Review of "Fish Defenses: Volume 2. Pathogens, Parasites and Predators" by G. Zaccone, C. Perrière, A. Mathis, B. G. Kapoor (eds.)

Book review of "Fish Defenses: Volume 2. Pathogens, Parasites and Predators" by G. Zaccone, C. Perrière, A. Mathis, B. G. Kapoor (eds.

Frictional Active Brownian Particles

Frictional forces affect the rheology of hard-sphere colloids, at high shear rate. Here we demonstrate, via numerical simulations, that they also affect the dynamics of active Brownian particles, and their motility induced phase separation. Frictional forces increase the angular diffusivity of the particles, in the dilute phase, and prevent colliding particles from resolving their collision by sliding one past to the other. This leads to qualitatively changes of motility-induced phase diagram in the volume-fraction motility plane. While frictionless systems become unstable towards phase separation as the motility increases only if their volume fraction overcomes a threshold, frictional system become unstable regardless of their volume fraction. These results suggest the possibility of controlling the motility induced phase diagram by tuning the roughness of the particles

Multifaceted Optimization of Energy Efficiency for Stationary WSN Applications

Stationary Wireless Sensor Networks (S-WSNs) consist of battery-powered and resource-constrained sensor nodes distributed at fixed locations to cooperatively monitor the environment or an object and provide persistent data acquisition. These systems are being practiced in many applications, ranging from disaster warning systems for instant event detection to structural health monitoring for effective maintenance. Despite the diversity of S-WSN applications, one common requirement is to achieve a long lifespan for a higher value-to-cost ratio. However, the variety of WSN deployment environments and use cases imply that there is no silver bullet to solve the energy issue completely. This thesis is a summary of six publications. Our  contributions include four energy optimization techniques on three layers for S-WSN applications. From the bottom up, we designed an ultra-low power smart trigger to integrate environment perceptibility into the hardware. On the network layer, we propose a reliable clustering protocol and a cluster-based data aggregation scheme. This scheme offers topology optimization together with in-network data processing. On the application layer, we extend an industrial standard protocol XMPP to incorporate WSN characteristics for unified information dissemination. Our protocol extensions facilitate WSN application development by adopting IMPS on the Internet. In addition, we conducted a performance analysis of one lightweight security protocol for WSNs called HIP Diet Exchange, which is being standardized by IETF. We suggested a few improvements and potential applications for HIP DEX. In the process of improving energy efficiency, we explore modular and generic design for better system integration and scalability. Our hardware invention can extend features by adding new transducers onboard. The clustering protocol and data aggregation scheme provides a general self-adaptive method to increase information throughput per energy cost while tolerating network dynamics. The unified XMPP extensions aim to support seamless information flow for the Web of Things. The results presented in this thesis demonstrate the importance of multifaceted optimization strategy in WSN development. An optimal WSN system should comprehend multiple factors to boost energy efficiency in a holistic approach

Origin and evolution of the RIG-I like RNA helicase gene family

Peer reviewedPublisher PD

Functional characterization of a short peptidoglycan recognition protein from Chinese giant salamander (Andrias davidianus)

This work was supported by the National Natural Science Foundation of China (Grant no. 31302221, 31172408 and 31272666) and Jiangsu Province (Grant no. BK20171274 and BK2011418), and partially by the Opening Project of Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland (Grant no. K2016-08). QZ was supported by the “Qinglan” project of Jiangsu province of China.Peer reviewedPublisher PD

Macrophage migration inhibitory factor (MIF) family in arthropods : Cloning and expression analysis of two MIF and one D-dopachrome tautomerase (DDT) homologues in Mud crabs, Scylla paramamosain

Acknowledgements This research was supported by grants from the National Natural Science Foundation of China (Nos. 31172438 and U1205123), the Natural Science Foundation of Fujian Province (No. 2012J06008 and 201311180002) and the projects-sponsored by SRF. TW received funding from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland) funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions.Peer reviewedPostprin

Molecular characterization and expression analysis of four fish-specific CC chemokine receptors CCR4La, CCR4Lc1, CCR4Lc2 and CCR11 in rainbow trout (Oncorhynchus mykiss)

ZQ was supported financially by the “Qinglan” project of Jiangsu Province and the Overseas Training Plan for Young and Middle-aged Teachers and Principals of College and Universities in Jiangsu Province, China. This work was partially supported by grants from the National Natural Science Foundation of China (31302221 and 31272666) and Jiangsu Province (BK2011418 and BK20151297). TW received funding from the Marine Alliance for Science and Technology for Scotland (MASTS), a pooling initiative funded by the Scottish Funding Council (grant reference HR09011), and JWH was supported by the Swiss National Science Foundation (grant reference CRSII3_147649-1).Peer reviewedPostprin

Utility of ITS1-5.8S-ITS2 sequences for species discrimination and phylogenetic inference of two closely related bucephalid digeneans (Digenea : Bucephalidae): Dollfustrema vaneyi and Dollfustrema hefeiensis

The complete internal transcribed spacer 1 (ITS1), 5.8S ribosomal DNA, and ITS2 region of the ribosomal DNA from 60 specimens belonging to two closely related bucephalid digeneans (Dollfustrema vaneyi and Dollfustrema hefeiensis) from different localities, hosts, and microhabitat sites were cloned to examine the level of sequence variation and the taxonomic levels to show utility in species identification and phylogeny estimation. Our data show that these molecular markers can help to discriminate the two species, which are morphologically very close and difficult to separate by classical methods. We found 21 haplotypes defined by 44 polymorphic positions in 38 individuals of D. vaneyi, and 16 haplotypes defined by 43 polymorphic positions in 22 individuals of D. hefeiensis. There is no shared haplotypes between the two species. Haplotype rather than nucleotide diversity is similar between the two species. Phylogenetic analyses reveal two robustly supported clades, one corresponding to D. vaneyi and the other corresponding to D. hefeiensis. However, the population structures between the two species seem to be incongruent and show no geographic and host-specific structure among them, further indicating that the two species may have had a more complex evolutionary history than expected.The complete internal transcribed spacer 1 (ITS1), 5.8S ribosomal DNA, and ITS2 region of the ribosomal DNA from 60 specimens belonging to two closely related bucephalid digeneans (Dollfustrema vaneyi and Dollfustrema hefeiensis) from different localities, hosts, and microhabitat sites were cloned to examine the level of sequence variation and the taxonomic levels to show utility in species identification and phylogeny estimation. Our data show that these molecular markers can help to discriminate the two species, which are morphologically very close and difficult to separate by classical methods. We found 21 haplotypes defined by 44 polymorphic positions in 38 individuals of D. vaneyi, and 16 haplotypes defined by 43 polymorphic positions in 22 individuals of D. hefeiensis. There is no shared haplotypes between the two species. Haplotype rather than nucleotide diversity is similar between the two species. Phylogenetic analyses reveal two robustly supported clades, one corresponding to D. vaneyi and the other corresponding to D. hefeiensis. However, the population structures between the two species seem to be incongruent and show no geographic and host-specific structure among them, further indicating that the two species may have had a more complex evolutionary history than expected

Flexible Single Sign-On for SIP: Bridging the Identity Chasm

Abstract-Identity federation is a key requirement for today's distributed services. This technology allows managed sharing of users' identity information between identity providers (IDP), and subsequently, the use of federated identities to access service providers (SP). Single Sign-On (SSO) is a core feature provided by these systems. The Session Initiation Protocol (SIP) is a signaling framework for session call control. It is becoming a widely accepted layer for applications and services, especially in the telecommunications and multimedia domain. In this paper, we explore solutions to incorporate SSO process into the SIP framework in order to simplify the services and resources access. Our design leverages the Liberty Alliance specifications and extends the existing SIP standards to support SSO functionality. We also present a prototype implementation at the end of this paper

Gene structure and transcription of IRF-2 in the mandarin fish Siniperca chuatsi with the finding of alternative transcripts and microsatellite in the coding region

The gene of interferon regulatory factor-2 (IRF-2) has been cloned from the mandarin fish (Siniperca chuatsi). The IRF-2 gene has 6,418 nucleotides (nt) and contains eight exons and seven introns, encoding two mRNAs. The two IRF-2 mRNAs each contained an open reading frame of 873 nt, which both translate into the same 291 amino acids but differed in their 5' untranslated region: one mRNA was transcribed initially from the exon 1 bypassing exon 2, while the other was transcribed from the exon 2. The microsatellites (CA repeats) could be found in the carboxyl terminal region of mandarin fish IRF-2, which result in the truncated form molecules. The microsatellites' polymorphism was investigated, and eight alleles were found in 16 individuals. The microsatellites were also examined in IRF-2 of several freshwater perciform fishes. The transcription of the IRF-2 in different tissues with or without poly inosine-cytidine stimulation was analyzed by real-time PCR, and the constitutive transcription of both molecules could be detected in all the tissues examined.The gene of interferon regulatory factor-2 (IRF-2) has been cloned from the mandarin fish (Siniperca chuatsi). The IRF-2 gene has 6,418 nucleotides (nt) and contains eight exons and seven introns, encoding two mRNAs. The two IRF-2 mRNAs each contained an open reading frame of 873 nt, which both translate into the same 291 amino acids but differed in their 5' untranslated region: one mRNA was transcribed initially from the exon 1 bypassing exon 2, while the other was transcribed from the exon 2. The microsatellites (CA repeats) could be found in the carboxyl terminal region of mandarin fish IRF-2, which result in the truncated form molecules. The microsatellites' polymorphism was investigated, and eight alleles were found in 16 individuals. The microsatellites were also examined in IRF-2 of several freshwater perciform fishes. The transcription of the IRF-2 in different tissues with or without poly inosine-cytidine stimulation was analyzed by real-time PCR, and the constitutive transcription of both molecules could be detected in all the tissues examined