Fast Physiological Processes Research Articles

Electroencephalography and analysis of functional brain activity

Electroencephalography (EEG) enables the recording and analysis of fast physiological processes in the cerebral cortex, which is currently virtually impossible for the majority of methods of functional brain examination. However, there is a certain stagnation in the EEG technology that requires some improvement in both methodological and technical approaches to EEG. Objective: to analyze the capacities of EEG and its role in current medical diagnostics. The majority of EEG machines have 8 to 32 recording channels and use the 10–20 electrode placement system. This results in loosing a substantial amount of information due to limited registration of some bioelectric activity and prevents using EEG data together with high-resolution neuroimaging. This issue can be addressed by EEG machines with high-density recording and multiple primary electroencephalographic sensors (at least 128), which ensures minimal loss of information at the first stage. However, such systems require an absolutely different approach to the analysis of EEG recordings. Larger amount of information (compared to conventional EEG) necessitates the implementation of various mathematical methods to analyze the recorded signals, as well as more extensive use of techniques for combining this data with findings of other diagnostic methods, primarily magnetic resonance imaging and functional magnetic resonance imaging. This will open new horizons for the investigation of bioelectric activity of the human brain.

Relative importance of chemical attractiveness to parasites for susceptibility to trematode infection.

While the host immune system is often considered the most important physiological mechanism against parasites, precontact mechanisms determining exposure to parasites may also affect infection dynamics. For instance, chemical cues released by hosts can attract parasite transmission stages. We used the freshwater snail Lymnaea stagnalis and its trematode parasite Echinoparyphium aconiatum to examine the role of host chemical attractiveness, physiological condition, and immune function in determining its susceptibility to infection. We assessed host attractiveness through parasite chemo‐orientation behavior; physiological condition through host body size, food consumption, and respiration rate; and immune function through two immune parameters (phenoloxidase‐like and antibacterial activity of hemolymph) at an individual level. We found that, although snails showed high variation in chemical attractiveness to E. aconiatum cercariae, this did not determine their overall susceptibility to infection. This was because large body size increased attractiveness, but also increased metabolic activity that reduced overall susceptibility. High metabolic rate indicates fast physiological processes, including immune activity. The examined immune traits, however, showed no association with susceptibility to infection. Our results indicate that postcontact mechanisms were more likely to determine snail susceptibility to infection than variation in attractiveness to parasites. These may include localized immune responses in the target tissue of the parasite. The lack of a relationship between food consumption and attractiveness to parasites contradicts earlier findings that show food deprivation reducing snail attractiveness. This suggests that, although variation in resource level over space and time can alter infection dynamics, variation in chemical attractiveness may not contribute to parasite‐induced fitness variation within populations when individuals experience similar environmental conditions.

Biological causal links on physiological and evolutionary time scales.

Correlation does not imply causation. If two variables, say A and B, are correlated, it could be because A causes B, or that B causes A, or because a third factor affects them both. We suggest that in many cases in biology, the causal link might be bi-directional: A causes B through a fast-acting physiological process, while B causes A through a slowly accumulating evolutionary process. Furthermore, many trained biologists tend to consistently focus at first on the fast-acting direction, and overlook the slower process in the opposite direction. We analyse several examples from modern biology that demonstrate this bias (codon usage optimality and gene expression, gene duplication and genetic dispensability, stem cell division and cancer risk, and the microbiome and host metabolism) and also discuss an example from linguistics. These examples demonstrate mutual effects between the fast physiological processes and the slow evolutionary ones. We believe that building awareness of inference biases among biologists who tend to prefer one causal direction over another could improve scientific reasoning.

Tools for Analyzing and Repairing Complex Biological Systems

To enable the understanding and repair of complex biological systems such as the brain, we are creating tools that enable molecular-resolution maps of large scale systems, as well as technologies for observing and controlling high-speed physiological dynamics in such systems. First, we have developed a method for imaging large 3-D specimens with nanoscale precision, by embedding them in a swellable polymer, which upon exposure to water expands isotropically severalfold. This method, which we call expansion microscopy, enables conventional diffraction-limited microscopes to do large-volume nanoscopy. Second, we have collaboratively developed strategies to image fast physiological processes in 3-D with millisecond precision, and used them to acquire neural activity maps throughout small organisms. Third, we have collaboratively developed nanotechnological and robotic methods to record high-speed electrical events with single cell resolution in living mammalian brain. Finally, we have developed a set of genetically-encoded reagents, known as optogenetic tools, that when expressed in specific neurons, enable their electrical activities to be precisely driven or silenced in response to millisecond timescale pulses of light. In this way we aim to enable the systematic mapping, dynamical observation, and control of complex biological systems like the brain.

64 A novel role for astrocytes in regulating glutamate clearance during stroke

We are building tools to confront a fundamental challenge of the brain and other complex biological systems: their molecular building blocks are nanoscale in size and organized with nanoscale precision, but support physiological processes and computations that occur over macroscopic length scales. To enable the understanding and fixing of such complex systems, we are creating tools that enable molecular-resolution maps of large scale systems, as well as technologies for observing and controlling information processing in such systems. First, we have developed a method for super-resolution optical imaging that can image large 3-D preserved specimens, with nanoscale precision (Chen et al., 2015). We embed a specimen in a swellable polymer, which upon exposure to water expands isotropically in size, enabling conventional diffraction-limited microscopes to do large-volume nanoscopy. Second, we have collaboratively developed plenoptic or light-field microscopy approaches to image fast physiological processes in 3-D with millisecond precision, and used them to image all the neural activity in small organisms (Prevedel et al., 2014). Third, we have collaboratively developed robotic and microfabricated methods for electrically recording the electrical activity of large numbers of cells in the brain (Kodandaramaiah et al., 2012). Finally, we have developed a set of genetically-encoded reagents known as optogenetic tools, that when expressed in specific neurons, enable their electrical activities to be precisely driven or silenced in response to millisecond timescale pulses of light (Boyden, 2011; Chuong et al., 2014; Klapoetke et al., 2014). In this way we aim to enable the systematic mapping, dynamical observation, and control of complex systems like the brain. References Boyden, E. S. (2011). A history of optogenetics: the development of tools for controlling brain circuits with light. F1000 Biology Reports 3(11). Chen, F., Tillberg, P. W., & Boyden, E. S. (2015). Expansion microscopy. Science 347, 543–548. Chuong, A. S., Miri, M. L., Busskamp, V., Matthews, G. A. C., Acker, L. C., Sorensen, A. T., ... Boyden, E. S. (2014) Noninvasive optical inhibition with a red-shifted microbial rhodopsin, Nature Neuroscience 17, 1123–1129. Klapoetke, N. C., Murata, Y., Kim, S. S., Pulver, S. R., Birdsey-Benson, A., Cho, Y. K., ... Boyden, E. S. (2014). Independent optical excitation of distinct neural populations. Nature Methods, 11, 338–346. Kodandaramaiah, S., Talei Franzesi, G., Chow, B., Boyden, E. S., & Forest, C. (2012). Automated whole-cell patch clamp electrophysiology of neurons in vivo. Nature Methods, 9, 585–587. Prevedel, R., Yoon, Y.-G., Hoffman, M., Pak, N., Wetzstein, G., Kato, S., ... Vaziri, A. (2014). Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy. Nature Methods, 11, 727–730.

Disentangling the response of forest and grassland energy exchange to heatwaves under idealized land–atmosphere coupling

Abstract. This study investigates the difference in land–atmosphere interactions between grassland and forest during typical heatwave conditions in order to understand the controversial results of Teuling et al. (2010) (hereafter T10), who found the systematic occurrence of higher sensible heat fluxes over forest than over grassland during heatwaves. With a simple but accurate coupled land–atmosphere model, we show that existing parametrizations are able to reproduce the findings of T10 for normal summer and heatwave conditions. Furthermore, we demonstrate the sensitivity of the coupled system to changes in incoming radiation and early-morning temperature typical for European heatwaves. Our results suggest that the fast atmospheric control of stomatal resistance can explain the observed differences between grassland and forest. The atmospheric boundary layer has a buffering function therein: increases in stomatal resistance are largely compensated for by increases in the potential evaporation due to atmospheric warming and drying. In order to disentangle the contributions of differences in several static and dynamic properties between forest and grassland, we have performed a virtual experiment with artificial land-use types that are equal to grassland, but with one of its properties replaced by that of forest. From these, we confirm the important role of the fast physiological processes that lead to the closure of stomata. Nonetheless, for a full explanation of T10's results, the other properties (albedo, roughness and the ratio of minimum stomatal resistance to leaf-area index) play an important but indirect role; their influences mainly consist of strengthening the feedback that leads to the closure of the stomata by providing more energy that can be converted into sensible heat. The model experiment also confirms that, in line with the larger sensible heat flux, higher atmospheric temperatures occur over forest. As our parametrization for stomatal resistance is empirical rather than mechanical, our study stresses the demand for a better mechanistic understanding of physiological processes in plants.

Noise-compensated homotopic non-local regularized reconstruction for rapid retinal optical coherence tomography image acquisitions.

BackgroundOptical coherence tomography (OCT) is a minimally invasive imaging technique, which utilizes the spatial and temporal coherence properties of optical waves backscattered from biological material. Recent advances in tunable lasers and infrared camera technologies have enabled an increase in the OCT imaging speed by a factor of more than 100, which is important for retinal imaging where we wish to study fast physiological processes in the biological tissue. However, the high scanning rate causes proportional decrease of the detector exposure time, resulting in a reduction of the system signal-to-noise ratio (SNR). One approach to improving the image quality of OCT tomograms acquired at high speed is to compensate for the noise component in the images without compromising the sharpness of the image details.MethodsIn this study, we propose a novel reconstruction method for rapid OCT image acquisitions, based on a noise-compensated homotopic modified James-Stein non-local regularized optimization strategy. The performance of the algorithm was tested on a series of high resolution OCT images of the human retina acquired at different imaging rates.ResultsQuantitative analysis was used to evaluate the performance of the algorithm using two state-of-art denoising strategies. Results demonstrate significant SNR improvements when using our proposed approach when compared to other approaches.ConclusionsA new reconstruction method based on a noise-compensated homotopic modified James-Stein non-local regularized optimization strategy was developed for the purpose of improving the quality of rapid OCT image acquisitions. Preliminary results show the proposed method shows considerable promise as a tool to improve the visualization and analysis of biological material using OCT.

FPGA Based High Speed Data Acquisition System for Electrical Impedance Tomography

Electrical Impedance Tomography (EIT) systems are used to image tissue bio-impedance. EIT provides a number of features making it attractive for use as a medical imaging device including the ability to image fast physiological processes (>60 Hz), to meet a range of clinical imaging needs through varying electrode geometries and configurations, to impart only non-ionizing radiation to a patient, and to map the significant electrical property contrasts present between numerous benign and pathological tissues. To leverage these potential advantages for medical imaging, we developed a modular 32 channel data acquisition (DAQ) system using National Instruments' PXI chassis, along with FPGA, ADC, Signal Generator and Timing and Synchronization modules. To achieve high frame rates, signal demodulation and spectral characteristics of higher order harmonics were computed using dedicated FFT-hardware built into the FPGA module. By offloading the computing onto FPGA, we were able to achieve a reduction in throughput required between the FPGA and PC by a factor of 32:1. A custom designed analog front end (AFE) was used to interface electrodes with our system. Our system is wideband, and capable of acquiring data for input signal frequencies ranging from 100 Hz to 12 MHz. The modular design of both the hardware and software will allow this system to be flexibly configured for the particular clinical application.

A compact acousto-optic lens for 2D and 3D femtosecond based 2-photon microscopy

We describe a high speed 3D Acousto-Optic Lens Microscope (AOLM) for femtosecond 2-photon imaging. By optimizing the design of the 4 AO Deflectors (AODs) and by deriving new control algorithms, we have developed a compact spherical AOL with a low temporal dispersion that enables 2-photon imaging at 10-fold lower power than previously reported. We show that the AOLM can perform high speed 2D raster-scan imaging (>150 Hz) without scan rate dependent astigmatism. It can deflect and focus a laser beam in a 3D random access sequence at 30 kHz and has an extended focusing range (>137 mum; 40X 0.8NA objective). These features are likely to make the AOLM a useful tool for studying fast physiological processes distributed in 3D space.

Monitoring Biological Membrane-Potential Changes: A CI QM/MM Study

In recent decades, new less-invasive, nonlinear optical methods have been proposed and optimized for monitoring fast physiological processes in biological cells. One of these methods allows the action potential (AP) in cardiomyocytes or neurons to be monitored by means of second-harmonic generation (SHG). We now present the first, to our knowledge, simulations of the dependency of the intensity of the second harmonic (I(SHG)) on variations of the transmembrane potential (TMP) in a cardiomyocyte during an action potential (AP). For this, an amphiphilic potential-sensitive styryl dye molecule with nonlinear optical properties was embedded in a dipalmitoylphosphatidylcholine (DPPC) bilayer, replacing one of the phospholipid molecules. External electrical fields with different strengths were applied across the membrane to simulate the AP of a heart-muscle cell. We used a combined classical/quantum mechanical approach to model the structure and the spectroscopic properties of the embedded chromophore. Two 10 ns molecular dynamics (MD) simulations provided input geometries for semiempirical molecular orbital (QM/MM) single-point configuration interaction (CI) calculations, which were used to calculate the wavelengths and oscillator strengths of electronic transitions in the di-8-ANEPPS dye molecule. The results were then used in a sum-over-states treatment to calculate the second-order hyperpolarizability. The square of the hyperpolarizability scales with the intensity of the second harmonic, which is used to monitor the action potentials of cardiomyocytes experimentally. Thus, we computed changes in the intensity of the second harmonic (DeltaI(SHG)) as function of TMP changes. Our results agree well with experimental measurements.

In vivo functional imaging of human cone photoreceptors

We evaluate a novel non-invasive optical technique for observing fast physiological processes, in particular phototransduction, in single photoreceptor cells in the living human eye. The method takes advantage of the interference of multiple reflections within the outer segments (OS) of cones. This self-interference phenomenon is highly sensitive to phase changes such as those caused by variations in refractive index and scatter within the photoreceptor cell. A high-speed (192 Hz) flood-illumination retina camera equipped with adaptive optics (AO) is used to observe individual photoreceptors, and to monitor changes in their reflectance in response to visible stimuli ("scintillation"). AO and high frame rates are necessary for resolving individual cones and their fast temporal dynamics, respectively. Scintillation initiates within 5 to 10 ms after the onset of the stimulus flash, lasts 300 to 400 ms, is observed at visible and near-infrared (NIR) wavelengths, and is highly sensitive to the coherence length of the imaging light source. To our knowledge this is the first demonstration of in vivo optical imaging of the fast physiological processes that accompany phototransduction in individual photoreceptors.

Use of Intrinsic Optical Signals to Monitor Physiological Changes in Brain Tissue Slices

Optical imaging techniques have the potential to bring a combination of high spatial and temporal resolution to studies of brain function. Many optical techniques require the addition of a dye or fluorescent marker to the tissue, and such methods have proven extremely valuable. It is also known that the intrinsic optical properties of neural tissue are affected by certain physiological changes and that these intrinsic optical signals can provide information not available by other means. Most authors attribute the intrinsic optical change to alterations in cell volume and concomitant change in the concentration of the cytosol. In this article we review the literature on intrinsic optical signals, covering both the mechanisms of the optical change and its use in various branches of neurophysiology. We also discuss technical aspects of the technique as used with hippocampal slices, including illumination methods, cameras, experimental methods, and data collection and analysis procedures. Finally we present data from investigations in which we used intrinsic optical signals in hippocampal slices to study the extent of spread of synaptic activation, propagation of spreading depression, extent and severity of the response to hypoxia, and tissue response to osmotic challenges. We conclude that (1) at least two processes generate intrinsic optical signals in hippocampal slices, one of which causes light scattering to change inversely with cell volume and is related to dilution of the cytoplasm, while the other, opposite in sign, may be due to mitochondrial swelling; and (2) the intrinsic optical signal can be a useful tool for spatial mapping of relatively slow events, but is not suitable for study of fast physiological processes.

T-jump study of calcium binding kinetics of calcium chelators

Recent experimental studies have investigated the kinetic competition between calcium chelators and the secretion apparatus at a fast central synapse. Simultaneously, mathematical modelling studies indicate the importance of a quantitative knowledge of the binding kinetics of the chelators in studying fast physiological processes operating on a millisecond time scale. Using the temperature-jump relaxation method, I have studied the in vitro kinetics of Bis-Fura-2, Furaptra, Fluo-3, Calcium-Green-1, Calcium-Green-5N, Calcium-Orange-5N as well as EGTA, BAPTA and H-EDTA in conditions which are identical to those implemented in our patch clamp recordings, i.e. 100–140 mM CsCl, 20–40 mM Cs-HEPES, 8 mM NaCl, pH = 7.2 at 22°C. The results can be summarized as follows: all fluorescent indicators have on rates in the range of 10 8–10 9 M −1s −1. They differ significantly with respect to their off-rates from each other according to their affinities, ranging from 100 s −1 up to 26 000 s −1. BAPTA is kinetically almost indistinguishable from Fura-2. EGTA and H-EDTA have small binding rate constants for calcium in the range of 3 × 108 M −1s −1 since, at pH 7.20, protons need to be dissociated from the chelators before they can bind calcium ions.

Kernspintomographie mit 100 ms Zeitauflösung

A technique for the measurement of image series with a temporal resolution of almost 100 ms was developed at a conventional magnetic resonance whole body imager for clinical applications. This was performed by modification of an echo-planar-imaging sequence for the detection of multiple images exploiting the fast gradient rise times of the imaging system. Furthermore, the handling of calculated data was optimized to avoid unnecessary idle time after the completion of the data acquisition. The imaging technique was used for the measurement of fast physiological processes as a part of clinical patient examinations.

On estimating freezing times during tissue rapid freezing.

For the study of morphological changes that are associated with fast physiological processes, it is important to know the times at which the surface regions of specimens are frozen during rapid freezing. A simple physical model has been used to estimate the freezing times and the cooling rates at 10 micron depths in specimens. The calculations indicate that cooling rates in excess of 4 X 10(4) K s-1 are associated with freezing times of less than 0.5 ms. Using the same model, experimental measurements of freezing times at much larger depths have been extrapolated to a depth of 10 micron, the times obtained are 0.1-0.6 ms for freezing by rapid immersion in cryogenic liquids, and 0.1 ms or less for freezing on a metal block. It is concluded that the delay time between contact with a cryogenic source and specimen freezing is less than 0.5 ms. The uncertainty in the time of freezing may be larger than this, because of an uncertainty of about +/- 0.5 ms in determining the exact time of contact and, for freeze fracture studies, because of an uncertainty of up to 0.5 ms due to imprecision in the depth of fracture. At the same time it is estimated that the time during which freezing takes place may be as high as 250 microseconds, which can be taken as an upper limit for the resolution time for rapid freezing.