Human p38 mitogen-activated protein kinase inhibitor drugs inhibit Plasmodium falciparum replication

We recently demonstrated that human p38 mitogen-activated protein kinase (MAPK) inhibitors reduced in vitro and in vivo replication of the protozoan parasites Toxoplasma gondii and Encephalitozoon cuniculi. In this study, we assessed the efficacy of five p38 MAPK inhibitors to block the replication of Plasmodium falciparum in human erythrocytes cultured ex vivo and demonstrate that the pyridinylimidazole RWJ67657 and the pyrrolobenzimidazole RWJ68198 reduced P. falciparum replication, yielded trophozoites that were greatly diminished in size at 24 h, and that these two agents interfered with stage differentiation. Interestingly, the chloroquine-resistant strain W2 was significantly more sensitive to these drugs than was the chloroquine-sensitive strain HB3. These results suggest that pyridinylimidazoles and pyrrolobenzimidazoles designed to inhibit human p38 MAPK activation can be developed to treat malaria.     

Subunit–subunit interactions are weakened in mutant forms of acetohydroxy acid synthase insensitive to valine inhibition

In acetohydroxy acid synthase from Streptomyces cinnamonensis mutants affected in valine regulation, the impact of mutations on interactions between the catalytic and the regulatory subunits was examined using yeast two-hybrid system. Mutations in the catalytic and the regulatory subunits were projected into homology models of the respective proteins. Two changes in the catalytic subunit, E139A (α domain) and ΔQ217 (β domain), both located on the surface of the catalytic subunit dimer, lowered the interaction with the regulatory subunit. Three consecutive changes in the N-terminal part of the regulatory subunit were examined. Changes G16D and V17D in a loop and adjacent α-helix of ACT domain affected the interaction considerably, indicating that this region might be in contact with the catalytic subunit during allosteric regulation. In contrast, the adjacent mutation L18F did not influence the interaction at all. Thus, L18 might participate in valine binding or conformational change transfer within the regulatory subunits. Shortening of the regulatory subunit to 107 residues reduced the interaction essentially, suggesting that the C-terminal part of the regulatory subunit is also important for the catalytic subunit binding.     

Overlaps and parallels in the regulation of intrinsic multiple-antibiotic resistance in Escherichia coli

Chromosomally encoded systems present in a variety of bacteria appear to play a central role in determining the intrinsic level of resistance to many commonly used antibiotics. Work with the Gram-negative bacterium Escherichia coli has shown that there is significant similarity at the amino acid sequence level among the structural components of these resistance systems as well as among their genetic regulators. This review describes two of the better-studied regulatory systems, marRAB and soxRS, as well as two regulated multidrug-efflux systems, encoded by emrAB and acrAB, and focuses on conserved themes in their primary structures and environmental stimuli. The observed resistance to clinically important antibiotics appears to reflect an overlap with broad-ranged adaptive responses by free-living bacteria to noxious plant materials in their natural environment.     

Frugivory by Small Vertebrates Within a Deforested, Dry Tropical Region of Central America

Small vertebrates were inventoried within three habitat types in a degraded dry forest region of Panama. Animals were classified as frugivorous if they were observed foraging on fruit or if fecal samples contained mostly or exclusively seeds. Overall, we found that eight bat species and 21 bird species consumed fruit. The greatest numbers of birds were observed within live fences and bird species richness was greatest within riparian forests. Bat assemblages were not significantly different between habitats. The implication is that ecosystem services such as seed dispersal may still be functional in this landscape.     

Plant mineral nutrition in ancient landscapes: high plant species diversity on infertile soils is linked to functional diversity for nutritional strategies

Ancient landscapes, which have not been glaciated in recent times or disturbed by other major catastrophic events such as volcanic eruptions, are dominated by nutrient-impoverished soils. If these parts of the world have had a relatively stable climate, due to buffering by oceans, their floras tend to be very biodiverse. This review compares the functional ecophysiological plant traits that dominate in old, climatically buffered, infertile landscapes (OCBILS) with those commonly found in young, frequently disturbed, fertile landscapes (YODFELs). We show that, within the OCBILs of Western Australia, non-mycorrhizal species with specialised root clusters predominantly occur on the most phosphate-impoverished soils, where they co-occur with mycorrhizal species without such specialised root clusters. In global comparisons, we show that plants in OCBILs, especially in Western Australia, are characterised by very low leaf phosphorus (P) concentrations, very high N:P ratios, and very high LMA values (LMA = leaf mass per unit leaf area). In addition, we show that species in OCBILs are far more likely to show P-toxicity symptoms when exposed to slightly elevated soil P levels when compared with plants in YODFELs. In addition, some species in OCBILs exhibit a remarkable P-resorption proficiency, with some plants in Western Australia achieving leaf P concentrations in recently shed leaves that are lower than ever reported before. We discuss how this knowledge on functional traits can guide us towards sustainable management of ancient landscapes.     

Central Nervous System Pathology Progresses Independently of KC and CXCR2 in Globoid-Cell Leukodystrophy

Globoid-cell Leukodystrophy (GLD; Krabbe’s disease) is a rapidly progressing inherited demyelinating disease caused by a deficiency of the lysosomal enzyme Galactosylceramidase (GALC). Deficiency of GALC leads to altered catabolism of galactosylceramide and the cytotoxic lipid, galactosylsphingosine (psychosine). This leads to a rapidly progressive fatal disease with spasticity, cognitive disability and seizures. The murine model of GLD (Twitcher; GALC−/−) lacks the same enzyme and has similar clinical features. The deficiency of GALC leads to oligodendrocyte death, profound neuroinflammation, and the influx of activated macrophages into the CNS. We showed previously that keratinocyte chemoattractant factor (KC) is highly elevated in the CNS of untreated Twitcher mice and significantly decreases after receiving a relatively effective therapy (bone marrow transplantation combined with gene therapy). The action of KC is mediated through the CXCR2 receptor and is a potent chemoattractant for macrophages and microglia. KC is also involved in oligodendrocyte migration and proliferation. Based on the commonalities between the disease presentation and the functions of KC, we hypothesized that KC and/or CXCR2 contribute to the pathogenesis of GLD. Interestingly, the course of the disease is not significantly altered in KC- or CXCR2-deficient Twitcher mice. There is also no alteration in inflammation or demyelination patterns in these mice. Furthermore, transplantation of CXCR2-deficient bone marrow does not alter the progression of the disease as it does in other models of demyelination. This study highlights the role of multiple redundant cytokines and growth factors in the pathogenesis of GLD.     

Breakage-reunion domain of Streptococcus pneumoniae topoisomerase IV: crystal structure of a gram-positive quinolone target

The 2.7 A crystal structure of the 55-kDa N-terminal breakage-reunion domain of topoisomerase (topo) IV subunit A (ParC) from Streptococcus pneumoniae, the first for the quinolone targets from a gram-positive bacterium, has been solved and reveals a 'closed' dimer similar in fold to Escherichia coli DNA gyrase subunit A (GyrA), but distinct from the 'open' gate structure of Escherichia coli ParC. Unlike GyrA whose DNA binding groove is largely positively charged, the DNA binding site of ParC exhibits a distinct pattern of alternating positively and negatively charged regions coincident with the predicted positions of the grooves and phosphate backbone of DNA. Based on the ParC structure, a new induced-fit model for sequence-specific recognition of the gate (G) segment by ParC has been proposed. These features may account for the unique DNA recognition and quinolone targeting properties of pneumococcal type II topoisomerases compared to their gram-negative counterparts.     

Synthesis and structures of mono and binuclear nickel(II) thiolate complexes of a dicompartmental pseudo-macrocycle with N(imine)2S2 and N(oxime)2S2 metal-binding sites

The reaction of [Ni(pftp)] [pftp = N,N-propane-1,3-diyl-(6-formyl-4-methyliminatothiophenolato)] with hydroxylamine hydrochloride in the presence potassium acetate in MeOH resulted in the formation of the complex [Ni(LH₂)] [L = N,N-propane-1,3-diyl-(4-methyl-2-methyliminato-6-methyloxime-thiophenolato)] in good yield. A single crystal X-ray diffraction structural determination showed a mononuclear nickel(II) complex with the new acyclic ligand LH₂ that had been functionalised with two oxime groups containing an empty N(oxime)₂S₂ pocket to which another metal ion could be added. A further reaction of [Ni(LH₂)] with NiCl₂·6H₂O, triethylamine and ammonium hexafluorophosphate in MeOH gave a dark red product that yielded red crystals of [Ni₂(LH)]PF₆·DMF via slow recrystallisation from a DMF/PrⁱOH solvent mixture. A single crystal X-ray diffraction study of these crystals confirmed the presence of a dinuclear nickel(II) complex linked by a dithiolato-bridge. Both nickel(II) ions exhibited square-planar geometry where the metal centres are coordinated in two distinct cis-S₂N(imine)₂ and cis-S₂N(oxime)₂ binding sites provided by the new dicompartmental oxime/thiolate-containing ligand LH.     

Gene expression changes reflect clinical response in a placebo-controlled randomized trial of abatacept in patients with diffuse cutaneous systemic sclerosis

IntroductionSystemic sclerosis is an autoimmune disease characterized by inflammation and fibrosis of the skin and internal organs. We sought to assess the clinical and molecular effects associated with response to intravenous abatacept in patients with diffuse cutaneous systemic.MethodsAdult diffuse cutaneous systemic sclerosis patients were randomized in a 2:1 double-blinded fashion to receive abatacept or placebo over 24 weeks. Primary outcomes were safety and the change in modified Rodnan Skin Score (mRSS) at week 24 compared with baseline. Improvers were defined as patients with a decrease in mRSS of ≥30 % post-treatment compared to baseline. Skin biopsies were obtained for differential gene expression and pathway enrichment analyses and intrinsic gene expression subset assignment.ResultsTen subjects were randomized to abatacept (n = 7) or placebo (n = 3). Disease duration from first non-Raynaud’s symptom was significantly longer (8.8 ± 3.8 years vs. 2.4 ± 1.6 years, p = 0.004) and median mRSS was higher (30 vs. 22, p = 0.05) in the placebo compared to abatacept group. Adverse events were similar in the two groups. Five out of seven patients (71 %) randomized to abatacept and one out of three patients (33 %) randomized to placebo experienced ≥30 % improvement in skin score. Subjects receiving abatacept showed a trend toward improvement in mRSS at week 24 (−8.6 ± 7.5, p = 0.0625) while those in the placebo group did not (−2.3 ± 15, p = 0.75). After adjusting for disease duration, mRSS significantly improved in the abatacept compared with the placebo group (abatacept vs. placebo mRSS decrease estimate −9.8, 95 % confidence interval −16.7 to −3.0, p = 0.0114). In the abatacept group, the patients in the inflammatory intrinsic subset showed a trend toward greater improvement in skin score at 24 weeks compared with the patients in the normal-like intrinsic subset (−13.5 ± 3.1 vs. −4.5 ± 6.4, p = 0.067). Abatacept resulted in decreased CD28 co-stimulatory gene expression in improvers consistent with its mechanism of action. Improvers mapped to the inflammatory intrinsic subset and showed decreased gene expression in inflammatory pathways, while non-improver and placebos showed stable or reverse gene expression over 24 weeks.ConclusionsClinical improvement following abatacept therapy was associated with modulation of inflammatory pathways in skin.

Trial registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00442611","term_id":"NCT00442611"}}NCT00442611. Registered 1 March 2007.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-015-0669-3) contains supplementary material, which is available to authorized users.     

NS-kNN: a modified <Emphasis Type="Italic">k</Emphasis>-nearest neighbors approach for imputing metabolomics data

Introduction

A common problem in metabolomics data analysis is the existence of a substantial number of missing values, which can complicate, bias, or even prevent certain downstream analyses. One of the most widely-used solutions to this problem is imputation of missing values using a k-nearest neighbors (kNN) algorithm to estimate missing metabolite abundances. kNN implicitly assumes that missing values are uniformly distributed at random in the dataset, but this is typically not true in metabolomics, where many values are missing because they are below the limit of detection of the analytical instrumentation.

Objectives

Here, we explore the impact of nonuniformly distributed missing values (missing not at random, or MNAR) on imputation performance. We present a new model for generating synthetic missing data and a new algorithm, No-Skip kNN (NS-kNN), that accounts for MNAR values to provide more accurate imputations.

Methods

We compare the imputation errors of the original kNN algorithm using two distance metrics, NS-kNN, and a recently developed algorithm KNN-TN, when applied to multiple experimental datasets with different types and levels of missing data.

Results

Our results show that NS-kNN typically outperforms kNN when at least 20–30% of missing values in a dataset are MNAR. NS-kNN also has lower imputation errors than KNN-TN on realistic datasets when at least 50% of missing values are MNAR.

Conclusion

Accounting for the nonuniform distribution of missing values in metabolomics data can significantly improve the results of imputation algorithms. The NS-kNN method imputes missing metabolomics data more accurately than existing kNN-based approaches when used on realistic datasets.