Hydrogel microparticles for biosensing

Due to their hydrophilic, biocompatible, and highly tunable nature, hydrogel materials have attracted strong interest in the recent years for numerous biotechnological applications. In particular, their solution-like environment and non-fouling nature in complex biological samples render hydrogels as ideal substrates for biosensing applications. Hydrogel coatings, and later, gel dot surface microarrays, were successfully used in sensitive nucleic acid assays and immunoassays. More recently, new microfabrication techniques for synthesizing encoded particles from hydrogel materials have enabled the development of hydrogel-based suspension arrays. Lithography processes and droplet-based microfluidic techniques enable generation of libraries of particles with unique spectral or graphical codes, for multiplexed sensing in biological samples. In this review, we discuss the key questions arising when designing hydrogel particles dedicated to biosensing. How can the hydrogel material be engineered in order to tune its properties and immobilize bioprobes inside? What are the strategies to fabricate and encode gel particles, and how can particles be processed and decoded after the assay? Finally, we review the bioassays reported so far in the literature that have used hydrogel particle arrays and give an outlook of further developments of the field. Keywords: Hydrogel; Biosensor; Microparticle; Multiplex assayNovartis Institutes of Biomedical Research (Presidential Fellowship)Novartis Institutes of Biomedical Research (Education Office)National Cancer Institute (U.S.) (Grant 5R21CA177393-02)National Science Foundation (U.S.) (Grant CMMI-1120724)Institute for Collaborative Biotechnologies (Grant W911NF-09-0001)United States. Army Research Offic

Designing Scalable Biological Interfaces

This thesis presents the analysis and design of biological interfacing technologies in light of a need for radical improvements in scalability. It focuses primarily on structural and functional neural data acquisition, but also extends to other problems including genomic editing and nanoscale spatial control. Its main contributions include analysis of the physical limits of large-scale neural recording, experimental development of a screening platform for ion-dependent molecular recording devices, characterization of the design space for molecularly-annotated neural connectomics, and new designs for high-speed genome engineering and bio-nano-fabrication. Articulating governing principles and roadmaps for these domains has contributed to the initiation of multi-institutional projects that are strategically targeted towards scalability

Current Trends in Cancer Nanotheranostics: Metallic, Polymeric, and Lipid-Based Systems

Theranostics has emerged in recent years to provide an efficient and safer alternative in cancer management. This review presents an updated description of nanotheranostic formulations under development for skin cancer (including melanoma), head and neck, thyroid, breast, gynecologic, prostate, and colon cancers, brain-related cancer, and hepatocellular carcinoma. With this focus, we appraised the clinical advantages and drawbacks of metallic, polymeric, and lipid-based nanosystems, such as low invasiveness, low toxicity to the surrounding healthy tissues, high precision, deeper tissue penetration, and dosage adjustment in a real-time setting. Particularly recognizing the increased complexity and multimodality in this area, multifunctional hybrid nanoparticles, comprising different nanomaterials and functionalized with targeting moieties and/or anticancer drugs, present the best characteristics for theranostics. Several examples, focusing on their design, composition, imaging and treatment modalities, and in vitro and in vivo characterization, are detailed herein. Briefly, all studies followed a common trend in the design of these theranostics modalities, such as the use of materials and/or drugs that share both inherent imaging (e.g., contrast agents) and therapeutic properties (e.g., heating or production reactive oxygen species). This rationale allows one to apparently overcome the heterogeneity, complexity, and harsh conditions of tumor microenvironments, leading to the development of successful targeted therapies.The authors acknowledge Fundação para a Ciência e a Tecnologia (FCT) for financial support through Projects UID/DTP/04138/2013, PTDC/MED-QUI/31721/2017 and for financial support through PhD fellowship SFRH/BD/117586/2016.info:eu-repo/semantics/publishedVersio

Encoded hydrogel microparticles for high-throughput molecular diagnostics and personalized medicine

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2012.Cataloged from PDF version of thesis.Includes bibliographical references (p. 141-161).The ability to accurately detect and quantify biological molecules in complex mixtures is crucial in basic research as well as in clinical settings. Advancements in genetic analysis, molecular diagnostics, and patient-tailored medicine require robust detection technologies that can obtain high-density information from a range of physiological samples in a rapid and cost-effective manner. Compared to conventional microarrays and methods based on polymerase chain reaction (PCR), suspension (particle-based) arrays offer several advantages in the multiplexed detection of biomolecules, including higher rates of sample processing, reduced consumption of sample and reagent, and rapid probe-set modification for customizable assays. This thesis expands the utility of a novel hydrogel-based microparticle array through (1) the creation of a microfluidic, flow-through fluorescence scanner for high-throughput particle analysis, (2) the development of a suite of techniques for the highly sensitive and specific detection of microRNA (miRNA) biomarkers, and (3) the investigation of new methods for directly measuring biomolecules at the single-cell level. Graphically-encoded hydrogel microparticles synthesized from non-fouling, bioinert poly(ethylene glycol) (PEG) and functionalized with biomolecule probes offer great promise in the development of high-performance, multiplexed bioassays. To extend this platform to applications in high-throughput analysis, particle design was optimized to ensure mechanical stability in high-velocity flow systems, and a single-color microfluidic scanner was constructed for the rapid fluorescence interrogation of each particle's spatially-segregated "code" and "probe" regions. The detection advantages of three-dimensional, probe-laden hydrogel scaffolds and the operational efficiencies of suspension array technology were then leveraged for the rapid multiplexed expression profiling of miRNA. The graphical encoding method and ligationbased labeling scheme implemented here allowed for scalable multiplexing with a simple workflow and an unprecedented combination of sensitivity, flexibility, and throughput. Through the rolling circle amplification of a labeling oligonucleotide, it was possible to further enhance the system's sensitivity and resolve single-molecule miRNA binding events on particle surfaces, enabling the first direct detection of low-abundance miRNA in human serum without the need for RNA extraction or target amplification. Finally, by arraying cells and gel particles in polydimethylsiloxane (PDMS) microwells, it was possible to dramatically improve the particles' target capture efficiency and thereby move closer to a regime in which miRNAs and other biological molecules may be directly detected without target amplification from single cells.by Stephen Clifford Chapin.Ph.D

Advanced flow lithography and barcoded particles

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2012.Cataloged from PDF version of thesis.Includes bibliographical references (p. 120-138).Anisotropic multifunctional particles have drawn much attention, leading to wide ranges of applications from biomedical areas to electronics. Despite their enormous potentials, particles with geometrically and chemically complex patterns are not widely used because existing methodologies have limitations in large scale, facile production and suffer from constraints of functionality and morphology. For example, the geometries of multifunctional particles prepared by liquid-phase particle synthesis have been mainly restricted to spheres, deformed spheres, or cylinders. This geometrical restriction has resulted from the tendency of liquid systems to adopt arrangements that minimize surface energy. Although template-assisted particle fabrication can overcome this, these methods are largely ineffective at producing particles with chemical anisotropy or patterning, as the precursor liquid is simply isolated in a non-wetting template and then crosslinked in situ. Currently, a technique that can provide both geometrical and chemical complexities to particles has been missing. Distinguished with the above techniques, flow lithography (FL) has been emerging as a powerful synthesis tool that enables the creation of microparticles with complex morphologies and chemical patterns. Combining photolithography with microfluidic methods, FL has provided precise control over particle size, shape, and chemical patchiness. However, in the primitive versions of FL, particle geometry and chemical patterning has been restricted to 2D and 1D, respectively. Also, these techniques have required the use of polydimethylsiloxane (PDMS) devices, greatly limiting the range of precursor materials which can be processed in FL. Here, we present advanced flow lithography to achieve much higher degree of geometrical and chemical complexity than before. For example, lock release lithography (LRL) can be used to introduce three-dimensional (3D) morphologies, and provide chemical anisotropy in the x-y dimensions (in-plane dimensions) of particles. Also, hydrodynamic focusing lithography (HFL) was developed to offer z-directional (particle height direction) chemical anisotropy to particles. Lastly, oxygen-free flow lithography was a technique designed to extend current PDMS-based FL to any kinds of devices and allow for the creation of particles from previously inaccessible reagents such as organic solvents. In this thesis, we have also demonstrated advanced barcoded particles as one application of advanced flow lithography. Previously, barcoded hydrogel particles were created as a promising diagnostic tool for high-throughput screening and multiplexed detection of biomolecules. Utilizing advanced flow lithography, we have added advanced functions to the hydrogel particles introducing magnetic beads, tri-layered structures or near-infrared sensing materials. As the first advanced barcoded particles, we present magnetic barcoded hydrogel particles that had led to practical applications in the efficient orientation and separation of the barcoded particles. Also, we show reinforced barcoded particles that combine the usually orthogonal characteristics of an open porous capture region for biomolecule detection with strong structural properties that resist deformation in flow. Finally, we demonstrate near-infrared barcoded particles which can exhibit label-free and real time detection of target molecules.by Ki Wan Bong.Ph.D

Enabling technologies for multiplexed biomolecule analysis and cell sorting

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2008.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Includes bibliographical references (p. [109]-122).The quantification and manipulation of biological entities from a physiological sample is extremely important for a broad range of applications in medical diagnostics, therapeutics, and basic science research. From a diagnostics standpoint, the cells, proteins, and nucleic acids that compose our bodies contain an enormous amount of information that can indicate the presence of, progression of, or even susceptibility to a given disease. However, extracting this information is often quite challenging. New tools are constantly being developed to make diagnostic testing more accurate, less invasive, faster, and less expensive. To this end, this thesis describes that advent of technologies to (1) precisely pattern biologically- and magnetically-active beads in hydrogel substrates for cell sorting and pattering, (2) synthesize morphologically and chemically-complex microparticles in a high-throughput fashion, and (3) perform rapid and accurate multiplexed biomolecule quantification using such particles. Bead-Patterned Hydrogels are a class of materials developed in this thesis that consist of microbeads precisely patterned in poly(ethylene glycol) (PEG) matrices. Using microfluidics and projection lithography on a standard microscope, magnetically-active or protein-decorated beads were patterned in close-packed or disperse-bead patterns on glass substrates with high resolution over large areas. Using slight alterations to ... bio-inert PEG matrix, or exposed from the PEG surface. It was shown that bead-patterned hydrogels could be used for the phenotype-specific sorting or patterning of lymphocytes. As was observed in the synthesis of bead-patterned hydrogels, free-radical polymerization is inhibited near microfluidic channel walls due to oxygen diffusion through the porous polydimethoxysilane (PDMS) elastomer composing devices.(cont.) By exploiting this phenomenon using ... an all-PDMS device, C graphy was developed. In stark contrast to traditional methods for anisotropic particle synthesis, this one-phase process provides a simple method to synthesize microparticles with complex morphologies and/or multiple adjacent chemistries in a high-throughput fashion. The processes is broadly applicable to any free-radical reacting monomer. For improved resolution and sharpened interfaces between adjacent chemistries ...by Daniel Colin Pregibon.Ph.D

A structural study of correlated materials: incipient mott insulators and low-dimensional systesm.

Current theories of high-temperature superconductivity suggest that electrons must organize into Cooper pairs in order for a material to exhibit a superconducting phase. Electrons in insulators experience significant repulsive interactions that tend to keep electrons localized at atomic positions. In contrast, electrons in metals are delocalized, interact weakly, and are free to conduct electricity. Therefore, the formation of Cooper pairs should have different mechanisms for metals compared to insulators. This contrast raises the debate about the origin of high-temperature superconductivity in iron-based material, whether it depends on the strong or weak coupling. Many iron-based materials are metallic in the normal phase; however, before entering the superconducting phase, iron-based superconductors are believed to harbor insulating characteristics in close proximity to a Mott insulator. Furthermore, because superconductivity in iron-based materials occurs the border of correlation-induced electronic order, it is crucial to understand the nature of the ordered states. The newly reported iron oxychalcogenide Ca2O2Fe2.6OS2 is an antiferromagnetic (AFM) insulator at room temperature. Oxychalcogenides are structurally similar to the iron-based superconductors and it is possible to tune the Fe-Fe ion distance to drive the material from an insulating to a metallic phase. It is unexpected that a decrease in the Fe-Fe ion distance for Ca2O2Fe2.6OS2 results in enhanced insulating properties instead of making the material more metallic. This violates the predictions of the well-established electron band theory. The first aim in this work was to examine the novel Mott insulator Ca2O2Fe2.6OS2, crystal structure, and the effect of selenium doping on the material. X-ray powder diffraction (XRD) and Rietveld analysis were used to study the crystal structure. Also, neutron powder diffraction was used to study the magnetic peak intensity behavior with changes in temperature. Transport measurements were performed on both samples and activation energies (E$_a$) was calculated as 0.0694 eV and 0.06098 eV for Ca2O2Fe2.6OS2 and Ca2O2Fe2.6OS1.75Se0.25 respectively. The Rietveld fits confirmed that the material had tetragonal crystal system with space group $P_4/mmm$ for both samples. The calculated $\beta$ showed that this Mott insulator has the two dimensional Ising model. The volume of crystal increased with decreasing temperature while the atomic site occupancy increased. Also, the doping did not affect the crystal structure, however it suppressed the magnetic behaviour in Ca2O2Fe2.6OS1.75Se0.25. The second aim of this work was to study the structure of iron oxychalcogenides La2O2Fe2O(S, Se)2, compare the short-range to the average structure and understand the short-range behavior in this type of Mott insulators. Neutron powder diffraction (NPD) was used to study the short and average structure of La2O2Fe2O(S, Se)2. The obtained NPD data were analyzed using Rietveld analysis and pair distribution function (PDF) method. We observe the presence of fluctuating nematic ordering from low temperature to room temperature. High values of the isotropic thermal parameter (U33) for the oxygen atom O2 along c-axis was observed. The results also suggested the presence of short-range local distortion in both La2O2Fe2O(S, Se)2 materials which can be evidence of nematic behavior in the short-range of these materials. The last part of this research investigated the transition metal dichalcogenides (TMDs). TMDs are receiving a large amount of attention because they have been posited as a potential successor to silicon in the future of electronics manufacturing. The fabrication of large TMD crystals is currently an active area of industrial work. Most TMDs are low dimensional materials in the sense that their structures consist of stacks of hexagonally atomic layers of transition metal atoms or chalcogens sandwiched by transition metal (TM) layers. In addition to this, TMD electronic properties are primarily contained in the 2D TM planes. The last aim of this research was to study the transition metal dichalcogenide MoTe2 in two of its three stable phases (2H-MoTe2 and 1T\u27-MoTe2). Also, we studied the Td phase, which results from the phase transition of 1T\u27-MoTe2 at low temperatures. Powder diffraction techniques were implemented to study the detail of the crystal structure of bulk phases. Rietveld analysis was used to analyze the powder diffraction data of all MoTe2 phases. Electron dispersion x-ray spectroscopy (EDX) and Raman spectroscopy were performed on both samples to check the purity of the samples. The EDX and Raman spectroscopy showed that the samples were clear from impurities. The Rietveld analysis determined the crystal structure of 2H-MoTe2, 1T\u27-MoTe2 and Td-MoTe2 were hexagonal P63/mmc, monoclinic P21/m, and orthorhombic Pmn21, respectively. Our results showed that temperature affected the atomic site occupancy in the studied MoTe2 phases, which might be related to the stacking faults in MoTe2 layers

Polymer-Coated Inorganic Nanoparticles: Nanotools for Life Science Applications

This dissertaion focus on the synthesis, surface modification and characterization of inorganic nanoparticles(NPs), including magnetic, plasmonic and semiconductor NPs. With controlling the reaction conditions during the synthesis, different particle diameters in the range of 4 nm to 30 nm can be synthesized. Afterwards, polymer coating process was successfully applied to different materials by overcoating the NPs with an amphiphoilic polymer, which can make the particle water soluble. This work aimed to produce the polymer-­ coated nanoparticles,analyze and compare their physico-­‐chemical properties based on different materials,and further, to test their potential for different biological applications

ICR ANNUAL REPORT 2019 (Volume 26)[All Pages]

This Annual Report covers from 1 January to 31 December 201