Review
Oncology
Carlo Ganini, Ivano Amelio, Riccardo Bertolo, Pierluigi Bove, Oreste Claudio Buonomo, Eleonora Candi, Chiara Cipriani, Nicola Di Daniele, Hartmut Juhl, Alessandro Mauriello, Carla Marani, John Marshall, Sonia Melino, Paolo Marchetti, Manuela Montanaro, Maria Emanuela Natale, Flavia Novelli, Giampiero Palmieri, Mauro Piacentini, Erino Angelo Rendina, Mario Roselli, Giuseppe Sica, Manfredi Tesauro, Valentina Rovella, Giuseppe Tisone, Yufang Shi, Ying Wang, Gerry Melino
Summary: Advancements in sequencing technologies have enabled more accurate and comprehensive cancer sequencing projects, such as deep sequencing of entire genomes, bypassing the high costs of whole-genome sequencing. Large-scale WGS applications on databases have allowed scientists to analyze molecular features, large structural variations, and noncoding regions of the genome globally for the first time. Thorough deciphering of the vast amount of data is needed, with the emergence of machine-learning approaches expected to lead to the development of personalized approaches for cancer medicine.
MOLECULAR ONCOLOGY
(2021)
Review
Genetics & Heredity
Laura K. White, Jay R. Hesselberth
Summary: This review provides an introduction to nanopore sequencing and its use in direct detection of nucleic acid modifications. Nanopore sequencing, as a third generation sequencing technology, offers advantages in high throughput and direct detection of nucleic acid modifications. Numerous endogenous and synthetic nucleic acid modifications have been studied using nanopore sequencing. Advances in sequencing chemistry and analysis methods are expected to improve the identification and quantification of these epigenetic marks.
FRONTIERS IN GENETICS
(2022)
Article
Chemistry, Multidisciplinary
Yuchen Wang, Anjelica Kucinic, Lilly Des Rosiers, Peter E. Beshay, Nicholas Wile, Michael W. Hudoba, Carlos E. Castro
Summary: DNA origami nanotechnology has potential for diverse applications, but its use in education is limited due to high cost and time requirements. We developed an experiment module for classroom implementation, focusing on a deformable hinge joint, that can be evaluated within 120 minutes using cost-effective equipment. Two beam-based models were presented to describe the joint deformation. This module can broaden access to and interest in the mechanical design of DNA origami.
APPLIED SCIENCES-BASEL
(2023)
Review
Geosciences, Multidisciplinary
Alida M. Bailleul, Zhiheng Li
Summary: The discovery of ancient DNA in fossils from extinct animals has opened up new research possibilities in paleobiology. Recent studies have shown evidence of endogenous DNA in cells from dinosaur and plant fossils, suggesting the potential for retrieving ancient sequences in fossils older than previously thought. Despite challenges like crosslinking and chemically modified nucleotides, there is hope for further understanding DNA preservation in deep time.
EARTH-SCIENCE REVIEWS
(2021)
Article
Engineering, Biomedical
James Joseph, Kevin N. Baumann, Alejandro Postigo, Laura Bollepalli, Sarah E. Bohndiek, Silvia Hernandez-Ainsa
Summary: Optoacoustic tomography allows non-invasive deep tissue imaging of optical contrast, with applications in cancer imaging utilizing molecular imaging contrast agents based on NIR dyes. Biodegradable DNA-based nanocarriers enable precise incorporation of NIR dyes for enhanced optoacoustic signal generation and prolonged blood circulation, leading to improved tumor accumulation through the EPR effect. In vivo imaging of tumor xenografts in mice using DNA-NCs shows enhanced OT signals compared to free fluorophores, indicating potential for improved tumor imaging efficacy with clinically relevant NIR dyes.
ADVANCED HEALTHCARE MATERIALS
(2021)
Article
Chemistry, Multidisciplinary
Arthur Rand, Philip Zimny, Roland Nagel, Chaitra Telang, Justin Mollison, Aaron Bruns, Emily Leff, Walter W. Reisner, William B. Dunbar
Summary: In this study, an electronic mapping of a bacterial genome using solid-state nanopore technology was presented. The method involves a dual-nano-pore architecture and active control logic to produce single-molecule data and estimate distances between physical tags on double-stranded DNA. Custom analysis methods were developed to generate consensus alignments from multiple scans, and this approach was applied to map the E. coli chromosome. The results showed a significant increase in alignment length with the recapture method, and the intertag resolution was determined to be around 150-166 bp.
Review
Biochemistry & Molecular Biology
Stefano Amente, Giovanni Scala, Barbara Majello, Somaiyeh Azmoun, Helen G. Tempest, Sanjay Premi, Marcus S. Cooke
Summary: Exposure from external and internal environments leads to modifications in genomic DNA, contributing to various diseases. Understanding the impact of damage on cellular function and pathogenesis remains unclear, but mapping DNA adductomics may provide valuable insights.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Eduardo Gonzalez-Grandio, Gozde S. Demirer, Christopher T. Jackson, Darwin Yang, Sophia Ebert, Kian Molawi, Harald Keller, Markita P. Landry
Summary: The surface chemistry of nanotubes plays a crucial role in their interaction with plants, with positively charged polymer-functionalized nanotubes causing cell death while pristine nanotubes are well tolerated. This highlights the importance of nanoparticle surface chemistry in their biocompatibility and agricultural applications.
JOURNAL OF NANOBIOTECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Shuai Zhao, Yuan Liu, Xiaokang Zhang, Rui Qin, Bin Wang, Qiang Zhang
Summary: This study proposes a DNA temporal logic circuit based on DNA strand displacement reactions, which can map temporally ordered inputs to corresponding binary message outputs. The circuit shows excellent responsiveness, flexibility, and expansibility, providing new ideas for future molecular encryption, information processing, and neural networks.
Article
Clinical Neurology
Giulia Berzero, Valentina Pieri, Pietro Mortini, Massimo Filippi, Gaetano Finocchiaro
Summary: The clinical use of liquid biopsy, specifically the analysis of cell-free DNA from plasma or cerebrospinal fluid, is increasingly important in oncology, particularly for brain tumours. It can provide valuable information for differential diagnosis, patient follow-up, and identifying targetable genetic alterations. However, there are challenges such as concomitant pathologies and invasive procedures to obtain cerebrospinal fluid, which could affect the accuracy and interpretation of the results. Further research and understanding of the mechanisms behind cfDNA shedding by tumours are needed to fully exploit its potential in clinical practice.
Article
Plant Sciences
Zeyu Zhang, Huihui Wang, Yongsheng Wang, Feihu Xi, Huiyuan Wang, Markus Kohnen, Pengfei Gao, Wentao Wei, Kai Chen, Xuqing Liu, Yubang Gao, Ximei Han, Kaiqiang Hu, Hangxiao Zhang, Qiang Zhu, Yushan Zheng, Bo Liu, Ayaz Ahmad, Yau-Heiu Hsu, Steven E. Jacobsen, Lianfeng Gu
Summary: The study found that CHH methylation gradually accumulates during the transition from vegetative to reproductive growth in moso bamboo, with differentially methylated regions mainly occurring at transcription start and termination sites. Genes with CG methylation changes are enriched in 'vegetative to reproductive phase transition of meristem' GO categories, while circRNA flanking introns are hypermethylated and enriched in LTR retrotransposons.
Review
Chemistry, Multidisciplinary
Yanfang Du, Ying Tang, Bingqian Lin, Xiaochen Xue, Yafen Wang, Yibin Liu
Summary: The mapping of DNA cytosine modifications is essential for understanding epigenetic regulation. While bisulfite sequencing has limitations, bisulfite-free methods have emerged as promising alternatives. This review provides an overview of both methods, discussing their advantages, limitations, and applications. Challenges and future perspectives for advancing bisulfite-free mapping methods are also explored.
SCIENCE CHINA-CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Xinpei Dai, Xiaoliang Chen, Xinxin Jing, Yinan Zhang, Muchen Pan, Mingqiang Li, Qian Li, Pi Liu, Chunhai Fan, Xiaoguo Liu
Summary: Integrating dissimilar materials at the nanoscale is crucial for modern electronics and optoelectronics. Researchers have developed a DNA origami-encoded strategy for integrating silica-metal heterostructures and revealed the underlying mechanisms. By programming the densities and lengths of protruding dsDNA strands on DNA origami, high site-addressability of material deposition was achieved.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Oncology
Verena Nilius-Eliliwi, Wanda M. Gerding, Roland Schroers, Huu Phuc Nguyen, Deepak B. Vangala
Summary: The classification of acute myeloid leukemia (AML) relies on genetic aberrations in leukemic cells, and accurate classification is crucial for risk stratification and treatment decisions. Current genetic diagnostics involve detecting single-nucleotide variants and larger structural and copy number variants. Optical Genome Mapping (OGM) is an unbiased method that can detect structural variants across the entire genome. This review summarizes the current knowledge of OGM in diagnosing hematological malignancies, particularly AML, and discusses its potential to replace older techniques and expand cytogenetic diagnostics.
Article
Multidisciplinary Sciences
Lizhi Dai, Xiaoxue Hu, Min Ji, Ningning Ma, Hang Xing, Jun- Jie Zhu, Qianhao Min, Ye Tian
Summary: Harnessing the programmable nature of DNA origami, researchers have demonstrated the ability to control structural features in crystalline materials and achieve different equilibrium phases and shapes using a single DNA origami morphology. By modulating the binding coordination with an allosteric factor, the DNA origami crystals undergo phase transitions and yield diverse crystal systems. This approach opens up new possibilities for developing crystalline materials with tunable properties and accessing a rich phase space.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Nanoscience & Nanotechnology
Shuyi Wu, Jonathan Jeffet, Assaf Grunwald, Hila Sharim, Noa Gilat, Dmitry Torchinsky, Quanshui Zheng, Shahar Zirkin, Luping Xu, Yuval Ebenstein
Review
Biochemical Research Methods
Christian Heck, Yael Michaeli, Ilko Bald, Yuval Ebenstein
CURRENT OPINION IN BIOTECHNOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Hila Sharim, Assaf Grunwald, Tslil Gabrieli, Yael Michaeli, Sapir Margalit, Dmitry Torchinsky, Rani Arielly, Gil Nifker, Matyas Juhasz, Felix Gularek, Miguel Almalvez, Brandon Dufault, Sreetama Sen Chandra, Alexander Liu, Surajit Bhattacharya, Yi-Wen Chen, Eric Vilain, Kathryn R. Wagner, Jonathan Pevsner, Jeff Reifenberger, Ernest T. Lam, Alex R. Hastie, Han Cao, Hayk Barseghyan, Elmar Weinhold, Yuval Ebenstein
Article
Biochemistry & Molecular Biology
Nikhil Jain, Tamar Shahal, Tslil Gabrieli, Noa Gilat, Dmitry Torchinsky, Yael Michaeli, Viola Vogel, Yuval Ebenstein
Article
Oncology
Sapir Margalit, Sigal Avraham, Tamar Shahal, Yael Michaeli, Noa Gilat, Prerna Magod, Michal Caspi, Shelly Loewenstein, Guy Lahat, Dinorah Friedmann-Morvinski, Revital Kariv, Rina Rosin-Arbesfeld, Shahar Zirkin, Yuval Ebenstein
INTERNATIONAL JOURNAL OF CANCER
(2020)
Article
Biochemistry & Molecular Biology
Vilhelm Mueller, Albertas Dvirnas, John Andersson, Vandana Singh, K. K. Sriram, Pegah Johansson, Yuval Ebenstein, Tobias Ambjornsson, Fredrik Westerlund
NUCLEIC ACIDS RESEARCH
(2019)
Article
Nanoscience & Nanotechnology
Nadezda Lapshina, Jonathan Jeffet, Gil Rosenman, Yuval Ebenstein, Tal Ellenbogen
Article
Chemistry, Analytical
Noa Gilat, Dmitry Torchinsky, Sapir Margalit, Yael Michaeli, Sigal Avraham, Hila Sharim, Nadav Elkoshi, Carmit Levy, Shahar Zirkin, Yuval Ebenstein
ANALYTICAL CHEMISTRY
(2020)
Article
Oncology
Vandana Singh, Pegah Johansson, Dmitry Torchinsky, Yii-Lih Lin, Robin Oz, Yuval Ebenstein, Ola Hammarsten, Fredrik Westerlund
TRANSLATIONAL ONCOLOGY
(2020)
Article
Chemistry, Multidisciplinary
Jonathan Jeffet, Sayan Mondal, Amit Federbush, Nadav Tenenboim, Miriam Neaman, Jasline Deek, Yuval Ebenstein, Yohai Bar-Sinai
Summary: This article presents a method for multiplexed single-molecule detection and quantification of a selected panel of miRs. The method does not depend on sequencing, requires a small amount of blood, and provides fast results by directly analyzing native, unamplified miRs. It combines compact spectral imaging and a machine learning-based detection scheme, allowing simultaneous multiplexed classification of multiple miR targets.
Article
Biochemical Research Methods
Yevgeni Nogin, Tahir Detinis Zur, Sapir Margalit, Ilana Barzilai, Onit Alalouf, Yuval Ebenstein, Yoav Shechtman
Summary: A new computational method called DeepOM, which utilizes deep learning, is presented for efficient retrieval of genomic information from a single microscopic image of intact DNA molecules. The method employs a convolutional neural network trained on simulated images of labeled DNA molecules to improve the alignment success rate of DNA images to genomic references.
Article
Biophysics
Noa Gilat, Dena Fridman, Hila Sharim, Sapir Margalit, Natalie R. Gassman, Yael Michaeli, Yuval Ebenstein
Summary: Mapping DNA damage and repair sites is crucial for understanding the impact of environmental exposures, genotoxicity, and human health. The RADD-seq technique allows for precise localization of DNA damage and repair sites, shedding light on cellular repair mechanisms and identifying genomic hotspots prone to mutation.
BIOPHYSICAL REPORTS
(2021)
Article
Biophysics
Jonathan Jeffet, Ariel Ionescu, Yael Michaeli, Dmitry Torchinsky, Eran Perlson, Timothy D. Craggs, Yuval Ebenstein
Summary: Color is a fundamental contrast mechanism in fluorescence microscopy, and CoCoS microscopy allows for real-time adjustment of spectral resolution to optimize sensitivity and throughput, enabling single-frame acquisition of multiple color channels with single-molecule sensitivity and significantly larger fields of view compared to previous techniques.
BIOPHYSICAL REPORTS
(2021)
Article
Chemistry, Multidisciplinary
Christian Heck, Dmitry Torchinsky, Gil Nifker, Felix Gularek, Yael Michaeli, Elmar Weinhold, Yuval Ebenstein
Article
Chemistry, Multidisciplinary
Dmitry Torchinsky, Yael Michaeli, Natalie R. Gassman, Yuval Ebenstein
CHEMICAL COMMUNICATIONS
(2019)
Review
Biochemical Research Methods
Pei-Ru Chen, Peng-Fei Xia
Summary: Carbon dioxide plays a crucial role in mitigating global climate change and supporting life on Earth. Synthetic biology and metabolic engineering offer a promising approach to enhance CO2 fixation by combining the advantages of autotrophic and heterotrophic organisms. This article reviews the current progress in constructing synthetic CO2 fixation pathways, discusses the underlying design principles and challenges, and provides insights into the future of carbon recycling through engineered synthetic carbon fixation pathways.
CURRENT OPINION IN BIOTECHNOLOGY
(2024)
