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Efficient plant breeding plays a significant role in increasing crop yields and attaining food security under climate change. Screening new cultivars through yield trials in multi-environments has improved crop yields, but the accumulated data from these trials has not been effectively upcycled. We propose a simple method that quantifies cultivar-specific productivity characteristics using two regression coefficients: yield-ability (β) and yield-plasticity (α). The recorded yields of each cultivar are expressed as a unique linear regression in response to the theoretical potential yield (Yp) calculated by a weather-driven crop growth model, called as the "YpCGM method". We apply this to 72510 independent datasets from yield trials of rice that used 237 cultivars measured at 110 locations in Japan over 38 years. The YpCGM method can upcycle accumulated yield data for use in genetic-gain analysis and genome-wide-association studies to guide future breeding programs for developing new cultivars suitable for the world's changing climate. Presentation of a methodology for integrating an empirical crop model and linear regression to characterize yield potential and yield plasticity of rice cultivars. [ABSTRACT FROM AUTHOR]

We constructed recombinant inbred lines (RILs) between a Japanese and a Taiwanese landrace of foxtail millet and employed next-generation sequencing, such as flexible ddRAD-seq and Nanopore sequencing to identify the candidate genes involved in the crop evolution of foxtail millet. We successfully constructed a linkage map using flexible ddRAD-seq with parents and RILs and detected major QTLs for each of three traits: leaf sheath colors, spikelet-tipped bristles (stb), and days to heading (DTH). (1) For leaf sheath colors, we identified the C gene on chromosome IV. (2) We identified a homeobox (HOX14) gene for stb on chromosome II, which shows homology with HvVrs1 in barley. (3) Finally, we identified a QTL with a large effect on DTH on chromosome II. A parent of the RILs from Taiwan and Yugu1 had a Harbinger-like TE in intron 3 of this gene. We also investigated the geographical distribution of the TE insertion type of this gene and found that the insertion type is distributed in the northern part of East Asia and intensively in South and Southeast Asia, suggesting that loss/reduction of function of this gene plays an important role in spreading into the northern part of East Asia and subtropical and tropical zones. [ABSTRACT FROM AUTHOR]

We constructed recombinant inbred lines (RILs) between a Japanese and a Taiwanese landrace of foxtail millet and employed next-generation sequencing, such as flexible ddRAD-seq and Nanopore sequencing to identify the candidate genes involved in the crop evolution of foxtail millet. We successfully constructed a linkage map using flexible ddRAD-seq with parents and RILs and detected major QTLs for each of three traits: leaf sheath colors, spikelet-tipped bristles (stb), and days to heading (DTH). (1) For leaf sheath colors, we identified the C gene on chromosome IV. (2) We identified a homeobox (HOX14) gene for stb on chromosome II, which shows homology with HvVrs1 in barley. (3) Finally, we identified a QTL with a large effect on DTH on chromosome II. A parent of the RILs from Taiwan and Yugu1 had a Harbinger-like TE in intron 3 of this gene. We also investigated the geographical distribution of the TE insertion type of this gene and found that the insertion type is distributed in the northern part of East Asia and intensively in South and Southeast Asia, suggesting that loss/reduction of function of this gene plays an important role in spreading into the northern part of East Asia and subtropical and tropical zones. [ABSTRACT FROM AUTHOR]

Lysosomal phospholipase A2 (LPLA2) is a key enzyme involved in the homeostasis of cellular phospholipids. Recently, LPLA2 was reported to preferentially degrade some truncated oxidized phospholipids at the sn -1 position. A commercially available, truncated oxidized phospholipid conjugated with a fluorescent dye, 1-palmitoyl-2-glutaroyl- sn -glycero-3-phosphoethanolamine- N -[4-(dipyrrometheneboron difluoride) butanoyl] (PGPE-BODIPY), was used to develop a specific assay for this enzyme. When recombinant mouse LPLA2 was incubated with liposomes consisting of 1,2- O -octadecyl- sn -glycero-3-phosphocholine/PGPE-BODIPY under acidic conditions, PGPE-BODIPY was converted to palmitic acid and a polar BODIPY-product. After phase partitioning by chloroform/methanol, the polar BODIPY-product was recovered in the aqueous phase and identified as 1-lyso-PGPE-BODIPY. The formation of 1-lyso-PGPE-BODIPY was quantitatively determined by fluorescent measurements. The Km and Vmax values of the recombinant LPLA2 for PGPE-BODIPY were 5.64 μM and 20.7 μmol/min/mg protein, respectively. Detectable activity against PGPE-BODIPY was present in LPLA2 deficient mouse sera, but the deacylase activity was completely suppressed by treatment with 4-(2-aminoethyl)benzenesulfonyl fluoride (AEBSF). AEBSF had no effect on LPLA2 activity. The LPLA2 activity of mouse serum pre-treated with AEBSF was specifically and quantitatively determined by this assay method. The PGPE-BODIPY and AEBSF based LPLA2 assay is convenient and can be used to measure LPLA2 activity in a variety of biological specimens. [ABSTRACT FROM AUTHOR]

Aim: The lysosomal enzyme in the anterior chamber has a crucial role in the digestion of the insoluble materials in the aqueous humor (AH). The dysfunction of AH filtration in the trabecular meshwork (TM) causes increasing AH outflow resistance in the TM. Those insoluble objects, including phospholipids, should be digested in the TM for normal outflow. The present study was conducted to explore the involvement of lysosomal phospholipase A2 (LPLA2), a phospholipid-degrading enzyme, of the AH in glaucoma using clinical AH specimens. Materials and Methods: One hundred and twenty-five AH specimens were collected from patients. The measurement of LPLA2 activity in the AH was carried out using liposomes consisting of phosphatidylglycerol andN-acetylsphingosine (NAS). The correlation between the LPLA2 activity in the AH and ocular diseases was investigated. Results: The human AH showed both transacylation of NAS and the release of fatty acids under acidic conditions but not at a neutral pH, which is consistent with the known properties of LPLA2. The LPLA2 activity in the AH was not affected by age or systemic disease. A comparison between ocular diseases showed that the AH specimens obtained from patients with glaucoma had significantly higher LPLA2 activity than the other ocular disease groups. Discussion: The present findings suggest that the ascended level of LPLA2 activity in the AH of glaucoma patients is associated with the development of glaucoma. [ABSTRACT FROM AUTHOR]

The significance of plastid terminal oxidase ( PTOX) in phytoene desaturation and chloroplast function has been demonstrated using PTOX-deficient mutants, particularly in Arabidopsis. However, studies on its role in monocots are lacking. Here, we report cloning and characterization of the rice ( Oryza sativa) PTOX1 gene., Using Ecotype Targeting Induced Local Lesions IN Genomes (Eco TILLING) and TILLING as forward genetic tools, we identified the causative mutation of an EMS mutant characterized by excessive tillering, semi-dwarfism and leaf variegation that corresponded to the PTOX1 gene., The tillering and semi-dwarf phenotypes of the ptox1 mutant are similar to phenotypes of known strigolactone ( SL)-related rice mutants, and both phenotypic traits could be rescued by application of the synthetic SL GR24. The ptox1 mutant accumulated phytoene in white leaf sectors with a corresponding deficiency in β-carotene, consistent with the expected function of PTOX1 in promoting phytoene desaturase activity. There was also no accumulation of the carotenoid-derived SL ent-2′- epi-5-deoxystrigol in root exudates. Elevated concentrations of auxin were detected in the mutant, supporting previous observations that SL interaction with auxin is important in shoot branching control., Our results demonstrate that PTOX1 is required for both carotenoid and SL synthesis resulting in SL-deficient phenotypes in rice. [ABSTRACT FROM AUTHOR]

Abstract: This study was conducted to elucidate pathophysiological roles of the lysosomal phospholipase A2 (LPLA2), a phospholipid-degrading enzyme, of the aqueous humor (AH) in uveitis using an animal model and clinical specimens. Endotoxin-induced uveitis (EIU) was induced by subcutaneous injections of lipopolysaccharide from Escherichia coli to seven-week-old male Lewis rats. Inflammation of the anterior chamber (AC) was evaluated by measurement of the protein concentration of rat AH. The LPLA2 activity in the AH, serum and cerebrospinal fluid obtained from EIU rats was detected using liposomes consisting of 1,2-dioleoylphosphatidylglycerol/N-acetylsphingosine as the substrate under acidic conditions. Immunohistochemical analysis was performed using antibodies against CD11b and LPLA2. Sixty-five human AH specimens, in which 11 eyes had a history of chronic uveitis, were collected during patient cataract surgeries and used to determine LPLA2 activity. The LPLA2 activity in rat AH was significantly increased by EIU induction, and was correlated to the extent of inflammation in the AC. By contrast, the LPLA2 activity in rat serum or cerebrospinal fluid was not influenced by EIU induction. According to the immunohistochemistry, LPLA2 was found in CD11b positive cells in the AC of the EIU rats. In the clinical specimens, the AH obtained from the patients with a history of uveitis possessed significantly higher LPLA2 activity than that from the senile patients with cataract but without other ocular diseases. These results demonstrate that the LPLA2 activity in the AH is augmented with the inflammation in the AC and suggest that the LPLA2 in the AH participates in the inflammation process in the AC. [Copyright &y& Elsevier]

The majority of agronomically important crop traits are quantitative, meaning that they are controlled by multiple genes each with a small effect (quantitative trait loci, QTLs). Mapping and isolation of QTLs is important for efficient crop breeding by marker-assisted selection ( MAS) and for a better understanding of the molecular mechanisms underlying the traits. However, since it requires the development and selection of DNA markers for linkage analysis, QTL analysis has been time-consuming and labor-intensive. Here we report the rapid identification of plant QTLs by whole-genome resequencing of DNAs from two populations each composed of 20-50 individuals showing extreme opposite trait values for a given phenotype in a segregating progeny. We propose to name this approach QTL-seq as applied to plant species. We applied QTL-seq to rice recombinant inbred lines and F2 populations and successfully identified QTLs for important agronomic traits, such as partial resistance to the fungal rice blast disease and seedling vigor. Simulation study showed that QTL-seq is able to detect QTLs over wide ranges of experimental variables, and the method can be generally applied in population genomics studies to rapidly identify genomic regions that underwent artificial or natural selective sweeps. [ABSTRACT FROM AUTHOR]

Abstract: There is a strong association between lysosome enzyme deficiencies and monogenic disorders resulting in lysosomal storage disease. Of the more than 75 characterized lysosomal proteins, two thirds are directly linked to inherited diseases of metabolism. Only one lysosomal storage disease, Niemann–Pick disease, is associated with impaired phospholipid metabolism. However, other phospholipases are found in the lysosome but remain poorly characterized. A recent exception is lysosomal phospholipase A2 (group XV phospholipase A2). Although no inherited disorder of lysosomal phospholipid metabolism has yet been associated with a loss of function of this lipase, this enzyme may be a target for an acquired form of lysosomal storage, drug induced phospholipidosis. This article is part of a Special Issue entitled Phospholipids and Phospholipid Metabolism. [Copyright &y& Elsevier]

Abstract: Lysosomal phospholipase A2 (group XV PLA2, LPLA2) is a lysosomal enzyme linked to drug-induced phospholipidosis. We developed phospholipid “smart probes” based on the conversion of a quenched fluorogenic substrate to a fluorescent product. Due to the preference of LPLA2 for phosphatidylglycerol, three fluorogenic phosphatidylglycerols were synthesized. Two fluorogenic phosphatidylglycerols were conjugated with one FAM (fluorescein amidite) group and one DABCYL [4-(4-dimethylaminophenylazo)-benzoyl] group; the third substrate consisted of two FAM groups conjugated at the sn-1 and sn-2 positions. The sn-1 ester linkage was replaced with an amide linkage. 1-FAM-2-DABCYL-PG was degraded by recombinant LPLA2 and mouse serum but not by the serum obtained from LPLA2-deficient mice when 1,2-dioleoyl-PG/1-FAM-2-DABCYL-PG liposomes were used. The formation of 1-FAM-lyso-PG generated from 1-FAM-2-DABCYL-PG in the presence of LPLA2 was quantitatively determined by fluorescent measurements. The 1-FAM-2-DABCYL-PG incorporated into 1,2-dioleoyl-phosphatidylcholine/sulfatide liposomes was used to evaluate the effect of the cationic amphiphilic drugs amiodarone and fluoxetine on LPLA2 activity. The IC50 values of amiodarone and fluoxetine estimated by fluorescent measurement were 10 and 19μM, respectively. These results indicate that 1-FAM-2-DABCYL-PG is a specific substrate for LPLA2 and a useful reagent for the detection of LPLA2 activity from multiple sources. [Copyright &y& Elsevier]

Seedling vigor is among the major determinants of stable stand establishment in direct-seeded rice ( Oryza sativa L.) in temperate regions. Quantitative trait loci (QTL) for seedling vigor were identified using 250 recombinant inbred lines (RILs) derived from a cross between two japonica rice cultivars Kakehashi and Dunghan Shali. Seedling heights measured at 14 days after sowing were 20.3 and 29.4 cm for Kakehashi and Dunghan Shali, respectively. For the RILs, the height ranged from 14.1 to 31.7 cm. Four putative QTLs associated with seedling height were detected. qPHS3- 2, the major QTL that was located on the long arm of chromosome 3, accounted for 26.2 % of the phenotypic variance. Using progeny of the near isogenic lines (NILs) produced by the backcross introduction of a chromosome segment carrying this major QTL into an elite cultivar Iwatekko, we fine-mapped qPHS3- 2 to a 81-kb interval between two markers, ID_CAPS_01 and RM16227. Within this mapped region, we identified the gene OsGA20ox1, which is related to gibberellin (GA) biosynthesis. The relative expression levels of GA20ox1 in seedlings of Dunghan Shali and NILs were higher than that of Iwatekko. Concomitantly, the amount of endogenous active GA was higher in Dunghan Shali and the NILs compared to the level detected in Iwatekko. These results indicate that OsGA20ox1 is a strong candidate gene for major QTL controlling seedling vigor in rice. [ABSTRACT FROM AUTHOR]

The majority of agronomic traits are controlled by multiple genes that cause minor phenotypic effects, making the identification of these genes difficult. Here we introduce MutMap, a method based on whole-genome resequencing of pooled DNA from a segregating population of plants that show a useful phenotype. In MutMap, a mutant is crossed directly to the original wild-type line and then selfed, allowing unequivocal segregation in second filial generation (F2) progeny of subtle phenotypic differences. This approach is particularly amenable to crop species because it minimizes the number of genetic crosses (n = 1 or 0) and mutant F2 progeny that are required. We applied MutMap to seven mutants of a Japanese elite rice cultivar and identified the unique genomic positions most probable to harbor mutations causing pale green leaves and semidwarfism, an agronomically relevant trait. These results show that MutMap can accelerate the genetic improvement of rice and other crop plants. [ABSTRACT FROM AUTHOR]

This paper presents a novel trajectory planning method for a flexible Cartesian robot manipulator in a point-to-point motion. In order to obtain an exact mathematical model, the parameters of the equation of motion are determined from an identification experiment. An artificial neural network is employed to generate the desired base position, and then, a particle swarm optimization technique is used as the learning algorithm, in which the sum of the displacements of the manipulator is chosen as the objective function. We show that the residual vibrations of the manipulator can be suppressed by minimizing the displacement of the manipulator. The effectiveness and validity of the proposed method are demonstrated by comparing the simulation and experimental results. [ABSTRACT FROM PUBLISHER]

Abstract: This study investigates the accuracy of nonlinear vibration analyses of a suspended cable, which possesses quadratic and cubic nonlinearities, with one-to-one internal resonance. To this end, we derive approximate solutions for primary resonance using two different approaches. In the first approach, the method of multiple scales is directly applied to governing equations, which are nonlinear partial differential equations. In the second approach, we first discretize the governing equations by using Galerkin’s procedure and then apply the shooting method. The accuracy of the results obtained by these approaches is confirmed by comparing them with results obtained by the finite difference method. [Copyright &y& Elsevier]

Abstract: For two-dimensional reversed-phase liquid chromatography–gas chromatography (2D RPLC–GC), a specially-designed needle packed with a polymer-coated fibrous stationary phase was introduced as a novel interface. The bundle of synthetic fibers coated with polydimethylsiloxane (PDMS) was packed into the head section of the needle, and served as the extraction medium. Using the post-column dilution of the LC eluent by water and subsequent extraction with the needle interface, the analyte was successfully concentrated to the PDMS phase on the fibrous support in the needle. The concentrated analytes were directly injected to GC system by inserting the needle to a heated GC injector. 2D separations of aliphatic and aromatic hydrocarbons, and also kerosene-extract were performed with the off-line RPLC–GC system interfaced by the needle extractor. The results suggested that the fiber-packed needle interface could be one of the simple and effective approaches to develop an on-line coupled LC–GC system. [Copyright &y& Elsevier]

Abstract: In this paper an optimal trajectory planning technique for suppressing residual vibrations in two-link rigid-flexible manipulators is proposed. In order to obtain an accurate mathematical model, the flexible link is modeled by taking the axial displacement and nonlinear curvature arising from large bending deformation into consideration. The equations of motion of the manipulator are derived using the Lagrangian approach and the assumed modes method. For the trajectory planning, the joint angle of the flexible link is expressed as a cubic spline function, and then the particle swarm optimization algorithm is used to determine the optimal trajectory. The optimal trajectory thus obtained satisfies the minimum vibration condition. By performing numerical simulations, the effectiveness of the proposed trajectory planning technique is verified. [Copyright &y& Elsevier]

This paper investigates one-to-one internal resonance of laminated shallow shells with rigidly clamped edges. It is assumed that the natural frequencies ω 2 and ω 3 of two asymmetric (second and third) vibration modes have the relationship ω 2≈ω 3. The displacements are expressed by using eigenvectors for linear vibration modes calculated by the Ritz method. Applying Galerkin''s procedure to the equation of motion, nonlinear differential equations are derived. By considering the first vibration mode in addition to the two asymmetric vibration modes, quadratic nonlinear terms expressing the interaction between the asymmetric and the first modes appear in the differential equations. Shooting method is used to obtain the steady-state response when the driving frequency Ω is near ω 2. The dynamic characteristics of the shells with the internal resonance are discussed. [Copyright &y& Elsevier]

Since the 1900s, proximate analysis has been the mainstream method of feed analysis. In addition to this method, the detergent method, which was developed in the 1960s, has become a popular methodology for feed composition and nutritive value evaluation. One fundamental characteristic of this method is that fractionated carbohydrates are classified as either the fiber of feed in terms of neutral detergent fiber (NDF) or non-fiber carbohydrates (NFC), which include sugar and starch. Meanwhile, in Japan another method, the enzymatic method, has been developed. The characteristic of this method is that fractionated carbohydrates are classified as either the fiber contained in feed in terms of organic cell wall (OCW) or nitrogen-cell wall free extracts (NCWFE, non-structural carbohydrates). One important fraction of feed nutrition is digestible carbohydrates, which are the sum of digestible non-structural carbohydrates and the digestible fiber. The content of digestible non-structural carbohydrates is obtained based on the nutritional uniformity of NFC and NCWFE in the detergent and enzymatic method, individually. The digestible fiber is obtained in the detergent method from the potential digestibility of NDF and lignifications, and obtained in the enzymatic method from the highly digestible organic a fraction and the poorly digestible organic b (Ob) fraction. The amount of digestible carbohydrates obtained by these two methods of analysis is sometimes significantly different. The Ob fraction obtained by the enzymatic method shows a significant negative correlation, and a 1% increase in the Ob content of hay dry matter suppresses the dry matter intake of dairy cattle by 0.17 kg. [ABSTRACT FROM AUTHOR]

Abstract: This paper examines the validity of non-linear vibration analyses of continuous systems with quadratic and cubic non-linearities. As an example, we treat a hinged–hinged Euler–Bernoulli beam resting on a non-linear elastic foundation with distributed quadratic and cubic non-linearities, and investigate the primary and subharmonic resonances, in which and are the driving and natural frequencies, respectively. The steady-state responses are found by using two different approaches. In the first approach, the method of multiple scales is applied directly to the governing equation that is a non-linear partial differential equation. In the second approach, we discretize the governing equation by using Galerkin''s procedure, and then apply the shooting method to the obtained ordinary differential equations. In order to check the validity of the solutions obtained by the two approaches, they are compared with the solutions obtained numerically by the finite difference method. [Copyright &y& Elsevier]

Lung surfactant is the surface-active agent comprised of phospholipids and proteins that lines pulmonary alveoli. Surfactant stabilizes the alveolar volume by reducing surface tension. Previously, we identified a lysosomal phospholipase A2, termed LPLA2, with specificity toward phosphatidylcholine and phosphatidylethanolamine. The phospholipase is localized to lysosomes, is calcium-independent, has an acidic pH optimum, and transacylates ceramide. Here, we demonstrate that LPLA2 is selectively expressed in alveolar macrophages but not in peritoneal macrophages, peripheral blood monocytes, or other tissues. Other macrophage-associated phospholipase A2s do not show a comparable distribution. LPLA2 is of high specific activity and recognizes disaturated phosphatidylcholine as a substrate. The lysosomal phospholipase A2 activity is six times lower in alveolar macrophages from mice with a targeted deletion of the granulocyte macrophage colonystimulating factor (GM-CSF), a model of impaired surfactant catabolism, compared with those from wild-type mice. However, LPLA2 activity and protein levels are measured in GM-CSF null mice in which GM-CSF is expressed as a transgene under the control of the surfactant protein C promoter. Thus LPLA2 may be a major enzyme of pulmonary surfactant phospholipid degradation by alveolar macrophages and may be deficient in disorders of surfactant metabolism. [ABSTRACT FROM AUTHOR]

Glycosphingolipid depletion in Fabry disease lymphoblasts with potent inhibitors of glucosylceramide synthase. Background. Fabry disease is an inherited X-linked disorder resulting in the loss of activity of the lysosomal hydrolase α-galactosidase A and causing the clinical manifestations of renal failure, cerebral vascular disease, and myocardial infarction. The phenotypic expression of this disorder is manifest by the accumulation of glycosphingolipids containing α-galactosyl linkages, most prominently globotriaosylceramide. Methods. Based on quantitative structure activity studies, we recently reported two newly designed glucosylceramide synthase inhibitors based on 1-phenyl-2-palmitoylamino-3-pyrrolidino-1-propanol (P4). These inhibitors, 4′-hydroxy-P4 and ethylenedioxy-P4, were evaluated for their ability to deplete globotriaosylceramide and other glucosylceramide-based lipids in Fabry lymphocytes and were compared with N-butyldeoxynojirimycin, another reported glucosylceramide synthase inhibitor. Results. Concentrations as low as 10 nmol/L of 4′-hydroxy-P4 and ethylenedioxy-P4 resulted in 70 and 80% depletion, respectively, of globotriaosylceramide, with maximal depletion occurring at three days of treatment. There was no impairment of cell growth. In contrast, N-butyldeoxynojirimycin only minimally lowered globotriaosylceramide levels, even at concentrations as high as 10 μmol/L. Globotriaosylceramide depletion was confirmed by the loss of binding of FITC-conjugated verotoxin B subunit to the lymphoblasts. Conclusions. These findings suggest that selective glucosylceramide synthase inhibitors are highly effective in the depletion of globotriaosylceramide from Fabry cell lines. We suggest that these compounds have potential therapeutic utility in the treatment of Fabry disease. [ABSTRACT FROM AUTHOR]

Recent studies have identified a potential role for glucosylceramide (GlcCer) in growth promotion and hormonal signalling. In an effort to demonstrate a growth-promoting activity of GlcCer, we prepared a GlcCer having a short-chain acid (octanoyl), in the belief that this glycolipid could be absorbed more readily and more uniformly by cultured cells. By using a mixture of two specific lecithins, dioleoylglycerophosphocholine and 1-stearoyl-2-palmitoylglycerophosphocholine, we were able to prepare dispersions containing a high molar proportion of the GlcCer and the related ceramide, octanoyl sphingosine. Unexpectedly, both sphingolipids inhibited protein and DNA synthesis in Madin-Darby canine kidney cells and produced large increases in the levels of the natural lipids, GlcCer, ceramide, free sphingosine, and an amine that may be glucosylsphingosine (GlcSph). Decreases were seen in the level of sphingomyelin and the proportion of protein kinase C in the cell membranes. The level of lactosylceramide was diminished by octanoyl GlcCer but elevated considerably by octanoyl sphingosine. Diacylglycerols were increased by the lecithins in the liposomes, but the exogenous sphingolipids had no effect. Octanoyl sphingosine labeled in the sphingoid base yielded labeled GlcCer and sphingomyelin labeled in both long-chain and very-long-chain fatty acid families, as well as the octanoyl version. The two families of ceramides, however, had relatively little radioactivity. Some of these changes are attributed to rapid hydrolysis of the added lipids with the formation, particularly from the ceramide, of sphingosine and its anabolic metabolite, GlcSph. Several observations support the idea that the octanoyl sphingosine inhibited the phosphocholinetransferase that synthesizes sphingomyelin while the octanoyl GlcCer inhibited GlcCer β-glucosidase and GlcCer galactosyltransferase. The use of unnatural short-chain lipids in the study of cell growth and other phenomena may result in unexpected changes in related metabolites and the findings from such experiments should therefore be interpreted cautiously. [ABSTRACT FROM AUTHOR]

Side-chain oxysterols produced from cholesterol either enzymatically or non-enzymatically show various bioactivities. Lecithin-cholesterol acyltransferase (LCAT) esterifies the C3-hydroxyl group of these sterols as well as cholesterol. Lysosomal phospholipase A2 (LPLA2) is related to LCAT but does not catalyze esterification of cholesterol. First, esterification of side-chain oxysterols by LPLA2 was investigated using recombinant mouse LPLA2 and dioleoyl-PC/sulfatide/oxysterol liposomes under acidic conditions. TLC and LC-MS/MS showed that the C3 and C27-hydroxyl groups of 27-hydroxycholesterol could be individually esterified by LPLA2 to form a monoester with the C27-hydroxyl preference. Cholesterol did not inhibit this reaction. Also, LPLA2 esterified other side-chain oxysterols. Their esterifications by mouse serum containing LCAT supported the idea that their esterifications by LPLA2 occur at the C3-hydroxyl group. N -acetylsphingosine (NAS) acting as an acyl acceptor in LPLA2 transacylation inhibited the side-chain oxysterol esterification by LPLA2. This suggests a competition between hydroxycholesterol and NAS on the acyl-LPLA2 intermediate formed during the reaction. Raising cationic amphiphilic drug concentration or ionic strength in the reaction mixture evoked a reduction of the side-chain oxysterol esterification by LPLA2. This indicates that the esterification could progress via an interfacial interaction of LPLA2 with the lipid membrane surface through an electrostatic interaction. The docking model of acyl-LPLA2 intermediate and side-chain oxysterol provided new insight to elucidate the transacylation mechanism of sterols by LPLA2. Finally, exogenous 25-hydroxycholesterol esterification within alveolar macrophages prepared from wild-type mice was significantly higher than that from LPLA2 deficient mice. This suggests that there is an esterification pathway of side-chain oxysterols via LPLA2. • LPLA2 catalyzes the esterification of side-chain oxysterols but not cholesterol. • The side-chain hydroxyl group plays a key role in the esterification by LPLA2. • The esterification of side-chain oxysterols by LPLA2 may be an alternative pathway. [ABSTRACT FROM AUTHOR]

Direct seeding is employed to circumvent the labor-intensive process of rice (Oryza sativa) transplantation, but this approach requires varieties with vigorous low-temperature germination (LTG) when sown in cold climates. To investigate the genetic basis of LTG, we identified the quantitative trait locus (QTL) qLTG11 from rice variety Arroz da Terra, which shows rapid seed germination at lower temperatures, using QTL-seq. We delineated the candidate region to a 52-kb interval containing GENERAL REGULATORY FACTOR14h (GF14h) gene, which is expressed during seed germination. The Arroz da Terra GF14h allele encodes functional GF14h, whereas Japanese rice variety Hitomebore harbors a 4-bp deletion in the coding region. Knocking out functional GF14h in a near-isogenic line (NIL) carrying the Arroz da Terra allele decreased LTG, whereas overexpressing functional GF14h in Hitomebore increased LTG, indicating that GF14h is the causal gene behind qLTG11. Analysis of numerous Japanese rice accessions revealed that the functional GF14h allele was lost from popular varieties during modern breeding. We generated a NIL in the Hitomebore background carrying a 172-kb genomic fragment from Arroz da Terra including GF14h. The NIL showed superior LTG compared to Hitomebore, with otherwise comparable agronomic traits. The functional GF14h allele from Arroz da Terra represents a valuable resource for direct seeding in cold regions. Author summary: Rice serves as a fundamental crop sustaining over half of the global population. With the rapid growth of the world's population, it will become increasingly important to improve rice productivity. On the other hand, the aging of rice farmers in Japan has resulted in a constant labor shortage. To address this, direct seeding, in which seeds are sown directly in rice fields without going through the most labor-intensive part of the rice cultivation process, i.e., seedling production and transplanting, has been recommended. However, prevalent elite rice varieties are known to be unsuitable for direct seeding due to their poor seed germination ability under low-temperature conditions. In this study, we show for the first time that GF14h gene from the Portuguese variety Arroz da Terra improves seed germination at low temperatures (LTG). In addition, a novel cross-bred line was generated by introducing the GF14h-containing genomic segment from Arroz da Terra into Hitomebore, a widely cultivated variety in northern Japan. This line is expected to be used as a pre-breeding material to enhance LTG. This study will provide a genetic basis for LTG and contribute to basic and applied research progress. [ABSTRACT FROM AUTHOR]

We hypothesised that mixing of rice lines with different maturity dates can improve the productivity per unit area while improving lodging resistance on account of the heterogeneous canopy. To test this hypothesis, we grew two lines, wild-type (WT) and early-maturing (EML), of each of two cultivars (Koshihikari and Hitomebore) in monoculture plantings and within-cultivar mixed plantings, with WT and EML plants alternating every one or two rows, over 2 years in northern Japan. The mixtures formed a canopy with different heading dates (5–7 days earlier than WT in Hitomebore and 14–19 days earlier in Koshihikari). For Koshihikari, the mixture increased grain yield per plant in the WT by 18–33%, but decreased it in the EML by 19–22%; however, for Hitomebore, there was no significant difference. Consequently, grain yield per unit area did not change relative to the mean of monocultures of WT and EML in either cultivar. Lodging tolerance improved significantly in the mixtures, especially for Koshihikari. Thus, mixing rice lines with different maturity dates improved lodging tolerance without decreasing productivity. As an alternative to monocultures, cultivar mixtures can reduce the risk of yield losses caused by climate change; hence, we studied mixed canopies of wild-type and early-maturing accessions of two cultivars of rice. There was no significant yield difference per unit area between the monoculture and mixed culture, but lodging tolerance increased in the mixed canopy. Our mixture of accessions with different maturity dates improved lodging tolerance of the mixed planting with no effect on productivity. [ABSTRACT FROM AUTHOR]

Purpose: Most complex gangliosides in vertebrates are formed from ganglioside GM3. GM3 deficiency in humans can result in epilepsy and visual impairment. To investigate whether a deficiency of GM3 is involved in visual function, ST3GAL5−/− mice with mutations in the ST3GAL5 gene-coded GM3 synthase were employed. Materials and Methods: Sixty mice were employed in this study. The glycosphingolipids of mice retinas were analyzed through high performance thin layer chromatography. The morphology of the optic nerves and retinas were evaluated by hematoxylin and eosin staining and immunohistochemical analysis using an anti-glial fibrillary acidic protein (GFAP) antibody. An electroretinogram (ERG) was applied on the eyes of 4, 9, 12, and 14-month-old mice. Also, visual evoked potential (VEP) was applied on 13-month-old mice. Results: The GM3 in the retinas was detected in ST3GAL5+/+ mice but not ST3GAL5−/− mice. Also, GM1b and GD1α expressions and lactosylceramide accumulation were found in the ST3GAL5−/− mouse retinas. There was no significant difference in GFAP expression in the retinas or optic discs between ST3GAL5+/+ and ST3GAL5−/− mice. Furthermore, the outcome of ERG and VEP analysis showed no disparity between the two strains in 13 and 14-month-old mice. Conclusion: In the eye, neither histopathological abnormalities nor abnormal functions of the retina were found in GM3-deficient mice. Differing from the situation in patients with GM3 deficiency, the lack of GM3 in mice did not lead to optic nerve atrophy. [ABSTRACT FROM AUTHOR]

Purpose: The goal of present study was to elucidate the pathophysiological roles of lysosomal phospholipase A2 (LPLA2) in intraocular pressure (IOP) levels and ocular inflammation. Methods: C57BL/6 (wild-type) and LPLA2-deficient mice with C57BL/6 background were employed. The IOPs were compared between wild-type and LPLA2-deficient mice during their aging, after topical administration of antiglaucoma medications such as travoprost, dorzolamide, or timolol maleate, or after induction of endotoxin-induced uveitis (EIU) using lipopolysaccharide (LPS). Concerning the EIU, ocular inflammation was also evaluated by immunohistochemical analysis by the anti-glial fibrillary acidic protein (GFAP) antibody. Results: The LPLA2-deficient mice showed higher IOP levels than the wild-type mice until 2 months of age (P= 1.60E-06); in older mice there was no difference between the two groups. Significant differences in the IOP changes between groups in young mice were seen after administration of 0.5% timolol (P< 0.05). Upon induction of EIU by LPS, compared with wild-type mice (P< 0.05), IOPs were significantly elevated in LPLA2-deficient mice at maximum levels of the ocular inflammation (48 h). Immunohistochemical analysis indicated that LPLA2-deficient mice showed more prolonged expression of GFAP at the inner plexiform layer and inner nuclear layer by EIU than that found in the wild-type mice (P< 0.05). Conclusions: These results confirm that LPLA2 plays a significant role in the control of IOP during mouse ocular development or with ocular inflammation by facilitating the digestion of intraocular insoluble materials. [ABSTRACT FROM PUBLISHER]

A lysosomal phospholipase A2, LPLA2, was recently characterized and shown to have substrate specificity for phosphatidylcholine and phosphatidylethanolamine. LPLA2 is ubiquitously expressed but is most highly expressed in alveolar macrophages. Double conditional gene targeting was employed to elucidate the function of LPLA2. LPLA2-deficient mice (Lpla2-/-) were generated by the systemic deletion of exon 5 of the Lpla2 gene, which encodes the lipase motif essential for the phospholipase A2 activity. The survival of the Lpla2-/- mice was normal. Lpla2-/- mouse mating pairs yielded normal litter sizes, indicating that the gene deficiency did not impair fertility or fecundity. Alveolar macrophages from wild-type but not Lpla2-/- mice readily degraded radiolabeled phosphatidylcholine. A marked accumulation of phospholipids, in particular phosphatidylethanolamine and phosphatidylcholine, was found in the alveolar macrophages, the peritoneal macrophages, and the spleens of Lpla2-/- mice. By 1 year of age, Lpla2-/- mice demonstrated marked splenomegaly and increased lung surfactant phospholipid levels. Ultrastructural examination of Lpla2-/- mouse alveolar and peritoneal macrophages revealed the appearance of foam cells with lamellar inclusion bodies, a hallmark of cellular phospholipidosis. Thus, a deficiency of lysosomal phospholipase A2 results in foam cell formation, surfactant lipid accumulation, splenomegaly, and phospholipidosis in mice. [ABSTRACT FROM AUTHOR]

Studies focused solely on single organisms can fail to identify the networks underlying host–pathogen gene-for-gene interactions. Here, we integrate genetic analyses of rice (Oryza sativa, host) and rice blast fungus (Magnaporthe oryzae, pathogen) and uncover a new pathogen recognition specificity of the rice nucleotide-binding domain and leucine-rich repeat protein (NLR) immune receptor Pik, which mediates resistance to M. oryzae expressing the avirulence effector gene AVR-Pik. Rice Piks-1, encoded by an allele of Pik-1, recognizes a previously unidentified effector encoded by the M. oryzae avirulence gene AVR-Mgk1, which is found on a mini-chromosome. AVR-Mgk1 has no sequence similarity to known AVR-Pik effectors and is prone to deletion from the mini-chromosome mediated by repeated Inago2 retrotransposon sequences. AVR-Mgk1 is detected by Piks-1 and by other Pik-1 alleles known to recognize AVR-Pik effectors; recognition is mediated by AVR-Mgk1 binding to the integrated heavy metal-associated (HMA) domain of Piks-1 and other Pik-1 alleles. Our findings highlight how complex gene-for-gene interaction networks can be disentangled by applying forward genetics approaches simultaneously to the host and pathogen. We demonstrate dynamic coevolution between an NLR integrated domain and multiple families of effector proteins. Studies focused solely on single organisms can fail to identify the networks underlying host–pathogen gene-for-gene interactions. Integrating genetic analyses of the pathogen rice blast fungus and its host plant helps to disentangle the complex interactions that determine the outcome of plant-pathogen interactions and reveals a previously overlooked pathogen effector. [ABSTRACT FROM AUTHOR]

Intraocular inflammation leads to oxidative stress and may generate lipid oxidation products. The present study was conducted to elucidate the pathophysiological roles of the lysosomal phospholipase A2 (LPLA2), a phospholipid-degrading enzyme, and the production of oxidized phospholipids (oxPLs) in autoimmune uveitis using a rat model. Lewis rats were immunized with a bovine interphotoreceptor retinoid-binding protein (bIRBP) peptide with complete Freund’s adjuvant (CFA) to induce experimental autoimmune uveitis (EAU). The aqueous humor (AH) and serum were collected every week for 4 weeks from the immunized rats. The LPLA2 activity of the AH and serum was detected using liposomes consisting of 1,2-dioleoylphosphatidylglycerol/N-acetylsphingosine as the substrate under acidic conditions. Immunohistochemical analysis was performed using antibodies against LPLA2 and oxPLs. The ocular inflammation was exacerbated at 2 weeks after immunization. The LPLA2 activity in the rat AH was increased by EAU induction, and was concomitant with the extent of inflammation in the anterior chamber (AC). In contrast, the LPLA2 activity in the rat serum was not influenced by EAU induction. At 2 weeks after immunization, immunoreactivity of LPLA2 was observed in infiltrated macrophages in the AC and vitreous cavity of the EAU rats. Furthermore, immunoreactivity of oxPLs was observed in the infiltrated macrophages of EAU rat eyes. These results demonstrated that the LPLA2 activity of the AH is augmented with the inflammation in the AC. The high expression of LPLA2 and production of oxPLs are found in the infiltrated macrophages in the acute inflammation of EAU rats. The present findings suggest the connection between LPLA2 activity and oxPL metabolism in the inflammation sites in the eye. [ABSTRACT FROM AUTHOR]

Understanding how plants allocate their resources to growth or defence is of long-term importance to the development of new and improved varieties of different crops., Using molecular genetics, plant physiology, hormone analysis and Next-Generation Sequencing ( NGS)-based transcript profiling, we have isolated and characterized the rice ( Oryza sativa) LESION AND LAMINA BENDING ( LLB) gene that encodes a chloroplast-targeted putative leucine carboxyl methyltransferase., Loss of LLB function results in reduced growth and yield, hypersensitive response ( HR)-like lesions, accumulation of the antimicrobial compounds momilactones and phytocassanes, and constitutive expression of pathogenesis-related genes. Consistent with these defence-associated responses, llb shows enhanced resistance to rice blast ( Magnaporthe oryzae) and bacterial blight ( Xanthomonas oryzae pv. oryzae). The lesion and resistance phenotypes are likely to be caused by the over-accumulation of jasmonates ( JAs) in the llb mutant including the JA precursor 12-oxo-phytodienoic acid. Additionally, llb shows an increased lamina inclination and enhanced early seedling growth due to elevated brassinosteroid ( BR) synthesis and/or signalling., These findings show that LLB functions in the chloroplast to either directly or indirectly repress both JA- and BR-mediated responses, revealing a possible mechanism for controlling how plants allocate resources for defence and growth. [ABSTRACT FROM AUTHOR]

A rhizomatous Dioscorea crop 'Edo-dokoro' was described in old records of Japan, but its botanical identity has not been characterized. We found that Edo-dokoro is still produced by four farmers in Tohoku-machi of the Aomori prefecture, Japan. The rhizomes of Edo-dokoro are a delicacy to the local people and are sold in the markets. Morphological characters of Edo-dokoro suggest its hybrid origin between the two species, Dioscorea tokoro and Dioscorea tenuipes. Genome analysis revealed that Edo-dokoro likely originated by hybridization of a male D. tokoro to a female D. tenuipes , followed by a backcross with a male plant of D. tokoro. Edo-dokoro is a typical minor crop possibly maintained for more than 300 years but now almost forgotten by the public. We hypothesize that there are many such uncharacterized genetic heritages passed over generations by small-scale farmers that await serious scientific investigation for future use and improvement by using modern genomics information. [ABSTRACT FROM AUTHOR]

Japanese cultivated gentians are perennial plants that flower in early summer to late autumn in Japan, depending on the cultivar. Several flowering-related genes, including GtFT1 and GtTFL1, are known to be involved in regulating flowering time, but many such genes remain unidentified. In this study, we obtained transcriptome profiling data using the Gentiana triflora cultivar 'Maciry', which typically flowers in late July. We conducted deep RNA sequencing analysis using gentian plants grown under natural field conditions for three months before flowering. To investigate diurnal changes, the plants were sampled at 4 h intervals over 24 h. Using these transcriptome data, we determined the expression profiles of leaves based on homology searches against the Flowering-Interactive Database of Arabidopsis. In particular, we focused on transcription factor genes, belonging to the BBX and MADS-box families, and analyzed their developmental and diurnal variation. The expression levels of representative BBX genes were also analyzed under long- and short-day conditions using in-vitro-grown seedlings, and the expression patterns of some BBX genes differed. Clustering analysis revealed that the transcription factor genes were coexpressed with GtFT1. Overall, these expression profiles will facilitate further analysis of the molecular mechanisms underlying the control of flowering time in gentians. [ABSTRACT FROM AUTHOR]

The article presents a study related to development of a salt-tolerant rice variety using a method called MutMap, which helps in identifying the loss-of-function mutations in rice that was further used in developing the variety. Topics discussed include physiological effects of excess amount of salts such as nitrates and potassium on rice, the MutMap, which is based on whole genome sequencing and pertinence of advantages of genomics-based crop breeding in improving traits such as yield.

When infecting plants, fungal pathogens secrete cell wall-degrading enzymes (CWDEs) that break down cellulose and hemicellulose, the primary components of plant cell walls. Some fungal CWDEs contain a unique domain, named the carbohydrate binding module (CBM), that facilitates their access to polysaccharides. However, little is known about how plants counteract pathogen degradation of their cell walls. Here, we show that the rice cysteine-rich repeat secretion protein OsRMC binds to and inhibits xylanase MoCel10A of the blast fungus pathogen Magnaporthe oryzae, interfering with its access to the rice cell wall and degradation of rice xylan. We found binding of OsRMC to various CBM1-containing enzymes, suggesting that it has a general role in inhibiting the action of CBM1. OsRMC is localized to the apoplast, and its expression is strongly induced in leaves infected with M. oryzae. Remarkably, knockdown and overexpression of OsRMC reduced and enhanced rice defense against M. oryzae, respectively, demonstrating that inhibition of CBM1-containing fungal enzymes by OsRMC is crucial for rice defense. We also identified additional CBM-interacting proteins (CBMIPs) from Arabidopsis thaliana and Setaria italica, indicating that a wide range of plants counteract pathogens through this mechanism. Author summary: Plants have evolved various activity-inhibiting proteins as a defense against fungal cell wall-degrading enzymes (CWDEs), but how plants counteract the function of fungal enzymes containing carbohydrate binding modules (CBMs) remains unknown. Here, we demonstrate that OsRMC, a member of the cysteine-rich repeat secretion protein family, interacts with fungal CBM1. OsRMC binding to CBM1 of a blast fungal xylanase blocks access to cellulose, resulting in the inhibition of xylanase enzymatic activity. Our study provides significant insights into plant countermeasures against CWDEs in the apoplastic space during plant-fungal pathogen interactions. It also reveals a molecular function of the DUF26 domain widely distributed in plant proteins. [ABSTRACT FROM AUTHOR]

Abstract: Active oxygen species for soot oxidation over Ag/ZrO2 were characterized by means of X-ray photoelectron spectroscopy (XPS) and temperature-programmed desorption and reduction methods. The temperature-programmed surface reaction (TPSR) between carbon black (CB), a model soot, and surface oxygen revealed that two kinds of adsorbed oxygen species were involved in CB oxidation over Ag/ZrO2. The results of XPS, temperature-programmed desorption of O2, and temperature-programmed reduction by H2 were insufficient to distinguish the two kinds of active oxygen species. Temperature-programmed reduction by NH3 (NH3-TPR) resulted in N2 and N2O formation as products of reduction of the Ag/ZrO2 surface and bulk oxygen. The N2O formation profile in NH3-TPR exhibited two peaks, corresponding to two kinds of oxygen species having a strong oxidation capacity. The effect of Ag loading on the total amount of N2O formation was in good agreement with that on the amount of active oxygen species observed by TPSR-CB. We concluded that NH3-TPR was an appropriate technique for quantitative characterization of the amount of active oxygen species for soot oxidation on Ag/ZrO2. [Copyright &y& Elsevier]

The Oryza sativa (rice) resistance gene Pia confers resistance to the blast fungus Magnaporthe oryzae carrying the AVR-Pia avirulence gene. To clone Pia, we employed a multifaceted genomics approach. First, we selected 12 R-gene analog (RGA) genes encoding nucleotide binding site-leucine rich repeats (NBS-LRRs) proteins from a region on chromosome 11 that shows linkage to Pia. By using seven rice accessions, we examined the association between Pia phenotypes and DNA polymorphisms in the 10 genes, which revealed three genes ( Os11gRGA3-Os11gRGA5) exhibiting a perfect association with the Pia phenotypes. We also screened ethyl methane sulfonate (EMS)-treated mutant lines of the rice cultivar 'Sasanishiki' harboring Pia, and isolated two mutants that lost the Pia phenotype. DNA sequencing of Os11gRGA3-Os11gRGA5 from the two mutant lines identified independent mutations of major effects in Os11gRGA4. The wild-type 'Sasanishiki' allele of Os11gRGA4 ( SasRGA4) complemented Pia function in both mutants, suggesting that SasRGA4 is necessary for Pia function. However, when the rice cultivar 'Himenomochi' lacking Pia was transfected with SasRGA4, the Pia phenotype was not recovered. An additional complementation study revealed that the two NBS-LRR-type R genes, SasRGA4 and SasRGA5, that are located next to each other and oriented in the opposite direction are necessary for Pia function. A population genetics analysis of SasRGA4 and SasRGA5 suggests that the two genes are under long-term balancing selection. [ABSTRACT FROM AUTHOR]

Reinforcement of the hydroperoxide-eliminating activity in the small and large intestines should prevent associated diseases. We previously isolated a lactic acid bacterium, Pediococcus pentosaceus Be1 that facilitates a 2-electron reduction of hydrogen peroxide to water. In this study, we successfully isolated an alternative lactic acid bacterium, Lactobacillus plantarum P1-2, that can efficiently reduce environmental alkyl hydroperoxides and fatty acid hydroperoxides to their corresponding hydroxyl derivatives through a 2-electron reduction. Each strain exhibited a wide concentration range with regard to the environmental reducing activity for each hydroperoxide. Given this, the two lactic acid bacteria were orally administered to an oxygen-sensitive short-lived nematode mutant, and this resulted in a significant expansion of its lifespan. This observation suggests that P. pentosaceus Be1 and L. plantarum P1-2 inhibit internal oxidative stress. To determine the specific organs involved in this response, we performed a similar experiment in rats, involving induced lipid peroxidation by iron-overloading. We observed that only L. plantarum P1-2 inhibited colonic mucosa lipid peroxidation in rats with induced oxidative stress. [ABSTRACT FROM AUTHOR]

Key message: An improved protocol of QTL-seq, an NGS-based method for bulked segregant analysis we previously developed in rice, allowed successful mapping of QTLs of interest in the highly heterozygous genome of B. rapa, demonstrating the power of this elegant method for genetic analyses in heterozygous species of economic importance. Recent advances in next-generation sequencing (NGS) and the various NGS-based methods developed for rapidly identifying candidate genes of interest have accelerated genetic analysis mainly in the model plants rice and Arabidopsis. Brassica rapa includes several economically important crops such as Chinese cabbage, turnip and various leafy vegetables. The application of NGS-based approaches for the analysis of B. rapa has been limited mainly due to its highly heterozygous genome and poor quality of the reference genome sequence currently available for this species. In this study, we have improved QTL-seq, a method for NGS-based bulked segregant analysis we previously developed in rice, extending its applicability for accelerating the genetic analysis and molecular breeding of B. rapa. Addition of new filters to the original QTL-seq pipeline allowed removal of spurious single-nucleotide polymorphisms caused by alignment/sequencing errors and variability between parents, significantly improving accuracy of the analysis. As proof of principle, we successfully applied the new approach to identify candidate genomic regions controlling flowering and trichome formation using segregating F2 progeny obtained from crosses made between cultivars of B. rapa showing contrasting phenotypes for these traits. We strongly believe that the improved QTL-seq method reported here will extend the applicability of NGS-based genetic analysis not only to B. rapa but also to other plant species of economic importance with heterozygous genomes. [ABSTRACT FROM AUTHOR]

During late 1960s Green Revolution, researchers utilized semidwarf 1 (sd1) to improve the yield and lodging resistance in rice (Oryza sativa L.). However, sd1 has a negative effect to culm strength and biomass production. To increase yield dramatically in 21th century, development of next generation long-culm rice for non-lodging and high grain yield independent of sd1 has been needed. The present study developed Monster Rice 1, a long-culm and heavy-panicle type of rice line and compared it with Takanari, a high-yielding semidwarf rice variety about yield and lodging resistance associated traits. Brown rice yield and bending moment at breaking of the basal elongated internode were higher in Monster Rice 1 than those in Takanari due to a large number of spikelets per panicle and thicker culm. Furthermore, to identify QTLs with superior alleles for these traits, QTL and haplotype analyses were performed using F2 population and recombinant inbred lines derived from a cross between Monster Rice 1 and Takanari. The results from this study suggest that long-culm and heavy-panicle type of rice with a superior lodging resistance by culm strength can perform its high yield potential by using these identified QTLs contributing yield and lodging resistance. [ABSTRACT FROM AUTHOR]

Phenotypic plasticity of plants in response to environmental changes is important for adapting to changing climate. Less attention has been paid to exploring the advantages of phenotypic plasticity in resource-rich environments to enhance the productivity of agricultural crops. Here, we examined genetic variation for phenotypic plasticity in indica rice ( Oryza sativa L.) across two diverse panels: (1) a Phenomics of Rice Adaptation and Yield (PRAY) population comprising 301 accessions; and (2) a Multi-parent Advanced Generation Inter-Cross (MAGIC) indica population comprising 151 accessions. Altered planting density was used as a proxy for elevated atmospheric CO2 response. Low planting density significantly increased panicle weight per plant compared with normal density, and the magnitude of the increase ranged from 1.10 to 2.78 times among accessions for the PRAY population and from 1.05 to 2.45 times for the MAGIC population. Genome-wide-association studies validate three Environmental Responsiveness (ER) candidate alleles (qER1-3) that were associated with relative response of panicle weight to low density. Two of these alleles were tested in 13 genotypes to clarify their biomass responses during vegetative growth under elevated CO2 in Japan. Our study provides evidence for polymorphisms that control rice phenotypic plasticity in environments that are rich in resources such as light and CO2. [ABSTRACT FROM AUTHOR]

Due to the recent advances in DNA sequencing technologies, whole genome sequencing (WGS)-based approaches are now accelerating the pace of our research toward a better understanding of host-pathogen interactions. Using WGS-based methods, we have isolated three avirulence ( AVR ) genes: AVR-Pia , AVR-Pii and AVR-Pik from Magnaporthe oryzae and two cognate rice resistance ( R -) genes: Pia and Pii . We briefly review our current understanding of the interactions between AVR-Pia and Pia , AVR-Pik and Pik , and AVR-Pii and Pii . [ABSTRACT FROM AUTHOR]

Lesion mimic mutants (LMMs) provide a useful tool to study defense-related programmed cell death (PCD) in plants. Although a number of LMMs have been identified in multiple species, most of the candidate genes are yet to be isolated. Here, we report the identification and characterization of a novel rice ( Oryza sativa L.) lesion mimic resembling ( lmr) mutant, and cloning of the corresponding LMR gene. The LMR locus was initially delineated to 1.2 Mb region on chromosome 6, which was further narrowed down to 155-kb using insertions/deletions (INDELs) and cleavage amplified polymorphic sequence markers developed in this study. We sequenced the open reading frames predicted within the candidate genomic region, and identified a G-A base substitution causing a premature translation termination in a gene that encodes an ATPase associated with various cellular activities type (AAA-type) protein. RNA interference transgenic lines with reduced LMR transcripts exhibited the lesion mimic phenotype similar to that of lmr plants. Furthermore, expression of the wild-type LMR in the mutant background complemented the lesion phenotype, confirming that the mutation identified in LMR is responsible for the mutant phenotype. The pathogenesis-related (PR) genes PBZ1 and PR1 were induced in lmr, which also showed enhanced resistance to rice blast ( Magnaporthe oryzae) and bacterial blight ( Xanthomonas oryzae pv. oryzae), suggesting LMR is a negative regulator of cell death in rice. The identification of lmr and cloning of the corresponding LMR gene provide an additional resource for the study of PCD in plants. [ABSTRACT FROM AUTHOR]

Genes involved in the transition from wild to cultivated crop species should be of great agronomic importance. Population genomic approaches utilizing genome resequencing data have been recently applied for this purpose, although it only reports a large list of candidate genes with no biological information. Here, by resequencing more than 30 genomes altogether of wild rice Oryza rufipogon and cultivated rice O. sativa, we identified a number of regions with clear footprints of selection during the domestication process. We then focused on identifying candidate domestication genes in these regions by utilizing the wealth of QTL information in rice. We were able to identify a number of interesting candidates such as transcription factors that should control key domestication traits such as shattering, awn length, and seed dormancy. Other candidates include those that might have been related to the improvement of grain quality and those that might have been involved in the local adaptation to dry conditions and colder environments. Our study shows that population genomic approaches and QTL mapping information can be used together to identify genes that might be of agronomic importance. [ABSTRACT FROM AUTHOR]

Next-generation sequencing allows the identification of mutations responsible for mutant phenotypes by whole-genome resequencing and alignment to a reference genome. However, when the resequenced cultivar/line displays significant structural variation from the reference genome, mutations in the genome regions missing from the reference (gaps) cannot be identified by simple alignment., Here we report on a method called ' Mut Map- Gap', which involves delineating a candidate region harboring a mutation of interest using the recently reported Mut Map method, followed by de novo assembly, alignment, and identification of the mutation within genome gaps., We applied Mut Map- Gap to isolate the blast resistant gene Pii from the rice cv Hitomebore using mutant lines that have lost Pii function., Mut Map- Gap should prove useful for cloning genes that exhibit significant structural variations such as disease resistance genes of the nucleotide-binding site-leucine rich repeat ( NBS- LRR) class. [ABSTRACT FROM AUTHOR]

Huntington disease is caused by cell death after the expansion of polyglutamine (polyQ) tracts longer than ~40 repeats encoded by exon 1 of the huntingtin (HTT) gene. Prefoldin is a molecular chaperone composed of six subunits, PFD1-6, and prevents misfolding of newly synthesized nascent polypeptides. In this study, we found that knockdown of PFD2 and PFD5 disrupted prefoldin formation in HTT-expressing cells, resulting in accumulation of aggregates of a pathogenic form of HTT and in induction of cell death. Dead cells, however, did not contain inclusions of HTT, and analysis by a fluorescence correlation spectroscopy indicated that knockdown of PFD2 and PFD5 also increased the size of soluble oligomers of pathogenic HTT in cells. In vitro single molecule observation demonstrated that prefoldin suppressed HTT aggregation at the small oligomer (dimer to tetramer) stage. These results indicate that prefoldin inhibits elongation of large oligomers of pathogenic Htt, thereby inhibiting subsequent inclusion formation, and suggest that soluble oligomers of polyQ-expanded HTT are more toxic than are inclusion to cells. [ABSTRACT FROM AUTHOR]

Advances in genome sequencing technologies have enabled researchers and breeders to rapidly associate phenotypic variation to genome sequence differences. We recently took advantage of next-generation sequencing technology to develop MutMap, a method that allows rapid identification of causal nucleotide changes of rice mutants by whole genome resequencing of pooled DNA of mutant F2 progeny derived from crosses made between candidate mutants and the parental line. Here we describe MutMap+, a versatile extension of MutMap, that identifies causal mutations by comparing SNP frequencies of bulked DNA of mutant and wild-type progeny of M3 generation derived from selfing of an M2 heterozygous individual. Notably, MutMap+ does not necessitate artificial crossing between mutants and the wild-type parental line. This method is therefore suitable for identifying mutations that cause early development lethality, sterility, or generally hamper crossing. Furthermore, MutMap+ is potentially useful for gene isolation in crops that are recalcitrant to artificial crosses. [ABSTRACT FROM AUTHOR]

Abstract: A phospholipase A2 was identified from MDCK cell homogenates with broad specificity toward glycerophospholipids including phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, and phosphatidylglycerol. The phospholipase has the unique ability to transacylate short chain ceramides. This phospholipase is calcium-independent, localized to lysosomes, and has an acidic pH optimum. The enzyme was purified from bovine brain and found to be a water-soluble glycoprotein consisting of a single peptide chain with a molecular weight of 45kDa. The primary structure deduced from the DNA sequences is highly conserved between chordates. The enzyme was named lysosomal phospholipase A2 (LPLA2) and subsequently designated group XV phospholipase A2. LPLA2 has 49% of amino acid sequence identity to lecithin–cholesterol acyltransferase and is a member of the αβ-hydrolase superfamily. LPLA2 is highly expressed in alveolar macrophages. A marked accumulation of glycerophospholipids and extensive lamellar inclusion bodies, a hallmark of cellular phospholipidosis, is observed in alveolar macrophages in LPLA 2 −/− mice. This defect can also be reproduced in macrophages that are exposed to cationic amphiphilic drugs such as amiodarone. In addition, older LPLA 2 −/− mice develop a phenotype similar to human autoimmune disease. These observations indicate that LPLA2 may play a primary role in phospholipid homeostasis, drug toxicity, and host defense. [ABSTRACT FROM AUTHOR]

The article discusses a study which examines the enzymatic components of Chlorella vulgaris. Findings of the study reveal that a free flavin-dependent Fenton reaction was identified on its cell-free extracts. It also indicates that its N-terminal sequence was similar to aldo-keto reductase family enzymes since it displayed aldehyde reductase activity as well.