Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana

Differential cytosine methylation of repeats and genes is important for coordination of genome stability and proper gene expression. Through genetic screen of mutants showing ectopic cytosine methylation in a genic region, we identified a jmjC-domain gene, IBM1 (increase in bonsai methylation 1), in Arabidopsis thaliana. In addition to the ectopic cytosine methylation, the ibm1 mutations induced a variety of developmental phenotypes, which depend on methylation of histone H3 at lysine 9. Paradoxically, the developmental phenotypes of the ibm1 were enhanced by the mutation in the chromatin-remodeling gene DDM1 (decrease in DNA methylation 1), which is necessary for keeping methylation and silencing of repeated heterochromatin loci. Our results demonstrate the importance of chromatin remodeling and histone modifications in the differential epigenetic control of repeats and genes.     

Tradition and change in postharvest pest management in Kenya

The hazard of postharvest pest losses is ubiquitous in peasant farming systems; as a result, farmers invariably have some response to the threat of these losses. Responses to postharvest pests may be more extensive than to field pests, even when, by statistical measures, the usual levels of losses are comparable. In studies of pest management practices in three contrasting areas in Kenya, it was found that farmers virtually always rely on an array of techniques and strategies, usually including both older and more modern practices. There is considerable variation among regions in the techniques used, due not only to climatic and socioeconomic factors, but also to variations in cultural history and preferences. The ways in which management practices have changed over time also vary by region. The major changes have been related to overall system change. Four main sources of change have been paramount: (1) population growth and the intensification of land use; (2) the introduction of new cash crops; (3) the introduction of new marketing infrastructure; and (4) the perception of increased environmental risk. Their effect on the replacement of older practices by newer ones is often interrelated. Traditional techniques are often based on materials derived from bushland, but increasing population density makes these difficult to continue as bushland and its common property resources disappear. Simultaneously, tolerance for losses is reduced as land availability is constrained. With the introduction of a cash crop infrastructure, new methods of pest management, especially pesticide use, become more readily available and may spread rapidly. Areas with good market infrastructure but varying population density may still differ considerably because with abundant land it is possible to compensate for expected losses by additional planting. A study of an FAO project to improve postharvest management through earlier harvesting and a redesigned storage crib indicate some reasons for its lack of widespread acceptance. Little or no attempt was made to adapt techniques to varying circumstances; instead, a single “solution” was meant to be applied across areas of vastly different conditions. In many cases, this project represented a radical response to a problem farmers considered they were coping with acceptably using existing methods. Although it probably represents an improvement over traditional storage methods in purely technical terms, the new technique also often involved major costs, readjustments, and cultural disruptions that may not have been anticipated by its designers. More likely to succeed would be a strategy that begins with some of farmers' existing practices and whose objective is to develop and offer a range of possible improvements from which farmers could select individual components appropriate to their conditions and needs.     

Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae

A computational analysis of the nuclear genome of a red alga, Cyanidioschyzon merolae, identified 11 transfer RNA (tRNA) genes in which the 3' half of the tRNA lies upstream of the 5' half in the genome. We verified that these genes are expressed and produce mature tRNAs that are aminoacylated. Analysis of tRNA-processing intermediates for these genes indicates an unusual processing pathway in which the termini of the tRNA precursor are ligated, resulting in formation of a characteristic circular RNA intermediate that is then processed at the acceptor stem to generate the correct termini.     

Incipient space weathering observed on the surface of Itokawa dust particles

The reflectance spectra of the most abundant meteorites, ordinary chondrites, are different from those of the abundant S-type (mnemonic for siliceous) asteroids. This discrepancy has been thought to be due to space weathering, which is an alteration of the surfaces of airless bodies exposed to the space environment. Here we report evidence of space weathering on particles returned from the S-type asteroid 25143 Itokawa by the Hayabusa spacecraft. Surface modification was found in 5 out of 10 particles, which varies depending on mineral species. Sulfur-bearing Fe-rich nanoparticles exist in a thin (5 to 15 nanometers) surface layer on olivine, low-Ca pyroxene, and plagioclase, which is suggestive of vapor deposition. Sulfur-free Fe-rich nanoparticles exist deeper inside (<60 nanometers) ferromagnesian silicates. Their texture suggests formation by metamictization and in situ reduction of Fe(2+).     

Neutron activation analysis of a particle returned from asteroid Itokawa

A single grain (~3 micrograms) returned by the Hayabusa spacecraft was analyzed by neutron activation analysis. This grain is mainly composed of olivine with minor amounts of plagioclase, troilite, and metal. Our results establish that the Itokawa sample has similar chemical characteristics (iron/scandium and nickel/cobalt ratios) to chondrites, confirming that this grain is extraterrestrial in origin and has primitive chemical compositions. Estimated iridium/nickel and iridium/cobalt ratios for metal in the Itokawa samples are about five times lower than CI carbonaceous chondrite values. A similar depletion of iridium was observed in chondrule metals of ordinary chondrites. These metals must have condensed from the nebular where refractory siderophile elements already condensed and were segregated.     

Oxygen isotopic compositions of asteroidal materials returned from Itokawa by the Hayabusa mission

Meteorite studies suggest that each solar system object has a unique oxygen isotopic composition. Chondrites, the most primitive of meteorites, have been believed to be derived from asteroids, but oxygen isotopic compositions of asteroids themselves have not been established. We measured, using secondary ion mass spectrometry, oxygen isotopic compositions of rock particles from asteroid 25143 Itokawa returned by the Hayabusa spacecraft. Compositions of the particles are depleted in (16)O relative to terrestrial materials and indicate that Itokawa, an S-type asteroid, is one of the sources of the LL or L group of equilibrated ordinary chondrites. This is a direct oxygen-isotope link between chondrites and their parent asteroid.     

Detection of the EGFP sequence in breast muscle of 3‐year‐old chicken after transfection using sonoporation

In our continuing effort to generate transgenic chickens, sonoporation was chosen to insert an exogenous gene into the chicken genome. An EGFP expression vector (pCAG‐EGFPac) and microbubbles were injected into the central disc of stage‐X blastoderm or the germinal crescent of stage‐4 embryos, followed by ultrasonic vibration. Nineteen chicks out of 108 treated embryos hatched, six females and six males out of these 19 chicks grew to sexual maturity and two females and three males lived for 3 years. Genomic DNA from 17 out of 35 gonads from embryos and chicks that died before sexual maturity was EGFP‐positive by PCR. No EGFP sequence was detected in the genomic DNA of 322 embryos from six sexually mature females and the semen from four sexually mature males by PCR. When genomic DNA was obtained from various tissues of five 3‐year‐old chickens, the EGFP sequence was amplified from the genomic DNA of the breast muscle of a female (No. 85). The above sequence was subjected to DNA sequencing and verified to be the EGFP sequence. These results showed that sonoporation is an effective tool for the transduction of exogenous genes into chicken embryos for the generation of transgenic chickens.     

Improvement of rice (Oryza sativa L.) growth in upland conditions with deep tillage and mulch

The productivity of upland rice in Japan as well as in the world is low and unstable owing to scarce and unpredictable rainfall. The objective of this study was to examine whether agronomic methods could enhance grain yield of upland rice. Four field experiments were conducted from 2001 to 2003 in Nishitokyo, Japan, under upland conditions with different water supplies, in order to quantify the effects of deep tillage combined with deep placement of manure (50-cm depth), straw mulch (6 t ha⁻¹), or their combinations on the growth and grain yield of rice. Mulch kept surface soil moisture higher than without mulch even at reproductive stage, and it increased yield to the greatest extent under the most favourable conditions with much rainfall before heading (i.e., 2003). Deep tillage with deep placement of manure induced deep root proliferation and higher nitrogen uptake, increasing biomass production, and panicle number, and consequently grain yield was enhanced under the two lowest yielding environments with less rainfall before heading. Rice plants with deep tillage with deep manure application without mulch tended to have lower leaf water potential and higher diffusion resistance during drought, and negative effects on grain filling and harvest index in some experiments compared with the control. When deep tillage with deep placement of manure was combined with mulching in two experiments in 2002 and 2003, grain yield always enhanced compared with the control (P < 0.10, 6.0 t ha⁻¹ versus 5.4 t ha⁻¹ on average), suggesting their synergetic mechanisms for yield increase and stabilization. The results showed that deep tillage or mulching can improve grain yield of rice under drought-prone rainfed upland conditions in a temperate climate on an Andosol, and their combination had more consistent and greater positive effects.