A novel method for assessing the 3-D orientation accuracy of inertial/magnetic sensors

A novel method for assessing the accuracy of inertial/magnetic sensors is presented. The method, referred to as the “residual matrix” method, is advantageous because it decouples the sensor's error with respect to Earth's gravity vector (attitude residual error: pitch and roll) from the sensor's error with respect to magnetic north (heading residual error), while remaining insensitive to singularity problems when the second Euler rotation is close to ±90°. As a demonstration, the accuracy of an inertial/magnetic sensor mounted to a participant's forearm was evaluated during a reaching task in a laboratory. Sensor orientation was measured internally (by the inertial/magnetic sensor) and externally using an optoelectronic measurement system with a marker cluster rigidly attached to the sensor's enclosure. Roll, pitch and heading residuals were calculated using the proposed novel method, as well as using a common orientation assessment method where the residuals are defined as the difference between the Euler angles measured by the inertial sensor and those measured by the optoelectronic system. Using the proposed residual matrix method, the roll and pitch residuals remained less than 1° and, as expected, no statistically significant difference between these two measures of attitude accuracy was found; the heading residuals were significantly larger than the attitude residuals but remained below 2°. Using the direct Euler angle comparison method, the residuals were in general larger due to singularity issues, and the expected significant difference between inertial/magnetic sensor attitude and heading accuracy was not present.     

Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia

Microbial hydrolysis of polysaccharides is critical to ecosystem functioning and is of great interest in diverse biotechnological applications, such as biofuel production and bioremediation. Here we demonstrate the use of a new, efficient approach to recover genomes of active polysaccharide degraders from natural, complex microbial assemblages, using a combination of fluorescently labeled substrates, fluorescence-activated cell sorting, and single cell genomics. We employed this approach to analyze freshwater and coastal bacterioplankton for degraders of laminarin and xylan, two of the most abundant storage and structural polysaccharides in nature. Our results suggest that a few phylotypes of Verrucomicrobia make a considerable contribution to polysaccharide degradation, although they constituted only a minor fraction of the total microbial community. Genomic sequencing of five cells, representing the most predominant, polysaccharide-active Verrucomicrobia phylotype, revealed significant enrichment in genes encoding a wide spectrum of glycoside hydrolases, sulfatases, peptidases, carbohydrate lyases and esterases, confirming that these organisms were well equipped for the hydrolysis of diverse polysaccharides. Remarkably, this enrichment was on average higher than in the sequenced representatives of Bacteroidetes, which are frequently regarded as highly efficient biopolymer degraders. These findings shed light on the ecological roles of uncultured Verrucomicrobia and suggest specific taxa as promising bioprospecting targets. The employed method offers a powerful tool to rapidly identify and recover discrete genomes of active players in polysaccharide degradation, without the need for cultivation.     

Quantitative Deep Sequencing Reveals Dynamic HIV-1 Escape and Large Population Shifts during CCR5 Antagonist Therapy In Vivo

High-throughput sequencing platforms provide an approach for detecting rare HIV-1 variants and documenting more fully quasispecies diversity. We applied this technology to the V3 loop-coding region of env in samples collected from 4 chronically HIV-infected subjects in whom CCR5 antagonist (vicriviroc [VVC]) therapy failed. Between 25,000–140,000 amplified sequences were obtained per sample. Profound baseline V3 loop sequence heterogeneity existed; predicted CXCR4-using populations were identified in a largely CCR5-using population. The V3 loop forms associated with subsequent virologic failure, either through CXCR4 use or the emergence of high-level VVC resistance, were present as minor variants at 0.8–2.8% of baseline samples. Extreme, rapid shifts in population frequencies toward these forms occurred, and deep sequencing provided a detailed view of the rapid evolutionary impact of VVC selection. Greater V3 diversity was observed post-selection. This previously unreported degree of V3 loop sequence diversity has implications for viral pathogenesis, vaccine design, and the optimal use of HIV-1 CCR5 antagonists.     

Rapid evaluation and quality control of next generation sequencing data with FaQCs

Background

Next generation sequencing (NGS) technologies that parallelize the sequencing process and produce thousands to millions, or even hundreds of millions of sequences in a single sequencing run, have revolutionized genomic and genetic research. Because of the vagaries of any platform’s sequencing chemistry, the experimental processing, machine failure, and so on, the quality of sequencing reads is never perfect, and often declines as the read is extended. These errors invariably affect downstream analysis/application and should therefore be identified early on to mitigate any unforeseen effects.

Results

Here we present a novel FastQ Quality Control Software (FaQCs) that can rapidly process large volumes of data, and which improves upon previous solutions to monitor the quality and remove poor quality data from sequencing runs. Both the speed of processing and the memory footprint of storing all required information have been optimized via algorithmic and parallel processing solutions. The trimmed output compared side-by-side with the original data is part of the automated PDF output. We show how this tool can help data analysis by providing a few examples, including an increased percentage of reads recruited to references, improved single nucleotide polymorphism identification as well as de novo sequence assembly metrics.

Conclusion

FaQCs combines several features of currently available applications into a single, user-friendly process, and includes additional unique capabilities such as filtering the PhiX control sequences, conversion of FASTQ formats, and multi-threading. The original data and trimmed summaries are reported within a variety of graphics and reports, providing a simple way to do data quality control and assurance.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0366-2) contains supplementary material, which is available to authorized users.     

Recruiting Human Microbiome Shotgun Data to Site-Specific Reference Genomes

The human body consists of innumerable multifaceted environments that predispose colonization by a number of distinct microbial communities, which play fundamental roles in human health and disease. In addition to community surveys and shotgun metagenomes that seek to explore the composition and diversity of these microbiomes, there are significant efforts to sequence reference microbial genomes from many body sites of healthy adults. To illustrate the utility of reference genomes when studying more complex metagenomes, we present a reference-based analysis of sequence reads generated from 55 shotgun metagenomes, selected from 5 major body sites, including 16 sub-sites. Interestingly, between 13% and 92% (62.3% average) of these shotgun reads were aligned to a then-complete list of 2780 reference genomes, including 1583 references for the human microbiome. However, no reference genome was universally found in all body sites. For any given metagenome, the body site-specific reference genomes, derived from the same body site as the sample, accounted for an average of 58.8% of the mapped reads. While different body sites did differ in abundant genera, proximal or symmetrical body sites were found to be most similar to one another. The extent of variation observed, both between individuals sampled within the same microenvironment, or at the same site within the same individual over time, calls into question comparative studies across individuals even if sampled at the same body site. This study illustrates the high utility of reference genomes and the need for further site-specific reference microbial genome sequencing, even within the already well-sampled human microbiome.     

Synthesis of Racemic 5-Substituted 1-(2,3-Dihydroxypropyl)-6-azauracils and Their Isosteric Isomers

Abstract

Acyclic nucleoside analogues of antiviral DHPA and HPMPA have been prepared. Coupling of silylated 6-azauracils with benzyl glycidyl ether and stannic chloride followed by the deprotection with boron trichloride gave 1-(2,3-dihydroxypropyl)-6-azauracils (3) in good overall yields. Reaction of silylated 6-azauracil and epichlorohydrin with or without catalytic stannic chloride afforded 1-(2-chloro-3-hydroxypropyl)-6-azauracil (4a) and 1-(3-chloro-2-hydroxypropyl)-6-azauracil (6a) respectively. Coupling of silylated 6-azaisocytosine under the same reaction conditions provided 1-(2,3-dihydroxypropyl)-6-azaisocytosine (9) and 1-(2-chloro-3-hydroxypropyl)-6-azaisocytosine (10) respectively. None of the compounds exhibited significant antiviral activity against herpes simplex viruses.     

Free-radical-mediated protein inactivation and recovery during protein photoencapsulation

Photoencapsulation of protein therapeutics is very attractive for preparing biomolecule-loaded hydrogels for a variety of biomedical applications. However, detrimental effects of highly active radical species generated during photoencapsulation must be carefully evaluated to maintain efficient hydrogel cross-linking while preserving the structure and bioactivity of encapsulated biomolecules. Here, we examine the free-radical-mediated inactivation and incomplete release of proteins from photocurable hydrogels utilizing lysozyme as a conservative model system. Various protein photoencapsulation conditions were tested to determine the factors affecting lysozyme structural integrity and bioactivity. It was found that a portion of the lysozyme becomes conjugated to polymer chains at high photoinitiator concentrations and long polymerization times. We also found that the more hydrophilic photoinitiator Irgacure-2959 (I-2959, 2-hydroxy-1-[4-(hydroxyethoxy)phenyl]-2-methyl-1-propanone) causes more damage to lysozyme compared to the hydrophobic photoinitiator Irgacure-651 (I-651, 2,2-dimethoxy-2-phenylacetophenone), even though I-2959 has been previously shown to be more cytocompatible. Furthermore, while nonacrylated PEG provides only limited protection from the denaturing free radicals that are present during hydrogel curing, acrylated PEG macromers effectively preserve lysozyme structural integrity and bioactivity in the presence of either photoinitiator. Overall, these findings indicate how photopolymerization conditions (e.g., photoinitiator type and concentration, UV exposure time, etc.) must be optimized to obtain a functional hydrogel device that can preserve protein bioactivity and provide maximal protein release.