Prediction of Biological Functions on Glycosylation Site Migrations in Human Influenza H1N1 Viruses

Protein glycosylation alteration is typically employed by various viruses for escaping immune pressures from their hosts. Our previous work had shown that not only the increase of glycosylation sites (glycosites) numbers, but also glycosite migration might be involved in the evolution of human seasonal influenza H1N1 viruses. More importantly, glycosite migration was likely a more effectively alteration way for the host adaption of human influenza H1N1 viruses. In this study, we provided more bioinformatics and statistic evidences for further predicting the significant biological functions of glycosite migration in the host adaptation of human influenza H1N1 viruses, by employing homology modeling and in silico protein glycosylation of representative HA and NA proteins as well as amino acid variability analysis at antigenic sites of HA and NA. The results showed that glycosite migrations in human influenza viruses have at least five possible functions: to more effectively mask the antigenic sites, to more effectively protect the enzymatic cleavage sites of neuraminidase (NA), to stabilize the polymeric structures, to regulate the receptor binding and catalytic activities and to balance the binding activity of hemagglutinin (HA) with the release activity of NA. The information here can provide some constructive suggestions for the function research related to protein glycosylation of influenza viruses, although these predictions still need to be supported by experimental data

A Missense Mutation in PPARD Causes a Major QTL Effect on Ear Size in Pigs

Chinese Erhualian is the most prolific pig breed in the world. The breed exhibits exceptionally large and floppy ears. To identify genes underlying this typical feature, we previously performed a genome scan in a large scale White Duroc × Erhualian cross and mapped a major QTL for ear size to a 2-cM region on chromosome 7. We herein performed an identical-by-descent analysis that defined the QTL within a 750-kb region. Historically, the large-ear feature has been selected for the ancient sacrificial culture in Erhualian pigs. By using a selective sweep analysis, we then refined the critical region to a 630-kb interval containing 9 annotated genes. Four of the 9 genes are expressed in ear tissues of piglets. Of the 4 genes, PPARD stood out as the strongest candidate gene for its established role in skin homeostasis, cartilage development, and fat metabolism. No differential expression of PPARD was found in ear tissues at different growth stages between large-eared Erhualian and small-eared Duroc pigs. We further screened coding sequence variants in the PPARD gene and identified only one missense mutation (G32E) in a conserved functionally important domain. The protein-altering mutation showed perfect concordance (100%) with the QTL genotypes of all 19 founder animals segregating in the White Duroc × Erhualian cross and occurred at high frequencies exclusively in Chinese large-eared breeds. Moreover, the mutation is of functional significance; it mediates down-regulation of β-catenin and its target gene expression that is crucial for fat deposition in skin. Furthermore, the mutation was significantly associated with ear size across the experimental cross and diverse outbred populations. A worldwide survey of haplotype diversity revealed that the mutation event is of Chinese origin, likely after domestication. Taken together, we provide evidence that PPARD G32E is the variation underlying this major QTL

Glycosylation Site Alteration in the Evolution of Influenza A (H1N1) Viruses

Influenza virus typically alters protein glycosylation in order to escape immune pressure from hosts and hence to facilitate survival in different host environments. In this study, the patterns and conservation of glycosylation sites on HA and NA of influenza A/H1N1 viruses isolated from various hosts at different time periods were systematically analyzed, by employing a new strategy combining genome-based glycosylation site prediction and 3D modeling of glycoprotein structures, for elucidation of the modes and laws of glycosylation site alteration in the evolution of influenza A/H1N1 viruses. The results showed that influenza H1N1 viruses underwent different alterations of protein glycosylation in different hosts. Two alternative modes of glycosylation site alteration were involved in the evolution of human influenza virus: One was an increase in glycosylation site numbers, which mainly occurred with high frequency in the early stages of evolution. The other was a change in the positional conversion of the glycosylation sites, which was the dominating mode with relatively low frequency in the later evolutionary stages. The mechanisms and possibly biological functions of glycosylation site alteration for the evolution of influenza A/H1N1 viruses were also discussed. Importantly, the significant role of positional alteration of glycosylation sites in the host adaptation of influenza virus was elucidated. Although the results still need to be supported by experimental data, the information here may provide some constructive suggestions for research into the glycosylation of influenza viruses as well as even the design of surveillance and the production of viral vaccines

Light-weight overlay path selection in a peer-to-peer environment

Large-scale peer-to-peer systems span a wide range of Internet locations. Such diversity can be leveraged to build overlay “detours” to circumvent periods of poor performance on the default path. However, identifying which peers are “good” relay choices in support of such detours is challenging, if one is to avoid incurring an overhead that grows with the size of the peer-to-peer system. This paper proposes and investigates the Earliest Branching Rule (EBR) to perform such a selection. EBR builds on the Earliest Diverging Rule (EDR) that selects relay nodes whose AS path diverges from the default path at the earliest possible point, but calls for monitoring a much smaller number of paths. As a result, it has a much lower overhead. The paper explores the performance and overhead of EBR, and compares them to that of EDR. The results demonstrate that EBR succeeds in selecting good relay nodes with minimum control overhead. Hence, providing a practical solution for dynamically building good overlays in large peer-to-peer systems

Output feedback control for a class of nonlinear systems with actuator degradation and sensor noise

This paper investigates the output feedback control problem of a class of nonlinear systems with sensor noise and actuator degradation. Firstly, by using the descriptor observer approach, the origin system is transformed into a descriptor system. On the basis of the descriptor system, a novel Proportional Derivative (PD) observer is developed to asymptotically estimate sensor noise and system state simultaneously. Then, by designing an adaptive law to estimate the effectiveness of actuator, an adaptive observer-based controller is constructed to ensure that system state can be regulated to the origin asymptotically. Finally, the design scheme is applied to address a flexible joint robot link problem

Grafting: a technique to modify ion accumulation in horticultural crops

Grafting is a centuries-old technique used in plants to obtain economic benefits. Grafting increases nutrient uptake and utilization efficiency in a number of plant species, including fruits, vegetables, and ornamentals. Selected rootstocks of the same species or close relatives are utilized in grafting. Rootstocks absorb more water and ions than self-rooted plants and transport these water and ions to the aboveground scion. Ion uptake is regulated by a complex communication mechanism between the scion and rootstock. Sugars, hormones, and miRNAs function as long-distance signaling molecules and regulate ion uptake and ion homeostasis by affecting the activity of ion transporters. This review summarizes available information on the effect of rootstock on nutrient uptake and utilization and the mechanisms involved. Information on specific nutrient-efficient rootstocks for different crops of commercial importance is also provided. Several other important approaches, such as interstocking (during double grafting), inarching, use of plant-growth-promoting rhizobacteria, use of arbuscular mycorrhizal fungi, use of plant growth substances (e.g., auxin and melatonin), and use of genetically engineered rootstocks and scions (transgrafting), are highlighted; these approaches can be combined with grafting to enhance nutrient uptake and utilization in commercially important plant species. Whether the rootstock and scion affect each other’s soil microbiota and their effect on the nutrient absorption of rootstocks remain largely unknown. Similarly, the physiological and molecular bases of grafting, crease formation, and incompatibility are not fully identified and require investigation. Grafting in horticultural crops can help reveal the basic biology of grafting, the reasons for incompatibility, sensing, and signaling of nutrients, ion uptake and transport, and the mechanism of heavy metal accumulation and restriction in rootstocks. Ion transporter and miRNA-regulated nutrient studies have focused on model and non-grafted plants, and information on grafted plants is limited. Such information will improve the development of nutrient-efficient rootstocks

Theoretical Analysis Based on Particle Electro-Mechanics for Au Pearl Chain Formation

This paper analyzes the fundamental mechanisms in driving Au Pearl Chain Formation (PCF) based on dielectrophoresis (DEP) force. From experimental results, the PCF process strongly depends on the voltage and the frequency applied on electrodes, but weakly on the sizes of particles, which appears to be contrary to theoretical expectations. To explain the above phenomenon, we estimated the DEP force and the Brownian motion imposed on the Au nanoparticles, and then investigated the AC electro-osmosis force and the electro-thermal force which may possibly affect the PCF rate. Numerical modeling to compare the forces is presented. By matching experimental and numerical results, we validate the scaling laws of the DEP force and electro-mechanics in the PCF of Au nanoparticles