QuISP: a Quantum Internet Simulation Package

We present an event-driven simulation package called QuISP for large-scale quantum networks built on top of the OMNeT++ discrete event simulation framework. Although the behavior of quantum networking devices have been revealed by recent research, it is still an open question how they will work in networks of a practical size. QuISP is designed to simulate large-scale quantum networks to investigate their behavior under realistic, noisy and heterogeneous configurations. The protocol architecture we propose enables studies of different choices for error management and other key decisions. Our confidence in the simulator is supported by comparing its output to analytic results for a small network. A key reason for simulation is to look for emergent behavior when large numbers of individually characterized devices are combined. QuISP can handle thousands of qubits in dozens of nodes on a laptop computer, preparing for full Quantum Internet simulation. This simulator promotes the development of protocols for larger and more complex quantum networks.Comment: 17 pages, 12 figure

Domesticating Vigna stipulacea: Chromosome-Level genome assembly reveals VsPSAT1 as a candidate gene decreasing hard-seededness

To increase food production under the challenges presented by global climate change, the concept of de novo domestication—utilizing stress-tolerant wild species as new crops—has recently gained considerable attention. We had previously identified mutants with desired domestication traits in a mutagenized population of the legume Vigna stipulacea Kuntze (minni payaru) as a pilot for de novo domestication. Given that there are multiple stress-tolerant wild legume species, it is important to establish efficient domestication processes using reverse genetics and identify the genes responsible for domestication traits. In this study, we identified VsPSAT1 as the candidate gene responsible for decreased hard-seededness, using a Vigna stipulacea isi2 mutant that takes up water from the lens groove. Scanning electron microscopy and computed tomography revealed that the isi2 mutant has lesser honeycomb-like wax sealing the lens groove than the wild-type, and takes up water from the lens groove. We also identified the pleiotropic effects of the isi2 mutant: accelerating leaf senescence, increasing seed size, and decreasing numbers of seeds per pod. While doing so, we produced a V. stipulacea whole-genome assembly of 441 Mbp in 11 chromosomes and 30,963 annotated protein-coding sequences. This study highlights the importance of wild legumes, especially those of the genus Vigna with pre-existing tolerance to biotic and abiotic stresses, for global food security during climate change

Rice immediately adapts the dynamics of photosynthates translocation to roots in response to changes in soil water environment

Rice is susceptible to abiotic stresses such as drought stress. To enhance drought resistance, elucidating the mechanisms by which rice plants adapt to intermittent drought stress that may occur in the field is an important requirement. Roots are directly exposed to changes in the soil water condition, and their responses to these environmental changes are driven by photosynthates. To visualize the distribution of photosynthates in the root system of rice plants under drought stress and recovery from drought stress, we combined X-ray computed tomography (CT) with open type positron emission tomography (OpenPET) and positron-emitting tracer imaging system (PETIS) with 11C tracer. The short half-life of 11C (20.39 min) allowed us to perform multiple experiments using the same plant, and thus photosynthate translocation was visualized as the same plant was subjected to drought stress and then re-irrigation for recovery. The results revealed that when soil is drier, 11C-photosynthates mainly translocated to the seminal roots, likely to promote elongation of the root with the aim of accessing water stored in the lower soil layers. The photosynthates translocation to seminal roots immediately stopped after rewatering then increased significantly in crown roots. We suggest that when rice plant experiencing drought is re-irrigated from the bottom of pot, the destination of 11C-photosynthates translocation immediately switches from seminal root to crown roots. We reveal that rice roots are responsive to changes in soil water conditions and that rice plants differentially adapts the dynamics of photosynthates translocation to crown roots and seminal roots depending on soil conditions

イネトランスポゾンPingの胚発生特異的な発現がMITE mPingの増殖を促進する

京都大学0048新制・課程博士博士(農学)甲第18526号農博第2083号新制||農||1026(附属図書館)学位論文||H26||N4870(農学部図書室)31412京都大学大学院農学研究科農学専攻(主査)教授 奥本 裕, 教授 米森 敬三, 教授 冨永 達学位規則第4条第1項該当Doctor of Agricultural ScienceKyoto UniversityDFA

Early embryogenesis-specific expression of the rice transposon Ping enhances amplification of the MITE mPing.

Miniature inverted-repeat transposable elements (MITEs) are numerically predominant transposable elements in the rice genome, and their activities have influenced the evolution of genes. Very little is known about how MITEs can rapidly amplify to thousands in the genome. The rice MITE mPing is quiescent in most cultivars under natural growth conditions, although it is activated by various stresses, such as tissue culture, gamma-ray irradiation, and high hydrostatic pressure. Exceptionally in the temperate japonica rice strain EG4 (cultivar Gimbozu), mPing has reached over 1000 copies in the genome, and is amplifying owing to its active transposition even under natural growth conditions. Being the only active MITE, mPing in EG4 is an appropriate material to study how MITEs amplify in the genome. Here, we provide important findings regarding the transposition and amplification of mPing in EG4. Transposon display of mPing using various tissues of a single EG4 plant revealed that most de novo mPing insertions arise in embryogenesis during the period from 3 to 5 days after pollination (DAP), and a large majority of these insertions are transmissible to the next generation. Locus-specific PCR showed that mPing excisions and insertions arose at the same time (3 to 5 DAP). Moreover, expression analysis and in situ hybridization analysis revealed that Ping, an autonomous partner for mPing, was markedly up-regulated in the 3 DAP embryo of EG4, whereas such up-regulation of Ping was not observed in the mPing-inactive cultivar Nipponbare. These results demonstrate that the early embryogenesis-specific expression of Ping is responsible for the successful amplification of mPing in EG4. This study helps not only to elucidate the whole mechanism of mPing amplification but also to further understand the contribution of MITEs to genome evolution

SNP in the first intronic region of <i>Ping</i>-ORF1.

<p>(A) Determination of the SNP sequence in the first intronic region of <i>Ping</i>-ORF1. The arrowhead indicates the position of the SNP. The number indicates the position of the <i>Ping</i> element. <i>Ping</i> harboring +1261C SNP and +1261T are named ‘C-type’ and ‘T-type’ <i>Ping</i>, respectively. (B) Box plots of <i>mPing</i> copy number in AG lines. The top and bottom of the boxes mark the first and third quartiles, respectively. The center line represents the median, and the whiskers show the range of observed values within 1.5 times the interquartile range from the hinges. Values beyond 1.5 times the interquartile range from the nearest hinge are marked by open circles. ‘No <i>Ping</i>’, ‘C-type <i>Ping</i>,’ and ‘T-type <i>Ping</i>’ indicate the groups having no <i>Ping</i>, C-type <i>Ping</i>, and T-type <i>Ping</i>, respectively. Expression of (C) <i>Ping</i>-ORF1 and (D) <i>Ping</i>-ORF2 during embryogenesis in <i>mPing</i>-active strains (A119 and A123) and <i>mPing</i>-inactive strains (A105 and G190). The results are presented as means of three biological replicates. Bars indicate SE. The ratio of (E) <i>Ping</i>-ORF1 and (F) -ORF2 expression level of A105, A119, A123, and G190 to that of Nipponbare. The means in (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004396#pgen-1004396-g003" target="_blank">Fig. 3C</a>) and (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004396#pgen-1004396-g003" target="_blank">Fig. 3D</a>) were used for calculation.</p

Transposition of <i>mPing</i> in reciprocal crosses between EG4 and Nipponbare.

<p>(A) Transposon display (TD) for <i>mPing</i> of the F₁ population from reciprocal crosses between EG4 and Nipponbare. One of the results of TD analysis using two selective bases is shown. The cross combinations are indicated at the top of the profiles, respectively. G and F indicate parental EG4 and the F₁ plants, respectively. White and black arrowheads indicate the bands representing the <i>de novo mPing</i> insertion and the band derived from Nipponbare genome, respectively. (B) Mean numbers of <i>de novo mPing</i> insertions in a single F₁ plant and in a self-pollinated plant. The cross combinations are indicated at the bottom of the profile. All 16 possible primer combinations were analyzed, and mean values were calculated using 16 individuals (n = 16). Bars indicate SE.</p

Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice

Abstract Root system architecture plays a crucial role in nutrient and water absorption during rice production. Genetic improvement of the rice root system requires elucidating its genetic control. Genome-wide association studies (GWASs) have identified genomic regions responsible for rice root phenotypes. However, candidate gene prioritization around the peak region often suffers from low statistical power and resolution. Transcriptomics enables other statistical mappings, such as transcriptome-wide association study (TWAS) and expression GWAS (eGWAS), which improve candidate gene identification by leveraging the natural variation of the expression profiles. To explore the genes responsible for root phenotypes, we conducted GWAS, TWAS, and eGWAS for 12 root phenotypes in 57 rice accessions using 427,751 single nucleotide polymorphisms (SNPs) and the expression profiles of 16,901 genes expressed in the roots. The GWAS identified three significant peaks, of which the most significant peak responsible for seven root phenotypes (crown root length, crown root surface area, number of crown root tips, lateral root length, lateral root surface area, lateral root volume, and number of lateral root tips) was detected at 6,199,732 bp on chromosome 8. In the most significant GWAS peak region, OsENT1 was prioritized as the most plausible candidate gene because its expression profile was strongly negatively correlated with the seven root phenotypes. In addition to OsENT1, OsEXPA31, OsSPL14, OsDEP1, and OsDEC1 were identified as candidate genes responsible for root phenotypes using TWAS. Furthermore, a cis-eGWAS peak SNP was detected for OsDjA6, which showed the eighth strongest association with lateral root volume in the TWAS. The cis-eGWAS peak SNP for OsDjA6 was in strong linkage disequilibrium (LD) with a GWAS peak SNP on the same chromosome for lateral root volume and in perfect LD with another SNP variant in a putative cis-element at the 518 bp upstream of the gene. These candidate genes provide new insights into the molecular breeding of root system architecture