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Association Between Sulfur-Metabolizing Bacterial Communities In Stool And Risk Of Distal Colorectal Cancer In Men, Long H. Nguyen, Wenjie Ma, Dong D. Wang, Yin Cao, Himel Mallick, Teklu K. Gerbaba, Jason Lloyd-Price, Galeb Abu-Ali, A. Brantley Hall, Daniel Sikavi, David A. Drew, Raaj S. Mehta, Cesar Arze, Amit D. Joshi, Yan Yan, Tobyn Branck, Casey Dulong, Kerry L. Ivey, Shuji Ogino, Eric B. Rimm, Mingyang Song, Wendy S. Garrett, Jacques Izard, Cutis Huttenhower, Andrew T. Chan Apr 2020

Association Between Sulfur-Metabolizing Bacterial Communities In Stool And Risk Of Distal Colorectal Cancer In Men, Long H. Nguyen, Wenjie Ma, Dong D. Wang, Yin Cao, Himel Mallick, Teklu K. Gerbaba, Jason Lloyd-Price, Galeb Abu-Ali, A. Brantley Hall, Daniel Sikavi, David A. Drew, Raaj S. Mehta, Cesar Arze, Amit D. Joshi, Yan Yan, Tobyn Branck, Casey Dulong, Kerry L. Ivey, Shuji Ogino, Eric B. Rimm, Mingyang Song, Wendy S. Garrett, Jacques Izard, Cutis Huttenhower, Andrew T. Chan

Faculty Publications in Food Science and Technology

Background & Aims: Sulfur-metabolizing microbes, which convert dietary sources of sulfur into genotoxic hydrogen sulfide (H2S), have been associated with development of colorectal cancer (CRC). We identified a dietary pattern associated with sulfur-metabolizing bacteria in stool and then investigated its association with risk of incident CRC using data from a large prospective study of men.

Methods: We collected data from 51,529 men enrolled in the Health Professionals Follow-up Study since 1986 to determine the association between sulfur-metabolizing bacteria in stool and risk of CRC over 26 years of follow-up. First, in a subcohort of 307 healthy men, we profiled serial stool metagenomes and metatranscriptomes and assessed diet using semiquantitative food frequency questionnaires to identify food groups associated with 43 bacterial species involved in sulfur metabolism. We used these data to develop a sulfur microbial dietary score. We then used Cox proportional hazards modeling to evaluate adherence to this pattern among eligible individuals (n = 48,246) from 1986 through 2012 with risk for incident CRC.

Results: Foods associated with higher sulfur microbial diet scores included increased consumption of processed meats and low-calorie drinks and lower consumption of vegetables and legumes. Increased sulfur microbial diet scores were associated with risk of distal colon and rectal cancers, after adjusting for other risk factors (multivariable relative risk, highest vs lowest quartile, 1.43; 95% confidence interval 1.14–1.81; P-trend = .002). In contrast, sulfur microbial diet scores were not associated with risk of proximal colon cancer (multivariable relative risk 0.86; 95% CI 0.65–1.14; P-trend = .31).

Conclusions: In an analysis of participants in the Health Professionals Follow-up Study, we found that long-term adherence to a dietary pattern associated with sulfur-metabolizing bacteria in stool was associated with an increased risk of distal CRC. Further studies are needed to determine how sulfur-metabolizing bacteria might contribute to CRC pathogenesis.


Antimicrobial Peptide Identification Using Multi-Scale Convolutional Network, Xin Su, Jing Xu, Yanbin Yin, Xiongwen Quan, Han Zhang Dec 2019

Antimicrobial Peptide Identification Using Multi-Scale Convolutional Network, Xin Su, Jing Xu, Yanbin Yin, Xiongwen Quan, Han Zhang

Faculty Publications in Food Science and Technology

Background: Antibiotic resistance has become an increasingly serious problem in the past decades. As an alternative choice, antimicrobial peptides (AMPs) have attracted lots of attention. To identify new AMPs, machine learning methods have been commonly used. More recently, some deep learning methods have also been applied to this problem.

Results: In this paper, we designed a deep learning model to identify AMP sequences. We employed the embedding layer and the multi-scale convolutional network in our model. The multi-scale convolutional network, which contains multiple convolutional layers of varying filter lengths, could utilize all latent features captured by the multiple convolutional layers ...


A Novel And Green Nanoparticle Formation Approach To Forming Low-Crystallinity Curcumin Nanoparticles To Improve Curcumin’S Bioaccessibility, Ali Ubeyitogullari, Ozan Ciftci Dec 2019

A Novel And Green Nanoparticle Formation Approach To Forming Low-Crystallinity Curcumin Nanoparticles To Improve Curcumin’S Bioaccessibility, Ali Ubeyitogullari, Ozan Ciftci

Faculty Publications in Food Science and Technology

Health-promoting effects of curcumin are well-known; however, curcumin has a very low bioavailability due to its crystalline structure. The main objective of this study was to develop a novel green nanoparticle formation method to generate low-crystallinity curcumin nanoparticles to enhance the bioavailability of curcumin. Nanoporous starch aerogels (NSAs) (surface area of 60 m2/g, pore size of 20 nm, density of 0.11 g/cm3, and porosity of 93%) were employed as a mold to produce curcumin nanoparticles with the help of supercritical carbon dioxide (SC-CO2). The average particle size of the curcumin nanoparticles was 66 nm. Impregnation into NSAs ...


Keeping Allergen Names Clear And Defined, Sanny K. Chan, Anna Pomés, Christiane Hilger, Janet M. Davies, Geoffrey Mueller, Annette Kuehn, Andreas L. Lopata, Gabriele Gadermaier, Marianne Van Hage, Monika Raulf, Richard E. Goodman Nov 2019

Keeping Allergen Names Clear And Defined, Sanny K. Chan, Anna Pomés, Christiane Hilger, Janet M. Davies, Geoffrey Mueller, Annette Kuehn, Andreas L. Lopata, Gabriele Gadermaier, Marianne Van Hage, Monika Raulf, Richard E. Goodman

Faculty Publications in Food Science and Technology

The World Health Organization/International Union of Immunological Societies (WHO/IUIS) Allergen Nomenclature Sub-Committee was established in 1986 by leading allergists to standardize names given to proteins that cause IgE-mediated reactions in humans. The Sub-Committee’s objective is to assign unique names to allergens based on a critical analysis of confidentially submitted biochemical and clinical data from researchers, often prior to publication to preserve consistency. The Sub-Committee maintains and revises the database as the understanding of allergens evolves. This report summarizes recent developments that led to updates in classification of cockroach group 1 and 5 allergens to animal as well ...


Gene Expression Value Prediction Based On Xgboost Algorithm, Wei Li, Yanbin Yin, Xiongwen Quan, Han Zhang Nov 2019

Gene Expression Value Prediction Based On Xgboost Algorithm, Wei Li, Yanbin Yin, Xiongwen Quan, Han Zhang

Faculty Publications in Food Science and Technology

Gene expression profiling has been widely used to characterize cell status to reflect the health of the body, to diagnose genetic diseases, etc. In recent years, although the cost of genome-wide expression profiling is gradually decreasing, the cost of collecting expression profiles for thousands of genes is still very high. Considering gene expressions are usually highly correlated in humans, the expression values of the remaining target genes can be predicted by analyzing the values of 943 landmark genes. Hence, we designed an algorithm for predicting gene expression values based on XGBoost, which integrates multiple tree models and has stronger interpretability ...


Prophylactic Effects Of Isomaltodextrin In A Balb/C Mouse Model Of Egg Allergy, Yoshinori Mine, Yan Jin, Hua Zhang, Prithy Rupa, Kaustav Majumder, Takeo Sakurai, Yoshifumi Taniguchi, Ryodai Takagaki, Hikaru Watanabe, Hitoshi Mitsuzumi Nov 2019

Prophylactic Effects Of Isomaltodextrin In A Balb/C Mouse Model Of Egg Allergy, Yoshinori Mine, Yan Jin, Hua Zhang, Prithy Rupa, Kaustav Majumder, Takeo Sakurai, Yoshifumi Taniguchi, Ryodai Takagaki, Hikaru Watanabe, Hitoshi Mitsuzumi

Faculty Publications in Food Science and Technology

The aim of this study was to evaluate the potential effects of isomaltodextrin (IMD), a dietary saccharide polymer derived from enzymatically produced from starch, on the ability to alter immune response (IR) bias to hen egg ovalbumin (Ova) induced allergic inflammation in mice. Groups of Balb/c mice were pre-treated with various doses of IMD in drinking water (1.0, 2.5, and 5.0% w/v) for 6 weeks and subsequently sensitized to the Ova together with continuous administration of IMD. To evaluate changes in immune response bias, immunoglobulin isotype-associated antibody activity, concentrations of type 1 and 2 cytokines ...


Role Of Dietary Flavonoid Compounds In Driving Patterns Of Microbial Community Assembly, Kerry L. Ivey, Andrew T. Chan, Jacques Izard, Aedin Cassidy, Geraint B. Rogers, Eric B. Rimm Sep 2019

Role Of Dietary Flavonoid Compounds In Driving Patterns Of Microbial Community Assembly, Kerry L. Ivey, Andrew T. Chan, Jacques Izard, Aedin Cassidy, Geraint B. Rogers, Eric B. Rimm

Faculty Publications in Food Science and Technology

Flavonoids are a group of polyphenolic dietary compounds found in many different plant-based foods. There is increasing evidence that higher flavonoid intake may be causally linked to a reduced risk of cardiovascular disease and other chronic diseases. The bioactivity and bioavailability of many dietary flavonoids can be influenced by gastrointestinal microbiome metabolism. However, the role that habitual flavonoid intake plays in shaping the human gut microbiome is poorly understood. We describe an application of an ecosystem-based analytic approach to nutritional, microbiome, and questionnaire data from a cohort of more than 240 generally healthy adult males to assess the role of ...


Bioinformatics Identification Of Anti-Crispr Loci By Using Homology, Guilt-By-Association, And Crispr Self-Targeting Spacer Approaches, Yanbin Yin, Bowen Yang, Sarah Entwistle Sep 2019

Bioinformatics Identification Of Anti-Crispr Loci By Using Homology, Guilt-By-Association, And Crispr Self-Targeting Spacer Approaches, Yanbin Yin, Bowen Yang, Sarah Entwistle

Faculty Publications in Food Science and Technology

Anti-CRISPR (Acr) loci/operons encode Acr proteins and Acr-associated (Aca) proteins. Forty-five Acr families have been experimentally characterized inhibiting seven subtypes of CRISPR-Cas systems. We have developed a bioinformatics pipeline to identify genomic loci containing Acr homologs and/or Aca homologs by combining three computational approaches: homology, guilt-by-association, and self-targeting spacers. Homology search found thousands of Acr homologs in bacterial and viral genomes, but most are homologous to AcrIIA7 and AcrIIA9. Investigating the gene neighborhood of these Acr homologs revealed that only a small percentage (23.0% in bacteria and 8.2% in viruses) of them have neighboring Aca homologs ...


Experimental Evidence For Adaptation To Species-Specific Gut Microbiota In House Mice, Andrew H. Moeller, João C. Gomes-Neto, Sara Mantz, Hatem Kittana, Rafael R. Segura Munoz, Robert J. Schmaltz, Amanda E. Ramer-Tait, Michael W. Nachman Jul 2019

Experimental Evidence For Adaptation To Species-Specific Gut Microbiota In House Mice, Andrew H. Moeller, João C. Gomes-Neto, Sara Mantz, Hatem Kittana, Rafael R. Segura Munoz, Robert J. Schmaltz, Amanda E. Ramer-Tait, Michael W. Nachman

Faculty Publications in Food Science and Technology

The gut microbial communities of mammals have codiversified with host species, and changes in the gut microbiota can have profound effects on host fitness. Therefore, the gut microbiota may drive adaptation in mammalian species, but this possibility is underexplored. Here, we show that the gut microbiota has codiversified with mice in the genus Mus over the past 6 million years, and we present experimental evidence that the gut microbiota has driven adaptive evolution of the house mouse, Mus musculus domesticus. Phylogenetic analyses of metagenomeassembled bacterial genomic sequences revealed that gut bacterial lineages have been retained within and diversified alongside Mus ...


Candida Albicans Quorum-Sensing Molecule Farnesol Modulates Staphyloxanthin Production And Activates The Thiol-Based Oxidative-Stress Response In Staphylococcus Aureus, Taissa Vila, Eric F. Kong, Ahmed Ibrahim, Kurt Piepenbrink, Amol C. Shetty, Carrie Mccracken, Vincent Bruno, Mary Ann Jabra-Rizk Jun 2019

Candida Albicans Quorum-Sensing Molecule Farnesol Modulates Staphyloxanthin Production And Activates The Thiol-Based Oxidative-Stress Response In Staphylococcus Aureus, Taissa Vila, Eric F. Kong, Ahmed Ibrahim, Kurt Piepenbrink, Amol C. Shetty, Carrie Mccracken, Vincent Bruno, Mary Ann Jabra-Rizk

Faculty Publications in Food Science and Technology

Microbial species utilize secreted-signaling molecules to coordinate their behavior. Our previous investigations demonstrated a key role for the Candida albicans-secreted quorum-sensing molecule farnesol in modulating Staphylococcus aureus response to antimicrobials in mixed biofilms. In this study, we aimed to provide mechanistic insights into the impact of farnesol on S. aureus within the context of inter-species interactions. To mimic biofilm dynamics, farnesol-sensitized S. aureus cells were generated via sequential farnesol exposure. The sensitized phenotype exhibited dramatic loss of the typical pigment, which we identified as staphyloxanthin, an important virulence factor synthesized by the Crt operon in S. aureus. Additionally, farnesol exposure ...


Cell Wall Enzymes In Zygnema Circumcarinatum Utex 1559 Respond To Osmotic Stress In A Plant-Like Fashion, Elisabeth Fitzek, Lauren Orton, Sarah Entwistle, W. Scott Grayburn, Catherine Ausland, Melvin R. Duvall, Yanbin Yin Jun 2019

Cell Wall Enzymes In Zygnema Circumcarinatum Utex 1559 Respond To Osmotic Stress In A Plant-Like Fashion, Elisabeth Fitzek, Lauren Orton, Sarah Entwistle, W. Scott Grayburn, Catherine Ausland, Melvin R. Duvall, Yanbin Yin

Faculty Publications in Food Science and Technology

Previous analysis of charophyte green algal (CGA) genomes and transcriptomes for specific protein families revealed that numerous land plant characteristics had already evolved in CGA. In this study, we have sequenced and assembled the transcriptome of Zygnema circumcarinatum UTEX 1559, and combined its predicted protein sequences with those of 13 additional species [five embryophytes (Emb), eight charophytes (Cha), and two chlorophytes (Chl) as the outgroup] for a comprehensive comparative genomics analysis. In total 25,485 orthologous gene clusters (OGCs, equivalent to protein families) of the 14 species were classified into nine OGC groups. For example, the ChaCEmb group contains 4 ...


Nitrogen, Cobalt Co-Doped Fluorescent Magnetic Carbon Dots As Ratiometric Fluorescent Probes For Cholesterol And Uric Acid In Human Blood Serum, Shan Huang, Erli Yang, Jiandong Yao, Xu Chu, Yi Liu, Yue Zhang, Qi Xiao May 2019

Nitrogen, Cobalt Co-Doped Fluorescent Magnetic Carbon Dots As Ratiometric Fluorescent Probes For Cholesterol And Uric Acid In Human Blood Serum, Shan Huang, Erli Yang, Jiandong Yao, Xu Chu, Yi Liu, Yue Zhang, Qi Xiao

Faculty Publications in Food Science and Technology

Detection of cholesterol and uric acid biomarkers is of great importance for clinical diagnosis of several serious diseases correlated with their variations in human blood serum. In this study, a new kind of well selective and highly sensitive ratiometric fluorescent probe for cholesterol and uric acid determination in human blood serum was innovatively developed on the basis of the inner filter effect (IFE) process of nitrogen, cobalt co-doped carbon dots (N,Co-CDs) with 2,3-diaminophenazine (DAP). DAP was the oxidative product during the oxidation reaction between ophenylenediamine and H2O2. Fluorescent magnetic N,Co-CDs possessing blue emission and magnetic property were ...


Long-Term Use Of Antibiotics And Risk Of Colorectal Adenoma, Yin Cao, Kana Wu, Raaj Mehta, David A. Drew, Mingyang Song, Paul Lochhead, Long H. Nguyen, Jacques Izard, Charles S. Fuchs, Wendy S. Garrett, Curtis Huttenhower, Shuji Ogino, Edward L. Giovannucci, Andrew T. Chan Apr 2019

Long-Term Use Of Antibiotics And Risk Of Colorectal Adenoma, Yin Cao, Kana Wu, Raaj Mehta, David A. Drew, Mingyang Song, Paul Lochhead, Long H. Nguyen, Jacques Izard, Charles S. Fuchs, Wendy S. Garrett, Curtis Huttenhower, Shuji Ogino, Edward L. Giovannucci, Andrew T. Chan

Faculty Publications in Food Science and Technology

Objective—Recent evidence suggests that antibiotic use, which alters the gut microbiome, is associated with an increased risk of colorectal cancer. However, the association between antibiotic use and risk of colorectal adenoma, the precursor for the majority of colorectal cancers, has not been investigated.

Design—We prospectively evaluated the association between antibiotic use at age 20–39 and 40–59 (assessed in 2004) and recent antibiotic use (assessed in 2008) with risk of subsequent colorectal adenoma among 16,642 women aged ≥60 enrolled in the Nurses’ Health Study who underwent at least one colonoscopy through 2010. We used multivariate logistic ...


Corrigendum: Use Of Uv Treated Milk Powder To Increase Vaccine Efficacy In The Elderly, Sara Schaefer, Kasper Arthur Hettinga, James Cullor, J. Bruce German, Bethany M. Henrick Mar 2019

Corrigendum: Use Of Uv Treated Milk Powder To Increase Vaccine Efficacy In The Elderly, Sara Schaefer, Kasper Arthur Hettinga, James Cullor, J. Bruce German, Bethany M. Henrick

Faculty Publications in Food Science and Technology

“Peripheral blood samples were collected at the time of enrollment (week 0) and serum was stored at −80◦C until subsequent analysis. Participants were then randomized into two groups and provided with equal concentration and quantity of either dairy or soy supplement provided in powdered form in coded, single-serving bags. Both participants and researchers were blinded to the type of protein received. Participants were asked to consume two servings of protein powder (6 grams/packet) with 4 ounces of water or applesauce twice per day, with meals, for a total of 8 weeks. At week 4, participants were vaccinated with ...


Tlr10 Senses Hiv-1 Proteins And Significantly Enhances Hiv-1 Infection, Bethany M. Henrick, Xiao-Dan Yao, Muhammad Atif Zahoor, Alash’Le Abimiku, Sophia Osawe, Kenneth L. Rosenthal Mar 2019

Tlr10 Senses Hiv-1 Proteins And Significantly Enhances Hiv-1 Infection, Bethany M. Henrick, Xiao-Dan Yao, Muhammad Atif Zahoor, Alash’Le Abimiku, Sophia Osawe, Kenneth L. Rosenthal

Faculty Publications in Food Science and Technology

Toll-like receptors (TLRs) play a crucial role in innate immunity and provide a first line of host defense against invading pathogens. Of the identified human TLRs, TLR10 remains an orphan receptor whose ligands and functions are poorly understood. In the present study, we sought to evaluate the level of TLR10 expression in breastmilk (BM) and explore its potential function in the context of HIV-1 infection. We evaluated HIV-1-infected (Nigerian: n = 40) and uninfected (Nigerian: n = 27; Canadian: n = 15) BM samples for TLR expression (i.e., TLR10, TLR2, and TLR1) and report here that HIV-1-infected BM from Nigerian women showed ...


Hydrodistillation Extraction Kinetics Regression Models For Essential Oil Yield And Composition In Juniperus Virginiana, J. Excelsa, And J. Sabina, Ivanka B. Semerdjieva, Santosh Shiwakoti, Charles L. Cantrell, Valtcho D. Zheljazkov, Tess Astatkie, Vicki L. Schlegel, Tzenka Radoukova Mar 2019

Hydrodistillation Extraction Kinetics Regression Models For Essential Oil Yield And Composition In Juniperus Virginiana, J. Excelsa, And J. Sabina, Ivanka B. Semerdjieva, Santosh Shiwakoti, Charles L. Cantrell, Valtcho D. Zheljazkov, Tess Astatkie, Vicki L. Schlegel, Tzenka Radoukova

Faculty Publications in Food Science and Technology

The chemical profile and antioxidant capacity of Juniperus virginiana, J. excelsa, and J. sabina essential oil (EO) fractions as a function of time was the subject of this study. The hypothesis was that, capturing EO in sequential timeframes during hydrodistillation would generate fractions containing unique compositions and antioxidant capacity. In J. virginiana, the highest limonene (43%) was found in the 0–5 min oil fraction, with safrole (37%) being highest in the 10–20 and 20–40 min fractions, and elemol (34%) being highest in the 160–240 min fraction. In J. excelsa, α-pinene (34-36%) was the highest in the ...


Orphan Genes Shared By Pathogenic Genomes Are More Associated With Bacterial Pathogenicity, Sarah Entwistle, Yanbin Yin Feb 2019

Orphan Genes Shared By Pathogenic Genomes Are More Associated With Bacterial Pathogenicity, Sarah Entwistle, Yanbin Yin

Faculty Publications in Food Science and Technology

Orphan genes (also known as ORFans [i.e., orphan open reading frames]) are new genes that enable an organism to adapt to its specific living environment. Our focus in this study is to compare ORFans between pathogens (P) and nonpathogens (NP) of the same genus. Using the pangenome idea, we have identified 130,169 ORFans in nine bacterial genera (505 genomes) and classified these ORFans into four groups: (i) SS-ORFans (P), which are only found in a single pathogenic genome; (ii) SS-ORFans (NP), which are only found in a single nonpathogenic genome; (iii) PS-ORFans (P), which are found in multiple ...


In Vitro Bioaccessibility Of Low-Crystallinity Phytosterol Nanoparticles Generated Using Nanoporous Starch Bioaerogels, Ali Ubeyitogullari, Regis Moreau, Devin J. Rose, Ozan Ciftci Jan 2019

In Vitro Bioaccessibility Of Low-Crystallinity Phytosterol Nanoparticles Generated Using Nanoporous Starch Bioaerogels, Ali Ubeyitogullari, Regis Moreau, Devin J. Rose, Ozan Ciftci

Faculty Publications in Food Science and Technology

Phytosterols are natural health-promoting bioactive compounds; however, phytosterols have very limited bioavailability due to their crystalline lipophilic structure. With the aim of improving bioaccessibility, low-crystallinity phytosterol nanoparticles were generated by supercritical carbon dioxide (SC-CO2) impregnation of phytosterols into nanoporous starch aerogels (NSAs). The in vitro bioaccessibility of the phytosterol nanoparticles (35%) was significantly higher than that of the crude phytosterols (3%) after sequential oral, gastric, and intestinal digestion. The percentages of starch hydrolysis were not different among the various NSA preparations and reached to 64% after sequential digestion. The zeta potential of the phytosterol nanoparticles was higher compared to that ...


In Vitro Bioaccessibility Of Novel Low-Crystallinity Phytosterol Nanoparticles In Non-Fat And Regular-Fat Foods, Ali Ubeyitogullari, Ozan Ciftci Jan 2019

In Vitro Bioaccessibility Of Novel Low-Crystallinity Phytosterol Nanoparticles In Non-Fat And Regular-Fat Foods, Ali Ubeyitogullari, Ozan Ciftci

Faculty Publications in Food Science and Technology

Crystalline structure of phytosterols leads to poor bioavailability and makes their incorporation into foods challenging. Bioaccessibility of first-of-their-kind low-crystallinity phytosterol nanoparticles impregnated in nanoporous starch aerogels (PS-NSA) was evaluated in non-, low-, and regular-fat solid and aqueous food formulations, namely, granola bars and puddings for the first time. Bioaccessibility of the phytosterol nanoparticles was significantly higher than that of crude phytosterols in all food formulations (p < .05); it was 88.2 and 91.8% for low- or regular-fat granola bars, respectively, whereas bioaccessibility of crude phytosterols was ca. 30% in those formulations. However, decreasing the lipid content to zero resulted in lower phytosterols' bioaccessibilities from both PS-NSA (53%) and crude phytosterols (ca. 16%) in non-fat granola bars. Bioaccessibility of crude phytosterols (2%) was significantly enhanced with PS-NSA (19%) in the pudding formulation. PS-NSA allows preparation of low- and non-fat foods enriched with phytosterols while enhancing the health benefits of phytosterols with smaller doses.


Mycoprotein: The Future Of Nutritious Nonmeat Protein, A Symposium Review, Tim Ja Finnigan, Benjamin T. Wall, Peter J. Wilde, Francis B. Stephens, Steve Taylor, Marjorie R. Freedman Jan 2019

Mycoprotein: The Future Of Nutritious Nonmeat Protein, A Symposium Review, Tim Ja Finnigan, Benjamin T. Wall, Peter J. Wilde, Francis B. Stephens, Steve Taylor, Marjorie R. Freedman

Faculty Publications in Food Science and Technology

Mycoprotein is an alternative, nutritious protein source with a meat-like texture made from Fusarium venenatum, a naturally occurring fungus. Its unique method of production yields a significantly reduced carbon and water footprint relative to beef and chicken. Mycoprotein, sold as Quorn, is consumed in 17 countries, including the United States. In line with current dietary guidelines, mycoprotein is high in protein and fiber, and low in fat, cholesterol, sodium, and sugar. Mycoprotein may help maintain healthy blood cholesterol levels, promote muscle synthesis, control glucose and insulin levels, and increase satiety. It is possible that some susceptible consumers will become sensitized ...


Extraction Of Astaxanthin From Engineered Camelina Sativa Seed Using Ethanol-Modified Supercritical Carbon Dioxide, Liyang Xie, Edgar B. Cahoon, Yue Zhang, Ozan Ciftci Jan 2019

Extraction Of Astaxanthin From Engineered Camelina Sativa Seed Using Ethanol-Modified Supercritical Carbon Dioxide, Liyang Xie, Edgar B. Cahoon, Yue Zhang, Ozan Ciftci

Faculty Publications in Food Science and Technology

Natural astaxanthin, a high-value carotenoid that is currently extracted mainly from marine organisms, was extracted from engineered camelina seed using ethanol-modified supercritical carbon dioxide (SC-CO2) for the first time, and compared with hexane and accelerated solvent extraction using hexane and ethanol. Response surface methodology (RSM) based on central composite rotatable design was employed to investigate the effect of pressure (30–45 MPa), temperature (40–60 °C), and ethanol concentration (10–35%, w/w). RSM-optimized conditions (41.6 MPa, 36.6 °C and 42.0% ethanol concentration) predicted the astaxanthin concentration as 437 μg/g oil, whereas the actual concentration ...


Gut Microbiota Dependent Anti-Tumor Immunity Restricts Melanoma Growth In Rnf5−/− Mice, Yan Li, Roberto Tinoco, Lisa Elmén, Igor Segota, Yibo Xian, Yu Fujita, Avinash Sahu, Raphy Zarecki, Kerrie Marie, Yongmei Feng, Ali Khateb, Dennie T. Frederick, Shiri K. Ashkenazi, Hyungsoo Kim, Eva Guijarro Perez, Chi-Ping Day, Rafael S. Segura Muñoz, Robert Schmaltz, Shibu Yooseph, Miguel A. Tam, Tongwu Zhang, Emily Avitan-Hersh, Lihi Tzur, Shoshana Roizman, Ilanit Boyango, Gil Bar-Sela, Amir Orian, Randal J. Kaufman, Marcus Bosenberg, Colin R. Goding, Bas Baaten, Mitchell P. Levesque, Reinhard Dummer, Kevin Brown, Glenn Merlino, Eytan Ruppin, Keith Flaherty, Amanda Ramer-Tait, Tao Long, Scott N. Peterson, Linda M. Bradley, Ze’Ev A. Ronai Jan 2019

Gut Microbiota Dependent Anti-Tumor Immunity Restricts Melanoma Growth In Rnf5−/− Mice, Yan Li, Roberto Tinoco, Lisa Elmén, Igor Segota, Yibo Xian, Yu Fujita, Avinash Sahu, Raphy Zarecki, Kerrie Marie, Yongmei Feng, Ali Khateb, Dennie T. Frederick, Shiri K. Ashkenazi, Hyungsoo Kim, Eva Guijarro Perez, Chi-Ping Day, Rafael S. Segura Muñoz, Robert Schmaltz, Shibu Yooseph, Miguel A. Tam, Tongwu Zhang, Emily Avitan-Hersh, Lihi Tzur, Shoshana Roizman, Ilanit Boyango, Gil Bar-Sela, Amir Orian, Randal J. Kaufman, Marcus Bosenberg, Colin R. Goding, Bas Baaten, Mitchell P. Levesque, Reinhard Dummer, Kevin Brown, Glenn Merlino, Eytan Ruppin, Keith Flaherty, Amanda Ramer-Tait, Tao Long, Scott N. Peterson, Linda M. Bradley, Ze’Ev A. Ronai

Faculty Publications in Food Science and Technology

Accumulating evidence points to an important role for the gut microbiome in anti-tumor immunity. Here, we show that altered intestinal microbiota contributes to anti-tumor immunity, limiting tumor expansion. Mice lacking the ubiquitin ligase RNF5 exhibit attenuated activation of the unfolded protein response (UPR) components, which coincides with increased expression of inflammasome components, recruitment and activation of dendritic cells and reduced expression of antimicrobial peptides in intestinal epithelial cells. Reduced UPR expression is also seen in murine and human melanoma tumor specimens that responded to immune checkpoint therapy. Co-housing of Rnf5−/− and WT mice abolishes the anti-tumor immunity and tumor inhibition ...


Formation Of Low-Density And Free-Flowing Hollow Microparticles From Butter And Fractionated Palm Oil Mixture, Joshua Gudeman, Junsi Yang, Ozan Ciftci Jan 2019

Formation Of Low-Density And Free-Flowing Hollow Microparticles From Butter And Fractionated Palm Oil Mixture, Joshua Gudeman, Junsi Yang, Ozan Ciftci

Faculty Publications in Food Science and Technology

The use of solid fats is challenging due to difficulty in incorporating into foods, handling during industrial food production, and relatively high-calorie contributions. The objective of this study was to form free-flowing and low-density hollow microparticles from nonhydrogenated fats, namely, butter and fractionated palm oil, using a novel method based on atomization of a carbon dioxide (CO2)- expanded lipid mixture. The melting point of the fractionated palm oil decreased from 66.2 to 47.3°C above 120 bar in the presence of pressurized CO2. The density of the particles decreased five-folds compared to that of the original ...


Use Of Uv Treated Milk Powder To Increase Vaccine Efficacy In The Elderly, Sara Schaefer, Kasper Arthur Hettinga, James Cullor, J. Bruce German, University Of Nebraska - Lincoln Oct 2018

Use Of Uv Treated Milk Powder To Increase Vaccine Efficacy In The Elderly, Sara Schaefer, Kasper Arthur Hettinga, James Cullor, J. Bruce German, University Of Nebraska - Lincoln

Faculty Publications in Food Science and Technology

Aging populations experience a decline in adaptive immune system function also known as immunosenesence. Protein nutrition has been shown to stimulate and strengthen the immune system, and such approaches are needed for this growing segment of the population. A controlled, randomized, double blind pilot study was conducted to compare two different protein sources (soy and dairy) as nutritional supplementation to enhance vaccine response. Our objective was to examine the immune stimulating effects of dairy protein subjected to ultraviolet radiation (UV-C) radiation treatment process instead of pasteurization. Participants were 21 healthy individuals over 60 years of age who consumed 6 g ...


Computational Modeling And Functional Characterization Of A Ggchi: A Class Iii Chitinase From Corms Of Gladiolus Grandiflorus, Maria Rafiq, Ashiq Hussain, Kausar Hussain Shah, Qamar Saeed, Muhammad Umair Sial, Zahid Ali, Friedrich Buck, Richard E. Goodman, Binish Khaliq, Uzma Ishaq, Mirza Ahsen Baig, Aisha Munawar, Seema Mahmood, Ahmed Akrem Oct 2018

Computational Modeling And Functional Characterization Of A Ggchi: A Class Iii Chitinase From Corms Of Gladiolus Grandiflorus, Maria Rafiq, Ashiq Hussain, Kausar Hussain Shah, Qamar Saeed, Muhammad Umair Sial, Zahid Ali, Friedrich Buck, Richard E. Goodman, Binish Khaliq, Uzma Ishaq, Mirza Ahsen Baig, Aisha Munawar, Seema Mahmood, Ahmed Akrem

Faculty Publications in Food Science and Technology

The present study describes the predicted model and functional characterization of an endochitinase (30 kDa) from corms of Gladiolus grandiflorus. ESI-QTOF-MS generated peptide showed 96% sequence homology with family 18, Class III acidic endochitinase of Gladiolus gandavensis. Purified G. grandiflorus chitinase (GgChi) hydrolyzed 4-methylumbelliferyl b-DN, N0,N00-triacetylchitotriose substrate showing specific endochitinase activity. Since no structural details of GgChi were available in the Protein Data Bank (PDB), a homology model was predicted using the coordinate information of Crocus vernus chitinase (PDB ID: 3SIM). Ramachandran plot indicated 84.5% in most favored region, 14.8% in additional and 0.6% in generously ...


Experimental Evaluation Of The Importance Of Colonization History In Early-Life Gut Microbiota Assembly, Inés Martínez, Maria X. Maldonado-Gomez, João Carlos Gomes-Neto, Hatem Kittana, Hua Ding, Robert J. Schmaltz, Payal Joglekar, Roberto Jiménez Cardona, Nathan L Marsteller, Steven W. Kembel, Andrew K. Benson, Daniel A. Peterson, Amanda Ramer-Tait, Jens C. Walter Sep 2018

Experimental Evaluation Of The Importance Of Colonization History In Early-Life Gut Microbiota Assembly, Inés Martínez, Maria X. Maldonado-Gomez, João Carlos Gomes-Neto, Hatem Kittana, Hua Ding, Robert J. Schmaltz, Payal Joglekar, Roberto Jiménez Cardona, Nathan L Marsteller, Steven W. Kembel, Andrew K. Benson, Daniel A. Peterson, Amanda Ramer-Tait, Jens C. Walter

Faculty Publications in Food Science and Technology

The factors that govern assembly of the gut microbiota are insufficiently understood. Here, we test the hypothesis that inter-individual microbiota variation can arise solely from differences in the order and timing by which the gut is colonized early in life. Experiments in which mice were inoculated in sequence either with two complex seed communities or a cocktail of four bacterial strains and a seed community revealed that colonization order influenced both the outcome of community assembly and the ecological success of individual colonizers. Historical contingency and priority effects also occurred in Rag1-/- mice, suggesting that the adaptive immune system is ...


The Msdin Family In Amanitin-Producing Mushrooms And Evolution Of The Prolyl Oligopeptidase Genes, Hong Luo, Qing Cai, Yungjiao Luli, Xuan Li, Rohita Sinha, Heather E. Hallen-Adams, Zhu L. Yang Aug 2018

The Msdin Family In Amanitin-Producing Mushrooms And Evolution Of The Prolyl Oligopeptidase Genes, Hong Luo, Qing Cai, Yungjiao Luli, Xuan Li, Rohita Sinha, Heather E. Hallen-Adams, Zhu L. Yang

Faculty Publications in Food Science and Technology

The biosynthetic pathway for amanitins and related cyclic peptides in deadly Amanita (Amanitace ae) mushrooms represents the first known ribosomal cyclic peptide pathway in the Fungi. Amanitins are found outside of the genus in distantly related agarics Galerina (Strophariaceae) and Lepiota (Agaricaceae). A long-standing question in the field persists: why is this pathway present in these phylogenetically disjunct agarics? Two deadly mushrooms, A. pallidorosea and A. subjunquillea, were deep sequenced, and sequences of biosynthetic genes encoding MSDINs (cyclic peptide presursor) and prolyl oligopeptidases (POPA and POPB) were obtained. The two Amanita species yielded 20 and 18 MSDINs, respectively. In addition ...


Dietary Patterns And Risk Of Colorectal Cancer Subtypes Classified By Fusobacterium Nucleatum In Tumor Tissue, Raaj S. Mehta, Reiko Nishihara, Yin Cao, Mingyang Song, Kosuke Mima, Zhi Rong Qian, Jonathan A. Nowak, Keisuke Kosumi, Tsuyoshi Hamada, Yohei Masugi, Susan Bullman, David A. Drew, Aleksandar D. Kostic, Teresa T. Fung, Wendy S. Garrett, Curtis Huttenhower, Kana Wu, Jeffrey A. Meyerhardt, Xuehong Zhang, Walter C. Willett, Edward L. Giovannucci, Charles S. Fuchs, Andrew T. Chan, Shuji Ogino Jul 2018

Dietary Patterns And Risk Of Colorectal Cancer Subtypes Classified By Fusobacterium Nucleatum In Tumor Tissue, Raaj S. Mehta, Reiko Nishihara, Yin Cao, Mingyang Song, Kosuke Mima, Zhi Rong Qian, Jonathan A. Nowak, Keisuke Kosumi, Tsuyoshi Hamada, Yohei Masugi, Susan Bullman, David A. Drew, Aleksandar D. Kostic, Teresa T. Fung, Wendy S. Garrett, Curtis Huttenhower, Kana Wu, Jeffrey A. Meyerhardt, Xuehong Zhang, Walter C. Willett, Edward L. Giovannucci, Charles S. Fuchs, Andrew T. Chan, Shuji Ogino

Faculty Publications in Food Science and Technology

Importance—Fusobacterium nucleatum appears to play a role in colorectal carcinogenesis through suppression of host immune response to tumor. Evidence also suggests that diet influences intestinal F. nucleatum. However, the role of F. nucleatum in mediating the relationship between diet and the risk of colorectal cancer is unknown.

Objective—To test the hypothesis that the associations of prudent diets (rich in whole grains and dietary fiber) and Western diets (rich in red and processed meat, refined grains, and desserts) with colorectal cancer risk may differ according to the presence of F. nucleatum in tumor tissue.

Design—Prospective cohort study.

Setting ...


Stability Of The Human Faecal Microbiome In A Cohort Of Adult Men, Raaj S. Mehta, David A. Drew, Jason Lloyd-Price, Ayshwarya Subramaian, Paul Lochhead, Amit D. Joshi, Kerry L. Ivey, Hamed Khalili, Gordon T. Brown, Casey Dulong, Mingyang Song, Long H. Nguyen, Himel Mallick, Eric B. Rimm, Jacques Izard, Curtis Huttenhower, Andrew T. Chan, Galeb S. Abu-Ali Jun 2018

Stability Of The Human Faecal Microbiome In A Cohort Of Adult Men, Raaj S. Mehta, David A. Drew, Jason Lloyd-Price, Ayshwarya Subramaian, Paul Lochhead, Amit D. Joshi, Kerry L. Ivey, Hamed Khalili, Gordon T. Brown, Casey Dulong, Mingyang Song, Long H. Nguyen, Himel Mallick, Eric B. Rimm, Jacques Izard, Curtis Huttenhower, Andrew T. Chan, Galeb S. Abu-Ali

Faculty Publications in Food Science and Technology

Characterizing the stability of the gut microbiome is important to exploit it as a therapeutic target and diagnostic biomarker. We metagenomically and metatranscriptomically sequenced the faecal microbiomes of 308 participants in the Health Professionals Follow-Up Study. Participants provided four stool samples—one pair collected 24–72 h apart and a second pair ~6 months later. Within-person taxonomic and functional variation was consistently lower than between-person variation over time. In contrast, metatranscriptomic profiles were comparably variable within and between subjects due to higher within-subject longitudinal variation. Metagenomic instability accounted for ~74% of corresponding metatranscriptomic instability. The rest was probably attributable to ...


Colonization Of Breastfed Infants By Bifidobacterium Longum Subsp. Infantis Evc001 Reduces Virulence Gene Abundance, Giorgio Casaburi, Steven A. Frese Jun 2018

Colonization Of Breastfed Infants By Bifidobacterium Longum Subsp. Infantis Evc001 Reduces Virulence Gene Abundance, Giorgio Casaburi, Steven A. Frese

Faculty Publications in Food Science and Technology

The infant gut microbiome is rapidly colonized by bacteria from the environment after birth, and this gut ecosystem can facilitate expansion of potential pathogens. Human milk shapes the infant gut microbiome and has evolved to foster the growth of specific bacteria. Breastfed infants fed the coevolved infant gut symbiont Bifidobacterium longum subsp. infantis EVC001 had significant modifications to their gut metagenome, including a decreased number of virulence factor genes.