Chemical vapor deposition and functionalization of fluorocarbon-organosilicon copolymer thin films

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2003.Includes bibliographical references.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Neural prostheses are micron-scale integrated circuit devices that are under development for the treatment of brain and spinal cord injuries. A key challenge in the fabrication of these silicon- based devices is the protection of the electronic components from the ambient body environment. There is a need for a biopassivation coating on these devices that is chemically inert and electrically insulating with good adhesion to the underlying silicon substrate. Fluorocarbon-organosilicon copolymers are of interest for this application because they have the desirable attributes of both fluorocarbon and organosilicon polymers, such as low dielectric constant, thermal stability, and good adhesion to silicon. Chemical vapor deposition (CVD) is an attractive synthetic technique for this application because it is single-step, requires no solvent, and allows conformal coatings to be deposited on substrates with complex topographies and small dimensions. Fluorocarbon-organosilicon copolymers have been synthesized by hot-filament CVD, a thermal CVD technique. Control over deposition rate and chemical structure is achieved by precursor choice and variation of filament temperature. Chemical characterization by infrared (FTIR), x-ray photoelectron (XPS), and solid-state nuclear magnetic resonance (NMR) spectroscopies indicates that the copolymer films range from highly cross-linked films to flexible films comprised mostly of linear polymer chains. This variation in chemical composition influences physical properties such as thermal stability and flexibility. The possibility of creating bioactive surface coatings has been explored by using the techniques of CVD and solution chemistry in combination. Chains of poly(acrylamide) have been grafted onto fluorocarbon-organosilicon films as a first step towards the design of bioactive coatings that could potentially enhance the performance of medical implants.by Shashi Krishna Murthy.Ph.D

Bridging the Divide between Neuroprosthetic Design, Tissue Engineering and Neurobiology

Neuroprosthetic devices have made a major impact in the treatment of a variety of disorders such as paralysis and stroke. However, a major impediment in the advancement of this technology is the challenge of maintaining device performance during chronic implantation (months to years) due to complex intrinsic host responses such as gliosis or glial scarring. The objective of this review is to bring together research communities in neurobiology, tissue engineering, and neuroprosthetics to address the major obstacles encountered in the translation of neuroprosthetics technology into long-term clinical use. This article draws connections between specific challenges faced by current neuroprosthetics technology and recent advances in the areas of nerve tissue engineering and neurobiology. Within the context of the device–nervous system interface and central nervous system implants, areas of synergistic opportunity are discussed, including platforms to present cells with multiple cues, controlled delivery of bioactive factors, three-dimensional constructs and in vitro models of gliosis and brain injury, nerve regeneration strategies, and neural stem/progenitor cell biology. Finally, recent insights gained from the fields of developmental neurobiology and cancer biology are discussed as examples of exciting new biological knowledge that may provide fresh inspiration toward novel technologies to address the complexities associated with long-term neuroprosthetic device performance

Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells - a benchmarking study

BACKGROUND: Proteomics research is enabled with the high-throughput technologies, but our ability to identify expressed proteome is limited in small samples. The coverage and consistency of proteome expression are critical problems in proteomics. Here, we propose pathway analysis and combination of microproteomics and transcriptomics analyses to improve mass-spectrometry protein identification from small size samples. RESULTS: Multiple proteomics runs using MCF-7 cell line detected 4,957 expressed proteins. About 80% of expressed proteins were present in MCF-7 transcripts data; highly expressed transcripts are more likely to have expressed proteins. Approximately 1,000 proteins were detected in each run of the small sample proteomics. These proteins were mapped to gene symbols and compared with gene sets representing canonical pathways, more than 4,000 genes were extracted from the enriched gene sets. The identified canonical pathways were largely overlapping between individual runs. Of identified pathways 182 were shared between three individual small sample runs. CONCLUSIONS: Current technologies enable us to directly detect 10% of expressed proteomes from small sample comprising as few as 50 cells. We used knowledge-based approaches to elucidate the missing proteome that can be verified by targeted proteomics. This knowledge-based approach includes pathway analysis and combination of gene expression and protein expression data for target prioritization. Genes present in both the enriched gene sets (canonical pathways collection) and in small sample proteomics data correspond to approximately 50% of expressed proteomes in larger sample proteomics data. In addition, 90% of targets from canonical pathways were estimated to be expressed. The comparison of proteomics and transcriptomics data, suggests that highly expressed transcripts have high probability of protein expression. However, approximately 10% of expressed proteins could not be matched with the expressed transcripts.The cost of this publication was funded by Vladimir Brusic. (Vladimir Brusic)Published versio

Improved diffuse fluorescence flow cytometer prototype for high sensitivity detection of rare circulating cells in vivo

Abstract. Detection and enumeration of rare circulating cells in mice are important problems in many areas of preclinical biomedical research. Recently, we developed a new method termed “diffuse fluorescence flow cytometry” (DFFC) that uses diffuse photons to increase the blood sampling volume and sensitivity versus existing in vivo flow cytometry methods. In this work, we describe a new DFFC prototype with approximately an order-of-magnitude improvement in sensitivity compared to our previous work. This sensitivity improvement is enabled by a number of technical innovations, which include a method for the removal of motion artifacts (allowing interrogation of mouse hindlegs that was less optically attenuating versus the tail) and improved collection optics and signal preamplification. We validated our system first in limb mimicking optical flow phantoms with fluorescent microspheres and then in nude mice with fluorescently labeled mesenchymal stem cells at injected concentrations of 5×103 cells/mL. In combination, these improvements resulted in an overall cell counting sensitivity of about 1 cell/mL or better in vivo

Toxicity of TiO2, SiO2, ZnO, CuO, Au and Ag engineered nanoparticles on hatching and early nauplii of Artemia sp.

The potential of environmental release enhances with increased commercial applications of the nanomaterials. In this work, a simple and efficient test to estimate the acute toxicity of nanoparticles is carried out on Artemia species and their hatching rates. We have tested six different engineered nanoparticles (silver, gold, copper oxide, zinc oxide, TiO2 and SiO2 nanoparticles) and three soluble salts (CuSO4, ZnSO4 and AgNO3) on Artemia sp. The physicochemical properties of the nanoparticles involved in this study were analyzed in normal water and marine water. Hydrated and bleached Artemia cysts were allowed to hatch in continuously aerated, filtered sterile salt water containing nanoparticles; hatching of viable nauplii and total hatchlings have been recorded. In parallel, standard Artemia toxicity test was conducted on the nauplii monitoring the viability. In hatching experiments, a reduction in hatching rate was observed along with mortality of newly hatched nauplii. The results of the hatching experiment and of the standard Artemia test showed a good correlation. The toxicity of the nanoparticles was compared and the order of toxicity was estimated as Ag>CuO>ZnO>Au>TiO2>SiO2. The study thus suggests that the hatching test itself is a reliable assay for determining the toxicity of nanomaterials

Soluble Receptor for Advanced Glycation End Products (sRAGE) Is a Sensitive Biomarker in Human Pulmonary Arterial Hypertension.

Pulmonary arterial hypertension (PAH) is a progressive condition with an unmet need for early diagnosis, better monitoring, and risk stratification. The receptor for advanced glycation end products (RAGE) is activated in response to hypoxia and vascular injury, and is associated with inflammation, cell proliferation and migration in PAH. For the adult cohort, we recruited 120 patients with PAH, 83 with idiopathic PAH (IPAH) and 37 with connective tissue disease-associated PAH (CTD-PAH), and 48 controls, and determined potential plasma biomarkers by enzyme-linked immunoassay. The established heart failure marker NTproBNP and IL-6 plasma levels were several-fold higher in both adult IPAH and CTD-PAH patients versus controls. Plasma soluble RAGE (sRAGE) was elevated in IPAH patients (3044 ± 215.2 pg/mL) and was even higher in CTD-PAH patients (3332 ± 321.6 pg/mL) versus controls (1766 ± 121.9 pg/mL; p < 0.01). All three markers were increased in WHO functional class II+III PAH versus controls (p < 0.001). Receiver-operating characteristic analysis revealed that sRAGE has diagnostic accuracy comparable to prognostic NTproBNP, and even outperforms NTproBNP in the distinction of PAH FC I from controls. Lung tissue RAGE expression was increased in IPAH versus controls (mRNA) and was located predominantly in the PA intima, media, and inflammatory cells in the perivascular space (immunohistochemistry). In the pediatric cohort, plasma sRAGE concentrations were higher than in adults, but were similar in PH (n = 10) and non-PH controls (n = 10). Taken together, in the largest adult sRAGE PAH study to date, we identify plasma sRAGE as a sensitive and accurate PAH biomarker with better performance than NTproBNP in the distinction of mild PAH from controls

Sensory and nutritional evaluation of nine types of millet substituted for polished white rice in select Indian meal preparations

This study was conducted to test the suitability of using nine types of millets namely finger millet, pearl millet, white and yellow sorghum, little millet, barnyard millet, proso millet, kodo millet, and browntop millet in seven popular Indian meal preparations based on sensory characteristics and nutrient value. The popular Indian meal preparations tested were boiled grain, dosa, idli, bisi belle bath, pulao, puttu, and pongal. In total, 53 variations in meal preparations were developed using the millets and seven polished white rice-based meal preparations were developed as control. The main findings indicated that meal preparation crafted from various millets garnered overall sensory scores closely resembling to those derived from polished white rice. Notably, little millet exhibited high scores in pongal and dosa, and achieved elevated overall sensory scores compared to meal preparation from polished white rice. Bisi belle bath made of barnyard millet scored higher in overall sensory score than polished white rice. Moreover, there was significant association between some types of millets’ overall sensory characteristics (p < 0.005) with polished white rice-based meal preparations. In terms of nutrient value, all the millet-based meal preparations had significantly high nutritional value compared to those made with polished white rice (p < 0.05). Especially calcium content of the meal prepared with finger millet was significantly higher compared to polished white rice-based meals (p < 0.05). Puttu, idli, and dosa prepared with finger millet had calcium content of 59.4, 10.8, and 70.9 mg/100 g compared to those prepared with the polished white rice which had only 1.3, 6.3, and 9.2 mg/100 g. The magnesium content of all millet-based meal preparations was generally several-folds higher compared to the polished white rice-based meal preparations (p < 0.05). There is a significant difference in the fiber content of the meals prepared with millets compared to the meals prepared with polished white rice (p < 0.05). This study was conducted using millets that are locally available and does not represent all the millet varieties available globally, as each type of millet has a wide range of varieties. Therefore, it is important to understand and choose the type and variety of millet while enhancing the nutritional value of diets