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1.  Abiotic Stresses Downregulate Key Genes Involved in Nitrogen Uptake and Assimilation in Brassica juncea L. 
PLoS ONE  2015;10(11):e0143645.
Abiotic stresses such as salinity, drought and extreme temperatures affect nitrogen (N) uptake and assimilation in plants. However, little is known about the regulation of N pathway genes at transcriptional level under abiotic stress conditions in Brassica juncea. In the present work, genes encoding nitrate transporters (NRT), ammonium transporters (AMT), nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate synthase (GOGAT), glutamate dehydrogenase (GDH), asparagines synthetase (ASN) were cloned from Brassica juncea L. var. Varuna. The deduced protein sequences were analyzed to predict their subcellular localization, which confirmed localization of all the proteins in their respective cellular organelles. The protein sequences were also subjected to conserved domain identification, which confirmed presence of characteristic domains in all the proteins, indicating their putative functions. Moreover, expression of these genes was studied after 1h and 24h of salt (150 mM NaCl), osmotic (250 mM Mannitol), cold (4°C) and heat (42°C) stresses. Most of the genes encoding nitrate transporters and enzymes responsible for N assimilation and remobilization were found to be downregulated under abiotic stresses. The expression of BjAMT1.2, BjAMT2, BjGS1.1, BjGDH1 and BjASN2 was downregulated after 1hr, while expression of BjNRT1.1, BjNRT2.1, BjNiR1, BjAMT2, BjGDH1 and BjASN2 was downregulated after 24h of all the stress treatments. However, expression of BjNRT1.1, BjNRT1.5 and BjGDH2 was upregulated after 1h of all stress treatments, while no gene was found to be upregulated after 24h of stress treatments, commonly. These observations indicate that expression of most of the genes is adversely affected under abiotic stress conditions, particularly under prolonged stress exposure (24h), which may be one of the reasons of reduction in plant growth and development under abiotic stresses.
doi:10.1371/journal.pone.0143645
PMCID: PMC4659633  PMID: 26605918
2.  Hydroxyethylamine Based Phthalimides as New Class of Plasmepsin Hits: Design, Synthesis and Antimalarial Evaluation 
PLoS ONE  2015;10(10):e0139347.
A novel class of phthalimides functionalized with privileged scaffolds was designed, synthesized and evaluated as potential inhibitors of plasmepsin 2 (Ki: 0.99 ± 0.1 μM for 6u) and plasmepsin 4 (Ki: 3.3 ± 0.3 μM for 6t), enzymes found in the digestive vacuole of the plasmodium parasite and considered as crucial drug targets. Three compounds were identified as potential candidates for further development. The listed compounds were also assayed for their antimalarial efficacy against chloroquine (CQ) sensitive strain (3D7) of Plasmodium falciparum. Assay of twenty seven hydroxyethylamine derivatives revealed four (5e, 6j, 6o and 6s) as strongly active, which were further evaluated against CQ resistant strain (7GB) of P. falciparum. Compound 5e possessing the piperidinopiperidine moiety exhibited promising antimalarial activity with an IC50 of 1.16 ± 0.04 μM. Further, compounds 5e, 6j, 6o and 6s exhibited low cytotoxic effect on MCF-7 cell line. Compound 6s possessing C2 symmetry was identified as the least cytotoxic with significant antimalarial activity (IC50: 1.30 ± 0.03 μM). The combined presence of hydroxyethylamine and cyclic amines (piperazines and piperidines) was observed as crucial for the activity. The current studies suggest that hydroxyethylamine based molecules act as potent antimalarial agent and may be helpful in drug development.
doi:10.1371/journal.pone.0139347
PMCID: PMC4621027  PMID: 26502278
3.  Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis 
BMC Genomics  2015;16(1):698.
Background
Crocus sativus stigmas form rich source of apocarotenoids like crocin, picrocrocin and saffranal which besides imparting color, flavour and aroma to saffron spice also have tremendous pharmacological properties. Inspite of their importance, the biosynthetic pathway of Crocus apocarotenoids is not fully elucidated. Moreover, the mechanism of their stigma specific accumulation remains unknown. Therefore, deep transcriptome sequencing of Crocus stigma and rest of the flower tissue was done to identify the genes and transcriptional regulators involved in the biosynthesis of these compounds.
Results
Transcriptome of stigma and rest of the flower tissue was sequenced using Illumina Genome Analyzer IIx platform which generated 64,604,402 flower and 51,350,714 stigma reads. Sequences were assembled de novo using trinity resulting in 64,438 transcripts which were classified into 32,204 unigenes comprising of 9853 clusters and 22,351 singletons. A comprehensive functional annotation and gene ontology (GO) analysis was carried out. 58.5 % of the transcripts showed similarity to sequences present in public databases while rest could be specific to Crocus. 5789 transcripts showed similarity to transcription factors representing 76 families out of which Myb family was most abundant. Many genes involved in carotenoid/apocarotenoid pathway were identified for the first time in this study which includes zeta-carotene isomerase and desaturase, carotenoid isomerase and lycopene epsilon-cyclase. GO analysis showed that the predominant classes in biological process category include metabolic process followed by cellular process and primary metabolic process. KEGG mapping analysis indicated that pathways involved in ribosome, carbon and starch and sucrose metabolism were highly represented. Differential expression analysis indicated that key carotenoid/apocarotenoid pathway genes including phytoene synthase, phytoene desaturase and carotenoid cleavage dioxygenase 2 are enriched in stigma thereby providing molecular proof for stigma to be the site of apocarotenoid biosynthesis.
Conclusions
This data would provide a rich source for understanding the carotenoid/apocarotenoid metabolism in Crocus. The database would also help in investigating many questions related to saffron biology including flower development.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1894-5) contains supplementary material, which is available to authorized users.
doi:10.1186/s12864-015-1894-5
PMCID: PMC4570256  PMID: 26370545
Crocus; Saffron; Apocarotenoids; Illumina; De novo assembly
4.  Metabolic enrichment of omega-3 polyunsaturated fatty acids does not reduce the onset of idiopathic knee osteoarthritis in mice 
Objective
We evaluated the effect of a reduction in the systemic ratio of n-6:n-3 polyunsaturated fatty acids (PUFAs) on changes in inflammation, glucose metabolism, and the idiopathic development of knee osteoarthritis (OA) in mice. We hypothesized that a lower ratio of n-6:n-3 PUFAs would protect against OA markers in cartilage and synovium, but not bone.
Design
Male and female fat-1 transgenic mice (Fat-1), which convert dietary n-6 to n-3 PUFAs endogenously, and their wild-type (WT) littermates were fed an n-6 PUFA enriched diet for 9-14 months. The effect of gender and genotype on serum PUFAs, IL-6, TNF-α, and glucose tolerance was tested by 2-factor analysis of variance. Cortical and trabecular subchondral bone changes were documented by micro-focal computed tomography, and knee OA was assessed by semi-quantitative histomorphometry grading.
Results
The n-6:n-3 ratio was reduced 12-fold and 7-fold in male and female Fat-1 mice, respectively, compared to WT littermates. IL-6 and TNF-α levels were reduced modestly in Fat-1 mice. However, these systemic changes did not reduce osteophyte development, synovial hyperplasia, or cartilage degeneration. Also the fat-1 transgene did not alter subchondral cortical or trabecular bone morphology or bone mineral density.
Conclusions
Reducing the systemic n-6:n-3 ratio does not slow idiopathic changes in cartilage, synovium, or bone associated with early-stage knee OA in mice. The anti-inflammatory and anti-catabolic effects of n-3 PUFAs previously reported for cartilage may be more evident at later stages of disease or in post-traumatic and other inflammatory models of OA.
doi:10.1016/j.joca.2014.06.033
PMCID: PMC4150746  PMID: 25008209
Cartilage; Subchondral Bone; Inflammation; Polyunsaturated Fatty Acids; Fat-1 Transgene; Synovitis; Aging; Mouse Models
5.  Postoperative analgesic efficacy of epidural tramadol as adjutant to ropivacaine in adult upper abdominal surgeries 
Background:
Postoperative pain control after major abdominal surgery is the prime concern of anesthesiologist. Among various methodologies, epidural analgesia is the most preferred technique because of the excellent quality of analgesia with minimum side-effects.
Aim:
The present study was designated to compare postoperative analgesic efficacy and safety of epidural tramadol as adjuvant to ropivacaine (0.2%) in adult upper abdominal surgery.
Settings and Design:
Prospective, randomized-controlled, double-blinded trial.
Materials and Methods:
Ninety patients planned for upper abdominal surgery under general anesthesia were randomized into three equal groups to receive epidural drug via epidural catheter at start of incisional wound closure: Group R to receive ropivacaine (0.2%); Group RT1 to receive tramadol 1 mg/kg with ropivacaine (0.2%); and RT2 to receive tramadol 2 mg/kg with ropivacaine (0.2%). Duration and quality of analgesia (visual analog scale [VAS] score), hemodynamic parameters, and adverse event were recorded and statistically analyzed.
Statistical Analysis:
One-way analysis of variance test, Fisher's exact test/Chi-square test, whichever appropriate. A P < 0.05 was considered significant.
Results:
Mean duration of analgesia after epidural bolus drug was significantly higher in Group RT2 (584 ± 58 min) when compared with RT1 (394 ± 46 min) or R Group (283 ± 35 min). VAS score was always lower in RT2 Group in comparison to other group during the study. Hemodynamic parameter remained stable in all three groups.
Conclusion:
We conclude that tramadol 2 mg/kg with ropivacaine (0.2%) provides more effective and longer-duration analgesia than tramadol 1 mg/kg with ropivacaine (0.2%).
doi:10.4103/0259-1162.161805
PMCID: PMC4683493  PMID: 26712976
Epidural analgesia; postoperative pain; ropivacaine; tramadol
6.  Genome-wide investigation and expression analysis of Sodium/Calcium exchanger gene family in rice and Arabidopsis 
Rice  2015;8:21.
Background
The Na+/Ca2+ Exchanger (NCX) protein family is a member of the Cation/Ca2+ exchanger superfamily and its members play important roles in cellular Ca2+ homeostasis. While the functions of NCX family of proteins is well understood in humans, not much is known about the total complement of Na+/Ca2+ exchangers in plants and their role in various physiological and developmental processes. In the present study, we have identified all the NCX proteins encoded in the genomes of rice and Arabidopsis and studied their phylogeny, domain architecture and expression profiles across different tissues, at various developmental stages and under stress conditions.
Results
Through whole genome investigation, we identified twenty-two NCX proteins encoded by fifteen genes in rice and sixteen NCX proteins encoded by thirteen genes in Arabidopsis. Based on phylogenetic reconstruction, these could be classified into five clades, members of most of which were found to possess distinct domain architecture. Expression profiling of the identified NCX genes using publicly available MPSS and microarray data showed differential expression patterns under abiotic stresses, and at various development stages. In rice, OsNCX1, OsNCX8, OsNCX9 and OsNCX15 were found to be highly expressed in all the plant parts and various developmental stages. qRT-PCR based expression analysis revealed that OsNCX3, OsNCX10 and OsNCX15 were highly induced by salt and dehydration stress. Besides, expression profiling showed differential regulation of rice NCX genes in response to calcium and EGTA. Interestingly, expression of none of the NCX genes was found to be co-regulated by NaCl and calcium.
Conclusions
Together, our results present insights into the potential role of NCX family of proteins in abiotic stresses and development. Findings of the present investigation should serve as a starting point for future studies aiming functional characterization of plant NCX family proteins.
Electronic supplementary material
The online version of this article (doi:10.1186/s12284-015-0054-5) contains supplementary material, which is available to authorized users.
doi:10.1186/s12284-015-0054-5
PMCID: PMC4488139  PMID: 26134707
Sodium calcium exchanger; Abiotic stress; Development; MPSS; Microarray; qRT-PCR
7.  Learning-guided automatic three dimensional synapse quantification for drosophila neurons 
BMC Bioinformatics  2015;16(1):177.
Background
The subcellular distribution of synapses is fundamentally important for the assembly, function, and plasticity of the nervous system. Automated and effective quantification tools are a prerequisite to large-scale studies of the molecular mechanisms of subcellular synapse distribution. Common practices for synapse quantification in neuroscience labs remain largely manual or semi-manual. This is mainly due to computational challenges in automatic quantification of synapses, including large volume, high dimensions and staining artifacts. In the case of confocal imaging, optical limit and xy-z resolution disparity also require special considerations to achieve the necessary robustness.
Results
A novel algorithm is presented in the paper for learning-guided automatic recognition and quantification of synaptic markers in 3D confocal images. The method developed a discriminative model based on 3D feature descriptors that detected the centers of synaptic markers. It made use of adaptive thresholding and multi-channel co-localization to improve the robustness. The detected markers then guided the splitting of synapse clumps, which further improved the precision and recall of the detected synapses. Algorithms were tested on lobula plate tangential cells (LPTCs) in the brain of Drosophila melanogaster, for GABAergic synaptic markers on axon terminals as well as dendrites.
Conclusions
The presented method was able to overcome the staining artifacts and the fuzzy boundaries of synapse clumps in 3D confocal image, and automatically quantify synaptic markers in a complex neuron such as LPTC. Comparison with some existing tools used in automatic 3D synapse quantification also proved the effectiveness of the proposed method.
doi:10.1186/s12859-015-0616-y
PMCID: PMC4445279  PMID: 26017624
Synapse detection; Automatic quantification; 3D confocal image; Model selection; BIOCAT
8.  Comparative evaluation of cost effectiveness and recovery profile between propofol and sevoflurane in laparoscopic cholecystectomy 
Background:
Anesthetic agents should be chosen not only on the basis of safety-efficacy profile, but also on the economic aspect. Propofol and sevoflurane are commonly utilized anesthetic agent for general anesthesia.
Aim:
The present study was designated to compare cost-effectiveness and recovery profile between propofol and sevoflurane for induction, maintenance or both.
Settings and Design:
Randomized controlled, participant and data operator blinded trial.
Materials and Methods:
Ninety patients undergoing laparoscopic cholecystectomy were randomized into three equal groups to receive: Group P to receive injection propofol for both induction and maintenance; Group PS to receive injection propofol for induction and sevoflurane for maintenance; and Group S to receive sevoflurane for both induction and maintenance of general anesthesia, respectively. Cost analysis, hemodynamic parameter, and recovery profile were compared between these groups.
Statistical Analysis:
One-way analysis of variance test or Fisher's exact test/Chi-square test whichever appropriate.
Results:
Total cost of anesthesia was highest in Group P and lowest in Group S. Mean time to extubation and time to follow verbal commands was lowest in Group S than Group P or Group P/S. Hemodynamic parameter was more stable in Group S.
Conclusion:
We conclude that sevoflurane appears to be better anesthetic agents in terms of cost-effectiveness and recovery profile.
doi:10.4103/0259-1162.156290
PMCID: PMC4563962  PMID: 26417120
Anesthesia; cost-effectiveness; propofol; sevoflurane
9.  Complete Genome Sequencing of Protease-Producing Novel Arthrobacter sp. Strain IHBB 11108 Using PacBio Single-Molecule Real-Time Sequencing Technology 
Genome Announcements  2015;3(2):e00346-15.
A previously uncharacterized species of the genus Arthrobacter, strain IHBB 11108 (MCC 2780), is a Gram-positive, strictly aerobic, nonmotile, cold-adapted, and protease-producing alkaliphilic actinobacterium, isolated from shallow undersurface water from Chandra Tal Lake, Lahaul-Spiti, India. The complete genome of the strain is 3.6 Mb in size with an average 58.97% G+C content.
doi:10.1128/genomeA.00346-15
PMCID: PMC4408344  PMID: 25908143
10.  Complete Genome Sequence of Paenibacillus sp. Strain IHBB 10380 Using PacBio Single-Molecule Real-Time Sequencing Technology 
Genome Announcements  2015;3(2):e00356-15.
The complete genome sequence of 5.77 Mb is reported for Paenibacillus sp. strain IHBB 10380, isolated from the cold desert area of the northwestern Himalayas and exhibiting amylase and cellulase activities. The gene-coding clusters predicted the presence of genes for hydrolytic enzymes in the genome.
doi:10.1128/genomeA.00356-15
PMCID: PMC4408346  PMID: 25908145
11.  The safety of ultrasound guided central venous cannulation in patients with liver disease 
Saudi Journal of Anaesthesia  2015;9(2):155-160.
Background:
Central venous cannulation (CVC) is frequently required during the management of patients with liver disease with deranged conventional coagulation parameters (CCP). Since CVC is known to be associated with vascular complications, it is standard practice to transfuse Fresh-Frozen Plasma or platelets to correct CCP. These CCP may not reflect true coagulopathy in liver disease. Additionally CVC when performed under ultrasound guidance (USG-CVC) in itself reduces the incidence of complications.
Aim:
To assess the safety of USG-CVC and to evaluate the incidence of complications among liver disease patients with coagulopathy.
Setting and Design:
An audit of all USG-CVCs was performed among adult patients with liver disease in a tertiary care center.
Materials and Methods:
Data was collected for all the adult patients (18-60 years) of either gender suffering from liver disease who had required USG-CVC. Univariate and multivariate regression analysis was done to identify possible risk factors for complications.
Results:
The mean age of the patients was 42.1 ± 11.6 years. Mean international normalized ratio was 2.17 ± 1.16 whereas median platelet count was 149.5 (range, 12-683) × 109/L. No major vascular or non-vascular complications were recorded in our patients. Overall incidence of minor vascular complications was 18.6%, of which 13% had significant ooze, 10.3% had hematoma formation and 4.7% had both hematoma and ooze. Arterial puncture and multiple attempts were independent risk factors for superficial hematoma formation whereas low platelet count and presence of ascites were independent risk factors for significant oozing.
Conclusion:
Ultrasound guidance -CVC in liver disease patients with deranged coagulation is a safe and highly successful modality.
doi:10.4103/1658-354X.152842
PMCID: PMC4374220  PMID: 25829903
Chronic liver disease; convention coagulation parameters; ultrasound guided central vein cannulation
12.  Śodhana: An Ayurvedic process for detoxification and modification of therapeutic activities of poisonous medicinal plants 
Ancient Science of Life  2015;34(4):188-197.
Ayurveda involves the use of drugs obtained from plants, animals, and mineral origin. All the three sources of drugs can be divided under poisonous and nonpoisonous category. There are various crude drugs, which generally possess unwanted impurities and toxic substances, which can lead to harmful health problems. Many authors have reported that not all medicinal plants are safe to use since they can bear many toxic and harmful phytoconstituents in them. Śodhana (detoxification/purification) is the process, which involves the conversion of any poisonous drug into beneficial, nonpoisonous/nontoxic ones. Vatsanābha (Aconitum species), Semecarpus anacardium, Strychnos nux-vomica, Acorus calamus, Abrus precatorius etc., are some of the interesting examples of toxic plants, which are still used in the Indian system of medicine. Aconite, bhilawanols, strychnine, β–asarone, abrin are some of the toxic components present in these plants and are relatively toxic in nature. Śodhana process involves the purification as well as reduction in the levels of toxic principles which sometimes results in an enhanced therapeutic efficacy. The present review is designed to extensively discuss and understand the scientific basis of the alternative use of toxic plants as a medicine after their purification process.
doi:10.4103/0257-7941.160862
PMCID: PMC4535066  PMID: 26283803
Ayurveda; detoxification; Śodhana; toxicity
13.  Draft Genome Sequence of a Cellulase-Producing Psychrotrophic Paenibacillus Strain, IHB B 3415, Isolated from the Cold Environment of the Western Himalayas, India 
Genome Announcements  2015;3(1):e01581-14.
Paenibacillus sp. strain IHB B 3415 is a cellulase-producing psychrotrophic bacterium isolated from a soil sample from the cold deserts of Himachal Pradesh, India. Here, we report an 8.44-Mb assembly of its genome sequence with a G+C content of 50.77%. The data presented here will provide insights into the mechanisms of cellulose degradation at low temperature.
doi:10.1128/genomeA.01581-14
PMCID: PMC4335335  PMID: 25700411
14.  Evaluation of exfoliative cytology in the diagnosis of oral premalignant and malignant lesions: A cytomorphometric analysis 
Dental Research Journal  2015;12(1):83-88.
Background:
Many oral squamous cell carcinomas (OSCCs) arise within regions that previously had premalignant lesion. Early diagnosis and prompt treatment of premalignant lesions offers the best hope of improving the prognosis in patients with OSCC. Exfoliative cytology is a simple and non-invasive diagnostic technique that could be used for early detection of oral premalignant and malignant lesions. This study was undertaken to evaluate the quantitative changes in nuclear area (NA), cytoplasmic area (CA) and nuclear-to-cytoplasmic ratio (NA/CA) in cytological buccal smears of oral leukoplakia with dysplasia (OLD) and OSCC patients while comparing with normal healthy mucosa.
Materials and Methods:
A quantitative study was conducted over 90 subjects including 30 cases each of OLD, OSCC and clinically normal oral mucosa. The smears obtained were stained with Papanicolaou (PAP) stain and cytomorphological assessment of the keratinocytes was carried out. The statistical tools included arithmetic mean, standard deviation, Chi-square test, analysis of variance, Tukey multiple comparison. P < 0.001 was considered as significant.
Results:
The mean NA of keratinocytes in the normal mucosa was 65.47 ± 4.77 μm2 while for OLD it was 107.97 ± 5.44 μm2 and 139.02 ± 8.10 μm2 for that of OSCC. The differences show a statistically significant increment in NA (P < 0.001). There was significant reduction (P < 0.001) in the CA of keratinocytes from OSCC when compared with those from smears of OLD and normal mucosa with the values of 1535.80 ± 79.38 μm2, 1078.51 ± 56.65 μm2 and 769.70 ± 38.77 μm2 respectively. The NA/CA ratio in the smears from normal oral mucosa, OLD and OSCC showed a mean value of 0.043 ± 0.004, 0.100 ± 0.008, 0.181 ± 0.015 respectively with a significant difference among the groups (P < 0.001).
Conclusion:
Evaluation of nuclear and CA of keratinocytes by cytomorphometry can serve as a useful adjunct in the diagnosis and prognosis of a dysplastic lesion which may lead to OSCC.
PMCID: PMC4336977  PMID: 25709680
Cytomorphometry; dysplasia; exfoliative cytology; oral leukoplakia; oral squamous cell carcinoma
15.  Draft Genome Sequence of Psychrotrophic Acinetobacter sp. Strain MN12 (MTCC 10786), Which Produces a Low-Temperature-Active and Alkaline-Stable Peptidase 
Genome Announcements  2014;2(6):e01167-14.
We report here the draft genome sequence of Acinetobacter sp. strain MN12 (MTCC 10786), which is a psychrotrophic bacterium that produces an extracellular low-temperature-active and alkaline-stable peptidase. The draft genome assembly of Acinetobacter sp. MN12 has a size of 4.31 Mbp, with a G+C content of 40.75%.
doi:10.1128/genomeA.01167-14
PMCID: PMC4239350  PMID: 25414495
16.  Effect of Neem oil and Haridra on non-healing wounds 
Ayu  2014;35(4):398-403.
Background:
In Ayurveda, Vrana (wound) has stated as tissue destruction and discoloration of viable tissue due to various etiology. In Sushruta Samhita, Sushruta described Vrana as a main subject. Most commonly Vrana can be classified into Shuddha and Dushta Vrana (chronic wound/nonhealing ulcers). Among the various drugs mentioned for Dushta Vrana, two of them, Neem (Azadirechta indica A. Juss) oil and Haridra (Curcuma longa Linn.) powder are selected for their wide spectrum action on wound.
Aim:
To compare the effect of Neem oil and Haridra in the treatment of chronic non-healing wounds.
Materials and Methods:
Total 60 patients of wounds with more than 6 weeks duration were enrolled and alternatively allocated to Group I (topical application of Neem oil), Group II (Haridra powder capsules, 1 g 3 times orally) and Group III (both drugs). Duration of treatment was considered until complete healing of the wound, whereas 4th and 8th week were considered for assessment of 50% healing. Wound size was measured and recorded at weekly intervals. Wound biopsy was repeated after 4 weeks for assessment of angiogenesis and deoxyribonucleic acid (DNA) analysis.
Results:
After 8 weeks of treatment, 50% wound healing was observed in 43.80% patients of Group I, 18.20% patients of Group II, and 70.00% patients of Group III. Microscopic angiogenesis grading system scores and DNA concentration showed highly significant effect of combined use of both drugs when compared before and after results of treatment (P < 0.001).
Conclusion:
Topical use of Neem oil and oral use of Haridra powder capsule used in combination were found effective for chronic non-healing wounds.
doi:10.4103/0974-8520.158998
PMCID: PMC4492024  PMID: 26195902
Chronic wound; Haridra; microscopic angiogenesis grading system score; Neem oil; wound healing
17.  Genome-Wide Identification and Expression Analysis of NBS-Encoding Genes in Malus x domestica and Expansion of NBS Genes Family in Rosaceae 
PLoS ONE  2014;9(9):e107987.
Nucleotide binding site leucine-rich repeats (NBS-LRR) disease resistance proteins play an important role in plant defense against pathogen attack. A number of recent studies have been carried out to identify and characterize NBS-LRR gene families in many important plant species. In this study, we identified NBS-LRR gene family comprising of 1015 NBS-LRRs using highly stringent computational methods. These NBS-LRRs were characterized on the basis of conserved protein motifs, gene duplication events, chromosomal locations, phylogenetic relationships and digital gene expression analysis. Surprisingly, equal distribution of Toll/interleukin-1 receptor (TIR) and coiled coil (CC) (1∶1) was detected in apple while the unequal distribution was reported in majority of all other known plant genome studies. Prediction of gene duplication events intriguingly revealed that not only tandem duplication but also segmental duplication may equally be responsible for the expansion of the apple NBS-LRR gene family. Gene expression profiling using expressed sequence tags database of apple and quantitative real-time PCR (qRT-PCR) revealed the expression of these genes in wide range of tissues and disease conditions, respectively. Taken together, this study will provide a blueprint for future efforts towards improvement of disease resistance in apple.
doi:10.1371/journal.pone.0107987
PMCID: PMC4169499  PMID: 25232838
19.  Mesenchymal chondrosarcoma of mandible: A rare case report and review 
Mesenchymal Chondrosarcomas (MCs) are rare malignant connective tissue neoplasms representing approximately 1% of all chondrosarcomas (CSs) that can arise from both soft and hard tissues. They are distinct tumors arising in unicentric or multicentric locations. The tumor is most unusual as it has been described as a particularly aggressive neoplasm with a high tendency for late recurrence and delayed metastasis. It is a biphasic tumor with areas comprising of spindle cell mesenchyme having areas of chondroid differentiation. Here we report a case of 60-year-old male with mesenchymal CS of the mandible.
doi:10.4103/0973-029X.141376
PMCID: PMC4211231  PMID: 25364172
Biphasic pattern; mesenchymal chondrosarcoma; mandible; tumor
20.  Evidence of Experimental Vertical Transmission of Emerging Novel ECSA Genotype of Chikungunya Virus in Aedes aegypti 
Background
Chikungunya virus (CHIKV) has emerged as one of the most important arboviruses of public health significance in the past decade. The virus is mainly maintained through human-mosquito-human cycle. Other routes of transmission and the mechanism of maintenance of the virus in nature are not clearly known. Vertical transmission may be a mechanism of sustaining the virus during inter-epidemic periods. Laboratory experiments were conducted to determine whether Aedes aegypti, a principal vector, is capable of vertically transmitting CHIKV or not.
Methodology/Principal Findings
Female Ae. aegypti were orally infected with a novel ECSA genotype of CHIKV in the 2nd gonotrophic cycle. On day 10 post infection, a non-infectious blood meal was provided to obtain another cycle of eggs. Larvae and adults developed from the eggs obtained following both infectious and non-infectious blood meal were tested for the presence of CHIKV specific RNA through real time RT-PCR. The results revealed that the larvae and adults developed from eggs derived from the infectious blood meal (2nd gonotrophic cycle) were negative for CHIKV RNA. However, the larvae and adults developed after subsequent non-infectious blood meal (3rd gonotrophic cycle) were positive with minimum filial infection rates of 28.2 (1∶35.5) and 20.2 (1∶49.5) respectively.
Conclusion/Significance
This study is the first to confirm experimental vertical transmission of emerging novel ECSA genotype of CHIKV in Ae. aegypti from India, indicating the possibilities of occurrence of this phenomenon in nature. This evidence may have important consequence for survival of CHIKV during adverse climatic conditions and inter-epidemic periods.
Author Summary
Although vertical transmission of arboviruses has been recognized for nearly a century, rates of transmission in laboratory experiments are low and their significance in terms of survival of virus during periods of low transmission appears debatable. Recently, major urban outbreaks of chikungunya have been recorded in many parts of Asia, Africa, and Europe. The occurrence of random sporadic cases of the disease in years following a major outbreak prompted us to investigate whether these might be attributable to survival of the virus by vertical transmission. Our experiments were designed to test two hypotheses: (1) The development of an egg-batch derived from an infectious blood meal is too rapid for the infection to reach ovaries; (2) The enormous distension of the membrane enveloping ovaries and ovarioles following oviposition, might facilitate virus penetration. We conclude that after the infected blood meal, oogenesis and oviposition were complete before virus had disseminated to infect the ovaries. Because similar experiments with infection in first gonotrophic cycle did not lead to infected progenies, it is presumed that expanded parous ovaries might support efficient infection. Therefore, it may be concluded that vertical transmission is a more common phenomena in mosquitoes during subsequent gonotrophic cycles following arboviral infection.
doi:10.1371/journal.pntd.0002990
PMCID: PMC4117456  PMID: 25080107
21.  Substrate dependent in vitro antifungal activity of Bacillus sp strain AR2 
Background
Biosurfactants are a structurally diverse group of secondary metabolites with lots of potential to serve mankind. Depending upon the structure and composition they may exhibit properties that make them suitable for a particular application. Structural and compositional diversity of biosurfactant is unambiguously substrate dependent. The present study investigates the qualitative and quantitative effect of different water soluble carbon source on the biosurfactant produced by Bacillus amylofaciens strain AR2.
Results
Strain AR2 produced lipopeptide type biosurfactant while growing on water soluble carbon sources. Maximum biosurfactant production was observed in the sucrose supplemented minimal salt medium (MSM). Strain AR2 exhibited carbon source dependent surface tension reduction in the range of 30-37 mN/m, critical micelle concentration (CMC) in the range 80-110 mg/l and emulsification index (EI24 kerosene) in the range of 32-66%. In dextrose, sucrose and glycerol supplemented MSM, strain AR2 produced lipopeptides as a mixture of surfactin, iturin and fengycin. However, in the presence of maltose, lactose and sorbitol only iturin was produced. This substrate dependent compositional variation in the lipopeptides significantly influenced antifungal activity. Lipopeptides produced by strain AR2 while growing on sucrose and dextrose based MSM was observed to be most efficient as an antifungal agent.
Conclusions
These results suggest that carbon source provided for the growth and biosurfactant production not only influences the yield but also the type of biosurfactant. Sucrose is the most suitable carbon source for production of lipopeptide biosurfactant with antifungal activity.
doi:10.1186/1475-2859-13-67
PMCID: PMC4028101  PMID: 24885467
Biosurfactant; Lipopeptides; Filamentous fungi; Fungicidal
22.  Plant profile, phytochemistry and pharmacology of Avartani (Helicteres isora Linn.): A review 
Plants are used as medicine since ancient time, in organized (Ayurveda, Unani & Siddha) and unorganized (folk, native & tribal) form. In these systems, drugs are described either in Sanskrit or vernacular languages. Avartani (Helicteres isora Linn.) is a medicinal plant which is used in several diseases. It is commonly known as Marodphali, Marorphali, Enthani etc. due to screw like appearance of its fruit. Avartani is used as a folk medicine to treat snake bite, diarrhoea and constipation of new born baby. In the research, antioxidant, hypolipidaemic, antibacterial and antiplasmid activities, cardiac antioxidant, antiperoxidative potency, brain-antioxidation potency, anticancer activity, antinociceptive activity, hepatoprotective activity, anti-diarrheal activity and wormicidal activity in this plant were reviewed.
doi:10.12980/APJTB.4.2014C872
PMCID: PMC4025269  PMID: 25183085
Avartani; Ayurveda; Helicteres isora Linn.; Marodphali; Anti-diarrheal
23.  Silver Binding Nucleolar Organizer Regions Dots in Oral Leukoplakia with Epithelial Dysplasia and Oral Squamous Cell Carcinoma: An In Vivo Study 
ISRN Dentistry  2014;2014:479187.
Silver binding nucleolar organizer regions (AgNOR) in normal oral mucosa (NOM), oral leukoplakia with epithelial dysplasia (ED), and oral squamous cell carcinoma (OSCC) were studied. The mean AgNOR count per nucleus increased from NOM to ED to OSCC. Tissue showing ED in oral leukoplakia and OSCC cases showed higher counts, wider scatter, and smaller size of AgNOR dots in the nuclei. The study seems to suggest that time method has some potential in distinguishing between NOM and oral leukoplakia with ED and OSCC. Studies of larger numbers are needed to arrive at more substantial conclusions.
doi:10.1155/2014/479187
PMCID: PMC4040188  PMID: 24944820
25.  First Draft Genome Sequence of a Member of the Genus Planomicrobium, Isolated from the Chandra River, India 
Genome Announcements  2014;2(1):e01259-13.
We report the first draft genome sequence of a member of the genus Planomicrobium, isolated from a soil sample from the Chandra River, located in the cold deserts of Himachal Pradesh, India. The draft genome assembly for Planomicrobium glaciei strain CHR43 has a size of 3,900,800 bp with a G+C content of 46.97%.
doi:10.1128/genomeA.01259-13
PMCID: PMC3916493  PMID: 24503999

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