Quantum chemistry as a tool in bioenergetics

Recent developments of quantum chemical methods have made it possible to tackle crucial questions in bioenergetics. The most important systems, cytochrome c oxidase in cellular respiration and photosystem II (PSII) in photosynthesis will here be used as examples to illustrate the power of the quantum chemical tools. One main contribution from quantum chemistry is to put mechanistic suggestions onto an energy scale. Accordingly, free energy profiles can be constructed both for reduction of molecular oxygen in cytochrome c oxidase and water oxidation in PSII, including O-O bond cleavage and formation, and also proton pumping in cytochrome c oxidase. For the construction of the energy diagrams, the computational results sometimes have to be combined with experimental information, such as reduction potentials and rate constants for individual steps in the reactions.     

Application of Solanum lycopersicum (tomato) hairy roots for production of passivated CdS nanocrystals with quantum dot properties

Semiconductor quantum dot particles have a wide range of applications in medicine, bioassays, computing and photovoltaics. Biological synthesis is an attractive approach for mass production of quantum dots as cells have the capacity to passivate the particles with organic ligands. In this work, hairy roots of Solanum lycopersicum (tomato) were used to produce CdS nanoparticles with quantum dot properties. Treatment of the roots with 100 μM Cd during the mid-growth phase of batch culture elicited cellular responses for Cd detoxification without affecting root growth. A combination of freeze-drying and freeze-thawing of the roots was used to extract Cd from the biomass; anion-exchange chromatography was then applied to selectively remove metal–phytochelatin complexes. Size-fractionation using gel filtration allowed the recovery of phytochelatin-capped Cd- and inorganic sulphide-containing nanoparticles displaying the size and size-dependent optical/electronic properties of CdS quantum dots. At 4–10 nm in diameter, these particles fluoresced at wavelengths corresponding to blue-violet on the colour spectrum and exhibited a high level of photostability with prolonged excitation. Whereas 69% of the Cd extracted from the roots was associated with phytochelatin peptides, the maximum yield of CdS nanocrystals with quantum dot properties was 1.4% of the total Cd taken up into the biomass. This work demonstrates a new culture-based approach for the biosynthesis of metallo-organic semiconductor quantum dots using hairy roots.     

Fluorescent labels in biosensors for pathogen detection

Infectious diseases caused by pathogens have become a life-threatening problem for millions of people around the world in recent years. Therefore, the need of efficient, fast, low-cost and user-friendly biosensing systems to monitor pathogen has increased enormously in the last few years. This paper presents an overview of different fluorescent labels and the utilization of fluorescence-based biosensor techniques for rapid, direct, sensitive and real-time identification of bacteria. In these biosensors, organic dyes, nanomaterials and rare-earth elements are playing an increasing role in the design of biosensing systems with an interest for applications in bacterial analysis.     

Nanoscale and functional heterogeneity of the hippocampal extracellular space

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Efficient manufacturing of therapeutic mesenchymal stromal cells with the use of the Quantum Cell Expansion System

BackgroundThe use of bone marrow–derived mesenchymal stromal cells (MSCs) as a cellular therapy for various diseases, such as graft-versus-host disease, diabetes, ischemic cardiomyopathy and Crohn's disease, has produced promising results in early-phase clinical trials. However, for widespread application and use in later phase studies, manufacture of these cells must be cost-effective, safe and reproducible. Current methods of manufacturing in flasks or cell factories are labor-intensive, involve a large number of open procedures and require prolonged culture times.MethodsWe evaluated the Quantum Cell Expansion System for the expansion of large numbers of MSCs from unprocessed bone marrow in a functionally closed system and compared the results with a flask-based method currently in clinical trials.ResultsAfter only two passages, we were able to expand a mean of 6.6 × 10⁸ MSCs from 25 mL of bone marrow reproducibly. The mean expansion time was 21 days, and cells obtained were able to differentiate into all three lineages: chondrocytes, osteoblasts and adipocytes. The Quantum was able to generate the target cell number of 2.0 × 10⁸ cells in an average of 9 fewer days and in half the number of passages required during flask-based expansion. We estimated that the Quantum would involve 133 open procedures versus 54,400 in flasks when manufacturing for a clinical trial. Quantum-expanded MSCs infused into an ischemic stroke rat model were therapeutically active.ConclusionsThe Quantum is a novel method of generating high numbers of MSCs in less time and at lower passages when compared with flasks. In the Quantum, the risk of contamination is substantially reduced because of the substantial decrease in open procedures.     

Near infrared sensing based on fluorescence resonance energy transfer between Mn:CdTe quantum dots and Au nanorods

A novel sensing system based on the near infrared (NIR) fluorescence resonance energy transfer (FRET) between Mn:CdTe quantum dots (Qdots) and Au nanorods (AuNRs) was established for the detection of human IgG. The NIR-emitting Qdots linked with goat anti-human IgG (Mn:CdTe-Ab1) and AuNRs linked with rabbit anti-human IgG (AuNRs-Ab2) acted as fluorescence donors and acceptors, respectively. FRET occurred by human IgG with the specific antigen–antibody interaction. And human IgG was detected based on the modulation in FRET efficiency. The calibration graph was linear over the range of 0.05–2.5 μM of human IgG under optimal conditions. The proposed sensing system can decrease the interference of biomolecules in NIR region and increase FRET efficiency in optimizing the spectral overlap of AuNRs with Mn:CdTe Qdots. This method has great potential for multiplex assay with different donor–acceptor pairs.     

A comparative study of galactose oxidase and active site analogs based on QM/MM Car-Parrinello simulations

A parallel study of the radical copper enzyme galactose oxidase (GOase) and a low molecular weight analog of the active site was performed with dynamical density functional and mixed quantum-classical calculations. This combined approach enables a direct comparison of the properties of the biomimetic and the natural systems throughout the course of the catalytic reaction. In both cases, five essential forms of the catalytic cycle have been investigated: the resting state in its semi-reduced (catalytically inactive) and its oxidized (catalytically active) form, A ^semi and A ^ox, respectively; a protonated intermediate B; the transition state for the rate-determining hydrogen abstraction step C, and its product D. For A and B the electronic properties of the biomimetic compound are qualitatively very similar to the ones of the natural target. However, in agreement with the experimentally observed difference in catalytic activity, the calculated activation energy for the hydrogen abstraction step is distinctly lower for GOase (16 kcal/mol) than for the mimetic compound (21 kcal/mol). The enzymatic transition state is stabilized by a delocalization of the unpaired spin density over the sulfur-modified equatorial tyrosine Tyr272, an effect that for geometric reasons is essentially absent in the biomimetic compound. Further differences between the mimic and its natural target concern the structure of the product of the abstraction step, which is characterized by a weakly coordinated aldehyde complex for the latter and a tightly bound linear complex for the former. Received 14 October 1999 · Accepted: 19 January 2000     

A critical assessment of the information processing capabilities of neuronal microtubules using coherent excitations

Evidence for signaling, communication, and conductivity in microtubules (MTs) has been shown through both direct and indirect means, and theoretical models predict their potential use in both classical and quantum information processing in neurons. The notion of quantum information processing within neurons has been implicated in the phenomena of consciousness, although controversies have arisen in regards to adverse physiological temperature effects on these capabilities. To investigate the possibility of quantum processes in relation to information processing in MTs, a biophysical MT model is used based on the electrostatic interior of the tubulin protein. The interior is taken to constitute a double-well potential structure within which a mobile electron is considered capable of occupying at least two distinct quantum states. These excitonic states together with MT lattice vibrations determine the state space of individual tubulin dimers within the MT lattice. Tubulin dimers are taken as quantum well structures containing an electron that can exist in either its ground state or first excited state. Following previous models involving the mechanisms of exciton energy propagation, we estimate the strength of exciton and phonon interactions and their effect on the formation and dynamics of coherent exciton domains within MTs. Also, estimates of energy and timescales for excitons, phonons, their interactions, and thermal effects are presented. Our conclusions cast doubt on the possibility of sufficiently long-lived coherent exciton/phonon structures existing at physiological temperatures in the absence of thermal isolation mechanisms. These results are discussed in comparison with previous models based on quantum effects in non-polar hydrophobic regions, which have yet to be disproved.     

Quantitation of Repetitive Sequences in Human Genomic DNA and Detection of an Elevated Ribosomal Repeat Copy Number in Schizophrenia: The Results of Molecular and Cytogenetic Analyses

A modified version of quantitating repetitive sequences in genomic DNA was developed to allow comparisons for numerous individual genomes and simultaneous analysis of several sequences in each DNA specimen. The relative genomic content of ribosomal repeats (rDNA) was estimated for 75 individuals, including 33 healthy donors (HD) and 42 schizophrenic patients (SP). The rDNA copy number in HD was 427 ± 18 (mean ± SE) per diploid nucleus, ranging 250–600. In SP, the rDNA copy number was 494 ± 15 and ranged 280–670, being significantly higher than in HD. The two samples did not differ in contents of sequences hybridizing with probes directed to a subfraction of human satellite III or to the histone genes. Cytogenetic analysis (silver staining of metaphase chromosomes) showed that the content of active rRNA genes in nucleolus organizer regions is higher in SP compared with HD. The possible causes of the elevated rRNA gene dosage in SP were considered. The method employed was proposed for studying the polymorphism for genomic content of various repeats in higher organisms, including humans.     

Effects of rotation length, fungicide treatment of seed tubers and nematicide on diseases and the quality of potato tubers

In 1982 – 88, potatoes were grown in 2-, 4- and 6-course rotations with spring barley on a field infested with Globodera rostochiensis. Severity of stem canker and black scurf increased with increasing frequency of previous potato crops, and seed tuber treatment with tolclofos-methyl became less effective in controlling diseases. This suggested that previous crops had increased the amounts of soil-borne inoculum of Rhizoctonia solani. Oxamyl soil treatment increased stem canker in one year and decreased black scurf in four years. Seed tuber treatment with imazalil or prochloraz decreased stem base infection by Polyscytalum pustulans and skin spot and silver scurf on tubers. Black dot was prevalent on tubers in all years and was not affected by seed tuber treatment or previous cropping. Oxamyl increased black dot and common scab in five years and decreased % tuber dry matter in six years. Cysts of G. rostochiensis were found attached to Désirée but not to Maris Piper tubers in August. At harvest tubers of both cultivars were affected by superficial pitting and its severity was related to soil populations of G. rostochiensis at planting. This damage was controlled by oxamyl. It is suggested that the pitting developed from holes made in the tuber skin at larval invasion. In 1989, Désirée seed tubers and healthy mini tubers were planted in all plots and severity of stem canker and black scurf increased with increasing proximity of previous potato crops and with the number of previous crops. Black dot on stems and tubers was not affected by previous cropping but was much less severe in a plot that had not grown potatoes during the seven years of the experiment. The severity of common scab generally decreased as the number of preceding potato crops increased.