Low-Cost Cryo-Light Microscopy Stage Fabrication for Correlated Light/Electron Microscopy

The coupling of cryo-light microscopy (cryo-LM) and cryo-electron microscopy (cryo-EM) poses a number of advantages for understanding cellular dynamics and ultrastructure. First, cells can be imaged in a near native environment for both techniques. Second, due to the vitrification process, samples are preserved by rapid physical immobilization rather than slow chemical fixation. Third, imaging the same sample with both cryo-LM and cryo-EM provides correlation of data from a single cell, rather than a comparison of "representative samples". While these benefits are well known from prior studies, the widespread use of correlative cryo-LM and cryo-EM remains limited due to the expense and complexity of buying or building a suitable cryogenic light microscopy stage. Here we demonstrate the assembly, and use of an inexpensive cryogenic stage that can be fabricated in any lab for less than $40 with parts found at local hardware and grocery stores. This cryo-LM stage is designed for use with reflected light microscopes that are fitted with long working distance air objectives. For correlative cryo-LM and cryo-EM studies, we adapt the use of carbon coated standard 3-mm cryo-EM grids as specimen supports. After adsorbing the sample to the grid, previously established protocols for vitrifying the sample and transferring/handling the grid are followed to permit multi-technique imaging. As a result, this setup allows any laboratory with a reflected light microscope to have access to direct correlative imaging of frozen hydrated samples

Neurogenesis Deep Learning

Neural machine learning methods, such as deep neural networks (DNN), have achieved remarkable success in a number of complex data processing tasks. These methods have arguably had their strongest impact on tasks such as image and audio processing - data processing domains in which humans have long held clear advantages over conventional algorithms. In contrast to biological neural systems, which are capable of learning continuously, deep artificial networks have a limited ability for incorporating new information in an already trained network. As a result, methods for continuous learning are potentially highly impactful in enabling the application of deep networks to dynamic data sets. Here, inspired by the process of adult neurogenesis in the hippocampus, we explore the potential for adding new neurons to deep layers of artificial neural networks in order to facilitate their acquisition of novel information while preserving previously trained data representations. Our results on the MNIST handwritten digit dataset and the NIST SD 19 dataset, which includes lower and upper case letters and digits, demonstrate that neurogenesis is well suited for addressing the stability-plasticity dilemma that has long challenged adaptive machine learning algorithms.Comment: 8 pages, 8 figures, Accepted to 2017 International Joint Conference on Neural Networks (IJCNN 2017

Intrinsic properties of a Burridge-Knopoff model of an earthquake fault

We present a detailed numerical study of certain fundamental aspects of a one-dimensional homogeneous, deterministic Burridge-Knopoff model. The model is described by a massive wave equation, in which the key nonlinearity is associated with the stick-slip velocity-weakening friction force at the interface between tectonic plates. In this paper, we present results for the statistical distribution of slipping events in the limit of a very long fault and infinitesimally slow driving rates. Typically, we find that the magnitude distribution of smaller events is consistent with the Gutenberg-Richter law, while the larger events occur in excess of this distribution. The crossover from smaller to larger events is identified with a correlation length describing the transition from localized to delocalized events. We also find that there is a sharp upper cutoff describing the maximum large event. We identify how the correlation length and this upper cutoff scale with the parameters in the model. We find that both are independent of system size, while both do depend on the spatial discretization. In addition to the magnitude distribution, we present a series of measurements of other seismologically relevant quantities, including the event duration, the size of the rupture zone, and the energy release, and discuss the relationship between our measurements and the corresponding empirical laws in seismology

Influence of coral and algal exudates on microbially mediated reef metabolism.

Benthic primary producers in tropical reef ecosystems can alter biogeochemical cycling and microbial processes in the surrounding seawater. In order to quantify these influences, we measured rates of photosynthesis, respiration, and dissolved organic carbon (DOC) exudate release by the dominant benthic primary producers (calcifying and non-calcifying macroalgae, turf-algae and corals) on reefs of Mo'orea French Polynesia. Subsequently, we examined planktonic and benthic microbial community response to these dissolved exudates by measuring bacterial growth rates and oxygen and DOC fluxes in dark and daylight incubation experiments. All benthic primary producers exuded significant quantities of DOC (roughly 10% of their daily fixed carbon) into the surrounding water over a diurnal cycle. The microbial community responses were dependent upon the source of the exudates and whether the inoculum of microbes included planktonic or planktonic plus benthic communities. The planktonic and benthic microbial communities in the unamended control treatments exhibited opposing influences on DO concentration where respiration dominated in treatments comprised solely of plankton and autotrophy dominated in treatments with benthic plus plankon microbial communities. Coral exudates (and associated inorganic nutrients) caused a shift towards a net autotrophic microbial metabolism by increasing the net production of oxygen by the benthic and decreasing the net consumption of oxygen by the planktonic microbial community. In contrast, the addition of algal exudates decreased the net primary production by the benthic communities and increased the net consumption of oxygen by the planktonic microbial community thereby resulting in a shift towards net heterotrophic community metabolism. When scaled up to the reef habitat, exudate-induced effects on microbial respiration did not outweigh the high oxygen production rates of benthic algae, such that reef areas dominated with benthic primary producers were always estimated to be net autotrophic. However, estimates of microbial consumption of DOC at the reef scale surpassed the DOC exudation rates suggesting net consumption of DOC at the reef-scale. In situ mesocosm experiments using custom-made benthic chambers placed over different types of benthic communities exhibited identical trends to those found in incubation experiments. Here we provide the first comprehensive dataset examining direct primary producer-induced, and indirect microbially mediated alterations of elemental cycling in both benthic and planktonic reef environments over diurnal cycles. Our results highlight the variability of the influence of different benthic primary producers on microbial metabolism in reef ecosystems and the potential implications for energy transfer to higher trophic levels during shifts from coral to algal dominance on reefs

Repellent Surface Applications for Pest Birds

Common pest birds in the United States include the non-native European starling (Sturnus vulgaris), house sparrow (Passer domesticus), and the pigeon (Columba livia domestica), as well as native birds including Canada geese (Branta canadensis) and gull species (Laridae). Large concentrations of pest birds can create human health hazards and monetary losses due to consumption of crops, depredation, and fecal contamination and accumulation. Fecal contamination hazards include the potential spread of zoonotic diseases including antimicrobial-resistant zoonoses and human injury due to the accumulation of fecal material on walking surfaces. Additionally, fecal accumulation causes structural and aesthetic damage due to the accelerated deterioration of building materials and increased maintenance costs. Methods to alleviate hazards and damages from aggregations of pest birds are needed. In a series of 3 experiments conducted in Fort Collins, Colorado, USA, between 2016 and 2018, we evaluated 3 surface-application repellent formulations for the reduction of fecal accumulations due to European starlings: Airepel® HC with castor oil, an anthraquinone-based repellent; Airepel HC with castor oil without anthraquinone; and MS2, a novel inert formulation with a tacky, oily texture. We compared each formulation directly to an untreated control. All 3 formulations reduced fecal accumulations beneath treated aluminum perches as compared to fecal accumulations beneath untreated aluminum perches. Interestingly, both formulations that contained no anthraquinone worked equally well or better than Airepel HC with castor oil, the anthraquinone-based formulation. The benefits of an exclusively inert formulation include less risk to applicators and non-target species. Comprehensive experimental field testing of these surface-application repellent formulations is warranted

Great Plains Soils May be C Sinks

Numerous studies with wide-ranging results have been conducted to resolve if Great Plains soils are a C source or sink. The authors addressed the source/sink question by examining the results from producer soil samples and production surveys that were analyzed and archived by the South Dakota Soil Testing Laboratory. Results showed that between 1985 and 2010, soil organic C content increased at a rate of 326 lb C/A/year, for a total increase of 24%. The increase was attributed to planting better adapted varieties and using better management practices that on average increased corn grain yields 2.29 bu/A/year. Higher soil organic C has impacts on water quality, soil productivity, and plant nutrition. For example, if we assume that the C:N ratio of organic matter is 10:1, then these findings would indicate that soils during this 25-year period were a sink for both C and N, and could have influenced the N needed to optimize crop yields

Overcoming Fas-mediated apoptosis accelerates Helicobacter-induced gastric cancer in mice

The initiating molecular events in Helicobacter-induced gastric carcinogenesis are not known. Early in infection, Fas antigen-mediated apoptosis depletes parietal and chief cell populations, leading to architectural distortion. As infection progresses, metaplastic and dysplastic glands appear, which are resistant to Fas-mediated apoptosis. These abnormal lineages precede, and are thought to be the precursor lesions of, gastric cancer. Acquisition of an antiapoptotic phenotype before transformation of cells suggests that loss of Fas sensitivity may be an early required trait for gastric cancer. We reasoned that forced Fas-apoptosis resistance would result in earlier and more aggressive gastric cancer in our mouse model. Fas antigen-deficient (lpr) mice or C57BL/6 wild-type mice were irradiated and reconstituted with C57BL/6 marrow forming partial lpr/wt chimera or wt/wt control mice, extending the life span of the lpr and ensuring a competent immune response to Helicobacter felis infection. Infected lpr/wt mice developed gastric cancer as early as 7 months after infection (compared with 15 months in wt/wt mice). At 10 months (90%) and 15 months (100%), mice developed aggressive invasive lesions. This earlier onset and more aggressive histology strongly argues that Fas-apoptosis resistance is an early and important feature of gastric cancer formation