Search for Low-Molecular-Weight Biomarkers in Plant Tissues and Seeds Using Metabolomics: Tools, Strategies, and Applications

This chapter summarises the metabolomic strategies currently in force used in plant science and describes the methods used. The metabolite profiling and fingerprinting of plant tissues through MS- and/or NMR-based approaches and the subsequent identification of biomarkers is detailed. Strategies for the microisolation and de novo identification of unknown biomarkers are also discussed. The various approaches are illustrated by a metabolomic study of the maize response to herbivory. A review of recent metabolomic studies performed on seed and crop plant tissues involving various analytical strategies is provided.

Descriptive/Inferential Cognitive Processes and Evaluative Cognitive Processes: Relationships Among Each Other and with Emotional Distress

We aimed to delineate key constructs from two forms of cognitive-behavioral therapy: cognitive therapy and rational-emotive behavior therapy. Furthermore, we aimed to investigate the interrelations among each other and with emotional distress. The key constructs of the underlying theories of these therapies (i.e., descriptive/inferential beliefs, evaluative beliefs) are often treated together as distorted cognitions and included as such in various scales. We used a cross-sectional design. Seventy-four undergraduate students (mean age = 24.68) completed measures of automatic thoughts and emotional distress. Three therapists trained in cognitive-behavioral therapy divided automatic thoughts into descriptive/inferential beliefs and evaluative beliefs by consensus. Correlation and mediation analyses were performed. These constructs showed medium to high associations to each other and to distress. The relationship between descriptive/inferential beliefs and distress was mediated by evaluative beliefs. Descriptive and inferential cognitions may not produce emotions without first being appraised in terms of personal relevance.

Electrochemical CO2 Reduction - A Critical View on Fundamentals, Materials and Applications

The electrochemical reduction of CO2 has been extensively studied over the past decades. Nevertheless, this topic has been tackled so far only by using a very fundamental approach and mostly by trying to improve kinetics and selectivities toward specific products in half-cell configurations and liquid-based electrolytes. The main drawback of this approach is that, due to the low solubility of CO2 in water, the maximum CO2 reduction current which could be drawn falls in the range of 0.01–0.02 A cm–2. This is at least an order of magnitude lower current density than the requirement to make CO2-electrolysis a technically and economically feasible option for transformation of CO2 into chemical feedstock or fuel thereby closing the CO2 cycle. This work attempts to give a short overview on the status of electrochemical CO2 reduction with respect to challenges at the electrolysis cell as well as at the catalyst level. We will critically discuss possible pathways to increase both operating current density and conversion efficiency in order to close the gap with established energy conversion technologies.

Otium et negotium. Reading processes and their cultural backgrounds in early Italian and German humanism

Reading and reading habits have radically changed in the digital age. Readers are no longer physically bound to textual objects and libraries, they deal with texts by copying, altering, and annotating them, and they mix established textual forms with other semiotic systems such as pictograms, icons and images. These circumstances also provoke a renewed research interest in the history of reading. In this talk, I will concentrate on reading processes as to how they were enacted and practised in early Italian and German humanism. I will start with some paradigmatic scenes described in Petrarch’s letters (among others the famous visit of the Mont Ventoux, where Petrarch, after having enjoyed a spectacular panorama, withdraws into the contemplative reading of St-Augustine). The transmission of Petrarch’s writings in humanist circles of Southern Germany (e.g. with the Schedel and Gossembrot families in Nurnberg, Augsburg and Strasburg) will then lead to specific reading practices documented in manuscripts that once belonged to coherent libraries and are nowadays spread all over Europe. In the case of the former tradesman and mayor Sigismund Gossembrot, complex habits of textual annotating and cross-referencing can be observed. The dichotomy of the Latin terms otium (‘rest’ and ‘leisure’) and negotium (‘activity’, but also ‘practice’, ‘negotiation’, ‘circulation of social energy’ in the sense of New Historicism) will be used as an ideal-type outline to describe the occurring processes of reading.

Otium et negotium. Reading processes and their cultural backgrounds in early Italian and German humanism

Reading and reading habits have radically changed in the digital age. Readers are no longer physically bound to textual objects and libraries, they deal with texts by copying, altering, and annotating them, and they mix established textual forms with other semiotic systems such as pictograms, icons and images. These circumstances also provoke a renewed research interest in the history of reading. In this talk, I will concentrate on reading processes as to how they were enacted and practised in early Italian and German humanism. I will start with some paradigmatic scenes described in Petrarch’s letters (among others the famous visit of the Mont Ventoux, where Petrarch, after having enjoyed a spectacular panorama, withdraws into the contemplative reading of St-Augustine). The transmission of Petrarch’s writings in humanist circles of Southern Germany (e.g. with the Schedel and Gossembrot families in Nurnberg, Augsburg and Strasburg) will then lead to specific reading practices documented in manuscripts that once belonged to coherent libraries and are nowadays spread all over Europe. In the case of the former tradesman and mayor Sigismund Gossembrot, complex habits of textual annotating and cross-referencing can be observed. The dichotomy of the Latin terms otium (‘rest’ and ‘leisure’) and negotium (‘activity’, but also ‘practice’, ‘negotiation’, ‘circulation of social energy’ in the sense of New Historicism) will be used as an ideal-type outline to describe the occurring processes of reading.

Sedimentological processes and environmental variability at Lake Ohrid (Macedonia, Albania) between 637 ka and the present

Lake Ohrid (Macedonia, Albania) is thought to be more than 1.2 million years old and host more than 300 endemic species. As a target of the International Continental scientific Drilling Program (ICDP), a successful deep drilling campaign was carried out within the scope of the Scientific Collaboration on Past Speciation Conditions in Lake Ohrid (SCOPSCO) project in 2013. Here, we present lithological, sedimentological, and (bio-)geochemical data from the upper 247.8 m composite depth of the overall 569 m long DEEP site sediment succession from the central part of the lake. According to an age model, which is based on 11 tephra layers (first-order tie points) and on tuning of bio-geochemical proxy data to orbital parameters (second-order tie points), the analyzed sediment sequence covers the last 637 kyr. The DEEP site sediment succession consists of hemipelagic sediments, which are interspersed by several tephra layers and infrequent, thin (< 5 cm) mass wasting deposits. The hemipelagic sediments can be classified into three different lithotypes. Lithotype 1 and 2 deposits comprise calcareous and slightly calcareous silty clay and are predominantly attributed to interglacial periods with high primary productivity in the lake during summer and reduced mixing during winter. The data suggest that high ion and nutrient concentrations in the lake water promoted calcite precipitation and diatom growth in the epilimnion during MIS15, 13, and 5. Following a strong primary productivity, highest interglacial temperatures can be reported for marine isotope stages (MIS) 11 and 5, whereas MIS15, 13, 9, and 7 were comparably cooler. Lithotype 3 deposits consist of clastic, silty clayey material and predominantly represent glacial periods with low primary productivity during summer and longer and intensified mixing during winter. The data imply that the most severe glacial conditions at Lake Ohrid persisted during MIS16, 12, 10, and 6, whereas somewhat warmer temperatures can be inferred for MIS14, 8, 4, and 2. Interglacial-like conditions occurred during parts of MIS14 and 8.

Innovation Processes and Industrial Districts

In this survey, we examine the operations of innovation processes within industrial districts by exploring the ways in which differentiation, specialization, and integration affect the generation, diffusion, and use of new knowledge in such districts. We begin with an analysis of the importance of the division of labor and then investigate the effects of social embeddedness on innovation. We also consider the effect of forms of organization within industrial districts at various stages of product and process life, and we examine the negative aspects of embeddedness for innovation. We conclude with a discussion of the possible consequences of new information and communications technologies on innovation in industrial districts.

Advanced Protein Modeling Method: Benchmarking and Applications in Computer-Aided Drug Discovery

Development of homology modeling methods will remain an area of active research. These methods aim to develop and model increasingly accurate three-dimensional structures of yet uncrystallized therapeutically relevant proteins e.g. Class A G-Protein Coupled Receptors. Incorporating protein flexibility is one way to achieve this goal. Here, I will discuss the enhancement and validation of the ligand-steered modeling, originally developed by Dr. Claudio Cavasotto, via cross modeling of the newly crystallized GPCR structures. This method uses known ligands and known experimental information to optimize relevant protein binding sites by incorporating protein flexibility. The ligand-steered models were able to model, reasonably reproduce binding sites and the co-crystallized native ligand poses of the β2 adrenergic and Adenosine 2A receptors using a single template structure. They also performed better than the choice of template, and crude models in a small scale high-throughput docking experiments and compound selectivity studies. Next, the application of this method to develop high-quality homology models of Cannabinoid Receptor 2, an emerging non-psychotic pain management target, is discussed. These models were validated by their ability to rationalize structure activity relationship data of two, inverse agonist and agonist, series of compounds. The method was also applied to improve the virtual screening performance of the β2 adrenergic crystal structure by optimizing the binding site using β2 specific compounds. These results show the feasibility of optimizing only the pharmacologically relevant protein binding sites and applicability to structure-based drug design projects.

Calmodulin -regulated processes and intracellular calcium in the heat stress response of mammalian cells

Three approaches were used to examine the role of Ca$\sp{2+}$- and/or calmodulin (CaM)-regulated processes in the mammalian heat stress response. The focus of the first approach was on the major Ca$\sp{2+}$-binding protein, CaM, and involved the use of CaM antagonists that perturbed CaM-regulated processes during heat stress. The second approach involved the use of a cell line and its BPV-1 transformants that express increased basal levels of CaM, or parvalbumin--a Ca$\sp{2+}$-binding protein not normally found in these cells. The last approach used Ca$\sp{2+}$ chelators to buffer Ca$\sp{2+}$-transients.^ The principle conclusions resulting from these three experimental approaches are: (1) CaM antagonists cause a temperature-dependent potentiation of heat killing, but do not inhibit the triggering and development of thermotolerance suggesting some targets for heat killing are different from those that lead to thermotolerance; (2) Members of major HSP families (especially HSP70) can bind to CaM in a Ca$\sp{2+}$-dependent manner in vitro, and HSP have been associated with events leading to thermotolerance. But, because thermotolerance is not affected by CaM antagonists, and antagonists should interfere with HSP binding to CaM, the events leading to triggering or developing thermotolerance were not strongly dependent on HSP binding to CaM; (3) CaM antagonists can also bind to HSP70 (and possibly other HSP) suggesting an alternative mechanism for the action of these agents in heat killing may involve direct binding to other proteins, like HSP70, whose function is important for survival following heating and inhibiting their activity; and (4) The signal governing the rate of synthesis of another major HSP group, the HSP26 family, can be largely abrogated by elevated Ca$\sp{2+}$-binding proteins or Ca$\sp{2+}$ chelators without significantly reducing survival or thermotolerance suggesting if the HSP26 family is involved in either end point, it may function in (Ca$\sp{2+}$) $\sb{\rm i}$ homeostasis. ^

(Table 1) Effects of desiccation on photochemical processes and nitrogenase activity in Nostoc commune s.l. colonies

The effects of desiccation on photochemical processes and nitrogenase activity were evaluated in Nostoc commune s.l. colonies in situ from a wet thufur meadow at Petuniabukta, Billefjorden, Central Svalbard, during the 2009 arctic summer. The colonies were collected in the fully hydrated state, and were subjected to slow desiccation at ambient temperatures (5 - 8°C) and low light (30 - 80 µmol/m**2/s). For each colony the weight, area, photochemical performance, and nitrogenase activity were determined at the beginning, as well as on every day during the first four days of the experiment; thereafter, on every second day until desiccation was complete. The photochemical performance was evaluated from variable chlorophyll fluorescence parameters (FV/FM, Phi(PSII) , qP, and NPQ), and the nitrogenase activity was estimated by an acetylene-ethylene reduction assay. A significant decrease in the photochemically active area was recorded from the third day, when the colony had lost approximately 40% of its original weight indicating some changes in the extracellular matrix, and stopped on the 14th to 18th day. No effects of the desiccation on the main photochemical parameters (FV/FM, Phi(PSII), qP) were observed up to the sixth to eighth days of desiccation. Slightly lower values of FV/FM and Phi(PSII) recorded in fully-hydrated colonies could be caused by impaired diffusion of CO2 into cells. The steep reduction of photochemical activity occurred between the eighth and tenth day of the experiment, when the colony had lost approximately 80% of its fully-hydrated weight. The nitrogenase activity was highest on the first day, probably due to improved diffusion of N2 into cells, then declined, but was detectable until the sixth day of the experiment. Since Nostoc commune s.l. colonies were capable of photosynthesis and nitrogen fixation to the level of ca. 60% of its fully-hydrated weight, even partly-hydrated colonies contribute substantially to carbon and nitrogen cycling in the High Arctic wet meadow tundra ecosystem.

Microsedimentological characterization as indicators of sedimentary processes and climate changes during Lateglacial at Laguna Potrok Aike, Santa Cruz, Argentina

Palaeoclimatic and paleoenvironmental high latitude records in the Southern Hemisphere are scarce compared to the northern counterpart. However, understanding global evolution of environmental systems during sudden climate changes is inseparable from an equivalent knowledge of both Hemispheres. In this context, a high-resolution study of lacustrine sediments from Laguna Potrok Aike, Santa Cruz province, Patagonia, Argentina, was conducted for the Lateglacial period using concurrent X-Ray Fluorescence (XRF) and Scanning electron microscope analyses. Peaks of Ca/Si and Mn, and occurrences of the green alga Phacotus lenticularis have been interpreted as variations in ventilation of the water column from 13.6 to 11.1 ka cal. BP. During this interval, mild climate conditions during the Younger Dryas are characterized by relatively weak westerlies favouring the formation of a stratified water body as indicated by preserved manganese and Ca/Si peaks and high Total Organic Carbon (TOC) values. In this environment, water in the epilimnion can reach sufficiently high temperature to allow P. lenticularis to grow. Colder conditions are marked by peaks in Ca without P. lenticularis and occur during the Antarctic Cold Reversal (ACR). In this Lateglacial interval, micropumices were also detected in large amount. Image analysis of thin sections allowed the counting and size measurement of detrital particles and micropumices separately. Micropumices significantly influence the iron and titanium content, hence preventing to use them as proxies of detrital input in this interval.

Seawater carbonate chemistry, processes and elements during experiments with planktonic foraminifera Orbulina universa, 2004

We investigate the sensitivity of U/Ca, Mg/Ca, and Sr/Ca to changes in seawater [CO3[2-]] and temperature in calcite produced by the two planktonic foraminifera species, Orbulina universa and Globigerina bulloides, in laboratory culture experiments. Our results demonstrate that at constant temperature, U/Ca in O. universa decreases by 25 +/- 7% per 100 µmol [CO3[2-]] kg**-1, as seawater [CO3[2-]] increases from 110 to 470 µmol kg**-1. Results from G. bulloides suggest a similar relationship, but U/Ca is consistently offset by ~+40% at the same environmental [CO3[2-]]. In O. universa, U/Ca is insensitive to temperature between 15°C and 25°C. Applying the O. universa relationship to three U/Ca records from a related species, Globigerinoides sacculifer, we estimate that Caribbean and tropical Atlantic [CO3[2-]] was 110 +/- 70 µmol kg**-1 and 80 +/- 40 µmol kg**-1 higher, respectively, during the last glacial period relative to the Holocene. This result is consistent with estimates of the glacial-interglacial change in surface water [CO3[2-]] based on both modeling and on boron isotope pH estimates. In settings where the addition of U by diagenetic processes is not a factor, down-core records of foraminiferal U/Ca have potential to provide information about changes in the ocean's carbonate concentration.

Comparison of CO2 From Coal Capture Processes and Valorisation Technologies

Coal is the most plentiful and evenly distributed fossil fuel worldwide. Based on current production, it is estimated that the reserves will last approximately 130 years. Its use worldwide has been increasing, mainly due to consumption by emerging countries. CO2 emissions generated by combustion and the repercussions of such on climate change support the view that it could no longer be used. CO2 capture may be the solution to continue using it, which would cater for the growing energy demand worldwide. The aim of this study is to compare different processes concerning CO2 capture that may be economically viable, ultimately showing that coal, a fossil energy source widely distributed around the world, can, as a result of using different CO2 capture processes, be used as a clean source of electricity. Hence, in places where geological hurdles may render the costs of CO2 storage considerably higher, since it might have to travel far, coal may be used for other purposes, thus valorising CO2 within the industrial sector. This research is focused on the technical and economic comparison of the most relevant CO2 capture projects designed in Spain using different existing technologies. The oxyfuel project in Ciuden (Leon, Spain), the IGCC Elcogas, precombustion CO2-capture project (Puertollano, Spain) and the postcombustion project in Carboneras (Almeria, Spain) will be analyzed in order to assess the options available to valorise captured CO2. Valorising captured CO2 may be an adequate solution in areas where, although CO2 capture is still possible, storage is not equally so, thus generating a further benefit. The possible uses of CO2 will be assessed in vegetable growing greenhouses, harnessing CO2 in vegetable life cycles. This will also be used in growing algae for subsequent biodiesel production. Both CO2 capture and valorising will eventually lead to the clean use of coal, which will thus enhance the level of self-supply, aiding the development of electric vehicles, which require large amounts of electricity, as well as improve the level of energy autonomy in countries around the world. Another type of fuel, biodiesel, will also be obtained, without this affecting international food prices.

First results obtained using the CENBG nanobeam line: performances and applications

A high resolution focused beam line has been recently installed on the AIFIRA (“Applications Interdisciplinaires des Faisceaux d’Ions en Région Aquitaine”) facility at CENBG. This nanobeam line, based on a doublet–triplet configuration of Oxford Microbeam Ltd. OM-50™ quadrupoles, offers the opportunity to focus protons, deuterons and alpha particles in the MeV energy range to a sub-micrometer beam spot. The beam optics design has been studied in detail and optimized using detailed ray-tracing simulations and the full mechanical design of the beam line was reported in the Debrecen ICNMTA conference in 2008. During the last two years, the lenses have been carefully aligned and the target chamber has been fully equipped with particle and X-ray detectors, microscopes and precise positioning stages. The beam line is now operational and has been used for its firstapplications to ion beam analysis. Interestingly, this set-up turned out to be a very versatile tool for a wide range of applications. Indeed, even if it was not intended during the design phase, the ion optics configuration offers the opportunity to work either with a high current microbeam (using the triplet only) or with a lower current beam presenting a sub-micrometer resolution (using the doublet–triplet configuration). The performances of the CENBGnanobeam line are presented for both configurations. Quantitative data concerning the beam lateral resolutions at different beam currents are provided. Finally, the firstresults obtained for different types of application are shown, including nuclear reaction analysis at the micrometer scale and the firstresults on biological samples