Testing the Bolam Test: consequences of recent developments.
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Clinical Competence↗
Biomedical subjects
K Shanmugam
Publications and source records attributed to K Shanmugam.
DiSSiMiL: Diverse Small Size Mini-Libraries applied to simple and rapid epitope mapping of a monoclonal antibody.
Methods for screening protein-protein interactions are useful in protein science and for the generation of drug leads. We set out to develop a simplified assay to rapidly test protein-protein interactions, with a library of 400 pentapeptides comprising the 20 natural amino acids at two variable positions followed by three glycines (NH2-X1X2GGG). The library was used to identify the epitope of monoclonal antibody (mAb) 10D11 directed against the HOXD4 protein. Three pentapeptide 'hits' were selected (VYGGG, PWGGG and WKGGG) from direct binding assays screening for pentapeptide-mAb interactions; and from assays using pentapeptides in solution to competitively block HOXD4-mAb interactions. Alignment of the three 'hit' pentapeptides to the HOXD4 sequence predicts the mAb 10D11 epitope as NH2-VYPWMK. Synthesis of NH2-VYPWMK hexapeptide confirmed this prediction; and an alanine scan of HOXD4 ablated binding by mAb 10D11 when amino acids in the putative epitope were mutated. We propose that these simplified but diverse libraries can be used for rapid epitope mapping of some mAbs, and for generating lead small peptide analogs that interfere with receptor-ligand or other protein-protein interactions, or with enzymatic activity.
Amino Acid Sequence↗
2,4-Toluene diamines--their carcinogenicity, biodegradation, analytical techniques and an approach towards development of biosensors.
2,4-Toluene diamine (TDA), a class A carcinogen, is a major raw material for the production of toluene diisocyanate (TDI), which is one of the precursors for the production of polyurethane foams (PU). This review deals with 2,4-toluene diamine's (TDA) carcinogenicity, analytical techniques, biodegradation and use as a biosensor for biogenic and synthetic amines, emphasizing various carcinogenicity studies by 2,4-TDA on animals and humans. This review reports some publications of the analysis of body fluid samples of workers from a PU producing factory for presence of TDA and TDI, since TDI gets absorbed into the worker's body, getting metabolized into TDA. Biodegradations of 2,4-TDA by various researchers are reported and also our own research experience with biodegradation of 2,4-TDA using Aspergillus nidulans isolated from soil site at a polyurethane foam dumping site have been discussed in this review. Biosensors for various biogenic and synthetic amines are discussed.
Animals↗
Cyclic voltammetric measurements of growth of Aspergillus terreus.
A detailed study using the cyclic voltammogram was done on the live cells of Aspergillus terreus. The peak current values were obtained for different days of growth and plotted against time. The response of cyclic voltammogram showed the phases of the growth of the fungus. The growth curve obtained matched well with the conventional methodology, which assesses the increase of dry weight of the organisms against time. The electrochemical method is more advantageous because it is easy to assess and consumes less time. Further the electrochemical method clearly shows the decline phase which is generally not very defined in the conventional method of assessment of the growth curve. It was confirmed by further experiments that the metabolites were responsible for the anodic peak and not the biomass. Further work is in progress in order to analyze the metabolite(s) that is/are responsible for the anodic peak.
Aspergillus↗
Assessment of growth of Fusarium solani by cyclic voltammetry and possible bioanalytical applications.
Fusarium solani, the fungus isolated from polyurethane waste scraps, was studied for its voltammetric response. The peak current values were obtained for different days and were plotted against time. This electrochemical method based on the voltammetric response showed all the four phases of the growth of the fungus. The growth curve obtained matched well with the conventional methodology, which is obtained by assessing the increase of dry weight of the organisms against time. The electrochemical method is more advantageous than the conventional method because the conventional method is very time consuming and difficult to work with. Further, the electrochemical method clearly shows the decline phase, which is generally not very well defined in the conventional method of assessment of the growth curve. It was confirmed by further experiments that the metabolites were responsible for the anodic peak and not the fungal biomass. Identification of the metabolites that are responsible for the anodic peak is presently being studied.
Biodegradation, Environmental↗
PBX and MEIS as non-DNA-binding partners in trimeric complexes with HOX proteins.
HOX, PBX, and MEIS transcription factors bind DNA through a homeodomain. PBX proteins bind DNA cooperatively as heterodimers with MEIS family members and also with HOX proteins from paralog groups 1 to 10. MEIS proteins cooperatively bind DNA with ABD-B class HOX proteins of groups 9 and 10. Here, we examine aspects of dimeric and higher-order interactions between these three homeodomain classes. The most significant results can be summarized as follows. (i) Most of PBX N terminal to the homeodomain is required for efficient cooperative binding with HOXD4 and HOXD9. (ii) MEIS and PBX proteins form higher-order complexes on a heterodimeric binding site. (iii) Although MEIS does not cooperatively bind DNA with ANTP class HOX proteins, it does form a trimer as a non-DNA-binding partner with DNA-bound PBX-HOXD4. (iv) The N terminus of HOXD4 negatively regulates trimer formation. (v) MEIS forms a similar trimer with DNA-bound PBX-HOXD9. (vi) A related trimer (where MEIS is a non-DNA-binding partner) is formed on a transcriptional promoter within the cell. (vii) We observe an additional trimer class involving non-DNA-bound PBX and DNA-bound MEIS-HOXD9 or MEIS-HOXD10 heterodimers that is enhanced by mutation of the PBX homeodomain. (viii) In this latter trimer, PBX is likely to contact both MEIS and HOXD9/D10. (ix) The stability of DNA binding by all trimers is enhanced relative to the heterodimers. These findings suggest novel functions for PBX and MEIS in modulating the function of DNA-bound MEIS-HOX and PBX-HOX heterodimers, respectively.
Antennapedia Homeodomain Protein↗
Residues flanking the HOX YPWM motif contribute to cooperative interactions with PBX.
Hox genes encode transcription factors that are major determinants of embryonic patterning. Recently, we and others have shown that specific recognition of target sites in DNA is partly achieved through cooperative interaction with the extradenticle/pre-B-cell transformation-related gene (EXD/PBX) family of homeodomain-containing proteins. This interaction is mediated by the YPWM motif present N-terminal to the homeodomain in HOX proteins. In the present study, we use YPWM peptides to confirm the importance of this motif for mediating HOX/PBX interactions. We also used a novel monoclonal antibody directed against the YPWM to show that occlusion of this motif abrogates cooperativity with PBX. In addition, we present evidence that residues flanking the YPWM, both N-terminally and C-terminally, stabilize the HOX.PBX cooperative complex. Because these flanking residues are also conserved among paralogs, they are likely to help distinguish the specificity of HOX/PBX interactions. Our data further show that the relative importance of individual residues within and flanking the YPWM is dependent on the identity of position 6 of the cooperative binding site (TGATTNATGG). These results suggest that interactions between PBX and the YPWM motif are modified by a base pair predicted to contact the N-terminal arm of the HOX homeodomain.
Alanine↗
Purification and characterization of a tRNA nucleotidyltransferase from Lupinus albus and functional complementation of a yeast mutation by corresponding cDNA.
ATP (CTP):tRNA nucleotidyltransferase (EC 2.7.7.25) was purified to apparent homogeneity from a crude extract of Lupinus albus seeds. Purification was accomplished using a multistep protocol including ammonium sulfate fractionation and chromatography on anion-exchange, hydroxylapatite and affinity columns. The lupin enzyme exhibited a pH optimum and salt and ion requirements that were similar to those of tRNA nucleotidyltransferases from other sources. Oligonucleotides, based on partial amino acid sequence of the purified protein, were used to isolate the corresponding cDNA. The cDNA potentially encodes a protein of 560 amino acids with a predicted molecular mass of 64 164 Da in good agreement with the apparent molecular mass of the pure protein determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis. The size and predicted amino acid sequence of the lupin enzyme are more similar to the enzyme from yeast than from Escherichia coli with some blocks of amino acid sequence conserved among all three enzymes. Functionality of the lupin cDNA was shown by complementation of a temperature-sensitive mutation in the yeast tRNA nucleotidyltransferase gene. While the lupin cDNA compensated for the nucleocytoplasmic defect in the yeast mutant it did not enable the mutant strain to grow at the non-permissive temperature on a non-fermentable carbon source.
Amino Acid Sequence↗
Heterocyclic tricycles as potential CNS agents I: 4-aminoalkylindeno[1,2-c]pyrazoles.
Series of 4-(3-dimethylaminopropyl)-4-hydroxyindeno[1,2-c]pyrazoles and 4-(1-methyl-4-piperidyl)-4-hydroxyindeno[1,2-c-]pyrazoles were synthesized and identified. The compounds were evaluated as potential CNS agents using spontaneous and forced motor activity in mice as an initial test. 2-Ethyl-3-methyl-4-(1-methyl-4-piperidyl)-4-hydroxyindeno[1,2-c]pyrazole possessed significant biological activity.
Animals↗