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To analyze cell to cell interaction effects on cell differentiation, we developed a new triple staining method for double in situ hybridization with cell lineage tracing in whole-mount Xenopus embryos. The method provides high color contrast views, and also enabled us to examine inside the embryos. Wild-type embryos whose blastomere(s) had been injected with a cell lineage tracer were cultured, fixed, hemisectioned when necessary, and first served for the double in situ hybridization, with two sequential chromogenic reactions. They were postfixed, and the labeled cells were retraced immunohistochemically. Finally, the pigment of the embryos was bleached to obtain a clear view. We applied this method to a blastomere transplantation experiment to examine whether the spatial gene expression patterns along the anteroposterior axis can be induced by cell to cell interactions. The presumptive organizer of a 32-cell embryo was replaced by the labeled presumptive epidermis of another synchronous embryo. The resultant triple-stained late gastrula showed quite similar anteroposterior expression patterns of gsc and Xbra to those of a normal embryo in the axial mesoderm derived from the transplanted presumptive epidermis, indicating that cell to cell interactions had induced these patterns. [ABSTRACT FROM AUTHOR]

We developed the RHiNET-2/SW high-speed network switch for a high-throughput parallel computing system consisting of optically interconnected distributed personal computers (PCs). RHiNET-2/SW enables high-throughput network switching (64 Gbit/s) by means of a switching LSI and eight pairs of synchronized parallel optical interconnection modules. To confirm the reliability of RHiNET-2/SW, we measured its bit error rate (BER), which was less than 10-11 (estimated value: 10-20). Five RHiNET-2/SWs and sixteen PC nodes can perform parallel computing. This result demonstrates the feasibility of optical interconnection in a high-speed, flexible network in a parallel computing system. © 2002 Wiley Periodicals, Inc. Electron Comm Jpn Pt 2, 85(6): 1–10, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecjb.10022 [ABSTRACT FROM AUTHOR]

Spinach (Spinacia oleracea L.) is a dioecious plant with male heterogametic sex determination and homomorphic sex chromosomes (XY). The dioecism is utilized for producing commercial hybrid seeds, and hence understanding the molecular-genetic basis of the species’ sex determining locus is an important issue for spinach breeding. In this study, seven dominant DNA markers were shown to completely co-segregate with the male-determining gene in segregating spinach populations comprising > 1500 plants. In addition, these seven dominant DNA markers were completely associated with the male-determining gene in over 100 spinach germplasm accessions and cultivars. These observations suggest that, in spinach, a Y-chromosomal region around the male-determining locus does not (or almost not) recombine with a counterpart region on the X chromosome. Using five of the seven DNA markers, five bacterial artificial chromosome (BAC) clone contigs with a total length of approximately 690 kbp were constructed. Full sequencing of six representative BAC clones (total insert length 504 kbp) from the five contigs and a transcriptome analysis by RNA-seq revealed that the Y-chromosomal region around the male-determining locus contains large amounts of repetitive elements, suggesting that the region might be poor in gene content. Most of the repeats found in this region are novel Ty1-copia-like and its derivative elements that accumulate predominantly in heterochromatic regions. Our findings may provide valuable insight into spinach genome structure and clues for future research into the evolution of the sex determining locus.Spinach (Spinacia oleracea L.) is a dioecious plant with male heterogametic sex determination and homomorphic sex chromosomes (XY). The dioecism is utilized for producing commercial hybrid seeds, and hence understanding the molecular-genetic basis of the species’ sex determining locus is an important issue for spinach breeding. In this study, seven dominant DNA markers were shown to completely co-segregate with the male-determining gene in segregating spinach populations comprising > 1500 plants. In addition, these seven dominant DNA markers were completely associated with the male-determining gene in over 100 spinach germplasm accessions and cultivars. These observations suggest that, in spinach, a Y-chromosomal region around the male-determining locus does not (or almost not) recombine with a counterpart region on the X chromosome. Using five of the seven DNA markers, five bacterial artificial chromosome (BAC) clone contigs with a total length of approximately 690 kbp were constructed. Full sequencing of six representative BAC clones (total insert length 504 kbp) from the five contigs and a transcriptome analysis by RNA-seq revealed that the Y-chromosomal region around the male-determining locus contains large amounts of repetitive elements, suggesting that the region might be poor in gene content. Most of the repeats found in this region are novel Ty1-copia-like and its derivative elements that accumulate predominantly in heterochromatic regions. Our findings may provide valuable insight into spinach genome structure and clues for future research into the evolution of the sex determining locus.Spinach (Spinacia oleracea L.) is a dioecious plant with male heterogametic sex determination and homomorphic sex chromosomes (XY). The dioecism is utilized for producing commercial hybrid seeds, and hence understanding the molecular-genetic basis of the species’ sex determining locus is an important issue for spinach breeding. In this study, seven dominant DNA markers were shown to completely co-segregate with the male-determining gene in segregating spinach populations comprising > 1500 plants. In addition, these seven dominant DNA markers were completely associated with the male-determining gene in over 100 spinach germplasm accessions and cultivars. These observations suggest that, in spinach, a Y-chromosomal region around the male-determining locus does not (or almost not) recombine with a counterpart region on the X chromosome. Using five of the seven DNA markers, five bacterial artificial chromosome (BAC) clone contigs with a total length of approximately 690 kbp were constructed. Full sequencing of six representative BAC clones (total insert length 504 kbp) from the five contigs and a transcriptome analysis by RNA-seq revealed that the Y-chromosomal region around the male-determining locus contains large amounts of repetitive elements, suggesting that the region might be poor in gene content. Most of the repeats found in this region are novel Ty1-copia-like and its derivative elements that accumulate predominantly in heterochromatic regions. Our findings may provide valuable insight into spinach genome structure and clues for future research into the evolution of the sex determining locus. [ABSTRACT FROM AUTHOR]

Programmable networks are a substantial part of current R&D on future internet (FI) in Europe and worldwide, with considerable impact generated by large-scale test bed infrastructures. In such test beds, researchers validate proof-of-concept prototypes for new algorithms and mechanisms for efficiently controlling and managing network resources. One of the key domains for FI research is software-defined networking (SDN), which creates innovations in existing Internet architectures by shifting the control and logic outside the network equipment to Data Centres. International cooperation among leading research centres in Europe, Americas and Asia is key to validate SDN foundations and tools. EU and Japan have jointly funded the FELIX project (federated test-beds for large-scale infrastructure experiments), which defines a common control and orchestration framework to manage federated FI test beds across continents. This framework enables an experimenter to (i) request and obtain resources across different test bed infrastructures dynamically; (ii) manage and control the network paths connecting the federated SDN test beds; (iii) monitor the underlying resources and (iv) use distributed applications executed on the federated infrastructures. This paper describes the high-level architecture of the FELIX framework and details six use cases that will be employed for validation. We present our analysis and end-user considerations, highlighting the necessity for resource accessibility and coherent use of physical connections over a large-scale test bed where different control technologies such as OpenFlow and the network service interface (NSI) are simultaneously used. [ABSTRACT FROM AUTHOR]

Ethernet has been used for connecting hosts in PC clusters, besides its use in local area networks. Although a layer-2 Ethernet topology is limited to a tree structure because of the need to avoid broadcast storms and deadlocks of frames, various deadlock-free routing algorithms on topologies that include loops suitable for parallel processing can be employed by the application of IEEE 802.1Q VLAN technology. However, the MPI communication libraries used in current PC clusters do not always support tagged VLAN technology; therefore, at present, the design of VLAN-based Ethernet cannot be applied to such PC clusters. In this study, we propose a switch-tagged routing methodology in order to implement various deadlock-free routing algorithms on such PC clusters by using at most the same number of VLANs as the degree of a switch. Since the MPI communication libraries do not need to perform VLAN operations, the proposed methodology has advantages in both simple host configuration and high portability. In addition, when it is used with on/off and multispeed link regulation, the power consumption of Ethernet switches can be reduced. Evaluation results using NAS parallel benchmarks showed that the performance of the topologies that include loops using the proposed methodology was comparable to that of an ideal one-switch (full crossbar) network, and the torus topology in particular had up to a 27 percent performance improvement compared with a tree topology with link aggregation. [ABSTRACT FROM AUTHOR]

In this paper, ‘Martini,’ a network interface controller chip for our original network called RHiNET, is described. Martini is designed to provide high-bandwidth and low-latency communication with a small overhead. To obtain high-performance communication, protected user-level zero-copy remote direct memory access (RDMA) communication functions are completely implemented by a hardwired logic. Also, to reduce the communication latency efficiently, we have proposed programmed I/O (PIO)-based communication mechanisms called ‘On the fly (OTF)‘ and have implemented them on Martini. The evaluation results show that Martini connected to a 64-bit/66-MHz peripheral component interconnect (PCI) bus achieves a 470-Mbyte maximum bidirectional bandwidth and a 1.74-μsec minimum latency on host-to-host memory copying. [ABSTRACT FROM AUTHOR]