Constructing a new integrated genetic linkage map and mapping quantitative trait loci for vegetative mycelium growth rate in Lentinula edodes

The most saturated linkage map for Lentinula edodes to date was constructed based on a mono-. karyotic population of 146 single spore isolates (SSIs) using sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), insertion deletion (InDel) markers, and the mating-type loci. Five hundred and twenty-four markers were located on 13 linkage groups (LGs). The map spanned a total length of 1006.1 cM, with an average marker spacing of 2.0 cM. Quantitative trait loci (QTLs) mapping was utilized to uncover the loci regulating and controlling the vegetative mycelium growth rate on various synthetic media, and complex medium for commercial cultivation of L. edodes. Two and 13 putative QTLs, identified respectively in the monokaryotic population and two testcross dikaryotic populations, were mapped on seven different LGs. Several vegetative mycelium growth rate-related QTLs uncovered here were clustered on LG4 (Qmgr1, Qdgr1, Qdgr2 and Qdgr9) and LG6 (Qdgr3, Qdgr4 and Qdgr5), implying the presence of main genomic areas responsible for growth rate regulation and control. The QTL hotspot region on LG4 was found to be in close proximity to:the region containing the mating-type A (MAT-A) locus. Moreover, Qdgr2 on LG4 was detected on different media, contributing 8.07%-23.71% of the phenotypic variation. The present study provides essential information for QTL mapping and marker-assisted selection (MAS) in L. edodes. (C) 2014 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.The most saturated linkage map for Lentinula edodes to date was constructed based on a mono-. karyotic population of 146 single spore isolates (SSIs) using sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), insertion deletion (InDel) markers, and the mating-type loci. Five hundred and twenty-four markers were located on 13 linkage groups (LGs). The map spanned a total length of 1006.1 cM, with an average marker spacing of 2.0 cM. Quantitative trait loci (QTLs) mapping was utilized to uncover the loci regulating and controlling the vegetative mycelium growth rate on various synthetic media, and complex medium for commercial cultivation of L. edodes. Two and 13 putative QTLs, identified respectively in the monokaryotic population and two testcross dikaryotic populations, were mapped on seven different LGs. Several vegetative mycelium growth rate-related QTLs uncovered here were clustered on LG4 (Qmgr1, Qdgr1, Qdgr2 and Qdgr9) and LG6 (Qdgr3, Qdgr4 and Qdgr5), implying the presence of main genomic areas responsible for growth rate regulation and control. The QTL hotspot region on LG4 was found to be in close proximity to:the region containing the mating-type A (MAT-A) locus. Moreover, Qdgr2 on LG4 was detected on different media, contributing 8.07%-23.71% of the phenotypic variation. The present study provides essential information for QTL mapping and marker-assisted selection (MAS) in L. edodes. (C) 2014 The British Mycological Society. Published by Elsevier Ltd. All rights reserved

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Estimating Surface Heat Fluxes Using Temperature and Wetness Information: A Particle Data Assimilation Framework

Surface heat fluxes (latent and sensible heat over the land surface) play a key role in the land-atmosphere interaction, and their spatial pattern as well as temporal evolution are vital to the terrestrial water cycle and surface energy balance. Ideally, we want to have accurate estimates of spatially distributed and temporally continuous fluxes. However, this cannot be achieved through interpolation of point measurements because of the limited number of flux stations and the high heterogeneity of fluxes, nor can this be done using large scale monitoring platforms such as remote sensing, since fluxes lack a unique signature that can be detected by satellites. Given the fact that surface heat fluxes are closely related to the thermal and wetness condition of the land surface, which are available from remote sensing instruments, this PhD research proposes a methodology to improve flux estimates by assimilating land surface temperature (LST) and soil wetness information into a coupled water and heat transfer model. The goal is to acquire accurate flux estimates over a large area using a simple model and a small suite of input data...Water Resource

Structural Control Method Research motivated for MAV Lift Force Modification

Micro Air Vehicle (MAV) is a group of unmanned aerial vehicles that is autonomous and with a size restriction. Thanks to its possible application ranging from civil search-and-rescue missions to military surveillance missions, there is rising interest in the MAV related topics. From the previous work of the Atlanta Project, a vehicle is designed that could generate upward lift force. However, for the agility of the vehicle, the ability of positioning and stabilizing is also required. Therefore, it is demanded there is a way to make the lift force on each wing unbalanced, which is also the aim of this thesis project. In this thesis project, the investigation is focused on what structure modification method is feasible to be applied on the vehicle. At first, different actuators and structural modification methods are analyzed and screened from perspective of effectiveness and weight. A passive stiffness method is nally selected as the best method among all methods, using piezo actuators. The mechanism of this method is that the piezo material's stiffness is different when electrodes of it is under open circuit and short circuit electrical condition. After the theoretical work, a test is done on a canti-lever beam for the verification of effectiveness of this method.Precision and Microsystems EngineeringMechanical, Maritime and Materials Engineerin

Analysis of streaming media systems

Multimedia services have been popping up at tremendous speed in recent years. A large number of these multimedia streaming systems are introduced to the consumer market. Internet Service Providers, Telecommunications Operators, Service/Content Providers, and end users are interested in the mechanisms they use, the Quality-of-Experience they provide (e.g. video/audio quality, audio-video synchronization, communication delay, start-up time, etc.), the resources they need, the system stability, and the service availability. The multimedia streaming systems analyzed in this thesis include IP layer multicast TV (IPTV), Peer-to-Peer TV (P2PTV), Content Delivery Networking (CDN), Peer-to-Peer Video-on-Demand (P2PVoD), Server-to-Client Video Conferencing (IPVC) and Peer-to-Peer Video Conferencing (P2PVC). This thesis aims to study various kinds of popular streaming systems, through analytical models, measurement experiments, and simulations, to reveal their characteristics and performance in different aspects. Based on this research, we can not only better understand the behavior and limitations of existing systems and find out the key parameters that affect their performance, but also investigate the potential problems and predict the system performance for future cases. By comparing the two general streaming content delivery methods (Server-Client and Peer-to-Peer), we gain in-depth insights on “which is better” and “what determines better” for different services and in different scenarios.TelecommunicationsElectrical Engineering, Mathematics and Computer Scienc

A “Transmission Time Reservation” method in a Wireless Lighting Control System

The lighting industry has been comprehensively developed and deployed during recent decades, especially with the rise of LED technology. As a related technique field, lighting control system has also draw more and more attention; therefore intelligent lighting control systems are needed. Nowadays, several famous lighting companies are working on a next generation of lighting control system, which apply not only a distributed network structure but also wireless communication. Rather than controlling by a single node, a distributed system will finish controlling operation in different control units. This guarantees the distributed system to be more robust and efficient. Wireless technology is also essential for a system because it is infeasible to connect distributed devices with cables. Of all the wireless communication standards, the zigbee protocol is regarded as the best solution for a lighting control system. This is because the zigbee protocol has features of low-rate and low-cost, which perfectly fit the features of a sensor network. However, this application also leads to a problem which cannot be ignored, the coexistence problem with other wireless protocols. Because both of the zigbee and other wireless protocols operate in the ISM 2.4 GHz frequency band, the coexistence problem happens. With different modulation and frequency spreading methods, different protocols will not detect each other correctly, for example if there are two different protocol packets being transmitted, a packet collision will happen. This problem is much more serious for the zigbee service, because the interference from wifi devices will be unacceptable for a zigbee transmission. How to solve this coexistence problem between zigbee and wifi devices in an indoor lighting environment is the main research question of this thesis. In this thesis, several solutions for the coexistence problem between zigbee and wifi are proposed and analyzed. With their different advantages and drawbacks, each of these methods has its own application scene. After comparing, the “Transmission Time Reservation” method has been proved to be a feasible solution as to the assumed problem, which has also been tested by simulations. Within this method, a gateway node between the zigbee and wifi network is designed cooperatively. Whenever there is a zigbee request, this node is programmed to do the reservation operation with the wifi AP node. The results of NS3 simulations and comparative tests have also shown that this method is effective to solve the coexistence problem in an indoor environment.Electrical EngineeringTelecommunicationsElectrical Engineering, Mathematics and Computer Scienc

Realistic Online Resource Management for Partially Reconfigurable Systems

In this dissertation, we focus our research on the problems related to efficient configurable resource management for partially reconfigurable systems. FPGA devices are used to build such systems for various application domains with telecommunication and energy efficient high performance computing being two prominent examples. Dynamic management of FPGA hardware resources is an important problem and is the main motivation for this dissertation. Our research starts with investigating an abstract view of configurable resources which represents the essential properties of FPGAs in respect to reconfiguration while leaving out many less important technology details. In this step, a realistic model with adequate complexity is exposed to the configurable resource management algorithms. Next, based on the abstract view, the hardware task's spatial requirements are studied and an efficient online task placement algorithm is proposed. Our placement algorithm dynamically redistributes the reconfigurable resources into blocks with various sizes and outperforms state of the art. In addition, a new model for measuring and analyzing the placement algorithms performance is built. In our next step we take into account also task's temporal requirements and consider holistic online task placement and scheduling. A novel algorithm with support for application specific scheduling heuristics is proposed. In addition, a reuse and partial reuse mechanism is applied to alleviate the single configuration port limitation present in modern systems. After that, a communication model is introduced into the abstract view and the proposed online scheduling algorithm is extended to account the communication paths among data dependent hardware tasks and between tasks and external peripherals. In this step, the complete realistic configurable resource management problem is addressed. Furthermore, mechanisms for hardware reuse and interrupt handling are proposed. The hardware reuse mechanism gives the required hardware support for the reuse and partial reuse mechanisms. The hardware interrupt handling mechanism enables real time applications on reconfigurable systems.Software Computer TechnologyElectrical Engineering, Mathematics and Computer Scienc

Olefin metathesis for effective polymer healing via dynamic exchange of strong carbon-carbon bonds

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Measurement study of multi-party video conferencing

More and more free multi-party video conferencing applications are readily available over the Internet and both Server-to-Client (S/C) or Peer-to-Peer (P2P) technologies are used. Investigating their mechanisms, analyzing their system performance, and measuring their quality are important objectives for researchers, developers and end users. In this paper, we take four representative video conferencing applications and reveal their characteristics and different aspects of Quality of Experience. Based on our observations and analysis, we recommend to incorporate the following aspects when designing video conferencing applications: 1) Traffic load control/balancing algorithms to better use the limited bandwidth resources and to have a stable conversation; 2) Use traffic shaping policy or adaptively re-encode streams in real time to limit the overall traffic. This work is, to our knowledge, the first measurement work to study and compare mechanisms and performance of existing free multi-party video conferencing systems.Network Architectures and ServicesElectrical Engineering, Mathematics and Computer Scienc