M. Shimizu

Bioengineering a plant NLR immune receptor with a robust binding interface towards a conserved fungal pathogen effector

The paper bioengineers a plant NLR receptor to recognize a conserved fungal effector, resulting in durable resistance against blast fungus isolates.

A large attachment organelle mediates interaction between a novel Nanobdellota archaeon YN1 and its host

This study isolates and characterizes a novel Nanobdellota archaeon and its host, revealing an attachment organelle that mediates their ectosymbiotic interaction.

Gluconeogenesis in the YSL-like tissue of cloudy catshark (Scyliorhinus torazame).

This study identifies gluconeogenic activity in the YSL-like tissue of cloudy catshark embryos, suggesting conserved yolk metabolism mechanisms between teleosts and elasmobranchs.

Impact of rice GENERAL REGULATORY FACTOR14h (GF14h) on low-temperature seed germination and its application to breeding

This paper identifies GF14h as the causal gene for low-temperature seed germination in rice and demonstrates its utility in breeding for direct seeding in cold climates.

Evolution of wheat blast resistance gene Rmg8 accompanied by differentiation of variants recognizing the powdery mildew fungus

The paper traces the evolutionary origin of wheat blast resistance gene Rmg8 and shows its ability to recognize both wheat blast and powdery mildew pathogens.

Downregulation of CYP7B1 caused by lipotoxicity associates with the progression of non-alcoholic steatohepatitis

This study shows that restoring CYP7B1 expression reduces NASH progression in mice, linking its downregulation to lipid and oxidative stress in the early stages of the disease.

Barley MLA3 recognizes the host-specificity determinant PWL2 from rice blast (M. oryzae)

The paper shows that the barley NLR Mla3 recognizes the rice blast effector PWL2, conferring resistance in a dosage-dependent manner.

Murine breast cancers disorganize the liver transcriptome in zonated manners

This study uses spatial transcriptomics to show that breast cancers disrupt liver zonation patterns, affecting specific metabolic and immune pathways in a zonated manner.

Disentangling the complex gene interaction networks between rice and the blast fungus identifies a new pathogen effector

Binding of a blast fungus Zinc-finger fold effector to a hydrophobic pocket in the host exocyst subunit Exo70 modulates immune recognition in rice

This paper reveals how the blast fungus effector AVR-Pii binds to rice Exo70, modulating immune recognition through a novel Zinc-finger fold and conserved hydrophobic interface.

Effector target-guided engineering of an integrated domain expands the disease resistance profile of a rice NLR immune receptor

The paper engineers rice NLR receptors to recognize new effector variants by incorporating effector targets, enhancing disease resistance against blast fungus.

Whole genome sequencing of a wild yam species Dioscorea tokoro reveals a genomic region associated with sex

The paper reports the whole genome sequence of Dioscorea tokoro and identifies a genomic region associated with sex determination.

A very long chain fatty acid responsive transcription factor, MYB93, regulates lateral root development in Arabidopsis

The paper identifies MYB93 as a VLCFA-responsive transcription factor that regulates lateral root development in Arabidopsis by modulating cell wall organization gene expression.

Hydroxylation site-specific and production-dependent roles of endogenous oxysterols in cellular cholesterol homeostasis

This study investigates how endogenously synthesized oxysterols regulate cholesterol homeostasis by affecting SREBP-2 and LXR, showing site-specific and production-dependent effects.

Apoplastic CBM1-interacting proteins bind conserved carbohydrate binding module 1 motifs in fungal hydrolases to counter pathogen invasion

The paper identifies OsCBMIP, a rice protein that binds to fungal CBM1 domains in xylanases, inhibiting their activity and enhancing rice defense against M. oryzae.

Skeletal muscle releases extracellular vesicles with distinct protein and miRNA signatures that accumulate and function within the muscle microenvironment

This study identifies markers for skeletal muscle-derived extracellular vesicles (SkM-EVs) and shows they mainly function within the muscle microenvironment rather than contributing significantly to plasma EVs.

The rice OsERF101 transcription factor regulates the NLR Xa1-mediated perception of TAL effectors and Xa1-mediated immunity

This study identifies OsERF101 as a regulator of Xa1-mediated immunity in rice by interacting with TAL effectors and modulating immune responses.

Pathogen-derived 9-methyl sphingoid base is perceived by a lectin receptor kinase in Arabidopsis

The paper shows that oomycete-derived ceramide is cleaved into sphingoid base by ceramidase and recognized by an Arabidopsis receptor kinase, enhancing plant immunity.

A genetically linked pair of NLR immune receptors show contrasting patterns of evolution

This paper studies the evolution of a rice NLR gene pair, showing that the sensor NLR undergoes dynamic domain integration under balancing selection, while the helper NLR remains functionally conserved under purifying selection.

Assessing the impacts of climate change on reproductive phenology in tropical rainforests of Southeast Asia

The paper analyzes climate change impacts on reproductive phenology in Southeast Asian tropical rainforests, finding decreased flowering and fruiting species proportions and reduced low-temperature flowering cues.

The blast pathogen effector AVR-Pik binds and stabilizes rice heavy metal-associated (HMA) proteins to co-opt their function in immunity

This study shows that the fungal effector AVR-Pik binds and stabilizes rice HMA proteins, co-opting their function to suppress immunity, while also triggering immunity in plants with integrated HMA domains in NLRs.

Genome analyses reveal the hybrid origin of the staple food crop white Guinea yam

This study reveals the hybrid origin of white Guinea yam through genomic analysis, showing it arose from crosses between D. praehensilis and D. abyssinica with significant introgression around the SWEETIE gene.

Lumi-Map, a real-time luciferase bioluminescence screen of mutants combined with MutMap, reveals Arabidopsis genes involved in PAMP-triggered immunity

Lumi-Map combines bioluminescence screening with MutMap to identify Arabidopsis genes involved in PAMP-triggered immunity, revealing three novel PTI-related genes.

Epidemiological survey of serum titers from adults against various Gram-negative bacterial V-antigens

The paper measures serum titers against five Gram-negative bacterial V-antigens in adults and finds high cross-correlation between some antigens, suggesting potential for epidemiological studies.

Anti-CD137 monoclonal antibody enhances trastuzumab-induced, natural killer cell-mediated cytotoxicity against pancreatic cancer cell lines with low human epidermal growth factor-like receptor 2 expression

This study shows that combining anti-CD137 mAb with trastuzumab enhances NK cell-mediated ADCC against HER2-low pancreatic cancer cells, particularly in individuals with FcγRIIIA-VV/VF genotype.

Reconstruction of atomistic structures from coarse-grained models for protein-DNA complexes

This study develops a method to reconstruct all-atom structures from coarse-grained protein-DNA complex models, improving accuracy at the interface and validating through multiple metrics.