Toshihiro Kogure

An acidic matrix protein, Pif, is a key macromolecule for nacre formation.

Making Mother of Pearl Nacre is an iridescent layer of calcium carbonate lining the inside of shells of marine mollusks and is commonly known as “mother of pearl.” It is composed of layers of uniformly oriented crystals of aragonite (a metastable form of calcium carbonate) separated by layers of organic matrix. How the ordered structure of aragonite layers is achieved has been unclear. Suzuki et al. (p. 1388, published online 13 August 2009; see the Perspective by Kröger) identified two acidic matrix proteins (Pif 97 and Pif 80) that regulate nacre formation in the Japanese pearl oyster. The proteins appear to form a complex in which Pif 80 binds to aragonite and Pif 97 binds to other macromolecules in the organic matrix. A matrix protein is identified that regulates nacre formation in the Japanese pearl oyster. The mollusk shell is a hard tissue consisting of calcium carbonate crystals and an organic matrix. The nacre of the shell is characterized by a stacked compartment structure with a uniformly oriented c axis of aragonite crystals in each compartment. Using a calcium carbonate–binding assay, we identified an acidic matrix protein, Pif, in the pearl oyster Pinctada fucata that specifically binds to aragonite crystals. The Pif complementary DNA (cDNA) encoded a precursor protein, which was posttranslationally cleaved to produce Pif 97 and Pif 80. The results from immunolocalization, a knockdown experiment that used RNA interference, and in vitro calcium carbonate crystallization studies strongly indicate that Pif regulates nacre formation.

Characterization of Prismalin-14, a novel matrix protein from the prismatic layer of the Japanese pearl oyster (Pinctada fucata)

The mollusc shell is a hard tissue consisting of calcium carbonate and organic matrices. The organic matrices are believed to play important roles in shell formation. In the present study, we extracted and purified a novel matrix protein, named Prismalin-14, from the acid-insoluble fraction of the prismatic layer of the shell of the Japanese pearl oyster (Pinctada fucata), and determined its whole amino acid sequence by a combination of amino acid sequence analysis and MS analysis of the intact protein and its enzymic digests. Prismalin-14 consisted of 105 amino acid residues, including PIYR repeats, a Gly/Tyr-rich region and N- and C-terminal Asp-rich regions. Prismalin-14 showed inhibitory activity on calcium carbonate precipitation and calcium-binding activity in vitro. The scanning electron microscopy images revealed that Prismalin-14 affected the crystallization of calcium carbonate in vitro. A cDNA encoding Prismalin-14 was cloned and its expression was analysed. The amino acid sequence deduced from the nucleotide sequence of Prismalin-14 cDNA was identical with that determined by peptide sequencing. Northern-blot analysis showed that a Prismalin-14 mRNA was expressed only at the mantle edge. In situ hybridization demonstrated that a Prismalin-14 mRNA was expressed strongly in the inner side of the outer fold of the mantle. These results suggest that Prismalin-14 is a framework protein that plays an important role in the regulation of calcification of the prismatic layer of the shell.

SUMMARY OF RECOMMENDATIONS OF NOMENCLATURE COMMITTEES RELEVANT TO CLAY MINERALOGY: REPORT OF THE ASSOCIATION INTERNATIONALE POUR L'ETUDE DES ARGILES (AIPEA) NOMENCLATURE COMMITTEE FOR 2006

Brindley et al. (1951) reported the earliest efforts to obtain international collaboration on nomenclature and classification of clay minerals, initiated at the International Soil Congress in Amsterdam in 1950. Since then, national clay groups were formed, and they proposed various changes in nomenclature at group meetings of the International Clay Conferences. Most of the national clay groups have representation on the Nomenclature Committee of the Association Internationale pour l’Etude des Argiles (AIPEA, International Association for the Study of Clays), which was established in 1966. The precursor committee to the AIPEA Nomenclature Committee was the Nomenclature Subcommittee of the Comite International pour l’Etude des Argiles (CIPEA, International Committee for the Study of Clays). The AIPEA Nomenclature Committee has worked closely with other international groups, including the Commission on New Minerals and Mineral Names (CNMMN) of the International Mineralogical Association (IMA), which is responsible for the formal recognition of new minerals and mineral names, and the International Union of Crystallography (IUCr), which considered extensions to the nomenclature of disordered, modulated and polytype structures (Guinier et al. , 1984) published earlier by a joint committee with the IMA (Bailey, 1977). In contrast to the other national clay groups, however, The Clay Minerals Society (CMS) Nomenclature Committee, which was established in 1963 at the same time as the CMS and predates the AIPEA Nomenclature Committee, remains in existence and occasionally produces recommendations. The precursor to this committee was the Nomenclature SubCommittee, which was organized in 1961 by the (US) National Research Council. The Chair of the AIPEA Nomenclature Committee is a standing member of the CMS Nomenclature Committee so that the committees are in close contact. The purpose of the AIPEA Nomenclature Committee has been to make general and specific recommendations concerning: (1) definitions of mineralogical and crystallographic clay-related terms; (2) classification and terminology …

Glycolytic intermediates induce amorphous calcium carbonate formation in crustaceans

It has been thought that phosphorus in biominerals made of amorphous calcium carbonate (ACC) might be related to ACC formation, but no such phosphorus-containing compounds have ever been identified. Crustaceans use ACC biominerals in exoskeleton and gastroliths so that they will have easy access to calcium carbonate inside the body before and after molting. We have identified phosphoenolpyruvate and 3-phosphoglycerate, intermediates of the glycolytic pathway, in exoskeleton and gastroliths and found them important for stabilizing ACC.

Speciation of Radioactive Soil Particles in the Fukushima Contaminated Area by IP Autoradiography and Microanalyses

Radioactive soil particles several tens of micrometers in size were collected from litter soil in the radiation contaminated area by the Fukushima nuclear plant accident and characterized using electron and X-ray microanalyses. The radioactive particles were discriminated by autoradiography using imaging plates (IP) on which microgrids were formed by laser ablation in order to find the particles under microscopy. Fifty radioactive particles were identified and classified into three types from their morphology and chemical composition, namely: (1) aggregates of clay minerals, (2) organic matter containing clay mineral particulates, and (3) weathered biotite originating from local granite. With respect to the second type, dissolution of the organic matter did not reduce the radiation, suggesting that the radionuclides were also fixed by the clay minerals. The weathered biotite grains have a plate-like shape with well-developed cleavages inside the grains, and kaolin group minerals and goethite filling the cleavage spaces. The reduction of the radiation intensity was measured before and after the trimming of the plate edges using a focused ion beam (FIB), to examine whether radioactive cesium primarily sorbed at frayed edges. The radiation was attenuated in proportion to the volume decrease by the edge trimming, implying that radioactive cesium was sorbed uniformly in the porous weathered biotite.

Cesium adsorption/desorption behavior of clay minerals considering actual contamination conditions in Fukushima.

Cesium adsorption/desorption experiments for various clay minerals, considering actual contamination conditions in Fukushima, were conducted using the 137Cs radioisotope and an autoradiography using imaging plates (IPs). A 50 μl solution containing 0.185 ~ 1.85 Bq of 137Cs (10−11 ~ 10−9 molL−1 of 137Cs) was dropped onto a substrate where various mineral particles were arranged. It was found that partially-vermiculitized biotite, which is termed “weathered biotite” (WB) in this study, from Fukushima sorbed 137Cs far more than the other clay minerals (fresh biotite, illite, smectite, kaolinite, halloysite, allophane, imogolite) on the same substrate. When WB was absent on the substrate, the amount of 137Cs sorbed to the other clay minerals was considerably increased, implying that selective sorption to WB caused depletion of radiocesium in the solution and less sorption to the coexisting minerals. Cs-sorption to WB continued for about one day, whereas that to ferruginous smectite was completed within one hour. The sorbed 137Cs in WB was hardly leached with hydrochloric acid at pH 1, particularly in samples with a longer sorption time. The presence/absence of WB sorbing radiocesium is a key factor affecting the dynamics and fate of radiocesium in Fukushima.

Determination of defect structures in kaolin-minerals by high-resolution transmission electron microscopy (HRTEM)

Abstract Near-atomic resolution TEM imaging has been successfully applied to determine the stacking defect structures in kaolin minerals, especially kaolinite. The specimen studied is from the middle stage of the depth-related kaolinite-to-dickite transformation in a sandstone reservoir. Several high-quality images were recorded on films in which the tetrahedral and octahedral positions in the kaolinite unit layers are clearly resolved, despite the obstacle of electron radiation damage. Electron diffraction and high-resolution imaging of dickite showed that few stacking defects exist in this polytype. On the other hand, kaolinite crystals contain a high density of stacking defects. These defects or stacking disorders are formed by a mixture of two kinds of lateral interlayer shifts, t1 (approximately −a/3) and t2(-a/3 + b/3), between adjacent layers. Disorder due to the coexistence of B and C layers (dickite-like stacking sequence) was never observed. These results provide not only an unambiguous settlement for the long -standing controversy of the defect structures in kaolinite, but also a new clue to understanding the kaolinite-to-dickite transformation mechanism.

Formation of Anatase Nanocrystals in Sol-Gel Derived TiO2-SiO2 Thin Films with Hot Water Treatment

We have successfully prepared transparent and porous anatase nanocrystals-dispersed films by treating the sol-gel derived TiO2-SiO2 films containing poly(ethylene glycol), PEG, with hot water. This process was done at temperatures lower than 100°C under atmospheric pressure, and thus anatase nanocrystals-dispersed films can be formed on various kinds of substrates including organic polymers with poor heat resistance. The changes in structure and composition of the TiO2-SiO2 gel films with hot water treatment were related to the formation process of anatase nanocrystals in the TiO2-SiO2 gel films with hot water treatment. The formation of anatase nanocrystals was found to proceed to hydrolysis of Si–O–Ti bonds and dissolution of SiO2 component. In addition, porous film structure formed by leaching of PEG with hot water treatment led to homogenous dispersion of anatase nonocrystals in the films.

Nucleation and growth of aragonite crystals at the growth front of nacres in pearl oyster, Pinctada fucata

The growth front of nacreous layer, which lies just above the outer prismatic layer, is one of the crucial areas to comprehend the formation of nacreous aragonite. The crystallographic properties of aragonite crystals at the growth front in pearl oyster, Pinctada fucata, were investigated using scanning electron microscopy with electron back-scattered diffraction, and transmission electron microscopy with focused ion beam sample preparation technique. Nano-sized aragonite crystals nucleate with random crystallographic orientation inside the dimples on the surface of the organic matrix that covers the outer prismatic columns. The dimples are filled with horn-like aragonite crystals, which enlarge from the bottom to the upper surface to form hemispheric domes. The domes grow concentrically and coalesce together to become the initial nacreous layer. The c-axes of aragonite at the top surface of the domes are preferentially oriented perpendicular to the surface. The horn-like aragonite and its crystallographic orientation are probably attained by geometrical selection with the fastest growth rate of aragonite along the c-axis, until organic sheets are continuously formed and interrupt the crystal growth of aragonite. The further crystal growth along the shell thickness is attained via mineral bridges through discontinuity or holes in the organic sheets. These results indicate that the crystal growth of aragonite at the growth front results from not only biotic process but also inorganic ones such as geometrical selection and mineral bridges.

Summary of recommendations of nomenclature committees relevant to clay mineralogy: report of the Association Internationale pour l’Etude des Argiles (AIPEA) Nomenclature Committee for 2006

Brindley et al. (1951) reported the earliest efforts to obtain international collaboration on nomenclature and classification of clay minerals, initiated at the International Soil Congress in Amsterdam in 1950. Since then, national clay groups were formed, and they proposed various changes in nomenclature at group meetings of the International Clay Conferences. Most of the national clay groups have representation on the Nomenclature Committee of the Association Internationale pour l’Etude des Argiles (AIPEA, International Association for the Study of Clays), which was established in 1966. The precursor committee to the AIPEA Nomenclature Committee was the Nomenclature Subcommittee of the Comite International pour l’Etude des Argiles (CIPEA, International Committee for the Study of Clays). The AIPEA Nomenclature Committee has worked closely with other international groups, including the Commission on New Minerals and Mineral Names (CNMMN) of the International Mineralogical Association (IMA), which is responsible for the formal recognition of new minerals and mineral names, and the International Union of Crystallography (IUCr), which considered extensions to the nomenclature of disordered, modulated and polytype structures (Guinier et al. , 1984) published earlier by a joint committee with the IMA (Bailey, 1977). In contrast to the other national clay groups, however, The Clay Minerals Society (CMS) Nomenclature Committee, which was established in 1963 at the same time as the CMS and predates the AIPEA Nomenclature Committee, remains in existence and occasionally produces recommendations. The precursor to this committee was the Nomenclature Sub-Committee, which was organized in 1961 by the (US) National Research Council. The Chair of the AIPEA Nomenclature Committee is a standing member of the CMS Nomenclature Committee so that the committees are in close contact. The purpose of the AIPEA Nomenclature Committee has been to make general and specific recommendations concerning: (1) definitions of mineralogical and crystallographic clay-related terms; (2) classification and terminology …