Biology subjects

Oldenkamp, R.

Publications and source records attributed to Oldenkamp, R..

7 recordsLinked to original sources

bioRxiv2025

Environmental exposure to antibiotics drives and sustains antibiotic resistance in Neisseria gonorrhoeae: A modelling study

Ciprofloxacin resistance is widespread in Neisseria gonorrhoeae, despite its discontinuation as recommended treatment option in 2007. Unintentional low-level exposure to ciprofloxacin, e.g., environmental or food-borne, might provide sufficiently high selection pressure to maintain resistance and compensate potential fitness costs. We used a mathematical within-host model of gonorrhoea to investigate the effect of low-level ciprofloxacin exposure on susceptibility. We present a mechanistic within-host model of gonococcal infections in the male urethra, to simulate the influence of low-level ciprofloxacin exposures on gonococcal ciprofloxacin susceptibility. We assessed the impact of repeated exposures to varying amounts of ciprofloxacin [Formula] in a chain of sequentially transmitted infections. Daily exposure to at least 0.15mg ciprofloxacin was sufficient to select for low-level resistance. Moreover, in the absence of ciprofloxacin treatment, resistant variants could revert back to variants with lower levels of resistance. However, background exposure can balance fitness costs of resistance and prevent a complete reversion to the fully susceptible variant. Even for human-host restricted pathogens such as Neisseria gonorrhoeae, a One Health approach that considers unintentional antibiotic exposures is needed to avoid the emergence and spread of resistance.

microbiology↗

bioRxiv2025

Visualizing homology search in living cells

Homologous recombination (HR) is a DNA repair process that requires a homologous sequence for the repair of DNA double-stranded breaks. The search for homology is the rate limiting step for HR, but the dynamics of homology search in vivo are currently poorly understood. This is largely due to a lack of tools to visualize homology search in action in living human cells. Here, we show that RAD51 and MND1, two proteins operating in homology search, become visible in long filamentous structures several hours after double-stranded break formation. Using GFP-MND1 we can visualize these filaments in living human cells and find that they are highly dynamic, explore the nuclear space, and can resolve over time. We show that the resolution of these filaments depends on RAD54L, known for its role in RAD51-driven homology search and strand-invasion. In addition, we find that loss of cohesin also inhibits the resolution of these filaments, in accordance with a role for cohesin in HR. Thus, our data suggest that these filaments are visible intermediates of an active DNA repair process, and that MND1-GFP can be used as a tool to study the dynamics of homology search in living human cells.

cell biology↗

bioRxiv2022

Genome-wide association reveals host-specific genomic traits in Escherichia coli

Escherichia coli is an opportunistic pathogen that can colonize or infect various host species. There is a significant gap in our understanding to what extent genetic lineages of E. coli are adapted or restricted to specific hosts. In addition, genomic determinants underlying such host specificity are unknown.By analyzing a randomly sampled collection of 1198 whole-genome sequenced E. coli isolates from four countries (Germany, UK, Spain, and Vietnam), obtained from five host species (human, pig, cattle, chicken, and wild boar) over 16 years, from both healthy and diseased hosts, we demonstrate that certain lineages of E. coli are frequently detected in specific hosts. We report a novel nan gene cluster, designated nan-9, putatively encoding acetylesterases and determinants of uptake and metabolism of sialic acid, to be associated with the human host as identified through genome wide association studies. In silico characterization predicts nan-9 to be involved in sialic acid (Sia) metabolism. In vitro growth experiments with a representative {Delta}nan E. coli mutant strain, using sialic acids 5-N-acetyl neuraminic acid (Neu5Ac) and N-glycolyl neuraminic acid (Neu5Gc) as the sole carbon source, indicate an impaired growth behaviour compared to the wild-type. In addition, we identified several additional E. coli genes that are potentially associated with adaptation to human, cattle and chicken hosts, but not for the pig host. Collectively, this study provides an extensive overview of genetic determinants which may mediate host specificity in E. coli. Our findings should inform risk analysis and epidemiological monitoring of (antimicrobial resistant) E. coli.

genomics↗

bioRxiv2020

Time-resolved structured illumination microscopy reveals key principles of Xist RNA spreading

Xist RNA directs the process of X-chromosome inactivation in mammals by spreading in cis along the chromosome from which it is transcribed and recruiting chromatin modifiers to silence gene transcription. To elucidate mechanisms of Xist RNA cis-confinement, we established a sequential dual color labeling, super-resolution imaging approach to trace individual Xist RNA molecules over time, enabling us to define fundamental parameters of spreading. We demonstrate a feedback mechanism linking Xist RNA synthesis and degradation, and an unexpected physical coupling between preceding and newly synthesized Xist RNA molecules. Additionally, we show that the protein SPEN, a key factor for Xist-mediated gene-silencing, has a distinct function in Xist RNA localization, stability and in coupling behavior. Our results provide important insights towards understanding the unique dynamic properties of Xist RNA. One Sentence SummaryVisualizing Xist RNA dynamics in single cells during X chromosome inactivation

developmental biology↗

bioRxiv2020

Cold induced chromatin compaction and nuclear retention of clock mRNAs resets the circadian rhythm

Cooling patients to sub-physiological temperatures is an integral part of modern medicine. We show that cold exposure induces temperature-specific changes to the higher-order chromatin and gene expression profiles of human cells. These changes are particularly dramatic at 18{degrees}C, a temperature synonymous with that experienced by patients undergoing controlled deep-hypothermia during surgery. Cells exposed to 18{degrees}C exhibit largely nuclear-restricted transcriptome changes. These include the nuclear accumulation of core circadian clock suppressor gene transcripts, most notably REV-ERB. This response is accompanied by compaction of higher-order chromatin and hindrance of mRNPs from engaging nuclear pores. Rewarming reverses chromatin compaction and releases the transcripts into the cytoplasm, triggering a pulse of suppressor gene proteins that resets the circadian clock. We show that cold-induced upregulation of REV-ERB alone is sufficient to trigger this resetting. Our findings uncover principles of the cellular cold-response that must be considered for current and future applications involving therapeutic deep-hypothermia.

molecular biology↗

bioRxiv2019

The CTCF Anatomy of Topologically Associating Domains

Topologically associated domains (TADs) are defined as regions of self-interaction. To date, it is unclear how to reconcile TAD structure with CTCF site orientation, which is known to coordinate chromatin loops anchored by Cohesin rings at convergent CTCF site pairs. We first approached this problem by 4C analysis of the FKBP5 locus. This uncovered a CTCF loop encompassing FKBP5 but not its entire TAD. However, adjacent CTCF sites were able to form back-up loops and these were located at TAD boundaries. We then analysed the spatial distribution of CTCF patterns along the genome together with a boundary identity conservation gradient obtained from primary blood cells. This revealed that divergent CTCF sites are enriched at boundaries and that convergent CTCF sites mark the interior of TADs. This conciliation of CTCF site orientation and TAD structure has deep implications for the further study and engineering of TADs and their boundaries.

genomics↗

bioRxiv2019

Chromatin arranges in filaments of blobs with nanoscale functional zonation

Three-dimensional (3D) chromatin organization plays a key role in regulating mammalian genome function, however many of its physical features at the single-cell level remain underexplored. Here we use 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify linked chromatin domains (CDs) composed of irregular [~]200-300-nm-wide aggregates of nucleosomes that can overlap with individual topologically associating domains and are distinct from a surrounding RNA-populated interchromatin region. High-content mapping uncovers confinement of cohesin and active histone modifications to surfaces and enrichment of repressive modifications towards the core of CDs in both hetero- and euchromatic regions. This nanoscale functional topography is temporarily relaxed in post-replicative chromatin, but remarkably persists after ablation of cohesin. Our findings establish CDs as physical and functional modules of mesoscale genome organization.

genomics↗