Composition Of The Adult Digestive Tract Bacterial Microbiome Based On Seven Mouth Surfaces, Tonsils, Throat And Stool Samples, Nicola Segata, Susan Kinder Haake, Peter Mannon, Katherine P. Lemon, Levi Waldron, Dirk Gevers, Curtis Huttenhower, Jacques Izard

Department of Food Science and Technology: Faculty Publications

Background: To understand the relationship between our bacterial microbiome and health, it is essential to define the microbiome in the absence of disease. The digestive tract includes diverse habitats and hosts the human body’s greatest bacterial density. We describe the bacterial community composition of ten digestive tract sites from more than 200 normal adults enrolled in the Human Microbiome Project, and metagenomically determined metabolic potentials of four representative sites.

Results: The microbiota of these diverse habitats formed four groups based on similar community compositions: buccal mucosa, keratinized gingiva, hard palate; saliva, tongue, tonsils, throat; sub- and supra-gingival plaques; …

Metabolic Reconstruction For Metagenomic Data And Its Application To The Human Microbiome, Sahar Abubucker, Nicola Segata, Johannes Goll, Alyxandria M. Schubert, Jacques Izard, Brandi L. Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker, Mathangi Thiagarajan, Bernard Henrissat, Owen White, Scott T. Scott, Barbara Methé, Patrick D. Schloss, Dirk Gever, Makedonka Mitreva, Curtis Huttenhower

Department of Food Science and Technology: Faculty Publications

Microbial communities carry out the majority of the biochemical activity on the planet, and they play integral roles in processes including metabolism and immune homeostasis in the human microbiome. Shotgun sequencing of such communities’ metagenomes provides information complementary to organismal abundances from taxonomic markers, but the resulting data typically comprise short reads from hundreds of different organisms and are at best challenging to assemble comparably to single-organism genomes. Here, we describe an alternative approach to infer the functional and metabolic potential of a microbial community metagenome. We determined the gene families and pathways present or absent within a community, as …

Cholesterol Lowering Effects Of Milk With Added Phytosterols, Laura Kells Cusack

Master's Theses

Foods incorporating plant sterols (PS) reduce Low-density lipoprotein (LDL) on average approximately 10%. PS with a higher lipid solubility may promote greater reductions. We examined the cholesterol lowering effect of a novel triglyceride recrystallized phystosterol (TRP). Twenty subjects (mean ± SD; age, 56 ± 10 years; BMI, 27 ± 5) with elevated LDL (>100 mg/dL) participated in three 4-week phases; Phase I, 2% milk; Phase II, milk with 2.0 grams (g) free PS; Phase III, milk with 2.0 g TRP. Before and after each phase two fasting blood draws were obtained for determination of serum cholesterol. Between the 2% …

The Effects Of Phytosterols On Lipoprotein Particle Size, Laura J. Kunces

Master's Theses

Phytosterols (PS) have become a recent popular medication alternative for treatment of hypercholesterolemia and have proven effective. Whether PS decrease risk of cardiovascular disease through other mechanisms, such as lipoprotein particle size and inflammatory markers, remains unclear. PURPOSE: The primary aim of this study was to examine the effects of two forms of PS in milk on lipoprotein particle size, inflammatory markers and fat-soluble vitamins. METHODS: Twenty subjects (13 males, 7 females; age; 55±6.1 years, height; 169±10 cm, weight; 77.9±16.9 kg, BMI; 27.3) consumed 16oz of cow’s milk daily for 12 weeks. The three sequential four-week phases consisted of 2% …

Role Of Lactic Acid Bacteria As A Bio-Sanitizer To Prevent Attachment Of Listeria Monocytogenes On Deli Slicer Contact Surfaces, And The Influence Of Listeria Innocua On The Attachment Of L. Monocytogenes On Selected Materials Located In The Food-Processing Environment, Jean Baptiste Ndahetuye

Graduate Theses and Dissertations

Listeria monocytogenes an important foodborne pathogen that continues to be a serious problem for the food industry. This pathogen contaminates food primarily during post-harvest in the food-processing environment. Its ecology in the food-processing environment is not well understood but previous research has demonstrated the ability of L. monocytogenes to survive on food contact surfaces after cleaning and disinfection. The current study explored the attachment of three lactic acid bacteria (LAB) strains, Lactobacillus animalis , Lb. amylovorus and Pediococcus acidilactici , their combination in a cocktail, and their influence to prevent the attachment of L. monocytogenes at room temperature by examining …

Feed Supplementation With Natural Extracts Of Cranberry And Its Efficacy On Campylobacter Colonization In Poultry, Ann Woo-Ming

Graduate Theses and Dissertations

Campylobacter spp. has been identified as one of the leading causative agents of food borne diarrheal illness. Epidemiological evidence has shown that poultry is the main source for human infection. Poultry are asymptomatic carriers of Campylobacter within their gastrointestinal tract, with colonization levels reaching 106-108 cfu/g cecal content. Surveys of domestic poultry flocks have estimated that approximately 90% of flocks are positive for Campylobacter colonization. Risk assessment studies have determined that by reducing levels of Campylobacter colonization during rearing, incidences of human infection will be significantly reduced. Currently there are no consistently effective treatments to eliminate Campylobacter from poultry flocks. …

Growing South Dakota (Spring 2012), College Of Agriculture &. Biological Sciences

Growing South Dakota (Publication of the College of Agriculture, Food and Environmental Sciences)

[Page] 2 Powerful Potential: Growing Global Population Spurs Need for Agbioscience
[Page] 4 Spring College News
[Page] 6 Enhanced Education: Students Complement Coursework With Extra-Curricular Opportunities
[Page] 8 Gaining Global Perspective: SDSU Delegation Visits Argentina
[Page] 9 Creative Collaboration: Students, Landowners & Industry Professionals Pair Up for a Positive Experience
[Page] 10 Wondrous Wheat: New Research Agreement & Wheat Varieties Announced
[Page] 12 Here and There
[Page] 14 New Era Underway: SDSU Extension Re-Energizes Programs, Delivery [Page] 16 iGrow Continues to Grow
[Page] 18 Focused on the Future: Field Specialists Strive to Serve Changing Landowner Needs
[Page] 19 Connecting with …

Pathogenicity Of Treponema Denticola Wild-Type And Mutant Strain Tested By An Active Mode Of Periodontal Infection Using Microinjection, Jacques Izard, Hajime Sasaki, Ralph Kent

Department of Food Science and Technology: Faculty Publications

The available passive mode of periodontal infections in mice requires high efficiency of bacterial attachment and invasiveness and is not always suitable to test the pathogenicity of genetically engineered mutant strains. We developed an active mode of oral infection, using microinjection in the marginal gingiva of mice, to test the pathogenicity of a genetically engineered Treponema denticola mutant strain deficient in intermediate-like filaments, compared to the wild-type strain. This targeted mode of infection inoculates the bacterial strain to be tested directly at a lesion site (needle entry point) located at the future periodontal lesion site. The efficiency of T. …

Identification And Analysis Of The Ige Binding By Parvalbumin And Other Potential Allergens In Different Fish And Frog Species, P. Lee, J. A. Nordlee, S. J. Koppelman, J. L. Baumert, Steve L. Taylor

Department of Food Science and Technology: Faculty Publications

Rationale: Serological cross-reactivity to different fish and frog species is common among fish-allergic individuals.We examined the intra- and inter-individual diversity in IgE responses of fish-allergic subjects to various fish and frog species and identified novel allergens besides parvalbumin.

Methods: Sera from 38 subjects with a clinical history of fish allergy were analyzed for IgE-binding profiles to crude extracts of 26 raw fish and frog species, and purified cod and carp parvalbumin using IgE-immunoblotting. Sera of 7 subjects showing similar IgE-binding profiles in the IgEimmmunoblotting were pooled to identify potential allergens in pilchard, herring, cod, cusk, and rainbow trout using two-dimensional …

Purification Of Alpha-Glucosidase Inhibitors From Grape Extract, Gayle M. Shipp

Wayne State University Theses

ABSTRACT

PURIFICATION OF ALPHA-GLUCOSIDASE INHIBITORS FROM GRAPE EXTRACT

by

GAYLE SHIPP

August 2012

Advisor: Dr. Kevin Zhou

Major: Nutrition and Food Science

Degree: Master of Science

Diabetes and its complications are steadily growing and remain major causes of morbidity and mortality in the U.S. Intestinal á-glucosidases play a crucial role in controlling postprandial blood glucose. For this reason, one attractive prevention and/or treatment strategy for type-2 diabetes is the inhibition of á-glucosidase. The effectiveness of á-glucosidase inhibitors (AGI's) for diabetes treatment is well documented in numerous animal and human clinical studies. Grape pomace extract (GPE) has recently found in our …

Recent Advances In The Application Of Non Thermal Methods For The Prevention Of Salmonella In Foods, Shilpi Gupta, Nissreen Abu-Ghannam

Books/Book Chapters/ Proceedings

Food-borne illness as a result of consumption of foods contaminated with pathogenic bacteria is a world-wide concern. The presence and subsequent growth of micro-organisms in food in addition to improper storage not only results in spoilage but also in a reduction of food quality. The microbiological safety in ready to eat products is a cause of big concern not only for the consumers and food industries but also for the regulatory agencies. The number of documented outbreaks of foodborne diseases has increased in the last decade with Salmonella spp., Listeria monocytogenes and Escherichia coli being responsible for the largest number …

The Effects Of Oil Palm Phenolics On Inflammation And Oxidative Stress In Relation To Amyloid Beta Plaques In Fad-Mutant And Wild Type B103 Cells, Lindsay Michelle Godsey

Wayne State University Theses

Alzheimer's disease (AD) affects approximately 35.6 million people in the world today (35). It is expected that by year 2050, an individual will develop AD every 33 seconds (8). Unfortunately, the etiology is not well known. Familial Alzheimer's disease (FAD) occurs due to specific genetic mutations, making it possible to replicate them in cells. Using B103 rat neuroblastoma cells transfected with a cDNA construct, wild type cells and FAD mutant cells were used in this research.

Natural ingredients such as oil palm phenolics (OPP) contain antioxidants. After finding the optimal experimental parameters, OPP was found to aid in the destabilization …

Efficient And Robust Rna-Seq Process For Cultured Bacteria And Complex Community Transcriptomes, Georgia Giannoukos, Dawn M. Ciulla, Katherine Huang, Brian J. Haas, Jacques Izard, Joshua Z. Levin, Jonathan Livny, Ashlee M. Earl, Dirk Gevers, Doyle V. Ward, Chad Nusbaum, Bruce W. Birren, Andreas Gnirke

Department of Food Science and Technology: Faculty Publications

We have developed a process for transcriptome analysis of bacterial communities that accommodates both intact and fragmented starting RNA and combines efficient rRNA removal with strand-specific RNA-seq. We applied this approach to an RNA mixture derived from three diverse cultured bacterial species and to RNA isolated from clinical stool samples. The resulting expression profiles were highly reproducible, enriched up to 40-fold for non-rRNA transcripts, and correlated well with profiles representing undepleted total RNA.

Supportive Weight Loss Program, Jenny Koscho Rd, Ldn, Cde

Clinical Nutrition Service

No abstract provided.

Parenteral Nutrition Order Entry Privileges For Registered Dietitians: Unique Approach To Improve Patient Outcomes (Poster), Judy Holaska Rd, Ms, Cnsc , Ldn

Clinical Nutrition Service

No abstract provided.

Parenteral Nutrition Web-Based Order Writing: Educating Prescribers And Registered Dietitians, Judy Holaska Rd, Ms, Cnsc , Ldn

Clinical Nutrition Service

No abstract provided.

Can Antioxidant-Rich Berries Improve Risk Factors Associated With Cardiovascular Disease In Postmenopausal Smokers?, Jordan Alaine Teeple

Graduate Theses and Dissertations

The purpose of this study was to examine the effects of smoking on risk factors associated with cardiovascular disease (CVD) and determine the efficacy of antioxidant-rich berries in ameliorating these risk factors in postmenopausal smokers. Menopause and cigarette smoking have been identified as major risk factors for CVD due to a decrease in antioxidant protection, increase in inflammation and oxidative stress, and adverse changes in serum lipids. Antioxidants, specifically flavonoid compounds found in blackberries and blueberries, have been shown to prevent low-density lipoprotein cholesterol oxidation and thus prevent downstream inflammation and oxidative stress. Healthy, postmenopausal nonsmokers (n=14) and smokers (n=31) …

Growing South Dakota (Fall 2011), College Of Agriculture &. Biological Sciences

Growing South Dakota (Publication of the College of Agriculture, Food and Environmental Sciences)

Page] 2 Adapting for the Future: South Dakota 4-H Efforts Move Forward
[Page] 5 Regional Transitions: Eight Extension Centers to Open in October
[Page] 6 College News [Page] 8 Making a Difference with Research: Ag Experiment Station Aids Industry & Economy
[Page] 10 Pig Potential: South Dakota's Swine Industry Offers Economic Opportunity [Page] 13 New Department Debuts: Natural Resource Disciplines Join Forces
[Page] 14 Autumn in the AIr: Grab Your Blue and Gold and Visit Campus
[Page] 16 iGrow Evolves: Usability And Content Are Being Enhanced
[Page] 18 Collection Effort: Despite Budget Cuts, Private Funds Allowed for Growth [Page] 21 …

Emerging Dynamics Of Human Campylobacteriosis In Southern Ireland, Susan Bullman, Daniel Corcoran, James O'Leary, Derry O'Hare, Brigid Lucey, Roy D. Sleator

Department of Biological Sciences Publications

Infections with Campylobacter spp. pose a significant health burden worldwide. The significance of Campylobacter jejuni/Campylobacter coli infection is well appreciated but the contribution of non-C. jejuni/C. coli spp. to human gastroenteritis is largely unknown. In this study, we employed a two-tiered molecular study on 7194 patient faecal samples received by the Microbiology Department in Cork University Hospital during 2009. The first step, using EntericBio® (Serosep), a multiplex PCR system, detected Campylobacter to the genus level. The second step, utilizing Campylobacter species-specific PCR identified to the species level. A total of 340 samples were confirmed as Campylobacter genus positive, 329 of …

Metagenomic Biomarker Discovery And Explanation, Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S. Garrett, Curtis Huttenhower

Department of Food Science and Technology: Faculty Publications

This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.

Includes supplemental materials.

Understanding Of Functions Of Selenoproteins And Dietary Selenium By Using Animal Models, Marina V. Kasaikina

Department of Biochemistry: Dissertations, Theses, and Student Research

Selenium (Se) is a trace element that is incorporated into proteins in the form of the 21^st amino acid, selenocysteine (Sec). Se supplementation was reported to have beneficial roles in prevention of cardiovascular and muscle disorders, cancer prevention and enhancement of the immune function. However, recent studies also showed that excessive dietary Se increases the risk of development of type 2 diabetes mellitus. Thus, better understanding of Se and selenoprotein functions is required. We used three approaches to address this problem.

First, we used high-throughput sequencing to examine composition of the gut microflora in mice maintained on selenium-deficient, selenium-sufficient, …

Estimation Of The Number Of Days Required To Determine Usual Antioxidant Intakes And Assessment Of The Prevalence Of Nutrient Inadequacy Among College Students, Catherine G. Davis

Master's Theses

High intake of antioxidant rich foods has been shown to decrease risk factors of chronic disease.  Young adulthood may be crucial in establishing healthy lifestyles including adequate nutrient consumption.

The present study was designed 1) to estimate usual nutrient intakes, 2) to calculate the number of days required to estimate usual antioxidant intake, and 3) to assess intake adequacy from diet and diet + supplement sources by using the Estimated Average Requirement (EAR).  The USDA Flavonoid and Proanthocyanidin databases, food consumption data, and dietary supplement use data from 60 students aged 18-25 years at the University of Connecticut were utilized. …

Growing South Dakota (Spring 2011), College Of Agriculture &. Biological Sciences

Growing South Dakota (Publication of the College of Agriculture, Food and Environmental Sciences)

[Page] 2 Classroom to Careers: An Optimistic Outlook Awaits Ag & Biological Sciences Graduates
[Page] 5 New Opportunities: Intro Ag Courses To Be Offered in Rapid City
[Page] 6 Budget Reality: Funding Cuts Prompt Structure and Staff Changes
[Page] 7 Gearing Up for DakotaFest: Replicated SDSU Campus, Educational Forums and Fundraising Auction Planned
[Page] 8 Continuing a Legacy: &1 Million Livestock Judging Endowment Being Established
[Page] 10 4-H Fun: Unique 4-H Activities Spark Student Interest in Science
[Page] 12 Innovative Outreach: BBQ Boot Camp Connect Consumers to Meat Industry
[Page] 13 College News
[Page] 14 Relevant Research: New, More Efficient …

Angiostatin Like Peptides In Milk: Potential Development For Dairy Products Capable Of Cancer Prevention, Erin Stefanutti

Master's Theses

For the past 40 years, antiangiogenic approaches have been of major interest in the development of methods to cure and prevent cancer. Angiogenesis, the development of blood vessels from pre-existing vascularization, is essential for cancer growth and spread of metastasis through the delivery of nutrients and oxygen essential to sustain the metabolic activity of these malignant cells. Blocking access to blood will cause cancerous cells to assume a dormant state creating inactive micro-tumors innocuous to the host. Angiostatin, the internal fragment of the fibrinolytic zymogen plasminogen, has shown great potential in reducing cancer size and number of metastatic colonies in …

Characterization Of Igg And Ige Binding To Parvalbumin Derived From Commercially Important Fish Species, P. Lee, Julie A. Nordlee, S. J. Koppelman, J. L. Baumert, Steve L. Taylor

Department of Food Science and Technology: Faculty Publications

Rationale: Parvalbumin is recognized as pan-allergen in fish and frog. However, previous studies demonstrated that the IgE- and IgG-binding patterns to parvalbumins vary depending on the fish species. We aimed to use 3 anti-parvalbumin IgG and human IgE to investigate the contributing factors for the binding differences.

Methods: Indirect enzyme-linked immunosorbent assay (ELISA) and IgG immunoblotting were used to determine the reactivity of the polyclonal anti-cod parvalbumin antibody and the commercially available, monoclonal anti-frog and anti-carp parvalbumin antibodies against raw muscle extracts of 25 fish species. Additionally, sera from 46 individuals with clinical history of fish allergy were analyzed for …

Growing South Dakota (Winter 2011), College Of Agriculture &. Biological Sciences

Growing South Dakota (Publication of the College of Agriculture, Food and Environmental Sciences)

[Page] 2 Introducing iGrow: New Web Portal Brings Information To One Location
[Page] 4 Crops, Cattle & Much More: Opportunities Farm Cultivates Research, Teaching And Scholarships
[Page] 7 College News
[Page] 8 Funding Fundamentals: Budget Cuts Have Far-Reaching Impact
[Page] 10 The Value Extension: Three Producers Share How They've Benefited [Page] 12 A Vision for Precision: Gregg Carlson Has Helped Guide Agronomy
[Page] 13 A Boost for Beginning Beef Producers: Training Program Offered Through USDA Grant
[Page] 14 Ethanol's Evolution: Promising New Research Goes Beyond Corn
[Page] 16 New Era for Cereal Grains: Seed Technology Lab Inspires Innovation
[Page] 18 …

Suggested Improvements For The Allergenicity Assessment Of Genetically Modified Plants Used In Foods, Richard E. Goodman

Department of Food Science and Technology: Faculty Publications

Genetically modified (GM) plants are increasingly used for food production and industrial applications. As the global population has surpassed 7 billion and per capita consumption rises, food production is challenged by loss of arable land, changing weather patterns, and evolving plant pests and disease. Previous gains in quantity and quality relied on natural or artificial breeding, random mutagenesis, increased pesticide and fertilizer use, and improved farming techniques, all without a formal safety evaluation. However, the direct introduction of novel genes raised questions regarding safety that are being addressed by an evaluation process that considers potential increases in the allergenicity, toxicity, …

Wild Buckwheat Is Unlikely To Pose A Risk To Buckwheat-Allergic Individuals, Julie A. Nordlee, Rakhi Panda, Joseph L. Baumert, Richard E. Goodman, Steve Taylor

Department of Food Science and Technology: Faculty Publications

Buckwheat (Fagopyrum esculentum) is a commonly allergenic food especially in Asia where buckwheat is more commonly consumed. Wild buckwheat (Polygonum convolvulus, recently changed to Fallopia convolvulus) is an annual weed prevalent in grain-growing areas of the United States. Wild buckwheat is not closely related to edible buckwheat although the seeds do have some physical resemblance. A large shipment of wheat into Japan was halted by the discovery of the adventitious presence of wild buckwheat seeds over possible concerns for buckwheat-allergic consumers. However, IgE-binding was not observed to an extract of wild buckwheat using sera from …

Evaluation And Comparison Of The Species-Specificity Of 3 Antiparvalbumin Igg Antibodies, Poi-Wah Lee, Julie A. Nordlee, Stef J. Koppelman, Joseph L. Baumert, Steve L. Taylor

Department of Food Science and Technology: Faculty Publications

Parvalbumin is a pan-allergen in fish and frogs that triggers IgE-mediated reactions in fish-allergic individuals. Previous studies demonstrated that antibodies raised against fish and frog parvalbumins displayed varying specificity for different fish species, and thus, the applicability of these antibodies for potential use in immunoassays to detect fish residues were limited. We aimed to determine the specificity of 3 IgG antibodies for various fish species. Indirect enzyme-linked immunosorbent assay (ELISA) and IgG-immunoblotting were used to compare the reactivity of the polyclonal anticod parvalbumin antibody and the commercially available, monoclonal antifrog and monoclonal anticarp parvalbumin antibodies against raw muscle extracts of …

Sodexo Nutrition Services Enhances Communication With Patients And Health Care Team (Poster), Melissa Faura Rd, Ldn, Ann Flickinger Ms, Rd, Ldn

Clinical Nutrition Service

No abstract provided.