Novel target genes of PsrA transcriptional regulator of Pseudomonas aeruginosa

The PsrA transcriptional regulator is involved in stationary phase induced transcriptional regulation of rpoS and in negative auto-regulation in Pseudomonas aeruginosa. This study was designed to determine whether other loci were regulated by PsrA in P. aeruginosa. Computer search was performed of the PsrA binding motif (G/CAAAC N2-4 GTTTG/C) against the P. aeruginosa genome sequence. Four of 14 analysed promoters responded to and bound PsrA; (i) divergent promoters controlling PA2952/ PA2951 and PA2953, (ii) promoter of PA0506 and (iii) upstream region of PA3571. Promoters PA0506 and PA2952-PA2951 were regulated negatively whereas promoters of PA2953 and PA3571 were regulated positively by PsrA. Two dimensional sodium dodecyl sulphate polyacrylamide gel electrophoresis (21) SDS-PAGE) analysis on total proteins from P. aeruginosa PAO1 and psrA knock-out derivative was also performed resulting in the identification of 11 protein spots which were differentially regulated. These studies have indicated PsrA as a global regulator

One-dimensional Ising ferromagnet frustrated by long-range interactions at finite temperatures

We consider a one-dimensional lattice of Ising-type variables where the ferromagnetic exchange interaction J between neighboring sites is frustrated by a long-ranged anti-ferromagnetic interaction of strength g between the sites i and j, decaying as |i-j|^-alpha, with alpha>1. For alpha smaller than a certain threshold alpha_0, which is larger than 2 and depends on the ratio J/g, the ground state consists of an ordered sequence of segments with equal length and alternating magnetization. The width of the segments depends on both alpha and the ratio J/g. Our Monte Carlo study shows that the on-site magnetization vanishes at finite temperatures and finds no indication of any phase transition. Yet, the modulation present in the ground state is recovered at finite temperatures in the two-point correlation function, which oscillates in space with a characteristic spatial period: The latter depends on alpha and J/g and decreases smoothly from the ground-state value as the temperature is increased. Such an oscillation of the correlation function is exponentially damped over a characteristic spatial scale, the correlation length, which asymptotically diverges roughly as the inverse of the temperature as T=0 is approached. This suggests that the long-range interaction causes the Ising chain to fall into a universality class consistent with an underlying continuous symmetry. The e^(Delta/T)-temperature dependence of the correlation length and the uniform ferromagnetic ground state, characteristic of the g=0 discrete Ising symmetry, are recovered for alpha > alpha_0.Comment: 12 pages, 7 figure

Low back pain risk factors in a large rural Australian Aboriginal community. An opportunity for managing co-morbidities?

BACKGROUND: Low back pain (LBP) is the most prevalent musculo-skeletal condition in rural and remote Australian Aboriginal communities. Smoking, physical inactivity and obesity are also prevalent amongst Indigenous people contributing to lifestyle diseases and concurrently to the high burden of low back pain. OBJECTIVES: This paper aims to examine the association between LBP and modifiable risk factors in a large rural Indigenous community as a basis for informing a musculo-skeletal and related health promotion program. METHODS: A community Advisory Group (CAG) comprising Elders, Aboriginal Health Workers, academics, nurses, a general practitioner and chiropractors assisted in the development of measures to assess self-reported musculo-skeletal conditions including LBP risk factors. The Kempsey survey included a community-based survey administered by Aboriginal Health Workers followed by a clinical assessment conducted by chiropractors. RESULTS: Age and gender characteristics of this Indigenous sample (n = 189) were comparable to those reported in previous Australian Bureau of Statistics (ABS) studies of the broader Indigenous population. A history of traumatic events was highly prevalent in the community, as were occupational risk factors. Thirty-four percent of participants reported a previous history of LBP. Sporting injuries were associated with multiple musculo-skeletal conditions, including LBP. Those reporting high levels of pain were often overweight or obese and obesity was associated with self-reported low back strain. Common barriers to medical management of LBP included an attitude of being able to cope with pain, poor health, and the lack of affordable and appropriate health care services. Though many of the modifiable risk factors known to be associated with LBP were highly prevalent in this study, none of these were statistically associated with LBP. CONCLUSION: Addressing particular modifiable risk factors associated with LBP such as smoking, physical inactivity and obesity may also present a wider opportunity to prevent and manage the high burden of illness imposed by co-morbidities such as heart disease and type-2 diabetes

A case-control study of cancers of the gastric cardia in Italy.

In a case-control study of gastric cancer (GC) in high-risk and low-risk areas in Italy, 923 GCs were reviewed by one pathologist and classified according to anatomic site. There were 68 (7.4%) cancers occurring in the gastric cardia. Compared to other GCs, cardia cancer tended to occur more often in males (sex ratio 2.8 vs 1.7) and as intestinal or unclassified histologic types. Nutritional factors for cardia tumours resembled those of other GCs, showing inverse associations with the consumption of raw vegetables, citrus and other fresh fruit, and ascorbic acid, and positive associations with the intake of traditional soups and meat, protein and cholesterol, and preference for salty foods. Cigarette smoking and wine consumption were unrelated to cardia cancer risk, and there was only a weak association with total alcohol intake. Cardia tumours showed a greater familial occurrence of GC than did other sites, with a 7-fold increase in risk for those reporting two first-degree relatives with GC. The authors discuss these findings in view of the rising incidence of adenocarcinomas of the cardia and lower oesophagus that has been reported in some western countries

Somatic mutations and deletions of the E-cadherin gene predict poor survival of patients with gastric cancer.

Purpose The prognosis of gastric cancer (GC) is poor, and the molecular pathogenesis players are vastly unknown. Surgery remains the primary option in GC treatment. The aim of this study was to investigate the impact of somatic CDH1 alterations in prognosis and survival of patients with GC. Patients and Methods A series of patients with sporadic and familial GC (diffuse and intestinal; n _ 246) were analyzed for somatic CDH1 mutations, promoter hypermethylation, and loss of heterozygosity (LOH) by polymerase chain reaction sequencing. E-cadherin protein expression was determined by immunohistochemistry. Associations between molecular, clinicopathologic, and survival data were analyzed. Results CDH1 somatic alterations were found in approximately 30% of all patients with GC. Both histologic types of sporadic GC displayed LOH in 7.5%, mutations in 1.7%, and hypermethylation in 18.4% of patients. Primary tumors from hereditary diffuse GC, lacking germline CDH1 alterations, showed exclusively CDH1 promoter hypermethylation in 50% of patients. Familial intestinal GC (FIGC) tumors showed LOH in 9.4% and hypermethylation in 17.0%. CDH1 alterations did not associate with a particular pattern of E-cadherin expression. Importantly, the worst patient survival rate among all GCs analyzed was seen in patients with tumors carrying CDH1 structural alterations, preferentially those belonging to FIGC families. Conclusion CDH1 somatic alterations exist in all clinical settings and histotypes of GC and associate with different survival rates. Their screening at GC diagnosis may predict patient prognosis and is likely to improve management of patients with this disease.Supported by the Portuguese Foundation for Science and Technology (Projects No. POCTI/SAUOBS/58111/2004, PIC/IC/82923/2007, PTDC/SAU-GMG/72168/2006, PTDC/SAUGMG/110785/2009, and PTDC/SAU-ONC/110294/2009; PhD Grants No. SFRH/BD/40090/2007-GC and SFRH/BD/44074/2008-JC); salary support to C.O. from POPHQREN/Type 4.2; European Social Fund and Portuguese Ministry of Science and Technology; European Molecular Biology Organization short-term fellowship (ASTF 338.00-2008-JC); Calouste Gulbenkian Foundation short-term fellowship (nr 92352-JC); and Istituto Toscano Tumori (Grant No. ITT-2007). IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology, and Higher Education and is partially supported by the Portuguese Foundation for Science and Technology

Electrostatic free energy calculations using the generalized solvent boundary potential method

Copyright 2002 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in The Journal of Chemical Physics and may be found at http://dx.doi.org/10.1063/1.1507108.Free energyperturbation (FEP) calculations using all-atom molecular dynamics simulations with a large number of explicit solvent molecules are a powerful approach to study ligand–macromolecule association processes at the atomic level. One strategy to carry out FEP calculations efficiently and reduce computational time is to consider the explicit dynamics of only a small number of atoms in a localized region around the ligand. Such an approximation is motivated by the observation that the factors governing binding specificity are dominated by interactions in the vicinity of the ligand. However, a straightforward truncation of the system may yield inaccurate results as the influence exerted by the remote regions of the macromolecule and the surrounding solvent through long-range electrostatic effects may be significant. To obtain meaningful results, it is important to incorporate the influence of the remote regions of the ligand–macromolecule complex implicitly using some effective potential. The generalized solvent boundary potential (GSBP) that was developed recently [W. Im, S. Bernèche, and B. Roux, J. Chem. Phys. 114, 2924 (2001)] is an efficient computational method to represent the long-range electrostaticinteractions arising from remote (outer) regions in simulations of a localized (inner) region with a small number of explicit atoms. In the present work, FEP calculations combined with GSBP are used to illustrate the importance of these long-range electrostatic factors in estimation of the charging free energy of an aspartate ligand bound to the aspartyl-tRNA synthetase. Calculations with explicit spherical simulation inner regions of different radii are used to test the accuracy of the GSBP method and also illustrate the importance of explicit protein and solvent dynamics in the free energy estimation. The influence of the represented outer region is tested using separate simulations in which the reaction field and/or the protein static field are excluded. Both components are shown to be essential to obtain quantitatively meaningful results. The ability of implicitly treating the influence of protein fluctuations in the outer region using a protein dielectric constant is examined. It is shown that accurate charging free energy calculations can be performed for this system with a spherical region of 15 to 20 Å radius, which roughly corresponds to 1500–3500 moving atoms. The results indicate that GSBP in combination with FEP calculations is a precise and efficient approach to include long-range electrostatic effects in the study of ligand binding to large macromolecules

A prominent β-hairpin structure in the winged-helix domain of RECQ1 is required for DNA unwinding and oligomer formation

RecQ helicases have attracted considerable interest in recent years due to their role in the suppression of genome instability and human diseases. These atypical helicases exert their function by resolving a number of highly specific DNA structures. The crystal structure of a truncated catalytic core of the human RECQ1 helicase (RECQ149–616) shows a prominent β-hairpin, with an aromatic residue (Y564) at the tip, located in the C-terminal winged-helix domain. Here, we show that the β-hairpin is required for the DNA unwinding and Holliday junction (HJ) resolution activity of full-length RECQ1, confirming that it represents an important determinant for the distinct substrate specificity of the five human RecQ helicases. In addition, we found that the β-hairpin is required for dimer formation in RECQ149–616 and tetramer formation in full-length RECQ1. We confirmed the presence of stable RECQ149–616 dimers in solution and demonstrated that dimer formation favours DNA unwinding; even though RECQ1 monomers are still active. Tetramers are instead necessary for more specialized activities such as HJ resolution and strand annealing. Interestingly, two independent protein–protein contacts are required for tetramer formation, one involves the β-hairpin and the other the N-terminus of RECQ1, suggesting a non-hierarchical mechanism of tetramer assembly