DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme

To cut DNA at their target sites, restriction enzymes assemble into different oligomeric structures. The Ecl18kI endonuclease in the crystal is arranged as a tetramer made of two dimers each bound to a DNA copy. However, free in solution Ecl18kI is a dimer. To find out whether the Ecl18kI dimer or tetramer represents the functionally important assembly, we generated mutants aimed at disrupting the putative dimer–dimer interface and analysed the functional properties of Ecl18kI and mutant variants. We show by atomic force microscopy that on two-site DNA, Ecl18kI loops out an intervening DNA fragment and forms a tetramer. Using the tethered particle motion technique, we demonstrate that in solution DNA looping is highly dynamic and involves a transient interaction between the two DNA-bound dimers. Furthermore, we show that Ecl18kI cleaves DNA in the synaptic complex much faster than when acting on a single recognition site. Contrary to Ecl18kI, the tetramerization interface mutant R174A binds DNA as a dimer, shows no DNA looping and is virtually inactive. We conclude that Ecl18kI follows the association model for the synaptic complex assembly in which it binds to the target site as a dimer and then associates into a transient tetrameric form to accomplish the cleavage reaction

Insights into the Molecular Evolution of the PDZ/LIM Family and Identification of a Novel Conserved Protein Motif

The PDZ and LIM domain-containing protein family is encoded by a diverse group of genes whose phylogeny has currently not been analyzed. In mammals, ten genes are found that encode both a PDZ- and one or several LIM-domains. These genes are: ALP, RIL, Elfin (CLP36), Mystique, Enigma (LMP-1), Enigma homologue (ENH), ZASP (Cypher, Oracle), LMO7 and the two LIM domain kinases (LIMK1 and LIMK2). As conventional alignment and phylogenetic procedures of full-length sequences fell short of elucidating the evolutionary history of these genes, we started to analyze the PDZ and LIM domain sequences themselves. Using information from most sequenced eukaryotic lineages, our phylogenetic analysis is based on full-length cDNA-, EST-derived- and genomic- PDZ and LIM domain sequences of over 25 species, ranging from yeast to humans. Plant and protozoan homologs were not found. Our phylogenetic analysis identifies a number of domain duplication and rearrangement events, and shows a single convergent event during evolution of the PDZ/LIM family. Further, we describe the separation of the ALP and Enigma subfamilies in lower vertebrates and identify a novel consensus motif, which we call ‘ALP-like motif’ (AM). This motif is highly-conserved between ALP subfamily proteins of diverse organisms. We used here a combinatorial approach to define the relation of the PDZ and LIM domain encoding genes and to reconstruct their phylogeny. This analysis allowed us to classify the PDZ/LIM family and to suggest a meaningful model for the molecular evolution of the diverse gene architectures found in this multi-domain family

Book-Talk: An Activity to Motivate Learners to Read Autonomously in a Foreign Language

In the last decade, extensive reading (ER) had been incorporated into English as a foreign language (EFL) education in various Japanese institutions. It restored the once broken balance of accuracy and fluency in traditional English education, and assisted reluctant EFL learners to start reading. However, ER required rather longer term for elementary learners to enjoy its benefits and the learners needed an extra encouragement to continue ER for the longer term. Book-talk was such an activity to encourage learners to read voluntary and to improve their language skills additionally. In a book-talk, several learners sat around a table, introduced the books they had read during the week, and accepted questions and comments from the others in turn. It also fitted well in lessons because 3-minute talks and 2-minute Q&A of six members took only 30 minutes. We will report how the activity motivated elder students, who had three or more years’ experience of ER, to continue their reading outside the class, and how it encouraged autonomous ER of adult EFL learners, who were reading English books borrowing from the college library. A combination of few talks and many readings worked well in EFL settings

Deodorant Activity of Black Cumin Seed Essential Oil against Garlic Organosulfur Compound

The deodorant activity of black cumin (Nigella sativa L.) seed, a spice used to flavor curry and vegetable foods in Southwest Asia, against garlic (Allium sativum L.) organosulfur compounds related to human malodor was evaluated. Black cumin seed essential oil showed remarkable deodorant activity against garlic essential oil. The mode of action of this deodorant activity was presumed to be that black cumin seed essential oil covalently reacted with the organosulfur compounds in garlic. Therefore, thymoquinone, which is a major constituent in black cumin seed essential oil, and allyl mercaptan, which is one of the organosulfur compounds produced by cutting garlic, were reacted in vitro, and the products were purified and elucidated using spectroscopic data. As a result, these substances were identified as different allyl mercaptan adducts to dihydrothymoquinone. This chemical reaction was presumed to play a key role in the deodorant activity of black cumin seed essential oil

A novel mutation of WFS1 gene in a Japanese man of Wolfram syndrome with positive diabetes-related antibodies

Wolfram syndrome is a rare, autosomal recessive disorder characterized by early-onset diabetes mellitus, optic atrophy and neurological and endocrinological abnormalities. A 47-year-old Japanese man with frequent severe hypoglycemic episodes was diagnosed as Wolfram syndrome based on clinical features and laboratory data. He had positive glutamic acid decarboxylase (GAD) and insulinoma-associated antigen-2 (IA-2) antibodies, both uncommon in this syndrome. Genetic analysis revealed that WFS1 gene of the patient has a homozygous 5 base pairs (AAGGC) insertion at position 1279 in exon 8, causing a frameshift at codon 371 leading to premature termination at codon 443