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Yuri S. Fantin Alexey D. Neverov Alexander V. Favorov Maria V. Alvarez-Figueroa Svetlana I. Braslavskaya Maria A. Gordukova Inga V. Karandashova Konstantin V. Kuleshov Anna I. Myznikova Maya S. Polishchuk Denis A. Reshetov Yana A. Voiciehovskaya Andrei A. Mironov Vladimir P. Chulanov 《PloS one》2013,8(1)
Sanger sequencing is a common method of reading DNA sequences. It is less expensive than high-throughput methods, and it is appropriate for numerous applications including molecular diagnostics. However, sequencing mixtures of similar DNA of pathogens with this method is challenging. This is important because most clinical samples contain such mixtures, rather than pure single strains. The traditional solution is to sequence selected clones of PCR products, a complicated, time-consuming, and expensive procedure. Here, we propose the base-calling with vocabulary (BCV) method that computationally deciphers Sanger chromatograms obtained from mixed DNA samples. The inputs to the BCV algorithm are a chromatogram and a dictionary of sequences that are similar to those we expect to obtain. We apply the base-calling function on a test dataset of chromatograms without ambiguous positions, as well as one with 3–14% sequence degeneracy. Furthermore, we use BCV to assemble a consensus sequence for an HIV genome fragment in a sample containing a mixture of viral DNA variants and to determine the positions of the indels. Finally, we detect drug-resistant Mycobacterium tuberculosis strains carrying frameshift mutations mixed with wild-type bacteria in the pncA gene, and roughly characterize bacterial communities in clinical samples by direct 16S rRNA sequencing. 相似文献
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Molecular Biology - Water soluble chlorophyll-binding proteins (WSCPs) of higher plants differ from most proteins containing chlorophyll or bacteriochlorophyll in that they are soluble in watr and... 相似文献
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Geert Zegels Geert AA Van Raemdonck Edmond P Coen Wiebren AA Tjalma Xaveer WM Van Ostade 《Proteome science》2009,7(1):17-16
Background
Cervical-vaginal fluid (CVF) plays an important role in the prevention of gynecological infections, although little is known about the contribution of CVF proteins to the immunity of the lower female genital tract. In order to analyze the protein composition of human CVF, we used CVF samples that are routinely collected during colposcopy, but are usually discarded. Since these samples are available in large quantities we aimed to analyze their usefulness for proteomics experiments. The samples were analyzed using different prefractionation techniques (ultrafiltration and C4(RP)-LC protein separation) followed by C18(RP)-LC peptide separation and identification by MALDI-TOF-TOF mass spectrometry. To determine the reproducibility of this proteomics platform we analyzed three technical replicates. Using spectral counting, protein abundances were estimated in a semiquantitative way. We also compared the results obtained in this study with those from previous studies derived from patients with different physiological conditions in order to determine an overlapping protein set. 相似文献8.
This investigation examined the exposure of Egyptian infants to Aflatoxin M1 (AfM1) and of lactating mothers to Aflatoxin B1, using AfM1 in human milk as a biomarker for exposure to AfB1. The presence of ochratoxin A (OA) in human milk was also investigated to determine the levels of infants exposure to OA
from human milk. The results indicated that AfM1 was found in 66 (55 %) of 120 human milk samples with a mean of 0.3 ± 0.53 ng/mL (range 0.02 to 2.09 ng/mL). OA was found
in 43 (35.8 %) of 120 human milk samples with a mean of 21.1 ± 13.7 ng/mL (range 5.07 to 45.01 ng/mL), which will cause a
daily intake of OA from human milk exceeding the suggested tolerable dose of 5 ng/kg-1 of OA body weight. On the other side AfM1 was found in 25 % of blood samples (5 out of 20 samples), at a mean of 1.18 ng/mL, but it was detected only in one urine
sample (1 out of 20 samples). OA was detected only in 2 out of 13 blood samples (15.4 %) with an average 3.67 ng/mL. Whereas
OA was not detected in all analyzed urine samples. 相似文献
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AA Smith 《Biotechnic & histochemistry》2014,89(3):215-219
One can find the optimal antibody dilution for immunostaining by repeated staining on the same tissue section by using a less dilute antibody for each attempt. Using secondary antibody and horseradish peroxidase conjugated to a dextran polymer, a section stained repeatedly with several dilutions of antibody appears as good as a section stained with only the last dilution. 相似文献