Life Sciences Commons^™

A Revision Of The Octocoral Genus Ovabunda Alderslade, 2001 (Anthozoa, Octocorallia, Xeniidae), Catherine S. Mcfadden, Yehuda Benayahu, Anna Halász, Dafna Aharonovich, Robert Toonen

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The family Xeniidae (Octocorallia) constitutes an abundant benthic component on many Indo-West Pacific coral reefs and is ecologically important in the Red Sea. The genus Ovabunda Alderslade, 2001 was recently established to accommodate previous Xenia species with sclerites comprised of a mass of minute corpuscle-shaped microscleres. The aim of the present study was to examine type material of Xenia species in order to verify their generic affiliation. We present here a comprehensive account of the genus Ovabunda, using scanning electron microscopy to depict sclerite microstructure. We assign three Xenia species to the genus: O. ainex comb. n., O. …

A New Species Of Ovabunda (Octocorallia, Xeniidae) From The Andaman Sea, Thailand With Notes On The Biogeography Of This Genus, Catherine S. Mcfadden, Michael P. Janes, Thanongsak Chanmethakul

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A survey of xeniid octocorals was carried out in the waters off Southwestern Thailand in September, 2007. Microscopic investigation of the colonies revealed that three specimens belonged to the genus Ovabunda. Gross morphological examination is presented here accompanied by scanning electron micrographs of the sclerites. Molecular phylogenetic analysis showed identical genotypes at mtMutS, COI, and 28S rDNA for all three specimens and supports their generic assignment. Colony size and shape, sclerite size, and pinnule arrangement differ from nominal species of Ovabunda and thus a new species, O. andamanensis is introduced here. This work also presents a new …

Social Aggregation In Pea Aphids: Experiment And Random Walk Modeling, Christa Nilsen, John Paige, Olivia Warner, Benjamin Mayhew, Ryan Sutley, Matthew Lam '15, Andrew J. Bernoff, Chad M. Topaz

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From bird flocks to fish schools and ungulate herds to insect swarms, social biological aggregations are found across the natural world. An ongoing challenge in the mathematical modeling of aggregations is to strengthen the connection between models and biological data by quantifying the rules that individuals follow. We model aggregation of the pea aphid, Acyrthosiphon pisum. Specifically, we conduct experiments to track the motion of aphids walking in a featureless circular arena in order to deduce individual-level rules. We observe that each aphid transitions stochastically between a moving and a stationary state. Moving aphids follow a correlated random walk. …

Sinularia Leptoclados (Ehrenberg, 1834) (Cnidaria: Octocorallia) Re-Examined, Catherine S. Mcfadden, Leen P. Van Ofwegen, Yehuda Benayahu

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Sinularia leptoclados (Ehrenberg, 1834) is re-described. Sinularia leptoclados var. gonatodes Kolonko, 1926 is synonymized with S. maxima Verseveldt, 1977. Two new species of Sinularia with digitiform lobules, leptoclados-type surface clubs and unbranched interior spindles, are described. An updated maximum likelihood tree of Sinularia species with leptoclados-type clubs (clade 5C) based on two mitochondrial genes (mtMutS, COI) and a nuclear gene (28S rDNA) is presented.

Molecular Phylogenetic Evidence Supports A New Family Of Octocorals And A New Genus Of Alcyoniidae (Octocorallia: Alcyonacea), Catherine S. Mcfadden, Leen P. Van Ofwegen

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Molecular phylogenetic evidence indicates that the octocoral family Alcyoniidae is highly polyphyletic, with genera distributed across Octocorallia in more than 10 separate clades. Most alcyoniid taxa belong to the large and poorly resolved Holaxonia–Alcyoniina clade of octocorals, but members of at least four genera of Alcyoniidae fall outside of that group. As a first step towards revision of the family, we describe a new genus, Parasphaerasclera gen. n., and family, Parasphaerascleridae fam. n., of Alcyonacea to accommodate species of Eleutherobia Pütter, 1900 and Alcyonium Linnaeus, 1758 that have digitiform to digitate or lobate growth forms, completely lack sclerites …

Deep-Sea Origin And In-Situ Diversification Of Chrysogorgiid Octocorals, Catherine S. Mcfadden, Eric Pante, Scott C. France, Arnaud Couloux, Corinne Cruaud, Sarah Samadi, Les Watling

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The diversity, ubiquity and prevalence in deep waters of the octocoral family Chrysogorgiidae Verrill, 1883 make it noteworthy as a model system to study radiation and diversification in the deep sea. Here we provide the first comprehensive phylogenetic analysis of the Chrysogorgiidae, and compare phylogeny and depth distribution. Phylogenetic relationships among 10 of 14 currently-described Chrysogorgiidae genera were inferred based on mitochondrial (mtMutS, cox1) and nuclear (18S) markers. Bathymetric distribution was estimated from multiple sources, including museum records, a literature review, and our own sampling records (985 stations, 2345 specimens). Genetic analyses suggest that the Chrysogorgiidae as currently described is …

How Muscles Function - The Work Loop Technique, Anna N. Ahn

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Anna Ahn discusses Bob Josephson’s 1985 paper entitled: ‘Mechanical power output from striated muscle during cyclic contraction’.

Escherichia Coli Lacking Rpos Are Rare In Natural Populations Of Non-Pathogens, Emily Snyder '11, David M. Gordon, Daniel M. Stoebel

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The alternative sigma factor RpoS controls a large regulon that allows E. coli to respond to a variety of stresses. Mutations in rpoS can increase rates of nutrient acquisition at the cost of a decrease in stress resistance. These kinds of mutations evolve rapidly under certain laboratory conditions where nutrient acquisition is especially challenging. The frequency of strains lacking RpoS in natural populations of E. coli is less clear. Such strains have been found at frequencies over 20% in some collections of wild isolates. However, laboratory handling can select for RpoS-null strains and may have affected some of these strain …

Evolution Of Spur-Length Diversity In Aquilegia Petals Is Achieved Solely Through Cell-Shape Anisotropy, Joshua R. Puzey, Sharon J. Gerbode, Scott A. Hodges, Elena M. Kramer, L. Mahadevan

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The role of petal spurs and specialized pollinator interactions has been studied since Darwin. Aquilegia petal spurs exhibit striking size and shape diversity, correlated with specialized pollinators ranging from bees to hawkmoths in a textbook example of adaptive radiation. Despite the evolutionary significance of spur length, remarkably little is known about Aquilegia spur morphogenesis and its evolution. Using experimental measurements, both at tissue and cellular levels, combined with numerical modelling, we have investigated the relative roles of cell divisions and cell shape in determining the morphology of the Aquilegia petal spur. Contrary to decades-old hypotheses implicating a discrete meristematic zone …

Effect Of Substrate Composition And Alignment On Corneal Cell Phenotype, Donna Phu '09, Lindsay S. Wray '08, Robert V. Warren '10, Richard C. Haskell, Elizabeth J. Orwin

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Corneal blindness is a significant problem treated primarily by corneal transplants. Donor tissue supply is low, creating a growing need for an alternative. A tissue-engineered cornea made from patient-derived cells and biopolymer scaffold materials would be widely accessible to all patients and would alleviate the need for donor sources. Previous work in this lab led to a method for electrospinning type I collagen scaffolds for culturing corneal fibroblasts ex vivo that mimics the microenvironment in the native cornea. This electrospun scaffold is composed of small-diameter, aligned collagen fibers. In this study, we investigate the effect of scaffold nanostructure and composition …

A New Genus Of Soft Coral Of The Family Alcyoniidae (Cnidaria, Octocorallia) With Re-Description Of A New Combination And Description Of A New Species, Catherine S. Mcfadden, Yehuda Benayahu

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A new genus, Aldersladum (family Alcyoniidae), is established to accommodate a previously described species, Effl atounaria sodwanae Benayahu, 1993 (family Xeniidae) from Sodwana Bay, South Africa that was wrongly assigned to the latter genus. Th is species is redescribed and a second new species, A. jengi from Penghu Is., Taiwan, is described. Th e diagnostic features of the new genus include the presence of only figure-eight shaped platelets in all parts of the colony, thus differentiating it from all known genera of the Alcyoniidae. Based on examination of additional material from other localities, the zoogeographical distribution of the genus is …

"Toward Integration: From Quantitative Biology To Mathbio-Biomath?", Pat Marsteller, Lisette G. De Pillis, Ann Findley, Karl Joplin, John Pelesko, Karen Nelson, Katerina Thompson, David Usher, Joseph Watkins

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In response to the call of BIO2010 for integrating quantitative skills into undergraduate biology education, 30 Howard Hughes Medical Institute (HHMI) Program Directors at the 2006 HHMI Program Directors Meeting established a consortium to investigate, implement, develop, and disseminate best practices resulting from the integration of math and biology. With the assistance of an HHMI-funded mini-grant, led by Karl Joplin of East Tennessee State University, and support in institutional HHMI grants at Emory and University of Delaware, these institutions held a series of summer institutes and workshops to document progress toward and address the challenges of implementing a more quantitative …

Kinematic Evidence For Superfast Locomotory Muscle In Two Species Of Teneriffiid Mites, Grace C. Wu, Jonathan C. Wright, Dwight L. Whitaker, Anna N. Ahn

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Locomotory muscles typically operate over a narrow range of contraction frequencies, characterized by the predominant fiber types and functional roles. The highest documented frequencies in the synchronous sound-producing muscles of insects (550 Hz) and toadfish (200 Hz) far exceed the contraction frequencies observed in weight-bearing locomotory muscles, which have maximum documented frequencies below 15-30 Hz. Laws of scaling, however, predict that smaller arthropods may employ stride frequencies exceeding this range. In this study we measured running speed and stride frequency in two undescribed species of teneriffiid mites from the coastal sage scrub of southern California. Relative speeds of both species …

Jane: A New Tool For The Cophylogeny Reconstruction Problem, Chris Conow, Daniel Fielder '11, Yaniv J. Ovadia '10, Ran Libeskind-Hadas

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Background

This paper describes the theory and implementation of a new software tool, called Jane, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecular systematics (associations of orderings and genes), and biogeography (associations of regions and orderings). The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costs associated with these events. Existing software tools for this problem have strengths and limitations, and the new Jane tool described here provides functionality that complements existing tools.

Results

The Jane software tool uses a polynomial time dynamic …

Sex, Mixability, And Modularity, Adi Livnat, Christos Papadimitriou, Nicholas Pippenger, Marcus W. Feldman

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The assumption that different genetic elements can make separate contributions to the same quantitative trait was originally made in order to reconcile biometry and Mendelism and ever since has been used in population genetics, specifically for the trait of fitness. Here we show that sex is responsible for the existence of separate genetic effects on fitness and, more generally, for the existence of a hierarchy of genetic evolutionary modules. Using the tools developed in the process, we also demonstrate that in terms of their fitness effects, separation and fusion of genes are associated with the increase and decrease of the …

Figs, Wasps, Gophers, And Lice: A Computational Exploration Of Coevolution, Ran Libeskind-Hadas

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This chapter explores the topic of coevolution: the genetic change in one species in response to the change in another. For example, in some cases, a parasite species might evolve to specialize with its host species. In other cases, the relationship between two species may be mutually beneficial and coevolution may serve to strengthen the benefits of that relationship.

Mathematical Biology At An Undergraduate Liberal Arts College, Stephen C. Adolph, Lisette G. De Pillis

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Since 2002 we have offered an undergraduate major in Mathematical Biology at Harvey Mudd College. The major was developed and is administered jointly by the mathematics and biology faculty. In this paper we describe the major, courses, and faculty and student research and discuss some of the challenges and opportunities we have experienced.

Thermal Links For The Implementation Of An Optical Refrigerator, John Parker, David Mar, Steven Von Der Porten, John Hankinson, Kevin Byram, Chris Lee, Michael K. Mayeda, Richard C. Haskell, Qimin Yang, Scott R. Greenfield, Richard I. Epstein

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Optical refrigeration has been demonstrated by several groups of researchers, but the cooling elements have not been thermally linked to realistic heat loads in ways that achieve the desired temperatures. The ideal thermal link will have minimal surface area, provide complete optical isolation for the load, and possess high thermal conductivity. We have designed thermal links that minimize the absorption of fluoresced photons by the heat load using multiple mirrors and geometric shapes including a hemisphere, a kinked waveguide, and a tapered waveguide. While total link performance is dependent on additional factors, we have observed net transmission of photons with …

Compensatory Evolution Of Gene Regulation In Response To Stress By Escherichia Coli Lacking Rpos, Daniel M. Stoebel, Karsten Hokamp, Michael S. Last, Charles J. Dorman

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The RpoS sigma factor protein of Escherichia coli RNA polymerase is the master transcriptional regulator of physiological responses to a variety of stresses. This stress response comes at the expense of scavenging for scarce resources, causing a trade-off between stress tolerance and nutrient acquisition. This trade-off favors non-functional rpoS alleles in nutrient-poor environments. We used experimental evolution to explore how natural selection modifies the regulatory network of strains lacking RpoS when they evolve in an osmotically stressful environment. We found that strains lacking RpoS adapt less variably, in terms of both fitness increase and changes in patterns of transcription, than …

The Shapley Value Of Phylogenetic Trees, Claus-Jochen Haake, Akemi Kashiwada '05, Francis E. Su

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Every weighted tree corresponds naturally to a cooperative game that we call a tree game; it assigns to each subset of leaves the sum of the weights of the minimal subtree spanned by those leaves. In the context of phylogenetic trees, the leaves are species and this assignment captures the diversity present in the coalition of species considered. We consider the Shapley value of tree games and suggest a biological interpretation. We determine the linear transformation M that shows the dependence of the Shapley value on the edge weights of the tree, and we also compute a null space …

Estimating Maximum Performance: Effects Of Intraindividual Variation, Stephen C. Adolph, Trevor Pickering '05

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Researchers often estimate the performance capabilities of animals using a small number of trials per individual. This procedure inevitably underestimates maximum performance, but few studies have examined the magnitude of this effect. In this study we explored the effects of intraindividual variation and individual sample size on the estimation of locomotor performance parameters. We measured sprint speed of the lizard Sceloporus occidentalis at two temperatures (20 degrees C and 35 degrees C), obtaining 20 measurements per individual. Speed did not vary temporally, indicating no training or fatigue effects. About 50% of the overall variation in speed at each temperature was …

The Phylum Cnidaria: A Review Of Phylogenetic Patterns And Diversity 300 Years After Linnaeus, Catherine S. Mcfadden, Marymegan Daly, Mercer R. Brugler, Paulyn Cartwright, Allen G. Collins, Michael N. Dawson, Daphne G. Fautin, Scott C. France, Dennis M. Opresko, Estefania Rodriguez, Sandra L. Romano, Joel L. Stake

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Systema Naturae includes representatives of every major lineage of the animal phylum Cnidaria. However, Linnaeus did not classify the members of the phylum as is now done, and the diversity of the group is not well represented. We contrast the Linnaean perspective on cnidarian diversity with the modern, phylogenetic perspective. For each order, we detail diversity at the family level, providing phylogenetic context where possible.

Testing The Persistence Of Phenotypic Plasticity After Incubation In The Western Fence Lizard, Sceloporus Occidentalis, Christine R. Buckley, Maddalena Jackson, Mina Youssef, Duncan J. Irschick, Stephen C. Adolph

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Hypothesis: Phenotypic variation in traits induced by different incubation temperatures does not persist into the lifetime of young lizards, and therefore contributes little to variation in long-term fitness.

Organism: Western fence lizard (Sceloporus occidentalis).

Methods: Split-clutch laboratory incubation experiment including eggs from two different populations under two different incubation regimes, measurement of morphological traits at hatching, and tracking of morphology and temperature preference behaviour for 7 weeks after hatching.

Results: Several morphological traits, including body mass, hindlimb length, inter-limb length, and tail length, initially differed between the two incubation treatments, but only the difference in tail length persisted …

Behavioural Plasticity In An Ecological Generalist: Microhabitat Use By Western Fence Lizards, Dee A. Asbury, Stephen C. Adolph

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Question: What is the basis for geographic variation in microhabitat use in fence lizards?

Hypothesis: Population differences in microhabitat use reflect behavioural plasticity rather than genetic or experiential differences.

Organisms: Western fence lizards (Sceloporus occidentalis).

Field site: Three sites (desert, valley, and mountain) in southern California, USA.

Methods: We compared habitat use by free-ranging lizards in three field populations. We also collected lizards from these three populations and studied their microhabitat use in experimental enclosures at a single field site.

Results: In the wild, lizards chose higher and shadier perches at the hottest (desert) site, lower and sunnier perches at …

Motion-Sensitive 3-D Optical Coherence Microscope Operating At 1300 Nm For The Visualization Of Early Frog Development, Barbara M. Hoeling, Stephanie S. Feldman, Daniel T. Strenge, Aaron Bernard, Emily R. Hogan, Daniel C. Petersen, Scott E. Fraser, Yun Kee, J. Michael Tyszka, Richard C. Haskell

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We present 3-dimensional volume-rendered in vivo images of developing embryos of the African clawed frog Xenopus laevis taken with our new en-face-scanning, focus-tracking OCM system at 1300 nm wavelength. Compared to our older instrument which operates at 850 nm, we measure a decrease in the attenuation coefficient by 33%, leading to a substantial improvement in depth penetration. Both instruments have motion-sensitivity capability. By evaluating the fast Fourier transform of the fringe signal, we can produce simultaneously images displaying the fringe amplitude of the backscattered light and images showing the random Brownian motion of the scatterers. We present time-lapse movies of …

Review Of Analysis Of Phylogenetics And Evolution With R By Emmanuel Paradis, Daniel M. Stoebel

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This is a book review.

Review Of Jewish Tradition And The Challenge Of Darwinism, Geoffery Cantor And Marc Swetlitz, Eds., Daniel M. Stoebel

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This is a book review.

Is A Basketball Free-Throw Sequence Nonrandom? A Group Exercise For Undergraduate Statistics Students, Stephen C. Adolph

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I describe a group exercise that I give to my undergraduate biostatistics class. The exercise involves analyzing a series of 200 consecutive basketball free-throw attempts to determine whether there is any evidence for sequential dependence in the probability of making a free-throw. The students are given the exercise before they have learned the appropriate statistical tests, so that they can come up with ideas on their own. Students spend a full class period working on the problem, with my guidance and hints. In the next class period, we discuss how each student group approached the problem. I then present several …

In Situ Muscle Power Differs Without Varying In Vitro Mechanical Properties In Two Insect Leg Muscles Innervated By The Same Motor Neuron, Anna N. Ahn, Kenneth Meijer, Robert J. Full

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The mechanical behavior of muscle during locomotion is often predicted by its anatomy, kinematics, activation pattern and contractile properties. The neuromuscular design of the cockroach leg provides a model system to examine these assumptions, because a single motor neuron innervates two extensor muscles operating at a single joint. Comparisons of the in situ measurements under in vivo running conditions of muscle 178 to a previously examined muscle (179) demonstrate that the same inputs (e.g. neural signal and kinematics) can result in different mechanical outputs. The same neural signal and kinematics, as determined during running, can result in different mechanical functions, …

An Optimal Brain Can Be Composed Of Conflicting Agents, Adi Livnat, Nicholas Pippenger

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Many behaviors have been attributed to internal conflict within the animal and human mind. However, internal conflict has not been reconciled with evolutionary principles, in that it appears maladaptive relative to a seamless decision-making process. We study this problem through a mathematical analysis of decision-making structures. We find that, under natural physiological limitations, an optimal decision-making system can involve “selfish” agents that are in conflict with one another, even though the system is designed for a single purpose. It follows that conflict can emerge within a collective even when natural selection acts on the level of the collective only.