Search

Abstract 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. 9 Gbp) with abundant repeat elements may have represented an obstacle for genetic analysis, this species is easily propagated by cutting, flowered by gibberellic acid, transformed by Agrobacterium, and edited by CRISPR/Cas9. These characteristics of C. japonica recommend it as a model conifer species for which reference genome sequences are necessary. Results Herein, we report the first chromosome-level assembly of C. japonica (2n = 22) using third-generation selfed progeny (estimated homozygosity rate = 0.96). Young leaf tissue was used to extract high molecular weight DNA (> 50 kb) for HiFi PacBio long-read sequencing and to construct an Hi-C/Omni-C library for Illumina short-read sequencing. The 29× and 26× genome coverage of HiFi and Illumina reads, respectively, for de novo assembly yielded 2,651 contigs (9.1 Gbp, N50 contig size 12.0 Mbp). Hi-C analysis mapped 97% of the nucleotides on 11 chromosomes. The assembly was verified through comparison with a consensus linkage map comprising 7,781 markers. BUSCO analysis identified ∼ 91% conserved genes. Conclusions Annotations of genes and comparisons of repeat elements with other Cupressaceae and Pinaceae species provide a fundamental resource for conifer research.

An inexpensive single-arm robot is widely utilized for recent laboratory automation solutions. The integration of a single-arm robot as a transfer system into a semi-automatic liquid dispenser without a transfer system can be realized as an inexpensive alternative to a fully automated liquid handling system. However, there has been no quantitative investigation of the positional accuracy of robot arms required to transfer microplates. In this study, we constructed a platform comprising aluminum frames and digital gauges to facilitate such measurements. We measured the position repeatability of a robot arm equipped with a custom-made finger by repeatedly transferring microplates. Further, the acceptable misalignment of plate transfer was evaluated by adding an artificial offset to the microplate position using this platform. The results of these experiments are expected to serve as benchmarks for the selection of robot arms for laboratory automation in biology. Furthermore, all information for replicating this device will be made publicly available, thereby allowing many researchers to collaborate and accumulate knowledge, hopefully contributing to advances in this field.

Abstract Neurofibromatosis type 1 (NF1) is an autosomal dominant nevus disease characterized by multiple manifestations, primarily café-au-lait macules and neurofibromas. Here, we present the case of an NF1 patient with 47,XYY mosaicism whose diagnosis was prompted by café-au-lait macules on the skin and mandibular neurofibromas. Targeted next-generation sequencing of the patient’s blood sample revealed a novel frameshift mutation in NF1 (NM_000267.3:c.6832dupA:p.Thr2278Asnfs*8) that is considered a pathogenic variant.

Glycosylation is a topic of intense current interest in the development of biopharmaceuticals because it is related to drug safety and efficacy. This work describes results of an interlaboratory study on the glycosylation of the Primary Sample (PS) of NISTmAb, a monoclonal antibody reference material. Seventy-six laboratories from industry, university, research, government, and hospital sectors in Europe, North America, Asia, and Australia submitted a total of 103 reports on glycan distributions. The principal objective of this study was to report and compare results for the full range of analytical methods presently used in the glycosylation analysis of mAbs. Therefore, participation was unrestricted, with laboratories choosing their own measurement techniques. Protein glycosylation was determined in various ways, including at the level of intact mAb, protein fragments, glycopeptides, or released glycans, using a wide variety of methods for derivatization, separation, identification, and quantification. Consequently, the diversity of results was enormous, with the number of glycan compositions identified by each laboratory ranging from 4 to 48. In total, one hundred sixteen glycan compositions were reported, of which 57 compositions could be assigned consensus abundance values. These consensus medians provide community-derived values for NISTmAb PS. Agreement with the consensus medians did not depend on the specific method or laboratory type. The study provides a view of the current state-of-the-art for biologic glycosylation measurement and suggests a clear need for harmonization of glycosylation analysis methods.

Osteoblastoma is a benign bone tumor with predominance in those < 20 years of age and rarely occurs in the maxillofacial region. The identification of FOS gene rearrangements in osteoblastomas has been reported, however, a small subset of osteoblastomas do not show FOS gene rearrangements. There are no reports discussing the relationship between age and FOS gene rearrangement in osteoblastomas. We report the case of a 66-year-old female patient with histological features of osteoblastoma in the mandible without FOS gene rearrangement. According to a review of previously reported cases of osteoblastoma, FOS gene rearrangement is significantly less common in patients > 40 years of age (P = 0.041). Osteoblastomas occurring in older adult patients may exhibit pathogeneses different from those of young patients. Further data, including the relationship between age and FOS gene rearrangement, is necessary to clarify the pathogenesis of osteoblastoma. [ABSTRACT FROM AUTHOR]

Wetlands are the largest global natural methane (CH4/ source, and emissions between 50 and 70° N latitude contribute 10-30% to this source. Predictive capability of land models for northern wetland CH4 emissions is still low due to limited site measurements, strong spatial and temporal variability in emissions, and complex hydrological and biogeochemical dynamics. To explore this issue, we compare wetland CH4 emission predictions from the Community Land Model 4.5 (CLM4.5-BGC) with siteto regional-scale observations. A comparison of the CH4 fluxes with eddy flux data highlighted needed changes to the model's estimate of aerenchyma area, which we implemented and tested. The model modification substantially reduced biases in CH4 emissions when compared with CarbonTracker CH4 predictions. CLM4.5 CH4 emission predictions agree well with growing season (May-September) CarbonTracker Alaskan regional-level CH4 predictions and sitelevel observations. However, CLM4.5 underestimated CH4 emissions in the cold season (October-April). The monthly atmospheric CH4 mole fraction enhancements due to wetland emissions are also assessed using the Weather Research and Forecasting-Stochastic Time-Inverted Lagrangian Transport (WRF-STILT) model coupled with daily emissions from CLM4.5 and compared with aircraft CH4 mole fraction measurements from the Carbon in Arctic Reservoirs Vulnerability Experiment (CARVE) campaign. Both the tower and aircraft analyses confirm the underestimate of cold-season CH4 emissions by CLM4.5. The greatest uncertainties in predicting the seasonal CH4 cycle are from the wetland extent, coldseason CH4 production and CH4 transport processes. We recommend more cold-season experimental studies in highlatitude systems, which could improve the understanding and parameterization of ecosystem structure and function during this period. Predicted CH4 emissions remain uncertain, but we show here that benchmarking against observations across spatial scales can inform model structural and parameter improvements.

The transcription factor tumour protein 63, encoded by the TP63 gene, is a regulator of epidermal development. Heterozygous mutations in TP63 cause a variety of human ectodermal dysplasia disorders, including ankyloblepharon-ectodermal defects-cleft lip/palate syndrome, ectrodactyly, ectodermal dysplasia, cleft lip/palate syndrome, split hand/foot malformation 4, Rapp-Hodgkin syndrome, limb mammary syndrome, and acro-dermato-ungual-lacrimal-tooth syndrome. There are genotype-phenotype correlations in some of these syndromes, and the number of cases with overlapping symptoms has been increasing. The phenotypic spectrum and expressivity of TP63 mutation-associated syndromes complicate its clinical diagnosis and classification. Here, we present an updated review of TP63 mutation mapping information, together with a comprehensive overview of TP63 mutation-associated syndromes. We show that several cases with the same mutation have been previously diagnosed with different syndromes. This study will be useful for the diagnosis and classification of TP63 mutation-associated syndromes.

Many nuclear power plants in Japan are approaching the end of their planned operational life spans. They must be decommissioned safely in the near future. Using augmented reality (AR), workers can intuitively understand information related to decommissioning work. Three-dimensional (work-site) reconstruction models of dismantling fields are useful for workers to observe the conditions of dismantling field situations without visiting the actual fields. This study, based on AR and work-site reconstruction models, developed and evaluated an information reference system. The evaluation consists of questionnaires and interview surveys administered to six nuclear power plant workers who used this system, along with a scenario. Results highlight the possibility of reducing time and mitigating mistakes in dismantling fields. Results also show the ease of referring to information in dismantling fields. Nevertheless, it is apparently difficult for workers to build reconstruction models of dismantling fields independently. Keywords: Annotation, Augmented Reality, Decommissioning Work Support, Planning

Emergency drills and drills against terrorism have been held at nuclear facilities. Shortcomings of these drills are that the numbers of emergency scenarios and roles are limited because many workers must participate in them simultaneously. The times during which all employees can participate simultaneously are limited. As a means of solving these problems, augmented reality (AR) training has been increasingly adopted in recent years, but difficulties of creating contents and the inadequate degrees of freedom in the created contents are becoming problematic. For this study, we developed an AR training environment construction system for users to create scenarios easily by simply assembling and placing blocks representing scenario components in a real-world environment. To realize the construction system, we also developed the "Program Block," which enables users to create scenarios in a puzzle-like style. The system can create and simulate various scenarios involving interaction between trainees and a real-world environment. To evaluate the ease of system usage and flexibility for scenario creation, a subjective experiment was conducted at a nuclear facility. Results indicate that users can construct an AR training environment easily. [ABSTRACT FROM AUTHOR]