Probabilistic Clustering of Sequences: Inferring new bacterial regulons by comparative genomics

Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as samples from weight matrices we derive a unique probability distribution for assignments of sites into clusters. Our algorithm, 'PROCSE' (probabilistic clustering of sequences), uses Monte-Carlo sampling of this distribution to partition and align thousands of short DNA sequences into clusters. The algorithm internally determines the number of clusters from the data, and assigns significance to the resulting clusters. We place theoretical limits on the ability of any algorithm to correctly cluster sequences drawn from weight matrices (WMs) when these WMs are unknown. Our analysis suggests that the set of all putative sites for a single genome (e.g. E. coli) is largely inadequate for clustering. When sites from different genomes are combined and all the homologous sites from the various species are used as a block, clustering becomes feasible. We predict 50-100 new regulons as well as many new members of existing regulons, potentially doubling the number of known regulatory sites in E. coli.Comment: 27 pages including 9 figures and 3 table

Bioengineered Nisin A Derivatives with Enhanced Activity against Both Gram Positive and Gram Negative Pathogens

peer-reviewedNisin is a bacteriocin widely utilized in more than 50 countries as a safe and natural antibacterial food preservative. It is the most extensively studied bacteriocin, having undergone decades of bioengineering with a view to improving function and physicochemical properties. The discovery of novel nisin variants with enhanced activity against clinical and foodborne pathogens has recently been described. We screened a randomized bank of nisin A producers and identified a variant with a serine to glycine change at position 29 (S29G), with enhanced efficacy against S. aureus SA113. Using a site-saturation mutagenesis approach we generated three more derivatives (S29A, S29D and S29E) with enhanced activity against a range of Gram positive drug resistant clinical, veterinary and food pathogens. In addition, a number of the nisin S29 derivatives displayed superior antimicrobial activity to nisin A when assessed against a range of Gram negative food-associated pathogens, including E. coli, Salmonella enterica serovar Typhimurium and Cronobacter sakazakii. This is the first report of derivatives of nisin, or indeed any lantibiotic, with enhanced antimicrobial activity against both Gram positive and Gram negative bacteria.This work was supported by the Irish Government under the National Development Plan, through Science Foundation Ireland Investigator awards (10/IN.1/B3027) and (06/IN.1/B98) (http://www.sfi.ie)

Human AlkB Homolog ABH8 Is a tRNA Methyltransferase Required for Wobble Uridine Modification and DNA Damage Survival

tRNA nucleosides are extensively modified to ensure their proper function in translation. However, many of the enzymes responsible for tRNA modifications in mammals await identification. Here, we show that human AlkB homolog 8 (ABH8) catalyzes tRNA methylation to generate 5-methylcarboxymethyl uridine (mcm[superscript 5]U) at the wobble position of certain tRNAs, a critical anticodon loop modification linked to DNA damage survival. We find that ABH8 interacts specifically with tRNAs containing mcm5U and that purified ABH8 complexes methylate RNA in vitro. Significantly, ABH8 depletion in human cells reduces endogenous levels of mcm[superscript 5]U in RNA and increases cellular sensitivity to DNA-damaging agents. Moreover, DNA-damaging agents induce ABH8 expression in an ATM-dependent manner. These results expand the role of mammalian AlkB proteins beyond that of direct DNA repair and support a regulatory mechanism in the DNA damage response pathway involving modulation of tRNA modification.United States. National Institutes of Health (grant CA055042)United States. National Institutes of Health (grant ES002109)United States. National Institutes of Health (grant ES01701)National Institutes of Health (U.S.). Intramural Research ProgramWestaway Research FundNational Center for Research Resources (U.S.) (grant S10-RR023783

Southern hemispheric halon trends and global halon emissions, 1978–2011

The atmospheric records of four halons, H-1211 (CBrClF2), H-1301 (CBrF3), H-2402 (CBrF2CBrF2) and H-1202 (CBr2F2), measured from air collected at Cape Grim, Tasmania, between 1978 and 2011, are reported. Mixing ratios of H-1211, H-2402 and H-1202 began to decline in the early to mid-2000s, but those of H-1301 continue to increase up to mid-2011. These trends are compared to those reported by NOAA (National Oceanic and Atmospheric Administration) and AGAGE (Advanced Global Atmospheric Experiment). The observations suggest that the contribution of the halons to total tropospheric bromine at Cape Grim has begun to decline from a peak in 2008 of about 8.1 ppt. An extrapolation of halon mixing ratios to 2060, based on reported banks and predicted release factors, shows this decline becoming more rapid in the coming decades, with a contribution to total tropospheric bromine of about 3 ppt in 2060. Top-down global annual emissions of the halons were derived using a two-dimensional atmospheric model. The emissions of all four have decreased since peaking in the late 1980s–mid-1990s, but this decline has slowed recently, particularly for H-1301 and H-2402 which have shown no decrease in emissions over the past five years. The UEA (University of East Anglia) top-down model-derived emissions are compared to those reported using a top-down approach by NOAA and AGAGE and the bottom-up estimates of HTOC (Halons Technical Options Committee). The implications of an alternative set of steady-state atmospheric lifetimes are discussed. Using a lifetime of 14 yr or less for H-1211 to calculate top-down emissions estimates would lead to small, or even negative, estimated banks given reported production data. Finally emissions of H-1202, a product of over-bromination during the production process of H-1211, have continued despite reported production of H-1211 ceasing in 2010. This raises questions as to the source of these H-1202 emissions

Structural and Magnetic Properties of Trigonal Iron

First principles calculations of the electronic structure of trigonal iron were performed using density function theory. The results are used to predict lattice spacings, magnetic moments and elastic properties; these are in good agreement with experiment for both the bcc and fcc structures. We find however, that in extracting these quantities great care must be taken in interpreting numerical fits to the calculated total energies. In addition, the results for bulk iron give insight into the properties of thin iron films. Thin films grown on substrates with mismatched lattice constants often have non-cubic symmetry. If they are thicker than a few monolayers their electronic structure is similar to a bulk material with an appropriately distorted geometry, as in our trigonal calculations. We recast our bulk results in terms of an iron film grown on the (111) surface of an fcc substrate, and find the predicted strain energies and moments accurately reflect the trends for iron growth on a variety of substrates.Comment: 11 pages, RevTeX,4 tar'd,compressed, uuencoded Postscript figure

Measurement in biological systems from the self-organisation point of view

Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological systems as dynamical systems far from not only their chemical equilibrium, but, in most cases, also of their Lyapunov stable states. Thus, in biological experiments, we do not observe states, but distinct trajectories followed by the examined organism. If one of the possible sequences is selected, a minute sub-section of the whole problem is obtained, sometimes in a seemingly highly reproducible manner. But the state of the organism is known only if a complete set of possible trajectories is known. And this is often practically impossible. Therefore, we propose a different framework for reporting and analysis of biological experiments, respecting the view of non-linear mathematics. This view should be used to avoid overoptimistic results, which have to be consequently retracted or largely complemented. An increase of specification of experimental procedures is the way for better understanding of the scope of paths, which the biological system may be evolving. And it is hidden in the evolution of experimental protocols.Comment: 13 pages, 5 figure

Charitable Food Systems' Capacity to Address Food Insecurity: An Australian Capital City Audit.

Australian efforts to address food insecurity are delivered by a charitable food system (CFS) which fails to meet demand. The scope and nature of the CFS is unknown. This study audits the organisational capacity of the CFS within the 10.9 square kilometres of inner-city Perth, Western Australia. A desktop analysis of services and 12 face-to-face interviews with representatives from CFS organisations was conducted. All CFS organisations were not-for⁻profit and guided by humanitarian or faith-based values. The CFS comprised three indirect services (IS) sourcing, banking and/or distributing food to 15 direct services (DS) providing food to recipients. DS offered 30 different food services at 34 locations feeding over 5670 people/week via 16 models including mobile and seated meals, food parcels, supermarket vouchers, and food pantries. Volunteer to paid staff ratios were 33:1 (DS) and 19:1 (IS). System-wide, food was mainly donated and most funding was philanthropic. Only three organisations received government funds. No organisation had a nutrition policy. The organisational capacity of the CFS was precarious due to unreliable, insufficient and inappropriate financial, human and food resources and structures. System-wide reforms are needed to ensure adequate and appropriate food relief for Australians experiencing food insecurity

Meanings of epilepsy in its sociocultural context and implications for stigma: Findings from ethnographic studies in local communities in China and Vietnam

We investigated beliefs about the causes, course, and treatment of epilepsy and its impact on quality of life (QOL) in key target groups, using “mini-ethnographies” involving 141 in-depth interviews and 12 focus groups in China, and 84 in-depth interviews and 16 focus groups in Vietnam. Data were analyzed thematically, using a qualitative data analysis package. In both countries, beliefs about causes and triggers of epilepsy and seizures were a complex interweaving of Western, traditional, and folk medicine concepts. Epilepsy was understood to be chronic, not curable, but controllable, and was seen as enormously socially disruptive, with wide-ranging impact on QOL. Our findings suggest a more “embodied” and benign set of theories about epilepsy than in some other cultural contexts; nonetheless, people with epilepsy are still seen as having low social value and face social rejection. By exploring meanings attached to epilepsy in these two cultural contexts, we have clarified reasons behind previously documented negative attitudes and foci for future intervention studies

Surface relaxation and ferromagnetism of Rh(001)

The significant discrepancy between first-principles calculations and experimental analyses for the relaxation of the (001) surface of rhodium has been a puzzle for some years. In this paper we present density functional theory calculations using the local-density approximation and the generalized gradient approximation of the exchange-correlation functional. We investigate the thermal expansion of the surface and the possibility of surface magnetism. The results throw light on several, hitherto overlooked, aspects of metal surfaces. We find, that, when the free energy is considered, density-functional theory provides results in good agreement with experiments.Comment: 6 pages, 4 figures, submitted to Phys. Rev. Lett. (April 28, 1996

Dopamine D_2-receptor activation elicits akinesia, rigidity, catalepsy, and tremor in mice expressing hypersensitive 4 nicotinic receptors via a cholinergic-dependent mechanism

Recent studies suggest that high-affinity neuronal nicotinic acetylcholine receptors (nAChRs) containing α4 and β2 subunits (α4β2*) functionally interact with G-protein-coupled dopamine (DA) D_2 receptors in basal ganglia. We hypothesized that if a functional interaction between these receptors exists, then mice expressing an M2 point mutation (Leu9'Ala) rendering 4 nAChRs hypersensitive to ACh may exhibit altered sensitivity to a D_2-receptor agonist. When challenged with the D_(2)R agonist, quinpirole (0.5–10 mg/kg), Leu9'Ala mice, but not wild-type (WT) littermates, developed severe, reversible motor impairment characterized by rigidity, catalepsy, akinesia, and tremor. While striatal DA tissue content, baseline release, and quinpirole-induced DA depletion did not differ between Leu9'Ala and WT mice, quinpirole dramatically increased activity of cholinergic striatal interneurons only in mutant animals, as measured by increased c-Fos expression in choline acetyltransferase (ChAT)-positive interneurons. Highlighting the importance of the cholinergic system in this mouse model, inhibiting the effects of ACh by blocking muscarinic receptors, or by selectively activating hypersensitive nAChRs with nicotine, rescued motor symptoms. This novel mouse model mimics the imbalance between striatal DA/ACh function associated with severe motor impairment in disorders such as Parkinson’s disease, and the data suggest that a D_(2)R–α4*-nAChR functional interaction regulates cholinergic interneuron activity.—Zhao-Shea, R., Cohen, B. N., Just, H., McClure-Begley, T., Whiteaker, P., Grady, S. R., Salminen, O., Gardner, P. D., Lester, H. A., Tapper, A. R. Dopamine D2-receptor activation elicits akinesia, rigidity, catalepsy, and tremor in mice expressing hypersensitive α4 nicotinic receptors via a cholinergic-dependent mechanism