Article
Biotechnology & Applied Microbiology
P. A. S. Fonseca, A. Suarez-Vega, C. Esteban-Blanco, R. Pelayo, H. Marina, B. Gutierrez-Gil, J. J. Arranz
Summary: Based on the results, the current study suggests potential candidate genes for the regulation of milk production traits in the sheep mammary gland. Further studies focusing on elucidating the genetic mechanisms affected by the identified differentially methylated regions (DMRs) may help to better understand the biological mechanisms modified in the mammary gland of dairy sheep as a response to nutritional challenges and their potential effects on milk production.
Review
Genetics & Heredity
John P. Brabson, Tiffany Leesang, Sofia Mohammad, Luisa Cimmino
Summary: DNA methylation is regulated by TET enzymes through oxidation, while vitamin C acts as a cofactor to promote DNA demethylation. This interaction plays a crucial role in maintaining genomic stability.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Nicolas Altemose, Glennis A. Logsdon, Andrey Bzikadze, Pragya Sidhwani, Sasha A. Langley, Gina Caldas, Savannah J. Hoyt, Lev Uralsky, Fedor D. Ryabov, Colin J. Shew, Michael E. G. Sauria, Matthew Borchers, Ariel Gershman, Alla Mikheenko, Valery A. Shepelev, Tatiana Dvorkina, Olga Kunyavskaya, Mitchell R. Vollger, Arang Rhie, Ann M. McCartney, Mobin Asri, Ryan Lorig-Roach, Kishwar Shafin, Julian K. Lucas, Sergey Aganezov, Daniel Olson, Leonardo Gomes de Lima, Tamara Potapova, Gabrielle A. Hartley, Marina Haukness, Peter Kerpedjiev, Fedor Gusev, Kristof Tigyi, Shelise Brooks, Alice Young, Sergey Nurk, Sergey Koren, Sofie R. Salama, Benedict Paten, Evgeny Rogaev, Aaron Streets, Gary H. Karpen, Abby F. Dernburg, Beth A. Sullivan, Aaron F. Straight, Travis J. Wheeler, Jennifer L. Gerton, Evan E. Eichler, Adam M. Phillippy, Winston Timp, Megan Y. Dennis, Rachel J. O'Neill, Justin M. Zook, Michael C. Schatz, Pavel A. Pevzner, Mark Diekhans, Charles H. Langley, Ivan A. Alexandrov, Karen H. Miga
Summary: Current human genome assemblies have neglected repetitive sequences near centromeres, hindering our understanding of their organization and evolution. A new approach has allowed researchers to comprehensively study these sequences, revealing their structural rearrangements and variations.
Review
Biochemistry & Molecular Biology
Finn E. von Eyben, Karsten Kristiansen, Daniel S. Kapp, Rong Hu, Ovidiu Preda, Francisco F. Nogales
Summary: This review summarizes the literature on the gene expression and epigenetic regulation of germ cell tumors of the testis type II (TGCT). The seminoma subtype of TGCT expresses a panel of induced pluripotent stem cell (iPSC) with four upregulated genes, while the embryonal carcinoma (EC) subtype has a different set of four upregulated genes. The epigenetic mechanisms, such as DNA methylation and histone modifications, regulate the expression of these driver genes and contribute to the clinical characteristics of TGCT.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Veterinary Sciences
Huaibing Yao, Xiaorui Liang, Zhihua Dou, Zhongkai Zhao, Wanpeng Ma, Zelin Hao, Hui Yan, Yuzhuo Wang, Zhuangyuan Wu, Gangliang Chen, Jie Yang
Summary: This study aimed to compare the morphological changes in mammary gland tissue and transcriptome expression profiles between young and adult female Bactrian camels, and explore the potential candidate genes and signaling pathways related to mammary gland development.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Oncology
Marina V. Nemtsova, Alexey I. Kalinkin, Ekaterina B. Kuznetsova, Irina V. Bure, Ekaterina A. Alekseeva, Igor I. Bykov, Tatiana V. Khorobrykh, Dmitry S. Mikhaylenko, Alexander S. Tanas, Vladimir V. Strelnikov
Summary: Epigenetic mechanisms play a crucial role in gene expression patterns, and their deregulations can affect oncogenesis and metastasis in gastric cancer. Mutations in epigenetic regulation genes, particularly in KMT2D, KMT2C, ARID1A, and CHD7, were found to be associated with reduced overall survival of patients, especially in those with metastases and signet ring cell tumors. This suggests that mutations in epigenetic regulation genes may serve as valuable clinical markers for prognosis in gastric cancer patients.
Article
Biotechnology & Applied Microbiology
Alessandro Giuliani, Thuy Tien Bui, Mohamed Helmy, Kumar Selvarajoo
Summary: The study investigates the transcriptome-wide scatter of 23 cell types and conditions across different levels of biological complexity, focusing on genes that act as toggle switches between pairwise replicates of the same cell type. It is found that the proportion of toggle genes dramatically increases from unicellular to multicellular organization, with a significant portion being non-coding genes such as tRNA, rRNA, lncRNA, sncRNA, and pseudogenes. The presence of disease associated microRNAs, pseudogenes, and uncharacterized transcripts in both development and cancer cells suggests toggle genes as a novel component creating transcriptome-wide variability.
Review
Cell Biology
Elly I. Lewerissa, Nael Nadif Kasri, Katrin Linda
Summary: Autophagy is a crucial metabolic process for maintaining cellular homeostasis and survival. Recent studies have shown the importance of autophagy in brain function, particularly in neuronal development and functioning. Mutations in autophagy-related genes as well as genes involved in epigenetic regulation have been linked to neurodevelopmental disorders (NDDs). This suggests that aberrant autophagic regulation may contribute to nervous system impairments in NDDs with disturbed epigenetic regulation.
Article
Microbiology
Patrizia D'Aquila, Francesco De Rango, Ersilia Paparazzo, Giuseppe Passarino, Dina Bellizzi
Summary: Adaptive antibiotic resistance is a transient metabolic adaptation of bacteria in response to low concentrations of antibiotics. Epigenetic modifications triggered by low concentrations of various antibiotics may modulate the sensitivity of bacteria to antibiotics. Understanding the molecular mechanisms behind adaptive resistance can suggest strategies to avoid it.
MICROBIOLOGY SPECTRUM
(2023)
Review
Cell Biology
Shawn Ying Xuan Tan, Jieqiong Zhang, Wee-Wei Tee
Summary: This review discusses the interplay between epigenetics and inflammation. External and internal microenvironments contribute to epigenetic processes, and dysregulation of these processes can lead to cancer. Chronic inflammation plays a crucial role in the tumor microenvironment, and inflammatory signaling can modulate changes in the global epigenetic landscape.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Reproductive Biology
Chuan Chen, Yawei Gao, Wenqiang Liu, Shaorong Gao
Summary: This article introduces the importance of epigenetic regulation in embryo development and somatic cell reprogramming. Using low-input sequencing techniques, researchers have revealed the epigenetic landscape during rapid transcriptome transitions and highlighted the essential roles of specific epigenetic regulators in transcription activity and chromatin remodeling.
BIOLOGY OF REPRODUCTION
(2022)
Article
Plant Sciences
Yan Shi, Yuan Qin, Fenglan Li, Haifeng Wang
Summary: The role of DNA methylation in regulating potato response to Fusarium toxin deoxynivalenol (DON) stress and potato disease resistance was investigated in this study. The results showed that different concentrations of DON treatment caused significant changes in global DNA methylation levels in potato tubers. Differentially methylated regions (DMRs)-associated differentially expressed genes (DEGs) were enriched in resistance-related metabolic pathways. In addition, DON stress potentially induced resistance in potato tubers, possibly related to epigenetic memory created after DNA methylation changes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Linshan Liu, Bin Xiao, Alison Hirukawa, Harvey W. Smith, Dongmei Zuo, Virginie Sanguin-Gendreau, Luke McCaffrey, Alice Jisoo Nam, William J. Muller
Summary: The regulation of gene expression through histone posttranslational modifications is crucial in breast cancer progression. Ezh2 integrates mTORC1 and Wnt signaling pathways in the early stages of mammary tumor progression, suggesting that targeting Ezh2 could be a potential treatment for early-stage luminal B breast cancer.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Ilona E. Grabowicz, Bartek Wilczynski, Bozena Kaminska, Adria-Jaume Roura, Bartosz Wojtas, Michal J. Dabrowski
Summary: Genome-wide studies have revealed specific genetic alterations, transcriptomic patterns, and epigenetic profiles associated with different types of glioma. The organization of chromatin and epigenetic landscape of enhancers have been shown to impact gene expression in low grade versus high grade gliomas. The identification of transcription factors and genes regulated by long-range contacts with enhancers provides important insights into the epigenetic differences associated with differential gene expression in gliomas of different malignancy.
SCIENTIFIC REPORTS
(2021)
Article
Agriculture, Dairy & Animal Science
Wenjing Wang, Xupeng Zang, Yonglun Liu, Yunyi Liang, Gengyuan Cai, Zhenfang Wu, Zicong Li
Summary: This study investigated the miRNA expression profiles in the mammary glands of mice at different developmental stages and identified a novel miRNA involved in regulating the expression of a milk protein gene. These findings are important for increasing milk production and improving milk quality.
Article
Microbiology
Samuel T. Westreich, Amir Ardeshir, Zeynep Alkan, Mary E. Kable, Ian Korf, Danielle G. Lemay
Article
Multidisciplinary Sciences
Jinxin Liu, Diana H. Taft, Maria X. Maldonado-Gomez, Daisy Johnson, Michelle L. Treiber, Danielle G. LemayQ, Edward J. DePeters, David A. Mills
NATURE COMMUNICATIONS
(2019)
Article
Nutrition & Dietetics
Elizabeth L. Chin, Liping Huang, Yasmine Y. Bouzid, Catherine P. Kirschke, Blythe Durbin-Johnson, Lacey M. Baldiviez, Ellen L. Bonnel, Nancy L. Keim, Ian Korf, Charles B. Stephensen, Danielle G. Lemay
Article
Biochemical Research Methods
Michelle L. Treiber, Diana H. Taft, Ian Korf, David A. Mills, Danielle G. Lemay
BMC BIOINFORMATICS
(2020)
Article
Biochemistry & Molecular Biology
Samuel T. Westreich, Jaime Salcedo, Blythe Durbin-Johnson, Jennifer T. Smilowitz, Ian Korf, David A. Mills, Daniela Barile, Danielle G. Lemay
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2020)
Article
Nutrition & Dietetics
Danielle G. Lemay, Lacey M. Baldiviez, Elizabeth L. Chin, Sarah S. Spearman, Eduardo Cervantes, Leslie R. Woodhouse, Nancy L. Keim, Charles B. Stephensen, Kevin D. Laugero
Summary: The study found that stool consistency in healthy adults is influenced by dietary intake and stress levels, with higher intake of saturated fat associated with hard stools, and higher stress levels associated with soft stools. Physical activity did not show a significant impact on stool consistency.
JOURNAL OF NUTRITION
(2021)
Article
Nutrition & Dietetics
Elizabeth L. Chin, Marta Van Loan, Sarah S. Spearman, Ellen L. Bonnel, Kevin D. Laugero, Charles B. Stephensen, Danielle G. Lemay
Summary: This study found that nonmodifiable factors, such as age, sex, and ethnicity, have a greater impact on bone health in healthy US men and women compared to directly modifiable factors like diet. Additionally, low stool pH was predictive of higher bone mineral content and density.
JOURNAL OF NUTRITION
(2021)
Article
Nutrition & Dietetics
Mary E. Kable, Elizabeth L. Chin, David Storms, Danielle G. Lemay, Charles B. Stephensen
Summary: This study investigated the relationship between diet patterns and gut microbial community composition in a diverse, healthy US adult cohort. Results showed significant correlations between diet dry weight, carbohydrates, fiber, and gut microbial diversity. Bifidobacterium and Lachnospira were found to be enriched in diets with specific nutrient profiles. The use of a tree structure annotated with grams of carbohydrates provided a robust method for comparing self-reported diet to gut microbial community composition.
JOURNAL OF NUTRITION
(2022)
Article
Nutrition & Dietetics
Juan J. Castillo, Garret Couture, Nikita P. Bacalzo, Ye Chen, Elizabeth L. Chin, Sarah E. Blecksmith, Yasmine Y. Bouzid, Yael Vainberg, Chad Masarweh, Qingwen Zhou, Jennifer T. Smilowitz, J. Bruce German, David A. Mills, Danielle G. Lemay, Carlito B. Lebrilla
Summary: The molecular complexity of carbohydrates consumed by humans has been oversimplified due to the lack of suitable analytical methods. This work presents a detailed catalogue of glycans in commonly consumed foods and establishes an open-access database. The Glycopedia can be used to formulate targeted diets that modulate the gut microbiome, opening possibilities for new preventative or therapeutic diets.
Article
Nutrition & Dietetics
Sierra D. Durham, Danielle G. Lemay, Zhe Wei, Kenneth F. Kalscheur, John W. Finley, Naomi K. Fukagawa, Daniela Barile
Summary: Consuming a low starch high fiber diet promoted greater overall bovine milk oligosaccharide production than a low fiber high starch diet in a population of midlactation Holstein dairy cattle.
CURRENT DEVELOPMENTS IN NUTRITION
(2022)
Article
Microbiology
Laurynne C. Coates, Sierra D. Durham, David H. Storms, Andrew D. Magnuson, Diane L. Van Hekken, Benjamin M. Plumier, John W. Finley, Naomi K. Fukagawa, Peggy M. Tomasula, Danielle G. Lemay, Matthew J. Picklo, Daniela Barile, Kenneth F. Kalscheur, Mary E. Kable
Summary: Milk oligosaccharides (MOs) and fatty acids (MFAs) have prebiotic, antiadhesive, and antimicrobial effects. Their relationships with milk microbes and inflammation have been studied in humans, but not in cows. Studying the relationships among milk microbiota, MFAs, MOs, lactose, and somatic cell counts in cows can provide valuable insights for improving milk quality and reducing waste.
MICROBIOLOGY SPECTRUM
(2023)
Article
Multidisciplinary Sciences
Sierra D. Durham, Zhe Wei, Danielle G. Lemay, Matthew C. Lange, Daniela Barile
Summary: The carbohydrate fraction in mammalian milks contains various oligosaccharides with different structures and compositions. Human milk oligosaccharides (HMOs) have been studied extensively due to their biological roles. However, understanding milk oligosaccharides in other mammals is challenging due to inconsistent data reporting methods. This study created a comprehensive database, MilkOligoDB, which consists of 3193 entries of milk oligosaccharides from 77 different species across 113 publications.
SCIENTIFIC REPORTS
(2023)
Article
Mathematical & Computational Biology
Andrew Oliver, Matthew Kay, Danielle G. Lemay
Summary: Biologists are increasingly using machine learning models not only for prediction but also for explanation. The algorithm TaxaHFE is designed to collapse information-poor features into higher taxonomic levels, leading to a significant reduction in the number of features and improved model performance. Compared to other hierarchical feature engineering implementations, TaxaHFE introduces the unique ability to consider both categorical and continuous response variables, enhancing model interpretability.
BIOINFORMATICS ADVANCES
(2023)
Article
Nutrition & Dietetics
Laurynne C. Coates, David Storms, John W. Finley, Naomi K. Fukagawa, Danielle G. Lemay, Kenneth F. Kalscheur, Mary E. Kable
Summary: This study found that feeding lactating cows a more sustainable, low-starch and high-fiber diet is associated with changes in raw milk microbiota composition and somatic cell count. It has implications for udder health and milk spoilage.
CURRENT DEVELOPMENTS IN NUTRITION
(2022)
Article
Computer Science, Information Systems
Cynthia S. Parr, Danielle G. Lemay, Christopher L. Owen, M. Jennifer Woodward-Greene, Jiayang Sun
Summary: Advances in natural language processing and computer vision are being applied to agricultural problems, but could be more powerful when combined with AI and numeric data sources. Challenges include obtaining high-quality training data and a lack of customized machine learning techniques.