Characterization of eukaryotic microbial diversity in hypersaline Lake Tyrrell, Australia.

This study describes the community structure of the microbial eukaryotic community from hypersaline Lake Tyrrell, Australia, using near full length 18S rRNA sequences. Water samples were taken in both summer and winter over a 4-year period. The extent of eukaryotic diversity detected was low, with only 35 unique phylotypes using a 97% sequence similarity threshold. The water samples were dominated (91%) by a novel cluster of the Alveolate, Apicomplexa Colpodella spp., most closely related to C. edax. The Chlorophyte, Dunaliella spp. accounted for less than 35% of water column samples. However, the eukaryotic community entrained in a salt crust sample was vastly different and was dominated (83%) by the Dunaliella spp. The patterns described here represent the first observation of microbial eukaryotic dynamics in this system and provide a multiyear comparison of community composition by season. The lack of expected seasonal distribution in eukaryotic communities paired with abundant nanoflagellates suggests that grazing may significantly structure microbial eukaryotic communities in this system

Modeling of biocatalytic reactions: A workflow for model calibration, selection and validation using Bayesian statistics

We present a workflow for kinetic modeling of biocatalytic reactions which combines methods from Bayesian learning and uncertainty quantification for model calibration, model selection, evaluation, and model reduction in a consistent statistical framework. Our workflow is particularly tailored to sparse data settings in which a considerable variability of the parameters remains after the models have been adapted to available data, a ubiquitous problem in many real‐world applications. Our workflow is exemplified on an enzyme‐catalyzed two‐substrate reaction mechanism describing the symmetric carboligation of 3,5‐dimethoxy‐benzaldehyde to (R )‐3,3′,5,5′‐tetramethoxybenzoin catalyzed by benzaldehyde lyase from Pseudomonas fluorescens . Results indicate a substrate‐dependent inactivation of enzyme, which is in accordance with other recent studies

Idiomatic Persistence and Querying for the W3C Web Annotation Data Model

Abstract. W3C Web annotations are a powerful way to support metadata information about digital resources. The Web Annotation Data Model proposes standardised RDF structures that express this by implementing a hierarchical annotation structure. Those annotations are designed to be shared, linked, tracked back as well as searched and discovered across different peers. However, non-Semantic Web experts may struggle to produce the corresponding RDF data or SPARQL queries. Therefore, we propose Anno4j, a Java-based library that gives developers the possibility to create and consume Web Annotations by using plain old Java objects. Anno4j follows natural Object-oriented idioms including inheritance, polymorphism, and composition to facilitate the development with Web Annotations. An extensible and modular architecture supports enhancements and use-case specific model alterations, while the plugin functionality of Anno4j allows to enrich querying by adding custom function evaluators

Performance Verification of the FlashCam Prototype Camera for the Cherenkov Telescope Array

The Cherenkov Telescope Array (CTA) is a future gamma-ray observatory that is planned to significantly improve upon the sensitivity and precision of the current generation of Cherenkov telescopes. The observatory will consist of several dozens of telescopes with different sizes and equipped with different types of cameras. Of these, the FlashCam camera system is the first to implement a fully digital signal processing chain which allows for a traceable, configurable trigger scheme and flexible signal reconstruction. As of autumn 2016, a prototype FlashCam camera for the medium-sized telescopes of CTA nears completion. First results of the ongoing system tests demonstrate that the signal chain and the readout system surpass CTA requirements. The stability of the system is shown using long-term temperature cycling.Comment: 5 pages, 13 figures, Proceedings of the 9th International Workshop on Ring Imaging Cherenkov Detectors (RICH 2016), Lake Bled, Sloveni

FlashCam: a fully-digital camera for the medium-sized telescopes of the Cherenkov Telescope Array

The FlashCam group is currently preparing photomultiplier-tube based cameras proposed for the medium-sized telescopes (MST) of the Cherenkov Telescope Array (CTA). The cameras are designed around the FlashCam readout concept which is the first fully-digital readout system for Cherenkov cameras, based on commercial FADCs and FPGAs as key components for the front-end electronics modules and a high performance camera server as back-end. This contribution describes the progress of the full-scale FlashCam camera prototype currently under construction, as well as performance results also obtained with earlier demonstrator setups. Plans towards the production and implementation of FlashCams on site are also briefly presented.Comment: 8 pages, 6 figures. In Proceedings of the 34th International Cosmic Ray Conference (ICRC2015), The Hague, The Netherlands. All CTA contributions at arXiv:1508.0589

Towards Protein Crystallization as a Process Step in Downstream Processing of Therapeutic Antibodies: Screening and Optimization at Microbatch Scale

Crystallization conditions of an intact monoclonal IgG4 (immunoglobulin G, subclass 4) antibody were established in vapor diffusion mode by sparse matrix screening and subsequent optimization. The procedure was transferred to microbatch conditions and a phase diagram was built showing surprisingly low solubility of the antibody at equilibrium. With up-scaling to process scale in mind, purification efficiency of the crystallization step was investigated. Added model protein contaminants were excluded from the crystals to more than 95%. No measurable loss of Fc-binding activity was observed in the crystallized and redissolved antibody. Conditions could be adapted to crystallize the antibody directly from concentrated and diafiltrated cell culture supernatant, showing purification efficiency similar to that of Protein A chromatography. We conclude that crystallization has the potential to be included in downstream processing as a low-cost purification or formulation step

The Effect of Osmolytes on Protein Fibrillation

Osmolytes are small molecules that are exploited by cells as a protective system against stress conditions. They favour compact protein states which makes them stabilize globular proteins in vitro and promote folding. Conversely, this preference for compact states promotes aggregation of unstructured proteins. Here we combine a brief review of the effect of osmolytes on protein fibrillation with a report of the effect of osmolytes on the unstructured peptide hormone glucagon. Our results show that osmolytes either accelerate the fibrillation kinetics or leave them unaffected, with the exception of the osmolyte taurine. Furthermore, the osmolytes that affected the shape of the fibrillation time profile led to fibrils with different structure as revealed by CD. The structural changes induced by Pro, Ser and choline-O-sulfate could be due to specific osmolytes binding to the peptides, stabilizing an otherwise labile fibrillation intermediate

Tolerance of allogromiid Foraminifera to severely elevated carbon dioxide concentrations : implications to future ecosystem functioning and paleoceanographic interpretations

Author Posting. © Elsevier B.V., 2009. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Global and Planetary Change 65 (2009): 107-114, doi:10.1016/j.gloplacha.2008.10.013.Increases in the partial pressure of carbon dioxide (pCO2) in the atmosphere will significantly affect a wide variety of terrestrial fauna and flora. Because of tight atmospheric-oceanic coupling, shallow-water marine species are also expected to be affected by increases in atmospheric carbon dioxide concentrations. One proposed way to slow increases in atmospheric pCO2 is to sequester CO2 in the deep sea. Thus, over the next few centuries marine species will be exposed to changing seawater chemistry caused by ocean-atmospheric exchange and/or deep-ocean sequestration. This initial case study on one allogromiid foraminiferal species (Allogromia laticollaris) was conducted to begin to ascertain the effect of elevated pCO2 on benthic Foraminifera, which are a major meiofaunal constituent of shallow- and deep-water marine communities. Cultures of this thecate foraminiferan protist were used for 10-14-day experiments. Experimental treatments were executed in an incubator that controlled CO2 (15 000; 30 000; 60 000; 90 000; 200 000 ppm), temperature and humidity; atmospheric controls (i.e., ~375 ppm CO2) were executed simultaneously. Although the experimental elevated pCO2 values are far above foreseeable surface water pCO2, they were selected to represent the spectrum of conditions expected for the benthos if deep-sea CO2 sequestration becomes a reality. Survival was assessed in two independent ways: pseudopodial presence/absence and measurement of adenosine triphosphate (ATP), which is an indicator of cellular energy. Substantial proportions of A. laticollaris populations survived 200 000 ppm CO2 although the mean of the median [ATP] of survivors was statistically lower for this treatment than for that of atmospheric control specimens. After individuals that had been incubated in 200 000 ppm CO2 for 12 days were transferred to atmospheric conditions for ~24 hours, the [ATP] of live specimens (survivors) approximated those of the comparable atmospheric control treatment. Incubation in 200 000 ppm CO2 also resulted in reproduction by some individuals. Results suggest that certain Foraminifera are able to tolerate deep-sea CO2 sequestration and perhaps thrive as a result of elevated pCO2 that is predicted for the next few centuries, in a high-pCO2 world. Thus, allogromiid foraminiferal “blooms” may result from climate change. Furthermore, because allogromiids consume a variety of prey, it is likely that they will be major players in ecosystem dynamics of future coastal sedimentary environments.This work was funded by US Department of Energy grant # DE-FG02-03ER63696 (to J. Kennett and J. Bernhard), NSF OCE-0725966, and the WHOI Summer Student Fellow Program, which is funded by NSF Research Experience for Undergraduates Program grant #OCE-0139423