Publications related to DNA extraction

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

Bart Deplancke, Daniel Migliozzi, Riccardo Dainese, Daniel Alpern, Gilles Weder, Mustafa Demir, Dariia Gudkova, Hüseyin Baris Atakan

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

Springer2024

A field-capable rapid plant DNA extraction protocol using microneedle patches for botanical surveying and monitoring

Sebastian Maerkl, Jonathan Selz, Nicolas Rémi Adam

PremiseA novel protocol for rapid plant DNA extraction using microneedles is proposed, which supports botanic surveys, taxonomy, and systematics. This protocol can be conducted in the field with limited laboratory skills and equipment. The protocol is vali ...

WILEY2023

Achieving high hybridization density at DNA biosensor surfaces using branched spacer and click chemistry

Sandrine Gerber, Alireza Kavand, Mounir Driss Mensi, Lucas Mayoraz, Perrine Agnes Edith Robin

The COVID-19 pandemic has highlighted the necessity to develop fast, highly sensitive and selective virus detection methods. Surface-based DNA-biosensors are interesting candidates for this purpose. Functionalization of solid substrates with DNA must be pr ...

2023

Polydimethylsiloxane microstructure-induced acoustic streaming for enhanced ultrasonic DNA fragmentation on a microfluidic chip

Martinus Gijs, Thomas Lehnert, Lin Sun

Next-generation sequencing (NGS) is an essential technology for DNA identification in genomic research. DNA fragmentation is a critical step for NGS and doing this on-chip is of great interest for future integrated genomic solutions. Here we demonstrate fa ...

ROYAL SOC CHEMISTRY2022

Bubble-enhanced ultrasonic microfluidic chip for rapid DNA fragmentation

Martinus Gijs, Thomas Lehnert, Lin Sun

DNA fragmentation is an essential process in developing genetic sequencing strategies, genetic research, as well as for the diagnosis of diseases with a genetic signature like cancer. Efficient on-chip DNA fragmentation protocols would be beneficial to pro ...

ROYAL SOC CHEMISTRY2022

Engineering Agrobacterium tumefaciens Adhesion to Target Cells

Alexandre Louis André Persat, Xavier Jean-Yves Pierrat, Jeremy Pak Hei Wong, Alix Kim Lan Pham

Agrobacterium tumefaciens is a plant pathogen commonly repurposed for genetic modification of crops. Despite its versatility, it remains inefficient at transferring DNA to many hosts, including to animal cells. Like many pathogens, physical contact between ...

AMER CHEMICAL SOC2022

m6A methylation potentiates cytosolic dsDNA recognition in a sequence-specific manner

Andrea Ablasser, Muhammet Fatih Gülen

Nucleic acid sensing through pattern recognition receptors is critical for immune recognition of microbial infections. Microbial DNA is frequently methylated at the N-6 position of adenines (m6A), a modification that is rare in mammalian host DNA. We show ...

ROYAL SOC2021

Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams

Tom Ian Battin, Hannes Markus Peter, Jade Brandani, Susheel Bhanu Busi, Stylianos Fodelianakis, Paraskevi Pramateftaki

Glacier-fed streams (GFS) are harsh ecosystems dominated by microbial life organized in benthic biofilms, yet the biodiversity and ecosystem functions provided by these communities remain under-appreciated. To better understand the microbial processes and ...

PEERJ INC2020

BAF restricts cGAS on nuclear DNA to prevent innate immune activation

Mahmut Selman Sakar, Beat Fierz, Andrea Ablasser, Baptiste Claude André Guey, Alexiane Clara Decout, Murat Kaynak, Kristina Makasheva, Marilena Wischnewski

The appearance of DNA in the cytosol is perceived as a danger signal that stimulates potent immune responses through cyclic guanosine monophosphate–adenosine monophosphate synthase (cGAS). How cells regulate the activity of cGAS toward self-DNA and guard a ...

American Association for the Advancement of Science2020

Establishing a Ternary System for Optical Monitoring of DNA-Protein Interactions with Single-Walled Carbon Nanotubes

Shang-Jung Wu

DNA-protein interactions lie at the crux of life's essential processes. As such, various technologies have been developed to characterize these interactions. The distinct advantages of these technologies can be leveraged to study different facets of these ...

EPFL2020

Redox Properties of Native and Damaged DNA from Mixed Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations

Ursula Röthlisberger, Ivano Tavernelli, Polydefkis Diamantis

The redox properties of two large DNA fragments composed of 39 base pairs, differing only by an 8-oxoguanine (8oxoG) defect replacing a guanine (G), were investigated in physiological conditions using mixed quantum mechanical/molecular mechanical (QM/MM) m ...

AMER CHEMICAL SOC2020

Neighbor predation linked to natural competence fosters the transfer of large genomic regions in Vibrio cholerae

Melanie Blokesch, Nicolas Jean Philippe Guex, Sandrine Stutzmann, Christian Iseli, Candice Stoudmann, Noémie Matthey

Natural competence for transformation is a primary mode of horizontal gene transfer. Competent bacteria are able to absorb free DNA from their surroundings and exchange this DNA against pieces of their own genome when sufficiently homologous. However, the ...

2019

Engineering a stable future for DNA-origami as a biomaterial

Maartje Martina Cornelia Bastings, Eva Eugene Kurisinkal, Hale Bila

DNA as a biomaterial has evoked great interest as a potential platform for therapeutics and diagnostics and as hydrogel scaffolds due to the relative ease of programming its robust and uniform shape, site-specific functionality and controlled responsive be ...

ROYAL SOC CHEMISTRY2019

Benchmarking protocols for the metagenomic analysis of stream biofilm viromes

Tom Ian Battin, Hannes Markus Peter, Jade Brandani, Massimo Bourquin, Meriem Bekliz

Viruses drive microbial diversity, function and evolution and influence important biogeochemical cycles in aquatic ecosystems. Despite their relevance, we currently lack an understanding of their potential impacts on stream biofilm structure and function. ...

PeerJ2019

Evaluation of Auramine O staining and conventional PCR for leprosy diagnosis: A comparative cross-sectional study from Ethiopia

Stewart Cole, Charlotte Avanzi, Philippe Busso

Background ...

PUBLIC LIBRARY SCIENCE2018

Simultaneous preservation of the DNA quality, the community composition and the density of freshwater oligochaetes for the development of genetically based biological indices

Régis Lionel Vivien

Introduction. Oligochaetes are recognized as valuable bioindicators of sediment quality in streams and lakes. The development of an oligochaete index based on the identification of specimens using DNA barcodes requires a method for simultaneously preservin ...

2018

Camera Attribution Forensic Analyzer in the Encrypted Domain

Juan Ramón Troncoso-Pastoriza

Digital media forensics must deal with constantly increasing volumes of data. In order to efficiently scale up, outsourcing computation becomes an appealing solution. However, due to the highly sensitive nature of forensic data, its privacy must be protect ...

IEEE2018

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

Giovanna Ambrosini, Philipp Bucher, Romain Fernand Pietro Groux

Transcription factors (TFs) regulate gene expression by binding to specific short DNA sequences of 5 to 20-bp to regulate the rate of transcription of genetic information from DNA to messenger RNA. We present PWMScan, a fast web-based tool to scan server-r ...

2018

Improvement of breast cancer diagnosis through microfluidics

Huu Tuan Nguyen

In breast cancer, 15-20% of cases are reported with overexpression of human epidermal growth factor receptor 2 (HER2) that causes rapid cancer progression and poor prognosis. Fortunately, HER2-targeted therapy using specific antibodies such as Trastuzumab ...

EPFL2018

Genomics: a Swiss army knife to fight leprosy

Charlotte Avanzi

Leprosy, a highly disabling and stigmatizing infectious disease, is caused by Mycobacterium leprae and the newly discovered agent, Mycobacterium lepromatosis. Though treatable with antibiotics, leprosy has still not been eradicated, and around 200,000 new ...

EPFL2018