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Concept

Métatranscriptomique

Publications associées (16)

Gene expression of Pocillopora damicornis coral larvae in response to acidification and ocean warming

Nils Rädecker

Objectives The endosymbiosis with Symbiodiniaceae is key to the ecological success of reef-building corals. However, climate change is threatening to destabilize this symbiosis on a global scale. Most studies looking into the response of corals to heat str ...

BMC2024

Surfactant Treatment for Efficient Gene Detection of Enteric Viruses and Indicators in Surface Water Concentrated by Ultrafiltration

Shotaro Torii

The hollow fiber ultrafiltration (HFUF)-based microbial concentration method is widely applied for monitoring pathogenic viruses and microbial indicators in environmental water samples. However, the HFUF-based method can co-concentrate substances that inte ...

SPRINGER2023

Sulfur-cycling chemolithoautotrophic microbial community dominates a cold, anoxic, hypersaline Arctic spring

Ianina Altshuler

Background Gypsum Hill Spring, located in Nunavut in the Canadian High Arctic, is a rare example of a cold saline spring arising through thick permafrost. It perennially discharges cold (similar to 7 degrees C), hypersaline (7-8% salinity), anoxic (similar ...

BMC2023

Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium

Rizlan Bernier-Latmani, Karin Lederballe Meibom, Karen Elda Viacava Romo, Nicolas Louis Maurice Jacquemin, Matthew Charles Reid, Jiangtao Qiao

Soil microbiomes harbor unparalleled functional and phylogenetic diversity and are sources of novel metabolisms. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype ...

2022

Dual proteomics of Drosophila melanogaster hemolymph infected with the heritable endosymbiont Spiroplasma poulsonii

Bruno Lemaitre, Florent François Masson, Samuel Rommelaere, Alice Marra, Fanny Schüpfer

Insects are frequently infected with heritable bacterial endosymbionts. Endosymbionts have a dramatic impact on their host physiology and evolution. Their tissue distribution is variable with some species being housed intracellularly, some extracellularly ...

2021

Intestinal stem cells differentiation and its application in cancer therapy

Maxim Norkin

Colorectal cancer (CRC) is one of the deadliest cancers worldwide. Despite extensive research in the field, new therapies targeting CRC are in urgent need. CRC is a highly heterogeneous disease with high levels of intra- and inter-patient heterogeneity. Ca ...

EPFL2021

A community-based transcriptomics classification and nomenclature of neocortical cell types

Parviz Ghaderi

To understand the function of cortical circuits, it is necessary to catalog their cellular diversity. Past attempts to do so using anatomical, physiological or molecular features of cortical cells have not resulted in a unified taxonomy of neuronal or glia ...

NATURE PUBLISHING GROUP2020

BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing

Bart Deplancke, David Hacker, Vincent Roland Julien Gardeux, Daniel Alpern, Bastien Mangeat, Antonio Carlos Alves Meireles Filho, Julie Marie Russeil

Despite its widespread use, RNA-seq is still too laborious and expensive to replace RT-qPCR as the default gene expression analysis method. We present a novel approach, BRB-seq, which uses early multiplexing to produce 3 cDNA libraries for dozens of sample ...

2019

Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation

Suliana Manley, Beat Fierz, David Michael Suter, Christian Sieben, Aleksandr Benke, Andrea Callegari

Transcription factors (TFs) regulate gene expression in both prokaryotes and eukaryotes by recognizing and binding to specific DNA promoter sequences. In higher eukaryotes, it remains unclear how the duration of TF binding to DNA relates to downstream tran ...

2019

SQC: Secure Quality Control for Meta-Analysis of Genome-Wide Association Studies

Jean-Pierre Hubaux, Jacques Fellay, Zhicong Huang, Huang Lin

Motivation: Due to the limited power of small-scale genome-wide association studies (GWAS), researchers tend to collaborate and establish a larger consortium in order to perform large-scale GWAS. Genome-wide association meta-analysis (GWAMA) is a statistic ...

Oxford University Press2017

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

GuavaH: a compendium of host genomic data in HIV biology and disease

Jacques Fellay, Paul Jack Mc Laren, Istvan Bartha

Background: There is an ever-increasing volume of data on host genes that are modulated during HIV infection, influence disease susceptibility or carry genetic variants that impact HIV infection. We created GuavaH (Genomic Utility for Association and Viral ...

BioMed Central2014

The restricted metabolism of the obligate organohalide respiring bacterium Dehalobacter restrictus: lessons from tiered functional genomics

Christof Holliger, Julien Maillard, Hauke Smidt, Aamani Rupakula Boyanapalli

Dehalobacter restrictus strain PER-K23 is an obligate organohalide respiring bacterium, which displays extremely narrow metabolic capabilities. It grows only via coupling energy conservation to anaerobic respiration of tetra- and trichloroethene with hydro ...

2013

Identification of HMX1 target genes: A predictive promoter model approach

Purpose: A homozygous mutation in the H6 family homeobox 1 (HMX1) gene is responsible for a new oculoauricular defect leading to eye and auricular developmental abnormalities as well as early retinal degeneration (MIM 612109). However, the HMX1 pathway rem ...

Molecular Vision2013

High-throughput approaches for the analysis of extrinsic regulators of stem cell fate

Matthias Lütolf, Adrian Ranga

The complexity of stem cell niches poses a tremendous challenge to understanding mechanisms of extrinsic regulation of stem cell fate. In order to better understand niche signaling and its effect on stem cell fate choices, in vitro systems are being engine ...

2012

Dissecting regulatory networks in host-pathogen interaction using chIP-on-chip technology

Stewart Cole, Claudia Sala

Understanding host-microbe interactions has been greatly enhanced by our broadening knowledge of the regulatory mechanisms at the heart of pathogenesis. The "transcriptomics" approach of measuring global gene expression has identified genes involved in bac ...

2009