Elastic properties of cubic crystals: Every's versus Blackman's diagram

Blackman's diagram of two dimensionless ratios of elastic constants is frequently used to correlate elastic properties of cubic crystals with interatomic bondings. Every's diagram of a different set of two dimensionless variables was used by us for classification of various properties of such crystals. We compare these two ways of characterization of elastic properties of cubic materials and consider the description of various groups of materials, e.g. simple metals, oxides, and alkali halides. With exception of intermediate valent compounds, the correlation coefficients for Every's diagrams of various groups of materials are greater than for Blackaman's diagrams, revealing the existence of a linear relationship between two dimensionless Every's variables. Alignment of elements and compounds along lines of constant Poisson's ratio $\nu(,\textbf{m})$, ($\textbf{m}$ arbitrary perpendicular to ) is observed. Division of the stability region in Blackman's diagram into region of complete auxetics, auxetics and non-auxetics is introduced. Correlations of a scaling and an acoustic anisotropy parameter are considered.Comment: 8 pages, 9 figures, presented on The Ninth International School on Theoretical Physics "Symmetry and Structural Properties of Condensed Matter", 5 - 12 September 2007, Myczkowce, Polan

Gene loss and lineage specific restriction-modification systems associated with niche differentiation in the Campylobacter jejuni Sequence Type 403 clonal complex

Campylobacter jejuni is a highly diverse species of bacteria commonly associated with infectious intestinal disease of humans and zoonotic carriage in poultry, cattle, pigs, and other animals. The species contains a large number of distinct clonal complexes that vary from host generalist lineages commonly found in poultry, livestock, and human disease cases to host-adapted specialized lineages primarily associated with livestock or poultry. Here, we present novel data on the ST403 clonal complex of C. jejuni, a lineage that has not been reported in avian hosts. Our data show that the lineage exhibits a distinctive pattern of intralineage recombination that is accompanied by the presence of lineage-specific restriction-modification systems. Furthermore, we show that the ST403 complex has undergone gene decay at a number of loci. Our data provide a putative link between the lack of association with avian hosts of C. jejuni ST403 and both gene gain and gene loss through nonsense mutations in coding sequences of genes, resulting in pseudogene formation

Reactivation of mitochondrial bioenergetics and dynamics during germination of Arabidopsis thaliana seed

Mitochondria are dynamic organelles in shoots and roots. Mitochondria move on F-actin using myosin motors, but movement can also result from remodelling of the actin cytoskeleton. This dynamism of mitochondria underpins their function and maintenance. For example, mitochondrial quality control underpins cell health and requires inter-mitochondrial fusion due to the uneven distribution of mtDNA within physically discrete mitochondria. Mitochondria are inactive in dry seed but must reactivate rapidly upon imbibition to provide ATP for germination. This reactivation requires not only a reactivation of mitochondrial metabolism but also of mitochondrial dynamics. Using a bioimaging approach we investigated reactivation using Arabidopsis as a model. Bioenergetic reactivation, visualised as the presence of a membrane potential, is almost immediate upon rehydration. However, reactivation of mitochondrial motility only occurs after transfer to optimal germination conditions. This late reactivation of mitochondrial motility appears specific: the actin cytoskeleton is present and dynamic early during imbibition as are other organelles that move in actin (e.g.ER). Reactivation of mitochondrial bioenergetics and dynamics is followed by dramatic reorganisation of the chondriome due to transient massive fusion, to form a perinuclear reticulum, followed by division. These data will be presented alongside results testing our hypothesis that the delay in activating mitochondrial motility is associated with the activation of mitochondrial quality control mechanisms to repair mtDNA damage incurred during maturation drying and imbibition

Draft Genome Sequence of Beneficial Rice Rhizosphere Isolate Pseudomonas aeruginosa PUPa3.

Published onlinePseudomonas aeruginosa PUPa3 is a rhizosphere-colonizing and plant growth-promoting strain isolated from the rhizosphere of rice. This strain has, however, been shown to be pathogenic in two nonmammalian infection models. Here we report the draft genome sequence of P. aeruginosa PUPa3.G.U. and M.K. were funded by the Ministry of Education, Science and Technological Development, Republic of Serbia (grant no. 173019). G.U. is also the beneficiary of FEMS Research Fellowship 2014-1. The laboratory of V.V. was financed by ICGEB core funding

Draft Genome Sequence of Erwinia toletana, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. Savastanoi.

Erwinia toletana was first reported in 2004 as a bacterial species isolated from olive knots caused by the plant bacterium Pseudomonas savastanoi pv. savastanoi. Recent studies have shown that the presence of this bacterium in the olive knot environment increases the virulence of the disease, indicating possible interspecies interactions with P. savastanoi pv. savastanoi. Here, we report the first draft genome sequence of an E. toletana strain.D.P.D.S. was the beneficiary of an ICGEB fellowship. The laboratory of V.V. was financed by Progetto AGER and ICGEB core funding

Arabidopsis seed mitochondria are bioenergetically active immediately upon imbibition and specialize via biogenesis in preparation for autotrophic growth

Seed germination is a vital developmental transition for production of progeny by sexual reproduction in spermatophytes. Quiescent cells in nondormant dry embryos are reawakened first by imbibition and then by perception of germination triggers. Reanimated tissues enter into a germination program requiring energy for expansion growth. However, germination requires that embryonic tissues develop to support the more energy-demanding processes of cell division and organogenesis of the new seedling. Reactivation of mitochondria to supply the required energy is thus a key process underpinning germination and seedling survival. Using live imaging, we investigated reactivation of mitochondrial bioenergetics and dynamics using Arabidopsis thaliana as a model. Bioenergetic reactivation, visualized by presence of a membrane potential, is immediate upon rehydration. However, reactivation of mitochondrial dynamics only occurs after transfer to germination conditions. Reactivation of mitochondrial bioenergetics is followed by dramatic reorganization of the chondriome (all mitochondrial in a cell, collectively) involving massive fusion and membrane biogenesis to form a perinuclear tubuloreticular structure enabling mixing of previously discrete mitochondrial DNA nucleoids. The end of germination coincides with fragmentation of the chondriome, doubling of mitochondrial number, and heterogeneous redistribution of nucleoids among the mitochondria, generating a population of mitochondria tailored to seedling growth

Imaging and analysis of mitochondrial dynamics in living cells.

One of the most striking features of plant mitochondria when visualized in living tissue is their dynamism. The beauty of cytoplasmic streaming, driving, and being driven by the motility of mitochondria and other small organelles belies the complexity of the process. Equally, capturing that dynamism and investigating the genes, proteins, and mechanisms underpinning the processes using molecular cell biology and bioimaging is a complex process. It requires the generation of fluorescent protein constructs, stable transgenic plants sometimes expressing multiple fusions, and generation of mutants, even before one is ready for analytical experimentation. Here, we describe some of the key tools and methods necessary to investigate plant mitochondrial dynamics

HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES1 Is Required for Circadian Periodicity through the Promotion of Nucleo-Cytoplasmic mRNA Export in Arabidopsis.

notes: PMCID: PMC3875725This is an open access article that is freely available in ORE or from the publisher's web site. Please cite the published version. © 2013 American Society of Plant Biologists. All rights reserved.Cold acclimation has been shown to be attenuated by the degradation of the INDUCER OF CBF EXPRESSION1 protein by the E3 ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES1 (HOS1). However, recent work has suggested that HOS1 may have a wider range of roles in plants than previously appreciated. Here, we show that hos1 mutants are affected in circadian clock function, exhibiting a long-period phenotype in a wide range of temperature and light environments. We demonstrate that hos1 mutants accumulate polyadenylated mRNA in the nucleus and that the circadian defect in hos1 is shared by multiple mutants with aberrant mRNA export, but not in a mutant attenuated in nucleo-cytoplasmic transport of microRNAs. As revealed by RNA sequencing, hos1 exhibits gross changes to the transcriptome with genes in multiple functional categories being affected. In addition, we show that hos1 and other previously described mutants with altered mRNA export affect cold signaling in a similar manner. Our data support a model in which altered mRNA export is important for the manifestation of hos1 circadian clock defects and suggest that HOS1 may indirectly affect cold signaling through disruption of the circadian clock.Biotechnology and Biological Science Research Counci

The Ubiquitous Distribution of Late Embryogenesis Abundant Proteins across Cell Compartments in Arabidopsis Offers Tailored Protection against Abiotic Stress

Late embryogenesis abundant (LEA) proteins are hydrophilic, mostly intrinsically disordered proteins, which play major roles in desiccation tolerance. In Arabidopsis thaliana, 51 genes encoding LEA proteins clustered into nine families have been inventoried. To increase our understanding of the yet enigmatic functions of these gene families, we report the subcellular location of each protein. Experimental data highlight the limits of in silico predictions for analysis of subcellular localization. Thirty-six LEA proteins localized to the cytosol, with most being able to diffuse into the nucleus. Three proteins were exclusively localized in plastids or mitochondria, while two others were found dually targeted to these organelles. Targeting cleavage sites could be determined for five of these proteins. Three proteins were found to be endoplasmic reticulum (ER) residents, two were vacuolar, and two were secreted. A single protein was identified in pexophagosomes. While most LEA protein families have a unique subcellular localization, members of the LEA_4 family are widely distributed (cytosol, mitochondria, plastid, ER, and pexophagosome) but share the presence of the class A α-helix motif. They are thus expected to establish interactions with various cellular membranes under stress conditions. The broad subcellular distribution of LEA proteins highlights the requirement for each cellular compartment to be provided with protective mechanisms to cope with desiccation or cold stress