Time-of-flight mass spectrometer for diagnostics of continuous plasma flow

This paper describes a version of the time-of-flight mass spectrometer based on a modified two-field acceleration approach of Wiley and McLaren. The aim of the device is a diagnostic of continuous plasma flow. The acceleration scheme idea, the construction of the spectrometer, and results of testing in plasma flow of Gd and CeO₂ generated by vacuum arc discharge are described. The instrument function of the spectrometer was measured, and its mass resolution was evaluated as ∼20. With the use of the instrument function, how to interpret the registered signal in the case of intersection of mass peaks was suggested. The presented device has a simple construction and relatively low values of applied acceleration voltages, so it has fewer requirements in manufacturability and cost.

A repeating fast radio burst source in a globular cluster

Fast radio bursts (FRBs) are flashes of unknown physical origin¹. The majority of FRBs have been seen only once, although some are known to generate multiple flashes^2,3. Many models invoke magnetically powered neutron stars (magnetars) as the source of the emission^4,5. Recently, the discovery⁶ of another repeater (FRB 20200120E) was announced, in the direction of the nearby galaxy M81, with four potential counterparts at other wavelengths⁶. Here we report observations that localized the FRB to a globular cluster associated with M81, where it is 2 parsecs away from the optical centre of the cluster. Globular clusters host old stellar populations, challenging FRB models that invoke young magnetars formed in a core-collapse supernova. We propose instead that FRB 20200120E originates from a highly magnetized neutron star formed either through the accretion-induced collapse of a white dwarf, or the merger of compact stars in a binary system⁷. Compact binaries are efficiently formed inside globular clusters, so a model invoking them could also be responsible for the observed bursts.

A synchrotron computed tomography dataset for validation of longitudinal tensile failure models based on fibre break and cluster development

We performed in-situ tensile tests on two carbon fibre/epoxy composites with continuous scanning using synchrotron computed tomography (CT). Both composites were cross-ply laminates, and two specimens were tested for each composite. The voxel size was sufficiently small to recognize individual fibres and fibre breaks. For each test, 16-19 volumes were reconstructed, cropped down to the 0° plies and analysed to track fibre break and cluster development. This dataset provides the last CT volume before failure for each of the four specimens as well as the individual fibre break locations in all reconstructed volumes. These data are then plotted against predictions from six state-of-the-art strength models. The target is that these data become a benchmark for the development of new models, inspiring researchers to set up refined experiments and develop improved models.

On Krylov’s estimates for optional semimartingales

The estimates of N. V. Krylov for distributions of stochastic integrals by means of the L d {L_{d}} -norm of a measurable function are well-known and are widely used in the theory of stochastic differential equations and controlled diffusion processes. We generalize estimates of this type for optional semimartingales, then apply these estimates to prove the change of variables formula for a general class of functions from the Sobolev space W d 2 {W^{2}_{d}} . We also show how to use these estimates for the investigation of L 2 {L^{2}} -convergence of solutions of optional SDE’s.

Magneto-optical properties of Au upon the injection of hot spin-polarized electrons across Fe/Au(0 0 1) interfaces

We demonstrate a novel method for the excitation of sizable magneto-optical effects in Au by means of the laser-induced injection of hot spin-polarized electrons in Au/Fe/MgO(0 0 1) heterostructures. It is based on the energy- and spin-dependent electron transmittance of Fe/Au interface which acts as a spin filter for non-thermalized electrons optically excited in Fe. We show that after crossing the interface, majority electrons propagate through the Au layer with the velocity on the order of 1 nm fs^-1 (close to the Fermi velocity) and the decay length on the order of 100 nm. Featuring ultrafast functionality and requiring no strong external magnetic fields, spin injection results in a distinct magneto-optical response of Au. We develop a formalism based on the phase of the transient complex MOKE response and demonstrate its robustness in a plethora of experimental and theoretical MOKE studies on Au, including our ab initio calculations. Our work introduces a flexible tool to manipulate magneto-optical properties of metals on the femtosecond timescale that holds high potential for active magneto-photonics, plasmonics, and spintronics.

Analysis of the time-resolved magneto-optical Kerr effect for ultrafast magnetization dynamics in ferromagnetic thin films

We discuss fundamental aspects of laser-induced ultrafast demagnetization probed by the time-resolved magneto-optical Kerr effect (MOKE). Studying thin Fe films on MgO substrate in the absence of electronic transport, we demonstrate how to disentangle pump-induced variations of magnetization and magneto-optical coefficients. We provide a mathematical formalism for retrieving genuine laser-induced magnetization dynamics and discuss its applicability in real experimental situations. We further stress the importance of temporal resolution achieved in the experiments and argue that measurements of both time-resolved MOKE rotation and ellipticity are needed for the correct assessment of magnetization dynamics on sub-picosecond timescales. The framework developed here sheds light onto the details of the time-resolved MOKE technique and contributes to the understanding of the interplay between ultrafast laser-induced optical and magnetic effects.

Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance

Background

Artemisinin-based combination therapies are the first line of treatment for Plasmodium falciparum infections worldwide, but artemisinin resistance has risen rapidly in Southeast Asia over the past decade. Mutations in the kelch13 gene have been implicated in this resistance. We used longitudinal genomic surveillance to detect signals in kelch13 and other loci that contribute to artemisinin or partner drug resistance. We retrospectively sequenced the genomes of 194 P. falciparum isolates from five sites in Northwest Thailand, over the period of a rapid increase in the emergence of artemisinin resistance (2001–2014).

Results

We evaluate statistical metrics for temporal change in the frequency of individual SNPs, assuming that SNPs associated with resistance increase in frequency over this period. After Kelch13-C580Y, the strongest temporal change is seen at a SNP in phosphatidylinositol 4-kinase, which is involved in a pathway recently implicated in artemisinin resistance. Furthermore, other loci exhibit strong temporal signatures which warrant further investigation for involvement in artemisinin resistance evolution. Through genome-wide association analysis we identify a variant in a kelch domain-containing gene on chromosome 10 that may epistatically modulate artemisinin resistance.

Conclusions

This analysis demonstrates the potential of a longitudinal genomic surveillance approach to detect resistance-associated gene loci to improve our mechanistic understanding of how resistance develops. Evidence for additional genomic regions outside of the kelch13 locus associated with artemisinin-resistant parasites may yield new molecular markers for resistance surveillance, which may be useful in efforts to reduce the emergence or spread of artemisinin resistance in African parasite populations.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-017-1204-4) contains supplementary material, which is available to authorized users.

Systematic dissection of genomic features determining transcription factor binding and enhancer function

Enhancers regulate gene expression through the binding of sequence-specific transcription factors (TFs) to cognate motifs. Various features influence TF binding and enhancer function-including the chromatin state of the genomic locus, the affinities of the binding site, the activity of the bound TFs, and interactions among TFs. However, the precise nature and relative contributions of these features remain unclear. Here, we used massively parallel reporter assays (MPRAs) involving 32,115 natural and synthetic enhancers, together with high-throughput in vivo binding assays, to systematically dissect the contribution of each of these features to the binding and activity of genomic regulatory elements that contain motifs for PPARγ, a TF that serves as a key regulator of adipogenesis. We show that distinct sets of features govern PPARγ binding vs. enhancer activity. PPARγ binding is largely governed by the affinity of the specific motif site and higher-order features of the larger genomic locus, such as chromatin accessibility. In contrast, the enhancer activity of PPARγ binding sites depends on varying contributions from dozens of TFs in the immediate vicinity, including interactions between combinations of these TFs. Different pairs of motifs follow different interaction rules, including subadditive, additive, and superadditive interactions among specific classes of TFs, with both spatially constrained and flexible grammars. Our results provide a paradigm for the systematic characterization of the genomic features underlying regulatory elements, applicable to the design of synthetic regulatory elements or the interpretation of human genetic variation.

Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits

Genome-wide association studies (GWAS) have successfully identified thousands of associations between common genetic variants and human disease phenotypes, but the majority of these variants are non-coding, often requiring genetic fine-mapping, epigenomic profiling, and individual reporter assays to delineate potential causal variants. We employ a massively parallel reporter assay (MPRA) to simultaneously screen 2,756 variants in strong linkage disequilibrium with 75 sentinel variants associated with red blood cell traits. We show that this assay identifies elements with endogenous erythroid regulatory activity. Across 23 sentinel variants, we conservatively identified 32 MPRA functional variants (MFVs). We used targeted genome editing to demonstrate endogenous enhancer activity across 3 MFVs that predominantly affect the transcription of SMIM1, RBM38, and CD164. Functional follow-up of RBM38 delineates a key role for this gene in the alternative splicing program occurring during terminal erythropoiesis. Finally, we provide evidence for how common GWAS-nominated variants can disrupt cell-type-specific transcriptional regulatory pathways.

Population genomics studies identify signatures of global dispersal and drug resistance in Plasmodium vivax

Plasmodium vivax is a major public health burden, responsible for the majority of malaria infections outside Africa. We explored the impact of demographic history and selective pressures on the P. vivax genome by sequencing 182 clinical isolates sampled from 11 countries across the globe, using hybrid selection to overcome human DNA contamination. We confirmed previous reports of high genomic diversity in P. vivax relative to the more virulent Plasmodium falciparum species; regional populations of P. vivax exhibited greater diversity than the global P. falciparum population, indicating a large and/or stable population. Signals of natural selection suggest that P. vivax is evolving in response to antimalarial drugs and is adapting to regional differences in the human host and the mosquito vector. These findings underline the variable epidemiology of this parasite species and highlight the breadth of approaches that may be required to eliminate P. vivax globally.

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

We recently used in situ Hi-C to create kilobase-resolution 3D maps of mammalian genomes. Here, we combine these maps with new Hi-C, microscopy, and genome-editing experiments to study the physical structure of chromatin fibers, domains, and loops. We find that the observed contact domains are inconsistent with the equilibrium state for an ordinary condensed polymer. Combining Hi-C data and novel mathematical theorems, we show that contact domains are also not consistent with a fractal globule. Instead, we use physical simulations to study two models of genome folding. In one, intermonomer attraction during polymer condensation leads to formation of an anisotropic "tension globule." In the other, CCCTC-binding factor (CTCF) and cohesin act together to extrude unknotted loops during interphase. Both models are consistent with the observed contact domains and with the observation that contact domains tend to form inside loops. However, the extrusion model explains a far wider array of observations, such as why loops tend not to overlap and why the CTCF-binding motifs at pairs of loop anchors lie in the convergent orientation. Finally, we perform 13 genome-editing experiments examining the effect of altering CTCF-binding sites on chromatin folding. The convergent rule correctly predicts the affected loops in every case. Moreover, the extrusion model accurately predicts in silico the 3D maps resulting from each experiment using only the location of CTCF-binding sites in the WT. Thus, we show that it is possible to disrupt, restore, and move loops and domains using targeted mutations as small as a single base pair.

Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections

Plasmodium vivax, one of the five species of Plasmodium parasites that cause human malaria, is responsible for 25–40% of malaria cases worldwide. Malaria global elimination efforts will benefit from accurate and effective genotyping tools that will provide insight into the population genetics and diversity of this parasite. The recent sequencing of P. vivax isolates from South America, Africa, and Asia presents a new opportunity by uncovering thousands of novel single nucleotide polymorphisms (SNPs). Genotyping a selection of these SNPs provides a robust, low-cost method of identifying parasite infections through their unique genetic signature or barcode. Based on our experience in generating a SNP barcode for P. falciparum using High Resolution Melting (HRM), we have developed a similar tool for P. vivax. We selected globally polymorphic SNPs from available P. vivax genome sequence data that were located in putatively selectively neutral sites (i.e., intergenic, intronic, or 4-fold degenerate coding). From these candidate SNPs we defined a barcode consisting of 42 SNPs. We analyzed the performance of the 42-SNP barcode on 87 P. vivax clinical samples from parasite populations in South America (Brazil, French Guiana), Africa (Ethiopia) and Asia (Sri Lanka). We found that the P. vivax barcode is robust, as it requires only a small quantity of DNA (limit of detection 0.3 ng/μl) to yield reproducible genotype calls, and detects polymorphic genotypes with high sensitivity. The markers are informative across all clinical samples evaluated (average minor allele frequency > 0.1). Population genetic and statistical analyses show the barcode captures high degrees of population diversity and differentiates geographically distinct populations. Our 42-SNP barcode provides a robust, informative, and standardized genetic marker set that accurately identifies a genomic signature for P. vivax infections.

Plasmodium vivax malaria is a major global public health problem, with nearly 2.5 billion people at risk for infection and approximately 132–391 million clinical infections annually. It has a wide geographical range, with a high disease burden in Asia, Central and South America, the Middle East, Oceania, and East Africa. Advances in sequencing technology and sample processing have made it possible to characterize the genetic diversity of P. vivax populations. This genetic variation provides a means to identify parasites by unique genetic signatures, or “barcodes.” We developed such a genetic barcode for P. vivax, composed of 42 robust and informative variants. Here we report its development and validation based on 87 clinical samples identified by microscopy to contain P. vivax from geographically diverse parasite populations from South America (Brazil, French Guiana), Africa (Ethiopia) and Asia (Sri Lanka). We show that the SNP barcode provides a genotyping tool that can be performed at low cost, providing a means to uniquely identify parasite infections and distinguish geographic origins, and that barcode data may offer new insights into P. vivax population structure and diversity.

Optoelectronic transport properties in amorphous/crystalline silicon solar cell heterojunctions measured by frequency-domain photocarrier radiometry: multi-parameter measurement reliability and precision studies

A theoretical one-dimensional two-layer linear photocarrier radiometry (PCR) model including the presence of effective interface carrier traps was used to evaluate the transport parameters of p-type hydrogenated amorphous silicon (a-Si:H) and n-type crystalline silicon (c-Si) passivated by an intrinsic hydrogenated amorphous silicon (i-layer) nanolayer. Several crystalline Si heterojunction structures were examined to investigate the influence of the i-layer thickness and the doping concentration of the a-Si:H layer. The experimental data of a series of heterojunction structures with intrinsic thin layers were fitted to PCR theory to gain insight into the transport properties of these devices. The quantitative multi-parameter results were studied with regard to measurement reliability (uniqueness) and precision using two independent computational best-fit programs. The considerable influence on the transport properties of the entire structure of two key parameters that can limit the performance of amorphous thin film solar cells, namely, the doping concentration of the a-Si:H layer and the i-layer thickness was demonstrated. It was shown that PCR can be applied to the non-destructive characterization of a-Si:H/c-Si heterojunction solar cells yielding reliable measurements of the key parameters.

Massively parallel reporter assays in cultured mammalian cells

The genetic reporter assay is a well-established and powerful tool for dissecting the relationship between DNA sequences and their gene regulatory activities. The potential throughput of this assay has, however, been limited by the need to individually clone and assay the activity of each sequence on interest using protein fluorescence or enzymatic activity as a proxy for regulatory activity. Advances in high-throughput DNA synthesis and sequencing technologies have recently made it possible to overcome these limitations by multiplexing the construction and interrogation of large libraries of reporter constructs. This protocol describes implementation of a Massively Parallel Reporter Assay (MPRA) that allows direct comparison of hundreds of thousands of putative regulatory sequences in a single cell culture dish.

Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes

Deep mutational scanning has emerged as a promising tool for mapping sequence-activity relationships in proteins, ribonucleic acid and deoxyribonucleic acid. In this approach, diverse variants of a sequence of interest are first ranked according to their activities in a relevant assay, and this ranking is then used to infer the shape of the fitness landscape around the wild-type sequence. Little is currently known, however, about the degree to which such fitness landscapes are dependent on the specific assay conditions from which they are inferred. To explore this issue, we performed comprehensive single-substitution mutational scanning of APH(3')II, a Tn5 transposon-derived kinase that confers resistance to aminoglycoside antibiotics, in Escherichia coli under selection with each of six structurally diverse antibiotics at a range of inhibitory concentrations. We found that the resulting local fitness landscapes showed significant dependence on both antibiotic structure and concentration, and that this dependence can be exploited to guide protein engineering. Specifically, we found that differential analysis of fitness landscapes allowed us to generate synthetic APH(3')II variants with orthogonal substrate specificities.

Abstract 242: Functional Characterization of a Cis-eQTL Locus for Plasma Cholesterol Using CRISPR/Cas Genome Editing in Human Pluripotent Stem Cells

Genome-wide association studies (GWASs) have discovered many novel genetic loci linked to serum lipid levels, yet pinpointing the causal variants remains a major challenge. Expression quantitative trait locus (eQTL) analysis of liver and adipose indicates that many lipid-associated variants influence gene expression in a cis-regulatory manner. To identify causal variants at 57 lipid-associated eQTL loci, we performed a massively parallel reporter assay (MPRA) in which the genomic region surrounding each candidate SNP was coupled to a reporter gene with a unique barcode identifier. This construct pool was transfected into 3T3-L1 adipocytes, and the copy number of each expressed barcode determined by RNAseq. Variants were prioritized according to allele-specific regulatory activity.

The top-ranked variant, rs2277862, is associated with total cholesterol and is flanked by the ERGIC3, CPNE1, and CEP250 genes, none of which have previous connections to lipid metabolism. We hypothesized that rs2277862 is causal for the eQTL at the 20q11 locus, and that it lies within a transcriptional regulatory site to influence local gene expression. We identified human pluripotent stem cell (hPSC) lines with different genotypes at rs2277862 and, using CRISPR/Cas genome-editing technology, either deleted the putative regulatory site encompassing rs2277862 or knocked in the alternate SNP allele. Analysis of undifferentiated rs2277862 homozygous major deletion mutants revealed diminished expression of ERGIC3, CPNE1, and CEP250; conversely, heterozygous deletion mutants had increased expression of the same three genes. Our results suggest that in hPSCs the major and minor alleles of rs2277862 have opposing effects on gene expression.

In ongoing work, we are validating these findings in differentiated adipocytes and seek to identify the factor(s) that binds the putative regulatory site to mediate allele-specific gene expression. We anticipate that this work will offer fresh insight into the mechanisms by which GWAS-implicated SNPs influence expression of causal genes for lipid metabolism and, more broadly, establish a novel methodology for finding causal variants for any phenotype of interest.

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

Genome-wide chromatin annotations have permitted the mapping of putative regulatory elements across multiple human cell types. However, their experimental dissection by directed regulatory motif disruption has remained unfeasible at the genome scale. Here, we use a massively parallel reporter assay (MPRA) to measure the transcriptional levels induced by 145-bp DNA segments centered on evolutionarily conserved regulatory motif instances within enhancer chromatin states. We select five predicted activators (HNF1, HNF4, FOXA, GATA, NFE2L2) and two predicted repressors (GFI1, ZFP161) and measure reporter expression in erythroleukemia (K562) and liver carcinoma (HepG2) cell lines. We test 2104 wild-type sequences and 3314 engineered enhancer variants containing targeted motif disruptions, each using 10 barcode tags and two replicates. The resulting data strongly confirm the enhancer activity and cell-type specificity of enhancer chromatin states, the ability of 145-bp segments to recapitulate both, the necessary role of regulatory motifs in enhancer function, and the complementary roles of activator and repressor motifs. We find statistically robust evidence that (1) disrupting the predicted activator motifs abolishes enhancer function, while silent or motif-improving changes maintain enhancer activity; (2) evolutionary conservation, nucleosome exclusion, binding of other factors, and strength of the motif match are predictive of enhancer activity; (3) scrambling repressor motifs leads to aberrant reporter expression in cell lines where the enhancers are usually inactive. Our results suggest a general strategy for deciphering cis-regulatory elements by systematic large-scale manipulation and provide quantitative enhancer activity measurements across thousands of constructs that can be mined to develop predictive models of gene expression.

Hybrid selection for sequencing pathogen genomes from clinical samples

We have adapted a solution hybrid selection protocol to enrich pathogen DNA in clinical samples dominated by human genetic material. Using mock mixtures of human and Plasmodium falciparum malaria parasite DNA as well as clinical samples from infected patients, we demonstrate an average of approximately 40-fold enrichment of parasite DNA after hybrid selection. This approach will enable efficient genome sequencing of pathogens from clinical samples, as well as sequencing of endosymbiotic organisms such as Wolbachia that live inside diverse metazoan phyla.

Targeted exon sequencing by in-solution hybrid selection

This unit describes a protocol for the targeted enrichment of exons from randomly sheared genomic DNA libraries using an in-solution hybrid selection approach for sequencing on an Illumina Genome Analyzer II. The steps for designing and ordering a hybrid selection oligo pool are reviewed, as are critical steps for performing the preparation and hybrid selection of an Illumina paired-end library. Critical parameters, performance metrics, and analysis workflow are discussed.

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts

Targeted RNA-Seq combines next-generation sequencing with capture of sequences from a relevant subset of a transcriptome. When testing by capturing sequences from a tumor cDNA library by hybridization to oligonucleotide probes specific for 467 cancer-related genes, this method showed high selectivity, improved mutation detection enabling discovery of novel chimeric transcripts, and provided RNA expression data. Thus, targeted RNA-Seq produces an enhanced view of the molecular state of a set of "high interest" genes.

Laser-induced magnetization dynamics of lanthanide-doped permalloy thin films

We investigate the effect of Ho, Dy, Tb, and Gd impurities on the femtosecond laser-induced magnetization dynamics of thin Permalloy films using the time-resolved magneto-optical Kerr effect. Varying the amount of Ho, Dy, Tb content from 0% to 8%, we observe a gradual change of the characteristic demagnetization time constant from approximately 60 to approximately 150 fs. In contrast, Gd concentrations up to 15% do not influence the time scale of the initial photoinduced magnetization loss. We propose a demagnetization mechanism that relies on strong magnetic inertia of the rare-earth dopant which stabilizes the ferrimagnetic ordering and thereby delays the demagnetization.

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

Targeting genomic loci by massively parallel sequencing requires new methods to enrich templates to be sequenced. We developed a capture method that uses biotinylated RNA “baits” to “fish” targets out of a “pond” of DNA fragments. The RNA is transcribed from PCR-amplified oligodeoxynucleotides originally synthesized on a microarray, generating sufficient bait for multiple captures at concentrations high enough to drive the hybridization. We tested this method with 170-mer baits that target >15,000 coding exons (2.5 Mb) and four regions (1.7 Mb total) using Illumina sequencing as read-out. About 90% of uniquely aligning bases fell on or near bait sequence; up to 50% lay on exons proper. The uniformity was such that ~60% of target bases in the exonic “catch”, and ~80% in the regional catch, had at least half the mean coverage. One lane of Illumina sequence was sufficient to call high-confidence genotypes for 89% of the targeted exon space.

Magnon-enhanced phonon damping at Gd(0001) and Tb(0001) surfaces using femtosecond time-resolved optical second-harmonic generation

Damping of coherent optical phonons is investigated by femtosecond time-resolved second-harmonic generation at Gd(0001) and Tb(0001) surfaces. At low temperature the damping rate increases monotonically with temperature, but close to the Curie point the damping rate is strongly reduced. We explain this behavior by phonon-magnon scattering originating from spin-orbit coupling proven by a larger effect for Tb than for Gd. Consideration of phonon-electron and phonon-phonon scattering shows that magnon-mediated damping is dominant almost up to the Curie temperature.

Nonequilibrium magnetization dynamics of gadolinium studied by magnetic linear dichroism in time-resolved 4f core-level photoemission

The magnetic linear dichroism of the gadolinium 4f core level is studied in a time-resolved photoemission experiment employing laser pump- and synchrotron-radiation probe pulses. Upon optical excitation of the 5d6s valence electrons with femtosecond laser pulses, the magnetic order in the 4f spin system is reduced. Remarkably, the linear dichroism remains at 80% of the equilibrium contrast while the lattice temperature reaches the Curie temperature due to electron-phonon scattering. Contrasting itinerant ferromagnets, this shows that equilibration between the lattice and spin subsystems takes in Gd about 80 ps and is established in parallel with heat diffusion.

Complex electrooptic research of nano-particle parameters in colloids

A research of some colloids has been carried out by means of dynamic light scattering, electrooptical and magnetooptical techniques. Intensity autocorrelation functions of scattered light have been compared to the relaxation curves of electrooptical effect for colloid particles of different shapes. The results of complex research confirm that the complicated character of light scattering by particles allows us to use the methods of birefringence and dichroism only formally when studying most colloid systems. Very thin nano-disperse structures are an exception to this rule. The investigation of polydispersity of some colloids was carried out by magnetooptical and two electrooptical techniques. Size distribution functions resulted from the different techniques agree. This justifies the suppositions about particle light scattering that are required for the use of the methods.

Algorithms for network analysis in systems-ADME/Tox using the MetaCore and MetaDrug platforms

The authors have previously applied two integrated platforms, MetaCore and MetaDrug, for the assembly and analysis of human biological networks as a useful method for the integration and functional interpretation of high-throughput experimental data. The present study demonstrates in detail the specific algorithms that are used in both software platforms. Using a standard set of genes as input, namely CYP3A4 (an enzyme), PXR (a nuclear hormone receptor), MDR1 (a transporter) and hERG (an ion channel) related to the absorption, distribution, metabolism, excretion and toxicity (ADME/Tox) of xenobiotics, we have now generated networks with each algorithm. The relative advantages and disadvantages of these algorithms are explained using these examples as well as appropriate instances of utility to illustrate further the particular circumstances for their use. In addition, the benefits of the different network algorithms are identified when compared with algorithms available in other products, where this information is available.

Scaling of the low-temperature dephasing rate in Kondo systems

We present phase coherence time measurements in quasi-one-dimensional Ag wires doped with Fe Kondo impurities of different concentrations n_{s}. Because of the relatively high Kondo temperature T_{K} approximately 4.3 K of this system, we are able to explore a temperature range from above T_{K} down to below 0.01T_{K}. We show that the magnetic contribution to the dephasing rate gamma_{m} per impurity is described by a single, universal curve when plotted as a function of T/T_{K}. For T>0.1T_{K}, the dephasing rate is remarkably well described by recent numerical results for spin S=1/2 impurities. At lower temperature, we observe deviations from this theory. Based on a comparison with theoretical calculations for S>1/2, we discuss possible explanations for the observed deviations.

Genome sequence, comparative analysis and haplotype structure of the domestic dog

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

Femtosecond electron and spin dynamics in Gd(0001) studied by time-resolved photoemission and magneto-optics

Femtosecond electron and spin dynamics of the Gd(0001) surface are investigated by time-resolved photoemission and second harmonic generation. Upon optical excitation the spin polarization of the surface state is reduced by half while its exchange splitting remains nearly unchanged. Electron-magnon interaction is proposed to facilitate electron-spin-flip scattering among spin-mixed surface and bulk states, which provides a mechanism for ultrafast demagnetization.

Coherent optical phonons and parametrically coupled magnons induced by femtosecond laser excitation of the Gd(0001) surface

Coherent spin dynamics in the THz domain coupled to a coherent phonon is observed in the time-resolved second harmonic response of the Gd(0001) ferromagnetic metal surface. An LO phonon of 2.9 THz is excited by a transient charge displacement at the surface caused by resonant absorption of a fs laser pulse in the exchange-split surface state. This lattice vibration modulates the interlayer distance inducing a coherent variation of the exchange interaction between spins in adjacent layers. The resulting magnetization dynamics is considered as optical magnon wave packets coupled to the phonon.

Clinical and environmental isolates of Burkholderia cepacia exhibit differential cytotoxicity towards macrophages and mast cells

Burkholderia cepacia is an emerging opportunistic pathogen that causes fatal infections in patients suffering from cystic fibrosis (CF) and chronic granulomatous disease. Various environmental isolates of B. cepacia are, however, capable of degrading environmental pollutants, such as trichloroethylene, 2,4,5-trichlorophenoxyacetic acid (2,4,5-T), etc., and are also highly effective in controlling plant diseases caused by nematodes and fungi. Such strains have therefore been proposed for environmental release to clean up toxic dump sites or as biopesticides. Various efforts to distinguish between clinical and environmental isolates of B. cepacia with regard to their virulence characteristics have produced ambiguous results, suggesting that newer methods are needed to test for the presence or absence of pathogenic potential in B. cepacia strains proposed for environmental release. We now report that several clinical strains of B. cepacia secrete cytotoxic factors that allow macrophage and mast cell death in the presence of external ATP. Several environmental strains had reduced activity in this regard. We also demonstrate that, while all the strains secrete enzymes that have nucleoside diphosphate kinase (Ndk), adenylate kinase (Ak) and 5'-nucleotidase activity, the level of secretion of the 5'-nucleotidase (and/or ATPase/phosphatase) appears to be lower in the environmental strains than in the clinical strains. The secretion of these enzymes is specifically activated in the presence of eukaryotic proteins such as alpha2-macroglobulin. As macrophage-or mast cell surface-associated P2Z receptors promote their cell death in the presence of mM concentrations of ATP, and as the secreted ATP-using enzymes generate various phosphorylated or non-phosphorylated adenine nucleotides that may even be better agonists than ATP in activating the P2Z receptors or may act through the activation of additional purinergic receptors, such enzymes may play an important role in allowing B. cepacia to evade host defence.

Random mutagenesis by recombinational capture of PCR products in Bacillus subtilis and Acinetobacter calcoaceticus

We describe a general method for random mutagenesis of cloned genes by error-prone PCR or DNA shuffling that eliminates the need for post-amplification subcloning following each cycle of mutagenesis. This method exploits the highly efficient and recombinogenic nature of DNA uptake during natural transformation in the Gram-positive bacterium Bacillus subtilis and the Gram-negative bacterium Acinetobacter calcoaceticus. Plasmid systems were designed that allow capture of PCR-amplified DNA fragments by marker-replacement recombination with a structurally similar helper plasmid resident in the transformation recipient. This recombination event simultaneously transfers the amplified sequences into the helper plasmid and restores the integrity of a drug resistance gene, thereby affording a direct selection for fragment capture. Although this strategy was sufficiently effective to permit recovery in B. subtilis of up to 10(3) transformants/microgram of PCR product, equivalent plasmid systems were approximately 100 times more efficient in A.calcoaceticus. Acinetobacter calcoaceticus also offers the advantage of essentially constitutive transformation competence in ordinary complex broth, such as LB, in contrast to two-step growth in semi-synthetic media required for optimal transformation of B.subtilis.

The Bacillus SpoIIGA protein is targeted to sites of spore septum formation in a SpoIIE-independent manner

The process of bacterial cell division involves the assembly of a complex of proteins at the site of septation that probably provides both the structural and the cytokinetic functions required for elaboration and closure of the septal annulus. During sporulation in Bacillus subtilis, this complex of proteins is modified by the inclusion of a sporulation-specific protein, SpoIIE, which plays a direct role in gene regulation and also has a genetically separable role in determining the gross structural properties of the specialized sporulation septum. We demonstrate by both green fluorescent protein (GFP) fusions and indirect immunofluorescence microscopy that SpoIIGA, a protein required for proteolytic cleavage of pro-sigmaE, is also targeted to the sporulation septum. Septal localization of SpoIIGA-GFP occurred even in the structurally abnormal septum formed by a SpoIIE null mutant. We also report the isolation of a spoIIGA homologue from Bacillus megaterium, a species in which the cells are significantly larger than those of B. subtilis. We have exploited the physical dimensions of the B. megaterium sporangium, in conjunction with wide-field deconvolution microscopy, to construct three-dimensional projections of sporulating cells. These projections indicate that SpoIIGA-GFP is initially localized in an annulus at the septal periphery and is only later localized uniformly throughout the septa. Localization was also detected in a B. subtilis spo0H null strain that fails to construct a spore septum. We propose that SpoIIGA is sequestered in the septum by an interaction with components of the septation machinery and that this interaction begins before the construction of the asymmetric septum.

Voltage-sensitive dye recordings of electrophysiological activation in a Langendorff-perfused mouse heart

The pattern of electrophysiological activation of adult mouse ventricles was measured with the use of voltage-sensitive dye methods. Di-4-ANEPPS was used to monitor membrane potential as small changes in fluorescence, which were detected by a state of the art, cooled, charged coupled device camera/image intensifier system. The extremely rapid conduction velocity, coupled with the small size of this preparation, necessitated taking these measurements at room temperature (22 to 23 degrees C). Initial experiments demonstrate that ventricular activation can be identified and its conduction pattern can be monitored reproducibly and with high resolution for extended time periods (10 to 20 mins) during spontaneous activity.