P. M. Shih

Genetically refactored Agrobacterium-mediated transformation

This paper refactors the Agrobacterium tumor-inducing plasmid into a minimal set of genes for plant and fungal transformation, demonstrating a bottom-up engineering approach.

Bacterial Form I' rubisco has smaller carbon isotope fractionation than its Form I counterpart

The paper measures the kinetic isotope effects (KIEs) of two Form I rubiscos and finds that the L8 variant has a smaller KIE than the L8S8 variant.

The trans-regulatory landscape of gene networks in plants

This study maps the trans-regulatory landscape of gene networks in plants by analyzing effector domains of Arabidopsis transcription factors to understand their functional roles in gene regulation.

A dolabralexin-deficient mutant provides insight into specialized diterpenoid metabolism in maize (Zea mays).

The paper identifies ZmKSL4 as the diterpene synthase for dolabralexin biosynthesis in maize and shows its role in root architecture under water deficit.

Carbon isotope fractionation by an ancestral rubisco suggests biological proxies for CO2 through geologic time should be re-evaluated

The paper measures carbon isotope fractionation of an ancestral rubisco in cyanobacteria, showing that evolutionary changes in photosynthesis physiology, not just atmospheric CO2, affect the carbon isotope record.

Nitrogen metabolism in Pseudomonas putida: functional analysis using random barcode transposon sequencing

This study identifies genes and proteins involved in nitrogen metabolism in Pseudomonas putida using transposon sequencing and provides an interactive visualization tool for the data.

Lignin-based resistance to Cuscuta campestris parasitism in Heinz resistant tomato cultivars

Four key regulators confer lignin accumulation in the tomato stem cortex to block C. campestris host penetration upon infection.

Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii

The paper sequenced genomes of photosynthesis mutants in Chlamydomonas reinhardtii to identify candidate genes involved in photosynthesis, validating two essential genes and uncovering 273 high-confidence candidates.

Phototrophy and carbon fixation in Chlorobi postdate the rise of oxygen

This study shows that Chlorobi bacteria evolved anoxygenic phototrophy and carbon fixation after the rise of oxygen, challenging their role in early Earth biosphere.

Phanerozoic Radiation of Ammonia Oxidizing Bacteria

This study estimates the timing of bacterial ammonia oxidation evolution using phylogenetic and molecular clock analyses, finding it originated in the Neoproterozoic and radiated during the Paleozoic.

Granick Revisited: Synthesizing Evolutionary and Ecological Evidence for the Late Origin of Bacteriochlorophyll via Ghost Lineages and Horizontal Gene Transfer

The paper re-examines the evolutionary history of photosynthesis by analyzing horizontal gene transfer and ecological factors in phototrophic organisms.

Population dynamics analysis of Saccharomyces cerevisiae deletion library during fed-batch cultivation using Bar-seq

The paper uses Bar-seq to analyze population dynamics of a yeast deletion library during fed-batch cultivation, identifying genes associated with stress responses in industrial fermentation.

Characterization of an ECF56-family sigma factor from Streptomyces venezuelae reveals a highly conserved regulome

This study characterizes the ECF56-family sigma factor from Streptomyces venezuelae, showing its C-terminal extension is conserved and regulates a highly conserved regulome across Actinobacteria.

Genomic Evidence for Phototrophic Oxidation of Small Alkanes in a Member of the Chloroflexi Phylum

The paper describes a new bacterial genome from the Chloroflexi phylum that exhibits both methanotrophy and phototrophy, suggesting a novel metabolic pathway for photomethanotrophy.