Quantum state engineering and precision metrology using state-insensitive light traps

Precision metrology and quantum measurement often demand that matter be prepared in well-defined quantum states for both internal and external degrees of freedom. Laser-cooled neutral atoms localized in a deeply confining optical potential satisfy this requirement. With an appropriate choice of wavelength and polarization for the optical trap, two electronic states of an atom can experience the same trapping potential, permitting coherent control of electronic transitions independent of the atomic center-of-mass motion. Here, we review a number of recent experiments that use this approach to investigate precision quantum metrology for optical atomic clocks and coherent control of optical interactions of single atoms and photons within the context of cavity quantum electrodynamics. We also provide a brief survey of promising prospects for future work.     

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.     

Preparation of phytate-removed deamidated soybean globulins by ion exchangers and characterization of their calcium-binding ability.

Phytate-removed deamidated soybean globulins were prepared using ion-exchange resins to provide them with a functional property to enhance calcium absorption in the body. The phosphorus level was reduced from 45 to 20 micromol/g using 0.05 g/mL of AE-4, an anion-exchange resin with a (2-hydroxyethyl)dimethylammonium group, in 0.2% soybean globulin solution for 1 h at 4 degrees C, and 90-92% of the phosphorus in defatted soybeans could be removed. As for deamidation, CE-4, a cation-exchange resin of the carboxylate type, showed a much higher deamidation activity than CE-1 and CE-2, cation-exchange resins of the sulfonate type. No peptide bond hydrolysis was observed for any cation-exchange resin treated at 4 degrees C. There was no significant difference in the amount of acid amide deamidated at temperatures between 4 and 50 degrees C. The deamidation level was able to increase to 73% using 0.10 g/mL of CE-4 in a 0.2% soybean globulin solution for 6 h at 4 degrees C. The amount of calcium bound to the soybean globulins decreased with removal of the phytate but increased with deamidation.     

Detection of Mycoplasma hyopneumoniae in lung and nasal swab samples from pigs by nested PCR and culture methods

We examined nasal swab and lung homogenate samples collected from pigs experimentally and naturally infected with Mycoplasma hyopneumoniae for the detection of M. hyopneumoniae by the nested PCR (nPCR) and culture methods. In the 23 experimentally infected pigs, M. hyopneumoniae was commonly detected in nasal swabs by the nPCR and culture methods at 4 weeks after inoculation, and there was a significant correlation (P<0.01) between the titers of viable organisms in nasal swabs and in lung homogenates in the experimentally inoculated pigs. In the naturally infected pigs, on the other hand, discrepancies in detection were found between nasal swab and lung homogenate samples in 17 of 36 cases, although the presence of gross lung lesions correlated relatively well with the detection of organisms from the samples. Our results indicated that the diagnosis of mycoplasmal pneumonia by nPCR in individual pigs with nasal swabs is reliable under these experimental conditions. At present, nPCR with nasal swabs should only be used for monitoring the disease status at the herd level under field conditions.     

Porcine MHC classical class I genes are coordinately expressed in superantigen-activated mononuclear cells

The expression of the major histocompatibility complex (MHC) classical class I genes is important for the adaptive immune response to target virus-infected cells and cancer cells. The up-regulation of the MHC is achieved by hormonal/cytokine signals including IFN-γ-inducible elements. The swine leukocyte antigen (SLA), the MHC class I region of pigs, consists of the duplicated classical class I genes, SLA-1, SLA-2 and SLA-3, but the molecular mechanisms involved in their up-regulation after T cell stimulation have not been fully elucidated. In order to better understand some of the putative regulatory mechanisms of SLA class I gene expression in activated T cells, we examined the coordinated expression of the SLA classical class I, IFN-γ and interferon regulatory factor-1 (IRF-1) genes in the peripheral blood mononuclear cells (PBMCs) of SLA homozygous Clawn miniature swine stimulated for 72h with either IFN-γ or an enterotoxin produced by Staphylococcus aureus. This enterotoxin, toxic shock syndrome-1 (TSST-1), is known to act as a superantigen (sAG) to activate the T cells in various vertebrate species. We showed by using mAbs and flow cytometry that the CD4(+)CD25(+) cell number of swine PBMCs was also increased by TSST-1 and to a lesser degree by IFN-γ. Time course analyses of the expression of the IFN-γ, IRF-1 and the three classical class I genes, SLA-1, SLA-2, and SLA-3, in PBMCs by quantitative real-time PCR revealed a transitory response to TSST-1 or IFN-γ stimulation. The IFN-γ mRNA levels in the PBMCs were continuously up-regulated over the first 48h by TSST-1 or IFN-γ. In contrast, SLA class I expression moderately increased at 24h and then decreased to a baseline level or less at 72h of IFN-γ or TSST-1 stimulation. The three classical SLA class I genes showed similar expression kinetics, although SLA-3 mRNA level was consistently lower than those of SLA-1 and -2. The expression of IRF-1, a modulator of SLA expression, showed similar kinetics to those of the three classical SLA class I genes. The expression profiles detected by flow cytometry of the SLA molecules on the cell surface of PBMCs were maintained at a consistently high level during cell stimulation with either TSST-1 or IFN-γ, which was distinct from the kinetics of mRNA expression. These results showed that miniature swine SLA class I mRNA expression was effectively and equally up-regulated among the three loci and coordinately with IRF-1 gene expression after stimulation of T cell activation by sAG or IFN-γ.     

Reliability in somatic cell count measurement of clinical mastitis milk using DeLaval cell counter

Somatic cell counts (SCC) measurements are typically performed using quantitative methods, such as the Breed method (Breed) and the Fossomatic method (FSCC). The DeLaval cell counter (DCC) developed recently is a quantitative somatic cell counter with a low initial cost and superior portability. However, since the DCC was specifically developed for measuring SCC of ≤ 4 × 10⁶ cells/mL milk from bulk tanks or individual cows, its reliability for estimating SCC that exceed this concentration has not yet been clarified. This study therefore examined whether it is possible to accurately measure SCC by diluting milk samples with initial SCC of 4 × 10⁶ cells/mL, as seen in clinical mastitis milk. We collected milk samples from 99 quarters of 99 Holstein cows with clinical mastitis. These milk samples were diluted 10‐fold with saline and thoroughly mixed before performing SCC measurement with the DCC. The correlation coefficients of SCC measured by the FSCC, Breed and DCC methods indicated strong correlations between each pair of methods. The findings showed that DCC can be used to identify bovine clinical mastitis milk and is useful as a quantitative SCC measurement device on farm sites.     

Phenotypic and functional analysis of bovine peripheral blood dendritic cells before parturition by a novel purification method

Dendritic cells (DCs) are specialized antigen presenting cells specializing in antigen uptake and processing, and play an important role in the innate and adaptive immune response. A subset of bovine peripheral blood DCs was identified as CD172a⁺/CD11c⁺/MHC (major histocompatibility complex) class II⁺ cells. Although DCs are identified at 0.1%–0.7% of peripheral blood mononuclear cells (PBMC), the phenotype and function of DCs remain poorly understood with regard to maintaining tolerance during the pregnancy. All cattle used in this study were 1 month before parturition. We have established a novel method for the purification of DCs from PBMC using magnetic‐activated cell sorting, and purified the CD172a⁺/CD11c⁺ DCs, with high expression of MHC class II and CD40, at 84.8% purity. There were individual differences in the expressions of CD205 and co‐stimulatory molecules CD80 and CD86 on DCs. There were positive correlations between expression of cytokine and co‐stimulatory molecules in DCs, and the DCs maintained their immune tolerance, evidenced by their low expressions of the co‐stimulatory molecules and cytokine production. These results suggest that before parturition a half of DCs may be immature and tend to maintain tolerance based on the low cytokine production, and the other DCs with high co‐stimulatory molecules may already have the ability of modulating the T‐cell linage.     

Drought-induced root plasticity of two upland NERICA varieties under conditions with contrasting soil depth characteristics

To identify differences in root plasticity patterns of two upland New Rice for Africa (NERICA) varieties, NERICA 1 and 4, in response to drought under conditions with contrasting soil profile characteristics, soil moisture gradients were imposed using a sloping bed system with depths ranging 30–65 cm and a line-source sprinkler system with a uniformly shallow soil layer of 20 cm depth. Varietal differences in shoot and root growths were identified only under moderate drought conditions, 11–18% v/v soil moisture content. Further, under moderate drought soil conditions where roots could penetrate into the deep soil layer, deep root development was greater in NERICA 4 than in NERICA 1, which contributed to maintaining dry matter production. However, under soil conditions with underground impediment to deep root development, higher shoot dry weight was noted for NERICA 1 than for NERICA 4 at 11–18% v/v soil moisture content, which was attributed to increased lateral root development in the shallow soil layer in NERICA 1. Enhanced lateral root development in the 0–20-cm soil layer was identified in NERICA 1 even under soil conditions without an impediment to deep root development; however, this did not contribute to maintaining dry matter production in upland rice. Thus, we show different root developmental traits associated with drought avoidance in the two NERICA varieties, and that desirable root traits for upland rice cultivation vary depending on the target soil environment, such as the distribution of soil moisture and root penetration resistance.     

Impact of land use on nitrogen concentration in groundwater and river water

Abstract

The aim of this study was to evaluate the impact of land use on nitrate nitrogen (NO₃-N) in shallow groundwater (G-N) and total nitrogen (N) in river water (R-N). The study area consisted of 26 watersheds (1342 km²) covering 72% of Kagawa Prefecture in Japan. We estimated G-N specific concentrations, which showed the magnitude of the upland fields, paddy fields, forests and urban land-use contributions to watershed-mean G-N. G-N specific concentrations were gained as partial regression coefficients using a multiple regression analysis of the watershed-mean G-N concentrations and the land-use ratios in each of the 26 watersheds. The results showed that the G-N specific concentration, which was gained as the partial regression coefficient for the multiple regression analysis, was 15.2 mg L^?1, 10.3 mg L^?1, 2.3 mg L^?1 and 2.5 mg L^?1 for the upland fields, paddy fields, forests and urban land-use types, respectively. R-N pollution load runoff to the river mouth was calculated by multiplying R-N specific concentration (previously reported) by river flow at the river mouth. Similarly, G-N pollution load arrival to groundwater was calculated by multiplying G-N specific concentration by the groundwater flow. The R-N pollution load runoff was 19.3 kg ha^?1 y^?1, 7.7 kg ha^?1 y^?1, 1.7 kg ha^?1 y^?1 and 7.6 kg ha^?1 y^?1, while the G-N pollution load arrival was 7.3 kg ha^?1 y^?1, 5.0 kg ha^?1 y^?1, 1.1 kg ha^?1 y^?1 and 1.2 kg ha^?1 y^?1, for upland fields, paddy fields, forests and urban areas, respectively. These results showed that the N in river water and groundwater was derived mainly from runoff and leaching from croplands. Therefore, the relationships between watershed-mean non-absorbed, applied nitrogen (NAA-N: nitrogen applied to cropland via fertilizer and manure without being absorbed by crops), R-N concentration and watershed-mean G-N concentration were investigated. A curvilinear correlation was observed between NAA-N and R-N concentrations (r² = 0.68) except for one small, high-density, urban watershed, and a weak linear correlation was observed between NAA-N and G-N concentrations (r² = 0.42).