Chemical and Biomolecular Engineering

Dietary lipids are transported from the intestine through contractile lymphatics. Chronic lipid loads can adversely affect lymphatic function. However, the acute lymphatic pump response in the mesentery to a postprandial lipid meal has gone unexplored. In this study, we used the rat mesenteric collecting vessel as an in vivo model to quantify the effect of lipoproteins on vessel function. Lipid load was continuously monitored by using the intensity of a fluorescent fatty-acid analog, which we infused along with a fat emulsion through a duodenal cannula. The vessel contractility was simultaneously quantified. We demonstrated for the first time that collecting lymphatic vessels respond to an acute lipid load by reducing pump function. High lipid levels decreased contraction frequency and amplitude. We also showed a strong tonic response through a reduction in the end-diastolic and systolic diameters. We further characterized the changes in flow rate and viscosity and showed that both ...

for serving as my committee members and for all the research ideas they bestowed on me. In addition, I would like to thank them for letting my defense be a pleasing event, and for their intellectual comments and suggestions. I would especially like to thank my research group (both past and present members) for supporting me throughout my defense and also for being a huge helping hand in all my research activities. In addition, I would also like to thank NSF as it was the primary source of my funding, without which this work would not have been possible. A special thanks to my parents for their unconditional love and support throughout my career. All the words in the world cannot describe how grateful I am to them for all of the sacrifices they made on my behalf. I would also like to thank all of my friends especially Swetha and Rajiv who constantly motivated me to reach my goal and for also being my writing buddies during the last few weeks. I am indebted to Karthik for helping me with my introduction section by proofreading it. I would also like to thank Keerti (now also my wife), Anusha, Bhavana, Praneeth & family, and Anirrudh for being my closest friends and making my life in Atlanta memorable. In the end, I would like express my iv deepest appreciation to the joy of my life, my wife Keerti who gave me love, happiness, hope, supported me during the difficult times and also helped me with my writing. v

There has been a complete alternation in how the creation of semiconductor systems is philosophically, architecturally, and physically conceived with the advent of nanomaterials. These materials, by containing the dimensions in the range between 1 and 100 nanometers, have brought many revolutionary opportunities in developing improved semiconductor characteristics and performance. Micro and nano electronics have played a pivotal role in introducing new methodologies in transistor technology, chip layout and manufacturing methods, enlargement in speed, consuming power, and miniaturization of electronic devices. This has become important especially as conventional silicon-based semiconductor technology is looming towards physical barriers of microfabrication where new approaches are being sought to satisfy the increasing requirements of future generation computing, communication, and electronic applications. The research employed a comprehensive literature review of scientific, academic, technical, and industrial articles regarding nanomaterials in use in semiconductor production. The subject matter incorporated data derived from numerous experimental investigations, industrial applications, and theoretical embodiment analyses of divergent forms of nanomaterials, their characteristics, and synthesis methods. The due review concerned the examination of the results of research pertaining to carbon nanotubes in semiconductor applications as well as graphene, quantum dots, and metallic nanoparticles. The assessment comprised manufacturing processes, relative performance measures, and comparisons of various nanomaterial applications and their effect on the efficiency and functionality of semiconductor devices. The findings confirm that nanomaterial integration results in the enhancement of semiconductor performance by large. Scientific research show that new achieved nanomaterials allow to amplify processing rate by 40% and reduce electrical power consumption by 35%. The application of two-dimensional materials such as graphene has demonstrated a 60% improvement in electron mobility over silicon-semiconductor references. Some of the quantum dot applications are now realizing at least 45 % of opto-electrical efficiency in the devices. New methods of nanofabrication production have led to decreased cost of manufacturing by thirty percent whereby the accuracy and reliability of devices being manufactured were improved. The research from outcomes demonstrates how nanomaterials could revolutionize current trends in semiconductor manufacturing. These improvements in the performance of the devices, energy consumption and in manufacturing prove the feasibility of applications of nanomaterials for future generation semiconductor devices. The major issues that were mentioned, such as scalability integration and process control, must be discussed further and researched in detail. The implications of this study point to the prospect for nanomaterials to make further improvements that can provide advanced marginal improvements to semiconductor technology depending on future breakthroughs in application, presumably reshaping the capabilities and production methods of electronic devices. This review provides comprehensive review to lay the foundation on how nanomaterials contribute towards improvement of the Semiconductor Manufacturing Technology. The lessons learned on improved small device performance, reducing power consumption, and refining manufacturing methods support the nanomaterial's imperative in semiconductor production. This view shows that despite a number of barriers to scale and implementation, the risks associated with the opportunities are much higher. The present research

CO hydrogenation to ethanol was carried out over Rh(1.5)/SiO 2 promoted with La and/or V oxides. Recent results at 230°C and 1.8 bar have shown 21% ethanol selectivity for the doubly promoted Rh-La/V/SiO 2. Here, we extend this work to examine the effects of reaction conditions-temperature, H 2 /CO ratio, space velocity, and pressure-on the activity and selectivity of these catalysts. An ethanol selectivity of 51.8% (close to the highest literature value) at a CO conversion of 7.9% was achieved with a corresponding methane selectivity of 15.4% at 270°C, 14 bar and H 2 /CO = 2 over the Rh-La/V/SiO 2 catalyst. Combined La/V promotion reduces methane selectivity and increases C 2+ oxygenates selectivity compared to the singly promoted catalysts by increasing the rate of CO insertion. Contrary to literature studies, higher pressures led to a dramatic increase in methane selectivity at the expense of ethanol, indicating increased CO dissociation activity at higher pressures, leaving fewer active CO molecules for insertion. The chain growth factor (a) for higher oxygenates differed significantly from that for hydrocarbons, suggesting that formation of these two types of products either proceeds by different mechanisms or on different active sites.

We have investigated the catalytic performance of novel In 2 O 3-Ga 2 O 3 mixed oxides synthesized by the alcoholic-coprecipitation method for propane dehydrogenation (PDH). Reactivity measurements reveal that the activities of In 2 O 3-Ga 2 O 3 catalysts are 1-3 fold (on an active metal basis) and 12-28 fold (on a surface area basis) higher than an In 2 O 3-Al 2 O 3 catalyst in terms of C 3 H 8 conversion. The structure, composition, and surface properties of the In 2 O 3-Ga 2 O 3 catalysts are thoroughly characterized. NH 3-TPD shows that the binary oxide system generates more acid sites than the corresponding single-component catalysts. Raman spectroscopy suggests that catalysts that produce coke of a more graphitic nature suppress cracking reactions, leading to higher C 3 H 6 selectivity. Lower reaction temperature also leads to higher C 3 H 6 selectivity by slowing down the rate of side reactions. XRD, XPS, and XANES measurements, strongly suggest that metallic indium and In 2 O 3 clusters are formed on the catalyst surface during the reaction. The agglomeration of In 2 O 3 domains and formation of a metallic indium phase are found to be irreversible under O 2 or H 2 treatment conditions used here, and may be responsible for loss of activity with increasing time on stream.

Aqueous phase reforming of glycerol was studied over a series of γ-Al2O3 supported metal nanoparticle catalysts for hydrogen production in a batch reactor. Of the metals studied, Pt/Al2O3 was found to be the most active catalyst under the conditions tested. A further systematic study on the impact of reaction parameters, including stirring speed, pressure, temperature, and substrate/metal molar ratio, was conducted and the optimum conditions for hydrogen production (and kinetic regime) were determined as 240 °C, 42 bar, 1000 rpm, and substrate/metal molar ratio ≥ 4100 for a 10 wt% glycerol feed. The glycerol conversion and hydrogen yield achieved at these conditions were 18% and 17%, respectively, with negligible CO and CH4 formation. Analysis of the spent catalyst using FTIR provides an indication that the reaction pathway includes glycerol dehydrogenation and dehydration steps in the liquid phase in addition to typical reforming and water gas shift reactions in the gas phase.

The effect of bis-(3-sulfopropyl)-disulfide (SPS) on the void-free electroless pillar-to-pillar bonding process has been investigated. Two dome-shaped Cu pillars were joined using electroless copper deposition with the addition of a suppressor to achieve solid, compliant Cu-to-Cu bonding without high temperature or pressure. SPS was added to the electroless copper plating bath which has strong suppression to the electroless plating in order to avoid the creation of an unbonded seam between the two Cu structures being bonded. The bath suppresses the deposition of copper near the entrance of the gap between the two pillars, while allowing high deposition rate in the geometrically restricted area between the copper structures being bonded. This phenomenon is due to diffusion of SPS through the narrow gap between the pillars being bonded. At adequate concentration of SPS, the two pillars were successfully joined without any remaining seam between the joined structures, by growth of copper from the center of the gap to the outside.

Enteropathogenic Escherichia coli (EPEC), enterohemorrhagic E. coli (EHEC) and enteroaggregative E. coli (EAEC) are intestinal pathogens that cause food and water-borne disease in humans. Using biochemical methods and NMR-based comparative metabolomics in conjunction with the nematode Caenorhabditis elegans, we developed a bioassay to identify secreted small molecules produced by these pathogens. We identified indole, indole-3-carboxaldehyde (ICA), and indole-3acetic acid (IAA), as factors that only in combination are sufficient to kill C. elegans. Importantly, although lethal to C. elegans, these molecules downregulate several bacterial processes important for pathogenesis in mammals. These include motility, biofilm formation and production of Shiga toxins. Some pathogenic E. coli strains are known to contain a Locus of Enterocyte Effacement (LEE), which encodes virulence factors that cause ''attaching and effacing'' (A/E) lesions in mammals, including formation of actin pedestals. We found that these indole derivatives also downregulate production of LEE virulence factors and inhibit pedestal formation on mammalian cells. Finally, upon oral administration, ICA inhibited virulence and promoted survival in a lethal mouse infection model. In summary, the C. elegans model in conjunction with metabolomics has facilitated identification of a family of indole derivatives that broadly regulate physiology in E. coli, and virulence in pathogenic strains. These molecules may enable development of new therapeutics that interfere with bacterial small-molecule signaling.

Enteropathogenic Escherichia coli (EPEC) cause intestinal inflammation, severe diarrhoea and mortality, particularly among children in developing nations. Upon attachment to intestinal epithelial cells, EPEC induces actin-filled membrane protrusions called ‘pedestals’ and disrupts microvilli to form attaching and effacing (A/E) lesions. EPEC also disrupts epithelial barrier function and causes colitis. Here we have investigated how virulence factors which orchestrate formation of actin pedestals interface with host tyrosine kinases. We show that Tec-family tyrosine kinases localize beneath EPEC and, with Abl-family kinases, comprise a set of redundant host kinases utilized by EPEC to form actin pedestals. We also show that Tir, a virulence factor required for pathogenesis, contains a polyproline region (PPR) that interacts with SH3 domains of redundant kinases, and a phosphorylation site (Y474) that interacts with kinase SH2 domains. These interactions are essential for pedestal formation, and mimic activation of kinases by cellular ligands. Our results suggest that a positive feedback loop exists in which initial phosphorylation of Tir on Y474 by tyrosine kinases causes recruitment of additional redundant kinases via PPR–SH3 interactions and PO3–Y474–SH2 interactions, which in turn phosphorylate other Tir molecules as well as proteins that catalyse formation of actin pedestals.

Enteropathogenic E.coli (EPEC) are deadly contaminants in water and food, and induce protrusion of actin-rich membrane pedestals beneath themselves upon attachment to intestinal epithelia. EPEC then causes intestinal inflammation, diarrhea, and, among children, death. Here we show that EPEC uses multiple tyrosine kinases for formation of pedestals, each of which is sufficient but not necessary. In particular, we show that Abl and Arg, members of the Abl family of tyrosine kinases, localize and are activated in pedestals. We also show that pyrido[2,3-d]pyrimidine (PD) compounds, which inhibit Abl, Arg and related kinases, block pedestal formation. Finally, we show that Abl and Arg are sufficient for pedestal formation in the absence of other tyrosine kinase activity, but are not necessary. Our results suggest that additional kinases which are sensitive to inhibition by PD also can suffice. Together, these results suggest that EPEC has evolved a mechanism to use any of several functionally redundant tyrosine kinases during pathogenesis, perhaps facilitating its capacity to infect different cell types. Moreover, PD compounds are being developed to treat cancers caused by dysregulated Abl. Our results raise the possibility that PD may be useful in treating EPEC infections, and because PD affects host and not bacterium, selecting resistant strains may be far less likely than with conventional antibiotics.

The Poxviridae family members vaccinia and variola virus enter mammalian cells, replicate outside the nucleus and produce virions that travel to the cell surface along microtubules, fuse with the plasma membrane and egress from infected cells toward apposing cells on actin-filled membranous protrusions. We show that cell-associated enveloped virions (CEV) use Abl-and Srcfamily tyrosine kinases for actin motility, and that these kinases act in a redundant fashion, perhaps permitting motility in a greater range of cell types. Additionally, release of CEV from the cell requires Abl-but not Src-family tyrosine kinases, and is blocked by STI-571 (Gleevec), an Abl-family kinase inhibitor used to treat chronic myelogenous leukemia in humans. Finally, we show that STI-571 reduces viral dissemination by five orders of magnitude and promotes survival in infected mice, suggesting possible use for this drug in treating smallpox or complications associated with vaccination. This therapeutic approach may prove generally efficacious in treating microbial infections that rely on host tyrosine kinases, and, because the drug targets host but not viral molecules, this strategy is much less likely to engender resistance compared to conventional antimicrobial therapies.

Enteropathogenic Escherichia coli (EPEC) are deadly contaminants in water and food and induce protrusion of actin-rich membrane pedestals beneath themselves upon attachment to intestinal epithelia. EPEC then causes intestinal inflammation, diarrhea, and, among children, death. Here, we show that EPEC uses multiple tyrosine kinases for formation of pedestals, each of which is sufficient but not necessary. In particular, we show that Abl and Arg, members of the Abl family of tyrosine kinases, localize and are activated in pedestals. We also show that pyrido[2,3-d]pyrimidine (PD) compounds, which inhibit Abl, Arg, and related kinases, block pedestal formation. Finally, we show that Abl and Arg are sufficient for pedestal formation in the absence of other tyrosine kinase activity, but they are not necessary. Our results suggest that additional kinases that are sensitive to inhibition by PD also can suffice. Together, these results suggest that EPEC has evolved a mechanism to use any of several functionally redundant tyrosine kinases during pathogenesis, perhaps facilitating its capacity to infect different cell types. Moreover, PD compounds are being developed to treat cancers caused by dysregulated Abl. Our results raise the possibility that PD may be useful in treating EPEC infections, and because PD affects host and not bacterium, selecting resistant strains may be far less likely than with conventional antibiotics.

Cationic antimicrobial host defense peptides (HDPs) combat infection by directly killing a wide variety of microbes, and/or modulating host immunity. HDPs have great therapeutic potential against antibiotic-resistant bacteria, viruses and even parasites, but there are substantial roadblocks to their therapeutic application. High manufacturing costs associated with amino acid precursors have limited the delivery of inexpensive therapeutics through industrial-scale chemical synthesis. Conversely, the production of peptides in bacteria by recombinant DNA technology has been impeded by the antimicrobial activity of these peptides and their susceptibility to proteolytic degradation, while subsequent purification of recombinant peptides often requires multiple steps and has not been cost-effective. Here we have developed methodologies appropriate for largescale industrial production of HDPs; in particular, we describe (i) a method, using fusions to SUMO, for producing high yields of intact recombinant HDPs in bacteria without significant toxicity; and (ii) a simplified 2-step purification method appropriate for industrial use. We have used this method to produce seven HDPs to date (IDR1, MX226, LL37, CRAMP, HHC-10, E5 and E6). Using this technology, pilot-scale fermentation (10 L) was performed to produce large quantities of biologically active cationic peptides. Together, these data indicate that this new method represents a cost-effective means to enable commercial enterprises to produce HDPs in large-scale under Good Laboratory Manufacturing Practice (GMP) conditions for therapeutic application in humans.

Enteropathogenic Escherichia coli, enterohemorrhagic E. coli, and Citrobacter rodentium are classified as attaching and effacing pathogens based on their ability to adhere to intestinal epithelium via actin-filled membranous protrusions (pedestals). Infection of mice with C. rodentium causes breach of the colonic epithelial barrier, a vigorous Th1 inflammatory response, and colitis. Ultimately, an adaptive immune response leads to clearance of the bacteria. Whereas much is known about the adaptive response to C. rodentium, the role of the innate immune response remains unclear. In this study, we demonstrate for the first time that the TLR adaptor MyD88 is essential for survival and optimal immunity following infection. MyD88 ؊/؊ mice suffer from bacteremia, gangrenous mucosal necrosis, severe colitis, and death following infection. Although an adaptive response occurs, MyD88-dependent signaling is necessary for efficient clearance of the pathogen. Based on reciprocal bone marrow transplants in conjunction with assessment of intestinal mucosal pathology, repair, and cytokine production, our findings suggest a model in which TLR signaling in hemopoietic and nonhemopoietic cells mediate three distinct processes: 1) induction of an epithelial repair response that maintains the protective barrier and limits access of bacteria to the lamina propria; 2) production of KC or other chemokines that attract neutrophils and thus facilitate killing of bacteria; and 3) efficient activation of an adaptive response that facilitates Ab-mediated clearance of the infection. Taken together, these experiments provide evidence for a protective role of innate immune signaling in infections caused by attaching and effacing pathogens.

Blue fluorescent proteins (BFPs) offer visualization of protein location and behavior, but often suffer from high autofluorescent background and poor signal discrimination. Through dual-laser excitation of bright and photoinduced dark states, mutations to the residues surrounding the BFP chromophore enable long-wavelength optical modulation of BFP emission. Such dark state engineering enables violet-excited blue emission to be increased upon lower energy, green coillumination. Turning this green co-illumination on and off at a specific frequency dynamically modulates collected blue fluorescence without generating additional background. Interpreted as transient photoconversion between neutral cis-and anionic trans-chromophoric forms, mutations tune photoisomerization and ground state tautomerizations to enable long-wavelength depopulation of the millisecond-lived, spectrally shifted dark states. Single mutations to the tyrosine-based blue fluorescent protein T203V/S205V exhibit enhanced modulation depth and varied frequency. Importantly, analogous single point mutations in the non-modulatable BFP, mKalama1, creates a modulatable variant. Building modulatable BFPs offers opportunities for improved BFP signal discrimination vs. background, greatly enhancing their utility.

We created a novel chimeric amine dehydrogenase (AmDH) via domain shuffling of two parent AmDHs ('L- and F-AmDH'), which in turn had been generated from leucine and phenylalanine DH, respectively. Unlike the parent proteins, the chimeric AmDH ('cFL-AmDH') catalyzes the amination of acetophenone to (R)-methylbenzylamine and adamantylmethylketone to adamantylethylamine.

The E-factor has become an important measure for the environmental impact of (bio)chemical reactions. However, summing up the obvious wastes generated in the laboratory neglects energy-related wastes (mostly greenhouse gases) which are generated elsewhere. To estimate these wastes, we propose to extend the E-factor by an energy-term (E þ-factor). At the example of a lab-scale enzyme fermentation, we demonstrate that the E þ-factor can constitute a multiple of the classical E-factor and therefore must not be neglected striving for a holistic estimation of the environmental impact.