Comparative proteomics and glycoproteomics of plasma proteins in Indian visceral leishmaniasis

Background

Visceral leishmaniasis (VL) is a deadly parasitic diseases caused by Leishmania donovani; it is a major health problem in many countries. A lack of proper understanding of the disease biology, poor diagnostic methods and increasing drug resistance are the main reasons for the growing burden of VL infection. Comparative plasma proteomics are a relatively useful technique that can be used to investigate disease-associated alterations that can help in understanding host responses against pathogens, and might be useful in disease management and diagnosis.

Result

In this study, a comparative proteomics and glycoproteomics approach using 2DE and 2D-DIGE was employed between early diagnosed VL patients of all age groups and healthy endemic and non-endemic controls in order to aid the recognition of disease-associated alterations in host plasma. Comparative proteomics was performed by the depletion of seven highly abundant plasma proteins. Comparative glycoproteomics was performed by the depletion of albumin and IgG, followed by purification of plasma glycoproteins using a multi lectin affinity column. From these two approaches, 39 differentially expressed protein spots were identified and sequenced using MALDI-TOF/TOF mass spectrometry. This revealed ten distinct proteins that appeared in multiple spots, suggesting micro-heterogeneity. Among these proteins, alpha-1-antitrypsin, alpha-1-B glycoprotein and amyloid-A1 precursor were up-regulated, whereas vitamin-D binding protein, apolipoprotein-A-I and transthyretin were down-regulated in VL. Alterations in the levels of these proteins in VL-infected plasma were further confirmed by western blot and ELISA.

Conclusions

These proteins may be involved in the survival of parasites, resisting neutrophil elastase, and in their multiplication in macrophages, potentially maintaining endogenous anti-inflammatory and immunosuppressive conditions. Consequently, the results of this study may help in understanding the host response against L.donovani, which could help in the discovery of new drugs and disease management. Finally, these alterations on protein levels might be beneficial in improving early diagnosis considering those as biomarkers in Indian VL.

Electronic supplementary material

The online version of this article (doi:10.1186/s12953-014-0048-z) contains supplementary material, which is available to authorized users.

Differential proteomics study of platelets in asymptomatic constitutional macrothrombocytopenia: altered levels of cytoskeletal proteins

OBJECTIVES

Harris platelet syndrome (HPS), also known as asymptomatic constitutional macrothrombocytopenia (ACMT), is an autosomal dominant platelet disorder characterized by mild-to-severe thrombocytopenia and giant platelets with normal platelet aggregation and absence of bleeding symptoms. We have attempted a comparative proteomics study for profiling of platelet proteins in healthy vs. pathological states to discover characteristic protein expression changes in macrothrombocytes and decipher the factors responsible for the functionally active yet morphologically distinct platelets.

METHODS

We have used 2-D gel-based protein separation techniques coupled with MALDI-ToF/ToF-based mass spectrometric identification and characterization of the proteins to investigate the differential proteome profiling of platelet proteins isolated from the peripheral blood samples of patients and normal volunteers.

RESULTS AND CONCLUSION

Our study revealed altered levels of actin-binding proteins such as myosin light chain, coactosin-like protein, actin-related protein 2/3 complex, and transgelin2 that hint toward the cytoskeletal changes necessary to maintain the structural and functional integrity of macrothrombocytes. We have also observed over expressed levels of peroxiredoxin2 that signifies the prevailing oxidative stress in these cells. Additionally, altered levels of protein disulfide isomerase and transthyretin provide insights into the measures adapted by the macrothrombocytes to maintain their normal functional activity. This first proteomics study of platelets from ACMT may provide an understanding of the structural stability and normal functioning of these platelets in spite of their large size.

Differential thermal stability and oxidative vulnerability of the hemoglobin variants, HbA2 and HbE

Apart from few early biophysical studies, the relative thermal instability of HbE has been only shown by clinical investigations. We have compared in vitro thermal stability of HbE with HbA2 and HbA using optical spectroscopy. From absorption measurements in the soret region, synchronous fluorescence spectroscopy and dynamic light scattering experiments, we have found thermal stability of the three hemoglobin variants following the order HbE<HbA<HbA2 in terms of structural unfolding and aggregation pattern. We have found formation of intermolecular dityrosine fluorophores with characteristic fluorescence signature, at pH >11.0 in all the three variants. Under oxidative stress conditions in presence of hydrogen peroxide, HbE has been found to be more vulnerable to aggregation compared to HbA and HbA2. Taken together, these studies have shown thermal and oxidative instability of HbE and points towards the role of HbE in the upregulation of redox regulators and chaperone proteins in erythrocyte proteome of patients suffering from HbEbeta thalassemia.

Defects in 6 MeV H+ irradiated hydrothermal ZnO single crystal

The effect of 6 MeV H(+) irradiation on hydrothermally grown ZnO single crystal has been investigated using high resolution x-ray diffraction (HRXRD) and optical absorption (ultraviolet-visible) spectroscopy. The increase of the diffuse scattering in the reciprocal space maps measured using HRXRD indicates an increase of the point defect density upon irradiation. Within the penetration depth of x-rays of several micrometres, the defect density increased with increasing distance from the sample surface. On the other hand, the near band gap optical absorption became sharper for the irradiated crystal. This reflects enhanced band to band absorption and reduced sub-band gap absorption due to defects. Temperature dependent photoluminescence spectra of the pristine sample show negative thermal quenching (NTQ) of the luminescence which is due to the presence of two or more donor related defects. Upon irradiation, a single dominant donor bound transition can be found without any temperature induced NTQ. Enhancement of the band edge luminescence and reduction of the defect related luminescence is observed at 10 K. Such changes have been discussed in the light of the hydrogen present in the as-grown state of hydrothermal ZnO.

Binding of polarity-sensitive hydrophobic ligands to erythroid and nonerythroid spectrin: fluorescence and molecular modeling studies

We have used three polarity-sensitive fluorescence probes, 6-propionyl 2-(N,N-dimethyl-amino) naphthalene (Prodan), pyrene and 8-anilino 1-naphthalene sulphonic acid, to study their binding with erythroid and nonerythroid spectrin, using fluorescence spectroscopy. We have found that both bind to prodan and pyrene with high affinities with apparent dissociation constants (Kd) of .50 and .17 μM, for prodan, and .04 and .02 μM, for pyrene, respectively. The most striking aspect of these bindings have been that the binding stoichiometry have been equal to 1 in erythroid spectrin, both in dimeric and tetrameric form, and in tetrameric nonerythroid spectrin. From an estimate of apparent dielectric constants, the polarity of the binding site in both erythroid and nonerythroid forms have been found to be extremely hydrophobic. Thermodynamic parameters associated with such binding revealed that the binding is favored by positive change in entropy. Molecular docking studies alone indicate that both prodan and pyrene bind to the four major structural domains, following the order in the strength of binding to the Ankyrin binding domain > SH3 domain > Self-association domain > N-terminal domain of α-spectrin of both forms of spectrin. The binding experiments, particularly with the tetrameric nonerythroid spectrin, however, indicate more toward the self association domain in offering the unique binding site, since the binding stoichiometry have been 1 in all forms of dimeric and tetrameric spectrin, so far studied by us. Further studies are needed to characterize the hydrophobic binding sites in both forms of spectrin.

DNA barcoding in Mucorales: an inventory of biodiversity

The order Mucorales comprises predominantly fast-growing saprotrophic fungi, some of which are used for the fermentation of foodstuffs but it also includes species known to cause infections in patients with severe immune or metabolic impairments. To inventory biodiversity in Mucorales ITS barcodes of 668 strains in 203 taxa were generated covering more than two thirds of the recognised species. Using the ITS sequences, Molecular Operational Taxonomic Units were defined by a similarity threshold of 99 %. An LSU sequence was generated for each unit as well. Analysis of the LSU sequences revealed that conventional phenotypic classifications of the Mucoraceae are highly artificial. The LSU- and ITS-based trees suggest that characters, such as rhizoids and sporangiola, traditionally used in mucoralean taxonomy are plesiomorphic traits. The ITS region turned out to be an appropriate barcoding marker in Mucorales. It could be sequenced directly in 82 % of the strains and its variability was sufficient to resolve most of the morphospecies. Molecular identification turned out to be problematic only for the species complexes of Mucor circinelloides, M. flavus, M. piriformis and Zygorhynchus moelleri. As many as 12 possibly undescribed species were detected. Intraspecific variability differed widely among mucorealean species ranging from 0 % in Backusella circina to 13.3 % in Cunninghamella echinulata. A high proportion of clinical strains was included for molecular identification. Clinical isolates of Cunninghamella elegans were identified molecularly for the first time. As a result of the phylogenetic analyses several taxonomic and nomenclatural changes became necessary. The genus Backusella was emended to include all species with transitorily recurved sporangiophores. Since this matched molecular data all Mucor species possessing this character were transferred to Backusella. The genus Zygorhynchus was shown to be polyphyletic based on ITS and LSU data. Consequently, Zygorhynchus was abandoned and all species were reclassified in Mucor. Our phylogenetic analyses showed, furthermore, that all non-thermophilic Rhizomucor species belong to Mucor. Accordingly, Rhizomucor endophyticus was transferred to Mucor and Rhizomucor chlamydosporus was synonymised with Mucor indicus. Lecto-, epi- or neotypes were designated for several taxa.

Bacteraemia caused by Sciscionella marina in a lymphoma patient: phenotypically mimicking Nocardia

A 55-year-old female patient with malignant lymphoma after induction chemotherapy developed fever. Blood culture yielded an organism biochemically identified as representing Nocardia spp., but molecular identification (16S rRNA gene sequencing) later identified it as representing Sciscionella marina. This is the first report, to the best of our knowledge, of Sciscionella being isolated from a human sample.

A gas-jet transport and catcher technique for on-line production of radioactive ion beams using an electron cyclotron resonance ion-source

Radioactive ion beams (RIB) have been produced on-line, using a gas-jet recoil transport coupled Electron Cyclotron Resonance (ECR) ion-source at the VECC-RIB facility. Radioactive atoms∕molecules carried through the gas-jet were stopped in a catcher placed inside the ECR plasma chamber. A skimmer has been used to remove bulk of the carrier gas at the ECR entrance. The diffusion of atoms∕molecules through the catcher has been verified off-line using stable isotopes and on-line through transmission of radioactive reaction products. Beams of (14)O (71 s), (42)K (12.4 h), (43)K (22.2 h), and (41)Ar (1.8 h) have been produced by bombarding nitrogen and argon gas targets with proton and alpha particle beams from the K130 cyclotron at VECC. Typical measured intensity of RIB at the separator focal plane is found to be a few times 10(3) particles per second (pps). About 3.2 × 10(3) pps of 1.4 MeV (14)O RIB has been measured after acceleration through a radiofrequency quadrupole linac. The details of the gas-jet coupled ECR ion-source and RIB production experiments are presented along with the plans for the future.

Nucleation in short-range attractive colloids: ordering and symmetry of clusters

Results from extensive Brownian dynamics simulations are presented for nucleation in a system of colloidal particles interacting via a short-range attractive potential. Our analysis shows that, even though the system is not in equilibrium, structures of small size clusters compare well with the theoretically predicted and experimentally observed ground state structures for short-range colloidal systems. In addition, the distribution of the symmetric structures in nucleation is comparable to the distribution seen in equilibrium. We also investigate how the shape and structure of fluctuating clusters in the prenucleation regime affect the formation of a stable nucleating cluster.

Evidence for oxidative stress in osteoarthritis

Evidence of increased oxidative stress in patients of osteoarthritis in comparison with healthy control subjects was investigated by measuring the thiobarbituric acid reactive substances (TBARS), vitamin C, reduced glutathione (GSH) and the activities of superoxide dismutase (SOD), catalase and glutathione peroxidase (GPx) in erythrocytes. It was observed that osteoarthritis patients were more susceptible to oxidative damage than controls as evident from increased TBARS and decreased ascorbic acid, GSH, catalase and GPx in erythrocytes. Significant increase in SOD activity found in patients might be an adaptive response. With the understanding of the role of antioxidants in arthritis, it is becoming increasingly clear that these agents seem to be beneficial in osteoarthritis.

Identical RNA-protein interactions in vivo and in vitro and a scheme of folding the newly synthesized proteins by ribosomes

A distinct three-dimensional shape of rRNA inside the ribosome is required for the peptidyl transfer activity of its peptidyltransferase center (PTC). In contrast, even the in vitro transcribed PTC RNA interacts with unfolded protein(s) at about five sites to let them attain their native states. We found that the same set of conserved nucleotides in the PTC interact identically with nascent and chemically unfolded proteins in vivo and in vitro, respectively. The time course of this interaction, difficult to follow in vivo, was observed in vitro. It suggested nucleation of folding of cytosolic globular proteins vectorially from hydrophilic N to hydrophobic C termini, consistent with our discovery of a regular arrangement of cumulative hydrophobic indices of the peptide segments of cytosolic proteins from N to C termini. Based on this observation, we propose a model here for the nucleation of folding of the nascent protein chain by the PTC.

Photoluminescence and positron annihilation spectroscopic investigation on a H(+) irradiated ZnO single crystal

Low temperature photoluminescence and room temperature positron annihilation spectroscopy have been employed to investigate the defects incorporated by 6 MeV H(+) ions in a hydrothermally grown ZnO single crystal. Prior to irradiation, the emission from donor bound excitons is at 3.378 eV (10 K). The irradiation creates an intense and narrow emission at 3.368 eV (10 K). The intensity of this peak is nearly four times that of the dominant near band edge peak of the pristine crystal. The characteristic features of the 3.368 eV emission indicate its origin as a 'hydrogen at oxygen vacancy' type defect. The positron annihilation lifetime measurement reveals a single component lifetime spectrum for both the unirradiated (164 ± 1 ps) and irradiated crystal (175 ± 1 ps). It reflects the fact that the positron lifetime and intensity of the new irradiation driven defect species are a little higher compared to those in the unirradiated crystal. However, the estimated defect concentration, even considering the high dynamic defect annihilation rate in ZnO, comes out to be ∼4 × 10(17) cm(-3) (using SRIM software). This is a very high defect concentration compared to the defect sensitivity of positron annihilation spectroscopy. A probable reason is the partial filling of the incorporated vacancies (positron traps), which in ZnO are zinc vacancies. The positron lifetime of ∼175 ps (in irradiated ZnO) is consistent with recent theoretical calculations for partially hydrogen-filled zinc vacancies in ZnO. Passivation of oxygen vacancies by hydrogen is also reflected in the photoluminescence results. A possible reason for such vacancy filling (at both Zn and O sites) due to irradiation has also been discussed.

Oxidative interaction between OxyHb and ATP: a spectroscopic study

The binding mode between oxyhemoglobin (oxyHb) and adenosine triphosphate (ATP) has been studied using absorption and fluorescence spectroscopy. OxyHb forms a ground state complex with ATP supported by five isosbestic points which appear in absorption spectra of oxyHb in buffer solution on addition of ATP. Moreover, the changes in absorption spectra suggest an oxidative interaction between the particular interacting systems. The binding constant has been determined from the quenching of fluorescence of oxyHb in the presence of a varied concentration of ATP, and that is 3.8 × 10(3) M(-1) at 25 °C. The negative changes in entropy and enthalpy indicate that the binding is enthalpy driven and the hydrogen bond and van der Waals (stacking) interactions play a major role. The oxygen affinity of oxyHb decreases with simultaneous formation of metHb in the presence of ATP. ATP-induced structural changes have been affirmed using both circular dichroism spectroscopy and synchronous fluorescence. A theoretical docking study gives the molecular details about the binding site of ATP in oxyHb.