Structure of the bundle-forming pilus from enteropathogenic Escherichia coli

Bundle-forming pili (BFP) are essential for the full virulence of enteropathogenic Escherichia coli (EPEC) because they are required for localized adherence to epithelial cells and auto-aggregation. We report the high resolution structure of bundlin, the monomer of BFP, solved by NMR. The structure reveals a new variation in the topology of type IVb pilins with significant differences in the composition and relative orientation of elements of secondary structure. In addition, the structural parameters of native BFP filaments were determined by electron microscopy after negative staining. The solution structure of bundlin was assembled according to these helical parameters to provide a plausible atomic resolution model for the BFP filament. We show that EPEC and Vibriocholerae type IVb pili display distinct differences in their monomer subunits consistent with data showing that bundlin and TcpA cannot complement each other, but assemble into filaments with similar helical organization.     

Agricultural greenhouse gas mitigation potential globally,in Europe and in the UK: what have we learnt in the last 20 years?

Agricultural lands occupy about 40–50% of the Earth's land surface. Agricultural practices can make a significant contribution at low cost to increasing soil carbon sinks, reducing greenhouse gas (GHG) emissions and contributing biomass feedstocks for energy use. Considering all gases, the global technical mitigation potential from agriculture (excluding fossil fuel offsets from biomass) by 2030 is estimated to be ca. 5500–6000 Mt CO₂‐eq. yr^?1. Economic potentials are estimated to be 1500–1600, 2500–2700 and 4000–4300 Mt CO₂‐eq. yr^?1 at carbon prices of up to $US20, 50 and 100 t CO₂‐eq.^?1, respectively. The value of the global agricultural GHG mitigation at the same three carbon prices is $US32 000, 130 000 and 420 000 million yr^?1, respectively. At the European level, early estimates of soil carbon sequestration potential in croplands were ca. 200 Mt CO₂ yr^?1, but this is a technical potential and is for geographical Europe as far east as the Urals. The economic potential is much smaller, with more recent estimates for the EU27 suggesting a maximum potential of ca. 20 Mt CO₂‐eq. yr^?1. The UK is small in global terms, but a large part of its land area (11 Mha) is used for agriculture. Agriculture accounts for about 7% of total UK GHG emissions. The mitigation potential of UK agriculture is estimated to be ca. 1–2 Mt CO₂‐eq. yr^?1, accounting for less than 1% of UK total GHG emissions.     

Fine-mapping and candidate gene analysis of bovine spinal muscular atrophy

Bovine spinal muscular atrophy (SMA), an autosomal recessive neurodegenerative disease, has been mapped at moderate resolution to the distal part of Chromosome 24. In this article we confirm this location and fine-map the SMA locus to an interval of approximately 0.8 cM at the very distal end of BTA24. Despite remarkable similarity to human SMA, the causative gene SMN can be excluded in bovine SMA. However, the interval where the disease now has been mapped contains BCL2, like SMN an antiapoptotic factor, and shown to bind to SMN. Moreover, knockout mice lacking the BCL2 gene show rapid motor neuron degeneration with early postnatal onset, as observed in bovine SMA. A comparative cattle/human map of the distal end of BTA24, based on the emerging bovine genome sequencing data, shows conserved synteny to HSA18 with hints of a segmental duplication and pericentic inversion just after the last available bovine marker DIK4971. This synteny lets us conclude that SMA is in immediate vicinity of the telomere. Candidate gene analysis of BCL2, however, excludes most of this gene, except its promoter region, and draws attention to the neighboring gene VPS4B, part of the endosomal protein-sorting machinery ESCRT-III which is involved in several neurodegenerative diseases. Stefan Krebs and Ivica Medugorac contributed equally to this work and agreed to be considered as first authors.     

Prevalence and Patterns of Tobacco Use in Bangladesh from 2009 to 2012: Evidence from International Tobacco Control (ITC) Study

Background

Smoking and passive smoking are collectively the biggest preventable cause of death in Bangladesh, with major public health burden of morbidity, disability, mortality and community costs. The available studies of tobacco use in Bangladesh, however, do not necessarily employ nationally representative samples needed to monitor the problem at a national scale. This paper examines the prevalence and patterns of tobacco use among adults in Bangladesh and the changes over time using large nationally representative comparable surveys.

Methods

Using data from two enumerations of the International Tobacco Control (ITC) Bangladesh Project conducted in 2009 and 2012, prevalence estimates are obtained for all tobacco products by socio-economic determinants and sample types of over 90,000 individuals drawn from over 30,000 households. Household level sample weights are used to obtain nationally representative prevalence estimates and standard errors. Statistical tests of difference in the estimates between two time periods are based on a logistic regression model that accounts for the complex sampling design. Using a multinomial logit model, the time trend in tobacco use status is identified to capture the effects of macro level determinants including changes in tobacco control policies.

Results

Between 2009 and 2012, overall tobacco use went down from 42.4% to 36.3%. The decline is more pronounced with respect to smokeless tobacco use than smoking. The prevalence of exclusive cigarette smoking went up from 7.2% to 10.6%; exclusive bidi smoking remained stable at around 2%; while smoking both cigarette and bidi went down from 4.6% to 1.8%; exclusive smokeless tobacco use went down from 20.2% to 16.9%; and both smokeless tobacco use and smoking went down from 8.4% to 5.1%. In general, the prevalence of tobacco use is higher among men, increases from younger to older age groups, and is higher among poorer people. Smoking prevalence is the highest among the slum population, followed by the tribal population, the national population and the border area population, suggesting greater burden of tobacco use among the disadvantaged groups.

Conclusions

The overall decline in tobacco use can be viewed as a structural shift in the tobacco market in Bangladesh from low value products such as bidi and smokeless tobacco to high value cigarettes, which is expected with the growth in income and purchasing power of the general population. Despite the reduction in overall tobacco use, the male smoking prevalence in Bangladesh is still high at 37%. The world average of daily smoking among men is 31.1%. The Tobacco Control Act 2005 and the Amendment have yet to make a significant impact in curbing tobacco usage in Bangladesh. The findings in this paper further suggest that the tobacco control policies in Bangladesh need to include targeted interventions to restrain the use of particular types of tobacco products among specific demographic and socio-economic groups of the population, such as smoked tobacco among men, smokeless tobacco among women, and both smoked and smokeless tobacco among those living in rural areas, those in low socio-economic status and those belonging to the tribal and the slum population.     

AL-12182, a novel 11-oxa prostaglandin analog with topical ocular hypotensive activity in the monkey

A series of 11-oxa prostaglandin analogs was evaluated for FP receptor binding and activation. Several compounds having aryloxy-terminated lower chains were found to be potent agonists. Topical ocular dosing of AL-12182, the isopropyl ester prodrug of the potent agonist 13, lowered intraocular pressure in the monkey by 40% accompanied by minimal conjunctival hyperemia in the rabbit. AL-12182 was synthesized on multigram scale starting with D-sorbitol.     

Unlocking the barley genome by chromosomal and comparative genomics

We used a novel approach that incorporated chromosome sorting, next-generation sequencing, array hybridization, and systematic exploitation of conserved synteny with model grasses to assign ~86% of the estimated ~32,000 barley (Hordeum vulgare) genes to individual chromosome arms. Using a series of bioinformatically constructed genome zippers that integrate gene indices of rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium distachyon in a conserved synteny model, we were able to assemble 21,766 barley genes in a putative linear order. We show that the barley (H) genome displays a mosaic of structural similarity to hexaploid bread wheat (Triticum aestivum) A, B, and D subgenomes and that orthologous genes in different grasses exhibit signatures of positive selection in different lineages. We present an ordered, information-rich scaffold of the barley genome that provides a valuable and robust framework for the development of novel strategies in cereal breeding.     

Compensating bends in a 16-base-pair DNA oligomer containing a T(3)A(3) segment: A NMR study of global DNA curvature

In-phase ligated DNA containing T(n)A(n) segments fail to exhibit the retarded polyacrylamide gel electrophoresis (PAGE) migration observed for in-phase ligated A(n)T(n) segments, a behavior thought to be correlated with macroscopic DNA curvature. The lack of macroscopic curvature in ligated T(n)A(n) segments is thought to be due to cancellation of bending in regions flanking the TpA steps. To address this issue, solution-state NMR, including residual dipolar coupling (RDC) restraints, was used to determine a high-resolution structure of [d(CGAGGTTTAAACCTCG)2], a DNA oligomer containing a T3A3 tract. The overall magnitude and direction of bending, including the regions flanking the central TpA step, was measured using a radius of curvature, Rc, analysis. The Rc for the overall molecule indicated a small magnitude of global bending (Rc = 138 +/- 23 nm) towards the major groove, whereas the Rc for the two halves (72 +/- 33 nm and 69 +/- 14 nm) indicated greater localized bending into the minor groove. The direction of bending in the regions flanking the TpA step is in partial opposition (109 degrees), contributing to cancellation of bending. The cancellation of bending did not correlate with a pattern of roll values at the TpA step, or at the 5' and 3' junctions, of the T3A3 segment, suggesting a simple junction/roll model is insufficient to predict cancellation of DNA bending in all T(n)A(n) junction sequence contexts. Importantly, Rc analysis of structures refined without RDC restraints lacked the precision and accuracy needed to reliably measure bending.