A number of diseases are linked to protein folding problems which lead to the deposition of insoluble protein plaques in the brain or other organs. These diseases include prion diseases such as Creutzfeld-Jakob disease, Alzheimer's disease, Parkinson's disease and type II (non-insulin dependent) diabetes. The protein plaques are found to consist of amyloid fibrils - cross-beta-sheet polymers with the beta-strands arranged perpendicular to the long axis of the fibre. Studies of ex vivo fibrils and fibrils produced in vitro showed that amyloid structures possess similar tinctorial and morphological properties. These suggest that the ability to form amyloid fibrils is an inherent property of polypeptide chains. The aims of this thesis were to investigate the structural properties of cytotoxic amyloid and examine the involved mechanisms. The model proteins used in the studies were the equine and hen lysozymes and de novo designed protein albebetin. Lysozymes are naturally ubiquitous proteins. Equine lysozyme belongs to an extended family of structurally related lysozymes and α-lactalbumins and can be considered as an evolutional bridge between them. Hen lysozyme is one of the most characterized protein and its amyloidogenic properties were described earlier. De novo protein albebetin and its constructs are designed to perform the function of grafted polypeptide sequence. Fibrils of equine lysozyme are formed at acidic pH and elevated temperatures where a partially folded molten globule state is populated. We have shown that lysozyme assembles into annular and linear protofilaments in a calcium-dependent manner. We showed that albebetin and its constructs are inherently highly amyloidogenic under physiological conditions. Fibrillation proceeds via multiple pathways and includes a hierarchy of amyloid structures ranging from oligomers to protofilaments and fibrils, among which two distinct types of oligomeric intermediates were characterized. Pivotal oligomers comprise of 10-12 monomers and on-pathway amyloid-prone oligomers constitute of 26-30 molecules. We suggest that transformation of the pivotal oligomers into the amyloid-prone ones is a limiting stage in albebetin fibrillation. Cytotoxic studies of albebetin amyloid species have revealed that initial, pivotal oligomers do not effect on cell viability while amyloid-prone ones induce cell death. We suggest that oligomeric size is important for the stabilizing cross-beta-sheet core which is crucial for cell toxicity. Cytotoxic studies of both oligomers and fibrils of hen lysozyme have revealed that both species induce cell death. The amyloid sample containing cross-β-sheet oligomers induces an apoptosis-like cell death. The oligomers without cross-β-sheet appeared to be non-toxic, indicating that the stabilization of this structural pattern is critical for the induced toxicity. In contrast, the fibrils induce more rapid, necrosis-like death. These studies gained insights into a structure–function relationship of different forms of amyloid and general pathways of cell death. This is an important step in understanding the mechanisms of amyloid-associated degeneration and defining specific therapeutic targets.

Advances in several research areas increase the need for more sophisticated fabrication techniques and better performing materials. Tackling this problem from a bottom-up perspective is currently an active field of research. The bottom-up fabrication procedure offers sub-nanometer accurate manipulation. At this time, candidates to achieve nanomanipulation include chemical (self-assembly), biotechnology methods (DNA-based), or using controllable physical forces (e.g. electrokinetic forces, mechanical forces). In this thesis, new methods and techniques for mechanical nanomanipulation using probe force interaction are developed. The considered probes are commonly used in Atomic Force Microscopes (AFMs) for high resolution imaging. AFM-based mechanical nanomanipulation will enable arranging nanoscale entities such as nanotubes and molecules in a precise and controlled manner to assemble and produce novel devices and systems at the nanoscale. The novelty of this research stems from the development of new modeling of the physics and mechanics of the tip interaction with nanoscale entities, coupled with the development of new smart cantilevers with multiple degrees of freedom. The gained knowledge from the conducted simulations and analysis is expected to enable true precision and repeatability of nanomanipulation tasks which is not feasible with existing methods and technologies.

<p>This research describes the development of a state-of-the-art atomic force microscope (AFM) for improved force spectroscopy. Although the AFM has been used extensively in this field of research, the performance of the instrument has been limited by inefficient operation techniques, incorrect experimental assumptions, and inadequate controller design. This research focuses on overcoming these deficiencies by providing precise control over the instrument for specialized research in a manner that is conducive to the natural science researcher.</p><p>To facilitate this research, a custom, multi-axis AFM system was constructed. The instrument was designed primarily for AFM-based force spectroscopy and as a result a substantial amount of research focused on the development of a wide variety of approach/retraction methods for the instrument. Defining research in this area included the development of methods to minimize potentially damaging compressive forces, form polymer bridges at different tip-sample gap widths, produce clean, deconvoluted force-extension curves, and limit single molecule force spectroscopy pulling geometry errors. In an effort to increase the efficiency of the instrument, the programs developed during this research were fully automated, allowing autonomous operation of the instrument for long periods of time. To compliment the data collection programs, both manual and automated analysis programs with force-volume imaging capabilities were also developed.</p><p>By studying the AFM from a dynamic systems, measurements, and controls approach, the resulting controllers were tailored to meet the process requirements of the intended applications. In doing so, the sensitivity of the instrument was improved for applications of interest. By incorporating control over the environment, contact force, loading rate, and pulling angle, the research has increased the accuracy of the AFM such that molecules and receptor-ligand binding events can be investigated with greater detail. Furthermore, the incorporation of a graphical user interface and automated data collection and analysis tools has made the AFM a more user-friendly, efficient instrument for the natural science researcher.</p> / Dissertation

No description available.

­ì¤l¤OÅã·LÃè(AFM)¯à¦b®ð¬Û¡B¯uªÅ¡B¤Î±µªñ¥Í²z±ø¥óªº²G¬Û¤¤ª½±µ¶i¦æªí­±³æ¤À¤lªºÆ[´ú¡C¦ý¼Ë«~¤À¤l³Q©T©w«á¡A¨äµ²ºc¬O§_»P¦ÛµMª¬ºA¬ÛÃö¡A»á¥O¤H½èºÃ¡C ¥»¬ã¨s°w¹ï¶³¥À¤ùªí­±¶i¦æ¤Æ¾Ç­×¹¢¡A§Q¥ÎºëÓi(spermine)¤j¤j´£°ª¤F°òªOªí­±§lªþDNAªº¯à¤O¡C¹B¥Î»E¦X¤À¤lÃì²Î­p¤ÀªR²z½×(statistical polymer chain analysis)¡A¥H¤TºØ¤£¦Pªø«×ªº½u«¬DNA¤À¤l¡A®Ú¾ÚAFM¼v¹³¤À§O§@¤À¤l½ü¹øÁ`ªø(contour length, L)¤Î¥¼ºÝ¨âÂI¶ZÂ÷(end-to-end distance, R)ªº´ú¶q¡A¥H<R2>»PL¤§¬ÛÃö©Ê±Àª¾¼v¹³¤¤ªºDNA¤À¤lªí²{ªº¬O3D¥ßÅé®·®»ºAºc«¬(three-dimensional trapped configuration)¡A¦Ó«D¤À¤l¦b2DªÅ¶¡­«·s«Ø¥ß¥­¿Å«áªºµ²ºc¡C¥t¥~¡AÂǧïÅÜDNA¼Ë«~²Gºw¦b¶³¥À¤ù¤W°®Àꪺ®É¶¡¡A©Ò³y¦¨°òªO§lªþ¤À¤l¼Æ¥ØªºÅܤơA°t¦X¤£¥i°fÂX´²¹B°Ê¼Ò«¬±o¨ì¤F¤À¤l¥Ñ²G¬Û¨ì¹Fªí­±¿é°e¹Lµ{¤§ÂX´²«Y¼Æ¡C ¦b©Ý¾ë²§ºc酶(topoisomerase)»P¶Ê¤ÆDNA¤À¤l¤ÏÀ³¹êÅ礤¡AAFM©úÅã¿ëÃÑ¥XDNA¤À¤l¦b©Ý¾ëºc§Î¤WªºÂà¤Æ¡A¬Æ¦Üª½±µ¬Ý¨ì¸Ñ±Û¾÷¨î¤¤©Ý¾ë酶¤À¤l»PÂùªÑDNA¤¤¤@±ø³æªÑªº§@¥Î¡C

Thesis (M.S.)--Worcester Polytechnic Institute. / Keywords: implant; medical; atomic force microscopy; fungi; bacteria. Includes bibliographical references (p. 82-100).

Thesis (Ph. D.)--University of Texas at Austin, 2001. / Vita. Includes bibliographical references (leaves 337-351). Available also in a digital version from Dissertation Abstracts.

This study was conducted to investigate the biofilm formation by using advanced microscopic and high-throughput sequencing techniques. The major tasks were (1) to quantitatively evaluate the initial bacterial attachment processes by Atomic Force Microscopy (AFM); (2) to characterize the chemical variation during biofilm formation by Raman microscopy; (3) to analyze the microbial structure and functions in the wastewater and drinking water biofilms by metagenomic analysis. To determine the lateral detachment force for bacteria, a quantitative method using contact mode of AFM was developed. The established method had good repeatability and sensitivity to various bacteria and substrata, and was applied to evaluate the roles of bacterial surface polymers in Phase I and II attachment, i.e. lipopolysaccharides, type 1 fimbria and capsular colanic acid. The results indicated lipopolysaccharides largely enhanced Phases I and II attachment. Fimbriae increased Phase I attachment but not significantly influence the adhesion strength in Phase II. Moreover, colanic acid had negative effect on attachment in both of Phases I and II. Surface-enhanced Raman scattering was applied to evaluate the chemical components in the biofilm matrix at different growth phases, including initial attached bacteria, colonies and mature biofilm. Three model bacteria, including Escherichia coli, Pseudomonas putida, and Bacillus subtilis, were used to cultivate biofilms. The results showed that the content of carbohydrates, proteins, and nucleic acids in biofilm matrix increased significantly along with the biofilm growth of three bacteria judging from the intensities and appearance probabilities of related marker peaks in the spectra. The content of lipids, however, only increased in the Gram-negative biofilms. Moreover, metagenomic data, coupled with PCR-based 454 pyrosequencing reads, were generated for activated sludge and biofilm from a full-scale hybrid reactor to study the microbial taxonomic and functional differences/connections between activated sludge and biofilm. The results showed that the dominant bacteria co-existed in two samples. Global functions in activated sludge and biofilm metagenomes showed quite similar pattern, revealing the limited differences of overall functions existed in two samples. For nitrogen removal, the diversity and abundance of nitrifiers and denitrifiers in biofilm did not surpass that in activated sludge. Whilst, higher abundances of nitrification and denitrification genes were indeed found in biofilm, suggesting the increased nitrogen removal by applying biofilm might be attributed to removal efficiency rather than biomass accumulation of nitrogen removal bacteria. To investigate the bacterial structure and functions of drinking water biofilm, PCR-based 454 pyrosequencing of 16S rRNA gene and Illumina metagenomic data were generated and analyzed. Significant differences of bacterial diversity and taxonomic structure were found between biofilms formed on stainless steel and plastics. Moreover, ecological succession could be obviously observed during biofilm formation. The metabolic network analysis for drinking water biofilm constructed for the first time. Moreover, the occurrence and abundance of specific genes involving in the bacterial pathway of glutathione metabolism and production/degradation of extracellular polymeric substances were also evaluated. / published_or_final_version / Civil Engineering / Doctoral / Doctor of Philosophy

No description available.

No description available.