Session J05: Physics of Biological Systems I

Single molecule biophysics perspective on SARS-CoV-2

COVID-19 is a novel threat which emerged at the end of 2019 and has caused enormous losses of human lives and had a significant effect on human health and worldwide economy. Although the viral spread seems to be very strongly influenced by population-scale factors such as prior exposure to the virus or vaccination state, it is informative to consider what biophysics tells us about the virus sensitivity to temperature and humidity. I will present our results from a variety of measurement techniques and their implication for how environmental conditions affect SARS-CoV-2. I will also briefly discuss our other recent biophysics efforts at the University of Utah.   

InnovaBug -- Handheld, Low-Cost, Rapid, Accurate, Small Fluid Volume Diagnostic (SFVD) Device for Pathogen Detection using Drops: Design and Proof-of-Concept

A third of blood cultures yield false positives for infection. The average hospital wastes over {\$}1M annually treating non-existent blood infections, leading to antibiotic-resistant bacteria and anxious testing. Cultures also require significant blood volumes, 10-30 mL and are often performed more than once in chronically ill patients and premature infants, leading to high rates of Hospital-Acquired Anemia. Culturing requires at least 72 hrs for results. InnovaBug is designed and prototyped as an accurate, rapid, low-cost, handheld, medical Small Fluid Volume Diagnostic (SFVD) device. Yogurt water is used as a model system for blood plasma, because its viscosity matches plasma and it offers various bacteria to identify and count. InnovaBug uses off-the-shelf microscope slides cladded with reflective Al, coated with a \textit{super-hydrophilic} coating, and SYBR Safe Green fluorescent dye. Drops are applied and fluoresced via UVA. Pathogens can be identified rapidly by shape. Quantitative analysis of the ratio between green fluorescence intensity versus UVA excitation intensity is correlated to Colony Forming Units (CFU) counting, showing pathogens are detected via macroscopic DNA/RNA fluorescence.   

Soft and stretchable microelectronic fibers for modulation of gut neural circuits.

Implantable neural interfaces are an important technology used to investigate the mechanisms that underlie the functioning of the central nervous system. However, these devices are known to instigate health issues characterized by neuronal death and glial scarring---problems that limit their quality and durability. Inspired by these challenges, as well as by the possibility to extend their application to the peripheral nervous system, the innovation of neural tools that aim at exploring the connection between the brain and the gastrointestinal tract has gained attention in recent years. In this contribution, a soft and fully stretchable multifunctional fiber consisting of a SEBS-based structure and PMMA cladding with gallium as the conductive medium was developed using the Thermal Drawing Process. Laser pattering was used to access the gallium and mount \textmu LEDs along the fiber's length. Mechanical tests revealed the preservation of conductivity when placed under deformation, and the I-V and light-output tests demonstrated the functionality of the microelectronics. The fibers represent a prototype of neural probes that could be used to gain a broader understanding of the peripheral nervous system, including that of gut-brain bidirectional communication.   

Quantitative Detection of Pathogen Load via a Rapid, Small Fluid Volume Diagnostic (SFVD) Device, using 0.03 -- 0.3mL of Fluids, vs Colony Forming Units (CFU) counting: InnovaBug

30{\%} of Blood Cultures for Pathogen detection (BCP) yield false positives, leading the US to spend more than 6 billions dollars per year on non-existent infections. On top, BCP uses large blood volumes, 10-30 mL and BCP causes a 74{\%} rate of Hospital-Acquired Anemia with daylong waits for results. InnovaBug is a new Small Fluid Volume Diagnostic (SFVD) device for rapid accurate, portable, low-cost pathogen detection in minutes. InnovaBug uses only 0.03-- 0.3 mL of fluid spread on a macroscopic region of a slide coated with a benign \textit{hyper-hydrophilic} film, called FluoFilm. FluoFilm contains a safe fluorescent nucleic acid dye, so that RNA/DNA from pathogens fluoresce at a macroscopic scale. The ratio R of RNA and DNA macroscopic fluorescence over the excitation intensity is measured via Color analysis on inexpensive SmartPhone images, and yields a rapid pathogen count comparable to Colony Forming Units (CFUs) counts in blood cultures. CFUs computed via R are tested quantitatively using UVC sterilization of calibrated pathogens such as LactoB and E.Coli. R decreases by 60-80{\%} after UVC sterilization and correlates well with CFUs from cultures   

Fast, Comprehensive, Accurate Small Volume Blood Diagnostics on Blood Drops via an Inexpensive Hand-held Collection Device, InnovaStrip and a Fast Blood Analysis App

Blood Diagnostics (BD) need mLs of blood, leading to Hospital Acquired Anemia in the chronically ill and infants. BD can take days for results, delaying treatment. A cheap, fast, portable BD device, InnovaStrip \texttrademark , is developed here for accurate Small Volume BD via a \textit{hyper-hydrophilic} coating, HemaDrop\texttrademark . \textit{Hyper-hydrophilicity }flattens droplets into flat, uniform films by absorbing H$_{2}$O in blood in minutes via rapid solidification into Homogeneous Thin Solid Films (HTSF) \textit{without coagulation}. HTSFs can be analyzed via hand-held X-ray Fluorescence (XRF) and Ion Beam Analysis (IBA). XRF and IBA can yield blood levels of electrolytes, Fe, heavy metals and radionuclides with an accuracy $\le \quad +$/-10{\%} in minutes. An App ,`Fast Accurate Blood Analysis', or FABA, converts data in blood levels as mg/dL, the medically accepted units in BD. InnovaStrip yields with FABA inexpensive, hand-held, blood levels of electrolytes, Fe, and metals, and has a high potential for deployment in remote and underserved areas with limited access to diagnostic labs   

Macroscopic vs Microscopic UV Fluorescence of DNA/RNA: a New Approach for Fast {\&} Accurate Detection {\&} Counting of Pathogens in Drops for a New Device InnovaBug\texttrademark

Accurate and reliable detection, identification and counting of pathogens is critical in the COVID-19 pandemic. Standard Colony Forming Units (CFUs) counting requires 24-72 hrs lab incubation, takes days and yields 30{\%} false positives. This work aims to detect and count quickly and accurately pathogens on surfaces before and after 254 nm UVC sterilization. First, benign pathogens are incubated, detected, identified and counted using UV Fluorescence microscopy via SYBR Safe fluorescent green stain for nucleic acids pairs. UV microscopy does not yield accurate pathogen counts because areas analyzed are \textless than 100x100 $\mu $m$^{\mathrm{2}}$. A new approach uses macroscopic imaging of 20x50 mm2 via SmartPhone and macroscopic fluorescence of \textless 1mL of dyed pathogen solutions on microscope slides. This new Small Fluid Volume Diagnostic (SFVD) device, InnovaBug\texttrademark , yields within min. the number of green 540 nm photons emitted by fluorescing DNA and RNA from pathogens. A simple color analysis App measures the number of green photons vs intensity of the UVA, making InnovaBug\texttrademark a convenient and practical device that can be deployed in many situations including, but not limited to, disaster sites and refugee camps