De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood

Background: The basidiomycete Rigidoporus microporus is a fungus that causes the white rot disease of the tropical rubber tree, Hevea brasiliensis, the major source of commercial natural rubber. Besides its lifestyle as a pathogen, the fungus is known to switch to saprotrophic growth on wood with the ability to degrade both lignin and cellulose. There is almost no genomic or transcriptomic information on the saprotrophic abilities of this fungus. In this study, we present the fungal transcriptomic profiles during saprotrophic growth on rubber wood. Results: A total of 266.6 million RNA-Seq reads were generated from six libraries of the fungus growing either on rubber wood or without wood. De novo assembly produced 34, 518 unigenes with an average length of 217(bp. Annotation of unigenes using public databases; GenBank, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups (COG) and Gene Ontology (GO) produced 25, 880 annotated unigenes. Transcriptomic profiling analysis revealed that the fungus expressed over 300 genes encoding lignocellulolytic enzymes. Among these, 175 genes were up-regulated in rubber wood. These include three members of the glycoside hydrolase family 43, as well as various glycosyl transferases, carbohydrate esterases and polysaccharide lyases. A large number of oxidoreductases which includes nine manganese peroxidases were also significantly up-regulated in rubber wood. Several genes involved in fatty acid metabolism and degradation as well as natural rubber degradation were expressed in the transcriptome. Four genes (acyl-CoA synthetase, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase and acyl-CoA acetyltransferase) potentially involved in rubber latex degradation pathway were also induced. A number of ATP binding cassette (ABC) transporters and hydrophobin genes were significantly expressed in the transcriptome during saprotrophic growth. Some genes related to energy metabolism were also induced. Conclusions: The analysed data gives an insight into the activation of lignocellulose breakdown machinery of R. microporus. This study also revealed genes with relevance in antibiotic metabolism (e.g. cephalosporin esterase) as well as those with potential applications in fatty acid degradation. This is the first study on the transcriptomic analysis of R. microporus on rubber wood and should serve as a pioneering resource for future studies of the fungus at the genomic or transcriptomic level.Peer reviewe

Analysis of Oscillator Neural Networks for Sparsely Coded Phase Patterns

We study a simple extended model of oscillator neural networks capable of storing sparsely coded phase patterns, in which information is encoded both in the mean firing rate and in the timing of spikes. Applying the methods of statistical neurodynamics to our model, we theoretically investigate the model's associative memory capability by evaluating its maximum storage capacities and deriving its basins of attraction. It is shown that, as in the Hopfield model, the storage capacity diverges as the activity level decreases. We consider various practically and theoretically important cases. For example, it is revealed that a dynamically adjusted threshold mechanism enhances the retrieval ability of the associative memory. It is also found that, under suitable conditions, the network can recall patterns even in the case that patterns with different activity levels are stored at the same time. In addition, we examine the robustness with respect to damage of the synaptic connections. The validity of these theoretical results is confirmed by reasonable agreement with numerical simulations.Comment: 23 pages, 11 figure

Solutions to the cosmological constant problems

We critically review several recent approaches to solving the two cosmological constant problems. The "old" problem is the discrepancy between the observed value of $\Lambda$ and the large values suggested by particle physics models. The second problem is the "time coincidence" between the epoch of galaxy formation $t_G$ and the epoch of $\Lambda$-domination t_\L. It is conceivable that the "old" problem can be resolved by fundamental physics alone, but we argue that in order to explain the "time coincidence" we must account for anthropic selection effects. Our main focus here is on the discrete-$\Lambda$ models in which $\Lambda$ can change through nucleation of branes. We consider the cosmology of this type of models in the context of inflation and discuss the observational constraints on the model parameters. The issue of multiple brane nucleation raised by Feng {\it et. al.} is discussed in some detail. We also review continuous-\L models in which the role of the cosmological constant is played by a slowly varying potential of a scalar field. We find that both continuous and discrete models can in principle solve both cosmological constant problems, although the required values of the parameters do not appear very natural. M-theory-motivated brane models, in which the brane tension is determined by the brane coupling to the four-form field, do not seem to be viable, except perhaps in a very tight corner of the parameter space. Finally, we point out that the time coincidence can also be explained in models where $\Lambda$ is fixed, but the primordial density contrast $Q=\delta\rho/\rho$ is treated as a random variable.Comment: 30 pages, 3 figures, two notes adde

Instantons in the nonperturbative QCD vacuum

The influence of nonperturbative fields on instantons in quantum chromodynamics is studied. Nonperturbative vacuum is described in terms of nonlocal gauge invariant vacuum averages of gluon field strength.Effective action for instanton is derived in bilocal approximation and it is demonstrated that stochastic background gluon fields are responsible for infra-red (IR) stabilization of instantons. Dependence of characteristic instanton size on gluon condensate and correlation length in nonperturbative vacuum is found. Comparison of obtained instanton size distribution with lattice data is made.Comment: 25 pages, 7 figures, 3 tables, RevTeX4, some corrections made and references adde

Narrow-band search of continuous gravitational-wave signals from Crab and Vela pulsars in Virgo VSR4 data

In this paper we present the results of a coherent narrow-band search for continuous gravitational-wave signals from the Crab and Vela pulsars conducted on Virgo VSR4 data. In order to take into account a possible small mismatch between the gravitational-wave frequency and two times the star rotation frequency, inferred from measurement of the electromagnetic pulse rate, a range of 0.02 Hz around two times the star rotational frequency has been searched for both the pulsars. No evidence for a signal has been found and 95% confidence level upper limits have been computed assuming both that polarization parameters are completely unknown and that they are known with some uncertainty, as derived from x-ray observations of the pulsar wind torii. For Vela the upper limits are comparable to the spin-down limit, computed assuming that all the observed spin-down is due to the emission of gravitational waves. For Crab the upper limits are about a factor of 2 below the spin-down limit, and represent a significant improvement with respect to past analysis. This is the first time the spin-down limit is significantly overcome in a narrow-band search.Fil: Quiroga, Gonzalo Damián. Universidad Nacional de Córdoba. Facultad de Matemática, Astronomia y Física. Sección Física. Grupo de Relatividad y Gravitacion; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Física Enrique Gaviola. Universidad Nacional de Córdoba. Instituto de Física Enrique Gaviola; ArgentinaFil: Maglione, Cesar German. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Física Enrique Gaviola. Universidad Nacional de Córdoba. Instituto de Física Enrique Gaviola; Argentina. Universidad Nacional de Córdoba. Facultad de Matemática, Astronomia y Física. Sección Física. Grupo de Relatividad y Gravitacion; ArgentinaFil: Reula, Oscar Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Física Enrique Gaviola. Universidad Nacional de Córdoba. Instituto de Física Enrique Gaviola; Argentina. Universidad Nacional de Córdoba. Facultad de Matemática, Astronomia y Física. Sección Física. Grupo de Relatividad y Gravitacion; ArgentinaFil: Aasi, J.. California Institute of Technology; Estados UnidosFil: Abbot, B. P.. California Institute of Technology; Estados UnidosFil: Abbot, R.. California Institute of Technology; Estados UnidosFil: Abbot, T.. State University of Louisiana; Estados UnidosFil: Abernathy, M. R.. California Institute of Technology; Estados UnidosFil: Acernese, F.. Universita di Salerno; Italia. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Ackley, K.. University of Florida; Estados UnidosFil: Adams, C.. LIGO Livingston Observatory; Estados UnidosFil: Adams, T.. Universite de Savoie. Laboratoire d’Annecy-le-Vieux de Physique des Particules; Francia. Cardiff University; Reino UnidoFil: Adams, T.. Universite de Savoie. Laboratoire d’Annecy-le-Vieux de Physique des Particules; FranciaFil: Addesso, P.. University of Sannio at Benevento; ItaliaFil: Adhikar, R. X.. California Institute of Technology; Estados UnidosFil: Adya, V.. Max-Planck-Institut für Gravitationsphysik; AlemaniaFil: Affeldt, C.. Max-Planck-Institut für Gravitationsphysik; AlemaniaFil: Agathos, M.. Nikhef; Science Park; Países BajosFil: Agatsuma, K.. Nikhef; Science Park; Países BajosFil: Aggarwal, N.. Massachusetts Institute of Technology; Estados UnidosFil: Aguiar, O. D.. Centro de Previsao de Tempo e Estudos Climáticos. Instituto Nacional de Pesquisas Espaciais; BrasilFil: Ain, A.. Inter-University Centre for Astronomy and Astrophysics; IndiaFil: Ajith, P.. Tata Institute of Fundamental Research; IndiaFil: Alemic, A.. Syracuse University; Estados UnidosFil: Allen, B.. Max-Planck-Institut für Gravitationsphysik; Alemania. University of Wisconsin; Estados UnidosFil: Allocca, A.. Università degli Studi di Siena; Italia. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Amariutei, D.. University of Florida; Estados UnidosFil: Anderson, S. B.. California Institute of Technology; Estados UnidosFil: Anderson, W. G.. University of Wisconsin; Estados UnidosFil: Arai, K.. California Institute of Technology; Estados Unido

Global structure of exact cosmological solutions in the brane world

We find the explicit coordinate transformation which links two exact cosmological solutions of the brane world which have been recently discovered. This means that both solutions are exactly the same with each other. One of two solutions is described by the motion of a domain wall in the well-known 5-dimensional Schwarzshild-AdS spacetime. Hence, we can easily understand the region covered by the coordinate used by another solution.Comment: Latex, 9 pages including 5 figures; references add, accepted for publication in Physical Review

On whether azimuthal isotropy and alongshelf translational invariance are present in low-frequency acoustic propagation along the New Jersey shelfbreak

Author Posting. © Acoustical Society of America, 2012. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 131 (2012): 1762-1781, doi:10.1121/1.3672644.To understand the issues associated with the presence (or lack) of azimuthal isotropy and horizontal (along isobath) invariance of low-frequency (center frequencies of 600 Hz and 900 Hz) acoustic propagation in a shelfbreak environment, a series of experiments were conducted under the Autonomous Wide-Aperture Cluster for Surveillance component of the Shallow Water 2006 experiment. Transmission loss data reported here were from two mobile acoustic sources executing (nearly) circular tracks transmitting to sonobuoy receivers in the circle centers, and from one 12.5 km alongshelf acoustic track. The circle radii were 7.5 km. Data are from September 8, 2006. Details of the acoustic and environmental measurements are presented. Simple analytic and computer models are used to assess the variability expected due to the ocean and seabed conditions encountered. A comparison of model results and data is made, which shows preliminary consistency between the data and the models, but also points towards further work that should be undertaken specifically in enlarging the range and frequency parameter space, and in looking at integrated transmission loss.Office of Naval Research Code 32

Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions

Correction: Scientific reports, vol. 10:1, art. 18199Fungal plant pathogens remain a serious threat to the sustainable agriculture and forestry, despite the extensive efforts undertaken to control their spread. White root rot disease is threatening rubber tree (Hevea brasiliensis) plantations throughout South and Southeast Asia and Western Africa, causing tree mortality and severe yield losses. Here, we report the complete genome sequence of the basidiomycete fungus Rigidoporus microporus, a causative agent of the disease. Our phylogenetic analysis confirmed the position of R. microporus among the members of Hymenochaetales, an understudied group of basidiomycetes. Our analysis further identified pathogen’s genes with a predicted role in the decay of plant cell wall polymers, in the utilization of latex components and in interspecific interactions between the pathogen and other fungi. We also detected putative horizontal gene transfer events in the genome of R. microporus. The reported first genome sequence of a tropical rubber tree pathogen R. microporus should contribute to the better understanding of how the fungus is able to facilitate wood decay and nutrient cycling as well as tolerate latex and utilize resinous extractives.Peer reviewe