Search

Multi-locus sequence typing (MLST) is widely used to investigate genetic relationships among eukaryotic taxa, including parasitic pathogens. MLST analysis workflows typically involve construction of alignment-based phylogenetic trees - i.e., where tree structures are computed from nucleotide differences observed in a multiple sequence alignment (MSA). Notably, alignment-based phylogenetic methods require that all isolates/taxa are represented by a single sequence. When multiple loci are sequenced these sequences may be concatenated to produce one tree that includes information from all loci. Alignment-based phylogenetic techniques are robust and widely used yet possess some shortcomings, including how heterozygous sites are handled, intolerance for missing data (i.e., partial genotypes), and differences in the way insertions-deletions (indels) are scored/treated during tree construction. In certain contexts, 'haplotype-based' methods may represent a viable alternative to alignment-based techniques, as they do not possess the aforementioned limitations. This is namely because haplotype-based methods assess genetic similarity based on numbers of shared (i.e., intersecting) haplotypes as opposed to similarities in nucleotide composition observed in an MSA. For haplotype-based comparisons, choosing an appropriate distance statistic is fundamental, and several statistics are available to choose from. However, a comprehensive assessment of various available statistics for their ability to produce a robust haplotype-based phylogenetic reconstruction has not yet been performed. We evaluated seven distance statistics by applying them to extant MLST datasets from the gastrointestinal parasite Cyclospora cayetanensis and two species of pathogenic nematode of the genus Strongyloides. We compare the genetic relationships identified using each statistic to epidemiologic, geographic, and host metadata. We show that Barratt's heuristic definition of genetic distance was the most robust among the statistics evaluated. Consequently, it is proposed that Barratt's heuristic represents a useful approach for use in the context of challenging MLST datasets possessing features (i.e., high heterozygosity, partial genotypes, and indel or repeat-based polymorphisms) that confound or preclude the use of alignment-based methods.

Although perceived stress has been shown to be related to online compulsive buying among women, little is known about the underlying mechanisms of this association. The present study examined the mediating role of negative coping and the moderating role of self-esteem in the association between perceived stress and online compulsive buying. A sample of 548 female consumers (M age = 21.41 years, SD = 4.40) completed questionnaire measures of perceived stress, self-esteem, negative coping, and online compulsive buying. Frequency of online buying and amount of money spent online per month were used as covariates. Results indicated that perceived stress was positively associated with online compulsive buying. Negative coping partially mediated this association. In addition, the direct effect of perceived stress on online compulsive buying, and the mediating effect of negative coping, were moderated by self-esteem. Specifically, these effects were weaker for women with higher self-esteem. These findings advance our understanding of how and when perceived stress is related to online compulsive buying among women. Limitations and implications are discussed.

PacBio and Illumina MiSeq platforms were used for genomic sequencing of a Leishmania (Leishmania) tropica strain isolated from a patient infected in Pakistan. PacBio assemblies were generated using Flye v2.4 and polished with MiSeq data. The results represent a considerable improvement of the currently available genome sequences in the GenBank database.

We investigated an autochthonous case of cutaneous leishmaniasis caused by a genetically different Leishmania sp. in a patient in Arizona, USA. This parasite was classified into the subgenus Leishmania on the basis of multilocus DNA sequence and phylogenetic analyses of the rRNA locus and 11 reference genes.

PacBio and Illumina MiSeq platforms were used for genomic sequencing of a Leishmania (Leishmania ) tropica strain isolated from a patient infected in Pakistan. PacBio assemblies were generated using Flye v2.4 and polished with MiSeq data. The results represent a considerable improvement of the currently available genome sequences in the GenBank database.

Previous research has documented that perceived stress is negatively associated with adolescent life satisfaction. However, the mediating mechanisms underlying this relation are largely unknown. The present study tested whether self-control and rumination mediate the link between perceived stress and adolescents’ lower life satisfaction. A sample of 1196 senior high school students (ages 13–19, 54% boys) completed questionnaires regarding demographics, perceived stress, self-control, rumination and life satisfaction. After controlling for gender, the results indicated that: (a) perceived stress was negatively associated with life satisfaction; (b) both self-control and rumination partially mediated the link between perceived stress and life satisfaction in a parallel pattern; and (c) self-control and rumination also sequentially mediated the relation between perceived stress and life satisfaction. The current study advances our understanding of how perceived stress might lead to poor life satisfaction. Furthermore, the multiple mediation analysis reveals that self-control and rumination can not only in parallel, but also sequentially mediate the relation between perceived stress and life satisfaction.

We present here the draft genome sequences of Leishmania ( Leishmania ) amazonensis , Leishmania ( Leishmania ) mexicana , and Leishmania ( Leishmania ) aethiopica , potential etiological agents of diffuse cutaneous leishmaniasis (DCL). Sequence data were obtained using PacBio and MiSeq platforms.

We present here the draft genome sequence for Leishmania ( Viannia) guyanensis . The isolate was obtained from a clinical case of cutaneous leishmaniasis in French Guiana.

We present here the first draft genome sequence of Leishmania (Viannia) lainsoni strain 216-34, sequenced using PacBio and MiSeq platforms. PacBio contigs were generated from de novo assemblies using CANU version 1.6 and polished using Illumina reads.

Although Social Network Site (SNS) usage has been shown to be related to online compulsive buying among women, little is known about the mediating mechanisms underlying this association. Based on the Interaction of Person-Affect-Cognition-Execution model (I-PACE) for addictive behaviors and social comparison theory, the present study examined the mediating roles of upward social comparison and state anxiety in the link between passive SNS usage and online compulsive buying among female undergraduate students. A sample of 799 Chinese female undergraduate students (mean age = 19.86 years, SD = 1.63) were recruited to complete questionnaires measuring passive SNS usage, upward social comparison on SNS, state anxiety, and online compulsive buying. After controlling for online shopping experience, the results showed that passive SNS usage was positively associated with online compulsive buying; upward social comparison and state anxiety partially mediated this link, which contained three mediating pathways – the separate mediating effect of upward social comparison and state anxiety, and the sequential mediating effect of upward social comparison and state anxiety. These findings can advance our understanding of how passive SNS usage is related to online compulsive buying among female undergraduate students. Limitations and implications of this study are discussed.

Under the perspective of self-perception theory and objectification theory, this study aims to examine the association between selfie-posting on social networking sites (SNSs) and exercise for weight control among Chinese young women, as well as the mediating role of body surveillance. A sample of 467 Chinese female students with a BMI lower than 24 were recruited. Participants voluntarily completed questionnaires assessing their selfie-posting behavior on SNSs, body surveillance, and their weight control motivation for exercise. The results show that selfie-posting on SNSs is positively associated with exercise for weight control, and that body surveillance significantly mediates this association. The results suggest that interventions targeting selfie behaviors on SNSs may be an effective way to prevent unhealthy exercise motivations, such as exercise for weight control, among young women with a low BMI.

We present here the draft genome sequence for Leishmania (Viannia) guyanensis. The isolate was obtained from a clinical case of cutaneous leishmaniasis in French Guiana., We present here the draft genome sequence for Leishmania (Viannia) guyanensis. The isolate was obtained from a clinical case of cutaneous leishmaniasis in French Guiana. Genomic DNA was sequenced using PacBio and MiSeq platforms.

Background The EMERGEncy ID Net Study Group is investigating whether advanced molecular tests (AMT) increase the detection of causative agents in the CSF of patients presenting with meningoencephalitis (ME). We report findings from a pilot study using AMT on 18 CSF samples from 10 US Urban Emergency Departments. The purpose of the pilot was to compare the performance of these four AMT to established clinical laboratory methods. Methods We investigated four AMT: (1) BioFire FilmArray ME Panel targeting 14 causative agents; (2) an in-house target-directed next generation sequencing assay targeting 25 agents; (3) a microarray capable of detecting >2,500 agents; and (4) deep metagenomic next generation sequencing. For targeted sequencing, loci from 12 DNA-based and 13 RNA-based pathogens were amplified from the extracts by multiplex PCR. All sequencing was performed on an Illumina MiSeq using 500 cycle v2 Reagent Kits. Reads from the targeted sequencing were aligned to the 25 specific reference target sequences using Bowtie2 while metagenomics reads were processed with the taxonomic sequence classifying software Kraken. For microarray analysis, Lawrence Livermore Microbial Detection Array v2 arrays were hybridized with Cy3-labeled DNA or cDNA. Scanned images of arrays were analyzed by CLiMax 3.1. Results Eight CSF samples had results positive for well-established causes of ME from prior testing (Table). The pilot study demonstrated none of the four AMT detected all causative agents in the eight CSF samples known to have well-established causes of ME. BioFire and targeted sequencing performed best, both detecting 6/8, metagenomics deep sequencing detected 3/8, and microarray detected 1/8. Conclusion Despite the sophistication of AMT, they cannot detect pathogens they do not target, that are present in small numbers, or that have been eliminated from the CSF by the immune response. Despite the theoretical potential for microarray and metagenomic sequencing to detect thousands of different agents, the agents probably must be present at high levels for detection. Disclosures All authors: No reported disclosures.

We report on the fluorescence properties and the combined effects of energy diffusion and energy transfer in polyfluorene nanoparticles doped with a variety of fluorescent dyes. As the doping host, polyfluorene possesses extraordinary "light harvesting" ability, resulting in higher per-particle brightness as compared to dye-loaded silica nanoparticles of similar dimensions. Both the steady-state fluorescence spectra and time-resolved fluorescence measurements indicate highly efficient energy transfer from the host polymer to the acceptor dye molecules. A model that takes into account the combined effects of energy diffusion, Förster transfer, and particle size was developed. Comparisons of experimental data to the model results elucidate the importance of particle size and energy diffusion within the polymer in determining the optical properties of the doped conjugated polymer nanoparticles. Fluorescence quantum yields of ~40% and peak extinction coefficients of 1.5 × 10(9) M(-1)cm(-1) were determined for aqueous suspensions of ~30 nm diameter polymer nanoparticles doped with perylene or coumarin 6 (2 wt %). Photobleaching experiments indicate that energy transfer phenomena strongly influence the photostability of these dye-doped nanoparticles. Significant features of these nanoparticles include the high brightness, highly red-shifted emission spectrum, and excellent photostability, which are promising for biological labeling and sensing applications. In addition, the nanoparticles are a useful model system for studying energy transfer in dense, nanostructured, multichromophoric systems.

Hepatitis C is a major public health problem in the United States and worldwide. Outbreaks of hepatitis C virus (HCV) infections associated with unsafe injection practices, drug diversion, and other exposures to blood are difficult to detect and investigate. Molecular analysis has been frequently used in the study of HCV outbreaks and transmission chains; helping identify a cluster of sequences as linked by transmission if their genetic distances are below a previously defined threshold.

Many computational science applications utilize complex workflow patterns that generate an intricately connected set of output files for subsequent analysis. Some types of applications, such as rare event sampling, additionally require guaranteed completion of all subtasks for analysis, and place significant demands on the workflow management and execution environment. SciFlow is a user interface built over the Hadoop infrastructure that provides a framework to support the complex process and data interactions and guaranteed completion requirements of scientific workflows. It provides an efficient mechanism for building a parallel scientific application with dataflow patterns, and enables the design, deployment, and execution of data intensive, many-task computing tasks on a Hadoop platform. The design principles of this framework emphasize simplicity, scalability and fault-tolerance. A case study using the forward flux sampling rare event simulation application validates the functionality, reliability and effectiveness of the framework.

Spermine synthase (SMS) is an enzyme which function is to convert spermidine into spermine. It was shown that gene defects resulting in amino acid changes of the wild type SMS cause Snyder-Robinson syndrome, which is a mild-to-moderate mental disability associated with osteoporosis, facial asymmetry, thin habitus, hypotonia, and a nonspecific movement disorder. These disease-causing missense mutations were demonstrated, both in silico and in vitro, to affect the wild type function of SMS by either destabilizing the SMS dimer/monomer or directly affecting the hydrogen bond network of the active site of SMS. In contrast to these studies, here we report an artificial engineering of a more efficient SMS variant by transferring sequence information from another organism. It is confirmed experimentally that the variant, bearing four amino acid substitutions, is catalytically more active than the wild type. The increased functionality is attributed to enhanced monomer stability, lowering the pKa of proton donor catalytic residue, optimized spatial distribution of the electrostatic potential around the SMS with respect to substrates, and increase of the frequency of mechanical vibration of the clefts presumed to be the gates toward the active sites. The study demonstrates that wild type SMS is not particularly evolutionarily optimized with respect to the reaction spermidine → spermine. Having in mind that currently there are no variations (non-synonymous single nucleotide polymorphism, nsSNP) detected in healthy individuals, it can be speculated that the human SMS function is precisely tuned toward its wild type and any deviation is unwanted and disease-causing., Author Summary Proteins are constantly subjected to evolutionary pressure to assure the organism's survival and reproduction. At the same time, the proteins' amino acid sequence undergoes mutations, some of which may cause diseases while others may be reflecting natural differences within the population (non-synonymous single nucleotide polymorphism, nsSNP). In this study we examine the human spermine synthase (HsSMS), for which currently there are no nsSNPs, while rare disease mutations are known to cause Snyder-Robinson syndrome. What is so special with this protein? Maybe the HsSMS is so well optimized for its function that any change of the wild type sequence should be degrading its performance. To check such a possibility, we engineered a mutant of HsSMS with enhanced stability, electrostatic and mechanical properties. The mutant was confirmed experimentally to be a better enzyme than the wild type. Thus, the HsSMS is not evolutionally optimized with respect to its enzymatic reaction, its amino acid sequence differs only in sick individuals and so far its sequence was found to be identical in all healthy individuals. Therefore, it can be speculated that the HsSMS function is precisely tuned toward the wild type characteristics such so any deviation is unwanted and is disease-causing.