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1.  A Chromosome Segment Substitution Library of Weedy Rice for Genetic Dissection of Complex Agronomic and Domestication Traits 
PLoS ONE  2015;10(6):e0130650.
Chromosome segment substitution lines (CSSLs) are a powerful alternative for locating quantitative trait loci (QTL), analyzing gene interactions, and providing starting materials for map-based cloning projects. We report the development and characterization of a CSSL library of a U.S. weedy rice accession ‘PSRR-1’ with genome-wide coverage in an adapted rice cultivar ‘Bengal’ background. The majority of the CSSLs carried a single defined weedy rice segment with an average introgression segment of 2.8 % of the donor genome. QTL mapping results for several agronomic and domestication traits from the CSSL population were compared with those obtained from two recombinant inbred line (RIL) populations involving the same weedy rice accession. There was congruence of major effect QTLs between both types of populations, but new and additional QTLs were detected in the CSSL population. Although, three major effect QTLs for plant height were detected on chromosomes 1, 4, and 8 in the CSSL population, the latter two escaped detection in both RIL populations. Since this was observed for many traits, epistasis may play a major role for the phenotypic variation observed in weedy rice. High levels of shattering and seed dormancy in weedy rice might result from an accumulation of many small effect QTLs. Several CSSLs with desirable agronomic traits (e.g. longer panicles, longer grains, and higher seed weight) identified in this study could be useful for rice breeding. Since weedy rice is a reservoir of genes for many weedy and agronomic attributes, the CSSL library will serve as a valuable resource to discover latent genetic diversity for improving crop productivity and understanding the plant domestication process through cloning and characterization of the underlying genes.
doi:10.1371/journal.pone.0130650
PMCID: PMC4472838  PMID: 26086245
2.  Cytotoxic Helix-Rich Oligomer Formation by Melittin and Pancreatic Polypeptide 
PLoS ONE  2015;10(3):e0120346.
Conversion of amyloid fibrils by many peptides/proteins involves cytotoxic helix-rich oligomers. However, their toxicity and biophysical studies remain largely unknown due to their highly dynamic nature. To address this, we chose two helical peptides (melittin, Mel and pancreatic polypeptide, PP) and studied their aggregation and toxicity. Mel converted its random coil structure to oligomeric helical structure upon binding to heparin; however, PP remained as helix after oligomerization. Interestingly, similar to Parkinson’s associated α-synuclein (AS) oligomers, Mel and PP also showed tinctorial properties, higher hydrophobic surface exposure, cellular toxicity and membrane pore formation after oligomerization in the presence of heparin. We suggest that helix-rich oligomers with exposed hydrophobic surface are highly cytotoxic to cells irrespective of their disease association. Moreover as Mel and PP (in the presence of heparin) instantly self-assemble into stable helix-rich amyloidogenic oligomers; they could be represented as models for understanding the biophysical and cytotoxic properties of helix-rich intermediates in detail.
doi:10.1371/journal.pone.0120346
PMCID: PMC4372375  PMID: 25803428
3.  Structure based aggregation studies reveal the presence of helix-rich intermediate during α-Synuclein aggregation 
Scientific Reports  2015;5:9228.
Mechanistic understanding of nucleation dependent polymerization by α-synuclein (α-Syn) into toxic oligomers and amyloids is important for the drug development against Parkinson's disease. However the structural and morphological characterization during nucleation and subsequent fibrillation process of α-Syn is not clearly understood. Using a variety of complementary biophysical techniques monitoring entire pathway of nine different synucleins, we found that transition of unstructured conformation into β-sheet rich fibril formation involves helix-rich intermediates. These intermediates are common for all aggregating synucleins, contain high solvent-exposed hydrophobic surfaces, are cytotoxic to SHSY-5Y cells and accelerate α-Syn aggregation efficiently. A multidimensional NMR study characterizing the intermediate accompanied with site-specific fluorescence study suggests that the N-terminal and central portions mainly participate in the helix-rich intermediate formation while the C-terminus remained in an extended conformation. However, significant conformational transitions occur at the middle and at the C-terminus during helix to β-sheet transition as evident from Trp fluorescence study. Since partial helix-rich intermediates were also observed for other amyloidogenic proteins such as Aβ and IAPP, we hypothesize that this class of intermediates may be one of the important intermediates for amyloid formation pathway by many natively unstructured protein/peptides and represent a potential target for drug development against amyloid diseases.
doi:10.1038/srep09228
PMCID: PMC4363886  PMID: 25784353
4.  Molecular Epidemiology and In-Vitro Antifungal Susceptibility of Aspergillus terreus Species Complex Isolates in Delhi, India: Evidence of Genetic Diversity by Amplified Fragment Length Polymorphism and Microsatellite Typing 
PLoS ONE  2015;10(3):e0118997.
Aspergillus terreus is emerging as an etiologic agent of invasive aspergillosis in immunocompromised individuals in several medical centers in the world. Infections due to A. terreus are of concern due to its resistance to amphotericin B, in vivo and in vitro, resulting in poor response to antifungal therapy and high mortality. Herein we examined a large collection of molecularly characterized, geographically diverse A. terreus isolates (n = 140) from clinical and environmental sources in India for the occurrence of cryptic A. terreus species. The population structure of the Indian A. terreus isolates and their association with those outside India was determined using microsatellite based typing (STR) technique and Amplified Fragment Length Polymorphism analysis (AFLP). Additionally, in vitro antifungal susceptibility of A. terreus isolates was determined against 7 antifungals. Sequence analyses of the calmodulin locus identified the recently described cryptic species A. hortai, comprising 1.4% of Aspergillus section Terrei isolates cultured from cases of aspergilloma and probable invasive aspergillosis not reported previously. All the nine markers used for STR typing of A. terreus species complex proved to be highly polymorphic. The presence of high genetic diversity revealing 75 distinct genotypes among 101 Indian A. terreus isolates was similar to the marked heterogeneity noticed in the 47 global A. terreus population exhibiting 38 unique genotypes mainly among isolates from North America and Europe. Also, AFLP analysis showed distinct banding patterns for genotypically diverse A. terreus isolates. Furthermore, no correlation between a particular genotype and amphotericin B susceptibility was observed. Overall, 8% of the A. terreus isolates exhibited low MICs of amphotericin B. All the echinocandins and azoles (voriconazole, posaconazole and isavuconazole) demonstrated high potency against all the isolates. The study emphasizes the need of molecular characterization of A. terreus species complex isolates to better understand the ecology, acquisition and transmission of this species.
doi:10.1371/journal.pone.0118997
PMCID: PMC4363790  PMID: 25781896
5.  Biological Cost of Pyocin Production during the SOS Response in Pseudomonas aeruginosa 
Journal of Bacteriology  2014;196(18):3351-3359.
LexA and two structurally related regulators, PrtR and PA0906, coordinate the Pseudomonas aeruginosa SOS response. RecA-mediated autocleavage of LexA induces the expression of a protective set of genes that increase DNA damage repair and tolerance. In contrast, RecA-mediated autocleavage of PrtR induces antimicrobial pyocin production and a program that lyses cells to release the newly synthesized pyocin. Recently, PrtR-regulated genes were shown to sensitize P. aeruginosa to quinolones, antibiotics that elicit a strong SOS response. Here, we investigated the mechanisms by which PrtR-regulated genes determine antimicrobial resistance and genotoxic stress survival. We found that induction of PrtR-regulated genes lowers resistance to clinically important antibiotics and impairs the survival of bacteria exposed to one of several genotoxic agents. Two distinct mechanisms mediated these effects. Cell lysis genes that are induced following PrtR autocleavage reduced resistance to bactericidal levels of ciprofloxacin, and production of extracellular R2 pyocin was lethal to cells that initially survived UV light treatment. Although typically resistant to R2 pyocin, P. aeruginosa becomes transiently sensitive to R2 pyocin following UV light treatment, likely because of the strong downregulation of lipopolysaccharide synthesis genes that are required for resistance to R2 pyocin. Our results demonstrate that pyocin production during the P. aeruginosa SOS response carries both expected and unexpected costs.
doi:10.1128/JB.01889-14
PMCID: PMC4135695  PMID: 25022851
6.  In Vitro Antifungal Susceptibility Profile and Correlation of Mycelial and Yeast Forms of Molecularly Characterized Histoplasma capsulatum Strains from India 
The antifungal susceptibility profiles of the mycelial and yeast forms of 23 Histoplasma capsulatum strains from pulmonary and disseminated histoplasmosis patients in India are reported here. The MIC data of this dimorphic fungus had good agreement between both forms for azoles, amphotericin B, and caspofungin. Therefore, the use of mycelial inocula for H. capsulatum antifungal susceptibility testing is suggested, which is less time-consuming vis-à-vis the yeast form, which requires 6 to 8 weeks for conversion.
doi:10.1128/AAC.02973-14
PMCID: PMC4135809  PMID: 24982084
7.  Hepatoprotective potential of ethanolic extract of Pandanus odoratissimus root against paracetamol-induced hepatotoxicity in rats 
Background:
Pandanus odoratissimus (Pandanaceae) is popular in the indigenous system of medicines like Ayurveda, Siddha, Unani and Homoeopathy. In the traditional system of medicine various plant parts such as leaves, root, flowers, and oils are used as anthelmintic, tonic, stomachic, digestive and in the treatment of jaundice and various liver disorders.
Objective:
The aim was to investigate the hepatoprotective activity of ethanolic extract of the root of P. odoratissimus against paracetamol (PCM) induced hepatotoxicity in rats.
Materials and Methods:
Hepatotoxicity was induced in male Wistar rat by PCM (2 g/kg b.w. p.o. for 7 days). The ethanolic extract of P. odoratissimus root was administered at the dose level of 200 mg/kg and 400 mg/kg b.w. orally for 7 days and silymarin (100 mg/kg b.w. p.o.) as standard drug was administered once daily for a week. The hepatoprotective effect of ethanolic extract was evaluated by assessment of biochemical parameters such as serum glutamic oxaloacetic transaminase, serum glutamic-pyruvic transaminase, serum alkaline phosphatase, total and direct bilirubin and triglycerides. Histopathological study of rat liver was also done.
Results:
Experimental findings revealed that the extract at dose level of 200 mg/kg and 400 mg/kg of b.w. showed dose dependant hepatoprotective effect against PCM induced hepatotoxicity by significantly restoring the levels of serum enzymes to normal that was comparable to that of silymarin, but the extract at dose level of 400 mg/kg was found to be more potent when compared to that of 200 mg/kg. Besides, the results obtained from histopathological study also support the study.
Conclusion:
From the results, it can be concluded that ethanolic extract of the root of P. odoratissimus afforded significant protection against PCM induced hepatotoxicity in rats.
doi:10.4103/0975-7406.148776
PMCID: PMC4333627  PMID: 25709336
Hepatoprotective activity; histopathology; Pandanus odoratissimus; paracetamol; silymarin
8.  The extracellular matrix protects Pseudomonas aeruginosa biofilms by limiting the penetration of tobramycin 
Environmental microbiology  2013;15(10):2865-2878.
SUMMARY
Biofilm cells are less susceptible to antimicrobials than their planktonic counterparts. While this phenomenon is multifactorial, the ability of the biofilm matrix to reduce antibiotic penetration into the biofilm is thought to be of limited importance, as previous studies suggest that antibiotics move fairly rapidly through biofilms. In this study, we monitored the transport of two clinically relevant antibiotics, tobramycin and ciprofloxacin, into non-mucoid P. aeruginosa biofilms. To our surprise, we showed that the positively charged antibiotic tobramycin is sequestered to the biofilm periphery, while the neutral antibiotic ciprofloxacin readily penetrated. We provide evidence that tobramycin in the biofilm periphery both stimulated a localized stress response and killed bacteria in these regions, but not in the underlying biofilm. Although it is unclear which matrix component binds tobramycin, its penetration was increased by the addition of cations in a dose-dependent manner, which led to increased biofilm death. These data suggest that ionic interactions of tobramycin with the biofilm matrix limit its penetration. We propose that tobramycin sequestration at the biofilm periphery is an important mechanism in protecting metabolically active cells that lie just below the zone of sequestration.
doi:10.1111/1462-2920.12155
PMCID: PMC4045617  PMID: 23751003
9.  Shrinking lung syndrome in systemic lupus erythematosus-scleroderma overlap 
Shrinking lung syndrome (SLS) is a infrequently reported manifestation of systemic lupus erythematosus (SLE). Reported prevalence of SLS is about 0.5% in SLE patients. Pathogenesis is not fully understood and different therapeutic modalities have been employed with variable results, as only 77 cases of SLS have been documented in literature. SLS in SLE-Scleroderma overlap has not been reported yet. We report a patient of SLE - scleroderma overlap presenting with dyspnea, intermittent orthopnea and pleuritic chest pain. Evaluation revealed elevated hemidiaphragms and severe restrictive defect. She was eventually diagnosed as a case of SLS. This case report is a reminder to the medical fraternity that SLS although a rare complication must be thought of in the special subset of patients of SLE having respiratory symptoms.
doi:10.4103/0970-2113.142152
PMCID: PMC4220329  PMID: 25378855
Scleroderma; scleroderma shrinking lung syndrome; systemic lupus erythematosus
10.  Conditions Associated with the Cystic Fibrosis Defect Promote Chronic Pseudomonas aeruginosa Infection 
Rationale: Progress has been made in understanding how the cystic fibrosis (CF) basic defect produces lung infection susceptibility. However, it remains unclear why CF exclusively leads to chronic infections that are noninvasive and highly resistant to eradication. Although biofilm formation has been suggested as a mechanism, recent work raises questions about the role of biofilms in CF.
Objectives: To learn how airway conditions attributed to CF transmembrane regulator dysfunction could lead to chronic infection, and to determine if biofilm-inhibiting genetic adaptations that are common in CF isolates affect the capacity of Pseudomonas aeruginosa to develop chronic infection phenotypes.
Methods: We studied P. aeruginosa isolates grown in agar and mucus gels containing sputum from patients with CF and measured their susceptibility to killing by antibiotics and host defenses. We also measured the invasive virulence of P. aeruginosa grown in sputum gels using airway epithelial cells and a murine infection model.
Measurements and Main Results: We found that conditions likely to result from increased mucus density, hyperinflammation, and defective bacterial killing could all cause P. aeruginosa to grow in bacterial aggregates. Aggregated growth markedly increased the resistance of bacteria to killing by host defenses and antibiotics, and reduced their invasiveness. In addition, we found that biofilm-inhibiting mutations do not impede aggregate formation in gel growth environments.
Conclusions: Our findings suggest that conditions associated with several CF pathogenesis hypotheses could cause the noninvasive and resistant infection phenotype, independently of the bacterial functions needed for biofilm formation.
doi:10.1164/rccm.201312-2142OC
PMCID: PMC4225830  PMID: 24467627
cystic fibrosis; chronic infection; Pseudomonas aeruginosa; biofilm
11.  Voriconazole-Resistant Penicillium oxalicum: An Emerging Pathogen in Immunocompromised Hosts 
Open Forum Infectious Diseases  2014;1(2):ofu029.
Penicillium species are rarely reported agents of infections in immunocompromised patients. We report 3 cases of invasive mycosis caused by voriconazole-resistant Penicillium oxalicum in patients with acute myeloid leukemia, diabetes mellitus, and chronic obstructive pulmonary disease, while on voriconazole therapy. Penicillium oxalicum has not been previously recognized as a cause of invasive mycoses.
doi:10.1093/ofid/ofu029
PMCID: PMC4281804  PMID: 25734109
immunocompromised; India; invasive; Penicillium oxalicum; posaconazole; voriconazole resistance
12.  Active starvation responses mediate antibiotic tolerance in biofilms and nutrient-limited bacteria 
Science (New York, N.Y.)  2011;334(6058):982-986.
Bacteria become highly tolerant to antibiotics when nutrients are limited. The inactivity of antibiotic targets caused by starvation-induced growth arrest is thought to be a key mechanism producing tolerance (1). Here we show that the antibiotic tolerance of nutrient-limited and biofilm Pseudomonas aeruginosa is mediated by active responses to starvation, rather than by the passive effects of growth arrest. The protective mechanism is controlled by the starvation-signaling stringent response (SR), and our experiments link SR–mediated tolerance to reduced levels of oxidant stress in bacterial cells. Furthermore, inactivating this protective mechanism sensitized biofilms by several orders of magnitude to four different classes of antibiotics, and markedly enhanced the efficacy of antibiotic treatment in experimental infections.
doi:10.1126/science.1211037
PMCID: PMC4046891  PMID: 22096200
13.  Pharmacognostical study and establishment of quality parameters of aerial parts of Costus speciosus-a well known tropical folklore medicine 
Objective
To evaluate the diagnostic pharmacognostical characters of Costus speciosus (aerial parts) along with their physico-chemical parameters and fluorosence analysis.
Method
The pharmacognostical characters were determined in terms of macroscopy, microscopy, powder microscopy, leaf constant, fluorescence analysis and preliminary phytochemical investigation.
Results
The findings of macroscopy revealed that leaves elliptic to oblong or oblong-lancoelate, thick, spirally arranged, with stem clasping sheaths up to 4 cm, flowers large, white, cone-like terminal spikes, with bright red bracts. Transverse section of leaflet showed the presence of cuticularised epidermis with polygonal cells on adaxial surface and bluntly angled cells on abaxial surface of lamina, mesophyll cells differentiated in to single layered palisade cells on each surface and 2-3 layered spongy parenchyma, unicellular and uniseriate multicellular covering trichomes, paracytic stomata and vascular bundles surrounded by sclerenchymatous multicellular sheath. Preliminary phytochemical screening exhibited the presence of various phytochemical groups like alkaloids, glycosides, steroids, phenolic constituents. Further, the leaf constants, powder microscopy and fluorescence characteristics indicated outstanding results from this investigation
Conclusions
Various pharmacognostical and physico-chemical parameters have pivotal roles in identification, authentication and establishment of quality parameters of the species.
doi:10.12980/APJTB.4.2014C1103
PMCID: PMC3994359  PMID: 25182951
Costus speciosus; Quality control; Physico-chemical parameters; Microscopy; Fluorescence analysis
14.  Bacterial Decolorization of Textile Azo Dye Acid Orange by Staphylococcus hominis RMLRT03 
Toxicology International  2014;21(2):160-166.
A bacterial strain RMLRT03 with ability to decolorize textile dye Acid Orange dye was isolated from textile effluent contaminated soil of Tanda, Ambedkar Nagar, Uttar Pradesh (India). The decolorization studies were performed in Bushnell and Haas medium (BHM) amended with Acid Orange dye. The bacterial strain was identified as Staphylococcus hominis on the basis of 16S rDNA sequence. The bacterial strain exhibited good decolorization ability with glucose and yeast extract supplementation as cosubstrate in static conditions. The optimal condition for the decolorization of Acid Orange dye by Staphylococcus hominis RMLRT03 strain were at pH 7.0 and 35°C in 60 h of incubation. The bacterial strain could tolerate high concentrations of Acid Orange dye up to 600 mg l-1. The high decolorizing activity under natural environmental conditions indicates that the bacterial strain has practical application in the treatment of dye containing wastewaters.
doi:10.4103/0971-6580.139797
PMCID: PMC4170557  PMID: 25253925
16S rDNA; BHM; cosubstrate; decolorization; textile dye
15.  Clinical Significance and Molecular Characterization of Nonsporulating Molds Isolated from the Respiratory Tracts of Bronchopulmonary Mycosis Patients with Special Reference to Basidiomycetes 
Journal of Clinical Microbiology  2013;51(10):3331-3337.
Nonsporulating molds (NSMs), especially basidiomycetes, have predominantly been reported as human pathogens responsible for allergic and invasive disease. Their conventional identification is problematic, as many isolates remain sterile in culture. Thus, inconclusive culture reports might adversely affect treatment decisions. The clinical significance of NSMs in pulmonary mycoses is poorly understood. We sequenced the internal transcribed spacer (ITS) region and D1/D2 domain of the larger subunit (LSU) of 52 NSMs isolated from respiratory specimens. The basidiomycetes were the predominant NSMs, of which Schizophyllum commune was the most common agent in allergic bronchopulmonary mycosis (ABPM), followed by Ceriporia lacerata in invasive fungal disease. Porostereum spadiceum, Phanaerochaete stereoides, Neosartorya fischeri, and Marasmiellus palmivorus were the other molds observed. Application of ITS and LSU region sequencing identified 92% of the isolates. The antifungal susceptibility data revealed that all basidiomycetes tested were susceptible to amphotericin B and resistant to caspofungin, fluconazole, and flucytosine. Except for 3 isolates of S. commune and a solitary isolate of M. palmivorus, all basidiomycetes had low MICs for itraconazole, posaconazole, and voriconazole. Basidiomycetes were isolated from patients with ABPM, invasive pulmonary mycosis/pneumonia, or fungal balls. In addition, the majority of the basidiomycetes were isolated from patients with chronic respiratory disorders who were sensitized to one of the basidiomycetous fungi and demonstrated precipitating antibodies against the incriminating fungi, indicating an indolent tissue reaction. Thus, isolation of basidiomycetes from the lower respiratory tract could be significant, and it is important to monitor these patients in order to prevent subsequent lung damage.
doi:10.1128/JCM.01486-13
PMCID: PMC3811655  PMID: 23903552
16.  Role of Decompression in Late Presentation of Cervical Spinal Cord Disorders 
Asian Spine Journal  2014;8(2):183-189.
Study Design
Prospective study conducted at Jawaharlal Nehru Medical College, Datta Meghe Institute of Medical Sciences, Wardha, India.
Purpose
To show the efficacy of decompression in the late presentation of cervical spinal cord disorders.
Overview of Literature
Studies by various authors have shown that early spinal decompression results in better neurological outcomes.
Methods
From January 2003 to January 2005, 11 of the 41 patients with cervical spinal cord compression, meeting the inclusion criteria, underwent anterior decompression; interbody graft placement and stabilization by anterior cervical locking plate. The neurologic and functional outcomes were recorded.
Results
Five patients had spinal cord injury and 6 patients had compressive cervical myelopathy. Complications included 1 death and 1 plate loosening. No patient lost their preoperative neurological status. One patient had no improvement, 2 patients showed full recovery. The mean follow-up is 28.3 month. At the of rehabilitation, 6 were able to walk without support), 2 could walk with support, and 1 needed a wheelchair. The average American Spinal Injury Association motor score on admission to the hospital, 32.8 (standard deviation [SD], 30.5); admission to rehabilitation, 38.6 (SD, 32.4); discharge from rehabilitation, 46.2 (SD, 33.7). The most recent follow-up was 64.0 (SD, 35.3).
Conclusions
The anterior approach for cervical decompression allows for adequate decompression. This decompression is the best chance offered in even late reported cases, including posttraumatic cases where there is no evidence of cord transactions. The use of anterior cervical plates reduces the chances of graft loosening, extruding, or collapsing.
doi:10.4184/asj.2014.8.2.183
PMCID: PMC3996343  PMID: 24761201
Cervical vertebrae; Neglected disease; Quadriparesis; Surgical decompression
17.  Curcumin Modulates α-Synuclein Aggregation and Toxicity 
ACS Chemical Neuroscience  2012;4(3):393-407.
In human beings, Parkinson’s disease (PD) is associated with the oligomerization and amyloid formation of α-synuclein (α-Syn). The polyphenolic Asian food ingredient curcumin has proven to be effective against a wide range of human diseases including cancers and neurological disorders. While curcumin has been shown to significantly reduce cell toxicity of α-Syn aggregates, its mechanism of action remains unexplored. Here, using a series of biophysical techniques, we demonstrate that curcumin reduces toxicity by binding to preformed oligomers and fibrils and altering their hydrophobic surface exposure. Further, our fluorescence and two-dimensional nuclear magnetic resonance (2D-NMR) data indicate that curcumin does not bind to monomeric α-Syn but binds specifically to oligomeric intermediates. The degree of curcumin binding correlates with the extent of α-Syn oligomerization, suggesting that the ordered structure of protein is required for effective curcumin binding. The acceleration of aggregation by curcumin may decrease the population of toxic oligomeric intermediates of α-Syn. Collectively; our results suggest that curcumin and related polyphenolic compounds can be pursued as candidate drug targets for treatment of PD and other neurological diseases.
doi:10.1021/cn3001203
PMCID: PMC3605819  PMID: 23509976
Curcumin; α-synuclein; amyloid; oligomers; toxicity; Parkinson’s disease
18.  Molecular Characterization and In Vitro Antifungal Susceptibility Profile of Schizophyllum commune, an Emerging Basidiomycete in Bronchopulmonary Mycoses 
Schizophyllum commune (n = 30) showed lowest geometric mean MICs of isavuconazole (0.19 μg/ml), itraconazole (0.2 μg/ml), voriconazole (0.24 μg/ml), and amphotericin B (0.29 μg/ml) and high geometric mean MICs of fluconazole (19.39 μg/ml) and flucytosine (17.28 μg/ml). Five cases (of 8) of allergic bronchopulmonary mycosis that were treated with itraconazole had no recrudescence after 6 to 24 months of follow-up. One case each of invasive pulmonary mycosis and fungal ball were treated successfully with voriconazole and itraconazole.
doi:10.1128/AAC.02619-12
PMCID: PMC3716139  PMID: 23507274
19.  Proteomic profiling of serum samples from chikungunya-infected patients provides insights into host response 
Clinical proteomics  2013;10(1):14.
Background
Chikungunya is a highly debilitating febrile illness caused by Chikungunya virus, a single-stranded RNA virus, which is transmitted by Aedes aegypti or Aedes albopictus mosquito species. The pathogenesis and host responses in individuals infected with the chikungunya virus are not well understood at the molecular level. We carried out proteomic profiling of serum samples from chikungunya patients in order to identify molecules associated with the host response to infection by this virus.
Results
Proteomic profiling of serum obtained from the infected individuals resulted in identification of 569 proteins. Of these, 63 proteins were found to be differentially expressed (≥ 2-fold) in patient as compared to control sera. These differentially expressed proteins were involved in various processes such as lipid metabolism, immune response, transport, signal transduction and apoptosis.
Conclusions
This is the first report providing a global proteomic profile of serum samples from individuals infected with the chikungunya virus. Our data provide an insight into the proteins that are involved as host response factors during an infection. These proteins include clusterin, apolipoproteins and S100A family of proteins.
doi:10.1186/1559-0275-10-14
PMCID: PMC3879382  PMID: 24124767
iTRAQ; Quantitative proteomics; Arthritis; Hyponatremia; Neuropathology
20.  New Clonal Strain of Candida auris, Delhi, India 
Emerging Infectious Diseases  2013;19(10):1670-1673.
A new clonal strain of Candida auris is an emerging etiologic agent of fungemia in Delhi, India. In 12 patients in 2 hospitals, it was resistant to fluconazole and genotypically distinct from isolates from South Korea and Japan, as revealed by M13 and amplified fragment length polymorphism typing.
doi:10.3201/eid1910.130393
PMCID: PMC3810747  PMID: 24048006
Candida auris; fungemia; M13 fingerprinting; AFLP; antifungal susceptibility; India; fungi; parasitic diseases
21.  Reconstruction of post-traumatic long bone defect with vascularised free fibula: A series of 28 cases 
Introduction:
The severe long bone defects usually follow high-energy trauma and are often associated with a significant soft-tissue injury. The goal of management of these open long bone defects is to provide stable fixation with maintenance of limb length and soft-tissue coverage. The purpose of this article is to present the clinic-radiological outcome, complications and treatment of post-traumatic long bone defect with vascularised fibula transfer.
Materials and Methods:
Retrospective records of 28 patients were analysed who presented with post-traumatic long bone defects and in whom reconstruction with vascularised free fibula was done. Demographic data were recorded and clinical and radiological assessment was done.
Results:
Out of 28 patients in whom vascularised free fibula transfer was carried out three flaps were lost while non-union occur in three patients. Three patients developed a stress fracture of transferred free fibula in the post-operative period. Few of the patients experienced some problems in the donor leg; however, all of them improved in subsequent follow-up.
Discussion:
It is clearly evident from this study that timing of surgery plays an important role in the micro-vascular reconstruction in trauma cases. All the complication like flap loss, non-union or delayed union occur in patients in whom reconstruction was delayed.
Conclusion:
The free vascularised fibula graft is a viable method for the reconstruction of skeletal defects of more than 6 cm, especially in cases of scarred and avascular recipient sites or in patients with combined bone and soft-tissue defects. Results are best when the reconstruction is done within 1 week of trauma.
doi:10.4103/0970-0358.122013
PMCID: PMC3897102  PMID: 24459347
Long bone defect; post-traumatic; vascularised free fibula
22.  Clinical Significance of Filamentous Basidiomycetes Illustrated by Isolates of the Novel Opportunist Ceriporia lacerata from the Human Respiratory Tract 
Journal of Clinical Microbiology  2013;51(2):585-590.
The filamentous basidiomycete Ceriporia lacerata, an agent of white rot on wood, has never been reported in human disease and its clinical significance is not yet known. We describe 4 patients with respiratory diseases where C. lacerata was implicated in a wide spectrum of clinical manifestations ranging from saprobic colonization to fungal pneumonia. The isolates did not show the morphological characteristics that facilitate recognition of filamentous basidiomycetes, such as the presence of clamp connections, spicules along hyphae, or fruiting bodies. The identity of the mold was confirmed by sequencing the internal transcribed spacer 1 and 4 (ITS-1 and ITS-4) and D1/D2 regions of the rRNA gene. All of the isolates exhibited the lowest MICs of posaconazole and isavuconazole (MIC range, 0.06 to 0.125 μg/ml), followed by itraconazole (MIC range, 0.06 to 0.5 μg/ml), voriconazole (MIC range, 0.125 to 0.5 μg/ml), and amphotericin B (MIC range, 0.25 to 1 μg/ml). The infections reported here occurred in patients with preexisting lung damage induced by tuberculosis or chronic obstructive pulmonary disease. Chronic, sometimes fatal infections by the ascomycete Aspergillus fumigatus and the basidiomycete Schizophyllum commune are well established in the presence of an anatomical pulmonary defect or in the background of immunodeficiency. It is postulated that C. lacerata, a novel opportunist basidiomycete, may be involved in similar pathological processes.
doi:10.1128/JCM.02943-12
PMCID: PMC3553890  PMID: 23241374
23.  Time Course Study of Delayed Wound Healing in a Biofilm-Challenged Diabetic Mouse Model 
Wound Repair and Regeneration  2012;20(3):342-352.
Bacterial biofilm has been shown to play a role in delaying wound healing of chronic wounds, a major medical problem that results in significant healthcare burden. A reproducible animal model could be very valuable for studying the mechanism and management of chronic wounds. Our previous work demonstrated that Pseudomonas aeruginosa (PAO1) biofilmchallenge on wounds in diabetic (db/db) mice significantly delayed wound healing. In this wound time course study, we further characterize the bacterial burden, delayed wound healing and certain aspects of the host inflammatory response in the PAO1 biofilm-challenged db/db mouse model. PAO1 biofilms were transferred onto 2 day old wounds created on the dorsal surface of db/db mice. Control wounds without biofilm-challenge healed by 4 weeks, consistent with previous studies; none of the biofilm-challenged wounds healed by 4 weeks; 64% of the biofilm-challenged wounds healed by 6 weeks; and all of the biofilm-challenged wounds healed by 8 weeks. During the wound healing process, P. aeruginosa were gradually cleared from the wounds while the presence of S. aureus (part of the normal mouse skin flora) increased. Scabs from all unhealed wounds contained 107 P. aeruginosa, which was 100 fold higher than the counts isolated from wound beds (i.e. 99% of the P. aeruginosa was in the scab). Histology and genetic analysis showed proliferative epidermis, deficient vascularization and increased inflammatory cytokines. Hypoxia inducible factor (HIF) expression increased 3 fold in 4 week wounds. In summary, our study demonstrates that biofilm-challenged wounds typically heal in approximately 6 weeks, at least 2 weeks longer than non biofilm-challenged normal wounds. These data suggest that this delayed wound healing model enables the in vivo study of bacterial biofilm responses to host defenses and the effects of biofilms on host wound healing pathways. It may also be used to test anti-biofilm strategies the treatment of chronic wounds.
doi:10.1111/j.1524-475X.2012.00793.x
PMCID: PMC3349451  PMID: 22564229
Pseudomonas aeruginosa; biofilm; wound infection; keratinocytes; inflammatory response; gene expression
24.  First Human Case of Pulmonary Fungal Ball Due to a Perenniporia Species (a Basidiomycete) 
Journal of Clinical Microbiology  2012;50(11):3786-3791.
Perenniporia species are basidiomycetes, resupinate shelf fungi responsible for white rot decay of wood. Here, we report for the first time an intracavitary pulmonary fungal ball due to a species of Perenniporia that has not been recognized so far as a human pathogen. The fungus was identified by sequencing of the partial ribosomal operon of a culture from a clinical specimen.
doi:10.1128/JCM.01863-12
PMCID: PMC3486195  PMID: 22895039
25.  Future Directions in Early Cystic Fibrosis Lung Disease Research 
Since the 1989 discovery that mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF), there has been substantial progress toward understanding the molecular basis for CF lung disease, leading to the discovery and development of new therapeutic approaches. However, the earliest impact of the loss of CFTR function on airway physiology and structure and its relationship to initial infection and inflammation are poorly understood. Universal newborn screening for CF in the United States represents an unprecedented opportunity for investigating CF clinical manifestations very early in life. Recently developed animal models with pulmonary phenotypic manifestations also provide a window into the early consequences of this genetic disorder. For these reasons, the National Heart, Lung, and Blood Institute (NHLBI) convened a working group of extramural experts, entitled “Future Research Directions in Early CF Lung Disease” on September 21–22, 2010, to identify future research directions of great promise in CF. The priority areas identified included (1) exploring pathogenic mechanisms of early CF lung disease; (2) leveraging newborn screening to elucidate the natural history of early lung disease; (3) developing a spectrum of biomarkers of early lung disease that reflects CF pathophysiology, clinical outcome, and response to treatment; (4) exploring the role of genetics/genomics (e.g., modifier genes, gene–environmental interactions, and epigenetics) in early CF pathogenesis; (5) defining early microbiological events in CF lung disease; and (6) elucidating the initial airway inflammatory, remodeling, and repair mechanisms in CF lung disease.
doi:10.1164/rccm.201111-2068WS
PMCID: PMC3360572  PMID: 22312017
cystic fibrosis; airway disease; innate immunity; microbiology; genetics

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