Browsing by Subject "Biotechnology"

Acoustic waves, as a form of mechanical vibration, not only induces the force directly on the object, but also induces the motion of the medium that propagates throughout the system. The study of acoustofluidic mainly focuses on the exploration of the underlying mechanism of the acoustic waves and fluid motion and the methodology of applying this technique to practical applications. Featuring its contactless, versatile, and biocompatible capabilities, the acoustofluidic method makes itself an ideal tool for biosample handling. As the majority of the bio-related samples (e.g., cell, small organism, exosome) possess their native environment within liquids, there is an urgent need to study the acoustic induced fluid motion in order to cooperate with the development of the acoustic tweezing technique. While both the theoretical study and application exploration have been established for the combination of acoustics and microfluidics, the fluid motion on a larger scale is still under-developed. One reason is that, although the acoustofluidic methods hold great potential in various biomedical applications, there is a limited way to form an organized motion in a larger fluid domain, which may lead to the imprecise manipulation of the target. On the other hand, the theoretical study for the microfluidic domain is on the basis of a simplified model with certain assumptions, when applying to the larger fluid area, and significantly influences both the accuracy and computation cost. In this dissertation, we have first developed a series of theoretical and numerical methods in order to provide insights into the acoustofluidic phenomenon in different domain scales. Specifically, we explored the non-linear acoustic dynamics in fluids with the perturbation theory and Reynolds’ stress theory. Then we presented that the vortex streaming can be predicted and designed with our theoretical and numerical study, which can be utilized for various fluid systems and expanded to practical biomedical applications. The boundary-driven streaming and Reynolds’ stress-induced streaming are studied and applied to the digital acoustofluidic droplet handling platform and droplet spinning system, respectively. We demonstrated that within the digital acoustofluidic platform, the droplet can be manipulated on the oil layer in a dynamic and biocompatible manner. Meanwhile, in the droplet spinning system, we can predict and guide the periodic liquid-air interface deformation, as well as the particle motion inside the droplet. We demonstrated that with the theoretical and experimental study, this platform can be utilized for the nanoscale particle (e.g., DNA molecule and exosome) concentration, separation, and transport. Next, based on our study of the acoustically induced fluid motion, we developed an integrated acoustofluidic rotational tweezing platform that can be utilized for zebrafish larvae rapid rotation (~1s/rotation), multi-spectral imaging, and phenotyping. In this study, we have conducted a systematic study including theory development, acoustofluidic device design/fabrication, and flow system implementation. Moreover, we have explored the multidisciplinary expansion combining the acoustofluidic zebrafish phenotyping device with the computer-vision-based 3D model reconstruction and characterization. With this method, we can obtain substantial information from a single zebrafish sample, including the 3D model, volume, surface area, and deformation ratio. Moreover, with the design of the continuous flow system, a flow-cytometry-like system was developed for zebrafish larvae morphological phenotyping. In this study, a standard workflow is established which can directly transfer the groups of samples to a statistical digital readout and provide a new guideline for applying acoustofluidic techniques to biomedical applications. This work represents a complete fusion of acoustofluidic theory, experimental function, and practical application implementation.

In the context of today's global mobility, information, bodies and goods are circulating across the globe, and even further into outer space. However, we face a paradox: the more we move, the more we become sedentary. The modes of transportation that enable our global mobility are working against us, insidiously dwindling our psycho-physical mobility. Globalization is thus not the world becoming bigger (or too big), but the world becoming immobile. Taking the body as the central non-place of political space, Architectures of Aliveness: Building Beyond Gravity interrogates the possibility of inhabiting circulation as a pragmatic form of resistance to the contemporary immobilization of life. In an era in which bodies and goods are ever more constantly in global circulation, architectures of aliveness ask, what would an experience of weightlessness do for us?

Biotechnology serves as the current dominant model for enlivening architecture and the mobility of its inhabitants. Architectures of aliveness invert the inquiry to look instead at outer space's modules of inhabitation. In questioning the possibility of making circulation inhabitable --as opposed to only inhabiting what is stationary--architectures of aliveness problematize architecture as a form of biomedia production in order to examine its capacity to impact psychic and bodily modalities toward an intensification of health. Problematized synchretically within life's mental and physical polarization, health is understood politically as an accretion of our capacity for action instead of essentially as an optimization of the biological body. The inquiry emerges at the intersection of biotechnology, neurosciences, outer space science and technology, and architecture. The analysis oscillates between historical and contemporary case studies toward an articulation that concentrates on contemporary phenomena while maintaining an historical perspective. The methodology combines archival research, interviews, and artistic and literary analysis. The analysis is informed by scientific research. More precisely, the objective is to construct an innovative mode of thinking about the fields of exchangeability between arts and sciences beyond a critique of instrumentality.

The outcomes suggest that architectures of aliveness are architectures that invite modes of inhabitation that deviate from habitualized everyday spatial engagements. It also finds that the feeling of aliveness emerges out of the production of analog or continuous space where the body is in relation with space as opposed to be represented in it. The analysis concludes that the impact of architecture on our sense of wellbeing is conditioned by proprioceptive experiences that are at once between vision and movement and yet at the same time in neither mode, suggesting an aesthetic of inhabitation based on our sense of weightedness and weightlessness.

These outcomes are thus transduced to the field of media studies to enchant biomediatic inquiry. Proposing a renewed definition of biomedia that interprets life as a form of aesthetic relation, architectures of aliveness also formulate a critique of the contemporary imperialism of visualization techniques. Architectures of aliveness conclude by questioning the political implications of its own method to suggest opacity and agonistic spaces as the biomediatic forms of political space.

Recombinant technology has given us the powerful ability to imagine and create novel biological entities, from potent therapeutics to functionally active materials. By harnessing nature’s building blocks and reconfiguring these components, recombinant engineering unlocks the potential to tailor drug specificity and pharmacokinetics, rationally design biomaterials, understand and define protein structure, and probe cellular function with molecular precision. These technological feats are made possible with a few simple biological ingredients: nucleotides, sugars, and amino acids. These components, exquisitely crafted by evolution, are individually combined in useful ratios and precise sequences in living systems to synthesize DNA, RNA, polysaccharides, and proteins. These macromolecules collectively support organismal structure and function and give rise to the incredible diversity in Charles Darwin’s “great tree” of life. However, the seemingly infinite potential for new materials built from these components is, in fact, limited. The chemical identity of these building blocks – with a particular focus herein on the twenty naturally-occurring amino acids – limits the scope and functionality of the recombinant materials we can produce. In order to functionalize these products, to fundamentally change their chemical identity while preserving their biological functionality, we require the finesse of bioorthogonal chemistries and modification techniques.

Bioorthogonal reactions modify biological materials within living systems without perturbing function, much as two orthogonal lines can extend in different directions and intersect only at a single point. That point of intersection can be precisely defined through recombinant technology and gives us access to new classes of biomaterials. The term “bioorthogonal”, coined by Carolyn Bertozzi, importantly defines these unique chemistries, which inertly co-exist with biology until the exact moment when the desired reactions are initiated, to enhance – and even transform – biological systems.

Bioorthogonal modification of proteins will, by definition, require expansion of the biochemical toolbox; there are a variety of techniques used to achieve this goal. In these studies, we explore the use of genetic code expansion for incorporation of unnatural amino acids. This technology permits co-translational incorporation of amino acids with unique and non-canonical R-groups directly into the polypeptide backbone of a protein or biopolymer. These residues introduce unique chemical reactivity for further functionalization with desired moieties or chemical transformation.

We have used this technology to develop novel therapeutic and material platforms comprised of a unique biopolymer, elastin-like polypeptide (ELP). This thermally responsive biopolymer is easily recombinantly synthesized, though more biochemically complex ELPs require successful bioorthogonal modification. We designed the unnatural amino acid-containing ELPs necessary to enable our strategies for developing three distinct biomaterial platforms: 1) photoreactive ELPs which can generate stable hydrogel particles spanning four orders of magnitude in size; 2) a universal strategy for drug-loaded, targeted ELP nanoparticles by incorporation of a unique site for drug attachment; 3) a sustained-release therapeutic for treatment of brain tumors combining proteins of distinct cellular origin.

We have combined existing tools, technologies, and materials to generate these novel platforms with utility in biomaterials, drug delivery, and cancer therapeutics. The optimizations performed in developing each of these systems will inform future studies with similar goals; similarly, the reactions and strategies employed will contribute to furthering our understanding of the full potential of these important bioorthogonal chemistries.

Searches for the genetic underpinnings of uniquely human traits have focused on human-specific divergence in conserved genomic regions, which reflects adaptive modifications of existing functional elements. However, the study of conserved regions excludes novel functional elements that descended from previously neutral regions. In this work, I integrate comparative genomic analyses with human population variation data to reveal that rapid divergence rate is associated with positive selection in human evolutionary history. Encouraged by this finding, I identified 1581 Human Ancestor Quickly Evolved Regions (HAQERs), which represent the fastest-evolved regions of the human genome. HAQERs rapidly diverged in an episodic burst of directional positive selection prior to the human-Neanderthal split before transitioning to constraint within hominins. HAQERs are enriched for bivalent chromatin states, particularly in gastrointestinal and neurodevelopmental tissues, and genetic variants linked to neurodevelopmental disease. I led a collaborative effort to develop scSTARR-seq as a multiplex single-cell in vivo enhancer assay to discover that rapid sequence divergence in HAQERs generated hominin-unique enhancers in the developing cerebral cortex. I propose that a lack of pleiotropic constraints and elevated mutation rates poised HAQERs for rapid adaptation and subsequent susceptibility to disease.