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Kool, E. T.

Publications and source records attributed to Kool, E. T..

3 recordsLinked to original sources

Microbial byproducts determine reproductive fitness of free-living and parasitic nematodes

A distinguishing feature of Trichuris nematodes is that these parasitic worms reproduce within the digestive tracts of humans and other mammalian hosts shedding thousands of eggs daily, facilitating their sustained presence in the environment and hampering eradication efforts. Although this aspect of the lifecycle places Trichuris in a microbiota-rich environment, metabolic byproducts of bacteria that facilitate the reproductive development of parasites are unknown. Here, we employ a pipeline using the well-characterized free-living nematode C. elegans to identify microbial factors with conserved roles in the reproduction of nematodes. A screen for E. coli mutants that impair C. elegans fertility identified genes in fatty acid biosynthesis and ethanolamine utilization pathways, including fabH and eutN. Trichuris muris eggs displayed defective hatching in the presence of E. coli deficient in fabH or eutN due to reduction in arginine or elevated levels of aldehydes, respectively. Remarkably, T. muris reared in gnotobiotic mice colonized with these E. coli mutants displayed profound abnormalities including morphological defects and a failure to lay viable eggs. These findings indicate that microbial byproducts mediate evolutionarily conserved transkingdom interactions that impact the reproductive fitness of distantly-related nematodes.

microbiology

Integrating transcription factor abundance with chromatin accessibility in human erythroid lineage commitment

We present InTAC-seq, a method for simultaneous quantification of genome-wide open chromatin and intracellular protein abundance in fixed cells. Using InTAC we directly observe variation in chromatin accessibility and transcription factor motif occupancy driven by differences in transcription factor protein abundance. By purifying bone marrow progenitor cells based on GATA1 protein expression, we establish its role in both functional and epigenetic restriction of erythroid cell identity in human hematopoiesis.

genomics

Site-specific RNA Functionalization via DNA-induced Structure

Site-specific RNA functionalization is in high demand, but remains a challenge, particularly for RNAs produced by transcription rather than by total synthesis. Recent studies have described acylimidazole reagents that react in high yields at 2-OH groups in RNAs. To date, the reactions occur stochastically at non-base-paired regions of RNA, covering much of the RNA in scattered acyl esters. Localized reactions, if possible, could prove useful in many applications, providing functional handles at specific sites and sequences of the biopolymer. Here we describe a DNA-directed strategy for in vitro functionalization of RNA at site-localized 2-OH groups. The method, RNA Acylation at Induced Loops (RAIL), utilizes complementary helper DNA oligonucleotides that expose gaps or loops at selected positions while protecting the remainder in DNA-RNA duplexes. Reaction with acylimidazole reagents is then carried out, providing high yields of 2-OH conjugation at predetermined sites. Subsequent removal of the DNA provides the RNA functionalized as desired. Experiments reveal optimal helper oligodeoxynucleotide designs and conditions for the reaction, and tests of the approach were carried out to control ribozyme activities and to label RNAs with dual-color fluorescent dyes. The RAIL approach offers a simple new strategy for site-specific labeling and controlling RNAs of any length and origin.

biochemistry