Biology Commons^™

Defining Life: A Conversation, K. Kofman, C. Adami, F. Baluška, J. Bongard, D. Brash, P. Calvo, G. Dodig-Crnkovic, P. Das, C. Fields, T. Froese, P. L. Gentili, G. Y. Georgiev, Scott F. Gilbert, T. N. W. Jackson, S. Kauffman, N. Lane, P. Marshall, D. Mcshea, W. Miller, S. Newman, A. Nunn, T. P. Pavlic, M. Picard, W. Ratcliff, A. Reber, J. Shapiro, A. Sloman, R. Solé, C. Sonnenschein, S. Stepney, R. Watson, O. Witkowski, M. Levin

Biology Faculty Works

Life is one of the most fascinating features of the physical world. Despite centuries of scientific study, experts still disagree about the definition, and even the possibility or utility of a definition, of this field. In a recent paper, we used AI to analyze the conceptual space formed by definitions of life given by a select set of modern workers in the life sciences and related fields. However, some of the most interesting material emerged as real-time conversations among those polled. In order to ensure that these ideas are not lost to the peer-reviewed scientific record, we here provide a …

Proximity Data And Social Networks: A Validation Study Of Two Models Of Mobile Dataloggers In The Semi-Fossorial And Social Rodent, Octodon Degus, L. D. Hayes, A. A. Maldonado-Chaparro, Jessica Morales Valenzuela, L. Platt, L. A. Ebensperger

Biology Faculty Works

The use of mobile dataloggers to gather proximity data has generated novel insights into the social network structure of animals. The performance of mobile dataloggers may be impacted by different environmental and social conditions. Thus, validation studies that account for species-specific habitat use and behavior are essential. We conducted a series of validation studies of two brands of mobile dataloggers (Gipsy6, Technosmart, Italy; ProxLog, IoSA, Belgium) on the semi-fossorial rodent, Octodon degus. First, we determined the sensitivity of both types of dataloggers to track position and closeness in different habitats (Experiments 1 and 2). To determine if the structure …

Neural Signaling Contributes To Heart Formation And Growth In The Invertebrate Chordate, Ciona Robusta, Hannah N. Gruner, C. J. Pickett, Jasmine Yimeng Bao , '24, Richard Garcia , '24, A. Hozumi, T. D. Scully, Sydney Popsuj, Shaoyang Ning, Mavis Gao , '26, Gia Bautista , '23, Keren Meze , '24, Haeun Karissa Lim , '25, T. Osugi, Mae Collins-Doijode , '26, Ofubofu Cairns , '24, Gabriel Levis , '23, Shu Yi Chen , '24, Taixi Gong , '24, H. Satake, A. M. Klein, Y. Sasakura, Bradley Justin Davidson

Biology Faculty Works

Neurons contribute to the complex interplay of signals that mediate heart development and homeostasis. Although a limited set of studies suggest that neuronal peptides impact vertebrate heart growth, the specific contributions of these peptides to cardiomyocyte progenitor differentiation or proliferation have not been elucidated. Here, we show that the neuropeptide tachykinin along with canonical Wnt signaling regulate cardiomyocyte progenitor proliferation in the chordate model Ciona robusta. In C. robusta, the heart continues to grow throughout adulthood and classic histological studies indicate that a line of undifferentiated cells may serve as a reserve progenitor lineage. We found that this line of …

Dna Barcoding And Metabarcoding Reveal Labeling Accuracy And Species Substitution In Squid And Surimi From Los Angeles Markets, Demian A. Willette, Margarita L. Joaquin

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Accurate species identification of seafood remains a persistent challenge in local and global marketplaces. This is particularly true for processed products that obscure diagnostic features. Here, we conduct a dual-molecular investigation into frozen squid and imitation crab products sold at American, Asian, and Hispanic grocery stores in Los Angeles, California, to assess label integrity under current U.S. Food & Drug Administration (FDA) guidance. Forty-eight squid samples from 13 retailers underwent DNA barcoding and yielded high percentage matches to 10 species across six genera. Despite broad labeling as ‘squid’, all samples matched FDA Acceptable Market Names with a 0 % mislabeling …

“Thou Hast Taught Me, Silent River, Many A Lesson, Deep And Long”: Metabolism, Development, And Evolution As Team Sports, Scott F. Gilbert

Biology Faculty Works

We recognize three great fluxes in nature. First there is the metabolic flow of molecules that pervades our cells and which creates organisms. Second, there is the developmental flow of cells that is our cycle of life. Third, there is the evolutionary flow of genes, organisms, and populations from the first single-celled prokaryotes to the extensive biodiversity present on earth today. Recent studies have shown that organisms are consortia of several species acting together. What we had thought of as metabolism based on a single genome is actually the co-metabolism of more than one species. What we had thought as …

Signs Of Life: Interkingdom Communication And The Sympoietic Organism, Scott F. Gilbert

Biology Faculty Works

No abstract provided.

Red Midge Larvae Are An Invertebrate Alternative Diet To Beef Liver For Planarian Husbandry, Jonah Pacis , '25, Danielle Ireland, Evangeline Coffinas, Jerome Sheehan, Kate Sun , '27, Eva-Maria S. Collins

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Freshwater planarians are an emerging model for toxicology and neuroscience because of their amenability to rapid behavioral screening and remarkable ability to regenerate a cephalized nervous system. As invertebrates, planarians can help reduce the use of vertebrates in research; however, laboratories typically maintain planarians on diets of homogenized organic beef or chicken liver, raising ethical concerns with feeding a vertebrate diet. Organic liver is difficult to obtain, and preparation methods vary, introducing intra- and interlaboratory variability. Here, we show that Dugesia japonica planarians can be maintained for over a year on commercially available red midge larvae (RML), a natural prey …

Multilevel Selection In The Margins: A Review Of Its Representation In Undergraduate Biology Textbooks, C. A. Greene, S. J. Mcpeek, L. Mitchem, A. B. Clark, Vincent A. Formica

Biology Faculty Works

Multilevel selection (MLS) is a foundational framework that expands the concept of natural selection beyond the traditional focus on individuals or genes to larger units, like groups. Despite strong empirical support and applications in a broad range of biological fields, MLS, often referred to as group selection, has a controversial history, which has impeded its wide use and led to incorrect inferences on the sources and strength of selection. Here, we explore how MLS is currently presented to undergraduate biology students by analyzing the content of nine commonly used Evolutionary Biology and Animal Behavior textbooks. We ask whether and how …

Draft Genome Sequences Of Burkholderia And Paraburkholderia Strains Isolated From Panicum Virgatum Soil And Roots At The Lux Arbor Reserve In Michigan, Usa, H. Kehlet-Delgado, R. H. Petipas, A. A. Antoch, Jeffrey S. Norman, X. Li, R. A. White Iii, S. E. Evans, L. K. Tiemann, M. L. Friesen

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We present draft genomes of two Paraburkholderia strains and two Burkholderia strains. Three strains were isolated from surrounding soils and one from roots of switchgrass (Panicum virgatum) in Michigan, USA.

Age-Dependent Changes In Reproductive Behaviour And Success In A Long-Lived Beetle (Bolitotherus Cornutus), C. A. Greene, L. D. Mitchem, Vitor Dos Anjos , '21, E. D. Brodie Iii, Vincent A. Formica

Biology Faculty Works

Age-related changes in behaviors often result in shifts in an individual’s competitive ability, reproductive success, and fitness. However, how mating behaviors, aggression, and mating success simultaneously change as individuals age in natural populations remains understudied. Investigating these age-dependent effects in wild populations could reveal how age-specific patterns shape social dynamics and influence natural selection. In this study, we ask how behaviors associated with mating and reproductive success vary across age in a wild metapopulation of a long-lived beetle, Bolitotherus cornutus. We used both cross-sectional and longitudinal data from a multi-year field study of individually marked beetles to investigate how …

Statistical Analysis Of Multi-Endpoint Phenotypic Screening Increases Sensitivity Of Planarian Neurotoxicity Testing, Danielle Ireland, L. J. Word, Eva-Maria S. Collins

Biology Faculty Works

There is an urgent need for high-throughput screening (HTS) models to replace, refine, and/or reduce (“3Rs”) vertebrate toxicity testing. Replacing in vivo animal studies is challenging for neurotoxicity and developmental neurotoxicity (DNT), where the functional relevancy of adverse outcomes needs to be assessed on the whole organism. We previously screened the NTP 87-compound library (NTP87), consisting of known and suspected developmental neurotoxicants, and showed that planarian HTS can identify known (developmental) neurotoxicants. Because analysis methods can impact screening results, and our original analysis used the lowest-observed-effect-level (LOEL) only, we hypothesized that the use of state-of-the-art statistical analysis would increase the …

Variation In Phenotype, Genotype, And Somatic Diversity Among Asexual Schmidtea Mediterranea Planarians, S. Kershenbaum, Danielle Ireland, Ziad Sabry , '20, Christina Rabeler, Vir Shetty , '22, A. Aboobaker, Eva-Maria S. Collins

Biology Faculty Works

Most multicellular life reproduces sexually, utilizing a single-celled stage that acts as a genetic bottleneck. This bottleneck limits the evolution of selfish cell adaptations by ensuring all cells descend from a single progenitor. We investigated an obligately asexual strain of Schmidtea mediterranea planarians that reproduces by self-bisection and lacks a single-cell bottleneck. Using 2.5 yearlong data on planarian reproductive behavior combined with genotyping, we revealed two previously undescribed genetically distinct substrains within the CIW4 strain. One substrain showed reduced fitness, which correlated with substantial losses of heterozygosity and increased somatic diversity. By genotyping consecutive head offspring over multiple generations, we …

Male Mating Preference For Larger Females Does Not Vary Among Age Classes In The Long-Lived Beetle Bolitotherus Cornutus, G. M. Jiron, C. A. Greene, E. D. Brodie Iii, Vincent A. Formica

Biology Faculty Works

Theory and past experimental work suggest that as males age, the strength of their mate preference should decrease. However, the empirical work investigating this question has primarily been conducted in insects that have very short life spans and often live for just a single mating season. This leaves a gap in our understanding of the relationship between male mate preference and age across taxa, as age can conflate with other ecological changes in a single mating season. In this study, we ask how the strength of preference for large female body size changes as males age in a long-lived insect, …

Using Published Undergraduate Biomechanics Research On Hydra Mouth Opening To Train Undergraduates, Stephen Hackler, T. Goel, Jonah Pacis , '25, Eva-Maria S. Collins

Biology Faculty Works

Biophysics research is exciting because physical approaches to biology can provide novel insights, and it is challenging because it requires knowledge and skills from multiple disciplines. We have developed an undergraduate biophysics laboratory module that teaches fundamental skills such as time-lapse microscopy, image analysis, programming, critical reading of scientific literature, and basics of scientific writing and peer review. The module is accessible to students who are familiar with introductory statistics, cell biology, and differential calculus. We used published research on the biomechanics of Hydra mouth opening as a framework because it describes a stunning biological phenomenon: Hydra, a freshwater …

Baseline Testosterone Levels Peak During The Inactive Period In Male Degus (Octodon Degus), Yuta Sato , '26, Tate M. S. Garcia , '26, Josephine S. Low , '27, Carolyn M. Bauer

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The steroid hormone testosterone is important for stimulating male reproductive processes including territory acquisition, mating displays, and spermatogenesis. When examining the relative effects of testosterone on reproductive processes, it is most reasonable to focus on peak baseline testosterone levels, especially for reproductive processes that may occur during specific times of day, such as mating and spermatogenesis. However, some studies have not found consistent positive relationships between circulating testosterone levels and reproductive variables. These nonsignificant relationships could be driven by methodology, as most studies in wild, free-living animals collect blood samples during an animals' active period, yet many species show peak …

Multiple Stressors Effects On The Physiological Performance Of Mytilus Trossulus, M. Christina Vasquez, Alana J. Borer, Claribel Y. Alcantar, Osiris Guinea Zepeda, Camya A. Brazil, Colin Carr, Emma Guerrini Romano, Alexander J. Provenzano, Min Jeon Roh

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Mytilus galloprovincialis and M. trossulus co-occur and hybridize along set biogeographical ranges of temperature and salinity along the Pacific coast, USA. However, the role of physiological traits in mussel distribution remains poorly understood. We investigated metabolic rate, antioxidant activity (superoxide dismutase, catalase), oxidative damage (malondialdehyde content, MDA), and clearance rate of M. trossulus under multiple stressors: 7 days of hyposalinity (20, 28, 34 ppt), followed by an acute heat shock (17, 20, 25 ◦C). We found a significant effect of temperature on metabolic rate, an interaction effect on antioxidant activity, and MDA, and independent temperature and salinity effects on clearance …

Spidr Enables Multiplexed Mapping Of Rna-Protein Interactions And Uncovers A Mechanism For Selective Translational Suppression Upon Cell Stress, Erica Wolin, Jimmy K. Guo, Mario R. Blanco, Isabel N. Goronzy, Darvesh Gorhe, Wenzhao Dong, Andrew A. Perez, Abdurrahman Keskin, Elizabeth Valenzuela, Ahmed A. Abdou, Carl R. Urbinati, Ross Kaufhold, H. Tomas Rube, Jailson Brito Querido, Mitchell Guttman, Marko Jovanovic

Biology Faculty Works

RNA-binding proteins (RBPs) regulate all stages of the mRNA life cycle, yet current methods generally map RNA targets of RBPs one protein at a time. To overcome this limitation, we developed SPIDR (split-and-pool identification of RBP targets), a highly multiplexed split-pool method that profiles the binding sites of dozens of RBPs simultaneously. SPIDR identifies precise, single-nucleotide binding sites for diverse classes of RBPs. Using SPIDR, we uncovered an interaction between LARP1 and the 18S rRNA and resolved this interaction to the mRNA entry channel of the 40S ribosome using cryoelectron microscopy (cryo-EM), providing a potential mechanistic explanation for LARP1’s role …

Ethical Implications Of Being A Holobiont, Scott F. Gilbert

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Developmental plasticity and holobiont theory have undermined the normative concepts of biological individuality. However, such traditional ideas of biological individuality have helped define and support Western ethical views into the 21st century. Guided by some of the ethical formulae of Simone Weil, Hans Jonas, and Alastair MacIntyre, this essay attempts to outline some possible trajectories for an ethics that is bounded by these new biological paradigms of environmental agency. Specifically, the ecological developmental biology concepts of plasticity and holobiont theory permit the “ethics of attention” to focus on the partnerships of living beings. Highlighting environmentally integrated life cycles and their …

​​Site Fidelity Is Associated With The Social Experience Of Forked Fungus Beetles (Bolitotherus Cornutus), Joo Yeon Kim , '22, C. W. Wood, E. D. Brodie Iii, Vincent A. Formica

Biology Faculty Works

Consistently returning to or remaining within a specific location, a behavior known as site fidelity, is a useful metric for quantifying animal space use. When multiple individuals display similar site fidelity patterns, they are likely to interact, shaping the degree and quality of their social interactions. However, the link between the expression of site fidelity behavior and an individual’s social experience has not been thoroughly investigated. In this study we examined (1) how intrinsic individual properties (body size and sex) predicted variation in site fidelity and (2) whether site fidelity was linked to the social experience of individuals in wild …

Teratogenic Effects Of Serotonin Receptor 2b Disruption On The Migration And Cardiac Derivatives Of The Cardiac Neural Crest, Brian K. Wells, Gwyneth K. Garramone, Amira Mahomed, Max Ezin

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Background: Cardiac neural crest cells (cNCCs) are critical for heart development, and their disruption can result in congenital heart defects. Serotonin (5-HT) signaling, specifically via 5-HT2B and 5-HT2C receptors, regulates diverse physiological processes, including neural crest migration. This study investigates how modulation of 5-HT2B and 5-HT2C receptor activity impacts cNCC migration and the development of their derivatives, with relevance to serotonergic drug safety during pregnancy.

Methods

Chicken embryos at HH8 were treated with 50 μL of 20 μM 1-Methylpsilocin (1-MP), an inverse agonist of 5-HT2B and agonist of 5-HT2C, and collected at HH14 to assess cNCC migration. Embryos were pre-treated …

Outreach & Dna-Based Monitoring Facilitate 3-Fold Reduction In Seafood Mislabeling In Los Angeles Over 10 Years, Demian A. Willette, Kelli Andrade, Ben Fitzpatrick, Kesterlyn Wilson

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Awareness and intervention can reduce fraudulent labeling in seafood. Using a 10-year longitudinal study approach, DNA-based monitoring data reveals a lower sushi mislabeling in Los Angeles restaurants over time. This is in part attributed to implemented recommendations by restaurants of a local academia-industry-government outreach initiative launched in 2018, The Los Angeles Seafood Monitoring Project. We found mislabeling was 3-fold lower among project-partnering restaurants than other restaurants. This difference was statistically significant, illustrating the combination of project partnering and implementation of recommendations was most impactful on reducing mislabeling rates. Lastly, the study period includes the COVID19 global pandemic, which additional monitoring …

Coyote (Canis Latrans) Macronutrient Consumption And Diet Relative To Seasonality And Urbanization, Katherine C. B. Weiss, Sean C. P. Coogan, Pierre Deviche, Jesse S. Lewis, Savage C. Hess, Jan Schipper, Eric G. Strauss, Beckett Sterner

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Diet selection informs the health, fitness, and behavior of wild predators. Due to assumptions that vertebrate prey contains similar compositions of macronutrients (i.e., protein, carbohydrates, and lipids), whole prey items traditionally define carnivore diets. However, increasing evidence suggests that prey differ in terms of their macronutrient compositions, particularly relative to body size. Furthermore, omnivorous predators, like coyotes (Canis latrans), integrate both prey and nonprey diet items whose macronutrient compositions vary. This is particularly important in urbanized systems, which introduce or alter the distributions of prey (e.g., domestic pets) and nonprey (e.g., ornamental plants) foods in ways that contribute …

Inflammasomes Primarily Restrict Cytosolic Salmonella Replication Within Human Macrophages, Marisa S. Egan, E. A. O'Rourke, S. Kumar Mageswaran, B. Zuo, I. Martynyuk, T. Demissie, E. N. Hunter, A. R. Bass, Y.-W. Chang, I. E. Brodsky, S. Shin

Biology Faculty Works

Salmonella enterica serovar Typhimurium is a facultative intracellular pathogen that utilizes its type III secretion systems (T3SSs) to inject virulence factors into host cells and colonize the host. In turn, a subset of cytosolic immune receptors respond to T3SS ligands by forming multimeric signaling complexes called inflammasomes, which activate caspases that induce interleukin-1 (IL-1) family cytokine release and an inflammatory form of cell death called pyroptosis. Human macrophages mount a multifaceted inflammasome response to Salmonella infection that ultimately restricts intracellular bacterial replication. However, how inflammasomes restrict Salmonella replication remains unknown. We find that caspase-1 is essential for mediating inflammasome responses …

Regeneration In Planarians Modifies Behavioral Switching, N. S. Tellakula, Eva-Maria S. Collins, W. B. Kristan Jr.

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The planarian Dugesia japonica responds differently to localized stimuli: anterior regions turn, middle regions elongate, and posterior regions contract. If cut into several pieces, each piece immediately produces the same three responses. Over several days, each piece regenerates all transected body parts. This study tested how the pieces coordinate behavioral responses during regeneration. We first determined the locations of the turning/elongation and elongation/contraction behavioral switches. Immediately, all transections moved both switching sites away from the cut sites so that the worm pieces produced the same three responses as intact worms. During regeneration, the sites of behavioral switching moved progressively closer …

Life Among The Sand Grains, Will M. Ballentine, N. G. Roberts, M. K. Yap-Chiongco, K. M. Halanych, K. M. Kocot

Biology Faculty Works

Have you ever played with sand at the beach? Did you know you were also playing with thousands of tiny animals? The sand in the ocean is home to many small creatures called meiofauna, but you can only see them under a magnifying glass or microscope. Meiofauna are so tiny that sand grains seem like boulders to them. Meiofauna are too small to move these boulders, so they wriggle through spaces between them. Living in such tight spaces has led them to evolve long, skinny body shapes like worms. They also have special body parts to grip sand grains and …

Distinguishing Classes Of Neuroactive Drugs Based On Computational Physicochemical Properties And Experimental Phenotypic Profiling In Planarians, Danielle Ireland, Christina Rabeler, Sagar Rao , '22, R. J. Richardson, Eva-Maria S. Collins

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Mental illnesses put a tremendous burden on afflicted individuals and society. Identification of novel drugs to treat such conditions is intrinsically challenging due to the complexity of neuropsychiatric diseases and the need for a systems-level understanding that goes beyond single molecule-target interactions. Thus far, drug discovery approaches focused on target-based in silico or in vitro high-throughput screening (HTS) have had limited success because they cannot capture pathway interactions or predict how a compound will affect the whole organism. Organismal behavioral testing is needed to fill the gap, but mammalian studies are too time-consuming and cost-prohibitive for the early stages of …

Validation Of Non-Invasive Methods For The Measurement Of Gonadal And Inter-Renal Steroid Hormones In A Desert-Adapted Amphibian (Scaphiopus Couchii), Alexander T. Baugh, Callie Cho , '23, Alice Onyango-Opiyo , '23, Sophie A. Rodner , '25, Senna Mieth , '25, Daniel Oakes , '24, Liam Halstead , '25

Biology Faculty Works

For aquatic and semi-aquatic vertebrates like amphibians, it is possible to estimate excreted hormone levels using non-invasive methods such as waterborne and salivary sampling. These techniques allow monitoring of endocrine activity over varying, repeated and simultaneous integration periods while minimizing handling-related stress that can ‘contaminate’ hormone estimates, including estimates of baseline glucocorticoids. Here we have validated the extraction and quantification of three steroid hormones (corticosterone, CORT; 17-b estradiol, E₂; testosterone, TST) in Couch’s spadefoots (Scaphiopus couchii)—a desert-adapted anuran of special interest for physiology, evolution and conservation—using non-invasive waterborne and minimally invasive salivary hormone methods. We combined extraction and …

Noncoding Rnas In Nuclear Organization, Thembalami Dube , '24, Dawn M. Carone

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No abstract provided.

Understanding Trends In Zostera Research, Stressors, And Response Variables, Hannah R. Lyford, Emma Guerrini Romano, Shayna A. Sura, Sarah Joy Bittick

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Background. Seagrass meadows are ecologically significant habitats that are globally threatened. Thus, there is increased interest in conservation of seagrasses as they face widespread decline. Biotic and abiotic factors that influence seagrass can be classified as stressors, such as rising temperature and eutrophication. Our study met an imminent need to consolidate data from previous studies to discern knowledge gaps and identify trends in studies, stressors, species, and geographic origination of research for the genus Zostera. For our systematic review, the objectives were to (A) qualitatively assess and summarize the current state of literature focused on seagrass species within the Zostera …

A Comprehensive Embryonic Staging Series Of The Turtle Trachemys Scripta, Christina M. Noravian, Perla G. Rand, Amira Mahomed, Maxellende Ezin, Annie Rickard, Oscar D. Juvera, Maria Elena De Bellard

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Background: Turtles hold a unique place in vertebrate evolutionary history, making them critical assets in embryology research. Yet, they remain understudied as potential model organisms in the field. Here, to support experimental manipulations with turtle embryos, we have created a complete normal table of development for comprehensive embryonic staging of Trachemys scripta, one of the most common invasive turtle species worldwide.

Results: The development of T. scripta embryos from 0 days post-oviposition (DPO) to hatching (~60 DPO) was described from approximately 300 viable eggs collected at California State University, Northridge during the 2021–2024 nesting seasons. Thirty-one stages between oviposition and …