A Bloch equation approach to intensity dependent optical spectra of light harvesting complex II

On the basis of the recent progress in the resolution of the structure of the antenna light harvesting complex II (LHC II) of the photosystem II, we propose a microscopically motivated theory to predict excitation intensity-dependent spectra. We show that optical Bloch equations provide the means to include all 2( N ) excited states of an oligomer complex of N coupled two-level systems and analyze the effects of Pauli Blocking and exciton-exciton annihilation on pump-probe spectra. We use LHC Bloch equations for 14 Coulomb coupled two-level systems, which describe the S (0) and S (1) level of every chlorophyll molecule. All parameter introduced into the Hamiltonian are based on microscopic structure and a quantum chemical model. The derived Bloch equations describe not only linear absorption but also the intensity dependence of optical spectra in a regime where the interplay of Pauli Blocking effects as well as exciton-exciton annihilation effects are important. As an example, pump-probe spectra are discussed. The observed saturation of the spectra for high intensities can be viewed as a relaxation channel blockade on short time scales due to Pauli blocking. The theoretical investigation is useful for the interpretation of the experimental data, if the experimental conditions exceed the low intensity pump limit and effects like strong Pauli Blocking and exciton-exciton annihilation need to be considered. These effects become important when multiple excitations are generated by the pump pulse in the complex.     

Regime shifts in marine ecosystems: detection, prediction and management

Regime shifts are abrupt changes between contrasting, persistent states of any complex system. The potential for their prediction in the ocean and possible management depends upon the characteristics of the regime shifts: their drivers (from anthropogenic to natural), scale (from the local to the basin) and potential for management action (from adaptation to mitigation). We present a conceptual framework that will enhance our ability to detect, predict and manage regime shifts in the ocean, illustrating our approach with three well-documented examples: the North Pacific, the North Sea and Caribbean coral reefs. We conclude that the ability to adapt to, or manage, regime shifts depends upon their uniqueness, our understanding of their causes and linkages among ecosystem components and our observational capabilities.     

Quantifying metabolic activity of filamentous fungi using a colorimetric XTT assay

The filamentous nature and robust cell walls of many fungi render traditional measurements of active biomass (e.g., turbidity, dry cell weight) ineffective for most fungal bioprocesses. To overcome this challenge, an assay for quantification of overall metabolic activity is developed using 2,3-bis(2-methoxy-4-nitro-5-sulfophenly)-5-[(phenylamino) carbonyl]-2H-tetrazolium hydroxide (XTT), which in the presence of active mitochondria is converted to a water-soluble formazan derivative that absorbs light in the visible spectrum (430-490 nm). Tests on the model fungus Aspergillus nidulans show that in actively growing cultures XTT absorbance is linearly related to dry cell weight below 0.2 g/kg broth. Validation through growth rate testing shows the developed XTT assay is able to accurately quantify reductions in culture metabolism during damaging physical treatment (heat, high shear, microwaving). Experiments in batch culture demonstrate that the developed XTT assay is capable of reporting on metabolic activity where dry cell weight is not. The developed assay is inexpensive, relatively rapid, and easy to conduct, making it ideally suited for assessment of fungal processes in the biotechnology industry.     

Early developmental failure of substantia nigra dopamine neurons in mice lacking the homeodomain gene Pitx3

The mesencephalic dopamine (mesDA) system is involved in the control of movement and behavior. The expression of Pitx3 in the brain is restricted to the mesDA system and the gene is induced relatively late, at E11.5, a time when tyrosine hydroxylase (Th) gene expression is initiated. We show here that, in the Pitx3-deficient aphakia (ak) mouse mutant, the mesDA system is malformed. Owing to the developmental failure of mesDA neurons in the lateral field of the midbrain, mesDA neurons are not found in the SNc and the projections to the caudate putamen are selectively lost. However, Pitx3 is expressed in all mesDA neurons in control animals. Therefore, mesDA neurons react specifically to the loss of Pitx3. Defects of motor control where not seen in the ak mice, suggesting that other neuronal systems compensate for the absence of the nigrostriatal pathway. However, an overall lower activity was observed. The results suggest that Pitx3 is specifically required for the formation of the SNc subfield at the onset of dopaminergic neuron differentiation.     

Protein translocation machineries: how organelles bring in matrix proteins

Eukaryotic cells contain several thousands of proteins that have to be accurately partitioned over the components of the cytoplasm (cytosol or any of the known organelles) to allow proper cell function. To this end, various specific topogenic signals have been designed as well as highly selective protein translocation machineries that ensure that each newly synthesized polypeptide reaches its correct subcellular destination or, in case of secretory proteins, is exported to the cell exterior. This contribution gives an overview regarding the principles of the main examples of polypeptide sorting and translocation, with emphasis on the function of cofactor binding in peroxisomal matrix protein import.     

Specific targeting of ultrasound contrast agent (USCA) for diagnostic application: an in vitro feasibility study based on SAW biosensor

The present study described a new strategy to examine the interaction between the targeted ultrasound contrast agent (USCA) and its target under flow conditions with a surface acoustic wave (SAW) transducer. The sensing principle is based on the measurement of the phase change on the sensing element upon the binding of specific biomolecules. Love-wave biosensor array was consisting of sensor elements and reference elements. The sensor elements have been prepared by coating the sensor surface with tumor marker EDB-fibronectin by means of SAM technique and carbodiimide chemistry. Reference elements were left blank or coated with fibronectin and used to eliminate thermal drift, unspecific binding, and turbulence from injection of liquids by calculating the differential phase shift with respect to the sensor elements. The binding of targeted USCA to the sensor surface was constantly recorded by monitoring the phase shift on the sensor element. The binding of targeted USCA generated a high phase shift on the sensor elements, but almost no change on the reference elements. Control experiments using non-targeted and isotype-targeted USCA confirmed the specificity of binding due to anti-EDB-fibronectin scFv-antibody-fragment-EDB-fibronectin antigen interaction. The suitability of the SAW technique to monitor the specific binding behavior of targeted micron-sized USCA in real time has been well established.     

Hepatitis C virus NS3-4A serine protease inhibitors: SAR of P'2 moiety with improved potency

We have discovered that introduction of appropriate amino acid derivatives at P'2 position improved the binding potency of P3-capped alpha-ketoamide inhibitors of HCV NS3 serine protease. X-ray crystal structure of one of the inhibitors (43) bound to the protease revealed the importance of the P'2 moiety.     

Mechanisms of light adaptation in Drosophila photoreceptors

Phototransduction in Drosophila is mediated by a phospholipase C (PLC) cascade culminating in activation of transient receptor potential (TRP) channels. Ca(2+) influx via these channels is required for light adaptation, but although several molecular targets of Ca(2+)-dependent feedback have been identified, their contribution to adaptation is unclear. By manipulating cytosolic Ca(2+) via the Na(+)/Ca(2+) exchange equilibrium, we found that Ca(2+) inhibited the light-induced current (LIC) over a range corresponding to steady-state light-adapted Ca(2+) levels (0.1-10 microM Ca(2+)) and accurately mimicked light adaptation. However, PLC activity monitored with genetically targeted PIP(2)-sensitive ion channels (Kir2.1) was first inhibited by much higher (>/= approximately 50 microM) Ca(2+) levels, which occur only transiently in vivo. Ca(2+)-dependent inhibition of PLC, but not the LIC, was impaired in mutants (inaC) of protein kinase C (PKC). The results indicate that light adaptation is primarily mediated downstream of PLC and independently of PKC by Ca(2+)-dependent inhibition of TRP channels. This is interpreted as a strategy to prevent inhibition of PLC by global steady-state light-adapted Ca(2+) levels, whereas rapid inhibition of PLC by local Ca(2+) transients is required to terminate the response and ensures that PIP(2) reserves are not depleted during stimulation.     

Role of arginine 220 in the oxygen sensor FixL from Bradyrhizobium japonicum

In the heme-based oxygen sensor protein FixL, conformational changes induced by oxygen binding to the heme sensor domain regulate the activity of a neighboring histidine kinase, eventually restricting expression of specific genes to hypoxic conditions. The conserved arginine 220 residue is suggested to play a key role in the signal transduction mechanism. To obtain detailed insights into the role of this residue, we replaced Arg(220) by histidine (R220H), glutamine (R220Q), glutamate (R220E), and isoleucine (R220I) in the heme domain FixLH from Bradyrhizobium japonicum. These mutations resulted in dramatic changes in the O(2) affinity with K(d) values in the order R220I < R220Q < wild type < R220H. For the R220H and R220Q mutants, residue 220 interacts with the bound O(2) or CO ligands, as seen by resonance Raman spectroscopy. For the oxy-adducts, this H-bond modifies the pi acidity of the O(2) ligand, and its strength is correlated with the back-bonding-sensitive nu(4) frequency, the k(off) value for O(2) dissociation, and heme core-size conformational changes. This effect is especially strong for the wild-type protein where Arg(220) is, in addition, positively charged. These observations strongly suggest that neither strong ligand fixation nor the displacement of residue 220 into the heme distal pocket are solely responsible for the reported heme conformational changes associated with kinase activity regulation, but that a significant decrease of the heme pi(*) electron density because of strong back-bonding toward the oxygen ligand also plays a key role.