Impacts of large and small barriers on fish assemblage composition assessed using environmental DNA metabarcoding.

River fragmentation caused by instream barriers is a leading cause of biodiversity loss, particularly for freshwater migratory fish, the vertebrate group that has suffered the steepest decline. However, most studies have tended to focus on the impacts of large dams on only a few taxa. We estimated the cumulative impact of both large and small barriers on fish species richness and relative abundance along an altitudinal gradient in the main stem of the River Allier (France). Using eDNA metabarcoding, we identified 24 fish zero-radius operational taxonomic units (zOTUs), corresponding to 26 species distributed along the main stem of the river. Elevation explained the greatest amount of variation in fish distribution, together with average flow, barrier density and its interaction with cumulative barrier height. Based on eDNA, the largest discontinuity in species richness was not related to the location of Poutès, the largest dam in the system, but located downstream from it. Our results indicate that, in addition to the more obvious effects of large dams on migratory fish such as the Atlantic salmon, the cumulative effects of small barriers can have widespread impacts on fish species richness and relative abundance, which should not be overlooked. We suggest that, as for other fragmented rivers, acting on numerous small barriers might bring about greater benefits in fish species richness than focusing only on the largest dams.

Quantitative assessment of fish larvae community composition in spawning areas using metabarcoding of bulk samples.

Accurate assessment of larval community composition in spawning areas is essential for fisheries management and conservation but is often hampered by the cryptic nature of many larvae, which renders them difficult to identify morphologically. Metabarcoding is a rapid and cost-effective method to monitor early life stages for management and environmental impact assessment purposes but its quantitative capability is under discussion. We compared metabarcoding with traditional morphological identification to evaluate taxonomic precision and reliability of abundance estimates, using 332 fish larvae from multinet hauls (0-50 m depth) collected at 14 offshore sampling sites in the Irish and Celtic seas. To improve quantification accuracy (relative abundance estimates), the amount of tissue for each specimen was standardized and mitochondrial primers (12S gene) with conserved binding sites were used. Relative family abundance estimated from metabarcoding reads and morphological assessment were positively correlated, as well as taxon richness (RS  = 0.81, P = 0.007) and diversity (RS  = 0.90, P = 0.002). Spatial patterns of community composition did not differ significantly between metabarcoding and morphological assessments. Our results show that DNA metabarcoding of bulk tissue samples can be used to monitor changes in fish larvae abundance and community composition. This represents a feasible, efficient, and faster alternative to morphological methods that can be applied to terrestrial and aquatic habitats.

A deep learning approach for designed diffraction-based acoustic patterning in microchannels.

Acoustic waves can be used to accurately position cells and particles and are appropriate for this activity owing to their biocompatibility and ability to generate microscale force gradients. Such fields, however, typically take the form of only periodic one or two-dimensional grids, limiting the scope of patterning activities that can be performed. Recent work has demonstrated that the interaction between microfluidic channel walls and travelling surface acoustic waves can generate spatially variable acoustic fields, opening the possibility that the channel geometry can be used to control the pressure field that develops. In this work we utilize this approach to create novel acoustic fields. Designing the channel that results in a desired acoustic field, however, is a non-trivial task. To rapidly generate designed acoustic fields from microchannel elements we utilize a deep learning approach based on a deep neural network (DNN) that is trained on images of pre-solved acoustic fields. We use then this trained DNN to create novel microchannel architectures for designed microparticle patterning.

Massively Multiplexed Submicron Particle Patterning in Acoustically Driven Oscillating Nanocavities.

Nanoacoustic fields are a promising method for particle actuation at the nanoscale, though THz frequencies are typically required to create nanoscale wavelengths. In this work, the generation of robust nanoscale force gradients is demonstrated using MHz driving frequencies via acoustic-structure interactions. A structured elastic layer at the interface between a microfluidic channel and a traveling surface acoustic wave (SAW) device results in submicron acoustic traps, each of which can trap individual submicron particles. The acoustically driven deformation of nanocavities gives rise to time-averaged acoustic fields which direct suspended particles toward, and trap them within, the nanocavities. The use of SAWs permits massively multiplexed particle manipulation with deterministic patterning at the single-particle level. In this work, 300 nm diameter particles are acoustically trapped in 500 nm diameter cavities using traveling SAWs with wavelengths in the range of 20-80 µm with one particle per cavity. On-demand generation of nanoscale acoustic force gradients has wide applications in nanoparticle manipulation, including bioparticle enrichment and enhanced catalytic reactions for industrial applications.

Slowness curve surface acoustic wave transducers for optimized acoustic streaming.

Surface acoustic waves can induce force gradients on the length scales of micro- and nanoparticles, allowing precise manipulation for particle capture, alignment and sorting activities. These waves typically occupy a spatial region much larger than a single particle, resulting in batch manipulation. Circular arc transducers can focus a SAW into a narrow beam on the order of the particle diameter for highly localised, single-particle manipulation by exciting wavelets which propagate to a common focal point. The anisotropic nature of SAW substrates, however, elongates and shifts the focal region. Acousto-microfluidic applications are highly dependent on the morphology of the underlying substrate displacement and, thus, become dependent on the microchannel position relative to the circular arc transducer. This requires either direct measurement or computational modelling of the SAW displacement field. We show that the directly measured elongation and shift in the focal region are recapitulated by an analytical model of beam steering, derived from a simulated slowness curve for 128° Y-cut lithium niobate. We show how the negative effects of beam steering can be negated by adjusting the curvature of arced transducers according to the slowness curve of the substrate, for which we present a simple function for convenient implementation in computational design software. Slowness-curve adjusted transducers do not require direct measurement of the SAW displacement field for microchannel placement and can capture smaller particles within the streaming vortices than can circular arc IDTs.

Mitogenomic diversity in Sacred Ibis Mummies sheds light on early Egyptian practices.

The ancient catacombs of Egypt harbor millions of well-preserved mummified Sacred Ibis (Threskiornis aethiopicus) dating from ~600BC. Although it is known that a very large number of these 'votive' mummies were sacrificed to the Egyptian God Thoth, how the ancient Egyptians obtained millions of these birds for mummification remains unresolved. Ancient Egyptian textual evidences suggest they may have been raised in dedicated large-scale farms. To investigate the most likely method used by the priests to secure birds for mummification, we report the first study of complete mitochondrial genomes of 14 Sacred Ibis mummies interred ~2500 years ago. We analysed and compared the mitogenomic diversity among Sacred Ibis mummies to that found in modern Sacred Ibis populations from throughout Africa. The ancient birds show a high level of genetic variation comparable to that identified in modern African populations, contrary to the suggestion in ancient hieroglyphics (or ancient writings) of centralized industrial scale farming of sacrificial birds. This suggests a sustained short-term taming of the wild migratory Sacred Ibis for the ritual yearly demand.

Acoustic fields and microfluidic patterning around embedded micro-structures subject to surface acoustic waves.

Recent research has shown that interactions between acoustic waves and microfluidic channels can generate microscale interference patterns with the application of a traveling surface acoustic wave (SAW), effectively creating standing wave patterns with a traveling wave. Forces arising from this interference can be utilized for precise manipulation of micron-sized particles and biological cells. The patterns that have been produced with this method, however, have been limited to straight lines and grids from flat channel walls, and where the spacing resulting from this interference has not previously been comprehensively explored. In this work we examine the interaction between both straight and curved channel interfaces with a SAW to derive geometrically deduced analytical models. These models predict the acoustic force-field periodicity near a channel interface as a function of its orientation to an underlying SAW, and are validated with experimental and simulation results. Notably, the spacing is larger for flat walls than for curved ones and is dependent on the ratio of sound speeds in the substrate and fluid. Generating these force-field gradients with only travelling waves has wide applications in acoustofluidic systems, where channel interfaces can potentially support a range of patterning, concentration, focusing and separation activities by creating locally defined acoustic forces.

Voltaglue Bioadhesives Energized with Interdigitated 3D-Graphene Electrodes.

Soft tissue fixation of implant and bioelectrodes relies on mechanical means (e.g., sutures, staples, and screws), with associated complications of tissue perforation, scarring, and interfacial stress concentrations. Adhesive bioelectrodes address these shortcomings with voltage cured carbene-based bioadhesives, locally energized through graphene interdigitated electrodes. Electrorheometry and adhesion structure activity relationships are explored with respect to voltage and electrolyte on bioelectrodes synthesized from graphene 3D-printed onto resorbable polyester substrates. Adhesive leachates effects on in vitro metabolism and human-derived platelet-rich plasma response serves to qualitatively assess biological response. The voltage activated bioadhesives are found to have gelation times of 60 s or less with maximum shear storage modulus (G') of 3 kPa. Shear modulus mimics reported values for human soft tissues (0.1-10 kPa). The maximum adhesion strength achieved for the ≈50 mg bioelectrode films is 170 g cm-2 (17 kPa), which exceeds the force required for tethering of electrodes on dynamic soft tissues. The method provides the groundwork for implantable bio/electrodes that may be permanently incorporated into soft tissues, vis-à-vis graphene backscattering wireless electronics since all components are bioresorbable.

Self-Aligned Acoustofluidic Particle Focusing and Patterning in Microfluidic Channels from Channel-Based Acoustic Waveguides.

Acoustic fields have been widely used for manipulation of particles and cells within microfluidic systems. In this Letter, we explore a novel acoustofluidic phenomenon for particle patterning and focusing, where a periodic acoustic pressure field is produced parallel to internal channel boundaries with the imposition of either a traveling or standing surface acoustic wave (SAW). This effect results from the propagation and intersection of edge waves from the channel walls according to the Huygens-Fresnel principle and classical wave fronts from the substrate-fluid interface. We demonstrate versatile control over this effect to produce both one- and two-dimensional acoustic patterning from one-dimensional SAW fields and its utility for continuous particle focusing. Uniquely, this channel-guided acoustic focusing permits the generation of robust acoustic fields without channel resonance conditions and particle focusing positions that are difficult or impossible to produce otherwise.

A rapid and meshless analytical model of acoustofluidic pressure fields for waveguide design.

Acoustofluidics has a strong pedigree in microscale manipulation, with particle and cell separation and patterning arising from acoustic pressure gradients. Acoustic waveguides are a promising candidate for localizing force fields in microfluidic devices, for which computational modelling is an important design tool. Meshed finite element analysis is a popular approach for this, yet its computation time increases rapidly when complex geometries are used, limiting its usefulness. Here, we present an analytical model of the acoustic pressure field in a microchannel arising from a surface acoustic wave (SAW) boundary condition that computes in milliseconds and provide the simulation code in the supplementary material. Unlike finite element analysis, the computation time of our model is independent of microchannel or waveguide shape, making it ideal for designing and optimising microscale waveguide structures. We provide experimental validation of our model with cases including near-field acoustic patterning of microparticles from a travelling SAW and two-dimensional patterning from a standing SAW and explore the design of waveguides for localised particle or cell capture.

Not just browsing: an animal that grazes phyllosphere microbes facilitates community heterogeneity.

Although grazers have long been recognized as top-down architects of plant communities, animal roles in determining microbial community composition have seldom been examined, particularly in aboveground systems. To determine the extent to which an animal can shape microbial communities, we conducted a controlled mesocosm study in situ to see if introducing mycophageous tree snails changed phyllosphere fungal community composition relative to matched control mesocosms. Fungal community composition and change was determined by Illumina sequencing of DNA collected from leaf surfaces before snails were introduced, daily for 3 days and weekly for 6 weeks thereafter. Scanning electron microscopy was used to confirm that grazing had occurred, and we recorded 3.5 times more cover of fungal hyphae in control mesocosms compared with those containing snails. Snails do not appear to vector novel microbes and despite grazing, a significant proportion of the initial leaf phyllosphere persisted in the mesocosms. Within-mesocosm diversities of fungi were similar regardless of whether or not snails were added. The greatest differences between the snail-treated and control mesocosms was that grazed mesocosms showed greater infiltration of microbes that were not sampled when the experiment commenced and that the variance in fungal community composition (beta diversity) was greater between leaves in snail-treated mesocosms indicating increased community heterogeneity and ecosystem fragmentation.

Self-assembled photoadditives in polyester films allow stop and go chemical release.

Near-infrared (NIR) triggered chemical delivery allows on-demand release with the advantage of external tissue stimulation. Bioresorbable polyester poly-l-lactic acid (PLLA) was compounded with photoadditives of neat zinc oxide (ZnO) nanoparticles and 980→365nm LiYF4:Tm3+, Yb3+ upconverting nanoparticles (UCNP). Subsequently, neat ZnO and UCNP blended PLLA films of sub-50µm thickness were knife casted with a hydrophobic small molecule drug mimic, fluorescein diacetate. The PLLA films displayed a 500 times increase in fluorescein diacetate release from the 50mW NIR irradiated PLLA/photoadditive film compared to non-irradiated PLLA control films. Larger ratios of UCNP/neat ZnO increased photocatalysis efficiency at low NIR duty cycles. The synergistic increase results from the self-assembled photoadditives of neat zinc oxide and upconverting nanoparticles (UCNPs), as seen in transmission electron microscopy. Colloidal ZnO, which does not self-assemble with UCNPs, had less than half the release kinetics of the self-assembled PLLA films under similar conditions, advocating Förster resonance energy transfer as the mechanism responsible for the synergistic increase. Alternative to intensity modulation, pulse width modulation (duty cycles from 0.1 to 1) of the low intensity 50mW NIR laser diode allowed tailorable release rates from 0.01 to 1.4% per day. With the low intensity NIR activation, tailorable release rates, and favorable biocompatibility of the constituents, implanted PLLA photoadditive thin films could allow feedback mediated chemical delivery. STATEMENT OF SIGNIFICANCE: Upconverting nanoparticles and zinc oxide nanorods were found to spontaneously self-assemble into submicron particles in organic solvents. Exposure of the submicron particles to near-infrared light allows stop and go chemical release from biocompatible polymers. Sample preparation of thin films is done with ease through physical mixing of the photoadditives followed by air-dried knife casting. A colloidal ZnO variant that does not self-assemble with upconverting nanoparticles had slower chemical release, suggesting that synergistic chemical release is brought upon by highly efficient energy transfer mechanisms when the nanoparticles are less than 10nm apart. Never before seen composite particles of UCNP/ZnO are displayed, which shows the close interaction of the photoadditives within the polymer matrix.

Rapid cell separation with minimal manipulation for autologous cell therapies.

The ability to isolate specific, viable cell populations from mixed ensembles with minimal manipulation and within intra-operative time would provide significant advantages for autologous, cell-based therapies in regenerative medicine. Current cell-enrichment technologies are either slow, lack specificity and/or require labelling. Thus a rapid, label-free separation technology that does not affect cell functionality, viability or phenotype is highly desirable. Here, we demonstrate separation of viable from non-viable human stromal cells using remote dielectrophoresis, in which an electric field is coupled into a microfluidic channel using shear-horizontal surface acoustic waves, producing an array of virtual electrodes within the channel. This allows high-throughput dielectrophoretic cell separation in high conductivity, physiological-like fluids, overcoming the limitations of conventional dielectrophoresis. We demonstrate viable/non-viable separation efficacy of >98% in pre-purified mesenchymal stromal cells, extracted from human dental pulp, with no adverse effects on cell viability, or on their subsequent osteogenic capabilities.

Addressing Unmet Clinical Needs with UV Bioadhesives.

The invasive practice of suturing for wound closure has persisted for millennia; with the rate of medical development, it is staggering that there are few viable alternatives to invasive mechanical fasteners. Biocompatible and biodegradable polymers are attractive candidates for versatile bioadhesives and could revolutionize surgical procedures. Bioadhesives can be broadly placed into two groups: activated and instant. Almost all commercially available bioadhesives are instant, which cross-link by mixing two components or on contact with moisture. Activated bioadhesives, on the other hand, allow control of when and where a bioadhesive cross-links and, in some cases, the extent of cross-linking. Despite significant progress, there has been little translation of activated bioadhesives to clinical use. This review discusses recent developments in UV-activated bioadhesives toward addressing unmet clinical needs.

Elastic Light Tunable Tissue Adhesive Dendrimers.

Development of bioadhesive formulations for tissue fixation remains a challenge. The major drawbacks of available bioadhesives are low adhesion strength, toxic byproducts, and complexity of application onto affected tissues. In order to address these problems, this study has developed a hydrogel bioadhesive system based on poly amido amine (PAMAM) dendrimer, grafted (conjugated) with UV-sensitive, 4-[3-(trifluoromethyl)-3H-diazirin-3-yl] benzyl bromide (PAMAM-g-diazirine). This particular diazirine molecule can be grafted to the surface amine groups of PAMAM in a one-pot synthesis. Diazirine functionalities are carbene precursors that form covalent crosslinks with hydrated tissues after low-power UV activation without necessity of free-radical initiators. The rheological properties and adhesion strength to ex vivo tissues are highly controllable depending on diazirine grafting, hydrogel concentration, and UV dose intensity fitting variety types of tissues. Covalent bonds at the tissue/bioadhesive interface provide robust adhesive and mechanical strength in a highly hydrated environment. The free flowing hydrogel conversion to elastic adhesive after UV activation allows intimate contact with the ex vivo swine tissue surfaces with low in vitro cytotoxicity observed, making it a promising bioadhesive formulation toward clinical applications.

Dining local: the microbial diet of a snail that grazes microbial communities is geographically structured.

Achatinella mustelina is a critically endangered tree snail that subsists entirely by grazing microbes from leaf surfaces of native trees. Little is known about the fundamental aspects of these microbe assemblages: not taxonomic composition, how this varies with host plant or location, nor whether snails selectively consume microbes. To address these questions, we collected 102 snail faecal samples as a proxy for diet, and 102 matched-leaf samples from four locations. We used Illumina amplicon sequencing to determine bacterial and fungal community composition. Microbial community structure was significantly distinct between snail faeces and leaf samples, but the same microbes occurred in both. We conclude that snails are not 'picky' eaters at the microbial level, but graze the surface of whatever plant they are on. In a second experiment, the gut was dissected from non-endangered native tree snails in the same family as Achatinella to confirm that faecal samples reflect gut contents. Over 60% of fungal reads were shared between faeces, gut and leaf samples. Overall, location, sample type (faeces or leaf) and host plant identity all significantly explained the community composition and variation among samples. Understanding the microbial ecology of microbes grazed by tree snails enables effective management when conservation requires captive breeding or field relocation.

Tuning model drug release and soft-tissue bioadhesion of polyester films by plasma post-treatment.

Plasma treatments are investigated as a post-production method of tuning drug release and bioadhesion of poly(lactic-co-glycolic acid) (PLGA) thin films. PLGA films were treated under varying conditions by controlling gas flow rate, composition, treatment time, and radio frequency (RF) power. In vitro release of the drug-like molecule fluorescein diacetate (FDAc) from plasma-treated PLGA was tunable by controlling RF power; an increase of 65% cumulative release is reported compared to controls. Bioadhesion was sensitive to RF power and treatment time, assessed using ex vivo shear-stress tests with wetted swine aorta. We report a maximum bioadhesion ∼6-fold that of controls and 5-fold that of DOPA-based mussel adhesives tested to swine skin.1 The novelty of this post-treatment is the activation of a hydrophobic polyester film for bioadhesion, which can be quenched, while simultaneously tuning drug-release kinetics. This exemplifies the promise of plasma post-treatment for in-clinic bioadhesive activation, along with technological advancements, i.e., atmospheric plasma and hand-held "plasma pencils".

Determining the diet of larvae of western rock lobster (Panulirus cygnus) using high-throughput DNA sequencing techniques.

The Western Australian rock lobster fishery has been both a highly productive and sustainable fishery. However, a recent dramatic and unexplained decline in post-larval recruitment threatens this sustainability. Our lack of knowledge of key processes in lobster larval ecology, such as their position in the food web, limits our ability to determine what underpins this decline. The present study uses a high-throughput amplicon sequencing approach on DNA obtained from the hepatopancreas of larvae to discover significant prey items. Two short regions of the 18S rRNA gene were amplified under the presence of lobster specific PNA to prevent lobster amplification and to improve prey amplification. In the resulting sequences either little prey was recovered, indicating that the larval gut was empty, or there was a high number of reads originating from multiple zooplankton taxa. The most abundant reads included colonial Radiolaria, Thaliacea, Actinopterygii, Hydrozoa and Sagittoidea, which supports the hypothesis that the larvae feed on multiple groups of mostly transparent gelatinous zooplankton. This hypothesis has prevailed as it has been tentatively inferred from the physiology of larvae, captive feeding trials and co-occurrence in situ. However, these prey have not been observed in the larval gut as traditional microscopic techniques cannot discern between transparent and gelatinous prey items in the gut. High-throughput amplicon sequencing of gut DNA has enabled us to classify these otherwise undetectable prey. The dominance of the colonial radiolarians among the gut contents is intriguing in that this group has been historically difficult to quantify in the water column, which may explain why they have not been connected to larval diet previously. Our results indicate that a PCR based technique is a very successful approach to identify the most abundant taxa in the natural diet of lobster larvae.