Biotic and abiotic processes of nitrogen immobilization in the soil-residue interface

The interface between decaying plant residues and soil is a hotspot for microbial immobilization of soil inorganic N. Recent studies on forest and grassland soils have demonstrated that rapid abiotic immobilization of inorganic N is also induced by the presence of plant residues. We, therefore, examined (1) how N immobilization varies with distance from the soil-residue interface and (2) whether abiotic immobilization occurs in agricultural soils. Spatiotemporal changes of N immobilization in the soil-residue interface were evaluated using a box that enabled soil to be sampled in 2 mm increments from a 4 mm-thick residue compartment (RC). The RC was filled with paddy soil containing ground plant residue (rice bran, rice straw or beech leaves) uniformly at a rate of 50 g dry matter kg⁻¹. Soil in the surrounding compartments contained no residue. After aerobic incubation for 5, 15 and 30 days at 25 °C, soils in each compartment were analyzed. After 5 days, significant depletion of inorganic N occurred throughout a volume of soil extending at least 10 mm from the RC in all residue treatments, suggesting extensive diffusion of inorganic N towards the RC. The depletion within 10 mm of the RC amounted to 5.0, 4.3 and 3.4 mg for rice bran, rice straw and beech leaf treatment, respectively. On the other hand, microbial N had increased significantly in the RC of the rice bran and rice straw treatments (11 mg and 5.5 mg, respectively) and insignificantly in the RC of the beech leaf treatment (0.06 mg). This increase amounted to 221% (rice bran), 129% (rice straw) and 1.7% (beech leaves) of the decrease in inorganic N within 10 mm of each RC. Thereafter the rate of N mineralization exceeded that of immobilization, and inorganic N levels had recovered almost to their original level by 15 days (rice bran) and 30 days (rice straw and beech leaves). These results suggested the predominance of biotic immobilization in soil near rice bran and rice straw and of abiotic immobilization in soil near beech leaves. No significant increase in both microbial and soluble organic N in the vicinity of beech leaves after incubation for 5 days further suggested that the abiotic process was responsible for the transformation of inorganic N into the insoluble organic N.     

Forest Floor Quality and N Transformations in a Temperate Forest Affected by Avian-Derived N Deposition

To evaluate the effects of avian-derived N deposition on forest C and N status, we investigated quantity and quality of litterfall, and chemical quality and N transformations in the forest floor from five sites that had been exposed to waterbird breeding colonies to differing degrees. The highest litterfall input of 2.6 t ha^?1 month^?1 was observed in the forest stand (Site 2) where intense bird breeding activity had been observed. Litterfall C/N was highest at the control site (no breeding activity) and decreased as the colonization stages advanced. Nitrogen concentration in litterfall and the forest floor was higher at those sites (Sites 3 and 4) where bird breeding had ceased and which represented the 'post-colony' situation, and consequently C/N and lignin/N of forest floor decreased. NH₄-N pool size in the forest floor was higher at Site 2, probably due to ongoing input and mineralization of bird excreta. Nitrification rate and percent nitrification were highest at Sites 3 and 4. From these results we conclude that study sites exposed to bird colonies show signs of N excess even after colonies are abandoned.     

Development of a multiplex PCR method for simultaneous detection of diagnostic DNA markers of five disease and pest resistance genes in potato

Multiplex PCR is practically a reasonable choice for molecular marker-assisted selection in potato breeding. We had developed and were using a multiplex PCR method for selection of resistance genes to cyst nematode (H1), Potato virus X (Rx1) and late blight (R1 and R2). Since then, more reliable and tightly linked markers for H1 and R2, and a new marker for resistance to Potato virus Y (Ry _chc ) were developed. In this article, all these superior markers, including a positive marker to eliminate PCR-failed samples, were incorporated into one multiplex PCR assay. Using the newly developed multiplex PCR technique, five plants potentially harboring all five resistance genes were selected from 96 hybrid plants approximately 5 h after DNA extraction, which is a third of the operation time compared with separate PCR reactions for each marker.     

QTL analysis of photoperiod sensitivity in common buckwheat by using markers for expressed sequence tags and photoperiod-sensitivity candidate genes

Photoperiod sensitivity is an important trait related to crop adaptation and ecological breeding in common buckwheat (Fagopyrum esculentum Moench). Although photoperiod sensitivity in this species is thought to be controlled by quantitative trait loci (QTLs), no genes or regions related to photoperiod sensitivity had been identified until now. Here, we identified QTLs controlling photoperiod sensitivity by QTL analysis in a segregating F₄ population (n = 100) derived from a cross of two autogamous lines, 02AL113(Kyukei SC2)LH.self and C0408-0 RP. The F₄ progenies were genotyped with three markers for photoperiod-sensitivity candidate genes, which were identified based on homology to photoperiod-sensitivity genes in Arabidopsis and 76 expressed sequence tag markers. Among the three photoperiod-sensitivity candidate genes (FeCCA1, FeELF3 and FeCOL3) identified in common buckwheat, FeELF3 was associated with photoperiod sensitivity. Two EST regions, Fest_L0606_4 and Fest_L0337_6, were associated with photoperiod sensitivity and explained 20.0% and 14.2% of the phenotypic variation, respectively. For both EST regions, the allele from 02AL113(Kyukei SC2)LH.self led to early flowering. An epistatic interaction was also confirmed between Fest_L0606_4 and Fest_L0337_6. These results demonstrate that photoperiod sensitivity in common buckwheat is controlled by a pathway consisting of photoperiod-sensitivity candidate genes as well as multiple gene action.     

Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus

Genomic imprinting causes parental origin-specific monoallelic gene expression through differential DNA methylation established in the parental germ line. However, the mechanisms underlying how specific sequences are selectively methylated are not fully understood. We have found that the components of the PIWI-interacting RNA (piRNA) pathway are required for de novo methylation of the differentially methylated region (DMR) of the imprinted mouse Rasgrf1 locus, but not other paternally imprinted loci. A retrotransposon sequence within a noncoding RNA spanning the DMR was targeted by piRNAs generated from a different locus. A direct repeat in the DMR, which is required for the methylation and imprinting of Rasgrf1, served as a promoter for this RNA. We propose a model in which piRNAs and a target RNA direct the sequence-specific methylation of Rasgrf1.     

Mutations in dynein link motor neuron degeneration to defects in retrograde transport

Degenerative disorders of motor neurons include a range of progressive fatal diseases such as amyotrophic lateral sclerosis (ALS), spinal-bulbar muscular atrophy (SBMA), and spinal muscular atrophy (SMA). Although the causative genetic alterations are known for some cases, the molecular basis of many SMA and SBMA-like syndromes and most ALS cases is unknown. Here we show that missense point mutations in the cytoplasmic dynein heavy chain result in progressive motor neuron degeneration in heterozygous mice, and in homozygotes this is accompanied by the formation of Lewy-like inclusion bodies, thus resembling key features of human pathology. These mutations exclusively perturb neuron-specific functions of dynein.     

CTLA-4 control over Foxp3+ regulatory T cell function

Naturally occurring Foxp3+CD4+ regulatory T cells (Tregs) are essential for maintaining immunological self-tolerance and immune homeostasis. Here, we show that a specific deficiency of cytotoxic T lymphocyte antigen 4 (CTLA-4) in Tregs results in spontaneous development of systemic lymphoproliferation, fatal T cell-mediated autoimmune disease, and hyperproduction of immunoglobulin E in mice, and it also produces potent tumor immunity. Treg-specific CTLA-4 deficiency impairs in vivo and in vitro suppressive function of Tregs-in particular, Treg-mediated down-regulation of CD80 and CD86 expression on dendritic cells. Thus, natural Tregs may critically require CTLA-4 to suppress immune responses by affecting the potency of antigen-presenting cells to activate other T cells.     

Cytokinin oxidase regulates rice grain production

Most agriculturally important traits are regulated by genes known as quantitative trait loci (QTLs) derived from natural allelic variations. We here show that a QTL that increases grain productivity in rice, Gn1a, is a gene for cytokinin oxidase/dehydrogenase (OsCKX2), an enzyme that degrades the phytohormone cytokinin. Reduced expression of OsCKX2 causes cytokinin accumulation in inflorescence meristems and increases the number of reproductive organs, resulting in enhanced grain yield. QTL pyramiding to combine loci for grain number and plant height in the same genetic background generated lines exhibiting both beneficial traits. These results provide a strategy for tailormade crop improvement.