Targeted Assembly of Short Sequence Reads

As next-generation sequence (NGS) production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole genome data sets in their entirety. Rather, NGS data sets can be mined for the presence of sequence variants of interest by localized assembly, which is a faster, easier, and more accurate approach. We present TASR, a streamlined assembler that interrogates very large NGS data sets for the presence of specific variants, by only considering reads within the sequence space of input target sequences provided by the user. The NGS data set is searched for reads with an exact match to all possible short words within the target sequence, and these reads are then assembled strin-gently to generate a consensus of the target and flanking sequence. Typically, variants of a particular locus are provided as different target sequences, and the presence of the variant in the data set being interrogated is revealed by a successful assembly outcome. However, TASR can also be used to find unknown sequences that flank a given target. We demonstrate that TASR has utility in finding or confirming ge-nomic mutations, polymorphism, fusion and integration events. Targeted assembly is a powerful method for interrogating large data sets for the presence of sequence variants of interest. TASR is a fast, flexible and easy to use tool for targeted assembly

Mechanistic studies of reactive oxygen species mediated electrochemical radical reactions of alkyl iodides

Mechanistic studies of a reactive oxygen species mediated electrochemical radical reaction of alkyl iodides are described. Hydroxyl radicals and ozone are identified to be the active species involved in the formation of alkyl radicals under mildly reducing potential (�1.0 V vs. Ag QRE) in buffered acidic conditions (pH 3.6)

An inducible transgene expression system for regulated phenotypic modification of human embryonic stem cells

Self-renewing pluripotent human embryonic stem (hES) cells are capable of regenerating such non-dividing cells as neurons and cardiomyocytes for therapies and can serve as an excellent experimental model for studying early human development. Both the spatial and temporal relationships of gene expression play a crucial role in determining differentiation; to obtain a better understanding of hES cell differentiation, it will be necessary to establish an inducible system in hES cells that enables specific transgene(s) to reversibly and conditionally express (1) at specific levels and (2) at particular time points during development. Using lentivirus (LV)-mediated gene transfer and a tetracycline-controlled trans-repressor (TR), we first established in hES cells a doxycycline (DOX)-inducible expression system of green fluorescent protein (GFP) to probe its reversibility and kinetics. Upon the addition of DOX, the percentage of GFP + hES cells increased time dependently: The time at which 50% of all green cells appeared (T 50 on) was 119.5 ± 3.2 h; upon DOX removal, GFP expression declined with a half-time (T 50 off) of 127.7 ± 3.9 h and became completely silenced at day 8. Both the proportion and total mean fluorescence intensity (MFI) were dose-dependent (EC 50 = 24.5 ± 2.2 ng/ml). The same system when incorporated into murine (m) ES cells similarly exhibited reversible dose-dependent responses with a similar sensitivity (EC 50 =49.5 ± 8.5 ng/ml), but the much faster kinetics (T 50 on = 35.5 ± 5.5 h, T 50 off = 71.5 ± 2.4 hours). DOX-induced expression of the Kir2.1 channels in mES and hES cells led to robust expression of the inwardly rectifying potassium (K +) current and thereby hyperpolarized the resting membrane potential (RMP). We conclude that the LV-inducible system established presents a unique tool for probing differentiation. © 2008 Mary Ann Liebert, Inc.published_or_final_versio

Illuminating Choices for Library Prep: A Comparison of Library Preparation Methods for Whole Genome Sequencing of Cryptococcus neoformans Using Illumina HiSeq.

The industry of next-generation sequencing is constantly evolving, with novel library preparation methods and new sequencing machines being released by the major sequencing technology companies annually. The Illumina TruSeq v2 library preparation method was the most widely used kit and the market leader; however, it has now been discontinued, and in 2013 was replaced by the TruSeq Nano and TruSeq PCR-free methods, leaving a gap in knowledge regarding which is the most appropriate library preparation method to use. Here, we used isolates from the pathogenic fungi Cryptococcus neoformans var. grubii and sequenced them using the existing TruSeq DNA v2 kit (Illumina), along with two new kits: the TruSeq Nano DNA kit (Illumina) and the NEBNext Ultra DNA kit (New England Biolabs) to provide a comparison. Compared to the original TruSeq DNA v2 kit, both newer kits gave equivalent or better sequencing data, with increased coverage. When comparing the two newer kits, we found little difference in cost and workflow, with the NEBNext Ultra both slightly cheaper and faster than the TruSeq Nano. However, the quality of data generated using the TruSeq Nano DNA kit was superior due to higher coverage at regions of low GC content, and more SNPs identified. Researchers should therefore evaluate their resources and the type of application (and hence data quality) being considered when ultimately deciding on which library prep method to use

Reaction pathways and mechanisms of the electrochemical degradation of phenol on different electrodes

Laboratory experiments were carried out on the kinetics and pathways of the electrochemical (EC) degradation of phenol at three different types of anodes, Ti/SnO2-Sb, Ti/RuO2, and Pt. Although phenol was oxidised by all of the anodes at a current density of 20 mA/cm2 or a cell voltage of 4.6 V, there was a considerable difference between the three anode types in the effectiveness and performance of EC organic degradation. Phenol was readily mineralized at the Ti/SnO2-Sb anode, but its degradation was much slower at the Ti/RuO2 and Pt anodes. The analytical results of high-performance liquid chromatography (HPLC) and gas chromatography coupled with mass spectrometry (GC/MS) indicated that the intermediate products of EC phenol degradation, including benzoquinone and organic acids, were subsequently oxidised rapidly by the Ti/SnO2-Sb anode, but accumulated in the cells of Ti/RuO2 and Pt. There was also a formation of dark-coloured polymeric compounds and precipitates in the solutions electrolyzed by the Ti/RuO2 and Pt anodes, which was not observed for the Ti/SnO 2-Sb cells. It is argued that anodic property not only affects the reaction kinetics of various steps of EC organic oxidation, but also alters the pathway of phenol electrolysis. Favourable surface treatment, such as the SnO2-Sb coating, provides the anode with an apparent catalytic function for rapid organic oxidation that is probably brought about by hydroxyl radicals generated from anodic water electrolysis. © 2005 Elsevier Ltd. All rights reserved.postprin

Microbial community analysis of fresh and old microbial biofilms on Bayon Temple sandstone of Angkor Thom, Cambodia

The temples of Angkor monuments including Angkor Thom and Bayon in Cambodia and surrounding countries were exclusively constructed using sandstone. They are severely threatened by biodeterioration caused by active growth of different microorganisms on the sandstone surfaces, but knowledge on the microbial community and composition of the biofilms on the sandstone is not available from this region. This study investigated the microbial community diversity by examining the fresh and old biofilms of the biodeteriorated bas-relief wall surfaces of the Bayon Temple by analysis of 16S and 18S rRNA gene sequences. The results showed that the retrieved sequences were clustered in 11 bacterial, 11 eukaryotic and two archaeal divisions with disparate communities (Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria; Alveolata, Fungi, Metazoa, Viridiplantae; Crenarchaeote, and Euyarchaeota). A comparison of the microbial communities between the fresh and old biofilms revealed that the bacterial community of old biofilm was very similar to the newly formed fresh biofilm in terms of bacterial composition, but the eukaryotic communities were distinctly different between these two. This information has important implications for understanding the formation process and development of the microbial diversity on the sandstone surfaces, and furthermore to the relationship between the extent of biodeterioration and succession of microbial communities on sandstone in tropic region. © 2010 The Author(s).published_or_final_versionSpringer Open Choice, 01 Dec 201

Capturing brain‐cognition relationship: Integrating task‐based fMRI across tasks markedly boosts prediction and test‐retest reliability

Capturing individual differences in cognition is central to human neuroscience. Yet our ability to estimate cognitive abilities via brain MRI is still poor in both prediction and reliability. Our study tested if this inability can be improved by integrating MRI signals across the whole brain and across modalities, including task-based functional MRI (tfMRI) of different tasks along with other non-task MRI modalities, such as structural MRI, resting-state functional connectivity. Using the Human Connectome Project (n = 873, 473 females, after quality control), we directly compared predictive models comprising different sets of MRI modalities (e.g., seven tasks vs. non-task modalities). We applied two approaches to integrate multimodal MRI, stacked vs. flat models, and implemented 16 combinations of machine-learning algorithms. The stacked model integrating all modalities via stacking Elastic Net provided the best prediction (r = 0.57), relatively to other models tested, as well as excellent test-retest reliability (ICC=∼.85) in capturing general cognitive abilities. Importantly, compared to the stacked model integrating across non-task modalities (r = 0.27), the stacked model integrating tfMRI across tasks led to significantly higher prediction (r = 0.56) while still providing excellent test-retest reliability (ICC=∼.83). The stacked model integrating tfMRI across tasks was driven by frontal and parietal areas and by tasks that are cognition-related (working-memory, relational processing, and language). This result is consistent with the parieto-frontal integration theory of intelligence. Accordingly, our results contradict the recently popular notion that tfMRI is not reliable enough to capture individual differences in cognition. Instead, our study suggests that tfMRI, when used appropriately (i.e., by drawing information across the whole brain and across tasks and by integrating with other modalities), provides predictive and reliable sources of information for individual differences in cognitive abilities, more so than non-task modalities

Web Service Discovery in a Semantically Extended UDDI Registry: the Case of FUSION

Service-oriented computing is being adopted at an unprecedented rate, making the effectiveness of automated service discovery an increasingly important challenge. UDDI has emerged as a de facto industry standard and fundamental building block within SOA infrastructures. Nevertheless, conventional UDDI registries lack means to provide unambiguous, semantically rich representations of Web service capabilities, and the logic inference power required for facilitating automated service discovery. To overcome this important limitation, a number of approaches have been proposed towards augmenting Web service discovery with semantics. This paper discusses the benefits of semantically extending Web service descriptions and UDDI registries, and presents an overview of the approach put forward in project FUSION, towards semantically-enhanced publication and discovery of services based on SAWSDL

A second Cretaceous ornithuromorph bird from the Changma Basin, Gansu Province, Northwestern China

Finely-bedded lacustrine deposits of the Aptian (Lower Cretaceous) Xiagou Formation exposed in the Changma Basin of Gansu Province, northwestern China, have yielded numerous fossil vertebrate remains, including approximately 100 avian specimens. Though the majority of these birds appear referable to the ornithuromorph Gansus yumenensis, a number of enantiornithine fossils have also been recovered. Here we report on a specimen consisting of a complete, three-dimensionally preserved sternum, furcula, and sternal ribs that represents a second ornithuromorph taxon from the Xiagou Formation at Changma. The fossil exhibits morphologies that distinguish it from all previously-known Xiagou birds and demonstrate that it represents a derived non-ornithurine member of Ornithuromorpha. Though it is morphologically distinct from the equivalent elements of all other described ornithuromorphs, the material is too incomplete to justify the erection of a new taxon. Nonetheless, it increases the taxonomic diversity of the Xiagou avifauna, thereby expanding our knowledge of Early Cretaceous avian diversity and evolution