Publications

@article{nokey_67,

title = {Rfam 15: RNA families database in 2025},

author = {Nancy Ontiveros-Palacios and Emma Cooke and Eric P. Nawrocki and Sandra Triebel and Manja Marz and Elena Rivas and Sam Griffiths-Jones and Anton I. Petrov and Alex Bateman and Blake Sweeney},

doi = {10.1101/2024.09.23.614430},

year  = {2024},

date = {2024-09-24},

journal = {bioRxiv},

keywords = {database, ncRNAs, RNA structure, RNA-RNA interactions},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Data report on gene expression after hepatic portal vein ligation (PVL) in rats},

author = {Daria Meyer and Joanna Kosacka and Martin von Bergen and Bruno Christ and Manja Marz},

doi = {10.3389/fgene.2024.1421955},

year  = {2024},

date = {2024-08-21},

journal = {Front Genet},

volume = {15},

pages = {1421955},

keywords = {liver, RNA / transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_66,

title = {Endogenous Bornavirus-like Elements in Bats: Evolutionary Insights from the Conserved Riboviral L-Gene in Microbats and Its Antisense Transcription in \textit{Myotis daubentonii}},

author = {Muriel Ritsch and Tom Eulenfeld and Kevin Lamkiewicz and Andreas Schoen and Friedemann Weber and Martin Hölzer and Manja Marz},

doi = {10.3390/v16081210},

issn = {1999-4915},

year  = {2024},

date = {2024-07-27},

urldate = {2024-07-27},

journal = {Viruses},

volume = {16},

issue = {8},

abstract = {Bats are ecologically diverse vertebrates characterized by their ability to host a wide range of viruses without apparent illness and the presence of numerous endogenous viral elements (EVEs). EVEs are well preserved, expressed, and may affect host biology and immunity, but their role in bat immune system evolution remains unclear. Among EVEs, endogenous bornavirus-like elements (EBLs) are bornavirus sequences integrated into animal genomes. Here, we identified a novel EBL in the microbat \textit{Myotis daubentonii}, EBLL-Cultervirus.10-MyoDau (short name is CV.10-MyoDau) that shows protein-level conservation with the L-protein of a \textit{Cultervirus} (Wuhan sharpbelly bornavirus). Surprisingly, we discovered a transcript on the antisense strand comprising three exons, which we named AMCR-MyoDau. The active transcription in \textit{Myotis daubentonii} tissues of AMCR-MyoDau, confirmed by RNA-Seq analysis and RT-PCR, highlights its potential role during viral infections. Using comparative genomics comprising 63 bat genomes, we demonstrate nucleotide-level conservation of CV.10-MyoDau and AMCR-MyoDau across various bat species and its detection in 22 \textit{Yangochiropera<i/> and 12 \textit{Yinpterochiroptera} species. To the best of our knowledge, this marks the first occurrence of a conserved EVE shared among diverse bat species, which is accompanied by a conserved antisense transcript. This highlights the need for future research to explore the role of EVEs in shaping the evolution of bat immunity.},

keywords = {phylogenetics, RNA / transcriptomics, virus host interaction, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_64,

title = {Exploring the impact of primer length on efficient gene detection via high-throughput sequencing},

author = {Julia Micheel and Aram Safrastyan and Franziska Aron and Damian Wollny},

doi = {10.1038/s41467-024-49685-0},

year  = {2024},

date = {2024-07-12},

journal = {Nature Communications},

volume = {15},

issue = {1},

abstract = {Reverse transcription (RT) is a crucial step in most RNA analysis methods. Optimizing protocols for this initial stage is critical for effective target detection, particularly when working with limited input RNA. Several factors, such as the input material quality and reaction conditions, influence RT efficiency. However, the effect of RT primer length on gene detection efficiency remains largely unknown. Thus, we investigate its impact by generating RNA-seq libraries with random RT primers of 6, 12, 18, or 24 nucleotides. To our surprise, the 18mer primer shows superior efficiency in overall transcript detection compared to the commonly used 6mer primer, especially in detecting longer RNA transcripts in complex human tissue samples. This study highlights the critical role of primer length in RT efficiency, which has significant potential to benefit various transcriptomic assays, from basic research to clinical diagnostics, given the central role of RT in RNA-related analyses.},

keywords = {RNA / transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_62,

title = {Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus},

author = {Sandra Triebel and Kevin Lamkiewicz and Nancy Ontiveros and Blake Sweeney and Peter F. Stadler and Anton I. Petrov and Michael Niepmann and Manja Marz},

doi = {10.1038/s41598-024-62897-0},

year  = {2024},

date = {2024-07-02},

urldate = {2024-07-02},

journal = {Scientific Reports},

volume = {14},

issue = {1},

abstract = {Hepatitis C virus (HCV) is a plus-stranded RNA virus that often chronically infects liver hepatocytes and causes liver cirrhosis and cancer. These viruses replicate their genomes employing error-prone replicases. Thereby, they routinely generate a large ‘cloud’ of RNA genomes (quasispecies) which—by trial and error—comprehensively explore the sequence space available for functional RNA genomes that maintain the ability for efficient replication and immune escape. In this context, it is important to identify which RNA secondary structures in the sequence space of the HCV genome are conserved, likely due to functional requirements. Here, we provide the first genome-wide multiple sequence alignment (MSA) with the prediction of RNA secondary structures throughout all representative full-length HCV genomes. We selected 57 representative genomes by clustering all complete HCV genomes from the BV-BRC database based on k-mer distributions and dimension reduction and adding RefSeq sequences. We include annotations of previously recognized features for easy comparison to other studies. Our results indicate that mainly the core coding region, the C-terminal NS5A region, and the NS5B region contain secondary structure elements that are conserved beyond coding sequence requirements, indicating functionality on the RNA level. In contrast, the genome regions in between contain less highly conserved structures. The results provide a complete description of all conserved RNA secondary structures and make clear that functionally important RNA secondary structures are present in certain HCV genome regions but are largely absent from other regions. Full-genome alignments of all branches of Hepacivirus C are provided in the supplement.},

keywords = {evolution, ncRNAs, phylogenetics, RNA structure, RNA-RNA interactions, virus host interaction, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_63,

title = {RIBAP: a comprehensive bacterial core genome annotation pipeline for pangenome calculation beyond the species level},

author = {Kevin Lamkiewicz and Lisa-Marie Barf and Konrad Sachse and Martin Hölzer},

doi = {10.1186/s13059-024-03312-9},

year  = {2024},

date = {2024-07-01},

journal = {Genome Biology},

volume = {25},

issue = {1},

abstract = {Microbial pangenome analysis identifies present or absent genes in prokaryotic genomes. However, current tools are limited when analyzing species with higher sequence diversity or higher taxonomic orders such as genera or families. The Roary ILP Bacterial core Annotation Pipeline (RIBAP) uses an integer linear programming approach to refine gene clusters predicted by Roary for identifying core genes. RIBAP successfully handles the complexity and diversity of Chlamydia, Klebsiella, Brucella, and Enterococcus genomes, outperforming other established and recent pangenome tools for identifying all-encompassing core genes at the genus level. RIBAP is a freely available Nextflow pipeline at github.com/hoelzer-lab/ribap and zenodo.org/doi/10.5281/zenodo.10890871.},

keywords = {annotation, bacteria, DNA / genomics, evolution, software},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_61,

title = {RNA-Protein Interaction Prediction without High-Throughput Data: An Overview and Benchmark of \textit{in silico} Tools},

author = {Sarah Krautwurst and Kevin Lamkiewicz},

doi = {10.1101/2024.06.24.600368},

year  = {2024},

date = {2024-06-27},

journal = {bioRxiv},

abstract = {RNA-protein interactions (RPIs) are crucial for accurately operating various processes in and between organisms across kingdoms of life. Mutual detection of RPI partner molecules depends on distinct sequential, structural, or thermodynamic features, which can be determined via experimental and bioinformatic methods. Still, the underlying molecular mechanisms of many RPIs are poorly understood. It is further hypothesized that many RPIs are not even described yet. Computational RPI prediction is continuously challenged by the lack of data and detailed research of very specific examples. With the discovery of novel RPI complexes in all kingdoms of life, adaptations of existing RPI prediction methods are necessary. Continuously improving computational RPI prediction is key in advancing the understanding of RPIs in detail and supplementing experimental RPI determination. The growing amount of data covering more species and detailed mechanisms support the accuracy of prediction tools, which in turn support specific experimental research on RPIs. Here, we give an overview of RPI prediction tools that do not use high-throughput data as the user's input. We review the tools according to their input, usability, and output. We then apply the tools to known RPI examples across different kingdoms of life. Our comparison shows that the investigated prediction tools do not favor a certain species and equip the user with results varying in degree of information, from an overall RPI score to detailed interacting residues. Furthermore, we provide a guide tree to assist users which RPI prediction tool is appropriate for their available input data and desired output.},

keywords = {ncRNAs, proteins, RNA structure},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_60,

title = {Detection of a novel genotype of \textit{Chlamydia buteonis} in falcons from the Emirates},

author = {F. Vorimore and R. Aaziz and L. {Al Qaysi} and U. Wernery and N. Borel and Konrad Sachse and K. Laroucau},

doi = {10.1016/j.vetmic.2024.110027},

year  = {2024},

date = {2024-02-16},

journal = {Veterinary Microbiology},

volume = {291},

pages = {110027},

abstract = {Chlamydiaceae are a family of obligate intracellular bacterial pathogens that affect both humans and animals. Recently, a new species named Chlamydia (C.) buteonis was isolated from hawks. In this study, we aimed to investigate the prevalence of Chlamydiaceae in 60 falcons that underwent a routine health check at a specialized clinic in Dubai, United Arab Emirates. Using real-time PCR, we analyzed cloacal and tracheal swabs from these birds and found that 39 of them tested positive for Chlamydiaceae. Subsequent real-time PCR assays specific for C. psittaci, C. abortus, C. avium, and C. gallinacea yielded negative results, while testing positive for C. buteonis. Analysis of ompA and MLST sequences indicated a highly conserved group of strains within this set of samples, but with sequences distinct from the C. buteonis RSHA reference strains and other C. buteonis strains isolated from hawks in the United States. Two strains were further isolated by cell culture and sequenced using whole-genome sequencing, confirming the clustering of these falcon strains within the C. buteonis species, but in a separate clade from the previously identified hawk strains. We also developed a SNP-based PCR-HRM assay to distinguish between these different genotypes. Overall, our findings suggest a high prevalence of C. buteonis in falcons in Dubai and highlight the importance of monitoring this pathogen in birds of prey.},

keywords = {bacteria, DNA / genomics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Maximizing the potential of genomic and transcriptomic studies by nanopore sequencing},

author = {Daria Meyer and Winfried Goettsch and Jannes Spangenberg and Patrick Bohn and Bettina Stieber and Sebastian Krautwurst and Christian {Höner zu Siederdissen} and Akash Srivastava and Milena Zarkovic and Damian Wollny and Manja Marz},

doi = {10.1101/2023.12.06.570356},

year  = {2023},

date = {2023-12-07},

urldate = {2023-12-07},

journal = {bioRxiv},

abstract = {Nucleic acid sequencing is the process of identifying the sequence of DNA or RNA, with DNA used for genomes and RNA for transcriptomes. Deciphering this information has the potential to greatly advance our understanding of genomic features and cellular functions. In comparison to other available sequencing methods, nanopore sequencing stands out due to its unique advantages of processing long nucleic acid strands in real time, within a small portable device, enabling the rapid analysis of samples in diverse settings. Evolving over the past decade, nanopore sequencing remains in a state of ongoing development and refinement, resulting in persistent challenges in protocols and technology. This article employs an interdisciplinary approach, evaluating experimental and computational methods to address critical gaps in our understanding in order to maximise the information gain from this advancing technology. We present a robust analysis of all aspects of nanopore sequencing by providing statistically supported insights, thus aiming to provide comprehensive guidelines for the diverse challenges that frequently impede optimal experimental outcomes. Here we present a robust analysis, bridging the gap by providing statistically supported insights into genomic and transcriptomic studies, providing fresh perspectives on sequencing.},

keywords = {DNA / genomics, nanopore, nucleic acid modifications},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Differential Transcriptional Responses of Human Granulocytes to Fungal Infection with \textit{Candida albicans} and \textit{Aspergillus fumigatus}},

author = {Tilman E. Klassert and Martin Hölzer and Cristina Zubiria-Barrera and Julia Bethge and Esther Klaile and Mario M. Müller and Manja Marz and Hortense Slevogt},

doi = {doi.org/10.3390/jof9101014},

year  = {2023},

date = {2023-10-14},

journal = {J Fungi},

volume = {9},

issue = {10},

pages = {1014},

abstract = {Neutrophils are critical phagocytic cells in innate immunity, playing a significant role in defending against invasive fungal pathogens. This study aimed to explore the transcriptional activation of human neutrophils in response to different fungal pathogens, including Candida albicans and Aspergillus fumigatus, compared to the bacterial pathogen Escherichia coli. We identified distinct transcriptional profiles and stress-related pathways in neutrophils during fungal infections, highlighting their functional diversity and adaptability. The transcriptional response was largely redundant across all pathogens in immune-relevant categories and cytokine pathway activation. However, differences in the magnitude of differentially expressed genes (DEGs) were observed, with A. fumigatus inducing a lower transcriptional effect compared to C. albicans and E. coli. Notably, specific gene signatures associated with cell death were differentially regulated by fungal pathogens, potentially increasing neutrophil susceptibility to autophagy, pyroptosis, and neutrophil extracellular trap (NET) formation. These findings provide valuable insights into the complex immunological responses of neutrophils during fungal infections, offering new avenues for diagnostic and therapeutic strategies, particularly in the management of invasive fungal diseases.},

keywords = {differential expression analysis, fungi, RNA / transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_49,

title = {Decoding cell-type contributions to the cfRNA transcriptomic landscape of liver cancer},

author = {Aram Safrastyan and Christian {Höner Zu Siederdissen} and Damian Wollny},

doi = {10.1186/s40246-023-00537-w},

year  = {2023},

date = {2023-10-05},

journal = {Hum Genomics},

volume = {17},

issue = {1},

pages = {90},

abstract = {Background

Liquid biopsy, particularly cell-free RNA (cfRNA), has emerged as a promising non-invasive diagnostic tool for various diseases, including cancer, due to its accessibility and the wealth of information it provides. A key area of interest is the composition and cellular origin of cfRNA in the blood and the alterations in the cfRNA transcriptomic landscape during carcinogenesis. Investigating these changes can offer insights into the manifestations of tissue alterations in the blood, potentially leading to more effective diagnostic strategies. However, the consistency of these findings across different studies and their clinical utility remains to be fully elucidated, highlighting the need for further research in this area.



Results

In this study, we analyzed over 350 blood samples from four distinct studies, investigating the cell type contributions to the cfRNA transcriptomic landscape in liver cancer. We found that an increase in hepatocyte proportions in the blood is a consistent feature across most studies and can be effectively utilized for classifying cancer and healthy samples. Moreover, our analysis revealed that in addition to hepatocytes, liver endothelial cell signatures are also prominent in the observed changes. By comparing the classification performance of cellular proportions to established markers, we demonstrated that cellular proportions could distinguish cancer from healthy samples as effectively as existing markers and can even enhance classification when used in combination with these markers.



Conclusions

Our comprehensive analysis of liver cell-type composition changes in blood revealed robust effects that help classify cancer from healthy samples. This is especially noteworthy, considering the heterogeneous nature of datasets and the etiological distinctions of samples. Furthermore, the observed differences in results across studies underscore the importance of integrative and comparative approaches in the future research to determine the consistency and robustness of findings. This study contributes to the understanding of cfRNA composition in liver cancer and highlights the potential of cellular deconvolution in liquid biopsy.},

keywords = {cancer, ncRNAs},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_47,

title = {The International Virus Bioinformatics Meeting 2023},

author = {Franziska Hufsky and Ana B. Abecasis and Artem Babaian and Sebastian Beck and Liam Brierley and Simon Dellicour and Christian Eggeling and Santiago F. Elena and Udo Gieraths and Anh D. Ha and Will Harvey and Terry C. Jones and Kevin Lamkiewicz and Gabriel Lencioni Lovate and Dominik Lücking and Martin Machyna and Luca Nishimura and Maximilian K. Nocke and Bernard Y. Renard and Shoichi Sakaguchi and Lygeri Sakellaridi and Jannes Spangenberg and Maria Tarradas-Alemany and Sandra Triebel and Yulia Vakulenko and Rajitha Yasas Wijesekara and Fernando González-Candelas and Sarah Krautwurst and Alba Pérez-Cataluña and Walter Randazzo and Gloria Sánchez and Manja Marz},

doi = {10.3390/v15102031},

issn = {1999-4915},

year  = {2023},

date = {2023-09-30},

urldate = {2023-09-30},

journal = {Viruses},

volume = {15},

issue = {10},

abstract = {The 2023 International Virus Bioinformatics Meeting was held in Valencia, Spain, from 24–26 May 2023, attracting approximately 180 participants worldwide. The primary objective of the conference was to establish a dynamic scientific environment conducive to discussion, collaboration, and the generation of novel research ideas. As the first in-person event following the SARS-CoV-2 pandemic, the meeting facilitated highly interactive exchanges among attendees. It served as a pivotal gathering for gaining insights into the current status of virus bioinformatics research and engaging with leading researchers and emerging scientists. The event comprised eight invited talks, 19 contributed talks, and 74 poster presentations across eleven sessions spanning three days. Topics covered included machine learning, bacteriophages, virus discovery, virus classification, virus visualization, viral infection, viromics, molecular epidemiology, phylodynamic analysis, RNA viruses, viral sequence analysis, viral surveillance, and metagenomics. This report provides rewritten abstracts of the presentations, a summary of the key research findings, and highlights shared during the meeting.},

keywords = {annotation, software, virus host interaction, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_46,

title = {RNA-based sensitive fungal pathogen detection},

author = {Julia Micheel and Franziska Aron and Abdulrahman A. Kelani and Christian Girbardt and Matthew G. Blango and Grit Walther and Damian Wollny},

doi = {10.1101/2023.09.26.559494},

year  = {2023},

date = {2023-09-26},

urldate = {2023-09-26},

journal = {bioRxiv},

abstract = {Detecting fungal pathogens, a major cause of severe systemic infections, remains challenging due to the difficulty and time-consuming nature of diagnostic methods. This delay in identification hinders targeted treatment decisions and may lead to unnecessary use of broad-spectrum antibiotics. To expedite treatment initiation, one promising approach is to directly detect pathogen nucleic acids such as DNA, which is often preferred to RNA because of its inherent stability. However, a higher number of RNA molecules per cell makes RNA a more promising diagnostic target which is particularly prominent for highly expressed genes such as rRNA. Here, we investigated the utility of a minimal input-specialized reverse transcription protocol to increase diagnostic sensitivity. This proof-of-concept study demonstrates that fungal rRNA detection by the minimal input protocol is drastically more sensitive compared to detection of genomic DNA even with high levels of human RNA background. This approach can detect several of the most relevant human pathogenic fungal genera, such as Aspergillus, Candida, and Fusarium and thus represents a powerful, cheap, and easily adaptable addition to currently available diagnostic assays.},

keywords = {fungi, ncRNAs, RNA / transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_48,

title = {Detection of reproducible liver cancer specific ligand-receptor signaling in blood},

author = {Aram Safrastyan and Damian Wollny},

doi = {10.1101/2023.09.25.559274},

year  = {2023},

date = {2023-09-25},

urldate = {2023-09-25},

journal = {bioRxiv},

abstract = {Cell-cell communication mediated by ligand-receptor interactions (LRI) is critical to coordinating diverse biological processes in homeostasis and disease. Lately, our understanding of these processes has greatly expanded through the inference of cellular communication, utilizing RNA extracted from bulk tissue or individual cells. Considering the challenge of obtaining tissue biopsies for these approaches, we considered the potential of studying cell-free RNA obtained from blood. To test the feasibility of this approach, we used the BulkSignalR algorithm across 295 cell-free RNA samples and compared the LRI profiles across multiple cancer types and healthy donors. Interestingly, we detected specific and reproducible LRIs particularly in the blood of liver cancer patients compared to healthy donors. We found an increase in the magnitude of hepatocyte interactions, notably hepatocyte autocrine interactions in liver cancer patients. Additionally, a robust panel of 30 liver cancer-specific LRIs presents a bridge linking liver cancer pathogenesis to discernible blood markers. In summary, our approach shows the plausibility of detecting liver LRIs in blood and builds upon the biological understanding of cell-free transcriptomes.},

keywords = {cancer, ncRNAs},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_45,

title = {Functional comparisons of the virus sensor RIG-I from humans, the microbat \textit{Myotis daubentonii}, and the megabat \textit{Rousettus aegyptiacus}, and their response to SARS-CoV-2 infection},

author = {Andreas Schoen and Martin Hölzer and Marcel A. Müller and Kai B. Wallerang and Christian Drosten and Manja Marz and Benjamin Lamp and Friedemann Weber},

doi = {10.1128/jvi.00205-23},

year  = {2023},

date = {2023-09-20},

urldate = {2023-09-20},

journal = {Journal of Virology},

volume = {0},

issue = {0},

pages = {e00205-23},

abstract = {Bats (order Chiroptera) are a major reservoir for emerging and re-emerging zoonotic viruses. Their tolerance toward highly pathogenic human viruses led to the hypothesis that bats may possess an especially active antiviral interferon (IFN) system. Here, we cloned and functionally characterized the virus RNA sensor, retinoic acid-inducible gene-I (RIG-I), from the "microbat" Myotis daubentonii (suborder Yangochiroptera) and the "megabat" Rousettus aegyptiacus (suborder Yinpterochiroptera) and compared them to the human ortholog. Our data show that the overall sequence and domain organization are highly conserved and that all three RIG-I orthologs can mediate a similar IFN induction in response to viral RNA at 37° and 39°C but not at 30°C. Like human RIG-I, bat RIG-Is were optimally activated by double stranded RNA containing a 5'-triphosphate end and required mitochondrial antiviral-signaling protein (MAVS) for antiviral signaling. Moreover, the RIG-I orthologs of humans and of R. aegyptiacus, but not of M. daubentonii, enable innate immune sensing of SARS-CoV-2 infection. Our results thus show that microbats and megabats express a RIG-I that is not substantially different from the human counterpart with respect to function, temperature dependency, antiviral signaling, and RNA ligand properties, and that human and megabat RIG-I are able to sense SARS-CoV-2 infection. IMPORTANCE A common hypothesis holds that bats (order Chiroptera) are outstanding reservoirs for zoonotic viruses because of a special antiviral interferon (IFN) system. However, functional studies about key components of the bat IFN system are rare. RIG-I is a cellular sensor for viral RNA signatures that activates the antiviral signaling chain to induce IFN. We cloned and functionally characterized RIG-I genes from two species of the suborders Yangochiroptera and Yinpterochiroptera. The bat RIG-Is were conserved in their sequence and domain organization, and similar to human RIG-I in (i) mediating virus- and IFN-activated gene expression, (ii) antiviral signaling, (iii) temperature dependence, and (iv) recognition of RNA ligands. Moreover, RIG-I of Rousettus aegyptiacus (suborder Yinpterochiroptera) and of humans were found to recognize SARS-CoV-2 infection. Thus, members of both bat suborders encode RIG-Is that are comparable to their human counterpart. The ability of bats to harbor zoonotic viruses therefore seems due to other features.},

keywords = {DNA / genomics, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_44,

title = {\textit{De novo} genome assembly resolving repetitive structures enables genomic analysis of 35 European \textit{Mycoplasmopsis bovis} strains},

author = {Sandra Triebel and Konrad Sachse and Michael Weber and Martin Heller and Celia Diezel and Martin Hölzer and Christiane Schnee and Manja Marz },

doi = {10.1186/s12864-023-09618-5},

isbn = {1471-2164},

year  = {2023},

date = {2023-09-16},

urldate = {2023-09-16},

journal = {BMC Genomics},

volume = {24},

number = {548},

issue = {1},

abstract = {Mycoplasmopsis (M.) bovis, the agent of mastitis, pneumonia, and arthritis in cattle, harbors a small genome of approximately 1 Mbp. Combining data from Illumina and Nanopore technologies, we sequenced and assembled the genomes of 35 European strains and isolate DL422_88 from Cuba. While the high proportion of repetitive structures in M. bovis genomes represent a particular challenge, implementation of our own pipeline Mycovista (available on GitHub www.github.com/sandraTriebel/mycovista ) in a hybrid approach enabled contiguous assembly of the genomes and, consequently, improved annotation rates considerably. To put our European strain panel in a global context, we analyzed the new genome sequences together with 175 genome assemblies from public databases. Construction of a phylogenetic tree based on core genes of these 219 strains revealed a clustering pattern according to geographical origin, with European isolates positioned on clades 4 and 5. Genomic data allowing assignment of strains to tissue specificity or certain disease manifestations could not be identified. Seven strains isolated from cattle with systemic circular condition (SCC), still a largely unknown manifestation of M. bovis disease, were located on both clades 4 and 5. Pairwise association analysis revealed 108 genomic elements associated with a particular clade of the phylogenetic tree. Further analyzing these hits, 25 genes are functionally annotated and could be linked to a M. bovis protein, e.g. various proteases and nucleases, as well as ten variable surface lipoproteins (Vsps) and other surface proteins. These clade-specific genes could serve as useful markers in epidemiological and clinical surveys.},

keywords = {assembly, bacteria, DNA / genomics, nanopore, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_43,

title = {Navigating the Landscape: A Comprehensive Review of Current Virus Databases},

author = {Muriel Ritsch and Noriko A. Cassman and Shahram Saghaei and Manja Marz},

doi = {10.3390/v15091834},

isbn = {1999-4915},

year  = {2023},

date = {2023-08-29},

journal = {Viruses},

volume = {15},

number = {1834},

issue = {9},

abstract = {Viruses are abundant and diverse entities that have important roles in public health, ecology, and agriculture. The identification and surveillance of viruses rely on an understanding of their genome organization, sequences, and replication strategy. Despite technological advancements in sequencing methods, our current understanding of virus diversity remains incomplete, highlighting the need to explore undiscovered viruses. Virus databases play a crucial role in providing access to sequences, annotations and other metadata, and analysis tools for studying viruses. However, there has not been a comprehensive review of virus databases in the last five years. This study aimed to fill this gap by identifying 24 active virus databases and included an extensive evaluation of their content, functionality and compliance with the FAIR principles. In this study, we thoroughly assessed the search capabilities of five database catalogs, which serve as comprehensive repositories housing a diverse array of databases and offering essential metadata. Moreover, we conducted a comprehensive review of different types of errors, encompassing taxonomy, names, missing information, sequences, sequence orientation, and chimeric sequences, with the intention of empowering users to effectively tackle these challenges. We expect this review to aid users in selecting suitable virus databases and other resources, and to help databases in error management and improve their adherence to the FAIR principles. The databases listed here represent the current knowledge of viruses and will help aid users find databases of interest based on content, functionality, and scope. The use of virus databases is integral to gaining new insights into the biology, evolution, and transmission of viruses, and developing new strategies to manage virus outbreaks and preserve global health.},

keywords = {database, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models},

author = {Guillermo Rangel-Pineros and Alexandre Almeida and Martin Beracochea and Ekaterina Sakharova and Manja Marz and Alejandro Reyes Muñoz and Martin Hölzer and Robert D. Finn },

doi = {10.1371/journal.pcbi.1011422},

year  = {2023},

date = {2023-08-28},

journal = {PLOS Comput Biol},

volume = {19},

issue = {8},

pages = {e1011422},

abstract = {The study of viral communities has revealed the enormous diversity and impact these biological entities have on various ecosystems. These observations have sparked widespread interest in developing computational strategies that support the comprehensive characterisation of viral communities based on sequencing data. Here we introduce VIRify, a new computational pipeline designed to provide a user-friendly and accurate functional and taxonomic characterisation of viral communities. VIRify identifies viral contigs and prophages from metagenomic assemblies and annotates them using a collection of viral profile hidden Markov models (HMMs). These include our manually-curated profile HMMs, which serve as specific taxonomic markers for a wide range of prokaryotic and eukaryotic viral taxa and are thus used to reliably classify viral contigs. We tested VIRify on assemblies from two microbial mock communities, a large metagenomics study, and a collection of publicly available viral genomic sequences from the human gut. The results showed that VIRify could identify sequences from both prokaryotic and eukaryotic viruses, and provided taxonomic classifications from the genus to the family rank with an average accuracy of 86.6%. In addition, VIRify allowed the detection and taxonomic classification of a range of prokaryotic and eukaryotic viruses present in 243 marine metagenomic assemblies. Finally, the use of VIRify led to a large expansion in the number of taxonomically classified human gut viral sequences and the improvement of outdated and shallow taxonomic classifications. Overall, we demonstrate that VIRify is a novel and powerful resource that offers an enhanced capability to detect a broad range of viral contigs and taxonomically classify them.},

keywords = {annotation, classification, metagenomics, phylogenetics, software, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {NFDI4Microbiota – national research data infrastructure for microbiota research},

author = {Konrad U. Förstner and Anke Becker and Jochen Blom and Peer Bork and Thomas Clavel and Marius Dieckmann and Alexander Goesmann and Barbara Götz and Thomas Gübitz and Franziska Hufsky and Sebastian Jünemann and Marie-Louise Körner and Manja Marz and Ulisses Nunes Da Rocha and Jörg Overmann and Alfred Pühler and Dietrich Rebholz-Schuhmann and Alexander Sczyrba and Jens Stoye and Justine Vandendorpe and Thea Van Rossum and Alice McHardy},

doi = {10.3897/rio.9.e110501},

year  = {2023},

date = {2023-08-24},

journal = {Research Ideas and Outcomes},

volume = {9},

pages = {e110501},

abstract = {Microbes – bacteria, archaea, unicellular eukaryotes, and viruses – play an important role in human and environmental health. Growing awareness of this fact has led to a huge increase in microbiological research and applications in a variety of fields. Driven by technological advances that allow high-throughput molecular characterization of microbial species and communities, microbiological research now offers unparalleled opportunities to address current and emerging needs. As well as helping to address global health threats such as antimicrobial resistance and viral pandemics, it also has a key role to play in areas such as agriculture, waste management, water treatment, ecosystems remediation, and the diagnosis, treatment and prevention of various diseases. Reflecting this broad potential, billions of euros have been invested in microbiota research programs worldwide. Though run independently, many of these projects are closely related. However, Germany currently has no infrastructure to connect such projects or even compare their results. Thus, the potential synergy of data and expertise is being squandered. The goal of the NFDI4Microbiota consortium is to serve and connect this broad and heterogeneous research community by elevating the availability and quality of research results through dedicated training, and by facilitating the generation, management, interpretation, sharing, and reuse of microbial data. In doing so, we will also foster interdisciplinary interactions between researchers. NFDI4Microbiota will achieve this by creating a German microbial research network through training and community-building activities, and by creating a cloud-based system that will make the storage, integration and analysis of microbial data, especially omics data, consistent, reproducible, and accessible across all areas of life sciences. In addition to increasing the quality of microbial research in Germany, our training program will support widespread and proper usage of these services. Through this dual emphasis on education and services, NFDI4Microbiota will ensure that microbial research in Germany is synergistic and efficient, and thus excellent. By creating a central resource for German microbial research, NDFDI4Microbiota will establish a connecting hub for all NFDI consortia that work with microbiological data, including GHGA, NFDI4Biodiversity, NFDI4Agri and several others. NFDI4Microbiota will provide non-microbial specialists from these consortia with direct and easy access to the necessary expertise and infrastructure in microbial research in order to facilitate their daily work and enhance their research. The links forged through NFDI4Microbiota will not only increase the synergy between NFDI consortia, but also elevate the overall quality and relevance of microbial research in Germany.},

keywords = {bacteria, fungi, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_41,

title = {\textit{Streptomyces marispadix} sp. nov., isolated from marine beach sediment},

author = {José Diogo Neves Dos Santos and Inês Rosado Vitorino and Nicolai Kallscheuer and Akash Srivastava and Sebastian Krautwurst and Manja Marz and Christian Jogler and Alexandre Lobo-da-Cunha and José Catita and Hugo Gonçalves and Ignacio González and Fernando Reyes and Olga Maria Lage},

doi = {10.1099/ijsem.0.005956},

isbn = {1466-5034},

year  = {2023},

date = {2023-07-25},

urldate = {2023-07-25},

journal = {International Journal of Systematic and Evolutionary Microbiology},

volume = {73},

number = {7},

abstract = {A novel actinomycetal strain, designated M600PL45_2T, was isolated from marine sediments obtained from Ingleses beach, Porto, on the Northern Coast of Portugal and was subjected to a polyphasic taxonomic characterisation study. The here described Gram-reaction-positive strain is characterised by the production of a brown pigment in both solid and liquid medium and forms typical helical hyphae that differentiate into smooth spores. The results of a phylogenetic analysis based on the 16S rRNA gene sequence indicated that M600PL45_2T has a high similarity to two members of the genus Streptomyces , Streptomyces bathyalis ASO4wetT (98.51 %) and Streptomyces daqingensis NEAU ZJC8T (98.44 %). The genome of M600PL45_2T has a size of 6 695 159 bp, a DNA G+C content of 70.71 mol% and 5538 coding sequences. M600PL45_2T grows at 15–37 °C and with a maximal growth rate between 25 °C and 30 °C. Growth at pH 6.0 to 9.0 with the optimal range between 6.0 and 7.5 was observed. M600PL45_2T showed a high salinity tolerance, growing with 0–10 % (w/v) NaCl, with best growth with 1–3% (w/v) NaCl. Major cellular fatty acids are iso-C15:0 (25.03 %), anteiso-C15:0 (17.70) and iso-C16:0 (26.90 %). The novel isolate was able to grow in media containing a variety of nitrogen and carbon sources. An antimicrobial activity screening indicated that an extract of M600PL45_2T has inhibitory activity against Staphylococcus aureus . On the basis of the polyphasic data, M600PL45_2T (= CECT 30365T = DSM 114036T) is introduced as the type strain of a novel species, that we named Streptomyces marispadix sp. nov.},

keywords = {bacteria, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_34,

title = {Sequential disruption of SPLASH-identified vRNA–vRNA interactions challenges their role in influenza A virus genome packaging},

author = {Celia Jakob and Gabriel Lencioni Lovate and Daniel Desirò and Lara Gießler and 

Redmond Patrick Smyth and Roland Marquet and Kevin Lamkiewicz and Manja Marz and Martin Schwemmle and Hardin Bolte},

doi = {10.1093/nar/gkad442},

isbn = {0305-1048},

year  = {2023},

date = {2023-07-07},

urldate = {2023-05-24},

journal = {Nucleic Acids Research},

abstract = {A fundamental step in the influenza A virus (IAV) replication cycle is the coordinated packaging of eight distinct genomic RNA segments (i.e. vRNAs) into a viral particle. Although this process is thought to be controlled by specific vRNA–vRNA interactions between the genome segments, few functional interactions have been validated. Recently, a large number of potentially functional vRNA–vRNA interactions have been detected in purified virions using the RNA interactome capture method SPLASH. However, their functional significance in coordinated genome packaging remains largely unclear. Here, we show by systematic mutational analysis that mutant A/SC35M (H7N7) viruses lacking several prominent SPLASH-identified vRNA–vRNA interactions involving the HA segment package the eight genome segments as efficiently as the wild-type virus. We therefore propose that the vRNA–vRNA interactions identified by SPLASH in IAV particles are not necessarily critical for the genome packaging process, leaving the underlying molecular mechanism elusive.},

keywords = {RNA-RNA interactions, splash, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_40,

title = {Oxford nanopore technologies-a valuable tool to generate whole-genome sequencing data for \textit{in silico} serotyping and the detection of genetic markers in \textit{Salmonella}},

author = {Christine Thomas and Ulrich Methner and Manja Marz and Jörg Linde},

doi = {10.3389/fvets.2023.1178922},

isbn = {2297-1769},

year  = {2023},

date = {2023-06-01},

urldate = {2023-06-01},

journal = {Frontiers in Veterinary Science},

volume = {10},

abstract = {Bacteria of the genus Salmonella pose a major risk to livestock, the food economy, and public health. Salmonella infections are one of the leading causes of food poisoning. The identification of serovars of Salmonella achieved by their diverse surface antigens is essential to gain information on their epidemiological context. Traditionally, slide agglutination has been used for serotyping. In recent years, whole-genome sequencing (WGS) followed by in silico serotyping has been established as an alternative method for serotyping and the detection of genetic markers for Salmonella. Until now, WGS data generated with Illumina sequencing are used to validate in silico serotyping methods. Oxford Nanopore Technologies (ONT) opens the possibility to sequence ultra-long reads and has frequently been used for bacterial sequencing. In this study, ONT sequencing data of 28 Salmonella strains of different serovars with epidemiological relevance in humans, food, and animals were taken to investigate the performance of the in silico serotyping tools SISTR and SeqSero2 compared to traditional slide agglutination tests. Moreover, the detection of genetic markers for resistance against antimicrobial agents, virulence, and plasmids was studied by comparing WGS data based on ONT with WGS data based on Illumina. Based on the ONT data from flow cell version R9.4.1, in silico serotyping achieved an accuracy of 96.4 and 92% for the tools SISTR and SeqSero2, respectively. Highly similar sets of genetic markers comparing both sequencing technologies were identified. Taking the ongoing improvement of basecalling and flow cells into account, ONT data can be used for Salmonella in silico serotyping and genetic marker detection.},

keywords = {bacteria, nanopore},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_35,

title = {Genomic analysis of 61 \textit{Chlamydia psittaci} strains reveals extensive divergence associated with host preference},

author = {Konrad Sachse and Martin Hölzer and Fabien Vorimore and Lisa-Marie Barf and Carsten Sachse and Karine Laroucau and Manja Marz and Kevin Lamkiewicz },

doi = {10.1186/s12864-023-09370-w},

isbn = {1471-2164},

year  = {2023},

date = {2023-05-29},

urldate = {2023-05-29},

journal = {BMC Genomics},

volume = {24},

issue = {1},

pages = {288},

abstract = {Background

Chlamydia (C.) psittaci, the causative agent of avian chlamydiosis and human psittacosis, is a genetically heterogeneous species. Its broad host range includes parrots and many other birds, but occasionally also humans (via zoonotic transmission), ruminants, horses, swine and rodents. To assess whether there are genetic markers associated with host tropism we comparatively analyzed whole-genome sequences of 61 C. psittaci strains, 47 of which carrying a 7.6-kbp plasmid.



Results

Following clean-up, reassembly and polishing of poorly assembled genomes from public databases, phylogenetic analyses using C. psittaci whole-genome sequence alignment revealed four major clades within this species. Clade 1 represents the most recent lineage comprising 40/61 strains and contains 9/10 of the psittacine strains, including type strain 6BC, and 10/13 of human isolates. Strains from different non-psittacine hosts clustered in Clades 2– 4. We found that clade membership correlates with typing schemes based on SNP types, ompA genotypes, multilocus sequence types as well as plasticity zone (PZ) structure and host preference. Genome analysis also revealed that i) sequence variation in the major outer membrane porin MOMP can result in 3D structural changes of immunogenic domains, ii) past host change of Clade 3 and 4 strains could be associated with loss of MAC/perforin in the PZ, rather than the large cytotoxin, iii) the distinct phylogeny of atypical strains (Clades 3 and 4) is also reflected in their repertoire of inclusion proteins (Inc family) and polymorphic membrane proteins (Pmps).



Conclusions

Our study identified a number of genomic features that can be correlated with the phylogeny and host preference of C. psittaci strains. Our data show that intra-species genomic divergence is associated with past host change and includes deletions in the plasticity zone, structural variations in immunogenic domains and distinct repertoires of virulence factors.},

keywords = {alignment, assembly, bacteria, DNA / genomics, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_42,

title = {PAPAS Suppresses Breast Carcinogenesis by Promoting Differentiation of Mammary Epithelial Cells},

author = {Sijia Ren and Feng Bai and Clara Stanko and Muriel Ritsch and Tino Schenk and Emanuel Barth and Xin-Hai Pei and Holger Bierhoff

},

doi = {10.2139/ssrn.4436847},

year  = {2023},

date = {2023-05-23},

journal = {Cell Reports},

abstract = {Extensive remodeling of the female mammary epithelium during development and pregnancy has been linked to cancer susceptibility. The faithful response of mammary epithelial cells (MECs) to hormone signaling is key to avoid breast cancer development. Here we show that lactogenic differentiation of murine MECs requires epigenetic silencing of genes encoding ribosomal RNA (rRNA) by the antisense transcript PAPAS. Accordingly, knockdown of PAPAS derepresses rRNA genes, attenuates the response to lactogenic hormones, and induces malignant transformation. Restoring PAPAS levels in breast cancer cells reduces tumorigenicity and, as revealed by transcriptomics, immune evasion potential. Mechanistically, we show that PAPAS transcription depends on R-loop formation at the 3’ end of rRNA genes, which is repressed by RNase H1 and replication protein A (RPA) overexpression in breast cancer cells. Depletion of PAPAS, and upregulation of RNase H1 and RPA in human breast cancer underpin the clinical relevance of our findings.},

keywords = {cancer, ncRNAs, RNA structure},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing},

author = {Annett Erkes and René P Grove and Milena Žarković and Sebastian Krautwurst and Ralf Koebnik and Richard D Morgan and Geoffrey G Wilson and Martin Hölzer and Manja Marz and Jens Boch and Jan Grau

},

doi = {10.1186/s12864-023-09228-1},

year  = {2023},

date = {2023-03-27},

journal = {BMC Genomics},

volume = {24},

issue = {1},

pages = {151},

abstract = {Background: Most plant-pathogenic Xanthomonas bacteria harbor transcription activator-like effector (TALE) genes, which function as transcriptional activators of host plant genes and support infection. The entire repertoire of up to 29 TALE genes of a Xanthomonas strain is also referred to as TALome. The DNA-binding domain of TALEs is comprised of highly conserved repeats and TALE genes often occur in gene clusters, which precludes the assembly of TALE-carrying Xanthomonas genomes based on standard sequencing approaches.



Results: Here, we report the successful assembly of the 5 Mbp genomes of five Xanthomonas strains from Oxford Nanopore Technologies (ONT) sequencing data. For one of these strains, Xanthomonas oryzae pv. oryzae (Xoo) PXO35, we illustrate why Illumina short reads and longer PacBio reads are insufficient to fully resolve the genome. While ONT reads are perfectly suited to yield highly contiguous genomes, they suffer from a specific error profile within homopolymers. To still yield complete and correct TALomes from ONT assemblies, we present a computational correction pipeline specifically tailored to TALE genes, which yields at least comparable accuracy as Illumina-based polishing. We further systematically assess the ONT-based pipeline for its multiplexing capacity and find that, combined with computational correction, the complete TALome of Xoo PXO35 could have been reconstructed from less than 20,000 ONT reads.



Conclusions: Our results indicate that multiplexed ONT sequencing combined with a computational correction of TALE genes constitutes a highly capable tool for characterizing the TALomes of huge collections of Xanthomonas strains in the future.},

keywords = {assembly, DNA / genomics, nanopore},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Magnipore: Prediction of differential single nucleotide changes in the Oxford Nanopore Technologies sequencing signal of SARS-CoV-2 samples},

author = {Jannes Spangenberg and Christian {Höner zu Siederdissen} and Milena Žarković and Sandra Triebel and Ruben Rose and Christina Martínez Christophersen and Lea Paltzow and Mohsen M. Hegab and Anna Wansorra and Akash Srivastava and Andi Krumbholz and Manja Marz},

doi = {10.1101/2023.03.17.533105},

year  = {2023},

date = {2023-03-17},

urldate = {2023-03-17},

journal = {bioRxiv},

abstract = {Oxford Nanopore Technologies (ONT) allows direct sequencing of ribonucleic acids (RNA) and, in addition, detection of possible RNA modifications due to deviations from the expected ONT signal. The software available so far for this purpose can only detect a small number of modifications. Alternatively, two samples can be compared for different RNA modifications. We present Magnipore, a novel tool to search for significant signal shifts between samples of Oxford Nanopore data from similar or related species. Magnipore classifies them into mutations and potential modifications. We use Magnipore to compare SARS-CoV-2 samples. Included were representatives of the early 2020s Pango lineages (n=6), samples from Pango lineages B.1.1.7 (n=2, Alpha), B.1.617.2 (n=1, Delta), and B.1.529 (n=7, Omicron). Magnipore utilizes position-wise Gaussian distribution models and a comprehensible significance threshold to find differential signals. In the case of Alpha and Delta, Magnipore identifies 55 detected mutations and 15 sites that hint at differential modifications. We predicted potential virus-variant and variant-group-specific differential modifications. Magnipore contributes to advancing RNA modification analysis in the context of viruses and virus variants.},

keywords = {coronavirus, nanopore, nucleic acid modifications, RNA / transcriptomics, software, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Identification of altered miRNAs and their targets in placenta accreta},

author = {José M Murrieta-Coxca and Emanuel Barth and Paulina Fuentes-Zacarias and Ruby N Gutiérrez-Samudio and Tanja Groten and Alexandra Gellhaus and Angela Köninger and Manja Marz and Udo R Markert and Diana M Morales-Prieto

},

doi = {10.3389/fendo.2023.1021640},

year  = {2023},

date = {2023-03-03},

journal = {Front Endocrinol},

volume = {14},

pages = {1021640},

abstract = {Placenta accreta spectrum (PAS) is one of the major causes of maternal morbidity and mortality worldwide with increasing incidence. PAS refers to a group of pathological conditions ranging from the abnormal attachment of the placenta to the uterus wall to its perforation and, in extreme cases, invasion into surrounding organs. Among them, placenta accreta is characterized by a direct adhesion of the villi to the myometrium without invasion and remains the most common diagnosis of PAS. Here, we identify the potential regulatory miRNA and target networks contributing to placenta accreta development. Using small RNA-Seq followed by RT-PCR confirmation, altered miRNA expression, including that of members of placenta-specific miRNA clusters (e.g., C19MC and C14MC), was identified in placenta accreta samples compared to normal placental tissues. In situ hybridization (ISH) revealed expression of altered miRNAs mostly in trophoblast but also in endothelial cells and this profile was similar among all evaluated degrees of PAS. Kyoto encyclopedia of genes and genomes (KEGG) analyses showed enriched pathways dysregulated in PAS associated with cell cycle regulation, inflammation, and invasion. mRNAs of genes associated with cell cycle and inflammation were downregulated in PAS. At the protein level, NF-κB was upregulated while PTEN was downregulated in placenta accreta tissue. The identified miRNAs and their targets are associated with signaling pathways relevant to controlling trophoblast function. Therefore, this study provides miRNA:mRNA associations that could be useful for understanding PAS onset and progression.},

keywords = {ncRNAs, pregnancy, RNA / transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Genome Structure, Life Cycle, and Taxonomy of Coronaviruses and the Evolution of SARS-CoV-2},

author = {Kevin Lamkiewicz and Luis Roger Esquivel Gomez and Denise Kühnert and Manja Marz

},

doi = {10.1007/978-3-031-15640-3_9},

year  = {2023},

date = {2023-01-03},

journal = {Curr Top Microbiol Immunol},

volume = {439},

pages = {305-339},

abstract = {Coronaviruses have a broad host range and exhibit high zoonotic potential. In this chapter, we describe their genomic organization in terms of encoded proteins and provide an introduction to the peculiar discontinuous transcription mechanism. Further, we present evolutionary conserved genomic RNA secondary structure features, which are involved in the complex replication mechanism. With a focus on computational methods, we review the emergence of SARS-CoV-2 starting with the 2019 strains. In that context, we also discuss the debated hypothesis of whether SARS-CoV-2 was created in a laboratory. We focus on the molecular evolution and the epidemiological dynamics of this recently emerged pathogen and we explain how variants of concern are detected and characterised. COVID-19, the disease caused by SARS-CoV-2, can spread through different transmission routes and also depends on a number of risk factors. We describe how current computational models of viral epidemiology, or more specifically, phylodynamics, have facilitated and will continue to enable a better understanding of the epidemic dynamics of SARS-CoV-2.},

keywords = {coronavirus, DNA / genomics, evolution, phylogenetics, RNA / transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Automatic, fast, hierarchical, and non-overlapping gating of flow cytometric data with flowEMMi v2},

author = {Carmen Bruckmann and Susann Müller and Christian {Höner zu Siederdissen}

},

doi = {10.1016/j.csbj.2022.11.033},

year  = {2022},

date = {2022-11-17},

urldate = {2022-11-17},

journal = {Comput Struct Biotechnol J},

volume = {20},

pages = {6473-6489},

abstract = {Flow cytometry has become a powerful technology for studying microbial community dynamics and ecology. These dynamics are tracked over long periods of time based on two-parameter community fingerprints consisting of subsets of cell distributions with similar cell properties. These subsets are highlighted by cytometric gates which are assembled into a gate template. Gate templates then are used to compare samples over time or between sites. The template is usually created manually by the operator which is time consuming, prone to human error and dependent on human expertise. Manual gating thus lacks reproducibility, which in turn might impact ecological downstream analyses such as various diversity parameters, turnover and nestedness or stability measures. We present a new version of our flowEMMi algorithm - originally designed for an automated construction of a gate template, which now (i) generates non-overlapping elliptical gates within a few minutes. Gate templates (ii) can be created for both single measurements and time-series measurements, allowing immediate downstream data analyses and on-line evaluation. Furthermore, it is possible to (iii) adjust gate sizes to Gaussian distribution confidence levels. This automatic approach (iv) makes the gate template creation objective and reproducible. Moreover, it can (v) generate hierarchies of gates. flowEMMi v2 is essential not only for exploratory studies, but also for routine monitoring and control of biotechnological processes. Therefore, flowEMMi v2 bridges a crucial bottleneck between automated cell sample collection and processing, and automated flow cytometric measurement on the one hand as well as automated downstream statistical analysis on the other hand.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021},

author = {Torsten Houwaart and Samir Belhaj and Emran Tawalbeh and Dirk Nagels and Yara Fröhlich and Patrick Finzer and Pilar Ciruela and Aurora Sabrià and Mercè Herrero and Cristina Andrés and Andrés Antón and Assia Benmoumene and Dounia Asskali and Hussein Haidar and Janina von Dahlen and Jessica Nicolai and Mygg Stiller and Jacqueline Blum and Christian Lange and Carla Adelmann and Britta Schroer and Ute Osmers and Christiane Grice and Phillipp P Kirfel and Hassan Jomaa and Daniel Strelow and Lisanna Hülse and Moritz Pigulla and Pascal Kreuzer and Alona Tyshaieva and Jonas Weber and Tobias Wienemann and Malte Kohns Vasconcelos and Katrin Hoffmann and Nadine Lübke and Sandra Hauka and Marcel Andree and Claus Jürgen Scholz and Nathalie Jazmati and Klaus Göbels and Rainer Zotz and Klaus Pfeffer and Jörg Timm and Lutz Ehlkes and Andreas Walker and Alexander T Dilthey and Deutsche COVID-19 OMICS Initiative (DeCOI)},

doi = {10.2807/1560-7917.ES.2022.27.43.2101089},

year  = {2022},

date = {2022-10-27},

urldate = {2022-10-27},

journal = {Euro Surveill},

volume = {27},

issue = {43},

pages = {2101089},

abstract = {BackgroundTracking person-to-person SARS-CoV-2 transmission in the population is important to understand the epidemiology of community transmission and may contribute to the containment of SARS-CoV-2. Neither contact tracing nor genomic surveillance alone, however, are typically sufficient to achieve this objective.AimWe demonstrate the successful application of the integrated genomic surveillance (IGS) system of the German city of Düsseldorf for tracing SARS-CoV-2 transmission chains in the population as well as detecting and investigating travel-associated SARS-CoV-2 infection clusters.MethodsGenomic surveillance, phylogenetic analysis, and structured case interviews were integrated to elucidate two genetically defined clusters of SARS-CoV-2 isolates detected by IGS in Düsseldorf in July 2021.ResultsCluster 1 (n = 67 Düsseldorf cases) and Cluster 2 (n = 36) were detected in a surveillance dataset of 518 high-quality SARS-CoV-2 genomes from Düsseldorf (53% of total cases, sampled mid-June to July 2021). Cluster 1 could be traced back to a complex pattern of transmission in nightlife venues following a putative importation by a SARS-CoV-2-infected return traveller (IP) in late June; 28 SARS-CoV-2 cases could be epidemiologically directly linked to IP. Supported by viral genome data from Spain, Cluster 2 was shown to represent multiple independent introduction events of a viral strain circulating in Catalonia and other European countries, followed by diffuse community transmission in Düsseldorf.ConclusionIGS enabled high-resolution tracing of SARS-CoV-2 transmission in an internationally connected city during community transmission and provided infection chain-level evidence of the downstream propagation of travel-imported SARS-CoV-2 cases.},

keywords = {coronavirus, nanopore, RNA / transcriptomics, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Mock2022,

title = {Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks},

author = {Florian Mock and Fleming Kretschmer and Anton Kriese and Sebastian Böcker and Manja Marz

},

doi = {10.1073/pnas.2122636119},

year  = {2022},

date = {2022-08-30},

journal = {Proc Natl Acad Sci},

volume = {119},

issue = {35},

pages = {e2122636119},

abstract = {Taxonomic classification, that is, the assignment to biological clades with shared ancestry, is a common task in genetics, mainly based on a genome similarity search of large genome databases. The classification quality depends heavily on the database, since representative relatives must be present. Many genomic sequences cannot be classified at all or only with a high misclassification rate. Here we present BERTax, a deep neural network program based on natural language processing to precisely classify the superkingdom and phylum of DNA sequences taxonomically without the need for a known representative relative from a database. We show BERTax to be at least on par with the state-of-the-art approaches when taxonomically similar species are part of the training data. For novel organisms, however, BERTax clearly outperforms any existing approach. Finally, we show that BERTax can also be combined with database approaches to further increase the prediction quality in almost all cases. Since BERTax is not based on similar entries in databases, it allows precise taxonomic classification of a broader range of genomic sequences, thus increasing the overall information gain.},

keywords = {classification, DNA / genomics, machine learning},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Network analysis of hepatocellular carcinoma liquid biopsies augmented by single-cell sequencing data},

author = {Aram Safrastyan and Damian Wollny},

doi = {10.3389/fgene.2022.921195},

year  = {2022},

date = {2022-08-25},

journal = {Front Genet},

volume = {13},

pages = {921195},

abstract = {Liquid biopsy, the analysis of body fluids, represents a promising approach for disease diagnosis and prognosis with minimal intervention. Sequencing cell-free RNA derived from liquid biopsies has been very promising for the diagnosis of several diseases. Cancer research, in particular, has emerged as a prominent candidate since early diagnosis has been shown to be a critical determinant of disease prognosis. Although high-throughput analysis of liquid biopsies has uncovered many differentially expressed genes in the context of cancer, the functional connection between these genes is not investigated in depth. An important approach to remedy this issue is the construction of gene networks which describes the correlation patterns between different genes, thereby allowing to infer their functional organization. In this study, we aimed at characterizing extracellular transcriptome gene networks of hepatocellular carcinoma patients compared to healthy controls. Our analysis revealed a number of genes previously associated with hepatocellular carcinoma and uncovered their association network in the blood. Our study thus demonstrates the feasibility of performing gene co-expression network analysis from cell-free RNA data and its utility in studying hepatocellular carcinoma. Furthermore, we augmented cell-free RNA network analysis with single-cell RNA sequencing data which enables the contextualization of the identified network modules with cell-type specific transcriptomes from the liver.},

keywords = {cancer, single-cell sequencing},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Comparative transcriptomics identifies candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae)},

author = {Lydia Gramzow and Katharina Klupsch and Noé Fernández-Pozo and Martin Hölzer and Manja Marz and Stefan A Rensing and Günter Theißen},

doi = {10.1186/s12870-022-03631-8},

year  = {2022},

date = {2022-07-14},

journal = {BMC Plant Biol},

volume = {22},

issue = {1},

pages = {340},

abstract = {Background: Fruits are the seed-bearing structures of flowering plants and are highly diverse in terms of morphology, texture and maturation. Dehiscent fruits split open upon maturation to discharge their seeds while indehiscent fruits are dispersed as a whole. Indehiscent fruits evolved from dehiscent fruits several times independently in the crucifer family (Brassicaceae). The fruits of Lepidium appelianum, for example, are indehiscent while the fruits of the closely related L. campestre are dehiscent. Here, we investigate the molecular and genetic mechanisms underlying the evolutionary transition from dehiscent to indehiscent fruits using these two Lepidium species as model system.



Results: We have sequenced the transcriptomes and small RNAs of floral buds, flowers and fruits of L. appelianum and L. campestre and analyzed differentially expressed genes (DEGs) and differently differentially expressed genes (DDEGs). DEGs are genes that show significantly different transcript levels in the same structures (buds, flowers and fruits) in different species, or in different structures in the same species. DDEGs are genes for which the change in expression level between two structures is significantly different in one species than in the other. Comparing the two species, the highest number of DEGs was found in flowers, followed by fruits and floral buds while the highest number of DDEGs was found in fruits versus flowers followed by flowers versus floral buds. Several gene ontology terms related to cell wall synthesis and degradation were overrepresented in different sets of DEGs highlighting the importance of these processes for fruit opening. Furthermore, the fruit valve identity genes FRUITFULL and YABBY3 were among the DEGs identified. Finally, the microRNA miR166 as well as the TCP transcription factors BRANCHED1 (BRC1) and TCP FAMILY TRANSCRIPTION FACTOR 4 (TCP4) were found to be DDEGs.



Conclusions: Our study reveals differences in gene expression between dehiscent and indehiscent fruits and uncovers miR166, BRC1 and TCP4 as candidate genes for the evolutionary transition from dehiscent to indehiscent fruits in Lepidium.},

keywords = {RNA / transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Women in the European Virus Bioinformatics Center},

author = {Franziska Hufsky and Ana B. Abecasis and Patricia Agudelo-Romero and Magda Bletsa and Katherine Brown and Claudia Claus and Stefanie Deinhardt-Emmer and Li Deng and Caroline C. Friedel and María Inés Gismondi and Evangelia Georgia Kostaki and Denise Kühnert and Urmila Kulkarni-Kale and Karin J. Metzner and Irmtraud M. Meyer and Laura Miozzi and Luca Nishimura and Sofia Paraskevopoulou and Alba Pérez-Cataluña and Janina Rahlff and Emma Thomson and Charlotte Tumescheit and Lia van der Hoek and Lore Van Espen and Anne-Mieke Vandamme and Maryam Zaheri and Neta Zuckerman and Manja Marz},

doi = {10.3390/v14071522},

year  = {2022},

date = {2022-07-12},

urldate = {2022-07-12},

journal = {Viruses},

volume = {14},

issue = {7},

pages = {1522},

abstract = {Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing “Big Data” offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.},

keywords = {viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Carbon fixation rates in groundwater similar to those in oligotrophic marine systems},

author = {Will A. Overholt and Susan Trumbore and Xiaomei Xu and Till L. V. Bornemann and Alexander J. Probst and Markus Krüger and Martina Herrmann and Bo Thamdrup and Laura A. Bristow and Martin Taubert and Valérie F. Schwab and Martin Hölzer and Manja Marz and Kirsten Küsel},

doi = {10.1038/s41561-022-00968-5},

year  = {2022},

date = {2022-06-30},

journal = {Nat Geosci},

volume = {15},

pages = {561–567},

abstract = {The terrestrial subsurface contains nearly all of Earth’s freshwater reserves and harbours the majority of our planet’s total prokaryotic biomass. Although genetic surveys suggest these organisms rely on in situ carbon fixation, rather than the photosynthetically derived organic carbon transported from surface environments, direct measurements of carbon fixation in the subsurface are absent. Using an ultra-low level 14C-labelling technique, we estimate in situ carbon fixation rates in a carbonate aquifer. We find these rates are similar to those measured in oligotrophic marine surface waters and up to six-fold greater than those observed in the lower euphotic zone. Our empirical carbon fixation rates agree with nitrification rate data. Metagenomic analyses reveal abundant putative chemolithoautotrophic members of an uncharacterized order of Nitrospiria that may be behind the carbon fixation. On the basis of our determined carbon fixation rates, we conservatively extrapolate global primary production in carbonate groundwaters (10% of global reserves) to be 0.11 Pg carbon per year. These rates fall within the range found for oligotrophic marine surface waters, indicating a substantial contribution of in situ primary production to subsurface ecosystem processes. We further suggest that, just as phototrophs are for marine biogeochemical cycling, such subsurface carbon fixation is potentially foundational to subsurface trophic webs.},

keywords = {groundwater},

pubstate = {published},

tppubtype = {article}

}

@article{Fuesslin2022,

title = {Prediction of Antibiotic Susceptibility Profiles of \textit{Vibrio cholerae} Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon},

author = {Valeria Fuesslin and Sebastian Krautwurst and Akash Srivastava and Doris Winter and Britta Liedigk and Thorsten Thye and Silvia Herrera-León and Shirlee Wohl and Jürgen May and Julius N. Fobil and Daniel Eibach and Manja Marz and Kathrin Schuldt},

url = {https://github.com/RaverJay/CholerAegon },

doi = {10.3389/fmicb.2022.909692},

year  = {2022},

date = {2022-06-22},

journal = {Front Microbiol},

volume = {13},

pages = {909692},

abstract = {During the last decades, antimicrobial resistance (AMR) has become a global public health concern. Nowadays multi-drug resistance is commonly observed in strains of Vibrio cholerae, the etiological agent of cholera. In order to limit the spread of pathogenic drug-resistant bacteria and to maintain treatment options the analysis of clinical samples and their AMR profiles are essential. Particularly, in low-resource settings a timely analysis of AMR profiles is often impaired due to lengthy culturing procedures for antibiotic susceptibility testing or lack of laboratory capacity. In this study, we explore the applicability of whole genome sequencing for the prediction of AMR profiles of V. cholerae. We developed the pipeline CholerAegon for the in silico prediction of AMR profiles of 82 V. cholerae genomes assembled from long and short sequencing reads. By correlating the predicted profiles with results from phenotypic antibiotic susceptibility testing we show that the prediction can replace in vitro susceptibility testing for five of seven antibiotics. Because of the relatively low costs, possibility for real-time data analyses, and portability, the Oxford Nanopore Technologies MinION sequencing platform—especially in light of an upcoming less error-prone technology for the platform—appears to be well suited for pathogen genomic analyses such as the one described here. Together with CholerAegon, it can leverage pathogen genomics to improve disease surveillance and to control further spread of antimicrobial resistance.},

keywords = {bacteria, DNA / genomics, nanopore},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Dogs as carriers of virulent and resistant genotypes of \textit{Clostridioides difficile}},

author = {SK Finsterwalder and I Loncaric and A Cabal and MP Szostak and Lisa-Marie Barf and Manja Marz and F Allerberger and IA Burgener and A Tichy and AT Feßler and S Schwarz and S Monecke and R Ehricht and W Ruppitsch and J Spergser and F Künzel},

doi = {10.1111/zph.12956},

year  = {2022},

date = {2022-05-12},

journal = {Zoonoses Public Health},

volume = {69},

issue = {6},

pages = {673-681},

abstract = {While previous research on zoonotic transmission of community-acquired Clostridioides difficile infection (CA-CDI) focused on food-producing animals, the present study aimed to investigate whether dogs are carriers of resistant and/or virulent C. difficile strains. Rectal swabs were collected from 323 dogs and 38 C. difficile isolates (11.8%) were obtained. Isolates were characterized by antimicrobial susceptibility testing, whole-genome sequencing (WGS) and a DNA hybridization assay. Multilocus sequence typing (MLST), core genome MLST (cgMLST) and screening for virulence and antimicrobial resistance genes were performed based on WGS. Minimum inhibitory concentrations for erythromycin, clindamycin, tetracycline, vancomycin and metronidazole were determined by E-test. Out of 38 C. difficile isolates, 28 (73.7%) carried genes for toxins. The majority of isolates belonged to MLST sequence types (STs) of clade I and one to clade V. Several isolates belonged to STs previously associated with human CA-CDI. However, cgMLST showed low genetic relatedness between the isolates of this study and C. difficile strains isolated from humans in Austria for which genome sequences were publicly available. Four isolates (10.5%) displayed resistance to three of the tested antimicrobial agents. Isolates exhibited resistance to erythromycin, clindamycin, tetracycline and metronidazole. These phenotypic resistances were supported by the presence of the resistance genes erm(B), cfr(C) and tet(M). All isolates were susceptible to vancomycin. Our results indicate that dogs may carry virulent and antimicrobial-resistant C. difficile strains.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Characterization of RNA content in individual phase-separated coacervate microdroplets},

author = {Damian Wollny and Benjamin Vernot and Jie Wang and Maria Hondele and Aram Safrastyan and Franziska Aron and Julia Micheel and Zhisong He and Anthony Hyman and Karsten Weis and J. Gray Camp and T-Y Dora Tang and Barbara Treutlein},

url = {10.1038/s41467-022-30158-1},

year  = {2022},

date = {2022-05-12},

urldate = {2022-05-12},

journal = {Nat Commun},

volume = {13},

issue = {1},

pages = {2626},

abstract = {Condensates formed by complex coacervation are hypothesized to have played a crucial part during the origin-of-life. In living cells, condensation organizes biomolecules into a wide range of membraneless compartments. Although RNA is a key component of biological condensates and the central component of the RNA world hypothesis, little is known about what determines RNA accumulation in condensates and to which extend single condensates differ in their RNA composition. To address this, we developed an approach to read the RNA content from single synthetic and protein-based condensates using high-throughput sequencing. We find that certain RNAs efficiently accumulate in condensates. These RNAs are strongly enriched in sequence motifs which show high sequence similarity to short interspersed elements (SINEs). We observe similar results for protein-derived condensates, demonstrating applicability across different in vitro reconstituted membraneless organelles. Thus, our results provide a new inroad to explore the RNA content of phase-separated droplets at single condensate resolution.},

keywords = {RNA / transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {The Role of Non-Coding RNAs in the Human Placenta},

author = {Milena Žarković and Franziska Hufsky and Udo R Markert and Manja Marz},

doi = {10.3390/cells11091588},

year  = {2022},

date = {2022-05-09},

journal = {Cells},

volume = {11},

issue = {9},

pages = {1588},

abstract = {Non-coding RNAs (ncRNAs) play a central and regulatory role in almost all cells, organs, and species, which has been broadly recognized since the human ENCODE project and several other genome projects. Nevertheless, a small fraction of ncRNAs have been identified, and in the placenta they have been investigated very marginally. To date, most examples of ncRNAs which have been identified to be specific for fetal tissues, including placenta, are members of the group of microRNAs (miRNAs). Due to their quantity, it can be expected that the fairly larger group of other ncRNAs exerts far stronger effects than miRNAs. The syncytiotrophoblast of fetal origin forms the interface between fetus and mother, and releases permanently extracellular vesicles (EVs) into the maternal circulation which contain fetal proteins and RNA, including ncRNA, for communication with neighboring and distant maternal cells. Disorders of ncRNA in placental tissue, especially in trophoblast cells, and in EVs seem to be involved in pregnancy disorders, potentially as a cause or consequence. This review summarizes the current knowledge on placental ncRNA, their transport in EVs, and their involvement and pregnancy pathologies, as well as their potential for novel diagnostic tools.},

keywords = {extracellular vesicles, ncRNAs, pregnancy, RNA / transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{Hufsky2022,

title = {The International Virus Bioinformatics Meeting 2022},

author = {Franziska Hufsky and Denis Beslic and Dimitri Boeckaerts and Sebastian Duchene and Enrique González-Tortuero and Andreas J Gruber and Jiarong Guo and Daan Jansen and John Juma and Kunaphas Kongkitimanon and Antoni Luque and Muriel Ritsch and Gabriel Lencioni Lovate and Luca Nishimura and Célia Pas and Esteban Domingo and Emma Hodcroft and Philippe Lemey and Matthew B Sullivan and Friedemann Weber and Fernando González-Candelas and Sarah Krautwurst and Alba Pérez-Cataluña and Walter Randazzo and Gloria Sánchez and Manja Marz },

doi = {10.3390/v14050973},

year  = {2022},

date = {2022-05-05},

urldate = {2022-05-05},

journal = {Viruses},

volume = {14},

issue = {5},

pages = {973},

abstract = {The International Virus Bioinformatics Meeting 2022 took place online, on 23-25 March 2022, and has attracted about 380 participants from all over the world. The goal of the meeting was to provide a meaningful and interactive scientific environment to promote discussion and collaboration and to inspire and suggest new research directions and questions. The participants created a highly interactive scientific environment even without physical face-to-face interactions. This meeting is a focal point to gain an insight into the state-of-the-art of the virus bioinformatics research landscape and to interact with researchers in the forefront as well as aspiring young scientists. The meeting featured eight invited and 18 contributed talks in eight sessions on three days, as well as 52 posters, which were presented during three virtual poster sessions. The main topics were: SARS-CoV-2, viral emergence and surveillance, virus-host interactions, viral sequence analysis, virus identification and annotation, phages, and viral diversity. This report summarizes the main research findings and highlights presented at the meeting.},

keywords = {annotation, software, virus host interaction, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Gib mir den Virus und ich sag dir den Wirt},

author = {Franziska Hufsky and Manja Marz},

doi = {10.1007/s12268-022-1732-7},

year  = {2022},

date = {2022-03-28},

journal = {BIOSpektrum},

volume = {28},

pages = {225–226},

keywords = {software, virus host interaction, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Nanopore sequencing for mapping of retrotransposon integration sites in the \textit{Dictyostelium discoideum} genome},

author = {Emanuel Barth and Johannes Burggraaff and Akash Srivastava and Thomas Winckler

},

doi = {10.17912/micropub.biology.000543},

year  = {2022},

date = {2022-03-18},

journal = {MicroPubl Biol},

abstract = {The unicellular eukaryote \textit{Dictyostelium discoideum} has a gene-dense haploid genome. This configuration presents mobile elements with the particular challenge of replicating without causing excessive damage to the host through insertional mutagenesis or recombination between repetitive sequences. \textit{D. discoideum} harbors an active population of the retrotransposon TRE5-A that integrates in a narrow window of ~50 bp upstream of tRNA genes. We assume that this integration preference was developed to avoid the disruption of protein-coding genes. Therefore, we recently mapped new integrations of a genetically tagged TRE5-A element at tRNA genes using PCR-based enrichment of integration junctions. However, the PCR-based enrichment produced several artificial DNA fusions that prevented the mapping of integration sites in unknown places of the genome. Here, we reanalyzed the previous experiment using nanopore sequencing. We summarize the advantages and limitations of direct genome resequencing for the mapping of mobile element integrations.},

keywords = {DNA / genomics, nanopore},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Draft genome assembly and sequencing dataset of the marine diatom Skeletonema cf. costatum RCC75},

author = {Maria Sorokina and Emanuel Barth and Mahnoor Zulfiqar and Michiel Kwantes and Georg Pohnert and Christoph Steinbeck

},

doi = {10.1016/j.dib.2022.107931},

year  = {2022},

date = {2022-02-19},

urldate = {2022-02-05},

journal = {Data Brief},

volume = {41},

pages = {107931},

abstract = {Diatoms (Bacillariophyceae) are a major constituent of the phytoplankton and have a universally recognized ecological importance. Between 1,000 and 1,300 diatom genera have been described in the literature, but only 10 nuclear genomes have been published and made available to the public up to date. Skeletonema costatum is a cosmopolitan marine diatom, principally occurring in coastal regions, and is one of the most abundant members of the Skeletonema genus. Here we present a draft assembly of the Skeletonema cf. costatum RCC75 genome, obtained from PacBio and Illumina NovaSeq data. This dataset will expand the knowledge of the Bacillariophyceae genetics and contribute to the global understanding of phytoplankton's physiological, ecological, and environmental functioning.},

keywords = {DNA / genomics},

pubstate = {published},

tppubtype = {article}

}

@article{Sofer2022,

title = {A genome-wide CRISPR activation screen reveals Hexokinase 1 as a critical factor in promoting resistance to multi-kinase inhibitors in hepatocellular carcinoma cells},

author = {Summer Sofer and Kevin Lamkiewicz and Shir Armoza Eilat and Shirly Partouche and Manja Marz and Neta Moskovits and Salomon M Stemmer and Amir Shlomai and Ella H Sklan},

doi = {10.1096/fj.202101507RR},

year  = {2022},

date = {2022-02-11},

urldate = {2022-02-11},

journal = {FASEB J },

volume = {36},

issue = {3},

pages = {e22191},

abstract = {Hepatocellular carcinoma (HCC) is often diagnosed at an advanced stage and is, therefore, treated with systemic drugs, such as tyrosine-kinase inhibitors (TKIs). These drugs, however, offer only modest survival benefits due to the rapid development of drug resistance. To identify genes implicated in TKI resistance, a cluster of regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 activation screen was performed in hepatoma cells treated with regorafenib, a TKI used as second-line therapy for advanced HCC. The screen results show that Hexokinase 1 (HK1), catalyzing the first step in glucose metabolism, is a top candidate for conferring TKI resistance. Compatible with this, HK1 was upregulated in regorafenib-resistant cells. Using several experimental approaches, both in vitro and in vivo, we show that TKI resistance correlates with HK1 expression. Furthermore, an HK inhibitor resensitized resistant cells to TKI treatment. Together, our data indicate that HK1 may function as a critical factor modulating TKI resistance in hepatoma cells and, therefore, may serve as a biomarker for treatment success.},

keywords = {cancer, DNA / genomics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Small Extracellular Vesicles from Peripheral Blood of Aged Mice Pass the Blood-Brain Barrier and Induce Glial Cell Activation.},

author = {Diana M Morales-Prieto and José M Murrieta-Coxca and Milan Stojiljkovic and Celia Diezel and Priska E Streicher and Julian A Henao-Restrepo and Franziska Röstel and Julia Lindner and Otto W Witte and Sebastian Weis and Christian Schmeer and Manja Marz},

doi = {10.3390/cells11040625},

year  = {2022},

date = {2022-02-11},

journal = {Cells},

volume = {11},

issue = {4},

pages = {625},

abstract = {Extracellular vesicles (EVs), including small EVs (sEVs), are involved in neuroinflammation and neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Yet, increased neuroinflammation can also be detected in the aging brain, and it is associated with increased glial activation. Changes in EV concentration are reported in aging tissues and senescence cells, suggesting a role of EVs in the process of aging. Here, we investigated the effect of peripheral sEVs from aged animals on neuroinflammation, specifically on glial activation. sEVs were isolated from the peripheral blood of young (3 months) and aged (24 months) C57BL/6J wildtype mice and injected into the peripheral blood from young animals via vein tail injections. The localization of EVs and the expression of selected genes involved in glial cell activation, including Gfap, Tgf-β, Cd68, and Iba1, were assessed in brain tissue 30 min, 4 h, and 24 h after injection. We found that sEVs from peripheral blood of aged mice but not from young mice altered gene expression in the brains of young animals. In particular, the expression of the specific astrocyte marker, Gfap, was significantly increased, indicating a strong response of this glial cell type. Our study shows that sEVs from aged mice can pass the blood-brain barrier (BBB) and induce glial cell activation.},

keywords = {aging, extracellular vesicles},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Comparative study of ten thogotovirus isolates and their distinct in vivo characteristics},

author = {Jonas Fuchs and Kevin Lamkiewicz and Larissa Kolesnikova and Martin Hölzer and Manja Marz and Georg Kochs},

doi = {10.1128/JVI.01556-21},

year  = {2022},

date = {2022-01-12},

journal = {J Virol},

abstract = {Thogotoviruses are tick-borne arboviruses that comprise a unique genus within the Orthomyxoviridae family. Infections with thogotoviruses primarily cause disease in livestock with occasional reports of human infections suggesting a zoonotic potential. In the past, multiple genetically distinct thogotoviruses were isolated mostly from collected ticks. However, many aspects regarding their phylogenetic relationships, morphological characteristics and virulence in mammals remain unclear. For the present comparative study, we used a collection of ten different thogotovirus isolates from different geographic areas. Next generation sequencing and subsequent phylogenetic analyses revealed a distinct separation of these viruses into two major clades - the Thogoto-like and Dhori-like viruses. Electron microscopy demonstrated a heterogeneous morphology with spherical and filamentous particles being present in virus preparations. To study their pathogenicity, we analyzed the viruses in a small animal model system. In intraperitoneally infected C57BL/6 mice, all isolates showed a tropism for liver, lung and spleen. Importantly, we did not observe horizontal transmission to uninfected, highly susceptible contact mice. The isolates enormously differed in their capacity to induce disease, ranging from subclinical to fatal outcomes. In vivo multi-step passaging experiments of two low-pathogenic isolates showed no increased virulence and sequence analyses of the passaged viruses indicated a high stability of the viral genomes after ten mouse passages. In summary, our analysis demonstrates the broad genetic and phenotypic variability within the thogotovirus genus. Moreover, thogotoviruses are well adapted to mammals but their horizontal transmission seems to depend on ticks as their vectors. Importance Since their discovery over sixty years ago, fifteen genetically distinct members of the thogotovirus genus have been isolated. These arboviruses belong to the Orthomyxovirus family and share many features with influenza viruses. However, numerous of these isolates have not been characterized in depth. In the present study, we comparatively analyzed a collection of ten different thogotovirus isolates to answer basic questions about their phylogenetic relationships, morphology and pathogenicity in mice. Our results highlight shared and unique characteristics of this diverse genus. Taken together, these observations provide a framework for the phylogenic classification and phenotypic characterization of newly identified thogotovirus isolates that could potentially cause severe human infections as exemplified by the recently reported, fatal Bourbon virus cases in the United States.},

keywords = {phylogenetics, viruses},

pubstate = {published},

tppubtype = {article}

}