Modelling aspects of oviduct fluid formation in vitro

© 2017 Society for Reproduction and Fertility. Oviduct fluid is the microenvironment that supports early reproductive processes including fertilisation, embryo cleavage and genome activation. However, the composition and regulation of this critical environment remain rather poorly defined. This study uses an in vitro preparation of the bovine oviduct epithelium to investigate the formation and composition of in vitro-derived oviduct fluid (ivDOF) within a controlled environment. We confirm the presence of oviduct-specific glycoprotein 1 in ivDOF and show that the amino acid and carbohydrate content resembles that of previously reported in vivo data. In parallel, using a different culture system, a panel of oviduct epithelial solute carrier genes and the corresponding flux of amino acids within ivDOF in response to steroid hormones were investigated. We next incorporated fibroblasts directly beneath the epithelium. This dual culture arrangement represents more faithfully the in vivo environment and impacts on ivDOF composition. Lastly, physiological and pathophysiological endocrine states were modelled and their impact on the in vitro oviduct preparation was evaluated. These experiments help clarify the dynamic function of the oviduct in vitro and suggest a number of future research avenues, such as investigating epithelial-fibroblast interactions, probing the molecular aetiologies of subfertility and optimising embryo culture media

An investigation on effectiveness of temperature treatment for fluorine-based reactive plasma jet machining of N-BK7®

In this study, a fluorine-based reactive plasma jet is investigated as a promising tool for ultraprecise surface machining of N-BK7®. Plasma-generated particles react with an N-BK7 surface to create volatile and nonvolatile compounds. The desorption of volatile compounds results in an etched surface, whereas nonvolatile compounds form a residual layer in the etched area, causing unpredictable effects on the etching rate. Surface temperature treatment is proposed to improve the machining procedure with respect to deterministic material removal, leading to predictable results. It is shown that, at an elevated surface temperature, the residual layer properties are modified in favor of improved etching performance. The etching behavior of N-BK7 is compared with fused silica to verify the optimality of the obtained results

A novel Deal–Grove-inspired model for fluorine-based plasma jet etching of borosilicate crown optical glass

The Deal–Grove model is a state-of-the-art approach proposed for describing the thermal oxidation of silicon and the oxide thickness over time. In this study, the Deal–Grove concept provided the inspiration for a mathematical model for simulating plasma jet-based dry etching process of borosilicate crown glass (N-BK7®). The whole process is contained in two so-called Deal–Grove parameters, which are extracted from experimental data including local etching depth and surface temperature distribution. The proposed model is extended for the evolution of dynamic etch profiles, and the obtained results are validated experimentally. By establishing such a model, it is possible to predict the effect of the residual layer and surface temperature on the evolution of local etching depths over dwell time

Development of a model for ultra-precise surface machining of N-BK7® using microwave-driven reactive plasma jet machining

In this paper, extensive studies are conducted as key to overcoming several challenging limitations in applying fluorine-based reactive plasma jet machining (PJM) to surface machining of N-BK7®, particularly regarding the manufacture of freeform optical elements. The chemical composition and lateral distributions of the residual layer are evaluated by X-ray photoelectron spectroscopy and scanning electron microscopy/energy-dispersive X-ray spectroscopy analysis aiming at clarifying the exact chemical kinetics between plasma generated active particles and the N-BK7 surface atoms. Subsequently, a model is developed by performing static etchings to consider the time-varying nonlinearity of the material removal rate and estimate the local etching rate function. Finally, the derived model is extended into the dynamic machining process, and the outcomes are compared with the experimental results

Impact of a Cold Pool Parameterization on the Diurnal Cycle and Intraseasonal Variability in the GEOS AGCM

A gradual transition from shallow to deep convection may be important both to the continental diurnal cycle of precipitation and to the tropical Madden-Julian Oscillation. However, many existing convection parameterizations transition too readily, with corresponding diurnal and intraseasonal biases. High entrainment rates can be used to delay deep convection, but typically produce mean state biases; this is the "entrainment dilemma." Cold pools and sub-grid organization offer a potential solution to this dilemma, and recent work shows parameterized cold pools can effectively modulate deep convection, with improvements to the diurnal cycle and intraseasonal variability. Here we investigate the effects of a simple prognostic cold pool scheme coupled to the Grell-Freitas convection parameterization, in a set of global simulations with the NASA GEOS model. Air detrained from parameterized downdrafts is maintained in vertically resolved cold pools, which evolve with simplified dynamics. We test several options for cold pool feedbacks on convection, including modifications to deep convective entrainment rates, convective source air properties, and thermodynamic profiles, based on the level of cold pool activity. Cold pool impacts on the diurnal cycle are evaluated against TRMM, and moisture and moist static energy budgets are used to understand changes in tropical intraseasonal variability. Preliminary results show delays in the diurnal cycle of precipitation

Proteomic analysis of Daphnia magna hints at molecular pathways involved in defensive plastic responses

Background: Phenotypic plasticity in defensive traits occurs in many species when facing heterogeneous predator regimes. The waterflea Daphnia is well-known for showing a variety of these so called inducible defences. However, molecular mechanisms underlying this plasticity are poorly understood so far. We performed proteomic analysis on Daphniamagna exposed to chemical cues of the predator Triops cancriformis. D. magna develops an array of morphological changes in the presence of Triops including changes of carapace morphology and cuticle hardening. Results: Using the 2D-DIGE technique, 1500 protein spots could be matched and quantified. We discovered 179 protein spots with altered intensity when comparing Triops exposed animals to a control group, and 69 spots were identified using nano-LC MS/MS. Kairomone exposure increased the intensity of spots containing muscle proteins, cuticle proteins and chitin-modifying enzymes as well as enzymes of carbohydrate and energy metabolism. The yolk precursor protein vitellogenin decreased in abundance in 41 of 43 spots. Conclusion: Identified proteins may be either directly involved in carapace stability or reflect changes in energy demand and allocation costs in animals exposed to predator kairomones. Our results present promising candidate proteins involved in the expression of inducible defences in Daphnia and enable further in depth analysis of this phenomenon

LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia

<p>Abstract</p> <p>Background</p> <p>Daphniids, commonly known as waterfleas, serve as important model systems for ecology, evolution and the environmental sciences. The sequencing and annotation of the <it>Daphnia pulex </it>genome both open future avenues of research on this model organism. As proteomics is not only essential to our understanding of cell function, and is also a powerful validation tool for predicted genes in genome annotation projects, a first proteomic dataset is presented in this article.</p> <p>Results</p> <p>A comprehensive set of 701,274 peptide tandem-mass-spectra, derived from <it>Daphnia pulex</it>, was generated, which lead to the identification of 531 proteins. To measure the impact of the <it>Daphnia pulex </it>filtered models database for mass spectrometry based <it>Daphnia </it>protein identification, this result was compared with results obtained with the Swiss-Prot and the <it>Drosophila melanogaster </it>database. To further validate the utility of the <it>Daphnia pulex </it>database for research on other <it>Daphnia </it>species, additional 407,778 peptide tandem-mass-spectra, obtained from <it>Daphnia longicephala</it>, were generated and evaluated, leading to the identification of 317 proteins.</p> <p>Conclusion</p> <p>Peptides identified in our approach provide the first experimental evidence for the translation of a broad variety of predicted coding regions within the <it>Daphnia </it>genome. Furthermore it could be demonstrated that identification of <it>Daphnia longicephala </it>proteins using the <it>Daphnia pulex </it>protein database is feasible but shows a slightly reduced identification rate. Data provided in this article clearly demonstrates that the <it>Daphnia </it>genome database is the key for mass spectrometry based high throughput proteomics in <it>Daphnia</it>.</p