Stable isotopes reveal dietary shifts associated with social change in Hellenistic, Roman and Late Antique Knossos

Knossos was an important city on Crete and within Mediterranean networks in terms of trade and political status, though its status differed throughout the Hellenistic, Roman and Late Antique periods. This paper uses stable carbon and nitrogen isotope analysis to consider whether people at Knossos had differential diets due to the social, political, cultural, and economic changes across this time frame, factoring in age, sex and social status. Samples of human bone were selected to represent this range of time periods and variables. In this initial study, a small but insignificant increase in δ13C values was observed between the Hellenistic and Roman periods and there was a significant increase in δ15N values for the Late Antique period. No relationship between δ13C or δ15N and age was observed and while the female and male means were similar, the females had wider ranging values. No significant differences were detected by social status as represented by tomb type but there were small sample sizes for several of the tomb types. The results indicated a C3 terrestrial diet with meat or other animal products included for most individuals. The slight increase in δ13C values in the Roman period may represent either the introduction of a small amount of C4 plant or marine food, or very low trophic level marine foods into some Roman diets. The higher δ13C and, in particular, δ15N values observed in the Late Antique samples, suggests an increased consumption of seafood, potentially linked to Christian dietary practices or advances in fishing technologies and preservation techniques. The wider spread values of females compared to males, indicating a more varied diet, could have resulted from differential participation in religious institutions connected to food or may have been caused by greater nutritional stress in females in relation to pregnancy and reproductive issues. This study does not show a pattern of higher animal protein consumption in times of economic and cultural growth and prosperity but differences were detected between the different time periods in connection with the concurrent socio-economic changes

Reversible Optogenetic Control of Subcellular Protein Localization in a Live Vertebrate Embryo.

We demonstrate the utility of the phytochrome system to rapidly and reversibly recruit proteins to specific subcellular regions within specific cells in a living vertebrate embryo. Light-induced heterodimerization using the phytochrome system has previously been used as a powerful tool to dissect signaling pathways for single cells in culture but has not previously been used to reversibly manipulate the precise subcellular location of proteins in multicellular organisms. Here we report the experimental conditions necessary to use this system to manipulate proteins in vivo. As proof of principle, we demonstrate that we can manipulate the localization of the apical polarity protein Pard3 with high temporal and spatial precision in both the neural tube and the embryo's enveloping layer epithelium. Our optimizations of optogenetic component expression and chromophore purification and delivery should significantly lower the barrier for establishing this powerful optogenetic system in other multicellular organisms

A functional genomic and proteomic perspective of sea urchin calcium signaling and egg activation

AbstractThe sea urchin egg has a rich history of contributions to our understanding of fundamental questions of egg activation at fertilization. Within seconds of sperm–egg interaction, calcium is released from the egg endoplasmic reticulum, launching the zygote into the mitotic cell cycle and the developmental program. The sequence of the Strongylocentrotus purpuratus genome offers unique opportunities to apply functional genomic and proteomic approaches to investigate the repertoire and regulation of Ca2+ signaling and homeostasis modules present in the egg and zygote. The sea urchin “calcium toolkit” as predicted by the genome is described. Emphasis is on the Ca2+ signaling modules operating during egg activation, but the Ca2+ signaling repertoire has ramifications for later developmental events and adult physiology as well. Presented here are the mechanisms that control the initial release of Ca2+ at fertilization and additional signaling components predicted by the genome and found to be expressed and operating in eggs at fertilization. The initial release of Ca2+ serves to coordinate egg activation, which is largely a phenomenon of post-translational modifications, especially dynamic protein phosphorylation. Functional proteomics can now be used to identify the phosphoproteome in general and specific kinase targets in particular. This approach is described along with findings to date. Key outstanding questions regarding the activation of the developmental program are framed in the context of what has been learned from the genome and how this knowledge can be applied to functional studies

Consensus guidelines for the use and interpretation of angiogenesis assays

The formation of new blood vessels, or angiogenesis, is a complex process that plays important roles in growth and development, tissue and organ regeneration, as well as numerous pathological conditions. Angiogenesis undergoes multiple discrete steps that can be individually evaluated and quantified by a large number of bioassays. These independent assessments hold advantages but also have limitations. This article describes in vivo, ex vivo, and in vitro bioassays that are available for the evaluation of angiogenesis and highlights critical aspects that are relevant for their execution and proper interpretation. As such, this collaborative work is the first edition of consensus guidelines on angiogenesis bioassays to serve for current and future reference

Nodal Gradient Interpretation During Zebrafish Germ Layer Patterning

This thesis presents work toward understanding how cells within an embryo receive fate and positional information. It concentrates on the Nodal morphogen gradient, which specifies germ layer identity through differing levels of Nodal signaling. Although much progress has been made in understanding the components and outcomes of the Nodal signaling pathway, there is very poor quantitative understanding of how cells translate the duration and concentration of Nodal signaling into fate/positional information. To address this question, several new technologies were employed or developed. Light sheet fluorescence microscopy was used to image Nodal signaling dynamics in vivo (Chapter 5). This new imaging technology allowed us to: determine which cells are exposed to the Nodal signal, quantitate the duration and level of this signaling, and directly correlate this with cellular response, i.e. which Nodal target genes are turned on and what germ layer fate is adopted. We will use this information to propose an initial model for how Nodal signaling is interpreted at a cellular level. We will test our model with additional data taken in the presence of an inhibitor, to access whether the system behaves as expected when the input is modified. In order to develop finer control of the spatial and temporal aspects of perturbing a biological system, we simultaneously developed optogenetic tools for use in zebrafish embryos. Most optogenetic systems, especially those that control protein localization and expression, have been developed at the tissue-culture level and do not transfer directly to the multicellular organism level. We were successfully able to optimize two optogenetic systems for use in zebrafish, the phytochrome system for protein localization control (Chapter 2) and the LOV system for transcriptional control (Chapters 3 and 4)

Reversible Optogenetic Control of Subcellular Protein Localization in a Live Vertebrate Embryo

We demonstrate the utility of the phytochrome system to rapidly and reversibly recruit proteins to specific subcellular regions within specific cells in a living vertebrate embryo. Light-induced heterodimerization using the phytochrome system has previously been used as a powerful tool to dissect signaling pathways for single cells in culture but has not previously been used to reversibly manipulate the precise subcellular location of proteins in multicellular organisms. Here we report the experimental conditions necessary to use this system to manipulate proteins in vivo. As proof of principle, we demonstrate that we can manipulate the localization of the apical polarity protein Pard3 with high temporal and spatial precision in both the neural tube and the embryo’s enveloping layer epithelium. Our optimizations of optogenetic component expression and chromophore purification and delivery should significantly lower the barrier for establishing this powerful optogenetic system in other multicellular organisms

Reversible Optogenetic Control of Subcellular Protein Localization in a Live Vertebrate Embryo.

We demonstrate the utility of the phytochrome system to rapidly and reversibly recruit proteins to specific subcellular regions within specific cells in a living vertebrate embryo. Light-induced heterodimerization using the phytochrome system has previously been used as a powerful tool to dissect signaling pathways for single cells in culture but has not previously been used to reversibly manipulate the precise subcellular location of proteins in multicellular organisms. Here we report the experimental conditions necessary to use this system to manipulate proteins in vivo. As proof of principle, we demonstrate that we can manipulate the localization of the apical polarity protein Pard3 with high temporal and spatial precision in both the neural tube and the embryo's enveloping layer epithelium. Our optimizations of optogenetic component expression and chromophore purification and delivery should significantly lower the barrier for establishing this powerful optogenetic system in other multicellular organisms