Structural insights into how Cas9 targets nucleosomes.

The CRISPR-associated endonuclease Cas9 derived from prokaryotes is used as a genome editing, which targets specific genomic loci by single guide RNAs (sgRNAs). The eukaryotes, the target of genome editing, store their genome DNA in chromatin, in which the nucleosome is a basic unit. Despite previous structural analyses focusing on Cas9 cleaving free DNA, structural insights into Cas9 targeting of DNA within nucleosomes are limited, leading to uncertainties in understanding how Cas9 operates in the eukaryotic genome.

Phenotypic and Genomic Signatures of Latitudinal Local Adaptation Along With Prevailing Ocean Current in a Coastal Goby.

In the marine realm, unidirectional ocean currents often lead to high migration rates of marine organisms and, therefore, inhibit the formation of their latitudinal genetic structure. In contrast, cryptic latitudinal structures associated with local adaptation may frequently exist in widespread species generally exposed to a strong environmental heterogeneity. However, our understanding of the evolvability of locally adapted populations in open marine environments still needs to be completed.

Motion-generation system for violin-playing robot using reinforcement learning differences in bowing parameters due to changes in learning conditions and sound pressure values.

Recently, research on human-robot communication attracts many researchers. We believe that music is one of the important channel between human and robot, because it can convey emotional information. In this research, we focus on the violin performance by a robot.

Using micro-CT to explore bone density variations in the skulls of the vulnerable Opsariichthys uncirostris uncirostris (Three-lips fish) during reproductive migration to a Lake Biwa tributary.

Not much is known about the changes in bone density due to fish reproductive migration. We used micro-CT and inferential statistics to determine whether the relative bone density in the skulls of adult Three-lips fish, that seasonally upstream migrated to a Lake Biwa tributary, changed across their known reproductive season. The relative bone density significantly decreased as standard length and condition factor (K) increased in both sexes.

Lasy-Seq: A High-Throughput 3' RNA-Seq Method for Large-Scale Transcriptome Profiling in Rice.

Lasy-Seq (low-cost and easy RNA-seq) is a high-throughput library preparation method for 3' RNA-seq. Usage of oligo(dT) primers with unique index sequences allows simultaneous reverse transcription (RT) reaction and sample indexing. Therefore, each post-RT step, which was performed on a sample-by-sample basis in a conventional method, can be performed on a large number of samples together in a single tube.

DeLTa-Seq: High-Throughput Targeted RNA-Seq of Rice Leaves Without RNA Purification.

DeLTa-seq is a high-throughput RNA-seq library preparation method that enables quantification of the expression of hundreds of arbitrarily selected genes without RNA purification. This method involves direct reverse transcription using rice leaf lysate and targeted RNA-seq library preparation. DeLTa-seq enables the precise quantification of gene expression with a small number of sequencing reads.

Precise Base Substitution Using CRISPR/Cas-Mediated Base Editor in Rice.

Base editors, CRISPR/Cas-based precise genome editing tools, enable base conversion at a target site without inducing DNA double-strand breaks. The genome editing targetable range is restricted by the requirement for protospacer adjacent motif (PAM) sequence. Cas9 derived from Streptococcus pyogenes (SpCas9)-most widely used for genome editing in many organisms-requires an NGG sequence adjacent to the target site as a PAM.

Gene Targeting via CRISPR/Cas9-Mediated DNA Double-Strand Break Induction in Rice.

Gene targeting (GT) is a precise genome editing tool to achieve desired modification of a target gene, e.g., introduction of point mutations, knock-in of a reporter gene, or swapping of a functional domain, through homologous recombination.

Agrobacterium-Mediated Transformation and Targeted Mutagenesis Using SpCas12f in Rice.

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) (CRISPR-Cas) is an adaptive prokaryote immune system against foreign DNA/RNA that is now applied widely to genome editing. A miniature Cas, CRISPR-Cas12f, is one-half to one-third the size of the CRISPR-Cas9 that is commonly used in genome editing experiments in many organisms, including higher plants. The compactness of CRISPR-Cas12f is expected to be advantageous in terms of vector construction and transformation frequency.

High β-carotene accumulation in transgenic eggplant fruits grown under artificial light.

Eggplant ( L.) fruits are known to contain few carotenoids such as β-carotene, which are abundant in congener tomato fruits. In a previous study, we introduced a fruit-specific gene promoter-driven gene encoding phytoene synthase (PSY) of into eggplant 'Senryo No.

Reducing herbivory in mixed planting by genomic prediction of neighbor effects in the field.

Genetically diverse populations can increase plant resistance to natural enemies. Yet, beneficial genotype pairs remain elusive due to the occurrence of positive or negative effects of mixed planting on plant resistance, respectively called associational resistance or susceptibility. Here, we identify key genotype pairs responsible for associational resistance to herbivory using the genome-wide polymorphism data of the plant species Arabidopsis thaliana.

Cy-1, a major QTL for tomato leaf curl New Delhi virus resistance, harbors a gene encoding a DFDGD-Class RNA-dependent RNA polymerase in cucumber (Cucumis sativus).

Background: Tomato leaf curl New Delhi virus (ToLCNDV) (family Geminiviridae, genus Begomovirus) is a significant threat to cucumber (Cucumis sativus) production in many regions. Previous studies have reported the genetic mapping of loci related to ToLCNDV resistance, but no resistance genes have been identified.

Results: We conducted map-based cloning of the ToLCNDV resistance gene in cucumber accession No.

Macroscale vertical power-law distribution of bacteria in dark oceans can emerge from microscale bacteria-particle interactions.

Microbes in the dark oceans are a key determinant of remineralization of sinking carbon particles. However, most marine ecosystem models overlook how microbes aggregate on particles and the microscale interactions between particle-associated microbes, making it difficult to obtain mechanistic insights on their vertical power-law decay pattern. Here, we present a spatial population model where the attachment and detachment processes of bacterial cells depend on local density of particle-associated bacteria.

NARO historical phenotype dataset from rice breeding.

Data from breeding, including phenotypic information, may improve the efficiency of breeding. Historical data from breeding trials accumulated over a long time are also useful. Here, by organizing data accumulated in the National Agriculture and Food Research Organization (NARO) rice breeding program, we developed a historical phenotype dataset, which includes 6052 records obtained for 667 varieties in yield trials in 1991-2018 at six NARO research stations.

Single candidate gene for salt tolerance of (Ohwi) Ohwi & Ohashi identified by QTL mapping, whole genome sequencing and triplicated RNA-seq analyses.

Salt tolerance has been an important issue as a solution for soil salinization and groundwater depletion. To challenge this issue, genetic diversity of wild plants must be harnessed. Here we report a discovery of a candidate gene for salt tolerance in , one of the coastal species in the genus .

Genetic parameters of behavior traits of beef cattle classified using wearable devices.

With the development of wearable devices, it is now possible to monitor livestock behavior 24 h a day. In this study, we estimated the genetic parameters of the daily duration of six behaviors (feeding, moving, lying, standing, ruminating while lying, and ruminating while standing) in beef cattle, automatically classified using wearable devices. The devices were attached to 332 Japanese beef cattle at two stations for approximately 5 months.

Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver.

Hepatic glucose metabolism serves dual purposes: maintaining glucose homeostasis and converting glucose into energy sources; however, the underlying mechanisms are unclear. We quantitatively measured liver metabolites, gene expression, and phosphorylated insulin signaling molecules in mice orally administered varying doses of glucose, and constructed a transomic network. Rapid phosphorylation of insulin signaling molecules in response to glucose intake was observed, in contrast to the more gradual changes in gene expression.

Evaluating the quantitative performance of environmental DNA metabarcoding for freshwater zooplankton community: a case study in Lake Biwa, Japan.

Zooplankton monitoring is important for understanding their population dynamics and life history, ecosystem health, and environmental changes. Compared with traditional morphological identification, environmental DNA (eDNA) analysis allows for more sensitive and efficient monitoring of zooplankton diversity. Previous eDNA studies have primarily used metabarcoding approaches to reveal their richness and composition, whereas its performance in predicting zooplankton abundance remains understudied.

Adaptive radiation of the genus in the Bonin Islands revealed through double-digest restriction site-associated DNA sequencing analysis.

The Bonin Islands, comprised of the Mukojima, Chichijima, and Hahajima Islands, are known for their isolated and distinctive habitats, hosting a diverse array of endemic flora and fauna. In these islands, adaptive radiation has played a remarkable role in speciation, particularly evident in the genus that is represented by three species: and exclusive to the Chichijima Islands, and , distributed across the entire Bonin Islands. Notably, exhibits multiple ecotypes, differing in leaf hair density, flowering time, and tree size.

Methodological assessment for efficient collection of Schistosoma mansoni environmental DNA and improved schistosomiasis surveillance in tropical wetlands.

Schistosomiasis, caused by trematodes of genus Schistosoma, is among the most seriously neglected tropical diseases. Although rapid surveillance of risk areas for Schistosoma transmission is vital to control schistosomiasis, the habitat and infection status of this parasite are difficult to assess. Environmental DNA (eDNA) analysis, involving the detection of extra-organismal DNA in water samples, facilitates cost-efficient and sensitive biomonitoring of aquatic environments and is a promising tool to identify Schistosoma habitat and infection risk areas.

Heritable Tissue-Culture-Free Gene Editing in Nicotiana benthamiana through Viral Delivery of SpCas9 and sgRNA.

Conventional plant gene editing requires laborious tissue-culture-mediated transformation, which restricts the range of applicable plant species. In this study, we developed a heritable and tissue-culture-free gene editing method in Nicotiana benthamiana using tobacco ringspot virus (TRSV) as a vector for in planta delivery of Cas9 and single-guide RNA (sgRNA) to shoot apical meristems. Agrobacterium-mediated inoculation of the TRSV vector induced systemic and heritable gene editing in Nicotiana benthamiana PHYTOENE DESATURASE.

Preying on cyprinid snout warts (pearl organs) as a novel and peculiar habit in the Lake Malawi cichlid Docimodus evelynae.

Cichlid fishes in the African Great Lakes have undergone explosive speciation, acquiring markedly varying ecologies and diets. There are multiple lineages of scale-eating cichlids, and their natural history and evolutionary ecology is only partially understood. We examined the feeding habit of Docimodus evelynae, a known scale eater, in Lake Malawi.

A Bayesian model for genomic prediction using metabolic networks.

Motivation: Genomic prediction is now an essential technique in breeding and medicine, and it is interesting to see how omics data can be used to improve prediction accuracy. Precedent work proposed a metabolic network-based method in biomass prediction of Arabidopsis; however, the method consists of multiple steps that possibly degrade prediction accuracy.

Results: We proposed a Bayesian model that integrates all steps and jointly infers all fluxes of reactions related to biomass production.