Biology Commons^™

To Stick Or Not To Stick: The Multiple Roles Of Cell Adhesion Molecules In Neural Circuit Assembly, Trevor Moreland, Fabienne E. Poulain

Faculty Publications

Precise wiring of neural circuits is essential for brain connectivity and function. During development, axons respond to diverse cues present in the extracellular matrix or at the surface of other cells to navigate to specific targets, where they establish precise connections with post-synaptic partners. Cell adhesion molecules (CAMs) represent a large group of structurally diverse proteins well known to mediate adhesion for neural circuit assembly. Through their adhesive properties, CAMs act as major regulators of axon navigation, fasciculation, and synapse formation. While the adhesive functions of CAMs have been known for decades, more recent studies have unraveled essential, non-adhesive functions …

Pickle Associates With Histone Deacetylase 9 To Mediate Vegetative Phase Change In Arabidopsis, Tieqiang Hu, Darren Manuela, Valerie Hinsch, Mingli Xu

Faculty Publications

• The juvenile-to-adult vegetative phase change in flowering plants is mediated by a decrease in miR156 levels. Downregulation of MIR156A/MIR156C, the two major sources of miR156, is accompanied by a decrease in acetylation of histone 3 lysine 27 (H3K27ac) and an increase in trimethylation of H3K27 (H3K27me3) at MIR156A/MIR156C in Arabidopsis.

• Here, we show that histone deacetylase 9 (HDA9) is recruited to MIR156A/MIR156C during the juvenile phase and associates with the CHD3 chromatin remodeler PICKLE (PKL) to erase H3K27ac at MIR156A/MIR156C.

• H2Aub and H3K27me3 become enriched at MIR156A/MIR156C, and the recruitment of Polycomb Repressive Complex …

The Interplay Between Hydrogen Sulfide And Phytohormone Signaling Pathways Under Challenging Environments, Muhammad Saad Shoaib Khan, Faisal Islam, Yajin Ye, Matthew Ashline, Daowen Wang, Biying Zhao, Zheng Qing Fu, Jian Chen

Faculty Publications

Hydrogen sulfide (H₂S) serves as an important gaseous signaling molecule that is involved in intra- and intercellular signal transduction in plant–environment interactions. In plants, H₂S is formed in sulfate/cysteine reduction pathways. The activation of endogenous H₂S and its exogenous application has been found to be highly effective in ameliorating a wide variety of stress conditions in plants. The H₂S interferes with the cellular redox regulatory network and prevents the degradation of proteins from oxidative stress via post-translational modifications (PTMs). H₂S-mediated persulfidation allows the rapid response of proteins in signaling networks …

Lis1 And Ndel1 Regulate Axonal Trafficking Of Mitochondria In Mature Neurons, Jai P. Pandey, Liang Shi, Remi A. Brebion, Deanna S. Smith

Faculty Publications

Defective mitochondrial dynamics in axons have been linked to both developmental and late-onset neurological disorders. Axonal trafficking is in large part governed by the microtubule motors kinesin-1 and cytoplasmic dynein 1 (dynein). Dynein is the primary retrograde transport motor in axons, and mutations in dynein and many of its regulators also cause neurological diseases. Depletion of LIS1, famous for linking dynein deregulation to lissencephaly (smooth brain), in adult mice leads to severe neurological phenotypes, demonstrating post-developmental roles. LIS1 stimulates retrograde transport of acidic organelles in cultured adult rat dorsal root ganglion (DRG) axons but findings on its role in mitochondrial …

Saving The Sea Turtles Of Anguilla: Combining Scientific Data With Community Perspectives To Inform Policy Decisions, L. M. Soanes, J. Johnson, K. Eckert, K. Gumbs, L. G. Halsey, G. Hughes, K. Levasseur, Joe Quattro, R. Richardson, J. P. Skinner, S. Wynee, F. Mukhida

Faculty Publications

Historic over-exploitation and the more recent threats caused by fisheries by-catch, disease and climate change have left sea turtle populations in the Wider Caribbean at risk of extinction. In 1995, following regional declines in nesting and foraging populations, the island of Anguilla implemented a moratorium on the hunting of turtles. At the request of the Government of Anguilla for scientific data to either support or remove the moratorium, comprehensive population estimates were obtained, and foraging, nesting and migratory movements were examined. In addition, community perspectives on turtles and their protection were assessed. Between 2015 and 18 surveys of 30 nesting …

Editorial: Pathways And Processes Underpinning Axonal Biology And Pathobiology, Pabitra K. Sahoo, Dianna E. Willis, James N. Sleigh

Faculty Publications

No abstract provided.

Identification And Characterization Of A Stem Canker And Twig Dieback Disease Of Pear Caused By Neofusicoccum Parvum In Chinese Mainland, Feng He, Jie Yang, Yancun Zhao, Pedro Laborda, Yifan Jia, Asma Safdar, Alex Machio Kange, Bingxin Li, Lan Zhou, Quan Zeng, Sally Brown, Zheng Qing Fu, Fengquan Liu

Faculty Publications

Pear (Pyrus spp.) is one of the most consumed fruits in China, but the pear production has to confront the growing threat from fatal diseases. In this study, we report two incidences of stem canker and twig dieback disease on pear plants, which led to death of pear seedlings (approximately 10% of total plants) in Guangxi and Jiangsu provinces. Using a combination of morphological and molecular diagnoses, along with pathogenicity test, the causal agent of the disease in these two locations was identified to be the fungus Neofusicoccum parvum. However, the isolates were divided into two clades: CY-2 …

The Ability To Classify Patients Based On Gene-Expression Data Varies By Algorithm And Performance Metric, Stephen Piccolo, Avery Mecham, Nathan P. Golightly, Jérémie L. Johnson, Dustin B. Miller

Faculty Publications

By classifying patients into subgroups, clinicians can provide more effective care than using a uniform approach for all patients. Such subgroups might include patients with a particular disease subtype, patients with a good (or poor) prognosis, or patients most (or least) likely to respond to a particular therapy. Transcriptomic measurements reflect the downstream effects of genomic and epigenomic variations. However, high-throughput technologies generate thousands of measurements per patient, and complex dependencies exist among genes, so it may be infeasible to classify patients using traditional statistical models. Machine-learning classification algorithms can help with this problem. However, hundreds of classification algorithms exist—and …

The Transcription Factor Vpxlnr Is Required For The Growth, Development, And Virulence Of The Fungal Pathogen Valsa Pyri, Feng He, Alex-Machio Kange, Jie Yang, Jiaxin Xiao, Rongbo Wang, Lu Yang, Yifan Jia, Zhengqing Fu, Yancun Zhao, Fengquan Liu

Faculty Publications

Pears (Pyrus sp.) are widely cultivated in China, and their yield accounts for more than 60% of global pear production. The fungal pathogen Valsa pyri is a major causal agent of pear canker disease, which results in enormous losses of pear production in northern China. In this study, we characterized a Zn₂Cys₆ transcription factor that contains one GAL4 domain and a fungal-trans domain, which are present in VpxlnR. The vpxlnR gene expression was upregulated in the invasion stage of V. pyri. To investigate its functions, we constructed gene deletion mutants and complementary strains. We observed …

The Global Virome In One Network (Virion): An Atlas Of Vertebrate-Virus Associations, Colin J. Carlson, Rory J. Gibb, Gregory F. Albery, Liam Brierley, Ryan P. Connor, Tad Dallas, Evan A. Eskew, Anna C. Fagre, Maxwell J. Farrell, Hannah K. Frank, Renata L. Muylaert, Timothée Poisot, Angela L. Rasmussen, Sadie J. Ryan, Stephanie N. Seifert

Faculty Publications

Data that catalogue viral diversity on Earth have been fragmented across sources, disciplines, formats, and various degrees of open sharing, posing challenges for research on macroecology, evolution, and public health. Here, we solve this problem by establishing a dynamically maintained database of vertebrate-virus associations, called The Global Virome in One Network (VIRION). The VIRION database has been assembled through both reconciliation of static data sets and integration of dynamically updated databases. These data sources are all harmonized against one taxonomic backbone, including metadata on host and virus taxonomic validity and higher classification; additional metadata on sampling methodology and evidence strength …

Relationship Between Oxidative Stress And Lifespan In Daphnia Pulex, Benedicth Ukhueduan, Charles Schumpert, Eunsuk Kim, Jeffry L. Dudycha, Rekha C. Patel

Faculty Publications

Macromolecular damage leading to cell, tissue and ultimately organ dysfunction is a major contributor to aging. Intracellular reactive oxygen species (ROS) resulting from normal metabolism cause most damage to macromolecules and the mitochondria play a central role in this process as they are the principle source of ROS. The relationship between naturally occurring variations in the mitochondrial (MT) genomes leading to correspondingly less or more ROS and macromolecular damage that changes the rate of aging associated organismal decline remains relatively unexplored. MT complex I, a component of the electron transport chain (ETC), is a key source of ROS and the …

Reply To Comment: Controls On Turnover Of Marine Dissolved Organic Matter-Testing The Null Hypothesis Of Purely Concentration-Driven Uptake, Yuan Shen, Ronald Benner

Faculty Publications

Our recent bioassay experiments indicate that molecular properties are a primary control on the microbial utilization of dissolved organic matter in the ocean. This finding is questioned by Lennartz and Dittmar who modeled our experiments and concluded that our observations could be largely explained by concentration-driven uptake independent from molecular properties. We suggest the authors' models are deficient for establishing the relative roles of molecular properties and concentration-driven uptake. Our conclusion is consistent with earlier and recent experimental results and biogeochemical observations, supporting a unified theory with molecular properties as a more prominent control than concentration-driven uptake on marine organic …

Transcriptional Coactivators: Driving Force Of Plant Immunity, Muhammad Saad Shoaib Khan, Faisal Islam, Huan Chen, Ming Chang, Daowen Wang, Fengquan Liu, Zhengqing Fu, Jian Chen

Faculty Publications

Salicylic acid (SA) is a plant defense signal that mediates local and systemic immune responses against pathogen invasion. However, the underlying mechanism of SA-mediated defense is very complex due to the involvement of various positive and negative regulators to fine-tune its signaling in diverse pathosystems. Upon pathogen infections, elevated level of SA promotes massive transcriptional reprogramming in which Non-expresser of PR genes 1 (NPR1) acts as a central hub and transcriptional coactivator in defense responses. Recent findings show that Enhanced Disease Susceptibility 1 (EDS1) also functions as a transcriptional coactivator and stimulates the expression of PR1 in the presence of …

Improved Chromosome-Level Genome Assembly Of The Glanville Fritillary Butterfly (Melitaea Cinxia) Integrating Pacific Biosciences Long Reads And A High-Density Linkage Map, Olli-Pekka Smolander, Daniel Blande, Virpi Ahola, Pasi Rastas, Jaakko Tanskanen, Juhana Kammonen, Vicencio Oostra, Lorenzo Pellegrini, Suvi Ikonen, Tad Dallas, Michelle F. Dileo, Anne Duplouy, Iihan Cem Duru, Pauliina Halimaa, Aapo Kahilainen, Suyog S. Kuwar, Sirpa O. Kärenlampi, Elvira Lafuente, Shiqi Luo, Jenny Makkonen, Abhilash Nair, Narua De La Paz Celorio-Mancera, Ville Pennanen, Annukka Ruokolainen, Tarja Sundell, Arja I. Tervahauta, Victoria Twort, Erik Van Bergen, Janina Österman-Udd, Lars Paulin, Mikko J. Frilander, Petri Auvinen, Marjo Saastamoinen

Faculty Publications

Background

The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses.

Results

The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92–94% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and …

Evolutionary Analyses Of Visual Opsin Genes In Frogs And Toads: Diversity, Duplication, And Positive Selection, Ryan K. Schott, Leah Perez, Matthew Kwiatkowski, Vance Imhoff, Jennifer M. Gumm

Faculty Publications

Among major vertebrate groups, anurans (frogs and toads) are understudied with regard to their visual systems, and little is known about variation among species that differ in ecology. We sampled North American anurans representing diverse evolutionary and life histories that likely possess visual systems adapted to meet different ecological needs. Using standard molecular techniques, visual opsin genes, which encode the protein component of visual pigments, were obtained from anuran retinas. Additionally, we extracted the visual opsins from publicly available genome and transcriptome assemblies, further increasing the phylogenetic and ecological diversity of our dataset to 33 species in total. We found …

Chronic Background Radiation Correlates With Sperm Swimming Endurance In Bank Voles From Chernobyl, Kati Kivisaari, Sara Calhim, Zbyszek Boratyríski, Timothy Mousseau, Anders P. Møller, Tapio Mappes

Faculty Publications

Sperm quantity and quality are key features explaining intra- and interspecific variation in male reproductive success. Spermatogenesis is sensitive to ionizing radiation and laboratory studies investigating acute effects of ionizing radiation have indeed found negative effects of radiation on sperm quantity and quality. In nature, levels of natural background radiation vary dramatically, and chronic effects of low-level background radiation exposure on spermatogenesis are poorly understood. The Chernobyl region offers a unique research opportunity for investigating effects of chronic low-level ionizing radiation on reproductive properties of wild organisms. We captured male bank voles (Myodes glareolus) from 24 locations in the Chernobyl …

Electrophysiological Responses To Conspecific Odorants In Xenopus Laevis Show Potential For Chemical Signaling, Heather J. Rhodes, Melanie Amo

Faculty Publications

No abstract provided.

Factors Related To Species Richness, Endemism, And Conservation Status Of The Herpetofauna (Amphibia And Reptilia) Of Mexican States, Geoffrey R. Smith, Julio A. Lemos-Espinal

Faculty Publications

No abstract provided.

Triophaser: Using Mendelian Inheritance Logic To Improve Genomic Phasing Of Trios, Dustin B. Miller, Stephen R. Piccolo

Faculty Publications

Background: When analyzing DNA sequence data of an individual, knowing which nucleotide was inherited from each parent can be benefcial when trying to identify certain types of DNA variants. Mendelian inheritance logic can be used to accurately phase (haplotype) the majority (67–83%) of an individual’s heterozygous nucleotide positions when genotypes are available for both parents (trio). However, when all members of a trio are heterozygous at a position, Mendelian inheritance logic cannot be used to phase. For such positions, a computational phasing algorithm can be used. Existing phasing algorithms use a haplotype reference panel, sequencing reads, and/or parental genotypes …

Panoramic Spatial Vision In The Bay Scallop Argopecten Irradians, Daniel R. Chappell, Tyler M. Horan, Daniel Isaac Speiser

Faculty Publications

We have a growing understanding of the light-sensing organs and light-influenced behaviours of animals with distributed visual systems, but we have yet to learn how these animals convert visual input into behavioural output. It has been suggested they consolidate visual information early in their sensory-motor pathways, resulting in them being able to detect visual cues (spatial resolution) without being able to locate them (spatial vision). To explore how an animal with dozens of eyes processes visual information, we analysed the responses of the bay scallop Argopecten irradians to both static and rotating visual stimuli. We found A. irradians distinguish between …

Cetacean Acousticwelfare In Wild And Managed-Care Settings: Gaps And Opportunities, Paige E. Stevens, Heather Hill, Jason N. Bruck

Faculty Publications

Cetaceans are potentially at risk of poor welfare due to the animals’ natural reliance on sound and the persistent nature of anthropogenic noise, especially in the wild. Industrial, commercial, and recreational human activity has expanded across the seas, resulting in a propagation of sound with varying frequency characteristics. In many countries, current regulations are based on the potential to induce hearing loss; however, a more nuanced approach is needed when shaping regulations, due to other non-hearing loss effects including activation of the stress response, acoustic masking, frequency shifts, alterations in behavior, and decreased foraging. Cetaceans in managedcare settings share the …

Low Light Intensity Delays Vegetative Phase Change, Mingli Xu, Tieqiang Hu, R Scott Poethig

Faculty Publications

Plants that develop under low light (LL) intensity often display a phenotype known as the “shade tolerance syndrome (STS)”. This syndrome is similar to the phenotype of plants in the juvenile phase of shoot development, but the basis for this similarity is unknown. We tested the hypothesis that the STS is regulated by the same mechanism that regulates the juvenile vegetative phase by examining the effect of LL on rosette development in Arabidopsis (Arabidopsis thaliana). We found that LL prolonged the juvenile vegetative phase and that this was associated with an increase in the expression of the master …

Simplifying The Development Of Portable, Scalable, And Reproducible Workflows, Stephen Piccolo, Zachary E. Ence, Elizabeth C. Anderson, Jeffrey T. Chang, Andrea H. Bild

Faculty Publications

Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool’s inputs, outputs, and other execution details. CWL documents can include instructions for executing tools inside software containers. Accordingly, CWL tools are portable—they can be executed on diverse computers—including personal workstations, high-performance clusters, or the cloud. CWL also supports workflows, which describe dependencies among tools and using outputs from one tool as inputs to others. To date, CWL has been used …

The Ghost Of Hosts Past: Impacts Of Host Extinction On Parasite Specificity, Maxwell J. Farrell, Andrew W. Park, Clayton E. Cressler, Tad Dallas, Shan Huang, Nicole Mideo, Ignacio Morales-Castilla, T. Jonathan Davies, Patrick Stephens

Faculty Publications

A growing body of research is focused on the extinction of parasite species in response to host endangerment and declines. Beyond the loss of parasite species richness, host extinction can impact apparent parasite host specificity, as measured by host richness or the phylogenetic distances among hosts. Such impacts on the distribution of parasites across the host phylogeny can have knock-on effects that may reshape the adaptation of both hosts and parasites, ultimately shifting the evolutionary landscape underlying the potential for emergence and the evolution of virulence across hosts. Here, we examine how the reshaping of host phylogenies through extinction may …

The Future Of Zoonotic Risk Prediction, Colin J. Carlson, Maxwell J. Farrell, Zoe Grange, Barbara A. Han, Nardus Mollentze, Alexandra L. Phelan, Angela L. Rasmussen, Gregory F. Albery, Bernard Bett, David M. Brett-Major, Lily E. Cohen, Tad Dallas, Evan A. Eskew, Anna C. Fagre, Kristian M. Forbes, Rory Gibb, Sam Halabi, Charlotte C. Hammer, Rebecca Katz, Jason Kindrachuk, Renata L. Muylaert, Felicia B. Nutter, Joseph Ogola, Kevin J. Olival, Michelle Rourke, Sadie J. Ryan, Noam Ross, Stephanie N. Seifert, Tarja Sironen, Claire J. Standley, Kishana Taylor, Marietjie Venter, Paul W. Webala

Faculty Publications

In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open …

Predicting Drug Sensitivity Of Cancer Cells Based On Dna Methylation Levels, Sofia P. Miranda, Fernanda A. Baião, Julia L. Fleck, Stephen R. Piccolo

Faculty Publications

Cancer cell lines, which are cell cultures derived from tumor samples, represent one of the least expensive and most studied preclinical models for drug development. Accurately predicting drug responses for a given cell line based on molecular features may help to optimize drug-development pipelines and explain mechanisms behind treatment responses. In this study, we focus on DNA methylation profiles as one type of molecular feature that is known to drive tumorigenesis and modulate treatment responses. Using genome-wide, DNA methylation profiles from 987 cell lines in the Genomics of Drug Sensitivity in Cancer database, we used machine-learning algorithms to evaluate the …

On The Human Appropriation Of Wetland Primary Production, James A. Cloern, Samuel M. Safran, Lydia Smith Vaughn, April Robinson, Alison A. Whipple, Katharyn E. Boyer, Judith Z. Drexler, Robert J. Naiman, James L. Pinckney, Emily R. Howe, Elizabeth A. Canuel, J. Letitia Grenier

Faculty Publications

Humans are changing the Earth's surface at an accelerating pace, with significant consequences for ecosystems and their biodiversity. Landscape transformation has far-reaching implications including reduced net primary production (NPP) available to support ecosystems, reduced energy supplies to consumers, and disruption of ecosystem services such as carbon storage. Anthropogenic activities have reduced global NPP available to terrestrial ecosystems by nearly 25%, but the loss of NPP from wetland ecosystems is unknown. We used a simple approach to estimate aquatic NPP from measured habitat areas and habitat-specific areal productivity in the largest wetland complex on the USA west coast, comparing historical and …

Local Translation Across Neural Development: A Focus On Radial Glial Cells, Axons, And Synaptogenesis, Manasu Agrawal, Kristy Welshhans

Faculty Publications

In the past two decades, significant progress has been made in our understanding of mRNA localization and translation at distal sites in axons and dendrites. The existing literature shows that local translation is regulated in a temporally and spatially restricted manner and is critical throughout embryonic and post-embryonic life. Here, recent key findings about mRNA localization and local translation across the various stages of neural development, including neurogenesis, axon development, and synaptogenesis, are reviewed. In the early stages of development, mRNAs are localized and locally translated in the endfeet of radial glial cells, but much is still unexplored about their …

Mitochondrial Genome Of Geomydoecus Aurei, A Pocket-Gopher Louse, Theresa A. Spradling, Alexandra C. Place, Ashley L. Campbell, James W. Demastes

Faculty Publications

Parasitic lice demonstrate an unusual array of mitochondrial genome architectures and gene arrangements. We characterized the mitochondrial genome of Geomydoecus aurei, a chewing louse (Phthiraptera: Trichodectidae) found on pocket gophers (Rodentia: Geomyidae) using reads from both Illumina and Oxford Nanopore sequencing coupled with PCR, cloning, and Sanger sequencing to verify structure and arrangement for each chromosome. The genome consisted of 12 circular mitochondrial chromosomes ranging in size from 1,318 to 2,088 nucleotides (nt). Total genome size was 19,015 nt. All 37 genes typical of metazoans (2 rRNA genes, 22 tRNA genes, and 13 protein-coding genes) were present. An average …

Individual Quality And Phenology Mediate The Effect Of Radioactive Contamination On Body Temperature In Chernobyl Barn Swallows, Zbyszek Boratynski, Timothy A. Mousseau, Anders Pape Moller

Faculty Publications

Anthropogenic stressors, such as radioactive contaminants released from the Chernobyl and Fukushima Daiichi accidents, deteriorate ecological and evolutionary processes, as evidence for damaging effects of radioactive contamination on wildlife is accumulating. Yet little is known about physiological traits of animals inhabiting contaminated areas, and how those are affected by individual quality and phenology. We investigated variation in body temperature of wild barn swallows, Hirundo rustica, exposed to radioactive contamination from the Chernobyl accident in Ukraine and Belarus. We tested whether exposure to variable levels of radioactive contamination modified core body temperature of birds, and whether individual and phenological characteristics modulated …