Engineering topics

Haseloff, Jim

Publications and source records attributed to Haseloff, Jim.

3 records

DOE OSTI2018

Opening options for material transfer

Material-transfer agreements (MTAs) underlie the legal frameworks within which biotechnology practitioners define the terms and conditions for sharing biomaterials ranging, for example, from plasmid DNA to patient samples. If MTAs are easy to use and well adapted to the needs of individual researchers, institutions, and broader communities, then more sharing, innovation, and translation can occur. However, the MTA frameworks currently in place were developed in the 1990s—before widespread adoption of the World Wide Web, genome sequencing, and gene synthesis—and are not always well adapted for contemporary research and translation practices or aligned with social objectives.

Kahl, Linda↗

DOE OSTI2017

Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome

The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

MarpoDB: An open registry for Marchantia polymorpha genetic parts

Marchantia polymorpha is an extant relative of the earliest terrestrial plants and has attracted a substantial interest as a model organism for evolutionary and developmental studies. Given its relatively simple genome, compact gene families, simple morphology, ease of propagation and transformation, M. polymorpha is becoming a promising platform for plant synthetic biology. Modular genetic parts have been essential for development of synthetic biology approaches, so we sought to design an engineering oriented database for M. polymorpha genetic parts where each gene is a standalone functional unit. MarpoDB is a database of M. polymorpha genes and genetic parts, which is tailored to become an integral tool for a synthetic biology workflow. Among its features are precompiled cross-database querying to InterPro, Pfam signatures and non-redundant Viridiplantae BLAST annotations; BLAST querying to M. polymorpha genes; sequence export in GenBank format; recoding of sequences to the common syntax for type IIS assembly and exchange of DNA parts; and a minimalistic, intuitive and interactive user interface for gene models and sequence exploration. Furthermore, we have implemented user input to encourage feedback, collaboration and exchange between the MarpoDB community. MarpoDB source-code is released on GitHub to promote development of computational tools for synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗