Aspects of Discrete Breathers and New Directions

We describe results concerning the existence proofs of Discrete Breathers (DBs) in the two classes of dynamical systems with optical linear phonons and with acoustic linear phonons. A standard approach is by continuation of DBs from an anticontinuous limit. A new approach, which is purely variational, is presented. We also review some numerical results on intraband DBs in random nonlinear systems. Some non-conventional physical applications of DBs are suggested. One of them is understanding slow relaxation properties of glassy materials. Another one concerns energy focusing and transport in biomolecules by targeted energy transfer of DBs. A similar theory could be used for describing targeted charge transfer of nonlinear electrons (polarons) and, more generally, for targeted transfer of several excitations (e.g. Davydov soliton).Comment: to appear in the Proceedings of NATO Advanced Research Workshop "Nonlinearity and Disorder: Theory and Applications", Tashkent,Uzbekistan,October 1-6, 200

An overview of the current status of CMB observations

In this paper we briefly review the current status of the Cosmic Microwave Background (CMB) observations, summarising the latest results obtained from CMB experiments, both in intensity and polarization, and the constraints imposed on the cosmological parameters. We also present a summary of current and future CMB experiments, with a special focus on the quest for the CMB B-mode polarization.Comment: Latest CMB results have been included. References added. To appear in "Highlights of Spanish Astrophysics V", Proceedings of the VIII Scientific Meeting of the Spanish Astronomical Society (SEA) held in Santander, 7-11 July, 200

Crystal structures of the NO sensor NsrR reveal how its iron-sulfur cluster modulates DNA binding

NsrR from Streptomyces coelicolor (Sc) regulates the expression of three genes through the progressive degradation of its [4Fe–4S] cluster on nitric oxide (NO) exposure. We report the 1.95 Å resolution crystal structure of dimeric holo-ScNsrR and show that the cluster is coordinated by the three invariant Cys residues from one monomer and, unexpectedly, Asp8 from the other. A cavity map suggests that NO displaces Asp8 as a cluster ligand and, while D8A and D8C variants remain NO sensitive, DNA binding is affected. A structural comparison of holo-ScNsrR with an apo-IscR-DNA complex shows that the [4Fe–4S] cluster stabilizes a turn between ScNsrR Cys93 and Cys99 properly oriented to interact with the DNA backbone. In addition, an apo ScNsrR structure suggests that Asn97 from this turn, along with Arg12, which forms a salt-bridge with Asp8, are instrumental in modulating the position of the DNA recognition helix region relative to its major groove

Structural and biochemical characterization of the exopolysaccharide deacetylase Agd3 required for Aspergillus fumigatus biofilm formation

The exopolysaccharide galactosaminogalactan (GAG) is an important virulence factor of the fungal pathogen Aspergillus fumigatus. Deletion of a gene encoding a putative deacetylase, Agd3, leads to defects in GAG deacetylation, biofilm formation, and virulence. Here, we show that Agd3 deacetylates GAG in a metal-dependent manner, and is the founding member of carbohydrate esterase family CE18. The active site is formed by four catalytic motifs that are essential for activity. The structure of Agd3 includes an elongated substrate-binding cleft formed by a carbohydrate binding module (CBM) that is the founding member of CBM family 87. Agd3 homologues are encoded in previously unidentified putative bacterial exopolysaccharide biosynthetic operons and in other fungal genomes. The exopolysaccharide galactosaminogalactan (GAG) is an important virulence factor of the fungal pathogen Aspergillus fumigatus. Here, the authors study an A. fumigatus enzyme that deacetylates GAG in a metal-dependent manner and constitutes a founding member of a new carbohydrate esterase family.Bio-organic Synthesi

Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli

Background: Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts.  Methodology/Principal Findings: The T. rangeli haploid genome is ,24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heatshock proteins.  Conclusions/Significance: Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets

First measurement of the cross-correlation of CMB lensing and galaxy lensing

We measure the cross-correlation of cosmic microwave background (CMB) lensing convergence maps derived from Atacama Cosmology Telescope data with galaxy lensing convergence maps as measured by the Canada-France-Hawaii Telescope Stripe 82 Survey. The CMB-galaxy lensing cross power spectrum is measured for the first time with a significance of 4.2σ, which corresponds to a 12% constraint on the amplitude of density fluctuations at redshifts ∼0.9. With upcoming improved lensing data, this novel type of measurement will become a powerful cosmological probe, providing a precise measurement of the mass distribution at intermediate redshifts and serving as a calibrator for systematic biases in weak lensing measurements

Structure of a bacterial type III secretion system in contact with a host membrane in situ

Many bacterial pathogens of animals and plants use a conserved type III secretion system (T3SS) to inject virulence effector proteins directly into eukaryotic cells to subvert host functions. Contact with host membranes is critical for T3SS activation, yet little is known about T3SS architecture in this state or the conformational changes that drive effector translocation. Here we use cryo-electron tomography and sub-tomogram averaging to derive the intact structure of the primordial Chlamydia trachomatis T3SS in the presence and absence of host membrane contact. Comparison of the averaged structures demonstrates a marked compaction of the basal body (4 nm) occurs when the needle tip contacts the host cell membrane. This compaction is coupled to a stabilization of the cytosolic sorting platform– ATPase. Our findings reveal the first structure of a bacterial T3SS from a major human pathogen engaged with a eukaryotic host, and reveal striking ‘pump-action’ conformational changes that underpin effector injection

Discrete breathers in ϕ4\phi^4 and related models

We touch upon the wide topic of discrete breather formation with a special emphasis on the the $\phi^4$ model. We start by introducing the model and discussing some of the application areas/motivational aspects of exploring time periodic, spatially localized structures, such as the discrete breathers. Our main emphasis is on the existence, and especially on the stability features of such solutions. We explore their spectral stability numerically, as well as in special limits (such as the vicinity of the so-called anti-continuum limit of vanishing coupling) analytically. We also provide and explore a simple, yet powerful stability criterion involving the sign of the derivative of the energy vs. frequency dependence of such solutions. We then turn our attention to nonlinear stability, bringing forth the importance of a topological notion, namely the Krein signature. Furthermore, we briefly touch upon linearly and nonlinearly unstable dynamics of such states. Some special aspects/extensions of such structures are only touched upon, including moving breathers and dissipative variations of the model and some possibilities for future work are highlighted