The ER stress-mediated apoptosis has been implicated in several neurodegenerative diseases; however, its role in HIV/neuroAIDS remains largely unexplored. The present study was undertaken to assess the involvement and detailed mechanism of IRE1α pathway in HIV-1 gp120-mediated ER stress and its possible involvement in cell death. Various signaling molecules for IRE1α pathway were assessed using SVGA cells, primary astrocytes and gp120 transgenic mice, which demonstrated gp120-mediated increase in phosphorylated JNK, XBP-1 and AP-1 leading to upregulation of CHOP. Furthermore, HIV-1 gp120-mediated activation of IRE1α also increased XBP-1 splicing. The functional consequence of gp120-mediated ER stress was determined via assessment of gp120-mediated cell death using PI staining and MTT assay. The gp120-mediated cell death also involved caspase-9/caspase-3-mediated apoptosis. These findings were confirmed with the help of specific siRNA for IRE1α, JNK, AP-1, BiP and CHOP showing significant reduction in gp120-mediated CHOP expression. Additionally, silencing all the intermediates also reduced the gp120-mediated cell death and caspase-9/caspase-3 activation at differential levels. This study provides ER-stress as a novel therapeutic target in the management of gp120-mediated cell death and possibly in the treatment of neuroAIDS.

Methamphetamine (MA), a psychostimulant drug has been associated with a variety of neurotoxic effects which are thought to be mediated by induction of pro-inflammatory cytokines/chemokines, oxidative stress and damage to blood-brain-barrier. Conversely, the ER stress-mediated apoptosis has been implicated in several neurodegenerative diseases. However, its involvement in MA-mediated neurodegenerative effects remains largely unexplored. The present study was undertaken to assess the effect of MA on ER stress and its possible involvement in apoptosis. For this purpose, SVGA astrocytes were treated with MA, which induced the expressions of BiP and CHOP at both, mRNA and protein levels. This phenomenon was also confirmed in HFA and various regions of mouse brain. Assessment of IRE1α, ATF6 and PERK pathways further elucidated the mechanistic details underlying MA-mediated ER stress. Knockdown of various intermediate molecules in ER stress pathways using siRNA demonstrated reduction in MA-mediated CHOP. Finally, MA-mediated apoptosis was demonstrated via MTT assay and TUNEL staining. The involvement of ER stress in the apoptosis was demonstrated with the help of MTT and TUNEL assays in the presence of siRNA against various ER stress proteins. The apoptosis also involved activation of caspase-3 and caspase-9, which was reversed by knockdown with various siRNAs. Altogether, this is the first report demonstrating mechanistic details responsible for MA-mediated ER stress and its role in apoptosis. This study provides a novel group of targets that can be explored in future for management of MA-mediated cell death and MA-associated neurodegenerative disorders.

Albizzia lebbeck Benth. (Mimosaceae) is a medicinal tree used to treat several inflammatory ailments in the Indian traditional Ayurvedic system of medicine. The aim of the present study was to evaluate the possible anti-inflammatory activity of the aqueous (AE) and ethanolic (EE) extracts of the leaves of A. lebbeck to support the ethnopharmacological claims. The study was carried out using Wistar rats (100-150 g). The AE and EE were prepared using the Soxhlet extraction process. The anti-inflammatory activity of the AE and EE of the leaves of A. lebbeck were studied using carrageenan-induced paw edema and cotton pellet-induced granuloma models. The AE and EE of the leaves of A. lebbeck at doses of 50, 100, and 200 mg/kg p.o. (oral administration) showed a dose-dependent and significant (p < 0.05) inhibition of carrageenan-induced hind paw edema with maximum percentage inhibition (PI) values of 22.34, 30.85, 39.36 and 22.53, 32.98, 42.55, respectively. The AE and EE at doses of 50, 100, 200 mg/kg p.o. significantly (p < 0.05) inhibited granuloma formation with PI values of 19.07, 27.57, 38.55 and 23.93, 32.23, 42.33, respectively. The AE and EE of the leaves of A. lebbeck showed significant (p < 0.05) anti-inflammatory activity.

Protein secretion systems used by almost all bacteria are highly significant for the normal existence and interaction of bacteria with their host. The accumulation of genome sequence data in past few years has provided great insights into the distribution and function of these secretion systems. In this study, a support vector machine (SVM)- based method, SSPred was developed for the automated functional annotation of proteins involved in secretion systems further classifying them into five major sub-types (Type-I, Type-II, Type-III, Type-IV and Sec systems). The dataset used in this study for training and testing was obtained from KEGG and SwissProt database and was curated in order to avoid redundancy. To overcome the problem of imbalance in positive and negative dataset, an ensemble of SVM modules, each trained on a balanced subset of the training data were used. Firstly, protein sequence features like amino-acid composition (AAC), dipeptide composition (DPC) and physico-chemical composition (PCC) were used to develop the SVM-based modules that achieved an average accuracy of 84%, 85.17% and 82.59%, respectively. Secondly, a hybrid module (hybrid-I) integrating all the previously used features was developed that achieved an average accuracy of 86.12%. Another hybrid module (hybrid-II) developed using evolutionary information of a protein sequence extracted from position-specific scoring matrix and amino-acid composition achieved a maximum average accuracy of 89.73%. On unbiased evaluation using an independent data set, SSPred showed good prediction performance in identification and classification of secretion systems. SSPred is a freely available World Wide Web server at http//www.bioinformatics.org/sspred.

HIV-associated neurocognitive disorders (HAND) exist in approximately 50% of infected individuals even after the introduction of highly active antiretroviral therapy. HIV-1 Tat has been implicated in HIV-associated neurotoxicity mediated through production of pro-inflammatory cytokines like IL-6 and IL-8 by astrocytes among others as well as oxidative stress. However, the underlying mechanism(s) in the up-regulation of IL-6 and IL-8 are not clearly understood. The present study was designed to determine the mechanism(s) responsible for IL-6 and IL-8 up-regulation by HIV-1 Tat.

Diabetes mellitus (DM) often causes chronic inflammation, hypertrophy, apoptosis and fibrosis in the heart and subsequently leads to myocardial remodeling, deteriorated cardiac function and heart failure. However, the etiology of the cardiac disease is unknown. Therefore, we assessed the gene expression in the left ventricle of diabetic and non-diabetic mice using Affymetrix microarray analysis. Allograft inflammatory factor-1 (AIF-1), one of the top downregulated B cell inflammatory genes, is associated with B cell functions in inflammatory responses. Real-time reverse transcriptase-polymerase chain reaction confirmed the Affymetrix data. The expression of CD19 and AIF-1 were downregulated in diabetic hearts as compared to control hearts. Using in vitro migration assay, we showed for the first time that AIF-1 is responsible for B cell migration as B cells migrated to GFP-AIF-1-transfected H9C2 cells compared to empty vector-transfected cells. Interestingly, overexpression of AIF-1 in diabetic mice prevented streptozotocin-induced cardiac dysfunction, inflammation and promoted B cell homing into the heart. Our results suggest that AIF-1 downregulation inhibited B cell homing into diabetic hearts, thus promoting inflammation that leads to the development of diabetic cardiomyopathy, and that overexpression of AIF-1 could be a novel treatment for this condition.

Karnal bunt disease of wheat is incited by quarantine fungal pathogen T. indica. Till date, there is little information on the pathogenic mechanisms involved in Karnal bunt. In order to understand the molecular mechanisms of disease pathogenesis, highly aggressive T. indica TiK isolate was cultured in the presence of host factor extracted from developing spikes of wheat variety WH-542. Modulation in protein profile of mycelial proteins and secretome from TiK cultured in the absence and presence of host factor was analyzed by 2-DE. Fifteen and twenty nine protein spots were up-regulated/differentially regulated in the proteome of mycelial and secreted proteins, respectively and identified using MALDI-TOF/TOF. Identified proteins are involved in suppression of host defense responses, lignin degradation of plant cell wall, penetration, adhesion of pathogen to host tissues, pathogen mediated reactive oxygen species generation, hydrolytic enzymes, detoxification of host generated reactive oxygen species. Further, integration of proteomic and genomic analysis has led to candidate pathogenicity/virulence factors identification. They were functionally annotated by sequence as well as structure based analysis. In this study, complementation of proteomics and genomics approaches resulted in novel pathogenicity/virulence factor(s) identification in T. indica.

Drugs of abuse, such as opiates, have been widely associated with enhancing HIV replication, accelerating disease progression and diminishing host-immune responses, thereby making it harder to effectively manage HIV infection. It is thus important to study the effects of drugs of abuse on HIV-infection and immune responses. Here, we develop mathematical models that incorporate the effects of morphine-altered antibody responses on HIV/SIV dynamics. Based on fitting the model to experimental data from simian immunodeficiency virus (SIV) infections in control and morphine-addicted macaques, we found that two of the most significant effects of virus specific antibodies are neutralizing viral particles and enhancing viral clearance. Using our model, we quantified how morphine alters virus-specific antibody responses, and how this alteration affects the key components of virus dynamics such as infection rate, virus clearance, viral load, CD4+ T cell count, and CD4+ T cell loss in SIV-infected macaques under conditioning with morphine. We found that in a subpopulation of SIV-infected morphine addicted macaques, the presence of drugs of abuse may cause significantly diminished antibody responses, resulting in more severe infection with increased SIV infectivity, a decreased viral clearance rate, increased viral load, and higher CD4+ T cell loss.

Aloe vera is a perennial, succulent, drought-resistant plant that exhibits many pharmacological characteristics such as wound healing ability against skin burns, anti-ulcer, anti-inflammatory, anti-tumor, anti-viral, anti-hypercholesterolemic, anti-hyperglycemic, anti-asthmatic and much more. Despite great medicinal worth, little genomic information is available on Aloe vera. This study is an initiative to explore the full-scale functional genomics of Aloe vera by generating whole transcriptome sequence database, using Illumina HiSeq technology and its progressive annotation specifically with respect to the metabolic specificity of the plant.

Mallotus philippensis L.(MP) commonly known as Kamala tree in Hindi,is a small to medium-sized monoecious tree.The objective of the study was to evaluate the anti-inflammatory activity of MPand a new flavanoneisolated from it by using in vivo models of inflammation.Albino wistar rats of either sex weighing 150-200g were used. Seven groups were made (n = 6), namely normal control group (normal saline, 1 ml/kg), standard control group (acetylsalicylic acid, 100 mg/kg), methanol crude extract (300 and 500 mg/kg), ethylacetate fraction (300 and 500 mg/kg) and active compound 4 (new flavanone, 50 mg/kg). The anti-inflammatory activity was studied using carrageenan induced paw edema method and cotton pellet granuloma method. Levels of cytokines (TNF-α, IL-1and IL-6) and activity of antioxidant enzymeslike catalase and glutathione peroxidase were estimated. It was found that the methanol extract, ethylacetate fraction and Flavanonedemonstrated significant reduction in paw edema in carrageenan induced paw edema method as compared to control. They also diminished the serum TNF-α, IL-6 and IL-1 levels. Significantly attenuated the malondialdehyde levels and increased the activities of catalase and glutathione peroxidase in paw tissue. Similarly there was asignificant decrease in granuloma formation in cotton pellet induced granuloma method. In conclusion, MP extracts and the newflavanonepossess anti-inflammatory activity and this might be due to the inhibition of various cytokines and increased free radical scavenging activity.

Canine Monocytic Ehrlichiosis (CME) is a serious tick-borne rickettsial disease affecting canine populations globally. Besides few reports from stray and pet dogs from localised geographical regions (cities/towns/small states), a comprehensive study on prevalence of Ehrlichia canis (E. canis) among working dogs from different geo-climatic zones of India was pertinently lacking. Study of CME among these dog populations was thus carried out, encompassing clinical aspects and different diagnostic methodologies viz., microscopy, serology and molecular biology. During the two-year study period, clinical specimens from 225 cases suspected of canine ehrlichiosis were examined for clinical pathology and presence of the haemoparasites. Overall prevalence of ehrlichiosis by microscopic examination, commercial dot-ELISA kit and nested PCR assay was estimated to be 1.3%, 19.1% and 5.8%, respectively, which were found to be statistically significant by McNemar Chi squared test (p<0.05). It was also observed that possibly due to widespread use of doxycycline therapy in field, CME presently does not remain a potential threat which it uses to pose earlier. However, concurrent infections of E. canis and Babesia gibsoni were found to be mostly fatal. Keeping in view of high number of apparently healthy dogs (24) out of total positive cases (46) observed during the study, it is recommended that prevalence studies on CME should also involve screening of apparently healthy dogs. Phylogenetic analysis carried on partial sequencing of 16S rRNA of E. canis strains revealed that all of the Indian strains clustered in a single clade with other E. canis species from India and rest of the world. Molecular divergence was observed among the sequences of Brazilian and American isolates which were also included in the present study. These findings have thus opened a new paradigm for planning of pragmatic control strategies against CME.

The incidence of HIV-associated neurological disorders (HAND) has increased during recent years even though the highly active antiretroviral therapy (HAART) has significantly curtailed the virus replication and increased the life expectancy among HIV-1 infected individuals. These neurological deficits have been attributed to HIV proteins including HIV-1 Tat. HIV-1 Tat is known to up-regulate CCL5 expression in mouse astrocytes, but the mechanism of up-regulation is not known. The present study was undertaken with the objective of determining the mechanism(s) underlying HIV-1 Tat-mediated expression of CCL5 in astrocytes. SVGA astrocytes were transiently transfected with a plasmid encoding Tat, and expression of CCL5 was studied at the mRNA and protein levels using real time RT-PCR and multiplex cytokine bead array, respectively. HIV-1 Tat showed a time-dependent increase in the CCL5 expression with peak mRNA and protein levels, observed at 1 h and 48 h post-transfection, respectively. In order to explore the mechanism(s), pharmacological inhibitors and siRNA against different pathway(s) were used. Pre-treatment with SC514 (NF-κB inhibitor), LY294002 (PI3K inhibitor), AG490 (JAK2 inhibitor) and Janex-1 (JAK3 inhibitor) showed partial reduction of the Tat-mediated induction of CCL5 suggesting involvement of JAK, PI3K/Akt and NF-κB in CCL5 expression. These results were further confirmed by knockdown of the respective genes using siRNA. Furthermore, p38 MAPK was found to be involved since the knockdown of p38δ but not other isoforms showed partial reduction in CCL5 induction. This was further confirmed at transcriptional level that AP-1, C/EBPα and C/EBPγ were involved in CCL5 up-regulation.

Monoterpenes, which are among the major components of plant essential oils, are known for their ecological roles as well for pharmaceutical properties. Geraniol, an acyclic monoterpene induces cell cycle arrest and apoptosis/senescence in various cancer cells and plants; however, the genes involved in the process and the underlying molecular mechanisms are not well understood. In this study, we demonstrate that treatment of tomato plants with geraniol results in induction of senescence due to a substantial alteration in transcriptome. We have identified several geraniol-responsive protein encoding genes in tomato using suppression subtractive hybridization (SSH) approach. These genes comprise of various components of signal transduction, cellular metabolism, reactive oxygen species (ROS), ethylene signalling, apoptosis and DNA damage response. Upregulation of NADPH oxidase and antioxidant genes, and increase in ROS level after geraniol treatment point towards the involvement of ROS in geraniol-mediated senescence. The delayed onset of seedling death and induced expression of geraniol-responsive genes in geraniol-treated ethylene receptor mutant (Nr) suggest that geraniol-mediated senescence involves both ethylene dependent and independent pathways. Moreover, expression analysis during tomato ripening revealed that geraniol-responsive genes are also associated with the natural organ senescence process.

In finger millet, calcium is one of the important and abundant mineral elements. The molecular mechanisms involved in calcium accumulation in plants remains poorly understood. Transcriptome sequencing of genetically diverse genotypes of finger millet differing in grain calcium content will help in understanding the trait.

Human immunodeficiency virus (HIV) has been associated with inflammatory effects that may potentially result in neurodegenerative changes and a number of newer chemotherapeutic agents are being tested to ameliorate these effects. In this study, we investigated the anti-neuroinflammatory activity of a novel resveratrol analog 4-(E)-{(p-tolylimino)-methylbenzene-1,2-diol} (TIMBD) against HIV1-gp120 induced neuroinflammation in SVG astrocytes. SVG astrocytic cells were pretreated with TIMBD or resveratrol (RES) and then transfected with a plasmid encoding HIV1-gp120. The mRNA and protein expression levels of proinflammatory cytokines IL6, IL8 and CCL5 were determined. Protein expression levels of NF-κB, AP1, p-STAT3, p-AKT, p-IKKs and p-p38 MAPK were also determined. TIMBD inhibited gp120-induced RNA and protein expression levels of IL6 and IL8, but not that of CCL5 in SVG astrocytes. Moreover, TIMBD attenuated gp120-induced phosphorylation of cJUN, cFOS, STAT3, p38-MAPK, AKT and IKKs, and the nuclear translocation of NF-κB p-65 subunit whereas RES mostly affected NF-κB protein expression levels. Our results suggest that TIMBD exerts anti-inflammatory effects better than that of RES in SVG astrocytes in vitro. These effects seem to be regulated by AP1, STAT-3 and NF-κB signaling pathways. TIMBD may thus have a potential of being a novel agent for treating HIV1-gp120-mediated neuroinflammatory diseases.

MAPK (Mitogen Activated Protein Kinase) is a Ser/Thr kinase, which plays a crucial role in plant growth and development, transferring the extra cellular stimuli into intracellular response etc. Manual identification of these MAPK in the plant genome is tedious and time taking process. There are number of online servers which predict the P-site (phosphorylation site), find the motifs and domain but there is no specific tool which can identify all them together. In order to identify the P-Site, phosphorylation site consensus sequences and domain of the MAPK in plant genome, we developed a tool, MAP Kinase analyzer. MAP kinase analyzer take protein sequence as input in the fasta format and the output of tool includes: 1) The prediction of the phosphorylation site viz., Serine (S), Threonine (T), and Tyrosine (Y), Contex, Position, Score and phosphorylating kinase as well as the graphical output; 2) Phosphorylation site consensus sequence pattern for different kinases and 3) Domain information about the MAPK's. The MAP kinase analyser tool and supplementary files can be downloaded from http://www.bioinfogbpuat/mapk_OWN_1/.

The mechanism of calcium uptake, translocation and accumulation in Poaceae has not yet been fully understood. To address this issue, we conducted genome-wide comparative in silico analysis of the calcium (Ca(2+)) transporter gene family of two crop species, rice and sorghum. Gene annotation, identification of upstream cis-acting elements, phylogenetic tree construction and syntenic mapping of the gene family were performed using several bioinformatics tools. A total of 31 Ca(2+) transporters, distributed on 9 out of 12 chromosomes, were predicted from rice genome, while 28 Ca(2+) transporters predicted from sorghum are distributed on all the chromosomes except chromosome 10 (Chr 10). Interestingly, most of the genes on Chr 1 and Chr 3 show an inverse syntenic relationship between rice and sorghum. Multiple sequence alignment and motif analysis of these transporter proteins revealed high conservation between the two species. Phylogenetic tree could very well identify the subclasses of channels, ATPases and exchangers among the gene family. The in silico cis-regulatory element analysis suggested diverse functions associated with light, stress and hormone responsiveness as well as endosperm- and meristem-specific gene expression. Further experiments are warranted to validate the in silico analysis of the predicted transporter gene family and elucidate the functions of Ca(2+) transporters in various biological processes.

Huntington's disease (HD) is a progressive neurodegenerative disorder characterized by a degeneration of striatal neurons. The possible role of COX and lipoxygenase (LOX) pathways has been well-documented in the pathology of several neurodegenerative disorders including HD. Licofelone is a competitive inhibitor of COX-1- and COX-2 and 5-LOX isoenzymes. Therefore, the present study was designed to investigate possible neuroinflammatory and apoptotic mechanisms in the neuroprotective effect of licofelone against 3-nitropropionic acid (3-NP)-induced HD-like symptoms in rats.

Perivascular mural cells of the choroid have been implicated in physiological functioning as well as in retinal disease pathogenesis. However details regarding their form and function are not well understood. We aim to characterize choroidal mural cells in the adult mouse choroid in terms of their distribution and morphology, and correlate these to their contractile behavior.

Oxidative stress appears to be an early event involved in the pathogenesis of Alzheimer's disease. The present study was designed to investigate the neuroprotective effects of Centella asiatica against colchicine-induced memory impairment and oxidative damage in rats. Colchicine (15 mug/5 muL) was administered intracerebroventricularly in the lateral ventricle of male wistar rats. Morris water maze and plus-maze performance tests were used to assess memory performance tasks. Various biochemical parameters such as lipid peroxidation, nitrite, reduced glutathione, glutathione-S-transferase, superoxide dismutase, acetylcholinesterase were also assessed. ICV colchicine resulted marked memory impairment and oxidative damage. Chronic treatment with Centella asiatica extract (150 and 300 mg/kg, p.o.) for a period of 25 days, beginning 4 days prior to colchicine administration, significantly attenuated colchicine-induced memory impairment and oxidative damage. Besides, Centella asiatica significantly reversed colchicines administered increase in acetylcholinesterase activity. Thus, present study indicates protective effect of Centella asiatica against colchicine-induced cognitive impairment and associated oxidative damage.