Transgenic tobacco plants expressing Tarin 1 inhibit the growth of Pseudomonas syringae pv. tomato and the development of Spodoptera frugiperda

The protein Tarin 1, from Colocasia esculenta, was expressed in Nicotiana tabacum. Bioassays were done on plants expressing Tarin 1 at different levels using Spodoptera frugiperda larvae, various bacteria and fungi and the root‐knot nematode Meloidogyne javanica. It was found that S. frugiperda larvae fed on transformed plants had retarded and lower pupation, lower accumulated biomass and higher mortality rate than larvae fed on control plants. Also, Tarin 1 was found to inhibit the growth in vitro of Pseudomonas syringae pv. tomato. For Meloidogyne javanica, both relative replication and root damage were greater in control plants than in transformed plants, but the results were not statistically significant. This work illustrates the effects of plants expressing Tarin 1, on the growth and development of insects and bacteria, and shows its potential for pest management.     

The IL-10R2 binding hot spot on IL-22 is located on the N-terminal helix and is dependent on N-linked glycosylation

IL-22 is a class 2 alpha-helical cytokine involved in the generation of inflammatory responses. These activities require IL-22 to engage the cell surface receptors IL-22R1 and the low-affinity signaling molecule IL-10R2. IL-10R2 also interacts with five other class 2 cytokines: IL-10, IL-26, and the interferon-like cytokines IL-28A, IL-28B, and IL-29. Here, we define the IL-10R2 binding site on IL-22 using surface plasmon resonance (SPR) and site-directed mutagenesis. Surprisingly, the binding hot spot on IL-22 includes asparagine 54 (N54), which is post-translationally modified by N-linked glycosylation. Further characterization of the glycosylation reveals that only a single fucosylated N-acetyl glucosamine on N54 is required for maximal IL-10R2 binding. Biological responses of IL-22 mutants measured in cell-based luciferase assays correlate with the in vitro SPR studies. Together, these data suggest that IL-22 activity may be modulated via changes in the glycosylation state of the ligand during inflammation.     

Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling

Background  

Proteochemometrics is a new methodology that allows prediction of protein function directly from real interaction measurement data without the need of 3D structure information. Several reported proteochemometric models of ligand-receptor interactions have already yielded significant insights into various forms of bio-molecular interactions. The proteochemometric models are multivariate regression models that predict binding affinity for a particular combination of features of the ligand and protein. Although proteochemometric models have already offered interesting results in various studies, no detailed statistical evaluation of their average predictive power has been performed. In particular, variable subset selection performed to date has always relied on using all available examples, a situation also encountered in microarray gene expression data analysis.     

Geographic Variation in Egg Size and Lipid Provisioning in the Diamondback Terrapin Malaclemys terrapin

Abstract Understanding phenotypic differentiation among populations of wide-ranging species remains at the core of life-history research, because adaptation to local environmental conditions is expected. For example, when energy resources influence offspring fitness (as in oviparous ectotherms), the egg and hatchling environments are expected to influence selection by acting on the amount of energy allocated to offspring. Here we identify population variation in egg mass, length, width, and volume from diamondback terrapin Malaclemys terrapin eggs collected in Rhode Island (RI), Maryland (MD), and South Carolina (SC). Egg size (mean volume: 7.6, 8.1, and 9.1 cc in RI, MD, and SC, respectively) and clutch size (mean no. eggs: 16.1, 12.2, and 6.0 in RI, MD, and SC, respectively) differed among populations, which indicated that females produce larger clutches with smaller eggs at high latitudes and smaller clutches of larger eggs at lower latitudes. Lipid analyses indicated that eggs from SC contained yolks with a higher proportion of nonpolar lipids than did eggs from MD or RI (mean percentage of nonpolar lipids: 22.3%, 22.5%, and 31.8% in RI, MD, and SC, respectively). Thus, female terrapins in SC are laying larger eggs with increased lipid content to provide more energy for the developing embryo. Interestingly, total triacylglycerol (energetic lipid) was greater in southern populations but occurred in higher proportions in northern populations (total triacylglycerol: 88.0%, 85.4%, and 81.9% in RI, MD, and SC, respectively). This variation in triacylglycerol levels demonstrates the necessity for quantifying each lipid component. These data indicate a difference in reproductive strategy by which females in northern populations invest in higher fecundity with less energetic resources per offspring, whereas females in southern populations invest in larger eggs with considerably greater energy reserves.     

XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services

Background  

Life sciences make heavily use of the web for both data provision and analysis. However, the increasing amount of available data and the diversity of analysis tools call for machine accessible interfaces in order to be effective. HTTP-based Web service technologies, like the Simple Object Access Protocol (SOAP) and REpresentational State Transfer (REST) services, are today the most common technologies for this in bioinformatics. However, these methods have severe drawbacks, including lack of discoverability, and the inability for services to send status notifications. Several complementary workarounds have been proposed, but the results are ad-hoc solutions of varying quality that can be difficult to use.