Jen and Sarah share their internship experiences in the TU Magazine.
This week, Michael and Jen left our group to continue their studies at their home universities. Michael is now working at Uni Marburg to earn his doctoral degree. Jen is back at UC San Diego to complete her undergraduate studies. Michael performed an amazing coexpression analysis on Arabidopsis thaliana data to identify novel genes in the anthocyanin biosynthesis. Many thanks for the excellent help in setting up the lab and also supporting the iGEM teams in 2022 and 2023! Jen studied cacao genomes to understand their specific properties. All the best for the future!
Boas presented some research of the group in his talk about comparative genomics at the section meeting biodiversity & evolution 2023 in Gießen. It was a successful meeting with many fruitful discussions, which might lead to future collaborations. The photo shows a figure from a study about the evolution of the Apiaceae FNS I (Pucker & Iorizzo, 2023).
Lena Fürstenberg examined the anthocyanin biosynthesis in the stinging nettle (Urtica dioica) for her bachelor's thesis. The medicinal plant of the year 2022 is renowned for producing various flavonoids, including anthocyanins. These compounds are formed in response to stress and accumulated within the plant, resulting in an intense red coloring of the leaves. The findings of this study were presented and discussed with the research group.
Rheum nobile grows in the Himalayas and is famous for its adaptation to the extreme conditions at high altitudes. The plant has an outer layer of leaves that serve for insulation and protection against UV radiation. This helps to increase the temperature inside the plant and safeguard the vital parts of the plant from the harmful effects of UV radiation. The genome sequence of Rheum nobile has now been published by Feng, Pucker, Kuang et al., 2023, providing an important foundation for understanding the biology of this species.
Our new BioInfTool server is online and allows the use of various bioinformatics tools without any installation. Through a web browser, genes involved in flavonoid biosynthesis can be identified in new plant species, or transcription factor families can be investigated. We welcome feedback and suggestions for additional tools that we should include in the future. Many thanks to Andreas Rempel and de.NBI for their excellent support!
Boas visited the research group Biochemistry of Plant Specialised Metabolites (University of Hannover) and enjoyed numerous discussions about biotechnology and specialized metabolism in plants. As part of a seminar, various projects for omics-based elucidation of biosynthetic pathways were presented. Many thanks for the invitation and the amazing time in Hannover!
We have performed direct RNA sequencing using our MinION. Melina extracted RNAs from flower samples of an aquatic plant. Melina and Benni prepared these RNAs for sequencing by creating complementary cDNA and attaching adaptors. After quality control, sequencing was performed on an R9 flow cell using one of our MinIONs. The length distribution shows an average read length of several hundred nucleotides, as many mRNAs are quite short. These data will provide an important foundation for gene identification. Many exciting experiments using this technology are planned!
As part of her Bachelor thesis, Corinna Thoben developed a tool for the automatic identification and annotation of bHLH transcription factors in the genome sequences of plants. A corresponding preprint was just published on bioRxiv: Automatic annotation of the bHLH gene family in plants. The bHLH_annotator is freely available via GitHub.
Today, the iGEM team 2023 of TU Braunschweig presented the plan for their project Li+onSwitch in a public talk in the BRICS. All interested members of TU Braunschweig and other research institutes in Braunschweig participated. Ronja and Susanna gave an excellent talk. Additional updates will be shared through the team's website.
All teaching materials of our "Data Literacy in Genome Research" course are now available through Twillo. The development of this course is funded by the Stiftung Innovation in der Hochschullehre. All files are available on github, but we hope for an increased visibility through Twillo. Additional information about this teaching innovation are available on the DaLiP website.
Our iGEM team TU Braunschweig 2023 was interviewed by the local newspaper. Now, you can find the content of that interview in the published newspaper article (in German).
We did a group trip and went bowling. It was a funny evening with many surprises.
Boas visited the research group Systematics, Biodiversity and Evolution of Plants (LMU Munich) and enjoyed numerous discussions about the evolution of biosynthesis pathways. The invited talk covered our recent projects about the evolution of biosynthesis pathways with a focus on genomics. Plants in the greenhouses of the Botanical Garden Munich-Nymphenberg are impressive. Many thanks for the invitation and the great time in Munich!
Boas visited the research group Physiology of Yield Stability (University of Hohenheim) and enjoyed inspiring discussions about the biosynthesis of specialized metabolites. The invited talk covered the recent insights into the mutual exclusion of anthocyanins and betalains in the Caryophyllales. Many thanks for the invitation and the excellent organisation!
The experiences and success of the iGEM team TU Braunschweig 2022 were summarized in the newsletter of the Braunschweiger Hochschulbunds (BHB) (in German) by Christian Köcher. Please find details about the 'LionDetect' project there.
We enjoyed a nice evening with snacks, waffles, and drinks.
On Friday evening, we enjoyed the Christmas market in the historic city center of Braunschweig. The relaxed atmosphere, hot wine punch, and tasty food facilitated conversations between the group members.
Due to the nice weather we decided to have a last barbecue in 2022. There is always something to celebrate and this is a great opportunity for exchange in the team.
For over 50 years, researchers have investigated the red, yellow, and blue pigments of plants in the Caryophyllales. Only plants in this order can have betalains, while most other land plants are pigmented by anthocyanins. However, the betalain-pigmented Caryophyllales plants do not accumulate anthocyanins. Recent studies by Fan et al., 2020 (now retracted) and Zhou et al., 2020 claimed that anthocyanins would contribute to the pigmentation of red pitayas. We previously addressed issues in the Fan et al., 2020 paper in our response (Pucker et al., 2022). Now, the paper by Zhou et al., 2020 was addressed by two correspondence articles just published in BMC Genomics. Both refute the contribution of anthocyanins to pigmentation in pitaya:
Pucker, B., Brockington, S.F. The evidence for anthocyanins in the betalain-pigmented genus Hylocereus is weak. BMC Genomics 23, 739 (2022). https://doi.org/10.1186/s12864-022-08947-1
Khan, M.I. The reported colour formation mechanism in pitaya fruit through co-accumulation of anthocyanins and betalains is inconsistent and fails to establish the co-accumulation. BMC Genomics 23, 740 (2022). https://doi.org/10.1186/s12864-022-08957-z
If you are interested in this topic, please have a look at these recent publications: Timoneda et al., 2019, Sheehan et al., 2020, and Pucker et al., 2022.
Shakunthala shares her experiences in Germany in a recent blog post. A particular focus is on her research experiences in our group at TU Braunschweig.
Maria offers a project with the title
Unwrapping the wonders of chocolate: from candy to functional food
for international students as part of the RISE program of the DAAD. Please contact Maria directly if you are interested in additional details. Would you like to apply? You can do this through the DAAD portal. Here is the project code: Braunschweig_BI_CH_4798.
Here is the blog post about the future of long read sequencing in plant genomics: "From finding flavonoids to the ‘dark matter’ of T-DNA insertions — investigating plant genomes with nanopore sequencing".
Boas was invited to give a talk about applications of long read sequencing in plant genomics as part of the APBioNET seminar series.
Life science students learnt the basis of Python3 and completed several application exercises. Slides and materials are available via github. Students can expressed there interest in taking this course in the future can send an email to Boas Pucker.
Melina and Benni (s. photo) are excited about the flower color change of Victoria spec. They collected samples during the summer of 2022 and would like to investigate these in detail to understand the molecular mechanisms. Therefore, they are collecting support through a crowd funding project at betterplace.
Many thanks to de.NBI for excellent support! Our research would not be possible without de.NBI. The details are described in a testimonial on the de.NBI website.
Successful (international) collaborations resulted in three new publications:
A proposal for "Freiraum 2022" received very positive evaluations and funding. As of September 2022, we are preparing several courses around 'plant genomics' and 'data literacy'. More details are available here (in German).
Boas Pucker gave a presentation at International Conference of the German Society for Plant Sciences 2022 in Bonn. Topic of this talk were molecular mechanisms that explain mutual exclusion of anthocyanins and betalains in the Caryophyllales. This involved KIPEs which was important for the identification of anthocyanin biosynthesis genes.
We enjoyed the nice weather in our beautiful garden. The visit of a future Master student, Michael, was an excellent reason for a barbecue.
We released an updated version of KIPEs on our web server. The changes between KIPEs3 and the original KIPEs version are described in a prepint:
We started the sequencing of two plant genomes. The picture shows the state of nanopores during the sequencing process. Green indicates that the nanopores are active and sequence DNA strands. First analysis of the datasets are promising. More details about this innovative sequencing technology are available in our recent review article.
We used the nice weather to take a new group picture.
A recent article in TU Magazin reports about the iGEM team TU_Braunschweig 2022, which is working on the laboratories of our group. The endless possibilities of an iGEM participation are highlighted in this article.
The iGEM team TU_Braunschweig 2022 is now officially registered for the competition. iGEM is a synthetic biology competition for student teams from around the world. Teams of TU Braunschweig participated very successfully in 2013 and 2014.
Our bioinformatic tools (MYB_annotator & KIPEs) are now available through a web server. This web server enables researchers without any bioinformatic skills to benefit from these tools. Files with sequences are uploaded to start the analysis. Once the analysis is completed, a compressed archive of all result files will be offered for download. Currently, the choices of parameters are restricted. The addition of other tools is in progress.
We wrote a review article about the development and current state of long read sequencing technologies with focus on plant genomics. This review covers the sequencing technologies provided by ONT and PacBio as well as applications of these technologies. Future challenges of plant genomics are presented.
Our publication "Comparison of Read Mapping and Variant Calling Tools for the Analysis of Plant NGS Data" was selected by the Editor as one of the promising and important studies in the field. We compared different bioinformatic tools for the alignment of reads against a reference sequence and the following identification of sequence differences.
We are currently informing students at TU Braunschweig about the opportunity to participate in iGEM, the international competition for synthetic biology. More details are available here: iGEM (in German).
An interview with Boas Pucker was published under the title "In Search of Drug Candidates in the Plant Genome" in the TU Magazin.
In October, the results of three projects were published as preprints on bioRxiv:
Boas Pucker was accepted as member of the Braunschweig Integrated Centre of Systems Biology (BRICS) on the 11th October 2021.
Since the 1st October 2021, the group is located at the TU Braunschweig in the Institute of Plant Biology (Mendelssohnstrasse 4). Details about research and resulting publications are available on the dedicated pages.
News regarding the group can be retrieved automatically via email. This includes open positions, publications, and other important events. Please click on the link below and enter your email address on the next page to subscribe/unsubscribe.
The offer to start a group with focus on Plant Biotechnology and Bioinformatics was accepted in spring 2021. There will be a PhD position available. Stay tuned for updates!