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

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

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

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

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

Tamar Kohn, Xavier Fernandez Cassi

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

2024

Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods

Jaspreet Singh Saini

Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral ...

Amer Soc Microbiology2024

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances

Hannes Markus Peter

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophicati ...

Amer Soc Microbiology2024

The microbial genomics of glacier-fed streams: adaptations to an extreme ecosystem

Massimo Bourquin

Glacier-fed streams are the cold, ultra-oligotrophic, and unstable streams that are fed by glacial meltwater. Despite these extreme conditions, they harbour a diverse and abundant microbial diversity that develops into biofilms, covering the boulders and s ...

EPFL2024

Optimised set of oligonucleotides for bulk rna barcoding and sequencing

Bart Deplancke, Riccardo Dainese, Daniel Alpern, Vincent Roland Julien Gardeux

The present invention relates generally to the field of nucleic acid sequencing and provides oligonucleotide molecules and barcodes contained therein. These oligonucleotide molecules and barcodes molecules are useful in sequencing to identify and resolve e ...

2023

Electronic readout of DNA amplification in nanoliter chambers. Strategies towards highly parallel semiconductor-based nucleic acid amplification testing

Saurabh Tomar

Polymerase chain reaction (PCR) has been the most significant driver in the field of nucleic acid testing (NAT) since its invention. Popularized as an abbreviation by the Covid-19 pandemic, PCR-based methods are the gold standard in the field of diagnostic ...

EPFL2023

Systematic benchmarking of single-cell ATAC-sequencing protocols

Bart Deplancke, Jörn Pezoldt, Camille Lucie Germaine Lambert

Benchmarking of scATAC-seq protocols demonstrates the effects of data quality on downstream analyses. ...

NATURE PORTFOLIO2023

Time-Resolved Scanning Ion Conductance Microscopy and Single-Molecule Spectroscopy

Samuel Mendes Leitão

The evolution of the 3D morphology is at the center of many relevant biological processes ranging from cellular differentiation to cancer invasion and metastasis. Microscopy techniques, such as electron microscopy (EM), super-resolution (SR) optical micros ...

EPFL2023

Hydromorphological assessment of sediment augmentation measures in gravel-bed rivers

Christian Mörtl

In the riverine environment, the riverscape, sediment and flow regime are essential drivers for natural habitat dynamics. Today, most water courses in Europe are regulated, and their natural dynamics are impaired. Flood releases coupled with the artificial ...

EPFL2023

Reduction of riverbed clogging related to sediment flushing

Giovanni De Cesare, Romain Maxime Dubuis

The ecological effects of dams on sediment and river flow have been subject to an increasing attention, leading to the implementation of mitigation measures such as environmental flow release and sediment replenishment. However, fine sediment dynamics have ...

CRC Press/Balkema2023

Clogging of riverbed substrates by fine sediment

Romain Maxime Dubuis

Riverbeds represent the habitat of numerous aquatic species. Exchanges between the groundwater, the hyporheic zone and the surface flow are also essential for river ecosystems. Fine sediment transported by rivers deposits inside or on top of the bed and mo ...

EPFL2023

Experimental characterization of root-reinforced riparian sediment deposits in a restored and widened river course

Giovanni De Cesare, Paolo Perona

The Arbogne River is located mainly in the Swiss canton of Fribourg. The River was meandering through the plane at a very low gradient and several exceptional historic floods with large sediment accumulation are mentioned. After important river training wo ...

2023

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics

Hamed Khakzad

Author summaryIn recent years, the application of deep learning represented a breakthrough in the mass spectrometry (MS) field by improving the assignment of the correct sequence of amino acids from observable MS spectra without prior knowledge, also known ...

PUBLIC LIBRARY SCIENCE2023

Modeling, analysis, and design of complex biological networks

Mohammadomid Oftadeh

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

EPFL2023

Ecosystem engineering by periphyton in Alpine proglacial streams

Matteo Roncoroni, Tom Ian Battin, Marc Aguet, Adrijan Selitaj, Davide Mancini

Stream periphytons are candidate ecosystem engineers in proglacial margins. Here, we quantify the extent to which they are engineers for the case of hillslope-fed tributaries in the terrace zones of proglacial margin alluvial plains. Candidate ecosystem en ...

WILEY2023

Ultrasonic sediment flux profiling with ACVP Technology: application to sediment-laden Boundary Layer flows

Giovanni De Cesare, David Hurther

Sediment transport in geophysical boundary layer flows has relevance to a broad spectrum of sciences ranging from the physical and chemical, to the biological, ecological and geological. Advances in sediment transport modelling and prediction strongly suff ...

2023

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

Construction of sequencing libraries from a ribonucleic acid (rna) using tailing and ligation of cdna (tlc)

Didier Trono, Christina Ernst

The present invention provides a method for preparing a sequencing library from a ribonucleic acid (RNA) sample. ...

2023

Iron Reduction in Profundal Sediments of Ultraoligotrophic Lake Tahoe under Oxygen-Limited Conditions

Meret Aeppli

Increased periods of bottom water anoxia in deep temperate lakes due to decreasing frequency and depth of water column mixing in a warming climate may result in the reductive dissolution of iron minerals and increased flux of nutrients from the sediment in ...

2023