The role of virus infection in a simple phytoplankton zooplankton system

Many planktonic species show spectacular bursts ("blooms") in population density. Though viral infections are known to cause behavioural and other changes in phytoplankton and other aquatic species, yet their role in regulating the phytoplankton population is still far from being understood. To study the role of viral diseases in the planktonic species, we model the phytoplankton-zooplankton system as a prey-predator system. Here the prey (phytoplankton) species is infected with a viral disease that divides the prey population into susceptible and infected classes, with the infected prey being more vulnerable to predation by the predator (zooplankton). The dynamical behaviour of the system is investigated from the point of view of stability and persistence both analytically and numerically. The model shows that infection can be sustained only above a threshold of force of infection, and, there exists a range in the infection rate where this system shows "bloom"-like stable limit cycle oscillations. The time series of natural "blooms" with different types of irregular oscillations can arise in this model simply from a biologically realistic feature, i.e., by the random variation of the epidemiological parameter (rate of infection) in the infected prey population. The difference in mean strength of infection alone can lead to the different types of patterns observed in natural planktonic blooms.     

Extracellular matrix proteome of chickpea (Cicer arietinum L.) illustrates pathway abundance, novel protein functions and evolutionary perspect

The extracellular matrix (ECM) or cell wall is a dynamic system and serves as the first line mediator in cell signaling to perceive and transmit extra- and intercellular signals in many pathways. Although ECM is a conserved compartment ubiquitously present throughout evolution, a compositional variation does exist among different organisms. ECM proteins account for 10% of the ECM mass, however, comprise several hundreds of different molecules with diverse functions. To understand the function of ECM proteins, we have developed the cell wall proteome of a crop legume, chickpea (Cicer arietinum). This comprehensive overview of the proteome would provide a basis for future comparative proteomic efforts for this important crop. Proteomic analyses revealed new ECM proteins of unknown functions vis-à-vis the presence of many known cell wall proteins. In addition, we report here evidence for the presence of unexpected proteins with known biochemical activities, which have never been associated with ECM.     

Synthesis and characterization of potent inhibitors of Trypanosoma cruzi dihydrofolate reductase

Dihydrofolate reductase (DHFR) of the parasite Trypanosoma cruzi (T. cruzi) is a potential target for developing drugs to treat Chagas’ disease. We have undertaken a detailed structure–activity study of this enzyme. We report here synthesis and characterization of six potent inhibitors of the parasitic enzyme. Inhibitory activity of each compound was determined against T. cruzi and human DHFR. One of these compounds, ethyl 4-(5-[(2,4-diamino-6-quinazolinyl)methyl]amino-2-methoxyphenoxy)butanoate (6b) was co-crystallized with the bifunctional dihydrofolate reductase-thymidylate synthase enzyme of T. cruzi and the crystal structure of the ternary enzyme:cofactor:inhibitor complex was determined. Molecular docking was used to analyze the potential interactions of all inhibitors with T. cruzi DHFR and human DHFR. Inhibitory activities of these compounds are discussed in the light of enzyme–ligand interactions. Binding affinities of each inhibitor for the respective enzymes were calculated based on the experimental or docked binding mode. An estimated 60–70% of the total binding energy is contributed by the 2,4-diaminoquinazoline scaffold.     

Computational identification of post-translational modification sites and functional families reveal possible moonlighting role of rotaviral proteins

Rotavirus (RV) diarrhoea causes huge number deaths in children less than 5 years of age. In spite of available vaccines, it has been difficult to combat RV due to large number of antigenically distinct genotypes, high mutation rates, generation of reassortant viruses due to segmented genome. RV is an eukaryotic virus which utilizes host cell machinery for its propagation. Since RV only encodes 12 proteins, post-translational modification (PTM) is important mechanism for modification, which consequently alters their function. A single protein exhibiting different functions in different locations or in different subcellular sites, are known to be 'moonlighting'. So there is a possibility that viral proteins moonlight in separate location and in different time to exhibit diverse cellular effects. Based on the primary sequence, the putative behaviour of proteins in cellular environment can be predicted, which helps to classify them into different functional families with high reliability score. In this study, sites for phosphorylation, glycosylation and SUMOylation of the six RV structural proteins (VP1, VP2, VP3, VP4, VP6 & VP7) & five non-structural proteins (NSP1, NSP2,NSP3,NSP4 & NSP5) and the functional families were predicted. As NSP6 is a very small protein and not required for virus growth & replication, it was not included in the study. Classification of RV proteins revealed multiple putative functions of each structural protein and varied number of PTM sites, indicating that RV proteins may also moonlight depending on requirements during viral life cycle. Targeting the crucial PTM sites on RV structural proteins may have implications in developing future anti-rotaviral strategies.     

A new blue luminescent dichlorido-bridged dinuclear copper(II) complex with DNA binding and cytotoxic activities: Synthesis, structure and DFT studies

A blue luminescent dichlorido-bridged dinuclear copper(II) (S = 1/2) complex, [Cu^II₂(HL)₂(μ-Cl)₂]·2H₂O, 1a was synthesized with the 1:1 reaction of the acyclic tridentate salicylaldehyde 2-pyridyl hydrazone ligand, HL, 1. The complex 1a displays multiple bands in the visible region (400-470 nm). The association constant (K_ass, UV-Vis) was found to be 1.186 × 10⁴ for 1a at 298 K. The copper(II)-copper(III) oxidation potential lies near 0.32 V versus Ag/AgCl electrode. On excitation at 390 nm, the ligand 1 strongly emits at 444 nm due to an intraligand ¹(π-π^∗) transition. Upon complexation with copper(II) the emission peak is slightly red shifted (λ_ex 390 nm, λ_em 450 nm, F/F₀ 0.81) with little quenching. Molecular structure of 1a (Cu···Cu 3.523 Å) has been determined by single crystal X-ray diffraction studies. DFT and TDDFT calculations strongly support the spectral behavior of the ligand and the complex. The complex 1a exhibits a strong interaction towards DNA as revealed from the K_b (intrinsic binding constant) 2.05 × 10⁴ M⁻¹ and K_sv (Stern-Volmer quenching constant) 2.47 values. The complex exhibits cytotoxic effect and the LD₅₀ value for HeLa cells was calculated as 5.44 μM at which the cell cycle was arrested at G₂/M phase.     

Binding of a cationic phenazinium dye in anionic liposomal membrane: a spectacular modification in the photophysics

Interaction of a cationic phenazinium dye, phenosafranin (PSF), with the anionic liposomal vesicle/bilayer of dimyristoyl-l-α-phosphatidylglycerol (DMPG) has been demonstrated using steady state and time resolved fluorescence and fluorescence anisotropy techniques. The charge transfer emission spectrum of PSF shows a dramatic modification in terms of fluorescence yield together with an appreciable hypsochromic shift in the lipid environment. The blue shift indicates a lowering in polarity inside the vesicle as compared to that in bulk water. The fluorescence and fluorescence quenching studies and micropolarity determination reveal that the cationic fluorophore has a profound binding interaction with the anionic DMPG membrane. Anisotropy study indicates the imposition of a motional restriction on the probe inside the bilayer. The electrostatic interaction between the cationic dye and the anionic lipid membrane has been argued to be the reason behind all these observations. The results could be useful in analyzing membrane organization and heterogeneity in natural membranes exploiting PSF or alike compounds as fluorescent probes.     

Structural basis of inducible costimulator ligand costimulatory function: determination of the cell surface oligomeric state and functional mapping of the receptor binding site of the protein

Inducible costimulator (ICOS) ligand (ICOSL), a B7-related transmembrane glycoprotein with extracellular IgV and IgC domains, binds to ICOS on activated T cells and delivers a positive costimulatory signal for optimal T cell function. Toward determining the structural features of ICOSL crucial for its costimulatory function, the present study shows that ICOSL displays a marked oligomerization potential, resembling more like B7-1 than B7-2. Use of ICOSL constructs lacking either the IgC or IgV domain demonstrates that receptor binding is mediated solely by the IgV domain but requires the IgC domain for maintaining the structural integrity of the protein. To map further the receptor recognition surface on ICOSL, a homology-based protein structure model of the ICOS:ICOSL complex was constructed. Based on predictions from the model, a series of mutations were generated targeting the potential receptor binding surface on ICOSL, and the mutants were tested for their biological function in terms of ICOS binding and T cell costimulation ability. The results provide experimental validation of the model and show that the receptor binding site on ICOSL is constituted chiefly by aromatic/hydrophobic residues. Critical ICOSL residues essential for ICOS binding map to the GFCC'C' beta-sheet face of the IgV domain and approximately overlap with the B7-1/B7-2 motif(s) that recognize CD28/CTLA-4. Altogether, similar structural features of ICOSL and B7 isoforms suggest a close evolutionary relationship between these costimulatory ligands, yet differences at the same time explain their unique specificity for the cognate binding partners, ICOS and CD28/CTLA-4, respectively.