Tyrosine Phosphorylation of 3BP2 Regulates B Cell Receptor-mediated Activation of NFAT

Adaptor protein c-Abl SH3 domain-binding protein-2 (3BP2, also referred to SH3BP2) regulates immune receptor-mediated signal transduction. In this report we focused on the molecular mechanism of 3BP2 function in B cell receptor (BCR) signaling. Engagement of BCR induces tyrosine phosphorylation of 3BP2. Genetic analysis demonstrated that Syk is critical for BCR-mediated tyrosine phosphorylation of 3BP2. Mutational analysis of 3BP2 revealed that both Tyr¹⁸³ and Src homology 2 (SH2) domain are necessary for 3BP2-mediated BCR-induced activation of nuclear factor of activated T cells (NFAT). Point mutation of Tyr¹⁸³ or Arg⁴⁸⁶ in the SH2 domain of 3BP2 diminished BCR-mediated tyrosine phosphorylation of 3BP2. Endogenous 3BP2 forms a complex with tyrosine-phosphorylated cellular signaling molecules. Peptide binding experiments demonstrated that only phosphorylated Tyr¹⁸³ in 3BP2 could form a complex with the SH2 domain(s) of phospholipase Cγ2 and Vav1 from B cell lysates. These interactions were represented by using bacterial glutathione S-transferase-phospholipase Cγ2 or -Vav1 SH2 domain. Furthermore, pulldown and Far Western experiments showed that the 3BP2-SH2 domain directly binds to B cell linker protein (BLNK) after BCR stimulation. These results demonstrated that 3BP2 induces the protein complex with cellular signaling molecules through phosphorylation of Tyr¹⁸³ and SH2 domain leading to the activation of NFAT in B cells.     

Modeling Susceptibility versus Resistance in Allergic Airway Disease Reveals Regulation by Tec Kinase Itk

Murine models of allergic asthma have been used to understand the mechanisms of development and pathology in this disease. In addition, knockout mice have contributed significantly to our understanding of the roles of specific molecules and cytokines in these models. However, results can vary significantly depending on the mouse strain used in the model, and in particularly in understanding the effect of specific knockouts. For example, it can be equivocal as to whether specific gene knockouts affect the susceptibility of the mice to developing the disease, or lead to resistance. Here we used a house dust mite model of allergic airway inflammation to examine the response of two strains of mice (C57BL/6 and BALB/c) which differ in their responses in allergic airway inflammation. We demonstrate an algorithm that can facilitate the understanding of the behavior of these models with regards to susceptibility (to allergic airway inflammation) (S_aai) or resistance (R_aai) in this model. We verify that both C57BL/6 and BALB/c develop disease, but BALB/c mice have higher S_aai for development. We then use this approach to show that the absence of the Tec family kinase Itk, which regulates the production of Th2 cytokines, leads to R_aai in the C57BL/6 background, but decreases S_aai on the BALB/c background. We suggest that the use of such approaches could clarify the behavior of various knockout mice in modeling allergic asthma.     

Flanking Microsatellite Markers for Breeding Varieties Against Asian Rice Gall Midge

The Asian rice gall midge, Orseolia oryzae Wood-Mason (Cecidomyiidae: Diptera) is a serious pest of wet season rice in South and Southeast Asia. Due to internal feeding habit and presence of biotypes of the pest, the most feasible way to control is breeding varieties resistant against multiple biotypes through marker-assisted breeding (MAB). But very few versatile co-dominant markers linked to the gall midge resistance genes are available. We used a set of F₉ recombinant inbred lines (RILs) of the cross TN1/PTB10 and identified microsatellite markers for the gall midge resistance gene in cv. PTB10 on short arm of rice chromosome 8. Markers RM22550 and RM547 flank the gene at a distance of 0.9 and 1.9 cM, respectively. Amplification of the markers in gall midge resistant and susceptible cultivars showed that these markers can be successfully used in MAB for development of gall midge resistant varieties.     

Toxicity of Crude Extracellular Products of <Emphasis Type="Italic">Aeromonas hydrophila</Emphasis> on Rohu, <Emphasis Type="Italic">Labeo rohita</Emphasis> (Ham.)

In the present study the haemolytic and proteolytic activity of extracellular products (ECP) secreted from Aeromonas hydrophila (CAHH14 strain) were studied with respect to temperature and different time of incubation as well as its lethal toxicity on rohu, Labeo rohita. The strain was isolated from Catla catla (showing abdominal dropsy symptom) collected from the pond of Central Institute of Freshwater Aquaculture (CIFA), Bhubaneswar, India and was characterized on the basis of biochemical tests. The highest production of haemolysin was achieved when the bacteria was grown at 35°C for 30 h. The proteolytic activity was found to be highest when the bacterium was grown at 30°C for 36 h. The haemolytic and proteolytic toxin produced by Aeromonas hydrophila was found to be lethal to rohu (LD₅₀ 1.7 × 10⁴ cfu/ml). The lethality of ECP was decreased by heating and completely inactivated by boiling at 100°C for 10 min. This indicates that protease activity and haemolytic activity of A. hydrophila ECP was temperature dependant.     

Comparative studies on carcass characteristics of marketable size farmed mrigal Cirrhinus mrigala, (Hamilton, 1822), and silver carp Hypophthalmichthys molitrix, (Val., 1844)

The carcass traits and commercial characteristics of farmed freshwater Cirrhinus mrigala and Hypophthalmichthys molitrix were investigated to calculate yield data useful for programming semi‐automated processing units. Specimens with average weights of 2500 and 3400 g were collected from both mrigal and silver carps, respectively. Samples were taken from grow‐out culture ponds of the Central Institute of Freshwater Aquaculture (CIFA), Odisha State, India. Carcass and offal yields as well as carcass cutability were assessed. Head yields were recorded as 14.9 and 27.5% for mrigal and silver carp, respectively. The gutted yield, headless yield and skinless dressed round percentages were determined as 89.4, 74.5 and 67.6% for mrigal and 92.8, 65.4 and 62.0% for silver carps, respectively. The meat: bone ratio in filleting averaged 4.8 for mrigal and 3.1 for silver carp. The middle cut of mrigal had both the highest total yield percentage and highest meat yield, whereas this was equally distributed between both the fore and middle cuts in silver carp. In both mrigal and silver carp the dry matter, ether extract and protein percentages were highest in the fore cut followed by middle and hind cut. In silver carp the percentage fat content was found to be significantly higher than in mrigal.     

Host response profile of human brain proteome in toxoplasma encephalitis co-infected with HIV

Background

Toxoplasma encephalitis is caused by the opportunistic protozoan parasite Toxoplasma gondii. Primary infection with T. gondii in immunocompetent individuals remains largely asymptomatic. In contrast, in immunocompromised individuals, reactivation of the parasite results in severe complications and mortality. Molecular changes at the protein level in the host central nervous system and proteins associated with pathogenesis of toxoplasma encephalitis are largely unexplored. We used a global quantitative proteomic strategy to identify differentially regulated proteins and affected molecular networks in the human host during T. gondii infection with HIV co-infection.

Results

We identified 3,496 proteins out of which 607 proteins were differentially expressed (≥1.5-fold) when frontal lobe of the brain from patients diagnosed with toxoplasma encephalitis was compared to control brain tissues. We validated differential expression of 3 proteins through immunohistochemistry, which was confirmed to be consistent with mass spectrometry analysis. Pathway analysis of differentially expressed proteins indicated deregulation of several pathways involved in antigen processing, immune response, neuronal growth, neurotransmitter transport and energy metabolism.

Conclusions

Global quantitative proteomic approach adopted in this study generated a comparative proteome profile of brain tissues from toxoplasma encephalitis patients co-infected with HIV. Differentially expressed proteins include previously reported and several new proteins in the context of T. gondii and HIV infection, which can be further investigated. Molecular pathways identified to be associated with the disease should enhance our understanding of pathogenesis in toxoplasma encephalitis.

Electronic supplementary material

The online version of this article (doi:10.1186/1559-0275-11-39) contains supplementary material, which is available to authorized users.     

Mathematical and computational modeling in biology at multiple scales

A variety of topics are reviewed in the area of mathematical and computational modeling in biology, covering the range of scales from populations of organisms to electrons in atoms. The use of maximum entropy as an inference tool in the fields of biology and drug discovery is discussed. Mathematical and computational methods and models in the areas of epidemiology, cell physiology and cancer are surveyed. The technique of molecular dynamics is covered, with special attention to force fields for protein simulations and methods for the calculation of solvation free energies. The utility of quantum mechanical methods in biophysical and biochemical modeling is explored. The field of computational enzymology is examined.     

Systematic study of photoluminescence,lyoluminescence and mechanoluminescence in Ce3+‐ and Eu3+‐activated Li3PO4 phosphors

Li₃PO₄ phosphor was prepared using a modified solid‐state diffusion technique. In this work, photoluminescence, lyoluminescence and mechanoluminescence studies were carried out in a Li₃PO₄ microcrystalline powder doped with different rare earths. In photoluminescence studies, characteristic emission of Ce and Eu was observed. The lyoluminescence glow curves of Li₃PO₄ microcrystals show that lyoluminescence intensity initially increases with time and then decreases exponentially. The decay time consists of two components for all masses. The dependence of decay time, especially the longer component, on mass has been investigated. Experiments on γ‐irradiated crystals have proved that the light emission originates from the recombination of released F‐centres with trapped holes (V₂‐centres) at the sulfuric acid–solid interface. Incorporation of bivalent alkali in solid lithium phosphate leads to an enhancement of lyoluminescence. A possible explanation for the experimental results has been attempted. The phosphor has a mechanoluminescence single glow peak. Mechanoluminescence intensity under various loading conditions was investigated. It is observed that mechanoluminescence intensity increases with increasing impurity concentration and increasing piston impact velocity. The results may be considered as only being of academic interest in solid‐state materials. Copyright © 2013 John Wiley & Sons, Ltd.     

Tomato Genomic Resources Database: An Integrated Repository of Useful Tomato Genomic Information for Basic and Applied Research

Tomato Genomic Resources Database (TGRD) allows interactive browsing of tomato genes, micro RNAs, simple sequence repeats (SSRs), important quantitative trait loci and Tomato-EXPEN 2000 genetic map altogether or separately along twelve chromosomes of tomato in a single window. The database is created using sequence of the cultivar Heinz 1706. High quality single nucleotide polymorphic (SNP) sites between the genes of Heinz 1706 and the wild tomato S. pimpinellifolium LA1589 are also included. Genes are classified into different families. 5′-upstream sequences (5′-US) of all the genes and their tissue-specific expression profiles are provided. Sequences of the microRNA loci and their putative target genes are catalogued. Genes and 5′-US show presence of SSRs and SNPs. SSRs located in the genomic, genic and 5′-US can be analysed separately for the presence of any particular motif. Primer sequences for all the SSRs and flanking sequences for all the genic SNPs have been provided. TGRD is a user-friendly web-accessible relational database and uses CMAP viewer for graphical scanning of all the features. Integration and graphical presentation of important genomic information will facilitate better and easier use of tomato genome. TGRD can be accessed as an open source repository at http://59.163.192.91/tomato2/.