Microbiology Commons^™

Diversity Of The Beneficial Bacterium Oxalobacter Formigenes Isolated From The Human Gut, Karen Shaw

Masters Theses

Oxalobacter formigenes is an anaerobic, oxalate degrading organism that colonizes in the mammalian intestinal tract. Currently, O. formigenes is divided into two groups via PCR of the oxc gene. Pulsed field gel electrophoresis (PFGE) is a technique used to resolve large pieces of DNA. Typically, PFGE is used to identify differences between strains for pathogenic bacteria, but this study sought to use it to further understand the diversity of a probiotic organism. This study aimed to develop a methodology for utilizing PFGE to examine O. formigenes. The methodology involved lysing O. formigenes cells in plugs, first in proteinase K, …

Microbial Community Analysis From Petroleum-Contaminated Sediments With High Magnetic Susceptibility, Anja E. Williams

Masters Theses

Microbial biodegradation is an increasingly incorporated method of hydrocarbon mineralization during oil spill cleanup. To monitor biodegradation, magnetic susceptibility (MS) is a geophysical tool that detects changes in sediments’ magnetism, possibly caused by microbial activity, for example by anaerobic iron reduction that can induce magnetite formation. Furthermore, the high input of carbon from an oil spill makes other required nutrients, like nitrogen, limiting. The first study goal was to characterize the microbial communities present at high levels of MS with 16S rRNA gene clone libraries at the petroleum-contaminated site in Bemidji, Minnesota. Sequences with high similarity to known iron-reducers were …

Exploring The Oncolytic Potentail Of A Double Knock-Out Tanapoxvirus Containing Flic Transgene, Esaw W. Kurban

Masters Theses

Since the emergence of oncolytic viruses (OVs), OVs have seen success in clinical trials and are a vital alternative treatment for cancer. Colorectal cancers are diseases which cause substantial health issues in the developed world, but current invasive treatment methods do not perform well in patients with advanced disease. We have explored the potential of tanapoxvirus (TPV) for its oncolytic virothrapy in two manners; specific gene deletion and non-targeted gene deletion. The non-targeted mutation of TPV’s genome was attempted using N-methyl-N-nitro-N-nitrosoguanidine (NTG) and N-ethyl-N-nitrosourea (ENU) as alkylating chemical. Specific gene deletion involved knocking-out a thymidine kinase gene (TPV-66R) and a …

Ph Dependent Antibiotic Resistance Of An Alkaliphilic, Halotolerant Bacterium Isolated From Soap Lake, Washington, Tiffany Charlynn Edwards

Masters Theses

"Soap Lake, located in Washington State, is a meromictic, soda lake. Many bacterial isolates retrieved from Soap Lake have been noted to possess resistance to multiple antibiotics. A likely explanation for the wide range of antibacterial resistance exhibited by these strains is due to the impact of high alkalinity on the antibiotics themselves and not due to the presence of antibiotic resistance genes. The aim of our study was to determine if select antibiotics are effective against Halomonas eurialkalitoleranis, a bacterium capable of growth over a wide range of neutral to alkaline pH values, to investigate the influence of alkalinity …

Effects Of Treated Wastewater Effluent On Microbial Community Structure In A Natural Receiving Aquatic System, Matthew D. Hladilek

Masters Theses

Despite our dependency on treatment facilities to condition wastewater for eventual release to the environment, our knowledge regarding the effects of treated water on the local watershed is extremely limited. Responses of these lotic systems to the treated wastewater effluent have been traditionally investigated by examining the benthic macroinvertebrate assemblages and community structure; however, these studies do not address the microbial diversity of the water systems. In the present study, planktonic and benthic bacterial community structure were examined at fourteen sites (from 60 m upstream to 12,100 m downstream) and at two time points along an aquatic system receiving treated …

Metagenomic Analysis Of The Lacrimal Caruncle Region Of Canis Lupus Familiaris Using Miseq Technology, Seun A. Ikugbayigbe

Masters Theses

The identification of ocular microbiota may allow early diagnosis and treatment strategies against eye diseases and disorders with canines. However, clinical microbial identification has been limited to cloning and conventional culture-based studies, which typically underestimate community diversity. In this report, lllumina MiSeq analysis of the 16S rRNA gene was used to examine the microbiome of the lacrimal caruncle region from five healthy dogs. The breeds sampled were a Golden Retriever (Dog A), a Weimaraner (Dog B), a Shih Tzu mix (Dog C), a Yorkie mix (Dog D), and a Dachshund (Dog E). MiSeq analysis revealed a total of 370 operational …

Examining The Nutritional Requirements Of Acidophilic Archaea "Ferroplasma Acidarmanus" Strain Fer1, Yudong Qu

Masters Theses

Ferroplasma acidarmanus strain fer1 (fer1) is an archaeal microaerophilic acidophile (pH 0 to pH 3) with a chemolithotrophic metabolism. As an efficient consumer of sulfate, fer1 plays an important role in the biogeochemical process of pyrite dissolution at acidic site. Confirming the genomic prediction of metabolic gene functions in this organism requires functional assays, which cannot be carried out until a defined medium is obtained. The objective of the current study was to replace the 0.1% (w/v) yeast extract component in the growth medium, mfer, with defined components for carbon, nitrogen, and vitamin needs. In order to replace the 0.1% …

Functional Annotation, Transcriptional Characterization And Enzymatic Contributions Of Essential Amino Acid Biosynthesis-Related Genes, Teresa J. Clark

Masters Theses

In plants, essential amino acid biosynthesis predominantly or exclusively occurs in the plastid. The plastid in the heterokont alga Nannochloropsis oceanica is surrounded by four membranes, which add great complexity to intracellular trafficking and communication. N. oceanica genes in essential amino acid biosynthesis were functionally annotated. The biosynthesis pathways resemble the pathways in Arabidopsis thaliana, but the gene content seems to be simpler in N. oceanica.

In addition, two A. thaliana mutants with loss-of-function mutations in the aspartate kinase-homoserine dehydrogenase 2 (AK-HSDH2) gene were characterized. These ak-hsdh2 mutants demonstrate unexpected accumulation of aspartate-derived amino acids (ADAAs), particularly threonine, in …

Resolving The Nutritional Requirements Of The Bile Acid-Dehydroxylating Gut Bacterium Clostridium Scindens, Oindrila Paul

Masters Theses

Compared to the other parts of the human body, the gastrointestinal tract harbors a complex microbiota. The impact of the indigenous microbiota on host physiology is most pronounced in the colon, where the primary bile acids chenodeoxycholic acid and cholic acid are converted, via 7α-dehydroxylation, to the toxic secondary bile acids lithocholic acid and deoxycholic acid, respectively, by Clostridium scindens, an obligate anaerobe. Interestingly, other than bile acid dehydroxylation, little is known about the basic physiology of C. scindens. Understanding the metabolism of C. scindens will hopefully provide much-needed information as to how this gut bacterium impacts human health and …

Lichen Use By Larval Leucochrysa Pavida (Neuroptera:Chrysopidae), Penni Jo Wilson

Masters Theses

Leucochrysa pavida is a species of green lacewing (Neuroptera:Chrysopidae) that uses lichen fragments to build a larval debris "packet." The "packet" is eventually used to form a cocoon used during pupation. Only minute lichen fragments are harvested for formation of the packets which makes identification of the actual lichens utilized difficult using morphological characteristics. For this reason, thin-layer chromatography was employed. The thin-layer chromatographic process identifies acetone-soluble lichen chemicals that are formed in lichen thalli. By comparing the chemistry of lichen communities at Tower Rock Recreation Area in Hardin County, Illinois, with the chemicals identified during thin-layer chromatography of larval …

Evidence For Dna Methylation-Sensitive Transactivator Mediated Regulation Of The Expression Of An Epstein-Barr Virus Neutralizing Antigen, Sridhar Chalasani

Masters Theses

DNA methylation has a profound effect on the expression of a number of eukaryotic genes. This study demonstrates that an Epstein-Barr virus (EBV) positive Burkitt's lymphoma cell line, Raji, contains the gene encoding gp350/220 but is not expressed. Frog virus 3 (FV3), an iridovirus, has the ability to overcome the inhibitory effect of DNA methylation. Fusion of FV3-infected cells with Raji cells resulted in expression of gp350/220, suggesting that gp350/220 is regulated by DNA methylation. Further evidence for this hypothesis was obtained by transfecting B95.8 cells with HpaII/HhaI methylated plasmid pLATE-CAT, containing the gp350/220 promoter. Southern blot analyses and a …

A Biosystematic Study Of Three Plant Pathogenic Fungi, Richard James Langham

Masters Theses

Isolates of Chalara australis, Eucalypt Ceratocystis, and Ceratocystis virescens were grown on Potato Dextrose Agar, Malt Extract Agar, and Czapek Agar and examined as part of a biosystematic study on these fungi. Basic micromorphological and macromorphological data on the cultures were recorded and the taxa were found to be morphologically similar. Tissue isolates and single spore isolates were crossed within these taxa and an interspecific cross performed. Chalara australis was found to be either asexual or have only one mating type present in the cultures studied. Eucalypt Ceratocystis was found to have a mating system characteristic of bipolar …

Relative Sensitivities Of Diatoms To Selected Heavy Metals, Jennifer E. Carlson

Masters Theses

Baseline data, including diatom community structure, metal concentrations of water, sediments and periphyton of the Embarras River were determined previously (Vaultonburg, 1991). Data on diatom community structure in conjunction with efforts to identify relative sensitivity of diatoms may be useful in establishing an effective method for biomonitoring metal pollution in the Embarras River and other aquatic systems. The main objectives of this project were: i) develop a bioassay method; ii) evaluate relative toxicities of several metals towards diatoms; and, iii) evaluate relative sensitivities of diatoms toward dissolved metals.

Unialgal cultures of Cyclotella meneghiniana, Navicula vaucheriae, and Nitzschia palea were isolated …

Direct Immunofluorescence Detection Of Giardia Spp. In Selected Mammals In Central Illinois, Using Anti-Giardia Polyclonal And Monoclonal Antibodies, Jeanette Aba Ackon Brown

Masters Theses

Giardia species occur in many kinds of mammals, and some of these hosts have been postulated as potential reservoirs for human infections. A study was initiated in fall 1990 to determine the distribution and frequency of giardiasis in populations of selected wild animals in 12 counties in Illinois. Fecal samples from 64 white-tailed deer, 13 coyotes, 9 muskrats, 6 raccoons, and 5 badgers were examined for the presence of Giardia spp. and specifically for G. lamblia. Anti-Giardia lamblia cysts polyclonal (PAb) and monoclonal (MAb), FITC-labeled antibody solutions were used for the direct immunofluorescence detection of Giardia cysts in …

The Isolation And Partial Characterization Of The Lipopolysaccharides From Rhizobium Leguminosarum Biovar Trifolii Strains Tb4, Tb104, And Tb112, Jill K. Miller

Masters Theses

The lipopolysaccharides (LPSs) from Rhizobium leguminosarum biovar trifolii TB4 and two transposon (Tn5) symbiotic mutants, R. leguminosarum bv. trifolii TB104 and TB112, were isolated and partially characterized. Bv. trifolii TB4 is a derivative of R. leguminosarum bv. trifolii ANU843. The two mutant strains elicited incompletely developed clover nodules that exhibited low bacterial populations and very low nitrogenase activity. The LPSs were extracted using the hot phenol-water method and purified with gel filtration column chromatography using Sepharose 4B with an elution buffer consisting of EDTA and triethylamine. The hexose compositions were determined by gas chromatography of the alditol acetate derivatives. LPS …

Quantitative Studies On Nodulation Competition Of Two Strains Of Bradyrhizobium Japonicum And Its Biological Control With A Bacteriophage, Jin Xiong

Masters Theses

Interstrain competition of Bradyrhizobium japonicum for nodulation of soybean (Glycine max) presents a serious problem to the field commercial inoculation practice. The more efficient, introduced strains are often outcompeted by the less efficient, indigenous strains. This study was conducted to determine if the competition could be effectively controlled by the massive introduction of a more efficient strain and/or the large scale reduction of a indigenous strain by the application of a bacteriophage specific to the indigenous one.

B. japonicum strain 61A123, common in Midwestern U.S. soils, and strain USDA110, representative of the strains used in commercial inocula, were chosen for …

Partial Characterization Of Lpss From Rhizobium Fredii Usda 205 Before And After Nod Gene Induction, Bradley Lawrence Reuhs

Masters Theses

The lipopolysaccharides (LPS) from Rhizobium fredii USDA 205 and its nod- mutant, HC 205, which has been cured of the 192-MDa symbiotic plasmid, were isolated by the phenol-water extraction method. The LPS from the wild-type strain which was grown in association with host-plant root extract or a flavone analog to a constituent of the root extract, which is required for the induction of at least a portion of the nodulation genes, was also isolated. The conditions required for the induction of the nod genes were determined by work with a nod- mutant of R. fredii USDA 201 which …

The Effects Of Frozen Storage And Repeated Freeze-Thawing On Salmonella In Varied Concentrations Of Waste Activated Sludge, Joseph Toman Jr.

Masters Theses

Commonly, waste activated sludge is applied to farmland as a fertilizer supplement and soil conditioner. The use of waste activated sludge is not only an efficient way of sludge disposal, but also an economical one. Much concern has been raised about the safety of such a practice. Harmful pathogens, like Salmonella, are commonly present in waste material. Treatment at wastewater plants is successful in eliminating these organisms from final effluent, but the solids generated are full of indigenous microorganisms, including Salmonella.

Work of this paper attempts to determine the safety of the sludge product after simulated winter conditions …

Antibiotic Effects On Coliform Enumeration, Keith Leonard Wozniak

Masters Theses

The inhibitory effects of Bacillus polymyxa on Escherichia coli were studied. Significant coliform inhibition was observed. The inhibitory agent (presumably polymyxin) was active against coliforms after a one hour holding time. Different suspending menstrua were analyzed for their effects on coliform inhibition. It was observed that Peptone water provided the highest recovery of coliforms while phosphate buffer provided less protection. Two methods of enumeration were also studied as to their ability to quantify coliforms inhibited by B. polymyxa. Comparable inhibition was shown using both methods. No significant differences exist between the Standard Plate Count and Membrane Filter techniques. Overall, …

The Effect Of A Bacteriophage On The Competition Of Rhizobium Japonicum Strains For Nodulation Of Glycine Max (L.) Merr, Lori Kelley

Masters Theses

The symbiotic relationship between Rhizobium japonicum (Kir.) Buch. and Glycine max (L.) Merr. was the concern of this thesis. This relationship occurs naturally in soybean fields. In the field there are many different strains of Rhizobium. Some of these strains fix atmospheric nitrogen more efficiently than others resulting in a higher crop yield. The problem is the more efficient nitrogen fixers are out-competed by less efficient nitrogen fixers. In order to solve this problem the more competitive strains have to be controlled. There are two main ways to do this. One is to increase the number of the desired …

Analysis Of The Charleston, Illinois Water Supply For The Presence Of Organic Mutagens Utilizing The Ames Salmonella/Microsome Assay, Steven Lee Washburn

Masters Theses

Water samples from the Charleston, Illinois water supply and selected agricultural run-off areas were tested for the presence of organic mutagenic chemicals. The Ames Salmonella/microsome mutagenicity assay utilizing strains TA98 and TA100 was used to analyze concentrated water samples. A special set of samples was exposed to the S9 activation system coupled with the TA98 strain to simulate the mammalian metabolic system.

No mutagens were detected in any of the samples tested. Several positive and negative control systems were included in the testing system. Negative control systems were used to determine the average spontaneous reversion rates for each strain for …

Response Of A Nitrifying Biofilm To Copper, Denise Moldroski Mott

Masters Theses

In pure cultures of Nitrosomonas, copper is known to cause a stimulation of nitrification at low levels (≤ 0.03 mg Cu⁺²/1) and an inhibition affect at higher levels (≥ 0.05 mg Cu⁺²/1). Nitrifying activated sludges are much more tolerant of copper showing only 75% inhibition at 150mg Cu⁺²/1. The purpose of this paper was to determine the copper sensitivity of a nitrifying biofilm grown in a continuous flow trickling filter system.

A continuous flow trickling filter system was built using limestone chips for the biofilm substrate. The biofilm was established from secondary effluent. …

Fecal Coliform Membrane Filtration Recovery Techniques, Pamela Rose Rinebold

Masters Theses

Researchers over the years have been trying to improve recovery techniques for fecal coliform bacteria. Improved techniques would provide better estimates of the number of fecal coliform bacteria as well as better estimates of fecal contamination with potential pathogenicity of food and water.

Stressed, but viable, fecal coliform bacteria if placed under the appropiate conditions, can recover, thus presenting the possibility of inadequate disinfection. Chlorine sanitization, as done in potable and wastewater treatment, is one such method of stressing bacteria.

Techniques of recovery were studied using presumably unstressed and chlorine stressed samples. Phase one of this study was the comparison …

A Comparison Of The Acidic Extracellular Polysaccharides From Rhizobium Trifolii Mutants Affected In Trifolium Repens Root Hair Curling, Brian Andrew Hanley

Masters Theses

The compositions and sugar linkages of the acidic extracellular polysaccharide (EPS) from several Rhizobium trifolii mutants were compared. These mutants were derived from a wild type Rhizobium trifolii, ANU843, and are unable to cause normal root hair curling, Hac-, or nodulate clover, Nod-. Three of the mutants contain a Tn5 insertion in a 5.3 kb BglII fragment of the symbiotic plasmid (pSym). A fourth mutant is missing the pSym, which includes much of the 5.3 kb BglII fragment, both of these deletions result in Hac-Nod- phenotypes. When the 5.3 kb BglII fragment is cloned (pRT150) and reinserted into the …

Partial Characterization Of The Extracellular Polysaccharides Produced By Mutants Of Rhizobium Leguminosarum And Rhizobium Trifolii, Lendell L. Cummins

Masters Theses

Extracellular polysaccharides (EPS) are suspected to be involved in some aspect of the Rhizobium-legume symbiotic process. Extracellular polysaccharides produced by R. leguminosarum and R. trifolii mutants were isolated and partially characterized by gas chromatography, column chromatography, double diffusion, polyacrylamide gel electrophoresis, and immunoelectrophoresis.

The R. leguminosarum mutants, derived from strain 128C53, all are deficient in EPS production (exo-). Strain ANU54 is missing the symbiotic plasmid, while plasmid-containing strains ANU54 pJB5JI and ANU54 pBR1AN nodulate (nod+) peas and clover respectively, but do not fix nitrogen (fix-).

R. leguminosarum mutants produce an EPS that is similar to parental LPS in composition. …

A Study Of The Mannitol Binding Protein Active Transport System And A Catabolite Repression Resistant Mutant In Pseudomonas Aeruginosa, Joseph Arthur Wolff

Masters Theses

Cold-shock extraction procedures were used for the efficient release of mannitol binding protein. Magnesium chloride and cold-shock released 92% of the total whole cell mannitol binding protein activity without release of detectable cytoplasmic marker protein glucose-6- phosphate dehydrogenase. Arsenate inhibited mannitol uptake to the same extent as azide. The simultaneous loss and gain of mannitol binding protein activity with mannitol uptake activity in mutants and reventants respectively, was consistant with periplasmic mannitol binding protein as a required component of mannitol uptake. A catabolite repression resistant mutant for mannitol uptake was isolated and described. This mutant, designated WEP-1, escaped catabolite repression …

Purification And Properties Of A Mannitol-Binding Protein From Pseudomonas Aeruginosa, Gregory V. Plano

Masters Theses

Mannitol-binding protein from Pseudomonas aeruginosa strain PAO has been purified 36-fold from magnesium chloride cold-shock supernatants. Sephadex G-100 gel filtration and carboxymethyl Sephadex ion exchange chromotography were utilized in the purification scheme. The position of the mannitol-binding protein band was identified on sodium dodeyl sulfate-polyacrylamide gels. The mannitol-binding protein has an apparent molecular weight of 45,000 as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

The Fungal Ecology Of The Activated Sludge Process, Douglas William Jaques

Masters Theses

Examination of wastewater secondary influent and activated sludge reveal that bacteria and fungi may exist in a negative correlation. Activated sludge may support a resident population of microfungi. All fungi isolated from secondary influent and activated sludge belong to the form-class Deuteromycetes. The density of geofungi in activated sludge may exceed that of bacterial chemolithotrophs and rival that of bacterial heterotrophs.

Characterization Of The Lipopolysaccharides (Lps) From Four Transposon Generated Symbiotic Mutants Of Rhizobium Trifolii, Robert G. Shatters Jr.

Masters Theses

The LPSs from four symbiotic mutants of R. trifolii were isolated and characterized. The mutants were obtained from Dr. Barry Rolfe of The Australian National University. Three mutants have Tn5 insertions in the "nod" regions of the symbiotic plasmid. The fourth has a 30 kb deletion. This deletion includes the majority of the "nod" regions. All mutants fail to nodulate clover and fail to induce markedly curled root hairs, i.e. they are hac-nod-. The LPSs were purified as described by Carlson et al. 1978.⁷ The polysaccharide portion of the LPSs was purified by treating the LPSs in 1% HAc …

Comparison Of Surface Polysaccharides Of R. Leguminosarum Anu57 (Exo-1), R. Leg. Anu57(Pbr1an) (Nod+, Nif-), And R. Leg. Anu57(Pjb5j1) (Nod+, Nif-), Frank G. Hustmyer

Masters Theses

Extracellular polysaccharides (EPS) and lipopolysaccharides (LPS) are suspected to be involved in the legume/Rhizobium symbiotic process. Polysaccharide compositions from the EPS, LPS, capsular polysaccharide (CPS), and small polysaccharide (SmPS) were compared between Rhizobium leguminosarum ANU57 (parent, Exo^-1) and two mutants R. leg. ANU57(pBR1AN) (nod⁺, nif^-) and R. leg. ANU57(pJB5J1) (nod⁺, nif^-) both containing a Sym (symbiotic) plasmid insertion. R. leg. ANU57(pBR1AN) and R. leg. ANU57(pJB5J1) are nod⁺ on clover and peas, respectively. The nod⁺ mutants produce larger amounts of EPS and decreased amounts of LPS compared to …