The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.     

Springiness of Pancake and Its Relation to Binding of Prime Starch to Tailings in Stored Wheat Flour

Wheat flours were stored at room temperature (15–25°C), 40, 60, 80, and 100°C for various times. The baking performance of these flours was then evaluated in terms of the springiness of pancakes (recovery from crushing). Baking performance improved with increased storage time at each temperature. Brabender Amylograph tests of the flours indicated that the onset temperature in viscosity decreased with increased storage time at each temperature. When the flours were fractionated by acetic acid (pH 3.5) with mortar and pestle, recoveries of the water-solubles and gluten fractions were unchanged, but recoveries of prime starch and tailings fractions changed remarkably with increased storage time. On the other hand, those changes were not observed when flours were fractionated with a Waring blender. The binding of prime starch to tailings was correlated significantly with baking performance.     

Transmission of mitochondrial plasmids in protoplast cell fusion between compatible monokaryons of <Emphasis Type="Italic">Lentinula edodes</Emphasis>

Electrophoretic analysis of the transmission pattern of mitochondrial plasmids in protoplast cell fusion between compatible monokaryons of Lentinula edodes indicates that three of the four plasmids carried in parental monokaryons are effectively transferred and replicated in the protoplast fusants. The two monokaryons, 1158a and 1569a, carried different plasmids that could be distinguished by a single restriction digest. Electrophoresis of intact plasmids and restriction analyses indicate that all but one of the fusants carry three of the four possible plasmids, indicating that transmission of plasmids in protoplast fusions is principally biparental in L. edodes. Thus, heterocytoplasmic cells of L. edodes can be effectively constructed by protoplast cell fusion. In addition, plasmids of the same homology group cannot coexist in the heteroplasmic cells after protoplast cell fusion. Contribution No. 382 of the Tottori Mycological Institute     

Analysis of the equine ovarian structure during the first twelve months of life by three-dimensional internal structure microscopy

A three-dimensional internal structure microscopy (3D-ISM) can clarify the anatomical arrangement of internal structures of equine ovaries. In this study, morphological changes of the equine ovary over the first 12 months of life were investigated by 3D-ISM in 59 fillies and by histological analysis in 2 fillies. The weight and volume of the paired ovaries initially decreased from 0 to 1 months to 2 to 3 months of age and then significantly increased at 8 to 12 months of age. The ovulation fossa was first observed around the 3rd month and became evident after the 6th month. The number of follicles with a diameter of ≥10 mm and the diameter of the largest follicle increased gradually after 6 months of age. On a volume basis, the medulla accounted for nearly 90% of the whole ovary at 0 to 1 months of age, but significantly decreased from 2 to 3 months of age. The volume of the cortex increased progressively after birth and reached approximately 60% of the total volume at 8 to 12 months of age. This significant development of the cortex coincided with the increased number and size of large follicles observed from 6 months of age. These results suggest that the development of the cortex plays a role in the maturation of the follicles and the equine ovary undergoes substantial morphological changes postnatally until puberty.     

A review of tower flux observation sites in Asia

Aggregating and sharing the metadata of flux observation sites results in a strong collaboration among various fields of study. Such data sharing will also be a part of the future design of a tower flux observation network in Asia. The aim of this review is to comprehend the state of tower flux observation sites in Asia. There are 109 tower flux observation sites in Asia including 51 forest sites. There are more new sites under construction in Asia than in America and Europe. These sites range from the taiga in Siberia to the rainforest in Southeast Asia, and from the equatorial to polar Koeppen climate zones. There are many highly humid areas in Asia, not only at low latitudes but also at middle latitudes. This climate condition has developed unique vegetation such as lucidophyllous (evergreen broadleaf) forest, which is distributed in warm areas with high precipitation in the growing season. However, there are only a few observations taking place in lucidophyllous forest. Rice paddy fields are also unique land cover in Asia. It is important to accumulate long-term data for rice fields with their management records, because plant activity depends highly on both climate conditions and land-use management. Flux data, especially net ecosystem exchange and related elements, are used for widespread studies not only within the flux-research community but also in other fields of study, for example remote sensing. At present, however, both the quantity and quality of the data are not sufficient for these studies. Regarding the quantity, there are many recently established sites that have not published data yet; regarding quality, flux data include uncertainties caused by methodological problems. Flux researchers are required not only to obtain flux data but also to improve their quality. Meanwhile, data users must understand there are still uncertainties in flux data. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Reduction in the IgE reactivity of Pacific mackerel parvalbumin by mutations at Ca2+-binding sites

ABSTRACT:   Parvalbumin is a sarcoplasmic Ca²⁺-binding protein of 12 kDa and represents the major fish allergen. Several peptide segments are identified as immunoglobulin E (IgE)-binding epitopes of cod parvalbumin. However, carp parvalbumin (Cyp c 1) shows a markedly reduced IgE-binding ability upon depletion of Ca²⁺, suggesting the importance of conformational epitopes associated with Ca²⁺-chelating. In this study, the IgE reactivity of Pacific mackerel Scomber japonicus parvalbumin (Sco j 1) was demonstrated to be markedly reduced (60–100% reduction) by Ca²⁺-depletion, similar to Cyp c 1. Three Sco j 1 mutants (D51A, D90A, D51/90A), with modifications in either one or both of the two Ca²⁺-binding sites, were then constructed by site-directed mutagenesis, followed by expression in Escherichia coli , and evaluated for their IgE reactivity. Interestingly, the double mutant (D51/90A), probably devoid of Ca²⁺-binding capacity, exhibited a significantly reduced IgE reactivity (equivalent to 0.0–7.5% of the IgE reactivity of natural Sco j 1). The results suggest that the IgE-binding ability of Sco j 1 largely depends on the solid conformation mediated by Ca²⁺-chelating, and that the hypoallergenic D51/90A will be a useful tool for the specific immunotherapy of fish allergy.     

Decomposition of coffee residue in soil

In this study the changes in the chemical properties of coffee residue during decomposition in soil were investigated. 1) Coffee residue contained about 20 g kg^-1 N. The main N compound was a structural protein-No However, the content of easily decomposable N (soluble protein-N and nonprotein-N) extracted by 800 mL L^-1 ethanol and 0.1 mol L^-1 phosphate buffer (pH 7.5) was very low. 2) The rates of nonprotein-N and soluble protein-N which remained reached values of 59 and 66% at 314 d after application of the coffee residue (DAA) to soil, respectively. However, the amount of structural protein-N reached a value of 96% at 314 DAA. 3) The lipid fraction of the coffee residue decreased from 186 to 47 g kg^-1 by 314 d after application. Coffee residue has a high content of lipid fraction and a large fraction corresponding to structural protein-No Therefore, the decomposition of the coffee residue is slower than that of other organic materials.