Aruna Pandey

Expression kinetics of ISG15, IRF3, IFNγ, IL10, IL2 and IL4 genes vis-a-vis virus shedding, tissue tropism and antibody dynamics in PPRV vaccinated, challenged, infected sheep and goats

Here, we studied the in vivo expression of Th1 (IL2 and IFN gamma) and Th2 (IL4 and IL10) - cytokines and antiviral molecules - IRF3 and ISG15 in peripheral blood mononuclear cells in relation to antigen and antibody dynamics under Peste des petits ruminants virus (PPRV) vaccination, infection and challenge in both sheep and goats. Vaccinated goats were seropositive by 9 days post vaccination (dpv) while in sheep idiosyncratic response was observed between 9 and 14 dpv for different animals. Expression of PPRV N gene was not detected in PBMCs of vaccinated and vaccinated challenged groups of both species, but was detected in unvaccinated infected PBMCs at 9 and 14 days post infection. The higher viral load at 9 dpi coincided with the peak clinical signs of the disease. The peak in viral replication at 9 dpi correlated with significant expression of antiviral molecules IRF3, ISG15 and IFN gamma in both the species. With the progression of disease, the decrease in N gene expression also correlated with the decrease in expression of IRF3, ISG15 and IFN gamma. In the unvaccinated infected animals ISG15, IRF3, IFN gamma and IL10 expression was higher than vaccinated animals. The IFN gamma expression predominated over IL4 in both vaccinated and infected animals with the infected exhibiting a stronger Th1 response. The persistent upregulation of this antiviral molecular signature - ISG15 and IRF3 even after 2 weeks post vaccination, presumably reflects the ongoing stimulation of innate immune cells.

Comparative and temporal transcriptome analysis of peste des petits ruminants virus infected goat peripheral blood mononuclear cells

Peste des petits ruminanats virus (PPRV), a morbillivirus causes an acute, highly contagious disease - peste des petits ruminants (PPR), affecting goats and sheep. Sungri/96 vaccine strain is widely used for mass vaccination programs in India against PPR and is considered the most potent vaccine providing long-term immunity. However, occurrence of outbreaks due to emerging PPR viruses may be a challenge. In this study, the temporal dynamics of immune response in goat peripheral blood mononuclear cells (PBMCs) infected with Sungri/96 vaccine virus was investigated by transcriptome analysis. Infected goat PBMCs at 48h and 120h post infection revealed 2540 and 2000 differentially expressed genes (DEGs), respectively, on comparison with respective controls. Comparison of the infected samples revealed 1416 DEGs to be altered across time points. Functional analysis of DEGs reflected enrichment of TLR signaling pathways, innate immune response, inflammatory response, positive regulation of signal transduction and cytokine production. The upregulation of innate immune genes during early phase (between 2-5 days) viz. interferon regulatory factors (IRFs), tripartite motifs (TRIM) and several interferon stimulated genes (ISGs) in infected PBMCs and interactome analysis indicated induction of broad-spectrum anti-viral state. Several Transcription factors - IRF3, FOXO3 and SP1 that govern immune regulatory pathways were identified to co-regulate the DEGs. The results from this study, highlighted the involvement of both innate and adaptive immune systems with the enrichment of complement cascade observed at 120h p.i., suggestive of a link between innate and adaptive immune response. Based on the transcriptome analysis and qRT-PCR validation, an in vitro mechanism for the induction of ISGs by IRFs in an interferon independent manner to trigger a robust immune response was predicted in PPRV infection.

Modulation of Host miRNAs Transcriptome in Lung and Spleen of Peste des Petits Ruminants Virus Infected Sheep and Goats

Peste des petits ruminants (PPR) is one of the highly contagious viral disease, characterized by fever, sore mouth, conjunctivitis, gastroenteritis, and pneumonia, primarily affecting sheep and goats. Reports suggested variable host response in goats and sheep and this host response vis-a-vis the expression of microRNAs (miRNAs) has not been investigated. Here, miRNAs were sequenced and proteomics data were generated to identify the role of differentially expressed miRNA (DEmiRNA) in PPR virus (PPRV) infected lung and spleen tissues of sheep and goats. In lungs, 67 and 37 DEmiRNAs have been identified in goats and sheep, respectively. Similarly, in spleen, 50 and 56 DEmiRNAs were identified in goats and sheep, respectively. A total of 20 and 11 miRNAs were found to be common differentially expressed in both the species in PPRV infected spleen and lung, respectively. Six DEmiRNAs—miR-21-3p, miR-1246, miR-27a-5p, miR-760-3p, miR-320a, and miR-363 were selected based on their role in viral infections, apoptosis, and fold change. The target prediction analysis of these six selected DEmiRNAs from the proteome data generated, revealed involvement of more number of genes in lung and spleen of goats than in sheep. On gene ontology analysis of host target genes these DEmiRNAs were found to regulate several immune response signaling pathways. It was observed that the pathways viz. T cell receptor signaling, Rap1 signaling, Toll-like receptor signaling, and B cell receptor signaling governed by DEmiRNAs were more perturbed in goats than in sheep. The data suggests that PPRV-induced miR-21-3p, miR-320a, and miR-363 might act cooperatively to enhance viral pathogenesis in the lung and spleen of sheep by downregulating several immune response genes. The study gives an important insight into the molecular pathogenesis of PPR by identifying that the PPRV—Izatnagar/94 isolate elicits a strong host response in goats than in sheep.

TIFR Near Infrared Imaging Camera-II on the 3.6 m Devasthal Optical Telescope

TIFR Near Infrared Imaging Camera-II is a closed-cycle Helium cryo-cooled imaging camera equipped with a Raytheon 512 x 512 pixels InSb Aladdin III Quadrant focal plane array having sensitivity to photons in the 1-5 microns wavelength band. In this paper, we present the performance of the camera on the newly installed 3.6-m Devasthal Optical Telescope (DOT) based on the calibration observations carried out during 2017 May 11-14 and 2017 October 7-31. After the preliminary characterization, the camera has been released to the Indian and Belgian astronomical community for science observations since 2017 May. The camera offers a field-of-view of ~86.5 arcsec x 86.5 arcsec on the DOT with a pixel scale of 0.169 arcsec. The seeing at the telescope site in the near-infrared bands is typically sub-arcsecond with the best seeing of ~0.45 arcsec realized in the near-infrared K-band on 2017 October 16. The camera is found to be capable of deep observations in the J, H and K bands comparable to other 4-m class telescopes available world-wide. Another highlight of this camera is the observational capability for sources up to Wide-field Infrared Survey Explorer (WISE) W1-band (3.4 microns) magnitudes of 9.2 in the narrow L-band (nbL; lambda_{cen} ~3.59 microns). Hence, the camera could be a good complementary instrument to observe the bright nbL-band sources that are saturated in the Spitzer-Infrared Array Camera ([3.6] <= 7.92 mag) and the WISE W1-band ([3.4] <= 8.1 mag). Sources with strong polycyclic aromatic hydrocarbon (PAH) emission at 3.3 microns are also detected. Details of the observations and estimated parameters are presented in this paper.

Selection and validation of suitable reference genes for qPCR gene expression analysis in goats and sheep under Peste des petits ruminants virus (PPRV), lineage IV infection

Identification of suitable candidate reference genes is an important prerequisite for validating the gene expression data obtained from downstream analysis of RNA sequencing using quantitative real time PCR (qRT-PCR). Though existence of a universal reference gene is myth, commonly used reference genes can be assessed for expression stability to confer their suitability to be used as candidate reference genes in gene expression studies. In this study, we evaluated the expression stability of ten most commonly used reference genes (GAPDH, ACTB, HSP90, HMBS, 18S rRNA, B2M, POLR2A, HPRT1, ACAC, YWHAZ) in fourteen different Peste des petits ruminants virus (PPRV) infected tissues of goats and sheep. RefFinder and RankAggreg software were used to deduce comprehensive ranking of reference genes. Our results suggested HMBS and B2M in goats and HMBS and HPRT1 in sheep can be used as suitable endogenous controls in gene expression studies of PPRV infection irrespective of tissues and condition as a whole, thus eliminating the use of tissue specific/ condition specific endogenous controls. We report for the first time suitable reference genes for gene expression studies in PPRV infected tissues. The reference genes determined here can be useful for future studies on gene expression in sheep and goat infected with PPRV, thus saving extra efforts and time of repeating the reference gene determination and validation.

Draft genome sequence of field isolate Brucella melitensis strain 2007BM/1 from India

OBJECTIVES Brucellosis is among one of the most widespread important global zoonotic diseases that is endemic in many parts of India. Brucella melitensis is supposed to be the most pathogenic species for humans. Here we report the draft genome sequence of B. melitensis strain 2007BM/1 isolated from a human in India. METHODS Genomic DNA was extracted from Brucella culture and was sequenced using an Illumina MiSeq platform. The generated reads were assembled using three de novo assemblers and the draft genome was annotated. RESULTS This monoisolate, with a genome length of 3268756bp, was found to be resistant to azithromycin and trimethoprim/sulfamethoxazole but susceptible to tetracycline, ofloxacin, rifampicin, ciprofloxacin and doxycycline. The presence of virulence genes in the strain was identified. CONCLUSIONS The results obtained will help in understanding drug resistance mechanisms and virulence factors in highly zoonotic B. melitensis and suggest the need for judicious use of antibiotics in livestock health and management practices.

Development and validation of IPM technology for ginger in Garhwal region of Uttarakhand

Intensive survey was conducted in different villages of Tehri district of Uttarakhand to identify the major ginger growing areas, where insectpests and diseases are major problem, to validate the IPM module under field conditions. Consequently, two villages i.e. Pali and Gaind were selected where, rhizome rot, leaf spot, white-grub and rhizome maggot were posing serious threat to ginger cultivation were identified. Therefore, an IPM module was formulated for existing pests problems based on the available control measures in literature against these pests which was further disseminated to the farmers through conductance of demonstrations at the farmers’ field in Tehri-Garhwal area. The results indicated that the IPM program provided 48.19, 63.94, 52.09 and 57.82% control of rhizome rot, leaf spot, white grub and rhizome maggots respectively, over non-IPM practice. Analysis of cost benefit ratio of IPM practice revealed that there was 32.82% increase in yield with net return of Rs. 92.04 thousand per hectare and a B: C ratio of 2.15 over Non-IPM practice. Over all study revealed that the ginger production under IPM situation proved comparatively more economically viable in terms of losses decreased by suppression of pest.

Validation of IPM module against major insect-pests and diseases of cabbage in mid-hills of Uttarakhand

Field trials were conducted to validate the formulated IPM programme for the management of insect-pests and diseases in cabbage grown in Jadipani village of Chamba block of district Tehri-Garhwal, Uttarakhand. The result showed that the IPM program provided 59.12, 57.12, 43.88, 55.98, 52.67, 49.41 and 52.24% reduction in white-grub, cut worm, cabbage butterfly, DBM, aphids, tobacco caterpillar, painted bug infestation, respectively, as compared to non-IPM practiced fields. Similarly, there was 52.15, 52.94 and 49.41% control of damping-off, black leg and white blight or head rot diseases, respectively, over non-IPM practice. Analysis of cost benefit ratio of IPM practice revealed that there was 58.88% increase in yield with net return of Rs. 65.59 thousand per ha over non-IPM practiced field. The B: C ratio of IPM practice field was 2.19. Overall study revealed that the cabbage production under IPM situation proved to be economically more viable in terms of reduction in crop losses by suppression of pest and consequently increase in yield.

Evaluation and validation of IPM technology for bell pepper (Capsicum annuum var. frutescens L.) through farmers' participatory approach in mid Garhwal hills of Uttarakhand.

Field experiments were conducted to evaluate the formulated IPM programme for the management of insect-pests and diseases in bell pepper (capsicum) in Jadipani village of Chamba block in Tehri Garhwal district (Uttarakhand). Comparative study indicated that IPM module was found to be very effective in terms of suppression of pest infestation and increase in yield over non-IPM. It was found that there was 61.30, 66.98 and 42.99 per cent control of white-grub, cut worm, thrips, respectively, in IPM practiced field as compared to non-IPM practice, respectively. Similarly, 72.27, 53.71 and 49.22 per cent control of damping-off, Colletotrichum leaf spot and Phytophthora fruit rot, respectively, was recorded in IPM practiced field. Analysis of cost benefit ratio of IPM practice revealed that there was 38.64 per cent increase in yield with net return of Rs. 51.87 thousand per hectare and a B:C ratio of 1.46 over farmers’ practice. Over all study revealed that the capsicum production under IPM situation proved comparatively more economically viable in terms of suppression of pest which resulted in increase of yield. How to view point the article : Kumar, Bijendra, Pandy, A.K. and Dev, Chandra (2016). Evaluation and validation of IPM technology for bell pepper (Capsicum annuum var. frutescens L.) through farmers’ participatory approach in mid Garhwal hills of Uttarakhand. in sorghum. Internat. J. Plant Protec., 9(1) : 109-114.

Systems biology approach: Panacea for unravelling host-virus interactions and dynamics of vaccine induced immune response

Abstract Systems biology is an interdisciplinary research field in life sciences, which involves a comprehensive and quantitative analysis of the interactions between all of the components of biological systems over time. For the past 50years the discipline of virology has overly focused on the pathogen itself. However, we now know that the host response is equally or more important in defining the eventual pathological outcome of infection. Systems biology has in recent years been increasingly recognised for its importance to infectious disease research. Host-virus interactions can be better understood by taking into account the dynamical molecular networks that constitute a biological system. To decipher the pathobiological mechanisms of any disease requires a deep knowledge of how multiple and concurrent signal-transduction pathways operate and are deregulated. Hence the intricacies of signalling pathways can be dissected only by system level approaches.