Improved photobiological H-2 production in engineered green algal cells

Oxygenic photosynthetic organisms use solar energy to split water (H2O) into protons (H+), electrons (e(-)), and oxygen. A select group of photosynthetic microorganisms, including the green alga Chlamydomonas reinhardtii, has evolved the additional ability to redirect the derived H+ and e(-) to drive hydrogen (H-2) production via the chloroplast hydrogenases HydA1 and A2 (H(2)ase). This process occurs under anaerobic conditions and provides a biological basis for solar-driven H-2 production. However, its relatively poor yield is a major limitation for the economic viability of this process. To improve H-2 production in Chlamydomonas, we have developed a new approach to increase H+ and e(-) supply to the hydrogenases. In a first step, mutants blocked in the state 1 transition were selected. These mutants are inhibited in cyclic e(-) transfer around photosystem I, eliminating possible competition for e(-) with H(2)ase. Selected strains were further screened for increased H-2 production rates, leading to the isolation of Stm6. This strain has a modified respiratory metabolism, providing it with two additional important properties as follows: large starch reserves ( i.e. enhanced substrate availability), and a low dissolved O-2 concentration (40% of the wild type (WT)), resulting in reduced inhibition of H2ase activation. The H-2 production rates of Stm6 were 5 - 13 times that of the control WT strain over a range of conditions ( light intensity, culture time, +/- uncoupler). Typically, similar to 540 ml of H-2 liter(-1) culture ( up to 98% pure) were produced over a 10-14-day period at a maximal rate of 4 ml h(-1) ( efficiency = similar to 5 times the WT). Stm6 therefore represents an important step toward the development of future solar-powered H-2 production systems.

The realisation of JSD specifications in object oriented languages

Jackson System Development (JSD) is an operational software development method which addresses most of the software lifecycle either directly or by providing a framework into which more specialised techniques can fit. The method has two major phases: first an abstract specification is derived that is in principle executable; second the specification is implemented using a variety of transformations. The object oriented paradigm is based on data abstraction and encapsulation coupled to an inheritance architecture that is able to support software reuse. Its claims of improved programmer productivity and easier program maintenance make it an important technology to be considered for building complex software systems. The mapping of JSD specifications into procedural languages typified by Cobol, Ada, etc., involves techniques such as inversion and state vector separation to produce executable systems of acceptable performance. However, at present, no strategy exists to map JSD specifications into object oriented languages. The aim of this research is to investigate the relationship between JSD and the object oriented paradigm, and to identify and implement transformations capable of mapping JSD specifications into an object oriented language typified by Smalltalk-80. The direction which the transformational strategy follows is one whereby the concurrency of a specification is removed. Two approaches implementing inversion - an architectural transformation resulting in a simulated coroutine mechanism being generated - are described in detail. The first approach directly realises inversions by manipulating Smalltalk-80 system contexts. This is possible in Smalltalk-80 because contexts are first class objects and are accessible to the user like any other system object. However, problems associated with this approach are expounded. The second approach realises coroutine-like behaviour in a structure called a `followmap'. A followmap is the results of a transformation on a JSD process in which a collection of followsets is generated. Each followset represents all possible state transitions a process can undergo from the current state of the process. Followsets, together with exploitation of the class/instance mechanism for implementing state vector separation, form the basis for mapping JSD specifications into Smalltalk-80. A tool, which is also built in Smalltalk-80, supports these derived transformations and enables a user to generate Smalltalk-80 prototypes of JSD specifications.

Steps and bumps:precision extraction of discrete states of molecular machines

We report statistical time-series analysis tools providing improvements in the rapid, precision extraction of discrete state dynamics from time traces of experimental observations of molecular machines. By building physical knowledge and statistical innovations into analysis tools, we provide techniques for estimating discrete state transitions buried in highly correlated molecular noise. We demonstrate the effectiveness of our approach on simulated and real examples of steplike rotation of the bacterial flagellar motor and the F1-ATPase enzyme. We show that our method can clearly identify molecular steps, periodicities and cascaded processes that are too weak for existing algorithms to detect, and can do so much faster than existing algorithms. Our techniques represent a step in the direction toward automated analysis of high-sample-rate, molecular-machine dynamics. Modular, open-source software that implements these techniques is provided.

Metastability and dynamics of stem cells: from direct observations to inference at the single cell level

Organismal development, homeostasis, and pathology are rooted in inherently probabilistic events. From gene expression to cellular differentiation, rates and likelihoods shape the form and function of biology. Processes ranging from growth to cancer homeostasis to reprogramming of stem cells all require transitions between distinct phenotypic states, and these occur at defined rates. Therefore, measuring the fidelity and dynamics with which such transitions occur is central to understanding natural biological phenomena and is critical for therapeutic interventions.

While these processes may produce robust population-level behaviors, decisions are made by individual cells. In certain circumstances, these minuscule computing units effectively roll dice to determine their fate. And while the 'omics' era has provided vast amounts of data on what these populations are doing en masse, the behaviors of the underlying units of these processes get washed out in averages.

Therefore, in order to understand the behavior of a sample of cells, it is critical to reveal how its underlying components, or mixture of cells in distinct states, each contribute to the overall phenotype. As such, we must first define what states exist in the population, determine what controls the stability of these states, and measure in high dimensionality the dynamics with which these cells transition between states.

To address a specific example of this general problem, we investigate the heterogeneity and dynamics of mouse embryonic stem cells (mESCs). While a number of reports have identified particular genes in ES cells that switch between 'high' and 'low' metastable expression states in culture, it remains unclear how levels of many of these regulators combine to form states in transcriptional space. Using a method called single molecule mRNA fluorescent in situ hybridization (smFISH), we quantitatively measure and fit distributions of core pluripotency regulators in single cells, identifying a wide range of variabilities between genes, but each explained by a simple model of bursty transcription. From this data, we also observed that strongly bimodal genes appear to be co-expressed, effectively limiting the occupancy of transcriptional space to two primary states across genes studied here. However, these states also appear punctuated by the conditional expression of the most highly variable genes, potentially defining smaller substates of pluripotency.

Having defined the transcriptional states, we next asked what might control their stability or persistence. Surprisingly, we found that DNA methylation, a mark normally associated with irreversible developmental progression, was itself differentially regulated between these two primary states. Furthermore, both acute or chronic inhibition of DNA methyltransferase activity led to reduced heterogeneity among the population, suggesting that metastability can be modulated by this strong epigenetic mark.

Finally, because understanding the dynamics of state transitions is fundamental to a variety of biological problems, we sought to develop a high-throughput method for the identification of cellular trajectories without the need for cell-line engineering. We achieved this by combining cell-lineage information gathered from time-lapse microscopy with endpoint smFISH for measurements of final expression states. Applying a simple mathematical framework to these lineage-tree associated expression states enables the inference of dynamic transitions. We apply our novel approach in order to infer temporal sequences of events, quantitative switching rates, and network topology among a set of ESC states.

Taken together, we identify distinct expression states in ES cells, gain fundamental insight into how a strong epigenetic modifier enforces the stability of these states, and develop and apply a new method for the identification of cellular trajectories using scalable in situ readouts of cellular state.

Glass transitions and state diagram for freeze-dried pineapple

Glass transition temperature of freeze-dried pineapple conditioned by adsorption at various water activities at 25 degreesC was determined by differential scanning calorimetry (DSC). High moisture content samples corresponding to water activities higher than 0.9, obtained by liquid water addition, were also analysed. The DSC traces showed a well-visible shift in baseline at the glass transition temperature (T(g)). Besides, no ice formation was observed until water activity was equal to 0.75. For water activities lower than 0.88, the glass transition curve showed that T(g) decreased with increasing moisture content and the experimental data could be well-correlated by the Gordon-Taylor equation. For higher water activities, this curve exhibited a discontinuity, with suddenly increasing glass transition temperatures approaching a constant value that corresponds to the T(g) of the maximally freeze-concentrated amorphous matrix. The unfreezable water content was determined through melting enthalpy dependence on the sample moisture content.

Sorption isotherm, glass transitions and state diagram for freeze-dried plum skin and pulp

Differential scanning calorimetry (DSC) was used to determine phase transitions of freeze-dried plums. Samples at low and intermediate moisture contents, were conditioned by adsorption at various water activities (0.11≤a w≤0.90) at 25°C, whereas in the high moisture content region (a w>0.90) samples were obtained by direct water addition, with the resulting sorption isotherm being well described by the Guggenheim-Anderson-deBoer (GAB) model. Freeze-dried samples of separated plum skin and pulp were also analysed. At a w≤0.75, two glass transitions were visible, with the glass transition temperature (T g) decreasing with increasing a w due to the water plasticising effect. The first T g was attributed to the matrix formed by sugars and water. The second one, less visible and less plasticised by water, was probably due to macromolecules of the fruit pulp. The Gordon-Taylor model represented satisfactorily the matrix glass transition curve for a w≤0.90. In the higher moisture content range T g remained practically constant around T g′ (-57.5°C). Analysis of the glass transition curve and the sorption isotherm indicated that stability at a temperature of 25°C, would be attained by freeze dried plum at a water activity of 0.04, corresponding to a moisture content of 12.9% (dry basis). © 2006 SAGE Publications.

Singular Temperatures Connected to Charge Transport Mechanism Transitions in Perylene Bisimides from Steady-State Photocurrent Measurements

Perylene bisimides (PBIs) are n-type semiconducting and photogenerating materials widely used in a variety of optoelectronic devices. Particularly interesting are PBIs that are simultaneously water-soluble and liquid-crystalline (PBI-W+LC) and, thus, attractive for the development of high-performing easily processable applications in biology and “green” organic electronics. In this work, singular temperatures connected to charge transport mechanism transitions in a PBI-W+LC derivative are determined with high accuracy by means of temperature-dependent photocurrent studies. These singular temperatures include not only the ones observed at 60 and 110 °C, corresponding to phase transition temperatures from crystalline to liquid-crystalline (LC) and from LC to the isotropic phase, respectively, as confirmed by differential scanning calorimetry (DSC), but also a transition at 45 °C, not observed by DSC. By analyzing the photocurrent dependence simultaneously on temperature and on light intensity, this transition is interpreted as a change from monomolecular to bimolecular recombination. These results might be useful for other semiconducting photogenerating materials, not necessarily PBIs or even organic semiconductors, which also show transport behavior changes at singular temperatures not connected with structural or phase transitions.

Entropy, chaos, and excited-state quantum phase transitions in the Dicke model

We study nonequilibrium processes in an isolated quantum system-the Dicke model-focusing on the role played by the transition from integrability to chaos and the presence of excited-state quantum phase transitions. We show that both diagonal and entanglement entropies are abruptly increased by the onset of chaos. Also, this increase ends in both cases just after the system crosses the critical energy of the excited-state quantum phase transition. The link between entropy production, the development of chaos, and the excited-state quantum phase transition is more clear for the entanglement entropy.

New constraints on muon-neutrino to electron-neutrino transitions in MINOS

This paper reports results from a search for nu(mu) -> nu(e) transitions by the MINOS experiment based on a 7 x 10(20) protons-on-target exposure. Our observation of 54 candidate nu(e) events in the far detector with a background of 49.1 +/- 7.0(stat) +/- 2.7(syst) events predicted by the measurements in the near detector requires 2sin(2)(2 theta(13))sin(2)theta(23) < 0.12(0.20) at the 90% C.L. for the normal (inverted) mass hierarchy at delta(CP) = 0. The experiment sets the tightest limits to date on the value of theta(13) for nearly all values of delta(CP) for the normal neutrino mass hierarchy and maximal sin(2)(2 theta(23)).

Search for Muon-Neutrino to Electron-Neutrino Transitions in MINOS

This Letter reports on a search for nu(mu)->nu(e) transitions by the MINOS experiment based on a 3.14x10(20) protons-on-target exposure in the Fermilab NuMI beam. We observe 35 events in the Far Detector with a background of 27 +/- 5(stat)+/- 2(syst) events predicted by the measurements in the Near Detector. If interpreted in terms of nu(mu)->nu(e) oscillations, this 1.5 sigma excess of events is consistent with sin(2)(2 theta(13)) comparable to the CHOOZ limit when |Delta m(2)|=2.43x10(-3) eV(2) and sin(2)(2 theta(23))=1.0 are assumed.