Y. Nakamura

Robust and accurate method for measuring tumor volume using optical 3D scanning for nonclinical in vivo efficacy study

This paper introduces a 3D optical scanning method to accurately measure tumor volume in mice, showing higher precision and lower variability than calipers and luminescence imaging.

Cold adaptation in Upper Paleolithic hunter-gatherers of eastern Eurasia

This study analyzes 42 genomes from Jomon hunter-gatherers to show they adapted to cold environments through positive selection during the Last Glacial Maximum.

Downregulation of Semaphorin 4A in keratinocytes reflects the features of non-lesional psoriasis

This study shows that downregulation of Sema4A in keratinocytes is associated with non-lesional psoriasis features and that Sema4A regulates skin homeostasis and inflammation.

Phenylphenalenones and Linear Diarylheptanoid Derivatives are Biosynthesized via Parallel Routes in Musella lasiocarpa, the Chinese Dwarf Banana

The paper identifies biosynthetic genes and pathways for phenylphenalenones and linear diarylheptanoid derivatives in Musella lasiocarpa using transcriptomics and biochemical assays.

Gelatinous matrix, an original strategy to cope with oligotrophy in Nassellaria (Radiolaria)

The paper identifies a gelatinous matrix in Nassellaria as an adaptation to oligotrophy, showing its evolutionary development and ecological significance in nutrient-depleted waters.

Overcoming antibody-resistant SARS-CoV-2 variants with bispecific antibodies constructed using non-neutralizing antibodies

This study develops bispecific antibodies that restore effectiveness against SARS-CoV-2 variants resistant to existing antibodies by combining non-neutralizing antibodies targeting different epitopes.

Thymically imprinted differential responsivity of naive CD4 T cells to IL2 results in a heterogeneity of both Treg induction and subsequent effector functioning

This study shows that thymic imprinting causes naive CD4 T cells to have different cytokine responses, leading to varied Treg induction and effector function.

Complete suspension culture of human induced pluripotent stem cells supplemented with suppressors of spontaneous differentiation

This study develops a suspension culture method for hiPSCs using PKCβ and Wnt inhibitors to prevent spontaneous differentiation, enabling scalable and stable clinical-grade hiPSC production.

Low albumin status accompanies multi-layered immunosuppressive phenotypes in metastatic breast cancer patients

The paper investigates the association between low albumin levels and immunosuppressive phenotypes in metastatic breast cancer patients using transcriptomic and metabolomic data.

Establishing a comprehensive web-based analysis platform for Nicotiana benthamiana genome and transcriptome

The paper develops a web-based platform for analyzing Nicotiana benthamiana genome and transcriptome data, enabling gene expression visualization, phylogenetic analysis, and functional enrichment.

Ikzf1 association with Foxp3 for Foxp3-dependent gene repression in Treg cells: induction of autoimmunity and tumor immunity by disrupting the association

This study shows that Ikzf1 associates with Foxp3 to repress genes in Treg cells, and disrupting this association leads to autoimmunity and enhanced tumor immunity.

Single-cell transcriptome landscape of circulating CD4+ T cell populations in human autoimmune diseases

The paper identifies 12 transcriptional gene programs in CD4+ T cells from autoimmune diseases and shows their utility in disease characterization and prediction.

Epigenetic silencing by SMYD3 represses tumor intrinsic interferon response in HPV-negative squamous cell carcinoma of the head and neck.

This study identifies SMYD3 as an epigenetic regulator that suppresses the intrinsic interferon response in HPV-negative HNSCC, offering a potential strategy to enhance immunotherapy response.

Retinoids rescue ceruloplasmin secretion and alleviate oxidative stress in Wilson's disease-specific hepatocytes

This study uses patient-derived iPSCs to identify retinoids as potential therapeutics for Wilson's disease by rescuing ceruloplasmin secretion and reducing oxidative stress.

Serum amyloid alpha 1-2 are not required for systemic inflammation in the 4T1 murine breast cancer model

This study shows that SAA1-2 proteins are not essential for systemic inflammation in the 4T1 murine breast cancer model.

A highly contiguous genome assembly of red perilla (Perilla frutescens) domesticated in Japan

This paper presents a high-quality genome assembly of red perilla, identifying potential targets for genome editing to enhance metabolite production.

Recycling upstream redox enzymes expands the regioselectivity of cycloaddition in pseudo-aspidosperma alkaloid biosynthesis

The paper shows that redox enzymes can alter the regioselectivity of cycloaddition reactions in alkaloid biosynthesis, enabling the formation of pseudo-aspidosperma alkaloids.

Genome analysis of Parmales, a sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs

This study compares parmalean and diatom genomes to show diatoms evolved from phago-mixotrophs to photoautotrophs by losing phagocytosis genes and gaining silica and nutrient metabolism capabilities.

Expansion of the Catalytic Repertoire of Alcohol Dehydrogenases in Plant Metabolism

The paper reports the crystal structure of an ADH enzyme that catalyzes a non-canonical 1,4 reduction, providing insights into how plant ADHs diversify their catalytic functions.

Editing the core region in HPFH deletions alters fetal and adult globin expression for treatment of β-hemoglobinopathies

This study edits the PRR-βE1 region in HSPCs to suppress HbA and enhance HbF production, showing therapeutic benefits for β-hemoglobinopathies.

Hydrodynamics shapes self-recruitment in anemonefishes

The paper compares self-recruitment and larval dispersal between a semi-enclosed bay and an open coast, finding that stronger cross-shore currents in the bay reduce local retention and self-recruitment.

MarpolBase Expression: A Web-based, Comprehensive Platform for Visualization and Analysis of Transcriptomes in the Liverwort Marchantia polymorpha

The paper introduces MBEX, a web-based platform for analyzing and visualizing transcriptomes in Marchantia polymorpha, demonstrating its utility through oil body biogenesis analysis.

Prostaglandin EP3 receptor-expressing preoptic neurons bidirectionally control body temperature via tonic GABAergic signaling

The paper identifies POAEP3R neurons as bidirectional regulators of body temperature through GABAergic signaling, showing both hypothermic and hyperthermic effects.

Dynamic interaction of BcsD subunit in type I bacterial cellulose synthase

This study investigates the dynamic interaction of BcsD in type I bacterial cellulose synthase, showing its role in regulating cellulose crystallization through two interaction modes.

Mitochondrial Genome of Garcinia mangostana L. variety Mesta

The paper reports the complete mitochondrial genome of Garcinia mangostana L. variety Mesta, revealing its structure, GC content, and phylogenetic placement within Malpighiales order.

Plastomes of Garcinia mangostana L. and comparative analysis with other Garcinia species

The paper reports the plastome of Garcinia mangostana L. Mesta variety and compares it with other Garcinia species to study gene conservation and phylogenetic relationships.

Myasthenia gravis-specific aberrant neuromuscular gene expression by medullary thymic epithelial cells in thymoma

This study identifies neuromuscular gene expression in thymoma-associated myasthenia gravis by analyzing bulk and single-cell RNA-seq data, linking it to specific thymic epithelial cell subpopulations.

Phosphatidylglycerol synthesis facilitates plastid gene expression and light induction of nuclear photosynthetic genes

This study investigates how phosphatidylglycerol (PG) deficiency affects gene expression and plant growth in Arabidopsis, showing its role in nuclear-encoded photosynthesis genes and chloroplast development.

Bark beetles locate fungal symbionts by detecting volatile fungal metabolites of host tree resin monoterpenes

This study shows bark beetles use volatile oxygenated metabolites from fungal symbionts to locate breeding sites with beneficial fungi.

Mieap forms membraneless organelles to compartmentalize and facilitate cardiolipin metabolism

The paper shows Mieap forms membraneless organelles to compartmentalize and facilitate cardiolipin metabolism, supporting mitochondrial quality control.