RnaseIII and T4 Polynucleotide Kinase Sequence Biases and Solutions During RNA-Seq Library Construction

Background: RNA-seq is a next generation sequencing method with a wide range of applications including single nucleotide polymorphism (SNP) detection, splice junction identification, and gene expression level measurement. However, the RNA-seq sequence data can be biased during library constructions resulting in incorrect data for SNP, splice junction, and gene expression studies. Here, we developed new library preparation methods to limit such biases. Results: A whole transcriptome library prepared for the SOLiD system displayed numerous read duplications (pile-ups) and gaps in known exons. The pile-ups and gaps of the whole transcriptome library caused a loss of SNP and splice junction information and reduced the quality of gene expression results. Further, we found clear sequence biases for both 5' and 3' end reads in the whole transcriptome library. To remove this bias, RNaseIII fragmentation was replaced with heat fragmentation. For adaptor ligation, T4 Polynucleotide Kinase (T4PNK) was used following heat fragmentation. However, its kinase and phosphatase activities introduced additional sequence biases. To minimize them, we used OptiKinase before T4PNK. Our study further revealed the specific target sequences of RNaseIII and T4PNK. Conclusions: Our results suggest that the heat fragmentation removed the RNaseIII sequence bias and significantly reduced the pile-ups and gaps. OptiKinase minimized the T4PNK sequence biases and removed most of the remaining pile-ups and gaps, thus maximizing the quality of RNA-seq data.National Institute on Alcohol Abuse and Alcoholism (NIAAA) AA12404, AA019382, AA020926, AA016648National Institutes of Health (NIH) R01 GM088344Waggoner Center for Alcohol and Addiction Researc

Soliton Resonances for MKP-II

Using the second flow - the Derivative Reaction-Diffusion system, and the third one of the dissipative SL(2,R) Kaup-Newell hierarchy, we show that the product of two functions, satisfying those systems is a solution of the modified Kadomtsev-Petviashvili equation in 2+1 dimension with negative dispersion (MKP-II). We construct Hirota's bilinear representation for both flows and combine them together as the bilinear system for MKP-II. Using this bilinear form we find one and two soliton solutions for the MKP-II. For special values of parameters our solution shows resonance behaviour with creation of four virtual solitons. Our approach allows one to interpret the resonance soliton as a composite object of two dissipative solitons in 1+1 dimensions.Comment: 11 pages, 2 figures, Talk on International Conference "Nonlinear Physics. Theory and Experiment. III", 24 June-3 July, 2004, Gallipoli(Lecce), Ital

When is an error not a prediction error? An electrophysiological investigation

A recent theory holds that the anterior cingulate cortex (ACC) uses reinforcement learning signals conveyed by the midbrain dopamine system to facilitate flexible action selection. According to this position, the impact of reward prediction error signals on ACC modulates the amplitude of a component of the event-related brain potential called the error-related negativity (ERN). The theory predicts that ERN amplitude is monotonically related to the expectedness of the event: It is larger for unexpected outcomes than for expected outcomes. However, a recent failure to confirm this prediction has called the theory into question. In the present article, we investigated this discrepancy in three trial-and-error learning experiments. All three experiments provided support for the theory, but the effect sizes were largest when an optimal response strategy could actually be learned. This observation suggests that ACC utilizes dopamine reward prediction error signals for adaptive decision making when the optimal behavior is, in fact, learnable

Damped Population Oscillation in a Spontaneously Decaying Two-Level Atom Coupled to a Monochromatic Field

We investigate the time evolution of atomic population in a two-level atom driven by a monochromatic radiation field, taking spontaneous emission into account. The Rabi oscillation exhibits amplitude damping in time caused by spontaneous emission. We show that the semiclassical master equation leads in general to an overestimation of the damping rate and that a correct quantitative description of the damped Rabi oscillation can thus be obtained only with a full quantum mechanical theory.Comment: 5 pages, 5 figure

Measurement of spontaneous emission from a two-dimensional photonic band gap defined microcavity at near-infrared wavelengths

An active, photonic band gap-based microcavity emitter in the near infrared is demonstrated. We present direct measurement of the spontaneous emission power and spectrum from a microcavity formed using a two-dimensional photonic band gap structure in a half wavelength thick slab waveguide. The appearance of cavity resonance peaks in the spectrum correspond to the photonic band gap energy. For detuned band gaps, no resonances are observed. For devices with correctly tuned band gaps, a two-time enhancement of the extraction efficiency was demonstrated compared to detuned band gaps and unpatterned material

Photonic bandgap disk laser

A two-dimensional photonic crystal defined hexagonal disk laser which relies on Bragg reflection rather than the total internal reflection as in traditional microdisk lasers is described. The devices are fabricated using a selective etch to form free standing membranes suspended in air. Room temperature lasing at 1650nm for a 150nm thick, ~15μm wide cavity fabricated in InP/GaAsP is demonstrated with pulsed optical pumping

Weighted feature selection criteria for visual servoing of a telerobot

Because of the continually changing environment of a space station, visual feedback is a vital element of a telerobotic system. A real time visual servoing system would allow a telerobot to track and manipulate randomly moving objects. Methodologies for the automatic selection of image features to be used to visually control the relative position between an eye-in-hand telerobot and a known object are devised. A weighted criteria function with both image recognition and control components is used to select the combination of image features which provides the best control. Simulation and experimental results of a PUMA robot arm visually tracking a randomly moving carburetor gasket with a visual update time of 70 milliseconds are discussed

Lasers incorporating 2D photonic bandgap mirrors

Semiconductor lasers incorporating a 2D photonic lattice as a one end mirror in a Fabry-Perot cavity are demonstrated. The photonic lattice is a 2D hexagonal close-packed array with a lattice constant of 220 nm. Pulsed threshold currents of 110 mA were observed from a 180 μm laser

The Carboxyl-Terminal Segment of Apolipoprotein A-V Undergoes a Lipid-Induced Conformational Change

Apolipoprotein (apo) A-V is a 343-residue, multidomain protein that plays an important role in regulation of plasma triglyceride homeostasis. Primary sequence analysis revealed a unique tetraproline sequence (Pro293-Pro296) near the carboxyl terminus of the protein. A peptide corresponding to the 48-residue segment beyond the tetraproline motif was generated from a recombinant apoA-V precursor wherein Pro295 was replaced by Met. Cyanogen bromide cleavage of the precursor protein, followed by negative affinity chromatography, yielded a purified peptide. Nondenaturing polyacrylamide gel electrophoresis verified that apoA-V(296-343) solubilizes phospholipid vesicles, forming a relatively heterogeneous population of reconstituted high-density lipoprotein with Stokes’ diameters\u3e17 nm. At the same time, apoA-V(296-343) failed to bind a spherical lipoprotein substrate in vitro. Far-UV circular dichroism spectroscopy revealed the peptide is unstructured in buffer yet adopts significant R-helical secondary structure in the presence of the lipid mimetic solvent trifluoroethanol (TFE; 50% v/v). Heteronuclear multidemensional NMR spectroscopy experiments were conducted with uniformly 15N- and 15N/13C-labeled peptide in 50% TFE. Peptide backbone assignment and secondary structure prediction using TALOSþ reveal the peptide adopts R-helix secondary structure from residues 309 to 334. In TFE, apoA-V(296-343) adopts an extended amphipathic R-helix, consistent with a role in lipoprotein binding as a component of full-length apoA-V