Biology Commons^™

Phenotype Bias Determines How Natural Rna Structures Occupy The Morphospace Of All Possible Shapes, Fatme Ghaddar, Dr Kamaludin Dingle, Dr Petr Sulc, Prof Ard A. Louis

Undergraduate Research Symposium

The relative prominence of developmental bias versus natural selection is a long standing controversy in evolutionary biology. Here we demonstrate quantitatively that developmental bias is the primary explanation for the occupation of the morphospace of RNA secondary structure (SS) shapes. By using the RNAshapes method to define coarse-grained SS classes, we can measure the frequencies that non-coding RNA SS shapes appear in nature. Our main findings are firstly that only the most frequent structures appear in nature; the vast majority of possible structures in the morphospace have not yet been explored. Secondly, and perhaps more surprisingly, these frequencies are accurately …

The Naked Truth: A Comprehensive Clarification And Classification Of Current ‘Myths’ In Naked Mole‐Rat Biology, Rochelle Buffenstein, Vincent Amoroso, Blazej Andziak, Stanislav Avdieiev, Jorge Azpurua, Alison J. Barker, Nigel C. Bennett, Miguel A. Brieño‐Enríquez, Gary N. Bronner, Clive Coen, Martha A. Delaney, Christine M. Dengler‐Crish, Yael H. Edrey, Chris G. Faulkes, Daniel Frankel, Gerard Friedlander, Patrick A. Gibney, Vera Gorbunova, Christopher Hine, Melissa M. Holmes, Jennifer U. M. Jarvis, Yoshimi Kawamura, Nobuyuki Kutsukake, Cynthia Kenyon, Walid T. Khaled, Takefumi Kikusui, Joseph Kissil, Samantha Lagestee, John Larson, Amanda Lauer, Leonid A. Lavrenchenko, Angela Lee, Jonathan B. Levitt, Gary R. Lewin, Kaitlyn N. Lewis Hardell, Tzuhua D. Lin, Matthew J. Mason, Dan Mccloskey, Mary Mcmahon, Kyoko Miura, Kazutaka Mogi, Vikram Narayan, Timothy P. O'Connor, Kazuo Okanoya, M. Justin O'Riain, Thomas J. Park, Ned J. Place, Katie Podshivalova, Matthew E. Pamenter, Sonja J. Pyott, Jane Reznick, J. Graham Ruby, Adam B. Salmon, Joseph Santos‐Sacchi, Diana K. Sarko, Andrei Seluanov, Alyssa Shepard, Megan Smith, Kenneth B. Storey, Xiao Tian, Emily N. Vice, Mélanie Viltard, Akiyuki Watarai, Ewa Wywial, Masanori Yamakawa, Elena D. Zemlemerova, Michael Zions, Ewan St. John Smith

Publications and Research

The naked mole‐rat (Heterocephalus glaber) has fascinated zoologists for at least half a century. It has also generated considerable biomedical interest not only because of its extraordinary longevity, but also because of unusual protective features (e.g. its tolerance of variable oxygen availability), which may be pertinent to several human disease states, including ischemia/reperfusion injury and neurodegeneration. A recent article entitled ‘Surprisingly long survival of premature conclusions about naked mole‐rat biology’ described 28 ‘myths’ which, those authors claimed, are a ‘perpetuation of beautiful, but falsified, hypotheses’ and impede our understanding of this enigmatic mammal. Here, we re‐examine each of …

Detecting Forest Response To Droughts With Global Observations Of Vegetation Water Content, Alexandra G. Konings, Sassan S. Saatchi, Christian Frankenberg, Michael Keller, Victor Leshyk, William R. L. Anderegg, Vincent Humphrey, Ashley M. Matheny, Anna Trugman, Bradley O. Christoffersen

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Droughts in a warming climate have become more common and more extreme, making understanding forest responses to water stress increasingly pressing. Analysis of water stress in trees has long focused on water potential in xylem and leaves, which influences stomatal closure and water flow through the soil-plant-atmosphere continuum. At the same time, changes of vegetation water content (VWC) are linked to a range of tree responses, including fluxes of water and carbon, mortality, flammability, and more. Unlike water potential, which requires demanding in situ measurements, VWC can be retrieved from remote sensing measurements, particularly at microwave frequencies using radar and …

Mutations In Several Auxin Biosynthesis Genes And Their Effects On Plant Phenotypes In Arabidopsis, Gabriela Hernandez, Lauren Huebner, Bethany Karlin Zolman

Undergraduate Research Symposium

Auxins are important hormones in plants that regulate growth and development. Disruptions in the auxin biosynthesis pathway result in morphological changes in phenotypes in the model plant Arabidopsis thaliana, including differences in root and leaf formation. Mutations in the Tryptophan Aminotransferase of Arabidopsis (TAA1) and YUCCA (YUC4) genes interfere with the plant's ability to synthesize Indole-3-acetic acid (IAA), the primary auxin involved in plant development. IBR1 and IBR3 act in the multistep conversion of indole-3-butyric acid (IBA) to IAA. ILL2, IAR3, and ILR1 hydrolyze IAA-amino acid conjugates into free IAA. The goal of …

Mara Repression Of Virulence Gene Hila In Salmonella, Alexandra King, Lauren Daugherty, Lon Chubiz Phd

Undergraduate Research Symposium

Salmonella is a bacteria most commonly known for causing the eponymous food-related illness. Due to their rapid reproduction rate and their ability to be propogated and maintained in a lab setting, they are commonly used in lab studies so that we can better understand how Salmonella causes disease in organisms that are more difficult to study. One area of interest is analyzing how Salmonella controls expression of the mechanisms that actually cause disease, called virulence traits, in response to the environment. In this study, antibiotic stress was used to analyze virulence gene expression. MarA is a gene that regulates ampicillin …

Mechanisms Of Substrate Recognition By The Cul3-Based E3 Ligase, Katia Graziella De Oliveira Rebola

Dissertations and Theses

Cul3-based E3 ligase is responsible for regulating a variety of cellular pathways, many of which are known to have profound effects on the proper function of multicellular organisms. Although progress over the past years has been truly impressive, our understanding of the mechanisms of E2 recruitment and selection by the BCR complex and all the roles that Cul3 plays on kidneys remains in its infancy. To explore these aspects, this dissertation aims to analyze the Cul3 complex using two different approaches: (1) We used the powerful tool of chimeric analysis to map the essential domain binding characteristics of Cul3 taking …

Weak Spatial-Genetic Structure In A Native Invasive, The Southern Pine Beetle (Dendroctonus Frontalis), Across The Eastern United States, Ryan C. Garrick, Ísis C. Arantes, Megan B. Stubbs, Nathan P. Havill

Faculty and Student Publications

The southern pine beetle, Dendroctonus frontalis, is a native pest of pine trees that has recently expanded its range into the northeastern United States. Understanding its colonization, dispersal, and connectivity will be critical for mitigating negative economic and ecological impacts in the newly invaded areas. Characterization of spatial-genetic structure can contribute to this; however, previous studies have reached different conclusions about regional population genetic structure, with one study reporting a weak east-west pattern, and the most recent reporting an absence of structure. Here we systematically assessed several explanations for the absence of spatial-genetic structure. To do this, we developed nine …

Linking Ecomechanical Models And Functional Traits To Understand Phenotypic Diversity, T. E. Higham, L. A. Ferry, L. Schmitz, D. J. Irschick, S. Starko, P. S L Anderson, P. J. Bergmann, H. A. Jamniczky, L. R. Monteiro, D. Navon, J. Messier, E. Carrington, S. C. Farina, K. L. Feilich, L. P. Hernandez, Michele A. Johnson, S. M. Kawano, C. J. Law, S. J. Longo, C. H. Martin, P. T. Martone, A. Rico-Guevara, S. E. Santana, K. J. Niklas

Biology Faculty Research

Physical principles and laws determine the set of possible organismal phenotypes. Constraints arising from development, the environment, and evolutionary history then yield workable, integrated phenotypes. We propose a theoretical and practical framework that considers the role of changing environments. This 'ecomechanical approach' integrates functional organismal traits with the ecological variables. This approach informs our ability to predict species shifts in survival and distribution and provides critical insights into phenotypic diversity. We outline how to use the ecomechanical paradigm using drag-induced bending in trees as an example. Our approach can be incorporated into existing research and help build interdisciplinary bridges. Finally, …

Otoliths Of South-Western Australian Fish: A Photographic Catalogue, Chris Dowling, Kim Smith, Elaine Lek, Joshua Brown

Fisheries Research Reports

Due to the species-specific nature of otoliths and given they are often the only part of the fish preserved when fish die, otolith catalogues can be used in numerous applications, such as diet studies in fish eating animals, including pinnipeds, fish and sea birds; archaeological purposes such as reconstructing indigenous people’s diets from otoliths found in middens or evolutionary history of fish species by comparing fossilized otoliths. Given the unique mixture of subtropical and temperate fish, including many endemic species that occur off the southwest corner of WA having a catalogue for this area is extremely important for people working …

Corticosterone's Roles In Avian Migration: Assessment Of Three Hypotheses, Carolyn M. Bauer, H. E. Watts

Biology Faculty Works

While corticosterone (CORT) is often suggested to be an important hormone regulating processes necessary for avian migration, there has been no systematic assessment of CORT's role in migration. Prior to migration, birds increase fat stores and flight muscle size to prepare for the high energetic costs associated with long-distance flight. After attaining sufficient energetic stores, birds then make the actual decision to depart from their origin site. Once en route birds alternate between periods of flight and stopovers, during which they rest and refuel for their next bouts of endurance flight. Here, we evaluate three non-mutually exclusive hypotheses that have …

College Of Natural Sciences Newsletter, September 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 9.

Page 1 Dean's Message
Page 2 Awards and Recognition
Page 3 Student Clubs in Natural Science
Page 4 Media Coverage of CNS
Page 5 Hobo Day Festivities
Page 6 Open PRAIRIE Data; Grants Awarded in CNS
Page 7 One Day for State Recap

Season Of Prescribed Fire Determines Grassland Restoration Outcomes After Fire Exclusion And Overgrazing, Erin N. Novak, Michelle Bertelsen, Dick Davis, Devin M. Grobert, Kelly G. Lyons, Jason P. Martina, W. Matt Mccaw, Matthew O'Toole, Joseph W. Veldman

Biology Faculty Research

Fire exclusion and mismanaged grazing are globally important drivers of environmental change in mesic C₄ grasslands and savannas. Although interest is growing in prescribed fire for grassland restoration, we have little long-term experimental evidence of the influence of burn season on the recovery of herbaceous plant communities, encroachment by trees and shrubs, and invasion by exotic grasses. We conducted a prescribed fire experiment (seven burns between 2001 and 2019) in historically fire-excluded and overgrazed grasslands of central Texas. Sites were assigned to one of four experimental treatments: summer burns (warm season, lightning season), fall burns (early cool season), winter …

Cellular Activity Of Salmonella Typhimurium Artab Toxin And Its Receptor-Binding Subunit, Elise Overgaard, Brad Morris, Omid Mohammad Mousa, Adriana Rodriguez, Leyla Cufurovic, Richard S. Beard, Juliette K. Tinker

Biology Faculty Publications and Presentations

Salmonellosis is among the most reported foodborne illnesses in the United States. The Salmonella enterica Typhimurium DT104 phage type, which is associated with multidrug-resistant disease in humans and animals, possesses an ADP-ribosylating toxin called ArtAB. Full-length artAB has been found on a number of broad-host-range non-typhoidal Salmonella species and serovars. ArtAB is also homologous to many AB₅ toxins from diverse Gram-negative pathogens, including cholera toxin (CT) and pertussis toxin (PT), and may be involved in Salmonella pathogenesis, however, in vitro cellular toxicity of ArtAB has not been characterized. artAB was cloned into E. coli and initially isolated …

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 …

Assesment Of Antibiotic Resistant Gene Expression In Clinical Isolates Of Pseudomonas Aeruginosa, Dustin Esmond

Biology Theses

Increasing prevalence of nosocomial infections by antimicrobial resistant pathogens resulting in higher mortality rates and financial burden is of great concern. Pseudomonas aeruginosa represents one of six highly virulent “ESKAPE” pathogens that exhibit considerable intrinsic drug resistance as well as mechanisms for acquiring further resistance. As many of these mechanisms are regulated through gene expression, we sought to identify regulatory strategies and patterns at play in 23 clinical isolates collected from Baku, Azerbaijan and Tyler, Texas, USA. Real-time quantitative polymerase chain reaction was performed on six gene targets implicated in resistance and contrasted with antibiotic phenotypes. We found AmpC cephalosporinase …

Ipla2-Via Is Required For Healthy Aging Of Neurons, Muscle, And The Female Germline In Drosophila Melanogaster, Surya Jyoti Banerjee, Adina Schonbrun, Sogol Eizadshenass, Shimshon Benji, Yaakov Tzvi Cantor, Liam Eliach, Matthew Lubin, Zev Narrowe, Jeremy Purow, Benjamin Shulman, Leib Wiener, Josefa Steinhauer

Faculty Publications - Biological Sciences

Neurodegenerative disease (ND) is a growing health burden worldwide, but its causes and treatments remain elusive. Although most cases of ND are sporadic, rare familial cases have been attributed to single genes, which can be investigated in animal models. We have generated a new mutation in the calcium-independent phospholipase A2 (iPLA2) VIA gene CG6718, the Drosophila melanogaster ortholog of human PLA2G6/PARK14, mutations in which cause a suite of NDs collectively called PLA2G6-associated neurodegeneration (PLAN). Our mutants display age-related loss of climbing ability, a symptom of neurodegeneration in flies. Although phospholipase activity commonly is presumed to underlie iPLA2VIA function, locomotor decline …

The Structural And Functional Role Of Photosensing In Rgs-Lov Proteins, Zaynab Jaber

Dissertations, Theses, and Capstone Projects

Light provides organisms with energy and spatiotemporal information. To survive and adapt, organisms have developed the ability to sense light to drive biochemical effects that underlie vision, entrainment of circadian rhythm, stress response, virulence, and many other important molecularly driven responses. Blue-light sensing Light-Oxygen-Voltage (LOV) domains are ubiquitous across multiple kingdoms of life and modulate various physiological events via diverse effector domains. Using a small molecule flavin chromophore, the LOV domain undergoes light-dependent structural changes leading to activation or repression of these catalytic and non-catalytic effectors. In silico analyses of high-throughput genomic sequencing data has led to the marked expansion …

Artificial Night Light And Anthropogenic Noise Interact To Influence Bird Abundance Over A Continental Scale, Ashley A. Wilson, Mark A. Ditmer, Jesse R. Barber, Neil H. Carter, Eliot T. Miller, Luke P. Tyrell, Clinton D. Francis

Biology Faculty Publications and Presentations

The extent of artificial night light and anthropogenic noise (i.e., “light” and “noise”) impacts is global and has the capacity to threaten species across diverse ecosystems. Existing research involving impacts of light or noise has primarily focused on noise or light alone and single species; however, these stimuli often co-occur and little is known about how co-exposure influences wildlife and if and why species may vary in their responses. Here, we had three aims: (1) to investigate species-specific responses to light, noise, and the interaction between the two using a spatially explicit approach to model changes in abundance of 140 …

The Slit-Binding Ig1 Domain Is Required For Multiple Axon Guidance Activities Of Drosophila Robo2, Lafreda J. Howard, Marie C. Reichert, Timonthy A. Evans

Biological Sciences Faculty Publications and Presentations

Drosophila Robo2 is a member of the evolutionarily conserved Roundabout (Robo) family of axon guidance receptors. Robo receptors signal midline repulsion in response to Slit ligands, which bind to the N-terminal Ig1 domain in most family members. In the Drosophila embryonic ventral nerve cord, Robo1 and Robo2 signal Slit-dependent midline repulsion, while Robo2 also regulates the medial-lateral position of longitudinal axon pathways and acts non-autonomously to promote midline crossing of commissural axons. While Robo2 signals midline repulsion in response to Slit, it is less clear whether Robo2's other activities are also Slit-dependent. To determine which of Robo2's axon guidance roles …

Biological Soil Crusts Of The Great Plains: A Review, Steven D. Warren, Roger Rosentreter, Nicole Pietrasiak

Biology Faculty Publications and Presentations

Biological soil crusts (BSCs), or biocrusts, are composed of fungi, bacteria, algae, and bryophytes (mosses, etc.) that occupy bare soil, entwining soil particles with filaments or rootlike structures and/or gluing them together with polysaccharide exudates to form a consolidated surface crust that stabilizes the soil against erosion. BSCs are common in arid and semiarid regions where vascular plant cover is naturally sparse, maximizing the exposure of surface-dwelling organisms to direct sunlight. Although less prominent and less studied there, BSC organisms are also present in more mesic areas such as the Great Plains where they can be found in shortgrass and …

Antibiotic Resistance Patterns Of Escherichia Coli Isolates From The Clinic Through The Wastewater Pathway, Brandon Bojar, Jennifer Sheridan, Rachelle E. Beattie, Caitlin Cahak, Elizabeth Liedhegner, L. Silvia Munoz-Price, Krassimira R. Hristova, Troy Skwor

Biological Sciences Faculty Research and Publications

Antimicrobial resistance (AMR) remains one of the leading global health threats. This study compared antimicrobial resistance patterns among E. coli isolates from clinical uropathogenic Escherichia coli (UPEC) to hospital wastewater populations and throughout an urban wastewater treatment facility – influent, pre- and post-chlorinated effluents. Antibiotic susceptibility of 201 isolates were analyzed against eleven different antibiotics, and the presence of twelve antibiotic resistant genes and type 1 integrase were identified. AMR exhibited the following pattern: UPEC (46.8%) > hospital wastewater (37.8%) > urban post-chlorinated effluent (27.6%) > pre-chlorinated effluent (21.4%) > urban influent wastewater (13.3%). However, multi-drug resistance against three or more antimicrobial classes was …

Heritable Cognitive Phenotypes Influence Appetitive Learning But Not Extinction In Honey Bees, Eda Sezen, Emily Dereszkiewicz, Alvin Hozan, Meghan M. Bennett, Cahit Ozturk, Brian H. Smith, Chelsea N. Cook

Biological Sciences Faculty Research and Publications

Learning and attention allow animals to better navigate complex environments. While foraging, honey bees (Apis mellifera L.) learn several aspects of their foraging environment, such as color and odor of flowers, which likely begins to happen before they evaluate the quality of the food. If bees begin to evaluate quality before they taste food, and then learn the food is depleted, this may create a conflict in what the bee learns and remembers. Individual honey bees differ in their sensitivity to information, thus creating variation in how they learn or do not learn certain environmental stimuli. For example, foraging …

A Chromosome-Level Genome Assembly Of The Parasitoid Wasp, Cotesia Glomerata (Hymenoptera: Braconidae), Brendan J. Pinto, Jerome J. Weis, Tony Gamble, Paul J. Ode, Ryan Paul, Jennifer M. Zaspel

Biological Sciences Faculty Research and Publications

Hymenopterans make up about 20% of all animal species, but most are poorly known and lack high-quality genomic resources. One group of important, yet understudied hymenopterans are parasitoid wasps in the family Braconidae. Among this understudied group is the genus Cotesia, a clade of ~1,000 species routinely used in studies of physiology, ecology, biological control, and genetics. However, our ability to understand these organisms has been hindered by a lack of genomic resources. We helped bridge this gap by generating a high-quality genome assembly for the parasitoid wasp, Cotesia glomerata (Braconidae; Microgastrinae). We generated this assembly using multiple sequencing …

Effects Of Low-Level Artificial Light At Night On Kentucky Bluegrass And An Introduced Herbivore, Morgan Crump, Cassandra Brown, Robert J. Griffin-Nolan, Lisa Angenoli, Nathan P. Lemoine, Brett M. 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 short-term, 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 …

Do Male And Female Heterogamety Really Differ In Expression Regulation? Lack Of Global Dosage Balance In Pygopodid Geckos, Michail Rovatsos, Tony Gamble, Stuart V. Nielsen, Arthur Georges, Tariq Ezaz, Lukáš Kratochvíl

Biological Sciences Faculty Research and Publications

Differentiation of sex chromosomes is thought to have evolved with cessation of recombination and subsequent loss of genes from the degenerated partner (Y and W) of sex chromosomes, which in turn leads to imbalance of gene dosage between sexes. Based on work with traditional model species, theory suggests that unequal gene copy numbers lead to the evolution of mechanisms to counter this imbalance. Dosage compensation, or at least achieving dosage balance in expression of sex-linked genes between sexes, has largely been documented in lineages with male heterogamety (XX/XY sex determination), while ZZ/ZW systems are assumed to be usually associated with …

Sex Chromosome Evolution Among Amniotes: Is The Origin Of Sex Chromosomes Non-Random?, Lukáš Kratochvíl, Tony Gamble, Michail Rovatsos

Biological Sciences Faculty Research and Publications

Sex chromosomes are a great example of a convergent evolution at the genomic level, having evolved dozens of times just within amniotes. An intriguing question is whether this repeated evolution was random, or whether some ancestral syntenic blocks have significantly higher chance to be co-opted for the role of sex chromosomes owing to their gene content related to gonad development. Here, we summarize current knowledge on the evolutionary history of sex determination and sex chromosomes in amniotes and evaluate the hypothesis of non-random emergence of sex chromosomes. The current data on the origin of sex chromosomes in amniotes suggest that …

Fire And Herbivory Drive Fungal And Bacterial Communities Through Distinct Above- And Belowground Mechanisms, M. L. Vermeire, J. Thoresen, K. Lennard, S. Vikram, K. Kirkman, A. M. Swemmer, M. Te Beest, F. Siebert, P. Gordijn, Z. Venter, C. Brunel, G. Wolfaard, J. A. Krumins, M. D. Cramer, H. J. Hawkins

Department of Biology Faculty Scholarship and Creative Works

Fire and herbivory are important natural disturbances in grassy biomes. Both drivers are likely to influence belowground microbial communities but no studies have unravelled the long-term impact of both fire and herbivory on bacterial and fungal communities. We hypothesized that soil bacterial communities change through disturbance-induced shifts in soil properties (e.g. pH, nutrients) while soil fungal communities change through vegetation modification (biomass and species composition). To test these ideas, we characterised soil physico-chemical properties (pH, acidity, C, N, P and exchangeable cations content, texture, bulk density, moisture), plant species richness and biomass, microbial biomass and bacterial and fungal community composition …

Antimicrobial Resistance: A Challenge Awaiting The Post-Covid-19 Era, Tekle Airgecho Lobie, Aklilu Abrham Roba, James Alexander Booth, Knut Ivan Kristiansen, Abraham Aseffa, Kirsten Skarstad, Magnar Bjørås

Research on Antimicrobial Resistance

Microbe exposure to pharmaceutical and non-pharmaceutical agents plays a role in the development of antibiotic resistance. The risks and consequences associated with extensive disinfectant use during the COVID-19 pandemic remain unclear. Some disinfectants, like sanitizers, contain genotoxic chemicals that damage microbial DNA, like phenol and hydrogen peroxide. This damage activates error-prone DNA repair enzymes, which can lead to mutations that induce antimicrobial resistance. Public health priority programs that have faced drug-resistance challenges associated with diseases, such as tuberculosis, HIV, and malaria, have given less attention to risks attributable to the COVID-19 pandemic. Pathogen-specific programs, like the directly observed treatment strategy …

The Hox Protein Conundrum: The “Specifics” Of Dna Binding For Hox Proteins And Their Partners, Bony De Kumar, Diane C. Darland

Biology Faculty Publications

Homeotic genes (Hox genes) are homeodomain-transcription factors involved in conferring segmental identity along the anterior-posterior body axis. Molecular characterization of HOX protein function raises some interesting questions regarding the source of the binding specificity of the HOX proteins. How do HOX proteins regulate common and unique target specificity across space and time? This review attempts to summarize and interpret findings in this area, largely focused on results from in vitro and in vivo studies in Drosophila and mouse systems. Recent studies related to HOX protein binding specificity compel us to reconsider some of our current models for transcription factor-DNA …

Linking Ecomechanical Models And Functional Traits To Understand Phenotypic Diversity, Timothy E. Higham, Lara A. Ferry, Lars Schmitz, Duncan J. Irschick, Samuel Starko, Philip S.L. Anderson, Philip J. Bergmann, Heather A. Jamniczky, Leandro R. Monteiro, Dina Navon, Julie Messier, Emily Carrington, Stacy C. Farina, Kara L. Feilich, L. Patricia Hernandez, Michele A. Johnson, Sandy M. Kawano, Chris J. Law, Sarah J. Longo, Christopher H. Martin, Patrick T. Martone, Alejandro Rico-Guevara, Sharlene E. Santana, Karl J. Niklas

Biology

Physical principles and laws determine the set of possible organismal phenotypes. Constraints arising from development, the environment, and evolutionary history then yield workable, integrated phenotypes. We propose a theoretical and practical framework that considers the role of changing environments. This ‘ecomechanical approach’ integrates functional organismal traits with the ecological variables. This approach informs our ability to predict species shifts in survival and distribution and provides critical insights into phenotypic diversity. We outline how to use the ecomechanical paradigm using drag-induced bending in trees as an example. Our approach can be incorporated into existing research and help build interdisciplinary bridges. Finally, …