Microbioreactor arrays with parametric control for high-throughput experimentation

A scalable array technology for parametric control of high-throughput cell cultivations is demonstrated. The technology makes use of commercial printed circuit board (PCB) technology, integrated circuit sensors, and an electrochemical gas generation system. We present results for an array of eight 250 microl microbioreactors. Each bioreactor contains an independently addressable suite that provides closed-loop temperature control, generates feed gas electrochemically, and continuously monitors optical density. The PCB technology allows for the assembly of additional off-the-shelf components into the microbioreactor array; we demonstrate the use of a commercial ISFET chip to continuously monitor culture pH. The electrochemical dosing system provides a powerful paradigm for reproducible gas delivery to high-density arrays of microreactors. Growth data are presented for Escherichia coli cultured in the array with varying microaerobic conditions using electrochemically generated oxygen. Additionally, we present data on carbon dioxide generation for pH dosing.     

A retrospective on the LBNL PEM project

We present a retrospective on the LBNL Positron Emission Mammography (PEM) project, looking back on our design and experiences. The LBNL PEM camera utilizes detector modules that are capable of measuring depth of interaction (DOI) and places them into 4 detector banks in a rectangular geometry. In order to build this camera, we had to develop the DOI detector module, LSO etching, Lumirror-epoxy reflector for the LSO array (to achieve optimal DOI), photodiode array, custom IC, rigid-flex readout board, packaging, DOI calibration and reconstruction algorithms for the rectangular camera geometry. We will discuss the high-lights (good and bad) of these developments.     

Analysis of aristolochic acids and analogues in medicinal plants and their commercial products by HPLC-PAD-ESI/MS

An HPLC-UV-MS method for the analysis of aristolochic acids A, B, C and D, 7-OH-aristolochic acid A, and aristolic acid in a number of plant materials and their commercial products has been developed. HPLC with photodiode array detection and electrospray ionisation-MS in the selected ion monitoring mode allowed the identification of the target compounds and increased the selectivity of complex analyses such as those associated with multi-botanical preparations. The presented method was used to analyse 10 plant samples and six commercial products that possibly contained aristolochic acids. The resulting chromatographic profiles of the samples were significantly different from each other, and the method was directly transferred to HPLC-MS, which was used to confirm the presence of the six aristolochic acids mentioned above.     

Static electric fields do not cause coleoptile movements

A photodiode array method has been used to record automatically minute lateral movements of Avena sativa L. (cv. Seger I) coleoptiles in a static electric field. The electric fields, 600 or 5000 V cm⁻¹ did not cause any significant movement of the coleoptiles, in contrast to reports in the literature. Likewise, in experiments where photographic recordings were made, no significant movements were found.     

Optical recording of the in vivo piriform cortex responses to electrical stimulation of the lateral olfactory tract in the rat

Using a voltage-sensitive styryl dye, optical recordings ofthe piriform cortex responses to bipolar electrical stimulationsof the rat lateral olfactory tract (LOT) were taken. Surgicalprocedures were performed on Wistar SPF male rats anaesthetizedwith equithesine. Anaesthesia was continued during the recording.In addition the animals were curarized and artificially ventilated.Piriform cortex was stained with RH795. Cortical fluorescencewas recorded with a 124-element photodiode array using epi-illuminationwhile electrical stimulations were delivered to the LOT. Mappingof the piriform activity indicated a very large overlap of therecorded responses. Nevertheless, some differences in locationof recorded responses were observed and seemed to correlatewith the location of the stimulation electrode on the LOT. Theresults are discussed in relation to the anatomy and histologyof the olfactory bulb projections to the piriform cortex.     

Scalable Fluidic Injector Arrays for Viral Targeting of Intact 3-D Brain Circuits

Our understanding of neural circuits--how they mediate the computations that subserve sensation, thought, emotion, and action, and how they are corrupted in neurological and psychiatric disorders--would be greatly facilitated by a technology for rapidly targeting genes to complex 3-dimensional neural circuits, enabling fast creation of "circuit-level transgenics." We have recently developed methods in which viruses encoding for light-sensitive proteins can sensitize specific cell types to millisecond-timescale activation and silencing in the intact brain. We here present the design and implementation of an injector array capable of delivering viruses (or other fluids) to dozens of defined points within the 3-dimensional structure of the brain (Figure. 1A, 1B). The injector array comprises one or more displacement pumps that each drive a set of syringes, each of which feeds into a polyimide/fused-silica capillary via a high-pressure-tolerant connector. The capillaries are sized, and then inserted into, desired locations specified by custom-milling a stereotactic positioning board, thus allowing viruses or other reagents to be delivered to the desired set of brain regions. To use the device, the surgeon first fills the fluidic subsystem entirely with oil, backfills the capillaries with the virus, inserts the device into the brain, and infuses reagents slowly (<0.1 microliters/min). The parallel nature of the injector array facilitates rapid, accurate, and robust labeling of entire neural circuits with viral payloads such as optical sensitizers to enable light-activation and silencing of defined brain circuits. Along with other technologies, such as optical fiber arrays for light delivery to desired sets of brain regions, we hope to create a toolbox that enables the systematic probing of causal neural functions in the intact brain. This technology may not only open up such systematic approaches to circuit-focused neuroscience in mammals, and facilitate labeling of brain regions in large animals such as non-human primates, but may also open up a clinical translational path for cell-specific optical control prosthetics, whose precision may enable improved treatment of intractable brain disorders. Finally, such devices as described here may facilitate precisely-timed fluidic delivery of other payloads, such as stem cells and pharmacological agents, to 3-dimensional structures, in an easily user-customizable fashion.     

Reproducibility of MUAP properties in array surface EMG recordings of the upper trapezius and sternocleidomastoid muscle

The use of array surface EMG recordings for detailed assessment of motor control and muscle properties is increasing. Motor unit action potentials (MUAPs) and their properties can be extracted from these recordings. The objective of this study was to determine the reproducibility of variables obtained from array surface EMG recordings of the shoulder and neck muscles during different functional tasks.Eight-channel linear arrays were placed on the upper trapezius (UT) and sternocleidomastoid (SCM) muscles of 12 healthy subjects. Subjects performed 3 tasks: shoulder abduction (90°), ironing (repetitively touching two ends of a horizontal bar in front of the subject), and 90° head turning. The protocol was performed twice while electrodes remained on and repeated a third time a week later.Three global and six MUAP-related variables were calculated. Intra-class correlation coefficients (ICC) were calculated to assess reliability and smallest detectable changes (SDC) were calculated to assess agreement.In general, the EMG variables showed high levels of reliability which suggests they may be effective for differentiating between-subjects. SDC was found to be considerably lower for the frequency-related (5–23%) than for the amplitude-related variables (15–78%), indicating that the frequency-related variables may be more suitable for investigating interventions which aim to modify motor control. There was no difference in reproducibility between global and MUAP-related variables, which justifies their complementary use.     

Control of hypocotyl phototropism by phytochrome in a dicotyledonous seedling (Sesamum indicum L.)

Abstract The phototropic response in stems of higher plants is brought about by blue/UV light. The problem studied here is to what extent long-wavelength light, which is absorbed by phytochrome, affects the phototropic response. A refined measurement of phototropism — a curvature index — was applied to the hypocotyl of the sesame seedling (Sesamum indicum L.). The time course of the phototropic response was followed in continuous unilateral weak blue light (B, 460 nm, 8 mW m^?2). Long term red light (R) pretreatments, operating through phytochrome, strongly increase the rate and extent of the phototropic response once it is elicited by unilateral B, while the pretreatments decrease the sensitivity towards B. If a R pulse is given immediately prior to the onset of unilateral B, the rate of the response is strongly reduced compared to the time course of curvature observed when the pretreatment was terminated with a long wavelength far-red light (FR) pulse. R and FR were then applied simultaneously with unilateral B to manipulate the status of the phytochrome system during actual curvature. It was found that a low Pfr/P ratio (established by FR) stimulates the phototropic response far above the control (B alone), while a high Pfr/P ratio (established by R) reduces the response below the control. During bending a positive effect of phytochrome on the rate and extent of the phototropic response, which is saturated at a low level of Pfr, appears to be counteracted by an inhibitory effect which dominates at higher levels of Pfr, such as established by omnilateral R. However, if R is applied unilaterally from the same direction as B, R increases the rate of curvature. Apparently the sesame seedling is capable of detecting the direction of R relative to the direction of B. While a mechanistic explanation of these effects cannot be advanced at present, it is clear that the seedling is capable of super-imposing information about the actual light conditions during bending on a ‘memory’ of the light conditions prior to the onset of bending. Thus, the previous as well as the actual light conditions determine its phototropic responsiveness.     

An active balance board system with real-time control of stiffness and time-delay to assess mechanisms of postural stability

Increased time-delay in the neuromuscular system caused by neurological disorders, concussions, or advancing age is an important factor contributing to balance loss (Chagdes et al., 2013, 2016a,b). We present the design and fabrication of an active balance board system that allows for a systematic study of stiffness and time-delay induced instabilities in standing posture. Although current commercial balance boards allow for variable stiffness, they do not allow for manipulation of time-delay. Having two controllable parameters can more accurately determine the cause of balance deficiencies, and allows us to induce instabilities even in healthy populations. An inverted pendulum model of human posture on such an active balance board predicts that reduced board rotational stiffness destabilizes upright posture through board tipping, and limit cycle oscillations about the upright position emerge as feedback time-delay is increased. We validate these two mechanisms of instability on the designed balance board, showing that rotational stiffness and board time-delay induced the predicted postural instabilities in healthy, young adults. Although current commercial balance boards utilize control of rotational stiffness, real-time control of both stiffness and time-delay on an active balance board is a novel and innovative manipulation to reveal balance deficiencies and potentially improve individualized balance training by targeting multiple dimensions contributing to standing balance.     

Mapping of the phosphorylation sites on the phototropic signal transducer, NPH3

The phototropic response in Arabidopsis thaliana is initiated by the blue-light photoreceptors, phototropin (phot)1 and phot2. A recent study has shown that one of the phototropic signal transducers, NPH3, is phosphorylated under dark conditions and dephosphorylated by blue-light irradiation. To further understand the function of phosphorylation and dephosphorylation of NPH3 during this phototropic response, we have mapped the phosphorylation sites of NPH3 in our current study. The NPH3 protein has at least three phosphorylation sites at serine residues, Ser212, Ser222, and Ser236, and these sites are dephosphorylated by blue-light irradiation. By immunoblotting analysis, these phosphorylation sites in phot1 mutants are not dephosphorylated following blue-light irradiation at both low and high fluence rates, even though such irradiations induce the phot2-dependent phototropic response in phot1. These results suggest that the dephosphorylated NPH3 is involved in the phot1-dependent phototropic response and is not essential for the phot2-dependent phototropic response. We generated two types of transgenic nph3 plants expressing a NPH3^{S212A/S222A/S232A/S236A} protein and a NPH3^Δ212–238 protein in which the phosphorylation region is deleted, and assessed the phototropic phenotype of these. Based upon our present findings, we discuss the role of dephosphorylated and phosphorylated NPH3 in mediating the phototropic response.     

Induction of myrosinase gene expression and myrosinase activity in radish hypocotyls by phototropic stimulation

The role of myrosinase (beta-thioglucoside glucohydrolase, EC 3.2.3.1) in the phototropic response in radish hypocotyls was investigated. Unilateral illumination with blue light abruptly up-regulated the activity of myrosinase, which releases bioactive 4-methylthio-3-butenyl isothiocyanate (MTBI) from inactive 4-methylthio-3-butenyl glucosinolate (MTBG), in the illuminated halves of radish hypocotyls 10 min after onset of phototropic stimulation, peaking after 30 min and decreasing thereafter. The myrosinase activity in the shaded halves also increased, but was significantly lower than that in the illuminated halves. Furthermore, whether blue light illumination induces myrosinase gene expression was studied. Northern blotting analysis indicated that myrosinase mRNA levels were increased markedly in unilaterally illuminated hypocotyls, reaching maximum signal intensity within 10 min after onset of blue illumination, declining nearly to the control level thereafter. These results suggested that phototropic stimulation promotes myrosinase gene expression and myrosinase activity in the illuminated side, resulting in the conversion of inactive MTBG to active MTBI and simultaneously producing more active raphanusanins, causing a phototropic response.     

Characterization of peptidyl-nucleoside antifungal antibiotics from fermentation broth

Summary Characterization of sinefungin related antifungal antibiotics from fermentation broth was accomplished by coupling photodiode array (PDA) detection to high performance liquid chromatography (HPLC). From the combined HPLC-PDA evaluation of broth filtrate, we detected five sinefungin related components. Fast atom bombardment (FAB) mass spectroscopic evaluations, mass-analysed ion kinetic energy spectra (MIKES) and collision activated (CA) MIKES of these components confirmed their respective identities. Our findings from the combination of HPLC photodiode array acquisition and FAB-mass spectrometry suggest we have detected the presence of a previously unreported sinefungin analogue.     

Practical genetic control strategies for industrial bioprocesses

Optimization of metabolism to maximize production of bio-based chemicals must consistently balance cellular resources for biocatalyst growth and desired compound synthesis. This mini-review discusses synthetic biology strategies for dynamically controlling expression of genes to enable dual-phase fermentations in which growth and production are separated into dedicated phases. Emphasis is placed on practical examples which can be reliably scaled to commercial production with the current state of technology. Recent case studies are presented, and recommendations are provided for environmental signals and genetic control circuits.     

Differential roles of auxin efflux carrier PIN proteins in hypocotyl phototropism of etiolated Arabidopsis seedlings depend on the direction of light stimulus

In a recent study, we demonstrated that although the auxin efflux carrier PIN-FORMED (PIN) proteins, such as PIN3 and PIN7, are required for the pulse-induced first positive phototropism in etiolated Arabidopsis hypocotyls, they are not necessary for the continuous-light-induced second positive phototropism when the seedlings are grown on the surface of agar medium, which causes the hypocotyls to separate from the agar surface. Previous reports have shown that hypocotyl phototropism is slightly impaired in pin3 single mutants when they are grown along the surface of agar medium, where the hypocotyls always contact the agar, producing some friction. To clarify the possible involvement of PIN3 and PIN7 in continuous-light-induced phototropism, we investigated hypocotyl phototropism in the pin3 pin7 double mutant grown along the surface of agar medium. Intriguingly, the phototropic curvature was slightly impaired in the double mutant when the phototropic stimulus was presented on the adaxial side of the hook, but was not impaired when the phototropic stimulus was presented on the abaxial side of the hook. These results indicate that PIN proteins are required for continuous-light-induced second positive phototropism, depending on the direction of the light stimulus, when the seedlings are in contact with agar medium.     

Blue and Green Light-Induced Phototropism in Arabidopsis thaliana and Lactuca sativa L. Seedlings

Exposure time-response curves for blue and green light-induced phototropic bending in hypocotyls of Arabidopsis thaliana (L.) Heynh. and Lactuca sativa L. seedlings are presented. These seedlings show significant phototropic sensitivity up to 540 to 550 nanometers. Since wave-lengths longer than 560 nanometers do not induce phototropic bending, it is suggested that the response to 510 to 550 nanometers light is mediated by the specific blue light photoreceptor of phototropism. We advise care in the use of green `safelights' for studies of phototropism.     

Mutagenic activity and heterocyclic amine carcinogens in commercial pet foods

Twenty-five commercial pet foods were analyzed for mutagenic activity using the Ames/Salmonella test with strain TA98 and added metabolic activation. All but one gave a positive mutagenic response. Fourteen of these samples were analyzed for heterocyclic amine mutagens/carcinogens and all but one contained 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx) and 10 of 14 contained 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) as analyzed by HPLC and confirmed by photodiode array peak matching. From these findings it is hypothesized that there is a connection between dietary heterocyclic amines and cancer in animals consuming these foods.     

PHOTOTROPISM OF SELAGINELLA: THE DIFFERENTIAL RESPONSE TO LIGHT

Selaginella kraussiana (Kunze) A. Braun has a plagiotropic dorsiventral stem with two rows of small leaves on the dorsal surface and two rows of large leaves inserted laterally. Stem tips exhibit a differential phototropic response. When stem tips are placed in their normal horizontal orientation and the dorsal surfaces are illumianted, the tips bend only 20” below the horizon and away from light. Stem curvature is limited to a zone 450 μm long located 1.5 mm behind the shoot apex. The dorsal cortical cells within this zone of curvature are about 1.44 times longer than the ventral cortical cells. Illumination of the ventral surface of the stem tips elicits a strong phototropic response. The stems bend from 123–158° below the horizon and toward light, and the zone of curvature increases in length to 10 mm of the explant. The curvature is large enough so that the previously shaded dorsal leaves of the stem tips become redirected toward the light. This phototropic response is promoted by white and blue light, whereas red or far-red light has no effect. When stem tips are cultured in total darkness, the length of the zone of curvature is 8.0 mm but the stems bend only 50–67°. Treatment of the small dorsal leaves with phenylacetic acid inhibits phototropic curvature, and the phototropic response is unaffected by gravity.     

High pigment1 mutation negatively regulates phototropic signal transduction in tomato seedlings

Phototropins and phytochromes are the major photosensory receptors in plants and they regulate distinct photomorphogenic responses. The molecular mechanisms underlying functional interactions of phototropins and phytochromes remain largely unclear. We show that the tomato (Lycopersicon esculentum) phytochrome A deficient mutant fri lacks phototropic curvature to low fluence blue light, indicating requirement for phytochrome A for expression of phototropic response. The hp1 mutant that exhibits hypersensitive responses to blue light and red light reverses the impairment of second-positive phototropic response in tomato in phytochrome A-deficient background. Physiological analyses indicate that HP1 functions as a negative regulator of phototropic signal transduction pathway, which is removed via action of phytochrome A. The loss of HP1 gene product in frihp1 double mutant allows the unhindered operation of phototropic signal transduction chain, obviating the need for the phytochrome action. Our results also indicate that the role of phytochrome in regulating phototropism is restricted to low fluence blue light only, and at high fluence blue light, the phytochrome A-deficient fri mutant shows the normal phototropic response.