Construction of a duck whole genome radiation hybrid panel : an aid for NGS whole genome assembly and a contribution to avian comparative maps

Le canard est une espèce d'importance agronomique en France, principalement à travers l'industrie de foie gras, qui représente plus de 75% de la production mondiale. De plus, c'est aussi un modèle important pour l'étude de l'infection par le virus influenza, pour lequel les oiseaux aquatiques sont un réservoir naturel, car porteurs asymptomatiques. Les travaux réalisés lors de la thèse se situent dans le contexte international de l'étude du génome du canard, comportant la séquence du génome, le séquençage d'EST et l'identification et la cartographie de SNP. Le but à terme pour l'INRA étant de disposer des connaissances sur le génome nécessaires pour la cartographie fine de QTL et l'identification de gènes impliqués dans l'expression de caractères agronomiques. Un panel de 90 d'hybrides irradiés (panel RH) a été réalisé par fusion de cellules donneuses de canard irradiées avec des cellules receveuses de hamster. Afin d'éviter la culture à grande échelle des clones cellulaires, des méthodes de génotypage par PCR utilisant l'amplification complète du génome (WGA) et/ou la réduction des volumes réactionnels ont été testées et deux premières cartes de chromosomes ont ainsi été réalisées. Nous avons également utilisé le génotypage par PCR pour vérifier la qualité de l'assemblage des scaffolds du génome du canard, réalisés par séquençage nouvelle génération Illumina au Beijing Genome Institute (BGI, Chine). Finalement, afin de couvrir le génome complet, nous avons entrepris un séquençage léger (0,1X de profondeur) d'hybrides, permettant une réalisation de cartes plus rapides que par PCR. Ces cartes permettent la détection des réarrangements chromosomiques existant entre les génomes de la poule et du canard, qui sont distants de 80 millions d'années.Duck is a very important agronomic species in France, especially for fatty liver industry which presents 75% worldwide production. Moreover, duck is also a scientific model for avian influenza research as it is a natural reservoir for avian influenza viruses. The work presented here is part of the international collaboration on duck genome sequencing, including SNP detection and mapping, EST sequencing. Our goal is to provide a genome map allowing for fine mapping QTL and identifying candidate genes involved in expression of agronomic traits. A panel composed of 90 radiation hybrids was produced by fusing irradiated duck donor cells with hamster cells. To avoid large-scale culture of the clones, PCR genotyping involving Whole Genome Amplification (WGA) and/or reduction of reaction volumes were tested and two first maps for duck chromosomes were made. We also used the PCR genotyping method to test for the quality of duck sequence scaffold assemblies, which had been produced by the Beijing Genome Institute (BGI, China). Finally, to cover the whole genome, we performed a low-pass sequencing (0.1X depth) of hybrids, allowing for rapid map development. These maps allow the detection of chromosomal rearrangements that have taken place between the duck and chicken genomes, which have diverged 80 million years ago

Behavioural investigation of the impact of different types of CEOs on innovation in family firms: moderating role of ownership divergence between cash flow rights and voting rights

In what way different types of CEOs within family firms, based on control diversity, behave towards R&D investment and how excess voting rights alter this behaviour of CEOs? This study has aimed to investigate the R&D investment behaviour of CEOs in family firms. This study has also investigated the moderating role of ownership divergence. The Pooled Ordinary Least Square (POLS) regression method is applied for data analysis purpose. Moreover, the Tobit regression model is also applied for robustness check. We obtained data (2008–2018) on Chinese A-share firms from CSMAR. The study found non-family CEOs exhibit negative behaviour towards R&D investment and that CEOs from family firms exhibit the same behaviour when do not have actual control rights. Family CEOs with actual control rights are more willing to R&D investment. The moderating effect of excess voting rights on family CEOs with actual control rights who change their willingness from positive to negative. The non-family CEOs and family CEOs without actual control rights show positive behaviour with existence of excess voting rights. This study is novel and pioneered the exploration of effects of different types of CEOs within family firms on R&D investment behaviour. This study is useful for directors to understand and select a suitable CEO for their firm, also for managers to devise an optimal level of ownership discrepancy to attain maximum benefits from R&D investment decisions

A two-base encoded DNA sequence alignment problem in computational biology

The recent introduction of instruments capable of producing millions of DNA sequence reads in a single run is rapidly changing the landscape of genetics. The primary objective of the "sequence alignment" problem is to search for a new algorithm that facilitates the use of two-base encoded data for large-scale re-sequencing projects. This algorithm should be able to perform local sequence alignment as well as error detection and correction in a reliable and systematic manner, enabling the direct comparison of encoded DNA sequence reads to a candidate reference DNA sequence. We will first briefly review two well-known sequence alignment approaches and provide a rudimentary improvement for implementation on parallel systems. Then, we carefully examin a unique sequencing technique known as the SOLiDTM System that can be implemented, and follow by the results from the global and local sequence alignment. In this report, the team presents an explanation of the algorithms for color space sequence data from the high-throughput re-sequencing technology and a theoretical parallel approach to the dynamic programming method for global and local alignment. The combination of the di-base approach and dynamic programming provides a possible viewpoint for large-scale re-sequencing projects. We anticipate the use of distributed computing to be the next-generation engine for large-scale problems like such

Switchable disposable passive RFID vapour sensors from inkjet printed electronic components integrated with PDMS as a stimulus responsive material

A route to cheap and disposable sensors for the chemical sensing market, with potential applications including monitoring of food spoilage, is reported herein. The sensor is the result of the direct integration of a stimuli-responsive material, poly(dimethylsiloxane) (PDMS), with an electronic component. The printing and sintering of colloidal silver ink solutions onto PDMS was optimized to allow the printing of conductive silver feed loops, which are the active sensing component in antennas for passive (battery-free) Radio Frequency Identification (RFID) tags. The response of these devices is related to the degree of swelling of the PDMS, which, in turn, has been shown to be correlated to the Hansen solubility parameters and the vapour pressures of the corresponding volatile organic compounds (VOCs). When exposed to solvent vapour the printed feed loop fractures, increasing resistance and ultimately breaking conductivity, leading to a change in the transmitted power and read range of the wireless device. Remarkably upon removal from the vapour, the fractured feed loops reassemble and become conductive again, making them switchable and “multi-use”. This work paves the way to a fully inkjet printed RFID substrate for vapour detection

Report on Selected Standardization Activities of the IEEE BASC and of the ATM Forum

This document describes the standardization activities which were performed during the first year period of the joint project named ﲁ Standardization and Research Project on an ATM/B-ISDN Switching Fabric System that is being jointly performed by Protocol Engineering Center (PEC) of Electronics and Telecommunications Research Institute (ETRI), Institute for Systems Research (ISR) of the University of Maryland at College Park (UMCP) and Modacom Co., Ltd. These standardization activities are related to the IEEE Bus Architecture Standards Committee (BASC) meetings and ATM Forum Meetings. This document also provides the general information about the IEEE Standards meetings and ATM Forum Standards meetings.<P

ATM/LAN Access Switch (ALAX): System Architecture

This document contains the hardware information for the ATM LAN Access Switch (ALAX) that was done as a collaborative research and development effort by the Institute for Systems Research at the University of Maryland, College Park, Protocol Engineering Center in Electronics and Telecommunications Research Institute, and Modacom Co., Ltd. of Korea.<P

Taxonomic and Functional Diversity of Soil and Hypolithic Microbial Communities in Miers Valley, McMurdo Dry Valleys, Antarctica

The McMurdo Dry Valleys of Antarctica are an extreme polar desert. Mineral soils support subsurface microbial communities and translucent rocks support development of hypolithic communities on ventral surfaces in soil contact. Despite significant research attention relatively little is known about taxonomic and functional diversity or their inter-relationships. Here we report a combined diversity and functional interrogation for soil and hypoliths of the Miers Valley in the McMurdo Dry Valleys of Antarctica. The study employed 16S rRNA fingerprinting and high throughput sequencing combined with the GeoChip functional microarray. The soil community was revealed as a highly diverse reservoir of bacterial diversity dominated by actinobacteria. Hypolithic communities were less diverse and dominated by cyanobacteria. Major differences in putative functionality were that soil communities displayed greater diversity in stress tolerance and recalcitrant substrate utilization pathways, whilst hypolithic communities supported greater diversity of nutrient limitation adaptation pathways. A relatively high level of functional redundancy in both soil and hypoliths may indicate adaptation of these communities to fluctuating environmental conditions

Antioxidative Characteristics of Anisomeles indica Extract and Inhibitory Effect of Ovatodiolide on Melanogenesis

The purpose of the study was to investigate the antioxidant characteristics of Anisomeles indica methanol extract and the inhibitory effect of ovatodiolide on melanogenesis. In the study, the antioxidant capacities of A. indica methanol extract such as DPPH assay, ABTS radical scavenging assay, reducing capacity and metal ion chelating capacity as well as total phenolic content of the extract were investigated. In addition, the inhibitory effects of ovatodiolide on mushroom tyrosinase, B16F10 intracellular tyrosinase and melanin content were determined spectrophotometrically. Our results revealed that the antioxidant capacities of A. indica methanol extract increased in a dose-dependent pattern. The purified ovatodiolide inhibited mushroom tyrosinase activity (IC50 = 0.253 mM), the compound also effectively suppressed intracellular tyrosinase activity (IC50 = 0.469 mM) and decreased the amount of melanin (IC50 = 0.435 mM) in a dose-dependent manner in B16F10 cells. Our results concluded that A. indica methanol extract displays antioxidant capacities and ovatodiolide purified from the extract inhibited melanogenesis in B16F10 cells. Hence, A. indica methanol extract and ovatodiolide could be applied as a type of dermatological whitening agent in skin care products

ALAX- A P1355-Based Architecture for An ATM LAN Access Switch, with Application to ATM Onboard Switching

We draw attention to the new IEEE P1355 Standard for Heterogeneous InterConnect as a possible platform to support several onboard processing functions, including onboard communications and onboard ATM switching. The main features of IEEE P1355 are illustrated through a discussion of the basic principles and protocol architecture of ALAX, the ATM LAN Access Switch, currently under design in the Laboratory for Advanced Switching Technologies at the University of Maryland, College Park