Density‐dependent and density‐independent drivers of population change in Barton Springs salamanders

Understanding population change is essential for conservation of imperiled species, such as amphibians. Worldwide amphibian declines have provided an impetus for investigating their population dynamics, which can involve both extrinsic (density‐independent) and intrinsic (density‐dependent) drivers acting differentially across multiple life stages or age classes. In this study, we examined the population dynamics of the endangered Barton Springs Salamander (Eurycea sosorum) using data from a long‐term monitoring program. We were interested in understanding both the potential environmental drivers (density‐independent factors) and demographic factors (interactions among size classes, negative density dependence) to better inform conservation and management activities. We used data from three different monitoring regimes and multivariate autoregressive state‐space models to quantify environmental effects (seasonality, discharge, algae, and sediment cover), intraspecific interactions among three size classes, and intra‐class density dependence. Results from our primary data set revealed similar patterns among sites and size classes and were corroborated by our out‐of‐sample data. Cross‐correlation analysis showed juvenile abundance was most strongly correlated with a 9‐month lag in aquifer discharge, which we suspect is related to inputs of organic carbon into the aquifer. However, sedimentation limited juvenile abundance at the surface, emphasizing the importance of continued sediment management. Recruitment from juveniles to the sub‐adult size class was evident, but negative density‐dependent feedback ultimately regulated each size class. Negative density dependence may be an encouraging sign for the conservation of E. sosorum because populations that can reach carrying capacity are less likely to go extinct compared to unregulated populations far below their carrying capacity. However, periodic population declines coupled with apparent migration into the aquifer complicate assessments of species status. Although both density‐dependent and density‐independent drivers of population change are not always apparent in time series of animal populations, both have important implications for conservation and management of E. sosorum.     

Correction: Talin tension sensor reveals novel features of focal adhesion force transmission and mechanosensitivity

The precise architecture of hair bundles, the arrays of mechanosensitive microvilli-like stereocilia crowning the auditory hair cells, is essential to hearing. Myosin IIIa, defective in the late-onset deafness form DFNB30, has been proposed to transport espin-1 to the tips of stereocilia, thereby promoting their elongation. We show that Myo3a^−/−Myo3b^−/− mice lacking myosin IIIa and myosin IIIb are profoundly deaf, whereas Myo3a-cKO Myo3b^−/− mice lacking myosin IIIb and losing myosin IIIa postnatally have normal hearing. Myo3a^−/−Myo3b^−/− cochlear hair bundles display robust mechanoelectrical transduction currents with normal kinetics but show severe embryonic abnormalities whose features rapidly change. These include abnormally tall and numerous microvilli or stereocilia, ungraded stereocilia bundles, and bundle rounding and closure. Surprisingly, espin-1 is properly targeted to Myo3a^−/−Myo3b^−/− stereocilia tips. Our results uncover the critical role that class III myosins play redundantly in hair-bundle morphogenesis; they unexpectedly limit the elongation of stereocilia and of subsequently regressing microvilli, thus contributing to the early hair bundle shaping.     

Talin tension sensor reveals novel features of focal adhesion force transmission and mechanosensitivity

Integrin-dependent adhesions are mechanosensitive structures in which talin mediates a linkage to actin filaments either directly or indirectly by recruiting vinculin. Here, we report the development and validation of a talin tension sensor. We find that talin in focal adhesions is under tension, which is higher in peripheral than central adhesions. Tension on talin is increased by vinculin and depends mainly on actin-binding site 2 (ABS2) within the middle of the rod domain, rather than ABS3 at the far C terminus. Unlike vinculin, talin is under lower tension on soft substrates. The difference between central and peripheral adhesions requires ABS3 but not vinculin or ABS2. However, differential stiffness sensing by talin requires ABS2 but not vinculin or ABS3. These results indicate that central versus peripheral adhesions must be organized and regulated differently, and that ABS2 and ABS3 have distinct functions in spatial variations and stiffness sensing. Overall, these results shed new light on talin function and constrain models for cellular mechanosensing.     

Temporal evolution of biochar's impact on soil nitrogen processes – a 15N tracing study

Biochar addition to soils has been proposed as a means to increase soil fertility and carbon sequestration. However, its effect on soil nitrogen (N) cycling and N availability is poorly understood. To gain better insight into the temporal variability of the impact of biochar on gross soil N dynamics, two ¹⁵N tracing experiments, in combination with numerical data analysis, were conducted with soil from a biochar field trial, 1 day and 1 year after application of a woody biochar type. The results showed accelerated soil N cycling immediately following biochar addition, with increased gross N mineralization (+34%), nitrification (+13%) and ammonium (NH₄⁺) and nitrate (NO₃⁻) immobilization rates (+4500% and +511%, respectively). One year after biochar application, the biochar acted as an inert substance with respect to N cycling. In the short term, biochar's labile C fraction and a pH increase can explain stimulated microbial activity, while in the longer term, when the labile C fraction has been mineralized and the pH effect has faded, the accelerating effect of biochar on N cycling ceases. In conclusion, biochar accelerates soil N transformations in the short-term through stimulating soil microbial activity, thereby increasing N bio-availability. This effect is, however, temporary.     

Understanding the Sub-Cellular Dynamics of Silicon Transportation and Synthesis in Diatoms Using Population-Level Data and Computational Optimization

Controlled synthesis of silicon is a major challenge in nanotechnology and material science. Diatoms, the unicellular algae, are an inspiring example of silica biosynthesis, producing complex and delicate nano-structures. This happens in several cell compartments, including cytoplasm and silica deposition vesicle (SDV). Considering the low concentration of silicic acid in oceans, cells have developed silicon transporter proteins (SIT). Moreover, cells change the level of active SITs during one cell cycle, likely as a response to the level of external nutrients and internal deposition rates. Despite this topic being of fundamental interest, the intracellular dynamics of nutrients and cell regulation strategies remain poorly understood. One reason is the difficulties in measurements and manipulation of these mechanisms at such small scales, and even when possible, data often contain large errors. Therefore, using computational techniques seems inevitable. We have constructed a mathematical model for silicon dynamics in the diatom Thalassiosira pseudonana in four compartments: external environment, cytoplasm, SDV and deposited silica. The model builds on mass conservation and Michaelis-Menten kinetics as mass transport equations. In order to find the free parameters of the model from sparse, noisy experimental data, an optimization technique (global and local search), together with enzyme related penalty terms, has been applied. We have connected population-level data to individual-cell-level quantities including the effect of early division of non-synchronized cells. Our model is robust, proven by sensitivity and perturbation analysis, and predicts dynamics of intracellular nutrients and enzymes in different compartments. The model produces different uptake regimes, previously recognized as surge, externally-controlled and internally-controlled uptakes. Finally, we imposed a flux of SITs to the model and compared it with previous classical kinetics. The model introduced can be generalized in order to analyze different biomineralizing organisms and to test different chemical pathways only by switching the system of mass transport equations.     

What factors shape female phenotypes of a poleward‐moving damselfly at the edge of its range?

Individuals at the expansion front during a climate‐driven range expansion are expected to differ phenotypically from those individuals in core populations. Little information is known about the joint, potentially opposing, effects of stressful conditions at the range edge versus evolutionary changes that take place during range expansion in shaping the phenotypes at the range front. We investigated the effect of range expansion on immune function, body condition and flight‐related morphology (flight muscle ratio, wing loading, and wing aspect ratio) of field‐collected females of the poleward‐moving damselfly Coenagrion scitulum. Individuals at the expansion front had a lower body condition, which indicated more stressful conditions at the range edge. Despite the counteracting effect of the shorter growth season, the higher flight muscle ratios at the expansion front indicated a strong selection for dispersal ability during range expansion. The current study suggests that models need to incorporate the interplay of stressful conditions and evolutionary processes at the expansion front to arrive at robust predictions of future species distributions under global warming. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 556–568.     

Optimizing I/O forwarding techniques for extreme-scale event tracing

Programming development tools are a vital component for understanding the behavior of parallel applications. Event tracing is a principal ingredient to these tools, but new and serious challenges place event tracing at risk on extreme-scale machines. As the quantity of captured events increases with concurrency, the additional data can overload the parallel file system and perturb the application being observed. In this work we present a solution for event tracing on extreme-scale machines. We enhance an I/O forwarding software layer to aggregate and reorganize log data prior to writing to the storage system, significantly reducing the burden on the underlying file system. Furthermore, we introduce a sophisticated write buffering capability to limit the impact. To validate the approach, we employ the Vampir tracing toolset using these new capabilities. Our results demonstrate that the approach increases the maximum traced application size by a factor of 5× to more than 200,000 processes.