bluuebunny/crossref_metadata_2025 huggingface dataset:
What fraction of the human genome is functional?
Authors: Ponting Chris P. , Hardison Ross C.
Published: August 2011

Many evolutionary studies over the past decade have estimated αsel, the proportion of all nucleotides in the human genome that are subject to purifying selection because of their biological function. Most of these studies have estimated the nucleotide substitution rates from genome sequence alignments across many diverse mammals. Some αsel estimates will be affected by the heterogeneity of substitution rates in neutral sequence across the genome. Most will also be inaccurate if change in the functional sequence repertoire occurs rapidly relative to the separation of lineages that are being compared. Evidence gathered from both evolutionary and experimental analyses now indicate that rates of “turnover” of functional, predominantly noncoding, sequence are, indeed, high. They are sufficiently high that an estimated 50% of mouse constrained noncoding sequence is predicted not to be shared with rat, a closely related rodent. The rapidity of turnover results in, at least, a twofold underestimate of αsel by analyses that measure constraint across the eutherian phylogeny. Approaches that take account of turnover estimate that the steady-state value of αsel lies between 10% and 15%. Experimental studies corroborate the predicted rates of loss and gain of noncoding functional sites. These studies show the limitations inherent in the use of deep sequence conservation for identifying functional sequence. Experimental investigations focusing on lineage-specific, noncoding, and functional sequence are now essential if we are to appreciate the complete functional repertoire of the human genome.
Discriminative prediction of mammalian enhancers from DNA sequence
Authors: Lee Dongwon , Karchin Rachel , Beer Michael A.
Published: August 2011

Accurately predicting regulatory sequences and enhancers in entire genomes is an important but difficult problem, especially in large vertebrate genomes. With the advent of ChIP-seq technology, experimental detection of genome-wide EP300/CREBBP bound regions provides a powerful platform to develop predictive tools for regulatory sequences and to study their sequence properties. Here, we develop a support vector machine (SVM) framework which can accurately identify EP300-bound enhancers using only genomic sequence and an unbiased set of general sequence features. Moreover, we find that the predictive sequence features identified by the SVM classifier reveal biologically relevant sequence elements enriched in the enhancers, but we also identify other features that are significantly depleted in enhancers. The predictive sequence features are evolutionarily conserved and spatially clustered, providing further support of their functional significance. Although our SVM is trained on experimental data, we also predict novel enhancers and show that these putative enhancers are significantly enriched in both ChIP-seq signal and DNase I hypersensitivity signal in the mouse brain and are located near relevant genes. Finally, we present results of comparisons between other EP300/CREBBP data sets using our SVM and uncover sequence elements enriched and/or depleted in the different classes of enhancers. Many of these sequence features play a role in specifying tissue-specific or developmental-stage-specific enhancer activity, but our results indicate that some features operate in a general or tissue-independent manner. In addition to providing a high confidence list of enhancer targets for subsequent experimental investigation, these results contribute to our understanding of the general sequence structure of vertebrate enhancers.
GeBP/GPL Transcription Factors Regulate a Subset ofCPR5-Dependent Processes
Authors: Perazza Daniel , Laporte Frédéric , Balagué Claudine , Chevalier Florian , Remo Shanterika , Bourge Mickaël , Larkin John , Herzog Michel , Vachon Gilles
Published: August 2011

The CONSTITUTIVE EXPRESSOR OF PATHOGENESIS-RELATED GENES5 (CPR5) gene of Arabidopsis (Arabidopsis thaliana) encodes a putative membrane protein of unknown biochemical function and displays highly pleiotropic functions, particularly in pathogen responses, cell proliferation, cell expansion, and cell death. Here, we demonstrate a link between CPR5 and the GLABRA1  ENHANCER BINDING PROTEIN (GeBP) family of transcription factors. We investigated the primary role of the GeBP/GeBP-like (GPL) genes using transcriptomic analysis of the quadruple gebp gpl1,2,3 mutant and one overexpressing line that displays several cpr5-like phenotypes including dwarfism, spontaneous necrotic lesions, and increased pathogen resistance. We found that GeBP/GPLs regulate a set of genes that represents a subset of the CPR5 pathway. This subset includes genes involved in response to stress as well as cell wall metabolism. Analysis of the quintuple gebp gpl1,2,3 cpr5 mutant indicates that GeBP/GPLs are involved in the control of cell expansion in a CPR5-dependent manner but not in the control of cell proliferation. In addition, to our knowledge, we provide the first evidence that the CPR5 protein is localized in the nucleus of plant cells and that a truncated version of the protein with no transmembrane domain can trigger cpr5-like processes when fused to the VP16 constitutive transcriptional activation domain. Our results provide clues on how CPR5 and GeBP/GPLs play opposite roles in the control of cell expansion and suggest that the CPR5 protein is involved in transcription.
Neutron powder diffraction refinement of PbZr1 − x
Ti
x
O3
Authors: Zhang N. , Yokota H. , Glazer A. M. , Thomas P. A.
Published: August 2011

Rietveld refinement of different structural models using neutron diffraction data for a series of powders of lead zirconate titanate, PbZr1 − x
Ti
x
O3 (PZT), is described. It is found that at all the compositions and temperatures studied the best results include contributions from more than one phase in order to fit the data. Consequently a new phase diagram is proposed.
Effects of the [OC6F5] moiety upon structural geometry: crystal structures of half-sandwich tantalum(V) aryloxide complexes from reaction of Cp*Ta(N
t
Bu)(CH2
R)2 with pentafluorophenol
Authors: Cole Jacqueline M. , Chan Michael C. W. , Gibson Vernon C. , Howard Judith A. K.
Published: August 2011

The synthesis, chemical and structural characterization of a series of pentamethylcyclopentadienyl (Cp*) tantalum imido complexes and aryloxide derivatives are presented. Specifically, the imido complexes Cp*Ta(N
t
Bu)(CH2
R)2, where R = Ph [dibenzyl(tert-butylamido) (η5-pentamethylcyclopentadienyl)tantalum(IV) (1)], Me2Ph [tert-butylamido)bis(2-methyl-2-phenylpropyl) (η5-pentamethylcyclopentadienyl)tantalum(IV) (2)], CMe3 [(tert-butylamido)bis(2,2-dimethylpropyl) (η5-pentamethylcyclopentadienyl)tantalum(IV) (3)], are reported. The crystal structure of (3) reveals α-agostic interactions with the Ta atom. The resulting increase in the tantalum core coordination improves electronic stability. As such it does not react with pentafluorophenol, in contrast to the other two reported imido complexes [(1) and (2)]. Addition of C6F5OH to (1) yields a dimeric aryl-oxide derivative, [Cp*Ta(CH2Ph)(OC6H5)(μ-O)]2 [di-μ-oxido-bis[benzyl(pentafluorophenolato) (η5-pentamethylcyclopentadienyl)tantalum(V)] (4)]. Its crystal structure reveals long Ta—O(C6H5) bonds but short oxo-bridging Ta—O bonds. This is explained by accounting for the fierce electronic competition for the vacant d
π orbitals of the electrophilic TaV centre. Steric congestion around each metal is alleviated by a large twist angle (77.1°) between the benzyl and pentafluorophenyl ligands and the ordering of each of these groups into stacked pairs. The imido complex (2) reacts with C6F5OH to produce a mixture of Cp*Ta(OC6F5)4 [tetrakis(pentafluorophenolato)(η5-pentamethylcyclopentadienyl)tantalum(V) (5)] and [Cp*Ta(OC6F5)2(μ-O)]2 [di-μ-oxido-bis[bis(pentafluorophenolato)(η5-pentamethylcyclopentadienyl)tantalum(V)] (6)]. Steric congestion is offset in both cases by the twisting of its pentafluorophenyl ligands. Particularly strong electronic competition for the empty d
π metal orbitals in (6) is reflected in its bond geometry, and owes itself to the more numerous electron-withdrawing pentafluorophenyl ligands. The balance of steric and electronic factors affecting the reactivity of Cp* tantalum imido based complexes with pentafluorophenol is therefore addressed.
Searching for small simple automorphic loops
Authors: Johnson Kenneth W. , Kinyon Michael K. , Nagy Gábor P. , Vojtěchovský Petr
Published: August 2011

A loop is (right) automorphic if all its (right) inner mappings are automorphisms. Using the classification of primitive groups of small degrees, we show that there is no non-associative simple commutative automorphic loop of order less than 212, and no non-associative simple automorphic loop of order less than 2500. We obtain numerous examples of non-associative simple right automorphic loops. We also prove that every automorphic loop has the antiautomorphic inverse property, and that a right automorphic loop is automorphic if and only if its conjugations are automorphisms.
Families of explicitly isogenous Jacobians of variable-separated curves
Authors: Smith Benjamin
Published: August 2011

We construct six infinite series of families of pairs of curves (X,Y) of arbitrarily high genus, defined over number fields, together with an explicit isogeny from the Jacobian ofXto the Jacobian ofYsplitting multiplication by 2, 3 or 4. For each family, we compute the isomorphism type of the isogeny kernel and the dimension of the image of the family in the appropriate moduli space. The families are derived from Cassou-Noguès and Couveignes’ explicit classification of pairs (f,g) of polynomials such thatf(x1)−g(x2) is reducible.

Supplementary materials are available with this article.
PARETO: A novel evolutionary optimization approach to multiobjective IMRT planning
Authors: Fiege Jason , McCurdy Boyd , Potrebko Peter , Champion Heather , Cull Andrew
Published: August 2011

Purpose:

In radiation therapy treatment planning, the clinical objectives of uniform high dose to the planning target volume (PTV) and low dose to the organs‐at‐risk (OARs) are invariably in conflict, often requiring compromises to be made between them when selecting the best treatment plan for a particular patient. In this work, the authors introduce Pareto‐Aware Radiotherapy Evolutionary Treatment Optimization (pareto), a multiobjective optimization tool to solve for beam angles and fluence patterns in intensity‐modulated radiation therapy (IMRT) treatment planning.

Methods:

pareto is built around a powerful multiobjective genetic algorithm (GA), which allows us to treat the problem of IMRT treatment plan optimization as a combined monolithic problem, where all beam fluence and angle parameters are treated equally during the optimization. We have employed a simple parameterized beam fluence representation with a realistic dose calculation approach, incorporating patient scatter effects, to demonstrate feasibility of the proposed approach on two phantoms. The first phantom is a simple cylindrical phantom containing a target surrounded by three OARs, while the second phantom is more complex and represents a paraspinal patient.

Results:

pareto results in a large database of Pareto nondominated solutions that represent the necessary trade‐offs between objectives. The solution quality was examined for several PTV and OAR fitness functions. The combination of a conformity‐based PTV fitness function and a dose‐volume histogram (DVH) or equivalent uniform dose (EUD) ‐based fitness function for the OAR produced relatively uniform and conformal PTV doses, with well‐spaced beams. A penalty function added to the fitness functions eliminates hotspots. Comparison of resulting DVHs to those from treatment plans developed with a single‐objective fluence optimizer (from a commercial treatment planning system) showed good correlation. Results also indicated that pareto shows promise in optimizing the number of beams.

Conclusions:

This initial evaluation of the evolutionary optimization software toolpareto for IMRT treatment planning demonstrates feasibility and provides motivation for continued development. Advantages of this approach over current commercial methods for treatment planning are many, including: (1) fully automated optimization that avoids human controlled iterative optimization and potentially improves overall process efficiency, (2) formulation of the problem as a true multiobjective one, which provides an optimized set of Pareto nondominated solutions refined over hundreds of generations and compiled from thousands of parameter sets explored during the run, and (3) rapid exploration of the final nondominated set accomplished by a graphical interface used to select the best treatment option for the patient.
Experimental generation of an arbitrarily rotated field‐free line for the use in magnetic particle imaging
Authors: Erbe Marlitt , Knopp Tobias , Sattel Timo F. , Biederer Sven , Buzug Thorsten M.
Published: August 2011

Purpose:

The concept of a magnetic field‐free line (FFL), with regard to the novel tomographic modality magnetic particle imaging (MPI), was recently introduced. Theoretical approaches predict the improvement of sensitivity of MPI by a factor of ten replacing the conventionally used field‐free point (FFP) by a FFL. In this work, an experimental apparatus for generating an arbitrarily rotated and translated FFL field is described and tested.

Methods:

A theoretical motivation for the implemented setup is provided and the required currents are derived in dependency of the coil sensitivities. A prototype of a FFL field generator is manufactured and the fields are measured using a Hall effect sensor. An evaluation of the generated fields is performed via comparison to simulated data.

Results:

To utilize the FFL concept for MPI, the setup generating the fields needs to be feasible in praxis with respect to power loss. Furthermore, rotating and translating the FFL, while keeping the setup static in space, is a crucial aspect for conveying FFL imaging to clinical applications. The implemented setup copes with both of these challenges and allows for experimental generation as well as evaluation of the required fields. The generated fields agree to within 3.5% of model predictions.

Conclusions:

This work transfers the FFL concept from theoretical considerations to the implementation of an experimental setup generating the required fields. The high agreement of the measured fields with simulated data indicates the feasibility of magnetic field generation for the implementation of FFL imaging in MPI.
AKT Promotes rRNA Synthesis and Cooperates with c-MYC to Stimulate Ribosome Biogenesis in Cancer
Authors: Chan Joanna C. , Hannan Katherine M. , Riddell Kim , Ng Pui Yee , Peck Abigail , Lee Rachel S. , Hung Sandy , Astle Megan V. , Bywater Megan , Wall Meaghan , Poortinga Gretchen , Jastrzebski Katarzyna , Sheppard Karen E. , Hemmings Brian A. , Hall Michael N. , Johnstone Ricky W. , McArthur Grant A. , Hannan Ross D. , Pearson Richard B.
Published: August 2011

In addition to promoting translation, AKT also stimulates protein synthesis and cell growth by enhancing ribosome biogenesis.
Actin on Yap
Authors: VanHook Annalisa M.
Published: August 2011

Stress fibers promote nuclear accumulation of Yap, thus promoting proliferation.
Playing Checkers
Authors: Hurtley Stella M.
Published: August 2011

Interactions between adhesion molecules support the checkerboard-like patterning of cells in the cochlea.
A Different Response to Acute and Chronic Stress
Authors: Adler Elizabeth M.
Published: August 2011

Neuronal regulation of chaperone production in nematodes leads to differential responses to misfolded proteins under conditions of acute or chronic stress.
Keeping T Cells Quiet
Authors: Foley John F.
Published: August 2011

The tumor suppressor protein Tsc1, an inhibitor of the mammalian target of rapamycin, is required to maintain naïve T cell quiescence.
Getting There Is Only Half the Fun
Authors: Hines Pamela J.
Published: August 2011

Active transfer of a transcription factor between plant cells is required for stem cell maintenance.
Clinical Carbapenem-Resistant Acinetobacter baylyi Strain Coharboring
bla
SIM-1
and
bla
OXA-23
from China
Authors: Zhou Zhihui , Du Xiaoxing , Wang Li , Yang Qing , Fu Yiqi , Yu Yunsong
Published: August 2011

bla
SIM-1
and
bla
OXA-23
were codetected in clinical carbapenem-resistant
Acinetobacter baylyi
strain NB09A30. Both of carbapenemase genes were located on a large plasmid (ca. 360 kb).
bla
SIM-1
was found as a gene cassette inserted into a class 1 integron identical to that determined in
Acinetobacter
sp. isolates from South Korea. The genetic structure of
bla
OXA-23
in NB09A30 was different from that in the prevalent
Acinetobacter baumannii
of clonal complex 92 (CC92) from the same hospital.
Biochemical Characterization of Sfh-I, a Subclass B2 Metallo-β-Lactamase from Serratia fonticola UTAD54
Authors: Fonseca Fátima , Arthur Christopher J. , Bromley Elizabeth H. C. , Samyn Bart , Moerman Pablo , Saavedra Maria José , Correia António , Spencer James
Published: August 2011

The subclass B2 metallo-β-lactamase (MBL) Sfh-I from
Serratia fonticola
UTAD54 was cloned and overexpressed in
Escherichia coli
. The recombinant protein binds one equivalent of zinc, as shown by mass spectrometry, and preferentially hydrolyzes carbapenem substrates. However, compared to other B2 MBLs, Sfh-I also shows limited hydrolytic activity against some additional substrates and is not inhibited by a second equivalent of zinc. These data confirm Sfh-I to be a subclass B2 metallo-β-lactamase with some distinctive properties.
Application of Bacterial Bioluminescence To Assess the Efficacy of Fast-Acting Biocides
Authors: Robinson Gareth M. , Tonks Katherine M. , Thorn Robin M. S. , Reynolds Darren M.
Published: August 2011

Traditional microbiological techniques are used to provide reliable data on the rate and extent of kill for a range of biocides. However, such techniques provide very limited data regarding the initial rate of kill of fast-acting biocides over very short time domains. This study describes the application of a recombinant strain ofEscherichia coliexpressing thePhotorhabdus luminescens luxoperon as a whole-cell biosensor. Light emission is linked directly to bacterial metabolism; therefore, by monitoring light output, the impact of fast-acting biocides can be assessed. Electrochemically activated solutions (ECASs), bleach, Virkon, and ethanol were assessed at three concentrations (1%, 10%, 80%) in the presence of organic soiling. Over a 2-s time course, 80% ECAS produced the greatest reduction in light output in the absence of organic load but was strongly inhibited by its presence. Eighty percent ethanol outperformed all tested biocides in the presence of organic soil. Bleach and Virkon produced similar reductions in bioluminescence at matched concentrations within the time course of the assay. It was also demonstrated that the assay can be used to rapidly assess the impact of organic soiling. The use of bioluminescent bacteria as whole-cell bioreporters allows assessment of the relative efficacies of fast-acting biocides within milliseconds of application. The assay can be used to investigate activity over short or extended time domains to confirm complete metabolic inhibition of the bioreporter. Moreover, the assay may enable further elucidation of their mechanism of action by allowing the investigation of activity over time domains precluded by traditional microbiology.
Pyrazinoic Acid Decreases the Proton Motive Force, Respiratory ATP Synthesis Activity, and Cellular ATP Levels
Authors: Lu Ping , Haagsma Anna C. , Pham Hoang , Maaskant Janneke J. , Mol Selena , Lill Holger , Bald Dirk
Published: August 2011

Pyrazinoic acid, the active form of the first-line antituberculosis drug pyrazinamide, decreased the proton motive force and respiratory ATP synthesis rates in subcellular mycobacterial membrane assays. Pyrazinoic acid also significantly lowered cellular ATP levels in
Mycobacterium bovis
BCG. These results indicate that the predominant mechanism of killing by this drug may operate by depletion of cellular ATP reserves.
Role of Lipid II and Membrane Thickness in the Mechanism of Action of the Lantibiotic Bovicin HC5
Authors: Paiva Aline Dias , Breukink Eefjan , Mantovani Hilário Cuquetto
Published: August 2011

Lantibiotics are antimicrobial peptides produced by Gram-positive bacteria, nisin being the most well-known member. Nisin inhibits peptidoglycan synthesis and forms pores at sensitive membranes upon interaction with lipid II, the essential bacterial cell wall precursor. Bovicin HC5, a bacteriocin produced by
Streptococcus bovis
HC5, has the putative N-terminal lipid II binding motif, and we investigated the mode of action of bovicin HC5 using both living bacteria and model membranes, with special emphasis on the role of lipid II. Bovicin HC5 showed activity against
Staphylococcus cohnii
and
Staphylococcus warneri
, but bovicin HC5 hardly interfered with the membrane potential of
S. cohnii
. In model membranes, bovicin HC5 was not able to cause carboxyfluorescein release or proton influx from DOPC vesicles containing lipid II. Bovicin HC5 blocked lipid II-dependent pore formation activity of nisin, and a high-affinity interaction with lipid II was observed (apparent binding constant [

K
a

] = 3.1 × 10
6
M
−1
), with a 1:1 stoichiometry. In DOPC vesicles containing lipid II, bovicin HC5 was able to assemble with lipid II into a prepore-like structure. Furthermore, we observed pore formation activity of bovicin HC5, which was stimulated by the presence of lipid II, in thin membranes. Moreover, bovicin HC5 induced the segregation of lipid II into domains in giant model membrane vesicles. In conclusion, bovicin HC5 has a primary mode of action similar to that of nisin, but some differences regarding the pore-forming capacity were demonstrated.
Efficient Identification of Human Immunodeficiency Virus Type 1 Mutants Resistant to a Protease Inhibitor by Using a Random Mutant Library
Authors: Kim Sanggu , Kim Yun-Cheol , Qi Hangfei , Su Kunkai , Morrison Sherie L. , Chow Samson A.
Published: August 2011

Emergence of drug-resistant mutant viruses during the course of antiretroviral therapy is a major hurdle that limits the success of chemotherapeutic treatment to suppress human immunodeficiency virus type 1 (HIV-1) replication and AIDS progression. Development of new drugs and careful patient management based on resistance genotyping data are important for enhancing therapeutic efficacy. However, identifying changes leading to drug resistance can take years of clinical studies, and conventional
in vitro
assays are limited in generating reliable drug resistance data. Here we present an efficient
in vitro
screening assay for selecting drug-resistant variants from a library of randomly mutated HIV-1 strains generated by transposon-directed base-exchange mutagenesis. As a test of principle, we screened a library of mutant HIV-1 strains containing random mutations in the protease gene by using a reporter T-cell line in the presence of the protease inhibitor (PI) nelfinavir (NFV). Analysis of replicating viruses from a single round of infection identified 50 amino acid substitutions at 35 HIV-1 protease residue positions. The selected mutant viruses showed specific resistance to NFV and included most of the known NFV resistance mutations. Therefore, the new assay is efficient for identifying changes leading to drug resistance. The data also provide insights into the molecular mechanisms underlying the development of drug resistance.
Current Prospects for the Fluoroquinolones as First-Line Tuberculosis Therapy
Authors: Takiff Howard , Guerrero Elba
Published: August 2011

While fluoroquinolones (FQs) have been successful in helping cure multidrug-resistant tuberculosis (MDR TB), studies in mice have suggested that if used as first-line agents they might reduce the duration of therapy required to cure drug-sensitive TB. The results of phase II trials with FQs as first-line agents have been mixed, but in at least three studies where moxifloxacin substituted for ethambutol, there was an increase in the early percentage of sputa that converted to negative for bacilli. Phase III trials are in progress to test the effectiveness of 4-month FQ-containing regimens, but there is concern that the widespread use of FQs for other infections could engender a high prevalence of FQ-resistant TB. However, several studies suggest that despite wide FQ use, the prevalence of FQ-resistant TB is low, and the majority of the resistance is low-level. The principal risk for resistance may be when FQs are used to treat nonspecific respiratory symptoms that are in fact TB, so curtailing this use of FQs could reduce the development of resistance and also the delays in TB diagnosis and treatment that have been documented when an FQ is given in this setting. While the future of FQs as first-line therapy will likely depend upon the results of the ongoing phase III trials, if they are to be effectively employed in high-TB-burden regions their use for community-acquired pneumonias should be restricted, the prevalence of FQ-resistant TB should be monitored, and the cost of the treatment should be comparable to that of current standard drug regimens.
Impact of Mutations Outside the V3 Region on Coreceptor Tropism Phenotypically Assessed in Patients Infected with HIV-1 Subtype B
Authors: Monno Laura , Saracino Annalisa , Scudeller Luigia , Punzi Grazia , Brindicci Gaetano , Altamura Maurantonio , Lagioia Antonella , Ladisa Nicoletta , Angarano Gioacchino
Published: August 2011

HIV coreceptor tropism (CTR) testing is a prerequisite for prescribing a coreceptor antagonist. CTR is increasingly deduced by analyzing the V3 loop sequence of gp120. We investigated the impact of mutations outside V3 on CTR as determined by the enhanced-sensitivity Trofile assay (ESTA). Paired ESTA and gp120 sequencing (population sequencing; from codon 32 of the conserved C1 to the variable V5 domains) were obtained from 60 antiretroviral treatment (ART)-naïve patients (15 with AIDS) infected with subtype B HIV-1. For gp120 sequence analysis, nucleotide mixtures were considered when the second highest electropherogram peak was >25%; sequences were translated into all possible permutations and classified as X4, dual/mixed (DM), and R5 based on coincident ESTA results. ESTA identified R5 and DM viruses in 72 and 28% of patients, respectively; no pure X4 was labeled. Forty percent of AIDS patients had R5 strains. Thirty-two positions, mostly outside V3, were significantly (P< 0.05) different between R5 and DM sequences. According to multivariate analysis, amino acid changes at 9 and 7 positions within the C1 to C4 and V1 to V5 regions, respectively, maintained a statistical significance, as did the net charge of V3 and C4. When analyzing only R5 sequences, 6 positions in the variable regions were found which, along with the V4 net charge, were significantly different for sequences from early- and end-stage disease patients. This study identifies specific amino acid changes outside V3 which contribute to CTR. Extending the analysis to include pure X4 and increasing the sample size would be desirable to define gp120 variables/changes which should be included in predictive algorithms.
Clinically Relevant Plasma Concentrations of Colistin in Combination with Imipenem Enhance Pharmacodynamic Activity against Multidrug-Resistant Pseudomonas aeruginosa at Multiple Inocula
Authors: Bergen Phillip J. , Forrest Alan , Bulitta Jürgen B. , Tsuji Brian T. , Sidjabat Hanna E. , Paterson David L. , Li Jian , Nation Roger L.
Published: August 2011

The use of combination antibiotic therapy may be beneficial against rapidly emerging resistance in
Pseudomonas aeruginosa
. The aim of this study was to systematically investigate
in vitro
bacterial killing and resistance emergence with colistin alone and in combination with imipenem against multidrug-resistant (MDR)
P. aeruginosa
. Time-kill studies were conducted over 48 h using 5 clinical isolates and ATCC 27853 at two inocula (∼10
6
and ∼10
8
CFU/ml); MDR, non-MDR, and colistin-heteroresistant and -resistant strains were included. Nine colistin-imipenem combinations were investigated. Microbiological response was examined by log changes at 6, 24, and 48 h. Colistin combined with imipenem at clinically relevant concentrations increased the levels of killing of MDR and colistin-heteroresistant isolates at both inocula. Substantial improvements in activity with combinations were observed across 48 h with all colistin concentrations at the low inoculum and with colistin at 4× and 16× MIC (or 4 and 32 mg/liter) at the high inoculum. Combinations were additive or synergistic against imipenem-resistant isolates (MICs, 16 and 32 mg/liter) at the 10
6
-CFU inoculum in 9, 11, and 12 of 18 cases (i.e., 9 combinations across 2 isolates) at 6, 24, and 48 h, respectively, and against the same isolates at the 10
8
-CFU inoculum in 11, 7, and 8 cases, respectively. Against a colistin-resistant strain (MIC, 128 mg/liter), combinations were additive or synergistic in 9 and 8 of 9 cases at 24 h at the 10
6
- and 10
8
-CFU inocula, respectively, and in 5 and 7 cases at 48 h. This systematic study provides important information for optimization of colistin-imipenem combinations targeting both colistin-susceptible and colistin-resistant subpopulations.
In Vitro
Activity of Antiretroviral Drugs against Plasmodium falciparum
Authors: Nsanzabana Christian , Rosenthal Philip J.
Published: August 2011

Malaria and HIV infection are both very common in many developing countries. With the increasing availability of therapy for HIV infection, it was of interest to determine whether antiretroviral drugs exert antimalarial effects. We therefore tested the
in vitro
activity of 19 antiretroviral drugs against the W2 and 3D7 strains of
Plasmodium falciparum
at concentrations up to 50 μM. None of 5 tested nucleoside reverse transcriptase inhibitors demonstrated activity. Two nonnucleoside reverse transcriptase inhibitors, efavirenz (mean 50% inhibitory concentration [IC
50
] of 22 to 30 μM against the two strains) and etravirine (3.1 to 3.4 μM), were active; nevirapine was not active. Also active were the fusion inhibitor enfuvirtide (6.2 to 7.9 μM) and the entry inhibitor maraviroc (15 to 21 μM). Raltegravir was not active. However, for all active drugs mentioned above, the IC
50
s were considerably greater than the concentrations achieved with standard dosing. The effects most likely to be clinically relevant were with HIV protease inhibitors. Of the tested compounds, activity was seen with lopinavir (2.7 to 2.9 μM), atazanavir (3.3 to 13.0 μM), saquinavir (5.0 to 12.1 μM), nelfinavir (6.5 to 12.1 μM), ritonavir (9.5 to 10.9 μM), tipranavir (15.5 to 22.3 μM), and amprenavir (28.1 to 40.8) but not darunavir. Lopinavir was active at levels well below those achieved with standard dosing of coformulated lopinavir-ritonavir. Lopinavir also demonstrated modest synergy with the antimalarial lumefantrine (mean fractional inhibitory concentration index of 0.66 for W2 and 0.53 for 3D7). Prior data showed that lopinavir-ritonavir also extends the pharmacokinetic exposure of lumefantrine. Thus, when used to treat HIV infection, lopinavir-ritonavir may have clinically relevant antimalarial activity and also enhance the activity of antimalarials.
Fractal Geometry and the Pharmacometrics of Micafungin in Overweight, Obese, and Extremely Obese People
Authors: Hall Ronald G. , Swancutt Mark A. , Gumbo Tawanda
Published: August 2011

The majority of Americans are overweight, and the incidence of obesity continues to increase. This trend predisposes people to a number of deleterious consequences, including the metabolic syndrome and other conditions that lead to a greater number of hospital admissions. Invasive candidiasis is an important nosocomial infection that results from these admissions. Echinocandins such as micafungin are indicated for treatment. We have previously demonstrated that overweight patients exhibit higher micafungin systemic clearance (SCL) than leaner patients. We hypothesized that obese and extremely obese people would show even higher SCL than merely overweight patients. To test this, we performed a prospective study of 36 adult volunteers randomized to receive a single dose of either 100 mg or 300 mg of micafungin whose body mass index fell within one of the following categories: <25, 25 to 40, and >40 kg/m
2
. The male-to-female ratio was 1:1. The minimum weight was 43 kg, the median 97 kg, and the maximum weight 155 kg. A two-compartment model was examined using the maximum likelihood solution via the expectation-maximization algorithm. Men had a higher median SCL of 1.53 liters/h versus 1.29 liters/h (
P
= 0.01) in the Mann-Whitney U-test. The typical SCL was 1.04 liters/h but increased by a factor of (weight/66)
0.75
as weight increased above 66 kg. Thus, the relationship between micafungin SCL and weight in adults is best described by fractal-geometry-based laws. Furthermore, micafungin SCL continues to increase as weight increases, with no obvious plateau. This leads to a requirement for strategies to determine individualized dosing levels for obese and extremely obese patients.
MK-0536 Inhibits HIV-1 Integrases Resistant to Raltegravir
Authors: Métifiot Mathieu , Johnson Barry , Smith Steven , Zhao Xue Zhi , Marchand Christophe , Burke Terrence , Hughes Stephen , Pommier Yves
Published: August 2011

With the U.S. Food and Drug Administration approval of raltegravir (RAL; MK-0518; Merck & Co.), HIV-1 integrase (IN) is the newest therapeutic target for AIDS and HIV infections. Recent structural analyses show that IN strand transfer inhibitors (INSTIs) share a common binding mode in the enzyme active site. While RAL represents a therapeutic breakthrough, the emergence of IN resistance mutations imposes the development of new INSTIs. We report here the biochemical and antiviral activities of MK-0536, a new IN inhibitor. We demonstrate that, like RAL, MK-0536 is highly potent against recombinant IN and viral replication. It is also effective against INs that carry the three main RAL resistance mutations (Y143R, N155H, and to a lesser extent G140S-Q148H) and against the G118R mutant. Modeling of IN developed from recent prototype foamy virus structures is presented to account for the differences in the drug activities of MK-0536 and RAL against the IN mutants.
Elicitation of Epithelial Cell-Derived Immune Effectors by Outer Membrane Vesicles of Nontypeable Haemophilus influenzae
Authors: Sharpe Samantha W. , Kuehn Meta J. , Mason Kevin M.
Published: August 2011

Outer membrane vesicles (OMVs) are produced by all Gram-negative microorganisms studied to date. The contributions of OMVs to biological processes are diverse and include mediation of bacterial stress responses, selective packaging and secretion of virulence determinants, modulation of the host immune response, and contributions to biofilm formation and stability. First characterized as transformasomes inHaemophilus, these membranous blebs facilitate transfer of DNA among bacteria. NontypeableHaemophilus influenzae(NTHI), an opportunistic pathogen of the upper and lower respiratory tracts, produces OMVsin vivo, but there is a paucity of information regarding both the composition and role of OMVs during NTHI colonization and pathogenesis. We demonstrated that purified NTHI vesicles are 20 to 200 nm in diameter and contain DNA, adhesin P5, IgA endopeptidase, serine protease, and heme utilization protein, suggesting a multifaceted role in virulence. NTHI OMVs can bind to human pharyngeal epithelial cells, resulting in a time- and temperature-dependent aggregation on the host cell surface, with subsequent internalization. OMVs colocalize with the endocytosis protein caveolin, indicating that internalization is mediated by caveolae, which are cholesterol-rich lipid raft domains. Upon interaction with epithelial cells, NTHI OMVs stimulate significant release of the immunomodulatory cytokine interleukin-8 (IL-8) as well as the antimicrobial peptide LL-37. Thus, we demonstrated that NTHI OMVs contain virulence-associated proteins that dynamically interact with and invade host epithelial cells. Beyond their ability to mediate DNA transfer inHaemophilus, OMV stimulation of host immunomodulatory cytokine and antimicrobial peptide release supports a dynamic role for vesiculation in NTHI pathogenesis and clinically relevant disease progression.
The Deubiquitinase Activity of the Salmonella Pathogenicity Island 2 Effector, SseL, Prevents Accumulation of Cellular Lipid Droplets
Authors: Arena Ellen T. , Auweter Sigrid D. , Antunes L. Caetano M. , Vogl A. Wayne , Han Jun , Guttman Julian A. , Croxen Matthew A. , Menendez Alfredo , Covey Scott D. , Borchers Christoph H. , Finlay B. Brett
Published: August 2011

To cause disease,
Salmonella enterica
serovar Typhimurium requires two type III secretion systems that are encoded by
Salmonella
pathogenicity islands 1 and 2 (SPI-1 and -2). These secretion systems serve to deliver specialized proteins (effectors) into the host cell cytosol. While the importance of these effectors to promote colonization and replication within the host has been established, the specific roles of individual secreted effectors in the disease process are not well understood. In this study, we used an
in vivo
gallbladder epithelial cell infection model to study the function of the SPI-2-encoded type III effector, SseL. The deletion of the
sseL
gene resulted in bacterial filamentation and elongation and the unusual localization of
Salmonella
within infected epithelial cells. Infection with the Δ
sseL
strain also caused dramatic changes in host cell lipid metabolism and led to the massive accumulation of lipid droplets in infected cells. This phenotype was directly attributable to the deubiquitinase activity of SseL, as a
Salmonella
strain carrying a single point mutation in the catalytic cysteine also resulted in extensive lipid droplet accumulation. The excessive buildup of lipids due to the absence of a functional
sseL
gene also was observed in murine livers during
S.
Typhimurium infection. These results suggest that SseL alters host lipid metabolism in infected epithelial cells by modifying the ubiquitination patterns of cellular targets.
Next-Generation Computational Genetic Analysis: Multiple Complement Alleles Control Survival after Candida albicans Infection
Authors: Peltz Gary , Zaas Aimee K. , Zheng Ming , Solis Norma V. , Zhang Mason X. , Liu Hong-Hsing , Hu Yajing , Boxx Gayle M. , Phan Quynh T. , Dill David , Filler Scott G.
Published: August 2011

Candida albicansis a fungal pathogen that causes severe disseminated infections that can be lethal in immunocompromised patients. Genetic factors are known to alter the initial susceptibility to and severity ofC. albicansinfection. We developed a next-generation computational genetic mapping program with advanced features to identify genetic factors affecting survival in a murine genetic model of hematogenousC. albicansinfection. This computational tool was used to analyze the median survival data after inbred mouse strains were infected withC. albicans, which provides a useful experimental model for identification of host susceptibility factors. The computational analysis indicated that genetic variation within early classical complement pathway components (C1q,C1r, andC1s) could affect survival. Consistent with the computational results, serum C1 binding to this pathogen was strongly affected byC1rsalleles, as was survival of chromosome substitution strains. These results led to a combinatorial, conditional genetic model, involving an interaction betweenC5andC1r/salleles, which accurately predicted survival after infection. Beyond applicability to infectious disease, this information could increase our understanding of the genetic factors affecting susceptibility to autoimmune and neurodegenerative diseases.
Exploring the therapeutic power of narrative at the end of life: a qualitative analysis of narratives emerging in dignity therapy
Authors: Tait Glendon R , Schryer Catherine , McDougall Allan , Lingard Lorelei
Published: August 2011

Objective

To understand the therapeutic effect of a narrative intervention, specifically dignity therapy, in patients at the end-of-life. To examine the thematic dimensions and shared narrative features of the stories that emerge in dignity therapy and theorise their relationship to the intervention's clinical impact.

Design

Resident physicians, as part of an educational intervention, co-administered the dignity therapy protocol with the principal investigator. Interviews were transcribed, edited, and then, within a week, read back to the patient and provided as a document for the patient to keep. A constant comparative approach was taken to identify narratives and thematic patterns.

Participants

12 Patients at the end-of-life were administered dignity interviews by 12 resident physicians, accompanied by the principal investigator.

Setting

Palliative care settings in two University of Toronto academic hospitals.

Results

Three narrative types emerged, each containing several themes. Evaluation narratives create a life lived before illness, with an overarching theme of overcoming adversity. Transition narratives describe a changing health situation and its meanings, including impact on family and on one's world view. Legacy narratives discuss the future without the patient and contain the parables and messages to be left for loved ones.

Conclusions

While the interview protocol guides patients' responses, the commonality of narrative structures across interviews suggests that patients draw on experiences with two familiar genres: the eulogy and the medical interview, to create a narrative order during the chaos of dying. The dignity interview's resonance with these genres appears to facilitate a powerful, and perhaps unexpected sense of agency.
Pressure–temperature evolution and thermal regimes in the Barrovian zones, Scotland
Authors: Vorhies Sarah H. , Ague Jay J.
Published: August 2011

We constrain the
P
–
T
evolution of the Barrovian metamorphic zones from the southwestern to the northeastern coasts of Scotland using thermobarometry and pseudosection analysis based on mineral composition data, garnet zoning profiles and 2D garnet maps. Twenty-five samples were investigated from the garnet to the sillimanite zones. In the western half of the field area there was relatively high-
P
metamorphism (0.9–1.1 GPa) followed by near-isothermal decompression. In and around the Barrovian type area of Glen Clova maximum pressures were also high (
c
. 0.8–0.9 GPa); however, peak-
T
conditions were driven by a brief (of the order of 1 Ma or less) thermal pulse or pulses during exhumation at
c
. 0.6 GPa. Pressures at peak-
T
conditions along the eastern coast were the lowest observed,
c
. 0.4–0.5 GPa. These rocks were probably affected by the same thermal pulse activity evident around Glen Clova. All three regions initially developed during regional metamorphism associated with thermal relaxation of tectonically overthickened crust. The eastern part of the sequence, including Glen Clova, is fundamentally different from the western part because it required additional advective heat input to achieve peak thermal conditions. This heat was probably supplied by synorogenic magmas (e.g. Newer Gabbros) and the associated elevated crustal heat flow.

Supplementary material:

Electron microprobe methods, mineral and rock analyses, mineral activity–composition relations, criteria for identifying prograde mineral compositions, pseudosection and diffusion modelling methods, and profiles of
X
Alm
and
X
Prp
from garnets in Figures
7
,
8
,
9
,
10
are available at
http://www.geolsoc.org.uk/SUP18491
.
Effects of melt percolation on platinum group elements and Re–Os systematics of peridotites from the Tan-Lu fault zone, eastern North China Craton
Authors: Xiao Yan , Zhang Hong-Fu
Published: August 2011

Concentrations of platinum group elements (PGE) and Re–Os isotopic compositions were determined for a suite of peridotite xenoliths from Cenozoic Beiyan volcanoes within the Tan-Lu fault zone, eastern North China Craton (NCC). Previous petrographic and geochemical data indicate the existence of considerable modification by melt–peridotite interaction for these xenoliths. Thus, this suite of xenoliths provides an unusual opportunity to examine the effects of melt percolation on PGE abundances and Re–Os isotopes. Our data show that most of the Beiyan peridotites have flat chondrite-normalized PGE patterns whereas a considerable variation in total PGE abundances has been observed in lherzolites to highly fertile cpx-rich lherzolites and wehrlites. Their total PGE contents range between 0.97 and 61.4 ppb and their PGE relative abundances from 0.1 to 0.0001 × CI-chondrites, respectively. In these rocks, the total PGE budget was reduced by more than 90% from lherzolite to cpx-rich lherzolite and to wehrlite, probably because intergranular sulphides were completely removed by silicate melt. However, Beiyan peridotites have low and variable Re (0.0002–0.5118 ppb) and Os (0.194–10.4 ppb) abundances and high
187
Os/
188
Os (0.12167–0.14978) ratios. The
187
Os/
188
Os ratios in some wehrlites are much higher than the value for the primitive mantle. The high
187
Os/
188
Os ratios have also been observed in peridotites found in other localities within the Tan-Lu fault zone such as Shanwang and Nüshan. This could be the result of the addition of radiogenic Os during the melt percolation. Extremely low Os abundances in Beiyan peridotites suggest that Os may behave as an incompatible element during melt percolation and could mobilize with the dissolution of sulphides. The suprachondritic
187
Os/
188
Os ratios in peridotites within the Tan-Lu fault zone relative to those away from it indicate that the Tan-Lu fault zone played an important role as a melt infiltrating channel in the radiogenic Os enrichment induced by melt percolation. This could be the reason for the Os isotopic heterogeneity observed in the eastern NCC. This study also confirms that Os isotopes and PGE appear to be mobile during massive melt percolation.
Age and composition of crystalline basement rocks on the Norwegian continental margin: offshore extension and continuity of the Caledonian–Appalachian orogenic belt
Authors: Slagstad Trond , Davidsen Børre , Daly J.Stephen
Published: August 2011

Twenty-two wells on the Norwegian continental margin have penetrated underlying basement. We present U–Pb zircon, whole-rock geochemical, and Sm–Nd and Rb–Sr isotopic data from nine wells in the North Sea and Norwegian Sea with relevance to the offshore continuation of the Norwegian Caledonides, and their correlation throughout the Caledonian–Appalachian orogenic belt. Palaeozoic magmatism in the North Sea can be divided into two groups. The older group consists of 460 Ma calc-alkaline granites with evolved isotopic compositions, correlative with similar rocks in the Uppermost Allochthon. The younger group consists of a 430 Ma dacite and a 421 Ma leucogabbro, with less evolved isotopic compositions. In the Norwegian Sea, isotopically evolved granitic magmatism at 437 Ma and more juvenile dioritic magmatism at 447 Ma are correlative with magmatism in the Bindal and Smøla–Hitra Batholiths in the Uppermost Allochthon. Metasedimentary basement rocks from the North Sea and Norwegian Sea, dominated by Late Palaeoproterozoic and Mesoproterozoic grains, resemble rocks found in the Caledonides of Scotland, Greenland and Svalbard. The new data, along with studies elsewhere along the belt, suggest that similar rocks may exist along much of the orogen.

Supplementary material:

U–Pb isotopic data are available at
http://www.geolsoc.org.uk/SUP18471
.