Conjugated Polymers in Bioelectronics.

The emerging field of organic bioelectronics bridges the electronic world of organic-semiconductor-based devices with the soft, predominantly ionic world of biology. This crosstalk can occur in both directions. For example, a biochemical reaction may change the doping state of an organic material, generating an electronic readout. Conversely, an electronic signal from a device may stimulate a biological event. Cutting-edge research in this field results in the development of a broad variety of meaningful applications, from biosensors and drug delivery systems to health monitoring devices and brain-machine interfaces. Conjugated polymers share similarities in chemical "nature" with biological molecules and can be engineered on various forms, including hydrogels that have Young's moduli similar to those of soft tissues and are ionically conducting. The structure of organic materials can be tuned through synthetic chemistry, and their biological properties can be controlled using a variety of functionalization strategies. Finally, organic electronic materials can be integrated with a variety of mechanical supports, giving rise to devices with form factors that enable integration with biological systems. While these developments are innovative and promising, it is important to note that the field is still in its infancy, with many unknowns and immense scope for exploration and highly collaborative research. The first part of this Account details the unique properties that render conjugated polymers excellent biointerfacing materials. We then offer an overview of the most common conjugated polymers that have been used as active layers in various organic bioelectronics devices, highlighting the importance of developing new materials. These materials are the most popular ethylenedioxythiophene derivatives as well as conjugated polyelectrolytes and ion-free organic semiconductors functionalized for the biological interface. We then discuss several applications and operation principles of state-of-the-art bioelectronics devices. These devices include electrodes applied to sense/trigger electrophysiological activity of cells as well as electrolyte-gated field-effect and electrochemical transistors used for sensing of biochemical markers. Another prime application example of conjugated polymers is cell actuators. External modulation of the redox state of the underlying conjugated polymer films controls the adhesion behavior and viability of cells. These smart surfaces can be also designed in the form of three-dimensional architectures because of the processability of conjugated polymers. As such, cell-loaded scaffolds based on electroactive polymers enable integrated sensing or stimulation within the engineered tissue itself. A last application example is organic neuromorphic devices, an alternative computing architecture that takes inspiration from biology and, in particular, from the way the brain works. Leveraging ion redistribution inside a conjugated polymer upon application of an electrical field and its coupling with electronic charges, conjugated polymers can be engineered to act as artificial neurons or synapses with complex, history-dependent behavior. We conclude this Account by highlighting main factors that need to be considered for the design of a conjugated polymer for applications in bioelectronics-although there can be various figures of merit given the broad range of applications, as emphasized in this Account.

Robotics-inspired biology.

For centuries, designers and engineers have looked to biology for inspiration. Biologically inspired robots are just one example of the application of knowledge of the natural world to engineering problems. However, recent work by biologists and interdisciplinary teams have flipped this approach, using robots and physical models to set the course for experiments on biological systems and to generate new hypotheses for biological research. We call this approach robotics-inspired biology; it involves performing experiments on robotic systems aimed at the discovery of new biological phenomena or generation of new hypotheses about how organisms function that can then be tested on living organisms. This new and exciting direction has emerged from the extensive use of physical models by biologists and is already making significant advances in the areas of biomechanics, locomotion, neuromechanics and sensorimotor control. Here, we provide an introduction and overview of robotics-inspired biology, describe two case studies and suggest several directions for the future of this exciting new research area.

A unique approach to demonstrating that apical bud temperature specifically determines leaf initiation rate in the dicot Cucumis sativus.

MAIN CONCLUSION: Leaf initiation rate is largely determined by the apical bud temperature even when apical bud temperature largely deviates from the temperature of other plant organs. We have long known that the rate of leaf initiation (LIR) is highly sensitive to temperature, but previous studies in dicots have not rigorously demonstrated that apical bud temperature controls LIR independent of other plant organs temperature. Many models assume that apical bud and leaf temperature are the same. In some environments, the temperature of the apical bud, where leaf initiation occurs, may differ by several degrees Celsius from the temperature of other plant organs. In a 28-days study, we maintained temperature differences between the apical bud and the rest of the individual Cucumis sativus plants from -7 to +8 °C by enclosing the apical buds in transparent, temperature-controlled, flow-through, spheres. Our results demonstrate that LIR was completely determined by apical bud temperature independent of other plant organs temperature. These results emphasize the need to measure or model apical bud temperatures in dicots to improve the prediction of crop development rates in simulation models.

Phase and absorption retrieval using incoherent X-ray sources.

X-ray phase contrast imaging has overcome the limitations of X-ray absorption imaging in many fields. Particular effort has been directed towards developing phase retrieval methods: These reveal quantitative information about a sample, which is a requirement for performing X-ray phase tomography, allows material identification and better distinction between tissue types, etc. Phase retrieval seems impossible with conventional X-ray sources due to their low spatial coherence. In the only previous example where conventional sources have been used, collimators were employed to produce spatially coherent secondary sources. We present a truly incoherent phase retrieval method, which removes the spatial coherence constraints and employs a conventional source without aperturing, collimation, or filtering. This is possible because our technique, based on the pixel edge illumination principle, is neither interferometric nor crystal based. Beams created by an X-ray mask to image the sample are smeared due to the incoherence of the source, yet we show that their displacements can still be measured accurately, obtaining strong phase contrast. Quantitative information is extracted from only two images rather than a sequence as required by several coherent methods. Our technique makes quantitative phase imaging and phase tomography possible in applications where exposure time and radiation dose are critical. The technique employs masks which are currently commercially available with linear dimensions in the tens of centimeters thus allowing for a large field of view. The technique works at high photon energy and thus promises to deliver much safer quantitative phase imaging and phase tomography in the future.

Poly(dimethylsiloxane)-based microdevices for studying plant reproduction.

Long-term holding and precise handling of growing plant tissues during in vitro cultivation has been a major hurdle for experimental studies related to plant development and reproduction. In the present review, we introduce two of our newly developed poly(dimethylsiloxane)-based microdevices: a T-shaped microchannel device for pollen tube chemoattraction and a microcage array for long-term live imaging of ovules. Their design, usage and advantages are described, and future prospects of experimental approaches to plant reproduction using such microdevices are discussed.

Science opportunities at the SwissFEL X-ray Laser.

Next-generation X-ray sources, based on the X-ray Free Electron Laser (XFEL) concept, will provide highly coherent, ultrashort pulses of soft and hard X-rays with peak intensity many orders of magnitude higher than that of a synchrotron. These pulses will allow studies of femtosecond dynamics at nanometer resolution and with chemical selectivity. They will produce diffraction images of organic and inorganic nanostructures without deleterious effects of radiation damage.

4273π: bioinformatics education on low cost ARM hardware.

BACKGROUND: Teaching bioinformatics at universities is complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration. For a future career in biology or bioinformatics, the installation of software is a useful skill. We propose that this may be taught by running the course on GNU/Linux running on inexpensive Raspberry Pi computer hardware, for which students may be granted full administrator access. RESULTS: We release 4273π, an operating system image for Raspberry Pi based on Raspbian Linux. This includes minor customisations for classroom use and includes our Open Access bioinformatics course, 4273π Bioinformatics for Biologists. This is based on the final-year undergraduate module BL4273, run on Raspberry Pi computers at the University of St Andrews, Semester 1, academic year 2012-2013. CONCLUSIONS: 4273π is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost.

X-ray lasers for structural and dynamic biology.

Research opportunities and techniques are reviewed for the application of hard x-ray pulsed free-electron lasers (XFEL) to structural biology. These include the imaging of protein nanocrystals, single particles such as viruses, pump--probe experiments for time-resolved nanocrystallography, and snapshot wide-angle x-ray scattering (WAXS) from molecules in solution. The use of femtosecond exposure times, rather than freezing of samples, as a means of minimizing radiation damage is shown to open up new opportunities for the molecular imaging of biochemical reactions at room temperature in solution. This is possible using a 'diffract-and-destroy' mode in which the incident pulse terminates before radiation damage begins. Methods for delivering hundreds of hydrated bioparticles per second (in random orientations) to a pulsed x-ray beam are described. New data analysis approaches are outlined for the correlated fluctuations in fast WAXS, for protein nanocrystals just a few molecules on a side, and for the continuous x-ray scattering from a single virus. Methods for determining the orientation of a molecule from its diffraction pattern are reviewed. Methods for the preparation of protein nanocrystals are also reviewed. New opportunities for solving the phase problem for XFEL data are outlined. A summary of the latest results is given, which now extend to atomic resolution for nanocrystals. Possibilities for time-resolved chemistry using fast WAXS (solution scattering) from mixtures is reviewed, toward the general goal of making molecular movies of biochemical processes.

Fluorescence correlation spectroscopy in biology, chemistry, and medicine.

This review describes the method of fluorescence correlation spectroscopy (FCS) and its applications. FCS is used for investigating processes associated with changes in the mobility of molecules and complexes and allows researchers to study aggregation of particles, binding of fluorescent molecules with supramolecular complexes, lipid vesicles, etc. The size of objects under study varies from a few angstroms for dye molecules to hundreds of nanometers for nanoparticles. The described applications of FCS comprise various fields from simple chemical systems of solution/micelle to sophisticated regulations on the level of living cells. Both the methodical bases and the theoretical principles of FCS are simple and available. The present review is concentrated preferentially on FCS applications for studies on artificial and natural membranes. At present, in contrast to the related approach of dynamic light scattering, FCS is poorly known in Russia, although it is widely employed in laboratories of other countries. The goal of this review is to promote the development of FCS in Russia so that this technique could occupy the position it deserves in modern Russian science.

Biological chemistry as a foundation of DNA genealogy: the emergence of "molecular history".

This paper presents the basis of DNA genealogy, a new field of science, which is currently emerging as an unusual blend of biochemistry, history, linguistics, and chemical kinetics. The methodology of the new approach is comprised of chemical (biological) kinetics applied to a pattern of mutations in non-recombinant fragments of DNA (Y chromosome and mtDNA, the latter not being considered in this overview). The goal of the analysis is to translate DNA mutation patterns into time spans to the most recent common ancestors of a given population or tribe and to the dating of ancient migration routes. To illustrate this approach, time spans to the common ancestors are calculated for ethnic Russians, that is Eastern Slavs (R1a1 tribe), Western Slavs (I1 and I2 tribes), and Northern (or Uralic) Slavs (N1c tribe), which were found to live around 4600 years before present (R1a1), 3650 ybp (I1), 3000 and 10,500 ybp (I2, two principal DNA lineages), and 3525 ybp (N1c) (confidence intervals are given in the main text). The data were compared with the respective dates for the nearest common ancestor of the R1a1 "Indo-European" population in India, who lived 4050 years before present, whose descendants represent the majority of the upper castes in India today (up to 72%). Furthermore, it was found that the haplotypes of ethnic Russians of the R1a1 haplogroup (up to 62% of the population in the Russian Federation) and those of the R1a1 Indians (more than 100 million today) are practically identical to each other, up to 67-marker haplotypes. This essentially solves a 200-year-old mystery of who were the Aryans who arrived in India around 3500 years before the present. Haplotypes and time spans to the ancient common ancestors were also compared for the ethnic Russians of haplogroups I1 and I2, on one hand, and the respective I1 and I2 populations in Eastern and Western Europe and Scandinavia, on the other. It is suggested that the approach described in this overview lays the foundation for "molecular history", in which the principal tool is high-technology analysis of DNA molecules of both our contemporaries and excavated ancient DNA samples, along with their biological kinetics.

Phase contrast optical tweezers.

In this paper, for the first time, we report on systematic theoretical and experimental investigation of Phase Contrast Optical Tweezers (PCOT) which could be an indispensable tool for micromanipulation of the transparent micro and nano objects such as biological tissues and vesicles. The quadrant photodiode detection scheme and the power-spectrum calibration method is shown to be valid for this case. We have shown that the phase objective with new designed phase plates can provide nearly aberration-free condition at a desired depth. This could be a valuable advantage for simultaneous in-depth micro-manipulations and visualization of the sample.

Optimizing the fluorescent yield in two-photon laser scanning microscopy with dispersion compensation.

A challenge for nonlinear imaging in living tissue is to maximize the total fluorescent yield from each fluorophore. We investigated the emission rates of three fluorophores-rhodamine B, a red fluorescent protein, and CdSe quantum dots-while manipulating the phase of the laser excitation pulse at the focus. In all cases a transform-limited pulse maximized the total yield to insure the highest signal-to-noise ratio. Further, we find evidence of fluorescence antibleaching in quantum dot samples.

Exploring biology with small organic molecules.

Small organic molecules have proven to be invaluable tools for investigating biological systems, but there is still much to learn from their use. To discover and to use more effectively new chemical tools to understand biology, strategies are needed that allow us to systematically explore 'biological-activity space'. Such strategies involve analysing both protein binding of, and phenotypic responses to, small organic molecules. The mapping of biological-activity space using small molecules is akin to mapping the stars--uncharted territory is explored using a system of coordinates that describes where each new feature lies.

Acoustic time-frequency domain imaging.

The axial resolution of conventional acoustic micro imaging is limited by the wavelength of acoustic waves. Acoustic time-frequency domain imaging was recently proposed to overcome the wavelength limit [Zhang et al., J. Acoust. Soc. Am. 118, 3706-3720 (2005)]. A continuous wavelet transform based acoustic time-frequency domain imaging technique is investigated in this paper. Experiments are performed on real 3D data collected from microelectronic packages. Results demonstrate the proposed technique reveals more image details and enhances the image contrast in comparison with conventional time domain imaging.