Article
Veterinary Sciences
Caijuan Yue, Jiakang Wang, Yifei Shen, Junli Zhang, Jian Liu, Aiping Xiao, Yisha Liu, Hehua Eer, Qiao-e Zhang
Summary: In this study, whole-genome bisulfite sequencing and bioinformatics analysis were used to compare the DNA methylation patterns between Tan sheep and Hu sheep. It was found that six genes - ACTA1, MYH11, WAS, VAV1, FN1, and ROCK2 - showed significant differences in methylation levels between Tan sheep and Hu sheep, and these genes are involved in muscle cell differentiation and development. This study highlights the importance of gene methylation in the formation of muscle-related traits.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Qian Yan, Ying Tang, Fan He, Jiao Xue, Ruisheng Zhou, Xiaoying Zhang, Huiyan Luo, Daihan Zhou, Xiongwen Wang
Summary: This study investigated alterations in DNA methylation patterns in hepatocellular carcinoma (HCC) using whole-genome bisulfite sequencing technology. The research identified a genome-wide hypomethylation pattern in HCC, with hyper-DMGs mainly involved in metabolism pathways and hypo-DMGs mainly involved in cell adhesion. By constructing a prognostic model based on aberrantly methylated genes, the study provided insights into the epigenetic mechanisms of HCC development.
Review
Biochemical Research Methods
Adam Nunn, Christian Otto, Peter F. Stadler, David Langenberger
Summary: Whole genome bisulfite sequencing has advanced epigenetic analysis by providing nucleotide-level resolution of 5-methylcytosine (5mC) on a genome-wide scale. Evaluations of nine short-read aligners suggest that BWA-meth and BSMAP are most effective in utilizing data during mapping. Downstream methylation analysis is influenced by handling multi-mapping reads and mapping quality.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Jacob Morrison, Julie M. Koeman, Benjamin K. Johnson, Kelly K. Foy, Ian Beddows, Wanding Zhou, David W. Chesla, Larissa L. Rossell, Emily J. Siegwald, Marie Adams, Hui Shen
Summary: This study extensively benchmarked common library preparation protocols for whole-genome DNA methylation sequencing, with NEBNext Enzymatic Methyl-seq and Swift Accel-NGS Methyl-Seq kits showing superior performance quantitatively. The NEBNext Enzymatic Methyl-seq kit is recommended for high-quality DNA samples, while the Swift kit is more suitable for degraded samples.
EPIGENETICS & CHROMATIN
(2021)
Article
Biotechnology & Applied Microbiology
Stefan Milosavljevic, Tony Kuo, Samuele Decarli, Lucas Mohn, Jun Sese, Kentaro K. Shimizu, Rie Shimizu-Inatsugi, Mark D. Robinson
Summary: ARPEGGIO is a workflow for analyzing epigenetic data in allopolyploids, utilizing the EAGLE-RC read classification algorithm to address sequence similarity challenges among parental genomes. This workflow offers automation and a complete set of analyses starting from raw WGBS data to outputting a list of genes showing differential methylation, ensuring reproducibility with simple set up and interpretation. ARPEGGIO stands out as the only workflow supporting polyploid data, as shown through its performance evaluation and agreement with published results.
Article
Biochemistry & Molecular Biology
Veronika N. Laine, Bernice Sepers, Melanie Lindner, Fleur Gawehns, Suvi Ruuskanen, Kees van Oers
Summary: The field of molecular biology is rapidly advancing and there is a growing interest in studying ecological epigenetics, particularly in wild vertebrates. This review provides a practical guide for researchers studying DNA methylation variation in wild vertebrates, discussing technical aspects, limitations, and data analysis methods.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemical Research Methods
Heesun Kim, Mikang Sim, Nayoung Park, Kisang Kwon, Junyoung Kim, Jaebum Kim
Summary: msPIPE is an end-to-end pipeline for DNA methylation analyses, allowing seamless connection of all necessary tasks from data pre-processing to downstream DNA methylation analyses. It generates various methylation profiles for analyzing methylation patterns, including statistical summaries and methylation levels. The pipeline also computes methylation levels in functional regions of the genome with proper annotation. The results can be visualized in high-quality figures. msPIPE can be easily used with a Docker image that includes all required packages and software for DNA methylation analyses.
BMC BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Mathia Colwell, Nicole M. Wanner, Chelsea Drown, Melissa Drown, Dana C. Dolinoy, Christopher Faulk
Summary: This study investigated the effects of chronic low doses of DAC on the DNA methylome and gene expression in mice. The results showed that DAC exposure led to more sensitive DNA methylation changes in testes and liver, as well as dysregulated gene expression targeting non-specific pathways. However, no dose level or regimen was found to cause systemic hypomethylation in whole mice.
Article
Genetics & Heredity
Elizabeth M. Martin, Sara A. Grimm, Zongli Xu, Jack A. Taylor, Paul A. Wade
Summary: This study compared the DNA methylation assessment using Illumina Mouse Methylation BeadChip (MMB) technology with the gold-standard method of whole-genome bisulfite sequencing (WGBS). The results showed that MMB produced similar measurements of methylation as WGBS, and the differentially methylated cytosines and regions identified by both methods overlapped and enriched for similar biological functions, indicating that MMB faithfully recapitulates the findings of WGBS.
Review
Biochemistry & Molecular Biology
Fabio Coppede, Utsa Bhaduri, Andrea Stoccoro, Vanessa Nicoli, Eleonora Di Venere, Giuseppe Merla
Summary: The central objective of combining discovery science with biomedical applications is to benefit patients and reduce the global disease burden. The conversion of DNA methylation (DNAm) from a biological process to a diagnostic tool is a prime example of this transformation, which took nearly a century. In recent years, DNAm studies have been standardized in clinical applications more than ever before, offering great potential for diagnosing various diseases associated with epigenetic alterations. DNAm detection plays a role in noninvasive prenatal testing and indicates prenatal risk factors in very preterm infants. In the field of cancer, liquid biopsy-based DNAm profiling provides valuable epigenetic biomarkers for early-stage diagnosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Xubin Zheng, Qiong Wu, Haonan Wu, Kwong-Sak Leung, Man-Hon Wong, Xueyan Liu, Lixin Cheng
Summary: This study introduced the most prevalent methods for processing bisulfite sequencing data and evaluated the consistency of the data acquired from different measurements in liver cancer. Differential methylated genes measured by various bisulfite sequencing assays and 450 k beadchip were consistently hypo-methylated in liver cancer with high functional similarity.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Antonella Sarnataro, Giulia De Riso, Sergio Cocozza, Antonio Pezone, Barbara Majello, Stefano Amente, Giovanni Scala
Summary: DNA methylation is an important epigenetic modification that influences gene regulation, genomic imprinting, and genome stability. EpiStatProfiler is an R package that allows the analysis of CpG and non-CpG epialleles based on bisulfite sequencing data, with additional features for genomic annotation and analysis. It is the first package to provide functionalities specifically for epiallele composition analysis from any type of bisulfite sequencing experiment.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Aleksandra Gorska, Maria Urbanowicz, Lukasz Grochowalski, Michal Seweryn, Marta Sobalska-Kwapis, Tomasz Wojdacz, Magdalena Lange, Marta Gruchala-Niedoszytko, Justyna Jarczak, Dominik Strapagiel, Magdalena Gorska-Ponikowska, Iwona Pelikant-Malecka, Leszek Kalinowski, Boguslaw Nedoszytko, Danuta Gutowska-Owsiak, Marek Niedoszytko
Summary: This study aimed to identify the differential methylation profiles and gene expression patterns associated with mastocytosis, a heterogenous disease of the mast cells. Genome-wide DNA methylation analysis was performed on peripheral blood samples from mastocytosis patients and healthy controls. The results showed significant differences in methylation levels of selected regions, including 31 genes located within the regulatory regions. Additionally, three oncogenes-FOXQ1, TWIST1, and ERG-were found to be differentially methylated in mastocytosis patients for the first time. These findings provide insights into the methylation landscape of mastocytosis and potential therapeutic targets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Pol Laanen, Eline Saenen, Mohamed Mysara, Jorden van de Walle, May Van Hees, Robin Nauts, Filip Van Nieuwerburgh, Stefan Voorspoels, Griet Jacobs, Ann Cuypers, Nele Horemans
Summary: The study reveals that exposure to gamma radiation can lead to DNA methylation changes in young Arabidopsis plants across multiple generations, with a significant increase in differentially methylated regions (DMRs) in the second generation exposed to the lowest dose rate. Surprisingly, there were no significant differences in plants exposed to the highest dose rate. Hypermethylation of transposable elements was found to increase genetic stability, while DMRs associated with genes were enriched for development and stress response-related functions, suggesting a role of DNA methylation in regulating gene expression in response to radiation.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Chemistry, Physical
Ting Gong, Heather Borgard, Zao Zhang, Shaoqiu Chen, Zitong Gao, Youping Deng
Summary: DNA methylation is a phenomenon associated with transcriptional repression, genomic imprinting, stem cell differentiation, embryonic development, and inflammation. Aberrant DNA methylation can indicate disease states, making the understanding of the prevalence and location of DNA methylation in the human genome important. Whole-genome bisulfite sequencing (WGBS) is a high-throughput method for analyzing DNA methylation, and this review compares and introduces the detailed experimental methodology of WGBS.
Article
Biotechnology & Applied Microbiology
Nadiya Romanova, Tarek Niemann, Johannes F. W. Greiner, Barbara Kaltschmidt, Christian Kaltschmidt, Thomas Noll
Summary: The study investigated the effects of hyperosmolality on CHO cells, revealing that exposure to high osmolality can lead to increased cell volume, decreased proliferation, enhanced mitochondrial activity, and the formation of multiple small nuclei in stressed cells. These findings demonstrate previously unknown morphological changes in CHO cells under hyperosmotic conditions and support existing data on the osmotic response in mammalian cells.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Article
Biochemistry & Molecular Biology
Leonie Herrmann, Louise Schelletter, Raimund Hoffrogge, Karsten Niehaus, Volker Rudolph, Martin Farr
Summary: During viral-induced myocarditis, neutrophil elastase may target and cleave CAR, reducing susceptibility to viral infections and potentially affecting the course of the disease.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Nadiya Romanova, Louise Schelletter, Raimund Hoffrogge, Thomas Noll
Summary: Chinese hamster ovary (CHO) cells are commonly used for therapeutic protein production. Exposure to high osmolality can affect cell physiology and protein expression. This study compared the proteome of CHO cells exposed to hyperosmolality with control cells, revealing differentially expressed proteins involved in mitochondrial activation, oxidative stress response, and cell cycle progression. The study also found that protein regulation can affect cell membrane stiffness and permeability.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Microbiology
Blanka Didak Ljubas, Mario Novak, Antonija Trontel, Ana Rajkovic, Zora Kelemen, Nenad Mardetko, Marina Grubisic, Mladen Pavlecic, Vlatka Petravic Tominac, Bozidar Santek
Summary: Brewers' spent grains, a by-product of the brewing industry, can be used to produce biofuels or biochemicals. Different experimental setups can direct the metabolism of Paenibacillus polymyxa DSM 742 towards the production of 2,3-butanediol and ethanol or lactate.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Cell Biology
Nadiya Romanova, Julian Schmitz, Marie Strakeljahn, Alexander Grunberger, Janina Bahnemann, Thomas Noll
Summary: This study investigates the impact of hyperosmolality and the effects of added osmotic-active reagents on CHO cells. The exposure to extreme hyperosmolality and glucose overfeeding leads to negative effects on cell growth and mitochondrial activity. These findings are important for process development in commercial production.
Article
Chemistry, Analytical
Lennard Karsten, Lukas Goett-Zink, Julian Schmitz, Raimund Hoffrogge, Alexander Grunberger, Tilman Kottke, Kristian M. Muller
Summary: In this study, ratiometric pH sensors with high dynamic ranges and dual-emission properties were developed for monitoring intra- and extracellular pH. These sensors can be applied in live-cell fluorescence microscopy and ratiometric flow cytometry to track pH changes in cells and culture chambers. The sensors also offer the potential to determine internalization rates, a promising parameter for characterizing protein-drug conjugates in cancer therapy.
Article
Biotechnology & Applied Microbiology
Oliver Hertel, Anne Neuss, Tobias Busche, David Brandt, Joern Kalinowski, Janina Bahnemann, Thomas Noll
Summary: This study established a CRISPR/Cas9-mediated site-specific integration strategy based on ChIP-seq data to improve stability and productivity of recombinant CHO cells.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Ecology
Birgit Gemeinholzer, Oliver Rupp, Annette Becker, Marc Strickert, Christina M. Mueller
Summary: Red clover is an important forage crop grown worldwide for cattle feed and soil improvement. There is a lack of knowledge about the natural genetic and phenotypic diversity of red clover. This study developed a low-cost mRNA analysis method and compared it with population genetic data to assess intraspecific variation and transcriptome responses.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Biotechnology & Applied Microbiology
Maximilian Klimpel, Monica Terrao, Nilakshi Ching, Vanessa Climenti, Thomas Noll, Vicky Pirzas, Holger Laux
Summary: This study describes the use of two suspension-adapted stable packaging cell lines for the development of a scalable and serum-free LV production process. Both cell lines are based on an inducible Tet-off system and can be used to produce LVs in suspension mode.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Multidisciplinary Sciences
Dewi Pramanik, Annette Becker, Clemens Roessner, Oliver Rupp, Diego Bogarin, Oscar Alejandro Perez-Escobar, Anita Dirks-Mulder, Kevin Droppert, Alexander Kocyan, Erik Smets, Barbara Gravendeel
Summary: This study analyzes the evolution and development of fruit dehiscence zones in orchids. Gene expression analysis reveals that orchids have different fruit dehiscence mechanisms compared to Arabidopsis thaliana. Genes involved in carpel, gynoecium, ovule development, and lipid biosynthesis may play a novel role in the formation of dehiscence zone tissues in orchids.
Article
Plant Sciences
Lucie Schroeder, Oliver Rupp, Michael Senkler, Nils Rugen, Natalija Hohnjec, Alexander Goesmann, Helge Kuester, Hans-Peter Braun
Summary: European mistletoe is a hemiparasitic flowering plant with an extremely large genome size. A transcriptome project was conducted to study its gene space, resulting in a database containing sequences of thousands of open reading frames encoding distinct proteins. A new database, VaGs II, was developed by combining data from a summer and winter transcriptome project, and it showed a higher completeness compared to the previous database. The quality of the new database was evaluated by re-analyzing proteome data, which provided new insights into the oxidative phosphorylation system of European mistletoe.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Christoph Keysberg, Oliver Hertel, Raimund Hoffrogge, Sibylle Reich, Nadine Hornung, Karlheinz Holzmann, Kerstin Otte
Summary: Researchers identified beneficial bioprocess conditions for small extracellular vesicle (sEV) production and found that short-term hyperthermia significantly increased the yield and quality of sEVs. Transcriptomics and proteomics analyses revealed an upregulation of heat-shock response and molecules related to exosome biogenesis and vesicle trafficking, which may contribute to the increased productivity. Overexpression of six genes was also found to enhance sEV secretion and production.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Meeting Abstract
Biotechnology & Applied Microbiology
M. T. Radukic, D. T. Le, S. Golm, C. Rothschild-Gronau, R. Hoffrogge, K. M. Mueller
HUMAN GENE THERAPY
(2022)
Article
Biotechnology & Applied Microbiology
Mladen Pavlecic, Mario Novak, Antonija Trontel, Nenad Mardetko, Marina Grubisic, Blanka Didak Ljubas, Vlatka Petravic Tominac, Rozelindra Coz Rakovac, Bozidar Santek
Summary: This study investigated the efficiency of bioethanol production from sugar beet cossettes using yeast in a horizontal rotating tubular bioreactor. A non-structural mathematical model was developed to describe substrate utilization and product formation. The results showed that rotation mode and speed greatly influenced the bioethanol yield.
FERMENTATION-BASEL
(2022)
