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1.  Assessing Cellular Response to Functionalized α-Helical Peptide Hydrogels 
Advanced Healthcare Materials  2014;3(9):1387-1391.
doi:10.1002/adhm.201400065
PMCID: PMC4276410  PMID: 24659615
2D cell culture; PC12 cells; peptide hydrogels; self-assembled fibers; tissue engineering
2.  The Ubiquitin C-Terminal Hydrolase L1 (UCH-L1) C Terminus Plays a Key Role in Protein Stability, but Its Farnesylation Is Not Required for Membrane Association in Primary Neurons* 
The Journal of Biological Chemistry  2014;289(52):36140-36149.
Background: Membrane-associated UCH-L1 has been proposed as a target for treating neurodegeneration.
Results: UCH-L1 association with neuronal membranes does not involve farnesylation. C-terminal truncation causes protein misfolding and neuronal death.
Conclusion: The C terminus of UCH-L1 regulates protein aggregation and stability.
Significance: The CTTΔ4 mutant provides a model for studying neurotoxic UCH-L1 aggregation events.
Ubiquitin C-terminal hydrolase L1 (UCH-L1) is a deubiquitinating enzyme that is highly expressed in neurons. A possible role for UCH-L1 in neurodegeneration has been highlighted because of its presence in Lewy bodies associated with Parkinson disease and neurofibrillary tangles observed in Alzheimer disease. UCH-L1 exists in two forms in neurons, a soluble cytoplasmic form (UCH-L1C) and a membrane-associated form (UCH-L1M). Alzheimer brains show reduced levels of soluble UCH-L1C correlating with the formation of UCH-L1-immunoreactive tau tangles, whereas UCH-L1M has been implicated in α-synuclein dysfunction. Given these reports of divergent roles, we investigated the properties of UCH-L1 membrane association. Surprisingly, our results indicate that UCH-L1 does not partition to the membrane in the cultured cell lines we tested. Furthermore, in primary cultured neurons, a proportion of UCH-L1M does partition to the membrane, but, contrary to a previous report, this does not require farnesylation. Deletion of the four C-terminal residues caused the loss of protein solubility, abrogation of substrate binding, increased cell death, and an abnormal intracellular distribution, consistent with protein dysfunction and aggregation. These data indicate that UCH-L1 is differently processed in neurons compared with clonal cell lines and that farnesylation does not account for the membrane association in neurons.
doi:10.1074/jbc.M114.557124
PMCID: PMC4276877  PMID: 25326379
Membrane Protein; Neurobiology; Posttranslational Modification (PTM); Protein Misfolding; Ubiquitination
3.  Influence of association state and DNA binding on the O2-reactivity of [4Fe-4S] fumarate and nitrate reduction (FNR) regulator 
Biochemical Journal  2014;463(Pt 1):83-92.
The fumarate and nitrate reduction (FNR) regulator is the master switch for the transition between anaerobic and aerobic respiration in Escherichia coli. Reaction of dimeric [4Fe-4S] FNR with O2 results in conversion of the cluster into a [2Fe-2S] form, via a [3Fe-4S] intermediate, leading to the loss of DNA binding through dissociation of the dimer into monomers. In the present paper, we report studies of two previously identified variants of FNR, D154A and I151A, in which the form of the cluster is decoupled from the association state. In vivo studies of permanently dimeric D154A FNR show that DNA binding does not affect the rate of cluster incorporation into the apoprotein or the rate of O2-mediated cluster loss. In vitro studies show that O2-mediated cluster conversion for D154A and the permanent monomer I151A FNR is the same as in wild-type FNR, but with altered kinetics. Decoupling leads to an increase in the rate of the [3Fe-4S]1+ into [2Fe-2S]2+ conversion step, consistent with the suggestion that this step drives association state changes in the wild-type protein. We have also shown that DNA-bound FNR reacts more rapidly with O2 than FNR free in solution, implying that transcriptionally active FNR is the preferred target for reaction with O2.
DNA-binding of [4Fe-4S] FNR and amino acid substitutions that decouple the dependence of the association state on the cluster are shown to have no effect on the overall cluster conversion mechanism but have a significant effect on reaction kinetics.
doi:10.1042/BJ20140169
PMCID: PMC4214427  PMID: 25019503
cluster conversion; dimerization; DNA regulation; fumarate and nitrate reduction (FNR) regulator; iron–sulfur cluster; O2-sensor; CRP, cAMP receptor protein; FNR, fumarate and nitrate reduction (regulator); Nm-FNR, Neisseria meningitidis FNR
4.  CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies 
Bioinformatics  2014;30(21):3029-3035.
Motivation: The ability to accurately model protein structures at the atomistic level underpins efforts to understand protein folding, to engineer natural proteins predictably and to design proteins de novo. Homology-based methods are well established and produce impressive results. However, these are limited to structures presented by and resolved for natural proteins. Addressing this problem more widely and deriving truly ab initio models requires mathematical descriptions for protein folds; the means to decorate these with natural, engineered or de novo sequences; and methods to score the resulting models.
Results: We present CCBuilder, a web-based application that tackles the problem for a defined but large class of protein structure, the α-helical coiled coils. CCBuilder generates coiled-coil backbones, builds side chains onto these frameworks and provides a range of metrics to measure the quality of the models. Its straightforward graphical user interface provides broad functionality that allows users to build and assess models, in which helix geometry, coiled-coil architecture and topology and protein sequence can be varied rapidly. We demonstrate the utility of CCBuilder by assembling models for 653 coiled-coil structures from the PDB, which cover >96% of the known coiled-coil types, and by generating models for rarer and de novo coiled-coil structures.
Availability and implementation: CCBuilder is freely available, without registration, at http://coiledcoils.chm.bris.ac.uk/app/cc_builder/
Contact: D.N.Woolfson@bristol.ac.uk or Chris.Wood@bristol.ac.uk
doi:10.1093/bioinformatics/btu502
PMCID: PMC4201159  PMID: 25064570
5.  Divergent LIN28-mRNA associations result in translational suppression upon the initiation of differentiation 
Nucleic Acids Research  2014;42(12):7997-8007.
LIN28 function is fundamental to the activity and behavior of human embryonic stem cells (hESCs) and induced pluripotent stem cells. Its main roles in these cell types are the regulation of translational efficiency and let-7 miRNA maturation. However, LIN28-associated mRNA cargo shifting and resultant regulation of translational efficiency upon the initiation of differentiation remain unknown. An RNA-immunoprecipitation and microarray analysis protocol, eRIP, that has high specificity and sensitivity was developed to test endogenous LIN28-associated mRNA cargo shifting. A combined eRIP and polysome analysis of early stage differentiation of hESCs with two distinct differentiation cues revealed close similarities between the dynamics of LIN28 association and translational modulation of genes involved in the Wnt signaling, cell cycle, RNA metabolism and proteasomal pathways. Our data demonstrate that change in translational efficiency is a major contributor to early stages of differentiation of hESCs, in which LIN28 plays a central role. This implies that eRIP analysis of LIN28-associated RNA cargoes may be used for rapid functional quality control of pluripotent stem cells under manufacture for therapeutic applications.
doi:10.1093/nar/gku430
PMCID: PMC4081066  PMID: 24860167
6.  Bacterial Iron–Sulfur Regulatory Proteins As Biological Sensor-Switches 
Antioxidants & Redox Signaling  2012;17(9):1215-1231.
Abstract
Significance: In recent years, bacterial iron–sulfur cluster proteins that function as regulators of gene transcription have emerged as a major new group. In all cases, the cluster acts as a sensor of the environment and enables the organism to adapt to the prevailing conditions. This can range from mounting a response to oxidative or nitrosative stress to switching between anaerobic and aerobic respiratory pathways. The sensitivity of these ancient cofactors to small molecule reactive oxygen and nitrogen species, in particular, makes them ideally suited to function as sensors. Recent Advances: An important challenge is to obtain mechanistic and structural information about how these regulators function and, in particular, how the chemistry occurring at the cluster drives the subsequent regulatory response. For several regulators, including FNR, SoxR, NsrR, IscR, and Wbl proteins, major advances in understanding have been gained recently and these are reviewed here. Critical Issues: A common theme emerging from these studies is that the sensitivity and specificity of the cluster of each regulatory protein must be exquisitely controlled by the protein environment of the cluster. Future Directions: A major future challenge is to determine, for a range of regulators, the key factors for achieving control of sensitivity/specificity. Such information will lead, eventually, to a system understanding of stress response, which often involves more than one regulator. Antioxid. Redox Signal. 17, 1215–1231.
doi:10.1089/ars.2012.4511
PMCID: PMC3430481  PMID: 22239203
7.  Focused Screening and Treatment (FSAT): A PCR-Based Strategy to Detect Malaria Parasite Carriers and Contain Drug Resistant P. falciparum, Pailin, Cambodia 
PLoS ONE  2012;7(10):e45797.
Recent studies have shown that Plasmodium falciparum malaria parasites in Pailin province, along the border between Thailand and Cambodia, have become resistant to artemisinin derivatives. To better define the epidemiology of P. falciparum populations and to assess the risk of the possible spread of these parasites outside Pailin, a new epidemiological tool named “Focused Screening and Treatment” (FSAT), based on active molecular detection of asymptomatic parasite carriers was introduced in 2010. Cross-sectional malariometric surveys using PCR were carried out in 20 out of 109 villages in Pailin province. Individuals detected as P. falciparum carriers were treated with atovaquone-proguanil combination plus a single dose of primaquine if the patient was non-G6PD deficient. Interviews were conducted to elicit history of cross-border travel that might contribute to the spread of artemisinin-resistant parasites. After directly observed treatment, patients were followed up and re-examined on day 7 and day 28. Among 6931 individuals screened, prevalence of P. falciparum carriers was less than 1%, of whom 96% were asymptomatic. Only 1.6% of the individuals had a travel history or plans to go outside Cambodia, with none of those tested being positive for P. falciparum. Retrospective analysis, using 2010 routine surveillance data, showed significant differences in the prevalence of asymptomatic carriers discovered by FSAT between villages classified as “high risk” and “low risk” based on malaria incidence data. All positive individuals treated and followed-up until day 28 were cured. No mutant-type allele related to atovaquone resistance was found. FSAT is a potentially useful tool to detect, treat and track clusters of asymptomatic carriers of P. falciparum along with providing valuable epidemiological information regarding cross-border movements of potential malaria parasite carriers and parasite gene flow.
doi:10.1371/journal.pone.0045797
PMCID: PMC3462177  PMID: 23049687
8.  A unique case of an alpha-fetoprotein-producing lung cancer with testicular metastasis 
Alpha-fetoprotein (AFP)-producing primary lung tumours are rare; we present the first case of an AFP-producing lung tumour with metastasis to testes. The patient, a 72-year-old man, presented with a history of flu-like symptoms and abdominal pain. On examination he had a hard, tender left scrotal mass. Imaging showed a 4.4-cm right lower lobe lung mass and the serum-AFP was raised (1189 ng/mL). Left orchidectomy excised a necrotic tumour. Microscopy showed complete hemorrhagic infarction and immunohistochemistry showed a lack of staining for AFP. Serum-AFP rose 3 days post-orchidectomy to 1466 ng/mL. The patient subsequently developed melaena and died. Autopsy revealed a 9 × 5-cm necrotic right lower lobe lung tumour. Immunohistochemistry showed the tumour cells reacted with a pan-cytokeratin antibody and less than 5% expressed AFP. Bilateral adrenal tumour deposits were also identified in addition to those in the bowel and spleen. The expression of AFP solely in the lung lesion and lack of expression in both testes, together with a rise in serum-AFP post-orchidectomy and the bilateral adrenal metastases, is overwhelming evidence for the reversal of the usual situation: a poorly differentiated AFP-secreting metastatic lung adenocarcinoma.
doi:10.5489/cuaj.11088
PMCID: PMC3478336  PMID: 23093628
9.  A de novo peptide hexamer with a mutable channel 
Nature chemical biology  2011;7(12):935-941.
The design of new proteins that expand the repertoire of natural protein structures represents a formidable challenge. Success in this area would increase understanding of protein structure, and present new scaffolds that could be exploited in biotechnology and synthetic biology. Here we describe the design, characterisation and X-ray crystal structure of a new coiled-coil protein. The de novo sequence forms a stand-alone, parallel, 6-helix bundle with a channel running through it. Although lined exclusively by hydrophobic leucine and isoleucine side chains, the 6 Å channel is permeable to water. One layer of leucine residues within the channel is mutable accepting polar aspartic acid (Asp) and histidine (His) side chains, and leading to subdivision and organization of solvent within the lumen. Moreover, these mutants can be combined to form a stable and unique (Asp-His)3 heterohexamer. These new structures provide a basis for engineering de novo proteins with new functions.
doi:10.1038/nchembio.692
PMCID: PMC3223406  PMID: 22037471
11.  Interleukin 18 and coronary heart disease: Prospective study and systematic review 
Atherosclerosis  2011;217(1):227-233.
Aim
Previous studies suggest that circulating levels of interleukin-18 (IL-18) may be prospectively related to risk of coronary heart disease (CHD) in the general population. We report new data from the largest prospective study to date, which are combined with data from all published prospective studies in a meta-analysis.
Methods
We measured baseline IL-18 levels in stored serum samples of subjects from a case–control study nested within a prospective study of 5661 men aged 40–59 years recruited from general practices in 18 British towns in 1978–1980 and followed-up for up to 16 years (median time to event 8.4 years) for fatal CHD and non-fatal myocardial infarction (595 cases, 1238 controls).
Results
IL-18 concentrations were strongly related to cigarette smoking, triglyceride, HDL-cholesterol (inversely) and to circulating levels of several inflammatory and haemostatic markers. Men in the top third of baseline IL-18 levels had an age-adjusted odds ratio (OR) for CHD of 1.55 (95% CI 1.21, 1.98) compared with those in the lowest third; this was reduced to 1.30 (95% CI 0.99, 1.69) after additional adjustment for vascular risk factors and 1.12 (95% CI 0.84, 1.49) after further adjustment for CRP and IL-6. In meta-analyses of CVD, associations (or effect sizes) were consistent between studies; RRs were 1.63 (95% CI 1.46, 1.82) after age adjustment, 1.39 (95% CI 1.24, 1.55) after additional risk factor adjustment and 1.34 (95% CI 1.17, 1.54) after additional adjustment for inflammatory markers.
Conclusions
Circulating IL-18 is prospectively and independently associated with CVD risk.
doi:10.1016/j.atherosclerosis.2011.03.015
PMCID: PMC3146704  PMID: 21481392
Coronary heart disease; Epidemiology; Interleukin-18; Cohort; Meta-analysis
12.  Voltage-dependent inactivation gating at the selectivity filter of the MthK K+ channel 
The Journal of General Physiology  2010;136(5):569-579.
Voltage-dependent K+ channels can undergo a gating process known as C-type inactivation, which involves entry into a nonconducting state through conformational changes near the channel’s selectivity filter. C-type inactivation may involve movements of transmembrane voltage sensor domains, although the mechanisms underlying this form of inactivation may be heterogeneous and are often unclear. Here, we report on a form of voltage-dependent inactivation gating observed in MthK, a prokaryotic K+ channel that lacks a canonical voltage sensor and may thus provide a reduced system to inform on mechanism. In single-channel recordings, we observe that Po decreases with depolarization, with a half-maximal voltage of 96 ± 3 mV. This gating is kinetically distinct from blockade by internal Ca2+ or Ba2+, suggesting that it may arise from an intrinsic inactivation mechanism. Inactivation gating was shifted toward more positive voltages by increasing external [K+] (47 mV per 10-fold increase in [K+]), suggesting that K+ binding at the extracellular side of the channel stabilizes the open-conductive state. The open-conductive state was stabilized by other external cations, and selectivity of the stabilizing site followed the sequence: K+ ≈ Rb+ > Cs+ > Na+ > Li+ ≈ NMG+. Selectivity of the stabilizing site is weaker than that of sites that determine permeability of these ions, suggesting that the site may lie toward the external end of the MthK selectivity filter. We could describe MthK gating over a wide range of positive voltages and external [K+] using kinetic schemes in which the open-conductive state is stabilized by K+ binding to a site that is not deep within the electric field, with the voltage dependence of inactivation arising from both voltage-dependent K+ dissociation and transitions between nonconducting (inactivated) states. These results provide a quantitative working hypothesis for voltage-dependent, K+-sensitive inactivation gating, a property that may be common to other K+ channels.
doi:10.1085/jgp.201010507
PMCID: PMC2964515  PMID: 20937694
13.  Characterization of [4Fe-4S]-containing and cluster-free forms of Streptomyces WhiD 
Biochemistry  2009;48(51):12252.
WhiD, a member of the WhiB-like (Wbl) family of iron-sulfur proteins found exclusively within the actinomycetes, is required for the late stages of sporulation in Streptomyces coelicolor. Like all other Wbl proteins, WhiD has not so far been purified in a soluble form that contains a significant amount of cluster and characterization has relied on cluster-reconstituted protein. Thus, a major goal in Wbl research is to obtain and characterize native protein containing iron-sulfur clusters. Here we report the analysis of S. coelicolor WhiD purified anaerobically from E. coli as a soluble protein containing a single [4Fe-4S]2+ cluster ligated by four cysteines. Upon exposure to oxygen, spectral features associated with the [4Fe-4S] cluster were lost in a slow reaction that unusually yielded apo-WhiD directly without significant concentrations of cluster intermediates. This process was found to be highly pH dependent with an optimal stability observed between pH 7.0 and 8.0. Low molecular weight thiols, including a mycothiol analogue and thioredoxin, exerted a small but significant protective effect against WhiD cluster loss, an activity that could be of physiological importance. [4Fe-4S]2+ WhiD was found to react much more rapidly with superoxide than with either oxygen or hydrogen peroxide, which may also be of physiological significance. Loss of the [4Fe-4S] cluster to form apo-protein destabilized the protein fold significantly, but did not lead to complete unfolding. Finally, apo-WhiD exhibited negligible activity in an insulin-based disulfide reductase assay demonstrating that it does not function as a general protein disulfide reductase.
doi:10.1021/bi901498v
PMCID: PMC2815329  PMID: 19954209
14.  Mycobacterium tuberculosis WhiB1 is an essential DNA-binding protein with a nitric oxide sensitive iron-sulphur cluster 
The Biochemical journal  2010;432(3):417-427.
Mycobacterium tuberculosis is a major pathogen that has the ability to establish, and emerge from, a persistent state. Wbl family proteins are associated with developmental processes in actinomycetes, and M. tuberculosis has seven such proteins. Here it is shown that the M. tuberculosis H37Rv whiB1 gene is essential. The WhiB1 protein possesses a [4Fe-4S]2+ cluster that is stable in air but reacts rapidly with eight equivalents of nitric oxide to yield two dinuclear dinitrosyl-iron thiol complexes. The [4Fe-4S] form of WhiB1 did not bind whiB1 promoter DNA, but the reduced and oxidized apo-WhiB1, and nitric oxide-treated holo-WhiB1 did bind to DNA. Mycobacterium smegmatis RNA polymerase induced transcription of whiB1 in vitro; however in the presence of apo-WhiB1 transcription was severely inhibited, irrespective of the presence or absence of the CRP protein Rv3676, which is known to activate whiB1 expression. Footprinting suggested that autorepression of whiB1 is achieved by apo-WhiB1 binding at a region that overlaps the core promoter elements. A model incorporating regulation of whiB1 expression in response to nitric oxide and cAMP is discussed with implications for sensing two important signals in establishing M. tuberculosis infections.
doi:10.1042/BJ20101440
PMCID: PMC2992795  PMID: 20929442
actinomycetes; iron-sulphur cluster; nitric oxide; TB; Wbl protein
15.  Subunit Organization in the TatA Complex of the Twin Arginine Protein Translocase 
The Journal of Biological Chemistry  2009;285(4):2294-2301.
The Tat system is used to transport folded proteins across the cytoplasmic membrane in bacteria and archaea and across the thylakoid membrane of plant chloroplasts. Multimers of the integral membrane TatA protein are thought to form the protein-conducting element of the Tat pathway. Nitroxide radicals were introduced at selected positions within the transmembrane helix of Escherichia coli TatA and used to probe the structure of detergent-solubilized TatA complexes by EPR spectroscopy. A comparison of spin label mobilities allowed classification of individual residues as buried within the TatA complex or exposed at the surface and suggested that residues Ile12 and Val14 are involved in interactions between helices. Analysis of inter-spin distances suggested that the transmembrane helices of TatA subunits are arranged as a single-walled ring containing a contact interface between Ile12 on one subunit and Val14 on an adjacent subunit. Experiments in which labeled and unlabeled TatA samples were mixed demonstrate that TatA subunits are exchanged between TatA complexes. This observation is consistent with the TatA dynamic polymerization model for the mechanism of Tat transport.
doi:10.1074/jbc.M109.065458
PMCID: PMC2807286  PMID: 19920142
Membrane/Channels; Membrane/Proteins; Methods/Electron Paramagnetic Resonance EPR; Protein/Structure; Protein/Translocation; Transport; Spin Labeling
16.  Iron and the translation of the amyloid precursor protein (APP) and ferritin 
Biochemical Society transactions  2008;36(Pt 6):1282-1287.
The essential metals iron, zinc and copper deposit near the Aβ (amyloid β-peptide) plaques in the brain cortex of AD (Alzheimer’s disease) patients. Plaque-associated iron and zinc are in neurotoxic excess at 1 mM concentrations. APP (amyloid precursor protein) is a single transmembrane metalloprotein cleaved to generate the 40-42-amino-acid Aβs, which exhibit metal-catalysed neurotoxicity. In health, ubiquitous APP is cleaved in a non-amyloidogenic pathway within its Aβ domain to release the neuroprotective APP ectodomain, APP(s). To adapt and counteract metal-catalysed oxidative stress, as during reperfusion from stroke, iron and cytokines induce the translation of both APP and ferritin (an iron storage protein) by similar mechanisms. We reported that APP was regulated at the translational level by active IL (interleukin)-1 (IL-1-responsive acute box) and IRE (iron-responsive element) RNA stem-loops in the 5′ untranslated region of APP mRNA. The APP IRE is homologous with the canonical IRE RNA stem-loop that binds the iron regulatory proteins (IRP1 and IRP2) to control intracellular iron homoeostasis by modulating ferritin mRNA translation and transferrin receptor mRNA stability. The APP IRE interacts with IRP1 (cytoplasmic cis-aconitase), whereas the canonical ferritin-H IRE RNA stem-loop binds to IRP2 in neural cell lines, and in human brain cortex tissue and in human blood lysates. The same constellation of RNA-binding proteins [IRP1/IRP2/poly(C) binding protein] control ferritin and APP translation with implications for the biology of metals in AD.
doi:10.1042/BST0361282
PMCID: PMC2746665  PMID: 19021541
amyloid precursor protein (APP); copper; ferritin; iron; oxidative stress; zinc
17.  Dissection of the DNA Mimicry of the Bacteriophage T7 Ocr Protein using Chemical Modification 
Journal of Molecular Biology  2009;391(3):565-576.
The homodimeric Ocr (overcome classical restriction) protein of bacteriophage T7 is a molecular mimic of double-stranded DNA and a highly effective competitive inhibitor of the bacterial type I restriction/modification system. The surface of Ocr is replete with acidic residues that mimic the phosphate backbone of DNA. In addition, Ocr also mimics the overall dimensions of a bent 24-bp DNA molecule. In this study, we attempted to delineate these two mechanisms of DNA mimicry by chemically modifying the negative charges on the Ocr surface. Our analysis reveals that removal of about 46% of the carboxylate groups per Ocr monomer results in an ∼ 50-fold reduction in binding affinity for a methyltransferase from a model type I restriction/modification system. The reduced affinity between Ocr with this degree of modification and the methyltransferase is comparable with the affinity of DNA for the methyltransferase. Additional modification to remove ∼ 86% of the carboxylate groups further reduces its binding affinity, although the modified Ocr still binds to the methyltransferase via a mechanism attributable to the shape mimicry of a bent DNA molecule. Our results show that the electrostatic mimicry of Ocr increases the binding affinity for its target enzyme by up to ∼ 800-fold.
doi:10.1016/j.jmb.2009.06.020
PMCID: PMC2806950  PMID: 19523474
Ocr, overcome classical restriction; R/M, restriction/modification; EDC, 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride; HOBt, hydroxybenzotriazole; MS, mass spectrometry; MALDI-TOF, matrix-assisted laser desorption/ionization time of flight; FT-ICR, Fourier transform ion cyclotron resonance; GdmCl, guanidinium hydrochloride; SAM, S-adenosyl-L-methionine; ITC, isothermal titration calorimetry; WT, wild type; DNA mimic; chemical modification; restriction/modification system
18.  Circulating TNFα levels in older men and women do not show independent prospective relations with MI or stroke 
Atherosclerosis  2009;205(1):302-308.
Background
Tumour necrosis factor alpha (TNFα) is a pro-inflammatory cytokine implicated in atherosclerotic plaque formation. We investigated whether circulating TNFα is prospectively associated with myocardial infarction (MI) or stroke in the older general population, independently of established cardiovascular risk factors and other inflammatory markers related to CHD risk.
Methods
We measured baseline TNFα concentrations in stored serum samples of 362 incident MI and 299 incident stroke cases and controls (2 per case, frequency matched by age, gender and town) who were ‘nested’ in parallel prospective studies of 4252 men and 4286 women aged 60–79 years assessed in general practices in 24 British towns in 1998–2000 and followed up for an average 7 years for fatal and non-fatal MI and stroke.
Results
TNFα levels were 11.4% (95% CI 9.5, 13.3%) higher among MI cases than controls; geometric mean 1.84 pg/mL compared to 1.63 pg/mL, p (difference) < 0.001. Participants in the top third of baseline TNFα levels had an age-adjusted odds ratio (OR) for MI of 1.75 (95%CI 1.22, 2.49) compared with those in the bottom third, which was reduced to 1.47 (95%CI 1.01, 2.14) after adjustment for established cardiovascular risk factors. However, further adjustment for C-reactive protein and interleukin-6 abolished the association OR 1.33 (95% CI 0.91, 1.66) and the linear trend. Excluding subjects with pre-existing CVD did not materially affect results. No significant association between TNFα and stroke was observed.
Conclusions
This study suggests that TNFα is not a strong independent risk marker for MI, and is not associated with risk of stroke.
doi:10.1016/j.atherosclerosis.2008.12.001
PMCID: PMC2706315  PMID: 19135670
TNFα, tumour necrosis factor alpha; MI, myocardial infarction; CVD, cardiovascular disease; CHD, coronary heart disease; OR, odds ratio; IQR, inter-quartile range; CI, confidence interval; CRP, C-reactive protein; IL-6, interleukin-6; BMI, body mass index; SBP, systolic blood pressure; DBP, diastolic blood pressure; t-PA, tissue plasminogen activator; LR, likelihood ratio; Myocardial infarction; Stroke; Inflammation; Epidemiology; TNFα; Prospective; Cohort
19.  Colonoscopic preoperative localization using submucosal injection of radiolabelled colloid 
Malignant colonic polyps can be removed endoscopically but surgical resection is sometimes required. However, the polypectomy site can be difficult to locate. Current methods use various tattooing agents, with varying degrees of success. A new technique using pre-operative injection of technetium-99m-labelled antimony colloid, with intraoperative localization using a handheld gamma probe, is described. Although unsuccessful in terms of localizing a previously partially resected polyp, the technique itself proved safe and simple, and has some advantages over other endoscopic approaches.
PMCID: PMC2661271  PMID: 18629395
Colonic polyps; Lymphoscintigraphy; Sentinel lymph node
20.  Changes in environmental tobacco smoke (ETS) exposure over a 20-year period: cross-sectional and longitudinal analyses 
Addiction (Abingdon, England)  2009;104(3):496-503.
Aims
To examine long-term changes in environmental tobacco smoke (ETS) exposure in British men between 1978 and 2000, using serum cotinine.
Design
Prospective cohort: British Regional Heart Study.
Setting
General practices in 24 towns in England, Wales and Scotland.
Participants
Non-smoking men: 2125 studied at baseline [questionnaire (Q1): 1978–80, aged 40–59 years], 3046 studied 20 years later (Q20: 1998–2000, aged 60–79 years) and 1208 studied at both times. Non-smokers were men reporting no current smoking with cotinine < 15 ng/ml at Q1 and/or Q20.
Measurements
Serum cotinine to assess ETS exposure.
Findings
In cross-sectional analysis, geometric mean cotinine level declined from 1.36 ng/ml [95% confidence interval (CI): 1.31, 1.42] at Q1 to 0.19 ng/ml (95% CI: 0.18, 0.19) at Q20. The prevalence of cotinine levels ≤ 0.7 ng/ml [associated with low coronary heart disease (CHD) risk] rose from 27.1% at Q1 to 83.3% at Q20. Manual social class and northern region of residence were associated with higher mean cotinine levels both at Q1 and Q20; older age was associated with lower cotinine level at Q20 only. Among 1208 persistent non-smokers, cotinine fell by 1.47 ng/ml (95% CI: 1.37, 1.57), 86% decline. Absolute falls in cotinine were greater in manual occupational groups, in the Midlands and Scotland compared to southern England, although percentage decline was very similar across groups.
Conclusions
A marked decline in ETS exposure occurred in Britain between 1978 and 2000, which is likely to have reduced ETS-related disease risks appreciably before the introduction of legislation banning smoking in public places.
doi:10.1111/j.1360-0443.2008.02473.x
PMCID: PMC2667894  PMID: 19207361
Cohort study; cotinine; environmental tobacco smoke; tobacco; trend
21.  How much of protein sequence space has been explored by life on Earth? 
We suggest that the vastness of protein sequence space is actually completely explorable during the populating of the Earth by life by considering upper and lower limits for the number of organisms, genome size, mutation rate and the number of functionally distinct classes of amino acids. We conclude that rather than life having explored only an infinitesimally small part of sequence space in the last 4 Gyr, it is instead quite plausible for all of functional protein sequence space to have been explored and that furthermore, at the molecular level, there is no role for contingency.
doi:10.1098/rsif.2008.0085
PMCID: PMC2459213  PMID: 18426772
protein sequence; evolution; contingency
22.  Fixation artefact in an intra-operative frozen section: a potential cause of misinterpretation 
The intra-operative histological assessment of fresh tissue can provide valuable diagnostic information and guide surgical management, however, even a limited exposure to standard fixation agents can potentially compromise analysis. Defined handling strategies should exist to facilitate the receipt of all specimens, in their optimal state, by the laboratory.
doi:10.1186/1749-8090-2-45
PMCID: PMC2117000  PMID: 17961203
23.  Perindopril: the evidence of its therapeutic impact in hypertension 
Core Evidence  2007;2(1):63-79.
Introduction:
Effective antihypertensive therapy reduces the risk of cardiovascular and cerebrovascular disease and death. Perindopril, a long-acting angiotensin-converting enzyme (ACE) inhibitor, is an established antihypertensive agent administered as a once-daily tablet.
Aims:
To review recent evidence for the use of perindopril in the treatment of hypertension.
Evidence review:
Evidence shows that perindopril alone or in combination with other antihypertensive agents can achieve clinically significant reductions in blood pressure after 12 weeks of treatment. There is strong evidence from large randomized studies that perindopril-based therapy reduces the risk of cardiovascular outcomes, including mortality, in patients with coronary artery disease and those who have had a prior stroke or transient ischemic attack. There is also some evidence that these effects are greater than those achieved by blood pressure reduction alone, suggesting other drug-related effects including improvements in endothelial function. Recent results have also shown that an amlodipine ± perindopril regimen prevented more major cardiovascular events than an atenolol-based regimen in patients with hypertension, as a result of better control of blood pressure. Economic evidence from one major study shows that, for most patients, the incremental cost per quality-adjusted life-year gained with perindopril 8 mg was lower than the threshold value of €20 000 (73–92% of patients) in Europe or £20 000 (94% of patients) in the UK.
Clinical value:
There is strong evidence supporting the use of perindopril-based therapy for the treatment of hypertension and reduction in the risk of cardiovascular disease, stroke, and death in a wide range of patients with stable coronary artery disease or hypertension.
PMCID: PMC3012553  PMID: 21221198
coronary artery disease; evidence-based review; hypertension; perindopril
24.  Etanercept in psoriasis: the evidence of its therapeutic impact 
Core Evidence  2007;2(1):51-62.
Introduction:
Psoriasis is a chronic inflammatory skin condition for which there is no cure. Treatment options are designed to control the disease symptoms and improve patients’ quality of life, and physical and mental function. Established treatments can be effective but are also limited by tolerability, convenience, cosmetic, and economic issues. Etanercept, a fully human soluble tumor necrosis factor (TNF) receptor protein, is a recently approved systemic treatment for chronic moderate to severe plaque psoriasis.
Aim:
To evaluate the evidence for the therapeutic value of etanercept in psoriasis.
Evidence review:
There is clear evidence that etanercept 25 mg or 50 mg twice per week reduces physician-assessed severity of psoriasis and can lead to clearing when compared with placebo. There is substantial evidence that etanercept improves patients’ quality of life as determined by both disease-specific and generic instruments. Emerging evidence includes improvements in symptoms associated with depression and fatigue. The tolerability of etanercept in patients with psoriasis appears to be similar to placebo. Initial indications from clinical trials suggest that there is no increased risk of infection or malignancy in etanercept-treated patients with psoriasis. The most common adverse events are reversible injection site reactions. Economic evidence is at present limited, although intermittent etanercept 25 mg is considered cost effective in patients with severe disease unsuitable for systemic treatment.
Clinical value:
Etanercept is an effective and efficient treatment for patients with moderate to severe psoriasis that may be suitable for intermittent use.
PMCID: PMC3012556  PMID: 21221197
etanercept; evidence; psoriasis; TNF inhibitor; treatment
25.  SIGMA: A System for Integrative Genomic Microarray Analysis of Cancer Genomes 
BMC Genomics  2006;7:324.
Background
The prevalence of high resolution profiling of genomes has created a need for the integrative analysis of information generated from multiple methodologies and platforms. Although the majority of data in the public domain are gene expression profiles, and expression analysis software are available, the increase of array CGH studies has enabled integration of high throughput genomic and gene expression datasets. However, tools for direct mining and analysis of array CGH data are limited. Hence, there is a great need for analytical and display software tailored to cross platform integrative analysis of cancer genomes.
Results
We have created a user-friendly java application to facilitate sophisticated visualization and analysis such as cross-tumor and cross-platform comparisons. To demonstrate the utility of this software, we assembled array CGH data representing Affymetrix SNP chip, Stanford cDNA arrays and whole genome tiling path array platforms for cross comparison. This cancer genome database contains 267 profiles from commonly used cancer cell lines representing 14 different tissue types.
Conclusion
In this study we have developed an application for the visualization and analysis of data from high resolution array CGH platforms that can be adapted for analysis of multiple types of high throughput genomic datasets. Furthermore, we invite researchers using array CGH technology to deposit both their raw and processed data, as this will be a continually expanding database of cancer genomes. This publicly available resource, the System for Integrative Genomic Microarray Analysis (SIGMA) of cancer genomes, can be accessed at .
doi:10.1186/1471-2164-7-324
PMCID: PMC1764892  PMID: 17192189

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