Universal primers for HBV genome DNA amplification across subtypes: a case study for designing more effective viral primers

<p>Abstract</p> <p>Background</p> <p>The highly heterogenic characteristic of viruses is the major obstacle to efficient DNA amplification. Taking advantage of the large number of virus DNA sequences in public databases to select conserved sites for primer design is an optimal way to tackle the difficulties in virus genome amplification.</p> <p>Results</p> <p>Here we use hepatitis B virus as an example to introduce a simple and efficient way for virus primer design. Based on the alignment of HBV sequences in public databases and a program BxB in Perl script, our method selected several optimal sites for HBV primer design. Polymerase chain reaction showed that compared with the success rate of the most popular primers for whole genome amplification of HBV, one set of primers for full length genome amplification and four sets of walking primers showed significant improvement. These newly designed primers are suitable for most subtypes of HBV.</p> <p>Conclusion</p> <p>Researchers can extend the method described here to design universal or subtype specific primers for various types of viruses. The BxB program based on multiple sequence alignment not only can be used as a separate tool but also can be integrated in any open source primer design software to select conserved regions for primer design.</p

Retraction: Universal primers for HBV genome DNA amplification across subtypes: a case study for designing more effective viral primers

Abstract This is a retraction of the article submitted by Zhang et al. Virology J 2007, 4:92</p

Ultrafast carrier dynamics of aluminum-doped silicon film irradiated by femtosecond laser pulse

An aluminum-doped p-type polycrystalline silicon film was fabricated on a glass substrate using magnetron sputtering. The ultrafast carrier dynamics of the silicon film were studied via its femtosecond transient reflectivity characteristics. The analysis of the transient reflectivity signal shows that the fast component of the relaxation time Ƭf is shorter than that found in previous studies with undoped silicon. The dynamics of the free carrier response and state filling dominate Ƭf in this sample, and owing to the existence of defects and boundaries, the state filling effect significantly increases Ƭf. On a longer time scale, the Auger recombination and carrier diffusion dominate the relaxation process. The slow component of the relaxation time Ƭfs is also shorter than any previously reported values for undoped silicon films

A Novel Richardson-Lucy Model with Dictionary Basis and Spatial Regularization for Isolating Isotropic Signals.

Diffusion-weighted magnetic resonance imaging is a non-invasive imaging method that has been increasingly used in neuroscience imaging over the last decade. Partial volume effects (PVEs) exist in sampling signal for many physical and actual reasons, which lead to inaccurate fiber imaging. We overcome the influence of PVEs by separating isotropic signal from diffusion-weighted signal, which can provide more accurate estimation of fiber orientations. In this work, we use a novel response function (RF) and the correspondent fiber orientation distribution function (fODF) to construct different signal models, in which case the fODF is represented using dictionary basis function. We then put forward a new index Piso, which is a part of fODF to quantify white and gray matter. The classic Richardson-Lucy (RL) model is usually used in the field of digital image processing to solve the problem of spherical deconvolution caused by highly ill-posed least-squares algorithm. In this case, we propose an innovative model integrating RL model with spatial regularization to settle the suggested double-models, which improve noise resistance and accuracy of imaging. Experimental results of simulated and real data show that the proposal method, which we call iRL, can robustly reconstruct a more accurate fODF and the quantitative index Piso performs better than fractional anisotropy and general fractional anisotropy

Universal primers for HBV genome DNA amplification across subtypes: a case study for designing more effective viral primers-1

<p><b>Copyright information:</b></p><p>Taken from "Universal primers for HBV genome DNA amplification across subtypes: a case study for designing more effective viral primers"</p><p>http://www.virologyj.com/content/4/1/92</p><p>Virology Journal 2007;4():92-92.</p><p>Published online 24 Sep 2007</p><p>PMCID:PMC2099425.</p><p></p>1059 bp), FA4-L/FA4-L' and FA4-R (amplicon size: 1072 bp) in red arrows represent the four sets of walking primers for fragment amplification. Here we select "CTTTTTC" of X ORF as the start point. FA1-L' and FA4-L' are degenerate primers

Universal primers for HBV genome DNA amplification across subtypes: a case study for designing more effective viral primers-0

<p><b>Copyright information:</b></p><p>Taken from "Universal primers for HBV genome DNA amplification across subtypes: a case study for designing more effective viral primers"</p><p>http://www.virologyj.com/content/4/1/92</p><p>Virology Journal 2007;4():92-92.</p><p>Published online 24 Sep 2007</p><p>PMCID:PMC2099425.</p><p></p>leotide, otherwise outputs a '-'. The cutoff was set to (0.05, 1), and the step length is 0.05. The frequency is listed in the left box and the nucleotides are in the right box

Universal primers for HBV genome DNA amplification across subtypes: a case study for designing more effective viral primers-2

<p><b>Copyright information:</b></p><p>Taken from "Universal primers for HBV genome DNA amplification across subtypes: a case study for designing more effective viral primers"</p><p>http://www.virologyj.com/content/4/1/92</p><p>Virology Journal 2007;4():92-92.</p><p>Published online 24 Sep 2007</p><p>PMCID:PMC2099425.</p><p></p>mplicon size: 1059 bp), FA1-L/FA1-L' and FA1-R (amplicon size: 1014 bp), FA4-L/FA4-L' and FA4-R (amplicon size: 1072 bp), FA2-L and FA2-R (amplicon size: 1074 bp) primer pairs respectively. Sample 3~7 are for full length genome amplification primers (WA-L and WA-R) testing (amplicon size: 3181 bp)