Life Sciences Commons^™

Contribution Of Pentose Catabolism To Molecular Hydrogen Formation By Targeted Disruption Of Arabinose Isomerase (Araa) In The Hyperthermophilic Bacterium Thermotoga Maritima, Derrick White, Raghuveer Singh, Deepak Rudrappa, Jackie Mateo, Levi Kramer, Laura Freese, Paul H. Blum

School of Biological Sciences: Faculty Publications

Thermotoga maritima ferments a broad range of sugars to form acetate, carbon dioxide, traces of lactate, and near theoretic yields of molecular hydrogen (H₂). In this organism, the catabolism of pentose sugars such as arabinose depends on the interaction of the pentose phosphate pathway with the Embden-Myerhoff and Entner-Doudoroff pathways. Although the values for H₂ yield have been determined using pentose-supplemented complex medium and predicted by metabolic pathway reconstruction, the actual effect of pathway elimination on hydrogen production has not been reported due to the lack of a genetic method for the creation of targeted mutations. Here, …

Cognition-Mediated Evolution Of Low-Quality Floral Nectars, Vladislav Nachev, Kai Petra Stich, Clemens Winter, Alan B. Bond, Alan Kamil, York Winter

Alan Bond Publications

Plants pollinated by hummingbirds or bats produce dilute nectars even though these animals prefer more concentrated sugar solutions. This mismatch is an unsolved evolutionary paradox. Here we show that lower quality, or more dilute, nectars evolve when the strength of preferring larger quantities or higher qualities of nectar diminishes as magnitudes of the physical stimuli increase. In a virtual evolution experiment conducted in the tropical rainforest, bats visited computer-automated flowers with simulated genomes that evolved relatively dilute nectars. Simulations replicated this evolution only when value functions, which relate the physical stimuli to subjective sensations, were nonlinear. Selection also depended on …

Cumulative Herbivory Outpaces Compensation For Early Floral Damage On A Monocarpic Perennial Thistle, Natalie M. West, Svata M. Louda

School of Biological Sciences: Faculty Publications

Floral herbivory represents a major threat to plant reproductive success, driving the importance of plant tolerance mechanisms that minimize fitness costs. However, the cumulative insect herbivory plants experience under natural conditions complicates predictions about tolerance contributions to net fitness. Apical damage can lead to compensatory seed production from late season flowering that ameliorates early season fitness losses. Yet, the compensation realized depends on successful development and herbivore escape by later season flowers. Using monocarpic perennial Cirsium canescens, we quantified seed-reproductive fitness of plants with vs. without experimental damage to the early-developing large apical flower head, with and without a …

Spatially Biased Dispersal Of Acorns By A Scatter-Hoarding Corvid May Accelerate Passive Restoration Of Oak Habitat On California’S Largest Island, Mario B. Pesendorfer, T. Scott Sillett, Scott A. Morrison

School of Biological Sciences: Faculty Publications

Scatter hoarding by corvids (crows, jays, magpies, and nutcrackers) provides seed dispersal for many large-seeded plants, including oaks and pines. When hoarding seeds, corvids often choose nonrandom locations throughout the landscape, resulting in differential survival of seeds. In the context of habitat restoration, such disproportional storing of seeds in areas suitable for germination and establishment can accelerate expansion and recovery of large-seeded tree populations and their associated ecosystems. Here, we investigate the spatial preferences of island scrub jays Aphelocoma insularis during scatter hoarding of acorns (Quercus spp.) on Santa Cruz Island. We use a large behavioral data set on …

Increased Insertion Number Leads To Increased Sperm Transfer And Fertilization Success In A Nursery Web Spider, Alissa G. Anderson, Eileen Hebets

Eileen Hebets Publications

Across animals, a male's fitness is largely dictated by his ability to fertilize eggs; and there exists a plethora of male adaptations associated with increasing fertilization success. In the nursery web spider, Pisaurina mira, males restrain females prior to and during copulation by wrapping them with silk. Previous research demonstrates that copulatory silk wrapping reduces a male's chance of being sexually cannibalized and increases the number of sperm transfer opportunities (termed insertions) that a male can achieve within a mating. While avoiding cannibalism provides an obvious survival benefit to males, the impact of insertion number on male fitness remains …

Distinct Transcriptome Profiles Of Gag-Specific Cd8+ T Cells Temporally Correlated With The Protection Elicited By Sivδnef Live Attenuated Vaccine, Wuxun Lu, Yanmin Wan, Fangrui Ma, R. Paul Johnson, Qingsheng Li

School of Biological Sciences: Faculty Publications

The live attenuated vaccine (LAV) SIVmac239Δnef (SIVΔnef) confers the best protection among all the vaccine modalities tested in rhesus macaque model of HIV-1 infection. This vaccine has a unique feature of time-dependent protection: macaques are not protected at 3±5 weeks post vaccination (WPV), whereas immune protection emerges between 15 and 20 WPV. Although the exact mechanisms of the time-dependent protection remain incompletely understood, studies suggested that both cellular and humoral immunities contribute to this time-dependent protection. To further elucidate the mechanisms of protection induced by SIVΔnef, we longitudinally compared the global gene expression profiles of SIV Gag-CM9+ CD8+ (Gag-specific CD8+) …

Neural Circuitry For Target Selection And Action Selection In Animal Behavior, Daizaburo Shizuka, Eileen Hebets, Kim L. Hoke

Papers in Behavior in Biological Sciences

Animal behaviorists have long strived for a comprehensive understanding of the proximate and ultimate causes of complex behavior, and we propose that recent advances in neurobiology can help reshape or clarify this behavior-oriented understanding. We begin with an overview of current views of neural circuit mechanisms that mediate target selection and action selection. In target selection, different stimuli compete for priority in sensory-motor process- ing. Action selection is the process by which multiple possible motor actions compete for priority in a manner which balances the needs of the animal with opportunities or threats in the environment. We next discuss spatial …

Online Dictionary Of Invertebrate Zoology: Complete Work, Mary Ann (Basinger) Maggenti, Armand R. Maggenti, Scott Lyell Gardner (Editor)

Armand R. Maggenti Online Dictionary of Invertebrate Zoology

An exhaustive dictionary of over 13,000 terms relating to invertebrate zoology, including etymologies, word derivations and taxonomic classification. Entries cover parasitology, nematology, marine invertebrates, insects, and anatomy, biology, and reproductive processes for the following phyla: Acanthocephala, Annelida, Arthropoda, Brachiopoda, Bryozoa, Chaetognatha, Cnidaria, Ctenophora, Echinodermata, Echiura, Entoprocta, Gastrotricha, Gnathostomulida, Kinorhyncha, Loricifera, Mesozoa, Mollusca, Nematoda, Nematomorpha, Nemertea, Onychophora, Pentastoma, Phoronida, Placozoa, Platyhelminthes, Pogonophora, Porifera, Priapula, Rotifera, Sipuncula, and Tardigrada.

Record Breaking Achievements By Spiders And The Scientists Who Study Them, Stefano Mammola, Peter Michalik, Eileen Hebets, Marco Isaia

Eileen Hebets Publications

Organismal biology has been steadily losing fashion in both formal education and scientific research. Simultaneous with this is an observable decrease in the connection between humans, their environment, and the organisms with which they share the planet. Nonetheless, we propose that organismal biology can facilitate scientific observation, discovery, research, and engagement, especially when the organisms of focus are ubiquitous and charismatic animals such as spiders. Despite being often feared, spiders are mysterious and intriguing, offering a useful foundation for the effective teaching and learning of scientific concepts and processes. In order to provide an entryway for teachers and students—as well …

Importance Of The Antenniform Legs, But Not Vision, For Homing By The Neotropical Whip Spider Paraphrynus Laevifrons, Verner P. Bingman, Jacob M. Graving, Eileen Hebets, Daniel D. Wiegmann

Eileen Hebets Publications

Amblypygids, or whip spiders, are nocturnal, predatory arthropods that display a robust ability to navigate to their home refuge. Prior field observations and displacement studies in amblypygids demonstrated an ability to home from distances as far away as 10 m. In the current study, micro-transmitters were used to take morning position fixes of individual Paraphrynus laevifrons following an experimental displacement of 10 m from their home refuge. The intention was to assess the relative importance of vision compared with sensory input acquired from the antenniform legs for navigation as well as other aspects of their spatial behavior. Displaced individuals were …

Host Allometry Influences The Evolution Of Parasite Host-Generalism: Theory And Meta-Analysis, Josephine G. Walker, Amy Hurford, Jo Cable, Amy R. Ellison, Stephen J. Price, Clayton E. Cressler

School of Biological Sciences: Faculty Publications

Parasites vary widely in the diversity of hosts they infect: some parasite species are specialists—infecting just a single host species, while others are generalists, capable of infecting many. Understanding the factors that drive parasite host-generalism is of basic biological interest, but also directly relevant to predicting disease emergence in new host species, identifying parasites that are likely to have unidentified additional hosts, and assessing transmission risk. Here, we use mathematical models to investigate how variation in host body size and environmental temperature affect the evolution of parasite host-generalism. We predict that parasites are more likely to evolve a generalist strategy …

Large But Uneven Reduction In Fish Size Across Species In Relation To Changing Sea Temperatures, Itai Van Rijn, Yehezkel Buba, John Delong, Moshe Kiflawi, Jonathan Belmaker

School of Biological Sciences: Faculty Publications

Ectotherms often attain smaller body sizes when they develop at higher temperatures. This phenomenon, known as the temperature size rule, has important consequences for global fisheries, whereby ocean warming is predicted to result in smaller fish and reduced biomass. However, the generality of this phenomenon and the mechanisms that drive it in natural populations remain unresolved. In this study we document the maximal size of 74 fish species along a steep temperature gradient in the Mediterranean Sea and find strong support for the temperature size rule. Importantly, we additionally find that size reduction in active fish species is dramatically larger …

The Economic Value Of Grassland Species For Carbon Storage, Bruce A. Hungate, Edward B. Barbier, Amy W. Ando, Samuel P. Marks, Peter B. Reich, Natasja Van Gestel, David Tilman, Johannes M. H. Knops, David U. Hooper, Bradley J. Butterfield, Bradley J. Cardinale

School of Biological Sciences: Faculty Publications

Carbon storage by ecosystems is valuable for climate protection. Biodiversity conservation may help increase carbon storage, but the value of this influence has been difficult to assess. We use plant, soil, and ecosystem carbon storage data from two grassland biodiversity experiments to show that greater species richness increases economic value: Increasing species richness from 1 to 10 had twice the economic value of increasing species richness from 1 to 2. The marginal value of each additional species declined as species accumulated, reflecting the nonlinear relationship between species richness and plant biomass production. Our demonstration of the economic value of biodiversity …

Increased Productivity In Wet Years Drives A Decline In Ecosystem Stability With Nitrogen Additions In Arid Grasslands, Junfeng Wang, Johannes M.H. Knops, Chad E. Brassil, Chunsheng Mu

School of Biological Sciences: Faculty Publications

Adding nutrients to nutrient-limited ecosystems typically lowers plant diversity and decreases species asynchrony. Both, in turn, decrease the stability of productivity in the response to negative climate fluctuations such as droughts. However, most classic studies examining stability have been done in relatively wet grasslands dominated by perennial grasses. We examined how nutrient additions influence the stability of productivity to rainfall variability in an arid grassland with a mix of perennial and annual species. Of the nutrients, only nitrogen increased productivity, and only in wet years. In addition, only nitrogen decreased the stability of productivity. Thus, nutrient addition makes ecosystem productivity …

Glaciation As A Migratory Switch, Robert M. Zink, Aubrey S. Gardner

School of Biological Sciences: Faculty Publications

Migratory behavior in birds is evolutionarily plastic, but it is unclear how this behavior responded during glacial cycles. One view is that at glacial maxima, species simply shifted their breeding ranges south of glacial ice and remained migratory. To test this hypothesis, we constructed ecological niche models for breeding and wintering ranges of 56 species, finding that 70% of currently long-distance North American migrant species likely lacked suitable breeding habitat in North America at the Last Glacial Maximum (LGM), and we hypothesized that they reverted to the ancestral state of being tropical sedentary residents. A smaller percentage of short-distance migrants …

Knowing Your Own: A Classroom Case Study Using The Scientific Method To Investigate How Birds Learn To Recognize Their Offspring, Joanna K. Hubbard, Daizaburo Shizuka, Brian A. Couch

School of Biological Sciences: Faculty Publications

Understanding the scientific method provides students with a necessary foundation for careers in science-related fields. Moreover, students can apply scientific inquiry skills in many aspects of their daily lives and decision making. Thus, the ability to apply the scientific method represents an essential skill that students should learn during undergraduate science education. We designed an interrupted case study in which students learn about and apply the scientific method to investigate and recapitulate the findings of a published research article. This research article addresses the question of how parents recognize their own young in a system where birds of the same …

Measurement Instrument For Scientific Teaching (Mist): A Tool To Measure The Frequencies Of Research-Based Teaching Practices In Undergraduate Science Courses, Mary F. Durham, Jennifer K. Knight, Brian A. Couch

School of Biological Sciences: Faculty Publications

The Scientific Teaching (ST) pedagogical framework provides various approaches for science instructors to teach in a way that more closely emulates how science is practiced by actively and inclusively engaging students in their own learning and by making instructional decisions based on student performance data. Fully understanding the impact of ST requires having mechanisms to quantify its implementation. While many useful instruments exist to document teaching practices, these instruments only partially align with the range of practices specified by ST, as described in a recently published taxonomy. Here, we describe the development, validation, and implementation of the Measurement Instrument for …

Student Buy-In Toward Formative Assessments: The Influence Of Student Factors And Importance For Course Success, Kathleen R. Brazeal, Brian A. Couch

School of Biological Sciences: Faculty Publications

Formative assessment (FA) techniques, such as pre-class assignments, in-class activities, and post-class homework, have been shown to improve student learning. While many students find these techniques beneficial, some students may not understand how they support learning or may resist their implementation. Improving our understanding of FA buy-in has important implications, since buy-in can potentially affect whether students fully engage with and learn from FAs. We investigated FAs in 12 undergraduate biology courses to understand which student characteristics influenced buy-in toward FAs and whether FA buy-in predicted course success. We administered a mid-semester survey that probed student perceptions toward several different …

First-Year And Non-First-Year Student Expectations Regarding In-Class And Out-Of-Class Learning Activities In Introductory Biology, Tanya L. Brown, Brian A. Couch

School of Biological Sciences: Faculty Publications

National calls for teaching transformation build on a constructivist learning theory and propose that students learn by actively engaging in course activities and interacting with other students. While interactive pedagogies can improve learning, they also have the potential to challenge traditional norms regarding class participation and learning strategies. To better understand the potential openness of students to interactive teaching practices, we administered a survey during the first week of two sections of an introductory biology course to characterize how students envisioned spending time during class as well as what activities they expected to complete outside of class during non-exam weeks …

Sigma Virus (Dmelsv) Incidence In Lines Of Drosophila Melanogaster Selected For Survival Following Infection With Bacillus Cereus, Meghan L. Bentz, Eve A. Humphrey, Lawrence G. Harshman

School of Biological Sciences: Faculty Publications

The immune response of Drosophila melanogaster is complex and involves both specific and general responses to parasites. In this study we tested for cross-immunity for bacteria and viruses by scoring the incidence of infection with the vertically transmitted Sigma virus (DMelSV) in the progeny of a cross between females transmitting DMelSV at high frequencies and males from lines subjected to three selection regimes related to resistance to Bacillus cereus. There was no significant difference in transmission of DMelSV among selection regimes, though results suggest that the B. cereus selected lines had lower rates of infection by DMelSV. We found …

Biotic Interchange Has Structured Western Hemisphere Mammal Communities, Danielle Fraser, S. Kathleen Lyons

School of Biological Sciences: Faculty Publications

Aim.— Many hypotheses posit that species-rich tropical communities are dominated by speciesspecies interactions, apparent as competitive exclusion or character displacement, whereas species-poor temperate communities are dominated by species-environment interactions. Recent studies demonstrate a strong influence of macroevolutionary and biogeographic factors. We simultaneously test for the effects of species interactions, climate, and biotic interchange on Western Hemisphere mammal communities using a phylogenetic and functional diversity approach.

Location.— Western Hemisphere.

Time period.— Modern

Major taxa studied.— Mammalia

Methods.— Using Western Hemisphere mammal distributional and body mass data, we calculate body mass dispersion, phylogenetic diversity (Net Relatedness Index), and assemblage-averaged rates of co-occurrence …

Cooperative Processing Of Primary Mirnas By Dus16 And Dcl3 In The Unicellular Green Alga Chlamydomonas Reinhardtii, Tomohito Yamasaki, Heriberto D. Cerutti

School of Biological Sciences: Faculty Publications

We have previously reported that the RNA-binding protein Dull slicer 16 (DUS16) plays a key role in the processing of primary miRNAs (pri-miRNAs) in the unicellular green alga Chlamydomonas reinhardtii. In the present report, we elaborate on the interaction of DUS16 with Dicer-like 3 (DCL3) during pri-miRNA processing. Comprehensive analyses of small RNA libraries derived from mutant and wild-type algal strains allowed the de novo prediction of 35 pri-miRNA genes, including 9 previously unknown ones. The pri-miRNAs dependent on DUS16 for processing largely overlapped with those dependent on DCL3. Our findings suggest that DUS16 and DCL3 work cooperatively, presumably …

Host Allometry Influences The Evolution Of Parasite Host-Generalism: Theory And Meta-Analysis, Josephine G. Walker, Amy Hurford, Jo Cable, Amy R. Ellison, Stephen J. Price, Clayton E. Cressler

School of Biological Sciences: Faculty Publications

Parasites vary widely in the diversity of hosts they infect: some parasite species are specialists—infecting just a single host species, while others are generalists, capable of infecting many. Understanding the factors that drive parasite host-generalism is of basic biological interest, but also directly relevant to predicting disease emergence in new host species, identifying parasites that are likely to have unidentified additional hosts, and assessing transmission risk. Here, we use mathematical models to investigate how variation in host body size and environmental temperature affect the evolution of parasite host-generalism. We predict that parasites are more likely to evolve a generalist strategy …

Sensory System Plasticity In A Visually Specialized, Nocturnal Spider, Jay A. Stafstrom, Peter Michalik, Eileen Hebets

School of Biological Sciences: Faculty Publications

The interplay between an animal’s environmental niche and its behavior can influence the evolutionary form and function of its sensory systems. While intraspecific variation in sensory systems has been documented across distant taxa, fewer studies have investigated how changes in behavior might relate to plasticity in sensory systems across developmental time. To investigate the relationships among behavior, peripheral sensory structures, and central processing regions in the brain, we take advantage of a dramatic within-species shift of behavior in a nocturnal, net-casting spider (Deinopis spinosa), where males cease visually-mediated foraging upon maturation. We compared eye diameters and brain region volumes across …

Phytophagous Insect Oviposition Shifts In Response To Probability Of Flower Abortion Owing To The Presence Of Basal Fruits, Shivani Jadeja, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

Phytophagous insects use a wide range of indicators or associated cues to avoid laying eggs in sites where offspring survival is low. For insects that lay eggs in flowers, these unsuitable sites may be created by the host plant’s resource allocation to flowers. In the sequentially flowering host plant, Yucca glauca, late-opening distal flowers are more likely to be aborted in the presence of already-initiated basal fruits because they are strong resource sinks. If flowers are aborted, all eggs of the phytophagous insect, Tegeticula yuccasella, within the flower die. We used the phytophagous insect T. yuccasella that lays …

The Emerging Contribution Of Social Wasps To Grape Rot Disease Ecology, Anne A. Madden, Sean D. Boyden, Jonathan-Andrew N. Soriano, Tyler B. Corey, Jonathan W. Leff, Noah Fierer, Philip T. Starks

School of Biological Sciences: Faculty Publications

Grape sour (bunch) rot is a polymicrobial disease of vineyards that causes millions of dollars in lost revenue per year due to decreased quality of grapes and resultant wine. The disease is associated with damaged berries infected with a community of acetic acid bacteria, yeasts, and filamentous fungi that results in rotting berries with high amounts of undesirable volatile acidity. Many insect species cause the initial grape berry damage that can lead to this disease, but most studies have focused on the role of fruit flies in facilitating symptoms and vectoring the microorganisms of this disease complex. Like fruit flies, …

Pseudopecoelus Mccauleyi N. Sp. And Podocotyle Sp. (Digenea: Opecoelidae) From The Deep Waters Off Oregon And British Columbia With An Updated Key To The Species Of Pseudopecoelus Von Wicklen, 1946 And Checklist Of Parasites From Lycodes Cortezianus (Perciformes: Zoarcidae), Charles K. Blend, Norman O. Dronen, Gábor R. Rácz, Scott Lyell Gardner

Scott L. Gardner Publications

Pseudopecoelus mccauleyi n. sp. (Opecoelidae: Opecoelinae) is described from the intestine of the bigfin eelpout, Lycodes cortezianus (Gilbert, 1890) (Perciformes: Zoarcidae), collected at 200–800 m depths in the northeastern Pacific Ocean off Oregon and Vancouver Island, British Columbia. The new species is distinguished by possessing a unique combination of the following diagnostic characters: vitelline fields that extend to the posterior margin of the ventral sucker; a slender, tubular and sinuous seminal vesicle that extends some distance into the hindbody; an unspecialized, protuberant ventral sucker; a genital pore at pharynx level; lobed to deeply multilobed testes; a lobed ovary; and an …

A New Species Of Catenotaenia (Cestoda: Catenotaeniidae) From Pygeretmus Pumilio Kerr, 1792 From The Gobi Of Mongolia, Altangerel Tsogtsaikhan Dursahinhan, Batsaikhan Nyamsuren, Danielle Marie Tufts, Scott Lyell Gardner

Scott L. Gardner Publications

From 1999 through 2012, a total of 541 individual rodents (jerboas of the family Dipodidae) were collected from several habitat types, primarily from the Gobi region of Mongolia, and were examined for helminth and protistan parasites. Of those rodents, 25 were identified as Pygeretmus pumilio Kerr, 1792 (Rodentia: Dipodidae), whereas 516 were other species of jerboa from the provinces of Dornogobi, Dundgobi, Omnogobi, Ovorhangai, Bayanhongor, Gobi Altai, and Hovd. During our field work, we collected several cestodes; some of which represented undescribed species, and these new species occurred in 40% of P. pumilio from four separate collecting localities. We designate …

Nematodes Associated With Mammals In The Great American Biotic Interchange (Gabi), F. Agustin Jimenez, Juliana Notarnicola, Scott Lyell Gardner

Scott L. Gardner Publications

The Great American Biotic Interchange (GABI) is a large-scale zoogeographic event that illustrates the exchange and diversification of mammals between North and South America. This phenomenon was accelerated by the connection of both landmasses during the Pliocene. Support for this phenomenon includes the extant distribution of xenarthrans, didelphiomorph marsupials, hystricognath and cricetine rodents, sciurids and carnivores, as well as the distribution of fossils in the stratigraphic record and the coalescence of genotypes. Contrasting with the relatively well-documented role and history of mammals in GABI, the role of their parasites has been largely neglected. As a consequence, the reconstructions of the …

A Method For Measuring The Attachment Strength Of The Cestode Hymenolepis Diminuta To The Rat Intestine, Wanchuan Xie, Gábor R. Rácz, Benjamin S. Terry, Scott Lyell Gardner

Scott L. Gardner Publications

A unique adaptation of many internal parasites of mammals is their ability to stay in the intestine for extended periods of time and resist the normal peristaltic movements and forces that push and expel material. To better understand parasite adhesion behavior and replicate their attachment method in medical devices, an experiment was designed and performed using the rat tapeworm, Hymenolepis diminuta. The experiment employed a tensile test machine and a digital scale and was designed to calculate the attachment strength of the scolex to the mucosa through the change of the value of the digital scale during the tensile …