Nutrition & Food Science Research Works

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    Experimental data for Development and evaluation of a modified most probable number (MPN) method for enumerating rifampicin-resistant Escherichia coli in agricultural, food, and environmental samples
    (2024) Gao, Zhujun; Tikekar, Rohan V.
    This is the dataset for manuscript titled Development and evaluation of a modified most probable number (MPN) method for enumerating rifampicin-resistant Escherichia coli in agricultural, food, and environmental samples that has a DOI of
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    Selenium Supranutrition: Are the Potential Benefits of Chemoprevention Outweighed by the Promotion of Diabetes and Insulin Resistance?
    (MDPI, 2013-04-19) Rocourt, Caroline R. B.; Cheng, Wen-Hsing
    Selenium was considered a toxin until 1957, when this mineral was shown to be essential in the prevention of necrotic liver damage in rats. The hypothesis of selenium chemoprevention is principally formulated by the observations that cancer incidence is inversely associated with selenium status. However, recent clinical and epidemiological studies demonstrate a role for some selenoproteins in exacerbating or promoting other disease states, specifically type 2 diabetes, although other data support a role of selenium in stimulating insulin sensitivity. Therefore, it is clear that our understanding in the role of selenium in glucose metabolism and chemoprevention is inadequate and incomplete. Research exploring the role of selenium in individual healthcare is of upmost importance and possibly will help explain how selenium is a double-edged sword in the pathologies of chronic diseases.
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    TCF4 Is a Molecular Target of Resveratrol in the Prevention of Colorectal Cancer
    (MDPI, 2015-05-07) Jeong, Jin Boo; Lee, Jihye; Lee, Seong-Ho
    The Wnt/β-catenin pathway plays an essential role in the tumorigenesis of colorectal cancer. T-cell factor-4 (TCF4) is a member of the TCF/LEF (lymphoid enhancer factor) family of transcription factors, and dysregulation of β-catenin is decisive for the initiation and progression of colorectal cancer. However, the role of TCF4 in the transcriptional regulation of its target gene remained poorly understood. Resveratrol is a dietary phytoalexin and present in many plants, including grape skin, nuts and fruits. Although resveratrol has been widely implicated in anti-tumorigenic and pro-apoptotic properties in several cancer models, the underlying cellular mechanisms are only partially understood. The current study was performed to elucidate the molecular mechanism of the anti-cancer activity of resveratrol in human colorectal cancer cells. The treatment of resveratrol and other phytochemicals decreased the expression of TCF4. Resveratrol decreases cellular accumulation of exogenously-introduced TCF4 protein, but did not change the TCF4 transcription. The inhibition of proteasomal degradation using MG132 (carbobenzoxy-Leu-Leu-leucinal) and lactacystin ameliorates resveratrol-stimulated down-regulation of TCF4. The half-life of TCF4 was decreased in the cells exposed to resveratrol. Resveratrol increased phosphorylation of TCF4 at serine/threonine residues through ERK (extracellular signal-regulated kinases) and p38-dependent pathways. The TCF4 knockdown decreased TCF/β-catenin-mediated transcriptional activity and sensitized resveratrol-induced apoptosis. The current study provides a new mechanistic link between resveratrol and TCF4 down-regulation and significant benefits for further preclinical and clinical practice.
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    Comparison of Metabolic Syndrome Indicators in Two Samples of Central and South Americans Living in the Washington, D.C. Area in 1993–1994 and 2008–2009: Secular Changes in Metabolic Syndrome in Hispanics
    (MDPI, 2017-08-05) Gill, Regina; Jackson, Robert T.; Duane, Marguerite; Miner, Allison; Khan, Saira A.
    The Central and South American populations are growing rapidly in the US; however, there is a paucity of information about their health status. Objectives: we estimated the prevalence of metabolic syndrome (MetS) and its individual components from two cohorts of Central and South Americans. Methods: This cross-sectional, medical record extraction survey sampled 1641 adults from a Washington, D.C clinic. A questionnaire was used to collect socio-demographic, medical history, anthropometric, biochemical, and clinical data. Results: among the 1993–1994 cohort, the MetS prevalence was 19.7%. The most prevalent MetS components were low high-density lipoprotein (HDL) cholesterol (40.4% men and 51.3% women), elevated triglycerides (40.9% men and 33.1% women), and high body mass index (BMI) ≥ 25 kg/m2 (27.6% men and 36.6% women). The overall prevalence of MetS in the 2008–2009 cohort was 28%. The most common abnormal metabolic indicator was an elevated BMI ≥ 25 kg/m2 (75.6%). 43.2% of men and 50.7% of women had HDL levels below normal, while the prevalence of hypertriglyceridemia was 46.5% and 32.5% for men and women, respectively. Conclusion: the prevalence of MetS was significantly greater in 2008–2009 compared with 1993–1994 (p ≤ 0.05). Dyslipidemia and high BMI have increased. Although similar components were identified in both the 1993–1994 and 2008–2009 study populations, the risks of MetS have increased over time.
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    Recent Developments in Food Packaging Based on Nanomaterials
    (MDPI, 2018-10-13) Huang, Yukun; Mei, Lei; Chen, Xianggui; Wang, Qin
    The increasing demand for high food quality and safety, and concerns of environment sustainable development have been encouraging researchers in the food industry to exploit the robust and green biodegradable nanocomposites, which provide new opportunities and challenges for the development of nanomaterials in the food industry. This review paper aims at summarizing the recent three years of research findings on the new development of nanomaterials for food packaging. Two categories of nanomaterials (i.e., inorganic and organic) are included. The synthetic methods, physical and chemical properties, biological activity, and applications in food systems and safety assessments of each nanomaterial are presented. This review also highlights the possible mechanisms of antimicrobial activity against bacteria of certain active nanomaterials and their health concerns. It concludes with an outlook of the nanomaterials functionalized in food packaging.
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    Antimicrobial Nanoparticles Incorporated in Edible Coatings and Films for the Preservation of Fruits and Vegetables
    (MDPI, 2019-04-30) Xing, Yage; Li, Wenxiu; Wang, Qin; Li, Xuanlin; Xu, Qinglian; Guo, Xunlian; Liu, Xiaocui; Shui, Yuru; Lin, Hongbin; Yang, Hua; Bi, Xiufang
    Edible coatings and films (ECF) are employed as matrixes for incorporating antimicrobial nanoparticles (NPs), and then they are applied on the fruits and vegetables to prolong shelf life and enhance storage quality. This paper provides a comprehensive review on the preparation, antimicrobial properties and mechanisms, surface and physical qualities of ECF containing antimicrobial NPs, and its efficient application to vegetables and fruits as well. Following an introduction on the properties of the main edible coating materials, the preparation technologies of ECF with NPs are summarized. The antimicrobial activity of ECF with NPs against the tested microorganism was observed by many researchers. This might be mainly due to the electrostatic interaction between the cationic polymer or free metal ions and the charged cell membrane, the photocatalytic reaction of NPs, the detachment of free metal ion, and partly due to the antimicrobial activity of edible materials. Moreover, their physical, mechanical and releasing properties are discussed in detail, which might be influenced by the concentration of NPs. The preservation potential on the quality of fruits and vegetables indicates that various ECF with NPs might be used as the ideal materials for food application. Following the introduction on these characteristics, an attempt is made to predict future trends in this field.
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    Food-Grade Nanoemulsions: Preparation, Stability and Application in Encapsulation of Bioactive Compounds
    (MDPI, 2019-11-21) Kiu, Qingqing; Huang, He; Chen, Honghong; Lin, Junfan; Wang, Qin
    Nanoemulsions have attracted significant attention in food fields and can increase the functionality of the bioactive compounds contained within them. In this paper, the preparation methods, including low-energy and high-energy methods, were first reviewed. Second, the physical and chemical destabilization mechanisms of nanoemulsions, such as gravitational separation (creaming or sedimentation), flocculation, coalescence, Ostwald ripening, lipid oxidation and so on, were reviewed. Then, the impact of different stabilizers, including emulsifiers, weighting agents, texture modifiers (thickening agents and gelling agents), ripening inhibitors, antioxidants and chelating agents, on the physicochemical stability of nanoemulsions were discussed. Finally, the applications of nanoemulsions for the delivery of functional ingredients, including bioactive lipids, essential oil, flavor compounds, vitamins, phenolic compounds and carotenoids, were summarized. This review can provide some reference for the selection of preparation methods and stabilizers that will improve performance in nanoemulsion-based products and expand their usage.
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    Urtica dioica Whole Vegetable as a Functional Food Targeting Fat Accumulation and Insulin Resistance-a Preliminary Study in a Mouse Pre-Diabetic Model
    (MDPI, 2020-04-10) Fan, Si; Raychaudhuri, Samnhita; Kraus, Olivia; Shahinozzaman, Md; Lofti, Leila; Obanda, Diana N.
    The shoot of Urtica dioica is used in several cultures as a vegetable or herb. However, not much has been studied about the potential of this plant when consumed as a whole food/vegetable rather than an extract for dietary supplements. In a 12-week dietary intervention study, we tested the effect of U. dioica vegetable on high fat diet induced obesity and insulin resistance in C57BL/6J mice. Mice were fed ad libitum with isocaloric diets containing 10% fat or 45% fat with or without U. dioica. The diet supplemented with U. dioica attenuated high fat diet induced weight gain (p < 0.005; n = 9), fat accumulation in adipose tissue (p < 0.005; n = 9), and whole-body insulin resistance (HOMA-IR index) (p < 0.001; n = 9). Analysis of gene expression in skeletal muscle showed no effect on the constituents of the insulin signaling pathway (AKT, IRS proteins, PI3K, GLUT4, and insulin receptor). Notable genes that impact lipid or glucose metabolism and whose expression was changed by U. dioica include fasting induced adipocyte factor (FIAF) in adipose and skeletal muscle, peroxisome proliferator-activated receptor-α (Ppar-α) and forkhead box protein (FOXO1) in muscle and liver, and Carnitine palmitoyltransferase I (Cpt1) in liver (p < 0.01). We conclude that U. dioica vegetable protects against diet induced obesity through mechanisms involving lipid accumulation and glucose metabolism in skeletal muscle, liver, and adipose tissue.
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    Benchmarking Long-Read Assemblers for Genomic Analyses of Bacterial Pathogens Using Oxford Nanopore Sequencing
    (MDPI, 2020-12-01) Chen, Zhao; Erickson, David L.; Meng, Jianghong
    Oxford Nanopore sequencing can be used to achieve complete bacterial genomes. However, the error rates of Oxford Nanopore long reads are greater compared to Illumina short reads. Long-read assemblers using a variety of assembly algorithms have been developed to overcome this deficiency, which have not been benchmarked for genomic analyses of bacterial pathogens using Oxford Nanopore long reads. In this study, long-read assemblers, namely Canu, Flye, Miniasm/Racon, Raven, Redbean, and Shasta, were thus benchmarked using Oxford Nanopore long reads of bacterial pathogens. Ten species were tested for mediocre- and low-quality simulated reads, and 10 species were tested for real reads. Raven was the most robust assembler, obtaining complete and accurate genomes. All Miniasm/Racon and Raven assemblies of mediocre-quality reads provided accurate antimicrobial resistance (AMR) profiles, while the Raven assembly of Klebsiella variicola with low-quality reads was the only assembly with an accurate AMR profile among all assemblers and species. All assemblers functioned well for predicting virulence genes using mediocre-quality and real reads, whereas only the Raven assemblies of low-quality reads had accurate numbers of virulence genes. Regarding multilocus sequence typing (MLST), Miniasm/Racon was the most effective assembler for mediocre-quality reads, while only the Raven assemblies of Escherichia coli O157:H7 and K. variicola with low-quality reads showed positive MLST results. Miniasm/Racon and Raven were the best performers for MLST using real reads. The Miniasm/Racon and Raven assemblies showed accurate phylogenetic inference. For the pan-genome analyses, Raven was the strongest assembler for simulated reads, whereas Miniasm/Racon and Raven performed the best for real reads. Overall, the most robust and accurate assembler was Raven, closely followed by Miniasm/Racon.
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    Kale Attenuates Inflammation and Modulates Gut Microbial Composition and Function in C57BL/6J Mice with Diet-Induced Obesity
    (MDPI, 2021-01-24) Shahinozzaman, Md; Raychaudhuri, Samnhita; Fan, Si; Obanda, Diana N.
    Kale (Brassica oleracea var. acephala) is a vegetable common in most cultures but is less studied as a functional food compared to other cruciferous vegetables, such as broccoli. We investigated the effect of supplementing a high-fat diet (HFD) with kale (HFKV) in C57BL/6J mice. We particularly explored its role in metabolic parameters, gut bacterial composition and diversity using 16S rRNA sequencing, systematically compared changes under each phylum and predicted the functional potential of the altered bacterial community using PICRUSt2. Like other cruciferous vegetables, kale attenuated HFD-induced inflammation. In addition, kale modulated HFD-induced changes in cecal microbiota composition. The HFD lowered bacterial diversity, increased the Firmicutes: Bacteroidetes (F/B) ratio and altered composition. Specifically, it lowered Actinobacteria and Bacteroidetes (Bacteroidia, Rikenellaceae and Prevotellaceae) but increased Firmicutes (mainly class Bacilli). Kale supplementation lowered the F/B ratio, increased both alpha and beta diversity and reduced class Bacilli and Erysipelotrichi but had no effect on Clostridia. Within Actinobacteria, HFKV particularly increased Coriobacteriales/Coriobacteriaceae about four-fold compared to the HFD (p < 0.05). Among Bacteroidia, HFKV increased the species Bacteroides thetaiotaomicron by over two-fold (p = 0.05) compared to the HFD. This species produces plant polysaccharide digesting enzymes. Compared to the HFD, kale supplementation enhanced several bacterial metabolic functions, including glycan degradation, thiamine metabolism and xenobiotic metabolism. Our findings provide evidence that kale is a functional food that modulates the microbiota and changes in inflammation phenotype.
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    Curcumin-Loaded Pickering Emulsion Formed by Ultrasound and Stabilized by Metal Organic Framework Optimization
    (MDPI, 2021-03-03) Ma, Peihua; Zhang, Zhi; Tsai, Shawn; Zhang, Hongchao; Li, Yuan; Yuan, Fang; Wang, Qin
    The ultrasound-assisted preparation of a curcumin-loaded metal organic framework (MOF) UiO-66-NH2 stabilized Pickering emulsion system was carried out in this study. A 3-level-4-factor Box–Behnken design (BBD) and response surface methodology (RSM) analysis were employed to systematically evaluate the effect of different experimental parameters (i.e., ultrasonic power, ultrasonic time, oil content, and MOF content) on curcumin loading capacity (LC) and encapsulation efficiency (EE). The results indicated that ultrasonic power and MOF content significantly affected LC and EE, whereas ultrasonic time and oil content had little effect. A mathematical model for optimizing the preparation of emulsion systems was established. Based on the ridge max analysis, an optimal condition for the newly developed curcumin-loaded MOF-Pickering emulsion was identified, i.e., ultrasonic power 150 W, ultrasonic time 11.17 min, oil content 20.0%, and MOF content 1.10%. At this condition, the LC and EE of curcumin obtained from the experiment reached 7.33% ± 0.54% and 56.18% ± 3.03%, respectively, which were within the prediction range of LC (7.35% ± 0.29%) and EE (54.34% ± 2.45%). The emulsion systems created in this study may find new applications for the delivery of bioactive compounds in food and pharmaceutical areas.
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    Polyphenol Containing Sorghum Brans Exhibit an Anti-Cancer Effect in Apc Min/+ Mice Treated with Dextran Sodium Sulfate
    (MDPI, 2021-08-01) Lee, Seong-Ho; Lee, Hee-Seop; Lee, Jihye; Amarakoon, Darshika; Lou, Zhiyuan; Noronha, Leela E.; Herald, Thomas J.; Perumal, Ramasamy; Smolensky, Dmitriy
    Colon cancer (CC) is considered a high-risk cancer in developed countries. Its etiology is correlated with a high consumption of red meat and low consumption of plant-based foods, including whole grains. Sorghum bran is rich in polyphenols. This study aimed to determine whether different high-phenolic sorghum brans suppress tumor formation in a genetic CC rodent model and elucidate mechanisms. Tissue culture experiments used colorectal cancer cell lines SW480, HCT-116 and Caco-2 and measured protein expression, and protein activity. The animal model used in this study was APC Min+/mouse model combined with dextram sodium sulfate. High phenolic sorghum bran extract treatment resulted in the inhibition of proliferation and induced apoptosis in CC cell lines. Treatment with high phenolic sorghum bran extracts repressed TNF-α-stimulated NF-κB transactivation and IGF-1-stimulated PI3K/AKT pathway via the downregulation of β-catenin transactivation. Furthermore, high-phenolic sorghum bran extracts activated AMPK and autophagy. Feeding with high-phenolic sorghum bran for 6 weeks significantly suppressed tumor formation in an APC Min/+ dextran sodium sulfate promoted CC mouse model. Our data demonstrates the potential application of high-phenolic sorghum bran as a functional food for the prevention of CC.
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    Persistence of Salmonella enterica and Enterococcus faecium NRRL B-2354 on Baby Spinach Subjected to Temperature Abuse after Exposure to Sub-Lethal Stresses
    (MDPI, 2021-09-10) Chen, Zhao; Meng, Jianghong
    The exposure of foodborne pathogens such as Salmonella enterica to a sub-lethal stress may protect bacterial cells against distinct stresses during the production of leafy greens, which can constitute potential health hazards to consumers. In this study, we evaluated how the prior exposure of S. enterica to sub-lethal food processing-related stresses influenced its subsequent persistence on baby spinach under cold (4 °C for 7 days) and temperature abuse (37 °C for 2 h + 4 °C for 7 days) conditions. We also compared the survival characteristics of pre-stressed S. enterica and Enterococcus faecium NRRL B-2354 as its surrogate on baby spinach. A cocktail of three S. enterica serovars, as well as S. Typhimurium ATCC 14028 wild type and its ΔrpoS mutant, and E. faecium NRRL B-2354, was first exposed to sub-lethal desiccation, oxidation, heat shock, and acid stresses. Afterward, baby spinach was inoculated with unstressed or pre-stressed cells at 7.0 log CFU/sample unit, followed by 7-day storage under cold and temperature abuse conditions. The unstressed S. enterica (fresh cells in sterile 0.85% saline) decreased rapidly within the first day and thereafter persisted around 5.5 log CFU/sample unit under both conditions. The desiccation-stressed S. enterica showed the highest bacterial counts (p < 0.05) compared to other conditions. The unstressed S. enterica survived better (p < 0.05) than the oxidation- and acid-stressed S. enterica, while there were no significant differences (p > 0.05) between the unstressed and heat-shocked S. enterica. Unlike the wild type, temperature abuse did not lead to the enhanced survival of the ΔrpoS mutant after exposure to desiccation stress, indicating that the rpoS gene could play a critical role in the persistence of desiccation-stressed S. enterica subjected to temperature abuse. E. faecium NRRL B-2354 was more persistent (p < 0.05) than the pre-stressed S. enterica under both conditions, suggesting its use as a suitable surrogate for pre-stressed S. enterica by providing a sufficient safety margin. Our results demonstrate the merit of considering the prior exposure of foodborne pathogens to sub-lethal stresses when validating the storage conditions for leafy greens.
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    Regulation Mechanism of ssDNA Aptamer in Nanozymes and Application of Nanozyme-Based Aptasensors in Food Safety
    (MDPI, 2022-02-14) Wang, Lijun; Zhou, Hong; Hu, Haixia; Wang, Qin; Chen, Xianggui
    Food safety issues are a worldwide concern. Pathogens, toxins, pesticides, veterinary drugs, heavy metals, and illegal additives are frequently reported to contaminate food and pose a serious threat to human health. Conventional detection methods have difficulties fulfilling the requirements for food development in a modern society. Therefore, novel rapid detection methods are urgently needed for on-site and rapid screening of massive food samples. Due to the extraordinary properties of nanozymes and aptamers, biosensors composed of both of them provide considerable advantages in analytical performances, including sensitivity, specificity, repeatability, and accuracy. They are considered a promising complementary detection method on top of conventional ones for the rapid and accurate detection of food contaminants. In recent years, we have witnessed a flourishing of analytical strategies based on aptamers and nanozymes for the detection of food contaminants, especially novel detection models based on the regulation by single-stranded DNA (ssDNA) of nanozyme activity. However, the applications of nanozyme-based aptasensors in food safety are seldom reviewed. Thus, this paper aims to provide a comprehensive review on nanozyme-based aptasensors in food safety, which are arranged according to the different interaction modes of ssDNA and nanozymes: aptasensors based on nanozyme activity either inhibited or enhanced by ssDNA, nanozymes as signal tags, and other methods. Before introducing the nanozyme-based aptasensors, the regulation by ssDNA of nanozyme activity via diverse factors is discussed systematically for precisely tailoring nanozyme activity in biosensors. Furthermore, current challenges are emphasized, and future perspectives are discussed.
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    Anti-Adipogenic Activity of High-Phenolic Sorghum Brans in Pre-Adipocytes
    (MDPI, 2022-04-02) Lee, Hee-Seop; Santana, Ádina L.; Peterson, Jaymi; Yucel, Umut; Perumal, Ramasamy; De Leon, Joaquin; Lee, Seong-Ho; Smolensky, Dmitriy
    Obesity is one of the leading public health problems that can result in life-threatening metabolic and chronic diseases such as cardiovascular diseases, diabetes, and cancer. Sorghum (Sorghum bicolor (L.) Moench) is the fifth most important cereal crop in the world and certain genotypes of sorghum have high polyphenol content. PI570481, SC84, and commercially available sumac sorghum are high-polyphenol genotypes that have demonstrated strong anti-cancer activities in previous studies. The objective of this study was to explore a potential anti-obesity use of extracts from sorghum bran in the differentiation of 3T3-L1 preadipocytes and to investigate cellular and molecular responses in differentiated adipocytes to elucidate related mechanisms. None of the four different sorghum bran extracts (PI570481, SC84, Sumac, and white sorghum as a low-polyphenol control) caused cytotoxicity in undifferentiated and differentiated 3T3-L1 cells at doses used in this study. Sorghum bran extracts (PI570481, SC84, and Sumac) reduced intracellular lipid accumulation and expression of adipogenic and lipogenic proteins in a dose-dependent manner in differentiated 3T3-L1 cells. The same polyphenol containing sorghum bran extracts also repressed production of reactive oxygen species (ROS) and MAPK signaling pathways and repressed insulin signaling and glucose uptake in differentiated 3T3-L1 cells. These data propose a potential use of high-phenolic sorghum bran for the prevention of obesity.
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    A Machine Learning Model for Food Source Attribution of Listeria monocytogenes
    (MDPI, 2022-06-16) Tanui, Collins K.; Benefo, Edmund O.; Karanth, Shraddha; Pradhan, Abani K.
    Despite its low morbidity, listeriosis has a high mortality rate due to the severity of its clinical manifestations. The source of human listeriosis is often unclear. In this study, we investigate the ability of machine learning to predict the food source from which clinical Listeria monocytogenes isolates originated. Four machine learning classification algorithms were trained on core genome multilocus sequence typing data of 1212 L. monocytogenes isolates from various food sources. The average accuracies of random forest, support vector machine radial kernel, stochastic gradient boosting, and logit boost were found to be 0.72, 0.61, 0.7, and 0.73, respectively. Logit boost showed the best performance and was used in model testing on 154 L. monocytogenes clinical isolates. The model attributed 17.5 % of human clinical cases to dairy, 32.5% to fruits, 14.3% to leafy greens, 9.7% to meat, 4.6% to poultry, and 18.8% to vegetables. The final model also provided us with genetic features that were predictive of specific sources. Thus, this combination of genomic data and machine learning-based models can greatly enhance our ability to track L. monocytogenes from different food sources.
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    Relationship between Live-In Grandparents and Grandchild’s Health and Well-Being in Palestinian Refugees in Lebanon
    (MDPI, 2022-12-26) Sheikomar, Olfat B.; Ghattas, Hala; Sahyoun, Nadine R.
    Grandparents (GP) play influential roles in grandchildren’s health, behavior, and life. However, this relationship has not been examined in the Arab region. This study assesses whether the presence of GP in the household is associated with grandchildren’s health and wellbeing. Health status was determined by a child experiencing chronic health conditions or an acute illness, and wellbeing was determined based on school attendance and child labor. Data were collected through surveys conducted in 2010 and 2015 of representative samples of Palestinian refugees living in Lebanon. Multivariate logistic regression showed that, even after controlling for potential confounders, including the presence of parents in the household and household food insecurity (FI), the presence of live-in GP was associated with lower odds of children experiencing acute illnesses (OR 0.74 95% CI 0.62–0.92) and higher odds of attending school (OR 2.22 95% CI 1.28–5.33), but not child labor. The presence of GP in the household may be protective to grandchildren’s health status and school attendance in this population.
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    Critical Assessment of Short-Read Assemblers for the Metagenomic Identification of Foodborne and Waterborne Pathogens Using Simulated Bacterial Communities
    (MDPI, 2022-12-06) Chen, Zhao; Meng, Jianghong
    Metagenomics offers the highest level of strain discrimination of bacterial pathogens from complex food and water microbiota. With the rapid evolvement of assembly algorithms, defining an optimal assembler based on the performance in the metagenomic identification of foodborne and waterborne pathogens is warranted. We aimed to benchmark short-read assemblers for the metagenomic identification of foodborne and waterborne pathogens using simulated bacterial communities. Bacterial communities on fresh spinach and in surface water were simulated by generating paired-end short reads of Illumina HiSeq, MiSeq, and NovaSeq at different sequencing depths. Multidrug-resistant Salmonella Indiana SI43 and Pseudomonas aeruginosa PAO1 were included in the simulated communities on fresh spinach and in surface water, respectively. ABySS, IDBA-UD, MaSuRCA, MEGAHIT, metaSPAdes, and Ray Meta were benchmarked in terms of assembly quality, identifications of plasmids, virulence genes, Salmonella pathogenicity island, antimicrobial resistance genes, chromosomal point mutations, serotyping, multilocus sequence typing, and whole-genome phylogeny. Overall, MEGHIT, metaSPAdes, and Ray Meta were more effective for metagenomic identification. We did not obtain an optimal assembler when using the extracted reads classified as Salmonella or P. aeruginosa for downstream genomic analyses, but the extracted reads showed consistent phylogenetic topology with the reference genome when they were aligned with Salmonella or P. aeruginosa strains. In most cases, HiSeq, MiSeq, and NovaSeq were comparable at the same sequencing depth, while higher sequencing depths generally led to more accurate results. As assembly algorithms advance and mature, the evaluation of assemblers should be a continuous process.
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    Genome-Wide Analysis on Transcriptome and Methylome in Prevention of Mammary Tumor Induced by Early Life Combined Botanicals
    (MDPI, 2022-12-21) Arora, Itika; Li, Shizhao; Crowley, Michael R.; Li, Yuanyuan; Tollefsbol, Trygve O.
    Breast cancer (BC) is the most common malignancy and the second leading cause of cancer death among women in the United States. The consumption of natural dietary components such as broccoli sprouts (BSp) and green tea polyphenols (GTPs) has demonstrated exciting potential in reducing the risk of BC through the regulation of epigenetic mechanisms. However, little is known about their impacts on reversing epigenomic aberrations that are centrally involved in the initiation and progression of BC. Previously, we have determined the efficacy of combined BSp and GTPs treatment on the inhibition of the growth of a mammary tumor in a transgenic Her2/neu mouse model. We sought to extend our previous study to identify universal biomarkers that represent common mechanistic changes among different mouse models in response to this dietary regime by including a new transgenic mouse model, C3(1)-SV40 TAg (SV40). As a result, we identified novel target genes that were differentially expressed and methylated in response to dietary botanicals when administered singly (BSp and GTPs) and in combination (BSp + GTPs) in both mouse models. We discovered more differentially expressed and methylated genes in the combination treatment group compared to the singly administered groups. Subsequently, several biological pathways related to epigenetic regulations were identified in response to the combination treatment. Furthermore, when compared to the BSp and GTPs treatment alone, the combinatorial treatment showed a more significant impact on the regulation of the epigenetic modifier activities involved in DNA methylation and histone modifications. Our study provides key insights about the impact of the combined administration of BSp and GTPs on BC using a multi-omics analysis, suggesting a combinatorial approach is more efficacious in preventing and inhibiting BC by impacting key tumor-related genes at transcriptomic and methylomic levels. Our findings could be further extrapolated as a comprehensive source for understanding the epigenetic modifications that are associated with the effects of these dietary botanicals on BC prevention.
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    Dietary Impacts on Gestational Diabetes: Connection between Gut Microbiome and Epigenetic Mechanisms
    (MDPI, 2022-12-10) Bankole, Taiwo; Winn, Hung; Li, Yuanyuan
    Gestational diabetes mellitus (GDM) is one of the most common obstetric complications due to an increased level of glucose intolerance during pregnancy. The prevalence of GDM increases due to the obesity epidemic. GDM is also associated with an increased risk of gestational hypertension and preeclampsia resulting in elevated maternal and perinatal morbidity and mortality. Diet is one of the most important environmental factors associated with etiology of GDM. Studies have shown that the consumption of certain bioactive diets and nutrients before and during pregnancy might have preventive effects against GDM leading to a healthy pregnancy outcome as well as beneficial metabolic outcomes later in the offspring’s life. Gut microbiome as a biological ecosystem bridges the gap between human health and diseases through diets. Maternal diets affect maternal and fetal gut microbiome and metabolomics profiles, which consequently regulate the host epigenome, thus contributing to later-life metabolic health in both mother and offspring. This review discusses the current knowledge regarding how epigenetic mechanisms mediate the interaction between maternal bioactive diets, the gut microbiome and the metabolome leading to improved metabolic health in both mother and offspring.