2016 CMC Faculty Publications and Grants

W.M. Keck Science Department

Chen, A., C. Chiu, S. Khan, R.D. Spence, and D. Prober. “QRFP and its receptors regulate locomotor activity and sleep in zebrafish.” Journal of Neuroscience, vol. 36, 2016, 1823-1840.

Abstract: The hypothalamus plays an important role in regulating sleep, but few hypothalamic sleep-promoting signaling pathways have been identified. Here we demonstrate a role for the neuropeptide QRFP (also known as P518 and 26RFa) and its receptors in regulating sleep in zebrafish, a diurnal vertebrate. We show that QRFP is expressed in ∼10 hypothalamic neurons in zebrafish larvae, which project to the hypothalamus, hindbrain, and spinal cord, including regions that express the two zebrafish QRFP receptor paralogs. We find that the overexpression of QRFP inhibits locomotor activity during the day, whereas mutation of qrfp or its receptors results in increased locomotor activity and decreased sleep during the day. Despite the restriction of these phenotypes to the day, the circadian clock does not regulate qrfp expression, and entrained circadian rhythms are not required for QRFP-induced rest. Instead, we find that QRFP overexpression decreases locomotor activity largely in a light-specific manner. Our results suggest that QRFP signaling plays an important role in promoting sleep and may underlie some aspects of hypothalamic sleep control. SIGNIFICANCE STATEMENT The hypothalamus is thought to play a key role in regulating sleep in vertebrate animals, but few sleep-promoting signaling pathways that function in the hypothalamus have been identified. Here we use the zebrafish, a diurnal vertebrate, to functionally and anatomically characterize the neuropeptide QRFP. We show that QRFP is exclusively expressed in a small number of neurons in the larval zebrafish hypothalamus that project widely in the brain. We also show that QRFP overexpression reduces locomotor activity, whereas animals that lack QRFP signaling are more active and sleep less. These results suggest that QRFP signaling participates in the hypothalamic regulation of sleep.

Tang, Zhaohua and Gretchen Edwalds-Gilbert. “Nucleic Acid and Protein Sample Preparation from Yeasts.” Sample Preparation Techniques for Soil, Plant, and Animal Samples, Springer Protocols Handbooks, edited by M. Micic, Springer Science+Business Media New York, 2016.

Abstract: The budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe, as unicellular eukaryotes, are popular model systems. They have greatly contributed to our understanding about biological principles of complex organisms. Although the two yeasts differ from one another in a range of features, both are genetically tractable, amenable to classical, molecular   genetics, and genomic-scale analyses. S. cerevisiae and S. pombe are ideal experimental systems for undergraduates learning about genetics and molecular and cell biology in laboratory course settings, as well as in research environments, because of their non-pathogenic nature, rapid reproduction cycles and suitability for diverse approaches and different types of courses. Both yeasts offer the opportunity for students to pursue inquiry-based learning. To facilitate students gaining knowledge in the laboratory, this chapter provides a guide for carrying out frequently used procedures for DNA isolation, RNA extraction, and protein lysate preparation from both S. cerevisiae and S. pombe yeast cells. Aimed at students learning through performing the experiments, each protocol also includes a brief explanation about relevant molecular concepts underlining the methods described, along with stepwise instructions.

Baker, J. and E.D. Ferree. “Foraging ontogeny in a suburban population of black phoebes (Sayornis nigricans).” Wilson Journal of Ornithology, 128, 2016, 368-377.

Abstract: The ability to forage successfully is intimately tied to juvenile survivorship in many avian species, yet may take varying amounts of time to develop in young birds. We examined the development of foraging skills in juvenile Black Phoebes (Sayornis nigricans). Black Phoebes are insectivorous and forage by scanning for and then pursuing potential prey while in flight. We hypothesized that before they disperse, approximately two months after fledging, juvenile phoebes should forage as successfully and with the same mechanics as adults. Because foraging proficiency should affect time allocation, we also compared how juveniles and adults divided their time among foraging and other activities. We found that by seven weeks of age juvenile phoebes foraged as successfully as adults, however, they spent more time flying and less time perched. In line with their gained efficiency, by around six weeks of age juvenile scanning rates and foraging flight durations were similar to adults. Overall, these results confirm that the complex foraging behaviors of Black Phoebes develop in juveniles in a relatively short time period. The development of proficient foraging abilities, however, appears to precede effective time allocation, which must occur sometime after independence or dispersal.


Dickinson, J.L, C. Akçay, E.D. Ferree, and C.A. Stern. “A hierarchical analysis of incest avoidance in a cooperative breeder.” Behavioral Ecology 27, 2016, 1132-1140.

Abstract: When animals live near family members, this creates potential for incest and inbreeding depression, especially with unfamiliar kin. We examined incest avoidance when birds paired in kin groups and after dispersal in western bluebirds, Sialia mexicana, a cooperative breeder with a persistent, but low frequency of adult males helping at the nest. During their first winter, sons usually live in family groups comprised of parents, brothers, immigrant females, and more rarely, immigrant males and philopatric sisters. Sons usually pair with females that have joined their winter group, although some pair with females they encounter after dispersal. Incestuous pairing among relatives with relatedness ≥0.25 rarely occurred in either context, even considering extrapair fertilizations and other sources of unfamiliar kin. Sons pairing in their winter groups preferentially mated with immigrant females and actively avoided pairing with relatives. After dispersal into kin neighborhoods in spring, active incest avoidance was still required to explain low levels of incest with females within 600 m (2–3 territories) of where sons first bred, whereas absence of incest over larger distances could be explained by random mating. The probability of encountering a female relative within 600 m of where a male settled declined rapidly with dispersal distance to near zero for males dispersing 2 km from home. Although recognition is required to avoid incest when pairing in winter groups or settling near home, female-biased dispersal reduces likelihood of incest to near zero, even when males disperse relatively short distances (e.g., 2 km) from where they were born.


Dickinson, J.L., C. Akçay, E. Ferree, and A. Stern. “Western bluebirds: lessons from a marginal cooperative breeder. “Cooperative Breeding in Vertebrates: Studies in Ecology, Evolution and Behavior, edited by W. Koenig and J. Dickinson, Cambridge University Press, 2016, 19-38.

Case, A. L, F. R. Finseth, C.M. Barr, and Lila Fishman. “Selfish evolution of cytonuclear hybrid incompatibility in Mimulus.” Proceedings of the Royal Society B Vol.283, No. 1838, 2016.

Abstract: Intraspecific coevolution between selfish elements and suppressors may promote interspecific hybrid incompatibility, but evidence of this process is rare. Here, we use genomic data to test alternative models for the evolution of cytonuclear hybrid male sterility in Mimulus. In hybrids between Iron Mountain (IM) Mimulus guttatus × Mimulus nasutus, two tightly linked M. guttatus alleles (Rf1/Rf2) each restore male fertility by suppressing a local mitochondrial male-sterility gene (IM-CMS). Unlike neutral models for the evolution of hybrid incompatibility loci, selfish evolution predicts that the Rf alleles experienced strong selection in the presence of IM-CMS. Using whole-genome sequences, we compared patterns of population-genetic variation in Rf at IM to a neighbouring population that lacks IM-CMS. Consistent with local selection in the presence of IM-CMS, the Rf region shows elevated FST, high local linkage disequilibrium and a distinct haplotype structure at IM, but not at Cone Peak (CP), suggesting a recent sweep in the presence of IM-CMS. In both populations, Rf2 exhibited lower polymorphism than other regions, but the low-diversity outliers were different between CP and IM. Our results confirm theoretical predictions of ubiquitous cytonuclear conflict in plants and provide a population-genetic mechanism for the evolution of a common form of hybrid incompatibility.


Hendrick, M.F., F. R. Finseth, M. E. Mathiasson, K. A. Palmer, E. M. Broder, P. Breigenzer, and L. Fishman. “The genetics of extreme microgeographic adaptation: an integrated approach identifies a major gene underlying leaf trichome divergence in Yellowstone Mimulus guttatus”. Molecular Ecology 25, 2016, 5647-5662.

Abstract: Microgeographic adaptation provides a particularly interesting context for understanding the genetic basis of phenotypic divergence and may also present unique empirical challenges. In particular, plant adaptation to extreme soil mosaics may generate barriers to gene flow or shifts in mating system that confound simple genomic scans for adaptive loci. Here, we combine three approaches – quantitative trait locus (QTL) mapping of candidate intervals in controlled crosses, population resequencing (PoolSeq) and analyses of wild recombinant individuals – to investigate one trait associated with Mimulus guttatus (yellow monkeyflower) adaptation to geothermal soils in Yellowstone National Park. We mapped a major QTL causing dense leaf trichomes in thermally adapted plants to a <50-kb region of linkage Group 14 (Tr14) previously implicated in trichome divergence between independent M. guttatus populations. A PoolSeq scan of Tr14 region revealed a cluster of six genes, coincident with the inferred QTL peak, with high allele frequency differences sufficient to explain observed phenotypic differentiation. One of these, the R2R3 MYB transcription factor Migut.N02661, is a plausible functional candidate and was also strongly associated (r2 = 0.27) with trichome phenotype in analyses of wild-collected admixed individuals. Although functional analyses will be necessary to definitively link molecular variants in Tr14 with trichome divergence, our analyses are a major step in that direction. They point to a simple, and parallel, genetic basis for one axis of Mimulus guttatus adaptation to an extreme habitat, suggest a broadly conserved genetic basis for trichome variation across flowering plants and pave the way for further investigations of this challenging case of microgeographic incipient speciation.

Salomon, M.P., W.L. Li, C.K. Edlund, J. Morrison, B.K. Fortini, A.K. Win, D.V. Conti, D.C. Thomas, D. Duggan, D.D. Buchanan, M.A. Jenkins, J.L. Hopper, S. Gallinger, L. Le Marchand, P.A. Newcomb, G. Casey, and P. Marjoram. “GWASeq: targeted re-sequencing follow up to GWAS” BMC Genomics 17(1), 2016, 176.

Abstract: For the last decade the conceptual framework of the Genome-Wide Association Study (GWAS) has dominated the investigation of human disease and other complex traits. While GWAS have been successful in identifying a large number of variants associated with various phenotypes, the overall amount of heritability explained by these variants remains small. This raises the question of how best to follow up on a GWAS, localize causal variants accounting for GWAS hits, and as a consequence explain more of the so-called "missing" heritability. Advances in high throughput sequencing technologies now allow for the efficient and cost-effective collection of vast amounts of fine-scale genomic data to complement GWAS. We investigate these issues using a colon cancer dataset. After QC, our data consisted of 1993 cases, 899 controls. Using marginal tests of associations, we identify 10 variants distributed among six targeted regions that are significantly associated with colorectal cancer, with eight of the variants being novel to this study. Additionally, we perform so-called 'SNP-set' tests of association and identify two sets of variants that implicate both common and rare variants in the etiology of colorectal cancer. Here we present a large-scale targeted re-sequencing resource focusing on genomic regions implicated in colorectal cancer susceptibility previously identified in several GWAS, which aims to 1) provide fine-scale targeted sequencing data for fine-mapping and 2) provide data resources to address methodological questions regarding the design of sequencing-based follow-up studies to GWAS. Additionally, we show that this strategy successfully identifies novel variants associated with colorectal cancer susceptibility and can implicate both common and rare variants.


Schmit, S.L., F.R. Schumacher, C.K. Edlund, D.V. Conti, U. Ihenacho, P. Wan, D. Van Den Berg, G. Casey, B.K. Fortini, H.J. Lenz, T. Tusié-Luna, C.A. Aguilar-Salinas, H. Moreno Macías, A. Huerta-Chagoya, M.L. Ordóñez-Sánchez, R. Rodríguez-Guillén, I. Cruz-Bautista, M. Rodríguez-Torres, L.L. Muñóz-Hernández, O. Arellano-Campos, D. Gómez, U. Alvirde, C. González-Villalpando, M.E. González-Villalpando, L. Le Marchand, C.A. Haiman, and J.C. Figueiredo. “Genome-wide Association Study of Colorectal Cancer in Hispanics” Carcinogenesis 37(6), 2016, 547-556.

Abstract: Genome-wide association studies (GWAS) have identified 58 susceptibility alleles across 37 regions associated with the risk of colorectal cancer (CRC) with P < 5×10(-8) Most studies have been conducted in non-Hispanic whites and East Asians; however, the generalizability of these findings and the potential for ethnic-specific risk variation in Hispanic and Latino (HL) individuals have been largely understudied. We describe the first GWAS of common genetic variation contributing to CRC risk in HL (1611 CRC cases and 4330 controls). We also examine known susceptibility alleles and implement imputation-based fine-mapping to identify potential ethnicity-specific association signals in known risk regions. We discovered 17 variants across 4 independent regions that merit further investigation due to suggestive CRC associations (P < 1×10(-6)) at 1p34.3 (rs7528276; Odds Ratio (OR) = 1.86 [95% confidence interval (CI): 1.47-2.36); P = 2.5×10(-7)], 2q23.3 (rs1367374; OR = 1.37 (95% CI: 1.21-1.55); P = 4.0×10(-7)), 14q24.2 (rs143046984; OR = 1.65 (95% CI: 1.36-2.01); P = 4.1×10(-7)) and 16q12.2 [rs142319636; OR = 1.69 (95% CI: 1.37-2.08); P=7.8×10(-7)]. Among the 57 previously published CRC susceptibility alleles with minor allele frequency ≥1%, 76.5% of SNPs had a consistent direction of effect and 19 (33.3%) were nominally statistically significant (P < 0.05). Further, rs185423955 and rs60892987 were identified as novel secondary susceptibility variants at 3q26.2 (P = 5.3×10(-5)) and 11q12.2 (P = 6.8×10(-5)), respectively. Our findings demonstrate the importance of fine mapping in HL. These results are informative for variant prioritization in functional studies and future risk prediction modeling in minority populations.

Helmuth, B., F. Choi, A. Matzelle, J. L. Torossian, S. L. Morello, K. A. S. Mislan, L. Yamane, D. Strickland, P. L. Szathmary, S. E. Gilman, A. Tockstein, T. J. Hilbish, M. T. Burrows, A. M. Power, E. Gosling, N. Mieszkowska, C. D. G. Harley, M. Nishizaki, E. Carrington, B. Menge, L. Petes, M. M. Foley, A. Johnson, M. Poole, M. M. Noble, E. L. Richmond, M. Robart, J. Robinson, J. Sapp, J. Sones, B. R. Broitman, M. W. Denny, K. J. Mach, L. P. Miller, M. O’Donnell, P. Ross, G. E. Hofmann, M. Zippay, C. Blanchette, J. A. Macfarlan, E. Carpizo-Ituarte, B. Ruttenberg, C. E. Peña Mejía, C. D. McQuaid, J. Lathlean, C. J. Monaco, K. R. Nicastro, and G. Zardi. “Long-term, high frequency in situ measurements of intertidal mussel bed temperatures using biomimetic sensors.” Nature Scientific Data 3:160087, 2016.

Abstract: At a proximal level, the physiological impacts of global climate change on ectothermic organisms are manifest as changes in body temperatures. Especially for plants and animals exposed to direct solar radiation, body temperatures can be substantially different from air temperatures. We deployed biomimetic sensors that approximate the thermal characteristics of intertidal mussels at 71 sites worldwide, from 1998-present. Loggers recorded temperatures at 10–30 min intervals nearly continuously at multiple intertidal elevations. Comparisons against direct measurements of mussel tissue temperature indicated errors of ~2.0–2.5 °C, during daily fluctuations that often exceeded 15°–20 °C. Geographic patterns in thermal stress based on biomimetic logger measurements were generally far more complex than anticipated based only on ‘habitat-level’ measurements of air or sea surface temperature. This unique data set provides an opportunity to link physiological measurements with spatially- and temporally-explicit field observations of body temperature.

External grant: Wenzel, A. (PI); Leconte, A. (co-PI); Hatcher, M. (co-PI) “Acquisition of a Fluorimeter for Undergraduate Instruction and Research.” Ellen Browning Scripps Foundation; 8/2016; $20,000 + $20,000 institutional match; Keck Science Department, Claremont, CA

Abstract: Fluorescence is the molecular absorption of light energy at one wavelength and its nearly instantaneous re-emission at another, usually longer, wavelength. Some molecules fluoresce naturally, while others can be modified to make fluorescent compounds. The instrument used to measure fluorescence is called a fluorometer. A fluorometer generates the wavelength of light required to excite a compound of interest; it then selectively transmits the wavelength of light emitted, measuring the intensity of that light. Fluorometers allow for the acquisition and measure of a sample’s fluorescence, including its intensity, spectral wavelengths, and lifetime. The fluorescence of a sample can be an indirect probe of the sample's environment, describing solvent-solute interactions, inter- and intramolecular interactions, etc. Analytical measurements provided by fluorometers can be used in multiple applications including chemistry, biochemistry, medical research, pharmaceuticals, food science, environmental studies, and nanotechnology. Within popular science, fluorescence instruments have been used to examine counterfeit banknotes, materials for optoelectronics, the efficacy of milk pasteurization, and the growth of coral in marine environments. This instrument can be used for both qualitative and quantitative analysis. Because of the sensitivity that this method affords, molecular concentrations as low as 1 part per trillion can be measured. While Keck has a fluorometer, the current software for the instrument is no longer supported by the manufacturer (Horiba). In addition, a mirror replacement to the Fluorolog is needed to improve performance.  The acquisition of this new instrument will be applied towards advanced instructional projects and faculty research.

External grant: Cottrell Scholar Award (Research Corporation for Science Advancement), “Biochemical characterization and engineering of luciferases through Statistical Coupling Analysis”, Principal Investigator, $100,000 (2016-2019)

Abstract: Luciferase Bioluminescence Imaging (BLI) is a non-invasive method for monitoring diverse processes in living systems. BLI couples in vitro and in vivo biological events to the bioluminescent output of the enzyme luciferase. BLI is constrained by the limitations of the luciferase enzyme—primarily insufficient emissions, limited emission colors, and thermal and pH instability. To date, efforts to biochemically characterize and/or engineer luciferase have imparted notable improvements to the luciferase enzyme; however, the improvements in one biochemical property (e.g. red-shifted emission) are typically accompanied by concomitant deterioration of other properties (e.g. decreased light output or decreased affinity for substrate).  Thus, optimization of luciferase is still necessary. Here, we propose to develop techniques that will maximize the potential of finding new, advantageous properties while minimizing the possibility of diminishing other, biochemically important properties.  We propose to apply a powerful, evolution-based heuristic method Statistical Coupling Analysis (SCA) to guide both biochemical characterization and engineering efforts for luciferase.  As our education proposal, we propose to incorporate the biochemical characterization of SCA-identified amino acid residues into an introductory chemistry course, enabling a large population of students to experience research as well as developing a potentially novel long-term strategy to incorporate research into introductory courses.  In the research proposal, we propose to engineer these enzymes; by using SCA coupled to a screen that focuses on identifying mutants that have multiple beneficial properties, we hope to create novel luciferase enzymes with biotechnologically useful properties as well as increase our biochemical understanding of this important enzyme. 


External grant: Wenzel, A. (PI); Leconte, A. (co-PI); Hatcher, M. (co-PI) “Acquisition of a Fluorimeter for Undergraduate Instruction and Research.”Ellen Browning Scripps Foundation; 8/2016; $20,000 + $20,000 institutional match; Keck Science Department, Claremont, CA

Abstract: Fluorescence is the molecular absorption of light energy at one wavelength and its nearly instantaneous re-emission at another, usually longer, wavelength. Some molecules fluoresce naturally, while others can be modified to make fluorescent compounds. The instrument used to measure fluorescence is called a fluorometer. A fluorometer generates the wavelength of light required to excite a compound of interest; it then selectively transmits the wavelength of light emitted, measuring the intensity of that light. Fluorometers allow for the acquisition and measure of a sample’s fluorescence, including its intensity, spectral wavelengths, and lifetime. The fluorescence of a sample can be an indirect probe of the sample's environment, describing solvent-solute interactions, inter- and intramolecular interactions, etc. Analytical measurements provided by fluorometers can be used in multiple applications including chemistry, biochemistry, medical research, pharmaceuticals, food science, environmental studies, and nanotechnology. Within popular science, fluorescence instruments have been used to examine counterfeit banknotes, materials for optoelectronics, the efficacy of milk pasteurization, and the growth of coral in marine environments. This instrument can be used for both qualitative and quantitative analysis. Because of the sensitivity that this method affords, molecular concentrations as low as 1 part per trillion can be measured. While Keck has a fluorometer, the current software for the instrument is no longer supported by the manufacturer (Horiba). In addition, a mirror replacement to the Fluorolog is needed to improve performance.  The acquisition of this new instrument will be applied towards advanced instructional projects and faculty research.

Hajdu, David, John Milton, and Tamas Insperger. "Extension of stability radius to neuromechanical systems with structured real perturbations." IEEE Trans. Neural Sys. Rehab Eng. 24, 2016, 1235-1242.

Abstract:The ability of humans to maintain balance about an unstable position in a continuously changing environment attests to the robustness of their balance control mechanisms to perturbations. A mathematical tool to analyze robust stabilization of unstable equilibria is the stability radius. Based on the pseudospectra, the stability radius gives a measure to the maximum change of the system parameters without resulting loss of stability. Here we compare stability radii for a model for human frontal plane balance controlled by a delayed proportional-derivative feedback to two types of perturbations: unstructured complex and weighted structured real. It is shown that 1) narrow stance widths are more robust to parameter variation; 2) stability is maintained for larger structured real perturbations than for unstructured complex perturbations; and 3) the most robust derivative gain to weighted structured real perturbations is located near the stability boundary. It is argued that stability radii can effectively be used to compare different control concepts associated with human motor control.


Milton J., R. Meyer, M. Zhvanetsky, S. Ridge, and T. Insperger. “Control at stability’s edge minimizes energetic costs: Expert stick balancing.”  J. Royal Society Interface 13, 2016.

Abstract: Stick balancing on the fingertip is a complex voluntary motor task that requires the stabilization of an unstable system. For seated expert stick balancers the time delay is 0.23s, the shortest stick that can be balanced for 240s is 0.32m and there is an approximately 0.8 degree dead zone for the estimation of the vertical displacement angle in the saggital plane. These observations motivate a switching-type, pendulum-cart model for balance control which utilizes an internal model to compensate for the time delay by predicting the sensory consequences of the stick's movements. Numerical simulations using the semi-discretization method suggest that the feedback gains are tuned near the edge of stability.  For these choices of the feedback gains the cost function which takes into account the position of the fingertip and the corrective forces is minimized. Thus expert stick balancers optimize control with a combination of quick maneuverability and minimum energy expenditures.

Monroy, J.A., K.L. Powers, C.M. Pace, T. Uyeno, and K.C. Nishikawa. "Effects of activation on the elastic properties of intact soleus muscles with a deletion in titin." Journal of Experimental Biology, 2016.

Abstract: Titin has long been known to contribute to muscle passive tension. Recently, it was also demonstrated that titin-based stiffness increases upon Ca2+-activation of wildtype mouse psoas myofibrils stretched beyond overlap of the thick and thin filaments. In addition, this increase in titin-based stiffness upon activation was impaired in single psoas myofibrils from mdm mice with a deletion in titin. Here, we investigate the effects of muscle activation on elastic properties of intact soleus muscles from wildtype and mdm mice to determine whether titin may contribute to active muscle stiffness. Using load-clamp experiments, we compared the stress-strain relationships of elastic elements in active and passive muscles during unloading, and quantified the change in stiffness upon activation. We used the mdm mutation, characterized by a deletion in the N2A region of the Ttn gene, to test the hypothesis that titin contributes to active muscle stiffness. Results show that the elastic modulus of wildtype muscles increases upon activation. Elastic elements began to develop force at lengths that were 15% shorter in active than in passive soleus, and there was a 2.9-fold increase in the slope of the stress - strain relationship. In contrast, mdm soleus showed no effect of activation on the slope or intercept of the stress - strain relationship. These results from intact soleus muscles are qualitatively and quantitatively similar to results from single wildtype psoas myofibrils stretched beyond overlap of the thick and thin filaments. Therefore, it is likely that titin plays a role in the increase of stiffness during rapid unloading that we observed in intact soleus muscles upon activation. The results from intact mdm soleus muscles are also consistent with impaired titin activation observed in single mdm psoas myofibrils stretched beyond filament overlap, further suggesting that the mechanism of titin activation is impaired in skeletal muscles from mdm mice. These results are consistent with the idea that, in addition to the thin filaments, titin is activated upon Ca2+-influx in skeletal muscle.


Pace, C.M., S. Mortimer, J.A. Monroy, and K.C. Nishikawa. "The effects of a skeletal muscle titin mutation on walking in mice." Journal of Comparative Physiology A, 2016, 1-10.

Abstract: Titin contributes to sarcomere assembly, muscle signaling, and mechanical properties of muscle. The mdm mouse exhibits a small deletion in the titin gene resulting in dystrophic mutants and phenotypically normal heterozygotes. We examined the effects of this mutation on locomotion to assess how, and if, changes to muscle phenotype explain observed locomotor differences. Mutant mice are much smaller in size than their siblings and gait abnormalities may be driven by differences in limb proportions and/or by changes to muscle phenotype caused by the titin mutation. We quantified differences in walking gait among mdm genotypes and also determined whether genotypes vary in limb morphometrics. Mice were filmed walking, and kinematic and morphological variables were measured. Mutant mice had a smaller range of motion at the ankle, shorter stride lengths, and shorter stance duration, but walked at the same relative speeds as the other genotypes. Although phenotypically similar to wildtype mice, heterozygous mice frequently exhibited intermediate gait mechanics. Morphological differences among genotypes in hindlimb proportions were small and do not explain the locomotor differences. We suggest that differences in locomotion among mdm genotypes are due to changes in muscle phenotype caused by the titin mutation.

Brown, W. and T. Poon. Introduction to Organic Chemistry, Sixth Edition, John Wiley and Sons, 2016. 

Abstract: Introduction to Organic Chemistry, 6th Edition provides an introduction to organic chemistry for students who require the fundamentals of organic chemistry as a requirement for their major. It is most suited for a one semester organic chemistry course. In an attempt to highlight the relevance of the material to students, the authors place a strong emphasis on showing the interrelationship between organic chemistry and other areas of science, particularly the biological and health sciences.  The text illustrates the use of organic chemistry as a tool in these sciences; it also stresses the organic compounds, both natural and synthetic, that surround us in everyday life: in pharmaceuticals, plastics, fibers, agrochemicals, surface coatings, toiletry preparations and cosmetics, food additives, adhesives, and elastomers.


Preest, M.R., M.J. Ward*, T. Poon, and J.W. Hermanson. “Chemical Prey Luring in Jackson's Chameleons.” Physiological and Biochemical Zoology 89, 2016, 110-117.

Abstract: Lizards in the family Chamaeleonidae have been described as wiping a viscous substance from a pouch (the temporal pouch) at the angle of the jaw on branches and then capturing flies that land near the area where the wiping occurs.  We confirmed the presence of this pouch in Jackson’s chameleons.  Histological work suggested that the material contained within is a result of decomposition of food and sloughed skin that has been trapped in the pouch, rather than a glandular secretion.  Gas chromatography-mass spectrometry indicated the presence of compounds that are both volatile and odiferous and similar to insect pheromones.  Choice tests with houseflies revealed attraction to the temporal pouch material.  Some authors have speculated that the temporal pouch material serves a function in territory marking and/or predator deterrence.  While it may play these roles, our results suggest that it also serves a role in chemical luring of prey.

Preest, M.R., M.J. Ward*, T. Poon, and J.W. Hermanson. “Chemical Prey Luring in Jackson's Chameleons.” Physiological and Biochemical Zoology 89, 2016, 110-117.

Abstract: Lizards in the family Chamaeleonidae have been described as wiping a viscous substance from a pouch (the temporal pouch) at the angle of the jaw on branches and then capturing flies that land near the area where the wiping occurs.  We confirmed the presence of this pouch in Jackson’s chameleons.  Histological work suggested that the material contained within is a result of decomposition of food and sloughed skin that has been trapped in the pouch, rather than a glandular secretion.  Gas chromatography-mass spectrometry indicated the presence of compounds that are both volatile and odiferous and similar to insect pheromones.  Choice tests with houseflies revealed attraction to the temporal pouch material.  Some authors have speculated that the temporal pouch material serves a function in territory marking and/or predator deterrence.  While it may play these roles, our results suggest that it also serves a role in chemical luring of prey.

Price, D.J., M.E. Kacarab, D.R. Cocker III, K.L. Purvis-Roberts, and P.J. Silva, "Effects of temperature on the formation of secondary organic aerosol from amine precursors." Aerosol Science and Technology 50.11, 2016, 1216-1226.

Abstract: Aerosol formation is directly influenced by meteorological properties such as temperature and relative humidity. This study examines the influence of temperature on the physical properties and chemical composition of the aerosol produced from radical oxidation of aliphatic amines. Aerosol formation for temperatures ranging from 10 to 40°C was investigated in dual 90 m3 indoor atmospheric chambers. Further, chemical and physical responses of aerosol formed at one temperature and then raised/cooled to another were investigated in detail. Around two to three times more aerosol formation occurred at 10°C than at 40°C. This has important implications for locations influenced by amine emissions during the winter months. Significant aerosol formation occurred with the oxidation of amines with nitrate radical (100–600 μg/m3) and consisted largely of amine nitrate salts. These reactions are important contributors to aerosol formation during the nighttime hours, when nitrate radical is the dominant oxidant and temperatures tend to be cooler. Solid/gas partitioning of amine nitrate salt aerosol was consistent with literature results. A novel, temperature dependent, mechanism describing peroxy and hydroperoxy radical reactions was observed in the trimethylamine with hydroxyl radical oxidation experiments.


External grant: Co-PI on NSF Proposal (GEO/ATM-1347071 June 2014-present) RUI: Collaborative Research: Aerosol Formation From Agricultural Volatile Organic Compounds in Collaboration with Professor David Cocker, University of California Riverside, Dr. Phil Silva, U.S. Department of Agriculture, Dr. Matthew Nee and Dr. Rezaul Mahmood, Western Kentucky University, ($699,985).


External grant:PI on Henry Dreyfus Teacher-Scholar Award, Chemical Mechanism for Particulate Matter Formation from Amines Utilized in Carbon Sequestration Technologies, August 2013-August 2018 ($60,000).

Robins, C. “Soils, Science, Society, and the Environment.” Oxford Research Encyclopedia of Environmental Science, 2016.

Abstract: Soils are the complex, dynamic, spatially diverse, living, and environmentally sensitive foundations of terrestrial ecosystems as well as human civilizations. The modern, environmental study of soil is a truly young scientific discipline that emerged only in the late 19th century from foundations in agricultural chemistry, land resource mapping, and geology. Today, little more than a century later, soil science is a rigorously interdisciplinary field with a wide range of exciting applications in agronomy, ecology, environmental policy, geology, public health, and many other environmentally relevant disciplines. Soils form slowly, in response to five inter-related factors: climate, organisms, topography, parent material, and time. Consequently, many soils are chemically, biologically, and/or geologically unique. The profound importance of soil, combined with the threats of erosion, urban development, pollution, climate change, and other factors, are now prompting soil scientists to consider the application of endangered species concepts to rare or threatened soil around the world.


W Wheeler, M.M., M.M. Dipman, T.A. Adams, A.V. Ruina, C.R. Robins, and W.M. Meyer, III. “Carbon and nitrogen storage in California sage scrub and non-native grassland habitats.” Journal of Arid Environments 129, 2016, 119-125.

Abstract: Human activity has altered global carbon and nitrogen cycles, leading to changes in global temperatures and plant communities. Because atmospheric carbon (C) and nitrogen (N) concentrations are affected by storage in terrestrial vegetation and soil, it is critical to understand how conversions from native to non-native vegetation may alter the C and N storage potential of terrestrial landscapes. In this study, we compared C and N storage in native California sage scrub, non-native grassland, and recovering California sage scrub habitats in the spring and fall by determining the C and N content in aboveground biomass, litter, and surface soil. Significantly more C and N were stored in intact and recovering California sage scrub than in grassland habitats. Intact and recovering sage scrub did not differ significantly in C or N storage. Our results highlight that preserving and restoring California sage scrub habitat not only provides habitat for native biodiversity, but also increases carbon and nitrogen storage potential even without restoration to intact sage scrub.

V. Nguyen, J. Rizzo, and B. Sanii. “An Assemblable, Multi-Angle Fluorescence and Ellipsometric Microscope.” PLOS ONE (included in Open Source Toolkit Collection), 2016.

Abstract: We introduce a multi-functional microscope for research laboratories that have significant cost and space limitations. The microscope pivots around the sample, operating in upright, inverted, side-on and oblique geometries. At these geometries it is able to perform bright-field, fluorescence and qualitative ellipsometric imaging. It is the first single instrument in the literature to be able to perform all of these functionalities. The system can be assembled by two undergraduate students from a provided manual in less than a day, from off-the-shelf and 3D printed components, which together cost approximately $16k at 2016 market prices. We include a highly specified assembly manual, a summary of design methodologies, and all associated 3D-printing files in hopes that the utility of the design outlives the current component market. This open design approach prepares readers to customize the instrument to specific needs and applications. We also discuss how to select household LEDs as low-cost light sources for fluorescence microscopy. We demonstrate the utility of the microscope in varied geometries and functionalities, with particular emphasis on studying hydrated, solid-supported lipid films and wet biological samples.

Chen A., C. Chiu, S. Khan, R.D. Spence, and D. Prober. “QRFP and its receptors regulate locomotor activity and sleep in zebrafish.” Journal of Neuroscience, vol. 36, 2016, 1823-1840.

Abstract:The hypothalamus plays an important role in regulating sleep, but few hypothalamic sleep-promoting signaling pathways have been identified. Here we demonstrate a role for the neuropeptide QRFP (also known as P518 and 26RFa) and its receptors in regulating sleep in zebrafish, a diurnal vertebrate. We show that QRFP is expressed in ∼10 hypothalamic neurons in zebrafish larvae, which project to the hypothalamus, hindbrain, and spinal cord, including regions that express the two zebrafish QRFP receptor paralogs. We find that the overexpression of QRFP inhibits locomotor activity during the day, whereas mutation of qrfp or its receptors results in increased locomotor activity and decreased sleep during the day. Despite the restriction of these phenotypes to the day, the circadian clock does not regulate qrfp expression, and entrained circadian rhythms are not required for QRFP-induced rest. Instead, we find that QRFP overexpression decreases locomotor activity largely in a light-specific manner. Our results suggest that QRFP signaling plays an important role in promoting sleep and may underlie some aspects of hypothalamic sleep control. SIGNIFICANCE STATEMENT The hypothalamus is thought to play a key role in regulating sleep in vertebrate animals, but few sleep-promoting signaling pathways that function in the hypothalamus have been identified. Here we use the zebrafish, a diurnal vertebrate, to functionally and anatomically characterize the neuropeptide QRFP. We show that QRFP is exclusively expressed in a small number of neurons in the larval zebrafish hypothalamus that project widely in the brain. We also show that QRFP overexpression reduces locomotor activity, whereas animals that lack QRFP signaling are more active and sleep less. These results suggest that QRFP signaling participates in the hypothalamic regulation of sleep.


Roberts D.G., H.B. Johnsonbaugh, R.D. Spence, and A.J. MacKenzie-Graham. “Optical Clearing of the Mouse Central Nervous System Using Passive CLARITY.” Journal of Visualized Experiments, vol. 112, 2016, e54025-e54025.

Abstract: Traditionally, tissue visualization has required that the tissue of interest be serially sectioned and imaged, subjecting each tissue section to unique non-linear deformations, dramatically hampering one's ability to evaluate cellular morphology, distribution and connectivity in the central nervous system (CNS). However, optical clearing techniques are changing the way tissues are visualized. These approaches permit one to probe deeply into intact organ preparations, providing tremendous insight into the structural organization of tissues in health and disease. Techniques such as Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging-compatible Tissue-hYdrogel (CLARITY) achieve this goal by providing a matrix that binds important biomolecules while permitting light-scattering lipids to freely diffuse out. Lipid removal, followed by refractive index matching, renders the tissue transparent and readily imaged in 3 dimensions (3D). Nevertheless, the electrophoretic tissue clearing (ETC) used in the original CLARITY protocol can be challenging to implement successfully and the use of a proprietary refraction index matching solution makes it expensive to use the technique routinely. This report demonstrates the implementation of a simple and inexpensive optical clearing protocol that combines passive CLARITY for improved tissue integrity and 2,2'-thiodiethanol (TDE), a previously described refractive index matching solution.

Tang, Zhaohua and Gretchen Edwalds-Gilbert. “Nucleic Acid and Protein Sample Preparation from Yeasts.” Sample Preparation Techniques for Soil, Plant, and Animal Samples, Springer Protocols Handbooks, edited by M. Micic, Springer Science+Business Media New York, 2016.

Abstract: The budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe, as unicellular eukaryotes, are popular model systems. They have greatly contributed to our understanding about biological principles of complex organisms. Although the two yeasts differ from one another in a range of features, both are genetically tractable, amenable to classical, molecular   genetics, and genomic-scale analyses. S. cerevisiae and S. pombe are ideal experimental systems for undergraduates learning about genetics and molecular and cell biology in laboratory course settings, as well as in research environments, because of their non-pathogenic nature, rapid reproduction cycles and suitability for diverse approaches and different types of courses. Both yeasts offer the opportunity for students to pursue inquiry-based learning. To facilitate students gaining knowledge in the laboratory, this chapter provides a guide for carrying out frequently used procedures for DNA isolation, RNA extraction, and protein lysate preparation from both S. cerevisiae and S. pombe yeast cells. Aimed at students learning through performing the experiments, each protocol also includes a brief explanation about relevant molecular concepts underlining the methods described, along with stepwise instructions.

Thomson. D.M. “Local Bombus decline linked to recovery of honey bees, drought effects on floral resources.” Ecology Letters 19 (10), 2016, 1247-1255.

Abstract: Time series of abundances are critical for understanding how abiotic factors and species interactions affect population dynamics, but are rarely linked with experiments and also scarce for bee pollinators. This gap is important given concerns about declines in some bee species. I monitored honey bee (Apis mellifera) and bumble bee (Bombus spp.) foragers in coastal California from 1999, when feral A. mellifera populations were low due to Varroa destructor, until 2014. Apis mellifera increased substantially, except between 2006 and 2011, coinciding with declines in managed populations. Increases in A. mellifera strongly correlated with declines in Bombus and reduced diet overlap between them, suggesting resource competition consistent with past experimental results. Lower Bombus numbers also correlated with diminished floral resources. Declines in floral abundances were associated with drought and reduced spring rainfall. These results illustrate how competition with an introduced species may interact with climate to drive local decline of native pollinators.


Thomson, D.M., Roxanne Cruz-de Hoyos*, Keala Cummings*, and Emily L. Schultz*.  “Why are native annual abundances low in invaded grasslands? Testing the effects of competition and seed limitation.” Plant Ecology 217, 2016, 431-442.

Abstract: Competitive suppression of native species has long been considered among the most important mechanisms allowing exotic plants to dominate some communities, but recent work has focused attention on the potential role of native seed limitation. We tested effects of competition from exotic annual grasses and seed limitation on the abundances of four native annual plants in invaded southern California grassland for two different years. Both initial responses and effects still present 1–3 years later were measured. In the wetter year of 2006, all four native species (Amsinckia menziesii var. intermedia, Phacelia distans, Camissonia bistorta and Clarkia purpurea ssp. quadrivulnera) increased in abundance with exotic grass removal, and two (Clarkia and Camissonia) responded significantly to seed addition. We observed limited treatment effects during the much drier growing season of 2007. By 2008–2009, any initial effects of exotic grass removal had disappeared. However, for both the 2006 and 2007 experiments seeding significantly increased native cover in 2009, independent of initial grass removal. Abundances of both Amsinckia and Phacelia, but not Camissonia or Clarkia, were significantly higher in seeded plots during 2008–2009. These delayed responses may have resulted from seed dormancy. Our results support the importance of both competition with exotics and seed limitation in determining native annual community composition of California grasslands. An interesting future question is whether traits related to resource use or germination phenology may predict differences in native species interactions with exotic grasses.

External grant: Wenzel, A. (PI) “RUI: Catalyst Systems to Effect Asymmetric Induction in the Hydroamination of Olefins.” National Science Foundation Grant #1566124; 9/2016; $193,099; Keck Science Department, Claremont, CA

Abstract: The Chemical Catalysis Program of the Chemistry Division supports the research project by Professor Wenzel. Professor Wenzel is a faculty member at the W. M. Keck Science Department at Claremont McKenna College. She is developing new molecules to catalyze selective hydroamination of alkenes. Hydroamination reactions are an efficient route for the preparation of amines, a common structure found in pharmaceutical and agrichemical products. The reactions are focused on making the synthesis sustainable. The catalyst molecules are designed to be readily available and to support robust reactions. The study is uncovering a wealth of fundamental information regarding the factors governing reaction design. The research is conducted entirely by undergraduate students. Professor Wenzel's program is well-poised to address the ongoing deficiency of underrepresented groups in science. She has an excellent record in training underrepresented minority students and successfully encouraging them to pursue graduate studies in chemistry. This research outlines the preparation of chiral heterodonor phosphorous/thioether (P/S) and phosphorous/amine (P/N) ligands as alternatives to classically-used bisphosphines for coordination onto palladium, ruthenium, and copper. The chiral, bidentate ligands are equipped with strong and weak donor-heteroatom pairs (e.g., P/S or P/N) to utilize favorable electronics to strongly influence the stability and reactivity associated with stereochemistry-defining reaction intermediates. The new catalysts are evaluated in two types of hydroamination reactions: an intermolecular, asymmetric anti-Markovnikov hydroamination of unactivated olefins and the enantioselective, Markovnikov hydroamination of dienes to produce dihydroquinolines. It is through a robust program in the training of undergraduate researchers that Professor Wenzel tries to advance of science as well as the education of future science professionals.


External grant: Wenzel, A. (PI); Leconte, A. (co-PI); Hatcher, M. (co-PI) “Acquisition of a Fluorimeter for Undergraduate Instruction and Research.”Ellen Browning Scripps Foundation; 8/2016; $20,000 + $20,000 institutional match; Keck Science Department, Claremont, CA

Abstract: Fluorescence is the molecular absorption of light energy at one wavelength and its nearly instantaneous re-emission at another, usually longer, wavelength. Some molecules fluoresce naturally, while others can be modified to make fluorescent compounds. The instrument used to measure fluorescence is called a fluorometer. A fluorometer generates the wavelength of light required to excite a compound of interest; it then selectively transmits the wavelength of light emitted, measuring the intensity of that light. Fluorometers allow for the acquisition and measure of a sample’s fluorescence, including its intensity, spectral wavelengths, and lifetime. The fluorescence of a sample can be an indirect probe of the sample's environment, describing solvent-solute interactions, inter- and intramolecular interactions, etc. Analytical measurements provided by fluorometers can be used in multiple applications including chemistry, biochemistry, medical research, pharmaceuticals, food science, environmental studies, and nanotechnology. Within popular science, fluorescence instruments have been used to examine counterfeit banknotes, materials for optoelectronics, the efficacy of milk pasteurization, and the growth of coral in marine environments. This instrument can be used for both qualitative and quantitative analysis. Because of the sensitivity that this method affords, molecular concentrations as low as 1 part per trillion can be measured. While Keck has a fluorometer, the current software for the instrument is no longer supported by the manufacturer (Horiba). In addition, a mirror replacement to the Fluorolog is needed to improve performance.  The acquisition of this new instrument will be applied towards advanced instructional projects and faculty research.

Gallagher, S.R. and E.A. Wiley, editors. Current Protocols: Essential Laboratory Techniques, Wiley and Sons, Inc., Online edition, Supplements 13 and 14, 2016.

Abstract: Current Protocols Essential Laboratory Techniques seeks to bridge the gap between the theory of the classroom and its application in the laboratory. By codifying and verifying basic information often taken for granted by more senior members of the lab, and presenting it in a clear and direct format, this title is intended to provide a resource upon which novice researchers can rely to become productive members of the modern life science laboratory. Current Protocols Essential Laboratory Techniques also serves to combat the so-called “kit mentality” by explaining the rationale behind many of the kits in common use today. The ultimate goal of Current Protocols Essential Laboratory Techniques is to equip the reader with a solid skill set that will continue to be applied and improved over the course of his or her research career.


Wiley, E.A. and D. Chalker. “A community model for course-based student research that advances faculty scholarship.” CUR Quarterly 37(2), 2016, 12-14.

Abstract: Embedding authentic experiences into course curricula has been touted for its broad impact on student learning and generating interest in science, but significant barriers limit implementation of this practice. Faculty struggle to balance teaching and research responsibilities, and the effort-intensive undertaking of designing classroom activities that generate meaningful data presents an added burden. One solution used by faculty is to engage students in classroom investigations that simultaneously advance scholarly productivity of the faculty member.  Commonly, these curricula are developed ad hoc by individuals to meld their research interests with the learning goals of a specific course, but as such, the exercises may not easily transfer to other classrooms taught by faculty with different scholarly interests and goals. Here we describe a collaborative faculty research consortium model that advances faculty scholarship while engaging students in authentic research experiences. This model should be transferrable to a broad range of research communities.


Yale, K., M. Neuman, E. Bulley, A.Tackett, B.T. Chait*,  and E.A. Wiley. “Phosphorylation-dependent targeting of Tetrahymena HP1 to condensed chromatin.” mSphere 1.4, 2016, e00142-16.

Abstract: The evolutionarily conserved proteins related to Heterochromatin Protein 1 (HP1), originally described in Drosophila, are well known for their roles in heterochromatin assembly and gene silencing. Targeting of HP1 proteins to specific chromatin locales is mediated at least in part by the HP1 chromodomain, which binds to histone H3 methylated at lysine 9 that marks condensed regions of the genome. Mechanisms that regulate HP1 targeting are emerging from studies in yeast and metazoans and point to roles for post-translational modifications.  Here, we report that modifications on an HP1 homolog (Hhp1) in the ciliate model Tetrahymena thermophila correlated with physiological state and with nuclear differentiation events involving the restructuring of chromatin. Results support the model that Hhp1 chromodomain binds lysine 27-methylated histone H3, and we show that co-localization with this histone mark depends on phosphorylation at a single Cdc2/Cdk1 kinase site in the "hinge region" adjacent to the chromodomain. These findings help elucidate important functional roles of reversible post-translational modifications on proteins in the HP1 family; in this case, regulating the targeting of a ciliate HP1 to chromatin regions marked with methylated H3 lysine 27.

Ng, J., B. Williams, D.M Thomson, and J. Halfar. “Developing a forward model of encrusting coralline algae.” Geochimica et Cosmochimica Acta, 194, 2016, 279-290.

Abstract: An increased number of climate proxy records and more refined interpretation of proxy data are crucial to improve projections of future climate at high latitudes, where internal feedbacks amplify warming and established high-resolution climate archives are especially sparse. Encrusting coralline algae are being developed as a mid- to high-latitude marine climate archive. These long-lived algae form a solid high-Mg calcite skeleton with annual growth bands similar to those of trees and tropical corals. The oxygen isotope ratio of the algal skeleton (d18Oalg) records local environmental and climatic factors, notably sea surface temperature and seawater d18O. Here we assess the d18Oalg–climate relationship in diverse environments across the algal habitat range utilizing two species of coralline algae from the genus Clathromorphum. Clathromorphum is widely distributed from the cold-temperate North Atlantic and Pacific to the Arctic Ocean and has recently yielded numerous climate reconstructions of up to 650 years in length. In this study, we calibrate d18Oalg of four specimens to gridded temperature and salinity data, the latter a proxy for seawater d18O. These specimens were collected from a variety of algal growth environments across the high-latitude Northern Hemisphere: two specimens from the Aleutian Archipelago, one from the Canadian Arctic, and one from the Gulf of Maine. Low winter temperatures and insolation restrict the months when algae record local climate in the d18O of their skeletons; we therefore determine these response seasons by correlating monthly temperature and salinity anomalies with annual d18Oalg anomalies at each site. We then average gridded data over months that correlate significantly (95% confidence interval) for regression with d18Oalg. While the timing and nature of the climate signal vary across sites, we find significant relationships between d18Oalg and either temperature or salinity averaged over the response season at three sites. Variation in local climatology among the four sites provides a physical explanation for calibration differences, compounded by uncertainties stemming from the proxy chronology, biological variability, temporal coverage, and sparse historical climate data. This work takes an essential step toward reconstructing high-latitude marine climate patterns with coralline algal d18O and developing algae proxy system models.


Williams, B., B. Thibodeau, Y. Chikaraishi, N. Ohkouchi, A. Walnum, A. Grottoli, and P. Colin. “Investigating variations in primary productivity in the Tropical Pacific Ocean due to multi-decadal nitricline depth fluctuation.” Limnology and Oceanography, 2016.

Abstract:The depth of the thermocline and associated nitricline in the western Pacific warm pool (WPWP) vary over time in response to changes in larger ocean-atmosphere climate patterns. A shoaling of the nitricline in the WPWP brings nitrate-rich seawater ( math formula > 4 μmol kg−1) above the base of the euphotic zone, stimulating primary productivity. Here, we test if decadal variability in the nitricline depth is driving changes in regional primary productivity and source nitrate dynamics. We use the nitrogen isotopic composition (δ15N) of amino acids in the skeleton of a proteinaceous coral collected from the base of the euphotic zone in the WPWP. In proteinaceous corals, as in most organic life, the δ15N of phenylalanine matches that of the ambient nitrate while the δ15N of trophic amino acids reflect subsequent trophic transfer of the nitrogen prior to incorporation into the coral's food, suspended particulate organic matter. Consistency of the trophic position of the coral calculated from the δ15N composition of the coral skeletal amino acids over its 56 yr lifespan suggest that decadal variability in nitricline depth and subsequent shifts in nitrate availability to the euphotic zone have not impacted primary productivity offshore of Palau in the WPWP. This is important when considering the current external forcing of Pacific Ocean climate patterns and the resulting impacts on the global carbon cycle in the Palau region of the WPWP.

External grant: NSF-TUES type 2, Senior Personnel, IONiC: Transforming education through collaborative development of materials at the frontiers of inorganic chemistry, $437,962, 2012-2017.