Life Sciences Commons^™

Impacts Of Plant-Microbe Interactions On Seedling Performance In A Riparian Forest Invaded By Lonicera Maackii, Taylor E. K. Strehl

Masters Theses

Soil microbes have profound impacts on plant growth and survival and can either promote or inhibit plant dominance. Exotic plants are often strongly invasive because they have escaped their natural enemies, potentially including antagonistic soil microbes. I examined how the invasive shrub Lonicera maackii and a common native tree, Acer negundo, responded to soil microbial communities to determine the role of soil microbes in regulating invasion success. This was done by growing both species with microbes from invaded (L. maackii) and uninvaded (A. negundo) soils collected from three locations within a riparian forest. Seedlings were …

Evaluation Of Intra-Species Diversity Of Oxalobacter Formigenes Strains Using Pulsed-Field Gel Electrophoresis (Pfge) And Multiplex Pcr, Nivedita Pareek

Masters Theses

Oxalobacter formigenes is a beneficial, strict anaerobic gut bacterium that plays an important role in the prevention of kidney stone disease with a unique characteristic of using only oxalate as a carbon and energy source. To date, twenty-one strains of O. formigenes have been isolated which are further divided into two groups based on differences in the patterns of cell membrane lipids, cellular proteins, and nucleic acid fragments. The objective of the study was to evaluate intra-species diversity of O. formigenes strains using pulsed-field gel electrophoresis (PFGE) and multiplex PCR.

Nine pure cultures of O. formigenes strains (5 strains group …

Xylan Metabolism By Caulobacter Crescentus, Viet Bui

Masters Theses

Bacteria present unique opportunities to explore the molecular mechanisms of nutrient acquisition processes at single cell level under various experimental conditions. Caulobacter crescentus is a gram-negative oligotrophic environmental bacterium with adaptive physiological responses, such as slow growth or complete arrest of cell cycle, presence of sessile and motile progenies with the sessile cells growing stalk to enhance nutrient uptake for growth in low-nutrient conditions. Details of plant polysaccharide-derived carbon compound, such as cellobiose, maltose, and xylose utilization by C. crescentus can be found but molecular details or mechanisms of polysaccharide utilization, such as xylan, has not been reported. Database analyses …

Detection Of Beta-Lactamase Variants In Municipal Wastewater And Fresh Water, Sunil Pandey

Masters Theses

The occurrence and spread of antibiotic-resistant genes (ARGs) are pressing public health problems worldwide. A key factor contributing to the spread of ARGs is lateral gene transfer. Wastewater treatment plants (WWTPs) are measured hot spots of microbial diversity and resistance because they receive polluted wastewater from diverse sources and contain a variety of different environments with dense bacterial loads. Due to the overuse of antibiotics the genetic capacities of microbes have profited. This helps every source of resistance gene and every means of horizontal gene transmission to develop the multiple mechanism of resistance to each antibiotic used clinically, agriculturally, or …

Analysis Of Gut Microbiota From Aedes Albopictus Mosquitoes Collected In Central Illinois, Megan E. Cooper

Undergraduate Honors Theses

Aedes albopictus, Asian tiger mosquitoes, are vectors of a wide number of human viral diseases including, West Nile virus, Dengue virus, Chikungunya virus and (recently) Zika virus. A large body of evidence has suggested that microbiomes of mosquito midguts are closely associated with specific mosquito life processes such as nutrition, reproduction, aggregation and defense against toxins. In this study we characterize the bacterial flora of the midguts of adult female Ae. albopictus collected from woodlots and residential areas in Champaign and Coles Counties of Central Illinois (40 samples in each category). After extraction of DNA from dissected midguts, we …

Biotransformation Of Oxo-Bile Acids Derivatives By Human Gut Bacteria, Laina Sallam

Masters Theses

Bile acids are one group of steroids that can be metabolically transformed by human gut anaerobes. One of these transformations is the conversion of primary bile acids to secondary bile acids by 7α-dehydroxylating gut bacteria such as Clostridium scindens, Clostridium hylemonae, and Clostridium hiranonis. These anaerobes metabolize bile acid derivatives via 3α- and 7α-hydroxysteroid dehydrogenases (HSDH). Studies to date have not reported if these organisms are capable of converting 12-oxolithocholic acid (12-oxoLCA) to deoxycholic acid (DCA). The emphasis of this study was to determine the ability of C. scindens ATCC 35704, C. hiranonis DSM 13275, and C. …

Resolution Of The Nutritional Requirements And Metabolic Profile Of Clostridium Scindens Atcc 35704, A Major Bile Acid-Dehydroxylating Anaerobe In The Human Gut, Rachana Shrestha

Masters Theses

Bile acids (cholate and chenodeoxycholate) are synthesized from cholesterol in the human liver, and secreted in small intestine for food digestion. However, a portion of these primary bile acids is converted in the colon to toxic secondary bile acids, deoxycholate and lithocholate. Secondary bile acid formation is the result of 7α-dehydroxylating anaerobes, and one of the key players in this conversion is Clostridium scindens. Interestingly, little is known about the basic physiology and nutrition of C. scindens. Therefore, the goal of this research was to understand the nutritional requirement, and determine the 7α-dehydroxylation activity and end products from …

Distiphallus Morphology And Its Role In Copulation Dynamics In Anastrepha Suspensa (Loew), Taylor J. Inboden

Masters Theses

Anastrepha suspensa (Diptera; Tephritidae) is an agricultural pest species

causing severe economic damage and is controlled, in part, by applying knowledge

of this species' reproduction (e.g., disrupting fertile copulations by SIT). During

copulation, males transfer sperm as well as protein rich fluids through an aedeagus

and distiphallus, which females then store in three spermathecae and one ventral

receptacle. Within the female reproductive tract, the ventral receptacle and the

three spermathecae are strategically separated from each other. I hypothesized

males' ability to direct sperm transfer within the female reproductive tract is

through the structures found in the distiphallus. Utilizing scanning electron …

Detection Of Antibiotic Resistance Loci In Wastewater And Fresh Water Samples, Mohammed Hamed Almalki

Masters Theses

Proper treatment of municipal wastewater is important not only for prevention of eutrophication but also for public health concerns. One consideration for wastewater treatment is the presence of organisms carrying antibiotic resistance genes. If these organisms survive the wastewater treatment process and are released into the streams, they can pose significant risks to public health. In addition, their presence also raises concerns for lateral gene transfer events at the wastewater plant. The spread of antibiotic loci has a major impact in public health and clinical therapy because resistant organisms render conventional treatments of important illnesses difficult. Beta-lactam drugs are known …

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, …

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 …

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 …

An Examination Of Keratinophilic Fungal On Eastern Bluebird Eggshells, Edward Anthony Hillman Iii

Undergraduate Honors Theses

This study was designed to evaluate the mycobiota of Eastern Bluebird eggshells and assess the abundance of keratinophilic fungi. Samples of fungi taken from Eastern Bluebird eggshells were subcultured for identification using macroscopic and microscopic characteristics. The occurrence of a significant number of keratinophilic fungi on Eastern Bluebird eggshells poses a potential threat to developing chicks.

Plant-Microbial Interactions Change Along A Prairie Restoration Chronosequence, Anna Herzberger

Undergraduate Honors Theses

Soil microbial communities are critical in determining the performance and density of species in plant communities. However, their role in regulating the success of restorations is much less clear. This study assessed the ability of soil microbial communities to regulate the growth and performance of two potentially dominant grasses and two common forbs in prairie restorations. Specifically, I examined the effects of soil microbial communities along a restoration chronosequence from agricultural fields to remnant prairies using experimentally inoculated soils. The two grass species, Andropogon gerardii and Sorghastrum nutans, produced larger biomass with the agricultural inoculates and experienced a decline …

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% …

Activities Of Methionine-Γ-Lyase In The Acidophilic Archaeon “Ferroplasma Acidarmanus” Strain Fer1, M. A. Khan, Madeline M. Lopez-Munoz, Charles W. Kaspar, Kai F. Hung

Kai F. Hung

Biogeochemical processes on exposed pyrite ores result in extremely high levels of sulfuric acid at these locations. Acidophiles that thrive in these conditions must overcome significant challenges, including an environment with proton concentrations at pH 3 or below. The role of sulfur metabolism in the archaeon “Ferroplasma acidarmanus” strain fer1’s ability to thrive in this environment was investigated due to its growth-dependent production of methanethiol, a volatile organic sulfur compound. Two putative sequences for methionine- γ-lyase (EC 4.4.1.11), an enzyme known to carry out α,γ-elimination on L-methionine to produce methanethiol, were identified in fer1. Bioinformatic analyses identified a conserved pyridoxal-5′-phosphate …

Activities Of Methionine-Γ-Lyase In The Acidophilic Archaeon “Ferroplasma Acidarmanus” Strain Fer1, M. Khan, Madeline Lopez-Munoz, Charles Kaspar, Kai Hung

Faculty Research & Creative Activity

Biogeochemical processes on exposed pyrite ores result in extremely high levels of sulfuric acid at these locations. Acidophiles that thrive in these conditions must overcome significant challenges, including an environment with proton concentrations at pH 3 or below. The role of sulfur metabolism in the archaeon “Ferroplasma acidarmanus” strain fer1’s ability to thrive in this environment was investigated due to its growth-dependent production of methanethiol, a volatile organic sulfur compound. Two putative sequences for methionine- γ-lyase (EC 4.4.1.11), an enzyme known to carry out α,γ-elimination on L-methionine to produce methanethiol, were identified in fer1. Bioinformatic analyses identified a conserved pyridoxal-5′-phosphate …

Activities Of Methionine-Γ-Lyase In The Acidophilic Archaeon “Ferroplasma Acidarmanus” Strain Fer1, M. A. Khan, Madeline M. Lopez-Munoz, Charles W. Kaspar, Kai F. Hung

Faculty Research & Creative Activity

Biogeochemical processes on exposed pyrite ores result in extremely high levels of sulfuric acid at these locations. Acidophiles that thrive in these conditions must overcome significant challenges, including an environment with proton concentrations at pH 3 or below. The role of sulfur metabolism in the archaeon “Ferroplasma acidarmanus” strain fer1’s ability to thrive in this environment was investigated due to its growth-dependent production of methanethiol, a volatile organic sulfur compound. Two putative sequences for methionine- γ-lyase (EC 4.4.1.11), an enzyme known to carry out α,γ-elimination on L-methionine to produce methanethiol, were identified in fer1. Bioinformatic analyses identified a conserved pyridoxal-5′-phosphate …

Phenotypic And Genotypic Characterization Of Escherichia Coli Isolated From Untreated Surface Waters, Steven L. Daniel, Kai F. Hung, Kristopher J. Janezic, Blake Ferry, Eric W. Hendricks, Brian A. Janiga, Tiffany Johnson, Samantha Murphy, Morgan E. Roberts, Sarah M. Scott, Alexandra N. Theisen

Steven L. Daniel

A common member of the intestinal microbiota in humans and animals is Escherichia coli. Based on the presence of virulence factors, E. coli can be potentially pathogenic. The focus of this study was to isolate E. coli from untreated surface waters (37 sites) in Illinois and Missouri and determine phenotypic and genotypic diversity among isolates. Water samples positive for fecal coliforms based on the Colisure® test were streaked directly onto Eosin Methylene Blue (EMB) agar (37°C) or transferred to EC broth (44.5°C). EC broth cultures producing gas were then streaked onto EMB agar. Forty-five isolates were identified as E. coli …

Phenotypic And Genotypic Characterization Of Escherichia Coli Isolated From Untreated Surface Waters, Kai F. Hung, Steven L. Daniel, Kristopher J. Janezic, Blake Ferry, Eric W. Hendricks, Brian A. Janiga, Tiffany Johnson, Samantha Murphy, Morgan E. Roberts, Sarah M. Scott, Alexandra N. Theisen

Kai F. Hung

A common member of the intestinal microbiota in humans and animals is Escherichia coli. Based on the presence of virulence factors, E. coli can be potentially pathogenic. The focus of this study was to isolate E. coli from untreated surface waters (37 sites) in Illinois and Missouri and determine phenotypic and genotypic diversity among isolates. Water samples positive for fecal coliforms based on the Colisure® test were streaked directly onto Eosin Methylene Blue (EMB) agar (37°C) or transferred to EC broth (44.5°C). EC broth cultures producing gas were then streaked onto EMB agar. Forty-five isolates were identified as E. coli …

Phenotypic And Genotypic Characterization Of Escherichia Coli Isolated From Untreated Surface Waters, Kai Hung, Steven Daniel, Kristopher Janezic, Blake Ferry, Eric Hendricks, Brian Janiga, Tiffany Johnson, Samantha Murphy, Morgan Roberts, Sarah Scott, Alexandra Theisen

Faculty Research & Creative Activity

A common member of the intestinal microbiota in humans and animals is Escherichia coli. Based on the presence of virulence factors, E. coli can be potentially pathogenic. The focus of this study was to isolate E. coli from untreated surface waters (37 sites) in Illinois and Missouri and determine phenotypic and genotypic diversity among isolates. Water samples positive for fecal coliforms based on the Colisure® test were streaked directly onto Eosin Methylene Blue (EMB) agar (37°C) or transferred to EC broth (44.5°C). EC broth cultures producing gas were then streaked onto EMB agar. Forty-five isolates were identified as E. coli …

Phenotypic And Genotypic Characterization Of Escherichia Coli Isolated From Untreated Surface Waters, Kai F. Hung, Steven L. Daniel, Kristopher J. Janezic, Blake Ferry, Eric W. Hendricks, Brian A. Janiga, Tiffany Johnson, Samantha Murphy, Morgan E. Roberts, Sarah M. Scott, Alexandra N. Theisen

Faculty Research & Creative Activity

A common member of the intestinal microbiota in humans and animals is Escherichia coli. Based on the presence of virulence factors, E. coli can be potentially pathogenic. The focus of this study was to isolate E. coli from untreated surface waters (37 sites) in Illinois and Missouri and determine phenotypic and genotypic diversity among isolates. Water samples positive for fecal coliforms based on the Colisure® test were streaked directly onto Eosin Methylene Blue (EMB) agar (37°C) or transferred to EC broth (44.5°C). EC broth cultures producing gas were then streaked onto EMB agar. Forty-five isolates were identified as E. coli …

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 …

Using Comparative Genomics For Inquiry-Based Learning To Dissect Virulence Of Escherichia Coli O157:H7 And Yersinia Pestis, David J. Baumler, Lois M. Banta, Kai F. Hung, Jodi A. Schwarz, Eric L. Cabot, Jeremy D. Glasner, Nicole T. Perna

Faculty Research & Creative Activity

Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples related to bacterial pathogenesis. Students first examine alignments of genomes of Escherichia coli O157:H7 strains isolated from three food-poisoning outbreaks using the multiple-genome alignment tool Mauve. Students investigate conservation of virulence factors using the Mauve viewer and by browsing annotations available at the A Systematic Annotation Package for Community Analysis of …

Using Comparative Genomics For Inquiry-Based Learning To Dissect Virulence Of Escherichia Coli O157:H7 And Yersinia Pestis, David J. Baumler, Lois M. Banta, Kai F. Hung, Jodi A. Schwarz, Eric L. Cabot, Jeremy D. Glasner, Nicole T. Perna

Kai F. Hung

Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples related to bacterial pathogenesis. Students first examine alignments of genomes of Escherichia coli O157:H7 strains isolated from three food-poisoning outbreaks using the multiple-genome alignment tool Mauve. Students investigate conservation of virulence factors using the Mauve viewer and by browsing annotations available at the A Systematic Annotation Package for Community Analysis of …

Using Comparative Genomics For Inquiry-Based Learning To Dissect Virulence Of Escherichia Coli O157:H7 And Yersinia Pestis, David Baumler, Lois Banta, Kai Hung, Jodi Schwarz, Eric Cabot, Jeremy Glasner, Nicole Perna

Faculty Research & Creative Activity

Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples related to bacterial pathogenesis. Students first examine alignments of genomes of Escherichia coli O157:H7 strains isolated from three food-poisoning outbreaks using the multiple-genome alignment tool Mauve. Students investigate conservation of virulence factors using the Mauve viewer and by browsing annotations available at the A Systematic Annotation Package for Community Analysis of …

Using Polymerase Chain Reaction To Detect Nifh And Vnfdgk In A Novel Acidophilic Microbial Community, Samantha L. Flowers

Undergraduate Honors Theses

Acidophiles are widely known for their ability to exploit harsh environments, typically consisting of high temperatures, dissolved metal concentrations, and acidic conditions. Consequently, different acidophilic species are employed industrially in applications such as biomining and bioleaching. However, their full potential in bioremediation, and in industrial practices, has yet to be fully explored because many of these acidophiles are difficult to culture in laboratory conditions or have yet to be properly identified. This investigation focuses on a novel community sampled from the Richmond Mine site in Iron Mountain, California, consisting of a filamentous fungus and prokaryotes. This consortium can be cultured …

Evaluation Of Glyphosate-Tolerant Soybean Cultivars For Resistance To Bacterial Pustule, Lopa Goradia, Glen Hartman, Steven L. Daniel

Steven L. Daniel

Xanthomonas axonopodis pv. glycines causes bacterial pustule of soybean, which is a common disease in many soybean-growing areas of the world and is controlled by a single recessive gene (rxp gene) commonly found in many conventional glyphosate-sensitive soybean cultivars. Since glyphosate-tolerant cultivars are commonly planted today, there has been no information about whether these new cultivars have bacterial pustule resistance. The goal of this study was to screen glyphosate-tolerant soybean cultivars for resistance to X. axonopodis pv. glycines. Three experiments were completed to evaluate resistance. In experiment 1, 525 commercial glyphosate-tolerant cultivars from 2001 were inoculated with X. axonopodis pv. …

Evaluation Of Glyphosate-Tolerant Soybean Cultivars For Resistance To Bacterial Pustule, Lopa Goradia, Glen Hartman, Steven Daniel

Faculty Research & Creative Activity

Xanthomonas axonopodis pv. glycines causes bacterial pustule of soybean, which is a common disease in many soybean-growing areas of the world and is controlled by a single recessive gene (rxp gene) commonly found in many conventional glyphosate-sensitive soybean cultivars. Since glyphosate-tolerant cultivars are commonly planted today, there has been no information about whether these new cultivars have bacterial pustule resistance. The goal of this study was to screen glyphosate-tolerant soybean cultivars for resistance to X. axonopodis pv. glycines. Three experiments were completed to evaluate resistance. In experiment 1, 525 commercial glyphosate-tolerant cultivars from 2001 were inoculated with X. axonopodis pv. …

Evaluation Of Glyphosate-Tolerant Soybean Cultivars For Resistance To Bacterial Pustule, Lopa Goradia, Glen Hartman, Steven L. Daniel

Faculty Research & Creative Activity

Xanthomonas axonopodis pv. glycines causes bacterial pustule of soybean, which is a common disease in many soybean-growing areas of the world and is controlled by a single recessive gene (rxp gene) commonly found in many conventional glyphosate-sensitive soybean cultivars. Since glyphosate-tolerant cultivars are commonly planted today, there has been no information about whether these new cultivars have bacterial pustule resistance. The goal of this study was to screen glyphosate-tolerant soybean cultivars for resistance to X. axonopodis pv. glycines. Three experiments were completed to evaluate resistance. In experiment 1, 525 commercial glyphosate-tolerant cultivars from 2001 were inoculated with X. axonopodis pv. …