Plant GARDEN: a portal website for cross-searching between different types of genomic and genetic resources in a wide variety of plant species.

BACKGROUND: Plant genome information is fundamental to plant research and development. Along with the increase in the number of published plant genomes, there is a need for an efficient system to retrieve various kinds of genome-related information from many plant species across plant kingdoms. Various plant databases have been developed, but no public database covers both genomic and genetic resources over a wide range of plant species. MAIN BODY: We have developed a plant genome portal site, Plant GARDEN (Genome And Resource Database Entry: https://plantgarden.jp/en/index ), to provide diverse information related to plant genomics and genetics in divergent plant species. Elasticsearch is used as a search engine, and cross-keyword search across species is available. Web-based user interfaces (WUI) for PCs and tablet computers were independently developed to make data searches more convenient. Several types of data are stored in Plant GARDEN: reference genomes, gene sequences, PCR-based DNA markers, trait-linked DNA markers identified in genetic studies, SNPs, and in/dels on publicly available sequence read archives (SRAs). The data registered in Plant GARDEN as of March 2023 included 304 assembled genome sequences, 11,331,614 gene sequences, 419,132 DNA markers, 8,225 QTLs, and 5,934 SNP lists (gvcf files). In addition, we have re-annotated all the genes registered in Plant GARDEN by using a functional annotation tool, Hayai-Annotation, to compare the orthologous relationships among genes. CONCLUSION: The aim of Plant GARDEN is to provide plant genome information for use in the fields of plant science as well as for plant-based industries, education, and other relevant areas. Therefore, we have designed a WUI that allows a diverse range of users to access such information in an easy-to-understand manner. Plant GARDEN will eventually include a wide range of plant species for which genome sequences are assembled, and thus the number of plant species in the database will continue to expand. We anticipate that Plant GARDEN will promote the understanding of genomes and gene diversity by facilitating comparisons of the registered sequences.

Dynamic depth-of-field projection mapping method based on a variable focus lens and visual feedback.

Dynamic projection mapping is an interactive display technology, which is capable with multiplayers with naked eyes for augmented reality. However, the fixed and shallow depth-of-field of the projector optics limits its potential applications. In this work, a high-speed projection mapping method with a dynamic focal tracking technology based on a variable focus lens will be illustrated. The proposed system included a high-speed variable focus lens, a high-speed camera, and a high- speed projector, so that the depth and rotation information would be detected and then served as feedback to correct the focal length and update the projection information in real time. As a result, the information would be well-focused projected even on a 3D dynamic moving object. The response speed of the high-speed prototype could reach around 5 ms, and the dynamic projection range covered from 0.5 to 2.0 m.

Modified Boyes' procedure for the multiple finger extensor tendon ruptures in patients with rheumatoid arthritis: A report of two cases.

Multiple subcutaneous extensor tendon ruptures in more than the ulnar three fingers sometimes occur in patients with rheumatoid arthritis accompanied by wrist deformity. In these situations, the flexor digitorum superficialis tendon of the middle finger (the FDS3 tendon) and that of the ring finger (the FDS4 tendon) are used for the transferred tendon (modified Boyes' procedure). Here, we treated two patients with rheumatoid arthritis, whose extensor tendons of more than three fingers were ruptured, using the modified Boyes' procedure. Case 1 had ruptures in four fingers (index through little), and Case 2 had ruptures in three fingers (middle through little). The FDS3 and FDS4 tendons were passed subcutaneously around the radial side of the wrist to the extensor sides and interlaced with the distal stump of the ruptured tendons. Switching of the finger movement was achieved smoothly in both cases. The post-operative evaluation showed an extension lag of -15° for the index finger 0° for the middle through the little fingers in Case 1, and 0° for the middle finger and -5° for the ring and little fingers in Case 2. The average post-operative extension lag was -3.5°. However, median nerve palsy occurred in both cases, and it gradually recovered. Stretching of the nerve by the correction of the wrist deformity and increased pressure in the carpal tunnel were supposed to be causes of this palsy. Modified Boyes' procedure is a useful method for more than three ulnar finger extensor tendon ruptures; however, post-operative median nerve palsy should be considered.

Characteristics of health-related quality of life and related factors in patients with brain tumors treated with rehabilitation therapy.

BACKGROUND: Rehabilitation therapy during hospitalization is effective in improving activities of daily living (ADL) and physical function in patients with brain tumors. However, there are few studies on the effect of rehabilitation therapy on health-related quality of life (HRQOL) in patients with brain tumors. Additionally, the EuroQol-5Dimension-5Level (EQ-5D-5L) index score has not been reported as an outcome. This study aimed to investigate the HRQOL of patients with brain tumors who underwent rehabilitation therapy and investigated the factors affecting the EQ-5D-5L index score from various perspectives, including various brain tumor type and recurrence. In addition, we examined the relationship between the EQ-5D-5L index score, disease-specific HRQOL scale, and ADL. METHODS: Patients with brain tumors who underwent treatment and rehabilitation at Single tertiary care academic medical center were included in this cross-sectional study. We used the EQ-5D-5L, European Organisation for Research and Treatment of Cancer (EORTC) quality of life questionnaire core 30, and EORTC quality of life questionnaire brain cancer module to evaluate HRQOL. ADL were assessed using the functional independence measure (FIM). The relationship between each HRQOL assessment score and the FIM was analyzed, and the influence of related factors was assessed by multiple regression analysis. RESULTS: This study included 76 patients. The EQ-5D-5L index score was 0.689 for all patients with brain tumors and 0.574 for those with glioblastomas, which was the lowest value. There was a moderate correlation between the EQ-5D-5L index score and FIM (r = 0.627, p < 0.001). In addition, the EQ-5D-5L index score was significantly correlated with most of the items of the disease-specific HRQOL scale. Multiple regression analysis revealed that glioblastoma histology (coefficient: - 0.373, p = 0.005) and recurrence (coefficient: - 0.273, p = 0.020) were independent factors affecting the EQ-5D-5L index score. CONCLUSIONS: Patients with glioblastoma undergoing rehabilitation have reduced HRQOL, which was influenced by glioblastoma histology and recurrence.

Accurate measurement of virtual image distance for near-eye displays based on auto-focusing.

Virtual reality (VR) and augmented reality (AR) are able to project virtual images to human eyes at a certain depth distance. This virtual image distance can be adjusted by controlling the diopter of the near-eye display. However, it is difficult to measure accurately and continuously since this virtual image distance spans a large range. In this work, we propose a method to accurately determine the virtual image distance of commercial VR/AR equipment. The measurement apparatus is built and calibrated to validate the feasibility. The focal distance of the focus-tunable lens can be automatically adjusted via a step motor by cooperating with the image sharpness analyzing program. Compared with other proposed methods, ours provides an effective means to achieve high accuracy, a wide and continuous testing range, and automatic evaluation of virtual image distance for compact near-eye displays.

Extended depth-of-field projection method using a high-speed projector with a synchronized oscillating variable-focus lens.

For a projector-based virtual reality (VR) or augmented reality (AR) display, a large depth of field and a high-speed image refresh rate are important keys to improve the projector's performance. Here, we propose a solution that extends the depth of field of the projection using a variable-focus lens and a high-speed projector as well as a control method that synchronizes oscillation of the variable-focus lens with the high-speed projector. The experiment confirms that the proposed system can project the well-focused and dynamically changeable contents on six different planes. Its projection range varies from 0.3 m to 1.5 m, and the refresh rate is 166.7 Hz.

Pixelwise Phase Unwrapping Based on Ordered Periods Phase Shift.

The existing phase-shift methods are effective in achieving high-speed, high-precision, high-resolution, real-time shape measurement of moving objects; however, a phase-unwrapping method that can handle the motion of target objects in a real environment and is robust against global illumination as well is yet to be established. Accordingly, a robust and highly accurate method for determining the absolute phase, using a minimum of three steps, is proposed in this study. In this proposed method, an order structure that rearranges the projection pattern for each period of the sine wave is introduced, so that solving the phase unwrapping problem comes down to calculating the pattern order. Using simulation experiments, it has been confirmed that the proposed method can be used in high-speed, high-precision, high-resolution, three-dimensional shape measurements even in situations with high-speed moving objects and presence of global illumination. In this study, an experimental measurement system was configured with a high-speed camera and projector, and real-time measurements were performed with a processing time of 1.05 ms and a throughput of 500 fps.

Laparoscopic decompression of a stricture of the celiac artery caused by the median arcuate ligament in a gastric cancer patient: A case of report.

Stricture of the celiac artery caused by the median arcuate ligament induces abdominal ischemic symptoms and aneurysm near the pancreatic head. However, the need to treat asymptomatic patients is unclear. We safely performed surgical decompression of a stricture of the celiac artery by MAL in an asymptomatic patient at the same time as gastrectomy for gastric cancer. After surgery, the stricture of the celiac artery had disappeared as demonstrated by CT scan and 3-D CT angiography.

Low-cost, readily available 3D microscopy imaging system with variable focus spinner.

A large open aperture in an optical system can capture high-resolution images but yields a shallow depth of field. To overcome this issue, we investigated a low-cost, readily available method for retrofitting microscopy imaging systems to achieve 3D focus scanning in this study. Specifically, a procedure for fabricating variable focus spinners with dissimilar plates was introduced, and a sequence of 12 images was captured in different focal planes. The image scale and phase were corrected, and the in-focus pixels were abstracted by employing the Laplacian operator. Finally, an all-in-focus sharp image was generated, and a depth map was obtained.

Synchronized High-Speed Vision Sensor Network for Expansion of Field of View.

We propose a 500-frames-per-second high-speed vision (HSV) sensor network that acquires frames at a timing that is precisely synchronized across the network. Multiple vision sensor nodes, individually comprising a camera and a PC, are connected via Ethernet for data transmission and for clock synchronization. A network of synchronized HSV sensors provides a significantly expanded field-of-view compared with that of each individual HSV sensor. In the proposed system, the shutter of each camera is controlled based on the clock of the PC locally provided inside the node, and the shutters are globally synchronized using the Precision Time Protocol (PTP) over the network. A theoretical analysis and experiment results indicate that the shutter trigger skew among the nodes is a few tens of microseconds at most, which is significantly smaller than the frame interval of 1000-fps-class high-speed cameras. Experimental results obtained with the proposed system comprising four nodes demonstrated the ability to capture the propagation of a small displacement along a large-scale structure.

Genome structure of Rosa multiflora, a wild ancestor of cultivated roses.

The draft genome sequence of a wild rose (Rosa multiflora Thunb.) was determined using Illumina MiSeq and HiSeq platforms. The total length of the scaffolds was 739,637,845 bp, consisting of 83,189 scaffolds, which was close to the 711 Mbp length estimated by k-mer analysis. N50 length of the scaffolds was 90,830 bp, and extent of the longest was 1,133,259 bp. The average GC content of the scaffolds was 38.9%. After gene prediction, 67,380 candidates exhibiting sequence homology to known genes and domains were extracted, which included complete and partial gene structures. This large number of genes for a diploid plant may reflect heterogeneity of the genome originating from self-incompatibility in R. multiflora. According to CEGMA analysis, 91.9% and 98.0% of the core eukaryotic genes were completely and partially conserved in the scaffolds, respectively. Genes presumably involved in flower color, scent and flowering are assigned. The results of this study will serve as a valuable resource for fundamental and applied research in the rose, including breeding and phylogenetic study of cultivated roses.

LjMOT1, a high-affinity molybdate transporter from Lotus japonicus, is essential for molybdate uptake, but not for the delivery to nodules.

Molybdenum (Mo) is an essential nutrient for plants, and is required for nitrogenase activity of legumes. However, the pathways of Mo uptake from soils and then delivery to the nodules have not been characterized in legumes. In this study, we characterized a high-affinity Mo transporter (LjMOT1) from Lotus japonicus. Mo concentrations in an ethyl methanesulfonate-mutagenized line (ljmot1) decreased by 70-95% compared with wild-type (WT). By comparing the DNA sequences of four AtMOT1 homologs between mutant and WT lines, one point mutation was found in LjMOT1, which altered Trp292 to a stop codon; no mutation was found in the other homologous genes. The phenotype of Mo concentrations in F2 progeny from ljmot1 and WT crosses were associated with genotypes of LjMOT1. Introduction of endogenous LjMOT1 to ljmot1 restored Mo accumulation to approximately 60-70% of the WT. Yeast expressing LjMOT1 exhibited high Mo uptake activity, and the Km was 182 nm. LjMOT1 was expressed mainly in roots, and its expression was not affected by Mo supply or rhizobium inoculation. Although Mo accumulation in the nodules of ljmot1 was significantly lower than that of WT, it was still high enough for normal nodulation and nitrogenase activity, even for cotyledons-removed ljmot1 plants grown under low Mo conditions, in this case the plant growth was significantly inhibited by Mo deficiency. Our results suggest that LjMOT1 is an essential Mo transporter in L. japonicus for Mo uptake from the soil and growth, but is not for Mo delivery to the nodules.

Plant Genome DataBase Japan (PGDBj).

A portal website that integrates a variety of information related to genomes of model and crop plants from databases (DBs) and the literature was generated. This website, named the Plant Genome DataBase Japan (PGDBj, http://pgdbj. jp/en/ ), is comprised of three component DBs and a cross-search engine which provides a seamless search over their contents. One of the three component DBs is the Ortholog DB, which provides gene cluster information based on the amino acid sequence similarity. Over 1,000,000 amino acid sequences of 40 Viridiplantae species were collected from the public DNA DBs, and plant genome DBs such as TAIR and RAP-DB were subjected to reciprocal BLAST searches for clustering. Another component DB is the Plant Resource DB for genomic- and bio-resources. This DB also integrates the SABRE DB, which provides cDNA and genome sequence resources maintained in the RIKEN BioResource Center and National BioResource Projects Japan. The third component DB of PGDBj is the DNA Marker DB, which manually or automatically collects curated information on DNA markers, quantitative trait loci (QTL), and related genetic linkage maps, from the literature and external DBs. By combining these component DBs and a cross-search engine, PGDBj serves as a useful platform to study genetic systems for both fundamental and applied researches for a wide range of plant species.

Genome sequence and analysis of the Japanese morning glory Ipomoea nil.

Ipomoea is the largest genus in the family Convolvulaceae. Ipomoea nil (Japanese morning glory) has been utilized as a model plant to study the genetic basis of floricultural traits, with over 1,500 mutant lines. In the present study, we have utilized second- and third-generation-sequencing platforms, and have reported a draft genome of I. nil with a scaffold N50 of 2.88 Mb (contig N50 of 1.87 Mb), covering 98% of the 750 Mb genome. Scaffolds covering 91.42% of the assembly are anchored to 15 pseudo-chromosomes. The draft genome has enabled the identification and cataloguing of the Tpn1 family transposons, known as the major mutagen of I. nil, and analysing the dwarf gene, CONTRACTED, located on the genetic map published in 1956. Comparative genomics has suggested that a whole genome duplication in Convolvulaceae, distinct from the recent Solanaceae event, has occurred after the divergence of the two sister families.

The LORE1 insertion mutant resource.

Long terminal repeat (LTR) retrotransposons are closely related to retroviruses, and their activities shape eukaryotic genomes. Here, we present a complete Lotus japonicus insertion mutant collection generated by identification of 640 653 new insertion events following de novo activation of the LTR element Lotus retrotransposon 1 (LORE1) (http://lotus.au.dk). Insertion preferences are critical for effective gene targeting, and we exploit our large dataset to analyse LTR element characteristics in this context. We infer the mechanism that generates the consensus palindromes typical of retroviral and LTR retrotransposon insertion sites, identify a short relaxed insertion site motif, and demonstrate selective integration into CHG-hypomethylated genes. These characteristics result in a steep increase in deleterious mutation rate following activation, and allow LORE1 active gene targeting to approach saturation within a population of 134 682 L. japonicus lines. We suggest that saturation mutagenesis using endogenous LTR retrotransposons with germinal activity can be used as a general and cost-efficient strategy for generation of non-transgenic mutant collections for unrestricted use in plant research.

Sequencing and analysis of the complete organellar genomes of Parmales, a closely related group to Bacillariophyta (diatoms).

We sequenced the complete plastid and mitochondrial genomes of the unicellular marine phytoplankton Triparma laevis, belonging to the order Parmales (Heterokonta). The cells of Parmales are surrounded by silicified cell walls, similar to Bacillariophyta (diatoms). T. laevis was recognized as a sister group of Bacillariophyta using a molecular phylogenetic analysis based on SSU rDNA and rbcL sequences. Bacillariophyta are the most successful group of phytoplankton in the modern ocean, but the origin and early evolution of them have not been clearly established. Detailed molecular analyses of T. laevis may increase our understanding of the evolutionary relationships among Parmales and Bacillariophyta. The gene contents of the plastid and mitochondrial genomes are similar between T. laevis and Bacillariophyta. The gene order of the plastid genome is also similar to Bacillariophyta, whereas the gene order of the mitochondrial genome is not conserved in Bacillariophyta, but the structure is more compact than Bacillariophyta. Phylogenetic analyses, using plastid-encoded concatenated amino acid datasets and mitochondria-encoded concatenated amino acid datasets suggest that T. laevis is a sister group of Bacillariophyta. These results suggest that the characteristics of the organellar genomes of T. laevis are similar and conserve ancestral characteristics more than Bacillariophyta.

Sequencing and comparative analyses of the genomes of zoysiagrasses.

Zoysiais a warm-season turfgrass, which comprises 11 allotetraploid species (2n= 4x= 40), each possessing different morphological and physiological traits. To characterize the genetic systems of Zoysia plants and to analyse their structural and functional differences in individual species and accessions, we sequenced the genomes of Zoysia species using HiSeq and MiSeq platforms. As a reference sequence of Zoysia species, we generated a high-quality draft sequence of the genome of Z. japonica accession 'Nagirizaki' (334 Mb) in which 59,271 protein-coding genes were predicted. In parallel, draft genome sequences of Z. matrella 'Wakaba' and Z. pacifica 'Zanpa' were also generated for comparative analyses. To investigate the genetic diversity among the Zoysia species, genome sequence reads of three additional accessions, Z. japonica'Kyoto', Z. japonica'Miyagi' and Z. matrella'Chiba Fair Green', were accumulated, and aligned against the reference genome of 'Nagirizaki' along with those from 'Wakaba' and 'Zanpa'. As a result, we detected 7,424,163 single-nucleotide polymorphisms and 852,488 short indels among these species. The information obtained in this study will be valuable for basic studies on zoysiagrass evolution and genetics as well as for the breeding of zoysiagrasses, and is made available in the 'Zoysia Genome Database' at http://zoysia.kazusa.or.jp.

Pleurochrysome: A Web Database of Pleurochrysis Transcripts and Orthologs Among Heterogeneous Algae.

Pleurochrysis is a coccolithophorid genus, which belongs to the Coccolithales in the Haptophyta. The genus has been used extensively for biological research, together with Emiliania in the Isochrysidales, to understand distinctive features between the two coccolithophorid-including orders. However, molecular biological research on Pleurochrysis such as elucidation of the molecular mechanism behind coccolith formation has not made great progress at least in part because of lack of comprehensive gene information. To provide such information to the research community, we built an open web database, the Pleurochrysome (http://bioinf.mind.meiji.ac.jp/phapt/), which currently stores 9,023 unique gene sequences (designated as UNIGENEs) assembled from expressed sequence tag sequences of P. haptonemofera as core information. The UNIGENEs were annotated with gene sequences sharing significant homology, conserved domains, Gene Ontology, KEGG Orthology, predicted subcellular localization, open reading frames and orthologous relationship with genes of 10 other algal species, a cyanobacterium and the yeast Saccharomyces cerevisiae. This sequence and annotation information can be easily accessed via several search functions. Besides fundamental functions such as BLAST and keyword searches, this database also offers search functions to explore orthologous genes in the 12 organisms and to seek novel genes. The Pleurochrysome will promote molecular biological and phylogenetic research on coccolithophorids and other haptophytes by helping scientists mine data from the primary transcriptome of P. haptonemofera.

Genome-wide survey of artificial mutations induced by ethyl methanesulfonate and gamma rays in tomato.

Genome-wide mutations induced by ethyl methanesulfonate (EMS) and gamma irradiation in the tomato Micro-Tom genome were identified by a whole-genome shotgun sequencing analysis to estimate the spectrum and distribution of whole-genome DNA mutations and the frequency of deleterious mutations. A total of ~370 Gb of paired-end reads for four EMS-induced mutants and three gamma-ray-irradiated lines as well as a wild-type line were obtained by next-generation sequencing technology. Using bioinformatics analyses, we identified 5920 induced single nucleotide variations and insertion/deletion (indel) mutations. The predominant mutations in the EMS mutants were C/G to T/A transitions, while in the gamma-ray mutants, C/G to T/A transitions, A/T to T/A transversions, A/T to G/C transitions and deletion mutations were equally common. Biases in the base composition flanking mutations differed between the mutagenesis types. Regarding the effects of the mutations on gene function, >90% of the mutations were located in intergenic regions, and only 0.2% were deleterious. In addition, we detected 1,140,687 spontaneous single nucleotide polymorphisms and indel polymorphisms in wild-type Micro-Tom lines. We also found copy number variation, deletions and insertions of chromosomal segments in both the mutant and wild-type lines. The results provide helpful information not only for mutation research, but also for mutant screening methodology with reverse-genetic approaches.

Molecular Characterization of LjABCG1, an ATP-Binding Cassette Protein in Lotus japonicus.

LjABCG1, a full-size ABCG subfamily of ATP-binding cassette proteins of a model legume, Lotus japonicus, was reported as a gene highly expressed during the early stages of nodulation, but have not been characterized in detail. In this study we showed that the induction of LjABCG1 expression was remarkable by methyl jasmonate treatment, and reporter gene experiments indicated that LjABCG1 was strongly expressed in the nodule parenchyma and cell layers adjacent to the root vascular tissue toward the nodule. LjABCG1 was suggested to be localized at the plasma membrane based on the fractionation of microsomal membranes as well as separation via aqueous two-phase partitioning. The physiological functions of LjABCG1 in symbiosis and pathogenesis were analyzed in homologous and heterologous systems. LjABCG1 knock-down L. japonicus plants did not show clear phenotypic differences in nodule formation, and not in defense against Pseudomonas syringae, either. In contrast, when LjABCG1 was expressed in the Arabidopsis pdr8-1 mutant, the penetration frequency of Phytophthora infestans, a potato late blight pathogen, was significantly reduced in LjABCG1/pdr8-1 than in pdr8-1 plants. This finding indicated that LjABCG1, at least partially, complemented the phenotype of pdr8 in Arabidopsis, suggesting the multiple roles of this protein in plant-microbe interactions.