The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications

Background: Rice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses. Therefore, decoding its entire genome will be a prerequisite for applied and basic research on this species and all other cereals. Results: We have determined and analyzed the complete sequences of two of its chromosomes, 11 and 12, which total 55.9 Mb (14.3% of the entire genome length), based on a set of overlapping clones. A total of 5,993 non-transposable element related genes are present on these chromosomes. Among them are 289 disease resistance-like and 28 defense-response genes, a higher proportion of these categories than on any other rice chromosome. A three-Mb segment on both chromosomes resulted from a duplication 7.7 million years ago (mya), the most recent large-scale duplication in the rice genome. Paralogous gene copies within this segmental duplication can be aligned with genomic assemblies from sorghum and maize. Although these gene copies are preserved on both chromosomes, their expression patterns have diverged. When the gene order of rice chromosomes 11 and 12 was compared to wheat gene loci, significant synteny between these orthologous regions was detected, illustrating the presence of conserved genes alternating with recently evolved genes. Conclusion: Because the resistance and defense response genes, enriched on these chromosomes relative to the whole genome, also occur in clusters, they provide a preferred target for breeding durable disease resistance in rice and the isolation of their allelic variants. The recent duplication of a large chromosomal segment coupled with the high density of disease resistance gene clusters makes this the most recently evolved part of the rice genome. Based on syntenic alignments of these chromosomes, rice chromosome 11 and 12 do not appear to have resulted from a single whole-genome duplication event as previously suggested

The pore structure of Clostridium perfringens epsilon toxin

Epsilon toxin (Etx), a potent pore forming toxin (PFT) produced by Clostridium perfringens, is responsible for the pathogenesis of enterotoxaemia of ruminants and has been suggested to play a role in multiple sclerosis in humans. Etx is a member of the aerolysin family of β-PFTs (aβ-PFTs). While the Etx soluble monomer structure was solved in 2004, Etx pore structure has remained elusive due to the difficulty of isolating the pore complex. Here we show the cryo-electron microscopy structure of Etx pore assembled on the membrane of susceptible cells. The pore structure explains important mutant phenotypes and suggests that the double β-barrel, a common feature of the aβ-PFTs, may be an important structural element in driving efficient pore formation. These insights provide the framework for the development of novel therapeutics to prevent human and animal infections, and are relevant for nano-biotechnology applications

Anomalous transparency in photonic crystals and its application to point-by-point grating inscription in photonic crystal fibers

Abstract It is common belief that photonic crystals behave similarly to isotropic and transparent media only when their feature sizes are much smaller than the wavelength of light. Here, we counter that belief and we report on photonic crystals that are transparent for anomalously high normalized frequencies up to 0.9, where the crystal’s feature sizes are comparable with the free space wavelength. Using traditional photonic band theory, we demonstrate that the isofrequency curves can be circular in the region above the first stop band for triangular lattice photonic crystals. In addition, by simulating how efficiently a tightly focused Gaussian beam propagates through the photonic crystal slab, we judge on the photonic crystal’s transparency rather than on isotropy only. Using this approach, we identified a wide range of photonic crystal parameters that provide anomalous transparency. Our findings indicate the possibility to scale up the features of photonic crystals and to extend their operational wavelength range for applications including optical cloaking and graded index guiding. We applied our result in the domain of femtosecond laser micromachining, by demonstrating what we believe to be the first point-by-point grating inscribed in a multi-ring photonic crystal fiber