Life Sciences Commons^™

The Human Oral Microbiome, Floyd E. Dewhirst, Tuste Chen, Jacques Izard, Bruce J. Paster, Anne C. R. Tanner, Wen-Han Yu, Abirami Lakshmanan, William G. Wade

Department of Food Science and Technology: Faculty Publications

The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome comprises over 600 prevalent taxa at the species level, with distinct subsets predominating at different habitats. The oral microbiome has been extensively characterized by cultivation and culture-independent molecular methods such as 16S rRNA cloning. Unfortunately, the vast majority of unnamed oral taxa are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic anchors. The first aim of this research was to collect 16S rRNA gene …

Ribosomal Biosynthesis Of The Cyclic Peptide Toxins Of Amanita Mushrooms (Invited Review), Jonathan D. Walton, Heather E. Hallen-Adams, Hong Luo

Department of Food Science and Technology: Faculty Publications

Some species of mushrooms in the genus Amanita are extremely poisonous and frequently fatal to mammals including humans and dogs. Their extreme toxicity is due to amatoxins such as α- and β-amanitin. Amanita mushrooms also biosynthesize a chemically related group of toxins, the phallotoxins, such as phalloidin. The amatoxins and phallotoxins (collectively known as the Amanita toxins) are bicyclic octa- and heptapeptides, respectively. Both contain an unusual Trp-Cys cross-bridge known as tryptathionine. We have shown that, in Amanita bisporigera, the amatoxins and phallotoxins are synthesized as proproteins on ribosomes and not by nonribosomal peptide synthetases. The proproteins are 34–35 …

Environment And Hybrid Influences On Food-Grade Sorghum Grain Yield And Hardness, Joni K. Griess, Stephen C. Mason, David S. Jackson, Tomie D. Galusha, Muhammad Yaseen, Jeffrey F. Pedersen

Department of Food Science and Technology: Faculty Publications

Few studies have examined grain quality of food-grade sorghum hybrids. The objective of this study was to determine the effects of environment and hybrid on grain quality of commercially available food-grade sorghums. A randomized complete block experiment with three replications was planted in 12 environments, which included the 2004 and 2005 growing seasons and irrigated and dryland water regimes in eastern, central, and west central Nebraska and a dryland low-N environment in eastern Nebraska. Environment accounted for 5 to 140 times greater variation in measured parameters than hybrid, and the hybrid × environment interaction accounted for less than 2% of …

The Human Oral Microbiome Database: A Web-Accessible Resource For Investigating Oral Microbe Taxonomic And Genomic Information, Tsute Chen, Wen-Han Yu, Jacques Izard, Oxana V. Baranova, Abirami Lakshmanan, Floyd E. Dewhirst

Department of Food Science and Technology: Faculty Publications

The human oral microbiome is the most studied human microflora, but 53% of the species have not yet been validly named and 35% remain uncultivated. The uncultivated taxa are known primarily from 16S rRNA sequence information. Sequence information tied solely to obscure isolate or clone numbers, and usually lacking accurate phylogenetic placement, is a major impediment to working with human oral microbiome data. The goal of creating the Human Oral Microbiome Database (HOMD) is to provide the scientific community with a body site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity …

Convergent Evolution Of Sequestrate Forms In Amanita Under Mediterranean Climate Conditions, Alfredo Justo, Ingo Morgenstern, Heather E. Hallen-Adams, David S. Hibbett

Department of Food Science and Technology: Faculty Publications

The systematic position of secotioid (Torrendia) and gasteroid (Amarrendia) forms within the agaricoid Amanita lineage (Agaricales, Basidiomycota) was studied with molecular (nLSU, ITS) data. Secotioid and gasteroid forms occur in four independent clades nested within agaricoid forms. One clade corresponds to the secotioid T. pulchella from southern Europe and northern Africa. The others correspond to Torrendia and Amarrendia species from Australia. Mediterranean climatic conditions are postulated as a force driving the convergent evolution of these secotioid and at least one of the gasteroid forms in geographically distant areas. Species formerly placed in Torrendia and Amarrendia are …

Co-Localization Of Amanitin And A Candidate Toxin-Processing Prolyl Oligopeptidase In Amanita Basidiocarps, Hong Lou, Heather E. Hallen-Adams, John S. Scott-Craig, Jonathan D. Walton

Department of Food Science and Technology: Faculty Publications

Fungi in the basidiomycetous ge nus Amanita owe their high mammalian toxicity to the bicyclic octapeptide amatoxins such as ∝-amanitin. Amatoxins and the related phallotoxins (such as the heptapeptide phalloidin) are encoded by members of the “MSDIN” gene family and synthesized on ribosomes as short (34 - 35 amino acid) proproteins. Anti-amanitin antibodies and confocal microscopy were used to determine the cellular and subcellular localization of amanitin accumulation in basidiocarps (mushrooms) of the Eastern North American destroying angel (Amanita bisporigera). Consistent with previous studies, amanitin is present throughout the basidiocarp (stipe, pileus, lamellae, trama, and universal veil), but …

A Partial Chromosomal Deletion Caused By Random Plasmid Integration Resulted In A Reduced Virulence Phenotype In Fusarium Graminearum, Thomas K. Baldwin, Iffa Gaffoor, John Antoniw, Corrie Andries, John Guenther, Martin Urban, Heather E. Hallen-Adams, John Pitkin, Kim E. Hammond-Kosack, Frances Trail

Department of Food Science and Technology: Faculty Publications

Fusarium graminearum (teleomorph: Gibberella zeae) is an Ascomycete fungal plant pathogen which infects a range of agriculturally important crops, including wheat, barley, and maize. A random plasmid insertion mutagenesis approach was used to analyze the pathogenicity of the PH-1 strain, for which full genomic information is available. Fungal transformants were initially screened for their ability to infect wheat ears. From a total of 1,170 transformants screened, eight were confirmed to be highly reduced in pathogenicity toward wheat ears and roots. These were designated disease-attenuated F. graminearum (daf) mutants. The in vitro growth rate and appearance of each daf …

Individuality In Gut Microbiota Composition Is A Complex Polygenic Trait Shaped By Multiple Environmental And Host Genetic Factors, Andrew K. Benson, Scott A. Kelly, Ryan Legge, Fangrui Ma, Soo Jen Low, Jaehyoung Kim, Min Zhang, Phaik Lyn Oh, Derrick Nehrenberg, Kunjie Hua, Stephen D. Kachman, Etsuko N. Moriyama, Jens Walter, Daniel A. Peterson, Daniel Pomp

Department of Food Science and Technology: Faculty Publications

In vertebrates, including humans, individuals harbor gut microbial communities whose species composition and relative proportions of dominant microbial groups are tremendously varied. Although external and stochastic factors clearly contribute to the individuality of the microbiota, the fundamental principles dictating how environmental factors and host genetic factors combine to shape this complex ecosystem are largely unknown and require systematic study. Here we examined factors that affect microbiota composition in a large (n = 645) mouse advanced intercross line originating from a cross between C57BL/6J and an ICR-derived outbred line (HR). Quantitative pyrosequencing of the microbiota defined a core measurable microbiota (CMM) …

Functionality Of Chemically Modified Wild-Type, Partial Waxy And Waxy Starches From Tetraploid Wheats, L. E. Hansen, David S. Jackson, R. L. Wehling, Robert A. Graybosch

Department of Food Science and Technology: Faculty Publications

Partial waxy (reduced-amylose) and fully waxy (amylose-free) tetraploid durum wheats (Triticum turgidum L. var durum) were developed by introgression of null alleles at the Wx-A1 and Wx-B1 loci from common hexaploid wheat (Triticum aestivum L.). Purified starches were obtained from each genotype, and chemically modified by: 1) cross-linking with phosphorus oxychloride, 2) substitution with propylene oxide, and 3) sequential cross-linking with phosphorus oxychloride followed by substitution with propylene oxide. Functional properties were compared to blends of waxy and wild-type durum starches of known amylose contents. Significant differences in functionality were observed amongst the …

Resistant Starches Types 2 And 4 Have Differential Effects On The Composition Of The Fecal Microbiota In Human Subjects, Ines Martinez, Jaehyoung Kim, Patrick R. Duffy, Vicki L. Schlegel, Jens Walter

Department of Food Science and Technology: Faculty Publications

Background: To systematically develop dietary strategies based on resistant starch (RS) that modulate the human gut microbiome, detailed in vivo studies that evaluate the effects of different forms of RS on the community structure and population dynamics of the gut microbiota are necessary. The aim of the present study was to gain a community wide perspective of the effects of RS types 2 (RS2) and 4 (RS4) on the fecal microbiota in human individuals.

Methods and Findings: Ten human subjects consumed crackers for three weeks each containing either RS2, RS4, or native starch in a double-blind, crossover design. Multiplex sequencing …

Factors Affecting The Alkaline Cooking Performance Of Selected Corn And Sorghum Hybrids, Weston B. Johnson, Wajira S. Ratnayake, David S. Jackson, Kyung-Min Lee, Timothy J. Herrman, Scott R. Bean, Stephen C. Mason

Department of Food Science and Technology: Faculty Publications

Dent com (Zea mays L.) and sorghum (Sorghum hieolor L. Moench) sample sets representative of commonly grown hybrids and diverse physical attributes were analyzed for alkaline cooking performance. The influence of kernel characteristics including hardness, density, starch properties (thermal, pasting, and crystallinity), starch content, protein content, and prolamin content on alkaline cooking performance was also determined. Corn nixtamal moisture content was lower for hard, dense kernels with high protein contents; sorghum nixtamal moisture content was lower for kernels with low moisture contents and low starch relative crystallinities. Statistically significant (P < 0.05) regression equations showed that corn nixtamal moisture content was influenced by TADD (tangential abrasive dehulling device) index, kernel moisture content, starch content, and protein content; sorghum nixtamal moisture content was influenced by starch relative crystallinity, kernel moisture content, and abrasive hardness index. Pericarp removal was not strongly correlated with kernel characterization tests. Location (environmental) and hybrid (genetic) factors influenced most kernel characteristics and nixtamalization processing variables.

Functionality Of Native Tetraploid Wheat Starches: Effects Of Waxy Loci Alleles And Amylose Concentration In Blends, L. E. Hansen, David S. Jackson, R. L. Wehling, J. D. Wilson, Robert A. Graybosch

Department of Food Science and Technology: Faculty Publications

Partial waxy (reduced amylose) and fully waxy (amylose-free) tetraploid durum wheats (Triticum turgidum L. var. durum) were used to investigate the relationships between both intra- and inter-granular variation in amylose concentration and starch functionality. Starches isolated from each genotype (intra-granular amylose variants) were compared to those of commercially available hexaploid wild-type and waxy starches, and functionalities compared to blends (inter-granular variants) of durum waxy and wild- type starches of 0, 6, 12, 18, 24, & 30% amylose content. Starch particle size distributions were not significantly different amongst partial waxy and wild-type genotypes; waxy samples had significantly smaller mean …

Responders And Non-Responders To Probiotic Interventions, Gregor Reid, Estelle Gaudier, Francisco Guarner, Gary B. Huffnagle, Jean M. Macklaim, Alicia Murcia Munoz, Margaret Martini, Tamar Ringel-Kulka, Balfor R. Sartor, Robert R. Unal, Kristin Verbeke, Jens Walter

Department of Food Science and Technology: Faculty Publications

As with many clinical studies, trials using probiotics have shown clearly that some patients benefit from the treatment while others do not. For example if treatment with probiotics leads to 36% cure rate of diarrhea, why did the other 64% not have the same result? The issue is important for human and indeed experimental animal studies for two main reasons: (i) Would changing the design of the study result in more subjects responding to treatment? (ii) If a subject does not respond what are the mechanistic reasons? In order to tackle the issue of responders and non-responders to therapy, a …

Threshold Dose For Peanut: Risk Characterization Based Upon Diagnostic Oral Challenge Of A Series Of 286 Peanut-Allergic Individuals, Steve L. Taylor, D. A. Moneret-Vautrin, Rene W. R. Crevel, David Sheffield, Martine Morisset, P. Dumont, Benjamin C. Remington, Joseph L. Baumert

Department of Food Science and Technology: Faculty Publications

Clinical records of 286 consecutive patients reacting positively with objective symptoms to double-blind, placebo-controlled oral peanut challenges at University Hospital, Nancy, France were examined for individual No Observed Adverse Effect Levels (NOAELs) and Lowest Observed Adverse Effect Levels (LOAELs). After fitting to a log-normal probability distribution model, the ED₁₀ and ED₀₅ were 14.4 and 7.3 mg (expressed as whole peanut), respectively, with 95% lower confidence intervals of 10.7 and 5.2 mg, respectively. Compared to results from a previous study where the ED₁₀ was based upon individual peanut thresholds gleaned from 12 publications, a statistically significant difference was …

Building The Genomic Base-Layer Of The Oral “Omic” World, The Forsyth Metagenomic Support Consortium, Jacques Izard

Department of Food Science and Technology: Faculty Publications

With the shift of molecular technologies directed toward the understanding of greater biological complexity of the oral cavity, a knowledge gap was created by the lack of genomic data from the diverse oral microorganisms. To facilitate and enable the interpretation of metagenomic, transcriptomic, and proteomic data generated or soon to be generated from oral biofilms, we are providing reference genomic information from phylogenetically diverse oral bacterial isolates. This work, initiated by the National Institute of Dental and Craniofacial Research as an isolated effort, is now part of the Human Microbiome Project. The goal of this effort is the public release …

Purification Of Parvalbumin From Carp: A Protocol That Avoids Heat Treatment, Stef J. Koppelman, Roland A. Romijn, Harmen H. J. De Jongh, Julie A. Nordlee, Sander Piersma, Martin Hessing, Steve L. Taylor

Department of Food Science and Technology: Faculty Publications

Parvalbumin from carp, a major allergen,was purified to homogeneity using ion exchange chromatography and size exclusion chromatography (estimated purity > 95% to 98% based on SDS-PAGE and native PAGE) with a yield of 318 mg, and a number of basic biochemical characteristics were determined. The identity was confirmed by peptide-mass fingerprinting, and IgE-binding was demonstrated. The UV/Vis absorbance spectra were explained using the previously published amino acid sequences. Far UV-CD spectroscopy was used to confirm the folding character of parvalbumin. We conclude that parvalbumin from carp can be purified on a comparatively large (hundreds of milligrams) scale using a purification protocol …