Background: The life-expectancy throughout the world has continuously increased in past years, mainly due to improvements in healthcare [1]. Lifespan extension will lead to a larger fraction of people being vulnerable to age-induced diseases such as Alzheimer’s. To address this issue, extensive studies are required to identify the mechanisms of diseases onset and progression. In addition, treatments need to be developed to prevent and control these diseases. Mammalian models can be used to study aging. However, these studies can suffer from being low-throughput, labor-intensive, and in many cases limited to qualitative assessments. In this work, we have integrated cutting-edge tools such as microfluidic platforms and machine learning techniques to study aging in a model organism, C.elegans, to address the limitations traditional studies face.

Results: We have focused on three projects that integrate microfluidics and quantitative image analysis for high-throughput, high-content biology. In our first project, we developed a novel microfluidic platform to perform life-long high-resolution high-throughput imaging of subtle phenotypes exhibited by a population of C. elegans as they age, in a drug free environment. This automated platform was used to track changes synapses undergo throughout the aging process quantitatively, while increasing the throughput of conventional microscopy [2]. To further increase the throughput and accuracy of neurodegeneration studies, we trained a Convolutional Neural Network algorithm to automate image processing of neuronal beading; a sign of neuro degradation. These phenotypes have traditionally been studied qualitatively or by manual image quantification, which could take a couple of hours per image. With MaskRCNN, a machine learning approach, we achieved 82% accuracy in image segmentation, while segmenting ~600 images in less than 5 hours. We were able to quantitatively characterize neurodegeneration caused by aging and cold-shock and track the changes such as increase in number of beads using this technology. Our last project was mainly focused on developing an affordable fully automated bead-sorting microfluidic platform for automated selection of protein-binding ligands. These screens traditionally required an experienced operator to sort through beads one by one, which is time consuming, labor-intensive, and subject to bias. Our platform fully automated the process of screening and achieved an accuracy of >90% and throughput of 125 beads/hour [3]. In this technology, we integrated online computer-based image processing to our platform to ensure that sorting is based on unbiased quantitative analysis of each bead.

Conclusions: In this work, we developed novel microfluidic and machine learning tools to facilitate complex image-based biological studies. These approaches enable otherwise unfeasible studies, greatly increase experimental accuracy and throughput, and ensure an unbiased approach to quantitative data acquisition.

References:

1. W. He, D. Goodkind and P. Kowal, Aging (Albany. NY)., 2016, 165.
2. S. Saberi-Bosari, J. Huayta and A. San-Miguel, Lab Chip, 2018, 18, 3090–3100.
3. S. Saberi-Bosari, M. Omary, A. Lavoie, R. Prodromou, K. Day, S. Menegatti and A. San-Miguel, Sci. Rep., 2019, 9, 7210.

Background: Protein-protein interactions (PPIs) are of great significance as they mediate the majority of cellular processes. PPIs are commonly identified using genetic based assays like yeast two hybrid (Y2H) and protein fragment complementation (PCA) where the protein of interest (“bait”) and its putative binding partner (“prey”) are fused to two different protein domains (Y2H) or protein fragments (PCA) using a cell-based system. Binding of the bait to the prey causes colocalization of the domains (Y2H) resulting in the stimulation of a readable output, like reporter gene activation, or reconstitution of a functional protein, like luciferase, by complementation of protein fragments (PCA). However, these methods are limited in scope as the affinity of the binding interaction cannot be efficiently quantitatively assessed or rank ordered. Generally, in vitro assays using soluble protein are performed for absolute binding affinity estimation. It is impractical for researchers to recombinantly express and purify soluble protein for each newly identified interaction pair. Hence, there is a need for a genetic based assay that can be used to estimate the absolute binding affinities of PPIs.

Results: Here, we describe a quantitative yeast-yeast two hybrid (qYY2H) that uses a luciferase-based assay for identification of putative PPIs and quantitative assessment of binding strength. In qYY2H, a prey protein is co-expressed with a luciferase reporter protein as yeast surface fusions. The bait protein is co-expressed with SsoFe2, an iron oxide binding protein; incubation of these cells with iron oxide nanoparticles results in their magnetization. Prey cells that complex with the magnetic bait cells are recovered using a magnet. A luciferase-based assay is used to quantify the number of prey cells captured by the bait cells. Standard curves can be used to estimate the exact number of prey cells complexed with the bait cells. Assay read out is proportional to the binding affinity of the interaction allowing for quantitative rank ordering between different prey. Absolute binding affinities can be estimated by fitting a multivalent binding model to titration curves generated using the qYY2H system. qYY2H assays were also used to characterize interacting pairs discovered from cDNA screens against SMAD3 and the WW domain. In addition, the qYY2H system allows for quantification of PPIs that rely on post-translational modifications, like phosphorylation, through the display of enzymatically modified proteins.

Conclusions: Unlike other PPI assays, the qYY2H system can provide absolute binding quantification using a multivalent binding model as the prey protein and luciferase reporter are co-displayed on the same surface. Because the interaction between the prey and bait cells is driven by avidity, even weak interactions can be detected. Noteworthy, the qYY2H system is one of the first genetic based assays that can be used to efficiently study interactions that rely on post-translationally modified domains. We expect qYY2H will be adopted by the protein engineering community for characterizing newly engineered interaction pairs discovered from combinatorial library screening.

Background: Increase of drug-resistance in pathogens has directly impacted healthcare industry. With only a few novel discoveries in the field of antibiotics since last two decades, often referred to as the discovery void, drug-resistance in pathogens has increased. Previously, infections that were easily treatable have now become fatal. Infections caused by drug-resistant pathogens can occur anywhere, but it is observed to take maximum effect in healthcare settings such as hospitals and nursing homes where patients are immune-compromised. The pathogens such as MRSA adhere to surfaces such as linens, counter tops, door handles, drapes, monitory equipment, sanitary ware and so on [1]. They infect personnel on contact, resulting in hospital acquired infections (HAIs). According to a recent report from CDC, 2.8 million people are affected by drug-resistant infections every year resulting in more than 35,000 deaths [2]. Over-prescription of antibiotics and improper disinfection protocols have only accelerated the problem of such infections. Instead of an ex post facto medical treatment by antibiotics, we intend to eliminate such pathogens before they infect anyone. In our work, this was achieved by continuous surface disinfection that serves as a preventive measure. We pursued two routes to achieve surface disinfection: a) antimicrobial photodynamic inactivation (aPDI) b) antimicrobial anionic inactivation (aAI).

Results: In the first method of aPDI, a photosensitizer (ZnTMPyP4+) was incorporated in an olefinic block copolymer (OBC) matrix. The photosensitizer is activated in the presence of visible light and produces singlet oxygen (1O2) that has a cytotoxic effect on pathogens. We have tested these materials against 5 bacterial, 3 viral and 1 fungal strain for an illumination time of 60 min with an illumination intensity of 65-80 mW/cm2 and achieved greater than ~ 99.9 % inactivation in all cases. The photosensitizer distribution was characterized by SEM, EDX & ToF-SIMS analyses. In the second method, we use a pentablock ionomer (TESET) containing charged sulfonic acid groups on the midblock. These materials act on pathogens by creating a large pH difference across the cell membrane that can disrupt the membrane, promote protein denaturation and eventually cell death. These ionomers were tested against 6 bacterial and 3 viral strains. Antimicrobial efficacy of 99.9999 % was achieved in 5 min of contact time.

Conclusions: In this work, antimicrobial efficacies of two chemically different thermoplastic elastomer systems have been investigated. The mechanism of disinfection of pathogens in the two routes was different. In the first method, aPDI, the disinfection was carried out in presence of visible light by production of cytotoxic singlet oxygen while in the second method, the disinfection was observed through a reduction in pH in the presence of moisture. We have demonstrated that both of the strategies considered, are highly effective, achieving ~ 99.9 % antimicrobial efficacy against most bacteria after reasonably quick exposure times (60 min for aPDI and 5 min for aAI).

References:

1. Kramer, A., Schwebke, I., Kampf, G. (2006) How long do nosocomial pathogens persist on inanimate surfaces? A systematic review. BMC Infect. Dis., 6: 130.
2. Antibiotic Resistance Threats in the United States, Centres for Disease Control and Prevention (CDC) 2019

Background: The development of robust affinity-based purification platforms is necessary to meet the increasing demand for emerging biotherapeutics, many of which cannot be purified with traditional techniques. Conventional ligands require dissociation conditions (e.g., pH, ionic strength, etc.) that are incompatible with labile biological targets, highlighting the need to identify new ligands whose binding and release activity responds to biocompatible stimuli. The identification of these ligands relies on the screening of combinatorial libraries of stimuli- responsive compounds. Azobenzene-cyclic peptides are ideal candidates to this goal, as they combine high binding specificity and biochemical stability with a reversible, light-controlled conformational switching behavior. To enable screening, sequencing, and validation of light-controlled ligands, we have developed (i) a novel chemistry, (ii) a microfluidic screening device, and (iii) a spectrophotometric apparatus for evaluating the photoswitching kinetics of azobenzene-cyclic peptides. A case study is presented on the design and study of novel light-controlled ligands for Vascular Cell Adhesion Molecule 1 (VCAM-1), a surface protein marker implicated in the differentiation of hematopoietic stem and progenitor cells.

Results: Our automated screening platform utilizes fluorescence microscopy and unsupervised image analysis to sort libraries of peptide-functionalized beads with high throughput (~ 125 beads per hour) and >90% yield and >90% accuracy [1]. Furthermore, our novel chemistry enables direct solid-phase peptide sequencing of the selected beads to identify ligand candidates. The device was first validated by screening a library of linear 8-mer peptides to identify novel ligands with high affinity and selectivity for Cas9. The identified sequences GYYRYSEY and YYHRHGLQ are the first short synthetic peptide ligands capable of purifying Cas9 from E. coli lysate with product recoveries between 86% – 89% and purities between 91% – 93% [2]. The device was then tested against model azobenzene-cyclic peptides to verify its ability to select light controlled ligands, using VCAM-1 as model target. Light irradiation triggered the release of up to 40% of the bound VCAM-1. Finally, we evaluated the photoswitching kinetics of model peptides to identify favorable conditions for the binding and elution of VCAM-1.

Conclusions: The proposed microfluidic sorting platform and spectrophotometric device offer a powerful approach to identify and study novel ligands for the processing of labile biotherapeutics. Coupled with our stimuli-responsive cyclic peptide design, we envision that these tools will streamline the development of biocompatible purification platforms for valuable biotherapeutics that are otherwise unachievable through traditional approaches.

References:

1. Saberi-Bosari, S., Omary, M., Lavoie, A., Prodromou, R., Day, K., Menegatti, S., and San-Miguel A. (2019) Affordable Microfluidic Bead-Sorting Platform for Automated Selection of Porous Particles Functionalized with Bioactive Compounds. Sci Rep, 9, 7210
2. Day, K., Prodromou, R., Saberi-Bosari, S., Omary, M., Market, C., San-Miguel, A., and Menegatti, S. Discovery and Evaluation of Peptide Ligands for Selective Adsorption and Release of Cas9 Nuclease on Solid Substrate, Bioconjugate Chem, (in press)

Background: Cells receive dynamic signals from their complex environments. There are a variety of ways in which cells could filter and process these signals including through protein signaling networks and gene regulatory networks. Interestingly, in eukaryotic cells, the process of expressing just a single gene can be quite complex, involving a series of steps and many chromatin regulators (CRs), including histone modifiers, Mediator components, nucleosome remodelers, and transcription factors. We hypothesize that the complexity of eukaryotic gene expression could not only process dynamic signals but be exploited through synthetic biology and optogenetic approaches to drive novel gene expression patterns. Here, we used light-inducible dimers, cryptochrome 2 (CRY2) and cryptochrome-interacting basic helix-loop-helix 1 (CIB1), to transiently recruit a transactivating protein,VP16. When exposed to blue light, CRY2 and CIB1 bind within a minute—recruiting VP16 to a synthetic reporter—and dissociate in about 5 minutes when blue light is removed [1]. This system provides a means to provide a range of dynamic inputs to chromatin, so we can explore the role chromatin plays in filtering various input signals.

Results: Using various signal input patterns using blue light, we were able to tune both the gene expression magnitude and noise by ~100 fold and 2 fold, respectively. By switching out VP16 with other CRs, we were able to characterize the distinct gene expression dynamics of each CR.

Conclusions: We have developed a tool that can provide robust gene expression control and provide a dynamic signal to chromatin using optogenetics. By expanding theCRY2/CIB1 system by changing the chromatin state, using a library of nearly 200 CRs, we will be able to study the effect chromatin has on signal processing and gene expression dynamics.

References:

1. A. Rademacher, F. Erdel, J. Trojanowski, S. Schumacher, K. Rippe, Real-time observation of light-controlled transcription in living cells. Journal of Cell Science 130, 4213-4224 (2017).

Background: Combination chemotherapy is currently the most widely utilized treatment strategy for cancer, owing to its distinct advantages over traditional single drug therapy [1]. By utilizing specific combination chemotherapeutic regimens, a synergistic treatment outcome can be achieved. Recent work suggests that the optimization of the molar ratio of the drug cohorts and the schedule, or sequence that the drugs are administered, are essential in maximizing synergistic treatment efficacy. To this end, researchers have designed drug delivery platforms that embrace this paradigm, using an array of carriers including nanoparticles, liposomes, polymer-drug conjugates, and hydrogels. Of these, hydrogels possess distinct advantages such as allowing local administration, thus maintaining a high drug concentration, and a flexible molecular architecture that affords tunable control of payload pharmacokinetics [2].

Results: In this work, two hydrogel-based drug delivery systems to deliver the combination regimen of doxorubicin (DOX) and gemcitabine (GEM), to treat triple negative breast cancer were developed. In the first study, a co-loaded, physical hydrogel comprising hydrophobically modified chitosan was prepared. Molecular dynamics simulations were performed to understand the molecular-level phenomena governing DOX transport through the network. The hydrophobic moieties provided selective control over DOX pharmacokinetics through a complex interplay between molecular level interactions and network morphology as evidenced in both simulations and experimentally. Further, the molecular dynamics simulations provide a pseudo-quantitative predictive capacity for DOX diffusion through the experimentally validated chitosan hydrogels. Building on the first study, the second study comprises a graphene oxide (GO)-peptide composite hydrogel to control release of DOX and GEM. A library of modifications on GO to tune DOX adsorption and desorption was initially employed. Again, molecular dynamics was employed to understand the molecular level interactions contributing to DOX adsorption/desorption and quantitatively captured DOX adsorption onto modified GO particles. The composite hydrogel was evaluated in vitro and confirmed the composite system can release the drug pair in a scheduled manner, resulting in improved drug synergism relative to concurrent regimen administration.

Conclusions: The studies presented represent two hydrogel-based systems embracing the current paradigm in drug delivery of scheduled and synergistic release that have demonstrated a synergistic therapeutic outcome. Combining drug delivery system design with in silico modeling can provide a powerful tool for molecular level understanding and a predictive capacity for design.

References:

1. K. Goto et al., (2016). The Lancet Oncology, 17, 1147.
2. K. Park, (2016). J. Controlled Release, 240, 2.

Background: Human neurodevelopment and its associated diseases are complex and challenging to study. In particular, prenatal neurodevelopmental periods are hard to access experimentally, especially in humans. The role of UBE3A in Angelman Syndrome and Autism Spectrum Disorder is an archetype for these challenges [1,2]. It is paternally imprinted in parts of the mouse brain, exhibits complex subcellular localization, and is suspected to dynamically establish these patterns in gestation [3,4].

Results: In this work, human cerebral organoids reveal that important spatiotemporal dynamics of UBE3A occur very early in human neurodevelopment. In particular, UBE3A localizes to the nucleus of neurons within a few weeks of organoid culture, with a stark transition established between EOMES and TBR1 cortical layers; these localization patterns are disrupted, and in some cases reversed, in Angelman Syndrome hiPSC-derived organoids. Organoids also exhibit early imprinting of paternal UBE3A within 6 weeks of culture, with topoisomerase inhibitors partially rescuing UBE3A levels in Angelman Syndrome organoids. One inhibitor also exhibits over two weeks of persistent rescue after just a single treatment.

Conclusions: This work establishes human cerebral organoids as an important model for studying UBE3A biology and motivates their broader use in understanding complex neurodevelopmental disorders.

References:

1. Lopez, S. J., Segal, D. J. & LaSalle, J. M. UBE3A: An E3 Ubiquitin Ligase with Genome-Wide Impact in Neurodevelopmental Disease. Frontiers in Molecular Neuroscience 11, 476, doi:10.3389/fnmol.2018.00476 (2019).
2. Vatsa, N. & Jana, N. R. UBE3A and Its Link with Autism. Front Mol Neurosci 11, 448,
   doi:10.3389/fnmol.2018.00448 (2018).
3. Burette, A. C. et al. Subcellular organization of UBE3A in neurons. Journal of Comparative Neurology 525, 233-251, doi:10.1002/cne.24063 (2017).
4. Judson, M. C., Sosa-Pagan, J. O., Del Cid, W. A., Han, J. E. & Philpot, B. D. Allelic specificity of Ube3a expression in the mouse brain during postnatal development. J Comp Neurol 522, 1874-1896, doi:10.1002/cne.23507 (2014).

Background: Several genes and pathways have been identified to play a role in longevity through study of the nematode C. elegans. Previous work has also identified phenotypic characteristics that are associated with a change in lifespan. One such phenotype is the formation of protein aggregates in aged C. elegans. Mutant worms with an increased lifespan have displayed a delayed increase in protein aggregation [1]. Forward genetic screens are one approach to identify mutations that yield a phenotype of interest, and thus helps discover genes at play, but are made difficult by the need to recover the progeny of each identified mutant. Our objective is to use protein aggregation as a tool for identifying C. elegans lifespan mutants using forward genetic screens.

Results: We developed a high-throughput, automated screening protocol for identifying aging mutants by measuring the aggregation of PAB-1 expressed in the C. elegans pharynx [1]. Unlike other proteins such as PolyQ, PAB-1 aggregates naturally in C. elegans. Moreover, increased aggregation of PAB-1 after egg-laying makes it a strong phenotype to study early onset of aging at the late reproductive stage. We utilized a microfluidic platform previously developed for C. elegans imaging and phenotypic sorting [2] and developed an automated screening program to identify animals with increased PAB-1 aggregation. The screen can be performed with minimal human intervention, and hundreds of worms can be screened over a period of hours. We conducted a high-throughput forward genetic screen for candidate mutants with high levels of PAB-1 aggregation in the pharynx at the end of their egg-laying period, taking advantage of a microfluidic platform that enables culturing animal age-synchronized populations [3]. We then further characterized the aggregation levels of candidate mutants and identified strains which displayed an increase in protein aggregation. From the verified aggregation mutants, we have identified multiple mutants with a reduced lifespan.

Conclusions: Using this screening method, we have achieved our goal of identifying aging mutants by screening for phenotypes in the late reproductive stage. The approach did not require screening populations of isogenic worms, as previously done with temperature-sensitive reproductive lines [4]. Moreover, EMS mutagenesis can produce a variety of alleles, unlike the partial knockdown induced by RNAi bacteria. Through this work, we aim to expand the capability of forward genetic screening methods to identify genes that regulate the natural aging process.

References:

1. Lechler, M. C., E. D. Crawford, N. Groh, K. Widmaier, R. Jung, J. Kirstein, J. C. Trinidad, A. L. Burlingame, and D. C. David (2017). Reduced Insulin/IGF-1 Signaling Restores the Dynamic Properties of Key Stress Granule Proteins during Aging. Cell Rep., 18: 454-467
2. San-Miguel, A., P. T. Kurshan, M. M. Crane, Y. Zhao, P. T. McGrath, K. Shen, and H. Lu (2016). Deep phenotyping unveils hidden traits and genetic relations in subtle mutants. Nature Comm., 7: 12990
3. Saberi-Bosari, S., J. Huayta, and A. San-Miguel. A microfluidic platform for lifelong high resolution and high throughput imaging of subtle aging phenotypes in C. elegans. Lab Chip, 18: 3090-3100.
4. Klass, M.R (1983). A method for the isolation of longevity mutants in the nematode Caenorhabditis elegans and initial results. Mech. Ageing. Dev., 22: 279-286

Background: Biological tissues are complex composite materials whose mechanical properties are often difficult to measure by traditional techniques. Quantification of bulk tissue properties, such as modulus and viscoelasticity, can be used to aid in disease diagnosis and design of novel therapies. We demonstrate the ability to measure multiple types of mammalian tissues, with elastic moduli ranging from 100-10,000 Pa, by dynamic oscillatory rheology on a commercially-available rheometer. We then present results from two case studies involving tumor digestion by injected collagenase enzymes and illustrate how rheology can be used to quantify treatment efficacy. In the first, we quantified the degree of in-vivo digestion of human uterine fibroid tissue (benign tumors) by a single injection of collagenase Clostridium histolyticum. In the second, we measured digestion of xenograft human breast cancer (malignant) tumors grown in mice by repeat injections of liberase (blend of collagenase isoforms.) In both studies, we co-injected Liquogel (LQG) [1], a thermoresponsive polymer that transitions upon heating from an injectable solution to a gel, to reduce diffusion of collagenase from the injection site.

Results: All tissues exhibited gel-like rheological behavior. We calculated average tissue moduli and viscoelasticity (tan δ) for all tissues. Data collected from reduction mammoplasty human breast tissues isolated from multiple individuals demonstrates that rheology can quantify tissue variability. Repeated freeze-thaw studies reveal the effect of sample history and highlight the need for consistent protocols for handling biological samples. We observed that injections of LQG & collagenase significantly reduced the modulus and increased the viscoelasticity of uterine fibroids compared to both buffer controls and free collagenase injections. The impact of collagenase injections on breast cancer tumors was less intuitive; in some instances, co-injection of LQG & collagenase led to the formation of smaller and stiffer tumors. We hypothesize this observation is due to collagenase softening the local microenvironment and discouraging outward tumor growth.

Conclusions: Dynamic rheology is a useful tool for characterizing the bulk modulus of biological tissues and for quantifying the effects of tumor digestion by collagenases. In-vivo tumor imaging and histological staining of parallel tissue samples complement rheological measurements to provide a more complete understanding of treatment effects on tumors.

References:

1. Jayes, F. L. et al. (2016). Loss of stiffness in collagen-rich uterine fibroids after digestion with purified collagenase Clostridium histolyticum. Am. J. Obstet. Gynecol., 215: 596.e1-596.e8.

Background: Light olefins such as ethylene and propylene are important chemical building blocks produced primarily via steam cracking of naphtha and light alkanes; however, commercial cracking processes suffer from high energy consumption and significant CO₂ intensity (up to 2 tons CO₂/ton C₂H₄). This is largely due to the endothermic cracking reactions, equilibrium-limited single-pass conversion, and complex product separations.[1] While oxidative cracking of naphtha using co-fed O₂ represents a potentially advantageous approach,[2] the need to co-feed gaseous oxygen introduces safety concerns and leads to significant COx formation. We propose a redox oxidative cracking (ROC) approach as an alternative scheme to intensify the production of light olefins from naphtha.[3]

Results: Here, we report Na2WO4-promoted perovskite oxides, e.g. CaMnO₃, as effective redox catalysts for ROC of naphtha. A 20 wt.% Na₂WO₄/CaMnO₃ redox catalyst demonstrated 64% and 58% olefin yields from n-hexane and cyclohexane feeds (representing naphtha), respectively, at T = 750°C and GHSV = 4500–5400 h^-1, representing absolute single-pass olefin yield increases of 12% and 40% over thermal cracking of each compound at identical conditions. COx yield as low as 1.7% was achieved along with >80% H₂ combustion over 25 redox cycles. Multiple characterizations including TEM-EDS and LEIS show the existence of a Na₂WO₄ surface layer and a Na- and W-enriched shell around the CaMnO₃ core. Moreover, in-situ XRD and TGA-DSC indicate that the Na₂WO₄ surface layer forms a molten shell covering the CaMnO₃ core under the working state of the redox catalyst. Na₂WO₄ played a key bifunctional role as (i) a catalytically active surface layer for hexane conversion and (ii) an O^2-/e^–conductor facilitating in-situ combustion of H₂ by CaMnO₃ lattice oxygen at the gas-molten shell interface.

Conclusions: Core-shell structured Na₂WO₄/CaMnO₃ was a highly effective redox catalyst for enhanced olefin production via naphtha ROC, evaluated here by using n-hexane and cyclohexane constituents. Over three-fold increase in olefin yield was achieved in the presence of the redox catalyst compared to thermal cracking. The redox reaction pathway, phase transition behavior of the perovskite oxides, and the role of Na₂WO₄ promoter were characterized in detail, providing important mechanistic insights for further optimization. Aspen Plus simulation of naphtha ROC demonstrated 52% energy savings and 50% reduction in CO₂ emissions on a per-ton ethylene basis compared to naphtha steam cracking.[4]

References:

1. Ren, T., Patel, M., and Blok, K. Energy. 31, 425 (2006).
2. Boyadjian, C., Lefferts, L., Seshan, K. Appl. Catal. A. Gen. 372 (2), 167 (2010).
3. Dudek, R.B., et al. Appl. Catal. B. Env. 246, 30 (2019).
4. Haribal, V.P., Chen, Y., Neal, L.M., Li, F. Engineering. 4 (5), 714 (2018).

Background: Metal catalyzed cross-coupling reactions are an integral part of the modern organic chemist’s synthetic toolbox with a wide scope of highly selective robust reactions with wide-scale applications in pharmaceutical and fine chemical manufacturing [1]. Cross-coupling reactions are commonly performed using either homogeneous or surface-bound heterogenous catalysts, each with various processing drawbacks. In homogeneous reactions the catalysts and ligands are commonly highly oxygen sensitive and must be separated from the product after the reaction. Heterogeneous catalysts are generally less active and the catalytic surface modifications can be less stable resulting in leaching and a loss of catalyst activity over time. Polymer-based catalysts are being developed to mitigate many of these issues. The polymer network offers the functionality for trapping and immobilizing the catalytic sites while still offering high transport rates and enabling volume loading of catalyst vs. a pure surface functionalization as on a rigid impermeable support like silica.

Results: One promising material is a palladium-loaded cross-linked poly hydromethylsiloxane (PHMS) network [2]. The catalyst material is formed by cross-linking the PHMS chains with multi-functional vinyl species to form a network that combines properties from both the PHMS backbones and the cross-linker. The Si-H functionality on the backbone serves as both a site for cross-linking as well as a reducing agent to convert the palladium acetate salt into its active Pd0 form. The Pd remains as an active catalyst for cross-coupling reactions even in the absence of conventional ligands. The reaction mixture is a representative cross-coupling of aryl halide and aryl boronic acid under basic conditions in a green solvent mixture of ethanol and water. Our previous work [3] focused on taking this bulk material and extending its application to use in packed bed reactors in addition to the previously reported batch methods. The cross-linker species was used as a handle to tune the yield and selectivity of the reaction by maximizing the affinity of the reagents and solvent to the catalytic material. Improving the affinity of the network for the reaction mixture improves the transport properties through the polymer network and improves access to the catalytic sites present in the bulk of the material.

Conclusions: The ability to tune a heterogeneous catalyst support material to improve reaction selectivity and yield with minimal separation requirements has promising impact on chemical manufacturing in fine chemical and pharmaceutical applications.

References:

1. Ruiz-Castillo, P., Buchwald, S.L., Applications of palladium-catalyzed C-N cross-coupling reactions. Chem Rev., 2016; 116(19):12564-12649.
2. Stibingerova, I., Voltrova, S., Kocova, S., Lindale, M., Srogl, J.. Modular approach to heterogeneous catalysis. Manipulation of cross-coupling catalyst activity. Org Lett., 2016; 18(2):312-315
3. Bennett, J. A., Kristof, A. J., Vasudevan, V., Genzer, J., Srogl, J., Abolhasani, M. Microfluidic synthesis of elastomeric microparticles: A case study in catalysis of palladium-mediated cross-coupling. AIChE Journal., 2018; 64(8):3188-3197

Background: High-pressure phenomena have been observed in many studies of adsorbed films on strongly wetting solid substrates. These include chemical reactions that normally require a high pressure (e.g. 10,000 bar or more), the formation of high-pressure solid phases and spectra indicating strong compression of the film. These recent results suggest that it should be possible to design nano-reactors to synthesize chemicals and materials that require pressures much greater than those that can be used in conventional manufacturing processes [1]. While it is possible to measure the pressure acting normal to the substrate surface, P_N, no method has been developed so far to measure the tangential pressure, P_T, parallel to the surface. However, this tangential pressure is of particular interest, since it is usually much larger than the normal pressure, and is the main driving force for high-pressure phenomena in adsorbed films. In the commonly used ‘virial route’ the average of the intermolecular forces acting in the direction parallel to the surface is obtained. The resulting local tangential pressure then depends on the fraction of these forces that are assigned to a particular point in space, r. Thus, the local tangential pressure is not a uniquely defined quantity.

Results: We show that by integrating P_T(r) over a small region of space, roughly the range of the intermolecular forces, we obtain an effective tangential pressure that is unique and free from the ambiguities in the definition of the ‘virial-route’ local tangential pressure [2]. The grand canonical Monte Carlo simulation results show that this characteristic integration range is independent of the wetting parameter which measures the strength of the solid-fluid interaction. For porous materials having slit-shaped pores this characteristic length is also independent of the pore width for large pores. Based on this characteristic length, we proposed a new route, the ‘2D-route’, to the effective tangential pressure [3]. The input parameters for this ‘2D-route’ are thickness and in-plane density of the adsorbed layer, and the system temperature.

Conclusions: We defined a unique effective tangential pressure to characterize high-pressure phenomena observed in adsorbed films near the substrate surface. We also developed a new ‘2D-route’ to the effective tangential pressure, based on statistical mechanics. We expect this ‘2D-route’ to provide the first experimental route to measure the pressure enhancement in adsorbed films.

References:

1. K.E. Gubbins, K. Gu, L. Huang, Y. Long, J.M. Mansell, E.E. Santiso, K. Shi, M. Śliwińska Bartkowiak, D. Srivastava (2018), “Surface-Driven High-Pressure Processing”, Engineering. 4: 311–320.
2. K. Shi, E.E. Santiso, K.E. Gubbins (2019), “Can we define a unique microscopic pressure?”, to be submitted
3. K. Shi, K. Gu, Y. Shen, D. Srivastava, E.E. Santiso, K.E. Gubbins (2018), “High-density equation of state for a two-dimensional Lennard-Jones solid”, J. Chem. Phys. 148: 174505.

Background: Lubricated friction on textured surfaces ubiquitously exist in natural world. Studies on textured tribopairs demonstrate different tribological behavior comparing with smooth ones. However, the basic mechanism of this distinction has not yet been covered. While emerging applications have sought design principles from biology, a general framework is lacking because soft interfaces experience a multiphysics coupling between solid deformation and fluid dissipation.

Results: In this study, we investigate >50 micro-patterned surfaces comprising elastomers, thermosets, and hydrogels, and discover that texturing induces a critical transition in the macroscopic friction coefficient.

Conclusions: This critical friction scales universally, without any fitting parameters, with the reduced elastic modulus and the pattern geometry. To capture the frictional dissipation, we separate the flow curve into two regimes and account for the contributions of shear and normal forces applied by the fluid on the patterns. Our model combines Reynolds’ equations and elastic deformation to provide physical insights that allow engineering of the elastohydrodynamic friction in a class of soft tribopairs using pattern geometry, material elasticity, and fluid properties.

Background: Our group has introduced a class of environmentally benign nanoparticles (EbNPs) for biotech applications [1]. These nanoparticles are made of biodegradable lignin and have low potential for nano-toxic impact. The lignin core nanoparticles are synthesized through flash nanoprecipitation, but until recently they were produced in mL-scale batches. EbNPs are functionalized for a variety of biotech application. EbNPs that serve as antimicrobials are created by infusing silver ions into the lignin core and are coated with a polyelectrolyte layer, enabling them to stick to bacteria. This formulation has the potential to decrease use of silver in consumer products and thus limits its eventual release into environment.

Results: We have developed a semi-continuous system featuring a recycle loop, making it possible to produce such nanoparticles in practical quantities for industrial applications [2]. We investigate the role of each variable in our process to determine how to control the size of our EbNPs and the final concentration of the EbNP suspensions. By changing the concentration of lignin in solvent, we are able to efficiently control the final size of synthesized nanoparticles. Then, by altering the anti-solvent volume, we control the final NP concentration of the dispersion. We discuss a few applications of our EbNPs, including their role as highly efficient antimicrobials and antifungals. We also investigate the application of the EbNPs on other biological surfaces, such as rose petals and human hair. We modify the lignin nanoparticles with a cationic biopolymer coating, chitosan, to inverse their surface charge and improve adherence to various surfaces.

Conclusions: With our semi-continuous system, we are now able to make liters of concentrated nanoparticle suspensions at a time. The nanoparticles can be functionalized with active ingredients as needed for different applications.

References:

1. Richter, Alex P., Joseph S. Brown, Bhuvnesh B. Bharti, Amy Wang, Sumit Gangwal, Keith Houck, Elaine A. Cohen Hubal, Vesselin N. Paunov, Simeon D. Stoyanov, and Orlin D. Velev (2015). An Environmentally Benign Antimicrobial Nanoparticle Based on a Silver-Infused Lignin Core. Nat. Nanotechnol., 10 (9): 817–823.
2. Conner, Cathryn G., Anka Veleva, Vesselin N. Paunov, Simeon Stoyanov, Orlin D. Velev (TBD). Scalable formation of concentrated monodisperse lignin nanoparticles by recirculation-enhanced flash nanoprecipitation. Small, to be submitted.

Background: In the development of next-generation photovoltaics and light emitting diodes, colloidal inorganic perovskite quantum dots (PQDs) have drawn notable attention for their highly tunable bandgap properties, high-charge carrier mobility and defect tolerance, and adaptability towards solution phase processing. However, studies of this material group and other colloidal semiconductor nanocrystals requires extensive exploration of their massive reaction parameter space within highly controlled reaction environments. Conventional flask-based, trial-and-error approaches are, therefore, highly unlikely to effectively capture the full potential and optimal synthesis conditions of these high-priority materials. Further complicating this process, across the accessible bandgap range, optimal synthesis parameters will vary significantly. Flow synthesis platforms have recently been demonstrated as a time- and material-efficient reaction monitoring strategy for synthesis, screening, and optimization of colloidal nanomaterials. The high sampling rate, low chemical consumption, and precise process control (automation) of flow reactors greatly reduces the challenges in exploring complex reaction spaces; however, high-throughput reaction screening technologies alone are likely not able to make significant breakthroughs, due to the massive scope of relevant colloidal synthesis conditions.

Results: In this work, we present a modular microfluidic platform integrated with a machine learning (ML)-enhanced reaction optimization algorithm for on-demand synthesis of high-quality inorganic perovskite QDs with desired optical properties. The intelligent QD synthesis platform consists of multiple computer-controlled pumps for on-demand reagent delivery/dosing, and an in-line flow cell for automatic UV-Vis absorption and photoluminescence spectroscopy. With this strategy, we have autonomously optimized reactant compositions for the simultaneous improvement of photoluminescence quantum yield (PLQY) and emission full-width at half-maximum (FWHM) at any desired peak emission energy (PE) – i.e. emission color. These optimizations are performed without any prior experimental information, and they reach desirable PLQY, FWHM, and PE values substantially faster than existing black box optimization techniques– in less than 25 samples. We then apply this same technique but instead pre-train the neural network models with prior experimental data before conducting the adaptive sampling procedure. As a result, we have further pushed the optimal measured values for nine of eleven target PE set points, in spite of performing the synthesis with a completely separate batch of precursors.

Conclusions: These techniques not only enable unsupervised material optimization and discovery, but they offer more consistent manufacturing of highly sensitive reactions. Further application of this strategy will advance the quality of commercial nanocrystals and expedite reaction studies, thereby leaving more time and resources available for creative material synthesis exploration.

Background: Traumatic brain injury (TBI) is a universal problem that can affect human health and lead to severe long-term disabilities. Recent studies have shown that suffering TBI may increase the chance of developing neurodegenerative diseases, such as Alzheimer’s disease (AD)[1]. As the urgency increases for a better understanding on how TBI might lead to the development of AD, tools and strategies using model organisms to study this occurrence are deeply needed. For this reason, this work aims to develop and implement a microfluidic platform for controlled neuronal injury to study neuronal degeneration and dysfunction using C. elegans AD models. C. elegans offers many excellent advantages as an in vivo model for the study of TBI and its relationship to AD. This platform integrates microfluidic devices with pressure and fluid control hardware, as well as high-resolution imaging and quantitative image analysis.

Results: Using PDMS-deflectable valves as injury features in our microfluidic device, we performed controlled head injury in the animals. Several conditions, such as culture temperature and injury frequency, were tested and compared, while keeping the animal age the same across all experiments. After insult, the main sign of neurodegeneration observed was the formation of beads along the dendrite of the AWC neurons. These results confirm that the current microfluidic device design is able to induce significant injury as assessed by neuronal morphological changes. We performed quantitative analysis of fluorescent images of the AWC neurons using MATLAB in order to identify morphological features indicative of neurodegeneration. To assess neurodegeneration progression, a second microfluidic device was designed to transfer the animals after the injury was inflicted. This microfluidic device includes 12 chambers were the animals can freely move and a tapered channel for immobilization for high-resolution imaging. The implementation of both devices will allow for a streamlined and effective way of further characterizing the neuronal morphological changes any time between one minute and up to 24 hours after injury.

Conclusions: A microfluidic platform was successfully fabricated for the purpose of neuronal injury and the characterization of morphological changes after injury. This platform includes two different microfluidic devices to be used in series. The first one allows to effectively perform controlled and localized head neuronal injury on a C. elegans age synchronized population. The second device will be used for day-long culture of the animals for further studies on how neurodegeneration changes as time passes. By incorporating a C. elegans AD model, with controlled injury and microfluidic platforms, this work will enable future studies of traumatic neuronal injury and neurodegeneration.

References:

1. S. M. Gentleman et al., “Long-term intracerebral inflammatory response after traumatic brain injury,” Forensic Sci. Int., vol. 146, no. 2–3, pp. 97–104, 2004.

Background: Genome editing has become an essential capability in bacteria to probe important phenotypes, study microbe-host interactions, and enhance beneficial properties. Currently, the most effective means of genome editing in bacteria combines low-efficiency recombineering with high-efficiency counter selection by nucleases from CRISPR-Cas systems, where the Cas9 nuclease from Streptococcus pyogenes (SpCas9) has been the most studied and utilized Cas nuclease. However, accumulating examples have reported cytotoxicity of expressing Cas9 in some bacteria for reasons that are poorly understood, limiting its use for genome editing^1-3

Results: Here, we report a distinct example in which co-expressing SpCas9 and its trans-activating CRISPR RNA (tracrRNA) is heavily cytotoxic in an industrial strain of the bacterium Lactobacillus paracasei. We found that transforming a plasmid containing SpCas9 and a tracrRNA resulted in very few colonies in this strain compared to transforming a plasmid containing SpCas9 or the tracrRNA alone. Furthermore, co-expressing a non-targeting crRNA significantly reduced cytotoxicity. Interestingly, DNA cleavage and DNA binding do not appear to be an important part of observed cytotoxicity. Systematic mutations to different portions of the tracrRNA revealed likely roles of RNA binding in a crRNA dependent matter.

Conclusions: We are currently investigating cytotoxicity by performing co immunoprecipitation and RNA-Seq to identify which endogenous RNAs are bound and potentially cleaved by Cas9. The results of this work are expected to help elucidate one mode of SpCas9 cytotoxicity in bacteria and, in turn, help others improve genome editing across Lactobacilli and other industrially relevant bacteria.

References:

1. Jiang Y, Qian F, Yang J, et al (2017) CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum. Nat Commun 8:15179
2. Cho S, Choe D, Lee E, et al (2018) High-level dCas9 expression induces abnormal cell morphology in Escherichia coli. ACS Synth Biol 7:1085–1094
3. Song X, Huang H, Xiong Z, et al (2017) CRISPR-Cas9 nickase-assisted genome editing in Lactobacillus casei. Appl Environ Microbiol 83:e01259–17

Background: Directed evolution enables biological function to be engineered in the absence of detailed biochemical models, and often suggests novel or counterintuitive routes to improved function. Recent advances in methods for directed evolution have overcome the traditionally laborious and costly steps for generating error-prone libraries, which include molecular cloning and transformation. However, all methods for directed evolution developed to date are limited either to small regions of DNA (<10kb) or allow the accumulation of off-target genomic mutations.

Results: Here, we present Autonomous Inducible Directed Evolution (AIDE) to overcome these limitations. AIDE combines P1 bacteriophage’s ability to package plasmids up to 90kb in size and transfer them efficiently to new Escherichia coli cells. Cells containing inducible mutation machinery (e.g. a re-engineered Mutagenesis Plasmid MP6 [1] (ISA265)) enable facile mutagenesis of the entire 90kb plasmid, of which ~85kb can consist of user-defined DNA. Mutated plasmids can then be transferred to new cells via P1 packaging to assay for improved phenotypes. AIDE relies on P1’s ability to switch between lysogenic to lytic cycles (e.g. via addition of the inducer arabinose), and the ability to turn on mutagenesis (e.g. via addition of the inducer anhydrotetracycline). P1’s ability to package phagemids is used to transfer plasmids from mutated cells to a wild-type strain, thus eliminating off-target genomic mutations.

Conclusions: Autonomous Inducible Directed Evolution is an addition to the directed evolution toolkit, which overcomes some of the challenges other methods do not address. These limitations primarily include the ability to evolve large (<85kb) DNA segments and avoiding the accumulation of off-target genomic mutations.

References:

1. Badran, A. H. & Liu, D. R. Development of potent in vivo mutagenesis plasmids with broad mutational spectra. Nat. Commun. 6, 8425 (2015).

Background: Current DNA-based information storage systems largely rely on polymerase chain reaction (PCR), which broadly informs how information is encoded, databases are organized, and files are accessed1-3. However, PCR presents three challenges that may preclude its broader use as a platform technology. First, information access through PCR amplification and enrichment of specific DNA strands could either destroy the entire database or significantly alter its compositions. Second, since dsDNA templates are melted in each PCR cycle, undesired off- target products could be generated due to the non-specific primer binding and amplification within data payloads. This requires encodings that sacrifice information density to avoid conflicting DNA sequences appearing in DNA strands3. Finally, as a method that actively creates new DNA strands, it is unclear whether PCR could facilitate in-storage file manipulations without altering the composition and strands balance of a database.

Results: This set of challenges could be overcome by using a hybrid file structure that included a single-stranded DNA (ssDNA) ‘toeholds’ and double-stranded (dsDNA) payload, and by the way organisms naturally access information from their genome through transcription. With the help of the toehold, we demonstrate that DNA strands that contain information of interest can be separated at room temperature (25 ̊C), accessed non-destructively through natural transcription driven by a modified T7 promoter sequence, and returned to the file database for recovery using functionalized magnetic beads4. In addition, since the accesses are without melting the file templates, non-specific amplification and off-target products are eliminated. This promotes the optimization of encodings, thereby improving oligo availability and information density of the system by orders of magnitude. Furthermore, we demonstrate that the toeholds of specific file strands can bind other appropriate designed oligos, thus providing in-storage file manipulation including file locking, renaming and deletion.

Conclusions: The DNA-based information storage system has captured enormous attention recently. Using the hybrid file structure has been shown to increase the theoretical information density and capacity of DNA storage by inhibiting non-specific binding within data payloads, enable transcription-based, non-destructive information access, and make possible in-storage file operations. This work demonstrates dynamic information access and manipulations are practical for DNA-based information storage systems.

References:

1. Organick, L. et al. Random access in large-scale DNA data storage. Nat. Biotechnol. 36, 242–248 (2018).
2. Tabatabaei Yazdi, S. M. H., Yuan, Y., Ma, J., Zhao, H. & Milenkovic, O. A Rewritable, Random Access DNA-Based Storage System. Sci. Rep. 5, 1–10 (2015).
3. Bornholt, J. et al. A DNA-Based Archival Storage System. ASPLOS ’16 337, 637–649 (ACM Press, 2016).
4. Bosnes, M. et al. Solid-phase in vitro Transcription and mRNA Purification using Dynabeads^TM Superparamagnetic Beads. 5th Int. mRNA Heal. Conf. (2017). doi:10.13140/RG.2.2.11334.16962

Background: The mesolimbic pathway, the connection between dopaminergic neurons in the VTA and medium spiny neurons in the striatum, remains important to study because it is affected by drugs of abuse[1]. Most research is currently performed on model organisms especially mice and rats. While this work has provided a good foundation, there remains a need for a new model system that can accurately capture dynamic changes at the molecular and cellular levels in a human cell system.

Results: Recent work has shown that embryonic stem cells grown in vitro can be differentiated into cell fate specific neurons that display similar characteristics as those seen in vivo[2]. Using similar techniques, a protocol for generating cerebral organoids, neurons differentiated from stem cells aggregated in 3D, containing dopaminergic or medium spiny neurons has been developed. The neurons in these two organoids can be tested for functionality and compared with in vivo neurons to confirm their identify. The organoids can then be fused together leading to synaptic connections between the dopaminergic neurons and medium spiny neurons. Once established, these organoid fusions can be used as an accurate model system for the human mesolimbic pathway which can be combined with recent advances in optogenetics and genome editing allowing us to study how this system responds to drugs of abuse.

Conclusions: An ex vivo> model of the human mesolimbic pathway has been derived from human embryonic stem cells. This system can be used to study how cocaine and other drugs of abuse affect these neurons on short and long-time scales.

References:

1. E. J. Nestler, “Molecular basis of long-term plasticity underlying addiction,” Nat. Rev. Neurosci., vol. 2, no. 2, pp. 119–128, 2001.
2. S. M. Chambers, C. A. Fasano, E. P. Papapetrou, M. Tomishima, M. Sadelain, and L. Studer, “Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling,” Nat. Biotechnol., vol. 27, no. 3, pp. 275–280, Mar. 2009.

Background: The order Sulfolobales is comprised of thermoacidophilic archaea (T_opt > 65°C, pH_opt < 3.5) [1], many of whom survive these harsh conditions through chemolithoautotrophy, or the fixation of CO2 by reduction or oxidation of metals and reduced inorganic sulfur compounds (RISCs) [1]. These organisms are industrially relevant to processes such as biomining, and their resiliency in extreme environments offers great potential as a biotechnology platform [2]. In particular, Sulfolobus acidocaldarius has a tractable genetic system, enabling metabolic engineering for the biosynthesis of industrial chemicals [3]. However, S. acidocaldarius is not currently capable of chemolithoautotrophic growth and must be engineered in order to fix CO₂ by oxidation of RISCs. Understanding sulfur oxidation in an acidic environment involves many species of sulfur interacting through both abiotic and enzymatic reactions [4]. Members of the Sulfolobales oxidize RISCs with varying effectiveness and exhibit substrate preferences. Comparative genomics of sequenced Sulfolobales provided insight into enzymes implicated in the sulfur oxidation process. Select enzymes from this analysis were introduced to S. acidocaldarius and enabled the organism to oxidize elemental sulfur [5].

Results: Select Sulfolobales are compared for differences in utilizing sulfur substrates through growth curves and rates of dissolved oxygen consumption. Bioinformatics approaches are employed to compare variations in the genomes of Sulfolobales based on their ability to oxidize different sulfur substrates. Two enzymes implicated in sulfur oxidation by this analysis were heterologously expressed in S. acidocaldarius, and the mutant strain exhibits the ability to oxidize elemental sulfur. Abiotic reactions of sulfur species relevant to the high temperature, low pH environment of thermoacidophiles were identified through thermodynamic free energy calculations.

Conclusions: The degree to which members of the Sulfolobales oxidize RISCs for energy can be linked to a core sulfur genome. Using the genetic tools available for S. acidocaldarius, sulfur oxidation can be enabled by introducing a set of enzymes within this core sulfur genome. Linking these enzymatic reactions to abiotic reactions of sulfur species, a mechanism for sulfur oxidation in the Sulfolobales is proposed.

References:

1. Wheaton, G. H., et al. (2015). The confluence of heavy metal biooxidation and heavy metal resistance: implications for bioleaching by extreme thermoacidophiles. Minerals-Basel 5: 397-451.
2. Auernik, K. S., et al. (2008). Life in hot acid: Pathway analyses in extremely thermoacidophilic archaea. Current Opinion in Biotechnology 19(5): 445-453.
3. Wagner, M., et al. (2012). Versatile genetic tool box for the Crenarchaeote Sulfolobus acidocaldarius. Front. Microbiol. 3: e214.
4. Suzuki, I. (1999). Oxidation of inorganic sulfur compounds: Chemical and enzymatic reactions. Canadian Journal of Microbiology 45(2): 97-105.
5. Zeldes, B. M., et al. (2019). Determinants of sulphur chemolithoautotrophy in the extremely thermoacidophilic Sulfolobales. Environmental Microbiology 21(10): 3696-3710.

Background: Chemical modifications, such as acetylations and methylations, decorate numerous residues of histone tails of human chromatin. These epigenetic marks influence proximal gene activity as well as the progression of many disease states [1]. Existing methods to perturb epigenetic landscapes use pharmacological or genetic manipulations that have pleiotropic effects, or use locus-targeted epigenome editors that lack control over the specific residues and modifications that are written. Thus, a tool to efficiently edit epigenetic states at specific genomic loci would shift our understanding of the relationship between epigenetics and gene regulation from correlative to causative [2]. Through my research, I aim to develop a robust platform that can rapidly measure the modifications made to histones by chromatin-modifying enzymes.

Results: Through my preliminary work with a human histone acetyltransferase, I have used the YESS [3] yeast surface display method to acetylate and display the N-terminal tails of histones.

Conclusions: This platform can be extended to other chromatin-editing enzymes to measure their natural residue specificities. The platform will be combined with random mutagenesis to evolve these editors to modify a specific single or combination of histone residue(s).

References:

1. Egger G., Liang G., Aparicio A., Jones A. Epigenetics in human disease and prospects for epigenetic therapy. Nature. 2004. Vol 429. pp457-463
2. Henikoff S., Shilatifard A. Histone modification: cause or cog? Trends in Genetics. 2011. Vol 27(10). Pp389-396
3. Yi L, Gebhard MC, Li Q, Taft JM, Georgiou G, Iverson BL. Engineering of TEV protease variants by yeast ER sequestration screening (YESS) of combinatorial libraries. Proc Natl Acad Sci. 2013. Vol 110(18). pp7229-7234

Background: Pregnancy disorders are typically the result of improper placentation and trophoblast differentiation. We aim to investigate key molecular mechanisms involved in placental development using human trophoblast stem cell models in order to better understand how pregnancy disorders arise in vivo. Previous work resulted in the discovery of two human trophoblast stem cell states, a more primitive, trophectoderm cell type (TEs) and a state that closer resembles cells from later stage-placental villi deemed villous cytotrophoblast cells (CTBs) [1,2]. CTBs could then further differentiate into the two terminal trophoblast subtypes, extravillous trophoblasts (EVTs) or syncytiotrophoblast (STB). Current CTB, EVT and STB media are chemically undefined, rendering investigation into molecular mechanisms difficult. Additionally, protocols used for EVT and STB differentiation are not representative of in vivo human development.

Results: We have proposed new CTB, EVT, and STB conditions that better represent in vivo cell environments and are fully defined. The CTB medium deemed TM5 has 5 major components that are necessary in maintaining the stem cell state. Additionally, the only variance between STB and EVT culture conditions is the addition of a basement extracellular matrix protein, laminin-111, in EVT differentiation. This signifies that the extracellular matrix acts as a switch in determining terminal trophoblast fate. This conclusion makes logical sense as EVTs are anchored in the maternal extracellular matrix while STB are free-floating, in contact with maternal blood.

Conclusions: This new media system allows for investigation into molecular mechanisms involved in CTB maintenance and differentiation to EVT and STB cell types. Additionally, this system may also be useful in reverting CTBs back to TEs which has implications in the ability to isolate trophoblast stem cells from term placenta and has never been accomplished.

References:

1. Mischler, A., Karakis, V., Mahinthakumar, J., Carberry, C., San Miguel, A., Rager, J., … & Rao, B. M. (2019). Two distinct trophectoderm lineage stem cells from human pluripotent stem cells. bioRxiv, 762542.
2. Okae, H., Toh, H., Sato, T., Hiura, H., Takahashi, S., Shirane, K., … & Arima, T. (2018). Derivation of human trophoblast stem cells. Cell stem cell, 22(1), 50-63.

Background: The genus Caldicellulosiruptor consists of extremely thermophilic, Gram-positive, fermentative anaerobic bacteria (T_opt > 70^oC), typically isolated from terrestrial thermal features. All species with available genome sequence information to date degrade hemicellulose, whereas only a subset degrade microcrystalline cellulose. Caldicellulosiruptor species physically associate with the substrate during growth on the plant biomass. One mechanism for this association is through multi-domain hemicellulases, which are anchored to the cell surface through S-layer homology (SLH) domains [1].

Results: Engineered strains of Caldicellulosiruptor bescii in which an SLH-domain hemicellulose from Caldicellulosiruptor kronotskyensis was inserted bound more tightly to certain xylans. These bacteria also deploy novel binding proteins, called tāpirins [2], which are encoded in proximity to the region of the genome referred to the Glucan Degradation Locus (GDL), which contains up to six multi-domain cellulases. Tāpirins specifically interact with microcrystalline cellulose to various extents [3]. For example, the tāpirin (Calkro_0844) from Caldicellulosiruptor kronotskyensis has a cellulose binding affinity comparable to family 3 carbohydrate binding modules (CBM3). The tāpirins from Caldicellulosiruptor hydrothermalis (Calhy_0908) and Caldicellulosiruptor kristjianssonii (Calkr_0826) bind to cellulose to a greater extent compared to other tāpirins, although these species are not prolific cellulose degraders. Furthermore, Caldicellulosiruptor bescii mutants lacking the tāpirin genes did not bind to the cellulose.

Conclusions: Discussed here are current efforts to engineer the surface of C. bescii to improve its capacity for biomass degradation. This includes inserting genes for non-native SLH-domain hemicellulases from other Caldicellulosiruptor species into the C. bescii genome. Furthermore, we are investigating the tāpirin cellulose binding mechanism through site-directed mutations in Calhy_0908, Calkr_0826, and Calkro_0844 in which cysteine residues are being inserted to strategically enable disulfide bridges within the protein to form. Our goal is to assess the significance of flexibility in hydrophobic binding pocket in the tāpirins as this relates to cellulose affinity.

References:

1. Conway, J.M.; et al (2016), Multidomain, surface layer-associated glycoside hydrolases contribute to plant polysaccharide degradation by Caldicellulosiruptor species. J of Biol Chem, 291(13): p. 6732-6747.
2. Blumer-Schuette, S.E.; et al (2015), Discrete and structurally unique proteins (tāpirins) mediate attachment of extremely thermophilic Caldicellulosiruptor species to cellulose. J of Biol Chem, 290(17): p. 10645-10656.
3. Lee, L.L.; et al (2019), Comparative Biochemical and Structural Analysis of Novel Cellulose Binding Proteins (Tāpirins) from Extremely Thermophilic Caldicellulosiruptor Species. J Appl Environ Microbiol, 85(3): p. 01983-18.

Background: Understanding microbial communities and the interactions between community members and their surroundings is a research field of growing interest [1]. Microbial communities that colonize plant roots are vital for plant growth and survival. A simplified, model microbiota for maize roots (ModCom) was recently identified and accelerates hypothesis testing in this community [2]. Interestingly, the complete ModCom achieves a stable level of colonization on maize roots, but when E. cloacae (Ecl) is removed C. pusillum (Cpu) dominates [2]. Ecl represents a “keystone” taxon that allows for community persistence. Through functional genomic screening methods, community persistence traits in Ecl’s genome can be identified.

Results: Of the seven member ModCom, O. pituitosum (Opi) was identified as the most efficient strain for transformation with an efficiency of 4.61*107 CFU/ug of DNA. Transformation was achieved by electroporation with a broad host range origin of replication plasmid (pBBR122). A functional genomic library from Ecl’s genome was created using a Covaris sonicator and fragments between 2-8 kb were extracted via Blue Pippin. The fragment pool was end repaired and will be transformed into Opi. Transformed Opi, with the rest of the ModCom minus Ecl, will be inoculated on Maize seedlings for inplanta selection of community persistence traits. Extracted DNA from inplanta selection experiments will be sequenced and assembled against Ecl’s genome using the annotation software PARFuMS[3].

Conclusions: Transformation of ModCom strains is dependent on endogenous restriction modification systems and methyltransferase expression. Persistence traits in Ecl were transformed into Opi and allowed for community survivability in planta. Future work will be to integrate specific operons and genes of the persistence genes into Opi and/or other community members to validate persistence traits of the identified genes.

References:

1. NIH Human Microbiome Portfolio Analysis Team. (2019) A Review of 10 Years of Human Microbiome Research Activities at the US National Institutes of Health, Fiscal Years 2007-2016. Microbiome, 7:31.
2. Niu, Ben, Joseph Nathaniel, Zheng, Xiaoqi, and Kolter, Roberto. (2017) Simplified and Representative Bacterial Community of Maize Roots. Proceedings of the National Academy of Sciences, 12: 2450-2459.
3. Crook, Nathan, et al. Adaptive Strategies of the Candidate Probiotic E. Coli Nissle in the Mammalian Gut. (2019) Cell Host & Microbe, 25: 499–51

Background: Next-generation probiotics offer unique attributes for the delivery of biomolecules to the gut [1]. By leveraging decades of work in metabolic engineering4, engineered probiotics have enabled the conversion of unused dietary material to beneficial products for the host. Furthermore, the ongoing development of biological sensing modalities advances the concept of drug synthesis tailored to the severity and location of disease within the host. Coupled with existing manufacturing expertise in food science and infrastructure in place for distributing probiotics, engineered probiotics promise to substantially reduce the costs associated with production of drug molecules.

Results: Saccharomyces boulardii is a widely used yeast probiotic which can counteract various gastrointestinal disorders[2]. As a relative of Saccharomyces cerevisiae, S. boulardii exhibits rapid growth and is easy to transform and thus represents a promising chassis for the engineered secretion of biomolecules. To establish S. boulardii as a platform for engineered delivery of biomolecules to the mammalian gut, we measured the amount and variance in protein expression enabled by a genetic part library consisting of promoters, terminators, selective markers, copy number control in S. boulardii. These genetic elements were characterized when encoded in plasmids and in various locations in the genome, revealing strategies for tunable control of gene expression and CRISPR-mediated genome editing in this strain. We then leveraged this set of genetic parts to combinatorially assemble pathways enabling a wide range of drug and vitamin titers. We next measured S. boulardii’s residence time in the gastrointestinal tracts of germ-free and antibiotic-treated mice, revealing the dosing strategies required to achieve long-term colonization. Finally, we demonstrated the synthesis of the vitamin β-carotene by engineered S. boulardii in the mouse gut, establishing genetic strategies that enable high levels of pathway activity in this in vivo context. This work thus establishes S. boulardii as a genetically tractable commensal fungus and provides a set of strategies for engineering S. boulardii to synthesize and deliver biomolecules during gut colonization.

Conclusions: Taken together, our results indicate that the decades of work developing S. cerevisiae as a platform for biomanufacturing and synthetic biology can be readily extended to S. boulardii. Coupled with the continued development of engineered commensal and probiotic bacteria, in situ biomanufacturing by gut-resident microbes has the potential to greatly reduce distributional complexity, improve site-specific delivery, and reduce production costs for a wide array of biomolecules.

References:

1. O’Toole, P. W., Marchesi, J. R. & Hill, C. Next-generation probiotics: the spectrum from probiotics to live biotherapeutics. Nat Microbiol 2, 17057 (2017).
2. Tiago, F. C. P. et al. Adhesion to the yeast cell surface as a mechanism for trapping pathogenic bacteria by Saccharomyces probiotics. J. Med. Microbiol. 61, 1194–1207 (2012).

Background: Microparticle filtration plays an important role in many medical and biological systems. However, most current technologies of microparticle filtration are limited by low-throughput or clogging [1]. Interestingly, the Manta Ray uses a non-clogging filtering mechanism to feed on 50 μm and greater zooplankton [2]. The Manta Ray’s mouth is lined with filter lobes creating small channels exiting the buccal cavity. Due to quick changes in fluid flow geometry, water and smaller particles are expelled through the channels, while larger particles follow their inertial path rather than the fluid path. Therefore, larger particles, which are smaller than the outlet channels, ricochet off the lobes, without passing through the filter lobe channels, effectively separating particles based on size [2]. However, most current applications of microparticle filtration, including blood cell and rare cell separation, require separation sizes under 50 μm. We intend to scale down this filtration mechanism to filter particles under 50 μm with precise control and high-throughput.

Results: Here we developed a microfluidic platform through standard photo and soft-lithography techniques to utilize the Manta Ray’s feeding mechanism to successfully filter 25 μm and larger fluorescent particles. ANSYS Fluent CFD simulations were used to help determine various device design choices prior to fabrication. To test device performance, combinations of 25 μm, 15 μm, 6 μm, and 2 μm fluorescent particles were pushed through the microfluidic device at various flow rates. Fluorescent images were taken of the device during operation, as well as representative samples of the inlet and both outlets. We wrote a custom-written MATLAB code to process the fluorescent images to determine the efficiency of the microparticle filter. Interestingly, we have identified two significantly different flow regimes that can result in high filtration efficiencies. Particle filtration efficiency is high at slower flows around 0.5 mL/min and drops drastically before increasing logarithmically with increasing flow rates. We have explored several parameters to explain filtration efficiency, including the Reynold’s Particle Number and fluid velocity profile. The device operates up to a maximum flow rate of 18 mL/min, permitting high-throughput filtration of 25 μm particles.

Conclusions: The microfluidic particle filtration platform enables high-throughput separation of 25 μm particles from smaller particles. Separation efficiency increases with fluid flow rate signaling particle inertial effects play a key role in ricochet filter separation. In further studies, we will explore different device design iterations to optimize the microfluidic filter to separate and filter various particle sizes with precise control.

References:

1. Cheng, Y., Ye, X., Ma, Z., Xie, S. & Wang, W. High-throughput and microfluidic filtration platform for on-chip cell separation from undiluted whole blood. Biomicrofluidics 10, 014118 (2016).
2. Divi, R. V., Strother, J. A. & Misty Paig-Tran, E. W. Manta rays feed using ricochet separation, a novel nonclogging filtration mechanism. Sci. Adv. 4, (2018).

Background: A feed forward loop (FFL) is commonly observed in several biological networks. The FFL network motif has been mostly been studied with respect to variation of the input signal in time, with only a few studies of FFL activity in a spatially distributed system such as morphogen-mediated tissue patterning. However, most morphogen gradients also evolve in time. We studied the spatiotemporal behavior of a coherent FFL in two contexts: (1) a generic, oscillating morphogen gradient and (2) the dorsal-ventral patterning of the early Drosophila embryo by a gradient of the NF-κB homolog Dorsal with its early target Twist.

Results: In both models, we found features in the dynamics of the intermediate node – phase difference and noise filtering – that were largely independent of the parameterization of the models, and thus were functions of the structure of the FFL itself. In the Dorsal gradient model, we also found that the dynamics of Dorsal require maternal pioneering factor Zelda for proper target gene expression.

Conclusions: Thus, an FFL network motif results in stable gene expression boundaries in the face of a spatially and temporally varying signal.

References:

1. Mangan, S., and Alon, U. (2003). Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A 100, 11980–11985
2. Schaerli, Y., Munteanu, A., Gili, M., Cotterell, J., Sharpe, J., and Isalan, M. (2014). A unified design space of synthetic stripe-forming networks. Nat. Commun. 5
3. Sagner, A., and Briscoe, J. (2017). Morphogen interpretation: concentration, time, competence, and signaling dynamics. Wiley Interdiscip. Rev. Dev. Biol. 6, 1–19.

Background: Reactive Oxygen Species (ROS) and their interplay with endogenous antioxidants allow to spatially control redox signaling in cells. Oxidative stress results from an imbalance between free radical generation and the antioxidant defense system. The depletion of antioxidant defense system namely Glutathione-S-Transferase protects the cells against xenobiotic stressors and maintains the equilibrium of redox signaling. GST-4 expression in C.elegans occurs through the SKN-1/Nrf2 Transcription Factor pathway, which regulates expression of genes involved in endogenous and exogeneous oxidative stress response. Previous hypothesis indicated that all pro-oxidants that invoke SKN1/Nrf2 pathway are indistinguishable in their ROS generation mechanisms [1]. Hence, it was assumed that simultaneous exposure to these compounds might only have an additive response. However, recent literature indicates that SKN-1/Nrf2 antioxidant response varies among different pro-oxidants [2]. A systemic approach is required to analyze the response of the SKN/Nrf2 pathway to simultaneous exposure to the pro-oxidant compounds of the same family to study potential synergistic or antagonistic response. A well-defined mixture experimental design can be helpful to understand the response surface upon exposure to mixtures to understand the synergistic/antagonistic effects with statistical models and reduce the experiment replications [3].

Results: An age synchronized CL2166 strain population expressing GFP tagged to the GST-4 promoter region was utilized for quantifying response to stimuli. The protocol for concurrent exposure to the pro-oxidant compounds from same family in liquid media was established. The fluorescent response is quantified with MATLAB image processing algorithm. Surprisingly, the organisms expressed differential antagonistic response upon exposure to binary and tertiary mixtures of the compounds Quantitative statistical model devised with the data enables in elucidating the differential response surface. Preliminary studies under dietary restriction reveals a synergistic effect of food and the pro-oxidant mixtures.

Conclusions: The statistical model enables understanding of the oxidative stress response under varying mixture stimulus with reduced experimentation. In future studies, the effect of dietary restriction and heat shock stimulus will be explored and studied in detail with other strains.

References:

1. Van Raamsdonk, Jeremy Michael, and Siegfried Hekimi. “Superoxide dismutase is dispensable for normal animal lifespan.” Proceedings of the National Academy of Sciences 109.15 (2012): 5785-5790.
2. Wu, Cheng-Wei, et al. “The Skp1 homologs SKR-1/2 are required for the Caenorhabditis elegans SKN-1 antioxidant/detoxification response independently of p38 MAPK.” PLoS genetics 12.10 (2016): e1006361.
3. Martin, Rubia M., Jonathan Stallrich, and Michael S. Bereman. “Mixture designs to investigate adverse effects upon co-exposure to environmental cyanotoxins.” Toxicology 421 (2019): 74-83.

Background: Molecular diagnoses of plant pathogens play a vital role for global crop protection, and the first step of molecular diagnoses is to isolate DNA from infected plant specimens. However, DNA isolation from plant cells is a complicated and time-consuming process due to the presence of rigid polysaccharide cell walls. As a result, isolation of high-quality plant DNA is mainly confined to well-equipped laboratories, and sample preparation becomes one of the major hurdles to perform molecular diagnostic assays of plant pathogens in the field. To expedite sample preparation and pathogen detection on site, a simple and rapid DNA extraction method has been developed using a polymer microneedle (MN) patch to isolate genomic or pathogenic DNA from plant leaves.

Results: MN patch-based DNA extraction method is minimally invasive, and isolates polymerase chain reaction (PCR) amplifiable DNA within one minute from several plant species such as tomato, potato, pepper, and banana. MN patches used for DNA extraction, are made of polyvinyl alcohol (PVA), and each patch consists of 225 microneedles. These conical microneedles penetrate deep into plant tissue and break hard-to-lyse plant cell walls to release encapsulated nucleic acid materials. For DNA extraction, a MN patch is gently pressed on the surface of the leaf for few seconds, and then, the patch is peeled off and rinsed with 100 μL TE buffer to collect absorbed DNA from microneedles. MN patches successfully extract Phytophthora infestans DNA from both laboratory-inoculated and field samples for detection of late blight disease in tomato. For laboratory-inoculated samples, the MN patch-based DNA extraction method achieved 100% detection rate compared to cetyltrimethylammonium (CTAB)-based DNA extraction method when the samples were taken 3 days after inoculation. For field samples, the MN extraction method successfully detected P. infestans in all blind samples tested from older lesions.

Conclusions: MN patch-based DNA extraction method reduces sample preparation time from 3-4 hours in a conventional assay to ~1 minute, and extracted DNA is directly applicable for amplification reactions without further purification. For applications, we have demonstrated that MN extraction detects P. infestans DNA in both inoculated and field-collected tomato leaf samples. Moreover, this simple and rapid extraction method could be used to isolate other plant pathogens’ DNA from various plant species directly in the field, and thus have great potential to become a universal sample preparation technique for on-site molecular diagnosis of plant pathogens.

References:

1. Paul, Rajesh, Amanda C. Saville, Jeana C. Hansel, Yanqi Ye, Carmin Ball, Alyssa Williams, Xinyuan Chang, Zhen Gu, Jean B. Ristaino, and Qingshan Wei (2019). Extraction of Plant DNA by Microneedle Patch for Rapid Detection of Plant Diseases. ACS nano, 13: 6540-6549

Background: As the predominant form of biomass on Earth, lignocellulose is a prime candidate for conversion into renewably sourced chemicals and fuels. The extremely thermophilic bacterium, Caldicellulosiruptor bescii (T_opt=78^oC), natively has the ability to metabolize the cellulose and hemicellulose contained in lignocellulose [1]. C. bescii can be genetically engineered to produce valuable chemicals such as ethanol and acetone [2,3]. Additionally, C. bescii can solubilize recalcitrant biomass, including switchgrass and poplar [1,4]. Populus trichocarpa provides a potential lignocellulose feedstock [4]. The Forest Biotechnology program at NCSU has the ability to genetically alter the monolignol synthesis pathway in the trees, allowing for feedstock improvements [5]. C. bescii grown on transgenic poplar biomass had improved solubilization and fermentation characteristics. C. bescii also demonstrated an ability to ferment poplar stem sections nearly as well as milled poplar, potentially eliminating the need for pretreatment milling [1].

Results: Efforts to create an optimal transgenic poplar line with good growth and fermentation characteristics is underway. C. bescii fermentations are used to quantify the recalcitrance of poplar lines. Highlights from these results are presented. Additional efforts are underway to produce acetone at industrially relevant levels. Progress toward this goal is presented.

Conclusions: The available genetic tools for both P. trichocarpa and C. bescii provide potential to optimize this microbe-feedstock pairing to become industrially relevant. Here we aim to produce high amounts of acetone from the fermentation of transgenic poplar biomass.

References:

1. C.T. Straub, et al., Quantitative Fermentation of Unpretreated Transgenic Poplar by Caldicellulosiruptor bescii. Nat. Commun. 10 (2019)
2. A.M. Williams-Rhaesa, et al., Engineering redox-balanced ethanol production in the cellulolytic and extremely thermophilic bacterium, Caldicellulosiruptor bescii, Metab. Eng. Commun. 7 (2018) 1–9.
3. B.M. Zeldes, et al., A synthetic enzymatic pathway for extremely thermophilic acetone production based on the unexpectedly thermostable acetoacetate decarboxylase from Clostridium acetobutylicum, Biotechnol. Bioeng. 115 (2018) 2951–2961.
4. P. Sannigrahi, A.J. Ragauskas, G.A. Tuskan, Poplar as a feedstock for biofuels : A review of compositional characteristics, Biofuels, Bioprod. Biorefining. 4 (2010) 209–226.
5. J.P. Wang, et al., Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis, Nat. Commun. 9 (2018).

Background: Ethylene oligomerization (EO) by heterogeneous catalysts has been studied for many years as part of efforts to upgrade stranded natural gas resources. Nickel supported on alumino-silicates has received recent attention [1]. Isolated Ni(II) in ion-exchange positions are the generally accepted EO active site in zeolite Ni-H-Beta, but the role of H⁺ BrØnsted acid sites (BAS) remains unclear [2]. Thus, we synthesized an Ni-NH4-Beta candidate by ion-exchanging NH4-Beta with Ni(II), without any subsequent calcination to decompose NH₄⁺ ions to BAS. We prepared Ni-H-Beta by Ni(II) exchange with H-Beta (as is standard) using 1 and 4 exchanges (denoted cB&A-1x/4x) and also with NH₄-Beta using 4 exchanges, but calcining afterward (denoted cA). For comparison, we prepared a highly active 2.5% Ni/Siral-30 by impregnation.

Results: A higher Ni concentration is obtained by ion-exchange of NH₄-Beta when compared to H-Beta. The Ni-Beta catalysts exhibit H2 TPR peaks at 370, 480, and 560 ^oC that indicate Ni(II) in the α, β and γ exchange sites of the Beta structure [3]. Ni-NH₄-Beta displays primarily α and cA primarily γ peaks. CO DRIFT spectra of cA and cB&A catalysts display geminal dicarbonyl bands [4] that are absent for Ni-NH₄-Beta. Instead, it displays an independent Ni-CO peak suggesting Ni ions at a distinct exchange site. Ni/Siral-30 exhibits only a weak band assigned to CO on NiO crystallites. NH₃-TPD spectra of the Ni-H-Beta catalysts evidence the generation of Ni(II) Lewis acid sites, the consumption of medium strength BAS, and the generation of strong BAS. The cB&A-4x/1x catalysts gave similar steady-state conversions in EO, despite their different Ni loadings, suggesting that Ni(II) species are not uniformly active [1]. Moreover, the EO reaction does not appear to be sensitive to Ni(II) ion location. Ni-H-Beta (cA) displayed higher EO conversion; however, this catalyst tended to deactivate more rapidly. This is attributed to long chain oligomers that accumulate and deny access to Ni sites by pore blockage. Ni-NH4-Beta displays comparable steady-state conversion with virtually no deactivation. Its selectivity to cracking products is significantly lower because of its lower BrØnsted acidity. Ni/Siral-30 exhibited higher activity than any of the Ni-Beta catalysts. NiO nanoparticles exposing coordinatively unsaturated (cus) Ni(II) ions are inferred to be the active sites. Whilst pore size may be a factor, given the relatively high WHSV under which the Ni/Siral-30 was tested, it is likely that these cus Ni(II) ions are more active than Ni(II) in Beta ion-exchange positions.

Conclusions: Ni(II) ions in Beta zeolite exchange sites are not uniformly active for EO. A Ni-NH₄-Beta catalyst without significant BrØnsted acidity is highly active for EO with low selectivity to cracking products. NiO nanoparticles supported on Siral-30 that expose cus Ni(II) ions are more active than Ni-Beta Zeolites for EO.

References:

1. S. Moussa, M. Arribas, P. Concepción, A. Martínez, Catal. Today 277, 78 (2016)
2. R. Henry, M. Komurcu, Y. Ganjkhanlou, R. Brogaard, L. Lu, K. Jens, G. Berlier, U. Olsbye, Catal. Today 299, 154 (2018)
3. A. Penkova, S. Dzwigaj, R. Kefirov, K. Hadjiivanov, M. Che, J. Phys.. Chem. C 111, 8623 (2007)
4. K. Hadjiivanov, H. Knözinger, M. Mihaylov, J. Phys. Chem. B 106, 2618 (2002)

Background: Biogas, produced by anaerobic digestion of agricultural waste, contains large amounts of CH4 and CO2. Both are potent greenhouse gases responsible for global climate change.[1] Rather than combusting the biogas for heat as often done, these compounds can be converted to syngas, a mixture of H₂ and CO, and used for production of carbon-neutral fuels or chemicals such as methanol and acetic acid. One process to produce syngas is dry reforming of methane, CH₄ + CO₂ → 2H₂ + 2CO.[2] This highly endothermic process (ΔH = +247 kJ/mol) requires high temperature and an active catalyst such as Rh to achieve desirable yields of syngas.[3,4] When Rh is dispersed on TiO₂, a wide band gap semiconductor material, photocatalytic activity of TiO₂ can potentially improve dry reforming performance. However, strong interactions between Rh and TiO₂ can lead to encapsulation of Rh by TiO₂ under reducing conditions and decrease the available Rh surface area.[5,6] Here we investigate the effect of temperature for calcination and reduction pretreatment steps on the nature of Rh particles on TiO₂.

Results: H2 chemisorption experiments showed a decrease in measured Rh surface area as calcination and reduction temperatures increased from 675°C to 850°C. For samples calcined at 750°C, an increase in the reduction temperature from 675°C to 850°C led to a 79% decrease in Rh dispersion. In dry reforming tests at 650°C, samples with higher initial Rh dispersion showed higher CH4 conversion and greater stability over 25 h on-stream than samples with lower initial Rh dispersion. Notably, samples pre-reduced above 675°C showed increased Rh dispersion after 25-h reforming tests, indicating an increase in Rh surface area under reforming conditions. S/TEM measurements were performed to determine the Rh particle morphology, Rh/TiO2 interface, and changes before and after reforming tests.

Conclusions: Rh dispersion on Rh/TiO₂ catalysts is highly dependent on pretreatment temperature and demonstrates complex behavior due to the strong metal-support interactions between Rh and TiO₂. High-temperature reduction of TiO₂ causes a decrease in available Rh surface area, which can be reversed under oxidizing conditions.

References:

1. Prasodjo, D., Vujic, T., Cooley, D., Yeh, K., Lee, M.-Y. (2013). A spatial-economic optimization study of swine waste-derived biogas infrastructure design in North Carolina. Nicholas Institute for Environmental Policy Solutions and Duke Carbon Offsets Initiative. Duke University, Durham, NC.
2. Pakhare, D., Spivey, J. (2014). A review of dry (CO2) reforming of methane over noble metal catalysts. Chem. Soc. Rev. 43: 7813–7837.
3. Rostrup-Nielsen, J.R., Hansen, J.H.B. (1993). CO2-Reforming of Methane over Transition Metals. J. Catal. 144: 38–49.
4. Tsipouriari, V.A., Efstathiou, A.M., Zhang, Z.L., Verykios, X.E. (1994). Reforming of methane with carbon dioxide to synthesis gas over supported Rh catalysts. Catal. Today 21: 579–587.
5. Logan, A.D., Braunschweig, E.J., Datye, A.K., Smith, D.J. (1988). Direct observation of the surfaces of small metal crystallites: rhodium supported on titania. Langmuir 4: 827–830.
6. Linsmeier, Ch., Taglauer, E. (2011). Strong metal–support interactions on rhodium model catalysts. Appl. Catal. A: General 391: 175–186.

Background: To understand the rates and selectivity of hemicellulose pyrolysis, we have probed the differences between pyrolysis of xylose, fucose and arabinose. Hemicellulose pyrolysis is an important part of making bio-oil from lignocellulosic biomass pyrolysis. Xylose is the monomer of xylan. Arabinose occurs in hemicellulose and has different hydroxyl group stereochemistry at carbon-2 and carbon-3 (third and fourth atom in the ring with oxygen numbered first). Fucose substitutes a methyl for an H onto arabinose’s carbon-5 (sixth atom in the ring with oxygen numbered first). Samples of D-arabinose (Fisher Scientific), L-fucose (Acros), and D-xylose (Sigma Aldrich) were flash-pyrolyzed (Pyroprobe 5200, CDS) at 250°C and 350°C. Product gases were analyzed by two-dimensional gas chromatography with time-of-flight mass spectrometry (Pegasus 4D, LECO).

Results: Acetaldehyde and water were the dominant products obtained in L-fucose pyrolysis and, glycolaldehyde and water in pyrolyses of D-arabinose and D-xylose. The yield of glycolaldehyde in pyrolysis of L-fucose was negligible compared to that found in the pyrolysis of D-arabinose and D-xylose. Formaldehyde was the second dominant species obtained from all the monosaccharides. The pyrolysis of the pentoses (arabinose and xylose) yielded other products like furfural, dihydroxyacetone and glycolaldehyde dimer. Other products obtained from the hexose (fucose) were butanedione, hydroxy acetone and 5-methyl furfural.

Conclusions: The methyl substitution on L-fucose changed the pathway adopted in fucose pyrolysis as opposed to that in D-arabinose and D-xylose. This helps us gain insight about the changes in mechanistic pathway adopted by intermediates in hemicellulose pyrolysis.

Background: Chemical looping-oxidative dehydrogenation (CL-ODH) of ethane is a promising alternative to produce ethylene, via thermal cracking or catalytic dehydrogenation coupled with selective hydrogen combustion (SHC) by a redox catalyst. Previous study has demonstrated that Na₂WO₄-promoted CaMnO₃ exhibited steady SHC performance in CL-ODH of ethane with 89% H₂ conversion and 88% selectivity at 850 °C over 50 redox cycles [1]. The kinetics parameters and reduction models of unpromoted and Na₂WO₄-promoted CaMnO₃ under H₂ and C₂H₄ have also been studied [2]. In this work, the reduction models of unpromoted and Na₂WO₄-promoted CaMn_0.9Fe_0.1O₃ under H₂ and C₂H₄ are reported.

Results: Comparing with the undoped CaMnO₃, the addition of 10% Fe on CaMnO₃ increases the reduction rate under H2 while it inhibits the reaction under C2H4. The reduction of unpromoted-CaMn0.9Fe0.1O₃ under H2 and C2H4 is well-described by reaction-order models. The activation energy for the reduction of unpromoted-CaMn0.9Fe0.1O3 under H2 is 44.3 kJ/mol, and the corresponding value is 122.2 kJ/mol under C2H4. The reduction models predict greater dependence on oxygen site density for CaMn0.9Fe0.1O₃ reduction under C2H4 as compared with H2. The addition of Na2WO4 enhances the SHC performance as evidenced by the fact that the reduction of the redox catalyst under C2H4 is almost completely inhibited. The nucleation and nuclei growth models show good agreement with the reduction of Na2WO4-promoted CaMn0.9Fe0.1O₃ under H2 and C2H4. The reduction rate under H2 is three order magnitude greater than that under C2H4.

Conclusions: The reduction kinetics of CaMn0.9Fe0.1O₃ redox catalyst under H2 and C2H4 was studied to explore the nature of selective hydrogen combustion (SHC) under CL-ODH of ethane, via a combination of redox TGA experiments and statistical analysis applied to fifteen empirical kinetic models [3]. The rate parameters obtained for CaMn0.9Fe0.1O₃ reduction by H2 and C2H4 provide insights and confirm the SHC performance of CaMn0.9Fe0.1O₃, indicating selective H2 combustion relative to C2H4 at intermediate to high solid conversion. The addition of Na2WO4 increases the activation energy for both the reduction under H2 and C2H4. It also exhibits better SHC performance by the promoted redox catalyst, demonstrated by the inhibition of the reduction under C2H4. The reported kinetics parameters and reaction models for the reduction of CaMn0.9Fe0.1O₃ under H2 and C2H4 provide insights to optimize the redox processes that employ these materials, such as the ethane CL-ODH process.

References:

1. Dudek, R. B., Gao, Y., Zhang, J., Li, F. (2018). Manganese-containing redox catalysts for selective hydrogen combustion under a cyclic redox scheme. AIChE Journal, 64(8), 3141–3150.
2. Dudek, R. B., Tian, Y., Jin, G., Blivin, M., Li, F. (2019). Reduction Kinetics of Perovskite Oxides for Selective Hydrogen Combustion in the Context of Olefin Production. Energy Technology, 1900738.
3. Zhou, Z., Han, L., Bollas, G. M. (2014). Kinetics of NiO reduction by H2 and Ni oxidation at conditions relevant to chemical-looping combustion and reforming. International Journal of Hydrogen Energy, 39(16), 8535–8556.

Background: Thermochemical air separation via cyclic redox reactions of an oxide-based oxygen sorbent has been extensively investigated recently. Although a number of promising oxygen sorbents have been proposed and investigated, further improvements in sorbent performance through fundamental understanding of the structure-performance relationships are highly desirable.

Results: In this study, we systematically investigated the effects of A and B site dopants on the oxygen uptake/release properties (i.e., vacancy formation energy, reduction enthalpy, reduction temperature, and oxygen capacity) of SrFeO₃ family of perovskites as oxygen sorbents. A monotonic correlation between DFT calculated oxygen vacancy formation energy and reduction temperature demonstrates the effectiveness of theoretical calculation for guiding selection of oxygen sorbents. Combining vacancy formation energy with stability analysis using tolerance factor, dopants such as Ba and Mn were identified for tuning redox property of SrFeO₃ sorbent, and increasing the oxygen capacity for temperature and pressure swings when compared to un-doped SrFeO₃. The Ca and Co co-doped sample proved extremely stable for air separation, with less than a 3% decrease in capacity over 2000 cycles, with little to no change in the particle size of the material. Although the dynamic nature of the redox process makes it difficult to use a single vacancy formation energy as the descriptor for the oxygen storage capacity a systematic approach was developed to correlate the oxygen storage capacities with the sorbents’ compositional properties and vacancy formation energies.

Conclusions: The systematic approach of combining DFT calculations with experimental oxygen vacancy studies from this study provides an effective strategy for developing improved sorbents for thermochemical air separation.

Background: Adhesives capable of sticking to various types of surfaces in underwater and high moisture conditions are required for a large array of applications such as marine coatings, sealants, medical devices, and wet living tissue repair. However, typical industrial adhesives are primarily developed for dry applications and perform poorly in wet environments or are highly specific to particular surfaces and not suitable for broad use. A viable and cost-effective strategy to address this issue is to develop generic adhesives that can be used for multiple types of surfaces in water or high moisture conditions. One approach researchers have taken to develop new adhesives is to draw inspiration from the natural glues produced by aquatic organisms capable of strong, moisture-resistant adhesion to various surfaces. Analysis of these glues has shown that these organisms’ abilities to adhere to a multitude of surfaces involve L-3,4-dihydroxyphenylalanine (DOPA) and functional amyloid nanostructures [1,2]. The objective of this project is to computationally design bio-inspired underwater adhesives that are stronger than those currently reported in the literature by analyzing and combining the adhesive capabilities of DOPA and amyloid-forming peptides in wet conditions. Explicit solvent atomistic simulations can give insight into the interactions underlying surface adhesion in the presence of water, which can then be used to guide the design of DOPA-amyloid conjugates for underwater adhesion.

Results: Motivated by the concern that DOPA groups might cluster in a way that interferes with their ability to adsorb to surfaces, we investigated the behavior of DOPA monomers in water and found that DOPA was unlikely to cluster significantly at concentrations lower than 1.0 M. We also simulated DOPA molecules on a silica surface and found that they readily adsorb onto silica. DOPA-containing chains (with alternating DOPA and glycine groups) were then simulated in water to examine the intra-molecular interactions of the chain, wherein we found that there were unlikely to be interactions detrimental to the adhesion process. We then began designing a DOPA-amyloid conjugate capable of generic underwater adsorption to varied surfaces. The amyloid-forming peptide KLVFFAE was chosen for the initial design as it is known to self-assemble into functional amyloid nanostructures. After several designs were tested for the ability their amyloid-forming propensity, it was found that the sequence KLVFFAE-G-ddGddGdd (where d represents DOPA) was the most favorable of the current designs.

Conclusions: Conjugated DOPA and amyloid-forming peptides have the potential to synergize and work as new designs for underwater adhesives. Our best current design KLVFFAE-G-ddGddGdd forms a defined amyloid structure while allowing for the DOPA-containing chain to be free to interact with the surface.

References:

1. Waite, J.H., Tanzer, M.L. (1981). Polyphenolic Substance of Mytilus edulis: Novel Adhesive Containing L-Dopa and Hydroxylproline. Science, 212: 1038-1040.
2. Mostaert, A.S., Higgins, M.J., Fukuma, T., Rindi, F., Jarvis, S.P. (2006) Nanoscale mechanical characterization of amyloid fibrils discovered in a natural adhesive. J. Biol. Phys., 32: 393-401.

Background: Wearable electronics have attracted great attention over the past decade due to their potential applications in health care and human-machine interfaces. Next generation wearable technology demands compatible energy sources that are soft, stretchable and sustainable. Efforts have been made to develop energy harvesters that can convert human motion/ambient mechanical energy to electrical energy.[1-4] Triboelectric, piezoelectric and thermoelectric generators convert mechanical energy to electrical energy.[1-4] Triboelectric harvesters have gained great popularity due to their relatively straightforward fabrication. They induce electrical current based on contact electrification (rubbing two surfaces) and electrostatic induction (oscillating the distance between charged surfaces).[1,3-5] Triboelectric harvesters generate high voltages and low currents. They require moisture-free environments to enable contact electrification.[1,3-5] Piezoelectric and thermoelectric generators, in contrast, require extensive fabrication techniques and loss in energy conversion when converted to flexible devices, as their fundamental materials are intrinsically hard and brittle.[1-3]

Results: We report a new approach to energy harvesting that utilizes liquid metals. These devices generate around 1mW/m² by harnessing energy from mechanical motion. We have characterized the behavior of these devices as a function of a variety of parameters including material properties and physical deformation. The devices behave as expected and the response of the devices to deformation match a physics-based model.

Conclusions:The liquid metal based soft device generate electrical signal when deformed, which may be useful for energy harvesting as well as self-powered sensors. These devices can be used to monitor human activities thereby find many applications in wearable electronics, dynamic tactile surfaces, healthcare systems like rehabilitation and prosthetics.

References:

1. Zhou, M. et al. A review on heat and mechanical energy harvesting from human – Principles, prototypes and perspectives. Renewable and Sustainable Energy Reviews 82, 3582–3609 (2018).
2. Sim, H. J. et al. Flexible, stretchable and weavable piezoelectric fiber: Flexible, Stretchable and Weavable Piezoelectric. Advanced Engineering Materials 17, 1270–1275 (2015).
3. Yang, Y. et al. Liquid-Metal-Based Super-Stretchable and Structure-Designable Triboelectric Nanogenerator for Wearable Electronics. ACS Nano 12, 2027–2034 (2018).
4. Gao, S. et al. Wearable high-dielectric-constant polymers with core–shell liquid metal inclusions for biomechanical energy harvesting and a self-powered user interface. Journal of Materials Chemistry A 7, 7109–7117 (2019).
5. Wang, Z. L., Jiang, T. & Xu, L. Toward the blue energy dream by triboelectric nanogenerator networks. Nano Energy 39, 9–23 (2017).

Background: Atomic layer deposition (ALD), consisting of sequential dosing and purging of two precursors¹, has been exploited for manufacturing semiconductor devices due to its uniformity and controllability but has inherent limitation in its selectivity to target surfaces.²

Results: Atomic layer etching (ALE) was periodically integrated into TiO₂ ALD to improve selectivity. 10~ nm selective deposition was achieved on silicon oxide vs hydrogen-terminated silicon, which is almost 10~ times improvement over ALD only process.

Conclusions: Periodic ALE integration can improve ALD selectivity when the surfaces after ALE are similar with the original surfaces.

References:

1. Parsons, Gregory., George, Steven., and Knez, Mato (2011). Progress and Future Directions for Atomic Layer Deposition and ALD-Based Chemistry. MRS Bulletin., 36; 865–871.
2. Fang, Ming., Ho, Johnny (2015). Area-Selective Atomic Layer Deposition: Conformal Coating, Subnanometer Thickness Control, and Smart Positioning. ACS Nano., 9; 8651–8654.

Background: Inorganic perovskite quantum dots (IPQDs) have demonstrated remarkable success as a more energy-efficient alternative to well-studied metal chalcogenide QDs, and are attracting attention from the energy and chemical industries for a wide range of applications including photovoltaic devices, LED displays, and solar-enabled organic synthesis (photocatalysis). The facile bandgap tunability at room temperature through anion exchange reactions, high photoluminescence quantum yield, and relatively high defect tolerance, differentiate IPQDs from the other colloidal semiconductor nanocrystals. Despite the groundbreaking advancements of IPQDs in the field, their unique ionic nature (different than metal chalcogenide QDs) require new colloidal synthesis routes and surface chemistries. Conventionally, batch synthesis methods are utilized to synthesize, screen, and optimize solution-processed QDs. However, the massive reaction parameter space associated with IPQDs, in combination with the inherent mass and heat transfer challenges of batch methods, necessitate utilization of material- and time-efficient synthesis methods for fundamental and applied studies of IQPDs. In this work, we develop and utilize a modular microfluidic platform for accelerated in-situ studies of IPQDs anion exchange reactions with minimum reagent consumption.

Results: Utilizing the modular microfluidic strategy, we study in detail the effects of halide composition, ligand ratios, and halide salt source across reaction (residence) times ranging from 0.5 to 90 s. Capitalizing on the wealth of the systematic studies of anion exchange reaction, enabled by the developed time- and material-efficient strategy, we postulate a three-stage reaction mechanism for the homogenoues IPQDs halide exchange reaction. We complement our in-situ findings of IPQDs anion exchange reactions with off-line material characterization techniques, gleaning new insights on the overall understanding of the anion-exchange reaction network.

Conclusions: In summary, we developed a facile and ambient condition/room‐temperature halide exchange strategy for inorganic perovskite QDs using a novel, material‐ and time‐efficient continuous flow reactor strategy, integrated with a translational spectral monitoring. The microfluidic platform enabled us to study reaction timescales that are not easily accessible using conventional reaction monitoring techniques (e.g., stopped‐flow injector). This insight into the early timescales allowed us to postulate a comprehensive three‐stage anion exchange mechanism that improves the overall understanding of this versatile process. In addition, we revealed, in detail, the effects of widely varying QDs anion exchange reaction parameter space, including precursors and ligand composition as well as halide salt source and concentration. The strategies and QD process controls integrated into our setup can be generalized and used for different QD synthesis schemes.

References:

1. Abdel‐Latif, K., Epps, R.W., Kerr, C.B., Papa, C.M., Castellano, F.N. and Abolhasani, M., 2019. Facile Room‐ Temperature Anion Exchange Reactions of Inorganic Perovskite Quantum Dots Enabled by a Modular Microfluidic Platform. Advanced Functional Materials, 29(23), p.1900712.

Background: CB protective textiles commonly include separate layers to prevent penetration from agents in aerosol and vapor form. However, combining the aerosol and vapor protection into one sorptive layer with filtering capability can reduce the thermal burden of the CB textile composite, and increase comfort to the Soldier. Recently, Polymers of Intrinsic Microporosity (PIMs) have attracted attention as a novel class of high free-volume polymers with highly rigid and contorted molecular structure. Most research on PIMs has focused on fundamental material and membrane properties, with only a few studies on materials in fiber form.

Results: In this study, PIM-1 polymer fiber mats were fabricated by electrospinning using different solvent systems consisting THF, DMF and toluene. The resulting fiber mats showed excellent breathability and high porosity, indicating potential for applications in protective clothing. The surface area of the PIM-1 fiber mats was typically 650 m²/g, which is close to 750 m²/g measured for the starting neat powder. A problem, however, is that the produced fiber mats have very poor mechanical integrity due to low interchain interactions of PIM-1, hindering their practical use. In our work, we have developed a unique PIM/PAN hetero-structure synthesis approach by incorporating PAN fibers as a structural reinforcing material into the PIM fiber matrix. The as-prepared PIM/PAN composite fibers exhibit 70 times improvement in tensile strength compared to the PIM fibers, with a net surface area of 548 m²/g, indicating only a moderate loss in porosity. In addition, metal-organic framework (MOF) particles with the capability of degrading toxic chemicals, such as chemical-warfare agent (CWA) simulants, were integrated into the composite fibers. The resultant PIM/PAN/MOF composite fibers show 2-3 times higher removal capacity of dimethyl methylphosphonate (DMMP) than the baseline material and demonstrate the detoxification of 4-nitrophenyl phosphate (DMNP) as monitored by UV−vis spectroscopy, among which DMMP and DMNP are both chemical nerve agent simulants.

Conclusions: These findings indicate that functionalized PIM-1-based fabrics are a promising material for applications in chemical protection and detoxification.

Background: We will report how we can form innovative, smart, multiphasic gel systems by controlling capillary forces and magnetic interactions. We have demonstrated the formation of soft micromagnets composed of polydimethylsiloxane (PDMS) beads with internally-embedded chained magnetic nanoparticles. Magnetic-field-directed assembly of the nanoparticles allows for the generation of anisotropic nanostructured PDMS beads which are capable of holding residual polar magnetization due to a permanently embedded dipole moment. Once magnetized, their magnetic interactions result in the formation of percolated networks. To determine key differences in magnetic interactions likely due to orientation differences of the magnetic particles, we have compared gels from these chained PDMS beads to PDMS beads with randomly dispersed magnetic nanoparticle, MNPs, from our previous work [1-3].

Results: We proved the tunability of the new chained bead system by conducting magnetization, demagnetization, and re-magnetization experiments which show evidence of successful reformation of percolating networks. We are currently using magnetic interaction templating to study and manipulate the magnetic response of our systems. Direct structure templating by anchoring these gels to 3D printed patterns could potentially improve the precision of rheological measurements. Preliminary data show that samples measured with a 3D printed structure have results with higher moduli.

Conclusions: Overall, we have constructed, and are currently developing, a rich toolbox of structures and interactions for producing novel, magneto-responsive gel networks. From our results, we see potential applications of our gel-system in water filtration systems.

References:

1. Butt, H.-J. (2011). Controlling the Flow of Suspensions. Science. 331: 868–869.
2. Yu, M., Ju, B., Liu, S., Choi, S-B. (2014). Magnetoresistance Characteristics of Magnetorheological Gel under a Magnetic Field. Ind. Eng. Chem. Res. 53: 4704−4710.
3. Huang, H-W., Huang, T-Y., Charilaou, M., Lyttle, S., Zhang, Q., Pane, S., Nelson, B.J. (2018). Investigation of Magnetotaxis of Reconfigurable Micro-Origami Swimmers with Competitive and Cooperative Anisotropy. Adv. Funct. Mater. 1802110: 1-9.

Background: Accumulation of bilgewater, a highly concentrated and complex amalgam of oils, particulates, and solvents, is a large issue for naval operations [1]. While there are set standards for its treatment and disposal, bilgewater discharge continues to be one of the largest anthropogenic pollution sources of marine environments, contributing around 20% of oily waste-water discharge from vessels into the sea [2, 3]. Introduction of new methods for on-board treatment bilgewater is necessary for optimizing resource use in naval operations and minimizing the Navy’s contribution to global wastewater discharge. I propose the use of a new class of colloidal matter, soft dendritic microparticles, as a physical method for particulate and oil adsorption and removal. This project will reveal the dendricolloids’ mechanism of operation with regards to the morphology, surface charge, and hydrophobicity. On a practical level, it will develop a new principle of bilgewater treatment that is based off of physical capture of waste rather than filtration.

Results: Soft dendritic microparticles, or dendricolloids, are formed through liquid nanofabrication processin which polymer is precipitated and/or cross-linked in turbulently sheared flow [4]. This results in unique hierarchical and nanofibrous morphology which gives large excluded volume and unusual structure-building capabilities to the dendricolloids. With their well-developed cavities, dendricolloids will act as micro-sponges, physically capturing contaminants from heavily polluted water. When fabricated from biodegradable polymers, these dendritic particles will further reduce the amount of post-processing pollution after waste collection as the dendricolloids themselves can degrade into more natural byproducts than non-biodegradable ones. Preliminary data shows more efficient particle capture with dendricolloids when compared against amorphous chitosan chunks with quick sedimentation due to formation of aggregates. Qualitatively, there is significant oil adsorption with those fabricated with poly(lactic acid).

Conclusions: Through this project, I will develop models that will correlate the effects of fluidic process parameters, colloidal interactions, and intrinsic polymer properties to oil and micro-plastic capture/separation efficiency from water. Characterizing dendricolloid properties can increase efficiency, reduce resource consumption, and limit environmental pollution during treatment process of bilgewater within Naval ships.

References:

1. Environmental Protection Agency, Office of Wastewater Management. Oily bilgewater separators. Washington, DC 20460.
2. Tomaszewska, M., Orecki, A., Karakulski, K. “Treatment of bilgewater using a combination of ultrafiltration and reverse osmosis,” Desalination, 185, 203-212 (2005).
3. Baltic Marine Environment Protection Commission. Baltic sea environment proceedings No. 50. Turku, Finland, 1992.
4. Roh, S., Williams, A.H., Bang, R.S., Stoyanov, S.D., Velev, O.D. “Soft dendritic microparticles with unusual adhesion and structuring properties,” Nat. Mater., 18, 1315-1320 (2019).

Background: Switchable hydrophilicity solvents (SHSs) are an emerging class of solvents for facile and energy-efficient liquid-liquid extraction (LLE) processes with “switching” of physiochemical properties of nitrogenous bases (e.g., amines or amidines). [1] In presence of carbon dioxide (CO₂) and water, SHSs undergo protonation caused by formation of carbonic acid (H₂CO₃). The CO₂-triggered tuning of the distribution coefficient of SHS in hydrophobic/hydrophilic media drives the reversible transfer of the SHS in presence of CO₂, dramatically reducing the energy needed for LLE processes. This unique characteristic of SHSs have opened a new frontier for energy-efficient chemical separations in various fields ranging from recycling of packaging materials [2] to extraction of algal biomass. [3] Since discovery of SHSs, the fundamental and applied studies of SHSs have typically been conducted using conventional flask-based techniques. However, the relatively low specific interfacial area (e.g., bubble columns offer 50-600 m²/m³) and gas-liquid contact time of conventional reactors for gas-liquid reactions have resulted in long solvent extraction times ranging from 2 h – 10 h, thereby hindering further development of this promising class of solvents. [4]

Results: In this work, we developed and utilized an intensified microfluidic reactor for accelerated fundamental studies of SHSs while minimizing the chemical consumption. The developed microfluidic reactor utilizes a highly CO₂-permeable membrane (Teflon AF-2400) in a tube-in-tube configuration, providing specific interfacial areas exceeding 4900 m²/m³. Utilizing the developed flow chemistry platform, we systematically studied the effects of both continuous (e.g., CO₂ pressure, and reaction time) and discrete (e.g., chemical structure of the SHS) process parameters on the kinetics and extent of the SHS recovery process.

Conclusions:The intensified flow reactor integrated with an in-situ process screening probe enables complete SHS recovery in 3~8 min (~25 times faster than a batch reactor), while utilizing only 4~8 μL of SHS mixture (~500 times less chemical consumption than a batch reactor). Utilizing the developed material-efficient microfluidic platform, a detailed framework for achieving the maximum single-pass extraction efficiency and accelerating the SHS extraction kinetics was provided.

References:

1. Jessop, P. G.; Mercer, S. M.; Heldebrant, D. J. CO2-Triggered Switchable Solvents, Surfactants, and Other Materials. Energy Environ. Sci. 2012, 5 (6), 7240–7253.
2. Samorì, C.; Cespi, D.; Blair, P.; Galletti, P.; Malferrari, D.; Passarini, F.; Vassura, I.; Tagliavini, E. Application of Switchable Hydrophilicity Solvents for Recycling Multilayer Packaging Materials. Green Chem. 2017, 19 (7), 1714–1720.
3. Cicci, A.; Sed, G.; Jessop, P. G.; Bravi, M. Circular Extraction: An Innovative Use of Switchable Solvents for the Biomass Biorefinery. Green Chem. 2018, 20 (17), 3908–3911.
4. Mallia, C. J.; Baxendale, I. R. The Use of Gases in Flow Synthesis. Org. Process Res. Dev. 2016, 20 (2), 327– 360.

Background: Renewable biopolymers such as cellulose and chitin have the potential to add value to a vast number of applications as society shifts away from petroleum-derived products. Colloidal nanomaterials based on these systems are particularly promising due to their nanoscale dimensions, water dispersibility, and other advantages. Optimization of these resources for targeted applications requires a detailed understanding of the material properties, especially flow behavior since they are often used in the form of aqueous suspensions. The goal of this work is to characterize the interactions between these particles in aqueous suspensions and the structures that develop under shear and at rest.

Results: A comparison of rheological properties and mechanisms that influence them is presented for several of the most prominent biobased nanomaterial systems: cellulose nanocrystals, micro/nanofibrillated cellulose, chitin nanocrystals, and nanofibrillated chitin. The viscosity profiles, gel characteristics, and yield stress properties of each material are discussed with respect to their morphology and the implications for their use in various applications are considered.

Conclusions: The stable of available biobased nanomaterials provides a range of available rheology profiles that can be selected to best suit the desired application while reducing environmental impact and improving biodegradability.

Background: Sweat is an important biofluid for monitoring individuals’ health as it contains number of essential biomarkers which are also present in blood. However, sampling sweat for analysis still remains challenging as most of the commercially available sweat sensing devices are either invasive in nature or work only under active perspiration [1][2]. These devices fail to function under low-sweating conditions and are incapable of deriving information in sweat from sedentary subjects. We demonstrate a new principle for the design of flexible and wearable devices, which are capable of extracting sweat under both sedentary and actively perspiring conditions using osmotic pressure difference for pumping, and evaporation for liquid disposal [3]. The device is composed of silicone, polyacrylamide hydrogel patch, and paper microfluidic conduit with a site of evaporation at the end (evaporation pad). The hydrogel is equilibrated with glycerin, glucose, or NaCl solution to build up the desired osmotic strength.

Results: In-vitro testing with gelatin-based model skin platform has initially revealed that both glucose and glycerin treated hydrogels facilitate high dye (model biomarker in model skin) accumulation on the evaporation pad, with glucose being the highest. Human trials with embedded glucose hydrogels has shown the potential of the prototype to extract sweat lactate under both resting and non-resting conditions within a period 2 hours. Results suggest that there is no direct correlation between the blood and sweat lactate. A continuous sweat lactate sensing platform is currently being established on the device by using enzymatic electrochemical sensors on a polyimide film, which is adhered directly onto the paper microfluidic channel. Initial testing with this integrated platform has shown that this wearable prototype can be easily tuned for continuous sweat lactate monitoring.

Conclusions: We are presently optimizing the design parameters of this osmotic wearable patch in order to have high sweat sampling and expedited fluid flow in the paper microfluid channel. We believe that more human trial experiments will provide a comprehensive understanding of the human lactate metabolism, that will eventually be useful for monitoring oxidative stress levels in athletes and military personnel. Such simple, low cost, continuous sweat sensing platform with specific sensors can either be worn directly onto the skin or be used as a wearable, that will reveal a great deal of health information.

References:

1. Min S, Balooch G, Kang D, Koh A, Kim J, Pielak RM, et al. (2016). A soft, wearable microfluidic device for the capture, storage, and colorimetric sensing of sweat. Sci Transl Med., 8(366), 366ra165-366ra165.
2. Jia, W. et al. Electrochemical Tattoo Biosensors for Real-Time Noninvasive Lactate Monitoring in Human Perspiration (2013) – Anal. Chem. 85, 6553–6560.
3. Shay, T., Dickey, M. D. & Velev, O. D. Hydrogel-enabled osmotic pumping for microfluidics: Towards wearable human-device interfaces (2017). Lab Chip 17, 710–716

Background: High shear processing of colloidal nanoemulsions are commonly encountered in instances of fiber extrusion, 3D printing and vial filling. When an attractive interaction is present between the colloidal nanodroplets at elevated temperatures, a gel network forms¹. An imposed shear flow on the gelled networks result in the development of structural heterogeneity that correlates with the overall applied shear rate².

Results: In order to quantify the influence of shear on the shear-induced structures, we report velocity profiles of thermoresponsive nanoemulsions through glass capillaries using particle tracking velocimetry. Fluorescent microbeads are imaged with a high-speed confocal microscope to map the impact of local shear rates on colloidal gel microstructures. This velocity profile was compared to a theoretically derived velocity profile computed from the Navier-Stokes equations and the Herschel-Bulkley fluid model.

Conclusions: We find that the experimental velocity profile reveals instances of wall slip and shear banding which are not captured in the theoretical velocity profile.

References:

1. Helgeson ME, Moran SE, An HZ, Doyle PS. (2012). Mesoporous organohydrogels from thermogelling photocrosslinkable nanoemulsions. Nat Mater.
2. Cardenas-Vasquez, ED, Smith, KM, Doolan TJ, and Hsiao LC (2019). Shear-induced microstructural gradients in nanoemulsion-laden organohydrogel fibers. Submitted.

Background: We aim to develop stimuli-responsive microgels for the rapid repair of damaged nonwovens and recovery of its initial permeability and mechanical properties. The objective is to imitate the bio-response of platelets in wound healing and reproduce it in repairing nonwoven (NW) systems with stimuli-responsive microgels. Upon damage to polypropylene (PP) NW, dual responsive microgels that resemble the platelets are drop cast on the NW. Then, a magnetic field is employed to guide them towards the point of damage, thereby imitating the platelet congregation at a wound site. After an accumulation of the microgels at the tear, ultraviolet light (UV) exposure is used to crosslink the microgels along and across the point of the tear to repair the damage which is similar to the formation of a blood clot to repair the wound. Such a system, owing to its chemistry, can be used for repairing different NW substrates like polyolefins, polyesters, and polyamides, thereby enabling in-situ repair of textiles without removing it from the point of application. The work comprises of two overarching objectives: design and optimization of a microgel system that responds to magnetic and UV stimulus; incorporation of the stimuli-responsive microgels in the nonwoven matrix and characterizing the recovery in terms of permeability and mechanical properties.

Results: We have successfully synthesized and characterized dual-responsive microgels that can be migrated using a magnetic field and crosslinked using UV-radiation. We have successfully demonstrated pinhole repairs of PP NW using functional microgels. By including the magnetic response in the microgels, we can locally concentrate the microgels and close the tear with UV-based crosslinking. This repair of NWs also recovers the permeability of the NW as compared to the original nonwoven before the tear.

Conclusions: The use of magnetic microgels for repair enables concentration and localization of the healing agents, thereby reducing the amount of material required for healing and pinhole repair as compared to repair using non-magnetic microgel. In the upcoming months, pinhole repairs of other nonwoven substrates (like polyethylene, polybutylene terephthalate, polyethylene terephthalate, etc..,) will be conducted to prove that this technology is substrate independent and can be used across different substrates.

References:

1. Y. H. Ding, M. Floren, and W. Tan, “Mussel-inspired polydopamine for bio-surface-functionalization,” Biosurface Biotribology, vol. 2, no. 4, pp. 121–136, Dec. 2016.

Background: The morphology of colloidal particles can critically determine the properties of soft materials such as gels, coatings, nonwovens, and composites.[1,2] Many efforts have been made to engineer methods to produce high aspect ratio polymeric materials such as electrospinning and melt blowing, however, these processes suffer from lack of scalability and versatility.[3] Polymer precipitation within a laminar nonsolvent flow has previously been shown to be a promising new method of producing nanofibers.[4] Herein, we investigate shear-driven polymer precipitation within a turbulent nonsolvent flow and show that the morphology of the resulting material is highly controllable.[5] Furthermore, we show that the capability of nanofibrous material production is expanded using this technique, as new precipitation mechanisms are utilized to produce previously undescribed colloidal materials.

Results: Polymer precipitation within a turbulent nonsolvent flow is shown to be capable of producing polymer materials with tunable morphologies from highly branched and nanofibrous soft dendritic colloids to mesoporous nano-sheets. Utilizing rapid precipitation mechanisms other than nonsolvent-induced phase separation such as hydrogel cross-linking and polyelectrolyte complexation allow the production of nanofibrous hydrogel and polyelectrolyte composite nanofibrous SDCs and expands the library of materials that can be produced by the shear-driven precipitation process. We show that SDCs have extraordinary adhesion and structuring properties due to their biomimetic, branched-fiber structure and the resulting van der Waals interactions with the substrate. The production process results in SDCs in suspension, which enables their two-dimensional use as physical adhesives, coatings, and nonwovens as well as three-dimensional applications as physical gels, rheology modifiers and composite fillers, and aerogels.

Conclusions: Shear-driven polymer precipitation is a powerful new technique that can produce nanofibrous colloidal structures from a nearly limitless number of materials. The SDC morphology is of particular interest due to its generations of bundled nanofibers comprising the greater particulates. This high aspect ratio material shows unrivaled efficiency in thickening and physical gelation properties in suspension as well as high adhesion and cohesion when deposited as a film or coating. The combination of these characteristics makes evident the vast potential of the shear-driven precipitation process as a technique to mass-produce the next generation of designer colloidal materials for any number of applications.

References:

1. Khan, S. A. & Zoeller, N. J. Dynamic rheological behavior of flocculated fumed silica suspensions. J. Rheol. (N. Y. N. Y). 37, 1225–1235 (1993).
2. Bahng, J. H. et al. Anomalous dispersions of ‘hedgehog’ particles. Nature 517, 596–599 (2015).
3. Xue, J., Wu, T., Dai, Y. & Xia, Y. Electrospinning and electrospun nanofibers: Methods, materials, and applications. Chem. Rev. 119, 5298–5415 (2019).
4. Smoukov, S. K. et al. Scalable liquid shear-driven fabrication of polymer nanofibers. Adv. Mater. 27, 2642– 2647 (2015).
5. Roh, S., Williams, A. H., Bang, R. S., Stoyanov, S. D. & Velev, O. D. Soft dendritic microparticles with unusual adhesion and structuring properties. Nat. Mater. 18, 1315–1320 (2019).

Background: Due to the increased environmental concern related to petroleum-based packaging systems, several calls are emerging from both the public and scientific communities to find suitable environmentally friendly alternatives. Polysaccharides derived films represent an attractive opportunity as the materials are sustainable, biodegradable, versatile and have great film forming properties. Through this context, this work is investigating the development of biopolymer-based packaging films that overcome the traditional limitations of biodegradable packaging materials, namely poor mechanical properties and excessive water uptake [1]. Through the incorporation of soft biopolymer based microparticles in the films, their functional properties could be enhanced and tailored for packaging applications. Reinforcing the matrix with these particles would produce composite, sustainable and biodegradable films that would reduce the environmental pollution and increase the shelf life of food products.

Results: Bio-composite films based on a polysaccharide hydrogel matrix of agarose and a reinforcing filling of soft microparticles made of chitosan (CS) and sodium alginate (SA) have been developed using solution casting method [2]. Several film functional properties have been tested like mechanical strength, elongation at break, light transmittance, water uptake and surface wettability. The preliminary results show a promising enhancement in the mechanical properties of the composite films compared to the pure agarose films; with the tensile strength and the elongation at break increasing by ca. 22% and 50% respectively. As the main limitation of the polysaccharide-based films is the excessive water uptake, the swelling capacity of the composite films decreased by 25%. The composite films show exceptional optical properties with more than 85% light transmission in the visible spectrum range. Preliminary FTIR results suggest the formation of hydrogen bonds between the agarose and the reinforcing matrix of CS or SA. The formation of these bonds can explain the reinforcing effect that the particles have on the film physicochemical properties.

Conclusions: The functional properties of a new class of biodegradable and sustainable composite films show promising enhancement over their pure counterpart. The enhanced properties could make these films suitable for sustainable packaging applications. Moving forward, other pivotal packaging film properties will be tested like water vapor transmission rate, oxygen barrier properties, water solubility and thermal characteristics.

References:

1. A. Awadhiya, D. Kumar, K. Rathore, B. Fatma, and V. Verma, “Synthesis and characterization of agarose–bacterial cellulose biodegradable composites,” Polym. Bull., vol. 74, no. 7, pp. 2887–2903, 2017.
2. R. M. Felfel, K. M. Z. Hossain, S. F. Kabir, S. Y. Liew, I. Ahmed, and D. M. Grant, “Flexible and transparent films produced from cellulose nanowhisker reinforced agarose,” Carbohydr. Polym., vol. 194, pp. 328–338, 2018.

Background: As nanomaterials become more common, available, and better understood, they are investigated in various applications, including plant protection. Several research groups have studied the use of different nanomaterials, including metal oxide nanoparticles and carbon nanotubes, as antifungals, but these materials remain in the environment for a very long time with potentially toxic effects. Our group has developed environmentally benign nanoparticles (EbNPs) of lignin, and we are investigating their use as an antifungal agent.

Results: Our EbNPs have the potential for a wide range of applications, and have been proven to be efficient antibacterial agents when loaded with silver ions. Preliminary experiments showed that EbNPs were almost as efficient at preventing fungal growth as a commercial chemical, and we are studying the fundamental interactions between all the components to understand these results. Through the use of bright-field and fluorescence microscopy, we are able to track the trends of fungal growth and where the EbNPs are going on the spores or substrate. Using various combinations and concentrations of EbNPs, spores, and different types of surfactants, we investigate colloidal interactions in solution, coffee ring formation on surfaces, and infectivity when applied to rose petals. We are also studying the spores and nanoparticle interactions over agar plates to macroscopically observe the difference between the systems.

Conclusions: EbNPs are interacting with fungal spores causing aggregation which is resisting the spore development. Further studies are currently ongoing to better understand the phenomenon. Such essential understanding of these interactions will assist in formulating efficient and environmentally benign antifungal products.

References:

1. Richter, Alexander P., Brown, Joseph S., Bharti Bhuvanesh, Wang Amy, Gangwal Sumit, Houck Keith, Cohen Hubal, Elaine A., Paunov, Vasselin N., Stoyanov, Simeon D. and Velev, Orlin D. (2015). An environmentally benign antimicrobial nanoparticle based on a silver-infused lignin core. Nat Nano, 10, 817.