­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 (Ph. D.)--Lehigh University, 2001. / Includes bibliographical references and vita.

Thesis (Ph. D.)--University of Texas at Austin, 2000. / Vita. Includes bibliographical references (leaves 124-130). Available also in a digital version from Dissertation Abstracts.

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.

Atomic force microscopy was used to image the action of cellulolytic enzymes in situ on never-dried native cellulose films. Cellomonas fimi, CenA was used as a model enzyme for proof of concept experiments and for the identification of different enzyme action on different cellulose structures. Inactive and active Trichoderma reesei enzymes EGI and CBHI were studied to disentangle the action of the cellulose binding domain from the catalytic domain. A novel procedure, volume analysis, was developed to quantify changes in cellulose fibers as a result of this action. Volume analysis was used to compare fibers in different experiments (with different structural features and enzymes) regardless of where the change in the fiber occurred. The site-specific nature of cellulose-enzyme interactions is accessible using this analysis technique. Additionally, the reported volume change reflects a change in mass that is of interest for industrial purposes. From inactive CBHI action there was no distinguishable change between enzyme action on defect or crystalline regions of the cellulose fiber. From the active enzyme results a quantifiable degradation event was measured. Digestion was initially quick then after one hour the volume plateaued. The crystalline cellulose region plateaued at -20 ± 1% and the defect region at -31 ± 2%. The inactive EGI enzyme was found to have significant non-hydrolytic action on insoluble cellulose fibers. There was more significant swelling effect on the defect than the crystalline regions of the cellulose fiber. From the active EGI results a quantifiable degradation event was measured followed by swelling events. Degradation was initially quick with the total mass loss occurring within the first hour of the experiment. The volume then increased as the enzyme induced swelling of the fiber structure. The extent of degradation and swelling is structure limited with more disordered regions showing larger decreases in volume and predominantly crystalline regions showing mainly swelling events.

No description available.