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Proteinuria selectivity index (PSI) is a potential tool for histological classification and prediction of treatment response in nephrotic syndrome, but evidence is insufficient. Clinical relevance of fractional excretion of sodium (FENa) in nephrotic syndrome remains largely unexplored. This multicenter retrospective study included patients with nephrotic syndrome who underwent kidney biopsy between January 2012 and June 2022. Optimal cutoffs for predicting complete remission based on PSI and FENa were determined using receiver operating characteristic curves. Patients were divided into two groups using these cutoffs and followed until complete remission. Of the 611 patients included, 177 had minimal change disease (MCD), 52 had focal segmental glomerulosclerosis (FSGS), and 149 had membranous nephropathy (MN). Median (interquartile range) PSI were 0.14 (0.09–0.19) for MCD, 0.33 (0.23–0.40) for FSGS, and 0.20 (0.14–0.30) for MN. FENa were 0.24 (0.09–0.68), 1.03 (0.50–2.14), and 0.78 (0.41–1.28). Patients with low PSI and FENa had a higher incidence of complete remission. Cox regression analyses demonstrated that both parameters were associated with achieving complete remission (HR 2.73 [95% CI 1.97–3.81] and HR 1.93 [95% CI 1.46–2.55], respectively). PSI and FENa may be useful for histological classification and predicting remission in nephrotic syndrome. [ABSTRACT FROM AUTHOR]

AgHST1 and AgHST3 genes encode sirtuins that are NAD+-dependent protein deacetylases. According to previous reports, their disruption leads to the overproduction of riboflavin in Ashbya gossypii. In this study, we investigated the potential causes of riboflavin overproduction in the AgHST1Δ and AgHST3Δ mutant strains of A. gossypii. The generation of reactive oxygen species was increasd in the mutants compared to in WT. Additionally, membrane potential was lower in the mutants than in WT. The NAD+/NADH ratio in AgHST1Δ mutant strain was lower than that in WT; however, the NAD+/NADH ratio in AgHST3Δ was slightly higher than that in WT. AgHST1Δ mutant strain was more sensitive to high temperatures and hydroxyurea treatment than WT or AgHST3Δ. Expression of the AgGLR1 gene, encoding glutathione reductase, was substantially decreased in AgHST1Δ and AgHST3Δ mutant strains. The addition of N-acetyl-L-cysteine, an antioxidant, suppressed the riboflavin production in the mutants, indicating that it was induced by oxidative stress. Therefore, high oxidative stress resulting from the disruption of sirtuin genes induces riboflavin overproduction in AgHST1Δ and AgHST3Δ mutant strains. This study established that oxidative stress is an important trigger for riboflavin overproduction in sirtuin gene-disrupted mutant strains of A. gossypii and helped to elucidate the mechanism of riboflavin production in A. gossypii. [ABSTRACT FROM AUTHOR]

Coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a global pandemic. Although several vaccines targeting SARS-CoV-2 spike proteins protect against COVID-19 infection, mutations affecting virus transmissibility and immune evasion potential have reduced their efficacy, leading to the need for a more efficient strategy. Available clinical evidence regarding COVID-19 suggests that endothelial dysfunction with thrombosis is a central pathogenesis of progression to systemic disease, in which overexpression of plasminogen activator inhibitor-1 (PAI-1) may be important. Here we developed a novel peptide vaccine against PAI-1 and evaluated its effect on lipopolysaccharide (LPS)-induced sepsis and SARS-CoV-2 infection in mice. Administration of LPS and mouse-adapted SARS-CoV-2 increased serum PAI-1 levels, although the latter showed smaller levels. In an LPS-induced sepsis model, mice immunized with PAI-1 vaccine showed reduced organ damage and microvascular thrombosis and improved survival compared with vehicle-treated mice. In plasma clot lysis assays, vaccination-induced serum IgG antibodies were fibrinolytic. However, in a SARS-CoV-2 infection model, survival and symptom severity (i.e., body weight reduction) did not differ between vaccine- and vehicle-treated groups. These results indicate that although PAI-1 may promote the severity of sepsis by increasing thrombus formation, it might not be a major contributor to COVID-19 exacerbation. [ABSTRACT FROM AUTHOR]

There is a critical need for efficient treatment of chronic kidney disease (CKD). Renal fibrosis is a final common pathway to end-stage renal disease independent of the underlying etiology, and connective tissue growth factor (CTGF) is a well-recognized profibrotic factor in fibrosis of various organ systems. Here, we developed a novel peptide vaccine against CTGF to attenuate the development of renal fibrosis. Three inoculations with this CTGF vaccine at 2-week intervals elicited antibodies specifically binding to human full-length CTGF, and the antigen-specific serum IgG antibody titers were maintained for > 30 weeks. The efficacy of the CTGF vaccine on renal fibrosis was evaluated in adenine-induced CKD and unilateral ureteral obstruction (UUO) murine models. In adenine-induced CKD model, immunization with the CTGF vaccine attenuated renal interstitial fibrosis. Vaccinated mice showed low levels of serum creatinine and urea nitrogen and low urine albumin–creatinine ratio compared with vehicle-treated mice. In UUO model, the CTGF vaccination also suppressed the onset of renal fibrosis. In an in vitro study, CTGF vaccine-elicited IgG antibodies efficiently suppressed CTGF-induced- and transforming growth factor-β-induced α-smooth muscle actin expression in kidney fibroblasts. These results demonstrate that the CTGF vaccine is a promising strategy to attenuate the development of renal fibrosis. [ABSTRACT FROM AUTHOR]

This paper presents a method to reduce the computational time required to solve shape optimization problems. A volume minimization problem under the mean compliance constraint is chosen as an example of the shape optimization problem. To solve this problem, an iterative algorithm based on the H 1 gradient method is considered as a conventional approach. In this study, we attempt to use a method of model order reduction for solving the linear elasticity problem based on the idea by Karhunen-Loève expansion (KLE). We consider the displacements obtained by the conventional method to be sampling data of a random variable; the orthonormal bases of KLE are defined as eigenfunctions of the eigenvalue problem obtained as the optimality condition of the variance maximization problem for the random variable. The feasibility of the proposed method is illustrated by testing the numerical scheme to a linear elastic body of the connecting rod type. [ABSTRACT FROM AUTHOR]

The exterior Bernoulli problem is rephrased into a shape optimization problem using a new type of objective function called the Dirichlet-data-gap cost function which measures the L 2 -distance between the Dirichlet data of two state functions. The first-order shape derivative of the cost function is explicitly determined via the chain rule approach. Using the same technique, the second-order shape derivative of the cost function at the solution of the free boundary problem is also computed. The gradient and Hessian informations are then used to formulate an efficient second-order gradient-based descent algorithm to numerically solve the minimization problem. The feasibility of the proposed method is illustrated through various numerical examples. [ABSTRACT FROM AUTHOR]

The present paper describes a shape optimization procedure for designing running shoes, focusing on two mechanical properties, namely, the shock absorption and the stability keeping the right posture. These properties are evaluated from two deformations of a sole at characteristic timings during running motion. We define approximate planes for the deformations of sole's upper boundary by least squares method. Using the planes, we choose the tilt angle in the shoe width direction at the mid stance phase of running motion as an objective function representing the stability, and the sunk amount at the contact phase of running motion as a constraint function representing the shock absorption. We assume that the sole is a bonded structure of soft and hard hyper-elastic materials, and the bonding and side boundaries are variable. In this study, we apply the formulation of nonparametric shape optimization to the sole considering finite deformation and contact condition of the bottom of the sole with the ground. Shape derivatives of the cost (objective and constraint) functions are obtained using the adjoint method. The H1 gradient method using these shape derivatives is applied as an iterative algorithm. To solve this optimization problem, we developed a computer program combined with some commercial softwares. The validity of the optimization method is confirmed by numerical examples. [ABSTRACT FROM AUTHOR]

Background: Low birth weight (LBW) is a risk factor for chronic kidney disease (CKD) in later life and is becoming increasingly common in developed countries, including Japan. Furthermore, a serial decrease in birth weight has been associated with an increasing prevalence of CKD stage 2 in male Japanese adolescents. Sex-specific differences affect CKD susceptibility, and the association between birth weight and CKD in women, has not been elucidated. In this study, we investigated the sex-specific effect of LBW on renal function. Methods: Annual cross-sectional data of 2417 Japanese adolescents (males 1736; females 681), aged 15–16 years, were evaluated over 8 years (2007–2014). Results: Over the study period, mean birth weights decreased significantly in males (p < 0.01) and females (p < 0.05). Furthermore, both sexes showed significant decrease in estimated glomerular filtration rates corresponding to the birth weight reduction. The prevalence of CKD stage 2 also increased in males (from 26.0 to 32.4%, p < 0.01) and females (from 6.3 to 18.5%, p < 0.05). The incidence of CKD stage 2 was significantly related to history of LBW (males: odds ratio 1.73; 95% confidence interval 1.06–2.80; p < 0.05; females: odds ratio 3.29; 95% confidence interval 1.25–8.02; p < 0.05). Conclusions: Our data revealed that renal function and birth weight have decreased over time, in healthy Japanese adolescents. In view of the recent declining trend demonstrated by birth weight in Japan, we speculate that the prevalence of CKD might increase in the future. [ABSTRACT FROM AUTHOR]

We propose a new shape optimization formulation of the Bernoulli problem by tracking the Neumann data. The associated state problem is an equivalent formulation of the Bernoulli problem with a Robin condition. We devise an iterative procedure based on a Lagrangian-like approach to numerically solve the minimization problem. The proposed scheme involves the knowledge of the shape gradient which is established through the minimax formulation. We illustrate the feasibility of the proposed method and highlight its advantage over the classical setting of tracking the Neumann data through several numerical examples. [ABSTRACT FROM AUTHOR]

We aim to identify the geometry (i.e., the shape and location) of a cavity inside an object through the concept of thermal imaging. More precisely, we present an identification procedure to determine the geometric shape of a cavity with convective boundary condition in a heat-conducting medium using the measured temperature on a part of the surface of the object. The inverse problem of identifying the cavity is resolved by shape optimization techniques, specifically by minimizing a least-squares type cost functional over a set of admissible geometries. The computation of the first-order shape derivative or shape gradient of the cost is carried out through minimax formulation, which is then justified by the Correa-Seeger theorem coupled with function space parametrization technique. We further characterize its boundary integral form using some identities from tangential calculus. Then, we utilize the computed expression for the shape gradient to implement an effective boundary variation algorithm for the numerical resolution of the shape optimization problem. To avoid boundary oscillations or irregular shapes in our approximations, we execute the gradient-based scheme using the H1 gradient method with perimeter regularization. Also, we propose a novel application of the said method in computing the mean curvature of the free boundary appearing in the shape gradient of the cost functional. We illustrate the feasibility of the proposed method by testing the numerical scheme to several cavity identification problems. Additionally, we also give some numerical examples for the case of corrosion detection since its inverse problem interpreted in the framework of electrostatic imaging is closely related to the focused problem. [ABSTRACT FROM AUTHOR]

This study demonstrates the use of Newton method to solve topology optimization problems of density type for linear elastic bodies to minimize the maximum von Mises stress. We use the Kreisselmeier-Steinhauser (KS) function with respect to von Mises stress as a cost function to avoid the non-differentiability of the maximum von Mises stress. For the design variable, we use a function defined in the domain of a linear elastic body with no restriction on the range and assume that a density is given by a sigmoid function of the function of design variable. The main aim of this study involves evaluating the second derivative of the KS function with respect to variation of the design variable and to propose an iterative scheme based on an H1 Newton method as opposed to the H1 gradient method that was presented in previous studies. The effectiveness of the scheme is demonstrated by numerical results for several linear elastic problems. The numerical results show that the speed of the proposed H1 Newton method exceeds that of the H1 gradient method. [ABSTRACT FROM AUTHOR]

This paper describes the shape optimization of an electrostatic capacitive sensor used to detect fingers. We consider two state determination problems. The first is a basic electrostatic field problem consisting of sensing electrodes, an earth electrode, and air. The second is an electrostatic field problem in which fingers are added to the basic electrostatic field problem. An objective cost function is defined using the negative-signed squared $$H^{1}$$ -norm of the difference between the solutions of the two state determination problems. The volume of the sensing electrode is used as the cost function. Using the solutions of the two state determination problems and the two adjoint problems, we present a method for evaluating the shape derivative of the objective cost function. To solve the shape optimization problem and minimize the negative-signed difference norm under the volume constraint, we use an iterative algorithm based on the $$H^{1}$$ gradient method. An algorithm for the shape optimization problem is developed to solve the boundary value problems. Numerical examples show that reasonable shapes are obtained using the present approach. [ABSTRACT FROM AUTHOR]

Key message: The first Good Manufacturing Practices production of a purification-free rice-based oral cholera vaccine (MucoRice-CTB) from transgenic plants in a closed cultivation system yielded a product meeting regulatory requirements. Abstract: Despite our knowledge of their advantages, plant-based vaccines remain unavailable for human use in both developing and industrialized countries. A leading, practical obstacle to their widespread use is producing plant-based vaccines that meet governmental regulatory requirements. Here, we report the first production according to current Good Manufacturing Practices of a rice-based vaccine, the cholera vaccine MucoRice-CTB, at an academic institution. To this end, we established specifications and methods for the master seed bank (MSB) of MucoRice-CTB, which was previously generated as a selection-marker-free line, evaluated its propagation, and given that the stored seeds must be renewed periodically. The production of MucoRice-CTB incorporated a closed hydroponic system for cultivating the transgenic plants, to minimize variations in expression and quality during vaccine manufacture. This type of molecular farming factory can be operated year-round, generating three harvests annually, and is cost- and production-effective. Rice was polished to a ratio of 95 % and then powdered to produce the MucoRice-CTB drug substance, and the identity, potency, and safety of the MucoRice-CTB product met pre-established release requirements. The formulation of MucoRice-CTB made by fine-powdering of drug substance and packaged in an aluminum pouch is being evaluated in a physician-initiated phase I study. [ABSTRACT FROM AUTHOR]

This paper presents a solution of a shape optimization problem of a flow field for delaying transition from a laminar flow to a turbulent flow. Mapping from an initial domain to a new domain is chosen as the design variable. Main problems are defined by the stationary Navier-Stokes problem and an eigenvalue problem assuming a linear disturbance on the solution of the stationary Navier-Stokes problem. The maximum value of the real part of the eigenvalue is used as an objective cost function. The shape derivative of the cost function is defined as the Fréchet derivative of the cost function with respect to arbitrary variation of the design variable, which denotes the domain variation, and is evaluated using the Lagrange multiplier method. To obtain a numerical solution, we use an iterative algorithm based on the $$H^{1}$$ gradient method using the finite element method. To confirm the validity of the solution, a numerical example for two-dimensional Poiseuille flow with a sudden expansion is presented. Results reveal that a critical Reynolds number increases by the iteration of reshaping. [ABSTRACT FROM AUTHOR]

The present paper describes a solution to a problem of identifying damage in a building based on experimentally measured vibrational eigenvalue and eigenmode pairs. The healthy rate, which is defined as the stiffness rate with respect to a perfect material, is chosen as the design target to be identified. The range of the healthy rate is restricted to within the range of 0-1. In order to overcome this restriction, we define a function with no restriction on the range defined in the domain of a linear elastic body for a building as a design variable and assume that the healthy rate is given by a sigmoid function of the function of the design variable. The linear coupling of the mean squared errors of vibrational eigenvalues and eigenmodes with respect to the measured values are used as a cost function. The derivative of the cost function with respect to the design variable is evaluated by the adjoint variable method. In order to resolve the identification problem of the damaged area, we use an iterative algorithm based on the $$H^{1}$$ gradient method using the finite-element method to obtain numerical solutions. A numerical example using experimental data demonstrates that a damaged area can be identified by the proposed approach. [ABSTRACT FROM AUTHOR]

Introduction: Macro-reentrant ventricular tachycardias (VT) utilizing the bundle branches and Purkinje fibers have been reported as verapamil sensitive VT (idiopathic left VT), bundle branch reentrant VT (BBRT) and inter-fascicular reentrant tachycardia (inter-fascicular VT). However, diagnostic confusion exists with these VTs due to the difficulty in differentiating between them with conventional electrophysiological (EP) studies. The aim of this study was to clarify the EP and anatomical entity of inter-fascicular VT, and provide successful methods for the radio frequency catheter ablation (RFCA) of inter-fascicular VT. Methods and results: A total of nine patients were included in this study. All patients were diagnosed with idiopathic left VT in the first session, and underwent a second session after a failed RFCA. Detailed EP studies guided by a three-dimensional (3D) mapping system were performed to further analyze the VTs. All VTs were finally diagnosed as inter-fascicular VT. They were successfully cured with RFCA targeting the left anterior or posterior fascicle, which was regarded as a requisite part of the reentrant circuit of the inter-fascicular VT, using 3D and fluoroscopic images combined with a detailed EP investigation instead of the conventional RFCA method targeting Purkinje potentials for the RFCA of idiopathic left VT. Conclusions: Inter-fascicular VT could be misdiagnosed as idiopathic left VT due to the limitations of the conventional EP study. Failed RFCA in presumptive idiopathic left VT cases has to be carefully investigated by further analysis, and a tailored RFCA strategy targeting the requisite portions of the left fascicles in the inter-fascicular VT reentrant circuit will be required for the successful elimination of the inter-fascicular VT. [ABSTRACT FROM AUTHOR]

This paper presents a numerical solution for shape optimization problems for link mechanisms, such as a piston-crank mechanism. The dynamic behavior of a link mechanism is described by a differential-algebraic equation (DAE) system consisting of motion equations for each single body and constraints of linkages and rigid motions. In a shape optimization problem, the objective function to maximize is constructed from the external work done by a given external force, which agrees with the kinetic energy of the link mechanism, for an assigned time interval, and the total volume of all the links forms the constraint function. The Fréchet derivatives of these cost functions with respect to the domain variation, which we call the shape derivatives of these cost functions, are evaluated theoretically. A scheme to solve the shape optimization problem is presented using the H gradient method (the traction method) proposed by the authors as a reshaping algorithm, since it retains the smoothness of the boundary. A numerical example shows that reasonable shapes for each link such that mobility of the link mechanism is improved are obtained by this approach. [ABSTRACT FROM AUTHOR]

Bacterial palea browning of rice, caused by Pantoea ananatis from infection during flowering, occurs widely in Japan and degrades the quality of rice. In a search for environmentally friendly control measures, effects of bacteriophages on the incidence of the disease were examined. Phages lytic to both pathogenic and nonpathogenic P. ananatis were isolated from an inflorescence of eulalia ( Miscanthus sinensis), a gramineous weed, and one of the phages was sprayed with and without a nonpathogenic isolate of P. ananatis on rice plants at the flowering stage. Coapplication of the phage and nonpathogenic P. ananatis suppressed the disease in sunlight. Surprisingly, application of the light-labile phage by itself was suppressive. The phage retarded the growth of the pathogen on rice plants and on LB medium. Because nonpathogenic Pantoea strains are abundant on rice panicles at the flowering stage and could be hosts of the phage and the optimum infection period of rice with P. ananatis is during the flowering stage, disease suppression by the phage is thought to be due to the combined effects of the phage, naturally inhabiting nonpathogenic bacteria, and the limited susceptible period. [ABSTRACT FROM AUTHOR]

There is growing evidence that symptomatic femoroacetabular impingement leads to intra-articular damage and the development of early-onset osteoarthritis. Symptoms of femoroacetabular impingement often do not manifest until adulthood, but have been increasingly recognised in the paediatric and adolescent population. The surgical treatment of femoroacetabular impingement is aimed at restoring a more normal femoral head-neck offset in order to increase the clearance and prevent femoral abutment against the acetabular edge. Current methods include open and arthroscopic techniques. The latter has been combined with an open approach to gain access to the head-neck junction for osteochondroplasty. Proximal femoral and/or periacetabular osteotomies are used to treat femoroacetabular impingement associated with deformity secondary to childhood hip conditions, such as slipped capital femoral epiphysis and Legg-Calvé-Perthes disease. Some adolescents have severe degenerative joint disease at the time of presentation and may require arthroplasty or arthrodesis. The aim of this review is to identify the major trends and advancements in the management of femoroacetabular impingement in adolescents, including the outcome of studies of the surgical treatment modalities used. [ABSTRACT FROM AUTHOR]

The present paper introduces a numerical solution to shape optimization problems of domains in which boundary value problems of partial differential equations are defined. In the present paper, the finite element method using NURBS as basis functions in the Galerkin method is applied to solve the boundary value problems and to solve a reshaping problem generated by the H1 gradient method for shape optimization, which has been developed as a general solution to shape optimization problems. Numerical examples of linear elastic continua illustrate that this solution works as well as using the conventional finite element method. [ABSTRACT FROM AUTHOR]

Black lesions on shoots of European pear trees observed in an orchard in Yamagata Prefecture in May 2007 were suspected to be caused by a bacterial pathogen. The surface of the colonies isolated on a high sucrose medium did not have the crater morphology that is characteristic of E. amylovora bvs. 1–3, and a specific DNA fragment was amplified from the isolates in the PCR using the EprpoD primer set. The partial sequences of the 16S rRNA gene placed the isolates in the genus Erwinia. The isolates differed serologically from E. amylovora biovars and E. pyrifoliae in an Ouchterlony double-diffusion test although their bacterial properties suggested that they are closely related to E. amylovora biovars and E. pyrifoliae. In a DNA–DNA hybridization test, the relatedness between the isolates and E. amylovora biovars or E. pyrifoliae did not exceed 70% level, indicating that they are independent species. Thus, the isolates belongs to the genus Erwnia but are not E. amylovra or E. pyrifoliae. After succulent pear shoots were injected with bacterial suspensions (109, 108, 107 and 106 cfu/ml) of the isolates, lesions formed with 109 and 108 cfu/ml, but the disease incidence with 108 cfu/ml was much lower than with E. amylovora and E. pyrifoliae. Virulence of the present isolates is thus thought to be very weak. On the basis of these results, we consider that this is a new shoot disease of European pear. In the 2007 season, all affected trees were pulled out after harvest. No symptoms have been observed in field surveys since the fruitlet season in 2007. [ABSTRACT FROM AUTHOR]

Xanthomonas oryzae pv. oryzae strain T7174R is lysed by bacteriophage OP1h and OP1h2. Three mutants tolerant to both OP1h and OP1h2 were isolated by transposon mutagenesis. The mutants had an insertion of the transposon in XOO1687, which is predicted to encode a TonB-dependent receptor gene. Plasmid pHMIroNB that contained XOO1687 of T7174R was constructed, and the mutant was transformed with the plasmid. The transformant recovered sensitivity to OP1h and OP1h2. Electron microscopic analysis demonstrated that OP1h and OP1h2 can adsorb to the wild type and the transformant, but they could not adsorb to the phage-tolerant mutant. These results suggest that the TonB-dependent receptor gene relates to adsorption and infection of T7174R by OP1h2 and OP1h. [ABSTRACT FROM AUTHOR]

The phylogenetic relationships among Erwinia amylovora biovar 4 (the pathogen of bacterial shoot blight of pear in Japan), other biovars of E. amylovora, and Erwinia pyrifoliae were investigated using the sequences of 16S rRNA, gyrB, and rpoD genes. The tested isolates formed two distinct monophyletic groups in the phylogenetic trees constructed based on the gyrB gene, rpoD gene, or a combination of the three genes: group 1 contained E. amylovora biovars 1, 2, and 3; group 2 contained E. amylovora bv. 4 and E. pyrifoliae. This phylogenetic analysis showed that E. amylovora bv. 4 was more closely related to E. pyrifoliae than to other biovars of E. amylovora. [ABSTRACT FROM AUTHOR]

The entire genome of bacteriophage OP1, lytic for Xanthomonas oryzae pv. oryzae causing bacterial leaf blight of rice, and the partial genomes of related phages were sequenced and analyzed. The OP1 genome comprises double-stranded, 4785-bp long DNA with 51.1% G + C content. Fifty-nine open reading frames (ORFs) were detected. ORF25 had similarity with the tail fiber gene of phages, whose product is related to host specificity. The ORF25 regions were amplified from four host-range mutants (OP1h, OP1hC, OP1h2, and OP1h2C) by polymerase chain reaction, and their deduced amino acid sequences were compared. Three mutants (OP1hC, OP1h2, OP1h2C) had duplications of a small domain in the N-terminal portion, although there were slight differences in the position of the duplicated sequences. One mutant OP1h had substituted amino acids in the duplication region. New mutants isolated in the laboratory (OP1hC and OP1h2C from OP1 and OP1h2) acquired the ability to lyse strain N5874 belonging to phagovar (lysotype) C. However, they rapidly lost this lytic ability when incubated with other phagovars. This loss was always accompanied by a loss of the characteristic repeats, suggesting that the host range of OP1-related phages changed mainly through duplication and deletion of a small domain in ORF25. [ABSTRACT FROM AUTHOR]

We sequenced and analyzed the genome of OP2 (MAFF 106404), a bacteriophage that lyses Xanthomonas oryzae pv. oryzae ( Xoo). It is 464bp, and the average G + C content is 60.9%. The results suggest that the genome sequence of OP2 is circularly permuted and terminally redundant, like that of coliphages T4 or P22. Sixty-two open reading frames (ORFs) were predicted in the genome. We constructed a circular map of the restriction enzyme sites and a gene map. The genome is clearly divided into four parts according to transcription direction. The directions of 27 ORFs are leftward and those of 35 are rightward. Most leftward ORFs are commonly conserved among many other phages, and some are structure-related or expression-related genes. In contrast, most rightward ORFs contain OP2-specific genes as well as DNA polymerase, helicase, dUTPase, and HNH family endonuclease genes. Nine rightward and 25 leftward ORFs have homology with the ORFs of bacteriophage Bcep1, which lyses Burkholderia cepacia. The leftward-transcribed OP2 genes and their orthologs in Bcep1 conserve a neighboring relationship, although the putative tail fiber gene does not have homology with that of Bcep1. Several ORFs have similarity (−5) to phage-related genes of Xylella fastidiosa and Xanthomonas spp. Exceptionally, the dUTPase gene had 94% identity with Xoo, and no insertions or deletions were detected in it. However, its neighboring regions did not have homology with the Xoo sequence. Although OP2 is a virulent phage of Xoo, some of the genetic characters have features of temperate phages. [ABSTRACT FROM AUTHOR]

The infection frequency of mature apple fruit by Erwinia amylovora and the survival of E. amylovora in the fruit stored at low temperature were investigated. The fruit stems (pedicels) of 460 mature apple fruit were inoculated with 105 or 104 cfu of bioluminescent E. amylovora, tagged with lux genes. Nine days after inoculation, 43% and 27% of the fruit inoculated with 105 and 104 cfu, respectively, were infected. All infected fruit looked healthy. After 6 months of storage at 5°C, almost all of the 142 infected fruit had viable E. amylovora. Of the fruit containing E. amylovora internally, 19.5% had latent infections and the rest had blight symptoms. E. amylovora was not uniformly distributed in the fruit flesh, and internal brown lesions were observed where E. amylovora was densely distributed. These findings showed that mature apple fruit may be infected with E. amylovora, especially as latent infections, and act as a source for long-range dissemination. [ABSTRACT FROM AUTHOR]

Invasion and colonization of mature apple fruit by a transformant ofErwinia amylovoratagged with bioluminescence genes fromVibrio fischeriwas examined. The transformant was deposited on cut surfaces of fruit stems, wounds on the shoulders and calyces, injured fruit-bearing twigs of harvested apple fruit, and cut fruit flesh. After incubation in closed stainless steel or plastic boxes at 25°C, fruit were periodically observed with a two-dimensional luminometer. The presence of the transformant in luminous areas was confirmed by isolating it on selective media.E. amylovora, when deposited in fruit stems: (1) can invade mature as well as immature apple fruit; (2) vertically and horizontally spreads and colonizes along vascular bundles, increasing its population; (3) reaches the calyx end and the flesh just under the exocarp within 3-4 days after inoculation; (4) when deposited on cut fruit flesh, irrespective of its maturity, can easily increase its population and survive 2-4 weeks or more at 25°C; and (5) even at the time of fruit maturation, can migrate within twigs rapidly and reaches the abscission layers between fruit-bearing twigs and fruit stems. [ABSTRACT FROM AUTHOR]

Two toxoflavin biosynthesis-related proteins (TRP-1, TRP-2) from wild strains of the phytopathogen Burkholderia glumae were previously identified, and toxA was determined to encode TRP-1, which has characteristics of a methyltransferase. An 8.2-kb region in the chromosomal DNA of B. glumae that contains the tox operon ( toxABCDE) and an upstream regulatory gene ( toxR) involved in phytotoxin toxoflavin biosynthesis was cloned and sequenced in this study. The sequence downstream of toxA contains four open reading frames ? toxB, toxC, toxD and toxE ? which encode polypeptides with calculated mole-cular masses of 23.3, 61.6, 34.9, and 38.3?kDa, respectively, all having the same transcriptional orientation as toxA. Mutants disrupted in the tox operon lost their ability to produce toxoflavin and did not induce typical chlorosis on infected rice panicles. Based on results from reverse transcription-polymerase chain reaction experiments, the message encoded by the tox operon may be polycistronic for all five genes. Also, the toxR gene was located upstream of this operon. The toxR gene product, with a calculated molecular mass of 37.5?kDa, might be a member of the LysR family of regulatory molecules and an activator that allows transcription of the tox operon. Furthermore, the deduced proteins of ToxB and ToxE had significant similarity to the GTP cyclohydrolase II and the deaminase, respectively, involved in riboflavin synthesis in several organisms. These results suggest that toxoflavin is synthesized in part through a biosynthetic pathway common to the synthesis of riboflavin, starting with GTP as the precursor. [ABSTRACT FROM AUTHOR]

Erwinia ananas, the causal agent of bacterial palea browning of rice, was transformed with bioluminescence genes to clarify their behavior on rice plants. Transformant CTB009T2 was used to inoculate rice plants, and the subsequent bioluminescence of CTB009T2 was observed using a two-dimensional luminometer. Luminous spots frequently appeared on anthers after flowering and on dead tissues such as leaf tips, lower leaf sheaths, and leaf blades. In spikelets that developed the disease symptom on the palea, luminous spots appeared 48 h after flowering on stigmas, basal parts of ovaries, and lodicules. These results indicate that postflowering anthers and dead tissues on rice plants are important sites for a rapid increase in the pathogen population, and that the multiplication of the pathogen on internal tissues of spikelets after flowering is associated with the appearance of browning. [ABSTRACT FROM AUTHOR]

Phytopathogenic Pseudomonas syringae is subdivided into about 50 pathovars due to their conspicuous differentiation with regard to pathogenicity. Based on the results of a phylogenetic analysis of four genes (gyrB, rpoD, hrpL, and hrpS), Sawada et al. (1999) showed that the ancestor of P. syringae had diverged into at least three monophyletic groups during its evolution. Physical maps of the genomes of representative strains of these three groups were constructed, which revealed that each strain had five rrn operons which existed on one circular genome. The fact that the structure and size of genomes vary greatly depending on the pathovar shows that P. syringae genomes are quite rich in plasticity and that they have undergone large-scale genomic rearrangements. Analyses of the codon usage and the GC content at the codon third position, in conjunction with phylogenomic analyses, showed that the gene cluster involved in phaseolotoxin synthesis (argK–tox cluster) expanded its distribution by conducting horizontal transfer onto the genomes of two P. syringae pathovars (pv. actinidiae and pv. phaseolicola) from bacterial species distantly related to P. syringae and that its acquisition was quite recent (i.e., after the ancestor of P. syringae diverged into the respective pathovars). Furthermore, the results of a detailed analysis of argK [an anabolic ornithine carbamoyltransferase (anabolic OCTase) gene], which is present within the argK–tox cluster, revealed the plausible process of generation of an unusual composition of the OCTase genes on the genomes of these two phaseolotoxin-producing pathovars: a catabolic OCTase gene (equivalent to the orthologue of arcB of P. aeruginosa) and an anabolic OCTase gene (argF), which must have been formed by gene duplication, have first been present on the genome of the ancestor of P. syringae; the catabolic OCTase gene has been deleted; the ancestor has diverged into the respective pathovars; the foreign-originated argK–tox cluster has horizontally transferred onto the genomes of pv. actinidiae and pv. phaseolicola; and hence two copies of only the anabolic OCTase genes (argK and argF) came to exist on the genomes of these two pathovars. Thus, the horizontal gene transfer and the genomic rearrangement were proven to have played an important role in the pathogenic differentiation and diversification of P. syringae. [ABSTRACT FROM AUTHOR]

Invasion of apple fruit by Erwinia amylovora from fruit-bearing twigs through the abscission layer at fruit maturation was examined. Erwinia amylovora (ca. 105 cfu) tagged with bioluminescence genes from Vibrio fischeri was deposited in artificial wounds on fruit-bearing twigs of apple trees grown in a containment greenhouse on September 22, 27, or October 5, 2004. On October 22, 176 apples were harvested and cut horizontally in half. The upper halves were stamped on plates of selective medium, and the lower halves were flooded with iodine solution to assess maturity. All fruit were symptomless and fully mature. The pathogen was recovered from 19 (10.8%) apples. The result showed that if at least ca. 105 cfu of E. amylovora are present in fruit-bearing twigs at the time of fruit maturation, the bacteria can pass through the abscission layer into the fruit, even though the mature fruit lack symptoms. [ABSTRACT FROM AUTHOR]

Presents a correction to the article "Invasion and colonization of mature apple fruit by Erwinia amylovora tagged with bioluminescence genes," that was previously published in the 2004 issue of the "Journal of General Plant Pathology."