Interrogation of metabolic and oxygen states of tumors with fiber-based luminescence lifetime spectroscopy.

The study of metabolic and oxygen states of cells in a tumor in vivo is crucial for understanding of the mechanisms responsible for tumor development and provides background for the relevant tumor's treatment. Here, we show that a specially designed implantable fiber-optic probe provides a promising tool for optical interrogation of metabolic and oxygen states of a tumor in vivo. In our experiments, the excitation light from a ps diode laser source is delivered to the sample through an exchangeable tip via a multimode fiber, and the emission light is transferred to the detector by another multimode fiber. Fluorescence lifetime of a nicotinamid adenine dinucleotide (NAD(P)H) and phosphorescence lifetime of an oxygen sensor based on an iridium (III) complex of enzothienylpyridine (BTPDM1) are explored both in model experiment in solutions and in living mice.

The fed-batch principle for the molecular biology lab: controlled nutrient diets in ready-made media improve production of recombinant proteins in Escherichia coli.

While the nutrient limited fed-batch technology is the standard of the cultivation of microorganisms and production of heterologous proteins in industry, despite its advantages in view of metabolic control and high cell density growth, shaken batch cultures are still the standard for protein production and expression screening in molecular biology and biochemistry laboratories. This is due to the difficulty and expenses to apply a controlled continuous glucose feed to shaken cultures. New ready-made growth media, e.g. by biocatalytic release of glucose from a polymer, offer a simple solution for the application of the fed-batch principle in shaken plate and flask cultures. Their wider use has shown that the controlled diet not only provides a solution to obtain significantly higher cell yields, but also in many cases folding of the target protein is improved by the applied lower growth rates; i.e. final volumetric yields for the active protein can be a multiple of what is obtained in complex medium cultures. The combination of the conventional optimization approaches with new and easy applicable growth systems has revolutionized recombinant protein production in Escherichia coli in view of product yield, culture robustness as well as significantly increased cell densities. This technical development establishes the basis for successful miniaturization and parallelization which is now an important tool for synthetic biology and protein engineering approaches. This review provides an overview of the recent developments, results and applications of advanced growth systems which use a controlled glucose release as substrate supply.

Influence of the Outer Ligands on Metal-to-Ligand Charge Transfer in Solvated Manganese Porphyrins.

Two manganese porphyrin complexes, manganese tetraphenylporphyrin chloride (MnTPP-Cl) and manganese octaethylporphyrin chloride (MnOEP-Cl), exhibit distinctive spectral features of metal-to-ligand charge-transfer (MLCT) when dissolved in dichloromethane, characterized by resonant inelastic X-ray scattering at the Mn L-edge and N K-edge. The metal-ligand orbital mixing that mediates the MLCT is analyzed with the help of density functional theory/restricted open-shell configuration interaction singles calculations. On the basis of experimental and theoretical analyses, the distinctive MLCT is argued to originate from alteration of the porphyrin outer ligands: phenyl groups in MnTPP-Cl and ethyl groups in MnOEP-Cl.

Ultrafast excited state dynamics of iridium(III) complexes and their changes upon immobilisation onto titanium dioxide layers.

Time-resolved spectroscopy was applied to investigate the excited state dynamics of two heteroleptic Ir(III) complexes with the general formula [Ir(C^N)2(N^N)](+), where C^N and N^N represent different cyclometalating and diimine ligands, respectively. The excited state relaxation is influenced by the ligand substitution as well as the light polarisation. Vibrational relaxation occurs in the sub-ps timescale and interligand charge transfer results in polarisation dependent signal dynamics with a time constant of about 30 ps. Electron injection from the iridium dye to TiO2 is analysed with respect to potential applications in solar energy conversion.

Fluorination-dependent molecular orbital occupancy in ring-shaped perfluorocarbons.

Perfluorocarbons are a family of molecules consisting mainly of carbon and fluorine atoms. They have interesting chemical properties and have diverse applications in biomedicine, physical chemistry and polymer science. In this work, carbon K-edge absorption and emission spectra of liquid decalin are presented and compared to perfluorodecalin. A comprehensive picture of the electronic structure of decalin is provided based on soft X-ray absorption and emission spectroscopies. Experimental data are compared to theoretical time-dependent density functional theory for the hydrocarbon, the perfluorocarbon and the stepwise fluorinated derivatives. We observed a molecular orbital change from unoccupied to occupied orbitals for perfluorodecalin, which was induced through the fluorination process.

Dinuclear Ru/Ni, Ir/Ni, and Ir/Pt complexes with bridging phenanthroline-5,6-dithiolate: synthesis, structure, and electrochemical and photophysical behavior.

We report the synthesis and full characterization of dinuclear complexes with the bridging ligand phenanthroline-5,6-dithiolate (phendt(2-)) featuring the [Ru(bpy)2](2+) or Ir(ppy)2](+) fragment at the diimine donor center and the [Ni(dppe)](2+) or [Pt(phen)](2+) complex moiety at the dithiolate group. The molecular structures of the mononuclear complexes [(C5H5)2Ti(S,S'-phendt)] and [(ppy)2Ir{N,N'-phendt-(C2H4CN)2}](PF6) as well as the dinuclear complex [(C5H5)(PPh3)Ru(phendt)Ni(dppe)](PF6) determined by X-ray diffraction (XRD) studies are compared. Photophysical studies with mononuclear [(bpy)2Ru{phendt-(C2H4CN)2}](2+) and [(ppy)2Ir{phendt-(C2H4CN)2}](+) as well as dinuclear [(bpy)2Ru(phendt)Ni(dppe)](2+) and [(ppy)2Ir(phendt)Ni(dppe)](+) uncovered an effective luminescence quenching in the dinuclear complexes. Lifetime measurements at room temperature, steady-state measurements at low temperature, electrochemical investigations, and DFT calculations provide evidence for a very efficient energy transfer from the Ru/Ir to the Ni complex moiety with a rate constant k > 5 × 10(9) s(-1). In comparison, the [Ru]phendt[Ni] complex displays a higher quenching efficiency with reduced excited state lifetime, whereas the [Ir]phendt[Ni] complex is characterized by an unaltered lifetime of the thermally equilibrated excited state.

Synthesis of fluorescent 2,3,5,6-tetraalkynylpyridines by site-selective Sonogashira-reactions of 2,3,5,6-tetrachloropyridines.

4-Substituted 2,3,5,6-tetraalkynylpyridines were prepared by tetra-fold Sonogashira reactions of the corresponding 2,3,5,6-tetrachloropyridines. 2,6-Dialkynyl-3,5-dichloropyridines were prepared by site-selective Sonogashira reactions from various 4-unsubstituted and 4-substituted tetrachloropyridines. Subsequent two-fold Sonogashira reactions of the products allowed for the synthesis of various 2,3,5,6-tetraalkynylpyridines containing different alkynyl groups. The products exhibit interesting UV/Vis and fluorescence properties. The position of absorption and emission bands can be tuned by systematic variation of the type of alkynyl substituent and by the type of substituent located at position 4 of the pyridine moiety. The presence of electron withdrawing substituents or of an alkynyl group at position 4 as well as the presence of donor substituted alkynyl groups at positions 2, 3, 5 and 6 resulted in high fluorescence quantum yields of up to 0.6, presumably due to the push-pull substitution pattern of the molecules.

Spin density distribution after electron transfer from triethylamine to an [Ir(ppy)2(bpy)]+ photosensitizer during photocatalytic water reduction.

The photoreduction of the bis(2-phenylpyridinato-)(2,2'-bipyridine)iridium(III) ion ([Ir(ppy)2(bpy)](+)), used as a photosensitizer in photocatalytic water splitting, by triethylamine was studied by means of UV/VIS, XANES, and EPR spectroscopies, supported by theoretical calculations at density functional theory (DFT) and complete active space self-consistent field (CASSCF/CASPT2) levels. The combination of these methods suggests a predominant bpy localization of the spin-density of the unpaired electron with notable delocalization to the Ir center. This is particularly evident from EPR and theoretical results and leads to broad EPR lines and a large anisotropy of the g-factor.

Photoswitching of enzyme activity by laser-induced pH-jump.

Controlled initiation of biochemical events and in particular of protein activity is a powerful tool in biochemical research. Specifically, optical trigger signals are an attractive approach for remote control of enzyme activity. We present a method for generating optical control of enzyme activity applicable to a widespread range of enzymes. The approach is based on short laser pulses as optical "switches" introducing an instantaneous change of the pH-value for activation of protein function. The pH-jump is induced by proton release from 2-nitrobenzaldehyde. Reaction conditions were chosen to yield a pH-jump of almost 3 units on switching from inactive to active conditions for the enzyme. In this experimental setup, irradiation can be realized without any loss of enzyme activity. Following this change in pH-value, a controlled activation of hydrolytic activity of acid phosphatase is successfully demonstrated. This application provides a general method for photocontrol of enzymatic function for proteins having a significant pH-profile. The kinetic data for the substrate 6-chloro-8-fluoro-4-methylumbelliferone phosphate are determined.

Synthesis and characterization of new iridium photosensitizers for catalytic hydrogen generation from water.

Novel phenylazole ligands were applied successfully in the synthesis of cyclometalated iridium(III) complexes of the general formula [Ir(phenylazole)(2)(bpy)]PF(6) (bpy=2,2'-bipyridine). All complexes were fully characterized by NMR, IR, and MS spectroscopic studies as well as by cyclic voltammetry. Three crystal structures obtained by X-ray analysis complemented the spectroscopic investigations. The excited-state lifetimes of the iridium complexes were determined and showed to be in the range of several hundred ns to multiple µs. All obtained iridium complexes were active as photosensitizers in catalytic hydrogen evolution from water in the presence of triethylamine as a sacrificial reducing agent. Applying an in situ formed iron-based water reduction catalyst derived from [HNEt(3)](+) [HFe(3)(CO)(11)](-) and tris[3,5-tris-(trifluoromethyl)-phenyl]phosphine as the ligand, [Ir(2-phenylbenz-oxazole)(2)-(bpy)]PF(6) proved to be the most efficient complex giving a quantum yield of 16% at 440 nm light irradiation.

Sandwich ELISA for quantitative detection of human collagen prolyl 4-hydroxylase.

BACKGROUND: We describe a method for specific, quantitative and quick detection of human collagen prolyl 4-hydroxylase (C-P4H), the key enzyme for collagen prolyl-4 hydroxylation, in crude samples based on a sandwich ELISA principle. The method is relevant to active C-P4H level monitoring during recombinant C-P4H and collagen production in different expression systems. The assay proves to be specific for the active C-P4H alpha2beta2 tetramer due to the use of antibodies against its both subunits. Thus in keeping with the method C-P4H is captured by coupled to an anti-alpha subunit antibody magnetic beads and an anti-beta subunit antibody binds to the PDI/beta subunit of the protein. Then the following holoenzyme detection is accomplished by a goat anti-rabbit IgG labeled with alkaline phosphatase which AP catalyzes the reaction of a substrate transformation with fluorescent signal generation. RESULTS: We applied an experimental design approach for the optimization of the antibody concentrations used in the sandwich ELISA. The assay sensitivity was 0.1 ng of C-P4H. The method was utilized for the analysis of C-P4H accumulation in crude cell extracts of E. coli overexpressing C-P4H. The sandwich ELISA signals obtained demonstrated a very good correlation with the detected protein activity levels measured with the standard radioactive assay. The developed assay was applied to optimize C-P4H production in E. coli Origami in a system where the C-P4H subunits expression acted under control by different promoters. The experiments performed in a shake flask fed-batch system (EnBase) verified earlier observations that cell density and oxygen supply are critical factors for the use of the inducer anhydrotetracycline and thus for the soluble C-P4H yield. CONCLUSIONS: Here we show an example of sandwich ELISA usage for quantifying multimeric proteins. The method was developed for monitoring the amount of recombinant C-P4H tetramer in crude E. coli extracts. Due to the specificity of the antibodies used in the assay against the different C-P4H subunits, the method detects the entire holoenzyme, and the signal is not disturbed by background expression of the separate subunits.

A novel fed-batch based cultivation method provides high cell-density and improves yield of soluble recombinant proteins in shaken cultures.

BACKGROUND: Cultivations for recombinant protein production in shake flasks should provide high cell densities, high protein productivity per cell and good protein quality. The methods described in laboratory handbooks often fail to reach these goals due to oxygen depletion, lack of pH control and the necessity to use low induction cell densities. In this article we describe the impact of a novel enzymatically controlled fed-batch cultivation technology on recombinant protein production in Escherichia coli in simple shaken cultures. RESULTS: The enzymatic glucose release system together with a well-balanced combination of mineral salts and complex medium additives provided high cell densities, high protein yields and a considerably improved proportion of soluble proteins in harvested cells. The cultivation method consists of three steps: 1) controlled growth by glucose-limited fed-batch to OD600 approximately 10, 2) addition of growth boosters together with an inducer providing efficient protein synthesis within a 3 to 6 hours period, and 3) a slow growth period (16 to 21 hours) during which the recombinant protein is slowly synthesized and folded. Cell densities corresponding to 10 to 15 g l(-1) cell dry weight could be achieved with the developed technique. In comparison to standard cultures in LB, Terrific Broth and mineral salt medium, we typically achieved over 10-fold higher volumetric yields of soluble recombinant proteins. CONCLUSIONS: We have demonstrated that by applying the novel EnBase Flo cultivation system in shaken cultures high cell densities can be obtained without impairing the productivity per cell. Especially the yield of soluble (correctly folded) proteins was significantly improved in comparison to commonly used LB, Terrific Broth or mineral salt media. This improvement is thought to result from a well controlled physiological state during the whole process. The higher volumetric yields enable the use of lower culture volumes and can thus significantly reduce the amount of time and effort needed for downstream processing or process optimization. We claim that the new cultivation system is widely applicable and, as it is very simple to apply, could widely replace standard shake flask approaches.

Improved production of human type II procollagen in the yeast Pichia pastoris in shake flasks by a wireless-controlled fed-batch system.

BACKGROUND: Here we describe a new technical solution for optimization of Pichia pastoris shake flask cultures with the example of production of stable human type II collagen. Production of recombinant proteins in P. pastoris is usually performed by controlling gene expression with the strong AOX1 promoter, which is induced by addition of methanol. Optimization of processes using the AOX1 promoter in P. pastoris is generally done in bioreactors by fed-batch fermentation with a controlled continuous addition of methanol for avoiding methanol toxification and carbon/energy starvation. The development of feeding protocols and the study of AOX1-controlled recombinant protein production have been largely made in shake flasks, although shake flasks have very limited possibilities for measurement and control. RESULTS: By applying on-line pO2 monitoring we demonstrate that the widely used pulse feeding of methanol results in long phases of methanol exhaustion and consequently low expression of AOX1 controlled genes. Furthermore, we provide a solution to apply the fed-batch strategy in shake flasks. The presented solution applies a wireless feeding unit which can be flexibly positioned and allows the use of computer-controlled feeding profiles. By using the human collagen II as an example we show that a quasi-continuous feeding profile, being the simplest way of a fed-batch fermentation, results in a higher production level of human collagen II. Moreover, the product has a higher proteolytic stability compared to control cultures due to the increased expression of human collagen prolyl 4-hydroxylase as monitored by mRNA and protein levels. CONCLUSION: The recommended standard protocol for methanol addition in shake flasks using pulse feeding is non-optimal and leads to repeated long phases of methanol starvation. The problem can be solved by applying the fed-batch technology. The presented wireless feeding unit, together with an on-line monitoring system offers a flexible, simple, and low-cost solution for initial optimization of the production in shake flasks which can be performed in parallel. By this way the fed-batch strategy can be applied from the early screening steps also in laboratories which do not have access to high-cost and complicated bioreactor systems.

Fermentation process for tetrameric human collagen prolyl 4-hydroxylase in Escherichia coli: improvement by gene optimisation of the PDI/beta subunit and repeated addition of the inducer anhydrotetracycline.

The collagen prolyl 4-hydroxylases (C-P4Hs) that reside within the lumen of the endoplasmic reticulum (ER) are the key enzymes in the biosynthesis of collagens. The vertebrate enzymes are alpha(2)beta(2) tetramers consisting of two catalytic alpha subunits and two beta subunits that are identical to protein disulfide isomerase (PDI). Cytoplasmic production of an active human C-P4H has recently been described in the Origami (trxB gor) mutant Escherichia coli using a bicistronic vector with independent control of the alpha and PDI/beta subunit expression by the tetA and T5-lac promoters, respectively, enabling sequential induction (Neubauer, A., Neubauer, P., Myllyharju, J., 2005. High-level production of human collagen prolyl 4-hydroxylase in Escherichia coli. Matrix Biol. 24, 59-68). We show here that the yield of active C-P4H in shake flasks is increased 50-fold by improving the expression level of the PDI/beta subunit through gene optimisation. We also found that stable expression of the alpha subunit mRNA in a fed-batch fermentation process requires repeated additions of anhydrotetracycline. This finding may be of a wider general importance for the use of the tetA promoter in fed-batch cultivations, especially if recombinant proteins are expressed during long production phases. We also show that growth of the E. coli Origami strain to high cell density on a complex medium with consecutive sequential induction is difficult to achieve and that optimisation of similarly complicated systems can greatly benefit from the use of quantitative mRNA analysis for the evaluation of transcriptional bottlenecks. The optimisation approach resulted in a fermentation yield of 143 mg L(-1) of active C-P4H, corresponding to approximately 7.5% of the total soluble cell protein.

High Yield of Recombinant Protein in Shaken E. coli Cultures with Enzymatic Glucose Release Medium EnPresso B.

Expression of recombinant proteins in sufficient quantities is essential for protein structure-function studies. The most commonly used method for recombinant protein production is overexpression in E. coli cultures. However, producing high yields of functional proteins in E. coli can be a challenge in conventional shaken cultures. This is often due to nonoptimal growth conditions, which result in low cell yields and insoluble or incorrectly folded target protein. To overcome the shortcomings of shake flask cultivation, we present a cultivation method based on enzymatic glucose delivery. This system mimics the fed-batch principle used in bioreactor cultivations and provides high yields of biomass and recombinant proteins in shaken cultivations.

Chemical bonding in aqueous hexacyano cobaltate from photon- and electron-detection perspectives.

The electronic structure of the [Co(CN)6]3- complex dissolved in water is studied using X-ray spectroscopy techniques. By combining electron and photon detection methods from the solutions ionized or excited by soft X-rays we experimentally identify chemical bonding between the metal center and the CN ligand. Non-resonant photoelectron spectroscopy provides solute electron binding energies, and nitrogen 1 s and cobalt 2p resonant core-level photoelectron spectroscopy identifies overlap between metal and ligand orbitals. By probing resonances we are able to qualitatively determine the ligand versus metal character of the respective occupied and non-occupied orbitals, purely by experiment. For the same excitations we also detect the emitted X-rays, yielding the complementary resonant inelastic X-ray scattering spectra. For a quantitative interpretation of the spectra, we perform theoretical electronic-structure calculations. The latter provide both orbital energies and orbital character which are found to be in good agreement with experimental energies and with experimentally inferred orbital mixing. We also report calculated X-ray absorption spectra, which in conjunction with our orbital-structure analysis, enables us to quantify various bonding interactions with a particular focus on the water-solvent - ligand interaction and the strength of π-backbonding between metal and ligand.

High-level production of human collagen prolyl 4-hydroxylase in Escherichia coli.

The collagen prolyl 4-hydroxylases (C-P4Hs), enzymes residing within the lumen of the endoplasmic reticulum, play a central role in the synthesis of all collagens. The vertebrate enzymes are alpha(2)beta(2) tetramers in which the two catalytic sites are located in the alpha subunits, and protein disulfide isomerase serves as the beta subunit. All attempts to assemble an active C-P4H tetramer from its subunits in in vitro cell-free systems have been unsuccessful, but assembly of a recombinant enzyme has been reported in several cell types by coexpression of the two types of subunit. An active type I C-P4H tetramer was obtained here by periplasmic expression in Escherichia coli strains BL21 and RB791. Further optimization for production by stepwise regulated coexpression of its subunits in the cytoplasm of a thioredoxin reductase and glutathione reductase mutant E. coli strain resulted in large amounts of human type I C-P4H tetramer. The specific activity of the C-P4H tetramer purified from the cytoplasmic expression was within the range of values reported for human type I C-P4H isolated as a nonrecombinant enzyme or produced in the endoplasmic reticulum of insect cells, but the expression level, about 25 mg/l in a fermenter, is about 5-10 times that obtained in insect cells. The enzyme expressed in E. coli differed from those present in vivo and those produced in other hosts in that it lacked the N glycosylation of its alpha subunits, which may be advantageous in crystallization experiments.

Modelling of translation of human protein disulfide isomerase in Escherichia coli-A case study of gene optimisation.

Recombinant human protein disulfide isomerase (PDI) was expressed in vivo in Escherichia coli using a non-optimised gene sequence and an optimised sequence with four 5' codons substituted by synonymous codons that take less time to translate. The optimisation resulted in a 2-fold increase of total PDI concentration and by successive optimisation with expression at low temperature in a 10-fold increase of the amount of soluble PDI in comparison with the original wild-type construct. The improvement can be due to a faster clearing of the ribosome binding site on the mRNA, elevating the translation initiation rate and resulting in higher ribosome loading and better ribosome protection of the PDI mRNA against endonucleolytic cleavage by RNase. This hypothesis was supported by a novel computer simulation model of E. coli translational ribosome traffic based upon the stochastic Gillespie algorithm. The study indicates the applicability of such models in optimisation of recombinant protein sequences.

Toward Microbioreactor Arrays: A Slow-Responding Oxygen Sensor for Monitoring of Microbial Cultures in Standard 96-Well Plates.

In this study, a slow-responding chemo-optical sensor for dissolved oxygen (DO) integrated into a 96-well plate was developed. The slow response time ensures that the measured oxygen value does not change much during plate transport to the microplate reader. The sensor therefore permits at-line DO measurement of microbial cultures. Moreover, it eliminates the necessity of individual optical measurement systems for each culture plate, as many plates can be measured successively. Combined with the 96-well format, this increases the experimental throughput enormously. The novel sensor plate (Slow OxoPlate) consists of fluorophores suspended in a polymer matrix that were placed into u-bottom 96-well plates. Response time was measured using sodium sulfite, and a t90 value of 9.7 min was recorded. For application, DO values were then measured in Escherichia coli and Saccharomyces cerevisiae cultures grown under fed-batch-like conditions. Depending on the DO sensor's response time, different information on the oxygenation state of the culture plate was obtained: a fast sensor variant detects disturbance through sampling, whereas the slow sensor indicates oxygen limitation during incubation. A combination of the commercially available OxoPlate and the Slow OxoPlate enables operators of screening facilities to validate their cultivation procedures with regard to oxygen availability.

Electron- and Energy-Transfer Processes in a Photocatalytic System Based on an Ir(III)-Photosensitizer and an Iron Catalyst.

The reaction pathways of bis-(2-phenylpyridinato-)(2,2'-bipyridine)iridium(III)hexafluorophosphate [Ir(ppy)2(bpy)]PF6 within a photocatalytic water reduction system for hydrogen generation based on an iron-catalyst were investigated by employing time-resolved photoluminescence spectroscopy and time-dependent density functional theory. Electron transfer (ET) from the sacrificial reagent to the photoexcited Ir complex has a surprisingly low probability of 0.4% per collision. Hence, this step limits the efficiency of the overall system. The calculations show that ET takes place only for specific encounter geometries. At the same time, the presence of the iron-catalyst represents an energy loss channel due to a triplet-triplet energy transfer of Dexter type. This loss channel is kept small by the employed concentration ratios, thus favoring the reductive ET necessary for the water reduction. The elucidated reaction mechanisms underline the further need to improve the sun light's energy pathway to the catalyst to increase the efficiency of the photocatalytic system.