J. Sri Widada

Development of loop-mediated isothermal amplification (LAMP) as a diagnostic tool of toxoplasmosis

Infection with Toxoplasma gondii is one of the most common parasitic infections in humans and other warm-blooded animals. This paper describes the development of loop-mediated isothermal amplification (LAMP) specific to the single-copy gene SAG1 as a diagnostic tool of toxoplasmosis. A set of primers, composed of outer primers, inner primers and loop primers was designed from a published sequence data (GeneBank Acc. no. AY651825). Experiments showed that when LAMP was applied to sample organs, amplification absolutely required the loop primers to complete. SAG1-based LAMP turned out to be very sensitive, exhibiting a degree of sensitivity higher than the conventional PCR. LAMP is a convenient and sensitive diagnostic tool for routine health control of toxoplasmosis.

Cloning and deletion mutagenesis using direct protein-protein interaction on an expression vector identification of the calmodulin binding domain of α-fodrin☆

We have screened a lambda gt11 library, constructed with mouse macrophage cDNA, in order to isolate clones that code for calmodulin binding proteins. We have developed a new approach for this purpose using radioactive calmodulin (produced by genetic engineering) to detect fusion proteins that interact with this protein with high affinity. A cDNA clone that codes for mouse macrophage fodrin was isolated, sequenced and identified. By deleting part of the sequence the calmodulin binding domain was located on the fodrin sequence. The site is situated on repeat 11 of fodrin and probably on the extra arm of this repeat. The method we developed is widely applicable to site-directed mutagenesis of interacting proteins.

Evolution of tropomyosin functional domains: Differential splicing and genomic constraints

SummaryWe have cloned and determined the nucleotide sequence of a complementary DNA (cDNA) encoded by a newly isolated human tropomyosin gene and expressed in liver. Using the leastsquare method of Fitch and Margoliash, we investigated the nucleotide divergences of this sequence and those published in the literature, which allowed us to clarify the classification and evolution of the tropomyosin genes expressed in vertebrates. Tropomyosin undergoes alternative splicing on three of its nine exons. Analysis of the exons not involved in differential splicing showed that the four human tropomyosin genes resulted from a duplication that probably occurred early, at the time of the amphibian radiation. The study of the sequences obtained from rat and chicken allowed a classification of these genes as one of the types identified for humans.The divergence of exons 6 and 9 indicates that functional pressure was exerted on these sequences, probably by an interaction with proteins in skeletal muscle and perhaps also in smooth muscle; such a constraint was not detected in the sequences obtained from nonmuscle cells. These results have led us to postulate the existence of a protein in smooth muscle that may be the counterpart of skeletal muscle troponin.We show that different kinds of functional pressure were exerted on a single gene, resulting in different evolutionary rates and different convergences in some regions of the same molecule.Codon usage analysis indicates that there is no strict relationship between tissue types (and hence the tRNA precursor pool) and codon usage. G+C content is characteristic of a gene and does not change significantly during evolution. These results are in good agreement with an isochore composition of the genome, and thus suggest a similar chromosomal environment in chicken, rat, and human.

Expression of tropomyosin genes during the development of the rat cerebellum.

Abstract: The expression of the tropomyosin genes in the rat nervous system was examined during the postnatal development of the cerebellum, using human‐specific α‐, β‐, γ‐, and d‐tropomyosin cDNA probes and rat‐specific α‐, β‐, and d‐tropomyosin oligonucleotide probes. The β‐ and γ‐genes do not seem to be expressed in the rat brain. The δ‐tropomyosin gene produces two mRNAs: a major one of 2.4 kb, which is highly concentrated during the first postnatal week and then decreases fourfold in level until the age of 35 days, and a minor one of 2 kb, with the same developmental profile as the 2.4‐kb mRNA. A 3‐kb mRNA is expressed by the α‐tropomyosin gene and is characteristic of the mature rat. The expression of the tropomyosin genes during the development of the rat cerebellum does not seem to be regulated through alternative splicing but rather implies the differential expression of two different isogenes. The multiple isoforms of tropomyosin produced during neuronal differentiation may be intimately involved in the regulation of the organization and function of actin microfilaments.

Identification of the calmodulin binding domain of α-fodrin and implications for folding

A cDNA clone producing a protein that binds calmodulin has been isolated from a mouse macrophage library. The cDNA was sequenced and identified as coding for fodrin. By deleting part of the sequence, the calmodulin binding domain was located. The site is situated on repeat 11 of fodrin probably on its extra arm. This part of the sequence exhibits great similarity to other calmodulin binding proteins. Analysis of the sequence and spatial structure of calmodulin revealed a domain which is quite complementary to the sequence identified on fodrin. These results provide a new insight into the structure of fodrin and consequently into the structure of proteins of the spectrin family. A model for the general folding of these molecules is proposed, involving a simple three-layer folding. The structure was further corroborated by analysis of charge distribution in the vicinity of the calmodulin binding site. The folding we propose is in good agreement with digestion experiments and explains observations in diseases resulting from mutations of human spectrin.