Biology subjects

Madsen, J. S.

Publications and source records attributed to Madsen, J. S..

5 recordsLinked to original sources

bioRxiv2021

CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids

Many prokaryotes encode CRISPR-Cas systems as immune protection against mobile genetic elements (MGEs), yet, a number of MGEs also harbor CRISPR-Cas components. With a few exceptions, CRISPR-Cas loci encoded on MGEs are uncharted and a comprehensive analysis of their distribution, prevalence, diversity, and function is lacking. Here, we systematically investigated CRISPR-Cas loci across the largest curated collection of natural bacterial and archaeal plasmids. CRISPR-Cas loci are widely but heterogeneously distributed across plasmids and, in comparison to host chromosomes, their mean prevalence per Mbp is higher and their distribution is markedly distinct. Furthermore, the spacer content of plasmid CRISPRs exhibits a strong targeting bias towards other plasmids, while chromosomal arrays are enriched with virus-targeting spacers. These contrasting targeting preferences dominate across the diversity of CRISPR-Cas subtypes and host taxa, highlighting the genetic independence of plasmids and suggesting a major role of CRISPR-Cas for mediating plasmid-plasmid conflicts. Altogether, CRISPR-Cas are frequent accessory components of many plasmids, which is an overlooked phenomenon that possibly facilitates their dissemination across microbiomes.

microbiology↗

bioRxiv2021

Deep Learning Shows Cellular Senescence Is a Barrier to Cancer Development

Cellular senescence is a critical component of aging and many age-related diseases, but understanding its role in human health is challenging in part due to the lack of exclusive or universal markers. Using neural networks, we achieve high accuracy in predicting senescence state and type from the nuclear morphology of DAPI-stained human fibroblasts, murine astrocytes and fibroblasts derived from premature aging diseases in vitro. After generalizing this approach, the predictor recognizes an increasing rate of senescent cells with age in H&E-stained murine liver tissue and human dermal biopsies. Evaluating corresponding medical records reveals that individuals with increased senescent cells have a significantly decreased rate of malignant neoplasms, lending support for the protective role of senescence in limiting cancer development. In sum, we introduce a novel predictor of cellular senescence and apply it to diagnostic medical images, indicating cancer occurs more frequently for those with a lower rate of senescence.

cell biology↗

bioRxiv2020

Adaptive evolution of phenotypic switching during environmental change

Microbes are faced with environmental fluctuations and it is therefore important to understand how change affects bacterial evolution and population dynamics. Here, we evolved a model bacterium, Pseudomonas aeruginosa PA14, under both constant and changing conditions where settlement by biofilm formation or migration by swimming motility was induced. In changing environments, a heterogeneous population evolved with both specialists and generalists. Interestingly, over time, generalists were outcompeted despite being better at both phenotypes compared to the ancestor. However, generalists became dominant when faced with local competition after resettlement. Reintroduction into a burn wound model, the environment PA14 originally was isolated from, further suggested a tradeoff between niche breadth and peak fitness in agreement with the evolution experiments. Mutations in the c-di-GMP system were key for adaptation of the phenotypes. No mutants lost their ability to regulate c-di-GMP, but generalists acquired mutations that optimized their phenotypic response by efficiently adjusting c-di-GMP levels.

evolutionary biology↗

bioRxiv2019

Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes

The current epidemic of antibiotic resistance has been facilitated by the wide and rapid horizontal dissemination of antibiotic resistance genes (ARGs) in microbial communities. Indeed, ARGs are often located on plasmids, which can efficiently shuttle genes across diverse taxa. While the existence conditions of plasmids have been extensively studied in a few model bacterial populations, their fate in complex bacterial communities is poorly understood. Here, we coupled plasmid transfer assays with serial growth experiments to investigate the persistence of the broad-host-range IncP-1 plasmid pKJK5 in microbial communities derived from a sewage treatment plant. The cultivation conditions combined different nutrient and oxygen levels, and were non-selective and non-conducive for liquid-phase conjugal transfer. Following initial transfer, the plasmid persisted in almost all conditions during a 10-day serial growth experiment (equivalent to 60 generations), with a transient transconjugant incidence up to 30%. By combining cell enumeration and sorting with amplicon sequencing, we mapped plasmid fitness effects across taxa of the microbial community. Unexpected plasmid fitness benefits were observed in multiple phylotypes of Aeromonas, Pseudomonas and Enterobacteriaceae, which resulted in community-level plasmid persistence. We demonstrate, for the first time, that plasmid fitness effects across community members can be estimated in a high-throughput way without prior isolation. By gaining a fitness benefit when carrying plasmids, members within complex microbial communities might have a hitherto unrecognized potential to maintain plasmids for long-term community-wide access.

ecology↗

bioRxiv2019

Developing single molecule methods for measuring the pathway proteins ERK, AKT, cyclin d and p70s6k in localized colon cancer in relation to mutation status

BackgroundThe aim of this study was to quantify the intracellular pathway proteins ERK, AKT, cyclin d and p70s6k in localized colon cancer tissue to investigate the possible prognostic values and the ability to be used as screening markers for upstream mutations.\n\nMethodsColon cancer tissue and autologous reference tissue were collected from 176 patients who underwent surgery for colon cancer. Assays for quantifying ERK, AKT, cyclin d and p70s6k proteins were developed using single molecule array (Simoa). KRAS/BRAF/PIK3CA mutation status was determined using droplet digital PCR.\n\nResultsPatients with BRAF mutations had decreased concentrations of ERK (p=0.0002), AKT (p=0.00004) and cyclin d (p=0.001) while no significant differences were found between patients with KRAS mutations and Wild type (Wt) patients. None of the investigated protein concentrations were associated with disease free survival or overall survival, if including all patients. However, when stratifying according to mutation status, significant correlations to overall survival were seen for patients with BRAF mutations and AKT (p=0.003) or ERK (p=0.046) and for patients with KRAS mutations and p70s6k (p=0.04). Furthermore, the combination of genetic mutations, stage 2 disease, and all of the investigated pathway proteins showed significant correlations to overall survival.\n\nConclusionsThere is a strong correlation between pathway protein concentrations and mutational BRAF status. Overall survival in colon cancer patients depend both on gene mutation status and pathway protein concentrations. As significant correlations were found between BRAF mutations and ERK, AKT and cyclin d, concentration measurements of these pathway proteins might be useful as screening for upstream mutations.

biochemistry↗