Force steps during viral DNA packaging ?

Biophysicists and structural biologists increasingly acknowledge the role played by the mechanical properties of macromolecules as a critical element in many biological processes. This change has been brought about, in part, by the advent of single molecule biophysics techniques that have made it possible to exert piconewton forces on key macromolecules and observe their deformations at nanometer length scales, as well as to observe the mechanical action of macromolecules such as molecular motors. This has opened up immense possibilities for a new generation of mechanical investigations that will respond to such measurements in an attempt to develop a coherent theory for the mechanical behavior of macromolecules under conditions where thermal and chemical effects are on an equal footing with deterministic forces. This paper presents an application of the principles of mechanics to the problem of DNA packaging, one of the key events in the life cycle of bacterial viruses with special reference to the nature of the internal forces that are built up during the DNA packaging process.Comment: 18 pages, 7 figures, To appear in the Journal of Mechanics and Physics of Solid

A Uniform CO Survey of the Molecular Clouds in Orion and Monoceros

We report the results of a new large scale survey of the Orion-Monoceros complex of molecular clouds made in the J = 1->0 line of CO with the Harvard-Smithsonian 1.2m millimetre-wave telescope. The survey consists of 52,288 uniformly spaced spectra that cover an area of 432 square degrees on the sky and is the most sensitive large-scale survey of the region to date. Distances to the constituent molecular clouds of the complex, estimated from an analysis of foreground and background stars, have provided information on the three dimensional structure of the entire complex.Comment: Accepted for publication in Astronomy and Astrophysics. 19 pages with 17 colour figures - 39 if you count the sub-figures separately. The figures here have been bit-mapped with some loss of quality and beauty. The paper version in A&A will be in greyscale with the on-line version in colour. In the meantime the colour version can be obtained by following links at http://www.star.bris.ac.uk/mrwm . The 9MB PostScript is recommended if you have appropriate bandwidth or otherwise the 2.3MB PDF is usabl

Shells, jets, and internal working surfaces in the molecular outflow from IRAS 04166+2706

Context: IRAS 04166+2706 in Taurus is one of the most nearby young stellar objects whose molecular outflow contains a highly collimated fast component. Methods: We have observed the IRAS 04166+2706 outflow with the IRAM Plateau de Bure interferometer in CO(J=2-1) and SiO(J=2-1) achieving angular resolutions between 2'' and 4''. To improve the quality of the CO(2-1) images, we have added single dish data to the interferometer visibilities. Results: The outflow consists of two distinct components. At velocities <10 km/s, the gas forms two opposed, approximately conical shells that have the YSO at their vertex. These shells coincide with the walls of evacuated cavities and seem to result from the acceleration of the ambient gas by a wide-angle wind. At velocities >30 km/s, the gas forms two opposed jets that travel along the center of the cavities and whose emission is dominated by a symmetric collection of at least 7 pairs of peaks. The velocity field of this component presents a sawtooth pattern with the gas in the tail of each peak moving faster than the gas in the head. This pattern, together with a systematic widening of the peaks with distance to the central source, is consistent with the emission arising from internal working surfaces traveling along the jet and resulting from variations in the velocity field of ejection. We interpret this component as the true protostellar wind, and we find its composition consistent with a chemical model of such type of wind. Conclusions: Our results support outflow wind models that have simultaneously wide-angle and narrow components, and suggest that the EHV peaks seen in a number of outflows consist of internally-shocked wind material.Comment: 13 pages, 10 figures. To appear in A&

TRPA1 gene polymorphisms and childhood asthma.

BACKGROUND: Animal data have suggested that the transient receptor potential ankyrin-1 (TRPA1) ion channel plays a key role in promoting airway inflammation in asthma and may mediate effects of paracetamol on asthma, yet confirmatory human data are lacking. To study associations of TRPA1 gene variants with childhood asthma and total IgE concentration, and interactions between TRPA1 and prenatal paracetamol exposure on these outcomes. METHODS: We analysed associations between 31 TRPA1 single nucleotide polymorphisms (SNPs) and current doctor-diagnosed asthma and total IgE concentration at 7.5 years in the Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort. We sought to confirm the most significant associations with comparable outcomes in the Prevention and Incidence of Asthma and Mite Allergy (PIAMA) and Generation R birth cohorts. In ALSPAC, we explored interactions with prenatal paracetamol exposure. RESULTS: In ALSPAC, there was strong evidence for association between six SNPs and asthma: rs959974 and rs1384001 (per-allele odds ratio for both: 1.30 (95% CI: 1.15-1.47), p = 0.00001), rs7010969 (OR 1.28 (1.13-1.46), p = 0.00004), rs3735945 (OR 1.30 (1.09-1.55), p = 0.003), rs920829 (OR 1.30 (1.09-1.54), p = 0.004) and rs4738202 (OR 1.22 (1.07-1.39), p = 0.004). In a meta-analysis across the three cohorts, the pooled effect estimates confirmed that all six SNPs were significantly associated with asthma. In ALSPAC, TRPA1 associations with asthma were not modified by prenatal paracetamol, although associations with IgE concentration were. CONCLUSION: This study suggests that TRPA1 may play a role in the development of childhood asthma. (249 words)

The role of effectors in nonhost resistance to filamentous plant pathogens

In nature, most plants are resistant to a wide range of phytopathogens. However, mechanisms contributing to this so-called nonhost resistance (NHR) are poorly understood. Besides constitutive defences, plants have developed two layers of inducible defence systems. Plant innate immunity relies on recognition of conserved pathogen-associated molecular patterns (PAMPs). In compatible interactions, pathogenicity effector molecules secreted by the invader can suppress host defence responses and facilitate the infection process. Additionally, plants have evolved pathogen-specific resistance mechanisms based on recognition of these effectors, which causes secondary defence responses. The current effector-driven hypothesis is that nonhost resistance in plants that are distantly related to the host plant is triggered by PAMP recognition that cannot be efficiently suppressed by the pathogen, whereas in more closely related species, nonhost recognition of effectors would play a crucial role. In this review we give an overview of current knowledge of the role of effector molecules in host and nonhost resistance and place these findings in the context of the model. We focus on examples from filamentous pathogens (fungi and oomycetes), discuss their implications for the field of plant-pathogen interactions and relevance in plant breeding strategies for development of durable resistance in crops

Spectral line survey of the ultracompact HII region Mon R2

Ultracompact (UC) HII regions constitute one of the earliest phases in the formation of a massive star and are characterized by extreme physical conditions (Go>10^5 Habing field and n>10^6 cm^-3). The UC HII Mon R2 is the closest one and therefore an excellent target to study the chemistry in these complex regions. We carried out a 3mm and 1mm spectral survey using the IRAM 30-m telescope towards three positions that represent different physical environments in Mon R2: (i) the ionization front (IF) at (0",0"); two peaks in the molecular cloud (ii) MP1 at the offset (+15",-15") and (iii) MP2 at the farther offset (0",40"). In addition, we carried out extensive modeling to explain the chemical differences between the three observed regions. We detected more than thirty different species. We detected SO+ and C4H suggesting that UV radiation plays an important role in the molecular chemistry of this region. We detected the typical PDR molecules CN, HCN, HCO, C2H, and c-C3H2. While the IF and the MP1 have a chemistry similar to that found in high UV field and dense PDRs like the Orion Bar, the MP2 is more similar to lower UV/density PDRs like the Horsehead nebula. We also detected complex molecules that are not usually found in PDRs (CH3CN, H2CO, HC3N, CH3OH and CH3C2H). Sulfur compounds CS, HCS+, C2S, H2CS, SO and SO2 and the deuterated species DCN and C2D were also identified. [DCN]/[HCN]=0.03 and [C2D]/[C2H]=0.05, are among the highest in warm regions. Our results show that the high UV/dense PDRs present a different chemistry from that of the low UV case. Abundance ratios like [CO+]/[HCO+] or [HCO]/[HCO+] are good diagnostics to differentiate between them. In Mon R2 we have the two classes of PDRs, a high UV PDR towards the IF and the adjacent molecular bar and a low-UV PDR which extends towards the north-west following the border of the cloud.Comment: 31 page

Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes

Large differences in plant genome sizes are mainly due to numerous events of insertions or deletions (indels). The balance between these events determines the evolutionary direction of genome changes. To address the question of what phenomena trigger these alterations, we compared the genomic sequences of two Arabidopsis thaliana lines, Columbia (Col) and Landsberg erecta (Ler). Based on the resulting alignments large indels (>100 bp) within these two genomes were analysed. There are ∼8500 large indels accounting for the differences between the two genomes. The genetic basis of their origin was distinguished as three main categories: unequal recombination (Urec)-derived, illegitimate recombination (Illrec)-derived and transposable elements (TE)-derived. A detailed study of their distribution and size variation along chromosomes, together with a correlation analyses, allowed us to demonstrate the impact of particular recombination-based mechanisms on the plant genome evolution. The results show that unequal recombination is not efficient in the removal of TEs within the pericentromeric regions. Moreover, we discovered an unexpectedly high influence of large indels on gene evolution pointing out significant differences between the various gene families. For the first time, we present convincing evidence that somatic events do play an important role in plant genome evolution

Investigating the health implications of social policy initiatives at the local level: study design and methods

<p>Abstract</p> <p>Background</p> <p>In this paper we present the research design and methods of a study that seeks to capture local level responses to an Australian national social policy initiative, aimed at reducing inequalities in the social determinants of health.</p> <p>Methods/Design</p> <p>The study takes a policy-to-practice approach and combines policy and stakeholder interviewing with a comparative case study analysis of two not-for-profit organisations involved in the delivery of federal government policy.</p> <p>Discussion</p> <p>Before the health impacts of broad-scale policies, such as the one described in this study, can be assessed at the population level, we need to understand the implementation process. This is consistent with current thinking in political science and social policy, which has emphasised the importance of investigating how, and if, policies are translated into operational realities.</p

Centre of pressure characteristics in normal, planus and cavus feet

Background The aim of this study was to compare centre of pressure (COP) characteristics between healthy adults with normal, planus or cavus feet who were allocated to groups based on reliable foot posture measurement techniques. Methods Ninety-two healthy adult participants (aged 18 to 45) were recruited and classified as either normal (n = 35), pes planus (n = 31) or pes cavus (n = 26) based on Foot Posture Index, Arch Index and normalised navicular height truncated measurements. Barefoot walking trials were conducted using an emed®-x 400 plantar pressure system (Novel GmbH, Munich, Germany). Average, maximum, minimum and range (difference between maximum and minimum) values were calculated for COP velocity and lateral-medial force index during loading response, midstance, terminal stance and pre-swing phases of stance. The COP excursion index was also calculated. One-way analyses of variance were used to compare the three foot posture groups. Results The cavus foot exhibited the slowest average and minimum COP velocity during terminal stance, but this pattern was reversed during pre-swing, when the cavus foot exhibited the fastest maximum COP velocity. The planus foot exhibited the smallest lateral medial force index range during terminal stance. There were no differences between the groups for COP excursion index. Conclusion These findings indicate that there are differences in COP characteristics between foot postures, which may represent different mechanisms for generating force to facilitate forward progression of the body during the propulsive phases of gait