EZ-SPOTs: A simple and robust high-throughput liquid handling platform.

Liquid handling is a fundamental capability for many scientific experiments. Previously, we introduced the Surface Patterned Omniphobic Tiles (SPOTs) platform, which enables manipulation of hundreds to thousands of independent experiments without costly equipment or excessive consumable expenses. However, the SPOTs platform requires a custom coating formulation and lacks robustness. To overcome these limitations, we introduce EZ-SPOTs. These devices can be created in an hour with common fabrication tools and just three components - glass, a hydrophobic coating, and acrylic. EZ-SPOTs preserve many of the SPOTs platform's strengths - ease of use, ability to handle a wide range of volumes, and scalability - and adopt a durable and abrasion resistant coating that enables multiple reuses of each device. Here, we describe the fabrication of EZ-SPOTs and showcase how its reusability allows antibiotic susceptibility testing of many isolates using a single device. These results quantitatively match current gold standard assays and the increased throughput provides substantially more information than standard approaches.

Marangoni spreading and contracting three-component droplets on completely wetting surfaces.

SignificanceThe shape and dynamics of small sessile droplets are dictated by capillary forces. For liquid mixtures, evaporation adds spatio-temporal modulation to these forces that can either enhance or inhibit droplet spreading, depending on the direction of the resulting Marangoni flow. This work experimentally and numerically demonstrates the coexistence of two antagonistic Marangoni flows in a ternary mixture. Played against each other, they can choreograph a boomerang-like wetting motion: Droplets initially rapidly spread, then contract into a compact cap shape. While such a behavior has been impossible in wetting scenarios of simple liquids, it enables spread-retract-remove surface processing with the addition of a single small liquid volume, demonstrated here in a surface-cleaning experiment.

Quantifying rapid bacterial evolution and transmission within the mouse intestine.

Due to limitations on high-resolution strain tracking, selection dynamics during gut microbiota colonization and transmission between hosts remain mostly mysterious. Here, we introduced hundreds of barcoded Escherichia coli strains into germ-free mice and quantified strain-level dynamics and metagenomic changes. Mutations in genes involved in motility and metabolite utilization are reproducibly selected within days. Even with rapid selection, coprophagy enforced similar barcode distributions across co-housed mice. Whole-genome sequencing of hundreds of isolates revealed linked alleles that demonstrate between-host transmission. A population-genetics model predicts substantial fitness advantages for certain mutants and that migration accounted for ∼10% of the resident microbiota each day. Treatment with ciprofloxacin suggests interplay between selection and transmission. While initial colonization was mostly uniform, in two mice a bottleneck reduced diversity and selected for ciprofloxacin resistance in the absence of drug. These findings highlight the interplay between environmental transmission and rapid, deterministic selection during evolution of the intestinal microbiota.

Thermal Marangoni Flow Impacts the Shape of Single Component Volatile Droplets on Thin, Completely Wetting Substrates.

Despite surface energies dictating complete wetting, it has been classically observed that volatile alkanes do not spread completely on glass substrates, and faster evaporation rates lead to higher contact angles. Here we investigate how substrate thickness influences this behavior. For sufficiently thin substrates, we find alkanes evaporate slower and display higher apparent contact angles, at odds with the typical explanations involving just evaporation, capillarity, and viscous dissipation. We derive the droplet temperature distribution and use it as part of a criteria to show that thermal Marangoni contraction plays a significant role in establishing droplet shape on thin substrates.

Neutral and selective dynamics in a synthetic microbial community.

Ecologists debate the relative importance of selective vs. neutral processes in understanding biodiversity. This debate is especially pertinent to microbial communities, which play crucial roles in areas such as health, disease, industry, and the environment. Here, we created a synthetic microbial community using heritable genetic barcodes and tracked community composition over repeated rounds of subculture with immigration. Consistent with theory, we find a transition exists between neutral and selective regimes, and the crossover point depends on the fraction of immigrants and the magnitude of fitness differences. Neutral models predict an increase in diversity with increased carrying capacity, while our selective model predicts a decrease in diversity. The community here lost diversity with an increase in carrying capacity, highlighting that using the correct model is essential for predicting community response to change. Together, these results emphasize the importance of including selection to obtain realistic models of even simple systems.

Two-component marangoni-contracted droplets: friction and shape.

When a mixture of propylene glycol and water is deposited on a clean glass slide, it forms a droplet of a given apparent contact angle rather than spreading as one would expect on such a high-energy surface. The droplet is stabilized by a Marangoni flow due to the non-uniformity of the components' concentrations between the border and the apex of the droplet, itself a result of evaporation. These self-contracting droplets have unusual properties such as absence of pinning and the ability to move under an external humidity gradient. The droplets' apparent contact angles are a function of their concentration and the external humidity. Here we study the motion of such droplets sliding down slopes and compare the results to normal non-volatile droplets. We precisely control the external humidity and explore the influence of the volume, viscosity, surface tension, and contact angle. We find that the droplets suffer a negligible pinning force so that for small velocities the capillary number (Ca) is directly proportional to the Bond number (Bo): Ca = Bo sin α with α the angle of the slope. Lastly we study the successive shapes the droplets take when sliding at larger and larger velocities.

Device and programming abstractions for spatiotemporal control of active micro-particle swarms.

We present a hardware setup and a set of executable commands for spatiotemporal programming and interactive control of a swarm of self-propelled microscopic agents inside a microfluidic chip. In particular, local and global spatiotemporal light stimuli are used to direct the motion of ensembles of Euglena gracilis, a unicellular phototactic organism. We develop three levels of programming abstractions (stimulus space, swarm space, and system space) to create a scripting language for directing swarms. We then implement a multi-level proof-of-concept biotic game using these commands to demonstrate their utility. These device and programming concepts will enhance our capabilities for manipulating natural and synthetic swarms, with future applications for on-chip processing, diagnostics, education, and research on collective behaviors.

Correction: LudusScope: Accessible Interactive Smartphone Microscopy for Life-Science Education.

[This corrects the article DOI: 10.1371/journal.pone.0162602.].

LudusScope: Accessible Interactive Smartphone Microscopy for Life-Science Education.

For centuries, observational microscopy has greatly facilitated biology education, but we still cannot easily and playfully interact with the microscopic world we see. We therefore developed the LudusScope, an accessible, interactive do-it-yourself smartphone microscopy platform that promotes exploratory stimulation and observation of microscopic organisms, in a design that combines the educational modalities of build, play, and inquire. The LudusScope's touchscreen and joystick allow the selection and stimulation of phototactic microorganisms such as Euglena gracilis with light. Organismal behavior is tracked and displayed in real time, enabling open and structured game play as well as scientific inquiry via quantitative experimentation. Furthermore, we used the Scratch programming language to incorporate biophysical modeling. This platform is designed as an accessible, low-cost educational kit for easy construction and expansion. User testing with both teachers and students demonstrates the educational potential of the LudusScope, and we anticipate additional synergy with the maker movement. Transforming observational microscopy into an interactive experience will make microbiology more tangible to society, and effectively support the interdisciplinary learning required by the Next Generation Science Standards.

A biotic game design project for integrated life science and engineering education.

Engaging, hands-on design experiences are key for formal and informal Science, Technology, Engineering, and Mathematics (STEM) education. Robotic and video game design challenges have been particularly effective in stimulating student interest, but equivalent experiences for the life sciences are not as developed. Here we present the concept of a "biotic game design project" to motivate student learning at the interface of life sciences and device engineering (as part of a cornerstone bioengineering devices course). We provide all course material and also present efforts in adapting the project's complexity to serve other time frames, age groups, learning focuses, and budgets. Students self-reported that they found the biotic game project fun and motivating, resulting in increased effort. Hence this type of design project could generate excitement and educational impact similar to robotics and video games.

Rapid identification of ESKAPE bacterial strains using an autonomous microfluidic device.

This article describes Bacteria ID Chips ('BacChips'): an inexpensive, portable, and autonomous microfluidic platform for identifying pathogenic strains of bacteria. BacChips consist of a set of microchambers and channels molded in the elastomeric polymer, poly(dimethylsiloxane) (PDMS). Each microchamber is preloaded with mono-, di-, or trisaccharides and dried. Pressing the layer of PDMS into contact with a glass coverslip forms the device; the footprint of the device in this article is ∼6 cm(2). After assembly, BacChips are degased under large negative pressure and are stored in vacuum-sealed plastic bags. To use the device, the bag is opened, a sample containing bacteria is introduced at the inlet of the device, and the degased PDMS draws the sample into the central channel and chambers. After the liquid at the inlet is consumed, air is drawn into the BacChip via the inlet and provides a physical barrier that separates the liquid samples in adjacent microchambers. A pH indicator is admixed with the samples prior to their loading, enabling the metabolism of the dissolved saccharides in the microchambers to be visualized. Importantly, BacChips operate without external equipment or instruments. By visually detecting the growth of bacteria using ambient light after ∼4 h, we demonstrate that BacChips with ten microchambers containing different saccharides can reproducibly detect the ESKAPE panel of pathogens, including strains of: Enterococcus faecalis, Enteroccocus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter aerogenes, and Enterobacter cloacae. This article describes a BacChip for point-of-care detection of ESKAPE pathogens and a starting point for designing multiplexed assays that identify bacterial strains from clinical samples and simultaneously determine their susceptibility to antibiotics.

A self-loading microfluidic device for determining the minimum inhibitory concentration of antibiotics.

This article describes a portable microfluidic technology for determining the minimum inhibitory concentration (MIC) of antibiotics against bacteria. The microfluidic platform consists of a set of chambers molded in poly(dimethylsiloxane) (PDMS) that are preloaded with antibiotic, dried, and reversibly sealed to a second layer of PDMS containing channels that connect the chambers. The assembled device is degassed via vacuum prior to its use, and the absorption of gas by PDMS provides the mechanism for actuating and metering the flow of fluid in the microfluidic channels and chambers. During the operation of the device, degas driven flow introduces a suspension of bacterial cells, dissolves the antibiotic, and isolates cells in individual chambers without cross contamination. The growth of bacteria in the chambers in the presence of a pH indicator produces a colorimetric change that can be detected visually using ambient light. Using this device we measured the MIC of vancomycin, tetracycline, and kanamycin against Enterococcus faecalis 1131, Proteus mirabilis HI4320, Klebsiella pneumoniae, and Escherichia coli MG1655 and report values that are comparable to standard liquid broth dilution measurements. The device provides a simple method for MIC determination of individual antibiotics against human pathogens that will have applications for clinical and point-of-care medicine. Importantly, this device is designed around simplicity: it requires a single pipetting step to introduce the sample, no additional components or external equipment for its operation, and provides a straightforward visual measurement of cell growth. As the device introduces a novel approach for filling and isolating dead-end microfluidic chambers that does not require valves and actuators, this technology should find applications in other portable assays and devices.