High-resolution mapping of nucleoprotein complexes by site-specific protein-DNA photocrosslinking: organization of the human TBP-TFIIA-TFIIB-DNA quaternary complex.

We have used a novel site-specific protein-DNA photocrosslinking procedure to define the positions of polypeptide chains relative to promoter DNA in binary, ternary, and quaternary complexes containing human TATA-binding protein, human or yeast transcription factor IIA (TFIIA), human transcription factor IIB (TFIIB), and promoter DNA. The results indicate that TFIIA and TFIIB make more extensive interactions with promoter DNA than previously anticipated. TATA-binding protein, TFIIA, and TFIIB surround promoter DNA for two turns of DNA helix and thus may form a "cylindrical clamp" effectively topologically linked to promoter DNA. Our results have implications for the energetics, DNA-sequence-specificity, and pathway of assembly of eukaryotic transcription complexes.

A mechanism for inducing plant development: the genesis of a specific inhibitor.

Parasitic strategies are widely distributed in the plant kingdom and frequently involve coupling parasite organogenesis with cues from the host. In Striga asiatica, for example, the cues that initiate the development of the host attachment organ, the haustorium, originate in the host and trigger the transition from vegetative to parasitic mode in the root meristem. This system therefore offers a unique opportunity to study the signals and mechanisms that control plant cell morphogenesis. Here we establish that the biological activity of structural analogs of the natural inducer displays a marked dependence on redox potential and suggest the existence of a semiquinone intermediate. Building on chemistry that exploits the energetics of such an intermediate, cyclopropyl-p-benzoquinone (CPBQ) is shown to be a specific inhibitor of haustorial development. These data are consistent with a model where haustorial development is initiated by the completion of a redox circuit.

Nitric oxide inhibits creatine kinase and regulates rat heart contractile reserve.

Cardiac myocytes express both constitutive and cytokine-inducible nitric oxide syntheses (NOS). NO and its congeners have been implicated in the regulation of cardiac contractile function. To determine whether NO could affect myocardial energetics, 31P NMR spectroscopy was used to evaluate high-energy phosphate metabolism in isolated rat hearts perfused with the NO donor S-nitrosoacetylcysteine (SNAC). All hearts were exposed to an initial high Ca2+ (3.5 mM) challenge followed by a recovery period, and then, either in the presence or absence of SNAC, to a second high Ca2+ challenge. This protocol allowed us to monitor simultaneously the effect of SNAC infusion on both contractile reserve (i.e., baseline versus high workload contractile function) and high-energy phosphate metabolism. The initial high Ca2+ challenge caused the rate-pressure product to increase by 74 +/- 5% in all hearts. As expected, ATP was maintained as phosphocreatine (PCr) content briefly dropped and then returned to baseline during the subsequent recovery period. Control hearts responded similarLy to the second high Ca2+ challenge, but SNAC-treated hearts did not demonstrate the expected increase in rate-pressure product. In these hearts, ATP declined significantly during the second high Ca2+ challenge, whereas phosphocreatine did not differ from controls, suggesting that phosphoryl transfer by creatine kinase (CK) was inhibited. CK activity, measured biochemically, was decreased by 61 +/- 13% in SNAC-treated hearts compared to controls. Purified CK in solution was also inhibited by SNAC, and reversal could be accomplished with DTT, a sulfhydryl reducing agent. Thus, NO can regulate contractile reserve, possibly by reversible nitrosothiol modification of CK.

Identification of residues linked to the slow-->fast transition of thrombin.

Residues energetically linked to the allosteric transition of thrombin from its anticoagulant slow form to the procoagulant fast form have been identified by site-directed mutagenesis. The energetics of recognition by the two forms of the enzyme were probed by using a synthetic chromogenic substrate, fibrinogen, and hirudin. The thrombin residues E39, W60d, E192, D221, and D222 are linked to the slow-->fast transition and are part of an "allosteric core" through which events originating at the Na+ binding loop propagate to other regions of the enzyme. The thrombin residues Y76, W96, W148, and R173 lie at the periphery of the allosteric core, affect recognition of fibrinogen and hirudin to the same extent in both forms, and are not linked to the slow-->fast transition.

Brownian Carnot engine

The Carnot cycle imposes a fundamental upper limit to the efficiency of a macroscopic motor operating between two thermal baths. However, this bound needs to be reinterpreted at microscopic scales, where molecular bio-motors and some artificial micro-engines operate. As described by stochastic thermodynamics, energy transfers in microscopic systems are random and thermal fluctuations induce transient decreases of entropy, allowing for possible violations of the Carnot limit. Here we report an experimental realization of a Carnot engine with a single optically trapped Brownian particle as the working substance. We present an exhaustive study of the energetics of the engine and analyse the fluctuations of the finite-time efficiency, showing that the Carnot bound can be surpassed for a small number of non-equilibrium cycles. As its macroscopic counterpart, the energetics of our Carnot device exhibits basic properties that one would expect to observe in any microscopic energy transducer operating with baths at different temperatures. Our results characterize the sources of irreversibility in the engine and the statistical properties of the efficiency-an insight that could inspire new strategies in the design of efficient nano-motors.

Modeling magnetar outbursts: flux enhancements and the connection with short bursts and glitches

The availability of a large amount of observational data recently collected from magnetar outbursts is now calling for a complete theoretical study of outburst characteristics. In this Letter (the first of a series dedicated to modeling magnetar outbursts), we tackle the long-standing open issue of whether or not short bursts and glitches are always connected to long-term radiative outbursts. We show that the recent detection of short bursts and glitches seemingly unconnected to outbursts is only misleading our understanding of these events. We show that, in the framework of the starquake model, neutrino emission processes in the magnetar crust limit the temperature, and therefore the luminosity. This natural limit to the maximum luminosity makes outbursts associated with bright persistent magnetars barely detectable. These events are simply seen as a small luminosity increase over the already bright quiescent state, followed by a fast return to quiescence. In particular, this is the case for 1RXS J1708–4009, 1E 1841–045, SGR 1806–20, and other bright persistent magnetars. On the other hand, a similar event (with the same energetics) in a fainter source will drive a more extreme luminosity variation and longer cooling time, as for sources such as XTE J1810–197, 1E 1547–5408, and SGR 1627–41. We conclude that the non-detection of large radiative outbursts in connection with glitches and bursts from bright persistent magnetars is not surprising per se, nor does it need any revision of the glitches and burst mechanisms as explained by current theoretical models.

Interplay Between Structure, Stoichiometry, and Electron Transfer Dynamics in SILAR-based Quantum Dot-Sensitized Oxides

We quantify the rate and efficiency of picosecond electron transfer (ET) from PbS nanocrystals, grown by successive ionic layer adsorption and reaction (SILAR), into a mesoporous SnO2 support. Successive SILAR deposition steps allow for stoichiometry- and size-variation of the QDs, characterized using transmission electron microscopy. Whereas for sulfur-rich (p-type) QD surfaces substantial electron trapping at the QD surface occurs, for lead-rich (n-type) QD surfaces, the QD trapping channel is suppressed and the ET efficiency is boosted. The ET efficiency increase achieved by lead-rich QD surfaces is found to be QD-size dependent, increasing linearly with QD surface area. On the other hand, ET rates are found to be independent of both QD size and surface stoichiometry, suggesting that the donor–acceptor energetics (constituting the driving force for ET) are fixed due to Fermi level pinning at the QD/oxide interface. Implications of our results for QD-sensitized solar cell design are discussed.

Adaptation of yeasts to fructose rich environments: a role for horizontal gene transfer of a fructose transporter

Abstract of the poster presented 33rd Small Meeting on Yeast Transport and Energetics, 21-24 July 2015, Lisbon, Portugal.

Strain-induced structural instability in FeRh

We perform density functional calculations to investigate the structure of the intermetallic alloy FeRh under epitaxial strain. Bulk FeRh exhibits a metamagnetic transition from a low-temperature antiferromagnetic (AFM) phase to a ferromagnetic phase at 350 K, and its strain dependence is of interest for tuning the transition temperature to the room-temperature operating conditions of typical memory devices. We find an unusually strong dependence of the structural energetics on the choice of exchange-correlation functional, with the usual local density approximation yielding the wrong ground-state structure, and generalized gradient (GGA) extensions being in better agreement with the bulk experimental structure. Using the GGA we show the existence of a metastable face-centered-cubic-like AFM structure that is reached from the ground-state body-centered-cubic-like AFM structure by following the epitaxial Bain path. We show that the behavior is well described using nonlinear elasticity theory, which captures the softening and eventual sign change of the orthorhombic shear modulus under compressive strain, consistent with this structural instability. Finally, we predict the existence of an additional unit-cell-doubling lattice instability, which should be observable at low temperature.

Biotelemetry: a mechanistic approach to ecology

Remote measurement of the physiology, behaviour and energetic status of free-living animals is made possible by a variety of techniques that we refer to collectively as 'biotelemetry'. This set of tools ranges from transmitters that send their signals to receivers up to a few kilometers away to those that send data to orbiting satellites and, more frequently, to devices that log data. They enable researchers to document, for long uninterrupted periods, how undisturbed organisms interact with each other and their environment in real time. In spite of advances enabling the monitoring of many physiological and behavioural variables across a range of taxa of various sizes, these devices have yet to be embraced widely by the ecological community. Our review suggests that this technology has immense potential for research in basic and applied animal ecology. Efforts to incorporate biotelemetry into broader ecological research programs should yield novel information that has been challenging to collect historically from free-ranging animals in their natural environments. Examples of research that would benefit from biotelemetry include the assessment of animal responses to different anthropogenic perturbations and the development of life-time energy budgets.

Costs increase as ritualized fighting progresses within and between phases in the sierra dome spider, Neriene litigiosa

Magnitudes and patterns of energy expenditure in animal contests are seldom measured, but can be critical for predicting contest dynamics and understanding the evolution of ritualized fighting behaviour. In the sierra dome spider, males compete for sexual access to females and their webs. They show three distinct phases of fighting behaviour, escalating from ritualized noncontact display (phase 1) to cooperative wrestling (phase 2), and finally to unritualized, potentially fatal fighting (phase 3). Using CO2 respirometry, we estimated energetic costs of male-male combat in terms of mean and maximum metabolic rates and the rate of increase in energy expenditure. We also investigated the energetic consequences of age and body mass, and compared fighting metabolism to metabolism during courtship. All three phases involved mean energy expenditures well above resting metabolic rate (3.5 X, 7.4 X and 11.5 X). Both mean and maximum energy expenditure became substantially greater as fights escalated through successive phases. The rates of increase in energy use during phases 2 and 3 were much higher than in phase 1. In addition, age and body mass affected contest energetics. These results are consistent with a basic prediction of evolutionarily stable strategy contest models, that sequences of agonistic behaviours should be organized into phases of escalating energetic costs. Finally, higher energetic costs of escalated fighting compared to courtship provide a rationale for first-male sperm precedence in this spider species. (C) 2004 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

On the microscopic mechanism of carbon gasification: A theoretical study

In this paper we report the results of ab initio calculations on the energetics and kinetics of oxygen-driven carbon gasification reactions using a small model cluster, with full characterisation of the stationary points on the reaction paths. We show that previously unconsidered pathways present significantly reduced barriers to reaction and must be considered as alternative viable paths. At least two electronic spin states of the model cluster must be considered for a complete description. (C) 2004 Elsevier Ltd. All rights reserved.

Locomotion and gaits of the northern brown bandicoot, Isoodon macrourus (Marsupalia: Peramelidae)

Gait repertoires of the northern brown bandicoot, Isoodon macrourus, were studied over a wide range of locomotor speeds. At low relative speeds, bandicoots used symmetrical gaits that included pacing, trotting, and lateral sequence strides. Forefoot contact duration was generally shorter than hind foot contact duration at all speeds. At moderate relative speeds bandicoots used half-bounding gaits with either no period of suspension or with a short gathered suspension. At high speeds the predominant gait had both a short extended and a short gathered suspension, although some strides comprised only an extended suspension. Increases in speed were accompanied by increases in spinal extension, presumably leading to the extended suspensions. On a stationary treadmill individuals occasionally used a bipedal gait. Maximum half-bounding speeds appear to be relatively low in this species.

Esterified astaxanthin levels in lobster epithelia correlate with shell colour intensity: Potential role in crustacean shell colour formation

Carotenoids, particularly astaxanthin, are the primary pigment in crustacean shell colour. Sub-adults of the western rock lobster, Panulirus cygnus, moult from a deep red colour (termed the red phase) to a much paler colour (the white phase) at sexual maturation. We observe a 2.4-fold difference in the amount of total carotenoid present in the shell extracts of reds compared to whites, as might be expected. However, analysis of the underlying epithelium shows that there is no correlation with shell colour and the amount of free (unesterified) astaxanthin-the level of free astaxanthin in reds and whites is not significantly different. Instead, we observe a correlated two-fold difference in the amount of esterified astaxanthin present in the epithelium of red versus white individuals. These data suggest a role for esterified astaxanthin in regulating shell colour formation and suggest that esterification may promote secretion and eventual incorporation of unesterified astaxanthin into the exoskeleton. (c) 2005 Elsevier Inc. All rights reserved.

Interpretation of the temperature dependence of rate constants in biosensor studies

A comparison is made between Arrhenius and transition-state analyses of the temperature dependence of rate constants reported in four published biosensor studies. Although the Eyring transition-state theory seemingly affords a more definitive solution to the problem of characterizing the activation energetics, the analysis is equivocal because of inherent assumptions about reaction mechanism and the magnitude of the transmission coefficient. In view of those uncertainties it is suggested that a preferable course of action entails reversion to the empirical Arrhenius analysis with regard to the energy of activation and a preexponential factor. The former is essentially equivalent to the enthalpy of activation, whereas the magnitude of the latter indicates directly the extent of disparity between the frequency of product formation and the universal frequency factor (temperature multiplied by the ratio of the Boltzmann and Planck constants) and hence the likelihood of a more complicated kinetic mechanism than that encompassed by the Eyring transition-state theory. (C) 2004 Elsevier Inc. All rights reserved.