Papers by Dr. Nurul Karim
Biological & Pharmaceutical Bulletin, 2006
Phytopathology®, 2009
Bursaphelenchus xylophilus is the causal agent of pine wilt disease, which is a major forest dise... more Bursaphelenchus xylophilus is the causal agent of pine wilt disease, which is a major forest disease in Japan, Korea, China, Taiwan, and Portugal. A diagnostic method which is rapid, precise, and simple could greatly help the proper management of this disease. Here, we present a novel detection method using loop-mediated isothermal amplification (LAMP) targeting the internal transcribed spacer region of ribosomal DNA of the nematode. Specificity of the primers and LAMP was confirmed using DNA from various nematode species related to B. xylophilus. Our experimental results suggest that LAMP can detect B. xylophilus faster and with higher sensitivity than the traditional diagnostic method. Moreover, because it does not require expensive equipment or specialized techniques, this LAMP-based diagnostic method has the potential to be used under field conditions.
BMC Genomics, 2009
Background The fungivorus nematode, Aphelenchus avenae is widespread in soil and is found in asso... more Background The fungivorus nematode, Aphelenchus avenae is widespread in soil and is found in association with decaying plant material. This nematode is also found in association with plants but its ability to cause plant disease remains largely undetermined. The taxonomic position and intermediate lifestyle of A. avenae make it an important model for studying the evolution of plant parasitism within the Nematoda. In addition, the exceptional capacity of this nematode to survive desiccation makes it an important system for study of anhydrobiosis. Expressed sequence tag (EST) analysis may therefore be useful in providing an initial insight into the poorly understood genetic background of A. avenae. Results We present the generation, analysis and annotation of over 5,000 ESTs from a mixed-stage A. avenae cDNA library. Clustering of 5,076 high-quality ESTs resulted in a set of 2,700 non-redundant sequences comprising 695 contigs and 2,005 singletons. Comparative analyses indicated that ...
Thermochimica Acta, 2004
Heat is a characteristic of all chemical reactions, and isothermal titration calorimetry (ITC) pr... more Heat is a characteristic of all chemical reactions, and isothermal titration calorimetry (ITC) provides a possible way to continuously detect the heat from catalytic reactions with high sensitivity and reproducibility. Cellulase, the enzyme of glycosyl hydrolase, catalyzes the cleavage of β-1,4 glycosidic bonds in cellulose. In this paper, ITC was applied to evaluate cellulase activity using cello-oligosaccharides as substrates. The hydrolysis heat of a single glycosidic bond of the substrate was successfully detected by combining ITC and normal-phase HPLC, and the time course of the enzymatic reaction was monitored continuously by ITC. The enzymatic parameters k cat and K M , obtained from calorimetric observables, clearly indicated that the reaction was well approximated by a simple Michaelis-Menten equation under the experimental conditions of this study. The normal-phase HPLC analysis was combined with the ITC approach to observe hydrolysis patterns and was found to be an effective and precise way to evaluate the activity of cellulase against cello-oligosaccharides.
Based on anti-idiotypic network theory in light of the need for new antifungal drugs, we attempte... more Based on anti-idiotypic network theory in light of the need for new antifungal drugs, we attempted to identify biologically active fragments from HM-1 yeast killer toxin and its anti-idiotypic antibody and to compare their potency as an antifungal agent. Thirteen overlapping peptides from HM-1 killer toxin and six peptides from its anti-idiotypic single-chain variable fragment (scFv) antibodies representing the complementarity determining regions were synthesized. The binding affinities of these peptides were investigated and measured by Dot blot and surface plasmon resonance analysis and finally their antifungal activities were investigated by inhibition of growth, colony forming unit assay. Peptide P6, containing the potential active site of HM-1 was highly capable of inhibiting the growth of Saccharomyces cerevisiae but was less effective on pathogenic fungi. However, peptide fragments derived from scFv antibody exerted remarkable inhibitory effect on the growth of pathogenic strains of Candida and Cryptococcus species in vitro. One scFv-derived decapeptide (SP6) was selected as the strongest killer peptide for its high binding affinity and antifungal abilities on both Candida and Cryptococcus species with IC(50) values from 2.33 × 10(-7) M to 36.0 × 10(-7) M. SP6 peptide activity was neutralized by laminarin, a β-1,3-glucan molecule, indicating this peptide derived from scFv anti-idiotypic antibody retains antifungal activity through interaction with cell wall β-glucan of their target fungal cells. Experimental evidence strongly suggested the possibility of development of anti-idiotypic scFv peptide-based antifungal agents which may lead to improve therapeutics for the management of varieties of fungal infections.
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Papers by Dr. Nurul Karim