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Title: DIRECTED EVOLUTION TO IMPROVE BIODESULFURIZATION OF PETROLEUM
Creator: Khayyat, Naghmeh Hassanzadeh
Date: 2013, 2013-12
Description: Dibenzothiophene (DBT) is an organosulfur compound found in petroleum that is refractory to the current hydrodesulfurization (HDS) method in...
Show moreDibenzothiophene (DBT) is an organosulfur compound found in petroleum that is refractory to the current hydrodesulfurization (HDS) method in refineries and raises the need for alternative methods such as biodesulfurization. Rhodococcus erythropolis strain IGTS8 naturally contains a dszABC operon, which encodes enzymes that can desulfurize DBT through the 4S pathway. Desulfurization-negative Rhodococcus opacus was transformed with plasmids pRESXdszABC and pRESXdszAS1BC, conferring the ability to desulfurize DBT. pRESXdszAS1BC had been modified from pRESXdszABC by placing a synthetic “sulpeptide gene” (S1) within the operon between dszA and dszB; S1 encodes a short polypeptide with high methionine and cysteine content, which puts additional sulfur demands on the 4S pathway when DBT is the only source of sulfur. Here we performed directed evolution on the two transformed R. opacus strains for 50 passages in a minimal (CDM) medium with DBT as the sole sulfur source in an attempt to drive evolution of greater DBT desulfurization activity. Desulfurization specific activity experiments were performed every 4 to 10 passages to compare the specific activities of these strains through the production of 2-HBP as measured by the Gibbs assay. Desulfurization positive strain Rhodococcus erythropolis IGTS8 was used as the control culture. R. opacus/pRESXdszABC demonstrated a maximum increase of 28-fold in desulfurization specific activity after 40 passages to a level as high as that of the control culture R. erythropolis IGTS8. Thereafter (passages 41-50), there was a 7% decrease from the maximum of desulfurization activity level (passage 40). R. opacus/pRESXdszAS1BC, however, showed only a maximum increase of 4-fold in specific activity after 37 passages. Moreover, there was a 61% decrease from the ix maximum of desulfurization activity level (passage 37) thereafter (passage 38-50). These could be due to the unexpected mutations and/or epigenetic changes in the pRESXdszAS1BC plasmid or host genomic sequences. Further DNA sequence analysis will be helpful in identification of these possible mutations.
M.S. in Biology, December 2013
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Title: Factors Affecting Sanitizer Efficacy on Preventing Cross-Contamination of E. Coli 0157:H7 During Postharvest Washing of Romaine Lettuce
Creator: Li, Yichen
Date: 2011-12-05, 2011-12
Description: Outbreaks of E. coli O157:H7 infections have been a continuing food safety challenge for the produce industry. Previous studies showed that...
Show moreOutbreaks of E. coli O157:H7 infections have been a continuing food safety challenge for the produce industry. Previous studies showed that contamination that originated in the farm can spread during postharvest processing. The objective of this study was to examine the spread of E. coli O157:H7 during postharvest washing of contaminated lettuce and to determine factors affecting the efficacy of sanitizer use in preventing cross-contamination. A bench-scale washing system was established to simulate industry operations. This system was equipped with a submersible pump and instruments to measure wash water properties including pH, temperature, chlorine level, oxidation reduction potential (ORP), turbidity and total organic carbon (TOC). Fresh-cut romaine lettuce (8 or 20 g) inoculated with approximately 8 log CFU/ml of E. coli O157:H7 with green fluorescence protein (GFP) were added into 40 L of tap water or industry water together with uninoculated lettuce (800 or 2000 g). The wash procedure lasted for 2 minutes. Washing operations were performed at two temperatures (3°C and 20°C) combined with different levels of chlorine treatments (0, 5, 20 and 30 ppm). Smaller-scale (50 – 100 mL) washing experiments were performed separately to determine the effects of organic contents and solid contents on the efficacy of sanitizer. Without chlorine treatment, the spread of E. coli O157:H7 occurred in both tap water and industry water at both 20°C and 3°C. With 20 ppm chlorine, no E. coli O157:H7 was detected in either wash water or uninoculated lettuce after washing in tap water. In industry water, chlorine level at 30 ppm or above could prevent crosscontamination of E. coli O157:H7. Neither the lettuce load nor the wash water temperature was proved to affect the efficacy of sanitizer. At 5 ppm of chlorine, increases in organic carbon (0% to 20%) led to the drop of free chlorine which resulted in a decrease in the microbial reduction from 2.51 to 0.01 log CFU/g. Increases in solid contents (0 g/L to 20 g/L) also caused a decrease in the microbial reduction from 2.52 to 1.17 log CFU/g but it did not change the free chlorine concentration. The utility of ORP as a measure of the antimicrobial efficiency of wash water was evaluated. ORP readings increased with increasing chlorine levels but reached a plateau and failed to correlate with the concentration of chlorine at chlorine levels > 20 ppm.
M.S. in Food Safety and Technology, December 2011
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Title: COMPLETE PLASTID GENOME OF THE HEMIPARASITIC PLANT PEDICULARIS REX
Creator: Yang, Jingyi
Date: 2015, 2015-07
Description: Pedicularis rex is a hemiparasitic plant from the Orobanchaceae family. Hemiparasites, also called semiparasites, are partly dependent on...
Show morePedicularis rex is a hemiparasitic plant from the Orobanchaceae family. Hemiparasites, also called semiparasites, are partly dependent on their host and, while they steal nutrients and other metabolites like other parasites, they have retained their photosynthesis ability. To better understand the hemiparasitic lifestyle of Pedicularis rex and what remains of its photosynthetic capability, we have determined the complete sequence of its plastid chromosome. The chloroplast genome of Pedicularis rex is 153,650 base pairs-long and exhibits a typical quadripartite structure with a large single copy (LSC) region and a small single copy (SSC) region separated by two inverted repeats (IR). A total of 79 unique protein-coding genes, including 9 pseudogenes, 30 tRNA- and 4 rRNA-encoding genes were retained in the plastid genome. Compared to the plastome of its close non-parasitic relative Lindenbergia philippensis, only one protein-coding gene and one intron are missing from P. rex but many genes show signs of pseudogenization. Pseudogenization in the P. rex plastid genome was found to be mainly caused by single site insertions, deletions or substitutions. The overall high level of homology between the P. rex and L. philippensis plastomes may explain why P. rex shows weak host dependence. However, how P. rex maintains its photosynthetic capability despite featuring a number of potentially dysfunctional pseudogenes involved in photosynthesis is unclear, and the minimal set of genes that is required for hemiparasitic plants to keep their autotrophic lifestyle is still unknown.
M.S. in Biology, July 2015
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Title: P21 IS A BIOMARKER OF CELL FATE AFTER UV IRRADIATION
Creator: Lu, Ziyan
Date: 2011-04-19, 2011-05
Description: UV irradiation can cause DNA damage, which leads to either cell cycle arrest or apoptosis. As a major transcriptional target of p53 protein in...
Show moreUV irradiation can cause DNA damage, which leads to either cell cycle arrest or apoptosis. As a major transcriptional target of p53 protein in response to DNA damage, p21 protein plays critical roles in both cell cycle arrest and apoptosis. However, the specific range of UV doses and functions of p21 protein leading to the determination of cell fate in human androgen-independent prostate cancer cells has not been completely elucidated. Here, we show that low doses of UV irradiation (< 40 J/m2) induced cell cycle arrest with up-regulation of p21 protein. However, high doses of UV irradiation (> 60 J/m2) can induce apoptotic cell death as indicated by caspase-3 activation, which is also consistent with apoptotic morphological changes. Interestingly, p21 protein is degraded at early time course of high-dose UV irradiation-induced apoptosis, pretreatment of proteasome inhibitor MG132 which can block p21 degradation but partially inhibits apoptotic cell death. Consistently, similar results were obtained in both 104-R1 cells and 104-IS cells. Taken together, the results suggest that there is a narrow window of UV doses range that serves as a “switch” point, in which cells make a decision: either cell cycle arrest or cell death. p21 protein serves as a good indicator for both cell cycle arrest and apoptotic cell death post-UV irradiation in human androgen-independent prostate cancer cells. Therefore, p21 may be a potential therapeutic target in prostate cancer.
M.S. in Biology, May 2011
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Title: CHARACTERIZATION OF A NOVEL TUMOR SUPPRESSOR BAX
Creator: Wang, Xin
Date: 2013-04-16, 2013-05
Description: Bax is a pro-death tumor suppressor. The loss of functional Bax expression can enhance the tumor growth. Recently we discovered a new family...
Show moreBax is a pro-death tumor suppressor. The loss of functional Bax expression can enhance the tumor growth. Recently we discovered a new family of functional Bax isoforms generated specifically in certain tumors; one of them is Bax 2 . In this thesis, I characterized the properties of Bax 2 protein by comparing with the parental Bax 2. Bax 2 was cloned into a GFP mammalian expression vector and transfected into the bax knockout cells. I examined Bax 2 expression, cellular distribution, and ability to induce cell death. The results show that the Bax 2 protein aggregated as granules around the nucleus in cytoplasm and induced more cell death than that from previously studied Bax 2. The results implicate that cancer patients with Bax 2 isoform might have better prognosis or response to treatment.
M.S. in Biology, May 2013
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Title: MOLECULAR AND GENETIC ENGINEERING STUDIES OF VITREOSCILLA HEMOGLOBIN
Creator: Chen, Yang
Date: 2014, 2014-05
Description: Biodesulfurization is a promising field that can be applied to the processing of crude oil for removing dibenzothiophene (DBT) and its...
Show moreBiodesulfurization is a promising field that can be applied to the processing of crude oil for removing dibenzothiophene (DBT) and its derivatives. A thermophilic bacterial strain Paenibacillus naphthalenovorans (32O-Y) was found to metabolize DBT as sole sulfur source. Another thermophilic strain Paenibacillus apiaries (32O-W) which cannot utilize DBT, however, was found to increase the desulfurization activity of 32O-Y in mixed 32O-Y+W culture in minimal-DBT medium at temperatures between 45 and 50 °C. In order to increase the desulfurization activity of these strains, we genetically engineered strain 32O-Y to express Vitreoscilla hemoglobin (VHb). VHb is the first hemoglobin found in bacteria and has been used to increase the growth and product yields various cells. The VHb gene (vgb) was successfully cloned into shuttle vector pNW33N. 32O-Y was successfully transformed with pNW33N-vgb while 32O-W was not. Compared to untransformed 32O-Y, 32O-Y[pNW33N-vgb] grew slower and reached a lower maximum OD600 when cultured in minimal-DBT medium at 45 °C. However, the Gibbs assay showed that VHb expression in 32O-Y increased its desulfurization activity by 18%. Thus, VHb can help 32O-Y metabolizing DBT while it might not promote growth. A series of high temperatures cultures need to be conducted to select an even more thermophilic strain which can fulfill the 60 °C requirement of industrial process. The VHb mutant (vgbM3) was also studied, which was previously found correlated with increased growth of E. coli DH5α, compared with the effect of wild type VHb. The effect that the mutant amino acids in VHbM3 was determined. Plasmid pUC- vgbM3 was obtained and successfully transformed to DH5α. After sequencing, two copies of vgbM3 were found in the plasmid. In order to study only one copy of vgbM3, x primers were designed for amplification. Fragment vgbM3 was successfully inserted into vector pUC18, followed by successful transformation into DH5α. Cell free extract was obtained from strains DH5α, DH5α[pUC8:16] and DH5α[pUC18-vgbM3] for CO-difference assay. As expected, DH5α expressed no hemoglobin. DH5α[pUC8:16] expressed wild type hemoglobin at 20 nmol/gm wet weight, while DH5α[pUC18-vgbM3] expressed mutant hemoglobin at 4 nmol/gm wet weight. Oxygen dissociation constant determination of VHbM3 will be the next step.
M.S. in Biology, May 2014
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Title: DIFFERENTIAL SENSITIVITY OF BAXΔ2 POSITIVE AND NEGATIVE CELLS TO ANTI-TUMOR AGENT BORTEZOMIB IN COLON CANCER
Creator: Chen, Wenjing
Date: 2015, 2015-05
Description: Tumor suppressor BaxΔ2 is a functional Bax isoform that is found in microsatellite unstable (MSI) colon cancer. However, BaxΔ2 proteins are...
Show moreTumor suppressor BaxΔ2 is a functional Bax isoform that is found in microsatellite unstable (MSI) colon cancer. However, BaxΔ2 proteins are not stable and are prone to be degraded by proteasomes in tumor cells. Bortezomib, a proteasome inhibitor, is an FDA approved anti-cancer drug mainly used for the treatment of myeloma and lymphoma. We tested if Bortezomib can block BaxΔ2 degradation and potentially be beneficial for the treatment of BaxΔ2 positive colon cancer. In this project, we compared the efficacy of Bortezomib-induced cell death in BaxΔ2-positive and BaxΔ2-negative colon cancer cells. We found that BaxΔ2-positive cells were highly sensitive to Bortezomib-induced cell death in comparison with that in BaxΔ2-negative cells. The half maximal inhibitory concentration (IC50) of cell viability for BaxΔ2-positive cells is 11.1 nM, while it is 453.8 nM for BaxΔ2-negative cells. The results indicate that Bortezomib has a selectivity towards BaxΔ2-expressive cells and could be a drug candidate for the treatment of BaxΔ2-positive colon cancer.
M.S. in Biology, May 2015
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Title: Thermal Resistance of Salmonella in Desiccation and Rehydration
Creator: Ahuja, Rameet
Date: 2011-12-06, 2011-12
Description: Transfer of salmonellae from a desiccated existence in dry food ingredients or processing environments to food products having higher water...
Show moreTransfer of salmonellae from a desiccated existence in dry food ingredients or processing environments to food products having higher water activities (e.g., peanut butter used in pie, chocolate in cake) leads to partial or full re-hydration of the bacteria. This study characterized the thermal behavior of Salmonella in response to desiccation and the subsequent rehydration. The thermal resistance of the desiccated S. enterica ser Tennessee was inversely correlated to aw: for example, desiccation at 11 to 97% equilibrated relative humidity (ERH) resulted in 0.5 to 3.3 log reduction, respectively, after 60ºC treatment for 10 min. Cells stored at lower ERH showed a lower survival rate, but higher thermal resistance. Once cells established their initial physiological response to desiccation, continual storage at 11% ERH up to three weeks did not further change the thermal resistance of Salmonella. Rehydration of the desiccated cells (11% ERH) to higher ERH conditions (84 to 97%) led to greater than 5 log reduction after heating cells at 60ºC for 10 min, in contrast, the same heat treatment resulted in approximate 3 log reduction for cells stored constantly at 84-97% ERH. There was no significant difference in regard to thermal sensitivity between cells rehydrated from 11% ERH to 33-55% ERH and that stored constantly at each ERH, only about 0.3-0.5 log CFU reduction in both cases. The study showed that rehydration moderately reduced cell viability, but greatly increased thermal sensitivity when a drastic aw shift occurred.
M.S. in Food Safety and Technology, December 2011
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Title: EFFECT OF SUCROSE AND HIGH PRESSURE PROCESSING ON FUNCTIONAL AND PHYCISOCHEMICAL PROPERTIES OF EGG WHITE PROTEINS
Creator: Liu, Hui
Date: 2013-04-25, 2013-05
Description: Egg white is widely used in food applications because of its nutritional benefits and versatile functionalities. Traditional treatment like...
Show moreEgg white is widely used in food applications because of its nutritional benefits and versatile functionalities. Traditional treatment like thermal pasteurization utilized for safety concern is disadvantageous to the egg white proteins due to the functionality impairment. High pressure processing (HPP) technology is known as a non-thermal food preserving method that can be operated at ambient temperatures. Sucrose is an essential ingredient that affects the functional behavior of egg white in numerous baking and pastry applications. The current study investigated the effect of sucrose and HPP on the functional and physicochemical properties of egg white proteins and verified the efficacy of HPP on microbial inactivation in egg white. Sucrose addition and HPP treatment were combined to study the foaming and physicochemical properties. Homogenized egg white samples were treated at selected HPP conditions (300-500 MPa) for 5-15 min, with an initial temperature of 4°C. Sucrose was added at 0-48% (w/v) to samples before or after HPP treatment. Foaming properties including foaming capacity and foam stability were measured immediately after whipping process. Turbidity and viscosity analyses were conducted within 24 hr after HPP treatment. The efficacy of HPP (500 MPa for 5 min) on microbial inactivation was verified using a pathogenic strain Salmonella enterica serotype Enteritidis (H7037) isolated from egg yolk implicated in a salmonellosis outbreak and a nonpathogenic Escherichia coli K12 strain (ATCC23716). All trials were completed in triplicate. Both addition of sucrose and HPP treatment decreased the foaming capacity but increased the foam stability of egg white proteins. Adding sucrose before HPP protected protein from turbidity and maintained foaming capacity, while adding sucrose after HPP greatly improved foam stability (p<0.05). Increasing HPP x holding time from 5 to 15 min did not affect the foaming properties significantly (p>0.05). A 5-log reduction of both strains was achieved after HPP treatment at 500 MPa for 5 min. These results exhibited that HPP can be used as a processing technology for the egg white safety control and that HPP could modify egg white foaming quality in food baking applications.
M.S. in Food Safety and Technology, May 2013
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Title: THE ELASTICITY AND PURIFICATION OF THE FLIGHT MUSCLE PROTEINS OF MENDUCA SEXTA
Creator: Dong, Sicong
Date: 2014, 2014-05
Description: Contraction of the DLM1 flight muscles of the Hawmoth, Manduca sexta are synchronous with the nervous impulse stimulation like mammalian...
Show moreContraction of the DLM1 flight muscles of the Hawmoth, Manduca sexta are synchronous with the nervous impulse stimulation like mammalian skeletal muscle. With cardiac-like behavior, DLM1 muscle of Manduca sexta can be a useful model to resemble mammalian cardiac muscle. Asynchronous flight muscles, like Lethocerus and Drosophila flight muscle, can only extend a few percent. But Manduca flight muscle has the ability to extend at least 100% in vitro and 9% in vivo. Very little is known about the protein composition and physiological behavior of Manduca flight muscle. Hence the length-tension behaviors of the DLM1 muscle of Manduca sexta are of considerable interest. In this experiment, we used PPi to remove thick filament in the sarcomere and focus on the passive tension generated by elastic proteins (projectin, kettin and sls proteins) in the sarcomere. The results showed elastic proteins (projectin, kettin and sls proteins)-based passive tension play a major role on muscle passive force in DLM1 muscles of Manduca sexta. We also tested a new way to prepare chemically skinned muscle samples where the dorsal and ventral muscle samples are pinned still in their shell on plates during the skinning step. In addition, preliminary experiments attempting to purify the DLM1 muscle proteins of Manduca sexta, fast protein liquid chromatography was used. Then 1% vertical SDS-agarose gel electrophoresis (VAGE) and 4-20% SDSPAGE gel are used to detect the samples after purification. We successfully purified 900kDa projectin and 700kDa kettin, which are major elastic proteins and useful for further research.
M.S. in Biology, May 2014
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Title: VITREOSCILLA HEMOGLOBIN: STRUCTURE-FUNCTION AND GENETIC ENGINEERING STUDIES
Creator: Li, Xiaodong
Date: 2014, 2014-05
Description: Paenibacillus strains 32O-W and 32O-Y were attempted to be transformed by electroporation with constructed plasmid pNW33N-vgb, modified to...
Show morePaenibacillus strains 32O-W and 32O-Y were attempted to be transformed by electroporation with constructed plasmid pNW33N-vgb, modified to contain the vgb gene which can be expressed as Vitreoscilla hemoglobin. Only attempts with 32O-Y were successful. Transformed 32O-Y/pNW33N-vgb was grown in CDM medium with dibenzothiophene (DBT) as the sole source of sulfur at different temperatures. Dramatic variability was observed in culture at different temperatures, so only the data at 45 °C was analyzed. The growth assay showed that the 32O-Y/pNW33N-vgb strain grew slower than untransformed 32O-Y, although Gibbs assay showed improvements in utilizing ability of DBT of 32O-Y/pNW33N-vgb compared to untransformed 32O-Y. This finding indicated that genetic engineering of introducing vgb into 32O-Y may cause deterioration in cell growth rate but improvement in desulfurization activities. Plasmid pUC-vgb-M2 was transformed into E. coli DH5α. The transformed DH5α/M2-vgb was cultured along with DH5α/pUC8:16, bearing plasmid pUC8:16 that was previously constructed in our lab and can be expressed to produce wild type VHb, and untransformed DH5α. CO-difference spectra were performed with the lysed cultures for the detection of VHb expression. As a result, DH5α/M2-vgb was confirmed to lack the ability to express functional VHb.
M.S. in Biology, May 2014
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Title: EFFECTS OF THERMAL TREATMENTS ON ELISA DETECTION OF MILK PROTEINS
Creator: Lu, Yingshuang
Date: 2011-07-27, 2011-07
Description: Cow’s milk allergy is one of the most prevalent food allergies in the United States. Commercial ELISA test kits, based on antigen-antibody...
Show moreCow’s milk allergy is one of the most prevalent food allergies in the United States. Commercial ELISA test kits, based on antigen-antibody reactions, are increasingly used by food manufacturers to detect the presence of allergen residues. Milk is a common ingredient used in a variety of foods that are subjected to different degrees of cooking. How thermal processing may affect the quantitative analysis of milk allergens by ELISA test kits needs to be determined. This study first examined the performance of four total protein assays (Pierce 660nm, Modified Lowry, Coomassie, BCA) for quantification of protein residues in thermally processed milk. BCA and Lowry assays were affected by lactose and its Maillard reaction byproducts resulting in the overestimation of protein concentrations in the samples. Pierce 660 nm assay was not affected and therefore was picked as the method for total protein analysis when evaluating commercial ELISA kits. Performances of four ELISA test kits (Veratox for Total Milk Allergen, BioKits BLG Assay Kits, ELISA SYSTEMS Casein and Beta-Lactoglobulin Residue assays) in comparison with the Pierce 660 nm assay for detection of thermally treated milk samples was also evaluated. NIST non-fat milk powder standard reference material 1549 and Backpacker’s Pantry Powdered Whole Milk were either heated in water at 60◦C, 63◦C, boiled, or autoclaved for 10 or 30 min, dry-heated in a mini-oven at 100 - 232◦C for 10 min, or fried in corn oil at 150◦C or 180◦C for 3 min in a deep fryer. Milk proteins in the oil samples were analyzed either directly or after extraction with phosphate-buffered saline with 0.05% Tween (PBST) followed by partitioning in hexane to remove residual oil. The results show that all four ELISA test kits were able to accurately quantify the amount of milk proteins in uncooked oils. Inclusion of the PBST/hexane extraction step prior to test kit analyses did not improve the detection. Elevated heat resulted in a lower level of proteins extracted. While the amount of protein residues determined by Veratox and ELISA SYSTEMS Casein kits were similar to those obtained by the Pierce assay, the BioKits BLG kits registered the highest amount of proteins in samples. On the other hand, ELISA SYSTEMS Beta-Lactoglobulin assay registered the lowest level of proteins in these samples. These results suggest that heat treatment could affect the solubility and possibly the antigenic properties of proteins. Depending on the test kits used, these changes could result in over- or underestimation of protein residues in thermally treated foods.
M.S. in Food Safety and Technology, July 2011
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Title: COMPARISON BETWEEN TWO CHITIN-PURIFIED PRO-DEATH PROTEINS IN MITOCHONDRIA TARGETING ANALYSIS
Creator: Yeap, Xin Yi
Date: 2011-04-19, 2011-05
Description: Bax protein belongs to the Bcl-2 family. It is pro-apoptotic and the most common form is Bax α. When a cell receives death stimuli, Bax...
Show moreBax protein belongs to the Bcl-2 family. It is pro-apoptotic and the most common form is Bax α. When a cell receives death stimuli, Bax protein will oligomerize and target to mitochondria. Another isoform of Bax called Bax 2, which has lost exon 2 and has a frame shift mutation, is verified to be more potent in inducing apoptosis than Bax α. Here, we would like to understand more about Bax 2 mitochondria targeting ability compared to the more common Bax α form. We first set up a cell-free system which contained purified Bax protein and purified mitochondria. The mitochondrial binding protein was identified using fractionation and Western blot with Bax isoformspecific antibodies. Integration of Bax protein into the mitochondrial membrane was determined using the alkaline stripping method. The results suggest that the majority of Bax α targeted and integrated into the mitochondria membrane, while the majority of Bax 2 did not target to mitochondria in the cell-free system. This may suggest that Bax 2 might need additional help from certain cytosol components such as co-factors to target to mitochondria or that Bax 2 induces cell death through a mechanism other than mitochondrial targeting.
M.S. in Biology, May 2011
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Title: The Effect of Salmonella Enteritidis on the Thermal Properties of Egg Albumen and Yolk
Creator: Chadha, Isha
Date: 2011-11-27, 2011-12
Description: Salmonella-inoculated and uninoculated fresh eggs were microwave processed to achieve pasteurization. However, quality degradation was...
Show moreSalmonella-inoculated and uninoculated fresh eggs were microwave processed to achieve pasteurization. However, quality degradation was observed in the albumen of inoculated eggs but not in the uninoculated eggs although the processing was the same. Previous work showed that dielectric properties of egg albumen and yolk do not change in the presence of the bacteria. A new hypothesis was therefore proposed that heat capacity is affected by its presence. If an egg has a lowered heat capacity it will become hotter for a given amount of microwave energy input than eggs having normal heat capacities. The goal of the experiments was to determine whether Salmonella at varying concentrations and different incubation times affects the temperature-dependent thermal properties of egg albumen and yolk during in-shell growth. Although the main concern was Salmonella’s effect on the heat capacity of albumen, the equipment used could measure thermal conductivity as well and measurements on yolk were included for completeness. The thermal properties of both egg albumen and yolk were measured by the KD2 Pro thermal properties analyzer (Decagon Instruments, Pullman, WA) via the supplied 30 mm dual-needle sensor. Variables were temperature (7oC, 30oC, 40oC, 50oC, 55oC and 60oC), bacterial inoculum (0, 103, 106, 108 cfu/ml) and incubation time (0 or 30 hours). The measurements showed no significant difference in thermal properties between inoculated and uninoculated samples of egg albumen and yolk regardless of change in temperature, bacterial concentration and incubation period. The absence of an effect on either the dielectric (previous study) or thermal (present study) parameters by the presence of Salmonella leaves unexplained the quality differences between similarly processed inoculated and uninoculated eggs. A biochemical explanation based on the interaction between metabolic byproducts and egg proteins, affecting how they denature, is a topic for future research.
M.S. in Food Safety and Technology, December 2011
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Title: AN EFFORT TO DISCOVER NOVEL BACTERIAL DSZ GENES TO HELP IMPROVE THE BIODESULFURIZATION OF CRUDE OIL
Creator: Salazar, Joelle Krieger
Date: 2011-04-25, 2011-05
Description: In this thesis study, soil samples were procured from various locations thought to contain high petroleum content, such as gas stations. Those...
Show moreIn this thesis study, soil samples were procured from various locations thought to contain high petroleum content, such as gas stations. Those samples were enriched for those that contained bacteria that were able to metabolize sulfur-containing compounds, such as DBT. The bacteria were then subjected to various experiments to determine if they possess any or all of the genes (dsz) encoding the three enzymes of the dibenzothiophene desulfurization pathway, as compared with R. erythropolis IGTS8. This feat was accomplished by using both growth experiments on medium containing dibenzothiophene as the sole sulfur source and genomic DNA extraction followed by PCR with dszABC universal primers. The resultant amplified DNA was then ligated to pGEM®-T Easy vector and transformed into electrocompetent E. coli cells. The transformants were subsequently screened and sent for sequencing. Using Blast, the sequences were analyzed. No obvious dsz homologies were identified although homologues in some cases to enzymes involved in sulfur metabolism were found. Several isolates were found to have dsz-like activity via the growth experiments as well as the Gibbs assay, which measures accumulation of the end product of the dsz-encoded pathway, 2-HBP Soil sample #32 showed promise in growth experiments in that the culture grew well in M9 with DBT as the sole sulfur source at temperatures of 30 °C, 37 °C, 45 °C, and 55 °C. Streaking the culture discovered two colonies with distinct morphology that were designated 32-W and 32-Y, for white and yellow colonies. 32-W and 32-Y also grew independently in M9 with DBT. Positive Gibbs Assays were obtained from the cultures 32-mixed, 32-W, and 32-Y.
M.S. in Biology, May 2011
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Title: EFFECTS OF CHROMIUM COMPOUNDS ON INSULIN-MEDIATED GLUCOSE UPTAKE
Creator: Yang, Liu
Date: 2012-04-13, 2012-05
Description: Chromium supplementation has been highlighted by its biological function in improvement of glucose metabolism. As essential trace nutrition,...
Show moreChromium supplementation has been highlighted by its biological function in improvement of glucose metabolism. As essential trace nutrition, chromium complex has great therapeutic potential in the alleviation of metabolic disorders, especially type II diabetes. This study is aimed at investigating the effect of two newly synthesized chromium (III) complexes Cr2(μ-OH)2(C4O4)2(H2O)4·(H2O)2, Cr2(μ-OH)2(μ1,2- C4O4)2(C2H6SO)4·(H2O)2 in comparison with a commercial compound CrCl3·6H2O on glucose uptake, as well as toxicity. We found that with 100 nM insulin stimulus, Cr2(μ- OH)2(C4O4)2(H2O)4·(H2O)2 significantly increased cellular glucose uptake, while Cr2(μ- OH)2(μ1,2-C4O4)2(C2H6SO)4·(H2O)2 inhibited the insulin-stimulated glucose uptake. Morphology study indicated that a relatively low concentration of these three complexes had little toxicity to cells within 24 h, but a higher concentration would lead to cell death. Cell growth curve supported the notion that the chromium (III) compounds in this study had no obvious cellular toxicity. Therefore, these results suggest that the newly synthesized less toxic chromium has a great potential in improvement of glucose metabolism in response to insulin. This study may provide valuable information in the treatment or management of diabetes. Keywords: Chromium, Insulin, Glucose uptake, Glucose metabolism, diabetes, type II diabetes
M.S. in Biology, May 2012
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Title: INTERACTION OF DAIRY BASED PROTEIN WITH PHENOLIC ANTIOXIDANT OF STRAWBERRY POWDER
Creator: Feng, Haoshi
Date: 2012-05-04, 2012-05
Description: Fruits contain an abundant amount of polyphenolic compounds that have antioxidant properties. These compounds have shown the ability of...
Show moreFruits contain an abundant amount of polyphenolic compounds that have antioxidant properties. These compounds have shown the ability of reducing the risk of major degenerative diseases, relief from allergies/asthma, weight loss and improved circulation. Dairy proteins have numerous benefits as enhancing muscle formation, weight and blood pressure control, beneficial effect in bone and dental health and protection against toxins, bacteria, and viruses. The combination of both fruit and dairy in commercial or homemade mixtures, such as smoothies, is readily available and popular. But in fact, the interactions which happen between proteins and fruit antioxidants could affect the availability and potential activity of antioxidants. This thesis will focus on the interaction of dairy proteins with antioxidant from freeze dried strawberry and measure the availability of the antioxidant capacity. Freeze dried strawberry powder at different concentrations (1.64%, 3.28% and 6.56%) was mixed with four types of proteins at different concentration to demonstrate the interaction over a range. The proteins used were skim milk powder (6.89%), whey from bovine milk (0.51%), casein from bovine milk (2.04%), and albumin from bovine serum (2.55%). The antioxidant content was measured by several analytical techniques using LCMS/MS, Oxygen Radical Absorbance Capacity (ORAC) assay and Folin-Ciocalteu assay. SDS-PAGE was used to examine the change of protein molecular weight before and after the reactions. The binding interaction resulted in significantly reduced ORAC and Folin- Ciocalteu assay values compared to the respective non-protein strawberry mixtures (P<0.001 and P<0.05). The SDS-PAGE images between protein strawberry mixtures and non-protein strawberry mixtures showed similar results. The (+)-catechin, cyanidin-3-O glucoside, pelargonidin-3-O-glucoside and kaempferol-3-coumaroylglucoside content were significantly reduced when comparing skim milk based strawberry powder mixtures and non-protein strawberry mixtures (P<0.05). This research indicates the binding interaction between dairy protein and freeze dried strawberry powder reduces the antioxidant activity of the freeze dried strawberry powder.
M.S. in Food Safety and Technology, May 2012
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Title: PANCREATIC ADENOCARCINOMA: SECRETORY MARKERS AND CORRELATION WITH PARKINSON’S DISEASE
Creator: Gayatri, Sitaram
Date: 2011-04-27, 2011-05
Description: Pancreatic adenocarcinoma (PDAC), the fourth highest cause of cancer related deaths in the United States, has the most aggressive presentation...
Show morePancreatic adenocarcinoma (PDAC), the fourth highest cause of cancer related deaths in the United States, has the most aggressive presentation resulting in a very short median survival time for the affected patients. Early detection of PDAC is confounded by lack of specific markers. Proteins of importance in neurodegenerative diseases like Parkinson’s disease (PD) are believed to be of etiological significance and correlated to or be the cause/effect of pancreatic disease. Expression of proteins like PD autosomal recessive, early onset 7 (PARK-7/DJ-1), α-Synuclein (SNCA) both of which are known to be pathognomonic to Parkinson’s disease was found altered in various stages of the disease. Purine Nucleoside Phosphorylase (NP) has been exploited to be a therapeutic target in cancers. The expression of all these three proteins was found to be variable with the stage and existence of metastatic lesions in PDAC tissues. The protein levels of NP were higher in PDAC sera compared to the benign samples. The serum NP levels of other cancers viz. lung, kidney, colon and breast were also not elevated. While the serum levels of NP and those of its downstream metabolites have the potential to differentiating PDAC from benign, the expression levels of SNCA and PARK-7/DJ-1 allude to a possible nuance in the etiology of PD and PDAC.
M.S. in Biology, May 2011
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Title: THE CHARACTERIZATION OF TWO THERMOPHILIC STRAINS CONCERNING BIO-DESULFURIZATION OF DIBENZOTHIOPHENE BY THE 4S PATHWAY
Creator: Li, Enze
Date: 2016, 2016-05
Description: A moderately thermophilic Mycobacterium strain (denoted Myco-U) was isolated in our lab as a contaminant during the cultivation of another...
Show moreA moderately thermophilic Mycobacterium strain (denoted Myco-U) was isolated in our lab as a contaminant during the cultivation of another thermophilic Paenibacillus strain, and has been proved to harbor the genes that encode the enzymes for dibenzothiophene (DBT) biodegradation via the 4S pathway; this makes it possible to efficiently remove organosulfur compounds (e.g. DBT and DBTO2) from the crude petroleum. Through directed evolution (continuous passage and selection with increasing temperature), the Myco-U strain has shown moderate capacity of metabolizing DBT to 2-hydroxybiphenyl (2-HBP) by the 4S pathway at a thermophilic temperature (~53 ℃). In the middle-to-late stages of the selections, a stubborn contaminant (denoted Bacillus X) arose and has remained difficult to get rid of from our medium and cultures ever since, leading to a persistent contamination and repetition of our experiments. The reason why Bacillus X is regarded as a contaminant is that it does not obtain sulfur by the expected means (e.g., DBT desulfurization), but utilizes the tiny amount of sulfate from the vitamin mix and 50 μg/ml yeast extract in our medium to grow. This is confirmed by the facts that Bacillus X does not yield any detectable 2-HBP, and a significant difference of growth has been detected between cultures with DBT as the sole sulfur source and the positive controls, which employs Na2SO4 as sulfur source. Through 16S rDNA amplification, cloning, and sequencing, Bacillus X was identified as a Bacillus species, and shows the highest homology (99 % identical) to a specific uncultured bacterium clone (NCBI #Accession: JN882111.1). The chromogenic mechanism and impacts of pH and carbonate upon the Gibbs assay, by which 2-HBP is quantified, were investigated. When DBT is absent or at undetectably low levels, cultures measured by the assay display a yellowish-to-brownish background after adding the Gibbs reagent (2,6-dichloroquinone-4-chloroimide). According to our results, the Gibbs reaction prefers alkaline conditions and pH 8.0 ranks the optimal (compared with pH 7.0, 7.5, 8.5 and 9.0) at which the maximum A610nm is detected.
M.S. in Biology, May 2016
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Title: CHANGES OF BACTERIAL SPECIES AND HEME PROTEIN LEVEL IN ACTIVATED SLUDGE COMMUNITIES ACCLIMATED TO LOW AERATION
Creator: Li, Hainan
Date: 2016, 2016-05
Description: Increasing oxygen utilization of activated sludge under low dissolved oxygen (DO) conditions can lead to energy savings in wastewater...
Show moreIncreasing oxygen utilization of activated sludge under low dissolved oxygen (DO) conditions can lead to energy savings in wastewater treatment systems. Adaptation of sludge communities to low oxygen conditions may be facilitated by increased expression of heme proteins. One way to assess heme protein expression in sludge is to analyze the species present in the sludge community during the adaptation process. In the work reported here, growth of a sludge culture adapted by Kunkel to low aeration for 48 weekly passages was continued for an additional 26 passages (182 days). The activated sludge was cultured in synthetic wastewater under low DO conditions. Temperature, dissolved oxygen, and specific oxygen uptake rates (SOUR) were measured at the end of each weekly passage. The community structures of passages 50, 53 and 65 were determined by 16S rDNA cloning techniques. The type of heme present was identified using the pyridine hemochromogen method. The SOUR values measured increased slightly in the first part of the experiment, when the culture DO was very low, but then decreased in the latter part of the experiment, when the culture DO increased. The community structure diversity in passage 50 in Kunkel’s study and passage 50 from this work are totally different in terms of species present, even though the two cultures were both derived from Kunkel’s passage 48 and were grown under conditions which were matched as closely as possible for two additional passages. This indicates that the community structure is highly sensitive to small changes in growth conditions. From the point of view of types of hemoglobin (Hb), the community became more diverse by passage 53, containing all three types of truncated Hb (trHbN, trHbO, and trHbP), possibly due to the need for NO scavenging and oxygen transfer enhancement. The proportion of cells that synthesize truncated Hb decreased slightly through passages 50 to 53 to 65. The percentage of cells that encode FlavoHbs decreased from 84 % to 50 % by passage 65. Overall there was an increase in Hb expression from passage 50 to passage 65. Heme b expression in the sludge culture was confirmed. Successful adaptation of the sludge culture to low DO conditions via enhancement of oxygen uptake was not obvious in this study. Yet the overall tendencies of SOUR and Hb expression suggest that it is possible to acquire a culture more efficient in oxygen uptake if a stable low aerobic environment can be maintained for an extended period.
M.S. in Biology, May 2016
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