A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation

BACKGROUND

Pyrosequencing techniques allow scientists to perform prokaryotic genome sequencing to achieve the draft genomic sequences within a few days. However, the assemblies with shotgun sequencing are usually composed of hundreds of contigs. A further multiplex PCR procedure is needed to fill all the gaps and link contigs into complete chromosomal sequence, which is the basis for prokaryotic comparative genomic studies. In this article, we study various pyrosequencing strategies by simulated assembling from 100 prokaryotic genomes.

FINDINGS

Simulation study shows that a single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) can produce: 1) ~90% of 100 assemblies with < 10 scaffolds and ~95% of 100 assemblies with < 150 contigs; 2) average contig N50 size is over 331 kb; 3) average single base accuracy is > 99.99%; 4) average false gene duplication rate is < 0.7%; 5) average false gene loss rate is < 0.4%.

CONCLUSIONS

A single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) is a cost-effective way for prokaryotic whole genome sequencing. This strategy provides solution to produce high quality draft assemblies for most of prokaryotic organisms within days. Due to the small number of assembled scaffolds, the following multiplex PCR procedure (for gap filling) would be easy. As a result, large scale prokaryotic whole genome sequencing projects may be finished within weeks.

Phenoloxidase in the scallop Chlamys farreri: purification and antibacterial activity of its reaction products generated in vitro

Phenoloxidase (PO) was purified from hemocytes of the scallop Chlamys farreri using native-PAGE and gel permeation column chromatography, and then substrate specificity and antibacterial activity generated from reaction products of purified PO were analyzed. The results showed purified PO had a molecular mass of 576 kDa in native-PAGE and 53 kDa in denatured PAGE, and could catalyze the substrates L-3,4-dihydroxyphenylalanine (L-DOPA), dopamine, catechol and hydroquinone suggesting it is a type of p-diphenoloxidase. Using dopamine as a substrate, PO reaction products significantly inhibited the growth of Vibrio alginolyticus, Vibrio parahaemolyticus and Aeromonas salmonicida. No significant inhibition was found in Streptococcus dysgalactiae, Streptococcus iniae, Micrococcus lysodeikticus and Edwardsiella tarda. When L-DOPA was used as a substrate, significant inhibition occurred in A. salmonicida only.

Analyses of CDC2L1 gene mutations in keloid tissue

BACKGROUND

Keloid disease is the result of a deregulated wound-healing process. Loss of heterozygosity on chromosome 1p36 has been shown to be associated with keloid formation in humans. The cell division cycle 2-like 1 (CDC2L1) gene is known to be essential for eukaryotic cell-cycle control, and has also been mapped to 1p36.

AIM

To verify the possible association between keloid disease and somatic mutation of the CDC2L1 gene on chromosome 1p36.

METHODS

Mutations of the CDC2L1 gene in keloid and healthy skin tissues were screened by denaturing high-performance liquid chromatography, and confirmed by DNA sequencing analysis.

RESULTS

Of the 27 patients with keloid assessed, 21 had mutations. The most prevalent exon affected was exon 7, with 15 patients affected: 10 patients (37%) had a base G deletion at codon 247, and 12 patients (44.4%) had a base A insertion at codon 267 (6 patients (25.9%) had both mutations). The remaining six patients had mutations in exons 11 (codon 433; n = 3) and 14 (codon 520; n = 3). Comparing the keloid skin tissues with the healthy control skin tissues, significant differences were seen between the groups for the base G deletion at codon 247 and the base A insertion at codon 267.

CONCLUSIONS

We have identified a correlation between two exon 7 mutations of the CDC2L1 gene and keloid disease. A further study of protein-kinase activity should be conducted to confirm the functionality of the CDC2L1 gene in the prevention of scar formation.

6-10× pyrosequencing is a practical approach for whole prokaryote genome studies

Next generation 454 pyrosequencing technology for whole bacterial genome sequencing involves a deep sequencing strategy with at least 15-20× in depth proposed by official protocols but usually done with over 20× in practices. In this study, we carried out a comprehensive evaluation of quality of the de novo assemblies based on realistic pyrosequencing simulated data from 1480 prokaryote genomes and 7 runs of machine-generated data. Our results demonstrated that for most of the prokaryote genomes, 6-10× sequencing in qualified runs with 400 bp reads could produce high quality draft assembly (>98% genome coverage, <100 contigs with N50 size >100 kb, single base accuracy >99.99, indel error rate <0.01%, false gene loss/duplication rate <0.5%). Our study proves the power of low depth pyrosequencing strategy, which provides a cost-effective way for sequencing whole prokaryote genomes in a short time and enables further studies in microbial population diversity and comparative genomics.

Treatment of cervical esophageal perforation caused by foreign bodies

In this article, we reviewed our experience of treatment of cervical esophageal perforation caused by foreign bodies. Between 1980 and 2010, 42 patients were included in this study. There were 18 women and 24 men with a median age of 54 years. We divided the patients into three groups: the patients whose foreign bodies could not be extracted by otolaryngologists using endoscope (n= 7), the patients who had some signs of abscess formation but the foreign bodies had been extracted using endoscope (n= 25), and the patients who had no signs of abscess formation and the foreign bodies had been extracted (n= 10). We treated the patients of the three groups with surgical treatment, drainage alone, and conservative treatment, respectively. The outcome of the current series was favorable. Our experience suggested that most of the cases can be treated conservatively or by drainage alone. If the foreign bodies of the esophagus could not be extracted using endoscope, surgical treatment including the removal of the foreign bodies, primary repair, and drainage should be performed.

Distinguishing amyloid fibril structures in Alzheimer's disease (AD) by two-dimensional ultraviolet (2DUV) spectroscopy

Understanding the aggregation mechanism of amyloid fibrils and characterizing their structures are important steps in the investigation of several neurodegenerative disorders associated with the misfolding of proteins. We report a simulation study of coherent two-dimensional chiral signals of three NMR structures of Aβ protein fibrils associated with Alzheimer's Disease, two models for Aβ(8-40) peptide wild-type (WT) and one for the Iowa (D23N) Aβ(15-40) mutant. Both far-ultraviolet (FUV) signals (λ = 190-250 nm), which originate from the backbone nπ* and ππ* transitions, and near-ultraviolet (NUV) signals (λ ≥ 250 nm) associated with aromatic side chains (Phe and Tyr) show distinct cross-peak patterns that can serve as novel signatures for the secondary structure.

Ambient pressure proton transfer mass spectrometry: detection of amines and ammonia

An instrument to detect gaseous amines and ammonia is described, and representative data from an urban site and a laboratory setting are presented. The instrument, an Ambient pressure Proton transfer Mass Spectrometer (AmPMS), consists of a chemical ionization and drift region at atmospheric pressure coupled to a standard quadrupole mass spectrometer. Calibrations show that AmPMS sensitivity is good for amines, and AmPMS backgrounds were suitably determined by diverting sampled air through a catalytic converter. In urban air at a site in Atlanta, amines were detected at subpptv levels for methyl and dimethyl amine which were generally at a low abundance of <1 and ∼3 pptv, respectively. Trimethyl amine (or isomers) was on average about 4 pptv in the morning and increased to 15 pptv in the afternoon, while triethyl amine (or isomers or amides) increased to 25 pptv on average in the late afternoon. The background levels for the 4 and 5 carbon amines and ammonia were high, and data are very limited for these species. Improvements in detecting amines and ammonia from a smog chamber were evident due to improvements in AmPMS background determination; notably dimethyl amine and its OH oxidation products were followed along with impurity ammonia and other species. Future work will focus on accurate calibration standards and on improving the sample gas inlet.

Supercontinuum generation in quasi-phase-matched LiNbO3 waveguide pumped by a Tm-doped fiber laser system

We demonstrate self-referencing of a Tm-doped fiber oscillator-amplifier system by performing octave-spanning supercontinuum generation in a periodically poled lithium niobate waveguide. We model the supercontinuum generation numerically and show good agreement with the experiment.

Predictors of relapse in chronic hepatitis B after discontinuation of anti-viral therapy

BACKGROUND

Optimal duration of anti-viral therapy in chronic hepatitis B virus (HBV) infection remains unclear.

AIM

To investigate factors that could predict relapse after stopping anti-viral agents.

METHODS

Chronic hepatitis B patients who were treated with anti-viral agents (lamivudine, adefovir, entecavir) and have stopped the treatment were recruited. Anti-viral agents were stopped according to the recommendations of the Asian Pacific Association for the Study of the Liver. Virological relapse was defined as an increase in serum HBV DNA to >1000 copies/mL after discontinuation of treatment.

RESULTS

Eighty-four (69 treatment naïve and 15 lamivudine resistant) patients were eligible for this study. Thirty-seven patients developed virological relapse at 4.3 ± 2.9 (range 1-11) months after discontinuation of therapy. The 1-year cumulative probability of virological relapse was 42% and 47% in HBeAg (hepatitis B e antigen)-positive (n = 41) and HBeAg (hepatitis B e antigen)-negative (n = 43) patients, respectively. On multivariate analysis by Cox proportional hazard model, pre-existing lamivudine resistance, delayed suppression of HBV DNA to undetectable level during anti-viral therapy and to a higher HBsAg (hepatitis B surface antigen) level at the end of treatment were associated with virological relapse. Twelve of the 15 (80%) lamivudine resistant patients developed virological relapse. Among the 11 treatment naïve patients who had HBsAg ≤ 2 log IU/mL at the end of treatment, 1 (9%) of them had virological relapse.

CONCLUSIONS

Treatment cessation among lamivudine resistant patients is associated with high risk of virological relapse. Serum HBsAg level at the end of treatment and rate of HBV DNA suppression can provide supplementary information to guide the timing of stopping anti-viral drugs.

Predictors of relapse in chronic hepatitis B after discontinuation of anti-viral therapy

BACKGROUND

Optimal duration of anti-viral therapy in chronic hepatitis B virus (HBV) infection remains unclear.

AIM

To investigate factors that could predict relapse after stopping anti-viral agents.

METHODS

Chronic hepatitis B patients who were treated with anti-viral agents (lamivudine, adefovir, entecavir) and have stopped the treatment were recruited. Anti-viral agents were stopped according to the recommendations of the Asian Pacific Association for the Study of the Liver. Virological relapse was defined as an increase in serum HBV DNA to >1000 copies/mL after discontinuation of treatment.

RESULTS

Eighty-four (69 treatment naïve and 15 lamivudine resistant) patients were eligible for this study. Thirty-seven patients developed virological relapse at 4.3 ± 2.9 (range 1-11) months after discontinuation of therapy. The 1-year cumulative probability of virological relapse was 42% and 47% in HBeAg (hepatitis B e antigen)-positive (n = 41) and HBeAg (hepatitis B e antigen)-negative (n = 43) patients, respectively. On multivariate analysis by Cox proportional hazard model, pre-existing lamivudine resistance, delayed suppression of HBV DNA to undetectable level during anti-viral therapy and to a higher HBsAg (hepatitis B surface antigen) level at the end of treatment were associated with virological relapse. Twelve of the 15 (80%) lamivudine resistant patients developed virological relapse. Among the 11 treatment naïve patients who had HBsAg ≤ 2 log IU/mL at the end of treatment, 1 (9%) of them had virological relapse.

CONCLUSIONS

Treatment cessation among lamivudine resistant patients is associated with high risk of virological relapse. Serum HBsAg level at the end of treatment and rate of HBV DNA suppression can provide supplementary information to guide the timing of stopping anti-viral drugs.

Effects of recipient oocyte age and interval from fusion to activation on development of buffalo (Bubalus bubalis) nuclear transfer embryos derived from fetal fibroblasts

The objective was to investigate the effect of recipient oocyte age and the interval from activation to fusion on developmental competence of buffalo nuclear transfer (NT) embryos. Buffalo oocytes matured in vitro for 22 h were enucleated by micromanipulation under the spindle view system, and a fetal fibroblast (pretreated with 0.1 μg/mL aphidicolin for 24 h, followed by culture for 48 h in 0.5% fetal bovine serum) was introduced into the enucleated oocyte, followed by electrofusion. Both oocytes and NT embryos were activated by exposure to 5 μM ionomycin for 5 min, followed by culture in 2 mM 6-dimethyl-aminopurine for 3 h. When oocytes matured in vitro for 28, 29, 30, 31, or 32 h were activated, more oocytes matured in vitro for 30 h developed into blastocysts in comparison with oocytes matured in vitro for 32 h (31.3 vs 19.9%, P < 0.05). When electrofusion was induced 27 h after the onset of oocyte maturation, the cleavage rate (78.0%) was higher than that of electrofusion induced at 28 h (67.2%, P < 0.05), and the blastocyst yield (18.1%) was higher (P < 0.05) than that of electrofusion induced at 25 or 26 h (7.4 and 8.5%, respectively). A higher proportion of NT embryos activated at 3 h after electrofusion developed to the blastocyst stage (18.6%) in comparison with NT embryos activated at 1 h (6.0%), 2 h (8.3%), or 4 h (10.6%) after fusion (P < 0.05). No recipient was pregnant 60 d after transfer of blastocysts developed from NT embryos activated at 1 h (0/8), 2 h (0/10), or 4 h (0/9) after fusion. However, 3 of 16 recipients were pregnant following transfer of blastocysts developed from the NT embryos activated at 3 h after fusion, and two of these recipients maintained pregnancy to term. We concluded that the developmental potential of buffalo NT embryos was related to recipient oocyte age and the interval from fusion to activation.