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2018 W.M. Keck Science Department Publications and Grants

*Indicates student co-author

Budischak, Sarah A. and Clayton E. Cressler. “Fueling Defense: Effects of Resources on the Ecology and Evolution of Tolerance to Parasite Infection.” Frontiers in Immunology, 2018, 9:2453.

Abstract: Resource availability is a key environmental constraint affecting the ecology and evolution of species. Resources have strong effects on disease resistance, but they can also affect the other main parasite defense strategy, tolerance. A small but growing number of animal studies are beginning to investigate the effects of resources on tolerance phenotypes. Here, we review how resources affect tolerance strategies across animal taxa ranging from fruit flies to frogs to mice. Surprisingly, resources (quality and quantity) can increase or reduce tolerance, dependent upon the particular host-parasite system. To explore this seeming contradiction, we recast predictions of models of sterility tolerance and mortality tolerance in a resource-dependent context. Doing so reveals that resources can have very different epidemiological and evolutionary effects, depending on what aspects of the tolerance phenotype are affected. Thus, it is critical to consider both sterility and mortality in future empirical studies of how behavioral and environmental resource availability affect tolerance to infection.


Budischak, Sarah A., Christina B. Hansen, Quentin Caudron, Romain Garnier, Tyler R. Kartzinel, István Pelczer, Clayton E. Cressler, Anieke van Leeuwen, and Andrea L. Graham. “Feeding Immunity Physiological and Behavioral Responses to Infection and Resource Limitation.” Frontiers in Immunology, 2018, 8:1914.

Abstract: Resources are a core currency of species interactions and ecology in general (e.g., think of food webs or competition). Within parasite-infected hosts, resources are divided among the competing demands of host immunity and growth as well as parasite reproduction and growth. Effects of resources on immune responses are increasingly understood at the cellular level (e.g., metabolic predictors of effector function), but there has been limited consideration of how these effects scale up to affect individual energetic regimes (e.g., allocation trade-offs), susceptibility to infection, and feeding behavior (e.g., responses to local resource quality and quantity). We experimentally rewilded laboratory mice (strain C57BL/6) in semi-natural enclosures to investigate the effects of dietary protein and gastrointestinal nematode (Trichuris muris) infection on individual-level immunity, activity, and behavior. The scale and realism of this field experiment, as well as the multiple physiological assays developed for laboratory mice, enabled us to detect costs, trade-offs, and potential compensatory mechanisms that mice employ to battle infection under different resource conditions. We found that mice on a low-protein diet spent more time feeding, which led to higher body fat stores (i.e., concentration of a satiety hormone, leptin) and altered metabolite profiles, but which did not fully compensate for the effects of poor nutrition on albumin or immune defenses. Specifically, immune defenses measured as interleukin 13 (IL13) (a primary cytokine coordinating defense against T. muris) and as T. muris-specific IgG1 titers were lower in mice on the low-protein diet. However, these reduced defenses did not result in higher worm counts in mice with poorer diets. The lab mice, living outside for the first time in thousands of generations, also consumed at least 26 wild plant species occurring in the enclosures, and DNA metabarcoding revealed that the consumption of different wild foods may be associated with differences in leptin concentrations. When individual foraging behavior was accounted for, worm infection significantly reduced rates of host weight gain. Housing laboratory mice in outdoor enclosures provided new insights into the resource costs of immune defense to helminth infection and how hosts modify their behavior to compensate for those costs.


Budischak, Sarah A., Dawn O’Neal, Anna E. Jolles, and Vanessa O. Ezenwa. “Differential Host Responses to Parasitism Shape Divergent Fitness Costs of Infection.” Functional Ecology, vol. 32, issue 2, 2018, pp. 324-333.

Abstract: Fitness costs of infection are fundamental to understanding the ecology and evolution of host–parasite interactions. However, these costs, and particularly their underlying mechanisms, are challenging to evaluate in wild populations. Here, we quantified total and species‐specific costs of gastrointestinal worms on African buffalo, by combining the power of an anthelmintic treatment experiment that perturbed the entire worm community with a longitudinal study that tracked the two most dominant community members. Reducing all worms improved buffalo body condition, which was strongly associated with increases in survival and reproduction. Species‐specific analyses revealed that condition‐mediated fitness costs of infection differed between parasite species. Hosts that gained the blood‐sucking worm Haemonchus, lost condition, and this loss may have been mediated by reductions in forage intake. Hosts that resisted Haemonchus by elevating IL‐4 and eosinophil immune defences were able to reduce their parasite loads and gain back condition. Conversely, hosts that gained Cooperia, a less pathogenic worm, gained condition and had higher survival and reproductive success. Elevating immune defences had no effect on Cooperia abundance. Coupled with the positive relationship observed between Cooperia and host condition, our data suggest that hosts might benefit from tolerating Cooperia rather than incurring the costs of resistance. Overall, our study reveals that differential host responses to parasites play a key role in mediating the costs of infection.


Budischak, Sarah A., Aprilianto E. Wiria, Firdaus Hamid, Linda J. Wammes, Maria M. M. Kaisar, Lisette van Lieshout, Erliyani Sartono, Taniawati Supali, Maria Yazdanbakhsh, and Andrea L. Graham. “Competing for Blood: The Ecology of Parasite Resource Competition in Human Malaria-Helminth Co-Infections.” Ecology Letters, vol. 21, 2018, pp. 536-545.

Abstract: Ecological theory suggests that co‐infecting parasite species can interact within hosts directly, via host immunity and/or via resource competition. In mice, competition for red blood cells (RBCs) between malaria and bloodsucking helminths can regulate malaria population dynamics, but the importance of RBC competition in human hosts was unknown. We analysed infection density (i.e. the concentration of parasites in infected hosts), from a 2‐year deworming study of over 4000 human subjects. After accounting for resource‐use differences among parasites, we find evidence of resource competition, priority effects and a competitive hierarchy within co‐infected individuals. For example reducing competition via deworming increased Plasmodium vivaxdensities 2.8‐fold, and this effect is limited to bloodsucking hookworms. Our ecological, resource‐based perspective sheds new light into decades of conflicting outcomes of malaria–helminth co‐infection studies with significant health and transmission consequences. Beyond blood, investigating within‐human resource competition may bring new insights for improving human health.


Dallas, Tad A., A. Alonso Aguirre, Sarah Budischak, Colin Carlson, Vanessa Ezenwa, Barbara Han, Shan Huang, and Patrick R. Stephens. “Gauging Support for Macroecological Patterns in Helminth Parasites.” Global Ecology and Biogeography, vol. 27, issue 12, 2018, pp. 1437-1447.

Abstract: To explore spatial patterns of helminth parasite diversity, and to investigate three main macroecological patterns – (a) latitude–diversity relationships, (b) positive scaling between parasite and host diversity, and (c) species–area relationships – using a largely underutilized global database of helminth parasite occurrence records. We examined the London Natural History Museum’s collection of helminth parasite occurrence records, consisting of over 18,000 unique host species and 27,000 unique helminth parasite species distributed across over 350 distinct terrestrial and aquatic localities. We find support for latitudinal gradients in parasite diversity and a strong relationship between host and parasite diversity at the global scale. Helminth species diversity–area relationships were not detectable as a function of host body mass, but larger geographic areas supported higher parasite richness, potentially mediated through higher host richness. Our findings indicate that helminth parasites may obey some of the macroecological relationships found in free‐living species, suggesting that parasites may offer further support for the generality of these patterns, while offering interesting counterexamples for others. We conclude with a discussion of future directions and potential challenges in the newly emerging macroecology of infectious disease.


Leung, Jacqueline M., Sarah A. Budischak, Hao Chung The, Christina Hansen, Rowann Bowcutt, Rebecca Neill, Mitchell Shellman, P’ng Loke, and Andrea L. Graham. “Rapid Environmental Effects on Gut Nematode Susceptibility in Rewilded Mice.” PLoS Biology, vol. 16, issue 3, 2018, e2004108.

Abstract: Genetic and environmental factors shape host susceptibility to infection, but how and how rapidly environmental variation might alter the susceptibility of mammalian genotypes remains unknown. Here, we investigate the impacts of seminatural environments upon the nematode susceptibility profiles of inbred C57BL/6 mice. We hypothesized that natural exposure to microbes might directly (e.g., via trophic interactions) or indirectly (e.g., via microbe-induced immune responses) alter the hatching, growth, and survival of nematodes in mice housed outdoors. We found that while C57BL/6 mice are resistant to high doses of nematode (Trichuris muris) eggs under clean laboratory conditions, exposure to outdoor environments significantly increased their susceptibility to infection, as evidenced by increased worm burdens and worm biomass. Indeed, mice kept outdoors harbored as many worms as signal transducer and activator of transcription 6 (STAT6) knockout mice, which are genetically deficient in the type 2 immune response essential for clearing nematodes. Using 16S ribosomal RNA sequencing of fecal samples, we discovered enhanced microbial diversity and specific bacterial taxa predictive of nematode burden in outdoor mice. We also observed decreased type 2 and increased type 1 immune responses in lamina propria and mesenteric lymph node (MLN) cells from infected mice residing outdoors. Importantly, in our experimental design, different groups of mice received nematode eggs either before or after moving outdoors. This contrasting timing of rewilding revealed that enhanced hatching of worms was not sufficient to explain the increased worm burdens; instead, microbial enhancement and type 1 immune facilitation of worm growth and survival, as hypothesized, were also necessary to explain our results. These findings demonstrate that environment can rapidly and significantly shape gut microbial communities and mucosal responses to nematode infections, leading to variation in parasite expulsion rates among genetically similar hosts.

Cao, Yu, Hualing Pi, Pete Chandrangsu, Yongtao Li, Yuqi Wang, Han Zhou, Hanqin Xiong, John D. Helmann, and Yanfei Cai. “Antagonism of Two Plant-Growth Promoting Bacillus velezensis Isolates Against Ralstonia solanacearum and Fusarium oxysporum.” Scientific Reports, vol. 8, 2018, 4360.

Abstract: Plant growth promoting rhizobacteria (PGPR) provide an effective and environmentally sustainable method to protect crops against pathogens. The spore-forming Bacilli are attractive PGPR due to their ease of storage and application. Here, we characterized two rhizosphere-associated Bacillus velezensis isolates (Y6 and F7) that possess strong antagonistic activity against Ralstonia solanacearum and Fusarium oxysporum under both laboratory and greenhouse conditions. We identified three lipopeptide (LP) compounds (surfactin, iturin and fengycin) as responsible for the antimicrobial activity of these two strains. We further dissected the contribution of LPs to various biological processes important for rhizosphere colonization. Although either iturin or fengycin is sufficient for antibacterial activity, cell motility and biofilm formation, only iturin plays a primary role in defense against the fungal pathogen F. oxysporum. Additionally, we found that LP production is significantly stimulated during interaction with R. solanacearum. These results demonstrate the different roles of LPs in the biology of B. velezensis and highlight the potential of these two isolates as biocontrol agents against phytopathogens.


Chandrangsu, Pete, Vu Van Loi, Haike Antelmann, and John D. Helmann. “The Role of Bacillithiol in Gram-Positive Firmicutes.” Antioxidants & Redox Signaling, vol. 28, no. 6, 2018, pp. 445-462.

Abstract: Since the discovery and structural characterization of bacillithiol (BSH), the biochemical functions of BSH-biosynthesis enzymes (BshA/B/C) and BSH-dependent detoxification enzymes (FosB, Bst, GlxA/B) have been explored in Bacillus and Staphylococcus species. It was shown that BSH plays an important role in detoxification of reactive oxygen and electrophilic species, alkylating agents, toxins, and antibiotics. More recently, new functions of BSH were discovered in metal homeostasis (Zn buffering, Fe-sulfur cluster, and copper homeostasis) and virulence control in Staphylococcus aureus. Unexpectedly, strains of the S. aureus NCTC8325 lineage were identified as natural BSH-deficient mutants. Modern mass spectrometry-based approaches have revealed the global reach of protein S-bacillithiolation in Firmicutes as an important regulatory redox modification under hypochlorite stress. S-bacillithiolation of OhrR, MetE, and glyceraldehyde-3-phosphate dehydrogenase (Gap) functions, analogous to S-glutathionylation, as both a redox-regulatory device and in thiol protection under oxidative stress. Although the functions of the bacilliredoxin (Brx) pathways in the reversal of S-bacillithiolations have been recently addressed, significantly more work is needed to establish the complete Brx reduction pathway, including the major enzyme(s), for reduction of oxidized BSH (BSSB) and the targets of Brx action in vivo. Despite the large number of identified S-bacillithiolated proteins, the physiological relevance of this redox modification was shown for only selected targets and should be a subject of future studies. In addition, many more BSH-dependent detoxification enzymes are evident from previous studies, although their roles and biochemical mechanisms require further study. This review of BSH research also pin-points these missing gaps for future research.


Patel, Vaidehi, Qun Wu, Pete Chandrangsu, and John D. Helmann. “A Metabolic Checkpoint Protein GlmR is Important for Diverting Carbon into Peptidoglycan Biosynthesis in Bacillus subtilis.” PLoS Genetics, vol. 14, no. 9, 2018, e1007689.

Abstract: The Bacillus subtilis GlmR (formerly YvcK) protein is essential for growth on gluconeogenic carbon sources. Mutants lacking GlmR display a variety of phenotypes suggestive of impaired cell wall synthesis including antibiotic sensitivity, aberrant cell morphology and lysis. To define the role of GlmR, we selected suppressor mutations that ameliorate the sensitivity of a glmRnull mutant to the beta-lactam antibiotic cefuroxime or restore growth on gluconeogenic carbon sources. Several of the resulting suppressors increase the expression of the GlmS and GlmM proteins that catalyze the first two committed steps in the diversion of carbon from central carbon metabolism into peptidoglycan biosynthesis. Chemical complementation studies indicate that the absence of GlmR can be overcome by provision of cells with N-acetylglucosamine (GlcNAc), even under conditions where GlcNAc cannot re-enter central metabolism and serve as a carbon source for growth. Our results indicate that GlmR facilitates the diversion of carbon from the central metabolite fructose-6-phosphate, which is limiting in cells growing on gluconeogenic carbon sources, into peptidoglycan biosynthesis. Our data suggest that GlmR stimulates GlmS activity, and we propose that this activation is antagonized by the known GlmR ligand and peptidoglycan intermediate UDP-GlcNAc. Thus, GlmR presides over a new mechanism for the regulation of carbon partitioning between central metabolism and peptidoglycan biosynthesis.

Coleman, Melissa and Eric Fortune. “Duet Singing in Plain-Tailed Wrens.” Current Biology, vol. 28, issue 11, 2018, pp. R643-R645.


Heston, Jonathan B., Joseph Simon IV, Nancy F. Day, Melissa J. Coleman, and Stephanie A. White. “Bidirectional Scaling of Vocal Variability by an Avian Cortico-Basal Ganglia Circuit.” Physiological Reports, vol. 6, issue 8, 2018, e13638.

Abstract: Behavioral variability is thought to be critical for trial and error learning, but where such motor exploration is generated in the central nervous system is unclear. The zebra finch songbird species offers a highly appropriate model in which to address this question. The male song is amenable to detailed measurements of variability, while the brain contains an identified cortico‐basal ganglia loop that underlies this behavior. We used pharmacogenetic interventions to separately interrogate cortical and basal ganglia nodes of zebra finch song control circuitry. We show that bidirectional manipulations of each node produce near mirror image changes in vocal control: Cortical activity promotes song variability, whereas basal ganglia activity promotes song stability. Furthermore, female conspecifics can detect these pharmacogenetically elicited changes in song quality. Our results indicate that cortex and striatopallidum can jointly and reciprocally affect behaviorally relevant levels of vocal variability, and point to endogenous mechanisms for its control.

Milton, John G., Tamas Insperger, Walter Cook, David Money Harris, and Gabor Stepan. “Microchaos in Human Postural Balance: Sensory Dead Zones and Sampled Time-Delayed Feedback.” Physical Review, vol. 98, 2018, 022223.

Abstract: Models for the stabilization of an inverted pendulum figure prominently in studies of human balance control. Surprisingly, fluctuations in measures related to the vertical displacement angle for quietly standing adults with eyes closed exhibit chaos. Here we show that small-amplitude chaotic fluctuations (“microchaos”) can be generated by the interplay between three essential components of human neural balance control, namely time-delayed feedback, a sensory dead zone, and frequency-dependent encoding of force. When the sampling frequency of the force encoding is decreased, the sensitivity of the balance control to changes in the initial conditions increases. The sampled, time-delayed nature of the balance control may provide insights into why falls are more common in the very young and the elderly.

Heston, Jonathan B., Joseph Simon IV, Nancy F. Day, Melissa J. Coleman, and Stephanie A. White. “Bidirectional Scaling of Vocal Variability by an Avian Cortico-Basal Ganglia Circuit.” Physiological Reports, vol. 6, issue 8, 2018, e13638.

Abstract: Behavioral variability is thought to be critical for trial and error learning, but where such motor exploration is generated in the central nervous system is unclear. The zebra finch songbird species offers a highly appropriate model in which to address this question. The male song is amenable to detailed measurements of variability, while the brain contains an identified cortico‐basal ganglia loop that underlies this behavior. We used pharmacogenetic interventions to separately interrogate cortical and basal ganglia nodes of zebra finch song control circuitry. We show that bidirectional manipulations of each node produce near mirror image changes in vocal control: Cortical activity promotes song variability, whereas basal ganglia activity promotes song stability. Furthermore, female conspecifics can detect these pharmacogenetically elicited changes in song quality. Our results indicate that cortex and striatopallidum can jointly and reciprocally affect behaviorally relevant levels of vocal variability, and point to endogenous mechanisms for its control.

Chung, Deanna M., Elise Ferree, Dawn M. Simon, and Pamel J. Yeh. “Patterns of Bird-Bacteria Associations.” EcoHealth, vol. 15, issue 3, 2018, pp. 627-641.

Abstract: Birds, with their broad geographic ranges and close association with humans, have historically played an important role as carriers of human disease and as reservoirs for drug-resistant bacteria. Here, we examine scientific literature over a 15-year timespan to identify reported avian-bacterial associations and factors that may impact zoonotic disease emergence by classifying traits of bird species and their bacteria. We find that the majority of wild birds studied were migratory, in temperate habitats, and in the order Passeriformes. The highest diversity of bacteria was found on birds in natural habitats. The most frequently reported bacteria were Escherichia coli, Salmonella enterica, and Campylobacter jejuni. Of the bacteria species reported, 54% have shown pathogenicity toward humans. Percentage-wise, more pathogens were found in tropical (vs. temperate) habitats and natural (vs. suburban, urban, or agricultural) habitats. Yet, only 22% were tested for antibiotic resistance, and of those tested, 75% of bacteria species were resistant to at least one antibiotic. There were no significant patterns of antibiotic resistance in migratory versus non-migratory birds, temperate versus tropical areas, or different habitats. We discuss biases in detection and representation, and suggest a need for increased sampling in non-temperate zones and in a wider range of avian species.


Ferree, Elise, Stephen Johnson*, Daniella Barraza*, Emma Crabo*, Jenna Florio*, Haley Godtfredsen*, Kennedy Holland*, Kanyarat Jitmana*, and Kaya Mark*. “Size-Dependent Variability in the Formation and Trade-Offs of Facultative Aggregations in Golden Orb-Web Spiders (Nephila clavipes).” Behavioral Ecology and Sociobiology, vol. 72, 2018, pp. 157-170.

Abstract: The vast majority (> 99.99%) of spiders are solitary, but in some species, individuals form stable groups or, alternatively, looser aggregations that fluctuate over space and time. While previous work has documented trade-offs associated with being part of intraspecific groups, rather than being solitary, we know less about why grouping behavior would be facultative. Residing in a group can reduce predation risk, but also lead to competition for food, and we hypothesized that variation in these trade-offs could provide insights into the optional nature of clustering. We used a Costa Rican population of golden orb-web spiders, Nephila clavipes, to ask two questions. First, we tested whether a spider’s size influenced the trade-offs of clustering, and second, whether inter-annual variation in predator and prey abundance could help explain clustering patterns. We also examined the process of cluster formation and dissolution in relation to spider size. Data collected on over 1500 spiders over 4 years indicated that in each year, small spiders experienced the greatest reduction in predation if clustered and also were most likely to initiate aggregations. Overall rates of predation varied significantly among years, and small spiders were most likely to cluster in the year with highest predation. We also detected a cost of clustering in the form of reduced prey capture, but only in years with relatively high overall prey acquisition. Together, these findings suggest that trade-offs that vary individually and over time could influence a spider’s decision to cluster and, hence, explain the facultative nature of aggregating in this population.

Finseth, Findley R., and Richard G. Harrison. “Genes Integral to the Reproductive Function of Male Tissues Drive Heterogeneity in Evolutionary Rate in Japanese Quail.” Genes: Genomes: Genetics, vol. 8, no. 1, 2018, pp. 39-51.

Abstract: Early comparative genomics studies originally uncovered a non-intuitive pattern - genes involved in reproduction appeared to evolve more rapidly than other classes of genes. Currently, however, the emerging consensus is that genes encoding reproductive proteins evolve under variable selective pressures, producing more heterogeneous divergence patterns than previously appreciated. We investigate a facet of that heterogeneity and explore the factors that drive male reproductive tissue-based heterogeneity in evolutionary rates. In Japanese quail (Coturnix japonica), genes with enriched expression in the testis evolve much more rapidly than those enriched in the foam gland, a novel gland that secretes an airy foam males transfer to females during mating. We compared molecular evolutionary patterns among 1) genes with induced expression in breeding versus wintering conditions for both tissues and 2) genes that encode foam proteins versus those with varying degrees of expression specificity in the foam gland. We report two major findings. First, genes up-regulated in breeding condition testis evolve exceptionally rapidly, while those induced in breeding condition foam glands evolve slowly. These differences hold even after correcting for hormonally-dependent gene expression and chromosomal location. Second, genes encoding foam proteins are extremely conserved in terms of gene identity and sequence. Together, these finding suggest that genes involved in the reproductive function of each tissue drive the marked rate heterogeneity.

Gilman, Sarah E. and Rhiannon L. Rognstad. “Influence of Food Supply and Shore Height on the Survival and Growth of the Barnacle Balanus glandula (Darwin).” Journal of Experimental Marine Biology and Ecology, vol. 498, 2018, pp. 32-38.

Abstract: The contribution of energy limitation to patterns of intertidal zonation and vertical range limits is not well understood. Higher vertical positions on an intertidal shore are typically associated with greater temperature and desiccation stress during emersion; yet, organisms at higher shore heights also experience reduced feeding time and thus also face greater energy limitation than their lower shore counterparts. Disentangling the roles of abiotic stress and food limitation is critical to accurately predicting intertidal species' responses to climate change. This experiment manipulated food supply and shore height for the intertidal barnacle Balanus glandula (Darwin 1854). Adults were maintained in the field for 39 days at one of four shore heights spanning the species' upper vertical range limit, with or without supplemental feeding during high tides. Higher shore animals showed significantly lower growth and higher mortality relative to those lower on the shore. Across all shore heights, fed animals had significantly higher overall growth (20–27% greater final body mass), but not survival, than animals in the control treatments. No significant interactions between height and feeding treatment were detected, although the benefits of supplemental feeding tended to be smaller at higher shore heights. Our results suggest that food limitation occurs across a large portion of B. glandula's vertical range and that it can influence the success of barnacles at and above the current upper vertical limit. As such, energy limitation may play an important role in the vertical limits of many high intertidal species, and in distributional limits more broadly.

Friedman, Eric J. and Adam S. Landsberg. “Duality and Nonlinear Graph Laplacians.” Theoretical Computer Science, vol. 713, 2018, pp. 21-30.

Abstract: In this paper we show that a recent nearly linear time algorithm for solving a system of equations arising from a graph Laplacian can be extended to a large class of nonlinear systems of equations, based on a nonlinear generalization of the graph Laplacian. This result follows from a nonlinear generalization of the notable duality between graph Laplacians and electrical flows. Beyond providing a fast algorithm for a class of nonlinear sets of equations, our work highlights the robustness of spectral graph theory and suggests new directions for research in spectral graph theory. Specifically, we present an iterative algorithm for solving a class of nonlinear system of equations arising from a nonlinear generalization of the graph Laplacian in Õ (k2m log(kn/ε)) iterations, where k is a measure of nonlinearity, n is the number of variables, m is the number of nonzero entries in the generalized graph Laplacian L, is the solution accuracy and Õ () neglects (non-leading) logarithmic terms. This algorithm is a natural nonlinear extension of the one in Kelner et al. (2013), which solves a linear Laplacian system of equations in nearly linear time. Unlike the linear case, in the nonlinear case each iteration takes Õ (n) time so the total running time is Õ (k2mn log(kn/ε)). For sparse graphs with m = O(n) and fixed k this nonlinear algorithm is Õ (n2 log(n/ε)) which is slightly faster than standard methods for solving linear equations, which require approximately O (n2.38) time.

Liu, Mira D*., Elliot A. Warner*, Charlotte E. Morrissey*, Caitlyn W. Fick*, Taia S. Wu*, Marya Y. Ornelas*, Gabriela V. Ochoa*, Brendan S. Zhang, Colin M. Rathbun, William B. Porterfield, Jennifer A. Prescher, and Aaron M. Leconte. “Statistical Coupling Analysis-Guided Library Design for the Discovery of Mutant Luciferases.” Biochemistry, vol. 57, 2018, pp. 663-671.

Abstract: Directed evolution has proven to be an invaluable tool for protein engineering; however, there is still a need for developing new approaches to continue to improve the efficiency and efficacy of these methods. Here, we demonstrate a new method for library design that applies a previously developed bioinformatic method, Statistical Coupling Analysis (SCA). SCA uses homologous enzymes to identify amino acid positions that are mutable, functionally important, and engage in synergistic interactions between amino acids. We use SCA to guide a library of the protein luciferase and demonstrate that, in a single round of selection, we can identify luciferase mutants with several valuable properties. Specifically, we identify luciferase mutants that possess both red-shifted emission spectra and improved stability relative to the wild type enzyme. We also identify luciferase mutants that possess a >50-fold change in specificity for modified luciferins. To understand the mutational origin of these improved mutants, we demonstrate the role of mutations at N229, S239, and G246 in unnatural function. These studies show that SCA can be used to guide library design and rapidly identify synergistic amino acid mutations from a small library.


External Grant: CAREER Award (National Science Foundation), "Development of DNA Polymerases Capable of High Fidelity Modified DNA Synthesis,” Principal Investigator: Aaron Leconte, $400,000 (2018-2023).

Abstract: DNA is widely known as the material that encodes information in all life forms. Besides this role, DNA is also one of the most valuable tools in modern biotechnology. Foundational technologies, such as the polymerase chain reaction and DNA sequencing, as well as emerging technologies, such as DNA-encoded drug discovery, rely on the unique functions of DNA. However, the usefulness of DNA-based tools is limited by DNA's susceptibility to destruction in a biological environment. With this award, the Chemistry of Life Processes Program in the Chemistry Division is funding Dr. Aaron Leconte from the W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges to develop proteins that can synthesize chemically-modified forms of DNA that are more stable than natural DNA in a biological environment. Consequently, the modified DNAs have the potential to expand the applications of DNA-based tools, such as high throughput DNA sequencing and synthetic biology used in a number of therapeutic and clinical diagnostics. Such research may benefit society by improving human health. Professor Leconte integrates research experiences in laboratory courses for undergraduate students to prepare these students for STEM graduate studies and careers. He is also developing videos that document the research experiences of current and former undergraduate students that can be used to inspire and attract more students to STEM studies.

Lundberg, Joyce, Charles Brewer-Carías, and Donald A. McFarlane. “On Biospeleothems from a Venezuelan Tepui Cave: U-Th Dating, Growth Rates, and Morphology.” International Journal of Speleology, vol. 47, issue 3, 2018, pp. 361-378.

Abstract: Seven silica biospeleothems from Cueva Charles Brewer, Chimantá Plateau, Venezuela have been successfully U-Th dated despite very low U and high detrital Th concentrations. Growth rates are low, between ~100 to ~800 μm/ka, and are greater closer to water level. Dates in unaltered material are in good stratigraphic order, but secondary silicification may compromise the U-Th system, yielding unreliable sequences of ages. Detritally-enriched layers correlate with global climate cycles of the Late Quaternary, in particular the cooler, drier phases of MIS 5d, 5a, and 4. SEM studies indicate that the peloidal material is made up of silica nano-particles assembled to form hollow tubules ~1 μm in diameter. Secondary silicification inside and outside the tubules fills most of the pores. Barite crystals are deposited close to the silicified core material. Chemical analyses suggest that the white peloidal material is deposited by stream-generated foam, while the silicified material and dark core material are closer to rock composition.


McFarlane, Donald A and Joyce Lundberg. “New Records of Guano-Associated Minerals from Caves in Northwest Borneo.” International Journal of Speleology, vol. 47, issue 2, 2018, pp. 119-126.

Abstract: Recent studies of ancient bat guano deposits in the caves of Gunung Mulu National Park and Niah National Park, Sarawak, Malaysia, have resulted in noteworthy records of phosphate minerals from these environments, including variscite, nano-particulate silica, fluorapatite, and niter.


McFarlane, Donald A., Joyce Lundberg, and Alan Gray. “A Pleistocene Horse from Upper Canada Cave, West Mendip, UK, and the Lost Cave of Hutton.” Cave and Karst Science, vol. 45, issue 2, 2018, pp. 62-66.

Abstract: Excavations at Upper Canada Cave, West Mendip, UK, have yielded bones of a Pleistocene horse, a radiocarbon date on the collagen returning 21,170 ±70 rcyBP (25,498 ±219 cal BP) which overlaps the Last Glacial Maximum in Britain. This date, some 8 kyr younger than previous finds, adds to the data on horses in Britain after the Last Interglacial. The confused history of the lost bone caves of Hutton Hill is reviewed on the basis of these Pleistocene remains, the morphology of the cave, and evidence of 18th century mining. Also, the timing and nature of the Hutton Hill cave faunal deposits are re-interpreted.


External grant: McFarlane, Donald A. “Plumbing the Depths of Hades; Bathymetry of the Kelimutu Crater Lakes, Indonesia, by Autonomous Surface Vehicle.” National Geographic Society. $11,368.00.

Abstract: Kelimutu volcano, Flores (Indonesia), is famous for its trio of volcanic lakes. Their fame derives in large part from the markedly different colors of these closely adjacent lakes, which in turn reflect differences in chemistry and probably depth. At least two of the three lakes are volcanically active, their chemistry dominated by magmatically-derived volatiles - notably sulphur dioxide and hydrogen chloride, resulting in very acidic conditions. The lakes' depths are poorly known and no bathymetric survey has ever been produced. Active crater lakes are inherently unstable, and their large volumes and toxic contents can make them hazardous to local communities. At the same time, warm (or hot) active crater lakes provide valuable windows into changes in the geothermal heat flux and can provide important insights and warnings for volcanic hazard monitoring. For both these reasons, active crater lakes have received a good deal of scientific attention. Lake bathymetry is necessary to establish lake volume, and accurate lake volume is needed for the heat-flux calculations that can provide insights into volcanic activity. When these lakes are quiescent, investigators have ventured onto them in a variety of boats and rafts, and more recently, have used sonar equipment to map their depths. However, when, as at Kelimutu, these lakes are subject to frequent phreatomagmatic eruptions, or are completely surrounded by precipitous cliffs, conventional boating becomes impractically hazardous. In response to this problem, we have developed, built and tested a unique autonomous, sonar equipped surface vehicle (ASV). Using relatively inexpensive, off-the-shelf components and open source software, the ASV is small enough to be carried by a single person across physically challenging terrain and is capable of generating detailed bathymetric profiles in extremely hostile conditions. Laguna Caliente, Volcan Poás (Costa Rica), which currently has a surface temperature of 55° C, a pH of 0.5, and is experiencing near-constant (< 1 hr intervals) phreatomagmatic eruptions (August 2016) was our first test site. We now propose to deploy our sonar-ASV unit into each of the three Kelimutu crater lakes and generate detailed bathymetric, thermal, pH and sediment maps of their structure. The refined volumetric calculations that we expect to produce will provide valuable baseline data for volcano hazard assessment at this remarkable site.

Milton, John G., Tamas Insperger, Walter Cook, David Money Harris, and Gabor Stepan. “Microchaos in Human Postural Balance: Sensory Dead Zones and Sampled Time-Delayed Feedback.” Physical Review, vol. 98, 2018, 022223.

Abstract: Models for the stabilization of an inverted pendulum figure prominently in studies of human balance control. Surprisingly, fluctuations in measures related to the vertical displacement angle for quietly standing adults with eyes closed exhibit chaos. Here we show that small-amplitude chaotic fluctuations (“microchaos”) can be generated by the interplay between three essential components of human neural balance control, namely time-delayed feedback, a sensory dead zone, and frequency-dependent encoding of force. When the sampling frequency of the force encoding is decreased, the sensitivity of the balance control to changes in the initial conditions increases. The sampled, time-delayed nature of the balance control may provide insights into why falls are more common in the very young and the elderly.

Nishikawa, Kiisa C., Jenna A. Monroy, and Uzma Tahir. “Muscle Function from Organisms to Molecules.” Integrative and Comparative Biology, vol. 58, issue 2, 2018, pp. 194-206.

Abstract: Gaps in our understanding of muscle contraction at the molecular level limit the ability to predict in vivo muscle forces in humans and animals during natural movements. Because muscles function as motors, springs, brakes, or struts, it is not surprising that uncertainties remain as to how sarcomeres produce these different behaviors. Current theories fail to explain why a single extra stimulus, added shortly after the onset of a train of stimuli, doubles the rate of force development. When stretch and doublet stimulation are combined in a work loop, muscle force doubles and work increases by 50% per cycle, yet no theory explains why this occurs. Current theories also fail to predict persistent increases in force after stretch and decreases in force after shortening. Early studies suggested that all of the instantaneous elasticity of muscle resides in the cross-bridges. Subsequent cross-bridge models explained the increase in force during active stretch, but required ad hoc assumptions that are now thought to be unreasonable. Recent estimates suggest that cross-bridges account for only 12% of the energy stored by muscles during active stretch. The inability of cross-bridges to account for the increase in force that persists after active stretching led to development of the sarcomere inhomogeneity theory. Nearly all predictions of this theory fail, yet the theory persists. In stretch-shortening cycles, muscles with similar activation and contractile properties function as motors or brakes. A change in the phase of activation relative to the phase of length changes can convert a muscle from a motor into a spring or brake. Based on these considerations, it is apparent that the current paradigm of muscle mechanics is incomplete. Recent advances in our understanding of giant muscle proteins, including twitchin and titin, allow us to expand our vision beyond cross-bridges to understand how muscles contribute to the biomechanics and control of movement.

Racicot, Rachel A. “Dolphins, Porpoises, and Monodontids, Evolution.” Encyclopedia of Marine Mammals, 3rd edition, edited by Bernd Würsig, J.G.M. Thewissen, and Kit M. Kovacs. Academic Press/Elsevier, 2018, pp. 271-274.


Racicot, Rachel A., Simon A.F. Darroch, and Naoki Kohno. “Neuroanatomy and Inner Ear Labyrinths of the Narwhal, Monodon monoceros, and Beluga, Delphinapterus leucas (Cetacea: Monodontidae).” Journal of Anatomy, vol. 233, issue 4, 2018, pp. 421-439.

Abstract: Narwhals (Monodon monoceros) and belugas (Delphinapterus leucas) are the only extant members of the Monodontidae, and are charismatic Arctic‐endemic cetaceans that are at risk from global change. Investigating the anatomy and sensory apparatuses of these animals is essential to understanding their ecology and evolution, and informs efforts for their conservation. Here, we use X‐ray CT scans to compare aspects of the endocranial and inner ear labyrinth anatomy of extant monodontids and use the overall morphology to draw larger inferences about the relationship between morphology and ecology. We show that differences in the shape of the brain, vasculature, and neural canals of both species may relate to differences in diving and other behaviors. The cochleae are similar in morphology in the two species, signifying similar hearing ranges and a close evolutionary relationship. Lastly, we compare two different methods for calculating 90var – a calculation independent of body size that is increasingly being used as a proxy for habitat preference. We show that a ‘direct’ angular measurement method shows significant differences between Arctic and other habitat preferences, but angle measurements based on planes through the semicircular canals do not, emphasizing the need for more detailed study and standardization of this measurement. This work represents the first comparative internal anatomical study of the endocranium and inner ear labyrinths of this small clade of toothed whales.

Caspi, Tal*, Leo Estrada*, Anna V. Dowling*, Erin Su*, Maxim Leschinskiy*, André R.O. Cavalcanti, Edward J. Crane III, Colin R. Robins, and Wallace W. Meyer III. “Carbon and Nitrogen in the Topsoils of Inceptisols and Mollisols Under Native Sage Scrub and Non-Native Grasslands in Southern California.” Geoderma Regional, vol. 14, 2018, e00172.

Abstract: Understanding how invasive plants influence terrestrial carbon (C) and nitrogen (N) budgets is important in the context of global climate change. In southern California, type-conversion, a process in which native California sage scrub is type-converted to non-native grassland, is thought to negatively impact total C and N storage in surface soil horizons. To better understand the extent to which type-conversion influences regional nutrient storage, we examined C and N concentration (%) and quantity (g/m2 ), key soil properties, and microbial abundances and assemblages in sage scrub and non-native grassland habitats at three sites that represent varying environmental conditions. Type-conversion decreased soil C concentration, but did not influence C quantity. Differences between these two metrics were driven by a higher aggregate soil density in the non-native grassland habitat compared to the sage scrub habitat at one site. Contrary to previous studies, we found that type-conversion did not impact total N storage, even in a site previously found to have increased soil N quantities under sage scrub. Sage scrub habitats contained more active fungi, and differences in microbial assemblages were found between habitat types. Despite the vast number of microbial OTUs, habitats harbored unique communities of microbial taxa with some species consistently more abundant in one habitat type across sites. Our results demonstrate that type-conversion negatively impacts topsoil C concentrations, but accurate modeling of nutrient stocks requires consideration of the links between vegetation structure, soil properties such as soil density, and microbial communities that vary significantly across small spatial scales. Collectively, we demonstrate that invasive grasses alter microbial communities and reduce soil C storage capacity in the region.


Del Vecchio, Joanmarie*, Karl A. Lang*, Colin R. Robins, Chris P. McGuire, and Edward J. Rhodes. “Storage and Weathering of Landslide Debris in the Eastern San Gabriel Mountains, California, USA: Implications for Mountain Solute Flux.” Earth Surface Processes and Landforms, vol. 43, 2018, pp. 2724-2737.

Abstract: The weathering of silicate minerals in mountain landscapes provides a critical source of chemical solutes in the global biogeochemical cycles that sustain life on Earth. Observations from across Earth’s surface indicate that the greatest flux of chemical solute is derived from rapidly eroding landscapes, where landsliding often limits the development of a continuous soil cover. In this study, we evaluate how weathering of landslide debris deposits may supplement the chemical solute flux from rapidly eroding, bedrock-dominated landscapes. We present new measurements of depositional surface and soil morphology, soil geochemistry, and luminescence-based depositional ages from debris stored in Cow Canyon, a tributary to the East Fork of the San Gabriel River in the eastern San Gabriel Mountains of California. Cow Canyon deposits include locally derived debris emplaced by dry colluvial and debris flow processes. Deposits have planar, low-angle, sloping surfaces with soils exhibiting a greater degree of weathering than nearby soils formed on bedrock. A ~33–40 ka depositional age of Cow Canyon deposits exceeds the estimated recurrence time for the largest landslides in the San Gabriel Mountains, suggesting the stored landslide debris may be a persistent source of chemical solute in this landscape. To quantitatively explore the significance of landslide debris on the landscape solute flux, we predict the flux of chemical solute from bedrock and debris soils using a generic, time-dependent model of soil mineral weathering. Our modeling illustrates that debris soils may be a primary source of chemical solute for a narrow range of conditions delimited by the initial landslide debris porosity and the comparative soil age. Broadly, we conclude that while landslide debris may be an important local reservoir of chemical solute, it is unlikely to dominate the long-term solute flux from rapidly eroding, bedrock-dominated landscapes.


External grant: Robins, Colin R., 2018. "Paleoenvironmental Analysis of Ancient (Petro)calcic Soil Horizons: Disentangling Climatic, Geomorphic, and Biological Records in the Mojave Desert." Keck Geology Consortium REU Program, $31,776. Work supported by the National Science Foundation under Grant No. 1659322.

Abstract: This four-student project will test a suite of related hypotheses regarding the mineralogical, morphological, and geomorphic history of Mormon Mesa, NV, a 5-4 million year old Mojave Desert landform containing a complex carbonate-cemented (petrocalcic) soil profile. The Mormon Mesa soil serves as an important and fascinating analog for other calcic and petrocalcic soils around the world, as well as for paleosols in the stratigraphic record. This work will expand upon past research by using stable isotope geochemistry alongside detailed soil-stratigraphic and micromorphological descriptions to constrain the relative timing, climate context (e.g., pluvial versus interpluvial), formation history and durability of horizon components including laminae, concretions, and cemented matrix across the Mormon Mesa soil profile, and especially within its morphologically complex "massive" horizon (Brock and Buck, 2009). This project will produce the first stable isotope data from Mormon Mesa's unique soil, and it will afford important, publishable new tests of closed-system assumptions for the use of isotope geochemistry and geochronology in (petro)calcic horizons and paleosols worldwide

Snell, Katherine*, Isabelle Lopez*, Brandon Louie*, Roxanna Kiessling*, and Babak Sanii. “Drawing and Hydrophobicity-Patterning Long Polydimethylsiloxane Silicone Filaments.” Journal of Visualized Experiments, vol. 143, 2018, e58826.

Abstract: Polydimethylsiloxane (PDMS) silicone is a versatile polymer that cannot readily be formed into long filaments. Traditional spinning methods fail because PDMS does not exhibit long-range fluidity at melting. We introduce an improved method to produce filaments of PDMS by a stepped temperature profile of the polymer as it cross-links from a fluid to an elastomer. By monitoring its warm-temperature viscosity, we estimate a window of time when its material properties are amendable to drawing into long filaments. The filaments pass through a high-temperature tube oven, curing them sufficiently to be harvested. These filaments are on the order of hundreds of micrometers in diameter and tens of centimeters in length, and even longer and thinner filaments are possible. These filaments retain many of the material properties of bulk PDMS, including switchable hydrophobicity. We demonstrate this capability with an automated corona-discharge patterning method. These patternable PDMS silicone filaments have applications in silicone weavings, gas-permeable sensor components, and model microscale foldamers.

Foster, Kathleen L., Theodore Garland Jr., Lars Schmitz, and Timothy E. Higham. “Skink Ecomorphology: Forelimb and Hind Limb Lengths, But Not Static Stability, Correlate with Habitat Use and Demonstrate Multiple Solutions.” Biological Journal of the Linnean Society, vol. 125, issue 4, 2018, pp. 673-692.

Abstract: Interspecific variation in animal form, function and behaviour is often associated with habitat use, implying co-adaptation. Numerous studies of the ‘ecomorphs’ of Greater Antillean anoles support this generality, but no other lizard group has shown unambiguous, consistent relationships between limb length and habitat use. We tested for such relationships in lygosomine skinks, a speciose and geographically widespread group that exhibits tremendous variation in relative limb length, has repeatedly invaded terrestrial, saxicolous and arboreal habitats, and uses a narrow range of substrates within these habitats. We combined new morphometric measurements of museum specimens and data from the literature (N = 101 total species) to determine if biomechanically founded ecomorphological predictions could successfully describe relationships of habitat with body size and with size-adjusted limb size, while also testing for differences among clades and for interactions between habitat and clade. In phylogenetically informed statistical analyses, both body size and size-adjusted hind limb length had a significant clade-by-habitat interaction and this interaction approached statistical significance for size-adjusted forelimb lengths. The ratio of forelimb to hind limb length varied among clades. However, size-adjusted limb spans, stance area and static stability were unrelated to either habitat or clade. Overall, although limbs tend to be longer in climbing than in terrestrial skinks, the clade-dependent nature of this relationship suggests that lygosomine skinks have achieved multiple solutions to similar selective regimes. We propose that longer limbs are probably more important for active climbing than for static clinging, and suggest that climbing and clinging ability may be somewhat independent.


Iglesias, Teresa L., Alex Dornburg, Dan L. Warren, Peter C. Wainwright, Lars Schmitz, and Evan P. Economo. “Eyes Wide Shut: The Impact of Dim-Light Vision on Neural Investment in Marine Teleosts.” Journal of Evolutionary Biology, vol. 31, issue 8, 2018, pp. 1082-1092.

Abstract: Understanding how organismal design evolves in response to environmental challenges is a central goal of evolutionary biology. In particular, assessing the extent to which environmental requirements drive general design features among distantly related groups is a major research question. The visual system is a critical sensory apparatus that evolves in response to changing light regimes. In vertebrates, the optic tectum is the primary visual processing centre of the brain and yet it is unclear how or whether this structure evolves while lineages adapt to changes in photic environment. On one hand, dim‐light adaptation is associated with larger eyes and enhanced light‐gathering power that could require larger information processing capacity. On the other hand, dim‐light vision may evolve to maximize light sensitivity at the cost of acuity and colour sensitivity, which could require less processing power. Here, we use X‐ray microtomography and phylogenetic comparative methods to examine the relationships between diel activity pattern, optic morphology, trophic guild and investment in the optic tectum across the largest radiation of vertebrates—teleost fishes. We find that despite driving the evolution of larger eyes, enhancement of the capacity for dim‐light vision generally is accompanied by a decrease in investment in the optic tectum. These findings underscore the importance of considering diel activity patterns in comparative studies and demonstrate how vision plays a role in brain evolution, illuminating common design principles of the vertebrate visual system.


Schmitz, Lars and Timothy E. Higham. “Non-Uniform Evolutionary Response of Gecko Eye Size to Changes in Diel Activity Patterns.” Biology Letters, vol. 14, issue 5, 2018, 20180064.

Abstract: Geckos feature a large range of eye sizes, but what drives this phenotypic diversity is currently unknown. Earlier studies point towards diel activity patterns (DAPs) and locomotory mode, but phylogenetic comparative studies in support of the proposed adaptive mode of eye evolution are lacking. Here, we test the hypothesis of DAPs as the driver of eye size evolution with a dataset on 99 species of gecko. Results from phylogenetic generalized least-square analysis (PGLS) and multivariate model-fitting reveal smaller eyes in diurnal geckos consistent with different phenotypic optima. However, Bayesian analyses of selective regime shifts demonstrate that only two of nine transitions from nocturnal to diurnal activity are coupled with decreases in eye size, and two other regime shifts are not associated with DAP transitions. This non-uniform evolutionary response suggests that eye size is not the only functionally relevant variable. Evolutionary adaptations may therefore include different combinations of several traits (e.g. photoreceptors), all with the same functional outcome. Our results further demonstrate that DAP only partially explains eye size diversity in geckos. As open habitats favour the evolution of large eyes while obstructed habitats favour small eyes, the degree of habitat clutter emerges as another potential axis of eye diversification.


Smith, Stephanie M., Kenneth D. Angielczyk, Lars Schmitz, and Steve C. Wang. “Do Bony Orbit Dimensions Predict Diel Activity Pattern in Sciurid Rodents?” The Anatomical Record, vol. 301, issue 10, 2018, pp. 1774-1787.

Abstract: Diel activity pattern (DAP) is a key aspect of an animal's ecology, but it is difficult to infer when behavior cannot be directly observed, as in the fossil record. Various anatomical correlates have therefore been used to attempt to classify DAP. Eyeball dimensions are good predictors of DAP because they relate directly to light sensitivity of the eye. Osteological characters, such as scleral ring dimensions, are also reliable proxies, but bony orbit dimensions alone have proven less reliable because soft tissues other than the eyeball can affect orbit size and shape. However, it would be useful if bony orbit dimensions could be used to determine DAP, particularly for mammals, which have no scleral ring, and nonmammalian synapsids, which infrequently preserve scleral rings. We investigated the possibility of predicting DAP in sciurids (Mammalia: Rodentia: Sciuridae) using orbit measurements and other cranial dimensions, and a variety of quantitative methods, including phylogenetic flexible discriminant analysis, classification trees, and logistic regression. The latter two methods do not require a priori assignment of DAP and therefore reflect the situation in a fossil data set. We find that although there are some interfering phylogenetic factors, nocturnal and non‐nocturnal sciurids can be differentiated from one another with over 80% accuracy using all methods investigated here; attempts to differentiate crepuscular animals from nocturnal and diurnal species proved much less successful. Our results indicate that these analyses offer several viable options for predicting DAP in the fossil record, but such analyses should be conducted in a phylogenetic context whenever possible. 

Thomson, Diane M., Jonas W. Kwok*, and Emily L. Schultz*. “Extreme Draught Alters Growth and Interactions with Exotic Grasses, But Not Survival, For a California Annual Forb.” Plant Ecology, vol. 219, no. 6, 2018, pp. 705-717.

Abstract: Climate change will not only alter mean conditions, but increase the frequency and intensity of extreme events such as severe droughts. Yet the consequences of extreme drought for plant demography are poorly understood. We compared phenology, demographic rates and effects of competition with exotic grasses for the California annual forb Phacelia distans between a year with slightly below average precipitation (2011–2012) and one in extreme drought (2012–2013). We also contrasted these demographic responses with changes in seedling emergence rates and cover in the annual plant community. Early Phacelia mortality actually fell in the extreme drought year, as low October rainfall shifted germination to cooler conditions in November. Survival from mid December to flowering did not change between years. In contrast to expectations, competition with early emerging exotic annual grasses did not reduce Phacelia spring survival in 2012–2013. A shorter window for fall germination that reduced priority effects may explain this result. Yet the 2012–2013 growing season ended a month earlier than in 2011–2012, significantly reducing Phacelia size at flowering and inflorescence production. Community

External grant: Van Arnam, Ethan. American Society of Pharmacognosy Research Starter Grant: "Field Collection and Isolation of Microbial Symbionts of North American Fungus-Growing Ants to Enable Ecologically-Guided Antibiotic Discovery,” 2018, $5,000.

Abstract: Defensive symbioses, in which a microbe provides chemical defenses that protect its animal host against parasites or predation, are now known to be widespread but remain underexplored. These symbiotic relationships have much to teach us about the evolutionary origins and dissemination of antibiotics in the natural world and also provide rich opportunities for ecologically guided antibiotic discovery. In particular, the bacterial symbionts of North American fungus-growing ants have outstanding potential for delivering novel antifungals and antibacterials. This Starter Grant will enable fieldwork and microbial isolations from these ants to build a foundational collection of symbiotic bacteria and fungi for my laboratory, currently in its first year at the Keck Science Department. This starter grant will launch our ecologically-guided chemical discovery efforts. Future activity screening, bioassay-guided fractionation, and structural elucidation will reveal bioactive molecules from this collection.

Wiley, Emily A., Scott Horrell, Alyssa Yoshino*, Cara C. Schornak, Claire Bagnani*, and Douglas L. Chalker “Diversification of HP1-like Chromo Domain Proteins in Tetrahymena thermophila.” Eukaryotic Microbiology, vol. 65, issue 1, 2018, pp. 104-116.

Abstract: Proteins that possess a chromo domain are well known for their roles in heterochromatin assembly and maintenance. The Heterochromatin Protein 1 (HP1) family, with a chromo domain and carboxy-terminal chromo shadow domain, targets heterochromatin through interaction with histone H3 methylated on lysine 9 (H3K9me2/3). The structural and functional diversity of these proteins observed in both fission yeast and metazoans correlate with chromatin specialization. To expand these studies, we examined chromo domain proteins in the ciliate Tetrahymena thermophila, which has functionally diverse and developmentally-regulated heterochromatin domains. We identified thirteen proteins similar to HP1. Together they possess only a fraction of the possible chromo domain subtypes and most lack a recognizable chromo shadow domain. Using fluorescence microscopy to track chromatin localization of tagged proteins through the life cycle, we show evidence that in T. thermophila this family has diversified with biological roles in RNAi-directed DNA elimination, germline genome structure, and somatic heterochromatin. Those proteins with H3K27me3 binding sequence characteristics localize to chromatin in mature nuclei, whereas those with H3K9me2/3 binding characteristics localize to developing nuclei undergoing DNA elimination. Findings point to an expanded and diversified family of chromo domain proteins that parallels heterochromatin diversity in ciliates.

Light, Tricia*, Branwen Williams, Jochen Halfar, Alicia Hou, Zoltan Zajacz, Alexandra Tsay, and Walter Adey. “Advancing Mg/Ca Analysis of Coralline Algae as a Climate Proxy by Assessing LA-ICP-OES Sampling and Coupled Mg/Ca-δ18O Analysis.” Geochemistry, Geophysics, Geosystems, vol. 19, issue 9, 2018, pp. 2876-2894.

Abstract: High-latitude climate reconstructions are essential for discerning anthropogenic climate change from natural climate variability. Since observational high-latitude climate records are rare prior to the satellite era, climate proxies such as the coralline algae Clathromorphum compactum are needed to generate these reconstructions. C. compactum is distributed across the northern high latitudes and documents environmental variability in the magnesium-to-calcium ratio (Mg/Ca) and δ18O composition of its calcite skeleton. Therefore, paired Mg/Ca and δ18Oa nalyses in C. compactum are a promising new tool for reconstructing historic high-latitude climate change. Here a new method for C. compactum Mg/Ca analysis, laser ablation-inductively coupled plasma-optical emission spectroscopy (LA-ICP-OES), was verified through comparisons with parallel Mg/Ca transects using established techniques in a specimen from Labrador, Canada. Next, LA-ICP-OES Mg/Ca analysis in two specimens from Nunavut, Canada, was paired with δ18O analyses. While Mg/Ca data across all specimens captured seasonal sea surface temperature (SST) variability, Mg/Ca values differed in replicate transects within skeleton formed at the same time regardless of technique used. This reduces the effectiveness of C. compactum Mg/Ca as a SST proxy on interannual time scales. Mg/Ca values and δ18O composition differed between the two Nunavut specimens, and only one of them documented local SST, sea ice cover, and sea surface salinity. This indicates that climate archive verification is required for each unique coralline algal specimen. In the specimen from Nunavut verified here, paired Mg/Ca and δ18O analyses produced more robust sea ice cover/sea surface salinity reconstructions than δ18Oa analyses alone, supporting further development of this proxy system.


McMahon, Kelton W., Branwen Williams, Thomas P. Guilderson, Danielle S. Glynn, and Matthew D. McCarthy. “Calibrating Amino Acid δ13 C and δ15 N Offsets Between Polyp and Protein Skeleton to Develop Proteinaceous Deep-Sea Corals as Paleoceanographic Archives”. Geochimica et Cosmochimica Acta, vol. 220, 2018, 261-275.

Abstract: Compound-specific stable isotopes of amino acids (CSI-AA) from proteinaceous deep-sea coral skeletons have the potential to improve paleoreconstructions of plankton community composition, and our understanding of the trophic dynamics and biogeochemical cycling of sinking organic matter in the Ocean. However, the assumption that the molecular isotopic values preserved in protein skeletal material reflect those of the living coral polyps has never been directly investigated in proteinaceous deep-sea corals. We examined CSI-AA from three genera of proteinaceous deep-sea corals from three oceanographically distinct regions of the North Pacific: Primnoa from the Gulf of Alaska, Isidella from the Central California Margin, and Kulamanamana from the North Pacific Subtropical Gyre. We found minimal offsets in the δ13C values of both essential and non-essential AAs, and in the δ15N values of source AAs, between paired samples of polyp tissue and protein skeleton. Using an essential AA δ13C fingerprinting approach, we show that estimates of the relative contribution of eukaryotic microalgae and prokaryotic cyanobacteria to the sinking organic matter supporting deep-sea corals are the same when calculated from polyp tissue or recently deposited skeletal tissue. The δ15N values of trophic AAs in skeletal tissue, on the other hand, were consistently 3–4‰ lower than polyp tissue for all three genera. We hypothesize that this offset reflects a partitioning of nitrogen flux through isotopic branch points in the synthesis of polyp (fast turnover tissue) and skeleton (slow, unidirectional incorporation). This offset indicates an underestimation, albeit correctable, of approximately half a trophic position from gorgonin protein-based deep-sea coral skeleton. Together, our observations open the door for applying many of the rapidly evolving CSI-AA based tools developed for metabolically active tissues in modern systems to archival coral tissues in a paleoceanographic context.


External grant: LaVigne, Michèle (lead-PI), Branwen Williams, Aaron Strong, and Alan Wanamaker (co-PIs). Maine Sea Grant: “From Paleoceanography to Policy: Applying Historical Coastal pH Baselines from Long-Lived Shells and Skeletons to Contemporary Shellfish Aquaculture.” $42,546 to Branwen Williams, total award: $149,972, 2018-2020.

Abstract: We propose to provide the first historical baseline data on coastal pH in Maine in order to help address the potential impact of these pH changes on local commercial shellfish to inform management. This study will, for the first time, bring together leading researchers in Gulf of Maine paleoceanography, OA policy, monitoring, and biology in order to address the following questions: Is the Gulf of Maine more acidic today than it was prior to human development? Has Gulf of Maine pH spatial variability changed in the last 100 years? What are the biological implications of these changes on commercial shellfish (mussels, clams, oysters)?


External grant: Williams, Branwen. “Do Mangrove Forests Reduce Coastal Aquaculture Nutrient Pollution While Increasing Carbon Storage? A Case Study of a Thai Shrimp Farm-Mangrove Ecosystem.” National Geographic Society, $28,170, 2018-2019.

Abstract: Mangrove forests are deteriorating rapidly because of human pressures, despite the fact that these forests perform many functions that are beneficial to people. These functions include buffering of excess nutrients received from land-use activities up stream of the mangroves and storing carbon as organic matter, decreasing atmospheric carbon dioxide. However, few studies have evaluated the impact of excess nutrients on the capacity of mangrove forests to store this carbon. This is particularly true in tropical Southeast Asia, where mangrove forest conversion into aquaculture is prevalent; and this aquaculture significantly contributes excess nutrients and reducing water quality in the absence of mangroves. Fortunately, a King's Project in eastern Thailand established a mangrove forest downstream from shrimp farms. This location is the ideal site to ask the question: do aquaculture-derived nutrients support carbon storage in mangrove forests? To address this question, we propose to use a comprehensive suite of chemical tracers in the coupled shrimp farm-mangrove system to evaluate the impact of aquaculture runoff on mangrove nutrient dynamics. We will 1) characterize across multiple levels in the food web the relative contributions of carbon and nitrogen from shrimp-farm runoff, marine-derived nutrients, and in situ production and 2) use sediment cores to reconstruct the relative changes of these nutrient sources and carbon storage through time. Results will quantify aquaculture runoff into the mangrove forest and any associated elevated carbon storage across space and through time, providing baseline information for future developments in aquaculture development/mangrove conservation policy in Southeast Asia.