Governing taste: data, temporality and everyday kiwifruit dry matter performances.

Data is essential to governing those emerging matters of concern that confront the agrifood every day. But data is no neutral intermediary. It disrupts, exposes, and creates new social, economic, political, and environmental possibilities, whilst simultaneously hiding, excluding, and foreclosing others. Scholars have become attuned to both the constitutive role of data in creating everyday worlds, and the need to develop critical accounts of the materialities, spatialities and multiplicities of data relationships. Whereas this emerging work develops insight to the capacity for data topologies to reterritorialise the spatial performances of everyday life, it has largely reduced the associated temporal dimensions to matters of fact. The effect of these performances has been to naturalize the temporal quality of speed and elide the multiple temporalities required to enact contemporary data worlds. Applying the lenses of infrastructuring, performativity and ferality, this paper explores temporality and data in the everyday worlds produced through the New Zealand kiwifruit industry's focus on dry matter. The paper argues that temporalities are deeply embedded in the kiwifruit industry's data relations. We show that while temporal data relations are critical to the industry, we also highlight ways in which those relations introduce new, potentially destabilizing performances into kiwifruit relations.

GC-IMS headspace analyses allow early recognition of bacterial growth and rapid pathogen differentiation in standard blood cultures.

Outcome of patients with blood stream infections (BSI) depends on the rapid initiation of adequate antibiotic therapy, which relies on the fast and reliable identification of the underlying pathogen. Blood cultures (BC) using CO2-sensitive colorimetric indicators and subsequent microbiological culturing are the diagnostic gold standard but turnaround times range between 24 and 48 h. The detection of volatile organic compounds of microbial origin (mVOC) has been described as a feasible method for identifying microbial growth and to differentiate between several microbial species. In this study, we aimed to investigate the ability of mVOC analyses using a gas chromatograph coupled to an ion mobility spectrometer (GC-IMS) for the recognition of bacterial growth and bacterial differentiation in BCs. Therefore, samples of whole blood and diluted bacterial suspension were injected into aerobic and anaerobic BC bottles and incubated for 8 h. Headspace samples from cultures of Escherichia coli (DSM 25944), Staphylococcus aureus (DSM 13661), and Pseudomonas aeruginosa (DSM 1117) were investigated hourly and we determined at which point of time a differentiation between the bacteria was possible. We found specific mVOC signals in the headspace over growing BCs of all three bacterial species. GC-IMS headspace analyses allowed faster recognition of bacterial growth than the colorimetric indicator of the BCs. A differentiation between the three investigated species was possible after 6 h of incubation with a high reliability in the principal component analysis. We concluded that GC-IMS headspace analyses could be a helpful method for the rapid detection and identification of bacteria in BSI.

Exploring the influence of natural cosolvents on the free energy and conformational landscape of filamentous actin and microtubules.

Actin and tubulin, the main components of the cytoskeleton, are responsible for many different cellular functions and can be found in nearly all eukaryotic cells. The formation of filamentous actin (F-actin) as well as microtubules depends strongly on environmental and solution conditions. The self-assembly of both, actin and tubulin, has been found to be among the most pressure sensitive process in vivo. Here, we explored the effects of various types of natural cosolvents, such as urea and the osmolyte trimethylamine-N-oxide (TMAO), on the temperature- and pressure-dependent stability of their polymeric states, F-actin and microtubules. Accumulation of TMAO by deep-sea animals is proposed to protect against destabilizing effects of pressure. The pressure and temperature of unfolding as well as associated enthalpy and volume changes have been determined using Fourier-transform infrared spectroscopy, covering a wide range of pressures and temperatures, ranging from 1 bar to 11 kbar and from 20 to 90 °C, respectively. Complementary thermodynamic measurements have been carried out using differential scanning and pressure perturbation calorimetry. The results obtained helped us explore the effect of the cellular milieu on the limitations of the pressure stability of cytoskeletal assemblies. Conversely to urea, the pressure stability of both polymers increases dramatically in the presence of TMAO, counteracting detrimental effects of both, urea and pressure.

Toward Extreme Biophysics: Deciphering the Infrared Response of Biomolecular Solutions at High Pressures.

Biophysics under extreme conditions is the fundamental platform for scrutinizing life in unusual habitats, such as those in the deep sea or continental subsurfaces, but also for putative extraterrestrial organisms. Therefore, an important thermodynamic variable to explore is pressure. It is shown that the combination of infrared spectroscopy with simulation is an exquisite approach for unraveling the intricate pressure response of the solvation pattern of TMAO in water, which is expected to be transferable to biomolecules in their native solvent. Pressure-enhanced hydrogen bonding was found for TMAO in water. TMAO is a molecule known to stabilize proteins against pressure-induced denaturation in deep-sea organisms.

Pressure and Temperature Effects on the Activity and Structure of the Catalytic Domain of Human MT1-MMP.

Membrane type 1-matrix metalloproteinase (MT1-MMP or MMP-14) is a zinc-transmembrane metalloprotease involved in the degradation of extracellular matrix and tumor invasion. While changes in solvation of MT1-MMP have been recently studied, little is known about the structural and energetic changes associated with MT1-MMP while interacting with substrates. Steady-state kinetic and thermodynamic data (including activation energies and activation volumes) were measured over a wide range of temperatures and pressures by means of a stopped-flow fluorescence technique. Complementary temperature- and pressure-dependent Fourier-transform infrared measurements provided corresponding structural information of the protein. MT1-MMP is stable and active over a wide range of temperatures (10-55 °C). A small conformational change was detected at 37 °C, which is responsible for the change in activity observed at the same temperature. Pressure decreases the enzymatic activity until complete inactivation occurs at 2 kbar. The inactivation is associated with changes in the rate-limiting step of the reaction caused by additional hydration of the active site upon compression and/or minor conformational changes in the active site region. Based on these data, an energy and volume diagram could be established for the various steps of the enzymatic reaction.

Combined effects of temperature, pressure, and co-solvents on the polymerization kinetics of actin.

In vivo studies have shown that the cytoskeleton of cells is very sensitive to changes in temperature and pressure. In particular, actin filaments get depolymerized when pressure is increased up to several hundred bars, conditions that are easily encountered in the deep sea. We quantitatively evaluate the effects of temperature, pressure, and osmolytes on the kinetics of the polymerization reaction of actin by high-pressure stopped-flow experiments in combination with fluorescence detection and an integrative stochastic simulation of the polymerization process. We show that the compatible osmolyte trimethylamine-N-oxide is not only able to compensate for the strongly retarding effect of chaotropic agents, such as urea, on actin polymerization, it is also able to largely offset the deteriorating effect of pressure on actin polymerization, thereby allowing biological cells to better cope with extreme environmental conditions.

Exploring the structure and phase behavior of plasma membrane vesicles under extreme environmental conditions.

Not only drastic temperature- but also pressure-induced perturbations of membrane organization pose a serious challenge to the biological cell. Although high hydrostatic pressure significantly influences the structural properties and thus functional characteristics of cells, this has not prevented life from invading the high pressure habitats of marine depths where pressures up to the 100 MPa level are encountered. Here, the temperature- and pressure-dependent structure and phase behavior of giant plasma membrane vesicles have been explored in the absence and presence of membrane proteins using a combined spectroscopic and microscopic approach. Demixing into extended liquid-ordered and liquid-disordered domains is observed over a wide range of temperatures and pressures. Only at pressures beyond 200 MPa a physiologically unfavorable all gel-like ordered lipid phase is reached at ambient temperature. This is in fact the pressure range where the membrane-protein function has generally been observed to cease, thereby shedding new light on the possible origin of this observation.

Cosolvent and crowding effects on the polymerization kinetics of actin.

We studied the effects of kosmotropic and chaotropic cosolvents, trimethylamine-N-oxide (TMAO) and urea, as well as crowding agents (dextran) on the polymerization reaction of actin. Time-lapse fluorescence intensity and anisotropy experiments were carried out to yield information about the kinetics of the polymerization process. To also quantitatively describe the effects, cosolvents and crowding impose on the underlying rate constants of the G-to-F-transformation, an integrative stochastic simulation model was applied. Drastic and diverse changes in the lag phase and association rates as well as the critical actin concentration were observed under different solvent conditions. The association rate constant is drastically increased by TMAO but decreased by urea. In mixtures of these osmolytes, TMAO counteracts not only the deleterious effect of urea on protein structure and stability, but also on the protein-protein interactions in the course of actin polymerization. Owing to the excluded volume effect, cell-like macromolecular crowding conditions increase the nucleation and association rates by one order of magnitude. Our results clearly reveal the pronounced sensitivity of the actin polymerization reaction to changes in cosolvent conditions and the presence of macromolecular crowding, and suggest that such effects should be taken into account in any discussion of the actin polymerization reaction in vivo.

Exploring the free energy and conformational landscape of tRNA at high temperature and pressure.

A combined temperature- and pressure-dependent study was employed to reveal the conformational and free-energy landscape of phenylalanine transfer RNA (tRNA(Phe) ), a known model for RNA function, to elucidate the features that are essential in determining its stability. These studies also help explore its structural properties under extreme environmental conditions, such as low/high temperatures and high pressures. To this end, fluorescence and FTIR spectroscopies, calorimetric and small-angle scattering measurements were carried out at different ion concentrations over a wide range of temperatures and pressures up to several hundred MPa. Compared with the pronounced temperature effect, the pressure-dependent structural changes of tRNA(Phe) are small. A maximum of only 15 % unpaired bases is observed upon pressurization up to 1 GPa. RNA unfolding differs not only from protein unfolding, but also from DNA melting. Its pressure stability seems to be similar to that of noncanonical DNA structures.

Exploring the stability limits of actin and its suprastructures.

Actin is the main component of the microfilament system in eukaryotic cells and can be found in distinct morphological states. Global (G)-actin is able to assemble into highly organized, supramolecular cellular structures known as filamentous (F)-actin and bundled (B)-actin. To evaluate the structure and stability of G-, F-, and B-actin over a wide range of temperatures and pressures, we used Fourier transform infrared spectroscopy in combination with differential scanning and pressure perturbation calorimetry, small-angle x-ray scattering, laser confocal scanning microscopy, and transmission electron microscopy. Our analysis was designed to provide new (to our knowledge) insights into the stabilizing forces of actin self-assembly and to reveal the stability of the actin polymorphs, including in conditions encountered in extreme environments. In addition, we sought to explain the limited pressure stability of actin self-assembly observed in vivo. G-actin is not only the least temperature-stable but also the least pressure-stable actin species. Under abyssal conditions, where temperatures as low as 1-4°C and pressures up to 1 kbar are reached, G-actin is hardly stable. However, the supramolecular assemblies of actin are stable enough to withstand the extreme conditions usually encountered on Earth. Beyond ∼3-4 kbar, filamentous structures disassemble, and beyond ∼4 kbar, complete dissociation of F-actin structures is observed. Between ∼1 and 2 kbar, some disordering of actin assemblies commences, in agreement with in vivo observations. The limited pressure stability of the monomeric building block seems to be responsible for the suppression of actin assembly in the kbar pressure range.

Game playing.

Game playing has been a core domain of artificial intelligence research since the beginnings of the field. Game playing provides clearly defined arenas within which computational approaches can be readily compared to human expertise through head-to-head competition and other benchmarks. Game playing research has identified several simple core algorithms that provide successful foundations, with development focused on the challenges of defeating human experts in specific games. Key developments include minimax search in chess, machine learning from self-play in backgammon, and Monte Carlo tree search in Go. These approaches have generalized successfully to additional games. While computers have surpassed human expertise in a wide variety of games, open challenges remain and research focuses on identifying and developing new successful algorithmic foundations. WIREs Cogn Sci 2014, 5:193-205. doi: 10.1002/wcs.1278 CONFLICT OF INTEREST: The author has declared no conflicts of interest for this article. For further resources related to this article, please visit the WIREs website.

Layer-by-layer assembly of a streptavidin-fibronectin multilayer on biotinylated TiO(X).

The biomodification of surfaces, especially titanium, is an important issue in current biomedical research. Regarding titanium, it is also important to ensure a specific protein modification of its surface because here protein binding that is too random can be observed. Specific nanoscale architectures can be applied to overcome this problem. As recently shown, streptavidin can be used as a coupling agent to immobilize biotinylated fibronectin (bFn) on a TiO(X) surface. Because of the conformation of adsorbed biotinylated fibronectin on a streptavidin monolayer, it is possible to adsorb more streptavidin and biotinylated fibronectin layers. On this basis, an alternating protein multilayer can be built up. In contrast to common layer-by-layer technology, in this procedure the mechanism of layer adsorption is very specific because of the interaction of biotin and streptavidin. In addition, we showed that the assembly of this multilayer system and its stability are dependent on the degree of labeling of biotinylated fibronectin. Hence we conclude that it is possible to build up well-defined nanoscale protein architectures by varying the degree of labeling of biotinylated fibronectin.

Adsorption and conformation behavior of biotinylated fibronectin on streptavidin-modified TiO(X) surfaces studied by SPR and AFM.

It is well-known that protein-modified implant surfaces such as TiO(2) show a higher bioconductivity. Fibronectin is a glycoprotein from the extracellular matrix (ECM) with a major role in cell adhesion. It can be applied on titanium oxide surfaces to accelerate implant integration. Not only the surface concentration but also the presentation of the protein plays an important role for the cellular response. We were able to show that TiO(X) surfaces modified with biotinylated fibronectin adsorbed on a streptavidin-silane self-assembly multilayer system are more effective regarding osteoblast adhesion than surfaces modified with nonspecifically bound fibronectin. The adsorption and conformation behavior of biotinylated and nonbiotinylated (native) fibronectin was studied by surface plasmon resonance (SPR) spectroscopy and atomic force microscopy (AFM). Imaging of the protein modification revealed that fibronectin adopts different conformations on nonmodified compared to streptavidin-modified TiO(X) surfaces. This conformational change of biotinylated fibronectin on the streptavidin monolayer delivers a fibronectin structure similar to the conformation inside the ECM and therefore explains the higher cell affinity for these surfaces.