Convergent evolution and predictability of gene copy numbers associated with diets in mammals.

Convergent evolution, the evolution of the same or similar phenotypes in phylogenetically independent lineages, is a widespread phenomenon in nature. If the genetic basis for convergent evolution is predictable to some extent, it may be possible to infer organismic phenotypes and the capability of organisms to utilize new ecological resources based on genome sequence data. While repeated amino acid changes have been studied in association with convergent evolution, relatively little is known about the potential contribution of repeated gene copy number changes.

Thermal gradient ring for analysis of temperature-dependent behaviors involving TRP channels in mice.

There are a lot of temperature-sensitive proteins including transient receptor potential (TRP) channels. Some TRP channels are temperature receptors having specific activation temperatures in vitro that are within the physiological temperature range. Mice deficient in specific TRP channels show abnormal thermal behaviors, but the role of TRP channels in these behaviors is not fully understood.

Synthesis of fully fused tetrapyrazinoporphyrazine polymers bearing three-dimensional structures controlled by steric repulsion.

The synthesis and characterization of fused aromatic networks composed of zinc tetrapyrazinoporphyrazines are reported. The steric repulsion of bulky substituents induced the formation of three-dimensional structures. Thus-obtained insoluble polymers adsorbed CO and had near-infrared absorption indicating their porosity and extended π-conjugation.

PI5P4K inhibitors: promising opportunities and challenges.

Phosphatidylinositol 5-phosphate 4-kinases (PI5P4K), also known as type II PIPKs or PIPKIIs, convert the lipid second messenger PI5P to PI(4,5)P. The PI5P4K family consists of three isozymes in mammals-PI5P4Kα, β, and γ-which notably utilize both GTP and ATP as phosphodonors. Unlike the other two isozymes, which can utilize both ATP and GTP, PI5P4Kβ exhibits a marked preference for GTP over ATP, acting as an intracellular GTP sensor that alters its kinase activity in response to physiological changes in GTP concentration.

Ligand-Independent Vitamin D Receptor Actions Essential for Keratinocyte Homeostasis in the Skin.

Recently, we demonstrated that the alopecia observed in vitamin D receptor gene-deficient (-KO) rats is not seen in rats with a mutant VDR(R270L/H301Q), which lacks ligand-binding ability, suggesting that the ligand-independent action of VDR plays a crucial role in maintaining the hair cycle. Since -KO rats also showed abnormalities in the skin, the relationship between alopecia and skin abnormalities was examined. To clarify the mechanism of actions of vitamin D and VDR in the skin, protein composition, and gene expression patterns in the skin were compared among -KO, -R270L/H301Q, and wild-type (WT) rats.

DFAST_QC: quality assessment and taxonomic identification tool for prokaryotic Genomes.

Background: Accurate taxonomic classification in genome databases is essential for reliable biological research and effective data sharing. Mislabeling or inaccuracies in genome annotations can lead to incorrect scientific conclusions and hinder the reproducibility of research findings. Despite advances in genome analysis techniques, challenges persist in ensuring precise and reliable taxonomic assignments.

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.

Polysulfur-based bulking of dynamin-related protein 1 prevents ischemic sulfide catabolism and heart failure in mice.

The presence of redox-active molecules containing catenated sulfur atoms (supersulfides) in living organisms has led to a review of the concepts of redox biology and its translational strategy. Glutathione (GSH) is the body's primary detoxifier and antioxidant, and its oxidized form (GSSG) has been considered as a marker of oxidative status. However, we report that GSSG, but not reduced GSH, prevents ischemic supersulfide catabolism-associated heart failure in male mice by electrophilic modification of dynamin-related protein (Drp1).

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.

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.

Bayesian Latent Class Models for Evaluating the Validity of Claim-based Definitions of Disease Outcomes.

Background: Large electronic databases have been widely used in recent years; however, they can be susceptible to bias due to incomplete information. To address this, validation studies have been conducted to assess the accuracy of disease diagnoses defined in databases. However, such studies may be constrained by potential misclassification in references and the interdependence between diagnoses from the same data source.

Molecular tag for promoting -glycan maturation in the cargo receptor-mediated secretion pathway.

MCFD2 and ERGIC-53 form a cargo receptor complex that plays a crucial role in transporting specific glycoproteins, including blood coagulation factor VIII, from the endoplasmic reticulum to the Golgi apparatus. We have demonstrated that MCFD2 recognizes a 10-amino-acid sequence in factor VIII, thereby facilitating its efficient transport. Moreover, the secretion of biopharmaceutical recombinant glycoproteins, such as erythropoietin, can be enhanced by tagging them with this sequence, which we have termed the "passport sequence" (PS).

Temporal dynamics in a red alga dominated geothermal feature in Yellowstone National Park.

Alga-dominated geothermal spring communities in Yellowstone National Park (YNP), USA, have been the focus of many studies, however, relatively little is known about the composition and community interactions which underpin these ecosystems. Our goal was to determine, in three neighboring yet distinct environments in Lemonade Creek, YNP, how cells cope with abiotic stressors over the diurnal cycle. All three environments are colonized by two photosynthetic lineages, and , both of which are extremophilic Cyanidiophyceae red algae.

Plastidial thioredoxin-like proteins are essential for normal embryogenesis and seed development in Arabidopsis thaliana.

Thiol/disulfide-based redox regulation is a key mechanism for modulating protein functions in response to changes in cellular redox status. Two thioredoxin (Trx)-like proteins [atypical Cys His-rich Trx (ACHT) and Trx-like2 (TrxL2)] have been identified as crucial for oxidizing and deactivating several chloroplast enzymes during light-to-dark transitions; however, their roles remain to be fully understood. In this study, we investigated the functions of Trx-like proteins in seed development.

Development of Molecular Dynamics Parameters and Theoretical Analysis of Excitonic and Optical Properties in the Light-Harvesting Complex II.

The light-harvesting complex II (LHCII) in green plants exhibits highly efficient excitation energy transfer (EET). A comprehensive understanding of the EET mechanism in LHCII requires quantum chemical, molecular dynamics (MD), and statistical mechanics calculations that can adequately describe pigment molecules in heterogeneous environments. Herein, we develop MD simulation parameters that accurately reproduce the quantum mechanical/molecular mechanical energies of both the ground and excited states of all chlorophyll (Chl) molecules in membrane embedded LHCII.

Population-specific reference panel improves imputation quality for genome-wide association studies conducted on the Japanese population.

To improve imputation quality for genome-wide association studies (GWAS) conducted on the Japanese population, we developed and evaluated four Japanese population-specific reference panels. These panels were constructed through the augmentation of the 1000 Genomes Project (1KG) panel using Japanese whole genome sequencing (WGS) data, with sample sizes ranging from 1 K to 7 K individuals enrolled through the Biobank Japan (BBJ) project, and sequencing depths ranging from 3× to 30×. Among these panels, an augmented reference panel comprising 7472 WGS samples of mixed depth (1KG+7K) exhibit the greatest improvement in imputation quality relative to the Trans-Omics for Precision Medicine (TOPMed) reference panel.

Metapopulation heterogeneities in host mobility, productivity, and immunocompetency always increase virulence and infectiousness.

The epidemiology and evolution of diseases unfold in populations that are rarely homogeneous. Instead, hosts infected by pathogens often form metapopulations, in which local populations connected by the movement of hosts experience different demographic and epidemiological conditions. Here, we develop a general theory of the evolution of pathogens in heterogeneous metapopulations.

Future spinal reflex is embedded in primary motor cortex output.

Mammals can execute intended limb movements despite the fact that spinal reflexes involuntarily modulate muscle activity. To generate appropriate muscle activity, the cortical descending motor output must coordinate with spinal reflexes, yet the underlying neural mechanism remains unclear. We simultaneously recorded activities in motor-related cortical areas, afferent neurons, and forelimb muscles of monkeys performing reaching movements.

Growth regulation bringing modularity to morphogenesis of complex three-dimensional exoskeletons.

Diverse three-dimensional morphologies of arthropods' outgrowths, including beetle horns, are formed through the non-uniform growth of epidermis. Prior to moulting, epidermal tissue peels off from the old cuticle and grows non-uniformly to shape protruding structures, which are often branching, curving or twisting, from the planar epidermis. This non-uniform growth is possibly regulated by the distribution of morphogens on the epidermal cell sheet.

A complete classification of evolutionary games with environmental feedback.

A tragedy of the commons, in which rational behavior of individuals to maximize their own payoffs depletes common resources, is one of the most important research topics in game theory. To better understand the social dilemma problem, recent studies have developed a theoretical framework of feedback-evolving game where individual behavior affects an environmental (renewable) resource and the environmental resource changes individual payoffs. While previous studies assumed that the frequency of defectors increases (prisoner's dilemma [PD] game) when the environmental resource is abundant to investigate an oscillating tragedy of the commons, it is also possible for other types of game to produce the social dilemma.

Rising trends of inbreeding in Japanese Thoroughbred horses.

We investigated the changes in inbreeding levels in Japanese Thoroughbred horses over the past 46 years. Our results show a significant increase in inbreeding over the past 30 years, primarily due to the influence of two sires, Northern Dancer and Sunday Silence. Northern Dancer's bloodline spread gradually through descendants like Northern Taste, leading to a slower increase in the inbreeding coefficient.