Femtosecond Pulse Temporal Overlap Estimation and Adjustment in SSFS-Based CARS System

This work is licensed under a Creative Commons Attribution 4.0 International License.We present and verify a residual-pump-based temporal overlap estimation method in soliton self-frequency shift-based coherent anti-Stokes Raman scattering system. The residual pump light, output by a highly nonlinear photonic crystal fiber, acts as a crucial link between the pump and Stokes pulses during the temporal overlap estimation. The wavelength-dependent optical delay is estimated to be 0.141 ps/nm when the Stokes wavelength is 900 nm ~1050 nm according to the temporal overlap estimation method. The actual measurement result is 0.138 ps/nm based on the nonresonant signal from a microscope slide, which is very close to the estimated result. In addition, the Raman resonant signals of liquid cyclohexane at 2853 cm -1 , 2923 cm -1 and 2938 cm -1 have also been successfully detected at the predicted optical delays 427.27 ps and 428.17 ps

The genomic and bulked segregant analysis of \u3ci\u3eCurcuma alismatifolia\u3c/i\u3e revealed its diverse bract pigmentation

Compared with most flowers where the showy part comprises specialized leaves (petals) directly subtending the reproductive structures, most Zingiberaceae species produce showy ‘‘flowers’’ through modifications of leaves (bracts) subtending the true flowers throughout an inflorescence. Curcuma alismatifolia, belonging to the Zingiberaceae family, a plant species originating from Southeast Asia, has become increasingly popular in the flower market worldwide because of its varied and esthetically pleasing bracts produced in different cultivars. Here, we present the chromosome-scale genome assembly of C. alismatifolia ‘‘Chiang Mai Pink’’ and explore the underlying mechanisms of bract pigmentation. Comparative genomic analysis revealed C. alismatifolia contains a residual signal of wholegenome duplication. Duplicated genes, including pigment-related genes, exhibit functional and structural differentiation resulting in diverse bract colors among C. alismatifolia cultivars. In addition, we identified the key genes that produce different colored bracts in C. alismatifolia, such as F3\u275’H, DFR, ANS and several transcription factors for anthocyanin synthesis, as well as chlH and CAO in the chlorophyll synthesis pathway by conducting transcriptomic analysis, bulked segregant analysis using both DNA and RNA data, and population genomic analysis. This work provides data for understanding the mechanism of bract pigmentation and will accelerate breeding in developing novel cultivars with richly colored bracts in C. alismatifolia and related species. It is also important to understand the variation in the evolution of the Zingiberaceae family

Antibiofilm Activity of an Exopolysaccharide from Marine Bacterium Vibrio sp. QY101

Bacterial exopolysaccharides have always been suggested to play crucial roles in the bacterial initial adhesion and the development of complex architecture in the later stages of bacterial biofilm formation. However, Escherichia coli group II capsular polysaccharide was characterized to exert broad-spectrum biofilm inhibition activity. In this study, we firstly reported that a bacterial exopolysaccharide (A101) not only inhibits biofilm formation of many bacteria but also disrupts established biofilm of some strains. A101 with an average molecular weight of up to 546 KDa, was isolated and purified from the culture supernatant of the marine bacterium Vibrio sp. QY101 by ethanol precipitation, iron-exchange chromatography and gel filtration chromatography. High performance liquid chromatography traces of the hydrolyzed polysaccharides showed that A101 is primarily consisted of galacturonic acid, glucuronic acid, rhamnose and glucosamine. A101 was demonstrated to inhibit biofilm formation by a wide range of Gram-negative and Gram-positive bacteria without antibacterial activity. Furthermore, A101 displayed a significant disruption on the established biofilm produced by Pseudomonas aeruginosa, but not by Staphylococcus aureus. Importantly, A101 increased the aminoglycosides antibiotics' capability of killing P. aeruginosa biofilm. Cell primary attachment to surfaces and intercellular aggregates assays suggested that A101 inhibited cell aggregates of both P. aeruginosa and S. aureus, while the cell-surface interactions inhibition only occurred in S. aureus, and the pre-formed cell aggregates dispersion induced by A101 only occurred in P. aeruginosa. Taken together, these data identify the antibiofilm activity of A101, which may make it potential in the design of new therapeutic strategies for bacterial biofilm-associated infections and limiting biofilm formation on medical indwelling devices. The found of A101 antibiofilm activity may also promote a new recognition about the functions of bacterial exopolysaccharides

Pathogenesis and modelling of infection dynamics in Ralstonia solanacearum

Le flétrissement bactérien causé par Ralstonia solanacearum limite la production mondiale de nombreuses cultures. La diversité génétique étendue de la bactérie a permis au cours des dernières années de concevoir le concept de complexe d'espèces de R. solanacearum (RSSC). Le séquençage génomique de plus de 30 souches représentatives de chaque groupe phylogénétique a élargi notre connaissance de l'évolution et de la spéciation du RSSC. Cela a permis d'identifier de nouvelles fonctions associées à la virulence. En outre, un grand nombre d'études ont été réalisées sur l'interaction plantes hôtes-R. solanacearum et éclairent la génétique, la biologie moléculaire et le développement de la maladie. Ces études ont documenté les stratégies d'infection qu'utilise R. solanacearum pour faire face aux défenses immunitaires des plantes. Bien que ces données qualitatives soient fondamentales pour comprendre l'infection par R. solanacearum, elles sont insuffisantes pour savoir si une plante sera infectées ou non. Cette question fondamentale nécessiteune compréhension quantitative des processus responsables de l'infection et colonisation de la plante par la populations de R. solanacearum. Ce travail a permis une étude quantitative permettant de répondre à la question suivante:"Combien d'individus de R. solanacearum entrent de la racine pour établir la base de l'infection donnant lieu a la maladie bactérienne dans la plante?" Cela nous a permis de déterminer quels facteurs contrôlent cette dynamique d'infection de R. solanacearum au sein de la plante hôte. Cette question scientifique nécessite un réexamen du cycle de vie de R. solanacearum et la caractérisation précise de l'ensemble du processus d'infection dans la plante. Sept paramètres dynamiques ont été affinés à partir de cinq étapes d'infection de R. solanacearum. Ensuite, nous avons établi un modèle mathématique de la dynamique dans l'hôte de la bactérie par l'intégration de ces paramètres. Le modèle suggère que toute la dynamique de la population influe sur la taille de la population de R. solanacearum. L'évaluation in vivo des paramètres et de leurs interactions prédit une petite taille de la population fondatrice, autour de quatre centaines de celluels bactériennes, ce qui a été confirmé par des mesures expérimentales avec une approche probabiliste. Pour comprendre les mécanismes qui restreignent la population de R. solanacearum, nous avons étudié les impacts de la virulence bactérienne, des barrières des plantes et du facteur environnemental sur la population fondatrice de l'infection. Nous avons montré que le goulot d'étranglement des infections est principalement modulé par l'agent pathogène (arsenal de virulence), l'hôte (caractéristiques physiques et immunitaires) et les conditions environnementales (température) en accord avec des études qualitatives.Bacterial wilt caused by Ralstonia solanacearum limits the global production of many crops. The extensive genetic diversity of the bacterium has in recent years led to the concept of a R. solanacearum Species Complex (RSSC). Genome sequencing of over 30 representative strains of the each phylogenetic groups has broadened our knowledge of the evolution and speciation of RSSC. This enabled the identification of novel virulence-associated functions. Furthermore, a large number of studies have been carried on plants-R. solanacearum interactions and shed light on the genetics, molecular biology, and disease development. These studies have documented the infection strategies of R. solanacearum employed to cope with plant immune defenses. Although these qualitative investigations are a basis to understand the pathogenesis of R. solanacearum, they are insufficient to know whether or not plants will be diseased. These fundamental questions require a quantitative understanding of the processes responsible for the rise, dissemination and fall of the infection populations of R. solanacearum. This work pioneered the quantitative study in plant bacterial pathogens by addressing the following question: "How many R. solanacearum individuals enter from the root to establish the bacterial wilt disease in plant?" It allowed us to determine what factors control the infection dynamics of R. solanacearum within the host plant. This scientific question requires a re-examination on the life cycle of R. solanacearum and the precise characterization of the whole infection process in plant. Seven dynamical parameters were refined from five subsequent infection steps of R. solanacearum in host plant. Then, we established a mathematical model of within-host dynamics of the bacterium by the integration of these parameters. The model suggests that the whole population dynamics influences the founding population/bottleneck size of R. solanacearum. The in vivo assessment of parameters and their interactions predicted a small founding population size, around four hundred bacterial cells, which was confirmed by experimental measurements with a probabilistic approach. To understand mechanisms restricting R. solanacearum population, we further investigated impacts of bacterial virulence, plant barriers and environmental factor on the infection founding population. We showed that infection bottleneck is mainly modulated by the pathogen (virulence arsenal), the host (physical and immunity traits) and the environmental conditions (temperature)

Modélisation et détermination des paramètres clefs gouvernant l'infection et la colonisation des plantes de tomate par la bactérie pathogène Ralstonia solanacearum

Le flétrissement bactérien causé par Ralstonia solanacearum limite la production mondiale de nombreuses cultures. La diversité génétique étendue de la bactérie a permis au cours des dernières années de concevoir le concept de complexe d'espèces de R. solanacearum (RSSC). Le séquençage génomique de plus de 30 souches représentatives de chaque groupe phylogénétique a élargi notre connaissance de l'évolution et de la spéciation du RSSC. Cela a permis d'identifier de nouvelles fonctions associées à la virulence. En outre, un grand nombre d'études ont été réalisées sur l'interaction plantes hôtes-R. solanacearum et éclairent la génétique, la biologie moléculaire et le développement de la maladie. Ces études ont documenté les stratégies d'infection qu'utilise R. solanacearum pour faire face aux défenses immunitaires des plantes. Bien que ces données qualitatives soient fondamentales pour comprendre l'infection par R. solanacearum, elles sont insuffisantes pour savoir si une plante sera infectées ou non. Cette question fondamentale nécessiteune compréhension quantitative des processus responsables de l'infection et colonisation de la plante par la populations de R. solanacearum. Ce travail a permis une étude quantitative permettant de répondre à la question suivante:"Combien d'individus de R. solanacearum entrent de la racine pour établir la base de l'infection donnant lieu a la maladie bactérienne dans la plante?" Cela nous a permis de déterminer quels facteurs contrôlent cette dynamique d'infection de R. solanacearum au sein de la plante hôte. Cette question scientifique nécessite un réexamen du cycle de vie de R. solanacearum et la caractérisation précise de l'ensemble du processus d'infection dans la plante. Sept paramètres dynamiques ont été affinés à partir de cinq étapes d'infection de R. solanacearum. Ensuite, nous avons établi un modèle mathématique de la dynamique dans l'hôte de la bactérie par l'intégration de ces paramètres. Le modèle suggère que toute la dynamique de la population influe sur la taille de la population de R. solanacearum. L'évaluation in vivo des paramètres et de leurs interactions prédit une petite taille de la population fondatrice, autour de quatre centaines de celluels bactériennes, ce qui a été confirmé par des mesures expérimentales avec une approche probabiliste. Pour comprendre les mécanismes qui restreignent la population de R. solanacearum, nous avons étudié les impacts de la virulence bactérienne, des barrières des plantes et du facteur environnemental sur la population fondatrice de l'infection. Nous avons montré que le goulot d'étranglement des infections est principalement modulé par l'agent pathogène (arsenal de virulence), l'hôte (caractéristiques physiques et immunitaires) et les conditions environnementales (température) en accord avec des études qualitatives.Bacterial wilt caused by Ralstonia solanacearum limits the global production of many crops. The extensive genetic diversity of the bacterium has in recent years led to the concept of a R. solanacearum Species Complex (RSSC). Genome sequencing of over 30 representative strains of the each phylogenetic groups has broadened our knowledge of the evolution and speciation of RSSC. This enabled the identification of novel virulence-associated functions. Furthermore, a large number of studies have been carried on plants-R. solanacearum interactions and shed light on the genetics, molecular biology, and disease development. These studies have documented the infection strategies of R. solanacearum employed to cope with plant immune defenses. Although these qualitative investigations are a basis to understand the pathogenesis of R. solanacearum, they are insufficient to know whether or not plants will be diseased. These fundamental questions require a quantitative understanding of the processes responsible for the rise, dissemination and fall of the infection populations of R. solanacearum. This work pioneered the quantitative study in plant bacterial pathogens by addressing the following question: "How many R. solanacearum individuals enter from the root to establish the bacterial wilt disease in plant?" It allowed us to determine what factors control the infection dynamics of R. solanacearum within the host plant. This scientific question requires a re-examination on the life cycle of R. solanacearum and the precise characterization of the whole infection process in plant. Seven dynamical parameters were refined from five subsequent infection steps of R. solanacearum in host plant. Then, we established a mathematical model of within-host dynamics of the bacterium by the integration of these parameters. The model suggests that the whole population dynamics influences the founding population/bottleneck size of R. solanacearum. The in vivo assessment of parameters and their interactions predicted a small founding population size, around four hundred bacterial cells, which was confirmed by experimental measurements with a probabilistic approach. To understand mechanisms restricting R. solanacearum population, we further investigated impacts of bacterial virulence, plant barriers and environmental factor on the infection founding population. We showed that infection bottleneck is mainly modulated by the pathogen (virulence arsenal), the host (physical and immunity traits) and the environmental conditions (temperature)

Genome Sequencing of Ralstonia solanacearum CQPS-1, a Phylotype I Strain Collected from a Highland Area with Continuous Cropping of Tobacco

Ralstonia solanacearum, an agent of bacterial wilt, is a highly variable species with a broad host range and wide geographic distribution. As a species complex, it has extensive genetic diversity and its living environment is polymorphic like the lowland and the highland area, so more genomes are needed for studying population evolution and environment adaptation. In this paper, we reported the genome sequencing of R. solanacearum strain CQPS-1 isolated from wilted tobacco in Pengshui, Chongqing, China, a highland area with severely acidified soil and continuous cropping of tobacco more than 20 years. The comparative genomic analysis among different R. solanacearum strains was also performed. The completed genome size of CQPS-1 was 5.89 Mb and contained the chromosome (3.83 Mb) and the megaplasmid (2.06 Mb). A total of 5229 coding sequences were predicted (the chromosome and megaplasmid encoded 3573 and 1656 genes, respectively). A comparative analysis with eight strains from four phylotypes showed that there was some variation among the species, e.g., a large set of specific genes in CQPS-1. Type III secretion system gene cluster (hrp gene cluster) was conserved in CQPS-1 compared with the reference strain GMI1000. In addition, most genes coding core type III effectors were also conserved with GMI1000, but significant gene variation was found in the gene ripAA: the identity compared with strain GMI1000 was 75% and the hrp(II) box promoter in the upstream had significantly mutated. This study provided a potential resource for further understanding of the relationship between variation of pathogenicity factors and adaptation to the host environment

Comparison of tragal perichondrium and COOK artificial material in endoscopic type 1 tympanoplasty

Objective: Various materials have been used for tympanic membrane reconstruction in middle ear surgery. This study aimed to evaluate the difference between the tragal perichondrium and COOK artificial material in patients who underwent endoscopic type 1 tympanoplasty. Method: This retrospective study included patients who underwent endoscopic type 1 tympanoplasty from June 2021 to June 2022 at Sir Run Run Shaw Hospital, Zhejiang University School of Medicine. Patients were divided into group A (tragal perichondrium) and group B (COOK artificial material) according to the material used in the operation. All patients were followed up for 6 months. The differences in age, gender, operation site, disease course, preoperative air-bone gap (ABG), operation time, blood loss, hearing gain, and wound healing rate were compared between the two groups. Results: This study enrolled 197 patients, with 120 patients in group A and 77 patients in group B. There were no significant differences in age, gender, operation site, disease course, or preoperative ABG between groups A and B (p > 0.05). Both groups had significant postoperative improvement in hearing (group A: 30.98 ± 9.58 dB vs. 17.07 ± 9.92 dB, p < 0.001; group B: 29.75 ± 7.52 dB vs. 14.25 ± 9.07 dB, p < 0.001). The mean hearing gain in group A and group B was comparable (14.02 ± 11.91 dB vs. 15.50 ± 7.05 dB, p = 0.609). The wound healing rates of groups A and B were no differences (93.33% vs. 87.01%, p = 0.133). The patients in group B had a shorter operation duration (72.57 ± 11.32 min vs. 61.86 ± 9.27 min, p = 0.045) and less blood loss (12.38 ± 3.7 mL vs. 8.10 ± 2.43 mL, p = 0.004). Conclusions: Tragal perichondrium and COOK artificial material are reliable for functional and anatomical outcomes in endoscopic type 1 tympanoplasty, and COOK artificial material can save operation time and blood loss in surgery compared to the tragal perichondrium