Gastroenterology Commons^™

Characterization Of Variant Rnas Encapsidated During Bromovirus Infection By High-Throughput Sequencing, Sarah Dexheimer, Nipin Shrestha, Bandana Sharma Chapagain, Jozef J. Bujarski, Yanbin Yin

Food for Health: Publications

Previously, we described the RNA recombinants accumulating in tissues infected with the bromoviruses BMV (Brome mosaic virus) and CCMV (Cowpea chlorotic mottle virus). In this work, we characterize the recombinants encapsidated inside the purified virion particles of BMV and CCMV. By using a tool called the Viral Recombination Mapper (ViReMa) that detects recombination junctions, we analyzed a high number of high-throughput sequencing (HTS) short RNA sequence reads. Over 28% of BMV or CCMV RNA reads did not perfectly map to the viral genomes. ViReMa identified 1.40% and 1.83% of these unmapped reads as the RNA recombinants, respectively, in BMV and …

Antibiotic-Induced Gut Dysbiosis Elicits Gut-Brain Axis Relevant Multi-Omic Signatures And Behavioral And Neuroendocrine Changes In A Nonhuman Primate Model, Shivdeep S. Hayer, Mackenzie Conrin, Jeffrey French, Andrew K. Benson, Sophie Alvarez, Kathryn Dempsey, Anne Fischer, Zahraa Wajih Alsafwani, William Gasper, Mallory J. Suhr Van Haute, Haley R. Hassenstab, Shayda Azadmanesh, Missy Briardy, Skyler Gerbers, Aliyah Jabenis, Jennifer L. Thompson, Jonathan B. Clayton

Food for Health: Publications

Emerging evidence indicates that antibiotic-induced dysbiosis can play an etiological role in the pathogenesis of neuropsychiatric disorders. However, most of this evidence comes from rodent models. The objective of this study was to evaluate if antibiotic-induced gut dysbiosis can elicit changes in gut metabolites and behavior indicative of gut-brain axis disruption in common marmosets (Callithrix jacchus) – a nonhuman primate model often used to study sociability and stress. We were able to successfully induce dysbiosis in marmosets using a custom antibiotic cocktail (vancomycin, enrofloxacin and neomycin) administered orally for 28 days. This gut dysbiosis altered gut metabolite profiles, …

Dbapis: A Database Of Anti-Prokaryotic Immune System Genes, Yuchen Yan, Jinfang Zheng, Xinpeng Zhang, Yanbin Yin

Food for Health: Publications

Anti-prokary otic immune sy stem (APIS) proteins, typically encoded b y phages, prophages, and plasmids, inhibit prokaryotic immune systems (e.g. restriction modification, to xin-antito xin, CRISPR-Cas). A gro wing number of APIS genes ha v e been characterized and dispersed in the literature. Here w e de v eloped dbAPIS ( https:// bcb.unl.edu/ dbAPIS ), as the first literature curated data repository for experimentally verified APIS genes and their associated protein f amilies. T he k e y features of dbAPIS include: (i) e xperimentally v erified APIS genes with their protein sequences, functional annotation, PDB or AlphaFold predicted str …

Antibiotic-Induced Gut Dysbiosis And Cognitive, Emotional, And Behavioral Changes In Rodents: A Systematic Review And Meta-Analysis, Shivdeep S. Hayer, Soonjo Hwang, Jonathan B. Clayton

Food for Health: Publications

There are previous epidemiological studies reporting associations between antibiotic use and psychiatric symptoms. Antibiotic-induced gut dysbiosis and alteration of microbiota-gut-brain axis communication has been proposed to play a role in this association. In this systematic review and meta-analysis, we reviewed published articles that have presented results on changes in cognition, emotion, and behavior in rodents (rats and mice) after antibiotic-induced gut dysbiosis. We searched three databases—PubMed, Web of Science, and SCOPUS to identify such articles using dedicated search strings and extracted data from 48 articles. Increase in anxiety and depression-like behavior was reported in 32.7 and 40.7 percent of the …

Antibiotic-Induced Gut Dysbiosis And Cognitive, Emotional, And Behavioral Changes In Rodents: A Systematic Review And Meta-Analysis, Shivdeep S. Hayer, Soonjo Hwang, Jonathan B. Clayton

Food for Health: Publications

There are previous epidemiological studies reporting associations between antibiotic use and psychiatric symptoms. Antibiotic-induced gut dysbiosis and alteration of microbiota-gut-brain axis communication has been proposed to play a role in this association. In this systematic review and meta-analysis, we reviewed published articles that have presented results on changes in cognition, emotion, and behavior in rodents (rats and mice) after antibiotic-induced gut dysbiosis. We searched three databases—PubMed, Web of Science, and SCOPUS to identify such articles using dedicated search strings and extracted data from 48 articles. Increase in anxiety and depression-like behavior was reported in 32.7 and 40.7 percent of the …

Exploring Celiac Disease: A Case Analysis Of Multi-Systemic Symptoms And Effective Dietary Intervention In A Young Female, Mahmoud Ahmed, Vyshnavidevi Sunkara, Muhammad S Khan, Maryam Affaf, Mohammad Ahsan Anwaar

Student and Faculty Publications

This study presents the case of a 23-year-old woman diagnosed with celiac disease (CD), a condition triggered by an immune response to gluten, leading to inflammation in the small intestine. The patient manifested typical gastrointestinal symptoms, including diarrhea, abdominal pain, and vomiting, complemented by extra-intestinal signs such as fatigue and skin rashes. Diagnosis was corroborated through the presence of tTG-IgA antibodies and distinct histological changes in the duodenum. A notable finding was the patient's iron deficiency anemia, directly linked to the duodenal damage caused by CD. Effective management, encompassing a strict gluten-free diet and iron supplementation, resulted in marked improvement …

Homeobox Transcription Factor Hbxa Influences Expression Of Over One Thousand Genes In The Model Fungus Aspergillus Nidulans, Sandesh S. Pandit, Jinfang Zheng, Yanbin Yan, Sophie Lorber, Olivier Puel, Sourabh Dhingra, Eduardo A. Espeso, Ana M. Calvo

Food for Health: Publications

In fungi, conserved homeobox-domain proteins are transcriptional regulators governing development. In Aspergillus species, several homeobox-domain transcription factor genes have been identified, among them, hbxA/hbx1. For instance, in the opportunistic human pathogen Aspergillus fumigatus, hbxA is involved in conidial production and germination, as well as virulence and secondary metabolism, including production of fumigaclavines, fumiquinazolines, and chaetominine. In the agriculturally important fungus Aspergillus flavus, disruption of hbx1 results in fluffy aconidial colonies unable to produce sclerotia. hbx1 also regulates production of aflatoxins, cyclopiazonic acid and aflatrem. Furthermore, transcriptome studies revealed that hbx1 has a broad effect on …

Distinct Gene Expression Profiles Between Human Preterm-Derived And Adult-Derived Intestinal Organoids Exposed To Enterococcus Faecalis: A Pilot Study, Andrea C. Masi, Tatiana Y. Fofanova, Christopher A. Lamb, Jennifer Auchtung, Robert A. Britton, Mary K. Estes, Sasirekha Ramani, Simon J. Cockell, Jonathan Coxhead, Nicholas D. Embleton, Janet E. Berrington, Joseph F. Petrosino, Christopher J. Stewart

Food for Health: Publications

We read with interest the study by Kayisoglu et al¹ comparing the gene expression between embryo-derived and adult-derived intestinal organoids. Some innate immune system genes were differentially expressed between the two organoid types, suggesting a potential role of exposure to the environment, including gut microbiota, in shaping the intestinal gene expression. In extremely preterm infants (<32 weeks gestation), microbial–host interaction at the epithelial surface has been associated with various morbidities including late onset sepsis and necrotising enterocolitis.² Thus, preterm intestinal organoids may provide a specific and robust model for this population.

The Inherited Intestinal Microbiota From Myeloid-Specific Zip8ko Mice Impairs Pulmonary Host Defense Against Pneumococcal Pneumonia, Derrick R. Samuelson, Deandra R. Smith, Kelly C. Cunningham, Sabah Haq, Daniel N. Villageliú, Christi Christi Ellis, Niaz Bahar Chowdhury, Amanda E. Ramer-Tait, Jeff Price, Daren L. Knoell

Food for Health: Publications

Intestinal dysbiosis increases susceptibility to infection through the alteration of metabolic profiles, which increases morbidity. Zinc (Zn) homeostasis in mammals is tightly regulated by 24 Zn transporters. ZIP8 is unique in that it is required by myeloid cells to maintain proper host defense against bacterial pneumonia. In addition, a frequently occurring ZIP8 defective variant (SLC39A8 rs13107325) is strongly associated with inflammation-based disorders and bacterial infection. In this study, we developed a novel model to study the effects of ZIP8-mediated intestinal dysbiosis on pulmonary host defense independent of the genetic effects. Cecal microbial communities from a myeloid-specific Zip8 knockout mouse …

"Keep Your Chin Up, And Keep Eating": Perceptions Of Barriers And Facilitators To Healthful Dietary Behaviors Among Individuals With Gastrointestinal Cancer And Caregivers, Brandy-Joe Milliron, Cynthia Klobodu, Jonathan Deutsch, Karon Martyn, Dan Dychtwald, Emily Riahi, Shawn Carro, Taylor Hisek, Natalie Darcy, Ann C. Klassen

Kimmel Cancer Center Faculty Papers

BACKGROUND: This study explored perceptions of barriers and facilitators to healthful dietary behaviors among patients with gastrointestinal (GI) cancer and their caregivers, including caregiver preparedness, patient and caregiver self-efficacy for symptom management, and other environmental, social, and familial factors that may serve as barriers and facilitators to healthful eating.

METHODS: Using a concurrent mixed methods cross-sectional study design, individuals with GI cancer receiving outpatient chemotherapy and their caregivers completed surveys, dietary assessments, and interviews. Caregiving preparedness, self-efficacy for symptom management, and dietary intake were assessed using validated instruments. Dietary quality was measured using the Healthy Eating Index (HEI)-2020. In-depth interviews …

Comparison Of Two Lipid Emulsions On The Incidence Of Parenteral Nutrition Associated Cholestasis In Neonates, Joy Greenberg, Mamta Naik, John Chapman, Allison Davidson, Essam Imseis

Student and Faculty Publications

OBJECTIVE: Lipid emulsion contributes to parenteral nutrition associated cholestasis (PNAC). For decades, soybean oil-based intravenous lipid emulsion (SO-ILE) was the predominant product. Recently, a multicomponent lipid emulsion containing soybean oil, medium-chain triglycerides, olive oil and fish oil (SMOF-ILE) has been used off-label in neonatal care. This study evaluates the incidence of PNAC in neonates who received SMOF-ILE or SO-ILE.

METHODS: This was a retrospective review of neonates who received SMOF-ILE or SO-ILE for at least 14 days. Patients receiving SMOF-ILE were matched based on gestational age (GA) and birth weight to a historical cohort receiving SO-ILE. The primary outcomes were …

Acafinder: Genome Mining For Anti-Crispr-Associated Genes, Bowen Yang, Jinfang Zheng, Yanbin Yin

Food for Health: Publications

Anti-CRISPR (Acr) proteins are encoded by (pro)viruses to inhibit their host’s CRISPR-Cas systems. Genes encoding Acr and Aca (Acr associated) proteins often colocalize to form acr-aca operons. Here, we present AcaFinder as the first Aca genome mining tool. AcaFinder can (i) predict Acas and their associated acr-aca operons using guilt-by-association (GBA); (ii) identify homologs of known Acas using an HMM (Hidden Markov model) database; (iii) take input genomes for potential prophages, CRISPR-Cas systems, and self-targeting spacers (STSs); and (iv) provide a standalone program (https://github.com/boweny920/AcaFinder) and a web server (http://aca .unl.edu/Aca). AcaFinder was applied to mining over …

The Unique Seed Protein Composition Of Quality Protein Popcorn Promotes Growth Of Beneficial Bacteria From The Human Gut Microbiome, Nate Korth, Leandra Parsons, Mallory J. Van Haute, Qinnan Yang, Preston Hurst, James C. Schnable, David R. Holding, Andrew K. Benson

Food for Health: Publications

The effects of fiber, complex carbohydrates, lipids, and small molecules from food matrices on the human gut microbiome have been increasingly studied. Much less is known about how dietary protein can influence the composition and function of the gut microbial community. Here, we used near-isogenic maize lines of conventional popcorn and quality-protein popcorn (QPP) to study the effects of the opaque-2 mutation and associated quality-protein modifiers on the human gut microbiome. Opaque-2 blocks the synthesis of major maize seed proteins (α-zeins), resulting in a compensatory synthesis of new seed proteins that are nutritionally beneficial with substantially higher levels …

Inflammatory Diseases And Resections Of The Digestive Tract Influence The Risk Of Circulating Food-Specific-Igg, Jacques Izard, Walker Carson, Joseph Baumert, Jennifer Clarke

Department of Food Science and Technology: Faculty Publications

Objectives: Individuals affected with inflammatory diseases of the digestive tract or have had surgical removal of sections of the digestive tract are often in need to adjust their diet. The symptomatology associated with food intake issues is often informally reported as food sensitivity. We investigated the circulating food-specific-IgG among ten conditions.

Conclusion: The risk of the having circulating food-specific IgG differed widely among the conditions investigated. The maintenance of a colonic environment might influence the risk of food sensitivity in ostomates.

The Chromosome-Level Rambutan Genome Reveals A Significant Role Of Segmental Duplication In The Expansion Of Resistance Genes, Jinfang Zheng1, Lyndel W. Meinhardt, Ricardo Goenaga, Tracie Matsumoto, Dapeng Zhang, Yanbin Yin

Food for Health: Publications

Rambutan (Nephelium lappaceum var. lappaceum), a tropical fruit tree native to southeastern Asia, belongs to the family Sapindaceae. Rambutan is a popular table fruit and is also processed into preserves, juices, wines, and sorbets [1]. At present, only three Sapindaceae genomes are publicly available: Xanthoceras sorbifolium [2], Dimocarpus longan (longan) [3], and Acer yangbiense [4]. During the process of submitting this manuscript, the genome paper for the rambutan cultivar Baoyan7 became available online, but its genome sequence has not yet been released [5].

(#Womeninddw) Persistent Speaker Gender Gap At The Premier Digestive Disease Event, Zubair Khan, Rabia Rukhshan, Asmeen Bhatt, Sushovan Guha, Srinivas Ramireddy, Prithvi Patil, Ricardo Badillo, Roy Tomas Davee, Nirav Thosani

Student and Faculty Publications

BACKGROUND: Over the last few decades, advances have been made regarding gender equality starting from medical students to trainees, to leadership in academics. The female representation in specialty academic conferences not only reflects the existing gender disparities in that specialty but also can influence young female trainees to join that field. Digestive Disease Week (DDW) is the premier digestive disease event. We aimed to calculate the proportion of female representation among speakers and moderators at the DDW meetings held from 2018 to 2020.

METHODS: The data for DDW 2018-2020 were collected via the online web-based planner. The gender of speakers …

Small Bowel Stomas Are Associated With Higher Risk Of Circulating Food-Specific-Igg Than Patients With Organic Gastrointestinal Conditions And Colostomies, Walker K. Carson, Joseph L. Baumert, Jennifer Clarke, Jacques Izard

Department of Food Science and Technology: Faculty Publications

Objective The effects of food sensitivity can easily be masked by other digestive symptoms in ostomates and are unknown. We investigated food-specific-IgG presence in ostomates relative to participants affected by other digestive diseases.

Design Food-specific-IgG was evaluated for 198 participants with a panel of 109 foods. Immunocompetency status was also tested. Jejunostomates, ileostomates, and colostomates were compared with individuals with digestive tract diseases with inflammatory components (periodontitis, eosinophilic esophagitis, duodenitis, ulcerative colitis, Crohn’s disease, and appendicitis), as well as food malabsorption due to intolerance. A logistic regression model with covariates was used to estimate the effect of the experimental data …

The Sulfur Microbial Diet Is Associated With Increased Risk Of Early-Onset Colorectal Cancer Precursors, Long H. Nguyen, Yin Cao, Jinhee Hur, Raaj S. Mehta, Daniel R. Sikavi, Yiqing Wang, Wenjie Ma, Kana Wu, Mingyang Song, Edward L. Giovannucci, Eric B. Rimm, Walter C. Willett, Wendy S. Garrett, Jacques Izard, Curtis Huttenhower, Andrew T. Chan

Food for Health: Publications

Background and aims: Diet may contribute to the increasing incidence of colorectal cancer (CRC) before age 50 (early-onset CRC). Microbial metabolism of dietary sulfur produces hydrogen sulfide (H₂S), a gastrointestinal carcinogen that cannot be easily measured at scale. As a result, evidence supporting its role in early neoplasia is lacking.

Methods: We evaluated long-term adherence to the sulfur microbial diet, a dietary index defined a priori based on increased abundance of 43 bacterial species involved with sulfur metabolism, with risk of CRC precursors among 59,013 individuals who underwent lower endoscopy in the Nurses’ Health Study II …

Output Consistency Scale To Standardize Ostomate Output Description In Clinical Practice And Studies, Lisa Whisenhunt, Linda Xu, Fan Yang, Jacques Izard

Food for Health: Publications

Stool descriptors have become popular due to the large diffusion of the Bristol Stool Form Scale (BSFS) via clinical studies, clinical trials, and social media. The applications have been numerous and centered around standardization of terminology that can be used by health care professionals and patients alike, as well as individuals interested in their wellness and the associated partners in the wellness industry. For a portion of the population, the digestive content is rerouted to an external manufactured pouch or bag, making the use of the BSFS visual descriptors of stool difficult. From day one post-resection surgery, ostomates are challenged …

Categorization Of Orthologous Gene Clusters In 92 Ascomycota Genomes Reveals Functions Important For Phytopathogenicity, Daniel Peterson, Tang Li, Ana M. Calvo, Yanbin Yin

Food for Health: Publications

Phytopathogenic Ascomycota are responsible for substantial economic losses each year, destroying valuable crops. The present study aims to provide new insights into phytopathogenicity in Ascomycota from a comparative genomic perspective. This has been achieved by categorizing orthologous gene groups (orthogroups) from 68 phytopathogenic and 24 non-phytopathogenic Ascomycota genomes into three classes: Core, (pathogen or non-pathogen) group-specific, and genome-specific accessory orthogroups. We found that (i) ~20% orthogroups are group-specific and accessory in the 92 Ascomycota genomes, (ii) phytopathogenicity is not phylogenetically determined, (iii) group-specific orthogroups have more enriched functional terms than accessory orthogroups and this trend is particularly evident in phytopathogenic …

The Chromosome-Level Genome Of Dragon Fruit Reveals Whole-Genome Duplication And Chromosomal Co-Localization Of Betacyanin Biosynthetic Genes, Jinfang Zheng, Lyndel W. Meinhardt, Ricardo Goenaga, Dapeng Zhang, Yanbin Yin

Food for Health: Publications

Dragon fruits are tropical fruits economically important for agricultural industries. As members of the family of Cactaceae, they have evolved to adapt to the arid environment. Here we report the draft genome of Hylocereus undatus, commercially known as the white-fleshed dragon fruit. The chromosomal level genome assembly contains 11 longest scaffolds corresponding to the 11 chromosomes of H. undatus. Genome annotation of H. undatus found ~29,000 protein-coding genes, similar to Carnegiea gigantea (saguaro). Whole-genome duplication (WGD) analysis revealed a WGD event in the last common ancestor of Cactaceae followed by extensive genome rearrangements. The divergence …

Characterization Of Two Zygnema Strains (Zygnema Circumcarinatum Sag 698-1a And Sag 698-1b) And A Rapid Method To Estimate Nuclear Genome Size Of Zygnematophycean Green Algae, Xuehuan Feng, Andreas Holzinger, Charlotte Permann, Dirk Anderson, Yanbin Yin

Food for Health: Publications

Zygnematophyceae green algae (ZGA) have been shown to be the closest relatives of land plants. Three nuclear genomes (Spirogloea muscicola, Mesotaenium endlicherianum, and Penium margaritaceum) of ZGA have been recently published, and more genomes are underway. Here we analyzed two Zygnema circumcarinatum strains SAG 698-1a (mating +) and SAG 698-1b (mating −) and found distinct cell sizes and other morphological differences. The molecular identities of the two strains were further investigated by sequencing their 18S rRNA, psaA and rbcL genes. These marker genes of SAG 698-1a were surprisingly much more similar to Z. cylindricum (SAG 698-2) than to SAG 698-1b. …

Characterization Of Two Zygnema Strains (Zygnema Circumcarinatum Sag 698-1a And Sag 698-1b) And A Rapid Method To Estimate Nuclear Genome Size Of Zygnematophycean Green Algae, Xuehuan Feng, Andreas Holzinger, Charlotte Permann, Dirk Anderson, Yanbin Yin

Food for Health: Publications

Zygnematophyceae green algae (ZGA) have been shown to be the closest relatives of land plants. Three nuclear genomes (Spirogloea muscicola, Mesotaenium endlicherianum, and Penium margaritaceum) of ZGA have been recently published, and more genomes are underway. Here we analyzed two Zygnema circumcarinatum strains SAG 698-1a (mating +) and SAG 698-1b (mating −) and found distinct cell sizes and other morphological differences. The molecular identities of the two strains were further investigated by sequencing their 18S rRNA, psaA and rbcL genes. These marker genes of SAG 698-1a were surprisingly much more similar to Z. cylindricum (SAG 698-2) than to SAG 698-1b. …

Characterization Of Two Zygnema Strains (Zygnema Circumcarinatum Sag 698-1a And Sag 698-1b) And A Rapid Method To Estimate Nuclear Genome Size Of Zygnematophycean Green Algae, Xuehuan Feng, Andreas Holzinger, Charlotte Permann, Dirk Anderson, Yanbin Yin

Food for Health: Publications

Zygnematophyceae green algae (ZGA) have been shown to be the closest relatives of land plants. Three nuclear genomes (Spirogloea muscicola, Mesotaenium endlicherianum, and Penium margaritaceum) of ZGA have been recently published, and more genomes are underway. Here we analyzed two Zygnema circumcarinatum strains SAG 698-1a (mating +) and SAG 698-1b (mating −) and found distinct cell sizes and other morphological differences. The molecular identities of the two strains were further investigated by sequencing their 18S rRNA, psaA and rbcL genes. These marker genes of SAG 698-1a were surprisingly much more similar to Z. cylindricum (SAG 698-2) than to SAG 698-1b. …

The Trait Repertoire Enabling Cyanobacteria To Bloom Assessed Through Comparative Genomic Complexity And Metatranscriptomics, Huansheng Cao, Yohei Shimura, Morgan M. Steffen, Zhou Yang, Jingrang Lu, Allen Joel, Landon Jenkins, Masanobu Kawachi, Yanbin Yin, Ferran Garcia-Pichel

Food for Health: Publications

Water bloom development due to eutrophication constitutes a case of niche specialization among planktonic cyanobacteria, but the genomic repertoire allowing bloom formation in only some species has not been fully characterized. We posited that the habitat relevance of a trait begets its underlying genomic complexity, so that traits within the repertoire would be differentially more complex in species successfully thriving in that habitat than in close species that cannot. To test this for the case of bloom-forming cyanobacteria, we curated 17 potentially relevant query metabolic pathways and five core pathways selected according to existing ecophysiological literature. The available 113 genomes …

Alteration Of The Gut Microbiome In Normal And Overweight School Children From Selangor With Lactobacillus Fermented Milk Administration, Narcisse Joseph, Jonathan B. Clayton, Susan L. Hoops, Carter A. Linhardt, Amalia Mohd Hashim, Barakatun Nisak Mohd Yusof, Suresh Kumar, Syafinaz Amin Nordin

Food for Health: Publications

Childhood obesity is a serious public health problem worldwide. Perturbations in the gut microbiota composition have been associated with the development of obesity in both children and adults. Probiotics, on the other hand, are proven to restore the composition of the gut microbiome which helps reduce the development of obesity. However, data on the effect of probiotics on gut microbiota and its association with childhood obesity is limited. This study aims to determine the effect of probiotics supplement intervention on gut microbiota profiles in obese and normal-weight children. A total of 37 children, 17 normal weight, and 20 overweight school …

Stool Microbiome, Ph And Short/Branched Chain Fatty Acids In Infants Receiving Extensively Hydrolyzed Formula, Amino Acid Formula, Or Human Milk Through Two Months Of Age, Car Reen Kok, Bradford Brabec, Maciej Chichlowski, Cheryl L. Harris, Nancy Moore, Jennifer L. Wampler, Jon Vanderhoof, Devin Rose, Robert Hutkins

Food for Health: Publications

CRISPR–Cas is an anti-viral mechanism of prokaryotes that has been widely adopted for genome editing. To make CRISPR–Cas genome editing more controllable and safer to use, anti-CRISPR proteins have been recently exploited to prevent excessive/prolonged Cas nuclease cleavage. Anti-CRISPR (Acr) proteins are encoded by (pro)phages/(pro)viruses, and have the ability to inhibit their host’s CRISPR–Cas systems. We have built an online database AcrDB (http://bcb.unl.edu/AcrDB) by scanning ∼19 000 genomes of prokaryotes and viruses with AcrFinder, a recently developed AcrAca (Acr-associated regulator) operon prediction program. Proteins in Acr-Aca operons were further processed by two machine learning-based programs (AcRanker and PaCRISPR) to obtain …

Somatic Symptoms And Binge Eating In Women's Daily Lives, Kelly A. Romano, Kristin E. Heron, Kathryn E. Smith, Ross D. Crosby, Scott G. Engel, Stephen A. Wonderlich, Raina D. Pang, Tyler B. Mason

Psychology Faculty Publications

Objective

The present study aimed to determine whether the momentary severity of women's somatic symptoms was concurrently and prospectively associated with their engagement in binge eating in naturalistic settings.

Method

Thirty women (M_age = 34.13, SD = 13.92) who had engaged in binge eating at least once over the month prior to study entry completed a 14-day ecological momentary assessment (EMA) protocol. During each of the 14 days, participants received five semi-random surveys via text message that assessed momentary somatic symptom severity (i.e., headaches, stomachaches/pain, chest/heart pain, faintness/dizziness, shortness of breath, fatigue) and disordered eating behaviors. Generalized estimating equations …

An In Vitro Enrichment Strategy For Formulating Synergistic Synbiotics, Car Reen Kok, David Fabian Gomez Quintero, Clement Niyirora, Devin Rose, Amanda Li, Robert Hutkins

Food for Health: Publications

ABSTRACT Research on the role of diet on gut and systemic health has led to considerable interest toward identifying novel therapeutic modulators of the gut microbiome, including the use of prebiotics and probiotics. However, various host responses have often been reported among many clinical trials. This is in part due to competitive exclusion as a result of the absence of ecological niches as well as host mediated constraints via colonization resistance. In this research, we developed a novel in vitro enrichment (IVE) method for isolating autochthonous strains that can function as synergistic synbiotics and overcome these constraints. The method relied …

Assessment Of Physical Fitness After Bariatric Surgery And Its Association With Protein Intake And Type Of Cholecalciferol Supplementation, Hendrika J M Smelt, Sjaak Pouwels, Alper Celik, Adarsh Gupta, Johannes F Smulders

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Background: Several studies showed that there is a relationship between vitamin and mineral status and muscle strength. In particular this is the case for handgrip strength (HS) and vitamin D deficiency. In bariatric surgery there is a risk of decrease in muscle strength after surgery and also vitamin and mineral deficiencies are not uncommon. The aim of this study is to assess the effect of low vitamin 25 (OH) cholecalciferol levels, high dose cholecalciferol supplementation regime and protein intake on physical fitness, measured using handgrip strength (HS) and the shuttle walk run test (SWRT). Methods: For this retrospective …