Call us  +49(0)201-1834053

University of Duisburg and Essen, Aquatic Ecosystems Research Group, Universitätsstr. 5, D-45141 Essen, Germany

6th iBOL Conference

Post Image

Arne Beerman and Vasco Elbrecht have presented new research from the GeneStream project on the 6th International Barcode of Life Conference in Guelph (Canada). Arne Beermann compared morphological identifications and DNA barcoding of marcoinvertebrates and provided an overview of the state of DNA reference databases. Vasco Elbrecht presented new metabarcoding protocols, and stressed the issue that primer bias prevents the estimation […]

Read More

New Publication

Post Image

A new paper by Vasco und Florian has just been published in PLOS ONE. In the study, we were able to detect over 80% of invertebrate taxa from a bulk samples using DNA metabarcoding. Further more we showed that with PCR based methods, estimating taxon abundance is not possible in such diverse bulk samples. Monitoring should thus focus primarily on presence absence data […]

Read More

New Lab ‘member’: Tissue homogeniser for metabarcoding samples.

Post Image

DNA metabarcoding allows the identification of hundreds of specimens at the same time. This holds great potential for the assessment of freshwater and other ecosystems. However, the appropriate homogenisation of bulk samples for DNA extraction is critical, as we have shown in a recent study. For our future metabarcoding studies using complete benthic kick samples […]

Read More

Visiting Andres Aguilar (California State University)

Post Image

Monday last week, Vasco visited Andres Aguilar from California State University, to discuss eDNA methods for invasive species detection and metabardocing approaches. We would like to thank Andy for taking time and the RUB Research School for funding this research visit. Picture 1: Visiting Andys molecular laboratory.   Picture 2: Vasco Elbrecht (left) and Andres (Andy) Aguilar.

Read More

SWS meeting 2015!

Post Image

We also presented our current metabarcoding research on the SWS Annual Meeting 2015 (Providence, Rhode Island, US). Vasco Elbrecht used this opportunity to talk with colleges from the university Guelph and other institutions about current research and future directions in DNA barcoding. We would like to thank the Rub Research School Plus for financing this stay. Video: This video summaries the metabardocing research we […]

Read More

Science Communication course

Post Image

Science communication is really important! Vasco Elbrecht has meet up with Eric Francavilla to learn more about science communication. Eric Francavilla works together with scientists at the Pacific Northwest National Laboratory in Richland, Washington and helps scientists to communicate their findings to the public. Like the GeneStream Team, he is also producing YouTube videos. We learned many useful and specific things and […]

Read More

SFS 2015 meeting, USA

Post Image

Vasco presented results of our latest metabarcoding experiments and protocols on the Society for Freshwater Sciences, SFS 2015 in Milwaukee. Our DNA based method for biodiversity assessment in rivers works reliably, but we could show that it will be dificult to obtain abundance data on invertebrate species sampled. The paper has been formally accepted by […]

Read More

Genome of the Arizona Snowfly published!

Post Image

We are happy to announce the publication of the mitochondrial genome of the Arizona Snowily Mesocapnia arizonensis (Plecoptera, Capniidae). This is already our second plecopteran genome which we assembled from existing next generation sequence data. We would like to thank Stacey Lance who publicly provided the Illumina data we used on NCBI. Our publication is available […]

Read More

Metabarcoding: Samples from Finland!

Post Image

In cooperation with Kristian Meissner from the Finnish Environment Institute SYKE we will start our first big metabarcoding test soon. In the next weeks we will analyse thousands of invertebrates from 30 finish streams with DNA based metabarcoding methods. Picture 1: Over 30 samples are ready for processing in the laboratory. Picture 2: Many samples contain […]

Read More

eLearning project receives 5×5000 award!

We are happy to announce that eLearning project “Blended Genome” from Vasco Elbrecht and Florian Leese was awarded with the 5×5000 award of the Ruhr University Bochum. We combine course teaching with video tutorials on YouTube to allow students flexible leaning of handling Next Generation Sequencing data. The first videos are already available on YouTube. Picture: The […]

Read More

Zeitraffer-Videos als Playlist

Post Image

Auf unserem neuen offiziellen GeneStream YouTube Channel, sind nun alle Zeitraffer Aufnahmen vom Mesokosmos Experiment am Breitenbach verfügbar. Das neue Experiment ist bereits in Planung. Wir werden auch in diesem Jahr wieder neue Videos zu aktuellen Projekten veröffentlichen.  

Read More

Fotoshooting: Metabarcoding

Post Image

Last week, our benthic macroinvertebrates took part in a rather unconventional photo shooting: As part of a planned method publication we want to apply for the cover picture and have therefore put our inverts into scene. See an example below. Picture 1: Several hundred animals are grinded to fine powder using liquid nitrogen and a […]

Read More

Second MiSeq run successful

Post Image

The second MiSeq run is now finished. We are testing how many species we can reliably identify with our method. The lab work is now finished and we will analyse the data over the next month. It is planned to get these exiting results published by the end of this year. Additionally we have produced […]

Read More

Video: DNA extraction

Post Image

In this video we show how we homogenise our samples with liquid nitrogen to validate our metabarcoding methods. Once we have grinded the tissues to a fine powder, we divide it up on several reaction tubes and extract the DNA. With DNA barcoding and illumina sequencing we can identify the different species wich were present […]

Read More

2. Metabarcoding analysis

Post Image

After successfully completing our first community barcoding analysis, we have started the preparations for a second metabarcoding analysis. Here, we want to test if we can recover the DNA of a variety of different freshwater organisms (resembling a typical macrozoobenthos sample) with our current protocol. This is important to identify bulk macrozoobenthos samples, so molecular data can be […]

Read More

New video of the mesocosm experiment 2014!

Post Image

This year we installed and ran our mesocosm system at the Felderbach (Ruhr area, near Hattingen). In today’s video, we show how we prepared the bottom substrate our experimental channels to represent the habitat of the stream as much as possible. All channels were prepared in the same way. Picture 1: All channels were filled with the […]

Read More

MiSeq run successful!

Post Image

Today we received the first sequences for our community barcoding analyses. From a MiSeq sequencer Run we obtained 32 million sequences of 2x300bp length (PE reads ~ 16 million). We will analyse over 20 GB of sequence data in the following weeks. Picture 1: A first look on the sequences shows that they have excellent […]

Read More

Labwork started!

Post Image

In the past week we started to process samples for the metabarcoding analysis. By combining classical CO1 barcoding to identify specimens with high throughput next generation sequencing, we will be able to identify hundreds to thousands of invertebrate specimens simultaneously. Implementing this novel technique for freshwater invertebrates will be useful to study the response of […]

Read More

Experiment successfully completed!

Post Image

Yesterday, we have successfully completed our mesocosm experiment at the Felderbach in Germany. We started early in the morning to collect all animals, algae and leaf packs from the experimental channels. We and our colleges will analyse and test for a variety of response variables to the different stressors from microbiota to insect communities.Here you […]

Read More

(Deutsch) Umweltstress bei Bachkrebsen

Sorry, this entry is only available in German.

Read More

(Deutsch) Hauptphase Experiment

Sorry, this entry is only available in German.

Read More

Seeding of macrozoobenthos

Post Image

Few days ago we collected and added several thousand macroozoobenthic organisms from the Felderbacht into the experimental channels. This additional “seeding” step is important, as not all organisms enter the channels via the natural drift from the stream. By the extensive sampling of invertebrates in the river and randomised distribution into all 64 channels, we […]

Read More

Experiment has started

We have finished the experimental setup and since last Saturday (8.3.) the experiment is now running. Over the course of the next 3 weeks, organisms from the natural drift of the small stream, the Felderbach, will colonise our experimental channels. After the initial colonisation phase, we will test for the impact of different anthropogenic stressors […]

Read More

Experimental setup day 2 and 3

Post Image

Over the past two days we have continued with our work on the experimental setup. Picture 1: We drilled 64 holes in the wooden planks, so the water can leave the channels. Picture 2: Substrate for the mesocosms was taken directly from the river and dried on a plane. Picture 3: With a wooden construction […]

Read More

Experimental setup has started

Today we have started with the setup of the ExStream mesocosm field experiment at the Felderbach (Hattingen, North Rhine-Westphalia, Germany). The scaffolding was set up and pumps installed. In the next days the setup will be completed and we can start with the experiment next monday. Picture 1: Today all necessary equipment was brought to […]

Read More