publications.bib

@article{Fu2021,
abstract = {The emergence and re-emergence of viral epidemics and the risks of antiviral drug resistance are a serious threat to global public health. New options to supplement or replace currently used drugs for antiviral therapy are urgently needed. The research in the field of ribosomally synthesized and post-translationally modified peptides (RiPPs) has been booming in the last few decades, in particular in view of their strong antimicrobial activities and high stability. The RiPPs with antiviral activity, especially those against enveloped viruses, are now also gaining more interest. RiPPs have a number of advantages over small molecule drugs in terms of specificity and affinity for targets, and over protein-based drugs in terms of cellular penetrability, stability and size. Moreover, the great engineering potential of RiPPs provides an efficient way to optimize them as potent antiviral drugs candidates. These intrinsic advantages underscore the good therapeutic prospects of RiPPs in viral treatment. With the aim to highlight the underrated antiviral potential of RiPPs and explore their development as antiviral drugs, we review the current literature describing the antiviral activities and mechanisms of action of RiPPs, discussing the ongoing efforts to improve their antiviral potential and demonstrate their suitability as antiviral therapeutics. We propose that antiviral RiPPs may overcome the limits of peptide-based antiviral therapy, providing an innovative option for the treatment of viral disease.},
author = {Fu, Yuxin and Jaarsma, Ate H. and Kuipers, Oscar P.},
doi = {10.1007/S00018-021-03759-0},
file = {:C$\backslash$:/Users/au681905/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Fu, Jaarsma, Kuipers - 2021 - Antiviral activities and applications of ribosomally synthesized and post-translationally modified peptide.pdf:pdf},
issn = {1420-9071},
journal = {Cellular and Molecular Life Sciences 2021 78:8},
keywords = {Biochemistry,Biomedicine,Cell Biology,Life Sciences,general},
month = {feb},
number = {8},
pages = {3921--3940},
publisher = {Springer},
title = {{Antiviral activities and applications of ribosomally synthesized and post-translationally modified peptides (RiPPs)}},
url = {https://link.springer.com/article/10.1007/s00018-021-03759-0},
volume = {78},
year = {2021}
}
@article{Jaarsma2023b,
abstract = {The microbiome of Greenland Ice Sheet supraglacial habitats is still underinvestigated, and as a result there is a lack of representative genomes from these environments. In this study, we investigated the supraglacial microbiome through a combination of culturing-dependent and -independent approaches. We explored ice, cryoconite, biofilm, and snow biodiversity to answer: (1) how microbial diversity differs between supraglacial habitats, (2) if obtained bacterial genomes reflect dominant community members, and (3) how culturing versus high throughput sequencing changes our observations of microbial diversity in supraglacial habitats. Genomes acquired through metagenomic sequencing (133 high-quality MAGs) and whole genome sequencing (73 bacterial isolates) were compared to the metagenome assemblies to investigate abundance within the total environmental DNA. Isolates obtained in this study were not dominant taxa in the habitat they were sampled from, in contrast to the obtained MAGs. We demonstrate here the advantages of using metagenome SSU rRNA genes to reflect whole-community diversity. Additionally, we demonstrate a proof-of-concept of the application of in situ culturing in a supraglacial setting.},
author = {Jaarsma, Ate H. and Sipes, Katie and Zervas, Athanasios and Jim{\'{e}}nez, Francisco Campuzano and Ellegaard-Jensen, Lea and Th{\o}gersen, Mariane S. and Stougaard, Peter and Benning, Liane G. and Tranter, Martyn and Anesio, Alexandre M.},
doi = {10.1093/femsec/fiad119},
file = {:C$\backslash$:/Users/au681905/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Jaarsma et al. - 2023 - Exploring microbial diversity in Greenland Ice Sheet supraglacial habitats through culturing-dependent and -inde.pdf:pdf},
issn = {15746941},
journal = {FEMS Microbiology Ecology},
keywords = {Greenland Ice Sheet,MAGs,amplicons,in situ culturing,isolates,metagenome},
number = {11},
pages = {1--16},
pmid = {37791411},
title = {{Exploring microbial diversity in Greenland Ice Sheet supraglacial habitats through culturing-dependent and -independent approaches}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/37791411},
volume = {99},
year = {2023}
}
@article{Jaarsma2023c,
abstract = {The Greenland Ice Sheet is a biome which is mainly microbially driven. Several different niches can be found within the glacial biome for those microbes able to withstand the harsh conditions, e.g., low temperatures, low nutrient conditions, high UV radiation in summer, and contrasting long and dark winters. Eukaryotic algae can form blooms during the summer on the ice surface, interacting with communities of bacteria, fungi, and viruses. Cryoconite holes and snow are also habitats with their own microbial community. Nevertheless, the microbiome of supraglacial habitats remains poorly studied, leading to a lack of representative genomes from these environments. Under-investigated extremophiles, like those living on the Greenland Ice Sheet, may provide an untapped reservoir of chemical diversity that is yet to be discovered. In this study, an inventory of the biosynthetic potential of these organisms is made, through cataloging the presence of biosynthetic gene clusters in their genomes. There were 133 high-quality metagenome-assembled genomes (MAGs) and 28 whole genomes of bacteria obtained from samples of the ice sheet surface, cryoconite, biofilm, and snow using culturing-dependent and -independent approaches. AntiSMASH and BiG-SCAPE were used to mine these genomes and subsequently analyze the resulting predicted gene clusters. Extensive sets of predicted Biosynthetic Gene Clusters (BGCs) were collected from the genome collection, with limited overlap between isolates and MAGs. Additionally, little overlap was found in the biosynthetic potential among different environments, suggesting specialization of organisms in specific habitats. The median number of BGCs per genome was significantly higher for the isolates compared to the MAGs. The most talented producers were found among Proteobacteria. We found evidence for the capacity of these microbes to produce antimicrobials, carotenoid pigments, siderophores, and osmoprotectants, indicating potential survival mechanisms to cope with extreme conditions. The majority of identified BGCs, including those in the most prevalent gene cluster families, have unknown functions, presenting a substantial potential for bioprospecting. This study underscores the diverse biosynthetic potential in Greenland Ice Sheet genomes, revealing insights into survival strategies and highlighting the need for further exploration and characterization of these untapped resources.},
author = {Jaarsma, Ate H. and Zervas, Athanasios and Sipes, Katie and {Campuzano Jim{\'{e}}nez}, Francisco and Smith, Andrea Claire and Svendsen, Liessel Victoria and Th{\o}gersen, Mariane S. and Stougaard, Peter and Benning, Liane G. and Tranter, Martyn and Anesio, Alexandre M.},
doi = {10.3389/fmicb.2023.1285791},
file = {:C$\backslash$:/Users/au681905/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Jaarsma et al. - 2023 - The undiscovered biosynthetic potential of the Greenland Ice Sheet microbiome.pdf:pdf},
issn = {1664302X},
journal = {Frontiers in Microbiology},
keywords = {bioprospecting,biosynthetic gene clusters,extremophiles,genome mining,metagenomic sequencing,supraglacial habitats},
title = {{The undiscovered biosynthetic potential of the Greenland Ice Sheet microbiome}},
volume = {14},
year = {2023}
}
@article{Viel2021,
abstract = {The lanthipeptide mersacidin is a ribosomally synthesized and post-translationally modified peptide (RiPP) produced by Bacillus amyloliquefaciens. It has antimicrobial activity against a range of G...},
author = {Viel, Jakob H. and Jaarsma, Ate H. and Kuipers, Oscar P.},
doi = {10.1021/ACSSYNBIO.0C00601},
file = {:C$\backslash$:/Users/au681905/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Viel, Jaarsma, Kuipers - 2021 - Heterologous Expression of Mersacidin in Escherichia coli Elucidates the Mode of Leader Processing.pdf:pdf},
journal = {ACS Synthetic Biology},
keywords = {E. coli,RiPPs,heterologous expression,lanthipeptides,leader processing,mersacidin,mutagenesis},
month = {mar},
number = {3},
pages = {600--608},
publisher = {American Chemical Society},
title = {{Heterologous Expression of Mersacidin in Escherichia coli Elucidates the Mode of Leader Processing}},
url = {https://pubs.acs.org/doi/full/10.1021/acssynbio.0c00601},
volume = {10},
year = {2021}
}
@article{Jaarsmaa,
author = {Jaarsma, Ate H and Sipes, Katie and Zervas, Athanasios and Feord, Helen and Jim, Francisco Campuzano and Th{\o}gersen, Mariane S and Benning, Liane G and Tranter, Martyn and Anesio, Alexandre M},
file = {:C$\backslash$:/Users/au681905/OneDrive - Aarhus universitet/DRIVE/PAPERS/STOIC/SUBMISSION/Jaarsma{\_}AH{\_}GrIS{\_}BGC.pdf:pdf},
journal = {ISME Journal},
keywords = {bgcs,biosynthetic gene clusters,metatranscriptomics,microbial community,supraglacial habitats},
pages = {1--12},
title = {{The encoded and expressed biosynthetic potential of Greenland Ice Sheet microbes}}
}