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Articles 1 - 18 of 18
Full-Text Articles in Life Sciences
Grnsight: A Web Application And Service For Visualizing Models Of Small- To Medium-Scale Gene Regulatory Networks, Kam D. Dahlquist, John David N. Dionisio, Ben G. Fitzpatrick, Nicole A. Anguiano, Anindita Varshneya, Britain J. Southwick, Mihir Samdarshi
Grnsight: A Web Application And Service For Visualizing Models Of Small- To Medium-Scale Gene Regulatory Networks, Kam D. Dahlquist, John David N. Dionisio, Ben G. Fitzpatrick, Nicole A. Anguiano, Anindita Varshneya, Britain J. Southwick, Mihir Samdarshi
Biology Faculty Works
GRNsight is a web application and service for visualizing models of gene regulatory networks (GRNs). A gene regulatory network (GRN) consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of mRNA and protein from genes. The original motivation came from our efforts to perform parameter estimation and forward simulation of the dynamics of a differential equations model of a small GRN with 21 nodes and 31 edges. We wanted a quick and easy way to visualize the weight parameters from the model which represent the direction and magnitude of the influence of …
Active Learning Outside The Classroom: Implementation And Outcomes Of Peer-Led Team-Learning Workshops In Introductory Biology, Philip Kudish, Robin Shores, A. Mcclung, Lisa Smulyan , '76, Elizabeth Ann Vallen, Kathleen King Siwicki
Active Learning Outside The Classroom: Implementation And Outcomes Of Peer-Led Team-Learning Workshops In Introductory Biology, Philip Kudish, Robin Shores, A. Mcclung, Lisa Smulyan , '76, Elizabeth Ann Vallen, Kathleen King Siwicki
Biology Faculty Works
Study group meetings (SGMs) are voluntary-attendance peer-led team-learning workshops that supplement introductory biology lectures at a selective liberal arts college. While supporting all students’ engagement with lecture material, specific aims are to improve the success of underrepresented minority (URM) students and those with weaker backgrounds in biology. Peer leaders with experience in biology courses and training in science pedagogy facilitate work on faculty-generated challenge problems. During the eight semesters assessed in this study, URM students and those with less preparation attended SGMs with equal or greater frequency than their counterparts. Most agreed that SGMs enhanced their comprehension of biology and …
Review Of "A Primer Of Human Genetics" By G. Gibson, John B. Jenkins
Review Of "A Primer Of Human Genetics" By G. Gibson, John B. Jenkins
Biology Faculty Works
No abstract provided.
Measures Of Relative Dentary Strength In Rancho La Brea Smilodon Fatalis Over Time, Wendy J. Binder, Kassaundra S. Cervantes, Julie A. Meachen
Measures Of Relative Dentary Strength In Rancho La Brea Smilodon Fatalis Over Time, Wendy J. Binder, Kassaundra S. Cervantes, Julie A. Meachen
Biology Faculty Works
The late Pleistocene megafaunal extinction of approximately 12,000 years ago, included the demise of Smilodon fatalis, a hypercarnivore from the Rancho La Brea deposits, which has been studied across time by looking at different deposits or pits to determine morphological size and shape changes and trends during this time. To better understand functional aspects of these changes, this study focused on a measure of jaw strength over time, which can give an indication of morphological changes within the jaw that cannot be seen using surface morphometrics. By radiographing dentaries, cortical bone can be seen, which provides an estimate of resistance …
Principles And Practices Fostering Inclusive Excellence: Lessons From The Howard Hughes Medical Institute’S Capstone Institutions, P. M. Dibartolo, L. Gregg-Jolly, D. Gross, C. A. Manduca, E. Iverson, D. B. Cooke Iii, G. K. Davis, C. Davidson, P. E. Hertz, L. Hibbard, S. K. Ireland, C. Mader, A. Pai, S. Raps, Kathleen King Siwicki, J. E. Swartz
Principles And Practices Fostering Inclusive Excellence: Lessons From The Howard Hughes Medical Institute’S Capstone Institutions, P. M. Dibartolo, L. Gregg-Jolly, D. Gross, C. A. Manduca, E. Iverson, D. B. Cooke Iii, G. K. Davis, C. Davidson, P. E. Hertz, L. Hibbard, S. K. Ireland, C. Mader, A. Pai, S. Raps, Kathleen King Siwicki, J. E. Swartz
Biology Faculty Works
Best-practices pedagogy in science, technology, engineering, and mathematics (STEM) aims for inclusive excellence that fosters student persistence. This paper describes principles of inclusivity across 11 primarily undergraduate institutions designated as Capstone Awardees in Howard Hughes Medical Institute’s (HHMI) 2012 competition. The Capstones represent a range of institutional missions, student profiles, and geographical locations. Each successfully directed activities toward persistence of STEM students, especially those from traditionally underrepresented groups, through a set of common elements: mentoring programs to build community; research experiences to strengthen scientific skill/identity; attention to quantitative skills; and outreach/bridge programs to broaden the student pool. This paper grounds …
Multitrophic Diversity Effects Of Network Degradation, Elizabeth Nichols, C. A. Peres, J. E. Hawes, S. Naeem
Multitrophic Diversity Effects Of Network Degradation, Elizabeth Nichols, C. A. Peres, J. E. Hawes, S. Naeem
Biology Faculty Works
Predicting the functional consequences of biodiversity loss in realistic, multitrophic communities remains a challenge. No existing biodiversity–ecosystem function study to date has simultaneously incorporated information on species traits, network topology, and extinction across multiple trophic levels, while all three factors are independently understood as critical drivers of post-extinction network structure and function. We fill this gap by comparing the functional consequences of simulated species loss both within (monotrophic) and across (bitrophic) trophic levels, in an ecological interaction network estimated from spatially explicit field data on tropical fecal detritus producer and consumers (mammals and dung beetles). We simulated trait-ordered beetle and …
Review Of "The Least Likely Man: Marshall Nirenberg And The Discovery Of The Genetic Code" By F. H. Portugal, John B. Jenkins
Review Of "The Least Likely Man: Marshall Nirenberg And The Discovery Of The Genetic Code" By F. H. Portugal, John B. Jenkins
Biology Faculty Works
No abstract provided.
A Potential Mate Influences Reproductive Development In Female, But Not Male, Pine Siskins, Heather E. Watts, Bruce Edley, Thomas P. Hahn
A Potential Mate Influences Reproductive Development In Female, But Not Male, Pine Siskins, Heather E. Watts, Bruce Edley, Thomas P. Hahn
Biology Faculty Works
The role of photoperiod in avian reproductive timing has been well studied, and we are increasingly recognizing the roles of other environmental cues such as social cues. However, few studies have evaluated the extent to which males and females of the same species respond similarly to the same type of cue. Moreover, previous studies have rarely examined how variation in the quality or nature of a given social cue might modulate its effect. Here, we examine the sensitivity of male and female pine siskins (Spinus pinus) to a potential mate as a stimulatory cue for gonadal recrudescence, and …
How Important Is A Postdoc For A Teaching Career?, Amy Cheng Vollmer, V. Balke, C. Frantz, T. E. Hanson
How Important Is A Postdoc For A Teaching Career?, Amy Cheng Vollmer, V. Balke, C. Frantz, T. E. Hanson
Biology Faculty Works
No abstract provided.
Distribution And Abundance Of Glucocorticoid And Mineralocorticoid Receptors Throughout The Brain Of The Great Tit (Parus Major), Rebecca A. Senft , '15, S. L. Meddle, Alexander T. Baugh
Distribution And Abundance Of Glucocorticoid And Mineralocorticoid Receptors Throughout The Brain Of The Great Tit (Parus Major), Rebecca A. Senft , '15, S. L. Meddle, Alexander T. Baugh
Biology Faculty Works
The glucocorticoid stress response, regulated by the hypothalamic-pituitary-adrenal (HPA) axis, enables individuals to cope with stressors through transcriptional effects in cells expressing the appropriate receptors. The two receptors that bind glucocorticoids—the mineralocorticoid receptor (MR) and glucocorticoid receptor (GR)—are present in a variety of vertebrate tissues, but their expression in the brain is especially important. Neural receptor patterns have the potential to integrate multiple behavioral and physiological traits simultaneously, including self-regulation of glucocorticoid secretion through negative feedback processes. In the present work, we quantified the expression of GR and MR mRNA throughout the brain of a female great tit (Parus major), …
Female Túngara Frogs Do Not Experience The Continuity Illusion, Alexander T. Baugh, M. J. Ryan, X. E. Bernal, A. S. Rand, M. A. Bee
Female Túngara Frogs Do Not Experience The Continuity Illusion, Alexander T. Baugh, M. J. Ryan, X. E. Bernal, A. S. Rand, M. A. Bee
Biology Faculty Works
In humans and some non-human vertebrates, a sound containing brief silent gaps can be rendered perceptually continuous by inserting noise into the gaps. This so-called ‘continuity illusion’ arises from a phenomenon known as ‘auditory induction’ and results in the perception of complete auditory objects despite fragmentary or incomplete acoustic information. Previous studies of auditory induction in gray treefrogs (Hyla versicolor and H. chrysoscelis) have demonstrated an absence of this phenomenon. These treefrog species produce pulsatile (non-continuous) vocalizations, whereas studies of auditory induction in other taxa, including humans, often present continuous sounds (e.g., frequency-modulated sweeps). This study investigated the continuity illusion …
Fibronectin Contributes To Notochord Intercalation In The Invertebrate Chordate, Ciona Intestinalis, F. Segade, C. Cota, A. Famiglietti, A. Cha, Bradley Justin Davidson , '91
Fibronectin Contributes To Notochord Intercalation In The Invertebrate Chordate, Ciona Intestinalis, F. Segade, C. Cota, A. Famiglietti, A. Cha, Bradley Justin Davidson , '91
Biology Faculty Works
Background: Genomic analysis has upended chordate phylogeny, placing the tunicates as the sister group to the vertebrates. This taxonomic rearrangement raises questions about the emergence of a tunicate/vertebrate ancestor. Results: Characterization of developmental genes uniquely shared by tunicates and vertebrates is one promising approach for deciphering developmental shifts underlying acquisition of novel, ancestral traits. The matrix glycoprotein Fibronectin (FN) has long been considered a vertebrate-specific gene, playing a major instructive role in vertebrate embryonic development. However, the recent computational prediction of an orthologous “vertebrate-like” Fn gene in the genome of a tunicate, Ciona savignyi, challenges this viewpoint suggesting that Fn …
Principles Of Differentiation And Morphogenesis, Scott F. Gilbert, R. Rice
Principles Of Differentiation And Morphogenesis, Scott F. Gilbert, R. Rice
Biology Faculty Works
Developmental biology is the science connecting genetics with anatomy, making sense out of both. The body builds itself from the instructions of the inherited DNA and the cytoplasmic system that interprets the DNA into genes and creates intracellular and cellular networks to generation the observable phenotype. Even ecological factors such as diet and stress may modify the DNA such that different phenotypes can be constructed from the same DNA. During the past two decades, the basic principles of development have become known; although this brief chapter cannot do them justice (see, for example, Gilbert, 2013), they cover the following: mechanisms …
A “Rule-Of-Five” Framework For Models And Modeling To Unify Mathematicians And Biologists And Improve Student Learning, Kam D. Dahlquist
A “Rule-Of-Five” Framework For Models And Modeling To Unify Mathematicians And Biologists And Improve Student Learning, Kam D. Dahlquist
Biology Faculty Works
Despite widespread calls for the incorporation of mathematical modeling into the undergraduate biology curriculum, there is lack of a common understanding around the definition of modeling, which inhibits progress. In this paper, we extend the “Rule-of-Four,” initially used in calculus reform efforts, to a “Rule-of-Five” framework for models and modeling that is inclusive of varying disciplinary definitions of each. This unifying framework allows us to both build on strengths that each discipline and its students bring, but also identify gaps in modeling activities practiced by each discipline. We also discuss benefits to student learning and interdisciplinary collaboration.
Bolstered Physical Defences Under Nutrient-Enriched Conditions May Facilitate A Secondary Foundational Algal Species In The South Pacific, Sarah Joy Bittick
Bolstered Physical Defences Under Nutrient-Enriched Conditions May Facilitate A Secondary Foundational Algal Species In The South Pacific, Sarah Joy Bittick
Biology Faculty Works
Humans have a long history of changing species' ranges and habitat distributions, making studies of the ecological processes that may facilitate these changes of key importance, particularly in cases where a primary foundation species is replaced by another, less desirable species. We investigated the impact of nutrients and herbivory on Turbinaria ornata, a secondary foundational macroalga that depends on and likely competes with coral, the primary foundational community. T. ornata is also rapidly expanding in range and habitat across the South Pacific. We conducted (i) a mesocosm experiment assessing relative nutrient limitation, (ii) a field experiment comparing importance of nutrients …
Nutrients Induce And Herbivores Maintain Thallus Toughness, A Structural Antiherbivory Defense In Turbinaria Ornata, Sarah Joy Bittick
Nutrients Induce And Herbivores Maintain Thallus Toughness, A Structural Antiherbivory Defense In Turbinaria Ornata, Sarah Joy Bittick
Biology Faculty Works
The loss of coral cover, frequently driven by anthropogenic disturbances, can result in a phase shift to dominance by fleshy macroalgae, many of which contain anti-herbivore defenses. Using field surveys, a mesocosm experiment, and field experiments, we evaluate whether 2 human impacts-nutrient enrichment and reduction in herbivory-affected production and maintenance of thallus toughness, a physical defense of the brown macroalgae Turbinari ornata that has recently expanded across the South Pacific. In contrast to our expectations, there was a weak negative relationship between herbivorous fish abundance and thallus toughness This relationship was driven by greater toughness in algae collected at the …
Preliminary Report: A Survey Of Aggressive Behaviors In The American Coot (Fulica Americana) At Ballona Wetlands, California, Victor D. Carmona-Galindo, Mariele Anne Courtois, Kiara Cerda
Preliminary Report: A Survey Of Aggressive Behaviors In The American Coot (Fulica Americana) At Ballona Wetlands, California, Victor D. Carmona-Galindo, Mariele Anne Courtois, Kiara Cerda
Biology Faculty Works
Understanding interspecific and intraspecific aggression is important for wildlife management and sustainability of populations. The objective of this study was to evaluate whether there is a difference in number of occurrences of interspecific aggression between American coots (Fulica americana) and mallard ducks (Anas platyrhynchos) and intraspecific aggression among American coots in the Ballona wetland habitat of Southern California. Trends in literature describe coots as highly aggressive toward other coots year-round and toward other bird species during the breeding season. Because we conducted observations outside the breeding season, we hypothesized that more instances of intraspecific aggression would …
Getting The Hologenome Concept Right: An Eco-Evolutionary Framework For Hosts And Their Microbiomes, K. R. Theis, N. M. Dheilly, J. L. Klassen, R. M. Brucker, J. F. Baines, T. C. G. Bosch, J. F. Cryan, Scott F. Gilbert, C. J. Goodnight, E. A. Lloyd, J. Sapp, P. Vandenkoornhuyse, I. Zilber-Rosenberg, E. Rosenberg, S. R. Bordenstein
Getting The Hologenome Concept Right: An Eco-Evolutionary Framework For Hosts And Their Microbiomes, K. R. Theis, N. M. Dheilly, J. L. Klassen, R. M. Brucker, J. F. Baines, T. C. G. Bosch, J. F. Cryan, Scott F. Gilbert, C. J. Goodnight, E. A. Lloyd, J. Sapp, P. Vandenkoornhuyse, I. Zilber-Rosenberg, E. Rosenberg, S. R. Bordenstein
Biology Faculty Works
Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization—what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not a primary unit of selection dismisses the fact that …