Quantum physics meets biology

Quantum physics and biology have long been regarded as unrelated disciplines, describing nature at the inanimate microlevel on the one hand and living species on the other hand. Over the last decades the life sciences have succeeded in providing ever more and refined explanations of macroscopic phenomena that were based on an improved understanding of molecular structures and mechanisms. Simultaneously, quantum physics, originally rooted in a world view of quantum coherences, entanglement and other non-classical effects, has been heading towards systems of increasing complexity. The present perspective article shall serve as a pedestrian guide to the growing interconnections between the two fields. We recapitulate the generic and sometimes unintuitive characteristics of quantum physics and point to a number of applications in the life sciences. We discuss our criteria for a future quantum biology, its current status, recent experimental progress and also the restrictions that nature imposes on bold extrapolations of quantum theory to macroscopic phenomena.Comment: 26 pages, 4 figures, Perspective article for the HFSP Journa

A Methodology for Detecting Field Potentials from the External Ear Canal: NEER and EVestG

An algorithm called the neural event extraction routine (NEER) and a method called Electrovestibulography (EVestG) for extracting field potentials (FPs) from artefact rich and noisy ear canal recordings is presented. Averaged FP waveforms can be used to aid detection of acoustic and or vestibular pathologies. FPs were recorded in the external ear canal proximal to the ear drum. These FPs were extracted using an algorithm called NEER. NEER utilises a modified complex Morlet wavelet analysis of phase change across multiple scales and a template matching (matched filter) methodology to detect FPs buried in noise and biological and environmental artefacts. Initial simulation with simulated FPs shows NEER detects FPs down to −30 dB SNR (power) but only 13–23% of those at SNR’s <−6 dB. This was deemed applicable to longer duration recordings wherein averaging could be applied as many FPs are present. NEER was applied to detect both spontaneous and whole body tilt evoked FPs. By subtracting the averaged tilt FP response from the averaged spontaneous FP response it is believed this difference is more representative of the vestibular response. Significant difference (p < 0.05) between up and down whole body (supine and sitting) movements was achieved. Pathologic and physiologic evidence in support of a vestibular and acoustic origin is also presented

The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing

We describe a statistical framework for QTL mapping using bulk segregant analysis (BSA) based on high throughput, short-read sequencing. Our proposed approach is based on a smoothed version of the standard statistic, and takes into account variation in allele frequency estimates due to sampling of segregants to form bulks as well as variation introduced during the sequencing of bulks. Using simulation, we explore the impact of key experimental variables such as bulk size and sequencing coverage on the ability to detect QTLs. Counterintuitively, we find that relatively large bulks maximize the power to detect QTLs even though this implies weaker selection and less extreme allele frequency differences. Our simulation studies suggest that with large bulks and sufficient sequencing depth, the methods we propose can be used to detect even weak effect QTLs and we demonstrate the utility of this framework by application to a BSA experiment in the budding yeast Saccharomyces cerevisiae

An online spike detection and spike classification algorithm capable of instantaneous resolution of overlapping spikes

For the analysis of neuronal cooperativity, simultaneously recorded extracellular signals from neighboring neurons need to be sorted reliably by a spike sorting method. Many algorithms have been developed to this end, however, to date, none of them manages to fulfill a set of demanding requirements. In particular, it is desirable to have an algorithm that operates online, detects and classifies overlapping spikes in real time, and that adapts to non-stationary data. Here, we present a combined spike detection and classification algorithm, which explicitly addresses these issues. Our approach makes use of linear filters to find a new representation of the data and to optimally enhance the signal-to-noise ratio. We introduce a method called “Deconfusion” which de-correlates the filter outputs and provides source separation. Finally, a set of well-defined thresholds is applied and leads to simultaneous spike detection and spike classification. By incorporating a direct feedback, the algorithm adapts to non-stationary data and is, therefore, well suited for acute recordings. We evaluate our method on simulated and experimental data, including simultaneous intra/extra-cellular recordings made in slices of a rat cortex and recordings from the prefrontal cortex of awake behaving macaques. We compare the results to existing spike detection as well as spike sorting methods. We conclude that our algorithm meets all of the mentioned requirements and outperforms other methods under realistic signal-to-noise ratios and in the presence of overlapping spikes

Mitochondrial effects of triarylmethane dyes

The mitochondrial effects of submicromolar concentrations of six triarylmethane dyes, with potential applications in antioncotic photodynamic therapy, were studied. All dyes promoted an inhibition of glutamate or succinate-supported respiration in uncoupled mitochondria, in a manner stimulated photodynamically. No inhibition of N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD) supported respiration was observed, indicating that these dyes do not affect mitochondrial complex IV. When mitochondria were energized with TMPD in the absence of an uncoupler, treatment with victoria blue R, B, or BO, promoted a dissipation of mitochondrial membrane potential and increase of respiratory rates, compatible with mitochondrial uncoupling. This effect was observed even in the dark, and was not prevented by EGTA, Mg2+ or cyclosporin A, suggesting that it is promoted by a direct effect of the dye on inner mitochondrial membrane permeability to protons. Indeed, victoria blue R, B, and BO promoted swelling of valinomycin-treated mitochondria incubated in a hyposmotic K+-acetate-based medium, confirming that these dyes act as classic protonophores such as FCCP. On the other hand, ethyl violet, crystal violet, and malachite green promoted a dissipation of mitochondrial membrane potential, accompanied by mitochondrial swelling, which was prevented by EGTA, Mg2+, and cyclosporin A, demonstrating that these drugs induce mitochondrial permeability transition. This mitochondrial permeabilization was followed by respiratory inhibition, attributable to cytochrome c release, and was caused by the oxidation of NAD(P)H promoted by these drugs.31658159