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Wei H, Yordanov Y, Kumari S, Georgieva T, Busov V. Genetic networks involved in poplar root response to low nitrogen. PLANT SIGNALING & BEHAVIOR 2013; 8:e27211. [PMID: 24300216 PMCID: PMC4091351 DOI: 10.4161/psb.27211] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Perception of environmental cues and adaptation to changing environmental conditions are crucial for survival of sessile organisms like plants. This is even more important for woody perennial species like trees that can occupy a site for thousands of years. We have previously shown that under low nitrogen (LN), poplar trees display a vigorous and long-lasting root growth associated with global transcriptomic reprogramming and an activation of hierarchical genetic networks. Here we use computational analysis to better understand the network among the genes showing distinct chronological patterns of expression during the response. Our analyses confirm the previous findings, define new potential signaling pathways and the possible downstream targets of these signaling events.
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Lin YC, Li W, Sun YH, Kumari S, Wei H, Li Q, Tunlaya-Anukit S, Sederoff RR, Chiang VL. SND1 transcription factor-directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa. THE PLANT CELL 2013; 25:4324-41. [PMID: 24280390 PMCID: PMC3875721 DOI: 10.1105/tpc.113.117697] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 10/13/2013] [Accepted: 10/23/2013] [Indexed: 05/18/2023]
Abstract
Wood is an essential renewable raw material for industrial products and energy. However, knowledge of the genetic regulation of wood formation is limited. We developed a genome-wide high-throughput system for the discovery and validation of specific transcription factor (TF)-directed hierarchical gene regulatory networks (hGRNs) in wood formation. This system depends on a new robust procedure for isolation and transfection of Populus trichocarpa stem differentiating xylem protoplasts. We overexpressed Secondary Wall-Associated NAC Domain 1s (Ptr-SND1-B1), a TF gene affecting wood formation, in these protoplasts and identified differentially expressed genes by RNA sequencing. Direct Ptr-SND1-B1-DNA interactions were then inferred by integration of time-course RNA sequencing data and top-down Graphical Gaussian Modeling-based algorithms. These Ptr-SND1-B1-DNA interactions were verified to function in differentiating xylem by anti-PtrSND1-B1 antibody-based chromatin immunoprecipitation (97% accuracy) and in stable transgenic P. trichocarpa (90% accuracy). In this way, we established a Ptr-SND1-B1-directed quantitative hGRN involving 76 direct targets, including eight TF and 61 enzyme-coding genes previously unidentified as targets. The network can be extended to the third layer from the second-layer TFs by computation or by overexpression of a second-layer TF to identify a new group of direct targets (third layer). This approach would allow the sequential establishment, one two-layered hGRN at a time, of all layers involved in a more comprehensive hGRN. Our approach may be particularly useful to study hGRNs in complex processes in plant species resistant to stable genetic transformation and where mutants are unavailable.
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Kumari S, Raines JM, Martin JM, Rodriguez JM. Thermal stability of kudzu root (Pueraria Radix) isoflavones as additives to beef patties. Journal of Food Science and Technology 2013; 52:1578-85. [PMID: 25745227 DOI: 10.1007/s13197-013-1112-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/18/2013] [Indexed: 11/30/2022]
Abstract
Kudzu root, Pueraria radix, extracts are a rich source of isoflavones. This study investigates the thermal stability of Pueraria radix extracts as a natural nutraceutical supplement in beef patties. The extract contained puerarin, diadzin, genistin, ononin, daidzein, glycitein, calycosin, genistein, formononetin and biochanin A; however, puerarin, daidzein and glycitein were the main components. The isoflavones concentrations in the spiked beef patties with kudzu root extracts were unaffected by cooking.
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Varma S, Sharma A, Malhotra P, Kumari S, Jain S, Varma N. Thrombotic complications of polycythemia vera. Hematology 2013; 13:319-23. [DOI: 10.1179/102453308x343400] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Kaur H, Kumari S, Gupta RC. Cytomorphological studies in some members of tribe Paniceae (Poaceae) from district Kangra of Himachal Pradesh (Western Himalayas). CYTOL GENET+ 2013. [DOI: 10.3103/s0095452713020060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Suri V, Singh A, Das R, Das A, Malhotra P, Jain S, Kumari S, Khandelwal N, Varma S. Osseous sarcoid with lytic lesions in skull. Rheumatol Int 2013; 34:579-82. [DOI: 10.1007/s00296-013-2752-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 04/04/2013] [Indexed: 11/30/2022]
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Kaur H, Kumari S, Gupta RC. Cytomorphological studies in some members of tribe Paniceae (Poaceae) from district Kangra of Himachal Pradesh (Western Himalayas). TSITOLOGIIA I GENETIKA 2013; 47:40-55. [PMID: 23745362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The present paper deals with cytological studies on the population basis of 21 species belonging to 9 genera of tribe Paniceae of family Poaceae from cytologically unexplored area of Western Himalayas i.e. district Kangra of Himachal Pradesh for the assessment of genetic diversity of grass flora. On world-wide basis, the chromosome counts have been made for the first time for three species such as Brachiaria remota (n = 16), Digitaria granularis (n = 36) and Isachne albens (n = 5). Similarly, on India basis, altogether new records are made for two species such as Echinochloa cruspavonis (n = 27) and Paspalum distichum (2n = 50). A comparison of the different euploid cytotypes studied at present for Digitaria adscendens, D. setigera and Oplismenus compositus revealed significant variations in their morphology, depicting increase in some of the characters of polyploid cytotypes. The course of meiosis has been observed to be normal in all the studied populations with high pollen fertility except for two species such as Paspalum dilatatum and P. distichum marked with abnormal meiosis and reduced pollen fertility.
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Jeelani SM, Rani S, Kumar S, Kumari S, Gupta RC. Cytological studies of Brassicaceae burn. (Cruciferae juss.) from Western Himalayas. TSITOLOGIIA I GENETIKA 2013; 47:26-36. [PMID: 23427609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Cytological studies have been carried out on 12 species of Brassicaceae Burn. on population basis from different geographical areas of Kashmir and Himachal Pradesh in the Western Himalayas. Variable chromosome reports for Barbaraea intermedia (n = 16), Cardamine loxostemonoides (n = 8), Nasturtium officinale (n = 8), Sisymbrium orientale (n = 14) on world-wide basis have been added to the previous reports of these species. The chromosome numbers in seven species as Barbaraea intermedia (n = 8), B. vulgaris (n = 8), Capsella bursa-pastoris (n = 8), Descuriania sophia (n = 10), Rorippa islandica (n = 8), Sisymbrium strictum (n = 7) and Thlaspi alpestre (n = 7) have been worked out for the first time from India. The meiotic course in the populations of seven species such as Barbaraea intermedia, Capsella bursa-pastoris, Coronopus didymus, Descuriania sophia, Nasturtium officinale, Sisymbrium orientale and S. strictum varies from normal to abnormal while all the populations of two species Barbaraea vulgaris and Sisymbrium irio show abnormal meiotic course. Meiotic abnormalities are in the form of cytomixis, chromosomal stickiness, unoriented bivalents, inter-bivalent connections, formation of laggards and bridges, all resulting into abnormal microsporogenesis. Heterogenous sized fertile pollen grains and reduced reproductive potentialities have invariably been observed in all the meiotically abnormal populations. However, the meiotic course in all the populations of Cardamine loxostemonoides, Rorippa islandica and Thalspi alpestre is found to be normal with high pollen fertility.
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Kumari S, Nie J, Chen HS, Ma H, Stewart R, Li X, Lu MZ, Taylor WM, Wei H. Evaluation of gene association methods for coexpression network construction and biological knowledge discovery. PLoS One 2012; 7:e50411. [PMID: 23226279 PMCID: PMC3511551 DOI: 10.1371/journal.pone.0050411] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 10/18/2012] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Constructing coexpression networks and performing network analysis using large-scale gene expression data sets is an effective way to uncover new biological knowledge; however, the methods used for gene association in constructing these coexpression networks have not been thoroughly evaluated. Since different methods lead to structurally different coexpression networks and provide different information, selecting the optimal gene association method is critical. METHODS AND RESULTS In this study, we compared eight gene association methods - Spearman rank correlation, Weighted Rank Correlation, Kendall, Hoeffding's D measure, Theil-Sen, Rank Theil-Sen, Distance Covariance, and Pearson - and focused on their true knowledge discovery rates in associating pathway genes and construction coordination networks of regulatory genes. We also examined the behaviors of different methods to microarray data with different properties, and whether the biological processes affect the efficiency of different methods. CONCLUSIONS We found that the Spearman, Hoeffding and Kendall methods are effective in identifying coexpressed pathway genes, whereas the Theil-sen, Rank Theil-Sen, Spearman, and Weighted Rank methods perform well in identifying coordinated transcription factors that control the same biological processes and traits. Surprisingly, the widely used Pearson method is generally less efficient, and so is the Distance Covariance method that can find gene pairs of multiple relationships. Some analyses we did clearly show Pearson and Distance Covariance methods have distinct behaviors as compared to all other six methods. The efficiencies of different methods vary with the data properties to some degree and are largely contingent upon the biological processes, which necessitates the pre-analysis to identify the best performing method for gene association and coexpression network construction.
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Kumar V, Sen MR, Nigam C, Gahlot R, Kumari S. Burden of different beta-lactamase classes among clinical isolates of AmpC-producing Pseudomonas aeruginosa in burn patients: A prospective study. Indian J Crit Care Med 2012. [PMID: 23188953 PMCID: PMC3506070 DOI: 10.4103/0972-5229.102077] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background: Pseudomonas aeruginosa is one of the most common pathogens causing infections in burns, and shows increasing resistance to β-lactam antibiotics by producing different classes of beta-lactamases. It is also not unusual to find a single isolate that expresses multiple β-lactamase enzymes, further complicating the treatment options. Thus, in this study, we aimed to determine the coexistence of different beta-lactamase enzymes in clinical isolates of P. aeruginosa in the burn ward. Materials and Methods: A total of 101 clinical isolates of P. aeruginosa from the burn ward were identified and tested for the presence of different beta-lactamase enzymes (extended spectrum beta lactamase (ESBL), Amp C and metallo β-lactamases (MBL) from October 2006 to May 2009. In vitro susceptibility pattern of antipseudomonal antibiotics was done by the Kirby Bauer disc diffusion method. Results: A total of 33 (32.7%) isolates were confirmed to be positive for AmpC beta-lactamase. Co-production of AmpC along with ESBL and MBL was reported in 24.5% and 45.5% isolates, respectively. A total of 12 (11.9%) isolates were resistant to three or more antibiotic classes (multidrug resistance). Imipenem and piperacillin/tazobactum showed high sensitivity, with 86.1% and 82.2%, respectively. Conclusion: This study reveals the high prevalence of multidrug- resistant P. aeruginosa producing beta-lactamase enzymes of different mechanisms in this region from burn patients. The emerging antimicrobial resistance in burn wound pathogens poses serious therapeutic challenge. Thus proper antibiotic policy and measures to restrict the indiscriminate use of cephalosporins and carbapenems should be taken to minimize the emergence of this multiple beta -lactamase producing pathogen.
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Ojha S, Goyal S, Sharma C, Arora S, Kumari S, Arya DS. Cardioprotective effect of lycopene against isoproterenol-induced myocardial infarction in rats. Hum Exp Toxicol 2012; 32:492-503. [PMID: 23060410 DOI: 10.1177/0960327112454890] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The present study was designed to evaluate the cardioprotective potential of lycopene (LCP) against isoproterenol (ISP)-induced myocardial infarction (MI), by assessing hemodynamic, biochemical and histopathological parameters. Wistar male albino rats were orally administered with LCP (0.5, 1.0 and 1.5 mg/kg) or with vehicle for 30 days, with concurrent subcutaneous injections of ISP (85 mg/kg) on days 28 and 29. ISP significantly (p < 0.05) decreased systolic, diastolic and mean arterial blood pressure (SAP, DAP and MAP, respectively) and heart rate (HR). ISP also decreased contractility (+LVdP/dt), relaxation (-LVdP/dt) and increased left ventricular end-diastolic pressure (LVEDP). In addition to functional impairment, ISP also caused a significant (p < 0.05) decrease in antioxidants, namely, superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GSHPx), glutathione (GSH), cardiac injury marker enzymes, creatine phosphokinase-MB (CK-MB) and lactate dehydrogenase (LDH), as well as induced lipid peroxidation, malonaldialdehyde (MDA) and histopathological alterations in heart. However, pretreatment with LCP significantly (p < 0.05) attenuated ISP-induced cardiac dysfunction as evidenced by improved SAP, DAP, MAP, HR, (±)LVdP/dt and reduced LVEDP. Pretreatment with LCP also significantly (p < 0.05) prevented the depletion of antioxidants (SOD, CAT, GSHPx and GSH), myocyte injury marker enzymes (CK-MB and LDH) and inhibited lipid peroxidation and MDA formation in the heart. Furthermore, reduced necrosis, edema and infiltration of inflammatory cells on histopathological examination also depicted the protective effect of LCP against the deleterious effect of ISP. Based on the results, it is suggested that LCP possesses significant cardioprotective potential and may serve as an adjunct in treatment and prophylaxis of MI.
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Kumari S. M428 PROLAPSE - AN INTERESTING CASE! Int J Gynaecol Obstet 2012. [DOI: 10.1016/s0020-7292(12)61618-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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88
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Mathur M, Kumari S. Contact dermatitis – Pathomechanism and understanding of disease in clinical setting. JOURNAL OF COLLEGE OF MEDICAL SCIENCES-NEPAL 2012. [DOI: 10.3126/jcmsn.v7i4.6816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
According to the pathophysiological mechanisms involved, two major types of contact dermatitis recognized irritant contact dermatitis (ICD) and allergic contact dermatitis (ACD). The diagnosis of either ICD or ACD is mainly depending on comprehensive clinical data (history and physical examination) as well as by performing appropriate diagnostic patch testing. Two forms of contact dermatitis may differ in early phase of development but development of clinical dermatitis have similar mechanism confusing the clinician and differentiating between ICD and ACD is often difficult in the clinical setting. This review will allow practicing physician to adopt rational clinical approach and the implementation of scientific information for therapeutic as well as preventive strategies. Journal of College of Medical Sciences-Nepal,2011,Vol-7,No-4, 70-77 DOI: http://dx.doi.org/10.3126/jcmsn.v7i4.6816
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Yousuf A, Malik M, Shamas IU, Beigh Z, Kumari S, Pampori PRA. Bacteriological Profile Of Ear Discharge And Their Antibiotic Sensitivity In Chronic Suppurative Otitis Media In Kashmir,India. BANGLADESH JOURNAL OF MEDICAL SCIENCE 2012. [DOI: 10.3329/bjms.v11i3.11731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The objective of the study was to study the microflora and the antibiograms of patients with chronic suppurative otitis media (CSOM) in Kashmir,in order to provide a guidelines for making a protocol for empirical antibiotic therapy. Study design:Prospective study Material and methods: This study was conducted on OPD basis in Department of Ear, Nose and Throat and HNS Government medical college Srinagar kashmir from july 2010 to june 1011 and one hundred twenty five(125) patients with unilateral or bilateral active chronic suppurative otitis media were prospectively studied.They had chronic ear discharge and had not received antibiotics for the previous five days. Swabs were taken from discharging ear's and sent to microbiological section of hospital were culture for bacteria was done Antibiotic sensitivity testing was done with standard antibiotic discs using Kirby-bauer disk diffusion method.4 Results:From the Clinical specimens off the 125 patients microbiological culture was positive in 110 specimens. The most common causal organisms isolated were Staphylococcus aureus (48%) including 8% of methcillin resistant staph aureus and Pseudomonas aeruginosa (16%) followed by coagulase negative.Antibiotic sensitivities of staph aureus (other than MRSA) showed that 72% isolates were sensitivity to gentamicin,55% to ciprofloxacin followed by 36% to cephalosporins (cetazidime,ceftriaxone) .For pseudomonas aeruginosa 72% isolates were sensitive to piperacillin/tazobactum 48% to ciprofloxacin and 32% to ceftazidime/ceftriaxone. Of the three antibiotics commonly available as topical eardrops,ciprofloxacin and gentamicin has the highest susceptibility rate. DOI: http://dx.doi.org/10.3329/bjms.v11i3.11731 Bangladesh Journal of Medical Science Vol. 11 No. 03 July12
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Agrawal A, Kumari S, Sahu KK. Studies on solvent extraction of iron(III) as a step for conversion of a waste effluent to a value added product. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2011; 92:3105-3111. [PMID: 21862202 DOI: 10.1016/j.jenvman.2011.07.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 07/14/2011] [Accepted: 07/25/2011] [Indexed: 05/31/2023]
Abstract
Solvent extraction of iron(III) from actual sulphate waste pickle liquor was investigated using trialkylphosphine oxide diluted with kerosene. The waste pickle liquor was procured from a local company which deals with the manufacturing of pipes and tubes made of iron and steel. Various parameters were studied to optimise a suitable condition for the maximum extraction of iron. The composition of the aqueous feed used in the experiment was 60.88 g/L Fe(III), 53 g/L acid with traces of Cu, Ni and Co. An ambient extraction at 30 °C yielded acceptable kinetics and loading efficiency for 40% trialkylphosphine oxide with a saturated loading capacity of 51.85 g/L in four contacts at O/A ratio of 1/1 in a multiple contact mode. Iron from the loaded organic was stripped using various strippants such as distilled water, H(2)SO(4) and oxalic acid. Since only 32% of loaded Fe could be stripped with 2 M H(2)SO(4) in five contacts, further stripping was done with 5% oxalic acid which showed a very promising result. It was found that almost 100% of Fe(III) could be stripped out with 5% oxalic acid at O/A of 1/1 in five contacts.
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Najar A, Kumari S, Attar N, Lababidi S. First Report of Chickpea chlorotic stunt virus Infecting Legume Crops in Tunisia. PLANT DISEASE 2011; 95:1321. [PMID: 30731675 DOI: 10.1094/pdis-10-10-0708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
During a survey of legume crops in the northeast and northwest regions of Tunisia in April 2010, plants showing yellowing, reddening, and stunting symptoms were observed. A total of 281 symptomatic samples were collected: 142 plants from 10 chickpea (Cicer arietinum L.) fields, 84 plants from six faba bean (Vicia faba L.) fields, and 55 plants from six pea (Pisum sativum L.) fields. All samples were tested by the tissue-blot immunoassay procedure with the following monoclonal antibodies (MAbs): a broad-spectrum legume-luteovirus MAb (5G4), Faba bean necrotic yellows virus (FBNYV; genus Nanovirus, family Nanovirudae) (3-2E9; provided by J. Vetten, BBA, Braunschweig, Germany), Beet western yellows virus (BWYV; genus Polerovirus, family Luteoviridae) (A5977; Agdia, Elkhart, IN), Bean leafroll virus (BLRV; genus Luteovirus, family Luteoviridae) (4B10), Soybean dwarf virus (SbDV; genus Luteovirus, family Luteoviridae) (ATCC PVAS-650; American Type Culture Collection ATCC, Rockville, MD,), and a mixture of three MAbs (5-2B8, -3D5, and -5B8) to a Syrian isolate of Chickpea chlorotic stunt virus (CpCSV) (1). Serological tests showed that CpCSV was detected in 121 samples (43.06%) (62 chickpea, 57 faba bean, and 2 pea), followed by FBNYV (detected in three faba bean and three pea), BWYV (detected in three chickpea and one faba bean), and BLRV (detected in one pea sample). FBNYV, BLRV, and BWYV have been previously detected in faba bean and chickpea in Tunisia (4), but to our knowledge, this is the first report of CpCSV affecting legumes in Tunisia, which was found in seven chickpea, seven faba bean, and two pea fields. CpCSV has been reported to naturally infect legume crops such as chickpea, lentil, field pea, and faba bean as well as some leguminous weeds and a few wild non-legume plants species in many countries in West Asia and North Africa and causes economic losses on chickpea in Eritrea, Ethiopia, and Syria (1-3). Serological results of CpCSV was confirmed in four (two pea, one faba bean, and one chickpea) samples by reverse transcription (RT)-PCR using CpCSV specific primers (F:5'-TAGGCGTACTGTTCAGCGGG-3' and R:5'-TCCTTTGTCCATTCGAGGTGA-3') (3), which produced an amplicon of expected size (413 bp). No amplification was observed from healthy plant extracts. Sequence analysis revealed that the four Tunisian isolates (TuV 258-201 collected from faba bean [GenBank Accession No. HQ199310], TuC 215-201 collected from chickpea [HQ199307], and TuP 163-201 [HQ199308] and TuP 166-201 collected from pea [HQ199309]) were most similar to each other with a high sequence identity (99%) and clustered with isolates of CpCSV from Syria (GenBank Accession No. EU541270), Egypt (EU541269), and Morocco (EU541267), to which they were most closely related (98%). The Tunisian isolates also showed high sequence identity (96%) in the coat protein region with Ethiopian (GenBank Accession No. EU541257) and Sudanese (EU541263) isolates. However, all isolates are distinct from BWYV, BLRV, and SbDV (less than 70% sequence identity). Since CpCSV is transmitted by aphids only, additional studies are needed to identify the host range of the virus and the efficient aphid vectors to better understand the epidemiology of this virus under Tunisian conditions References: (1) A. D. Abraham et al. Arch.Virol. 154:791; 2009. (2) N. Y. Asaad et al. J. Phytopathol. 157:756, 2009. (3) S. G. Kumari et al. Phytopathol. Mediterr. 47:42, 2008. (4) A. Najar et al. Phytopathol. Mediterr. 39:423, 2000.
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Shafqat K, Pal SK, Kumari S, Kyriacou PA. Empirical mode decomposition analysis of HRV data from patients undergoing local anaesthesia (brachial plexus block). Physiol Meas 2011; 32:483-97. [PMID: 21411870 DOI: 10.1088/0967-3334/32/4/008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Spectral analysis of heart rate variability (HRV) is used for the assessment of cardiovascular autonomic control. In this study, a data-driven adaptive technique called empirical mode decomposition (EMD) and the associated Hilbert spectrum has been used to evaluate the effect of local anaesthesia on HRV parameters in a group of 14 patients undergoing axillary brachial plexus block. The normalized amplitude Hilbert spectrum was used to calculate the error index associated with the instantaneous frequency. The amplitude and the frequency values were corrected in the region where the error was higher than twice standard deviation. The intrinsic mode function (IMF) components were assigned to the LF and the HF part of the signal by making use of the centre frequency and the standard deviation spectral extension estimated from the marginal spectrum of the IMF components. The optimal range of the stopping criterion was found to be between 4 and 9 for the HRV data. The statistical analysis showed that the LF/HF ratio decreased within an hour of the application of the brachial plexus block compared to the values at the start of the procedure. These changes were observed in 13 of the 14 patients included in this study.
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Kashyap R, Mittal B, Kumari S, Bhattacharya A, Singh B. Retroperitoneal fibrosis masquerading as para-aortic lymphadenopathy on F-18 FDG PET/CT in a patient with carcinoma cervix. World J Nucl Med 2011; 10:23-4. [PMID: 22034580 PMCID: PMC3198043 DOI: 10.4103/1450-1147.82113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
We present a case of carcinoma cervix found to have a soft tissue lesion in retroperitoneal region with intense FDG uptake. However, this FDG uptake was false positive as the final diagnosis was retroperitoneal fibrosis.
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Mutanda T, Ramesh D, Karthikeyan S, Kumari S, Anandraj A, Bux F. Bioprospecting for hyper-lipid producing microalgal strains for sustainable biofuel production. BIORESOURCE TECHNOLOGY 2011; 102:57-70. [PMID: 20624676 DOI: 10.1016/j.biortech.2010.06.077] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 06/09/2010] [Accepted: 06/17/2010] [Indexed: 05/06/2023]
Abstract
Global petroleum reserves are shrinking at a fast pace, increasing the demand for alternate fuels. Microalgae have the ability to grow rapidly, and synthesize and accumulate large amounts (approximately 20-50% of dry weight) of neutral lipid stored in cytosolic lipid bodies. A successful and economically viable algae based biofuel industry mainly depends on the selection of appropriate algal strains. The main focus of bioprospecting for microalgae is to identify unique high lipid producing microalgae from different habitats. Indigenous species of microalgae with high lipid yields are especially valuable in the biofuel industry. Isolation, purification and identification of natural microalgal assemblages using conventional techniques is generally time consuming. However, the recent use of micromanipulation as a rapid isolating tool allows for a higher screening throughput. The appropriate media and growth conditions are also important for successful microalgal proliferation. Environmental parameters recorded at the sampling site are necessary to optimize in vitro growth. Identification of species generally requires a combination of morphological and genetic characterization. The selected microalgal strains are grown in upscale systems such as raceway ponds or photobireactors for biomass and lipid production. This paper reviews the recent methodologies adopted for site selection, sampling, strain selection and identification, optimization of cultural conditions for superior lipid yield for biofuel production. Energy generation routes of microalgal lipids and biomass are discussed in detail.
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Shafqat K, Pal SK, Kumari S, Kyriacou PA. HRV analysis in local anesthesia using Continuous Wavelet Transform (CWT). ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2011; 2011:4808-4811. [PMID: 22255414 DOI: 10.1109/iembs.2011.6091191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Spectral analysis of Heart Rate Variability (HRV) is used for the assessment of cardiovascular autonomic control. In this study Continuous Wavelet Transform (CWT) has been used to evaluate the effect of local anesthesia on HRV parameters in a group of fourteen patients undergoing axillary brachial plexus block. A new method which takes signal characteristics into account has been presented for the estimation of the variable boundaries associated with the low and the high frequency band of the HRV signal. The variable boundary method might be useful in cases when the power related to respiration component extends beyond the traditionally excepted range of the high frequency band (0.15-0.4 Hz). The statistical analysis (non-parametric Wilcoxon signed rank test) showed that the LF/HF ratio decreased within an hour of the application of the brachial plexus block compared to the values fifteen minutes prior to the application of the block. These changes were observed in thirteen of the fourteen patients included in this study.
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Kumari S, Harjai K, Chhibber S. Isolation and characterization of Klebsiella pneumoniae specific bacteriophages from sewage samples. Folia Microbiol (Praha) 2010; 55:221-7. [PMID: 20526833 DOI: 10.1007/s12223-010-0032-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2009] [Revised: 02/12/2010] [Indexed: 10/19/2022]
Abstract
Five bacteriophages (Kpn5, Kpn12, Kpn13, Kpn17 and Kpn22), each having specificity against Klebsiella pneumoniae strain B5055, were isolated from sewage samples and characterized in terms of growth characteristics, genetic material, morphology and structural proteins. Adsorption rate as well as single step growth curve experiments showed variation among phages. Restriction enzyme digestion of DNA confirmed the presence of double stranded DNA as well as the heterogeneous nature of genetic material. RAPD-PCR was performed to further distinguish these closely related phages. Their genome fingerprint confirmed their diversity. Transmission electron microscopy, on the other hand, showed their morphological similarity; they were assigned to family Podoviridae, order Caudovirales on the basis of their head and tail morphology. Structural proteins resolved on SDS-PAGE showed the presence of similar major outer membrane proteins. The bacteriophages, belonging to Podoviridae family with short stumpy tails, were found to be nontoxic to mice. They showed maximum count in various organs at 6 h post inoculation, which persisted till 36 h. These phages thus have the potential to be used for phage therapy.
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Kaur N, Kumari S, Jain S, Majumdar S, Ghosh S. P427 ROLE OF DIFFERENT FORMS OF HDL (Ox-HDL AND nHDL) ON Ox-LDL INDUCED APOPTOSIS IN DIFFERENTIATED MONOCYTES. ATHEROSCLEROSIS SUPP 2010. [DOI: 10.1016/s1567-5688(10)70494-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Shafqat K, Pal SK, Kumari S, Kyriacou PA. Time-frequency analysis of HRV data from locally anesthetized patients. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2010; 2009:1824-7. [PMID: 19963516 DOI: 10.1109/iembs.2009.5332604] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Spectral analysis of Heart Rate Variability (HRV) can be used for the assessment of cardiovascular autonomic control. In this study Smoothed-Pseudo Wigner-Ville Distribution (SPWVD) has been used to evaluate the effect of local anesthesia on HRV parameters in a group of fourteen patients undergoing brachial plexus block (local anesthesia) using the transarterial technique. Instead of using the fixed boundaries of the LF (0.04-0.15 Hz) and the HF (0.15-0.4 Hz) components, the center frequency and the standard deviation spectral extension was used to estimate the boundaries related to the two components of the HRV signal. The boundaries related to the HF component of the signal were estimated using the cross-spectrum between the HRV signal and the respiration signal. The LF component boundaries were estimated directly from the time-frequency representation of the HRV signal. The statistical analysis showed that the (LF)/HF amplitude ratio decreased within an hour of the application of the brachial plexus block compared to the values at the start of the procedure. These changes were observed in eleven of the fourteen patients included in this study.
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Shafqat K, Pal SK, Kumari S, Kyriacou PA. Empirical mode decomposition (EMD) analysis of HRV data from locally anesthetized patients. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2010; 2009:2244-7. [PMID: 19965157 DOI: 10.1109/iembs.2009.5335000] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Spectral analysis of Heart Rate Variability (HRV) is used for the assessment of cardiovascular autonomic control. In this study data driven adaptive technique Empirical Mode Decomposition (EMD) and the associated Hilbert spectrum has been used to evaluate the effect of local anesthesia on HRV parameters in a group of fourteen patients undergoing brachial plexus block (local anesthesia) using transarterial technique. The confidence limit for the stopping criteria was establish and the S value that gave the smallest squared deviation from the mean was considered optimal. The normalized amplitude Hilbert spectrum was used to calculate the error index associated with the instantaneous frequency. The amplitude and the frequency values were corrected in the region where the error was higher than twice the standard deviation. The Intrinsic Mode Function (IMF) components were assigned to the Low Frequency (LF) and the High Frequency (HF) part of the signal by making use of the center frequency and the standard deviation spectral extension estimated from the marginal spectrum of the IMF components. The analysis procedure was validated with the help of a simulated signal which consisted of two components in the LF and the HF region of the HRV signal with varying amplitude and frequency. The optimal range of the stopping criterion was found to be between 4 and 9 for the HRV data. The statistical analysis showed that the LF/HF amplitude ratio decreased within an hour of the application of the brachial plexus block compared to the values at the start of the procedure. These changes were observed in thirteen of the fourteen patients included in this study.
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Goyal SN, Arora S, Sharma AK, Joshi S, Ray R, Bhatia J, Kumari S, Arya DS. Preventive effect of crocin of Crocus sativus on hemodynamic, biochemical, histopathological and ultrastuctural alterations in isoproterenol-induced cardiotoxicity in rats. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2010; 17:227-232. [PMID: 19747807 DOI: 10.1016/j.phymed.2009.08.009] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2009] [Revised: 07/09/2009] [Accepted: 08/06/2009] [Indexed: 05/28/2023]
Abstract
We investigated the effects of crocin, a pharmacologically active constituent of Crocus sativus L., in isoproterenol (ISO)-induced cardiotoxicity with reference to hemodynamic, antioxidant, histopathological and ultrastructural parameters. Rats were administered crocin (5, 10 and 20mg/kg/day) or vehicle orally for 21 days along with ISO (85mg/kg, subcutaneously, at 24h interval) on 20th and 21st day. On 22nd day ISO-control rats showed cardiac dysfunction as indicated by lowering of systolic, diastolic and mean arterial blood pressures. In addition, a significant decrease in maximum positive and negative rate of developed left ventricular pressure (+/-LVdp/dt(max)) and an increase in left ventricular end-diastolic pressure (LVEDP) were observed. Furthermore, a marked reduction in the activities of myocardial creatine kinase-MB (CK-MB) isoenzyme, lactate dehydrogenase (LDH), superoxide dismutase (SOD), catalase (CAT), and reduced glutathione (GSH) levels along with an increase in content of malondialdehyde (MDA) were observed. Myocardial necrosis, edema and inflammation were evident from the light microscopic and ultrastructural changes. Crocin at the dose of 20mg/kg/day significantly modulated hemodynamic and antioxidant derangements. The preventive role of crocin on ISO-induced MI was reconfirmed by histopathological and ultrastructural examinations. The effect at the dose of 20mg/kg/day of crocin was more pronounced than that of other two doses (5 and 10mg/kg/day). The results suggest that crocin may have cardioprotective effect in ISO-induced cardiac toxicity through modulation of oxidative stress in such a way that maintains the redox status of the cell.
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