Publications related to DNA barcoding

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

DNA modifications impact natural transformation of Acinetobacter baumannii

Melanie Blokesch, Nicolas Jean Philippe Guex, Christian Iseli, Alexandre Lemopoulos, Nina Vesel

Acinetobacter baumannii is a dangerous nosocomial pathogen, especially due to its ability to rapidly acquire new genetic traits, including antibiotic resistance genes (ARG). In A. baumannii, natural competence for transformation, one of the primary modes o ...

2023

Evaluation of genetic demultiplexing of single-cell sequencing data from model species

Clement Helsens

Single-cell sequencing (sc-seq) provides a species agnostic tool to study cellular processes. However, these technologies are expensive and require sufficient cell quantities and biological replicates to avoid artifactual results. An option to address thes ...

LIFE SCIENCE ALLIANCE LLC2023

From Trees to Barcodes and Back Again: A Combinatorial, Probabilistic and Geometric Study of a Topological Inverse Problem

Adélie Eliane Garin

In this thesis, we investigate the inverse problem of trees and barcodes from a combinatorial, geometric, probabilistic and statistical point of view. Computing the persistent homology of a merge tree yields a barcode B. Reconstructing a tree from B invol ...

EPFL2022

Taxonomic revision of the Eudicella White, 1839 complex, with description of three new subgenera

Michele De Palma

Morphological and DNA barcoding analysis of representative taxa in the Eudicella White complex identified five distinct subgenera, three of which are established herein: Eudicella (Coelorrhinella) n. subg., Eudicella (Aneurhina) n. subg., and Eudicella (Ce ...

2021

High-throughput DNA barcoding of oligochaetes for abundance-based indices to assess the biological quality of sediments in streams and lakes

Benoît Jean Dominique Ferrari, Régis Lionel Vivien

Aquatic oligochaete communities are valuable indicators of the biological quality of sediments in streams and lakes, but identification of specimens to the species level based on morphological features requires solid expertise in taxonomy and is possible o ...

Nature Research2020

Barcoding analysis and taxonomic revision of Goliathus Lamarck, 1802 (Scarabaeidae, Cetoniinae)

Michele De Palma

We conducted barcoding analysis of valid taxa in the genus Goliathus Lamarck, 1802 and clarified their relationships. Specimens of Goliathus goliatus (Drury, 1770) sampled in tropical rainforests from Cameroon to Kenya display degrees of genetic and phenot ...

2020

The foreign oligochaete species Quistadrilus multisetosus (Smith, 1900) in Lake Geneva: morphological and molecular characterization and environmental influences on its distribution

Benoît Jean Dominique Ferrari, Régis Lionel Vivien

The presence of the oligochaete species Quistadrilus multisetosus (Smith, 1900) originating from North America has been mentioned for several decades in Europe, the Middle East and Russia. Its distribution and abundance in Europe is still unknown but it ca ...

2020

The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards

Jeffrey David Jensen, Kristen Kay Irwin, Susanne Petra Pfeifer, Stefan Jean Laurent

By combining well-established population genetic theory with high-throughput sequencing data from natural populations, major strides have recently been made in understanding how, why, and when vertebrate populations evolve crypsis. Here, we focus on backgr ...

NATURE PUBLISHING GROUP2020

Self-organization of parS centromeres by the ParB CTP hydrolase

Paolo De Los Rios, Stefano Zamuner

ParABS systems facilitate chromosome segregation and plasmid partitioning in bacteria and archaea. ParB protein binds centromeric parS DNA sequences and spreads to flanking DNA. We show that ParB is an enzyme that hydrolyzes cytidine triphosphate (CTP) to ...

American Association for the Advancement of Science2019

280 Birds with One Stone: Inducing Multilingual Taxonomies from Wikipedia Using Character-Level Classification

Karl Aberer, Rémi Philippe Lebret, Hamza Harkous, Amit Gupta

We propose a novel fully-automated approach towards inducing multilingual taxonomies fromWikipedia. Given an English taxonomy, our approach first leverages the interlanguage links of Wikipedia to automatically construct training datasets for the is-a relat ...

ASSOC ADVANCEMENT ARTIFICIAL INTELLIGENCE2018

A microfluidic array for high-content screening at whole-organism resolution

Johan Auwerx, Martinus Gijs, Matteo Cornaglia, Laurent Mouchiroud, Daniel Migliozzi

A main step for the development and the validation of medical drugs is the screening on whole organisms, which gives the systemic information that is missing when using cellular models. Among the organisms of choice, Caenorhabditis elegans is a soil worm w ...

SPIE-INT SOC OPTICAL ENGINEERING2018

Extraction of cell-free DNA from urine, using polylysine-coated silica particles

Paul Refinetti, Sho Takano

DNA analysis is used for a variety of purposes, including disease diagnosis and DNA profiling; this involves extracting DNA from living organisms. In this study, we prepared polycationic silica particles to extract DNA that has the negatively charged phosp ...

Springer Heidelberg2017

Integrating Gene Synthesis and MITOMI for Rapid Protein Engineering

Matthew Christopher Blackburn

The research described within this thesis is primarily motivated by two fields of science with reversed, yet complementary, approaches to addressing the same essential objective: manipulating and understanding the complex program of life. Whereas synthetic ...

EPFL2016

COI Barcoding of Nebelid Testate Amoebae (Amoebozoa: Arcellinida): Extensive Cryptic Diversity and Redefinition of the Hyalospheniidae Schultze

Edward Mitchell, Enrique Lara, Thierry Jean Heger

We used Cytochrome Oxidase Subunit 1 (COI) to assess the phylogenetic relationships and taxonomy of Nebela sensu stricto and similar taxa (Nebela group, Arcellinida) in order to clarify the taxonomic validity of morphological characters. The COI data not o ...

2012

Controlling a Single DNA Molecule in an Electric Field by Means of In Situ Atomic Force Microscopy

Giovanni Dietler, Jae Sun Jeong

DNA is the bio-polymer containing the genetic information needed for the development and functioning for all living organisms. It has a polymeric structure consisting of units called nucleotides, each consisting of a non-polar, hydrophobic interior (the ba ...

Electrochemical Society2012

PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data

Christof Holliger, Julien Maillard, Pierre Rossi, David Gregory Weissbrodt, Jacques Rougemont, Noam Shani, Lucas Sinclair

Background: In molecular microbial ecology, massive sequencing is gradually replacing classical fingerprinting techniques such as terminal-restriction fragment length polymorphism (T-RFLP) combined with cloning-sequencing for the characterization of microb ...

BioMed Central2012

Comparing COI and SSU rDNA barcodes for assessing the diversity and phylogenetic relationships of cyphoderiid testate amoebae (Rhizaria: Euglyphida)

Edward Mitchell, Enrique Lara, Thierry Jean Heger

The mitochondrial Cytochrome Oxidase Subunit 1 gene (COI) has been promoted as an ideal “DNA barcode” for animal species and other groups of eukaryotes. However, the utility of the COI marker for species level discrimination and for phylogenetic analyses h ...

2011

Quorum Sensing Contributes to Natural Transformation of Vibrio cholerae in a Species-Specific Manner

Melanie Blokesch, Patrick Martin Seitz, Gaia Francesca Marianne Suckow

Although it is a human pathogen, Vibrio cholerae is a regular member of aquatic habitats, such as coastal regions and estuaries. Within these environments, V. cholerae often takes advantage of the abundance of zooplankton and their chitinous molts as a nut ...

American Society for Microbiology2011