Genomic regions, cellular components and gene regulatory basis underlying pod length variations in cowpea (V. unguiculata L. Walp).

Cowpea (V. unguiculata L. Walp) is a climate resilient legume crop important for food security. Cultivated cowpea (V. unguiculata L) generally comprises the bushy, short-podded grain cowpea dominant in Africa and the climbing, long-podded vegetable cowpea popular in Asia. How selection has contributed to the diversification of the two types of cowpea remains largely unknown. In the current study, a novel genotyping assay for over 50 000 SNPs was employed to delineate genomic regions governing pod length. Major, minor and epistatic QTLs were identified through QTL mapping. Seventy-two SNPs associated with pod length were detected by genome-wide association studies (GWAS). Population stratification analysis revealed subdivision among a cowpea germplasm collection consisting of 299 accessions, which is consistent with pod length groups. Genomic scan for selective signals suggested that domestication of vegetable cowpea was accompanied by selection of multiple traits including pod length, while the further improvement process was featured by selection of pod length primarily. Pod growth kinetics assay demonstrated that more durable cell proliferation rather than cell elongation or enlargement was the main reason for longer pods. Transcriptomic analysis suggested the involvement of sugar, gibberellin and nutritional signalling in regulation of pod length. This study establishes the basis for map-based cloning of pod length genes in cowpea and for marker-assisted selection of this trait in breeding programmes

Optimization of CNOT circuits on topological superconducting processors

We focus on optimization of the depth/size of CNOT circuits under topological connectivity constraints. We prove that any $n$-qubit CNOT circuit can be paralleled to $O(n)$ depth with $n^2$ ancillas for $2$-dimensional grid structure. For the high dimensional grid topological structure in which every quibit connects to $2\log n$ other qubits, we achieves the asymptotically optimal depth $O(\log n)$ with only $n^2$ ancillas. We also consider the synthesis without ancillas. We propose an algorithm uses at most $2n^2$ CNOT gates for arbitrary connected graph, considerably better than previous works. Experiments also confirmed the performance of our algorithm. We also designed an algorithm for dense graph, which is asymptotically optimal for regular graph. All these results can be applied to stabilizer circuits

VHF data transmission experiments using MBC equipment conducted during the period from JARE-43 to JARE-45

In order to study the ability of meteor burst communications (MBC) as a new medium of data collection networks in Antarctica, we have performed a series of VHF data transmission experiments. In the experiment during the period of JARE-43 (the 43rd Japanese Antarctic Research Expedition), a remote station at Zhongshan Station sent data packets to a master station at Syowa Station using a commercial MBC system. Together with meteor burst propagations, non-meteoric propagations were frequently observed during local nighttime. We found that they worked effectively for packet transmissions and greatly increased the data throughput. Overall data throughput obtained by this experiment was 0.63bps. In JARE-44, we added another remote station at Dome Fuji Station. Since the transmitted power from the master unit was split into two directions, data throughput from Zhongshan Station was reduced to 0.36bps. That from Dome Fuji Station was only 0.13bps. For the experiment in JARE-45, we replaced the commercial MBC system with a RANDOM (RAdio Network for Data Over Meteor) system developed by the authors. The experiment is being conducted between Syowa and Zhongshan Stations. The estimated data throughput during the period from April 1st, 2004 to August 31st, 2004 was 2.9bps

Genome-wide identification of new reference genes for RT-qPCR normalization in CGMMV-infected Lagenaria siceraria

Lagenaria siceraria is an economically important cucurbitaceous crop, but suitable reference genes (RGs) to use when the plants are infected by cucumber green mottle mosaic virus (CGMMV) have not been determined. Sixteen candidate RGs of both leaf and fruit and 18 candidate RGs mostly from separate RNA-Seq datasets of bottle gourd leaf or fruit were screened and assessed by RT-qPCR. The expression stability of these genes was determined and ranked using geNorm, NormFinder, BestKeeper and RefFinder. Comprehensive analysis resulted in the selection of LsCYP, LsH3, and LsTBP as the optimal RGs for bottle gourd leaves, and LsP4H, LsADP, and LsTBP for fruits. LsWD, LsGAPDH, and LsH3 were optimal for use in both leaves and fruits under the infection of CGMMV. Isopentenyl transferase (IPT) and DNA-directed RNA polymerase (DdRP) were used to validate the applicability of the most stable identified RGs from bottle gourd in response to CGMMV. All the candidate RGs performed in RT-qPCR consistently with the data from the transcriptome database. The results demonstrated that LsWD, LsGAPDH and LsH3 were the most suitable internal RGs for the leaf, and LsH3, LsGAPDH, LsP4H and LsCYP for the fruit

Comparison of osteogenic capability of 3D-printed bioceramic scaffolds and granules with different porosities for clinical translation

Pore parameters, structural stability, and filler morphology of artificial implants are key factors influencing the process of bone tissue repair. However, the extent to which each of these factors contributes to bone formation in the preparation of porous bioceramics is currently unclear, with the two often being coupled. Herein, we prepared magnesium-doped wollastonite (Mg-CSi) scaffolds with 57% and 70% porosity (57-S and 70-S) via a 3D printing technique. Meanwhile, the bioceramic granules (57-G and 70-G) with curved pore topography (IWP) were prepared by physically disrupting the 57-S and 70-S scaffolds, respectively, and compared for in vivo osteogenesis at 4, 10, and 16 weeks. The pore parameters and the mechanical and biodegradable properties of different porous bioceramics were characterized systematically. The four groups of porous scaffolds and granules were then implanted into a rabbit femoral defect model to evaluate the osteogenic behavior in vivo. 2D/3D reconstruction and histological analysis showed that significant bone tissue production was visible in the central zone of porous granule groups at the early stage but bone tissue ingrowth was slower in the porous scaffold groups. The bone tissue regeneration and reconstruction capacity were stronger after 10 weeks, and the porous architecture of the 57-S scaffold was maintained stably at 16 weeks. These experimental results demonstrated that the structure-collapsed porous bioceramic is favorable for early-stage osteoconduction and that the 3D topological scaffolds may provide more structural stability for bone tissue growth for a long-term stage. These findings provide new ideas for the selection of different types of porous bioceramics for clinical bone repair

Partial sequencing of the bottle gourd genome reveals markers useful for phylogenetic analysis and breeding

<p>Abstract</p> <p>Background</p> <p>Bottle gourd [<it>Lagenaria siceraria </it>(Mol.) Standl.] is an important cucurbit crop worldwide. Archaeological research indicates that bottle gourd was domesticated more than 10,000 years ago, making it one of the earliest plants cultivated by man. In spite of its widespread importance and long history of cultivation almost nothing has been known about the genome of this species thus far.</p> <p>Results</p> <p>We report here the partial sequencing of bottle gourd genome using the 454 GS-FLX Titanium sequencing platform. A total of 150,253 sequence reads, which were assembled into 3,994 contigs and 82,522 singletons were generated. The total length of the non-redundant singletons/assemblies is 32 Mb, theoretically covering ~ 10% of the bottle gourd genome. Functional annotation of the sequences revealed a broad range of functional types, covering all the three top-level ontologies. Comparison of the gene sequences between bottle gourd and the model cucurbit cucumber (<it>Cucumis sativus</it>) revealed a 90% sequence similarity on average. Using the sequence information, 4395 microsatellite-containing sequences were identified and 400 SSR markers were developed, of which 94% amplified bands of anticipated sizes. Transferability of these markers to four other cucurbit species showed obvious decline with increasing phylogenetic distance. From analyzing polymorphisms of a subset of 14 SSR markers assayed on 44 representative China bottle gourd varieties/landraces, a principal coordinates (PCo) analysis output and a UPGMA-based dendrogram were constructed. Bottle gourd accessions tended to group by fruit shape rather than geographic origin, although in certain subclades the lines from the same or close origin did tend to cluster.</p> <p>Conclusions</p> <p>This work provides an initial basis for genome characterization, gene isolation and comparative genomics analysis in bottle gourd. The SSR markers developed would facilitate marker assisted breeding schemes for efficient introduction of desired traits.</p

A SNP and SSR Based Genetic Map of Asparagus Bean (Vigna. unguiculata ssp. sesquipedialis) and Comparison with the Broader Species

Asparagus bean (Vigna. unguiculata ssp. sesquipedialis) is a distinctive subspecies of cowpea [Vigna. unguiculata (L.) Walp.] that apparently originated in East Asia and is characterized by extremely long and thin pods and an aggressive climbing growth habit. The crop is widely cultivated throughout Asia for the production of immature pods known as ‘long beans’ or ‘asparagus beans’. While the genome of cowpea ssp. unguiculata has been characterized recently by high-density genetic mapping and partial sequencing, little is known about the genome of asparagus bean. We report here the first genetic map of asparagus bean based on SNP and SSR markers. The current map consists of 375 loci mapped onto 11 linkage groups (LGs), with 191 loci detected by SNP markers and 184 loci by SSR markers. The overall map length is 745 cM, with an average marker distance of 1.98 cM. There are four high marker-density blocks distributed on three LGs and three regions of segregation distortion (SDRs) identified on two other LGs, two of which co-locate in chromosomal regions syntenic to SDRs in soybean. Synteny between asparagus bean and the model legume Lotus. japonica was also established. This work provides the basis for mapping and functional analysis of genes/QTLs of particular interest in asparagus bean, as well as for comparative genomics study of cowpea at the subspecies level

Dual-Level Regulation of ACC Synthase Activity by MPK3/MPK6 Cascade and Its Downstream WRKY Transcription Factor during Ethylene Induction in Arabidopsis

Plants under pathogen attack produce high levels of ethylene, which plays important roles in plant immunity. Previously, we reported the involvement of ACS2 and ACS6, two Type I ACS isoforms, in Botrytis cinerea–induced ethylene biosynthesis and their regulation at the protein stability level by MPK3 and MPK6, two Arabidopsis pathogen-responsive mitogen-activated protein kinases (MAPKs). The residual ethylene induction in the acs2/acs6 double mutant suggests the involvement of additional ACS isoforms. It is also known that a subset of ACS genes, including ACS6, is transcriptionally induced in plants under stress or pathogen attack. However, the importance of ACS gene activation and the regulatory mechanism(s) are not clear. In this report, we demonstrate using genetic analysis that ACS7 and ACS11, two Type III ACS isoforms, and ACS8, a Type II ACS isoform, also contribute to the B. cinerea–induced ethylene production. In addition to post-translational regulation, transcriptional activation of the ACS genes also plays a critical role in sustaining high levels of ethylene induction. Interestingly, MPK3 and MPK6 not only control the stability of ACS2 and ACS6 proteins via direct protein phosphorylation but also regulate the expression of ACS2 and ACS6 genes. WRKY33, another MPK3/MPK6 substrate, is involved in the MPK3/MPK6-induced ACS2/ACS6 gene expression based on genetic analyses. Furthermore, chromatin-immunoprecipitation assay reveals the direct binding of WRKY33 to the W-boxes in the promoters of ACS2 and ACS6 genes in vivo, suggesting that WRKY33 is directly involved in the activation of ACS2 and ACS6 expression downstream of MPK3/MPK6 cascade in response to pathogen invasion. Regulation of ACS activity by MPK3/MPK6 at both transcriptional and protein stability levels plays a key role in determining the kinetics and magnitude of ethylene induction