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Chhabra ML, Parameswari B, Viswanathan R. Pathogenic behaviour pattern of Colletotrichum falcatum isolates of sugarcane in sub-tropical India. ACTA ACUST UNITED AC 2016. [DOI: 10.5958/2229-4473.2016.00103.8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Chinnaraja C, Viswanathan R. Quantification of sugarcane yellow leaf virus in sugarcane following transmission through aphid vector, Melanaphis sacchari. Virusdisease 2015; 26:237-42. [PMID: 26645033 PMCID: PMC4663716 DOI: 10.1007/s13337-015-0267-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/07/2015] [Indexed: 02/05/2023] Open
Abstract
Yellow leaf caused by Sugarcane yellow leaf virus (SCYLV) is a serious constraint to sugarcane production in India and currently the disease epidemics occur on many of the susceptible varieties under field conditions. Studies were conducted on the virus transmission by sugarcane aphid Melanaphis sacchari in sugarcane by inoculating virus-free meristem derived from micro- propagated plants of sugarcane cv Co 86032 with viruliferous aphids. Virus transmission was confirmed through RT-PCR assays and subsequently SCYLV population was established through RT-qPCR. A maximum of 22.3 × 10(3), 3.16 × 10(6) and 4.78 × 10(6) copies of SCYLV-RNA targets were recorded in the plants after 7, 180 and 300 days, respectively. This study showed that the aphid species M. sacchari acts as an effective vector of SCYLV. The relative standard curve method in RT-qPCR efficiently detected the increment in SCYLV copy numbers in sugarcane following transmission through M. sacchari.
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Sathyabhama M, Viswanathan R, Nandakumar M, Malathi P, Ramesh Sundar A. Understanding sugarcane defence responses during the initial phase of Colletotrichum falcatum pathogenesis by suppression subtractive hybridization (SSH). PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY 2015. [DOI: 10.1016/j.pmpp.2015.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Viswanathan R, Rana R, Lee Y, Alagkiozidis I, Reinhardt M, Arain A, Tolentino J, Pradhan T. Relationship of locus of control and depression to treatment adherence in gynecologic oncology patients. Gynecol Oncol 2015. [DOI: 10.1016/j.ygyno.2015.01.203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Viswanathan R. Varietal Degeneration in Sugarcane and its Management in India. SUGAR TECH 2015. [DOI: 10.1007/s12355-015-0369-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Sathyabhama M, Viswanathan R, Malathi P, Ramesh Sundar A. Identification of Differentially Expressed Genes in Sugarcane During Pathogenesis of Colletotrichum falcatum by Suppression Subtractive Hybridization (SSH). SUGAR TECH 2015. [DOI: 10.1007/s12355-014-0364-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Viswanathan R, Hoffman EA, Shetty SJ, Bekiranov S, Auble DT. Analysis of chromatin binding dynamics using the crosslinking kinetics (CLK) method. Methods 2014; 70:97-107. [PMID: 25448301 PMCID: PMC4267959 DOI: 10.1016/j.ymeth.2014.10.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 10/17/2014] [Accepted: 10/27/2014] [Indexed: 02/03/2023] Open
Abstract
Transcription factor binding sites in chromatin are routinely inventoried by the chromatin immunoprecipitation assay, and these binding patterns can provide precise and detailed information about cell state. However, some fundamental molecular questions regarding transcription factor function require an understanding of in vivo binding dynamics as well as location information. Here we describe the crosslinking kinetics (CLK) assay, in which the time-dependence of formaldehyde crosslinking is used to extract on- and off-rates for chromatin binding in vivo.
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Rahul PR, Ganesh Kumar V, Viswanathan R, Ramesh Sundar A, Malathi P, Naveen Prasanth C, Pratima PT. Defense Transcriptome Analysis of Sugarcane and Colletotrichum falcatum Interaction Using Host Suspension Cells and Pathogen Elicitor. SUGAR TECH 2014. [DOI: 10.1007/s12355-014-0356-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Parameswari B, Bagyalakshmi K, Chinnaraja C, Viswanathan R. Molecular characterization of Indian Sugarcane streak mosaic virus isolates reveals recombination and negative selection in the P1 gene. Gene 2014; 552:199-203. [PMID: 25225126 DOI: 10.1016/j.gene.2014.09.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 09/05/2014] [Accepted: 09/12/2014] [Indexed: 02/08/2023]
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Cheow LF, Viswanathan R, Chin CS, Jennifer N, Jones RC, Guccione E, Quake SR, Burkholder WF. Multiplexed Analysis of Protein–Ligand Interactions by Fluorescence Anisotropy in a Microfluidic Platform. Anal Chem 2014; 86:9901-8. [DOI: 10.1021/ac502605f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Anna Durai A, Premachandran MN, Govindaraj P, Malathi P, Viswanathan R. Variability in Breeding Pool of Sugarcane (Saccharum spp.) for Yield, Quality and Resistance to Different Biotic and Abiotic Stress Factors. SUGAR TECH 2014. [DOI: 10.1007/s12355-014-0301-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Viswanathan R. Infectious hepatitis in Delhi (1955-56): a critical study-epidemiology. 1957. THE NATIONAL MEDICAL JOURNAL OF INDIA 2013; 26:362-377. [PMID: 25074004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
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Poorey K, Viswanathan R, Carver MN, Karpova TS, Cirimotich SM, McNally JG, Bekiranov S, Auble DT. Measuring chromatin interaction dynamics on the second time scale at single-copy genes. Science 2013; 342:369-72. [PMID: 24091704 PMCID: PMC3997053 DOI: 10.1126/science.1242369] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The chromatin immunoprecipitation (ChIP) assay is widely used to capture interactions between chromatin and regulatory proteins, but it is unknown how stable most native interactions are. Although live-cell imaging suggests short-lived interactions at tandem gene arrays, current methods cannot measure rapid binding dynamics at single-copy genes. We show, by using a modified ChIP assay with subsecond temporal resolution, that the time dependence of formaldehyde cross-linking can be used to extract in vivo on and off rates for site-specific chromatin interactions varying over a ~100-fold dynamic range. By using the method, we show that a regulatory process can shift weakly bound TATA-binding protein to stable promoter interactions, thereby facilitating transcription complex formation. This assay provides an approach for systematic, quantitative analyses of chromatin binding dynamics in vivo.
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Prathima PT, Raveendran M, Kumar KK, Rahul PR, Kumar VG, Viswanathan R, Sundar AR, Malathi P, Sudhakar D, Balasubramaniam P. Differential regulation of defense-related gene expression in response to red rot pathogen Colletotrichum falcatum infection in sugarcane. Appl Biochem Biotechnol 2013; 171:488-503. [PMID: 23861092 DOI: 10.1007/s12010-013-0346-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 06/17/2013] [Indexed: 02/08/2023]
Abstract
Red rot is a serious disease of sugarcane caused by the fungus Colletotrichum falcatum imposing a considerable economic loss annually in all sugarcane-producing countries. In this study, we analyzed the early resistance response of sugarcane to red rot fungus by comparing the differences between control and inoculated stalk tissues. Differential display reverse transcription polymerase chain reaction (DD-RT-PCR) was employed to identify altered expression of genes in disease-resistant cv Co 93009, in response to pathogen infection. DD-RT-PCR identified 300 differentially expressed transcripts of which 112 were selected for further analysis. Cloning and sequence analysis of the isolated cDNA fragments resulted in functional categorization of these clones into five categories, of which the defense/stress/signaling group was the largest, with clones homologous to genes known to be actively involved in various pathogenesis-related functions in plant species. This group showed overexpression of several transcripts related to ethylene-mediated and jasmonic acid pathway of plant defense mechanisms. Of the 112 expressed sequence tags, validation of expression was carried out for five important genes whose role in plant defense mechanisms is well established. This is the first report of Colletotrichum-mediated gene regulation in sugarcane which has provided a set of candidate genes for detailed molecular dissection of signaling and defense responses in tropical sugarcane during the onset of red rot resistance.
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Viswanathan R, Ganesh Kumar V, Karuppaiah R, Scindiya M, Chinnaraja C. Development of Duplex-Immunocapture (Duplex-IC) RT-PCR for the Detection of Sugarcane streak mosaic virus and Sugarcane mosaic virus in Sugarcane. SUGAR TECH 2013. [DOI: 10.1007/s12355-013-0216-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Karuppaiah R, Viswanathan R, Kumar VG. Genetic diversity of Sugarcane bacilliform virus isolates infecting Saccharum spp. in India. Virus Genes 2013; 46:505-16. [PMID: 23430710 DOI: 10.1007/s11262-013-0890-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 02/05/2013] [Indexed: 02/05/2023]
Abstract
Sugarcane bacilliform virus (SCBV), which causes leaf freckle in sugarcane, is a member of the genus Badnavirus. Studies were conducted to characterize SCBV in Saccharum officinarum germplasm and cultivated varieties in India by sequencing the complete genomes of five isolates. Genome lengths ranged from 7,553 to 7,884 nucleotides. Duplications in ORF3 and insertions in the RNase H-domain in some of the isolates were found to contribute to the large size of their genomes. The Indian SCBV isolates share identities of 69-85 % for the complete genomic sequence, indicating wide genetic diversity among them, and share 70-82 % identity with Sugarcane bacilliform Ireng Maleng virus (SCBIMV) and Sugarcane bacilliform Morocco virus (SCBMV), as well as 43-46 % identity with Banana streak virus (BSV) and BSV-related SCBV species from Guadeloupe, indicating that the Indian SCBV isolates are distinct from SCBV isolates reported to date. Irrespective of the region compared, SCBV isolates from India, Australia, and Morocco clustered together. BSV and BSV-related SCBV isolates from Guadeloupe formed another cluster. A phylogenetic analysis based on the partial RT/RNase H-sequence separated SCBV and BSV-related SCBV sequences into 11 SCBV groups viz. SCBV-A to -K. Among the 11 groups, the SCBV sequences separated under H, I, J, and K are newly identified in this study, representing three new species and are tentatively named as SCBBBV, SCBBOV, and SCBBRV. Thus, the PASC and phylogenetic analyses evidenced that the symptoms associated with badnaviruses in sugarcane in India are caused by at least three new species, SCBBBV, SCBBOV, and SCBBRV, besides SCBIMV and SCBMV represented by SCBV-BT and SCBV-Iscam, respectively.
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Parameswari B, Bagyalakshmi K, Viswanathan R, Chinnaraja C. Molecular characterization of Indian sugarcane streak mosaic virus isolate. Virus Genes 2012; 46:186-9. [PMID: 23011777 DOI: 10.1007/s11262-012-0827-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Accepted: 09/14/2012] [Indexed: 02/05/2023]
Abstract
Sugarcane streak mosaic virus (SCSMV), a member of the genus Poacevirus, family Potyviridae, is an important viral pathogen affecting sugarcane cultivation in India. The complete nucleotide sequence of a SCSMV isolate from India (SCSMV-IND) was determined. The linear, assembled, single-stranded positive-sense RNA genome of SCSMV-IND was 9,786 nucleotides in length (excluding the poly (A) tail) and encoded a polyprotein of 3,131 amino acid residues. The genome of SCSMV-IND shared high degree of sequence identity with SCSMV-PAK (93 % at nucleotide and 97 % at amino acid), and shared only 81 % nucleotide and 94 % amino acid identities with all the four SCSMV isolates (SCSMV-JP1, -JP2, -ID, and -THA). Phylogenetic tree analysis of the complete genome sequences of SCSMV isolates revealed that they can be clustered into two groups. SCSMV-IND and -AP isolates showed 18 % (nucleotide) divergence within the highly conserved 3' partial genome, suggesting a high level of genetic diversity among the Indian SCSMV isolates.
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Chinnaraja C, Viswanathan R, Karuppaiah R, Bagyalakshmi K, Malathi P, Parameswari B. Complete genome characterization of Sugarcane yellow leaf virus from India: Evidence for RNA recombination. EUROPEAN JOURNAL OF PLANT PATHOLOGY 2012. [DOI: 10.1007/s10658-012-0090-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Malathi P, Viswanathan R. Identification of Pathogenicity Determinants in Colletotrichum falcatum Using Wild and Mutant Cultures. SUGAR TECH 2012. [DOI: 10.1007/s12355-012-0161-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Malathi P, Viswanathan R. Variation in Colletotrichum falcatum-Red Rot Pathogen of Sugarcane in Relation to Host Resistance. SUGAR TECH 2012. [DOI: 10.1007/s12355-012-0150-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Bagyalakshmi K, Parameswari B, Chinnaraja C, Karuppaiah R, Ganesh Kumar V, Viswanathan R. Genetic variability and potential recombination events in the HC-Pro gene of sugarcane streak mosaic virus. Arch Virol 2012; 157:1371-5. [PMID: 22481599 DOI: 10.1007/s00705-012-1297-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 02/27/2012] [Indexed: 02/08/2023]
Abstract
Sugarcane streak mosaic virus (SCSMV), a member of the family Potyviridae, is an important viral pathogen affecting sugarcane production in India. The variability in the nucleotide (nt) and amino acid (aa) sequences of helper component proteinase (HC-Pro) of SCSMV isolates from India was investigated and compared with those of previously published virus isolates from different Asian countries. Comparison of all of the sequenced virus isolates revealed a high level of diversity in the HC-Pro gene (72-97% nt sequence identity; 83-99% aa sequence identity), and the Indian isolates were found to be the most divergent (up to 12% variation at the amino acid level). Phylogenetic analysis revealed clustering of 16 SCSMV isolates into two groups. Group I included isolates from India and Pakistan, and group II consisted of isolates from Japan and Indonesia. Recombination analysis revealed nine potentially significant recombination events, and putative recombination sites were identified throughout the HC-Pro gene. Analysis of selection pressure indicated that the HC-Pro gene of SCSMV is under strong negative selection. It is likely that recombination, along with strong negative selection, enhances the speed of elimination of deleterious mutations in the HC-Pro gene.
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Moyle-Heyrman G, Viswanathan R, Widom J, Auble DT. Two-step mechanism for modifier of transcription 1 (Mot1) enzyme-catalyzed displacement of TATA-binding protein (TBP) from DNA. J Biol Chem 2012; 287:9002-12. [PMID: 22298788 DOI: 10.1074/jbc.m111.333484] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The TATA box binding protein (TBP) is a central component of the transcription preinitiation complex, and its occupancy at a promoter is correlated with transcription levels. The TBP-promoter DNA complex contains sharply bent DNA and its interaction lifetime is limited by the ATP-dependent TBP displacement activity of the Snf2/Swi2 ATPase Mot1. Several mechanisms for Mot1 action have been proposed, but how it catalyzes TBP removal from DNA is unknown. To better understand the Mot1 mechanism, native gel electrophoresis and FRET were used to determine how Mot1 affects the trajectory of DNA in the TBP-DNA complex. Strikingly, in the absence of ATP, Mot1 acts to unbend DNA, whereas TBP remains closely associated with the DNA in a stable Mot1-TBP-DNA ternary complex. Interestingly, and in contrast to full-length Mot1, the isolated Mot1 ATPase domain binds DNA, and its affinity for DNA is nucleotide-dependent, suggesting parallels between the Mot1 mechanism and DNA translocation-based mechanisms of chromatin remodeling enzymes. Based on these findings, a model is presented for Mot1 that links a DNA conformational change with ATP-induced DNA translocation.
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Viswanathan R, Shashibhushan KK, Subba Reddy VV. Short communication: pre- and co-curing effect of adhesives on shear bond strengths of composite resins to primary enamel and dentine: an in vitro study. Eur Arch Paediatr Dent 2012; 12:308-11. [PMID: 22122850 DOI: 10.1007/bf03262829] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIM To evaluate and compare shear bond strengths of composite resins to primary enamel and dentine when the adhesives are pre-cured (light cured before the application of the resin) or co-cured (adhesive and the resin light cured together). METHODS Buccal surfaces of 80 caries-free primary molars were wet ground to create bonding surfaces on enamel and dentine and specimens mounted on acrylic blocks. Two bonding agents (Prime and Bond NT® and Xeno III®) were applied to either enamel or dentine as per manufacturer's instructions. In 40 specimens, the bonding agent was light cured immediately after the application (pre-cured). The other 40 specimens were not light cured until the composite resin application (co-cured). Resin composite cylinders were made incrementally using acrylic moulds over the adhesives and light cured. Specimens were stored in deionised water for 24 hours at room temperature. Shear bond strength was measured using an Instron universal testing machine (in MPa) and was analysed with Student's unpaired t test. RESULTS Light curing the adhesive separately produced significantly higher bond strengths to primary dentine than co-curing (p<0.001). At the same time light curing the adhesive separately did not produce significantly different bond strengths to primary enamel (p>0.05). CONCLUSION Curing sequence had no significant effect on shear bond strength of adhesives on the primary enamel. Pre-curing adhesives before curing composite resins produced greater shear bond strength to primary dentine.
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Heiss G, Viswanathan R, Auble D, Lamb DC. Freeing the Promoter Site: Mechanistic Insights into the Interaction of Mot1 with TBP using spFRET. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.1573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Sangeetha G, Anandan A, Viswanathan R. Morphological and molecular characterization of Colletotrichum musaeisolates from various banana ( Musaspp.) cultivars. ACTA PHYTOPATHOLOGICA ET ENTOMOLOGICA HUNGARICA 2011. [DOI: 10.1556/aphyt.46.2011.2.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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