Quantitative method for specific nucleic acid sequences using competitive polymerase chain reaction with an alternately binding probe

We have developed a simple, cost-effective, and accurate method for the quantification of specific nucleic acid sequences by the combined use of competitive PCR and a sequence-specific fluorescent probe that binds to either the gene of interest (target) or internal standard (competitor), referred to as alternately binding probe (ABProbe). In this method, the target and competitor were coamplified with the ABProbe, and then the fluorescence intensity was measured. The ratio of the target to the competitor can be calculated from the fluorescence intensity of the ABProbe using fluorescence quenching and fluorescence resonance energy transfer, that is, the starting quantity of the target is successfully calculated by end-point fluorescence measurement. Therefore, this method eliminates the complex post-PCR steps and expensive devices for real-time fluorescence measurement. We called this method alternately binding probe competitive PCR (ABC-PCR). We quantified amoA as a model target by ABC-PCR and real-time PCR. By comparison, the sensitivity, accuracy, and precision of ABC-PCR were similar to those of real-time PCR. Moreover, ABC-PCR was able to correctly quantify DNA even when PCR was inhibited by humic acid; therefore, this method will enable accurate DNA quantification for biological samples that contain PCR inhibitors.     

Warm Laser Shock Peening: New developments and process optimization

Laser Shock Peening is a well-known technology able to enhance the fatigue life of mechanical components. Surface residual stress is induced by means of the recoil pressure of an ablated coating in a confining medium interacting with a high power density laser.Warm Laser Shock Peening is obtained by laser peening a pre-warmed workpiece surface: combining the thermal effect of the pre-heated surface and the mechanical phenomenon of the recoil shock pressure, the dynamic aging of the surface microstructure is obtained. Precipitates surrounded by dense dislocation together with residual stress considerable increase the mechanical properties of the workpiece.     

Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops

Although epigenetic modifications have been intensely investigated over the last decade due to their role in crop adaptation to rapid climate change, it is unclear which epigenetic changes are heritable and therefore transmitted to their progeny. The identification of epigenetic marks that are transmitted to the next generations is of primary importance for their use in breeding and for the development of new cultivars with a broad-spectrum of tolerance/resistance to abiotic and biotic stresses. In this review, we discuss general aspects of plant responses to environmental stresses and provide an overview of recent findings on the role of transgenerational epigenetic modifications in crops. In addition, we take the opportunity to describe the aims of EPI-CATCH, an international COST action consortium composed by researchers from 28 countries. The aim of this COST action launched in 2020 is: (1) to define standardized pipelines and methods used in the study of epigenetic mechanisms in plants, (2) update, share, and exchange findings in epigenetic responses to environmental stresses in plants, (3) develop new concepts and frontiers in plant epigenetics and epigenomics, (4) enhance dissemination, communication, and transfer of knowledge in plant epigenetics and epigenomics.     

Opioid antagonist peptides derived from kappa-casein

Opioid antagonists were sought in the fragments of kappa-casein which were obtained by chemical synthesis and enzymic digestion. A synthetic bovine kappa-casein peptide (35-41), Tyr-Pro-Ser-Tyr-Gly-Leu-Asn (casoxin A) showed opioid antagonist activity at 200 microM in the guinea pig ileum assay. A synthetic peptide Tyr-Pro-Tyr-Tyr (casoxin B) which is found in bovine and human kappa-casein, also showed opioid antagonist activity at 100 microM. Another opioid antagonist peptide (casoxin C) was isolated from tryptic digests of bovine kappa-casein by reverse-phase HPLC. The structure of the peptide was Tyr-Ile-Pro-Ile-Gln-Tyr-Val-Leu-Ser-Arg, which corresponded to kappa-casein (25-34). Casoxin C was active at 5 microM in the guinea pig ileum assay. Thus, bovine kappa-casein contains three potential opioid antagonist sequences.     

Bacterial communities in petroleum oil in stockpiles

Bacterial communities in crude-oil samples from Japanese oil stockpiles were investigated by 16S rRNA gene cloning, followed by denaturing gradient gel electrophoresis (DGGE) analysis. 16S rRNA genes were successfully amplified by PCR after isooctane treatment from three kinds of crude-oil sample collected at four oil stockpiles in Japan. DGGE profiles showed that bacteria related to Ochrobactrum anthropi, Burkholderia cepacia, Stenotrophomonas maltophilia, Propionibacterium acnes, and Brevundimonas diminuta were frequently detected in most crude-oil samples. The bacterial communities differed in the sampling time and layer. Among the predominant bacteria detected in the crude oil, only three species were found for bacteria isolated on agar plates and were related to Burkholderia, Stenotrophomonas, and Propionibacterium, while Ochrobactrum sp. could not be isolated although this species seemed to be the most abundant bacterium in crude oil from the DGGE profiles. Using an archaea-specific primer set, methanogens were found in crude-oil sludge but not in crude-oil samples, indicating that methanogens might be involved in sludge formation in oil stockpiles.     

Mechanism for degradation of poly(sodium acrylate) by bacterial consortium no. L7-98

Poly(sodium acrylate) (PSA) can be degraded by consortia of several bacterial species. We investigated the degradation mechanism for PSA (average molecular weight, 2100) by consortium no. L7-98. PSA was used as the sole carbon source in a mineral salt medium. After cultivation, the PSA had a range of molecular weights, including low-molecular-weight compounds, which were purified by gel-permeation and reversed-phase column chromatography. One purified compound, B1, with the molecular weight of 200, had a carbonyl group next to the terminus, according to 1H and 13C nuclear magnetic resonance spectrometry and X-ray analysis of the crystal structure. Two categories of metabolites of PSA were detected in the culture by electrospray ionization mass spectrometry. Results of high-resolution mass spectrometry (HR-MS) suggested that one kind of compounds had a carbonyl group and that the other kind of compounds had an aldehyde group and a double bond. Compounds having the molecular weights of 200 and 272 were rapidly produced from an acrylic acid oligomer with the molecular weight of 258 by resting cells of the consortium. HR-MS showed that a methylene group at the terminal unit was oxidized to a carbonyl group and that the compound with the molecular weight of 200 was compound B1. From these results, we propose that the degradation pathway of PSA involves (i) oxidation of a methylene group to a carbonyl group next to the terminus, (ii) decarboxylation to form an aldehyde group and dehydrogenation to form a double bond between the terminal unit and the next unit, and (iii) oxidation of the aldehyde group to a carboxyl group followed by elimination of an acetic acid.     

A study of mesh deformation methods for magnetic field analysis

In this paper, we describe a study of mesh deformation methods for magnetic field analysis. We propose an efficient method that is a combination of two conventional mesh deformation methods. We numerically estimate the basic performance of the proposed method and conventional methods using three‐dimensional mesh models for magnetic field analysis. We highlight the advantages of the proposed method with respect to its robustness and computational cost. © 2011 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.     

Extractive solubilization, structural change, and functional conversion of cytochrome c in ionic liquids via crown ether complexation

This article reports on the extraction behavior of heme proteins from an aqueous phase into ionic liquids (ILs) with dicyclohexano-18-crown-6 (DCH18C6), and the structure-function relationship of cytochrome c (Cyt-c) dissolved in ILs. We have found that DCH18C6 enables transfer of Lys-rich proteins into ILs via supramolecular complexation. The hydrophobicity and functional groups of ILs have a great influence on protein partitioning, and a hydroxyl group-containing IL with DCH18C6 is capable of the quantitative partitioning of Cyt-c. On the other hand, protein transfer using conventional organic solvents is negligibly small. UV-visible, CD, and resonance Raman spectroscopic characterizations indicate that the sixth ligand Met 80 in the heme group of the Cyt-c-DCH18C6 complex in IL is replaced by other amino acid residues of the peptide chain and that a non-natural, six-coordinate, low-spin ferric heme structure is induced in IL. Solubilization of Cyt-c in IL causes the environmental change of the heme vicinity of Cyt-c, which triggers the functional conversion of Cyt-c from an electron-transfer protein to peroxidase. The Cyt-c-DCH18C6 complex in IL provides remarkably high peroxidase activity compared with native Cyt-c, because of enhancement of the affinity for H2O2.     

Random Forest classification model of basal stem rot disease caused by Ganoderma boninense in oil palm plantations

Ganoderma boninense is a fungus that causes basal stem rot (BSR) disease in oil palm plantations. BSR is a major disease in oil palm plantations in both Indonesia and Malaysia. There is no effective treatment for curing BSR; current treatments only prolong the life of oil palms. One strategy to control BSR is early detection of G. boninense infection. Based on the infection symptoms, many researchers have applied remote-sensing techniques for early detection and mapping of BSR disease in oil palms. The main objectives of this article were to evaluate the potential of machine-learning models for predicting BSR disease in oil palm plantations and to produce maps of the distribution of BSR disease. QuickBird imagery archived on 4 August 2008 was applied in three classifier models: Support Vector Machine, Random Forest (RF), and classification and regression tree models The RF model was best at predicting, classifying, and mapping oil palm BSR in terms of overall accuracy (OA), producer accuracy, user accuracy, and kappa value. Using 75% of the data for training and 25% for testing, the RF classifier model achieved 91% OA. In addition, this model separated the healthy and unhealthy oil palms in the study sites into 37,617 (75%) and 12,320 (25%) individuals, respectively.