A5073216193- Cancer Genomics and Diagnostics
- Fungal and yeast genetics research
- Microbial Metabolic Engineering and Bioproduction
- Chromosomal and Genetic Variations
- CRISPR and Genetic Engineering
- Evolution and Genetic Dynamics
- Genetic factors in colorectal cancer
- Genomics and Chromatin Dynamics
- Bacterial biofilms and quorum sensing
- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Plant nutrient uptake and metabolism
- DNA Repair Mechanisms
- Genomic variations and chromosomal abnormalities
- Pancreatic and Hepatic Oncology Research
- Biofuel production and bioconversion
- Antifungal resistance and susceptibility
- Plant and animal studies
- Polyamine Metabolism and Applications
- Epigenetics and DNA Methylation
- Gene Regulatory Network Analysis
- Plant-Microbe Interactions and Immunity
- Fermentation and Sensory Analysis
- Evolutionary Game Theory and Cooperation
- Antimicrobial Peptides and Activities
University of Copenhagen
2016-2025
Aarhus University
2024
Botswana Geoscience Institute
2024
BGI Research
2024
Universitat Autònoma de Barcelona
2024
Technical University of Denmark
2003-2010
Goethe University Frankfurt
2006
Carlsberg Laboratory
1998-2001
The human genome is generally organized into stable chromosomes, and only tumor cells are known to accumulate kilobase (kb)-sized extrachromosomal circular DNA elements (eccDNAs). However, it must be expected that kb eccDNAs exist in normal as a result of mutations. Here, we purify sequence from muscle blood samples 16 healthy men, detecting ~100,000 unique eccDNA types million nuclei. Half these structures carry genes or gene fragments the majority smaller than 25 kb. Transcription suggests...
Examples of extrachromosomal circular DNAs (eccDNAs) are found in many organisms, but their impact on genetic variation at the genome scale has not been investigated. We mapped 1,756 eccDNAs Saccharomyces cerevisiae using Circle-Seq, a highly sensitive eccDNA purification method. Yeast ranged from an arbitrary lower limit 1 kb up to 38 and covered 23% genome, representing thousands genes. EccDNA arose both genomic regions with repetitive sequences ≥ 15 bases long short or no sequences. Some...
Abstract Background Growth rate is central to the development of cells in all organisms. However, little known about impact changing growth rates. We used continuous cultures control and studied transcriptional program model eukaryote Saccharomyces cerevisiae , with generation times varying between 2 35 hours. Results A total 5930 transcripts were identified at different rates studied. Consensus clustering these revealed that half yeast genes are affected by specific rate, changes similar...
Assessment of reproducibility DNA-microarray analysis from published data sets is complicated by the use different microbial strains, cultivation techniques, and analytical procedures. Because intra- interlaboratory highly relevant for application in functional genomics metabolic engineering, we designed a set experiments to specifically address this issue. Saccharomyces cerevisiae CEN.PK113-7D was grown under defined conditions glucose-limited chemostats, followed transcriptome with...
Amino acid transporters of the yeast plasma membrane (permeases) belong to a family integral proteins with pronounced structural similarity. We present evidence that member this family, encoded by open reading frame (ORF) YDR160w ( SSY1 ), is required for expression set transporter genes. Thus, deletion gene causes loss leucine‐inducible transcription amino permease genes BAP2 , TAT1 and BAP3 (ORF YDR046c) peptide transporter, PTR2 . D ‐leucine can generate signal without entering cell....
To study adaptive evolution in defined environments, we performed experiments with Saccharomyces cerevisiae (yeast) nitrogen-limited chemostat cultures. We used DNA microarrays to identify copy-number variation associated adaptation and observed frequent amplifications deletions at the GAP1 locus. encodes general amino acid permease, which transports acids across plasma membrane. identified a self-propagating extrachromosomal circular molecule that results from intrachromosomal recombination...
Circular DNA has recently been identified across different species including human normal and cancerous tissue, but short-read mappers are unable to align many of the reads crossing circle junctions hence limiting their detection from sequencing data.Here, we propose a new method, Circle-Map that guides realignment partially aligned using information discordantly mapped map short unaligned portions probabilistic model. We compared similar up-to-date methods for circular RNA demonstrate how...
Abstract Lifelong regular physical activity is associated with reduced risk of type 2 diabetes (T2D), maintenance muscle mass and increased metabolic capacity. However, little known about epigenetic mechanisms that might contribute to these beneficial effects in aged individuals. We investigated the effect lifelong on global DNA methylation patterns skeletal healthy men, who had either performed exercise or remained sedentary their entire lives (average age 62 years). was significantly lower...
Extrachromosomal circular DNA (eccDNA) and ring chromosomes are genetic alterations found in humans with disorders. However, there is a lack of engineering tools to recapitulate study the biogenesis eccDNAs. Here, we created dual-fluorescence biosensor cassette, which upon delivery pairs CRISPR/Cas9 guide RNAs, CRISPR-C, allows us specific fluorophore expressing eccDNA human cells. We show that CRISPR-C can generate functional eccDNA, using novel system. further reveal also eccDNAs from...
Extrachromosomal circular DNA (eccDNA) elements of chromosomal origin are known to be common in a number eukaryotic species. However, it remains addressed whether genomic features such as genome size, the load repetitive within genome, and/or animal physiology affect eccDNAs. Here, we investigate distribution and numbers eccDNAs condensed less repeat-rich compared with human using Columba livia domestica (domestic rock pigeon) model organism. By sequencing eccDNA blood breast muscle from...
Abstract Extrachromosomal DNA (ecDNA) presents a promising target for cancer therapy; however, its spatial-temporal diversity and influence on tumor evolution the immune microenvironment remain largely unclear. We apply computational methods to analyze ecDNA from whole-genome sequencing data of 595 urothelial carcinoma (UC) patients. demonstrate that drives clonal through structural rearrangements during malignant transformation recurrence UC. This supports model wherein tumors evolve via...
The plasma membrane proton pump (H(+)-ATPase) energizes solute uptake by secondary transporters. Wild-type Arabidopsis H(+)-ATPase (AHA2) and truncated lacking 38, 51, 61, 66, 77, 92, 96, 104 C-terminal amino acids were produced in yeast. All AHA2 species correctly targeted to the yeast and, addition, accumulated internal membranes. Removal of 38 residues from a high-affinity state plant with low Km value (0.1 mM) for ATP. an additional 12 C terminus resulted significant increase molecular...
ABSTRACT Through genome-wide transcript analysis of a reference strain and two recombinant Saccharomyces cerevisiae strains with different rates galactose uptake, we obtained information about the global transcriptional response to metabolic engineering GAL gene regulatory network. One overexpressed encoding activator Gal4, in other genes Gal80, Gal6, Mig1, which are negative regulators system, were deleted. Even though uptake significantly three strains, surprisingly did not find any...
Extrachromosomal circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and reported other eukaryotes as well. EccDNAs contribute to variation among somatic cells multicellular organisms evolution of unicellular eukaryotes. Sensitive methods for detecting eccDNA needed clarify how these affect genome stability environmental biological factors induce their formation eukaryotic cells. This video presents a sensitive eccDNA-purification method called Circle-Seq. The...
Extrachromosomal circular DNA (eccDNA) of chromosomal origin is found in many eukaryotic species and cell types, including cancer, where eccDNAs with oncogenes drive tumorigenesis. Most studies eccDNA employ short-read sequencing for their identification. However, cannot resolve the complexity genomic repeats, which can lead to missing products. Long-read technologies provide an alternative constructing complete maps. We present a software suite, Construction-based...
Lithium is highly toxic to yeast when grown in galactose medium mainly because phosphoglucomutase, a key enzyme of metabolism, inhibited. We studied the global protein and gene expression profiles Saccharomyces cerevisiae different time intervals after addition lithium. These results were related physiological studies where both secreted intracellular metabolites determined. Microarray analysis showed that 664 open reading frames down-regulated 725 up-regulated response Genes involved...
The uptake and catabolism of galactose by the yeast Saccharomyces cerevisiae is much lower than for glucose fructose, in applications this utilization complex substrates that contain galactose, example, lignocellulose raffinose, causes prolonged fermentations. Galactose metabolized via Leloir pathway, besides industrial interest improving flux through pathway it also medical relevance to study pathway. Thus, genetic disorders genes encoding galactose-1-phosphate uridylyltransferase or...
Many microbial cells have the ability to form sessile communities defined as biofilms that altered physiological and pathological properties compared free living microorganisms.Biofilms in nature are often difficult investigate reside under poorly conditions 1 .Using a transparent substratum it is possible device system where simple can be examined non-destructive way realtime: here we demonstrate assembly operation of flow cell model system, for vitro 3D studies generating high...