A divide-and-conquer algorithm for large-scale de novo transcriptome assembly through combining small assemblies from existing algorithms

While the continued development of high-throughput sequencing has facilitated studies of entire transcriptomes in non-model organisms, the incorporation of an increasing amount of RNA-Seq libraries has made de novo transcriptome assembly difficult. Although algorithms that can assemble a large amount of RNA-Seq data are available, they are generally very memory-intensive and can only be used to construct small assemblies. We develop a divide-and-conquer strategy that allows these algorithms to be utilized, by subdividing a large RNA-Seq data set into small libraries. Each individual library is assembled independently by an existing algorithm, and a merging algorithm is developed to combine these assemblies by picking a subset of high quality transcripts to form a large transcriptome. When compared to existing algorithms that return a single assembly directly, this strategy achieves comparable or increased accuracy as memory-efficient algorithms that can be used to process a large amount of RNA-Seq data, and comparable or decreased accuracy as memory-intensive algorithms that can only be used to construct small assemblies. Our divide-and-conquer strategy allows memory-intensive de novo transcriptome assembly algorithms to be utilized to construct large assemblies

The Rice Miniature Inverted Repeat Transposable Element mPing Is an Effective Insertional Mutagen in Soybean

Insertional mutagenesis of legume genomes such as soybean (Glycine max) should aid in identifying genes responsible for key traits such as nitrogen fixation and seed quality. The relatively low throughput of soybean transformation necessitates the use of a transposon-tagging strategy where a single transformation event will produce many mutations over a number of generations. However, existing transposon-tagging tools being used in legumes are of limited utility because of restricted transposition (Ac/Ds: soybean) or the requirement for tissue culture activation (Tnt1: Medicago truncatula). A recently discovered transposable element from rice (Oryza sativa), mPing, and the genes required for its mobilization, were transferred to soybean to determine if it will be an improvement over the other available transposon-tagging tools. Stable transformation events in soybean were tested for mPing transposition. Analysis of mPing excision at early and late embryo developmental stages revealed increased excision during late development in most transgenic lines, suggesting that transposition is developmentally regulated. Transgenic lines that produced heritable mPing insertions were identified, with the plants from the highest activity line producing at least one new insertion per generation. Analysis of the mPing insertion sites in the soybean genome revealed that features displayed in rice were retained including transposition to unlinked sites and a preference for insertion within 2.5 kb of a gene. Taken together these findings indicate that mPing has the characteristics necessary for an effective transposon-tagging resource

Virulence-related genotypic differences among Bacillus cereus ocular and gastrointestinal isolates and the relationship to endophthalmitis pathogenesis

BackgroundBacillus cereus (Bc) can cause self-limiting gastrointestinal infections, but when infecting the eye, can cause rapid and irreversible blindness. This study investigated whether clinical ocular and gastrointestinal Bc isolates differed in terms of virulence-related genotypes and endophthalmitis virulence.MethodsTwenty-eight Bc ocular, gastrointestinal, and laboratory reference isolates were evaluated. Hemolysis assays were performed to assess potential differences in hemolytic activity. The presence of twenty Bc virulence-related genes was assessed by PCR. A subset of ocular and gastrointestinal isolates differing in PCR positivity for 5 virulence genes was compared to strain ATCC14579 in an experimental murine model of endophthalmitis. At 8 hours post infection, retinal function was evaluated by electroretinography, and intraocular bacterial concentrations were determined by plate counts.ResultsGastrointestinal Bc isolates were more hemolytic than the Bc ocular isolates and ATCC14579 (p < 0.0001). Bc ocular isolates were more frequently PCR-positive for capK, cytK, hblA, hblC, and plcR compared to the gastrointestinal isolates (p ≤ 0.0002). In the endophthalmitis model, mean A-wave retention did not differ significantly between eyes infected with ATCC14579 and eyes infected with the selected ocular or gastrointestinal isolates (p ≥ 0.3528). Similar results were observed for mean B-wave retention (p ≥ 0.0640). Only one diarrheal isolate showed significantly greater B-wave retention when compared to ATCC14579 (p = 0.0303). No significant differences in mean A-wave (p ≥ 0.1535) or B-wave (p ≥ 0.0727) retention between the selected ocular and gastrointestinal isolates were observed. Intraocular concentrations of ATCC14579 were significantly higher than the selected ocular isolate and 3 of the gastrointestinal isolates (p ≤ 0.0303). Intraocular concentrations of the selected ocular isolate were not significantly different from the gastrointestinal isolates (p ≥ 0.1923).ConclusionsAmong the subset of virulence-related genes assessed, 5 were significantly enriched among the ocular isolates compared to gastrointestinal isolates. While hemolytic activity was higher among gastrointestinal isolates, retinal function retention and intraocular growth was not significantly different between the selected ocular and gastrointestinal isolates. These results suggest that Bc strains causing gastrointestinal infections, while differing from ocular isolates in hemolytic activity and virulence-related gene profile, are similarly virulent in endophthalmitis

Coordinated Quadrotor Unmanned Aerial Vehicles

The objective of this project is to design and implement coordinated estimation and control algorithms for a pair of quadrotor unmanned aerial vehicles (UAVs). These algorithms enable one of the UAVs to observe and reduce navigational uncertainty for the other UAV, which carries a relatively small number of sensors. The sensors installed include a LiDAR depth sensor and a camera. The commercially available 3DR Solo UAV is used as a platform. For each UAV, this platform is modified by attaching a Raspberry Pi embedded flight controller. A socket server is designed to enable communication between UAVs. The LQR and EKF tools from control theory are used to design the desired algorithms. The system is demonstrated via a flight test involving the two UAVs following a straight line trajectory

PCBs can diminish the influence of temperature on thyroid indices in rainbow trout (Oncorhynchus mykiss)

The influence of PCBs on the thyroid status of rainbow trout was assessed at various temperatures to identify if PCB mixtures, as well OH-PCBs produced via biotransformation of parent PCBs, can illicit thyroid effects in fish. Juvenile rainbow trout (Oncorhynchus mykiss) held at 8, 12 or 16 °C were exposed to dietary concentrations of an environmentally relevant mixture of PCBs for 30 days followed by a depuration phase. Two additional treatments at 12 °C included higher concentrations of PCBs (congeners 77, 126 and 169) known to induce CYP1A in fish (referred to as CYP1A treatment) and PCBs (congeners 87, 99, 101, 153, 180, 183 and 194) known to induce CYP2B in mammals (referred to as CYP2 treatment), to assess the influence of more biologically relevant PCB congeners on thyroid indices in fish. Growth rate and liver somatic index varied with water temperature (p \u3c 0.05) but did not differ between PCB exposed and control fish (p \u3e 0.05) and mortality was low in all treatments. Changes in some measures of thyroid status were apparent in PCB-exposed fish held in the 12 and 16 °C treatments while other measures showed no change in any treatment. The natural inverse relationship between thyroid epithelial cell height (TECH) and temperature, was diminished after 30 days of exposure to PCBs as the epithelial cell height in PCB-exposed fish was significantly augmented in the 12 and 16 °C treatments compared to controls at these temperatures (p \u3c 0.05). However, after 20 days of depuration, TECH values in the PCB exposed fish returned to control values. The natural linear gradient between T4 outer-ring deiodinase activity (ORD) and temperature was also diminished after 30 days of exposure to PCBs. PCB-exposed fish from the 16 °C treatment had significantly lower deiodinase activities (p \u3c 0.05) compared to controls at this temperature, but deiodinase activities returned to normal by day 20 of depuration. No differences were observed in T3 inner-ring deiodinase (IRD) activities and plasma concentrations of T3 and T4 in any of the treatments (p \u3e 0.05). EROD activity in fish from the CYP1A and CYP2 treatments were elevated compared to control and high dose PCB-exposed treatments (p \u3c 0.05), but the inclusion of CYP inducing congeners did not appear to influence any index of thyroid status. Results of this study suggest that exposure of rainbow trout to high concentrations of PCBs and/or OH-PCBs may alter some indices of thyroid status when water temperatures are high, but these changes are within the compensatory scope of the thyroid system based on no change in circulating hormone concentrations, growth rates or mortality. © 2007 Elsevier B.V. All rights reserved

Portraying fathers: Reproductive journeys in Malawi

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