Genome Analysis Revives a Forgotten Hybrid Crop Edo-dokoro in the Genus Dioscorea

忘れられた作物「えどどころ」の起原 --ゲノム解析が明らかにする青森県三八上北地域に残る栽培イモの歴史--. 京都大学プレスリリース. 2022-08-10.A rhizomatous Dioscorea crop “Edo-dokoro” was described in old records of Japan, but its botanical identify has not been characterized. We found that Edo-dokoro is still produced by four farmers in Tohoku-machi of Aomori Prefecture, Japan. Rhizomes of Edo-dokoro are a delicacy to the local people and are sold in the markets. Morphological characters of Edo-dokoro suggest its hybrid origin between the two species, D. tokoro and D. tenuipes. Genome analysis revealed that Edo-dokoro is likely originated by hybridization of a male D. tokoro to a female D. tenuipes, followed by a backcross with a male plant of D. tokoro. Edo-dokoro is a typical minor crop possibly maintained for more than 300 years but now almost forgotten from the public. We hypothesize that there are many such uncharacterized genetic heritages passed over generations by small scale farmers that await serious scientific investigation for future use and improvement by using modern genomics information

エンタメ小説における会話文の発話意図分析―発話文表現文型辞書の改良に向けて―

Nagoya UniversityNagoya University会議名: 言語資源ワークショップ2022, 開催地: オンライン, 会期: 2022年8月30日-31日, 主催: 国立国語研究所 言語資源開発センター小説の会話文を生成するためのツールとして『発話文表現文型辞書』を編纂し改訂を重ねている。本辞書は、「発話意図」と「表現文型」と「話し方の特徴」で構成されており、「発話意図」の項目の抜本的な見直しが目下の課題である。本研究では、エンタメ小説の会話文を発話意図分析することによって、現在の辞書の発話意図（60種）で対応できない発話文はどれか、追加すべき発話意図は何か、どのような発話意図のラベルや体系を採用すれば、小説発話文生成時に使いやすいかなどを検討する

発話文表現文型辞書の設計と編纂

Nagoya UniversityNagoya University会議名: 言語資源活用ワークショップ2019, 開催地: 国立国語研究所, 会期: 2019年9月2日−4日, 主催: 国立国語研究所 コーパス開発センター旧版の『日本語表現文型辞書』を改訂した、『発話文表現文型辞書』について報告する。旧版では、小説の発話文を生成する際に、「ある目的で発話する時、ある話し方をする人物は、この表現文型を使う」という情報を提供することを目標に、発話意図・話し方の特徴ベクトル・表現文型という3種類の情報から成る辞書のしくみを定めた。しかしながら、日本語の発話文では、話し相手との関係に応じて様々な表現文型が使い分けられる。そのため、新版では、話し方の特徴ベクトルを見直し、敬意の有無・距離・場面差・品格などを表す、待遇表現に関する要素を増強した。さらに、実際の発話文では、同じ人物が状況や感情に応じて様々な表現文型を用いるため、辞書作成の目標を、「ある目的で発話する時、ある話し方で表すならば、この表現文型を使う」という情報の提供に変更した。辞書のサイズは、発話意図が68項目（旧版50）、話し方の特徴ベクトルは20次元（旧版8）、表現文型エントリが1,099（旧版675）である

High-performance pipeline for MutMap and QTL-seq

[Summary] Bulked segregant analysis implemented in MutMap and QTL-seq is a powerful and efficient method to identify loci contributing to important phenotypic traits. However, the previous pipelines were not user-friendly to install and run. Here, we describe new pipelines for MutMap and QTL-seq. These updated pipelines are approximately 5–8 times faster than the previous pipeline, are easier for novice users to use, and can be easily installed through bioconda with all dependencies. [Availability] The new pipelines of MutMap and QTL-seq are written in Python and can be installed via bioconda. The source code and manuals are available online (MutMap: https://github.com/YuSugihara/MutMap, QTL-seq: https://github.com/YuSugihara/QTL-seq)

発話文自動生成のための日本語表現文型辞書の作成

会議名: 言語資源活用ワークショップ2016, 開催地: 国立国語研究所, 会期: 2017年3月7日-8日, 主催: 国立国語研究所 コーパス開発センター発話文の自動生成の実現基盤となる日本語表現文型辞書を作成した。この辞書は，依頼や勧誘といった発話の目的（発話意図）に対して，それを伝達する際に使用する複数の言語形式（表現文型）を整理したもので，現在，50 の発話意図に対して，のべ675 件の表現文型が収録されている。たとえば，発話意図【依頼-実行】には，表現文型「V-てくださらない？」，「V-てくれんか？」，「お願い，V-て」などの31 種類の表現文型が収録されている。この辞書の特徴は，それぞれの表現文型に，話し方の特徴を表す情報が付与されている点にある。たとえば，「V-てくださらない？」には，「女性的-2，大人っぽい-1，婉曲的-2，丁寧-1」という情報が付与されている。これらの情報を利用することにより，話者の特徴に応じた表現文型の選択が可能となる

How many times can patients tolerate reoperation?

The frequency of resection for the recurrence of colorectal cancer has not been investigated in previous studies. Likewise, the related postoperative complications and the limit for indicating surgical resection has not been reported. Herein, we reported the complications of a highly frequent surgical approach for rectal cancer recurrence, i.e., exceeding three reoperations, based on our clinical experience. We included 15 cases exceeding two operations for the local recurrence of colorectal cancer from 2014 to 2019. We examined the postoperative complications classified as Clavien–Dindo IIIb. The positive rates of the complications were 0 (0.0%), 0 (0.0%), 2 (13.3%), 3 (37.5%), and 0 (0.0%) for the primary, 1st recurrent, 2nd recurrent, 3rd recurrent, and 4th recurrent operation group (p = 0.027), respectively. It is important to exercise caution in handling cases exceeding two reoperations (exceeding three reoperations including the primary operation)

Identification of candidate flowering and sex genes in white Guinea yam (D. rotundata Poir.) by SuperSAGE transcriptome profiling

Open Access JournalDioecy (distinct male and female individuals) combined with scarce to non-flowering are common features of cultivated yam (Dioscorea spp.). However, the molecular mechanisms underlying flowering and sex determination in Dioscorea are unknown. We conducted SuperSAGE transcriptome profiling of male, female and monoecious individuals to identify flowering and sex-related genes in white Guinea yam (D. rotundata). SuperSAGE analysis generated a total of 20,236 unique tags, of which 13,901 were represented by a minimum of 10 tags. Of these, 88 tags were significantly differentially expressed in male, female and monoecious plants. Of the 88 differentially expressed SuperSAGE tags, 18 corresponded to genes previously implicated in flower development and sex determination in multiple plant species. We validated the SuperSAGE data with quantitative real-time PCR (qRT-PCR)-based analysis of the expression of four candidate genes. Our findings suggest that mechanisms of flowering and sex determination are likely conserved in Dioscorea. We further investigated the flowering patterns of 1938 D. rotundata accessions representing diverse geographical origins over two years, revealing that over 85% of the accessions are either male or non-flowering, and that less than 15% are female, while monoecious plants are rare. Intensity of flowering appeared to be a function of sex, with male plants flowering more abundantly than female ones. Candidate genes identified in this study can be targeted with the aim to induce regular flowering in poor to non-flowering cultivars. Findings of the study provide important inputs for further studies aiming to overcome the challenge of flowering in yams and to improve the efficiency of yam breeding

Genome analyses reveal the hybrid origin of the staple crop white Guinea yam (Dioscorea rotundata)

西アフリカの主食作物ギニアヤムの起源を解明 --ギニアヤムはサバンナと熱帯雨林に生育する野生種の雑種起源--. 京都大学プレスリリース. 2020-12-11.White Guinea yam (Dioscorea rotundata) is an important staple tuber crop in West Africa. However, its origin remains unclear. In this study, we resequenced 336 accessions of white Guinea yam and compared them with the sequences of wild Dioscorea species using an improved reference genome sequence of D. rotundata. In contrast to a previous study suggesting that D. rotundata originated from a subgroup of Dioscorea praehensilis, our results suggest a hybrid origin of white Guinea yam from crosses between the wild rainforest species D. praehensilis and the savannah-adapted species Dioscorea abyssinica. We identified a greater genomic contribution from D. abyssinica in the sex chromosome of Guinea yam and extensive introgression around the SWEETIE gene. Our findings point to a complex domestication scenario for Guinea yam and highlight the importance of wild species as gene donors for improving this crop through molecular breeding

Detection of Transgenes in Gene Delivery Model Mice by Adenoviral Vector Using ddPCR

With the rapid progress of genetic engineering and gene therapy, the World Anti-Doping Agency has been alerted to gene doping and prohibited its use in sports. However, there is no standard method available yet for the detection of transgenes delivered by recombinant adenoviral (rAdV) vectors. Here, we aim to develop a detection method for transgenes delivered by rAdV vectors in a mouse model that mimics gene doping. These rAdV vectors containing the mCherry gene was delivered in mice through intravenous injection or local muscular injection. After five days, stool and whole blood samples were collected, and total DNA was extracted. As additional experiments, whole blood was also collected from the mouse tail tip until 15 days from injection of the rAdv vector. Transgene fragments from different DNA samples were analyzed using semi-quantitative PCR (sqPCR), quantitative PCR (qPCR), and droplet digital PCR (ddPCR). In the results, transgene fragments could be directly detected from blood cell fraction DNA, plasma cell-free DNA, and stool DNA by qPCR and ddPCR, depending on specimen type and injection methods. We observed that a combination of blood cell fraction DNA and ddPCR was more sensitive than other combinations used in this model. These results could accelerate the development of detection methods for gene doping