[Show abstract][Hide abstract] ABSTRACT: Objective:
The occurrence of yeast infections in humans has increased, with the species belonging to genus Candida still being the most common cause of infection. Nevertheless, infections caused by less common yeasts have been widely reported in recent years. The main objective of this study was to assess the potential of these less common saprophytic yeasts to invade the host cell, which is essential for causing systemic infections.
Material and methods:
Various yeast isolates were identified by DNA sequence information of PCR amplified ITS region. The purported saprophytic yeasts were characterized for internalization by mammalian cells in vitro, by staining the F-actin.
The identification of different yeast isolates from various patients revealed that 70% of the isolates belonged to the genus Candida, while remaining 30% of the isolates were yeasts not belonging to genus Candida. These non-Candida clinical isolates, either in yeast or hyphal forms, were efficiently internalized by human epithelial cells. The internalization was marked by a process of actin polymerization surrounding the invading yeast. Such uptake by epithelial cells signifies traversal of cell barrier by yeast cells during infection in vivo.
[Show abstract][Hide abstract] ABSTRACT: The recent 2013-15 epidemic of Ebola virus disease (EVD) has initiated extensive sequencing and analysis of ebolavirus genomes. All ebolavirus genomes available until December 2014 have been collated and analyzed in this study to obtain phylogenetic relationship and uncover the variations amongst them. The terminal 'leader' and 'trailer' nucleotide sequences of the genomes were omitted and analysis of the intermediate region accommodating the sole seven genes (hepta-CDS region) of the virus showed the relative stability of the genome, including the ones isolated from the current epidemic. The genome information was scrutinized to detect the variation in the surface glycoprotein gene and annotate its three protein products, resulting from its atypical transcription. This study will make an easy understanding of the genomes for those who desire to exploit the genome sequences for different investigations in EVD.
No preview · Article · Jun 2015 · Biochemical and Biophysical Research Communications
[Show abstract][Hide abstract] ABSTRACT: Wolbachia are maternally inherited bacterial endo-symbionts of arthropods distributed among a wide range of hosts. It is now well known that they induce reproductive manipulations in their arthropod hosts by various phenotypic effects. The objective of the present study was to investigate Wolbachia infection among the insect order Odonata comprising 16 species from 5 families. Fifteen odonate species representing five families were found to harbour Wolbachia with the overall infection rate of 70%, out of which four-teen species are reported for the first time. According to multilocus sequence typing (MLST) data and phylo-genetic analysis, all odonate Wolbachia species belong to supergroup F, except Trithemis pallindinervis, which belongs to supergroup B. MLST data reveal 20 new, highly similar STs (99.32 ± 0.34). We found a high rate of Wolbachia infection in Odonata of India, which indicates importance of this association. The charac-terization of these Wolbachia strains promises to lead to a deeper insight into this interaction, which is essential for further studies based on their phenotypic effects. The study suggests that all the characterized Wolbachia STs are totally new and arise as a result of point mutation.
[Show abstract][Hide abstract] ABSTRACT: Leishmania donovani is a kinetoplastid protozoan that causes a severe and fatal disease kala-azar, or visceral leishmaniasis. L. donovani infects human host after the phlebotomine sandfly takes a blood meal and resides within the phagolysosome of infected macrophages. Previous studies on host-parasite interactions have not focused on Leishmania organelles and the role that they play in the survival of this parasite within macrophages. Leishmania possess glycosomes that are unique and specialized subcellular microbody organelles. Glycosomes are known to harbor most peroxisomal enzymes and, in addition, they also possess nine glycolytic enzymes. In the present study, we have carried out proteomic profiling using high resolution mass spectrometry of a sucrose density gradient-enriched glycosomal fraction isolated from L. donovani promastigotes. This study resulted in the identification of 4022 unique peptides, leading to the identification of 1355 unique proteins from a preparation enriched in L. donovani glycosomes. Based on protein annotation, 566 (41.8%) were identified as hypothetical proteins with no known function. A majority of the identified proteins are involved in metabolic processes such as carbohydrate, lipid, and nucleic acid metabolism. Our present proteomic analysis is the most comprehensive study to date to map the proteome of L. donovani glycosomes.
No preview · Article · Mar 2015 · Omics A Journal of Integrative Biology
[Show abstract][Hide abstract] ABSTRACT: Leishmania donovani is a kinetoplastid protozoan parasite which causes a fatal disease visceral leishmaniasis in humans. Genome sequencing of L. donovani revealed information about the arrangement of genes and genome architecture. After curation of the genome sequence, many genes in L. donovani were assigned as truncated or "partial" genes by the genome sequencing group. In the present study, we have carried out an extensive analysis and attempted to improve the gene models of these partial genes. Our analysis resulted in the identification of 308 partial genes in L. donovani, which were further categorized as C-terminal extensions, joining of genes, tandemly repeated paralogs and wrong chromosomal assignments. We have analyzed each of these genes from these categories and have improved the annotation of existing gene models in L. donovani. Some of these corrections have been confirmed by mass spectrometry derived peptide data from our previous comparative proteogenomics study in L. donovani.
[Show abstract][Hide abstract] ABSTRACT: Background: Oral therapy for pulmonary tuberculosis (TB) treatment suffers from the limitation of hepatic metabolism leading insufficient concentration of antitubercular (anti‑TB) drugs in alveolar macrophage which harbors Mycobacterium tuberculosis (MTB). Targeted aerosol delivery of antituberculous drug to lung is efficient for treating local lung TB infection. Objective: The present study was aimed to evaluate rifapentine (RPT) loaded proliposomal dry powder for inhalation (RLDPI) for anti‑TBactivity and cytotoxicity in vitro. In vivo toxicity study was also undertaken in Wistar rats to determine safe concentration of RLDPI for administration.
Materials and Methods: Anti‑TB activity of developed RLDPI was assessed using drug susceptibility testing (DST) on Mycobacteria growth indicator tube (MGIT) method. In vitro cytotoxicity was performed in A549 cell lines and IC50 values were used to compare the cytotoxicity of formulation with pure RPT. In vivo repeated dose toxicity study was undertaken using Wistar rats at three different doses for 28‑days by intratracheal insufflations method. Results: The results of DST study revealed sensitivity of tubercle bacteria to RLDPI at concentration equivalent to 10 μg/mL of RPT. This study confirmed anti‑TB potential of RPT in spray‑dried RLDPI, though the spray drying method is reported to reduce activity of drugs. Cytotoxicity study in A549 cells demonstrated that RPT when encapsulated in liposomes as RLDPI was safe to cells as compared to pure RPT. In vivo toxicity study revealed that RPT in the form of RLDPI was safe at 1 and 5 mg/kg dose. However, mortality was seen at higher dose (10 mg/kg), possibly because of liver and kidney damage. Conclusion: Thus, these studies demonstrated safety of RLDPI for the treatment of pulmonary TB.
Full-text · Article · Sep 2014 · Toxicology International
[Show abstract][Hide abstract] ABSTRACT: The aim of the present study was to establish the potential of montelukast loaded nanostructured lipid carrier (MNLC) for pulmonary application. The formulated nanoparticles were evaluated in vitro for aerodynamic characterization and in vivo for pulmokinetics in Wistar rats. The in vitro cytotoxicity was performed on A549 cell line and compared with montelukast-aqueous solution. MNLC was prepared with montelukast (0.2%), Precirol ATO5 (solid lipid), and Capryol-90 (liquid lipid) in the ratio of 7:3 using melt-emulsification-homogenization method. dl-Pyrrolidonecarboxylic acid salt of l-cocyl arginine ethyl ester (CAE), a biodegradable surfactant in the concentration of 1% was used to stabilize the nanoparticles. The particle size and encapsulation efficiency (EE) were 184.6 ± 2.7 nm and >95%, respectively. MNLC-Dry powder for inhalation (DPI) was prepared by lyophilization using 3% mannitol as cryoprotectant and carrier. MNLC-DPI was evaluated for flow, crystallographic and thermal properties. Mass median diameters (MMD) and density for MNLC-DPI were found to be 15.1 ± 1.4 μm and 0.051 ± 0.002 g/cc, respectively. In vitro aerosol performance study indicated more than 95% of the emitted dose (ED) at both the flow rates studied. Mass median aerodynamic diameters (MMAD) of 3.24 ± 0.67 μm with 69.98 ± 1.9% fine particle fraction (FPF) were obtained at 30 L/min flow rate, whereas at 60 L/min MMAD and FPF were found to be 2.83 ± 0.46 μm and 90.22 ± 2.6%, respectively. In vitro cytotoxicity study on A549 cells revealed higher safety of MNLC than pure drug. The pulmonary pharmacokinetic study demonstrated improved bioavailability, longer residence of drug in the lung and targeting factor of 11.76 for MNLC as compared to montelukast-aqueous solution. Thus, the results of the study demonstrated the potential of montelukast lipidic nanoparticulate formulation to improve the efficacy with reduced toxicity leading to better performance of drug as MNLC-DPI for inhalation use.
No preview · Article · Jul 2014 · European Journal of Pharmaceutics and Biopharmaceutics
[Show abstract][Hide abstract] ABSTRACT: Abstract Among the neglected tropical diseases, leishmaniasis is one of the most devastating, resulting in significant mortality and contributing to nearly 2 million disability-adjusted life years. Cutaneous leishmaniasis is a debilitating disorder caused by the kinetoplastid protozoan parasite Leishmania major, which results in disfiguration and scars. L. major genome was the first to be sequenced within the genus Leishmania. Use of proteomic data for annotating genomes is a complementary approach to conventional genome annotation approaches and is referred to as proteogenomics. We have used a proteogenomics-based approach to map the proteome of L. major and also annotate its genome. In this study, we searched L. major promastigote proteomic data against the annotated L. major protein database. Additionally, we searched the proteomic data against six-frame translated L. major genome. In all, we identified 3613 proteins in L. major promastigotes, which covered 43% of its proteome. We also identified 26 genome search-specific peptides, which led to the identification of three novel genes previously not identified in L. major. We also corrected the annotation of N-termini of 15 genes, which resulted in extension of their protein products. We have validated our proteogenomics findings by RT-PCR and sequencing. In addition, our study resulted in identification of 266 N-terminally acetylated peptides in L. major, one of the largest acetylated peptide datasets thus far in Leishmania. This dataset should be a valuable resource to researchers focusing on neglected tropical diseases.
Full-text · Article · Jun 2014 · Omics A Journal of Integrative Biology
[Show abstract][Hide abstract] ABSTRACT: The Lonar crater is an unusually well-preserved meteorite impact structure that is located in one of the largest volcanic provinces on Earth (i.e., the Deccan Traps in India). The diversity of endoliths in Lonar crater basalts or Deccan flood basalts is not known. Here, the phylogenetic diversity of endolithic Bacteria and Archaea inhabiting basalts retrieved from four discrete sampling sites on the Lonar crater walls and the lake-bed was assessed using culture-independent molecular methods. Taxonomic classification of 16S rRNA gene sequences from all four basalt samples revealed similarities as well as dissimilarities in the presence or absence of several prokaryotic taxa. Cluster analysis of Denaturing gradient gel electrophoresis fingerprints and UniFrac analysis of clone library sequences suggested substantial variations in bacterial and archaeal diversity between crater-wall and lake-bed sites. Although sequences affiliated to the bacterial phyla Actinobacteria, Acidobacteria and Chloroflexi were relatively more abundant in crater-wall basalts than in lake-bed basalts; the reverse was observed for sequences related to Proteobacteria, Firmicutes, Cyanobacteria and Bacteroidetes. Archaea in crater-wall and lake-bed basalt libraries were almost completely represented by Thaumarchaeota and Euryarchaeota, respectively. Diversity indices and richness estimates suggested the diversity of endolithic Bacteria to be higher than that of Archaea in the Lonar crater basalts. A substantial number of clone library sequences did not affiliate with extant Bacteria and Archaea. The detection of several putative lineages associated with C, N and S cycling suggests that the Lonar crater basalts are colonized by metabolically diverse prokaryotic communities involved in biogeochemical cycling of major elements.
[Show abstract][Hide abstract] ABSTRACT: Network of signaling proteins and functional interaction between the infected cell and the leishmanial parasite, though are not well understood, may be deciphered computationally by reconstructing the immune signaling network. As we all know signaling pathways are well-known abstractions that explain the mechanisms whereby cells respond to signals, collections of pathways form networks, and interactions between pathways in a network, known as cross-talk, enables further complex signaling behaviours. In silico perturbations can help identify sensitive crosstalk points in the network which can be pharmacologically tested. In this study, we have developed a model for immune signaling cascade in leishmaniasis and based upon the interaction analysis obtained through simulation, we have developed a model network, between four signaling pathways i.e., CD14, epidermal growth factor (EGF), tumor necrotic factor (TNF) and PI3 K mediated signaling. Principal component analysis of the signaling network showed that EGF and TNF pathways can be potent pharmacological targets to curb leishmaniasis. The approach is illustrated with a proposed workable model of epidermal growth factor receptor (EGFR) that modulates the immune response. EGFR signaling represents a critical junction between inflammation related signal and potent cell regulation machinery that modulates the expression of cytokines.
No preview · Article · Dec 2013 · Systems and Synthetic Biology
[Show abstract][Hide abstract] ABSTRACT: Modulated immune signal (CD14-TLR and TNF) in leishmaniasis can be linked to EGFR pathway involved in wound healing, through crosstalk points. This signaling network can be further linked to a synthetic gene circuit acting as a positive feedback loop to elicit a synchronized intercellular communication among the immune cells which may contribute to a better understanding of signaling dynamics in leishmaniasis.
Network reconstruction with positive feedback loop, simulation (ODE 15s solver) and sensitivity analysis of CD14-TLR, TNF and EGFR was done in Simbiology (MATLAB 7.11.1). Cytoscape and adjacency matrix was used to calculate network topology. PCA was extracted by using sensitivity coefficient in MATLAB. Model reduction was done using time, flux and sensitivity score.
Network has five crosstalk points: NIK, IkB_NFkB and MKK (4/7, 3/6, 1/2) which shows high flux and sensitivity. PI3K in EGFR pathway show high flux and sensitivity. PCA score was high for cytoplasmic ERK1/2, PI3K, Atk, STAT1/3 and nuclear JNK. Of the 125 parameters, 20% are crucial as deduced by model reduction.
EGFR can be linked to CD14-TLR and TNF through the MAPK crosstalk points. These pathways may be controlled through Ras and Raf that lie upstream of signaling components ERK ½ (c) and JNK (n) that have a high PCA score via a synthetic gene circuit for activating cell-cell communication to elicit an inflammatory response. Also a disease resolving effect may be achieved through PI3K in the EGFR pathway.
The reconstructed signaling network can be linked to a gene circuit with a positive feedback loop, for cell-cell communication resulting in synchronized response in the immune cell population, for disease resolving effect in leishmaniasis.
No preview · Article · Aug 2013 · Biochimica et Biophysica Acta
[Show abstract][Hide abstract] ABSTRACT: Germ band retraction (GBR) stage is one of the important stages during insect development. It is associated with an extensive epithelial morphogenesis and may also be pivotal in generation of morphological diversity in insects. Despite its importance, only a handful of studies report the transcriptome repertoire of this stage in insects. Here, we report generation, annotation and analysis of ESTs from the embryonic stage (16-22 h post fertilization) of laboratoryreared Anopheles stephensi mosquitoes. A total of 1002 contigs were obtained upon clustering of 1140 high-quality ESTs, which demonstrates an astonishingly low transcript redundancy (12.1 percent). Putative functions were assigned only to 213 contigs (21 percent), comprising mainly of transcripts encoding protein synthesis machinery. Approximately 78 percent of the transcripts remain uncharacterized, illustrating a lack of sequence information about the genes expressed in the embryonic stages of mosquitoes. This study highlights several novel transcripts, which apart from insect development, may significantly contribute to the essential biological complexity underlying insect viability in adverse environments. Nonetheless, the generated sequence information from this work provides a comprehensive resource for genome annotation, microarray development, phylogenetic analysis and other molecular biology applications in entomology.
Full-text · Article · Jun 2013 · Journal of Biosciences
[Show abstract][Hide abstract] ABSTRACT: Differences in midgut bacterial communities of Aedes aegypti, the primary mosquito vector of dengue viruses (DENV), might influence the susceptibility of these mosquitoes to infection by DENV. As a first step toward addressing this hypothesis, comparative analysis of bacterial communities from midguts of mosquito strains with differential genetic susceptibility to DENV was performed. 16S rRNA gene libraries and real-time PCR approaches were used to characterize midgut bacterial community composition and abundance in three Aedes aegypti strains: MOYO, MOYO-R, and MOYO-S. Although Pseudomonas spp.-related clones were predominant across all libraries, some interesting and potentially significant differences were found in midgut bacterial communities among the three strains. Pedobacter sp.- and Janthinobacterium sp.-related phylotypes were identified only in the MOYO-R strain libraries, while Bacillus sp. was detected only in the MOYO-S strain. Rahnella sp. was found in MOYO-R and MOYO strains libraries but was absent in MOYO-S libraries. Both 16S rRNA gene library and real-time PCR approaches confirmed the presence of Pedobacter sp. only in the MOYO-R strain. Further, real-time PCR-based quantification of 16S rRNA gene copies showed bacterial abundance in midguts of the MOYO-R strain mosquitoes to be at least 10-100-folds higher than in the MOYO-S and MOYO strain mosquitoes. Our study identified some putative bacteria with characteristic physiological properties that could affect the infectivity of dengue virus. This analysis represents the first report of comparisons of midgut bacterial communities with respect to refractoriness and susceptibility of Aedes aegypti mosquitoes to DENV and will guide future efforts to address the potential interactive role of midgut bacteria of Aedes aegypti mosquitoes in determining vectorial capacity for DENV.
Full-text · Article · May 2013 · Parasitology Research
[Show abstract][Hide abstract] ABSTRACT: Unlabelled:
The kinetoplastid protozoan parasite, Leishmania donovani, is the causative agent of kala azar or visceral leishmaniasis. Kala azar is a severe form of leishmaniasis that is fatal in the majority of untreated cases. Studies on proteomic analysis of L. donovani thus far have been carried out using homology-based identification based on related Leishmania species (L. infantum, L. major and L. braziliensis) whose genomes have been sequenced. Recently, the genome of L. donovani was fully sequenced and the data became publicly available. We took advantage of the availability of its genomic sequence to carry out a more accurate proteogenomic analysis of L. donovani proteome using our previously generated dataset. This resulted in identification of 17,504 unique peptides upon database-dependent search against the annotated proteins in L. donovani. These peptides were assigned to 3999 unique proteins in L. donovani. 2296 proteins were identified in both the life stages of L. donovani, while 613 and 1090 proteins were identified only from amastigote and promastigote stages, respectively. The proteomic data was also searched against six-frame translated L. donovani genome, which led to 255 genome search-specific peptides (GSSPs) resulting in identification of 20 novel genes and correction of 40 existing gene models in L. donovani.
Leishmania donovani genome sequencing was recently completed, which permitted us to use a proteogenomic approach to map its proteome and to carry out annotation of it genome. This resulted in mapping of 50% (3999 proteins) of L. donovani proteome. Our study identified 20 novel genes previously not predicted from the L. donovani genome in addition to correcting annotations of 40 existing gene models. The identified proteins may help in better understanding of stage-specific protein expression profiles in L. donovani and to identify novel stage-specific drug targets in L. donovani which could be used in the treatment of leishmaniasis. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
Full-text · Article · Apr 2013 · Journal of proteomics
[Show abstract][Hide abstract] ABSTRACT: Background
Ochrobactrum intermedium is an emerging opportunistic pathogen of humans that is closely related to members of the genus Brucella. Earlier, we reported the case of an Indian subject with non-ulcer dyspeptic symptoms whose urease positive gastric biopsy revealed the presence of Helicobacter pylori along with non-Helicobacter like bacteria, eventually cultured and identified as O. intermedium strain M86.
Here, we describe the unclosed draft genome of the strain M86 with a length of 5,188,688 bp and mean G+C content of 57.9%. We have also identified many putative gene clusters that might be responsible for its persistence in the gastric mucosa.Comparative analysis of genomic features of Ochrobactrum intermedium strain M86 and Ochrobactrum intermedium LMG 3301T was also done.
This paper attempts to gain whole-genome based insights into the putative gene determinants of O. intermedium for survival in the highly acidic stomach lumen environment .Identification of genes putatively involved in the various metabolic pathways may lead to a better understanding of the survival of O. intermdedium in acidic condition.
[Show abstract][Hide abstract] ABSTRACT: Bacillus lentus BI377 (B. lentus BI377) an alkaliphilic strain has accomplished the discriminate color removal strategy for Reactive Red sulfonated azoic recalcitrant irrespective of their molecular structure. During the decolorization experiment, it was observed that the diazo dye first followed chromophoric cleavage by azoreductase via typical azoreduction whereas, in case of monoazo dye, cleavage took place by peroxidase via successive electron transfers to oxide surface resulting in the asymmetric cleavage of the azo bond. Dismutation of oxidative stress by reactive metabolites has confirmed by superoxide dismutase activity. Carbon monoxide (CO) binding spectra, the content of cytochrome P450 and spectroscopy analysis by GCMS, FTIR and (1)H NMR of intermediate metabolites indicated the differentiate pattern of diazo and monoazo dye decolorization fuse to central metabolic pathway. Declined percentage of TOC and the cytotoxicity (MTT) study confirmed that environmentally benign intermediates may lead to mineralization.
Full-text · Article · Dec 2012 · Bioresource Technology