Monitoring the microbiome for food safety and quality using deep shotgun sequencing.

In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced the total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic matrix filtering step that improved microbe detection specificity to >99.96% during in silico validation. The pipeline identified 119 microbial genera per HPP sample on average with 65 genera present in all samples. The most abundant of these were Bacteroides, Clostridium, Lactococcus, Aeromonas, and Citrobacter. We also observed shifts in the microbial community corresponding to ingredient composition differences. When comparing culture-based results for Salmonella with total RNA sequencing, we found that Salmonella growth did not correlate with multiple sequence analyses. We conclude that microbiome sequencing is useful to characterize complex food microbial communities, while additional work is required for predicting specific species' viability from total RNA sequencing.

Food authentication from shotgun sequencing reads with an application on high protein powders.

Here we propose that using shotgun sequencing to examine food leads to accurate authentication of ingredients and detection of contaminants. To demonstrate this, we developed a bioinformatic pipeline, FASER (Food Authentication from SEquencing Reads), designed to resolve the relative composition of mixtures of eukaryotic species using RNA or DNA sequencing. Our comprehensive database includes >6000 plants and animals that may be present in food. FASER accurately identified eukaryotic species with 0.4% median absolute difference between observed and expected proportions on sequence data from various sources including sausage meat, plants, and fish. FASER was applied to 31 high protein powder raw factory ingredient total RNA samples. The samples mostly contained the expected source ingredient, chicken, while three samples unexpectedly contained pork and beef. Our results demonstrate that DNA/RNA sequencing of food ingredients, combined with a robust analysis, can be used to find contaminants and authenticate food ingredients in a single assay.

Using Unentangled Oligomers To Toughen Materials.

Entanglements between polymer chains are responsible for the strength and toughness of polymeric materials. When the chains are too short to form entanglements, the polymer becomes weak and brittle. Here we show that molecular bridging of oligomers in molecular-scale confinement can dramatically toughen materials even when intermolecular entanglements are completely absent. We describe the fabrication of nanocomposite materials that confine oligomer chains to molecular-scale dimensions and demonstrate that partially confined unentangled oligomers can toughen materials far beyond rule-of-mixtures estimates. We also characterize how partially confined oligomers affect the kinetics of nanocomposite cracking in moist environments and show that the presence of a backfilled oligomeric phase within a nanoporous organosilicate matrix leads to atomistic crack path meandering in which the failure path is preferentially located within the matrix phase.

Synthesis of Polyimides in Molecular-Scale Confinement for Low-Density Hybrid Nanocomposites.

In this work, we exploit a confinement-induced molecular synthesis and a resulting bridging mechanism to create confined polyimide thermoset nanocomposites that couple molecular confinement-enhanced toughening with an unprecedented combination of high-temperature properties at low density. We describe a synthesis strategy that involves the infiltration of individual polymer chains through a nanoscale porous network while simultaneous imidization reactions increase the molecular backbone stiffness. In the extreme limit where the confinement length scale is much smaller than the polymer's molecular size, confinement-induced molecular mechanisms give rise to exceptional mechanical properties. We find that polyimide oligomers can undergo cross-linking reactions even in such molecular-scale confinement, increasing the molecular weight of the organic phase and toughening the nanocomposite through a confinement-induced energy dissipation mechanism. This work demonstrates that the confinement-induced molecular bridging mechanism can be extended to thermoset polymers with multifunctional properties, such as excellent thermo-oxidative stability and high service temperatures (>350 °C).

Hyperconnected molecular glass network architectures with exceptional elastic properties.

Hyperconnected network architectures can endow nanomaterials with remarkable mechanical properties that are fundamentally controlled by designing connectivity into the intrinsic molecular structure. For hybrid organic-inorganic nanomaterials, here we show that by using 1,3,5 silyl benzene precursors, the connectivity of a silicon atom within the network extends beyond its chemical coordination number, resulting in a hyperconnected network with exceptional elastic stiffness, higher than that of fully dense silica. The exceptional intrinsic stiffness of these hyperconnected glass networks is demonstrated with molecular dynamics models and these model predictions are calibrated through the synthesis and characterization of an intrinsically porous hybrid glass processed from 1,3,5(triethoxysilyl)benzene. The proposed molecular design strategy applies to any materials system wherein the mechanical properties are controlled by the underlying network connectivity.

Amine-functionalized, multi-arm star polymers: A novel platform for removing glyphosate from aqueous media.

We describe a novel method for efficiently removing glyphosate from aqueous media via adsorption onto highly functionalized star-shaped polymeric particles. These particles have a polystyrene core with more than 35 attached methacrylate polymer arms, each containing a plurality of pendant amines (poly(dimethylamino ethyl methacrylate): PDMAEMA) that are partially protonated in water. Kinetic studies demonstrate that these star-polymers successfully remove up to 93% of glyphosate present in aqueous solution (feed concentration: 5 ppm), within 10 min contact time, outperforming activated carbon, which removed 33% after 20 min. On these star-polymers, glyphosate adsorption closely follows the Langmuir model indicating monolayer coverage at most. Ionic interaction between the protonated amines and glyphosate's dissociated carboxylic and phosphoric acid groups lead to effective glyphosate capture even at feed concentrations below 1 ppm. Surface charge of these star polymers and dissociation of glyphosate are both influenced by pH, thus glyphosate removal efficiency increases from 63% to 93% when pH increases from 4.2 to 7.7. NMR studies conducted with butylamine as a proxy for these polymeric particles confirm that the amine group binds with both glyphosate's carboxylic and phosphoric acid groups when its concentrations are in a 2:1 or higher molar ratio with glyphosate.

Fundamental limits of material toughening in molecularly confined polymers.

The exceptional mechanical properties of polymer nanocomposites are achieved through intimate mixing of the polymer and inorganic phases, which leads to spatial confinement of the polymer phase. In this study we probe the mechanical and fracture properties of polymers in the extreme limits of molecular confinement, where a stiff inorganic phase confines the polymer chains to dimensions far smaller than their bulk radius of gyration. We show that polymers confined at molecular length scales dissipate energy through a confinement-induced molecular bridging mechanism that is distinct from existing entanglement-based theories of polymer deformation and fracture. We demonstrate that the toughening is controlled by the molecular size and the degree of confinement, but is ultimately limited by the strength of individual molecules.

Carbon-Bridge Incorporation in Organosilicate Coatings Using Oxidative Atmospheric Plasma Deposition.

Carbon-bridges were successfully incorporated into the molecular structure of inorganic silicate films deposited onto polymer substrates using an oxidative atmospheric plasma deposition process. Key process parameters that include the precursor chemistry and delivery rate are discussed in the context of a deposition model. The resulting coating exhibited significantly improved adhesion and a 4-fold increase in moisture resistance as determined from the threshold for debonding in humid air compared to dense silica or commercial sol-gel polysiloxane coatings. Other important parameters for obtaining highly adhesive coating deposition on oxidation-sensitive polymer substrates using atmospheric plasma were also investigated to fully activate but not overoxidize the substrate. The resulting carbon molecular bridged adhesive coating showed enhanced moisture resistance, important for functional membrane applications.

Molecular design for moisture insensitivity of compositionally graded hybrid films.

Effective bonding of organic/inorganic interfaces especially in high humidity environments is paramount to the structural reliability of modern multilayer device technologies, such as flexible electronics, photovoltaics, microelectronic devices, and fiber-metal laminates used in aerospace applications. We demonstrate the ability to design compositionally graded hybrid organic/inorganic films with an inorganic zirconium network capable of forming a moisture-insensitive bond at the interface between an oxide and organic material. By controlling the chemistry of the deposited films and utilizing time-dependent debonding studies, we were able to correlate the behavior of the hybrid films at high humidity to their underlying molecular structure. As a result, an outstanding threefold improvement in adhesion of silicon/epoxy interfaces can be obtained with the introduction of these films even in high humidity environments.

Highly transparent multifunctional bilayer coatings on polymers using low-temperature atmospheric plasma deposition.

We report on the synthesis of hard, adhesive, and highly transparent bilayer organosilicate thin films on large poly(methyl methacrylate) substrates by atmospheric plasma, in ambient air, at room temperature, in a one-step process, using a single precursor. The method overcomes the challenge of fabricating coatings with high mechanical and interfacial properties in a one-step process. The bottom layer is a carbon-bridged hybrid silica with excellent adhesion with the poly(methyl methacrylate) substrate, and the top layer is a dense silica with high Young's modulus, hardness, and scratch resistance. The bilayer structure exhibited ~100% transmittance in the visible wavelength range, twice the adhesion energy and three times the Young's modulus of commercial polysiloxane sol­gel coatings.

Independent control of adhesive and bulk properties of hybrid silica coatings on polycarbonate.

Transparent polymers are widely used in many applications ranging from automotive windows to microelectronics packaging. However, their intrinsic characteristics, in particular their mechanical properties, are significantly degraded with exposure to different weather conditions. For instance, under humid environment or UV-irradiation, polycarbonate (PC) undergoes depolymerization, leading to the release of Bisphenol A, a molecule presumed to be a hormonal disruptor, potentially causing health problems. This is a serious concern and the new REACH (Registration, Evaluation, Authorization and Restriction of Chemical substances ) program dictates that materials releasing Bisphenol A should be removed from the market by January 1st, 2015 (2012-1442 law). Manufacturers have tried to satisfy this new regulation by depositing atop the PC a dense oxide-like protective coating that would act as a barrier layer. While high hardness, modulus, and density can be achieved by this approach, these coatings suffer from poor adhesion to the PC as evidenced by the numerous delamination events occurring under low scratch constraints. Here, we show that the combination of a N2/H2-plasma treatment of PC before depositing a hybrid organic-inorganic solution leads to a coating displaying elevated hardness, modulus, and density, along with a very high adherence to PC (> 20 J/m(2) as measured by double cantilever beam test). In this study, the sol-gel coatings were composed of hybrid O/I silica (based on organoalkoxysilanes and colloidal silica) and designed to favor covalent bonding between the hybrid network and the surface treated PC, hence increasing the contribution of the plastic deformation from the substrate. Interestingly, double-cantilever beam (DCB) tests showed that the coating's adhesion to PC was the same irrespective of the organoalkoxysilanes/colloidal silica ratio. The versatility of the sol-gel deposition techniques (dip-coating, spray-coating, etc.), together with the excellent mechanical properties and exceptional adherence of this hybrid material to PC should lead to interesting new applications in diverse fields: optical eye-glasses, medical materials, packaging, and so forth.

Heterogeneous solution deposition of high-performance adhesive hybrid films.

Interfaces between organic and inorganic materials are of critical importance to the lifetime of devices found in microelectronic chips, organic electronics, photovoltaics, and high-performance laminates. Hybrid organic/inorganic materials synthesized through sol-gel processing are best suited to address these challenges because of the intimate mixing of both components. We demonstrate that deposition from heterogeneous sol-gel solutions leads to the unique nanolength-scale control of the through-thickness film composition and therefore the independent optimization of both the bulk and interfacial film properties. Consequently, an outstanding 3-fold improvement in the adhesive/cohesive properties of these hybrid films can be obtained from otherwise identical precursors.

Improved adhesion of dense silica coatings on polymers by atmospheric plasma pretreatment.

Oxygen atmospheric plasma was used to pretreat polycarbonate (PC) and stretched poly(methyl methacrylate) (PMMA) surfaces in order to enhance the adhesion of the dense silica coatings deposited by atmospheric plasma on the polymer substrates. The treatment time and chemical structure of the polymers were found to be important factors. For PC, a short treatment increased the adhesion energy, while longer treatment times decreased the adhesion. In contrast, plasma pretreatment monotonically decreased the adhesion of PMMA, and pristine PMMA exhibited much higher adhesion than the PC counterpart. We found that adhesion enhancement was achieved through improved chemical bonding, chain interdiffusion, and mechanical interlocking at the coating/substrate interface, after a short atmospheric plasma treatment. Decreased adhesion resulted from overoxidation and low-molecular-weight weak layer formation on the polymer surface by prolonged atmospheric plasma treatment. The dramatic differences in the behavior of PC and PMMA in relation to the plasma treatment time were due to their dissimilar resistance to atmospheric plasma exposure.

Atmospheric plasma deposited dense silica coatings on plastics.

We explore the application of a high-temperature precursor delivery system for depositing high boiling point organosilicate precursors on plastics using atmospheric plasma. Dense silica coatings were deposited on stretched poly(methyl methacrylate), polycarbonate and silicon substrates from the high boiling temperature precursor, 1, 2-bis(triethoxysilyl)ethane, and from two widely used low boiling temperature precursors, tetraethoxysilane and tetramethylcyclotetrasiloxane. The coating deposition rate, molecular network structure, density, Young's modulus and adhesion to plastics exhibited a strong dependence on the precursor delivery temperature and rate, and the functionality and number of silicon atoms in the precursor molecules. The Young's modulus of the coatings ranged from 6 to 34 GPa, depending strongly on the coating density. The adhesion of the coatings to plastics was affected by both the chemical structure of the precursor and the extent of exposure of the plastic substrate to the plasma during the initial stage of deposition. The optimum combinations of Young's modulus and adhesion were achieved with the high boiling point precursor which produced coatings with high Young's modulus and good adhesion compared to commercial polysiloxane hard coatings on plastics.

Cryogenic plasmas for controlled processing of nanoporous materials.

Plasma processing at cryogenic temperatures tremendously suppresses the depth penetration of plasma radical species within nanoporous materials. We demonstrate that this confining effect is surprisingly unrelated to changes in the phase diffusivity of radical species gas, but is determined by the increase of the sticking coefficient and the radical recombination and reaction factors, favoring an early irreversible surface adsorption of the plasma radical species.

Organic thin film transistor using a photo-curable organic/inorganic hybrid material as a gate dielectric.

A polyhedral oligomeric silsesquioxane derivative (POSS-OXT) containing photo-curable 4-membered cyclic oxetane functional groups was used as a gate dielectric of organic field effect transistor. The POSS-OXT was cross-linked and completely solidified by UV irradiation in the presence of a selected photo acid generator, and pinhole free uniform thin film was obtained. We fabricated a metal/insulator/metal device of Au/POSS-OXT (300 nm)/Au with area of 0.7 mm2 and the measured leakage current and capacitance of the device to evaluate the insulating properties of the POSS-OXT thin film. The maximum current was about 0.25 nA when 40 V was applied to the device. The observed values of the capacitance per unit area and dissipation factor were 11.4 nF/cm2 and 0.025, respectively. We fabricated an organic thin film transistor with pentacene as the active semiconductor and the photo-cross-linked POSS-OXT as an insulator. A field effect carrier mobility of 0.03 cm2/VN s was obtained with the device.

Organocatalytic living ring-opening polymerization of cyclic carbosiloxanes.

[reaction: see text] An organocatalytic route to narrowly dispersed poly(carbosiloxanes) of predictable molecular weight and end group fidelity is described. N-Heterocyclic carbenes (NHC) and 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) catalyze the ring opening of cyclic carbosiloxanes. The pK(b) of the catalyst is important in preventing adverse transetherification reactions and obtaining well-defined polymers. Mechanistic studies indicate that hydrogen bonding to TBD or the NHC activates alcohols or silanols for ring-opening reactions.