Biology subjects

Shih, A. J.

Publications and source records attributed to Shih, A. J..

4 recordsLinked to original sources

bioRxiv2026

Blood-brain barrier disrupting stimuli induce production of extracellular vesicles with distinct protein cargoes and functionality

The blood-brain barrier (BBB) protects the brain from substances in the circulation; yet, this barrier can be breached. Systemic lupus erythematosus is a disease in which over 50% of patients experience manifestations of neuropsychiatric lupus (NPSLE), with many displaying BBB dysfunction. High levels of TNF, IL-1{beta}, C5a, and epinephrine, which have all been shown to cause BBB permeability, may be present in the serum of SLE patients. Brain microvascular endothelial cells (BMVECs) are a major structural element of the BBB. We asked whether BMVECs stimulated with barrier-disrupting factors release extracellular vesicles (EVs) which might participate in autocrine signaling or might have utility as diagnostic biomarkers of BBB permeability. We analyzed proteins in EVs secreted by unstimulated and stimulated BMVECs by mass spectrometry and used secreted EVs for further BMVEC stimulation. We subjected BMVECs to bulk RNA-seq to identify response signatures to the initial stimulus and to secondary stimulation with EVs. We show that there are agent-specific EV-associated protein profiles. EVs from BMVECs subjected to BBB-breaching stimuli alter the BMVEC transcriptional program, representing a potential feed-forward mechanism. Finally, we suggest that the proteins associated with EVs might be markers of BBB disruption.

molecular biology↗

bioRxiv2022

Automated assembly of high-density carbon fiber electrode arrays for single unit electrophysiological recordings

ObjectiveCarbon fiber (CF) is good for chronic neural recording due to the small diameter (7 {micro}m), high Youngs modulus, and low electrical resistance, but most high-density carbon fiber (HDCF) arrays are manually assembled with labor-intensive procedures and limited by the accuracy and repeatability of the operator handling. A machine to automate the assembly is desired. ApproachThe HDCF array assembly machine contains: 1) a roller-based CF extruder, 2) a motion system with three linear and one rotary stages, 3) an imaging system with two digital microscope cameras, and 4) a laser cutter. The roller-based extruder automatically feeds single CF as raw material. The motion system aligns the CF with the array backend then places it. The imaging system observes the relative position between the CF and the backend. The laser cutter cuts off the CF. Two image processing algorithms are implemented to align the CF with the support shanks and circuit connection pads. Main resultsThe machine was capable of precisely handling 6.8 m carbon fiber electrodes. Each electrode was placed into a 12 m wide trenches in a silicon support shank. Two HDCF arrays with 16 CF electrodes populated on 3 mm shanks (with 80 m pitch) were fully assembled. Impedance measurements were found to be in good agreement with manual assembled arrays. One HDCF array was implanted in the motor cortex in an anesthetized rat and was able to detect single unit activity. SignificanceThis machine can eliminate the manual labor-intensive handling, alignment and placement of single carbon fiber during assembly, providing a proof-of-concepts towards fully automated HDCF array assembly and batch production.

bioengineering↗

bioRxiv2021

Proteomic and single-cell transcriptomic dissection of human plasmacytoid dendritic cell response to influenza virus

Plasmacytoid dendritic cells [pDCs] represent a rare innate immune subset uniquely endowed with the capacity to produce substantial amounts of type-I interferons [IFN-I]. This function of pDCs is critical for effective antiviral defenses and has been implicated in autoimmunity. While IFN-I and select cytokines have been recognized as pDC secreted products, a comprehensive agnostic profiling of the pDC secretome in response to a physiologic stimulus has not been reported. We applied LC-MS/MS to catalogue the repertoire of proteins secreted by pDCs in response to challenge with live influenza H1N1. Additionally, using single-cell RNA-seq [scRNA-seq], we perform multidimensional analyses of pDC transcriptional diversification following stimulation. Our data reveal an abundance of protein species released by pDCs in addition to IFN-I, and evidence highly specialized roles within the pDC population ranging from dedicated cytokine super-producers to cells with APC-like functions. Moreover, dynamic expression of transcription factors and surface markers characterize activated pDC fates.

immunology↗

bioRxiv2021

Benchtop Carbon Fiber Microelectrode Array Fabrication Toolkit

BackgroundConventional neural probes are primarily fabricated in a cleanroom, requiring the use of multiple expensive and highly specialized tools. New methodWe propose a cleanroom "light" fabrication process of carbon fiber neural electrode arrays that can be learned quickly by an inexperienced cleanroom user. This carbon fiber electrode array fabrication process requires just one cleanroom tool, a parylene-c deposition machine, that can be learned quickly or outsourced to a commercial processing facility at marginal cost. Our fabrication process also includes hand-populating printed circuit boards, insulation, and tip optimization. ResultsThe three different tip optimizations explored here (Nd:YAG laser, blowtorch, and UV laser) result in a range of tip geometries and 1kHz impedances, with blowtorched fibers resulting in the lowest impedance. While previous experiments have proven laser and blowtorch electrode efficacy, this paper also shows UV laser cut fibers can record neural signals in vivo. Comparison with existing methodsExisting carbon fiber arrays either do not have individuated electrodes in favor of bundles or require cleanroom fabricated guides for population and insulation. The proposed arrays use only tools that can be used at a benchtop for fiber population. ConclusionsThis carbon fiber electrode array fabrication process allows for quick customization of bulk array fabrication at a reduced price compared to commercially available probes.

bioengineering↗