Automated high resolution optical mapping using arrayed, fluid-fixed DNA molecules

Diagnostic and Prognostic/Therapeutic Significance of Comprehensive Analysis of Bone and Soft Tissue Tumors Using Optical Genome Mapping and Next-Generation Sequencing

Detecting somatic structural variants (SVs), copy number variants (CNVs), and mutations in bone and soft tissue tumors is essential for accurately diagnosing, treating, and prognosticating outcomes. Optical genome mapping (OGM) holds promise to yield useful data on SVs and CNVs but requires fresh or snap-frozen tissues. This study aimed to evaluate the clinical utility of data from OGM compared with current standard-of-care cytogenetic testing. We evaluated 60 consecutive specimens from bone and soft tissue tumors using OGM and karyotyping, fluorescence in situ hybridization, gene fusion assays, and deep next-generation sequencing. OGM accurately identified diagnostic SVs/CNVs previously detected by karyotyping and fluorescence in situ hybridization (specificity = 100%). OGM identified diagnostic and pathogenic SVs/CNVs (∼23% of cases) undetected by karyotyping (cryptic/submicroscopic). OGM allowed the detection and further characterization of complex structural rearrangements including chromoanagenesis (27% of cases) and complex 3- to 6-way translocations (15% of cases). In addition to identifying 321 SVs and CNVs among cases with chromoanagenesis events, OGM identified approximately 9 SVs and 12 CNVs per sample. A combination of OGM and deep next-generation sequencing data identified diagnostic, disease-associated, and pathogenic SVs, CNVs, and mutations in ∼98% of the cases. Our cohort contained the most extensive collection of bone and soft tissue tumors profiled by OGM. OGM had excellent concordance with standard-of-care cytogenetic testing, detecting and assigning high-resolution genome-wide genomic abnormalities with higher sensitivity than routine testing. This is the first and largest study to provide insights into the clinical utility of combined OGM and deep sequencing for the pathologic diagnosis and potential prognostication of bone and soft tissue tumors in routine clinical practice.

'Gel-Stacks' gently confine or reversibly immobilize arrays of single DNA molecules for manipulation and study

Large DNA molecules (>20 kb) are difficult analytes prone to breakage during serial manipulations and cannot be 'rescued' as full-length amplicons. Accordingly, to present, modify and analyze arrays of large, single DNA molecules, we created an easily realizable approach offering gentle confinement conditions or immobilization via spermidine condensation for controlled delivery of reagents that support live imaging by epifluorescence microscopy termed 'Gel-Stacks.' Molecules are locally confined between two hydrogel surfaces without covalent tethering to support time-lapse imaging and multistep workflows that accommodate large DNA molecules. With a thin polyacrylamide gel layer covalently bound to a glass surface as the base and swappable, reagent-infused, agarose slabs on top, DNA molecules are stably presented for imaging during reagent delivery by passive diffusion.

Identification of errors in draft genome assemblies at single-nucleotide resolution for quality assessment and improvement

Assembly of a high-quality genome is important for downstream comparative and functional genomic studies. However, most tools for genome assembly assessment only give qualitative reports, which do not pinpoint assembly errors at specific regions. Here, we develop a new reference-free tool, Clipping information for Revealing Assembly Quality (CRAQ), which maps raw reads back to assembled sequences to identify regional and structural assembly errors based on effective clipped alignment information. Error counts are transformed into corresponding assembly evaluation indexes to reflect the assembly quality at single-nucleotide resolution. Notably, CRAQ distinguishes assembly errors from heterozygous sites or structural differences between haplotypes. This tool can clearly indicate low-quality regions and potential structural error breakpoints; thus, it can identify misjoined regions that should be split for further scaffold building and improvement of the assembly. We have benchmarked CRAQ on multiple genomes assembled using different strategies, and demonstrated the misjoin correction for improving the constructed pseudomolecules.

Optical Genome Mapping for Oncology Applications

Optical genome mapping (OGM) is a next-generation cytogenomic technology that has the potential to replace standard-of-care technologies used in the genetic workup of various malignancies. The ability to detect various classes of structural variations that include copy number variations, deletions, duplications, balanced and unbalanced events (insertions, inversions, and translocation) and complex genomic rearrangements in a single assay and analysis demonstrates the utility of the technology in tumor research and clinical application. Herein, we provide the methodological details for performing OGM and pre- and post-analytical quality control (QC) checks and describe critical steps that should be performed with caution, probable causes for specific QC failures, and potential method modifications that could be implemented as part of troubleshooting. The protocol description and troubleshooting guide should help new and current users of the technology to improve or troubleshoot the problems (if any) in their workflow. © 2023 Wiley Periodicals LLC. Basic Protocol: Optical genome mapping.

Evaporation-Driven Liquid-Liquid Crystalline Phase Separation in Droplets of Anisotropic Colloids

Drying a colloidal droplet involves complex physics that is often accompanied by evaporation-induced concentration gradients inside of the droplet, offering a platform for fundamental and technological opportunities, including self-assembly, thin film deposition, microfabrication, and DNA stretching. Here, we investigate the drying, liquid crystalline structures, and deposit patterns of colloidal liquid crystalline droplets undergoing liquid-liquid crystalline phase separation (LLCPS) during evaporation. We show that evaporation-induced progressive up-concentration inside the drying droplets makes it possible to cross, at different speeds, various thermodynamic stability states in solutions of amyloid fibril rigid filamentous colloids, thus allowing access to both metastable states, where phase separation occurs via nucleation and growth, as well as to unstable states, where phase separation occurs via the more elusive spinodal decomposition, leading to the formation of liquid crystalline microdroplets (or tactoids) of different shapes. We present the tactoids "phase diagram" as a function of the position within the droplet and elucidate their hydrodynamics. Furthermore, we demonstrate that the presence of the amyloid fibrils not only does not enhance the pinning behavior during droplet evaporation but also slightly suppresses it, thus minimizing the coffee-ring effect. We observed that microsize domains with cholesteric structure emerge in the drying droplet close to the droplet's initial edge, yet such domains are not connected to form a uniform cholesteric dried film. Finally, we demonstrate that a fully cholesteric dried layer can be generated from the drying droplets by regulating the kinetics of the evaporation process.

Era of gapless plant genomes: innovations in sequencing and mapping technologies revolutionize genomics and breeding

Whole-genome sequencing and assembly have revolutionized plant genetics and molecular biology over the last two decades. However, significant shortcomings in first- and second-generation technology resulted in imperfect reference genomes: numerous and large gaps of low quality or undeterminable sequence in areas of highly repetitive DNA along with limited chromosomal phasing restricted the ability of researchers to characterize regulatory noncoding elements and genic regions that underwent recent duplication events. Recently, advances in long-read sequencing have resulted in the first gapless, telomere-to-telomere (T2T) assemblies of plant genomes. This leap forward has the potential to increase the speed and confidence of genomics and molecular experimentation while reducing costs for the research community.

Semicrystalline Polymer Micro/Nanostructures Formed by Droplet Evaporation of Aqueous Poly(ethylene oxide) Solutions: Effect of Solution Concentration

Deposits formed after evaporation of sessile droplets, containing aqueous solutions of poly(ethylene oxide), on hydrophilic glass substrates were studied experimentally and mathematically as a function of the initial solution concentration. The macrostructure and micro/nanostructures of deposits were studied using stereo microscopy and atomic force microscopy. A model, based on thin-film lubrication theory, was developed to evaluate the deposit macrostructure by estimating the droplet final height. Moreover, the model was extended to evaluate the micro/nanostructure of deposits by estimating the rate of supersaturation development in connection with the driving force of crystallization. Previous studies had only described the macrostructure of poly(ethylene oxide) deposits formed after droplet evaporation, whereas the focus of our study was the deposit micro/nanostructures. Our atomic force microscopy study showed that regions close to the deposit periphery were composed of predominantly semicrystalline micro/nanostructures in the form of out-of-plane lamellae, which require a high driving force of crystallization. However, deposit central areas presented semicrystalline micro/nanostructures in the form of in-plane terraces and spirals, which require a lower driving force of crystallization. Increasing the initial concentration of solutions led to an increase in the lengths and thicknesses of the out-of-plane lamellae at the deposits' periphery and enhanced the tendency to form spirals in the central areas. Our numerical study suggested that the rate of supersaturation development and thus the driving force of crystallization increased from the center toward the periphery of droplets, and the supersaturation rate was lower for solutions with higher initial concentrations at each radius. Therefore, periphery areas of droplets with lower initial concentrations were suitable for the formation of micro/nanostructures which require higher driving forces, whereas central areas of droplets with higher initial concentration were desirable for the formation of micro/nanostructures which require lower driving forces. These numerical results were in good qualitative agreement with the experimental findings.

Investigation of Water Evaporation Process at Air/Water Interface using Hofmeister Ions

Evaporation is an interfacial phenomenon in which a water molecule breaks the intermolecular hydrogen (H-) bonds and enters the vapor phase. However, a detailed demonstration of the role of interfacial water structure in the evaporation process is still lacking. Here, we purposefully perturb the H-bonding environment at the air/water interface by introducing kosmotropic (HPO₄^-2, SO₄^-2, and CO₃^-2) and chaotropic ions (NO₃^- and I^-) to determine their influence on the evaporation process. Using time-resolved interferometry on aqueous salt droplets, we found that kosmotropes reduce evaporation, whereas chaotropes accelerate the evaporation process, following the Hofmeister series: HPO₄^-2 < SO₄^-2 < CO₃^-2 < Cl^- < NO₃^- < I^-. To extract deeper molecular-level insights into the observed Hofmeister trend in the evaporation rates, we investigated the air/water interface in the presence of ions using surface-specific sum frequency generation (SFG) vibrational spectroscopy. The SFG vibrational spectra reveal the significant impact of ions on the strength of the H-bonding environment and the orientation of free OH oscillators from ∼36.2 to 48.4° at the air/water interface, where both the effects follow the Hofmeister series. It is established that the slow evaporating water molecules experience a strong H-bonding environment with free OH oscillators tilted away from the surface normal in the presence of kosmotropes. In contrast, the fast evaporating water molecules experience a weak H-bonding environment with free OH oscillators tilted toward the surface normal in the presence of chaotropes at the air/water interface. Our experimental outcomes showcase the complex bonding environment of interfacial water molecules and their decisive role in the evaporation process.

ToxR is a c-di-GMP binding protein that modulates surface-associated behaviour in Pseudomonas aeruginosa

Pseudomonas aeruginosa uses multiple protein regulators that work in tandem to control the production of a wide range of virulence factors and facilitate rapid adaptation to diverse environmental conditions. In this opportunistic pathogen, ToxR was known to positively regulate the production of the major virulence factor exotoxin A and now, through analysis of genetic changes between two sublines of P. aeruginosa PAO1 and functional complementation of swarming, we have identified a previously unknown role of ToxR in surface-associated motility in P. aeruginosa. Further analysis revealed that ToxR had an impact on swarming motility by regulating the Rhl quorum sensing system and subsequent production of rhamnolipid surfactants. Additionally, ToxR was found to tightly bind cyclic diguanylate (c-di-GMP) and negatively affect traits controlled by this second messenger including reducing biofilm formation and the expression of Psl and Pel exopolysaccharides, necessary for attachment and sessile communities matrix scaffolding, in P. aeruginosa. Moreover, a link between the post-transcriptional regulator RsmA and toxR expression via the alternative sigma factor PvdS, induced under iron-limiting conditions, is established. This study reveals the importance of ToxR in a sophisticated regulation of free-living and biofilm-associated lifestyles, appropriate for establishing acute or chronic P. aeruginosa infections.

Evaporation of Water Nanodroplets on Heated Surfaces: Does Nano Matter?

While experiments and continuum models have provided a relatively good understanding of the evaporation of macroscopic water droplets, elucidating how sessile nanodroplets evaporate is an open question critical for advancing nanotechnological applications where nanodroplets can play an essential role. Here, using molecular dynamics simulations, we find that evaporating nanodroplets, in contrast to their macroscopic counterparts, are not always in thermal equilibrium with the substrate and that the vapor concentration on the nanodroplet surface does not reach a steady state. As a result, the evaporative behavior of nanodroplets is significantly different. Regardless of hydrophobicity, nanodroplets do not follow conventional evaporation modes but instead exhibit dynamic wetting behavior characterized by huge, non-equilibrium, isovolumetric fluctuations in the contact angle and contact radius. For hydrophilic nanodroplets, the evaporation rate, controlled by the vapor concentration, decays exponentially over time. Hydrophobic nanodroplets follow stretched exponential kinetics arising from the slower thermalization with the substrate. The evaporative half-lifetime of the nanodroplets is directly related to the thermalization time scale and therefore increases monotonically with the hydrophobicity of the substrate. Finally, the evaporative flux profile along the nanodroplet surface is highly nonuniform but does not diverge at the contact line as the macroscopic continuum models predict.

A Parallelized Nanofluidic Device for High-Throughput Optical DNA Mapping of Bacterial Plasmids

Optical DNA mapping (ODM) has developed into an important technique for DNA analysis, where single DNA molecules are sequence-specifically labeled and stretched, for example, in nanofluidic channels. We have developed an ODM assay to analyze bacterial plasmids-circular extrachromosomal DNA that often carry genes that make bacteria resistant to antibiotics. As for most techniques, the next important step is to increase throughput and automation. In this work, we designed and fabricated a nanofluidic device that, together with a simple automation routine, allows parallel analysis of up to 10 samples at the same time. Using plasmids encoding extended-spectrum beta-lactamases (ESBL), isolated from Escherichiacoli and Klebsiellapneumoniae, we demonstrate the multiplexing capabilities of the device when it comes to both many samples in parallel and different resistance genes. As a final example, we combined the device with a novel protocol for rapid cultivation and extraction of plasmids from fecal samples collected from patients. This combined protocol will make it possible to analyze many patient samples in one device already on the day the sample is collected, which is an important step forward for the ODM analysis of plasmids in clinical diagnostics.

Gas-Phase Temperature Mapping of Evaporating Microdroplets

Evaporation is a ubiquitous and complex phenomenon of importance to many natural and industrial systems. Evaporation occurs when molecules near the free interface overcome intermolecular attractions with the bulk liquid. As molecules escape the liquid phase, heat is removed, causing evaporative cooling. The influence of evaporative cooling on inducing a temperature difference with the surrounding atmosphere as well as within the liquid is poorly understood. Here, we develop a technique to overcome past difficulties encountered during the study of heterogeneous droplet evaporation by coupling a piezo-driven droplet generation mechanism to a controlled micro-thermocouple to probe microdroplet evaporation. The technique allowed us to probe the gas-phase temperature distribution using a micro-thermocouple (50 μm) in the vicinity of the liquid-vapor interface with high spatial (±10 μm) and temporal (±100 ms) resolution. We experimentally map the temperature gradient formed surrounding sessile water droplets having varying curvature dictated by the apparent advancing contact angle (100° ≲ θ ≲ 165°). The experiments were carried out at temperatures below and above ambient for a range of fixed droplet radii (130 μm ≲ R ≲ 330 μm). Our results provide a primary validation of the centuries-old theoretical framework underpinning heterogeneous droplet evaporation mediated by the working fluid, substrate, and gas thermophysical properties, droplet apparent contact angle, and droplet size. We show that microscale droplets residing on low-thermal-conductivity substrates such as glass absorb up to 8× more heat from the surrounding gas compared to droplets residing on high-thermal-conductivity substrates such as copper. Our work not only develops an experimental understanding of the heat transfer mechanisms governing droplet evaporation but also presents a powerful platform for the study and characterization of liquid-vapor transport at curved interfaces wetting and nonwetting advanced functional surfaces.

Customized optical mapping by CRISPR-Cas9 mediated DNA labeling with multiple sgRNAs

Whole-genome mapping technologies have been developed as a complementary tool to provide scaffolds for genome assembly and structural variation analysis (1,2). We recently introduced a novel DNA labeling strategy based on a CRISPR-Cas9 genome editing system, which can target any 20bp sequences. The labeling strategy is specifically useful in targeting repetitive sequences, and sequences not accessible to other labeling methods. In this report, we present customized mapping strategies that extend the applications of CRISPR-Cas9 DNA labeling. We first design a CRISPR-Cas9 labeling strategy to interrogate and differentiate the single allele differences in NGG protospacer adjacent motifs (PAM sequence). Combined with sequence motif labeling, we can pinpoint the single-base differences in highly conserved sequences. In the second strategy, we design mapping patterns across a genome by selecting sets of specific single-guide RNAs (sgRNAs) for labeling multiple loci of a genomic region or a whole genome. By developing and optimizing a single tube synthesis of multiple sgRNAs, we demonstrate the utility of CRISPR-Cas9 mapping with 162 sgRNAs targeting the 2Mb Haemophilus influenzae chromosome. These CRISPR-Cas9 mapping approaches could be particularly useful for applications in defining long-distance haplotypes and pinpointing the breakpoints in large structural variants in complex genomes and microbial mixtures.

Toward Controlling Evaporative Deposition: Effects of Substrate, Solvent, and Solute

Understanding evaporative deposition from a colloidal suspension and on-demand control over it are important due to its industrial and biomedical applications. In particular, it is known that interactions among substrate, solute, and solvent have important consequences on evaporative depositions; however, how these are affecting the deposition patterns and at which conditions these interactions are prominent need detailed investigations. Here we report that the total time of deposition (t_d) and the geometric shape of the droplet (L_c = initial footprint diameter/height) have a significant role in determining the evaporative deposition patterns. We have identified four zones based on t_d and L_c, and found that with longer deposition time (high t_d) and larger available space for particle motion within a liquid droplet (high L_c), deposition patterns were governed by the interactions among the substrate, solute, and solvent. We also experimentally demonstrated that the pinned contact line is indispensable for the "coffee ring" effect by comparing the deposition on surfaces with and without hysteresis. The effect of the Marangoni flow is also discussed, and it is shown that by controlling Marangoni flow, one can manipulate the droplet deposition from uniform disk-like to coffee ring with a central deposition.

Evaporation of squeezed water droplets between two parallel hydrophobic/superhydrophobic surfaces

HYPOTHESIS

A liquid droplet is apt to be deformed within a compact space in various applications. The morphological change of a droplet and vapor accumulation in the confined space between two parallel surfaces with different gaps and surface wettability are expected to significantly affect the evaporation dynamics of the squeezed droplet therein.

EXPERIMENTS

Here the evaporation dynamics of a squeezed droplet between two parallel hydrophobic/superhydrophobic surfaces are experimentally explored. By reducing the surface gap from 1000 μm to 400 μm, the evolution of contact angle, contact radius and volume of the evaporating droplet are measured. A diffusion-driven model based on a two-parameter ellipsoidal segment geometry is developed to predict the morphology and volume evolution of a squeezed droplet during evaporation.

FINDINGS

Evaporation dynamics of a squeezed water droplet via the constant contact radius (CCR) mode, the constant contact angle (CCA) mode, or the mixed mode are experimentally observed. Confirmed by our ellipsoidal segment model, the evaporation of the squeezed droplet is significantly depressed with the decreasing surface gap, which is primarily attributed to vapor enrichment in a more confined geometry. A linear scaling law between droplet volume and evaporation time is unveiled, which is verified by a simplified cylindrical model.

Pinning-depinning of the contact line during drop evaporation on textured surfaces: A lattice Boltzmann study

The evaporation of the liquid droplet on a structured surface is numerically investigated using the lattice Boltzmann method. Simulations are carried out for different contact angles and pillar widths. From the simulation for the Cassie state, it is found that the evaporation starts in a pinned contact line mode. Then, when the droplet reaches the receding state, the contact line jumps to the neighboring pillar. Also, the depinning force decreases with increasing the contact angle or the pillar width. In the Wenzel state, the droplet contact line remains on the initial pillar for all of its lifetime.

Competitive Electrohydrodynamic and Electrosolutal Advection Arrests Evaporation Kinetics of Droplets

This article reports the hitherto unreported phenomenon of arrested evaporation dynamics in pendant droplets because of electric field stimulus. The evaporation kinetics of pendant droplets of electrically conducting saline solutions in the presence of a transverse, alternating electric field is investigated experimentally. While the increase of field strength reduces the evaporation rate, increment in field frequency has the opposite effect. The same has been explained on the solvation kinetics of ions in polar water. Theoretical analysis reveals that change in surface tension and the diffusion-driven evaporation model cannot predict the decelerated evaporation. With the aid of particle image velocimetry, suppression of internal circulation velocity within the droplet is observed under electric field stimulus, which directly affects the evaporation rate. A mathematical scaling model is proposed to quantify the effects of electrohydrodynamic circulation and electrothermal and electrosolutal advection on the evaporation kinetics. The analysis encompasses major governing parameters, namely, the thermal and solutal Marangoni numbers, the electrohydrodynamic number, the electro-Prandtl and electro-Schmidt numbers, and their respective contributions. It has been shown that the electrothermal Marangoni effect is suppressed by the electric field, leading to deteriorated evaporation rates. Additionally, the electrosolutal Marangoni effect further suppresses the internal advection, further reducing the evaporation rate by a larger proportion. Stability analysis reveals that the electric body force retards the stable internal advection. The stability mapping also illustrates that if the field strength is high enough for the electrosolutal advection to overshadow the solutal Marangoni effect completely, it can lead to improvement in evaporation rates.

Advances in optical mapping for genomic research

Recent advances in optical mapping have allowed the construction of improved genome assemblies with greater contiguity. Optical mapping also enables genome comparison and identification of large-scale structural variations. Association of these large-scale genomic features with biological functions is an important goal in plant and animal breeding and in medical research. Optical mapping has also been used in microbiology and still plays an important role in strain typing and epidemiological studies. Here, we review the development of optical mapping in recent decades to illustrate its importance in genomic research. We detail its applications and algorithms to show its specific advantages. Finally, we discuss the challenges required to facilitate the optimization of optical mapping and improve its future development and application.

Molecular Dynamics Study of Binary Nanodroplet Evaporation on a Heated Homogeneous Substrate

The evaporation mechanism of miscible binary nanodroplets from heated homogeneous surfaces was studied by molecular dynamics simulations, which has never been studied before. The binary droplets contain a hydrophilic component (type-2 particles) and a hydrophobic component (type-3 particles). It is shown that liquid-liquid interaction strength (ε₂₃) and hydrophilic particle number fraction (φ) have great influence on the surface tension, wetting characteristics, evaporation patterns, evaporation rate, and local mass flux. It is observed that when ε₂₃ ≥ 1, or φ ≈ 0.5, the evaporation mode is the constant-contact-angle mode. Otherwise, it is the mixed mode. We found that the evaporation rate becomes faster when φ and ε₂₃ increase. The droplets become more hydrophilic when φ increases, which promotes heat transfer efficiency between the liquid-solid interface. Besides, a larger ε₂₃ promotes the heat transfer inside the droplet. The mass transfer to the vapor phase occurs preferentially in the vicinity of TPCL (three phase contact line) in the hydrophilic systems (θ < θ_c), where θ_c is the critical contact angle, while in most hydrophobic systems (θ > θ_c), the mass flux close to the TPCL is suppressed. We found that θ_c ∈ (102°-106°), which is different from the theoretical one, θ_c = 90°. The discrepancy is attributed to the existence of the adsorption layer near the TPCL.

Nanopore-Enhanced Drop Evaporation: When Cooler or More Saline Water Droplets Evaporate Faster

The evaporation of water droplets on surfaces is a ubiquitous phenomenon in nature and has critical importance in a broad range of technical applications. Here, we show a substantial enhancement of liquid evaporation rate when droplets are on nanoporous thin film surfaces. We also reveal how this nanopore-enhanced evaporation leads to counterintuitive phenomena: cooler or more saline water droplets evaporate faster. We find indeed that, contrary to typical evaporation behavior of sessile droplets on nonporous surfaces, the droplets placed on nanoporous thin films evaporate more rapidly when salt concentration increases or when the temperature decreases. This peculiar droplet evaporation behavior is related to the key role of the steady wetted annulus that is self-generated into the nanopore network in the drop periphery, which leads to an effectively enhanced evaporation area that controls the overall evaporation process. Our results provide the prospect of conceiving fresh scenarios in the evaporation of drops on surfaces in both relevant applications and fundamental insights.

Toward a Common Coordinate Framework for the Human Body

Understanding the genetic and molecular drivers of phenotypic heterogeneity across individuals is central to biology. As new technologies enable fine-grained and spatially resolved molecular profiling, we need new computational approaches to integrate data from the same organ across different individuals into a consistent reference and to construct maps of molecular and cellular organization at histological and anatomical scales. Here, we review previous efforts and discuss challenges involved in establishing such a common coordinate framework, the underlying map of tissues and organs. We focus on strategies to handle anatomical variation across individuals and highlight the need for new technologies and analytical methods spanning multiple hierarchical scales of spatial resolution.

In Situ Sensing of Reactive Oxygen Species on Dye-Stained Single DNA Molecules under Illumination

Reactive oxygen species (ROS) are a necessary evil in many biological systems and have been measured with fluorescent probes at the ensemble levels both in vitro and in vivo. Measuring ROS generated from a single molecule is important for mechanistic studies, yet measuring ROS near a dye-labeled single-molecule under illumination has been challenging. Here, we use CellROX, a group of ROS probes, to sense ROS near dye-stained DNA that has been flow-stretched and immobilized on a surface. ROS is responsible for the photodamage of DNA molecules under this circumstance. In this report, we confirmed the ROS sensing reaction in bulk solutions and optimized the conditions for single-molecule experiments including the selection of substrates, dye concentrations, probes in the CellROX series, excitation lasers, and emission filter-sets. We observed a correlation between ROS and the dye-labeled DNA and localized the ROS-activated CellROX probe molecules at both the ensemble level and the single-molecule level.

Arthropod Genome Sequencing and Assembly Strategies

As in any endeavor, the strategy applied to a genome project can mean the difference between success and failure. This is especially important when limited funding often means only a single approach may be tried at a given time. Although the advance of all areas of genomics and transcriptomics in recent years has led to an embarrassment of riches, methods in the field have not quite reached the turn-key production status for all species, despite being closer than ever. Here I contrast and compare the technical approaches to genome projects in the hope of enabling strategy choices with higher probabilities of success. Finally, I review the new technologies that are not yet widely distributed which are revolutionizing the future of genomics.

Morphology Transformation of Supramolecular Structures in Aqueous Mixtures of Two Oppositely Charged Amphiphiles

The co-assembly of oppositely charged amphiphiles provides a fascinating approach for forming complex supramolecular structures, which are interesting from both fundamental and technological viewpoints. Here, we report a stepwise morphology transformation of co-assembled supramolecular structures in the aqueous mixture of lithocholic acid (LCA) and cetyltrimethylammonium bromide (CTAB) at mixed molar ratios of 1:1 and 2:1. The co-assembly of LCA and CTAB initially forms multilamellar vesicles followed by the spontaneous growth of membrane tubes from the vesicles. The vesicle-to-tube transition is accompanied by a fluidic-to-crystalline phase transition. After being aged, the membrane tubes twist into left-handed helices, which then intertwine into left-handed double helices and multihelix bundles. The single handedness of these supramolecular structures is a reflection of the amplification of the chirality of LCA. An understanding of the co-assembly mechanism and pathway is a key step toward producing supramolecular structures with distinguished morphologies.

Dynamical Clustering and Band Formation of Particles in a Marangoni Vortexing Droplet

Drying a droplet containing microparticles results in the deposition of particles in various patterns, including the so-called "coffee-ring" pattern. The particle deposition is dependent on the internal flow dynamics, such as the capillary flow and Marangoni vortex (MV), of the droplet. Particle migration and self-assembly on a substrate are interesting phenomena that have critical implications in many applications such as inkjet printing, coating, and many other droplet-based industrial processes. In this work, we observed the formation of bands of particles in a rotating MV during the evaporation of a water droplet containing particles. We investigated the mechanism underlying the formation of banded MV caused by capillary meniscus forces between two particles near the air-liquid interface. In particular, we show that the banded MV can be manipulated by tuning the surfactant concentration and particle concentration. Our findings would provide a new direction in understanding the particle deposition pattern of a colloidal droplet.

Interplay of electro-thermo-solutal advection and internal electrohydrodynamics governed enhanced evaporation of droplets

The article experimentally examines and theoretically establishes the influence of electric field on the evaporation kinetics of pendant droplets. It is observed that the evaporation of saline-pendant droplets can be augmented by the application of an external alternating electric field. The evaporation behaviour is modulated by an increase in the field strength and frequency. The classical diffusion driven evaporation model is found insufficient in predicting the improved evaporation rates. The change in surface tension due to field constraint is also unable to explain the observed physics. Consequently, the internal hydrodynamics of the droplet is investigated through particle image velocimetry. The electric field is found to induce enhanced internal advection, which improves the evaporation rates. A scaled analytical model is proposed to quantify the role of internal electrohydrodynamics, electro-thermal and electro-solutal effects. Stability maps reveal that the advection is caused nearly equally by the electro-solutal and electro-thermal effects within the droplet. The model is able to illustrate the influence played by the governing thermal and solutal Marangoni number, the electro-Prandtl and electro-Schmidt number, and the associated electrohydrodynamic number. The magnitude of the internal circulation can be predicted by the proposed model, which validates the proposed mechanism.

Pinning-Depinning Mechanism of the Contact Line during Evaporation of Nanodroplets on Heated Heterogeneous Surfaces: A Molecular Dynamics Simulation

Droplet evaporation on heterogeneous or patterned surfaces has numerous potential applications, for example, inkjet printing. The effect of surface heterogeneities on the evaporation of a nanometer-sized cylindrical droplet on a solid surface is studied using molecular dynamics simulations of Lennard-Jones particles. Different heterogeneities of the surface were achieved through alternating stripes of equal width but two chemical types, which lead to different contact angles. The evaporation induced by the heated substrate instead of the isothermal evaporation is investigated. It is found that the whole evaporation process is generally dominated by the nonuniform evaporation effect. However, at the initial moment, the volume expansion and local evaporation effects play important roles. From the nanoscale point of view, the slow movement of the contact line during the pinning process is observed, which is different from the macroscopic stationary pinning. Particularly, we found that the speed of the contact line may be not only affected by the intrinsic energy barrier between the two adjacent stripes ( ũ) but also relevant to the evaporation rate. Generally speaking, the larger the intrinsic energy barrier, the slower the movement of the contact line. At the specified temperature, when ũ is less than a critical energy barrier ( ũ*), the speed of the contact line would increase with the evaporate rate. When ũ > ũ*, the speed of the contact line is determined only by ũ and no longer affected by the evaporation rate at different stages (the first stick and the second stick).

Experimental and Theoretical Investigation of Droplet Evaporation on Heated Hydrophilic and Hydrophobic Surfaces

The evaporation characteristics of sessile droplets on heated hydrophobic and hydrophilic surfaces are investigated. Results are reported for the evaporation of water droplet volumes covering a range of shapes dominated by surface tension or gravity and over a range of temperatures between 40 and 60 °C. The weight evolution and total time of evaporation is measured using a novel self-contained heating stage on a high resolution analytical balance, which has advantages over visualization measurement techniques as it allows free choice of the initial droplet size and surface and the ability to record the droplet evaporation right through to the final stages of droplet life. Evaporation is modeled through a combination of a constant contact area and a constant contact angle model with the switch from the former to the latter occurring when the contact angle falls below its predetermined receding value. Theoretical results compare well with the experimental results for the hydrophobic substrate. However, a significant deviation is observed for the hydrophilic substrate due to the combined effects of the droplet surface cooling due to evaporation and buoyancy effects that are not included in the model. The proposed method of using the stick-slip model offers a convenient means of modeling droplet evaporation by mimicking the drying modes based on initial measurements of the static and receding contact angles.

Overview of Next-Generation Sequencing Technologies

High throughput DNA sequencing methodology (next generation sequencing; NGS) has rapidly evolved over the past 15 years and new methods are continually being commercialized. As the technology develops, so do increases in the number of corresponding applications for basic and applied science. The purpose of this review is to provide a compendium of NGS methodologies and associated applications. Each brief discussion is followed by web links to the manufacturer and/or web-based visualizations. Keyword searches, such as with Google, may also provide helpful internet links and information. © 2018 by John Wiley & Sons, Inc.

Gravitational Effect in Evaporating Binary Microdroplets

The flow in an evaporating glycerol-water binary submillimeter droplet with a Bond number Bo≪1 is studied both experimentally and numerically. First, we measure the flow fields near the substrate by microparticle image velocimetry for both sessile and pendant droplets during the evaporation process, which surprisingly show opposite radial flow directions-inward and outward, respectively. This observation clearly reveals that in spite of the small droplet size, gravitational effects play a crucial role in controlling the flow fields in the evaporating droplets. We theoretically analyze that this gravity-driven effect is triggered by the lower volatility of glycerol which leads to a preferential evaporation of water then the local concentration difference of the two components leads to a density gradient that drives the convective flow. We show that the Archimedes number Ar is the nondimensional control parameter for the occurrence of the gravitational effects. We confirm our hypothesis by experimentally comparing two evaporating microdroplet systems, namely, a glycerol-water droplet and a 1,2-propanediol-water droplet. We obtain different Ar, larger or smaller than a unit by varying a series of droplet heights, which corresponds to cases with or without gravitational effects, respectively. Finally, we simulate the process numerically, finding good agreement with the experimental results and again confirming our interpretation.

Evaporation of Water on Suspended Graphene: Suppressing the Effect of Physically Heterogeneous Surfaces

Evaporation of water nanodroplets on a hydrophilically adjusted graphene sheet was studied based on a molecular dynamics approach. Suspended graphene was used as a physically heterogeneous surface, and fixed graphene was considered as an ideally flat surface. State of the triple-phase contact line (TPCL) and shape evolution were addressed at four different temperatures on both substrates. Additionally, contact angle (CA) was studied during 3 and 22.5 ns simulations in both closed and opened conditions. The observed constant contact angle regime was predictable for the fixed graphene. However, it was not expected for the suspended system and was attributed to the oscillations of the substrate atoms. The size of the nanodroplet also affects the constant-contact-angle mode in both systems, when the number of water molecules decreases to less than 500. The oscillations created a surface on which physical heterogeneities were varying through time. Examination of the evaporation and condensation processes revealed higher rates for the fixed systems. Local mass fluxes were calculated to reveal the contribution of TPCL and meridian surface (MS) of the nanodroplet to evaporation and condensation. The obtained results indicate similar values for the mass flux ratio at the TPCL, which remains twice as large as the MS for both suspended and fixed graphene. The results confirm the assumption that a surface with varying heterogeneities can overwhelm the droplet and act as an ideally flat surface.

Morphology modulation in evaporative drying mediated crystallization of sodium chloride solution droplet with surfactant

We report the evaporative drying of an aqueous droplet containing a dilute solution of sodium chloride (NaCl) on a hydrophobic substrate made of cross-linked poly-dimethyl siloxane (PDMS). The salt concentration Cn was varied between 0.08 molar (M) and 2.0 M. The contact line of the evaporating droplets shows significant initial retraction for all Cn, before they get pinned. While the final morphology comprises a few small NaCl crystals deposited around the pinned contact line, in droplets with a low Cn (<0.5 M), it transforms to a single large salt crystal when Cn > 0.7 M with no peripheral deposition. We further show that the deposition morphology drastically changes when an anionic surfactant, sodium dodecyl sulfate (SDS), is added into the salt-solutions. Even in the surfactant-laden droplets, the final deposition morphology changes significantly as a function of Cn. It transforms from a thick SDS ring surrounding a fractal-like deposit of NaCl crystallites at lower Cn to a peripheral deposit of NaCl crystals at higher Cn due to competition between micelle formation and crystallization. However, the crystallographic orientation of the deposited NaCl crystals remains unaltered irrespective of the presence of surfactant.

Magnetohydrodynamics- and magnetosolutal-transport-mediated evaporation dynamics in paramagnetic pendant droplets under field stimulus

Evaporation kinetics of pendant droplets is an area of immense importance in several applications, in addition to possessing rich fluid dynamics and thermal transport physics. This article experimentally and analytically sheds insight into the augmented evaporation dynamics of paramagnetic pendant droplets in the presence of a magnetic field stimulus. The literature provides information that solutal advection and the solutal Marangoni effect lead to enhanced evaporation in droplets with solvated ions. The main focus of this article is to modulate the thermosolutal advection with the aid of an external magnetic field and comprehend the dynamics of the evaporation process under such complex multiphysics interactions. Experimental observations reveal that the evaporation rate enhances as a direct function of the magnetic moment of the solvated magnetic element ions, thereby pointing at the magnetophoretic and magnetosolutal advection. Additionally, flow visualization by particle image velocimetry illustrates that the internal advection currents within the droplet increase in magnitude and are distorted in orientation by the magnetic field. A mathematical formalism based on magnetothermal and magnetosolutal advection has been proposed via scaling analysis of the species and energy conservation equations. The formalism takes into account all major governing factors, viz., the magnetothermal and magnetosolutal Marangoni numbers, magneto-Prandtl and magneto-Schmidt numbers, and the Hartmann number. The modeling establishes the magnetosolutal advection to be the dominant factor behind the augmented evaporation dynamics. Accurate validation of the experimental internal circulation velocity is obtained from the proposed model. This study reveals rich insight into the magnetothermosolutal hydrodynamics in paramagnetic droplets.

Evaporation-Triggered Segregation of Sessile Binary Droplets

Droplet evaporation of multicomponent droplets is essential for various physiochemical applications, e.g., in inkjet printing, spray cooling, and microfabrication. In this work, we observe and study the phase segregation of an evaporating sessile binary droplet, consisting of a miscible mixture of water and a surfactantlike liquid (1,2-hexanediol). The phase segregation (i.e., demixing) leads to a reduced water evaporation rate of the droplet, and eventually the evaporation process ceases due to shielding of the water by the nonvolatile 1,2-hexanediol. Visualizations of the flow field by particle image velocimetry and numerical simulations reveal that the timescale of water evaporation at the droplet rim is faster than that of the Marangoni flow, which originates from the surface tension difference between water and 1,2-hexanediol, eventually leading to segregation.

Transverse dielectrophoretic-based DNA nanoscale confinement

Confinement of single molecules within nanoscale environments is crucial in a range of fields, including biomedicine, genomics, and biophysics. Here, we present a method that can concentrate, confine, and linearly stretch DNA molecules within a single optical field of view using dielectrophoretic (DEP) force. The method can convert an open surface into one confining DNA molecules without a requirement for bonding, hydrodynamic or mechanical components. We use a transverse DEP field between a top coverslip and a bottom substrate, both of which are coated with a transparent conductive material. Both layers are attached using double-sided tape, defining the chamber. The nanofeatures lie at the “floor” and do not require any bonding. With the application of an alternating (AC) electric field (2 V_p-p) between the top and bottom electrodes, a DEP field gradient is established and used to concentrate, confine and linearly extend DNA in nanogrooves as small as 100-nm in width. We also demonstrate reversible loading/unloading of DNA molecules into nanogrooves and nanopits by switching frequency (between 10 kHz to 100 kHz). The technology presented in this paper provides a new method for single-molecule trapping and analysis.

Molecular investigation of evaporation of biodroplets containing single-strand DNA on graphene surface

In this study, the water droplet behaviour of four different types of single-strand DNA with homogeneous base sequence on a graphene substrate during evaporation of the droplet was investigated using molecular dynamics (MD) simulation. The simulation results indicated that the evaporation depended on the DNA sequence. The observed changes can be divided into four parts: (i) vaporization mode, (ii) evaporation flux, (iii) mechanism of single-strand placement on the surface, and (iv) consideration of remaining single strands after evaporation. Our simulation observations indicated different evaporation modes for thymine biodroplets as compared to those for other biodroplets. The evaporation of the thymine biodroplets occurred with an increase in the contact angle, while that of the other biodroplets occur in a constant contact angle mode. Moreover, thymine biodroplets generate the lowest contact line compared to other single strands, and it is always placed far away from the centre of the droplets during evaporation. Investigating variations in the evaporation flux shows that thymine has the highest evaporation flux and guanine has the lowest. Moreover, during initial evaporation, the flux of evaporation increases at the triple point of the biodroplets containing thymine single strands, while it decreases in the other biodroplets. The following observation was obtained from the study of the placement of single strands on the substrate: guanine and thymine interacted slower than other single strands during evaporation with graphene, adenine single strand had a higher folding during evaporation, and guanine single strand showed the lowest end-to-end distance. The investigation of single-strand DNA after evaporation shows that adenine produces the most stable structure at the end of evaporation. In addition, cytosine is the most stretched single-strand DNA due to its lack of internal π-π stacking and hydrogen bonding. Therefore, cytosine single strand is more accessible for use in microarrays to detect target single strands.

Simple scaling laws for the evaporation of droplets pinned on pillars: Transfer-rate- and diffusion-limited regimes

The evaporation of droplets can give rise to a wide range of interesting phenomena in which the dynamics of the evaporation are crucial. In this work, we find simple scaling laws for the evaporation dynamics of axisymmetric droplets pinned on millimeter-sized pillars. Different laws are found depending on whether evaporation is limited by the diffusion of vapor molecules or by the transfer rate across the liquid-vapor interface. For the diffusion-limited regime, we find that a mass-loss rate equal to 3/7 of that of a free-standing evaporating droplet brings a good balance between simplicity and physical correctness. We also find a scaling law for the evaporation of multicomponent solutions. The scaling laws found are validated against experiments of the evaporation of droplets of (1) water, (2) blood plasma, and (3) a mixture of water and polyethylene glycol, pinned on acrylic pillars of different diameters. These results shed light on the macroscopic dynamics of evaporation on pillars as a first step towards the understanding of other complex phenomena that may be taking place during the evaporation process, such as particle transport and chemical reactions.

DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle

Progress in whole-genome sequencing using short-read (e.g., <150 bp), next-generation sequencing technologies has reinvigorated interest in high-resolution physical mapping to fill technical gaps that are not well addressed by sequencing. Here, we report two technical advances in DNA nanotechnology and single-molecule genomics: (1) we describe a labeling technique (CRISPR-Cas9 nanoparticles) for high-speed AFM-based physical mapping of DNA and (2) the first successful demonstration of using DVD optics to image DNA molecules with high-speed AFM. As a proof of principle, we used this new “nanomapping” method to detect and map precisely BCL2–IGH translocations present in lymph node biopsies of follicular lymphoma patents. This HS-AFM “nanomapping” technique can be complementary to both sequencing and other physical mapping approaches.

Physical mapping of DNA can be used to detect structural variants and for whole-genome haplotype assembly. Here, the authors use CRISPR-Cas9 and high-speed atomic force microscopy to ‘nanomap’ single molecules of DNA.

Chip-scale alignment of long DNA nanofibers on a patterned self-assembled monolayer

Controlled alignment of long DNA nanofibers is challenging. This communication reports a method to align human genomic DNA with nearly unlimited length using lithographically produced micro-patterns of self-assembled monolayers (SAMs) with positively charged terminal groups. The micro-patterns act as local DNA reservoirs to supply DNAs for nanofiber formation, and can also stretch and align DNA nanofibers to form an ordered array by controlling the dewetting profile. By reducing the size and inter-patch distance of a micro-patch, a nearly uniform array of long DNA nanofibers can be patterned over a large area. A controlled motion of a DNA containing droplet allows for free patterning of DNA nanofibers and production of complex structures without a transfer process. Bending of DNA nanofibers due to local distortion of the contact line bridges more adjacent micro-patches and increases the chance of producing continuous nanofibers. The interplay between surface tension and electrostatic attraction of positively charged micro-patterns allows the production of long DNA nanofibers in a simple yet powerful way.

Molecular conformations of DNA targets captured by model nanoarrays

An open question in single molecule nanoarrays is how the chemical and morphological heterogeneities of the solid support affect the properties of biomacromolecules. We generated arrays that allowed individually-resolvable DNA molecules to interact with tailored surface heterogeneities and revealed how molecular conformations are impacted by surface interactions.

Microscopic origin of wall slip during flow of an entangled DNA solution in microfluidics: Flow induced chain stretching versus chain desorption

Despite the relevance and importance of slip, a fundamental understanding of the underlying molecular mechanisms of wall slip in polymer flow is still missing. In this work, we investigate the slip behavior of an entangled DNA solution at a molecular scale using a confocal microscope coupled to a microfluidic device. From microscopic measurement, we obtain both the velocity profile and conformation of polymeric chains by visualizing DNA molecules during flow on various surfaces (ranging from weak to strong interactions with DNA molecules). In channel flow at a low Weissenberg number (Wi = 0.14), we observe a parabolic flow for an APTES-treated glass (with strong interaction with DNA) in the absence of slip, while a significant amount of slip has been observed for a regular glass (with a weak interaction with DNA). At higher flow rates (Wi > 1.0), strong slip appears during flow on APTES-treated surfaces. In this case, only immobile DNA molecules are stretched on the surface and other bulk chains remain coiled. This observation suggests that the flow induced chain stretching at the interface is the main mechanism of slip during flow on strong surfaces. Conversely, for slip flow on surfaces with weak interactions (such as unmodified or acrylate-modified glasses), polymeric chains are desorbed from the surface and a thin layer of water is present near the surface, which induces an effective slip during flow. By imaging DNA conformations during both channel and shear flows on different surfaces, we elucidate that either chain desorption or flow-induced stretching of adsorbed chains occurs depending on the surface condition. In general, we expect that these new insights into the slip phenomenon will be useful for studying the biological flow involving single DNA molecule experiments in micro/nanofluidic devices.

Applications of optical DNA mapping in microbiology

Optical mapping (OM) has been used in microbiology for the past 20 years, initially as a technique to facilitate DNA sequence-based studies; however, with decreases in DNA sequencing costs and increases in sequence output from automated sequencing platforms, OM has grown into an important auxiliary tool for genome assembly and comparison. Currently, there are a number of new and exciting applications for OM in the field of microbiology, including investigation of disease outbreaks, identification of specific genes of clinical and/or epidemiological relevance, and the possibility of single-cell analysis when combined with cell-sorting approaches. In addition, designing lab-on-a-chip systems based on OM is now feasible and will allow the integrated and automated microbiological analysis of biological fluids. Here, we review the basic technology of OM, detail the current state of the art of the field, and look ahead to possible future developments in OM technology for microbiological applications.

Nanopores and Nanochannels: From Gene Sequencing to Genome Mapping

DNA strands can be analyzed at the single-molecule level by isolating them inside nanoscale holes. The strategy is used for the label-free and portable sequencing with nanopores. Nanochannels can also be applied to map genomes with high resolution, as shown by Jeffet et al. in this issue of ACS Nano. Here, we compare the two strategies in terms of biophysical similarities and differences and describe that both are complementary and can improve the DNA analysis for genomic research and diagnostics.