Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 61-65). / Novel sequencing technologies are rapidly advancing studies of microbial community structure and diversity. Sequencing platforms like the Illumina Genome Analyzer II (GAI1) and the Applied Biosystems SOLiD enable experiments that were previously too expensive or time-consuming by providing a very large number of short reads at a significantly lower cost per base pair (bp) than conventional longer-read systems like the Roche-454 GS FLX pyrosequencing instrument. Short-read platforms, however, are not readily amenable to some applications like metagenomics and metatranscriptomics, and therefore pyrosequencing remains the dominant sequencing technique in these fields. The primary reason short-read technologies have not been used for metagenomic analyses is due to the difficulty of confidently assigning phylogeny or putative gene function to short sequences. In an effort to overcome this limitation, a strategy was developed for preparing libraries from sheared genomic DNA with tunable size distributions using solid phase reversible immobilization (SPRI). This size selection captures DNA fragments of the necessary length to enable the generation of overlapping reads when sequenced from both ends. The lower-quality ends of mated reads were then used to produce a high-quality consensus sequence in the region of overlap. The fraction of composite reads that could be assigned to a taxon was similar to those from 454-FLX, despite the slightly shorter average read length of the composite Illumina reads. This technique successfully demonstrates a practical and economical alternative to 454-FLX for metagenomics. In addition, a scalable, fully automated process for creating sequence-ready, barcoded libraries of 16S rDNA for microbial diversity studies was developed for the Illumina platform. This process will enable sequencing of hundreds of environmental samples on a single Illumina flowcell, greatly decreasing the cost per sample while providing thousands of short-reads for microbial ecology studies. The incorporation of error-correcting, short DNA "barcodes" (also called tags or indexes) during polymerase chain reaction (PCR) amplification of the 16S sequence facilitates sample multiplexing. This process also utilizes the SPRI method to replace column-based reaction clean-ups, enabling the library preparation procedure to be performed almost entirely by a robotic liquid handling workstation. Finally, two unique PCR primer systems (primer-clipping and primer-skipping) were engineered to increase the informative read length of 16S sequence by either cutting the known universal tract out of the final-product to be sequenced, or by omitting sequencing of the universal regions using specially-crafted primers designed to be compatible with Illumina platform conditions. By applying both the overlapping-read technique and multiplexed 16S library preparation workflow, a streamlined approach for efficient gene and species discovery has been assembled to accommodate new metagenomic applications for the Illumina sequencing platform. / by Matthew Christopher Blackburn. / S.M.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1998. / Includes bibliographical references (leaves 245-265). / by Steffen Ernst. / Ph.D.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1995. / Includes bibliographical references (leaves 78-79). / by Katsuya Ishikawa. / M.S.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1996. / Includes bibliographical references. / by Susan J. Sofia Allgor. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1996. / Includes bibliographical references (v. 2, leaves 343-356). / by Michael Tevriz Kezirian. / Ph.D.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1984. / MICROFICHE COPY AVAILABLE IN ARCHIVES AND SCIENCE. / Bibliography: leaves 562-586. / by Michael Anthony Serio. / Ph.D.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, February 2000. / Vita. / Includes bibliographical references (p. 114-133). / Interleukin-2 (IL-2) has been widely studied as a protein therapeutic due primarily to its central role in potentiating cell-based immunity. The effects of IL-2 on its cellular targets are mediated solely through interaction with one or more forms of the IL-2 receptor (IL- 2R). The overall goal of this thesis is to quantitatively characterize IL-2/IL-2R interactions toward the scientific end of advancing the understanding of the effects of molecular perturbations on cell function, and the technological end of providing insight into the design of improved IL-2 therapies. An interleukin-2 (IL-2) variant displays binding affinity to the heterotrimeric IL-2 receptor similar to that of wild-type (WT) IL-2, and was previously found to exhibit increased bioactivity in a T cell proliferation assay. Dedicated trafficking studies show that endocytic trafficking of this 20 I variant might be responsible for this increased potency, as a significantly increased fraction of internalized 201 is sorted to recycling instead of to lysosomal degradation. Denaturation experiments indicate that wild-type IL-2 and the 201 analog have similar stabilities at neutral pH; however, the analog displays decreased stability of the native and intermediate states under endosomal sorting conditions when compared to wild-type IL-2. This behavior correlates with differential pH-sensitivities of receptor binding affinity measured for IL-2 and the 201 variant. improved sorting leads to an extended half-life of intact 20 I, providing enhanced mitogenesis as compared to IL-2. We further conclude that this IL-2 variant minimizes undesired stimulation of NK cells. We describe a mathematical model that relates ligand-receptor trafficking properties to T cell proliferation in response to interleukin-2 (IL-2). The steady-state sorting behavior of the 201 variant is predictable from the model, as are criteria for designing IL-2 variants with further improvements in bioactivity. The concept of altering trafficking dynamics may offer a generalizable approach to generating improvements in the pharmacological efficacy of therapeutic cytokines. / by Eric Michael Fallon. / Ph.D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references. / On-chip flow chemistry synthesis has advanced rapidly in recent years as a fast and effective means to discover and screen suitable reaction candidates for continuous production. Among the many chemical reactions, multiphase reactions constitute a major category with important industrial applications, and microreactors have been shown to effectively enhance the efficiency of such reactions. However, compared to single-phase flow chemistry systems, many unknowns remain in the design, optimization and scale-up of multiphase microreactors - primarily due to the complex nature of the multiphase flow. Therefore, this work aims to obtain fundamental knowledge of the hydrodynamics, transport and reactions in multiphase microreactors through a combination of computation, theory and characterization. Specifically, I studied five typical multiphase flow chemistry modules: the segmented flow microreactor, the post microreactor, the tube-in-tube microreactor, the capillary microseparator and the membrane microseparator. A series of C++ solvers that simultaneously model multiphase hydrodynamics, transport and reactions on the microscale were developed and validated. Parallel computation with up to 128 cores were performed to accelerate simulation. Laser-induced fluorescence visualization combined with image analysis was used to systematically quantify key features such as interfacial area and phase holdup. A variety of analytic models were also developed to provide guidelines for enhanced reactor design. The integrated strategy elucidated the complex hydrodynamics and transport in microreactors with full physical details. The enhanced physical insight into multiphase microreactors would be crucial to predicting reactor performance, reducing experimental cost, and achieving reactor scale-up. / by Lu Yang. / Ph. D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2016. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Cataloged from student-submitted PDF version of thesis. / Includes bibliographical references (pages 153-162). / Desalination systems have become an important part of many water supply networks, and they have also been considered as solutions for water shortages and in areas in which access to clean and safe water is still a problem. The quality of available water that is encountered in these situations tends to vary significantly, ranging from seawater to just slightly brackish water to even just water with trace amounts of toxic ions or small amounts of infectious bacteria or viral particles. While current technologies provide a very good solution to desalinating seawater via reverse osmosis, the solutions that are currently used for brackish water or contaminated water are often suboptimal in that they often operate inefficiently in this regime. It is also often difficult to deploy these systems in environments with little infrastructure. In this thesis, shock electrodialysis is proposed and examined for its potential to effectively provide a solution for use with brackish and contaminated water. Shock electrodialysis is in many ways related to electrodialysis, but it is based on the emerging science of desalination shocks in porous media, giving it the distinct advantage of using fewer membranes and separating fresh and brine stream via a non-physical internal barrier (i.e. the shock), which then also allows for removal of particles. Furthermore, in contrast to electrodialysis, it is able to completely deionize water, which is extremely important when dealing with water sources that are contaminated with traces of toxic ions. Experimental results from a proof-of-concept prototype are presented and compared with numerical and analytical modeling results with the aim to better understand the important factors in shock electrodialysis. These results suggest that, while shock electrodialysis can indeed fully deionize water, the energy efficiency is still very poor and needs to be significantly improved before this technology can be effectively employed in the field. In addition to shock electrodialysis, this thesis also explores the use of a 4th-order Poisson equation to include ion-ion correlations in a simple manner when modeling two different electrolyte systems. The first system considered is a surface that was coated with a polyelectrolyte in solution with a simple electrolyte of varying concentration. This system is of interest, because, as the concentration changes, inversion of the apparent difference in potential between this surface and a surface that is not coated with polyelectrolyte is found to occur, a phenomenon that is not explained by traditional models. The second system considered is simply a bulk electrolyte solution in which the aim was to improve the Debye- Hückel theory for ionic activity to be able to more accurately predict the activity using a very simple model. In both systems, correlations proved to be important to varying degrees and the 4th-order equation proved to be useful in better predicting the observed phenomena. / by Sven Schlumpberger. / Ph. D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2007. / Includes bibliographical references (p. 437-458). / Sequential motif discovery, the ability to identify conserved patterns in ordered datasets without a priori knowledge of exactly what those patterns will be, is a frequently encountered and difficult problem in computational biology and biochemical engineering. The most prevalent example of such a problem is finding conserved DNA sequences in the upstream regions of genes that are believed to be coregulated. Other examples are as diverse as identifying conserved secondary structure in proteins and interpreting time-series data. This thesis creates a unified, generic approach to addressing these (and other) problems in sequential motif discovery and demonstrates the utility of that approach on a number of applications. A generic motif discovery algorithm was created for the purpose of finding conserved patterns in arbitrary data types. This approach and implementation, name Gemoda, decouples three key steps in the motif discovery process: comparison, clustering, and convolution. Since it decouples these steps, Gemoda is a modular algorithm; that is, any comparison metric can be used with any clustering algorithm and any convolution scheme. The comparison metric is a data-specific function that transforms the motif discovery problem into a solvable graph-theoretic problem that still adequately represents the important similarities in the data. / (cont.) This thesis presents the development of Gemoda as well as applications of this approach in a number of different contexts. One application is an exhaustive solution of an abstraction of the transcription factor binding site discovery problem in DNA. A similar application is to the analysis of upstream regions of regulons in microbial DNA. Another application is the identification of protein sequence homologies in a set of related proteins in the presence of significant noise. A quite different application is the discovery of extended local secondary structure homology between a protein and a protein complex known to be in the same structural family. The final application is to the analysis of metabolomic datasets. The diversity of these sample applications, which range from the analysis of strings (like DNA and amino acid sequences) to real-valued data (like protein structures and metabolomic datasets) demonstrates that our generic approach is successful and useful for solving established and novel problems alike. The last application, of analyzing metabolomic datasets, is of particular interest. Using Gemoda, an appropriate comparison function, and appropriate data handling, a novel and useful approach to the interpretation of metabolite profiling datasets obtained from gas chromatography coupled to mass spectrometry is developed. / (cont.) The use of a motif discovery approach allows for the expansion of the scope of metabolites that can be tracked and analyzed in an untargeted metabolite profiling (or metabolomic) experiment. This new approach, named SpectConnect, is presented herein along with examples that verify its efficacy and utility in some validation experiments. The beginning of a broader application of SpectConnect's potential is presented as well. The success of SpectConnect, a novel application of Gemoda, validates the utility of a truly generic approach to motif discovery. By not getting bogged down in the specifics of a type of data and a problem unique to that type of data, a broader class of problems can be addressed that otherwise would have been extremely difficult to handle. / by Mark Philip-Walter Styczynski. / Ph.D.