Search bioRxiv⌕ Search

Biology subjects

Hansen, D. M.

Publications and source records attributed to Hansen, D. M..

3 recordsLinked to original sources

A mobile CRISPRi collection enables genetic interaction studies for the essential genes of Escherichia coli

Ordered collections of precise gene deletions in E. coli and other model microbes have proven to be invaluable resources to study the dispensability of the non-essential genome in different environmental and genetic contexts. The dispensability of canonically essential genes, however, has been largely unstudied in such contexts. Advances in gene editing, in particular CRISPR interference (CRISPRi), have enabled depletion of essential cellular machinery to study the downstream effects on bacterial physiology. Here, we describe the construction of an ordered E. coli CRISPRi collection, designed to knock down the expression of 356 essential genes with the induction of a catalytically inactive Cas9, harbored on the conjugative plasmid pFD152, that also encodes for expression of specific guide RNA scaffolds. This mobile CRISPRi library can be conjugated into other ordered genetic libraries, to assess combined effects of essential gene knockdowns with non-essential gene deletions. As proof of concept, we probed cell envelope synthesis with two crosses. First, we crossed a deletion in the gene lpp with the entire CRISPRi library. Similarly, we crossed the CRISPRi knockdown of lolA with [~]4,000 deletion strains of the Keio collection. These experiments revealed a number of notable genetic interactions for the essential phenotype probed and, in particular, showed supressing interactions for the loci in question.

systems biology↗

A Holistic Analysis of the Intestinal Stem Cell Niche Network

Although many studies into the intestinal stem cell (ISC) niche have been carried out, they have focused on the role of a single cell type or molecular signal. However, no holistic comparisons of the predominant cell types and signals present within the intestinal mucosa have been conducted to date. We utilize bulk RNA sequencing to profile 20 different mucosal cell types covering four major cell categories: epithelial, stromal, endothelial and immune. We further examined the stromal signaling environment using scRNAseq to provide a more comprehensive view of the signaling microenvironment within the intestinal mucosa. We identified the primary signals for the major ISC regulatory pathways and their respective cellular sources. Our analysis suggests that a niche network exists, with no single cell type being responsible for ISC self-renewal, proliferation, or differentiation; rather, each cell type within the network carries out specific functions in a highly cooperative and coordinated manner.

cell biology↗

Frugivory and seed dispersal by chelonians: A review and synthesis

In recent years, it has become clear that frugivory and seed dispersal (FSD) by turtles and tortoises is much more common than previously thought. Yet, a review and synthesis is lacking. We here review published and unpublished records of chelonian FSD, and assess the role of chelonians as seed dispersers, from individual species to the community level. We first discuss the distribution of chelonian FSD and the characteristics of the fruit and/or seed species eaten and dispersed by chelonians. We then use the seed dispersal efficiency framework to explore the quantitative and qualitative components of seed dispersal by tortoises and turtles, embarking on a journey from when the fruits and/or seeds are consumed, to when and where they are deposited, and assess how efficient chelonians are as seed dispersers. We finally discuss chelonian FSD in the context of communities and chelonians as megafauna. We found that a substantial proportion of the worlds aquatic and terrestrial turtles and a major part of testudinid tortoises (70 species in 12 families) include fruits and/or seeds in their diet, and that furits of at least 588 plant species in 120 families are ingested and/or dispersed by chelonians. For some chelonians, overall or in certain seasons, fruit may even form the largest part of their diet. Contrary to seed dispersal by lizards, the other major reptilian frugivores, chelonian FSD is not an island phenomenon in terms of geographic distribution. Nevertheless, on islands especially tortoises are often among the largest native terrestrial vertebrates--or were, until humans got there. We synthesize our knowledge of chelonian FSD, and discuss the relevance of our findings for conservation and restoration, especially in relation to rewilding with large and giant tortoises.\n\nResumenEn anos recientes, se ha hecho claro que la frugivoria y dispersion de semillas (FDS) llevada a cabo por tortugas (quelonidos) es mas comun de lo antes pensado. No obstante, todavia careciamos de una revision y sintesis sobre este tema. En este articulo, revisamos records (publicados y no publicados) sobre FDS por quelonidos, y evaluamos su rol como dispersores de semillas, desde el nivel de individuos, al nivel de comunidades. Primero, discutimos la distribucion de FDS por quelonidos, y las caracteristicas de las especies de frutos y/o semillas consumidas y dispersadas por tortugas. Luego hacemos uso del concepto de la eficiencia de dispersion de semillas como marco de referencia para explorar los componentes cualitativos y cuantitativos de la FDS por quelonidos, embarcandonos en un viaje desde cuando los frutos y/o semillas son consumidas, hasta cuando son depositadas. Tambien evaluamos cuan eficientes son los quelonidos como dispersores de semillas. Finalmente procedemos a discutir la FDS por quelonidos en el contexto de comunidades, y como megafauna. Encontramos que una proporcion substancial de las tortugas acuaticas del mundo y la mayor parte de las tortugas testudinidas (70 especies en 12 familias) incluyen frutos y/o semillas en su dieta que abarcan al menos 588 especies de plantas en 120 familias. En algunas especies, en general o en algunas estaciones, la mayor parte de su dieta esta conformada por frutas y/o semillas. Mas importante aun, y contrario a las lagartijas, que son otro grupo importante de reptiles que incurre en FDS, la frugivoria y dispersion de semillas por quelonidos no es un fenomeno de islas solamente, en terminos de distribucion geografica. Empero, en islas, especialmente las tortugas terrestres, estan entre los vertebrados nativos de mayor tamano-o lo estuvieron, hasta que los humanos llegaron a ellas. En este articulo, hacemos una sintesis de las lecciones aprendidas hasta ahora sobre la FDS por quelonidos, y discutimos la relevancia de nuestros hallazgos para la conservacion y restauracion, especialmente en relacion a proyectos de resilvestrar ( rewilding) con tortugas gigantes o de gran tamano.

ecology↗