From Workstations to Workbenches: Towards Predicting Physicochemically Viable Protein-Protein Interactions Across a Host and a Pathogen

The understanding of protein-protein interactions is indispensable in comprehending most of the biological processes in a cell. Small-scale experiments as well as large-scale high-throughput techniques over the past few decades have facilitated identification and analysis of protein-protein interactions which form the basis of much of our knowledge on functional and regulatory aspects of proteins. However, such rich catalog of interaction data should be used with caution when establishing protein-protein interactions in silico, as the high-throughput datasets are prone to false positives. Numerous computational means developed to pursue genome-wide studies on protein-protein interactions at times overlook the mechanistic and molecular details, thus questioning the reliability of predicted protein-protein interactions. We review the development, advantages, and shortcomings of varied approaches and demonstrate that by providing a structural viewpoint in terms of shape complementarity and interaction energies at protein-protein interfaces coupled with information on expression and localization of proteins homologous to an interacting pair, it is possible to assess the credibility of predicted interactions in biological context. With a focus on human pathogen Mycobacterium tuberculosis H37Rv, we show that such scrupulous use of details at the molecular level can predict physicochemically viable protein-protein interactions across host and pathogen. Such predicted interactions have the potential to provide molecular basis of probable mechanisms of pathogenesis and hence open up ways to explore their usefulness as targets in the light of drug discovery. (c) 2014 IUBMB Life, 66(11):759-774, 2014

An alluaudite Na-2+Fe-2x(2-x)(SO4)(3)(x=0.2) derivative phase as insertion host for lithium battery

A new desodiated derivative compound, Na0.89Fe1.8(SO4)(3), was prepared by the chemical oxidation of alluaudite Na2.4Fe1.8(SO4)(3) Phase using NOBF4 as oxidant. The structure and valency of Fe were characterized by X-ray diffraction (XRD) and Fe-57 Mossbauer spectroscopy. Intercalation behavior of lithium ions in the structure of Na0.89Fe1.8(SO4)(3) was gauged by electrochemical analyses and ex-situ X-ray diffraction. A high capacity of 110 mAh g(-1) at 0.1 C was obtained with a good rate kinetics within a range of 0.1-10 C(1 C = 118 mAh g-1) involving a high Fe3+/Fe2+ redox potential of 3.75 V (vs. Li/Li+). These results confirmed that the Na2.4-delta Fe1.8(SO4)(3) framework was stable even after oxidation and forms a new competitive cathode for the reversible intercalation of lithium ions. (C) 2014 Elsevier B.V. All rights reserved.

Effects of large-scale deforestation on precipitation in the monsoon regions: Remote versus local effects

In this paper, using idealized climate model simulations, we investigate the biogeophysical effects of large-scale deforestation on monsoon regions. We find that the remote forcing from large-scale deforestation in the northern middle and high latitudes shifts the Intertropical Convergence Zone southward. This results in a significant decrease in precipitation in the Northern Hemisphere monsoon regions (East Asia, North America, North Africa, and South Asia) and moderate precipitation increases in the Southern Hemisphere monsoon regions (South Africa, South America, and Australia). The magnitude of the monsoonal precipitation changes depends on the location of deforestation, with remote effects showing a larger influence than local effects. The South Asian Monsoon region is affected the most, with 18% decline in precipitation over India. Our results indicate that any comprehensive assessment of afforestation/reforestation as climate change mitigation strategies should carefully evaluate the remote effects on monsoonal precipitation alongside the large local impacts on temperatures.

Large-Scale Multiuser SM-MIMO Versus Massive MIMO

Spatial modulation (SM) is attractive for multiantenna wireless communications. SM uses multiple transmit antenna elements but only one transmit radio frequency (RF) chain. In SM, in addition to the information bits conveyed through conventional modulation symbols (e.g., QAM), the index of the active transmit antenna also conveys information bits. In this paper, we establish that SM has significant signal-to-noise (SNR) advantage over conventional modulation in large-scale multiuser (multiple-input multiple-output) MIMO systems. Our new contribution in this paper addresses the key issue of large-dimension signal processing at the base station (BS) receiver (e.g., signal detection) in large-scale multiuser SM-MIMO systems, where each user is equipped with multiple transmit antennas (e.g., 2 or 4 antennas) but only one transmit RF chain, and the BS is equipped with tens to hundreds of (e.g., 128) receive antennas. Specifically, we propose two novel algorithms for detection of large-scale SM-MIMO signals at the BS; one is based on message passing and the other is based on local search. The proposed algorithms achieve very good performance and scale well. For the same spectral efficiency, multiuser SM-MIMO outperforms conventional multiuser MIMO (recently being referred to as massive MIMO) by several dBs. The SNR advantage of SM-MIMO over massive MIMO can be attributed to: (i) because of the spatial index bits, SM-MIMO can use a lower-order QAM alphabet compared to that in massive MIMO to achieve the same spectral efficiency, and (ii) for the same spectral efficiency and QAM size, massive MIMO will need more spatial streams per user which leads to increased spatial interference.

Interferon-Gamma and Nitric Oxide Synthase 2 Mediate the Aggregation of Resident Adherent Peritoneal Exudate Cells: Implications for the Host Response to Pathogens

Interferon-gamma (Ifn gamma), a key macrophage activating cytokine, plays pleiotropic roles in host immunity. In this study, the ability of Ifn gamma to induce the aggregation of resident mouse adherent peritoneal exudate cells (APECs), consisting primarily of macrophages, was investigated. Cell-cell interactions involve adhesion molecules and, upon addition of Ifn gamma, CD11b re-localizes preferentially to the sites of interaction on APECs. A functional role of CD11b in enhancing aggregation is demonstrated using Reopro, a blocking reagent, and siRNA to Cd11b. Studies with NG-methyl-L-arginine (LNMA), an inhibitor of Nitric oxide synthase (Nos), NO donors, e.g., S-nitroso-N-acetyl-DL-penicillamine (SNAP) or Diethylenetriamine/ nitric oxide adduct (DETA/NO), and Nos2(-/-) mice identified Nitric oxide (NO) induced by Ifn gamma as a key regulator of aggregation of APECs. Further studies with Nos2(-/-) APECs revealed that some Ifn. responses are independent of NO: induction of MHC class II and CD80. On the other hand, Nos2 derived NO is important for other functions: motility, phagocytosis, morphology and aggregation. Studies with cytoskeleton depolymerizing agents revealed that Ifn gamma and NO mediate the cortical stabilization of Actin and Tubulin which contribute to aggregation of APECs. The biological relevance of aggregation of APECs was delineated using infection experiments with Salmonella Typhimurium (S. Typhimurium). APECs from orally infected, but not uninfected, mice produce high amounts of NO and aggregate upon ex vivo culture in a Nos2-dependent manner. Importantly, aggregated APECs induced by Ifn gamma contain fewer intracellular S. Typhimurium compared to their single counterparts post infection. Further experiments with LNMA or Reopro revealed that both NO and CD11b are important for aggregation; in addition, NO is bactericidal. Overall, this study elucidates novel roles for Ifn gamma and Nos2 in regulating Actin, Tubulin, CD11b, motility and morphology during the aggregation response of APECs. The implications of aggregation or ``group behavior'' of APECs are discussed in the context of host resistance to infectious organisms.

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

The annotated whole-genome sequence of Mycobacterium tuberculosis indicated that Rv1388 (Mtihf) likely encodes a putative 20 kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or organization of mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF-duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg170, Arg171, and Arg173, which might be involved in DNA binding, and a conserved proline (P150) in the tight turn. The phenotypic sensitivity of Escherichia coli Delta ihfA and Delta ihfB strains to UV and methylmethanesulfonate could be complemented with the wild-type Mtihf, but not its alleles bearing mutations in the DNA-binding residues. Protein DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, bind with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHF alpha beta. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes compaction of DNA into nucleoid-like or higher-order filamentous structures. We hence propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.

Differences in host species relationships and biogeographic influences produce contrasting patterns of prevalence, community composition and genetic structure in two genera of avian malaria parasites in southern Melanesia

1. Host-parasite interactions have the potential to influence broadscale ecological and evolutionary processes, levels of endemism, divergence patterns and distributions in host populations. Understanding the mechanisms involved requires identification of the factors that shape parasite distribution and prevalence. 2. A lack of comparative information on community-level host-parasite associations limits our understanding of the role of parasites in host population divergence processes. Avian malaria (haemosporidian) parasites in bird communities offer a tractable model system to examine the potential for pathogens to influence evolutionary processes in natural host populations. 3. Using cytochrome b variation, we characterized phylogenetic diversity and prevalence of two genera of avian haemosporidian parasites, Plasmodium and Haemoproteus, and analysed biogeographic patterns of lineages across islands and avian hosts, in southern Melanesian bird communities to identify factors that explain patterns of infection. 4. Plasmodium spp. displayed isolation-by-distance effects, a significant amount of genetic variation distributed among islands but insignificant amounts among host species and families, and strong local island effects with respect to prevalence. Haemoproteus spp. did not display isolation-by-distance patterns, showed marked structuring of genetic variation among avian host species and families, and significant host species prevalence patterns. 5. These differences suggest that Plasmodium spp. infection patterns were shaped by geography and the abiotic environment, whereas Haemoproteus spp. infection patterns were shaped predominantly by host associations. Heterogeneity in the complement and prevalence of parasite lineages infecting local bird communities likely exposes host species to a mosaic of spatially divergent disease selection pressures across their naturally fragmented distributions in southern Melanesia. Host associations for Haemoproteus spp. indicate a capacity for the formation of locally co-adapted host-parasite relationships, a feature that may limit intraspecific gene flow or range expansions of closely related host species.

Epigenetics and miRNA during bacteria-induced host immune responses

Various cellular processes including the pathogen-specific immune responses, host-pathogen interactions and the related evasion mechanisms rely on the ability of the immune cells to be reprogrammed accurately and in many cases instantaneously. In this context, the exact functions of epigenetic and miRNA-mediated regulation of genes, coupled with recent advent in techniques that aid such studies, make it an attractive field for research. Here, we review examples that involve the epigenetic and miRNA control of the host immune system during infection with bacteria. Interestingly, many pathogens utilize the epigenetic and miRNA machinery to modify and evade the host immune responses. Thus, we believe that global epigenetic and miRNA mapping of such host-pathogen interactions would provide key insights into their cellular functions and help to identify various determinants for therapeutic value.

Exploring the Colour of 3d Transition-Metal Ions in Trigonal Bipyramidal Coordination: Identification of Purple-Blue (CoO5) and Beige-Red (NiO5) Chromophores in LiMgBO3 Host

In an attempt to develop new coloured inorganic oxides, we have investigated the substitution of 3d transition-metal ions in LiMgBO3 host where Mg-II has a trigonal bipyramidal (TBP) oxygen coordination]. We find that single-phase materials are formed for (LiMg1-xCoxBO3)-B-II (0 < x 1.0), (LiMg1-xNixBO3)-B-II (0 < x 0.1), (LiMg1-xCuxBO3)-B-II (0 < x 0.1) and also (Li1-xMg1-xFexBO3)-B-III (0 < x 0.1) of which the Co-II and Ni-II derivatives are strongly coloured, purple-blue and beige-red, respectively, thus identifying TBP CoO5 and NiO5 as new chromophores for these colours.

Designing Novel Sulphate-based Ceramic Materials as Insertion Host Compounds for Secondary Batteries

Rechargeable batteries have propelled the wireless revolution and automobiles market over the past 25 years. Developing better batteries with improved energy density demands unveiling of new cathode ceramic materials with suitable diffusion channels and open framework structure. In this pursuit of achieving higher energy density, one approach is to realize enhanced redox voltage of insertion of ceramic compounds. This can be accomplished by incorporating highly electronegative anions in the cathode ceramics. Building on this idea, recently various sulphate- based compounds have been reported as high voltage cathode materials. The current article highlights the use of sulphate (SO4) based cathodes to realize the highest ever Fe3+/Fe2+ redox potentials in Li-ion batteries (LiFeSO4F fluorosulphate: 3.9V vs Li/Li+) and Na-ion batteries (Na2Fe2(SO4)(3) polysulphate: 3.8V vs Na/Na+). These sulphate-based cathode ceramic compounds pave way for newer avenues to design better batteries for future applications.

Anthropogenic aerosol fraction over the Indian region: model simulations versus multi-satellite data analysis

Anthropogenic aerosols play a crucial role in our environment, climate, and health. Assessment of spatial and temporal variation in anthropogenic aerosols is essential to determine their impact. Aerosols are of natural and anthropogenic origin and together constitute a composite aerosol system. Information about either component needs elimination of the other from the composite aerosol system. In the present work we estimated the anthropogenic aerosol fraction (AF) over the Indian region following two different approaches and inter-compared the estimates. We espouse multi-satellite data analysis and model simulations (using the CHIMERE Chemical transport model) to derive natural aerosol distribution, which was subsequently used to estimate AF over the Indian subcontinent. These two approaches are significantly different from each other. Natural aerosol satellite-derived information was extracted in terms of optical depth while model simulations yielded mass concentration. Anthropogenic aerosol fraction distribution was studied over two periods in 2008: premonsoon (March-May) and winter (November-February) in regard to the known distinct seasonality in aerosol loading and type over the Indian region. Although both techniques have derived the same property, considerable differences were noted in temporal and spatial distribution. Satellite retrieval of AF showed maximum values during the pre-monsoon and summer months while lowest values were observed in winter. On the other hand, model simulations showed the highest concentration of AF in winter and the lowest during pre-monsoon and summer months. Both techniques provided an annual average AF of comparable magnitude (similar to 0.43 +/- 0.06 from the satellite and similar to 0.48 +/- 0.19 from the model). For winter months the model-estimated AF was similar to 0.62 +/- 0.09, significantly higher than that (0.39 +/- 0.05) estimated from the satellite, while during pre-monsoon months satellite-estimated AF was similar to 0.46 +/- 0.06 and the model simulation estimation similar to 0.53 +/- 0.14. Preliminary results from this work indicate that model-simulated results are nearer to the actual variation as compared to satellite estimation in view of general seasonal variation in aerosol concentrations.

Air-pollution and economics: diesel bus versus electric bus

The Bangalore Metropolitan Transport Corporation (BMTC) took an initiative to check the overall benefits of introducing electric buses as a suitable replacement for the diesel buses to tackle the burgeoning pollution in the city of Bengaluru, India. For a trial run of three months, an electric bus was procured from a Chinese company `Build Your Dreams' (BYD). Data were collected by BMTC on the operation and maintenance of the bus. This new initiative, if rightly guided, could have a direct impact on the lives of those in the city. An economic analysis of the running as well as maintenance of the electric buses within the city limits was performed. For comparison, the same analysis was performed for the data from the existing diesel bus operating on the same route. On the basis of the study, it can be concluded that the introduction of electric buses as a means of public transport in the city would be beneficial both economically as well as environmentally. The electric bus also makes much less noise, thereby helping reduce noise pollution and makes less vibration when compared to the diesel bus. This results in a more comfortable journey for the passengers.

Three-dimensional plotted hydroxyapatite scaffolds with predefined architecture: comparison of stabilization by alginate cross-linking versus sintering

Scaffolds for bone tissue engineering are essentially characterized by porous three-dimensional structures with interconnected pores to facilitate the exchange of nutrients and removal of waste products from cells, thereby promoting cell proliferation in such engineered scaffolds. Although hydroxyapatite is widely being considered for bone tissue engineering applications due to its occurrence in the natural extracellular matrix of this tissue, limited reports are available on additive manufacturing of hydroxyapatite-based materials. In this perspective, hydroxyapatite-based three-dimensional porous scaffolds with two different binders (maltodextrin and sodium alginate) were fabricated using the extrusion method of three-dimensional plotting and the results were compared in reference to the structural properties of scaffolds processed via chemical stabilization and sintering routes, respectively. With the optimal processing conditions regarding to pH and viscosity of binder-loaded hydroxyapatite pastes, scaffolds with parallelepiped porous architecture having up to 74% porosity were fabricated. Interestingly, sintering of the as-plotted hydroxyapatite-sodium alginate (cross-linked with CaCl2 solution) scaffolds led to the formation of chlorapatite (Ca9.54P5.98O23.8Cl1.60(OH)(2.74)). Both the sintered scaffolds displayed progressive deformation and delayed fracture under compressive loading, with hydroxyapatite-alginate scaffolds exhibiting a higher compressive strength (9.5 +/- 0.5MPa) than hydroxyapatite-maltodextrin scaffolds (7.0 +/- 0.6MPa). The difference in properties is explained in terms of the phase assemblage and microstructure.

Virulent Salmonella enterica infections can be exacerbated by concomitant infection of the host with a live attenuated S. enterica vaccine via Toll-like receptor 4-dependent interleukin-10 production with the involvement of both TRIF and MyD88.

During systemic disease in mice, Salmonella enterica grows intracellularly within discrete foci of infection in the spleen and liver. In concomitant infections, foci containing different S. enterica strains are spatially separated. We have investigated whether functional interactions between bacterial populations within the same host can occur despite the known spatial separation of the foci and independence of growth of salmonellae residing in different foci. In this study we have demonstrated that bacterial numbers of virulent S. enterica serovar Typhimurium C5 strain in mouse tissues can be increased by the presence of the attenuated aroA S. Typhimurium SL3261 vaccine strain in the same tissue. Disease exacerbation does not require simultaneous coinjection of the attenuated bacteria. SL3261 can be administered up to 48 hr after or 24 hr before the administration of C5 and still determine higher tissue numbers of the virulent bacteria. This indicates that intravenous administration of a S. enterica vaccine strain could potentially exacerbate an established infection with wild-type bacteria. These data also suggest that the severity of an infection with a virulent S. enterica strain can be increased by the prior administration of a live attenuated vaccine strain if infection occurs within 48 hr of vaccination. Exacerbation of the growth of C5 requires Toll-like receptor 4-dependent interleukin-10 production with the involvement of both Toll/interleukin-1 receptor-domain-containing adaptor inducing interferon-beta and myeloid differentiation factor 88.

Modelling within-host spatiotemporal dynamics of invasive bacterial disease

Mechanistic determinants of bacterial growth, death, and spread within mammalian hosts cannot be fully resolved studying a single bacterial population. They are also currently poorly understood. Here, we report on the application of sophisticated experimental approaches to map spatiotemporal population dynamics of bacteria during an infection. We analyzed heterogeneous traits of simultaneous infections with tagged Salmonella enterica populations (wild-type isogenic tagged strains [WITS]) in wild-type and gene-targeted mice. WITS are phenotypically identical but can be distinguished and enumerated by quantitative PCR, making it possible, using probabilistic models, to estimate bacterial death rate based on the disappearance of strains through time. This multidisciplinary approach allowed us to establish the timing, relative occurrence, and immune control of key infection parameters in a true host-pathogen combination. Our analyses support a model in which shortly after infection, concomitant death and rapid bacterial replication lead to the establishment of independent bacterial subpopulations in different organs, a process controlled by host antimicrobial mechanisms. Later, decreased microbial mortality leads to an exponential increase in the number of bacteria that spread locally, with subsequent mixing of bacteria between organs via bacteraemia and further stochastic selection. This approach provides us with an unprecedented outlook on the pathogenesis of S. enterica infections, illustrating the complex spatial and stochastic effects that drive an infectious disease. The application of the novel method that we present in appropriate and diverse host-pathogen combinations, together with modelling of the data that result, will facilitate a comprehensive view of the spatial and stochastic nature of within-host dynamics. © 2008 Grant et al.