Nohemi Huanca Nuñez, Robin L. Chazdon, Sabrina E. Russo

School of Biological Sciences: Faculty Publications

Abstract

Tropical forest regeneration after abandonment of former agricultural land depends critically on the input of tree seeds, yet seed dispersal is increasingly disrupted in contemporary human-modified landscapes. Here, we introduce the concept of seed rain–successional feedbacks as a deterministic process in which seed rain is shaped by successional dynamics internal to a forest site and that acts to reinforce priority effects. We used a combination of time series and chronosequence approaches to investigate how the quantity and taxonomic and functional composition of seed rain change during succession and to evaluate the strength of seed rain–successional feedbacks, relative to other …

Development Of A Preventive Influenza D Virus Vaccine, Qingsheng Li, Yanmin Wan, Feng Li

School of Biological Sciences: Faculty Publications

The present disclosure provides a DNA vaccine or immunogenic composition expressing consensus hemagglutinin esterase - fusion ( HEF ) protein ( FluD - Vax ) and a protein based vaccine utilizing the HEF consensus protein . Methods of making and using the compositions are also provided herein.

Evolution Of Genome Structure In The Drosophila Simulans Species Complex, Mahul Chakraborty, Ching-Ho Chang, Danielle E. Khost, Jeffrey Vedanayagam, Jeffrey R. Adrion, Yi Liao, Kristi L. Montooth, Colin D. Meiklejohn, Amanda M. Larracuente, J J. Emerson

School of Biological Sciences: Faculty Publications

The rapid evolution of repetitive DNA sequences, including satellite DNA, tandem duplications, and transposable elements, underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genomic regions are fragmented and misassembled in most contemporary genome assemblies. We generated highly contiguous de novo reference genomes for the Drosophila simulans species complex (D. simulans, D. mauritiana, and D. sechellia), which speciated ∼250,000 yr ago. Our assemblies are comparable in contiguity and accuracy to the current D. melanogaster genome, allowing us to directly compare repetitive sequences between these four species. We find that at least 15% of the D. simulans complex …

The Influence Of Juvenile Dinosaurs On Community Structure And Diversity, Katlin Schroeder, S. Kathleen Lyons, Felisa A. Smith

School of Biological Sciences: Faculty Publications

Despite dominating biodiversity in the Mesozoic, dinosaurs were not speciose. Oviparity constrained even gigantic dinosaurs to less than 15 kg at birth; growth through multiple morphologies led to the consumption of different resources at each stage. Such disparity between neonates and adults could have influenced the structure and diversity of dinosaur communities. Here, we quantified this effect for 43 communities across 136 million years and seven continents. We found that megatheropods (more than 1000 kg) such as tyrannosaurs had specific effects on dinosaur community structure. Although herbivores spanned the body size range, communities with megatheropods lacked carnivores weighing 100 to …

Epigraph Hemagglutinin Vaccine Induces Broad Cross-Reactive Immunity Against Swine H3 Influenza Virus, Brianna L. Bullard, Brigette N. Corder, Jennifer Debeauchamp, Adam Rubrum, Bette Korber, Richard J. Webby, Eric A. Weaver

School of Biological Sciences: Faculty Publications

Influenza A virus infection in swine impacts the agricultural industry in addition to its zoonotic potential. Here, we utilize epigraph, a computational algorithm, to design a universal swine H3 influenza vaccine. The epigraph hemagglutinin proteins are delivered using an Adenovirus type 5 vector and are compared to a wild type hemagglutinin and the commercial inactivated vaccine, FluSure. In mice, epigraph vaccination leads to significant cross-reactive antibody and T-cell responses against a diverse panel of swH3 isolates. Epigraph vaccination also reduces weight loss and lung viral titers in mice after challenge with three divergent swH3 viruses. Vaccination studies in swine, the …

What Questions Are On The Minds Of Stem Undergraduate Students And How Can They Be Addressed?, Clara L. Meaders, Michelle K. Smith, Timothy Boester, Anne Bracy, Brian A. Couch, Abby G. Drake, Saima Farooq, Bashir Khoda, Cynthia Kinsland, A. Kelly Lane, Sarah E. Lindahl, William H. Livingston, Ayesha Maliwal Bundy, Amber Mccormick, Anya I. Morozov, Jennifer L. Newell-Caito, Katharine J. Ruskin, Mark A. Sarvary, Marilyne Stains, Justin R. St. Juliana, Stephanie R. Thomas, Cindy Van Es, Erin L. Vinson, Maren N. Vitousek, Mackenzie R. Stetzer

School of Biological Sciences: Faculty Publications

Addressing common student questions in introductory STEM courses early in the term is one way that instructors can ensure that their students have all been presented with information about how to succeed in their courses. However, categorizing student questions and identifying evidence-based resources to address student questions takes time, and instructors may not be able to easily collect and respond to student questions at the beginning of every course. To help faculty effectively anticipate and respond to student questions, we 1) administered surveys in multiple STEM courses to identify common student questions, 2) conducted a qualitative analysis to determine categories …

Temperature But Not Ocean Acidification Affects Energy Metabolism And Enzyme Activities In The Blue Mussel, Mytilus Edulis, Omera B. Matoo, Gisela Lannig, Christian Bock, Inna M. Sokolova

School of Biological Sciences: Faculty Publications

1. In mosaic marine habitats, such as intertidal zones, ocean acidification (OA) is exacerbated by high variability of pH, temperature, and biological CO2 production. The nonlinear interactions among these drivers can be context-specific and their effect on organisms in these habitats remains largely unknown, warranting further investigation. 2. We were particularly interested in Mytilus edulis (the blue mussel) from intertidal zones of the Gulf of Maine (GOM), USA, for this study. GOM is a hot spot of global climate change (average sea surface temperature (SST) increasing by >0.2°C/year) with >60% decline in mussel population over the past 40 years. 3. …

Genome-Wide Discovery Of Natural Variation In Pre-Mrna Splicing And Prioritising Causal Alternative Splicing To Salt Stress Response In Rice, Huihui Yu, Qian Du, Malachy Campbell, Bin Yu, Harkamal Walia, Chi Zhang

School of Biological Sciences: Faculty Publications

• Pre-mRNA splicing is an essential step for the regulation of gene expression. In order to specifically capture splicing variants in plants for genome-wide association studies (GWAS), we developed a software tool to quantify and visualise Variations of Splicing in Population (VASP).
• VASP can quantify splicing variants from short-read RNA-seq datasets and discover genotype-specific splicing (GSS) events, which can be used to prioritise causal pre-mRNA splicing events in GWAS. We applied our method to an RNA-seq dataset with 328 samples from 82 genotypes from a rice diversity panel exposed to optimal and saline growing conditions.
• In total, 764 significant GSS events …

Complete Genome Sequence Of Geobacter Sp. Strain Feam09, A Moderately Acidophilic Soil Bacterium, Pooja Yadav, Sanjay Antony-Babu, Erin Hayes, Olivia M. Healy, Donald Pan, Wendy H. Yang, Whendee L. Silver, Christopher L. Anderson, Adam Voshall, Samodha C. Fernando, Etsuko N. Moriyama, Joshua R. Herr, Karrie A. Weber

School of Biological Sciences: Faculty Publications

A moderately acidophilic Geobacter sp. strain, FeAm09, was isolated from forest soil. The complete genome sequence is 4,099,068 bp with an average GC content of 61.1%. No plasmids were detected. The genome contains a total of 3,843 genes and 3,608 protein-coding genes, including genes supporting iron and nitrogen biogeochemical cycling.

Body Mass-Related Changes In Mammal Community Assembly Patterns During The Late Quaternary Of North America, Silvia Pineda-Munoz, Advait M. Jukar, Anikó B. Toth, Danielle Fraser, Andrew Du, W. Andrew Barr, Kathryn L. Amatangelo, Meghan A. Balk, Anna K. Behrensmeyer, Jessica Blois, Matt Davis, Jussi T. Eronen, Nicholas J. Gotelli, Cindy Looy, Joshua H. Miller, Alexandria B. Shupinski, Laura C. Soul, Amelia Villaseñor, Scott Wing, S. Kathleen Lyons

School of Biological Sciences: Faculty Publications

The late Quaternary of North America was marked by prominent ecological changes, including the end-Pleistocene megafaunal extinction, the spread of human settlements and the rise of agriculture. Here we examine the mechanistic reasons for temporal changes in mammal species association and body size during this time period. Building upon the co-occurrence results from Lyons et al. (2016) – wherein each species pair was classified as spatially aggregated, segregated or random – we examined body mass differences (BMD) between each species pair for each association type and time period (Late Pleistocene: 40 000 ¹⁴C–11 700 ¹⁴C ybp, Holocene: 11 …

The Potential Use Of Radiomics With Pre-Radiation Therapy Mr Imaging In Predicting Risk Of Pseudoprogression In Glioblastoma Patients, Michael J. Baine, Justin Burr, Qian Du, Chi Zhang, Xiaoying Liang, Luke Krajewski, Laura Zima, Gerard Rux, Chi Zhang, Dandan Zheng

School of Biological Sciences: Faculty Publications

Glioblastoma (GBM) is the most common adult glioma. Differentiating post-treatment effects such as pseudoprogression from true progression is paramount for treatment. Radiomics has been shown to predict overall survival and MGMT (methylguanine-DNA methyltransferase) pro- moter status in those with GBM. A potential application of radiomics is predicting pseudoprogression on pre-radiotherapy (RT) scans for patients with GBM. A retrospective review was performed with radiomic data analyzed using pre-RT MRI scans. Pseudoprogression was defined as post-treatment findings on imaging that resolved with steroids or spontaneously on subsequent imaging. Of the 72 patients identified for the study, 35 were able to be assessed …

Pollinator Assemblage And Pollen Load Differences On Sympatric Diploid And Tetraploid Cytotypes Of The Desert-Dominant Larrea Tridentata, Robert G. Laport, Robert L. Minckley, Diana Pilson

School of Biological Sciences: Faculty Publications

PREMISE: Whole-genome duplication (polyploidy) is an important force shaping flowering-plant evolution. Ploidy-specific plant–pollinator interactions represent important community-level biotic interactions that can lead to nonrandom mating and the persistence of mixed-ploidy populations.

METHODS: At a naturally occurring diploid–tetraploid contact zone of the autopolyploid desert shrub Larrea tridentata, we combined flower phenology analyses, collections of bees on plants of known cytotype, and flow cytometry analyses of bee-collected pollen loads to investigate whether (1) diploid and tetraploid plants have unique bee pollinator assemblages, (2) bee taxa exhibit ploidy-specific visitation and pollen collection biases, and (3) specialist and generalist bee taxa …