For the past 25 years, it has been known that alterations in DNA methylation (DNAm) occur in cancer, including hypomethylation of oncogenes and hypermethylation of tumor suppressor genes. However, most studies of cancer methylation have assumed that…
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Toll-like receptors (TLRs) play a crucial role in host defense against microbial infection. The microbial ligands recognized by TLRs are not unique to pathogens, however, and are produced by both pathogenic and commensal microorganisms. It is…
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Colon cancer is one of the best-understood neoplasms from a genetic perspective, yet it remains the second most common cause of cancer-related death, indicating that some of its cancer cells are not eradicated by current therapies. What has yet to…
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Bisulfite sequencing measures absolute levels of DNA methylation at single-nucleotide resolution, providing a robust platform for molecular diagnostics. We optimized bisulfite sequencing for genome-scale analysis of clinical samples: here we outline…
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We review recent developments in spatially realistic metapopulation theory, which leads to quantitative models of the dynamics of species inhabiting highly fragmented landscapes. Our emphasis is in stochastic patch occupancy models, which describe…
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We examined the impact of three forms of dispersal, stepping-stone, normal and leptokurtic, on spatial genetic structure of expanding populations using computer simulations. When dispersal beyond neighbouring demes is allowed, rare long-distance…
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Colon carcinoma is the second most common cause of death from cancer. The isolation and characterization of tumorigenic colon cancer cells may help to devise novel diagnostic and therapeutic procedures. Although there is increasing evidence that a…
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Intestinal cancer is initiated by Wnt- pathway- activating mutations in genes such as adenomatous polyposis coli APC). As in most cancers, the cell of origin has remained elusive. In a previously established Lgr5 leucine- rich- repeat containing G-…
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Seed dispersal can be advantageous (1) in escape from density- or distance-dependent seed and seedling mortality, (2) by colonization of suitable sites unpredictable in space and time, and (3) by directed dispersal to particular sites with a…
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Accurate normalization is an absolute prerequisite for correct measurement of gene expression. For quantitative real-time reverse transcription-PCR (RT-PCR), the most commonly used normalization strategy involves standardization to a single…
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Oncogenic mutations in the small GTPase Ras are highly prevalent in cancer, but an understanding of the vulnerabilities of these cancers is lacking. We undertook a genome-wide RNAi screen to identify synthetic lethal interactions with the KRAS…
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MicroRNAs (miRNAs) are a class of small noncoding RNAs that have important regulatory roles in multicellular organisms. The public miRNA database contains 321 human miRNA sequences, 234 of which have been experimentally verified. To explore the…
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A single layer of epithelial cells lines the small and large intestines and functions as a barrier between commensal bacteria and the rest of the body. Ligation of Toll-like receptors (TLRs) on intestinal epithelial cells by bacterial products…
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The human gut is the natural habitat for a large and dynamic bacterial community, but a substantial part of these bacterial populations are still to be described. However, the relevance and effect of resident bacteria on a host's physiology and…
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To estimate absolute protein contents in complex mixtures, we previously defined a protein abundance index (PAI) as the number of observed peptides divided by the number of observable peptides per protein (Rappsilber, J., Ryder, U., Lamond, A. I.,…
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All organisms, especially terrestrial plants and other sessile species, interact mainly with their neighbors, but neighborhoods can differ in composition because of dispersal and mortality. There is increasingly strong evidence that the spatial…
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I reviewed and reconciled predictions of four models oil the effect of habitat fragmentation on the population extinction threshold, and I compared these predictions to results, from empirical studies. All four models predict that habitat…
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Species presence/absence surveys are commonly used in monitoring programs, metapopulation studies and habitat modelling, yet they can never be used to confirm that a species is absent from a location. Was the species there but not detected, or was…
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I reviewed and reconciled predictions of four models oil the effect of habitat fragmentation on the population extinction threshold, and I compared these predictions to results, from empirical studies. All four models predict that habitat…
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The use of fossil sediments and genetic markers has allowed reconstruction of range shifts of forest trees induced by past climatic changes. Independently, studies of the ecology and population biology of human-induced tree invasions have started to…
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