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1.  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.
PMCID: PMC4335335
2.  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%.
PMCID: PMC4239350  PMID: 25414495
3.  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.
PMCID: PMC4169499  PMID: 25232838
5.  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.
PMCID: PMC4211231  PMID: 25364172
Biphasic pattern; mesenchymal chondrosarcoma; mandible; tumor
6.  Evidence of Experimental Vertical Transmission of Emerging Novel ECSA Genotype of Chikungunya Virus in Aedes aegypti 
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.
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.
PMCID: PMC4117456  PMID: 25080107
7.  Substrate dependent in vitro antifungal activity of Bacillus sp strain AR2 
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.
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.
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.
PMCID: PMC4028101  PMID: 24885467
Biosurfactant; Lipopeptides; Filamentous fungi; Fungicidal
8.  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.
PMCID: PMC4025269  PMID: 25183085
Avartani; Ayurveda; Helicteres isora Linn.; Marodphali; Anti-diarrheal
9.  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.
PMCID: PMC4040188  PMID: 24944820
11.  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%.
PMCID: PMC3916493  PMID: 24503999
12.  Efficient extraction of proteins from formalin-fixed paraffin-embedded tissues requires higher concentration of tris(hydroxymethyl)aminomethane 
Clinical proteomics  2014;11(1):4.
Numerous formaldehyde-fixed and paraffin-embedded clinical tissues have been created in the past decades and stored in pathological depositories at hospitals as well as in clinical laboratories worldwide. In addition to the archived tissues, formaldehyde-fixation is also mandatory for preparing proteomics samples from diseased patients or animal models in order to inactivate contagious agents. Protein extraction from formaldehyde-fixed tissues is hampered by the Schiff base formation between the amino groups of proteins and formaldehyde. Although achievement of the highest extraction efficiency of proteins from the formaldehyde-fixed tissues is essential for obtaining maximum proteomics information, no attention has been paid to the concentration dependence of tris(hydroxymethyl)aminomethane on the extraction efficacy. We suspected that the concentration of tris(hydroxymethyl)aminomethane affects the protein extraction efficiency because of its property as a primary amine that reverses the Schiff base formation between the primary amines of proteins and formaldehyde. Thus we pursued optimization of the component and protocol of protein extraction buffer to achieve better extraction efficiency of proteins from formaldehyde-fixed and paraffin-embedded tissues.
In order to simulate protein extraction from diseased tissues we made formaldehyde-fixed and paraffin-embedded samples from mouse liver slices and investigated the protein extraction efficiency and speed by changing the concentration of the protein extraction buffer component tris(hydroxymethyl)aminomethane under various extraction conditions. We find, as expected, that tris(hydroxymethyl)aminomethane significantly affects the performance of protein extraction from the formaldehyde-fixed and paraffin-embedded samples both in the extraction yield and in the extraction speed.
We recommend the concentration of tris(hydroxymethyl)aminomethane in protein extraction buffer to be higher than 300 mM when extraction is conducted for 90 min at 90°C to achieve the most efficient protein extraction in a shorter time. The information will be essential for performing the most efficient protein extraction from formaldehyde-fixed and paraffin-embedded tissue samples for proteomics analysis.
PMCID: PMC3922997  PMID: 24484752
FFPE; Protein extraction; TRIS concentration; Proteomics
13.  Decadorial of a burn center in Central India 
Burn injuries are a serious public health problem. In our study we have identified different epidemiological factors based on 10 years of our experience at a burn unit in central India and recommend some strategies to prevent burn injuries.
Materials and Methods:
This is a retrospective analysis (2001-2010) of database from burn unit of S.S. Medical College, Rewa, India.
2499 patients with burn injury were analysed. 66.8% and 38.2% patients were females and males respectively, with a median age of 25 years. Flame (80.1%) was most common cause, home (96%) was most common place, traditional Indian stove (28.8%), kerosene lamp (26.7%), hot liquid (12.2%) and kerosene stove (10.4%) were common causes. Median Total Body Surface Area (TBSA) burn was 40.0%; females had significantly greater (P < 0.001) burn than males (median 50% vs 26.0%). High mortality (40.3%) seen; female sex (OR 3.22, 95% CI 2.65-3.92); young age (15-29 year) (OR 3.48, 95% CI 2.45-4.94); flame burn (OR 12.9, 95% CI 1.69-98.32); suicidal burn OR 6.82 95%CI 4.44-10.48) and TBSA > 76% (OR 3099, 95%CI 1302-7380) were significant risk factors for death. Median hospital stays was 8 days; shorter hospital stays seen among TBSA burn > 76% (2 days), suicidal intent (4 days), and those who expired (4 days). Septicemia (45.8%) and burn shock (41%) were the major cause for death.
Cooking and lighting equipments are major cause of burn injury among females and young age group. Equipment modification to improve safety features and public awareness programs are necessary to reduce burn incidents.
PMCID: PMC3961915  PMID: 24678209
Burns; epidemiology; female; flame; kitchen; mortality; septicemia; suicidal
14.  Molecular and Virological Investigation of a Focal Chikungunya Outbreak in Northern India 
The Scientific World Journal  2013;2013:367382.
Chikungunya (CHIK) fever is one of the most important arboviral infections of medical significance. The objective of the present study is to identify and characterize the etiology of a focal febrile arthritis outbreak from Gwalior, northern India, during October-November 2010. A detailed virological (isolation) and molecular (end-point RT-PCR, quantitative RT-PCR, and nucleotide sequencing) investigation of this outbreak was carried out by collecting and studying 52 clinical samples and 15 mosquito pools from the affected region. The investigation revealed the presence of CHIK viral RNA in 29% of clinical samples and 13% mosquito pool by RT-PCR. The quantification of CHIK viral RNA in samples varied from 102.50 to 106.67 copies/mL, as demonstrated through quantitative RT-PCR. In addition, six CHIK viruses were isolated from RT-PCR positive samples. The nucleotide sequences of partial E1 gene of five representative CHIK viruses were deciphered, which revealed that all the viral strains from this outbreak belong to the recently emerging ECS African genotype. Identification of Chikungunya virus ECSA African genotype as the etiology of the present outbreak confirms the continued circulation of the novel genotype, since 2006, in India. The identification of CHIK virus in Aedes aegypti also confirmed it as the major vector in northern India.
PMCID: PMC3886578  PMID: 24453838
15.  SHetA2 interference with mortalin binding to p66shc and p53 identified using drug-conjugated magnetic microspheres 
Investigational New Drugs  2013;32(3):412-423.
SHetA2 is a small molecule flexible heteroarotinoid (Flex-Het) with promising cancer prevention and therapeutic activity. Extensive preclinical testing documented lack of SHetA2 toxicity at doses 25 to 150 fold above effective doses. Knowledge of the SHetA2 molecular target(s) that mediate(s) the mechanism of SHetA2 action is critical to appropriate design of clinical trials and improved analogs. The aim of this study was to develop a method to identify SHetA2 binding proteins in cancer cells. A known metabolite of SHetA2 that has a hydroxyl group available for attachment was synthesized and conjugated to a linker for attachment to a magnetic microsphere. SHetA2-conjugated magnetic microspheres and unconjugated magnetic microspheres were separately incubated with aliquots of a whole cell protein extract from the A2780 human ovarian cancer cell line. After washing away non-specifically bound proteins with the protein extraction buffer, SHetA2-binding proteins were eluted with an excess of free SHetA2. In two independent experiments, an SDS gel band of about 72 kDa was present at differential levels in wells of eluent from SHetA2-microspheres in comparison to wells of eluent from unconjugated microspheres. Mass spectrometry analysis of the bands (QStar) and straight eluents (Orbitrap) identified mortalin (HSPA9) to be present in the eluent from SHetA2-microspheres and not in eluent from unconjugated microspheres. Co-immunoprecipitation experiments demonstrated that SHetA2 interfered with mortalin binding to p53 and p66 Src homologous-collagen homologue (p66shc) inside cancer cells. Mortalin and SHetA2 conflictingly regulate the same molecules involved in mitochondria-mediated intrinsic apoptosis. The results validate the power of this protocol for revealing drug targets.
Electronic supplementary material
The online version of this article (doi:10.1007/s10637-013-0041-x) contains supplementary material, which is available to authorized users.
PMCID: PMC4045313  PMID: 24254390
Mortalin; HSPA9; Heteroarotinoids; Ovarian cancer; p66shc; p53
16.  Nebulised fentanyl for post-operative pain relief, a prospective double-blind controlled randomised clinical trial 
Indian Journal of Anaesthesia  2013;57(6):583-586.
Background and Aim:
Intravenous (IV) route for fentanyl administration is the gold standard for post-operative pain relief, but complications such as respiratory depression, bradycardia and hypotension have limited this route. The aim of this randomised controlled trial was to compare the efficacy of nebulised fentanyl with IV fentanyl for post-operative pain relief after lower abdominal surgery.
In the post-operative care unit, at the time of first onset of pain (visual analogue scale- VAS score > 4) patients were randomised into three groups and fentanyl was administered either IV 2 μg/kg or by nebulisation of solution containing 3 or 4 μg/kg fentanyl over 8 min in 90 patients divided into three groups of 30 each. Observation were made for pain relief by visual analogue scale score 0-10. Adverse effects such as respiratory depression, bradycardia and hypotension were also recoded. Statistical analysis was performed using Medcalc software version 12, 2012. (MedCalc Software, Ostend, Belgium).
In the nebulisation group, it was observed that the analgesic efficacy of fentanyl was dose dependent with a delayed onset of analgesia (10 min vs. 5 min). Nebulisation with 4 μg/kg fentanyl produced analgesia at par to 2 μg/kg IV fentanyl with prolonged duration (90 min vs. 30 min) and with significantly less adverse effects.
This study shows that nebulisation with 4 μg/kg fentanyl may be used as an alternative to IV 2 μg/kg fentanyl for adequate post-operative pain relief.
PMCID: PMC3883393  PMID: 24403618
Fentanyl; post-operative analgesia; pulmonary administration; side-effects
17.  Orbital myiasis caused by green bottle fly 
The Australasian Medical Journal  2013;6(10):504-506.
An 80-year-old farmer, presented with large, maggot infested ulceration involving the medial part of the right upper lid. The left eye was phthisical. There was history of untreated traumatic laceration of the right upper lid. Mechanical removal of maggots was done under turpentine coverage with regular antibiotic dressing. Microbiological examination of maggots revealed the larvae to be of Lucilia sericata (green bottle fly). The ulceration completely healed in two weeks following manual removal of maggots and regular dressing. Orbital myiasis is an uncommon clinical condition, with isolated case reports in literature.
PMCID: PMC3821047  PMID: 24223066
Green bottle fly; Lucilia sericata; maggots; orbital myiasis
18.  Comprehensive transcriptomic study on horse gram (Macrotyloma uniflorum): De novo assembly, functional characterization and comparative analysis in relation to drought stress 
BMC Genomics  2013;14:647.
Drought tolerance is an attribute maintained in plants by cross-talk between multiple and cascading metabolic pathways. Without a sequenced genome available for horse gram, it is difficult to comprehend such complex networks and intercalated genes associated with drought tolerance of horse gram (Macrotyloma uniflorum). Therefore, de novo transcriptome discovery and associated analyses was done for this highly drought tolerant yet under exploited legume to decipher its genetic makeup.
Eight samples comprising of shoot and root tissues of two horse gram genotypes (drought-sensitive; M-191 and drought-tolerant; M-249) were used for comparison under control and polyethylene glycol-induced drought stress conditions. Using Illumina sequencing technology, a total of 229,297,896 paired end read pairs were generated and utilized for de novo assembly of horse gram. Significant BLAST hits were obtained for 26,045 transcripts while, 3,558 transcripts had no hits but contained important conserved domains. A total of 21,887 unigenes were identified. SSRs containing sequences covered 16.25% of the transcriptome with predominant tri- and mono-nucleotides (43%). The total GC content of the transcriptome was found to be 43.44%. Under Gene Ontology response to stimulus, DNA binding and catalytic activity was highly expressed during drought stress conditions. Serine/threonine protein kinase was found to dominate in Enzyme Classification while pathways belonging to ribosome metabolism followed by plant pathogen interaction and plant hormone signal transduction were predominant in Kyoto Encyclopedia of Genes and Genomes analysis. Independent search on plant metabolic network pathways suggested valine degradation, gluconeogenesis and purine nucleotide degradation to be highly influenced under drought stress in horse gram. Transcription factors belonging to NAC, MYB-related, and WRKY families were found highly represented under drought stress. qRT-PCR validated the expression profile for 9 out of 10 genes analyzed in response to drought stress.
De novo transcriptome discovery and analysis has generated enormous information over horse gram genomics. The genes and pathways identified suggest efficient regulation leading to active adaptation as a basal defense response against drought stress by horse gram. The knowledge generated can be further utilized for exploring other underexploited plants for stress responsive genes and improving plant tolerance.
PMCID: PMC3853109  PMID: 24059455
Horse gram; Illumina sequencing; De novo assembly; Drought responsive genes
19.  An unusual case of paradoxical enlargement of lymph nodes during treatment of tuberculous lymphadenitis in immunocompetent patient and literature review 
Female, 21
Final Diagnosis:
Tuberculous lyphadenitis
Cough dry • fever • subcutaneous mass • weight loss
Clinical Procedure:
Unusual clinical course
Enlargement of lymph nodes during treatment of Tuberculous lymphadenitis is well recognized phenomenon in HIV infected patient with ample literature to help guide management. On the contrary, it poses a clinical challenge to distinguish between paradoxical reaction and treatment failure in HIV-seronegative patients and require high index of suspicion.
Case Report:
We report a case of 21 year old female of Bangladeshi origin with tuberculous lymphadenitis diagnosed on the basis of strong clinical history and radiologic findings. Patient’s clinical symptoms and lymphadenopathy initially improved but worsened after three months of RIPE therapy. This prompted re imaging and excision biopsy of enlarging lymph node to exclude other masqueraders. Patient was continued on same antituberculous treatment. Oral prednisone was added with subsequent clinical improvement and decrease in the size of lymphadenopathy.
Paradoxical reaction during anti tuberculous treatment must be considered after careful exclusion of medication non adherence, development of resistance and other similar conditions.
PMCID: PMC3700484  PMID: 23826468
paradoxical reaction (PR); highly active anti-retroviral therapy (HAART); rifampin; isoniazid; pyrazinamide and ethambutol (RIPE); tuberculosis (TB); Kikuchi’s disease (KD); tuberculosis lymphadenitis (TL)
20.  Genome-Wide Organization and Expression Profiling of the NAC Transcription Factor Family in Potato (Solanum tuberosum L.) 
NAC [no apical meristem (NAM), Arabidopsis thaliana transcription activation factor [ATAF1/2] and cup-shaped cotyledon (CUC2)] proteins belong to one of the largest plant-specific transcription factor (TF) families and play important roles in plant development processes, response to biotic and abiotic cues and hormone signalling. Our genome-wide analysis identified 110 StNAC genes in potato encoding for 136 proteins, including 14 membrane-bound TFs. The physical map positions of StNAC genes on 12 potato chromosomes were non-random, and 40 genes were found to be distributed in 16 clusters. The StNAC proteins were phylogenetically clustered into 12 subgroups. Phylogenetic analysis of StNACs along with their Arabidopsis and rice counterparts divided these proteins into 18 subgroups. Our comparative analysis has also identified 36 putative TNAC proteins, which appear to be restricted to Solanaceae family. In silico expression analysis, using Illumina RNA-seq transcriptome data, revealed tissue-specific, biotic, abiotic stress and hormone-responsive expression profile of StNAC genes. Several StNAC genes, including StNAC072 and StNAC101that are orthologs of known stress-responsive Arabidopsis RESPONSIVE TO DEHYDRATION 26 (RD26) were identified as highly abiotic stress responsive. Quantitative real-time polymerase chain reaction analysis largely corroborated the expression profile of StNAC genes as revealed by the RNA-seq data. Taken together, this analysis indicates towards putative functions of several StNAC TFs, which will provide blue-print for their functional characterization and utilization in potato improvement.
PMCID: PMC3738166  PMID: 23649897
abiotic stress; genome-wide analysis; Illumina RNA-seq; NAC transcription factor; potato
21.  Antibacterial activity of actinomycetes isolated from different soil samples of Sheopur (A city of central India) 
The main objective of the present study was isolation, purification, and characterization of actinomycetes from soil samples, having antimicrobial activity against 12 selected pathogenic strains. Soils samples were taken from different niche habitats of Sheopur district, Madhya Pradesh, India. These samples were serially diluted and plated on actinomycete isolation agar media. Potential colonies were screened, purified, and stored in glycerol stock. Isolates were morphologically and biochemically characterized. These isolates were subjected to extraction for production of the antibacterial compound. Antibacterial activity and Minimum Inhibitory Concentration (MIC) of the purified extract of isolates were evaluated. Totally 31 actinomycete isolates were tested for antagonistic activity against 12 pathogenic microorganisms. Isolates AS14, AS27, and AS28 were highly active, while AS1 showed less activity against the pathogenic microorganisms. Isolate AS7 exhibited the highest antagonistic activity against Bacillus cereus (24 mm) and AS16 showed the highest activity against Enterococcus faecalis (21 mm). MIC was also determined for actinomycete isolates against all the tested microorganisms. MIC of actinomycete isolates was found to be 2.5 mg/ml against Shigella dysenteriae, Vancomycin-resistant enterococci, and Klebsiella pneumoniae, and was 1.25 mg/ml for Staphylococcus saprophyticus, Streptococcus pyogenes, Staphylococcus epidermidis, Methicillin-resistant Staphylococcus, Bacillus cereus, Staphylococcus xylosus, Methicillin-resistant Staphylococcus aureus, Enterococcus faecalis, and Staphylococcus aureus. All actinomycetes isolates showed antibacterial activity against S. aureus, while they showed less activity against S. dysenteriae. These isolates had antibacterial activity and could be used in the development of new antibiotics for pharmaceutical or agricultural purposes.
PMCID: PMC3696223  PMID: 23833752
Agar well diffusion method; antimicrobial activity; minimum inhibitory concentration; pathogenic microorganisms; Sheopur
22.  Metastatic papillary thyroid carcinoma with absence of tumor focus in thyroid gland 
Papillary thyroid carcinoma presenting as isolated cervical lymphadenopathy with clinically and histologically normal thyroid gland is rarely reported.
Case Report:
We report a case of 31 years old female who presented with a left cervical mass and clinically normal thyroid gland. After inconclusive FANC, excision biopsy of her cervical lymph nodes revealed metastatic papillary thyroid carcinoma. The patient subsequently underwent total thyroidectomy with bilateral lymph node dissection. Interestingly pathological examination showed no primary carcinoma in the gland. Postoperative radioactive iodine scan revealed no other metastasis.
Total thyroidectomy is the next best step despite clinically and radiologically normal appearing thyroid gland once cervical lymph nodes are proven to be metastatic in nature followed by a RAI therapy to treat occult foci of PTC.
PMCID: PMC3619041  PMID: 23569568
papillary thyroid micro carcinoma (PTMC); fine needle aspiration cytology (FNAC); computed tomography (CT); papillary thyroid carcinoma (PTC)
23.  Degree of modification of Ro60 by the lipid peroxidation by-product 4-hydroxy-2-nonenal may differentially induce Sjögren's syndrome or systemic lupus erythematosus in BALB/c mice 
Free radical biology & medicine  2010;50(10):1222-1233.
Our previous work showed that immunization of rabbits with 4-hydroxy 2-nonenal-modified Ro60 (HNE-Ro60) accelerates autoimmunity. We extended this model into mice, hypothesizing that the severity of autoimmunity would be dependent on degree of HNE-modification of Ro60. Five groups of BALB/c mice (ten/group) were used. Group I was immunized with Ro60. Groups II to IV were immunized with Ro60 modified with 0.4 mM (low), 2 mM (medium) and 10 mM (high) HNE respectively. Group V controls received Freund's adjuvant. A rapid abrogation of tolerance to Ro60/La antigens occurred in mice immunized with HNE-modified Ro60, especially in the low and medium HNE-Ro60 groups. Lymphocytic infiltration and significantly high decrement in salivary flow (37%) compared to controls was observed only in high HNE-Ro60 group, suggesting induction of a SS-like condition in this group. Anti-dsDNA occurred only in mice immunized with medium HNE-Ro60. This group did not have significant decrement in salivary flow, suggesting induction of SLE-like manifestation in this group. Significantly high antibodies to Ro60 were found in saliva of mice in low and medium HNE-Ro60, and Ro60 groups as well as anti-HNE Ro60 in low and medium HNE-Ro60 groups. Understanding the mechanism of this differential induction may help delineate between these two autoimmune diseases.
PMCID: PMC3591494  PMID: 20946951
Sjögren's syndrome; SLE; autoimmunity; epitope spreading; autoantibodies; antigens; 4-hydroxy-2-nonenal; oxidative damage
24.  Draft Genome Sequence of Pseudomonas aeruginosa Strain N002, Isolated from Crude Oil-Contaminated Soil from Geleky, Assam, India 
Genome Announcements  2013;1(1):e00104-12.
Here, we report the draft genome sequence of crude oil-degrading Pseudomonas aeruginosa strain N002, isolated from a crude oil-polluted soil sample from Geleky, Assam, India. Multiple genes potentially involved in crude oil degradation were identified.
PMCID: PMC3569314  PMID: 23405324
25.  Braving the attitude of altitude: Caragana jubata at work in cold desert of Himalaya 
Scientific Reports  2013;3:1022.
The present work was conducted to understand the basis of adaptation in Caragana jubata in its niche environment at high altitude cold desert of Himalaya. Molecular data showed predominance of genes encoding chaperones and those involved in growth and development at low temperature (LT), a major cue operative at high altitude. Importantly, these genes expressed in C. jubata in its natural habitat. Their homologues in Arabidopsis thaliana, Oryza sativa, and Glycine max did not exhibit similar trend of gene expression at LT. Constitutive expression and a quick up-regulation of the above genes suggested the ability of C. jubata to adjust its cellular machinery to maintain growth and development in its niche. This was reflected in LT50 (the temperature at which 50% injury occurred) and LT mediated photosynthetic acclimatory response. Such molecular and physiological plasticity enables C. jubata to thrive in the high altitude cold desert of Himalayas.
PMCID: PMC3535672  PMID: 23289064

Results 1-25 (52)