A Quantum Electrodynamics Description of Quantum Coherence and Damping in Condensed-Phase Energy Transfer.

Quantum coherence in condensed-phase electronic resonance energy transfer (RET) is described within the context of quantum electrodynamics (QED) theory. Mediating dressed virtual photons (polaritons) are explicitly incorporated into the treatment, and coherence is understood within the context of interfering Feynman pathways connecting the initial and final states for the RET process. The model investigated is that of an oriented three-body donor, acceptor, and mediator RET system embedded within a dispersive and absorbing polarizable medium. We show how quantum coherence can significantly enhance the rate of RET and give a rigorous picture for subsequent decoherence that is driven by both phase and amplitude damping. Energy-conserving phase damping occurs as a result of geometric and dispersive effects and is associated with destructive interference between Feynman pathways. Dissipative amplitude damping, on the other hand, is attributed to vibronic relaxation and absorptivity of the medium and can be understood as virtual photons (polaritons) leaking into the environment. This model offers insights into the emergence of coherence and subsequent decoherence for energy transfer in photosynthetic systems.

Nonlocalized Generation of Correlated Photon Pairs in Degenerate Down-Conversion.

The achievement of optimum conversion efficiency in conventional spontaneous parametric down-conversion requires consideration of quantum processes that entail multisite electrodynamic coupling, actively taking place within the conversion material. The physical mechanism, which operates through virtual photon propagation, provides for photon pairs to be emitted from spatially separated sites of photon interaction; occasionally pairs are produced in which each photon emerges from a different point in space. The extent of such nonlocalized generation is influenced by individual variations in both distance and phase correlation. Mathematical analysis of the global contributions from this mechanism provides a quantitative measure for a degree of positional uncertainty in the origin of down-converted emission.

Hyper-Rayleigh scattering in centrosymmetric systems.

Hyper-Rayleigh scattering (HRS) is an incoherent mechanism for optical second harmonic generation. The frequency-doubled light that emerges from this mechanism is not emitted in a laser-like manner, in the forward direction; it is scattered in all directions. The underlying theory for this effect involves terms that are quadratic in the incident field and involves an even-order optical susceptibility (for a molecule, its associated hyperpolarizability). In consequence, HRS is often regarded as formally forbidden in centrosymmetric media. However, for the fundamental three-photon interaction, theory based on the standard electric dipole approximation, representable as E1(3), does not account for all experimental observations. The relevant results emerge upon extending the theory to include E1(2)M1 and E1(2)E2 contributions, incorporating one magnetic dipolar or electric quadrupolar interaction, respectively, to a consistent level of multipolar expansion. Both additional interactions require the deployment of higher orders in the multipole expansion, with the E1(2)E2 interaction analogous in rank and parity to a four-wave susceptibility. To elicit the correct form of response from fluid or disordered media invites a tensor representation which does not oversimplify the molecular components, yet which can produce results to facilitate the interpretation of experimental observations. The detailed derivation in this work leads to results which are summarized for the following: perpendicular detection of polarization components both parallel and perpendicular to the pump radiation, leading to distinct polarization ratio results, as well as a reversal ratio for forward scattered circular polarizations. The results provide a route to handling data with direct physical interpretation, to enable the more sophisticated design of molecules with sought nonlinear optical properties.

Resonance energy transfer: influence of neighboring matter absorbing in the wavelength region of the acceptor.

In many of the materials and systems in which resonance energy transfer occurs, the individual chromophores are embedded within a superstructure of significantly different chemical composition. In accounting for the influence of the surrounding matter, the simplest and most widely used representation is commonly cast in terms of a dependence on local refractive index. However, such a depiction is a significant oversimplification, as it fails to register the electronic and local geometric effects of material specifically in the vicinity of the chromophores undergoing energy transfer. The principal objective of this study is to construct a detailed picture of how individual photon interaction events are modified by vicinal, non-absorbing chromophores. A specific aim is to discover what effects arise when input excitation is located in the neighborhood of other chromophores that have a slightly shorter wavelength of absorption; this involves a passive effect exerted on the transfer of energy at wavelengths where they themselves display no significant absorption. The theory is based on a thorough quantum electrodynamical analysis that allows the identification of specific optical and electronic chromophore attributes to expedite or inhibit electronic energy transfer. The Clausius-Mossotti dispersion relationship is then deployed to elicit a dependence on the bulk refractive index of the surroundings. A distinction is drawn between cases in which the influence on the electromagnetic coupling between the donor and the acceptor is primarily due to the static electric field produced by a polar medium, and converse cases in which the mechanism for modifying the form of energy transfer involves the medium acquiring an induced electric dipole. The results provide insights into the detailed quantum mechanisms that operate in multi-chromophore systems, pointing to factors that contribute to the optimization of photosystem characteristics.

A deacetylase-deficient SIRT1 variant opposes full-length SIRT1 in regulating tumor suppressor p53 and governs expression of cancer-related genes.

SIRT1 is an NAD-dependent deacetylase and epigenetic regulator essential for normal mammalian development and homeostasis. Here we describe a human SIRT1 splice variant, designated SIRT1-Δ2/9, in which the deacetylase coding sequence is lost due to splicing between exons 2 and 9. This work aimed to determine if SIRT1-Δ2/9 is a novel functional product of the SIRT1 gene. Endogenous SIRT1-Δ2/9 protein was identified in human cell lysate by immunoblotting and splice variant-specific RNA interference (RNAi). SIRT1-Δ2/9 mRNA is bound by CUGBP2, which downregulates its translation. Using pulldown assays, we demonstrate that SIRT1-Δ2/9 binds p53 protein. SIRT1-Δ2/9 maintains basal p53 protein levels and supports p53 function in response to DNA damage, as evidenced by RNAi-mediated depletion of SIRT1-Δ2/9 prior to damage. In turn, basal p53 downregulates SIRT1-Δ2/9 RNA levels, while stress-activated p53 eliminates SIRT1-Δ2/9. Loss of wild-type (wt) p53 has been correlated with overexpression of SIRT1-Δ2/9 in a range of human cancers. Exogenous SIRT1-Δ2/9 protein associates with specific promoters in chromatin and can regulate cancer-related gene expression, as evidenced by chromatin immunoprecipitation analysis and RNAi/genomic array data. SIRT1 is of major therapeutic importance, and potential therapeutic drugs are screened against SIRT1 deacetylase activity. Our discovery of SIRT1-Δ2/9 identifies a new, deacetylase-independent therapeutic target for SIRT1-related diseases, including cancer.

SIRT1 undergoes alternative splicing in a novel auto-regulatory loop with p53.

BACKGROUND: The NAD-dependent deacetylase SIRT1 is a nutrient-sensitive coordinator of stress-tolerance, multiple homeostatic processes and healthspan, while p53 is a stress-responsive transcription factor and our paramount tumour suppressor. Thus, SIRT1-mediated inhibition of p53 has been identified as a key node in the common biology of cancer, metabolism, development and ageing. However, precisely how SIRT1 integrates such diverse processes remains to be elucidated. METHODOLOGY/PRINCIPAL FINDINGS: Here we report that SIRT1 is alternatively spliced in mammals, generating a novel SIRT1 isoform: SIRT1-ΔExon8. We show that SIRT1-ΔExon8 is expressed widely throughout normal human and mouse tissues, suggesting evolutionary conservation and critical function. Further studies demonstrate that the SIRT1-ΔExon8 isoform retains minimal deacetylase activity and exhibits distinct stress sensitivity, RNA/protein stability, and protein-protein interactions compared to classical SIRT1-Full-Length (SIRT1-FL). We also identify an auto-regulatory loop whereby SIRT1-ΔExon8 can regulate p53, while in reciprocal p53 can influence SIRT1 splice variation. CONCLUSIONS/SIGNIFICANCE: We characterize the first alternative isoform of SIRT1 and demonstrate its evolutionary conservation in mammalian tissues. The results also reveal a new level of inter-dependency between p53 and SIRT1, two master regulators of multiple phenomena. Thus, previously-attributed SIRT1 functions may in fact be distributed between SIRT1 isoforms, with important implications for SIRT1 functional studies and the current search for SIRT1-activating therapeutics to combat age-related decline.

JNK2-dependent regulation of SIRT1 protein stability.

Mammalian SIRT1 is an NAD-dependent deacetylase with critical roles in the maintenance of homeostasis and cell survival. Elevated levels of SIRT1 protein are evident in cancer in which SIRT1 can function as a cancer-specific survival factor. Here we demonstrate that elevated SIRT1 protein in human cells is not attributable to increased SIRT1 mRNA levels but, instead, reflects SIRT1 protein stability. RNAi-mediated depletion of JNK2 reduced the half-life of SIRT1 protein from >9 h to <2 h and this correlated with lack of SIRT1 protein phosphorylation at serine 27. In contrast, depletion of JNK1 had no effect upon SIRT1 protein stability and SIRT1 phosphorylation at serine 47 showed no correlation with SIRT1 protein stability. Thus we show that JNK2 is linked, directly or indirectly, with SIRT1 protein stability and that this function is coupled with SIRT1 phosphorylation at serine 27. Our observations identify a route for therapeutic modulation of SIRT1 protein levels in SIRT1-linked diseases including cancer, neurodegeneration and diabetes.

Development and comparisons of efficient gas-cultivation systems for anaerobic carbon monoxide-utilizing microorganisms.

We describe a system for the cultivation of gaseous substrate utilizing microorganisms that overcomes some of the limitations of fixed volume culture vessels and the costs associated with sparging. Cali-5-Bond gas-sampling bag was used as the culture vessel. The bags contain approximately six times more mass of CO than the 40 mL vials at 1 atm of pressure and performed equally to the 40 mL vials in terms of their ability to maintain the composition of the gas over extended incubation times. Experiments using Clostridium ljungdahlii and CO as the sole carbon and energy source in both the gas sampling bag cultivation system and the traditional vial system demonstrated that this culture had a 15x increase in optical density in 24 h of incubation. The gas-sampling bags offer a viable alternative to gas sparging while overcoming the limitations of fixed volume culture vessels.

Cancer-specific functions of SIRT1 enable human epithelial cancer cell growth and survival.

SIRT1 is a conserved NAD-dependent deacetylase that regulates life span in accord with nutritional provision. In mammalian cells, SIRT1 also down-regulates stress-induced p53 and FoxO pathways for apoptosis, thus favoring survival under stress. The functioning of SIRT1 under normal, nonstressed conditions of cell growth is unknown. Here we have asked if SIRT1 has the capacity to influence cell viability in the absence of applied stress. For this purpose we used synthetic small interfering RNA to silence SIRT1 gene expression by RNA interference (RNAi). We show that the process of RNAi, by itself, does not affect cell growth and is not sufficient to activate a cellular stress response (indicated by lack of activation of endogenous p53). We also show that, in the absence of applied stress, SIRT1 silencing induces growth arrest and/or apoptosis in human epithelial cancer cells. In contrast, normal human epithelial cells and normal human diploid fibroblasts seem to be refractory to SIRT1 silencing. Combined gene knockout with RNAi cosilencing experiments indicate that SIRT1 and Bcl-2 may suppress separable apoptotic pathways in the same cell lineage and that the SIRT1-regulated pathway is independent of p53, Bax, and caspase-2. Alternatively, SIRT1 may suppress apoptosis downstream from these apoptotic factors. In either case, we show that FoxO4 (but not FoxO3) is required as proapoptotic mediator. We further identify caspase-3 and caspase-7 as downstream executioners of SIRT1/FoxO4-regulated apoptosis. Our work identifies SIRT1 as a novel target for selective killing of cancer versus noncancer epithelial cells.