In vivo robotics: the automation of neuroscience and other intact-system biological fields

High-throughput genetic manipulation of multicellular organisms using a machine-vision guided embryonic microinjection robot

Microinjection is a technique used for transgenesis, mutagenesis, cell labeling, cryopreservation, and in vitro fertilization in multiple single and multicellular organisms. Microinjection requires specialized skills and involves rate-limiting and labor-intensive preparatory steps. Here, we constructed a machine-vision guided generalized robot that fully automates the process of microinjection in fruit fly (Drosophila melanogaster) and zebrafish (Danio rerio) embryos. The robot uses machine learning models trained to detect embryos in images of agar plates and identify specific anatomical locations within each embryo in 3D space using dual view microscopes. The robot then serially performs a microinjection in each detected embryo. We constructed and used three such robots to automatically microinject tens of thousands of Drosophila and zebrafish embryos. We systematically optimized robotic microinjection for each species and performed routine transgenesis with proficiency comparable to highly skilled human practitioners while achieving up to 4× increases in microinjection throughput in Drosophila. The robot was utilized to microinject pools of over 20,000 uniquely barcoded plasmids into 1,713 embryos in 2 days to rapidly generate more than 400 unique transgenic Drosophila lines. This experiment enabled a novel measurement of the number of independent germline integration events per successfully injected embryo. Finally, we showed that robotic microinjection of cryoprotective agents in zebrafish embryos significantly improves vitrification rates and survival of cryopreserved embryos post-thaw as compared to manual microinjection. We anticipate that the robot can be used to carry out microinjection for genome-wide manipulation and cryopreservation at scale in a wide range of organisms.

AutoRG: An automatized reach-to-grasp platform technology for assessing forelimb motor function, neural circuit activation, and cognition in rodents

BACKGROUND

Rodent reach-to-grasp function assessment is a translationally powerful model for evaluating neurological function impairments and recovery responses. Existing assessment platforms are experimenter-dependent, costly, or low-throughput with limited output measures. Further, a direct histologic comparison of neural activation has never been conducted between any novel, automated platform and the well-established single pellet skilled reach task (SRT).

NEW METHOD

To address these technological and knowledge gaps, we designed an open-source, low-cost Automatized Reach-to-Grasp (AutoRG) pull platform that reduces experimenter interventions and variability. We assessed reach-to-grasp function in rats across seven progressively difficult stages using AutoRG. We mapped AutoRG and SRT-activated motor circuitries in the rat brain using volumetric imaging of the immediate early gene-encoded Arc (activity-regulated cytoskeleton-associated) protein.

RESULTS

Rats demonstrated robust forelimb reaching and pulling behavior after training in AutoRG. Reliable force versus time responses were recorded for individual reach events in real time, which were used to derive several secondary functional measures of performance. Moreover, we provide the first demonstration that for a training period of 30 min, AutoRG and SRT both engage similar neural responses in the caudal forelimb area (CFA), rostral forelimb area (RFA), and sensorimotor area (S1).

CONCLUSION

AutoRG is the first low-cost, open-source pull system designed for the scale-up of volitional forelimb motor function testing and characterization of rodent reaching behavior. The similarities in neuronal activation patterns observed in the rat motor cortex after SRT and AutoRG assessments validate the AutoRG as a rigorously characterized, scalable alternative to the conventional SRT and expensive commercial systems.

Cleaning patch-clamp pipettes for immediate reuse

Patch-clamp recording has enabled single-cell electrical, morphological and genetic studies at unparalleled resolution. Yet it remains a laborious and low-throughput technique, making it largely impractical for large-scale measurements such as cell type and connectivity characterization of neurons in the brain. Specifically, the technique is critically limited by the ubiquitous practice of manually replacing patch-clamp pipettes after each recording. To circumvent this limitation, we developed a simple, fast, and automated method for cleaning glass pipette electrodes that enables their reuse within one minute. By immersing pipette tips into Alconox, a commercially-available detergent, followed by rinsing, we were able to reuse pipettes 10 times with no degradation in signal fidelity, in experimental preparations ranging from human embryonic kidney cells to neurons in culture, slices, and in vivo. Undetectable trace amounts of Alconox remaining in the pipette after cleaning did not affect ion channel pharmacology. We demonstrate the utility of pipette cleaning by developing the first robot to perform sequential patch-clamp recordings in cell culture and in vivo without a human operator.

Assembly and operation of the autopatcher for automated intracellular neural recording in vivo

Whole-cell patch clamping in vivo is an important neuroscience technique that uniquely provides access to both suprathreshold spiking and subthreshold synaptic events of single neurons in the brain. This article describes how to set up and use the autopatcher, which is a robot for automatically obtaining high-yield and high-quality whole-cell patch clamp recordings in vivo. By following this protocol, a functional experimental rig for automated whole-cell patch clamping can be set up in 1 week. High-quality surgical preparation of mice takes ∼1 h, and each autopatching experiment can be carried out over periods lasting several hours. Autopatching should enable in vivo intracellular investigations to be accessible by a substantial number of neuroscience laboratories, and it enables labs that are already doing in vivo patch clamping to scale up their efforts by reducing training time for new lab members and increasing experimental durations by handling mentally intensive tasks automatically.

MATLAB-based automated patch-clamp system for awake behaving mice

Automation has been an important part of biomedical research for decades, and the use of automated and robotic systems is now standard for such tasks as DNA sequencing, microfluidics, and high-throughput screening. Recently, Kodandaramaiah and colleagues (Nat Methods 9: 585-587, 2012) demonstrated, using anesthetized animals, the feasibility of automating blind patch-clamp recordings in vivo. Blind patch is a good target for automation because it is a complex yet highly stereotyped process that revolves around analysis of a single signal (electrode impedance) and movement along a single axis. Here, we introduce an automated system for blind patch-clamp recordings from awake, head-fixed mice running on a wheel. In its design, we were guided by 3 requirements: easy-to-use and easy-to-modify software; seamless integration of behavioral equipment; and efficient use of time. The resulting system employs equipment that is standard for patch recording rigs, moderately priced, or simple to make. It is written entirely in MATLAB, a programming environment that has an enormous user base in the neuroscience community and many available resources for analysis and instrument control. Using this system, we obtained 19 whole cell patch recordings from neurons in the prefrontal cortex of awake mice, aged 8-9 wk. Successful recordings had series resistances that averaged 52 ± 4 MΩ and required 5.7 ± 0.6 attempts to obtain. These numbers are comparable with those of experienced electrophysiologists working manually, and this system, written in a simple and familiar language, will be useful to many cellular electrophysiologists who wish to study awake behaving mice.

Protection and Repair After Spinal Cord Injury: Accomplishments and Future Directions

It was an honor for me to present the 2014 G. Heiner Sell Memorial Lecture at the annual American Spinal Injury Association (ASIA) meeting in San Antonio. For this purpose, I provided a comprehensive review of the scope of research targeting discovery and translational and clinical investigations into spinal cord injury (SCI) research. Indeed, these are exciting times in the area of spinal cord research and clinical initiatives. Many laboratories and clinical programs throughout the world are publishing data related to the pathophysiology of SCI and new strategies for protecting and promoting recovery in both animal models and humans. For this lecture, several topics were discussed including neuroprotective and reparative strategies, neurorehabilitation, quality of life issues, and future directions. In the area of neuroprotection, pathophysiological events that may be targeted with therapeutic strategies, including pharmacological and targeted temperature management were reviewed. For reparative approaches, the importance of both intrinsic and extrinsic mechanisms of axonal regeneration was highlighted. Various cell therapies currently being tested in preclinical and clinical arenas were reviewed as well as ongoing US Food and Drug Administration approved trials for SCI patients. Neurorehabilitation is an evolving research field with locomotive training strategies, electrical stimulation, and brain-machine interface programs targeting various types of SCI. The importance of testing combination approaches including neuroprotective, reparative, and rehabilitative strategies to maximize recovery mechanisms was therefore emphasized. Finally, quality of life issues that affect thousands of individuals living with paralysis were also presented. Future directions and specific obstacles that require attention as we continue to move the SCI field forward were discussed.

Microchip amplifier for in vitro, in vivo, and automated whole cell patch-clamp recording

Patch clamping is a gold-standard electrophysiology technique that has the temporal resolution and signal-to-noise ratio capable of reporting single ion channel currents, as well as electrical activity of excitable single cells. Despite its usefulness and decades of development, the amplifiers required for patch clamping are expensive and bulky. This has limited the scalability and throughput of patch clamping for single-ion channel and single-cell analyses. In this work, we have developed a custom patch-clamp amplifier microchip that can be fabricated using standard commercial silicon processes capable of performing both voltage- and current-clamp measurements. A key innovation is the use of nonlinear feedback elements in the voltage-clamp amplifier circuit to convert measured currents into logarithmically encoded voltages, thereby eliminating the need for large high-valued resistors, a factor that has limited previous attempts at integration. Benchtop characterization of the chip shows low levels of current noise [1.1 pA root mean square (rms) over 5 kHz] during voltage-clamp measurements and low levels of voltage noise (8.2 μV rms over 10 kHz) during current-clamp measurements. We demonstrate the ability of the chip to perform both current- and voltage-clamp measurement in vitro in HEK293FT cells and cultured neurons. We also demonstrate its ability to perform in vivo recordings as part of a robotic patch-clamping system. The performance of the patch-clamp amplifier microchip compares favorably with much larger commercial instrumentation, enabling benchtop commoditization, miniaturization, and scalable patch-clamp instrumentation.