Characterizing the regulatory mechanisms in fusarium verticillioides secondary metabolism using functional genomics approaches

Fusarium verticillioides is one of the most important fungal pathogens of maize and has also received increasing attention due to its ability to produce various secondary metabolites, including fumonisin B1 (FB1) and bikaverin. However, little is known about the regulatory mechanisms associated with F. verticillioides secondary metabolism. In this study, I utilized functional genomics, forward and reverse genetics, proteomics, and high efficiency homologous recombination, to better understand the complex secondary metabolism regulations in F. verticillioides. First, using the reverse genetics approach, I characterized a putative protein phosphatase gene, CPP1 as a negative regulator of FB1 biosynthesis. CPP1 gene deletion also affected multiple phenotypes such as radial growth, conidia germination rates, macroconidia formation, and hyphal swelling. Through gene complementation, I also demonstrated that the F. verticillioides CPP1 and Neurospora crassa wild-type ppe-1 gene are functionally conserved. Second, I used proteomics and quantitative real-time (qRT)-PCR, to advance our understanding of genes associated with fumonisin production. I analyzed the proteomic changes associated with the mutation in FCC1, a key positive regulator of fumonisins biosynthesis. I isolated proteins that were significantly up-regulated in either the wild-type or the fcc1 mutant, and transcriptional profiles of the genes corresponding to the selected proteins were analyzed via qRT-PCR. These genes showing expression patterns concomitant with fumonisin biosynthesis can be identified as primary targets for functional analysis. Next, I utilized REMI (Restriction Enzyme Mediated Integration) to isolate GAC1 gene, which encodes a GTPase activating protein, that serve as a negative regulator of bikaverin biosynthesis in F. verticillioides. AREA and PKS4 are downstream genes that are regulated positively and negatively by GAC1, respectively. Lastly, I generated a highly efficient homologous recombination strain of F. verticillioides. In eukaryotes, KU70 and KU80 play important roles in nonhomologous end-joining process, which leads to a high percentage of ectopic integration events during fungal transformation. By generating a KU70 gene deletion mutant (SF41), I have established a resource that will contribute to functional genomic research in F. verticillioides

Dynamic model for failures in biological systems

A dynamic model for failures in biological organisms is proposed and studied both analytically and numerically. Each cell in the organism becomes dead under sufficiently strong stress, and is then allowed to be healed with some probability. It is found that unlike the case of no healing, the organism in general does not completely break down even in the presence of noise. Revealed is the characteristic time evolution that the system tends to resist the stress longer than the system without healing, followed by sudden breakdown with some fraction of cells surviving. When the noise is weak, the critical stress beyond which the system breaks down increases rapidly as the healing parameter is raised from zero, indicative of the importance of healing in biological systems.Comment: To appear in Europhys. Let

Dynamic model of fiber bundles

A realistic continuous-time dynamics for fiber bundles is introduced and studied both analytically and numerically. The equation of motion reproduces known stationary-state results in the deterministic limit while the system under non-vanishing stress always breaks down in the presence of noise. Revealed in particular is the characteristic time evolution that the system tends to resist the stress for considerable time, followed by sudden complete rupture. The critical stress beyond which the complete rupture emerges is also obtained

Characterizing the regulatory mechanisms in fusarium verticillioides secondary metabolism using functional genomics approaches

Fusarium verticillioides is one of the most important fungal pathogens of maize and has also received increasing attention due to its ability to produce various secondary metabolites, including fumonisin B1 (FB1) and bikaverin. However, little is known about the regulatory mechanisms associated with F. verticillioides secondary metabolism. In this study, I utilized functional genomics, forward and reverse genetics, proteomics, and high efficiency homologous recombination, to better understand the complex secondary metabolism regulations in F. verticillioides. First, using the reverse genetics approach, I characterized a putative protein phosphatase gene, CPP1 as a negative regulator of FB1 biosynthesis. CPP1 gene deletion also affected multiple phenotypes such as radial growth, conidia germination rates, macroconidia formation, and hyphal swelling. Through gene complementation, I also demonstrated that the F. verticillioides CPP1 and Neurospora crassa wild-type ppe-1 gene are functionally conserved. Second, I used proteomics and quantitative real-time (qRT)-PCR, to advance our understanding of genes associated with fumonisin production. I analyzed the proteomic changes associated with the mutation in FCC1, a key positive regulator of fumonisins biosynthesis. I isolated proteins that were significantly up-regulated in either the wild-type or the fcc1 mutant, and transcriptional profiles of the genes corresponding to the selected proteins were analyzed via qRT-PCR. These genes showing expression patterns concomitant with fumonisin biosynthesis can be identified as primary targets for functional analysis. Next, I utilized REMI (Restriction Enzyme Mediated Integration) to isolate GAC1 gene, which encodes a GTPase activating protein, that serve as a negative regulator of bikaverin biosynthesis in F. verticillioides. AREA and PKS4 are downstream genes that are regulated positively and negatively by GAC1, respectively. Lastly, I generated a highly efficient homologous recombination strain of F. verticillioides. In eukaryotes, KU70 and KU80 play important roles in nonhomologous end-joining process, which leads to a high percentage of ectopic integration events during fungal transformation. By generating a KU70 gene deletion mutant (SF41), I have established a resource that will contribute to functional genomic research in F. verticillioides

A Novel Cross-Layer Authentication Protocol for the Internet of Things

An innovative cross-layer authentication protocol that integrates cryptography-based authentication and physical layer authentication (PLA) is proposed for massive cellular Internet of things (IoT) systems. Due to dramatic increases in the number of cellular IoT devices, a centralized authentication architecture in which a mobility management entity in core networks administers authentication of massive numbers of IoT devices may cause network congestion with large signaling overhead. Thus, a distributed authentication architecture in which a base station in radio access networks authenticates IoT devices locally is presented. In addition, a cross-layer authentication protocol is designed with a novel integration strategy under the distributed authentication architecture, where PLA, which employs physical features for authentication, is used as preemptive authentication in the proposed protocol. Theoretical analysis and numerical simulations were performed to analyze the trade-off between authentication performance and overhead in the proposed authentication method compared with existing authentication protocols. The results demonstrate that the proposed protocol outperforms conventional authentication and key agreement protocols in terms of overhead and computational complexity while guaranteeing low authentication error probability

Putative spin liquid in the triangle-based iridate Ba3_3IrTi2_2O9_9

We report on thermodynamic, magnetization, and muon spin relaxation measurements of the strong spin-orbit coupled iridate Ba$_3$IrTi$_2$O$_9$, which constitutes a new frustration motif made up a mixture of edge- and corner-sharing triangles. In spite of strong antiferromagnetic exchange interaction of the order of 100~K, we find no hint for long-range magnetic order down to 23 mK. The magnetic specific heat data unveil the $T$-linear and -squared dependences at low temperatures below 1~K. At the respective temperatures, the zero-field muon spin relaxation features a persistent spin dynamics, indicative of unconventional low-energy excitations. A comparison to the $4d$ isostructural compound Ba$_3$RuTi$_2$O$_9$ suggests that a concerted interplay of compass-like magnetic interactions and frustrated geometry promotes a dynamically fluctuating state in a triangle-based iridate.Comment: Physical Review B accepte

Topological quantization and degeneracy in Josephson-junction arrays

We consider the conductivity quantization in two-dimensional arrays of mesoscopic Josephson junctions, and examine the associated degeneracy in various regimes of the system. The filling factor of the system may be controlled by the gate voltage as well as the magnetic field, and its appropriate values for quantization is obtained by employing the Jain hierarchy scheme both in the charge description and in the vortex description. The duality between the two descriptions then suggests the possibility that the system undergoes a change in degeneracy while the quantized conductivity remains fixed.Comment: To appear in Phys. Rev.

Mathematical modelling long-term effects of replacing Prevnar7 with Prevnar13 on invasive pneumococcal diseases in England and Wales

England and Wales recently replaced the 7-valent pneumococcal conjugate vaccine (PCV7) with its 13-valent equivalent (PCV13), partly based on projections from mathematical models of the long-term impact of such a switch compared to ceasing pneumococcal conjugate vaccination altogether. A compartmental deterministic model was used to estimate parameters governing transmission of infection and competition between different groups of pneumococcal serotypes prior to the introduction of PCV13. The best-fitting parameters were used in an individual based model to describe pneumococcal transmission dynamics and effects of various options for the vaccination programme change in England and Wales. A number of scenarios were conducted using (i) different assumptions about the number of invasive pneumococcal disease cases adjusted for the increasing trend in disease incidence prior to PCV7 introduction in England and Wales, and (ii) a range of values representing serotype replacement induced by vaccination of the additional six serotypes in PCV13. Most of the scenarios considered suggest that ceasing pneumococcal conjugate vaccine use would cause an increase in invasive pneumococcal disease incidence, while replacing PCV7 with PCV13 would cause an overall decrease. However, the size of this reduction largely depends on the level of competition induced by the additional serotypes in PCV13. The model estimates that over 20 years of PCV13 vaccination, around 5000–62000 IPD cases could be prevented compared to stopping pneumococcal conjugate vaccination altogether. Despite inevitable uncertainty around serotype replacement effects following introduction of PCV13, the model suggests a reduction in overall invasive pneumococcal disease incidence in all cases. Our results provide useful evidence on the benefits of PCV13 to countries replacing or considering replacing PCV7 with PCV13, as well as data that can be used to evaluate the cost-effectiveness of such a switch

Staphylococcal enterotoxin sensitization in a community-based population : a potential role in adult-onset asthma

Background: Recent studies suggest that Staphylococcus aureus enterotoxin sensitization is a risk factor for asthma. However, there is a paucity of epidemiologic evidence on adult-onset asthma in community-based populations. Objective: We sought to evaluate the epidemiology and the clinical significance of staphylococcal enterotoxin sensitization in community-based adult populations. Methods: The present analyses were performed using the baseline data set of Korean adult population surveys, consisting of 1080 adults (mean age=60.2years) recruited from an urban and a rural community. Questionnaires, methacholine challenge tests, and allergen skin tests were performed for defining clinical phenotypes. Sera were analysed for total IgE and enterotoxin-specific IgE using ImmunoCAP. Results: Staphylococcal enterotoxin sensitization (0.35kU/L) had a prevalence of 27.0%. Risk factors were identified as male sex, current smoking, advanced age (61years), and inhalant allergen sensitization. Current asthma was mostly adult onset (18years old) and showed independent associations with high enterotoxin-specific IgE levels in multivariate logistic regression tests. In multivariate linear regressions, staphylococcal enterotoxin-specific IgE level was identified as the major determinant factor for total IgE level. Conclusions and Clinical Relevance: Staphylococcal enterotoxin sensitization was independently associated with adult-onset asthma in adult community populations. Strong correlations between the enterotoxin-specific IgE and total IgE levels support the clinical significance. The present findings warrant further studies for the precise roles of staphylococcal enterotoxin sensitization in the asthma pathogenesis

Optical observations of NEA 3200 Phaethon (1983 TB) during the 2017 apparition

The near-Earth asteroid 3200 Phaethon (1983 TB) is an attractive object not only from a scientific viewpoint but also because of JAXA's DESTINY+ target. The rotational lightcurve and spin properties were investigated based on the data obtained in the ground-based observation campaign of Phaethon. We aim to refine the lightcurves and shape model of Phaethon using all available lightcurve datasets obtained via optical observation, as well as our time-series observation data from the 2017 apparition. Using eight 1-2-m telescopes and an optical imager, we acquired the optical lightcurves and derived the spin parameters of Phaethon. We applied the lightcurve inversion method and SAGE algorithm to deduce the convex and non-convex shape model and pole orientations. We analysed the optical lightcurve of Phaethon and derived a synodic and a sidereal rotational period of 3.6039 h, with an axis ratio of a/b = 1.07. The ecliptic longitude (lambda) and latitude (beta) of the pole orientation were determined as (308, -52) and (322, -40) via two independent methods. A non-convex model from the SAGE method, which exhibits a concavity feature, is also presented.Comment: 14 pages, 4 figures, 1 figure in Appendix A. Accepted for publication in Astronomy & Astrophysics (A&A