Article
Microbiology
Haojie Jin, Rick Kim, Devaki Bhaya
Summary: This study demonstrates the presence of a dual degron at the N-terminus of the UmuD protein in Synechocystis sp. PCC6803, which requires ClpA/P protease and the ClpS adaptor for proteolysis.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Xiangzhen Zan, Ling Chu, Ranze Xie, Yanqing Su, Xiangyu Yao, Peng Xu, Wenbin Liu
Summary: In this article, an image encryption method based on the modulation-based storage architecture is proposed to encrypt images in highly error-prone DNA storage channels. Numerical results have shown that this method is feasible and effective with excellent security against various attacks. It is more reliable and suitable for large-scale applications compared to other methods such as hybridization reactions of DNA molecules.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Yaolei Zhang, Guangyi Fan, Xin Liu, Kerstin Skovgaard, Michael Sturek, Peter M. H. Heegaard
Summary: The feral pigs on Ossabaw Island have a strong tendency towards obesity and can develop metabolic syndrome on a high energy diet. The high-quality genome of the Ossabaw pig revealed unique genomic variations that may be related to its thrifty phenotype, including a significant inversion. Additionally, a positively selected gene, leptin receptor, was identified as potentially playing a key role in obesity and inflammation development.
Review
Oncology
Daniele Caracciolo, Caterina Riillo, Maria Teresa Di Martino, Pierosandro Tagliaferri, Pierfrancesco Tassone
Summary: Cancer onset and progression result in high levels of DNA damage, with error-prone DNA repair pathways promoting genomic instability that leads to the appearance of cancer hallmarks through progressive genetic aberrations in tumor cells. This provides a potential target for precision oncology through the inhibition of Alternative Non-Homologous End Joining (Alt-NHEJ) as a new cancer vulnerability.
Article
Biotechnology & Applied Microbiology
Ian C. C. Nova, Justas Ritmejeris, Henry Brinkerhoff, Theo J. R. Koenig, Jens H. H. Gundlach, Cees Dekker
Summary: Drawing peptides through a nanopore allows for the detection of individual phosphorylation sites; Current methods cannot measure single molecules or differentiate between closely spaced phosphorylation sites; We can detect cancer-associated post-translational modifications at the single-molecule level by controlling the peptide's movement through a nanopore; With individual reads of single molecules, we can discriminate peptide sequences with one or two closely spaced phosphates with 95% accuracy.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Sea On Lee, Stephen D. Fried
Summary: An improved error-prone PCR protocol using a Touchdown approach and commercially available components is reported, which can efficiently concentrate mutations into a small region of plasmid DNA and achieve very high mutational loads on a standard-sized amplicon.
ANALYTICAL BIOCHEMISTRY
(2021)
Review
Genetics & Heredity
Ritesh K. Shukla, Ashish Badiye, Kamayani Vajpayee, Neeti Kapoor
Summary: The rapid development of nanotechnology has led to enhanced production of nanoparticles, which poses potential threats to human health. Interaction between nanoparticles and DNA can result in structural and functional modifications, impacting the cellular system negatively.
FRONTIERS IN GENETICS
(2021)
Article
Biochemical Research Methods
Ramin Shirali Hossein Zade, Aysun Urhan, Alvaro Assis de Souza, Akash Singh, Thomas Abeel
Summary: This study introduces a new tool called HAT for haplotype assembly, which utilizes short and long reads along with a reference genome to obtain higher-quality continuous haplotypes.
Review
Cell Biology
Yanli Zou, Jing Jing Li, Wei Xue, Xiangbin Kong, Hucheng Duan, Yiqun Li, Lai Wei
Summary: Uveitis is a vision-threatening intraocular inflammation with unclear pathogenesis. While genetic variations have been identified in its onset and progression, epigenetic regulation also plays crucial roles in immunoregulation. Epigenetic therapies show promise in treating intraocular inflammation, offering hope for the future development of treatments for these devastating conditions.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Celia Maria Curieses Andres, Jose Manuel Perez de la Lastra, Celia Andres Juan, Francisco J. Plou, Eduardo Perez-Lebena
Summary: This review focuses on the DNA damage caused by various oxidizing, alkylating, and nitrating species, which may play a crucial role in the pathophysiology of inflammation, cancer, and degenerative diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Benjamin B. Morris, Nolan A. Wages, Patrick A. Grant, P. Todd Stukenberg, Ryan D. Gentzler, Richard D. Hall, Wallace L. Akerley, Thomas K. Varghese, Susanne M. Arnold, Terence M. Williams, Vincenzo Coppola, David R. Jones, David T. Auble, Marty W. Mayo
Summary: Evidence suggests that many patients with lung adenocarcinoma exhibit significant genome instability and overexpress the transcription factor MYBL2, which is associated with poor prognostic outcomes and potential disruption of DNA repair pathways.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ying Ge, Athina Masoura, Jingzhou Yang, Francesco A. Aprile
Summary: Neurodegenerative diseases are associated with the formation of fibrillar protein aggregates called amyloids in the nervous system. The aggregation process is influenced by various post-translational modifications whose specific mechanisms are not fully understood. Currently, emerging chemical mutagenesis technology is being developed to introduce protein post-translational modifications while maintaining stability and solubility during the modification reaction. However, the precipitation of amyloidogenic proteins during modification procedures can affect yield and downstream characterization. This study presents a method to maintain solubility of amyloidogenic proteins during chemical mutagenesis, using phosphorylation and acetylation as examples.
ACS CHEMICAL NEUROSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Ying Ge, Athina Masoura, Jingzhou Yang, Francesco A. Aprile
Summary: Neurodegenerative diseases are associated with the formation of amyloid fibrillar protein aggregates in the nervous system. The mechanisms of post-translational modifications that affect this aggregation process are not fully understood. Chemical mutagenesis technology is being developed to introduce protein post-translational modifications while maintaining stability and solubility. This article presents a method to maintain solubility of amyloidogenic proteins during chemical mutagenesis, using the amyloid-beta peptide as an example.
ACS CHEMICAL NEUROSCIENCE
(2022)
Article
Statistics & Probability
Li-Pang Chen
Summary: In statistical analysis or supervised learning, classification is an attractive topic. We propose a valid inferential method to deal with measurement error and handle variable selection simultaneously in logistic regression or probit models. Through numerical studies, we find that the proposed method accurately retains informative predictors and gives precise estimators, and its performance is generally better than that without measurement error correction.
JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS
(2023)
Review
Genetics & Heredity
Laura Niiranen, Dawid Leciej, Hanna Edlund, Carolina Bernhardsson, Magdalena Fraser, Federico Sanchez Quinto, Karl-Heinz Herzig, Mattias Jakobsson, Jaroslaw Walkowiak, Olaf Thalmann
Summary: Epigenetic changes play a major role in fundamental metabolic pathways and have been closely linked to various diseases. This review focuses on the study of epigenetic changes in animals, with a special emphasis on human DNA methylation using ancient and modern genomes. Through ancient DNA research, we can infer past epigenetic changes and gain a comprehensive understanding of how our ancestors adapted to the changing environment and modified their lifestyles. However, working with ancient DNA presents challenges, but new paleoepigenomic data holds promise for future studies.
Article
Biotechnology & Applied Microbiology
Yibin Liu, Paulina Siejka-Zielinska, Gergana Velikova, Ying Bi, Fang Yuan, Marketa Tomkova, Chunsen Bai, Lei Chen, Benjamin Schuster-Bockler, Chun-Xiao Song
NATURE BIOTECHNOLOGY
(2019)
Article
Physiology
Jakub Tomek, Guoliang Hao, Marketa Tomkova, Andrew Lewis, Carolyn Carr, David J. Paterson, Blanca Rodriguez, Gil Bub, Neil Herring
FRONTIERS IN PHYSIOLOGY
(2019)
Article
Genetics & Heredity
Vassili Kusmartsev, Magdalena Drozdz, Benjamin Schuster-Bockler, Tobias Warnecke
Article
Biochemistry & Molecular Biology
Pakavarin Louphrasitthiphol, Robert Siddaway, Alessia Loffreda, Vivian Pogenberg, Hans Friedrichsen, Alexander Schepsky, Zhiqiang Zeng, Min Lu, Thomas Strub, Rasmus Freter, Richard Lisle, Eda Suer, Benjamin Thomas, Benjamin Schuster-Bockler, Panagis Filippakopoulos, Mark Middleton, Xin Lu, E. Elizabeth Patton, Irwin Davidson, Jean-Philippe Lambert, Matthias Wilmanns, Eirikur Steingrimsson, Davide Mazza, Colin R. Goding
Article
Multidisciplinary Sciences
Martin Popel, Marketa Tomkova, Jakub Tomek, Lukasz Kaiser, Jakob Uszkoreit, Ondrej Bojar, Zdenek Zabokrtsky
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Paulina Siejka-Zielinska, Jingfei Cheng, Felix Jackson, Yibin Liu, Zahir Soonawalla, Srikanth Reddy, Michael Silva, Luminita Puta, Misti Vanette McCain, Emma L. Culver, Noor Bekkali, Benjamin Schuster-Bockler, Pier Francesco Palamara, Derek Mann, Helen Reeves, Eleanor Barnes, Shivan Sivakumar, Chun-Xiao Song
Summary: In this study, the researchers optimized TAPS for cfDNA, allowing high-quality and high-depth whole-genome methylome profiling of patients with HCC and PDAC. They demonstrated that cfTAPS can provide multimodal information about cfDNA characteristics, and that integrated analysis of DNA methylation and other features enables accurate identification of early HCC and PDAC.
Article
Biochemistry & Molecular Biology
Henriette O'Geen, Marketa Tomkova, Jacquelyn A. Combs, Emma K. Tilley, David J. Segal
Summary: This study systematically investigated the ability of CRISPR/dCas9-based epigenome editors to engineer persistent epigenetic silencing. It revealed the importance of cis regulatory features and chromatin marks in the stability of epigenetic reprogramming, providing insights into engineering predictable and long-lasting gene expression changes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cardiac & Cardiovascular Systems
Jana Rubackova Popelova, Marketa Tomkova, Jakub Tomek, Renata Zivna
Summary: ASD closure appears to be associated with improved long-term survival independently of age, PH, and other clinical variables.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)
Article
Cardiac & Cardiovascular Systems
Jana Rubackova Popelova, Jakub Tomek, Marketa Tomkova, Renata Zivna
Summary: Four types of hemodynamic PH can be found in adult patients with ASD and can be used to stratify patients by their likelihood of PH normalization and survival after ASD closure.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Marketa Tomkova, Jakub Tomek, Julie Chow, John D. McPherson, David J. Segal, Fereydoun Hormozdiari
Summary: The study presents a novel framework called Dr.Nod for the detection of non-coding cis-regulatory candidate driver mutations. Applying the framework to tumor data reveals an enrichment of candidate driver mutations in regulatory regions of known cancer driver genes. The study demonstrates the significance of tissue-matched enhancer-gene maps and functional impact of non-coding regulatory driver mutations in cancer.
NUCLEIC ACIDS RESEARCH
(2023)
Meeting Abstract
Biotechnology & Applied Microbiology
Henriette O'Geen, Marketa Tomkova, David J. Segal
Meeting Abstract
Oncology
Marketa Tomkova, Claire Renard, Lara Urban, Souad Kolli, Maude Ardin, Manuraj Pandey, Maria Zhivagui, Hana Huskova, Magali Olivier, Hiroyuki Marusawa, Benjamin Schuster-Bockler, Jiri Zavadil
Meeting Abstract
Oncology
Yibin Liu, Paulina Siejka, Gergana Velikova, Ying Bi, Marketa Tomkova, Benjamin Schuster-Boeckler, Chun-Xiao Song
Article
Cardiac & Cardiovascular Systems
Jana Rubackova Popelova, Renata Zivna, Marketa Tomkova, Jakub Tomek