Data from: Mechanisms of Gill-Clogging by Hagfish Slime
Luke Taylor, Gaurav Chaudhary, Gaurav Jain, Andrew Lowe, Andre Hupe, Atsuko Negishi, Yu Zeng, Randy Ewoldt, and Douglas Fudge
Abstract of Proc. Roy. Soc. article:
Hagfishes defend themselves from gill-breathing predators by producing large volumes of fibrous slime when attacked. The slime’s effectiveness comes from its ability to clog predators’ gills, but the mechanisms by which hagfish slime clogs are uncertain, especially given its remarkably dilute concentration of solids. We quantified the clogging performance of hagfish slime over a range of concentrations, measured the contributions of its mucous and thread components, and measured the effect of turbulent mixing on clogging. To assess the porous structure of hagfish slime, we used a custom device to measure its Darcy permeability. We show that hagfish slime clogs at extremely dilute concentrations like those found in native hagfish slime and displays clogging performance that is superior to three thickening agents. We report an extremely low Darcy permeability for hagfish slime, and an effective pore size of 10-300 nm. We also show that the mucous and thread components play distinct yet crucial roles, with mucus being responsible for effective clogging and low permeability and the threads imparting mechanical strength and retaining clogging function over time. Our results provide new insights into the mechanisms by which hagfish slime clogs gills and may inspire the development of ultra-soft materials with novel properties.
Nematode Epicuticlin and Collagen Sequences with YGD/GYR Amino Acid Motifs
Bruno Betschart, Marco Bisoffi, and Ferial Alaeddine
Nematoda and Arthropoda have a complex exoskeleton, the cuticle, which is replaced via molts during their development. Major constituents of nematode cuticles are specific collagens and insoluble proteins called cuticlins. The epicuticle is composed of an insoluble protein called epicuticlin. Our objective was to identify and characterize genes and their encoded proteins forming the epicuticle. We were able to complete the identification of the first epicuticlin gene, Asu-epicut1 of Ascaris suum which is composed of 7 tandem repeats. The deduced protein, Asu-EPICUT1, consists of a signal peptide of 20 amino acids followed by 353 amino acids composed of seven tandem repeats (TR) of 49 or 51 amino acids each. Each repeat has three highly conserved tyrosine motives. Interestingly one of them (GYR) is the Pfam motif PF02756 present in several cuticular proteins of arthropods. Blast search in different databases using parts of epicuticular proteins as queries showed the presence of homologous proteins in 50 other nematode species. They are all characterized by TR, each composed of around 60 amino acids and two to four motifs with a conserved tyrosine. Some of the putative epicuticular proteins detected in nematodes of Clade V (Rhabditina) contain beside the tyrosine residues one cysteine residue per repeat. This new category of cuticular proteins might crosslink with specific cuticular collagens, which also have tyrosine motifs. The localization in the outermost layer of the nematode body and their unique structure renders them important candidates for biochemical and molecular interaction studies.
Demographic Data Collection in STEM Organizations
Nicholas P. Burnett, Alyssa Hernandez, Emily King, Richelle Tanner, and Kathryn Wilsterman
Professional organizations in STEM (science, technology, engineering, and mathematics) can use demographic data to quantify recruitment and retention (R&R) of underrepresented groups within their memberships. However, variation in the types of demographic data collected can influence the targeting and perceived impacts of R&R efforts - e.g., giving false signals of R&R for some groups. We obtained demographic surveys from 73 U.S.-affiliated STEM organizations, collectively representing 712,000 members and conference-attendees. We found large differences in the demographic categories surveyed (e.g., disability status, sexual orientation) and the available response options. These discrepancies indicate a lack of consensus regarding the demographic groups that should be recognized and, for groups that are omitted from surveys, an inability of organizations to prioritize and evaluate R&R initiatives. Aligning inclusive demographic surveys across organizations will provide baseline data that can be used to target and evaluate R&R initiatives to better serve underrepresented groups throughout STEM.
Data from: Climatic Influences on Winter Precipitation Use by Trees in Summer
Gregory R. Goldsmith
Trees in seasonal climates may use water originating from both winter and summer precipitation. However, the seasonal origins of water used by trees have not been systematically studied. We used stable isotopes of water to compare the seasonal origins of water found in three common tree species across 24 Swiss forest sites sampled in two different years. The data set provides information on the sites (e.g., latitude/longitude, site name), site characteristics (e.g., weather/climate), tree species studied (beech, spruce and oak), and corresponding observations of stable isotopes of hydrogen and oxygen in tree xylem water.
Data from: Structural and Defensive Roles of Angiosperm Leaf Venation Network Reticulation Across an Andes-Amazon Elevation Gradient
Benjamin Blonder, Lisa Patrick Bentley, Alexander Shenkin, Percy O. Chambi Porroa, Yolvi Valdez Tejeira, Tatiana Erika Boza Espinoza, Gregory R. Goldsmith, Lucas Enrico, Roberta E. Martin, Gregory P. Asner, Sandra Díaz, Brian J. Enquist, and Yadvinder Malhi
1.The network of minor veins of angiosperm leaves may include loops (reticulation). Variation in network architecture has been hypothesized to have hydraulic and also structural and defensive functions. 2.We measured venation network trait space in eight dimensions for 136 biomass-dominant angiosperm tree species along a 3,300 m elevation gradient in southeastern Peru. We then examined the relative importance of multiple ecological, and evolutionary predictors of reticulation. 3.Variation in minor venation network reticulation was constrained to three axes. These axes described branching vs. reconnecting veins, elongated vs. compact areoles, and high vs. low density veins. Variation in the first two axes was predicted by traits related to mechanical strength and secondary compounds, and in the third axis by site temperature. 4.Synthesis. Defensive and structural factors primarily explain variation in multiple axes of reticulation, with a smaller role for climate-linked hydraulic factors. These results suggest that venation network reticulation may be determined more by species interactions than by hydraulic functions.
Data from: A Selfish Genetic Element Linked to Increased Lifespan Impacts Metabolism in Female House Mice
Patricia C. Lopes and Anna K. Lindholm
Gene drive systems can lead to the evolution of traits that further enhance the transmission of the driving element. In gene drive, one allele is transmitted to offspring at a higher frequency than the homologous allele. This has a range of consequences, which generally include a reduction in fitness of the carrier of the driving allele, making such systems selfish. The t haplotype is one such driver, found in house mice. It is linked to a reduction in litter size in matings among heterozygous animals, but also to increased lifespan in wild females that carry it. Here, we tested whether carrying the t haplotype was associated with altered resting metabolic rate (RMR). We show that females carrying the t haplotype decrease RMR as they increase in size, compared to wildtype females or males of either genotype. Our study elucidates a plausible mechanism by which a selfish genetic element increases lifespan.
Data from: Spatial Variation in Throughfall, Soil, and Plant Water Isotopes in a Temperate Forest
Gregory R. Goldsmith, Scott T. Allen, Sabine Braun, Nadine Engbersen, Clara Romero González-Quijano, James W. Kirchner, and Rolf T. W. Siegwolf
Studies of stable isotopes of water in the environment have been fundamental to advancing our understanding of how water moves through the soil-plant-atmosphere continuum; however, much of this research focuses on how water isotopes vary in time, rather than in space. We examined the spatial variation in the δ18O and δ2H of throughfall and bulk soil water, as well as branch xylem and bulk leaf water of Picea abies (Norway Spruce) and Fagus sylvatica (Beech), in a 1 ha forest plot in the northern Alps of Switzerland. Means and ranges of water isotope ratios varied considerably among throughfall, soil, and xylem samples. Soil water isotope ratios were often poorly explained by soil characteristics and often not predictable from proximal samples. Branch xylem water isotope values varied less than either soil water or bulk leaf water. The isotopic range observed within an individual tree crown was often similar to that observed among different crowns. As a result of the heterogeneity in isotope ratios, inferences about the depth of plant root water uptake drawn from a two end-member mixing model were highly sensitive to the soil sampling location. Our results clearly demonstrate that studies using water isotopes to infer root water uptake must explicitly consider how to characterize soil water, incorporating measures of both vertical and lateral variation. By accounting for this spatial variation and the processes that shape it, we can improve the application of water isotopes to studies of plant ecophysiology, ecohydrology, soil hydrology, and paleoclimatology.
Eddy Flux Measurements and Transfer Velocities of Momentum, Sensible Heat, Water Vapor, and Sulfur Dioxide at Scripps Pier
Eric Saltzman, Jack G. Porter, and Warren de Bruyn
This data set contains air/sea eddy covariance fluxes and related data measured at Scripps Pier in La Jolla, California. The goal of this study was to determine transfer velocities for momentum, sensible heat, water vapor, and sulfur dioxide in order to study the process of air/sea deposition of highly soluble gases. The measurements were made during April, 2014.
Data from: What Controls Variation in Carbon Use Efficiency Among Amazonian Tropical Forests?
Christopher E. Doughty, Gregory R. Goldsmith, Nicolas Raab, Cecile A. J. Girardin, Filio Farfan-Amezquita, Walter Huaraca Huasco, Javier E. Silva-Espejo, Alejandro Araujo-Murakami, Antonino C.L. da Costa, Wanderley Rocha, David Galbraith, Patrick Meir, Dan B. Metcalfe, Yadvinder Malhi, and Walter Huaraca-Huasco
Why do some forests produce biomass more efficiently than others? Variations in Carbon Use Efficiency (CUE: total Net Primary Production (NPP)/ Gross Primary Production (GPP)) may be due to changes in wood residence time (Biomass/NPPwood), temperature, or soil nutrient status. We tested these hypotheses in 14, one ha plots across Amazonian and Andean forests where we measured most key components of net primary production (NPP: wood, fine roots, and leaves) and autotrophic respiration (Ra; wood, rhizosphere, and leaf respiration). We found that lower fertility sites were less efficient at producing biomass and had higher rhizosphere respiration, indicating increased carbon allocation to belowground components. We then compared wood respiration to wood growth and rhizosphere respiration to fine root growth and found that forests with residence times 40 yrs. A comparison of rhizosphere respiration to fine root growth showed that rhizosphere growth respiration was significantly greater at low fertility sites. Overall, we found that Amazonian forests produce biomass less efficiently in stands with residence times >40 yrs and in stands with lower fertility, but changes to long-term mean annual temperatures do not impact CUE.
Loon Project Database
Walter H. Piper
Data collected since 1993 in Oneida County, Wisconsin, on the breeding and territorial behavior of the common loon, Gavia immer. This study population is marked with USGS metal bands and colored leg bands for individual identification. It includes many individuals banded as chicks, whose life histories are known thoroughly. Data are collected from April through August of most years on this migratory species.
Data from: Investment in Territorial Defence Relates to Recent Reproductive Success in Common Loons Gavia immer
Jeremy A. Spool, Lauren V. Riters, and Walter H. Piper
As the value of a limited resource such as a territory increases, animals should invest more in the defence of that resource. Because reproductive success often depends on the quality of a breeding territory, reproductive success or failure may alter the perceived value of territory and affect an animal's investment in territorial defence. We used common loons (Gavia immer) to test the hypothesis that animals with recent breeding success would show stronger territorial defence than those with no recent breeding success. Surprisingly, successful loons responded less, not more, to a simulated intrusion. However, birds with success in the previous season also increased their territorial response as the breeding season progressed. In conjunction with past data showing that recently successful loons experience an increase in conspecific intrusions on their territories, we interpret our data to suggest that loons with recent success offset the cost of increased intrusions by adopting a more efficient strategy for territorial defence (e.g., limiting investment in resource defence until the time of the season when it is most critical).
"Probing the Transition State Region in Catalytic CO Oxidation on Ru" data files
H. Öström, H. Öberg, H. Xin, Jerry L. LaRue, M. Beye, M. Dell'Angela, J. Gladh, M. L. Ng, J. A. Sellberg, S. Kaya, G. Mercurio, D. Nordlund, W. F. Schlotter, A. Föhlisch, M. Wolf, W. Wurth, M. Persson, J. K. Nørskov, F. Abild-Pedersen, H. Ogasawara, L. G. M. Pettersson, and A. Nilsson
Femtosecond x-ray laser pulses are used to probe the CO oxidation reaction on Ru initiated by an optical laser pulse. On a timescale of a few hundred femtoseconds, the optical laser pulse excites motions of CO and O on the surface allowing the reactants to collide and, with a transient close to a picosecond (ps), new electronic states appear in the O K-edge x-ray absorption spectrum. Density functional theory calculations indicate that these result from changes in the adsorption site and bond-formation between CO and O with a distribution of OC—O bond lengths close to the transition state (TS). After 1 ps 10 % of the CO populate the TS region, which is consistent with predictions based on a quantum oscillator model.
Below you may find selected data sets from Biology, Chemistry, and Environmental Sciences faculty in the Schmid College of Science and Technology.
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