Co-profiling of single-cell gene expression and chromatin landscapes in stickleback pituitary.

The pituitary gland is a key endocrine gland with various physiological functions including metabolism, growth, and reproduction. It comprises several distinct cell populations that release multiple polypeptide hormones. Although the major endocrine cell types are conserved across taxa, the regulatory mechanisms of gene expression and chromatin organization in specific cell types remain poorly understood.

Urodele amphibian newt bridges the missing link in evo-devo of the pancreas.

Background: The pancreas exhibits diverse structures and roles across vertebrates. The pancreas has evolved to include both endocrine and exocrine cells, a change that occurred during the transition from fish to amphibian. This event emphasizes the evolutionary significance of amphibians.

A chromosome-level genome assembly of wild silkmoth, Bombyx mandarina.

The wild silk moth, Bombyx mandarina, is the closest relative of the domesticated silk moth, Bombyx mori. National BioResource Project of Japan (NBRP) maintains a B. mandarina strain derived from individuals captured at Sakado (Saitama, Japan) in 1982.

DEAD/H Box 5 (DDX5) Augments E2F1-Induced Cell Death Independent of the Tumor Suppressor p53.

In almost all cancers, the p53 pathway is disabled and cancer cells survive. Hence, it is crucially important to induce cell death independent of p53 in the treatment of cancers. The transcription factor E2F1 is controlled by binding of the tumor suppressor pRB, and induces apoptosis by activating the gene, an upstream activator of p53, when deregulated from pRB by loss of pRB function.

Spatially ordered recruitment of fast muscles in accordance with movement strengths in larval zebrafish.

In vertebrates, skeletal muscle comprises fast and slow fibers. Slow and fast muscle cells in fish are spatially segregated; slow muscle cells are located only in a superficial region, and comprise a small fraction of the total muscle cell mass. Slow muscles support low-speed, low-force movements, while fast muscles are responsible for high-speed, high-force movements.

Genome-scale evolution in local populations of wild chimpanzees.

Analysis of genome-scale evolution has been difficult in large, endangered animals because opportunities to collect high-quality genetic samples are limited. There is a need for novel field-friendly, cost-effective genetic techniques. This study conducted an exome-wide analysis of a total of 42 chimpanzees (Pan troglodytes) across six African regions, providing insights into population discrimination techniques.

Polymerase-Usage Sequencing Identifies Initiation Zones with Less Bias Across S phase in Mouse Embryonic Stem Cells.

Various methods have been developed to map replication initiation zones (IZs) genome-wide, often finding far fewer IZs than expected. In particular, IZs corresponding to later stages of S phase are under-represented. Here, we re-analyzed IZs with respect to replication timing in mouse ES cells.

Cell cycle-dependent regulation of CRISPR-Cas9 repetitive activation by anti-CRISPR and Cdt1 fusion in the CRISPRa system.

CRISPR-Cas9 is a widely used genome-editing tool. We previously developed a method with improved homology-directed repair efficiency and reduced off-target effects by utilizing a fusion protein of AcrIIA4, a Cas9 inhibitor, and Cdt1, which accumulates in the G1 phase and activates Cas9 only in the S/G2 phase. However, it is unknown whether Cas9 inhibition by AcrIIA4 + Cdt1 occurs repeatedly in the G1 phase as the cell cycle progresses.

Physcomitrium LATERAL SUPPRESSOR genes promote formative cell divisions to produce germ cell lineages in both male and female gametangia.

The evolution of green plants from aquatic to terrestrial environments is thought to have been facilitated by the acquisition of gametangia, specialized multicellular organs housing gametes. Antheridia and archegonia, responsible for producing and protecting sperm and egg cells, undergo formative cell divisions to produce a cell to differentiate into germ cell lineages and the other cell to give rise to surrounding structures. However, the genes governing this process remain unidentified.

Egg Microinjection for the Ladybird Beetle .

In this paper, we present a detailed protocol for microinjecting DNA, RNA, or protein solutions into fertilized eggs of the multicolored Asian ladybird beetle, Harmonia axyridis, under a stereomicroscope equipped with an injection apparatus. is an emerging model organism for studying various biological fields, showing intraspecific polymorphisms exhibiting highly diverse color patterns on the elytra. Here, we describe how to rear ladybird beetles in a laboratory and obtain fertilized eggs for microinjection experiments.

Novel function of Hox13 in regulating outgrowth of the newt hindlimb bud through interaction with Fgf10 and Tbx4.

5'Hox genes regulate pattern formation along the axes of the limb. Previously, we showed that Hoxa13/Hoxd13 double-mutant newts lacked all digits of the forelimbs during development and regeneration, showing that newt Hox13 is necessary for digit formation in development and regeneration. In addition, we found another unique phenotype.

γ-Secretase Cleaves Bifunctional Fatty Acid-Conjugated Small Molecules with Amide Bonds in Mammalian Cells.

Connecting two small molecules, such as ligands, fluorophores, or lipids, together via a linker with amide bonds is a widely used strategy to generate synthetic bifunctional molecules for various biological and biomedical applications. Such bifunctional molecules have been used in live-cell experiments under the assumption that they should be stable in cells. However, we recently found that a membrane-targeting bifunctional molecule, composed of a lipopeptide and the small-molecule ligand trimethoprim, referred to as mgcTMP, underwent amide-bond cleavage in mammalian cells.

Possible roles of CAHS proteins from Tardigrade in osmotic stress tolerance in mammalian cells.

Anhydrobiosis, a phenomenon in which organisms survive extreme dehydration by entering a reversible ametabolic state, is a remarkable example of survival strategies. This study focuses on anhydrobiosis in tardigrades, which are known for their resilience to severe environmental conditions. Tardigrades utilize several protective mechanisms against desiccation, notably the constitutive expression of cytoplasmic abundant heat soluble (CAHS) proteins in Ramazzottius varieornatus.

The significance of social interactions in synchronized swarming flight in a termite.

In social insects, individuals of working caste coordinate their actions to manage various collective tasks. Such collective behaviours exist not only in workers but also in winged reproductives (alates). During certain seasons, newly emerged alates fly from the nest to disperse and find mating partners in a synchronized manner.

Spatial Transcriptomics Reveals the Temporal Architecture of the Seminiferous Epithelial Cycle and Precise Sertoli-Germ Synchronization.

Spermatogenesis is characterized by the seminiferous epithelial cycle, a periodic pattern of germ cell differentiation with a wave-like progression along the length of seminiferous tubules. While key signaling and metabolic components of the cycle are known, the transcriptional changes across the cycle and the correlations between germ cell and somatic lineages remain undefined. Here, we use spatial transcriptomics via RNA SeqFISH+ to profile 2,638 genes in 216,090 cells in mouse testis and identify a periodic transcriptional pattern across tubules that precisely recapitulates the seminiferous epithelial cycle, enabling us to map cells to specific timepoints along the developmental cycle.

Structural diversity and function of the granulocyte colony-stimulating factor in medaka fish.

Diversity in the granulocyte repertoire, including neutrophils, basophils, and eosinophils, has been reported in vertebrate species. Medaka fish (Oryzias latipes) have only neutrophils; however, the storage pool of granulopoiesis tissues and the molecular mechanism of granulopoiesis in medaka fish have not been explored. Granulocyte colony-stimulating factor (G-CSF) is a cytokine responsible for neutrophil differentiation, survival, and proliferation.

A mitochondrial metalloprotease FtsH4 is required for symbiotic nitrogen fixation in Lotus japonicus nodules.

Symbiotic nitrogen fixation is a highly coordinated process involving legume plants and nitrogen-fixing bacteria known as rhizobia. In this study, we investigated a novel Fix mutant of the model legume Lotus japonicus that develops root nodules with endosymbiotic rhizobia but fails in nitrogen fixation. Map-based cloning identified the causal gene encoding the filamentation temperature-sensitive H (FtsH) protein, designated as LjFtsH4.

Labor- and cost-effective long-read amplicon sequencing using a plasmid analysis service: Application to transposon-inserted alleles in Japanese morning glory.

The sequencing of PCR fragments amplified from specific regions of genomes is a fundamental technique in molecular genetics. Sanger sequencing is commonly used for this analysis; however, amplicon sequencing utilizing next-generation sequencing has become widespread. In addition, long-read amplicon sequencing, using Nanopore or PacBio sequencers to analyze long PCR fragments, has emerged, although it is often more expensive than Sanger sequencing.

Infrared laser-induced gene expression in single cells characterized by quantitative imaging in Physcomitrium patens.

A spatiotemporal understanding of gene function requires the precise control of gene expression in each cell. Here, we use an infrared laser-evoked gene operator (IR-LEGO) system to induce gene expression at the single-cell level in the moss Physcomitrium patens by heating a living cell with an IR laser and thereby activating the heat shock response. We identify the laser irradiation conditions that provide higher inducibility with lower invasiveness by changing the laser power and irradiation duration.

A chromosome-level genome assembly of a model conifer plant, the Japanese cedar, Cryptomeria japonica D. Don.

Background: The Japanese cedar (Cryptomeria japonica D. Don) is one of the most important Japanese forest trees, occupying approximately 44% of artificial forests and planted in East Asia, the Azores Archipelago, and certain islands in the Indian Ocean. Although the huge genome of the species (ca.

Arabidopsis KNS3 and its two homologs mediate endoplasmic reticulum-to-plasma membrane traffic of boric acid channels.

Membrane proteins targeted to the plasma membrane are first transported from the endoplasmic reticulum (ER) to the Golgi apparatus. This study explored the mechanisms controlling plasma membrane trafficking of the boric acid channel AtNIP5;1 from the ER. Imaging-based screening using transgenic Arabidopsis identified six mutants in which GFP-NIP5;1 was localized in the ER in addition to the plasma membrane.

Spatiotemporal control of transgene expression using an infrared laser in the crustacean Daphnia magna.

The crustacean Daphnia magna is an emerging model for ecological and toxicological genomics. However, the lack of methods for spatial and temporal control of gene expression has impaired the elucidation of molecular mechanisms underlying responses to environments in vivo. Here we report local activation of the hsp70 promoter-driven gene cassette in D.