Yeast-based automated high-throughput screens to identify anti-parasitic lead compounds

We have developed a robust, fully automated anti-parasitic drug-screening method that selects compounds specifically targeting parasite enzymes and not their host counterparts, thus allowing the early elimination of compounds with potential side effects. Our yeast system permits multiple parasite targets to be assayed in parallel owing to the strains’ expression of different fluorescent proteins. A strain expressing the human target is included in the multiplexed screen to exclude compounds that do not discriminate between host and parasite enzymes. This form of assay has the advantages of using known targets and not requiring the in vitro culture of parasites. We performed automated screens for inhibitors of parasite dihydrofolate reductases, N-myristoyltransferases and phosphoglycerate kinases, finding specific inhibitors of parasite targets. We found that our ‘hits’ have significant structural similarities to compounds with in vitro anti-parasitic activity, validating our screens and suggesting targets for hits identified in parasite-based assays. Finally, we demonstrate a 60 per cent success rate for our hit compounds in killing or severely inhibiting the growth of Trypanosoma brucei, the causative agent of African sleeping sickness.     

Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia

Searching for genetic variants with unusual differentiation between subpopulations is an established approach for identifying signals of natural selection. However, existing methods generally require discrete subpopulations. We introduce a method that infers selection using principal components (PCs) by identifying variants whose differentiation along top PCs is significantly greater than the null distribution of genetic drift. To enable the application of this method to large datasets, we developed the FastPCA software, which employs recent advances in random matrix theory to accurately approximate top PCs while reducing time and memory cost from quadratic to linear in the number of individuals, a computational improvement of many orders of magnitude. We apply FastPCA to a cohort of 54,734 European Americans, identifying 5 distinct subpopulations spanning the top 4 PCs. Using the PC-based test for natural selection, we replicate previously known selected loci and identify three new genome-wide significant signals of selection, including selection in Europeans at ADH1B. The coding variant rs1229984^∗T has previously been associated to a decreased risk of alcoholism and shown to be under selection in East Asians; we show that it is a rare example of independent evolution on two continents. We also detect selection signals at IGFBP3 and IGH, which have also previously been associated to human disease.     

Phylogenetic analysis of the formin homology 2 domain

Formin proteins are key regulators of eukaryotic actin filament assembly and elongation, and many species possess multiple formin isoforms. A nomenclature system based on fundamental features would be desirable, to aid the rapid identification and characterization of novel formins. In this article, we attempt to systematize the formin family by performing phylogenetic analyses of the formin homology 2 (FH2) domain, an independently folding region common to all formins, which alone can influence actin dynamics. Through database searches, we identify 101 FH2 domains from 26 eukaryotic species, including 15 in mice. Sequence alignments reveal a highly conserved yeast-specific insert in the "knob loop" region of the FH2 domain, with unknown functional consequences. Phylogenetic analysis using minimum evolution (ME), maximum parsimony (MP), and maximum likelihood (ML) algorithms strongly supports the existence of seven metazoan groups. Yeast FH2 domains segregate from all other eukaryotes, including metazoans, other fungi, plants, and protists. Sequence comparisons of non-FH2 regions support relationships between three metazoan groups (Dia, DAAM, and FRL) and examine previously identified coiled-coil and Diaphanous auto-regulatory domain sequences. This analysis allows for a formin nomenclature system based on sequence relationships, as well as suggesting strategies for the determination of biochemical and cellular activities of these proteins.     

Luminescent α-diimine complexes of ruthenium(II) containing scorpionate ligands

We describe the synthesis, characterization, and reactivity of several Ru(II) complexes of the type cis-L₂Ru(Z)ⁿ⁺, where L is an α-diimine [e.g. 2,2′-bipyridine (bpy) or 1,10-phenanthroline (phen)] ligand and Z is a bis-coordinated scorpionate ligand such as tris-(1-pyrazolyl)methane (HC(pz)₃, PZ=1-pyrazolyl; n=2) or tetrakis-(1-pyrazolyl)borate anion (B(pz)₄ ⁻; n=1). The complexes each exhibit strong visible absorption assigned as a π*(L)←dπ(Ru) metal-to-ligand charge-transfer (MLCT) transition characteristic of the cis-L₂Ru²⁺ kernel. A corresponding MLCT excited state emission is observed in room temperature CH₃CN solution, although emission energies, lifetimes, and quantum yields are reduced relative to Ru(bpy)₃ ²⁺. Electronic spectra and cyclic voltammetry measurements indicate that the relative π-acceptor abilities of the coordinated Z are: Z=(1H-pyrazolyl)₂(pz)₂B(pz)₂<(pyridine)₂<(pz)₂CH(pz). Uncoordinated pz groups of cis-(bpy)₂Ru(pz)₂B(pz)₂ ⁺ can be reacted to form a sterically hindered, localized-valence (K_com33 l mol⁻¹) cis,cis-(bpy)₂Ru^II(pz)₂B(pz)₂Ru^II(bpy)₂ ³⁺ dimer. The dimer properties are interpreted by comparison to the known cis-(bpy)₂Ru^II(pz)₂Ru^II(bpy)₂ ²⁺ analog. The dimer is photoreactive and undergoes an asymmetrical photocleavage in CH₃CN (yielding cis-(bpy)₂Ru^III(pz)₂B(pz)₂ ²⁺ and cis-(bpy)₂Ru^II(CH₃CN)₂ ²⁺), similar to the corresponding thermal reaction observed for the mixed-valence cis-(bpy)₂Ru^II(pz)₂Ru^III(bpy)₂ ³⁺ system.     

Abnormal Hypermethylation at Imprinting Control Regions in Patients with S-Adenosylhomocysteine Hydrolase (AHCY) Deficiency

S-adenosylhomocysteine hydrolase (AHCY) deficiency is a rare autosomal recessive disorder in methionine metabolism caused by mutations in the AHCY gene. Main characteristics are psychomotor delay including delayed myelination and myopathy (hypotonia, absent tendon reflexes etc.) from birth, mostly associated with hypermethioninaemia, elevated serum creatine kinase levels and increased genome wide DNA methylation. The prime function of AHCY is to hydrolyse and efficiently remove S-adenosylhomocysteine, the by-product of transmethylation reactions and one of the most potent methyltransferase inhibitors. In this study, we set out to more specifically characterize DNA methylation changes in blood samples from patients with AHCY deficiency. Global DNA methylation was increased in two of three analysed patients. In addition, we analysed the DNA methylation levels at differentially methylated regions (DMRs) of six imprinted genes (MEST, SNRPN, LIT1, H19, GTL2 and PEG3) as well as Alu and LINE1 repetitive elements in seven patients. Three patients showed a hypermethylation in up to five imprinted gene DMRs. Abnormal methylation in Alu and LINE1 repetitive elements was not observed. We conclude that DNA hypermethylation seems to be a frequent but not a constant feature associated with AHCY deficiency that affects different genomic regions to different degrees. Thus AHCY deficiency may represent an ideal model disease for studying the molecular origins and biological consequences of DNA hypermethylation due to impaired cellular methylation status.     

Potent Inhibition of Pseudogymnoascus destructans,the Causative Agent of White-Nose Syndrome in Bats,by Cold-Pressed,Terpeneless, Valencia Orange Oil

The causative agent of White-nose Syndrome (WNS), Pseudogymnoascus destructans, has been shown to be fatal to several species of bats in North America. To date, no compounds or chemical control measures have been developed which eliminates the growth of the fungus in the environment or in affected animals. In the current study, we evaluated the activity of cold-pressed, terpeneless orange oil (CPT) against multiple isolates of P. destructans in vitro. For all assays, a modified Kirby-Bauer disk diffusion assay was used. Standardized spore suspensions were prepared, adjusted to a specific optical density, and used to plate fungal lawns. Plates were incubated at either 15°C or 4°C for up to 6 months and checked at regular intervals for growth. Once controls had grown, zones of inhibition were measured (mm) on test plates and compared to those obtained using current antifungal drugs. All P. destructans isolates were completely inhibited by 100% CPT (10 μL) at 1 month of incubation regardless of temperature (4°C and 15°C). Complete inhibition persisted up to 6 months following a single exposure at this concentration. Of the standard antifungals, only amphotericin B demonstrated any activity, resulting in zone diameters ranging from 58 mm to 74 mm. CPT, at the highest concentration tested (100%), had no significant effect against a variety of other environmental organisms including various filamentous fungi, bacteria and aerobic actinomycetes. Given that CPT is relatively non-toxic, the possibility exists that the all-natural, mixture could be used as an environmental pre-treatment to eradicate P. destructans from bat habitats. Additional studies are needed to assess any undesirable effects of CPT on bat behavior and health and overall impacts on other members of the interconnected ecosystem(s).     

The RNA Domain Vc1 Regulates Downstream Gene Expression in Response to Cyclic Diguanylate in Vibrio cholerae

In many bacterial species, including the aquatic bacterium and human pathogen Vibrio cholerae, the second messenger cyclic diguanylate (c-di-GMP) modulates processes such as biofilm formation, motility, and virulence factor production. By interacting with various effectors, c-di-GMP regulates gene expression or protein function. One type of c-di-GMP receptor is the class I riboswitch, representatives of which have been shown to bind c-di-GMP in vitro. Herein, we examined the in vitro and in vivo function of the putative class I riboswitch in Vibrio cholerae, Vc1, which lies upstream of the gene encoding GbpA, a colonization factor that contributes to attachment of V. cholerae to environmental and host surfaces containing N-acetylglucosamine moieties. We provide evidence that Vc1 RNA interacts directly with c-di-GMP in vitro, and that nucleotides conserved among this class of riboswitch are important for binding. Yet the mutation of these conserved residues individually in the V. cholerae chromosome inconsistently affects the expression of gbpA and production of the GbpA protein. By isolating the regulatory function of Vc1, we show that the Vc1 element positively regulates downstream gene expression in response to c-di-GMP. Together these data suggest that the Vc1 element responds to c-di-GMP in vivo. Positive regulation of gbpA expression by c-di-GMP via Vc1 may influence the ability of V. cholerae to associate with chitin in the aquatic environment and the host intestinal environment.     

Improved Heterojunction Quality in Cu2O-based Solar Cells Through the Optimization of Atmospheric Pressure Spatial Atomic Layer Deposited Zn1-xMgxO

Atmospheric pressure spatial atomic layer deposition (AP-SALD) was used to deposit n-type ZnO and Zn_1-xMg_xO thin films onto p-type thermally oxidized Cu₂O substrates outside vacuum at low temperature. The performance of photovoltaic devices featuring atmospherically fabricated ZnO/Cu₂O heterojunction was dependent on the conditions of AP-SALD film deposition, namely, the substrate temperature and deposition time, as well as on the Cu₂O substrate exposure to oxidizing agents prior to and during the ZnO deposition. Superficial Cu₂O to CuO oxidation was identified as a limiting factor to heterojunction quality due to recombination at the ZnO/Cu₂O interface. Optimization of AP-SALD conditions as well as keeping Cu₂O away from air and moisture in order to minimize Cu₂O surface oxidation led to improved device performance. A three-fold increase in the open-circuit voltage (up to 0.65 V) and a two-fold increase in the short-circuit current density produced solar cells with a record 2.2% power conversion efficiency (PCE). This PCE is the highest reported for a Zn_1-xMg_xO/Cu₂O heterojunction formed outside vacuum, which highlights atmospheric pressure spatial ALD as a promising technique for inexpensive and scalable fabrication of Cu₂O-based photovoltaics.     

New Approach to Develop Optimized Sunscreens that Enable Cutaneous Vitamin D Formation with Minimal Erythema Risk

Sunscreens protect the skin against erythemal radiation (E_er). But at the same time they reduce the effective radiation dose (E_VD) responsible for the formation of previtamin D in the skin. The paper describes a calculation method for optimizing the ratio E_VD/E_er behind sunscreens e.g. with SPF 5, 15 and 30 respectively. Taking into account that a majority of people in industrialized countries suffer from a shortage in vitamin D even in summer time, the ratio E_vd/E_er is a new and important criterion for the quality of sunscreens. Furthermore the exposure time t_vd needed per day for forming the equivalent of the recommended amount of 2000 IU of vitamin D per day for skin type 2 is estimated when sunscreens with different filter compositions are used. In vitro experiments show a significant increase of the conversion of 7-dehydrocholesterol (7-DHC) to previtamin D when exposed to artificial solar radiation behind an experimental sunscreen optimized for previtamin D production compared to a commercial sunscreen having the same SPF.     

The duality of stability: towards a stochastic theory of species interactions

Understanding the dynamics of ecological systems using stability concepts has been a key driver in ecological research from the inception of the field. Despite the tremendous effort put into this area, progress has been limited due to the bewildering number of metrics used to describe ecological stability. Here, we seek to resolve some of the confusion by unfolding the dynamics of a simple consumer-resource interaction module. In what follows, we first review common dynamical metrics of stability (CV, eigenvalues). We argue using the classical type II consumer-resource model as an example where the empirical stability metric, CV, hides two different, but important, aspects of stability: (i) stability due to mean population density processes and (ii) stability due to population density variance processes. We then employ a simple stochastic consumer-resource framework in order to elucidate (i) when we expect these two different aspects of stability to arise in ecological systems and, importantly, highlight (ii) the fact that these two different aspects of stability respond differentially, but predictably, to changes in fundamental parameters that govern biomass flux and loss in any consumer-resource interaction (e.g., attack rates, carrying capacity, mortality).