Low-complexity and highly robust barcodes for error-rich single molecular sequencing.

DNA barcodes are frequently corrupted due to insertion, deletion, and substitution errors during DNA synthesis, amplification and sequencing, resulting in index hopping. In this paper, we propose a new DNA barcode construction scheme that combines a cyclic block code with a predetermined pseudo-random sequence bit by bit to form bit pairs, and then converts the bit pairs to bases, i.e., the DNA barcodes. Then, we present a barcode identification scheme for noisy sequencing reads, which uses a combination of cyclic shifting and traditional dynamic programming to mark the insertion and deletion positions, and then performs erasure-and-error-correction decoding on the corrupted codewords. Furthermore, we verify the identification error rate of barcodes for multiple errors and evaluate the reliability of the barcodes in DNA context. This method can be easily generalized for constructing long barcodes, which may be used in scenarios with serious errors. Simulation results show that the bit error rate after identifying insertions/deletions is greatly reduced using the combination of cyclic shift and dynamic programming compared to using dynamic programming only. It indicates that the proposed method can effectively improve the accuracy for estimating insertion/deletion errors. And the overall identification error rate of the proposed method is lower than 10 - 5 when the probability of each base mutation is less than 0.1, which is the typical scenario in third-generation sequencing.

Impact of Cold Ischemic Time and Freeze-Thaw Cycles on RNA, DNA and Protein Quality in Colorectal Cancer Tissues Biobanking.

Tissue-derived RNA, DNA and protein samples become more and more crucial for molecular detection in clinical research, personalized and targeted cancer therapy. This study evaluated how to biobanking colorectal tissues through examining the influences of cold ischemic time and freeze-thaw cycles on RNA, DNA and protein integrity. Here, 144 pairs of tumor and normal colorectal tissues were used to investigate the impact of cold ischemic times (0-48h) on RNA, DNA and protein integrity at on ice or room temperature conditions. Additionally, 45 pairs of tissues experienced 0-9 freeze-thaw cycles, and then the RNA, DNA and protein quality were analyzed. On ice, RNA, DNA and protein from colorectal tumor and normal tissues were all stable up to 48h after surgery. At room temperature, RNA in colorectal tumor and normal tissues began to degrade at 8h and 24h, respectively. Meanwhile, the tumor tissues DNA degradation occurred at 24h after surgery at room temperature. Similarly, the protein expression level of tumor and normal tissues began to change at 24h after the surgery at room temperature. Interestingly, tissue RNA and DNA remained stable even after 9 freeze-thaw cycles, whereas the proteins levels were remarkably changed after 7 freeze-thaw cycles. This study provided a useful evidence on how to store human colorectal tissues for biobanking. Preserving the surgical colorectal tissue on ice was an effective way to prevent RNA, DNA and protein degradation. Importantly, more than 7 repeated freeze-thaw cycles were not recommended for colorectal tissues.

Electrophoretic deposition of carbon nanotube on reticulated vitreous carbon for hexavalent chromium removal in a biocathode microbial fuel cell.

For Cr(VI)-removal microbial fuel cell (MFC), a more efficient biocathode in MFCs is required to improve the Cr(VI) removal and electricity generation. RVC-CNT electrode was prepared through the electrophoretic deposition of carbon nanotube (CNT) on reticulated vitreous carbon (RVC). The power density of MFC with an RVC-CNT electrode increased to 132.1 ± 2.8 mW m-2, and 80.9% removal of Cr(VI) was achieved within 48 h; compared to only 44.5% removal of Cr(VI) in unmodified RVC. Cyclic voltammetry, energy-dispersive spectrometry and X-ray photoelectron spectrometry showed that the RVC-CNT electrode enhanced the electrical conductivity and the electron transfer rate; and provided more reaction sites for Cr(VI) reduction. This approach provides process simplicity and a thickness control method for fabricating three-dimensional biocathodes to improve the performance of MFCs for Cr(VI) removal.

High efficiency microbial electrosynthesis of acetate from carbon dioxide by a self-assembled electroactive biofilm.

Microbial electrosynthesis (MES) is a biocathode-driven process, producing high-value chemicals from CO2. Here, an in situ self-assembled graphene oxide (rGO)/biofilm was constructed, in MES, for high efficient acetate production. GO has been successfully reduced by electroautotrophic bacteria for the first time. An increase, of 1.5 times, in the volumetric acetate production rate, was obtained by self-assembling rGO/biofilm, as compared to the control group. In MES with rGO/biofilm, a volumetric acetate production rate of 0.17gl-1d-1 has been achieved, 77% of the electrons consumed, were recovered and the final acetate concentration reached 7.1gl-1, within 40days. A three-dimensional rGO/biofilm was constructed enabling highly efficient electron transfer rates within biofilms, and between biofilm and electrode, demonstrating that the development of 3D electroactive biofilms, with higher extracellular electron transfer rates, is an effective approach to improving MES efficiency.

Characterization of a novel N-acetylneuraminic acid lyase favoring industrial N-acetylneuraminic acid synthesis.

N-Acetylneuraminic acid lyase (NAL, E.C. number 4.1.3.3) is a Class I aldolase that catalyzes the reversible aldol cleavage of N-acetylneuraminic acid (Neu5Ac) from pyruvate and N-acetyl-D-mannosamine (ManNAc). Due to the high Neu5Ac cleavage activity in most isozyme forms, the enzyme catalyzes the rate-limiting step of two biocatalytic reactions producing Neu5Ac in industry. We report the biochemical characterization of a novel NAL from a "GRAS" (General recognized as safe) strain C. glutamicum ATCC 13032 (CgNal). Compared to all previously reported NALs, CgNal exhibited the lowest kcat/Km value for Neu5Ac and highest kcat/Km values for ManNAc and pyruvate, which makes CgNal favor industrial Neu5Ac synthesis process in a non-equilibrium condition. The recombinant CgNal reached the highest expression level (480 mg/L culture), and the highest reported yield of Neu5Ac was achieved (194 g/L, 0.63 M). All these unique properties make CgNal a promising biocatalyst for industrial Neu5Ac biosynthesis. Additionally, although showing the best Neu5Ac synthesis activity among the NAL family, CgNal is more related to dihydrodipicolinate synthase (DHDPS) by phylogenetic analysis. The activities of CgNal towards both NAL's and DHDPS' substrates are fairly high, which indicates CgNal a bi-functional enzyme. The sequence analysis suggests that CgNal might have adopted a unique set of residues for substrates recognition.

Engineered cytidine triphosphate synthetase with reduced product inhibition.

Cytidine triphosphate (CTP) synthetase (CTPS) (EC number 6.3.4.2) is a key enzyme involved in de novo synthesis of CTP. It catalyzes the rate-limiting step of the process due to the product inhibition effects on the enzyme. In this study, a novel CTPS from Corynebacterium glutamicum ATCC 13032 (CgCTPS) was cloned, expressed and characterized. A series of mutagenesis in its N-terminal ammonia ligase (ALase) domain was performed in order to reduce CTP product inhibition. All single mutation variants (D160E, E162A, E168K) lowered product inhibition by lowering the enzyme's binding affinity for CTP. The homology model of CgCTPS showed that D160E mutant caused steric hindrance for the pyrimidine ring of CTP stacking, E162A disrupted the hydrogen bond between CTP ribose and side chain and D168K caused minor localized structure perturbations of CTP binding pocket. The triple mutant of CTPS (D160E-E162A-E168K) with halved Km, doubled Vmax and the 23.5-fold increased IC50 for CTP shows a potential for use in industrial-scale CTP production by its better performance in enzyme kinetics and product inhibition.

A microsecond microfluidic mixer for characterizing fast biochemical reactions.

Analysis of fast biochemical reactions requires rapid mixing of solutions. Micromixers can achieve uniform mixing of solutions in a short time and have been recognized as an attractive tool to analyze fast reactions. However, it is still a challenge to design mixers with simple structure and short dead time. Here, a zigzag turbulent micromixer was developed with a rapid mixing time of 16 µs at sample consumption of 10 µL/s. Numerical simulations and confocal imaging validated this result. Application of the chemiluminescence (CL) reaction demonstrated the use of this mixer in analyzing the kinetic process of the CL reaction. In comparison to the turbulent micromixers reported previously, this zigzag mixer has advantages of short dead time, simple structure and low sample consumption. We anticipate the developed mixer to be a useful tool in studying biochemical kinetics or be integrated to Lab-on-a-chip device as a pretreatment functional unit.

Are randomized trials conducted in China or India biased? A comparative empirical analysis.

CONTEXT: China and India are two emerging forces in undertaking randomized clinical trials. The quality of trials from these countries may affect not just their substantial populations but also their contribution to health policy throughout the world. OBJECTIVE: The objectives of this study were to describe and contrast the quality and biases in reports of trials conducted in China and India with a set of "gold standard" trials reported in leading European and North American journals. METHOD: A systematic review and comparative empirical analysis of randomized controlled trial reports published in selected Chinese, Indian, and European or North American medical journals were performed. Quality was assessed against a subset of criteria from the CONSORT statement. We compared the rate of reporting of positive outcomes in clinical trials to describe potential bias. RESULT: In total, 307 Chinese papers, 117 Indian papers, and 304 Western papers were included. Reports of Indian trials were slightly better than Chinese papers on the trial reporting quality indicators and much better than Chinese papers on reporting patients' ethical issues. However, the gold standard Western trial reports scored considerably higher on all quality criteria. Chinese papers were substantially more likely to report statistically significant results (odds ratio [OR]=2.96, 95% confidence interval [CI]=2.23-3.94; P<0.0001). Indian trials reported a similar rate of positive results to Western papers (OR=0.92, 95% CI=0.69-1.24; P=0.59). CONCLUSION: Reporting of trials in major Chinese and Indian journals falls short of that achieved in the gold standard Western journals we appraised and may reflect underlying inadequacies in the design and conduct of these trials. Chinese trials appear biased and may selectively report positive outcomes while ignoring neutral or negative outcomes. Trialists and journal editors in China and India should adopt the CONSORT reporting guidelines, should ensure that a primary outcome is prespecified and reported, and should ensure that analysis is conducted according to the intention-to-treat principle. Ethical questions in the conduct of trials in China must be addressed.

An assessment of the quality of randomised controlled trials conducted in China.

BACKGROUND: Despite the rapid increase in research in China, little is known about the quality of clinical trials conducted there. METHODS: A systematic review and critical appraisal of randomised controlled trials (RCTs) conducted in China and published in 2004 was undertaken to describe their characteristics, assess the quality of their reporting, and where possible, the quality of their conduct. Randomised controlled trials in all disease areas and types of interventions, which took place in China and included Chinese citizens were identified using PubMed and hand searching the Journal Series of the Chinese Medical Association. Quality was assessed against a subset of criteria adapted from the CONSORT statement. RESULTS: Three hundred and seven RCTs were included. One hundred and ninety-nine (64.8%) failed to report methods of randomization and 254 (82.4%) did not mention blinding of either participants or investigators. Reporting of baseline characteristics, primary outcome and length of follow-up was inadequate in a substantial proportion of studies. Fewer than 11% of RCTs mentioned ethical approval and only 18.0% adequately discussed informed consent. However, dropout rates were very favourable with nearly 44% of trials reporting a zero dropout rate. CONCLUSION: Reporting of RCTs in China requires substantial improvement to meet the targets of the CONSORT statement. The conduct of Chinese RCTs cannot be directly inferred from the standard of reporting; however without good reporting the methods of the trials cannot be clearly ascertained.

[Probe into characteristics of Taraxacum mongolicum ultramicro-power].

OBJECTIVE: To observe and study the tissue characteristics of T. mongolicum ultramicro-power and dissolving-out characteristics of effective compositions. METHOD: By microscopic observation and thin-layer chromatography. RESULT: Nearly all cell walls of T. mongolicum are broken and dissolving-out characteristics of effective compositions are remarkably improved, after it is ultramicro-porphyrized.

[Study on pharmacology of ultra-fine particles compound Rehmannia].

OBJECTIVE: To observe pharmacological difference between ultra-fine particles of six ingredient Rehmannia pill and traditional six ingredient Rehmannia pill. METHOD: Pharmacokinetic index was measured by death rate, and pharmacology actions were compared by anti-fatigue, hypoglycemic, clearance rate of charcoal particle, hypoxia resistance and serum hemolysin concentration experiment. RESULT: Dose-effection was significant and pharmacology actions were more than traditional six ingredient Rehmannia pill in six ingredient Rehmannia pill. CONCLUSION: Ultra-fine particles of six ingredient Rehmannia pill are better than traditional six ingredient Rehmannia pill in bioavailability and pharmacology actions, and the weight of pill is reduced while efficacy is enhenced by ultra-fine particles.