Cementing proteins provide extra mechanical stabilization to viral cages

The study of virus shell stability is key not only for gaining insights into viral biological cycles but also for using viral capsids in materials science. The strength of viral particles depends profoundly on their structural changes occurring during maturation, whose final step often requires the specific binding of ‘decoration’ proteins (such as gpD in bacteriophage lambda) to the viral shell. Here we characterize the mechanical stability of gpD-free and gpD-decorated bacteriophage lambda capsids. The incorporation of gpD into the lambda shell imparts a major mechanical reinforcement that resists punctual deformations. We further interrogate lambda particle stability with molecular fatigue experiments that resemble the sub-lethal Brownian collisions of virus shells with macromolecules in crowded environments. Decorated particles are especially robust against collisions of a few kBT (where kB is the Boltzmann’s constant and T is the temperature ~300 K), which approximate those anticipated from molecular insults in the environmentWe acknowledge the MINECO of Spain (PIB2010US-00233, FIS3011-29493, Consolider CSD2010-00024, CAMprojectNo.S3009/MAT-1467), and the US National Science Foundation (MCB-1158107) for their financial support of this researc

How long can you hold the filler:Maintenance and retrieval

This study attempts to reveal the mechanisms behind the online formation of Wh-Filler-Gap Dependencies (WhFGD). Specifically, we aim to uncover the way in which maintenance and retrieval work in WhFGD processing, by paying special attention to the information that is retrieved when the gap is recognized. We use the agreement attraction phenomenon (Wagers, M. W., Lau, E. F., & Phillips, C. (2009). Agreement attraction in comprehension: Representations and processes. Journal of Memory and Language, 61(2), 206-237) as a probe. The first and second experiments examined the type of information that is maintained and how maintenance is motivated, investigating the retrieved information at the gap for reactivated fillers and definite NPs. The third experiment examined the role of the retrieval, comparing reactivated and active fillers. We contend that the information being accessed reflects the extent to which the filler is maintained, where the reader is able to access fine-grained information including category information as well as a representation of both the head and the modifier at the verb

Steady State of microemulsions in shear flow

Steady-state properties of microemulsions in shear flow are studied in the context of a Ginzburg-Landau free-energy approach. Explicit expressions are given for the structure factor and the time correlation function at the one loop level of approximation. Our results predict a four-peak pattern for the structure factor, implying the simultaneous presence of interfaces aligned with two different orientations. Due to the peculiar interface structure a non-monotonous relaxation of the time correlator is also found.Comment: 5 pages, 3 figure

Solution Structure of a TBP–TAFII230 Complex Protein Mimicry of the Minor Groove Surface of the TATA Box Unwound by TBP

AbstractGeneral transcription factor TFIID consists of TATA box–binding protein (TBP) and TBP-associated factors (TAFIIs), which together play a central role in both positive and negative regulation of transcription. The N-terminal region of the 230 kDa Drosophila TAFII (dTAFII230) binds directly to TBP and inhibits TBP binding to the TATA box. We report here the solution structure of the complex formed by dTAFII230 N-terminal region (residues 11–77) and TBP. dTAFII23011–77 comprises three α helices and a β hairpin, forming a core that occupies the concave DNA-binding surface of TBP. The TBP-binding surface of dTAFII230 markedly resembles the minor groove surface of the partially unwound TATA box in the TBP–TATA complex. This protein mimicry of the TATA element surface provides the structural basis of the mechanism by which dTAFII230 negatively controls the TATA box–binding activity within the TFIID complex

Comparative genomics of Bradyrhizobium japonicum CPAC 15 and Bradyrhizobium diazoefficiens CPAC 7: elite model strains for understanding symbiotic performance with soybean.

The soybean-Bradyrhizobium symbiosis can be highly efficient in fixing nitrogen, but few genomic sequences of elite inoculant strains are available. Here we contribute with information on the genomes of two commercial strains that are broadly applied to soybean crops in the tropics. B. japonicum CPAC 15 (=SEMIA 5079) is outstanding in its saprophytic capacity and competitiveness, whereas B. diazoefficiens CPAC 7 (=SEMIA 5080) is known for its high efficiency in fixing nitrogen. Both are well adapted to tropical soils. The genomes of CPAC 15 and CPAC 7 were compared to each other and also to those of B. japonicum USDA 6T and B. diazoefficiens USDA 110T. Differences in genome size were found between species, with B. japonicum having larger genomes than B. diazoefficiens. Although most of the four genomes were syntenic, genome rearrangements within and between species were observed, including events in the symbiosis island. In addition to the symbiotic region, several genomic islands were identified. Altogether, these features must confer high genomic plasticity that might explain adaptation and differences in symbiotic performance. It was not possible to attribute known functions to half of the predicted genes. About 10% of the genomes was composed of exclusive genes of each strain, but up to 98% of them were of unknown function or coded for mobile genetic elements. In CPAC 15, more genes were associated with secondary metabolites, nutrient transport, iron-acquisition and IAA metabolism, potentially correlated with higher saprophytic capacity and competitiveness than seen with CPAC 7. In CPAC 7, more genes were related to the metabolism of amino acids and hydrogen uptake, potentially correlated with higher efficiency of nitrogen fixation than seen with CPAC 15. Several differences and similarities detected between the two elite soybean-inoculant strains and between the two species of Bradyrhizobium provide new insights into adaptation to tropical soils, efficiency of N2 fixation, nodulation and competitiveness

Mechanisms for slow strengthening in granular materials

Several mechanisms cause a granular material to strengthen over time at low applied stress. The strength is determined from the maximum frictional force F_max experienced by a shearing plate in contact with wet or dry granular material after the layer has been at rest for a waiting time \tau. The layer strength increases roughly logarithmically with \tau -only- if a shear stress is applied during the waiting time. The mechanisms of strengthening are investigated by sensitive displacement measurements and by imaging of particle motion in the shear zone. Granular matter can strengthen due to a slow shift in the particle arrangement under shear stress. Humidity also leads to strengthening, but is found not to be its sole cause. In addition to these time dependent effects, the static friction coefficient can also be increased by compaction of the granular material under some circumstances, and by cycling of the applied shear stress.Comment: 21 pages, 11 figures, submitted to Phys. Rev.