A Customized Light Sheet Microscope to Measure Spatio-Temporal Protein Dynamics in Small Model Organisms

We describe a customizable and cost-effective light sheet microscopy (LSM) platform for rapid three-dimensional imaging of protein dynamics in small model organisms. The system is designed for high acquisition speeds and enables extended time-lapse in vivo experiments when using fluorescently labeled specimens. We demonstrate the capability of the setup to monitor gene expression and protein localization during ageing and upon starvation stress in longitudinal studies in individual or small groups of adult Caenorhabditis elegans nematodes. The system is equipped to readily perform fluorescence recovery after photobleaching (FRAP), which allows monitoring protein recovery and distribution under low photobleaching conditions. Our imaging platform is designed to easily switch between light sheet microscopy and optical projection tomography (OPT) modalities. The setup permits monitoring of spatio-temporal expression and localization of ageing biomarkers of subcellular size and can be conveniently adapted to image a wide range of small model organisms and tissue samples.     

Mechanical stress induces DNA synthesis in PDL fibroblasts by a mechanism unrelated to autocrine growth factor action

Periodontal regeneration is thought to require the proliferation of stress-sensitive periodontal ligament (PDL) fibroblast cells. The influence of physiological amounts of mechanical stretching on the DNA synthesis potential of human PDL fibroblasts was examined by means of an established, simple in vitro system of stretch application. A significant increase in the relative levels of incorporation of tritiated thymidine was observed in cultures stretched for 1–6 h. Neutralising antibodies for platelet-derived growth factor (PDGF) and transforming growth factor-beta (TGF-β) did not blunt the DNA synthesis induction. This mitogenic response to stretch appears to be independent of an autocrine mechanism involving growth factors in general, because stretch-conditioned medium, when transferred to non-stretched fibroblasts, did not mimic the mitogenic effect of stretch.     

On the role of an unusual tRNAGly isoacceptor in Staphylococcus aureus

In the available Staphylococcus aureus genomes, four different genes have been annotated to encode tRNA^Gly isoacceptors. Besides their prominent role in protein synthesis, some of them also participate in the formation of pentaglycine bridges during cell wall synthesis. However, until today, it is not known how many and which of them are actually involved in this essential procedure. In the present study we identified, apart from the four annotated tRNA^Gly genes, a putative pseudogene which encodes and expresses an unusual fifth tRNA^Gly isoacceptor in S. aureus (as detected via RT-PCR and subsequent direct sequencing analysis). All the in vitro transcribed tRNA^Gly molecules (including the “pseudogene-encoded” tRNA^Gly) can be efficiently aminoacylated by the recombinant S. aureus glycyl-tRNA synthetase. Furthermore, bioinformatic analysis suggests that the “pseudo”-tRNA^Gly(UCC) identified in the present study and two of the annotated isoacceptors bearing the same anticodon carry specific sequence elements that do not favour the strong interaction with EF-Tu that proteinogenic tRNAs would promote. This observation was verified by the differential capacity of Gly-tRNA^Gly molecules to form ternary complexes with activated S. aureus EF-Tu·GTP. These tRNA^Gly molecules display high sequence similarities with their S. epidermidis orthologs which also actively participate in cell wall synthesis. Both bioinformatic and biochemical data suggest that in S. aureus these three glycylated tRNA^Gly isoacceptors that are weak EF-Tu binders, possibly escape protein synthesis and serve as glycine donors for the formation of pentaglycine bridges that are essential for stabilization of the staphylococcal cell wall.     

Whey valorisation: A complete and novel technology development for dairy industry starter culture production

Whey is the major by-product of the dairy industry, produced in large quantities and usually disposed off causing major environmental pollution, due to its high organic load that makes treatment cost prohibitive. This paper comprises a contribution on the valorisation of this high polluting liquid waste of the dairy industry, based on research for the production of novel dairy starter cultures using whey as raw material. Starter cultures are used for cheese ripening in order to: (i) accelerate ripening, (ii) improve quality and (iii) increase shelf-life. The developed technology involves biomass production from whey followed by thermal drying of cultures. Specifically, Kluyveromyces marxianus, Lactobacillus bulgaricus and kefir yeasts were thermally dried, and their efficiency in lactose and milk whey fermentations was studied. The most suitable culture regarding its technological properties was kefir, which was used for cheese ripening in freeze-dried and thermally dried form. Besides the reduction of production cost, which is an essential requirement for the food industry, the use of thermally dried kefir displayed several other advantages such as acceleration of ripening, increase of shelf-life, and improvement of hard-type cheese quality.     

Production of human osteoclasts in a three-dimensional bone marrow culture system

Osteoclasts, which are derived from hemopoietic stem cells, play important roles in bone remodeling and resorption. Osteoclast development is critically dependent on the bone microenvironment. We have developed a novel human ex vivo bone marrow model that mimics bone marrow both structurally and functionally by providing artificial scaffolding, thus obtaining a three-dimensional growth configuration with high cell density and intimate physical contact between hemopoietic and stromal cells. In this study, we utilized the 3-D culture system to produce multinucleated cells (MNCs) from human bone marrow cells cultured in the presence of Vitamin D₃ and the absence of hydrocortisone and any exogenous growth factors. These multinucleated cells had the phenotypic and functional characteristics of osteoclasts as determined by their morphology, expression of tartarate resistant acid phosphatase (TRAP), and the ability to resorb bone. Scoring of the resorption pits revealed a dose response to Vitamin D₃ stimulation with 10⁻⁷ M being the optimal concentration. Furthermore, addition of parathyroid hormone (10⁻⁸ M) resulted in an up-to three-fold enhancement of bone resorption. These findings suggest that the 3-D culture system represent a physiologically relevant model to study osteoclastogenesis and elucidate the molecular and cellular signals associated with this process.     

Application of the OECD 301F respirometric test for the biodegradability assessment of various potential endocrine disrupting chemicals

The biodegradability of several potential endocrine disrupting compounds, namely 4-n-nonylphenol (4-n-NP), nonylphenol monoethoxylate (NP1EO), nonylphenol diethoxylate (NP2EO), bisphenol A (BPA), triclosan (TCS), di-(2-ethylhexyl)-phthalate (DEHP), perfluorooctanoate (PFOA) and perfluorononanoate (PFNA) was evaluated in this study, using OECD method 301F (manometric respirometry test) and activated sludge as inoculum. According to the results, 4-n-NP and BPA meet the strict definition of ready biodegradability and they are not expected to be persistent during the activated sludge process. Partial biodegradation was observed for DEHP (58.7+/-5.7%, n=3), TCS (52.1+/-8.5%, n=3) and NP1EO (25.9+/-8.1%, n=3), indicating their possible biodegradation in wastewater treatment systems, while no biodegradation was observed for NP2EO, PFOA and PFNA. Experiments in the co-presence of a readily biodegradable compound showed the absence of co-metabolic phenomena during 4-n-NP, BPA and TCS biodegradation. Using first order kinetics to describe biodegradation of the target compounds, half-lives of 4.3+/-0.6, 1.3+/-0.2, 1.8+/-0.5, 6.9+/-2.6 days were calculated for 4-n-NP, BPA, TCS and DEHP, respectively. Toxicity tests using marine bacterium Vibrio fischeri showed that biodegradation of 4-n-NP, NP1EO, BPA and TCS is a simultaneous detoxification process, while possible abiotic or biotic transformations of NP2EO, DEHP, PFOA and PFNA during respirometric test resulted to significant increase of their toxicities.     

Do long-term changes in sea surface temperature at the breeding areas affect the breeding dates and reproduction performance of Mediterranean loggerhead turtles? Implications for climate change

Global climate change is likely to have an important influence on the phenology, behaviour and population dynamics of many species. We investigate climatic related changes in the breeding phenology of Mediterranean loggerhead marine turtles Caretta caretta over a 19 year period and the potential relationship between these changes and reproductive success and performance. We found that the studied population has experienced fluctuating sea surface temperatures (SST) with an increasing trend during the last century. With increasing spring SST there is a trend towards earlier nesting. However, there is no significant relationship between SST and nesting season, defined as the duration between the first recorded emergence and the last nest laid. Our analyses indicate that marine turtles display phenological changes, and thus maintain favorable thermal conditions at the nesting sites. Furthermore, increasing spring SST was correlated with decreasing clutch size and increasing hatching success that resulted in an apparent lack of correlation between SST and hatchling production. This apparent independence might be misleading since it only holds for a limited range of SST values. Thus, if we estimate the effect of climate change on loggerhead population growth as neutral, based on the apparent independence between SST and total number of hatchlings, we will be underestimating the population extinction risk.     

Advanced model‐based control strategies for the intensification of upstream and downstream processing in mAb production

Current industrial trends encourage the development of sustainable, environmentally friendly processes with minimal energy and material consumption. In particular, the increasing market demand in biopharmaceutical industry and the tight regulations in product quality necessitate efficient operating procedures that guarantee products of high purity. In this direction, process intensification via continuous operation paves the way for the development of novel, eco‐friendly processes, characterized by higher productivity and lower production costs. This work focuses on the development of advanced control strategies for (i) a cell culture system in a bioreactor and (ii) a semicontinuous purification process. More specifically, we consider a fed‐batch culture of GS‐NS0 cells and the semicontinuous Multicolumn Countercurrent Solvent Gradient Purification (MCSGP) for the purification process. The controllers are designed following the PAROC framework/software platform and their capabilities are assessed in silico, against the process models. It is demonstrated that the proposed controllers efficiently manage to increase the system productivity, returning strategies that can lead to continuous, stable process operation. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:966–988, 2017