Molecular characterization of cyclophilin A-like protein from Piriformospora indica for its potential role to abiotic stress tolerance in E. coli

BACKGROUND: Cyclophilins (CyP), conserved in all genera, are known to have regulatory responses of various cellular processes including stress tolerance. Interestingly, CyP has a crucial role as peptidyl-prolyl cis–trans isomerases (PPIases). Our earlier in silico based approach resulted into the identification of cyclophilin family from rice, Arabidopsis and yeast. In our recent report, we discovered a new OsCYP-25 from rice. Here, we identified a novel cyclophylin A-like protein (PiCyP) from Piriformospora indica which is responsible for abiotic stress tolerance in E. coli. RESULTS: Cyclophylin A-like protein (CyPA) (accession number GQ214003) was selected from cDNA library. The genomic organization CyPA revealed a 1304 bp of CyPA in P. indica genome, showing 10 exons and 9 introns. Further, CyPA was evident in PCR with gDNA and cDNA and Southern blot analysis. The phylogenetic examination of CyPA of P. indica showed that it is closed to human cyclophilin. The uniqueness of PiCyPA protein was apparent in western blot study. Kinetics of purified PiCyPA protein for its PPIas activity was determined via first order rate constant (0.104 s(-1)) in the presence of 1 μg of PiCyPA, with increasing PiCyPA concentration, in the presence of cyclosporin A (CsA) and the inhibition constant (4.435 nM) of CsA for inhibition of PiCyPA. The differential response of E. coli harbouring pET28a-PiCypA was observed for their different degree of tolerance to different abiotic stresses as compared to empty pET28a vector. CONCLUSIONS: Overexpression of PiCyPA protein E. coli cells confer enhanced tolerance to wide range of abiotic stresses. Thus, this study provides the significance of PiCypA as a molecular chaperone which advanced cellular stress responses of E. coli cells under adverse conditions, and it, furthermore, confirms the mounting the sustainability of E. coli for exploitation in recombinant proteins production. Additionally, the PiCyPA gene cooperates substantial functions in cellular network of stress tolerance mechanism, essentially required for various developmental stages, and might be a potential paramount candidate for crop improvement and its sustainable production under adverse conditions

Exported plasmodial J domain protein, PFE0055c, and PfHsp70-x form a specific co-chaperone-chaperone partnership

Plasmodium falciparum is a unicellular protozoan parasite and causative agent of a severe form of malaria in humans, accounting for very high worldwide fatality rates. At the molecular level, survival of the parasite within the human host is mediated by P. falciparum heat shock proteins (PfHsps) that provide protection during febrile episodes. The ATP-dependent chaperone activity of Hsp70 relies on the co-chaperone J domain protein (JDP), with which it forms a chaperone-co-chaperone complex. The exported P. falciparum JDP (PfJDP), PFA0660w, has been shown to stimulate the ATPase activity of the exported chaperone, PfHsp70-x. Furthermore, PFA0660w has been shown to associate with another exported PfJDP, PFE0055c, and PfHsp70-x in J-dots, highly mobile structures found in the infected erythrocyte cytosol. Therefore, the present study aims to conduct a structural and functional characterization of the full-length exported PfJDP, PFE0055c. Recombinant PFE0055c was successfully expressed and purified and found to stimulate the basal ATPase activity of PfHsp70-x to a greater extent than PFA0660w but, like PFA0660w, did not significantly stimulate the basal ATPase activity of human Hsp70. Small-molecule inhibition assays were conducted to determine the effect of known inhibitors of JDPs (chalcone, C86) and Hsp70 (benzothiazole rhodacyanines, JG231 and JG98) on the basal and PFE0055c-stimulated ATPase activity of PfHsp70-x. In this study, JG231 and JG98 were found to inhibit both the basal and PFE0055c-stimulated ATPase activity of PfHsp70-x. C86 only inhibited the PFE0055c-stimulated ATPase activity of PfHsp70-x, consistent with PFE0055c binding to PfHsp70-x through its J domain. This research has provided further insight into the molecular basis of the interaction between these exported plasmodial chaperones, which could inform future antimalarial drug discovery studies

Improving Age of Information with Interference Problem in Long-Range Wide Area Networks

Low Power Wide Area Networks (LPWAN) offer a promising wireless communications technology for Internet of Things (IoT) applications. Among various existing LPWAN technologies, Long-Range WAN (LoRaWAN) consumes minimal power and provides virtual channels for communication through spreading factors. However, LoRaWAN suffers from the interference problem among nodes connected to a gateway that uses the same spreading factor. Such interference increases data communication time, thus reducing data freshness and suitability of LoRaWAN for delay-sensitive applications. To minimize the interference problem, an optimal allocation of the spreading factor is requisite for determining the time duration of data transmission. This paper proposes a game-theoretic approach to estimate the time duration of using a spreading factor that ensures on-time data delivery with maximum network utilization. We incorporate the Age of Information (AoI) metric to capture the freshness of information as demanded by the applications. Our proposed approach is validated through simulation experiments, and its applicability is demonstrated for a crop protection system that ensures real-time monitoring and intrusion control of animals in an agricultural field. The simulation and prototype results demonstrate the impact of the number of nodes, AoI metric, and game-theoretic parameters on the performance of the IoT network

An Energy Efficient Smart Metering System using Edge Computing in LoRa Network

An important research issue in smart metering is to correctly transfer the smart meter readings from consumers to the operator within the given time period by consuming minimum energy. In this paper, we propose an energy efficient smart metering system using Edge computing in Long Range (LoRa). We assume that all appliances in a house are connected to a smart meter that is affixed with Edge device and LoRa node for processing and transferring the processed smart meter readings, respectively. The energy consumption of the appliances can be represented as an energy multivariate time series. The system first proposes a deep learning-based compression-decompression model for reducing the size of the energy time series at the Edge devices. Next, it formulates an optimization problem for finding the suitable compressed energy time series to reduce the energy consumption and delay of the system. Finally, the system presents an algorithm for selecting the suitable spreading factors to transfer the compressed time series to the operator in the given time. Our simulation and prototype results demonstrate the impact of the parameters of the compression model, network, and the number of smart meters and appliances on delay, energy consumption, and accuracy of the system

Proteomic analysis of human plasma in chronic rheumatic mitral stenosis reveals proteins involved in the complement and coagulation cascade

BACKGROUND: Rheumatic fever in childhood is the most common cause of Mitral Stenosis in developing countries. The disease is characterized by damaged and deformed mitral valves predisposing them to scarring and narrowing (stenosis) that results in left atrial hypertrophy followed by heart failure. Presently, echocardiography is the main imaging technique used to diagnose Mitral Stenosis. Despite the high prevalence and increased morbidity, no biochemical indicators are available for prediction, diagnosis and management of the disease. Adopting a proteomic approach to study Rheumatic Mitral Stenosis may therefore throw some light in this direction. In our study, we undertook plasma proteomics of human subjects suffering from Rheumatic Mitral Stenosis (n = 6) and Control subjects (n = 6). Six plasma samples, three each from the control and patient groups were pooled and subjected to low abundance protein enrichment. Pooled plasma samples (crude and equalized) were then subjected to in-solution trypsin digestion separately. Digests were analyzed using nano LC-MS(E). Data was acquired with the Protein Lynx Global Server v2.5.2 software and searches made against reviewed Homo sapiens database (UniProtKB) for protein identification. Label-free protein quantification was performed in crude plasma only. RESULTS: A total of 130 proteins spanning 9–192 kDa were identified. Of these 83 proteins were common to both groups and 34 were differentially regulated. Functional annotation of overlapping and differential proteins revealed that more than 50% proteins are involved in inflammation and immune response. This was corroborated by findings from pathway analysis and histopathological studies on excised tissue sections of stenotic mitral valves. Verification of selected protein candidates by immunotechniques in crude plasma corroborated our findings from label-free protein quantification. CONCLUSIONS: We propose that this protein profile of blood plasma, or any of the individual proteins, could serve as a focal point for future mechanistic studies on Mitral Stenosis. In addition, some of the proteins associated with this disorder may be candidate biomarkers for disease diagnosis and prognosis. Our findings might help to enrich existing knowledge on the molecular mechanisms involved in Mitral Stenosis and improve the current diagnostic tools in the long run. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1559-0275-11-35) contains supplementary material, which is available to authorized users

In silico identification of modulators of J domain protein-Hsp70 interactions in Plasmodium falciparum: a drug repurposing strategy against malaria

Plasmodium falciparum is a unicellular, intracellular protozoan parasite, and the causative agent of malaria in humans, a deadly vector borne infectious disease. A key phase of malaria pathology, is the invasion of human erythrocytes, resulting in drastic remodeling by exported parasite proteins, including molecular chaperones and co-chaperones. The survival of the parasite within the human host is mediated by P. falciparum heat shock protein 70s (PfHsp70s) and J domain proteins (PfJDPs), functioning as chaperones-co-chaperones partnerships. Two complexes have been shown to be important for survival and pathology of the malaria parasite: PfHsp70-x-PFE0055c (exported); and PfHsp70-2-PfSec63 (endoplasmic reticulum). Virtual screening was conducted on the drug repurposing library, the Pandemic Response Box, to identify small-molecules that could specifically disrupt these chaperone complexes. Five top ranked compounds possessing preferential binding affinity for the malarial chaperone system compared to the human system, were identified; three top PfHsp70-PfJDP binders, MBX 1641, zoliflodacin and itraconazole; and two top J domain binders, ezetimibe and a benzo-diazepinone. These compounds were validated by repeat molecular dockings and molecular dynamics simulation, resulting in all the compounds, except for MBX 1461, being confirmed to bind preferentially to the malarial chaperone system. A detailed contact analysis of the PfHsp70-PfJDP binders identified two different types of modulators, those that potentially inhibit complex formation (MBX 1461), and those that potentially stabilize the complex (zoliflodacin and itraconazole). These data suggested that zoliflodacin and itraconazole are potential novel modulators specific to the malarial system. A detailed contact analysis of the J domain binders (ezetimibe and the benzo-diazepinone), revealed that they bound with not only greater affinity but also a better pose to the malarial J domain compared to that of the human system. These data suggested that ezetimibe and the benzo-diazepinone are potential specific inhibitors of the malarial chaperone system. Both itraconazole and ezetimibe are FDA-approved drugs, possess anti-malarial activity and have recently been repurposed for the treatment of cancer. This is the first time that such drug-like compounds have been identified as potential modulators of PfHsp70-PfJDP complexes, and they represent novel candidates for validation and development into anti-malarial drugs

Integrating sequence stratigraphy and rock-physics to interpret seismic amplitudes and predict reservoir quality

This dissertation focuses on the link between seismic amplitudes and reservoir properties. Prediction of reservoir properties, such as sorting, sand/shale ratio, and cement-volume from seismic amplitudes improves by integrating knowledge from multiple disciplines. The key contribution of this dissertation is to improve the prediction of reservoir properties by integrating sequence stratigraphy and rock physics. Sequence stratigraphy has been successfully used for qualitative interpretation of seismic amplitudes to predict reservoir properties. Rock physics modeling allows quantitative interpretation of seismic amplitudes. However, often there is uncertainty about selecting geologically appropriate rock physics model and its input parameters, away from the wells. In the present dissertation, we exploit the predictive power of sequence stratigraphy to extract the spatial trends of sedimentological parameters that control seismic amplitudes. These spatial trends of sedimentological parameters can serve as valuable constraints in rock physics modeling, especially away from the wells. Consequently, rock physics modeling, integrated with the trends from sequence stratigraphy, become useful for interpreting observed seismic amplitudes away from the wells in terms of underlying sedimentological parameters. We illustrate this methodology using a comprehensive dataset from channelized turbidite systems, deposited in minibasin settings in the offshore Equatorial Guinea, West Africa. First, we present a practical recipe for using closed-form expressions of effective medium models to predict seismic velocities in unconsolidated sandstones. We use an effective medium model that combines perfectly rough and smooth grains (the extended Walton model), and use that model to derive coordination number, porosity, and pressure relations for P and S wave velocities from experimental data. Our recipe provides reasonable fits to other experimental and borehole data, and specifically improves the predictions of shear wave velocities. In addition, we provide empirical relations on normal compaction depth trends of porosity, velocities, and VP/VS ratio for shale and clean sands in shallow, supra-salt sediments in the Gulf of Mexico. Next, we identify probable spatial trends of sand/shale ratio and sorting as predicted by the conventional sequence stratigraphic model in minibasin settings (spill-and-fill model). These spatial trends are evaluated using well data from offshore West Africa, and the same well data are used to calibrate rock physics models (modified soft-sand model) that provide links between P-impedance and quartz/clay ratio, and sorting. The spatial increase in sand/shale ratio and sorting corresponds to an overall increase in P-impedance, and AVO intercept and gradient. The results are used as a guide to interpret sedimentological parameters from seismic attributes, away from the well locations. We present a quantitative link between carbonate cement and seismic attributes by combining stratigraphie cycles and the rock physics model (modified differential effective medium model). The variation in carbonate cement volume in West Africa can be linked with two distinct stratigraphic cycles: the coarsening-upward cycles and the fining-upward cycles. Cemented sandstones associated with these cycles exhibit distinct signatures on P-impedance vs. porosity and AVO intercept vs. gradient crossplots. These observations are important for assessing reservoir properties in the West Africa as well as in other analogous depositional environments. Finally, we investigate the relationship between seismic velocities and time temperature index (TTI) using basin and petroleum system modeling at Rio Muni basin, West Africa. We find that both VP and VS increase exponentially with TTI. The results can be applied to predict TTI, and thereby thermal maturity, from observed velocities