毛细管阵列电泳与规模化DNA测序

 根据 10 0 80份基因组DNA测序的结果 ,讨论了毛细管阵列电泳测序方法的技术特点 ,并对影响测序结果的一些因素进行了分析。在此基础上与平板凝胶电泳方法进行比较 ,显示了毛细管阵列电泳的优点。同时也对大规模测序技术环节之间的协调进行了探讨 。     

From NGS assembly challenges to instability of fungal mitochondrial genomes: A case study in genome complexity

The presence of repetitive or non-unique DNA persisting over sizable regions of a eukaryotic genome can hinder the genome's successful de novo assembly from short reads: ambiguities in assigning genome locations to the non-unique subsequences can result in premature termination of contigs and thus overfragmented assemblies. Fungal mitochondrial (mtDNA) genomes are compact (typically less than 100 kb), yet often contain short non-unique sequences that can be shown to impede their successful de novo assembly in silico. Such repeats can also confuse processes in the cell in vivo. A well-studied example is ectopic (out-of-register, illegitimate) recombination associated with repeat pairs, which can lead to deletion of functionally important genes that are located between the repeats. Repeats that remain conserved over micro- or macroevolutionary timescales despite such risks may indicate functionally or structurally (e.g., for replication) important regions. This principle could form the basis of a mining strategy for accelerating discovery of function in genome sequences. We present here our screening of a sample of 11 fully sequenced fungal mitochondrial genomes by observing where exact k-mer repeats occurred several times; initial analyses motivated us to focus on 17-mers occurring more than three times. Based on the diverse repeats we observe, we propose that such screening may serve as an efficient expedient for gaining a rapid but representative first insight into the repeat landscapes of sparsely characterized mitochondrial chromosomes. Our matching of the flagged repeats to previously reported regions of interest supports the idea that systems of persisting, non-trivial repeats in genomes can often highlight features meriting further attention.     

Liquid chromatographic methods for the therapeutic drug monitoring of methotrexate as clinical decision support for personalized medicine: A brief review

Methotrexate (MTX) is an antifolate drug used for several diseases. Depending on the disease, MTX can be administered at low dose (LDMTX) in some autoimmune diseases, like rheumatoid arthritis, or at high dose (HDMTX) in some cancers, such as acute lymphoblastic leukemia. After absorption, MTX is metabolized in the liver to 7‐hydroxymethotrexate and in the intestine to 2,4‐diamino‐N10‐methylpteroic acid (DAMPA). Moreover, inside red blood cells, MTX is converted to active metabolites, MTX polyglutamates (MTXPGs), contributing to its pharmacodynamics. Owing to its narrow therapeutic range, and inter‐ and intra‐patient variability, either noneffectiveness and/or toxicity may occur. Because of the existence of a relationship between drug therapeutic outcome and its systemic concentration, therapeutic drug monitoring (TDM) may ensure the effectiveness and safety of MTX use. In order to monitor the optimization of patient clinical response profile, several analytical methods have been described for TDM in biological samples. These include liquid chromatography (LC) coupled with ultraviolet detection, fluorescence detection or mass spectrometry, each one presenting advantages and drawbacks. This paper reviews the most commonly used techniques for sample preparation and critically discusses the current LC methods applied for the TDM of MTX in biological samples, at LDMTX and HDMTX.     

Molecular deformation and free-solution electrophoresis of DNA-uncharged polymer conjugates at high field strengths: theoretical predictions Part 2: Stretching

DNA sequencing by electrophoresis can be dramatically sped up by overcoming the need for the sieving medium. Normally it is possible to separate DNA based on size in free solution; however, not end-labeled free-solution electrophoresis (ELFSE) uses a neutral drag-tag molecule to make it possible. In experiments to date, the drag-tag and DNA together form a random coil conformation; while with future generation drag-tags and high fields, deformation of this conformation may occur. In the first paper in this series we investigated the conditions under which the DNA and label become hydrodynamically distinct (or segregated), based on a theoretical approach developed for the electrophoresis of polyampholytes. In this paper we study further deformation wherein either the DNA and/or a polymeric label stretch. We show that deformation may dramatically improve the capabilities of ELFSE, especially when both the DNA and a polymeric drag-tag fully stretch; however, reaching these regimes will require extremely high field intensities, something that only microchip technologies may be able to achieve.     

Surrogate docking: structure-based virtual screening at high throughput speed

Summary Structure-based screening using fully flexible docking is still too slow for large molecular libraries. High quality docking of a million molecule library can take days even on a cluster with hundreds of CPUs. This performance issue prohibits the use of fully flexible docking in the design of large combinatorial libraries. We have developed a fast structure-based screening method, which utilizes docking of a limited number of compounds to build a 2D QSAR model used to rapidly score the rest of the database. We compare here a model based on radial basis functions and a Bayesian categorization model. The number of compounds that need to be actually docked depends on the number of docking hits found. In our case studies reasonable quality models are built after docking of the number of molecules containing 50 docking hits. The rest of the library is screened by the QSAR model. Optionally a fraction of the QSAR-prioritized library can be docked in order to find the true docking hits. The quality of the model only depends on the training set size – not on the size of the library to be screened. Therefore, for larger libraries the method yields higher gain in speed no change in performance. Prioritizing a large library with these models provides a significant enrichment with docking hits: it attains the values of 13 and 35 at the beginning of the score-sorted libraries in our two case studies: screening of the NCI collection and a combinatorial libraries on CDK2 kinase structure. With such enrichments, only a fraction of the database must actually be docked to find many of the true hits. The throughput of the method allows its use in screening of large compound collections and in the design of large combinatorial libraries. The strategy proposed has an important effect on efficiency but does not affect retrieval of actives, the latter being determined by the quality of the docking method itself. Electronic supplementary material is available at http://dx.doi.org/10.1007/s10822-005-9002-6.     

SnpFilt: A pipeline for reference-free assembly-based identification of SNPs in bacterial genomes

De novo assembly of bacterial genomes from next-generation sequencing (NGS) data allows a reference-free discovery of single nucleotide polymorphisms (SNP). However, substantial rates of errors in genomes assembled by this approach remain a major barrier for the reference-free analysis of genome variations in medically important bacteria. The aim of this report was to improve the quality of SNP identification in bacterial genomes without closely related references. We developed a bioinformatics pipeline (SnpFilt) that constructs an assembly using SPAdes and then removes unreliable regions based on the quality and coverage of re-aligned reads at neighbouring regions. The performance of the pipeline was compared against reference-based SNP calling for Illumina HiSeq, MiSeq and NextSeq reads from a range of bacterial pathogens including Salmonella, which is one of the most common causes of food-borne disease. The SnpFilt pipeline removed all false SNP in all test NGS datasets consisting of paired-end Illumina reads. We also showed that for reliable and complete SNP calls, at least 40-fold coverage is required. Analysis of bacterial isolates associated with epidemiologically confirmed outbreaks using the SnpFilt pipeline produced results consistent with previously published findings. The SnpFilt pipeline improves the quality of de-novo assembly and precision of SNP calling in bacterial genomes by removal of regions of the assembly that may potentially contain assembly errors. SnpFilt is available from https://github.com/LanLab/SnpFilt.     

Hippocampal regenerative medicine: neurogenic implications for addiction and mental disorders

Psychiatric illness is a prevalent and highly debilitating disorder, and more than 50% of the general population in both middle- and high-income countries experience at least one psychiatric disorder at some point in their lives. As we continue to learn how pervasive psychiatric episodes are in society, we must acknowledge that psychiatric disorders are not solely relegated to a small group of predisposed individuals but rather occur in significant portions of all societal groups. Several distinct brain regions have been implicated in neuropsychiatric disease. These brain regions include corticolimbic structures, which regulate executive function and decision making (e.g., the prefrontal cortex), as well as striatal subregions known to control motivated behavior under normal and stressful conditions. Importantly, the corticolimbic neural circuitry includes the hippocampus, a critical brain structure that sends projections to both the cortex and striatum to coordinate learning, memory, and mood. In this review, we will discuss past and recent discoveries of how neurobiological processes in the hippocampus and corticolimbic structures work in concert to control executive function, memory, and mood in the context of mental disorders.Subject terms: Adult neurogenesis, Addiction     

CRISPR‐Cas: From the Bacterial Adaptive Immune System to a Versatile Tool for Genome Engineering

The field of biology has been revolutionized by the recent advancement of an adaptive bacterial immune system as a universal genome engineering tool. Bacteria and archaea use repetitive genomic elements termed clustered regularly interspaced short palindromic repeats (CRISPR) in combination with an RNA‐guided nuclease (CRISPR‐associated nuclease: Cas) to target and destroy invading DNA. By choosing the appropriate sequence of the guide RNA, this two‐component system can be used to efficiently modify, target, and edit genomic loci of interest in plants, insects, fungi, mammalian cells, and whole organisms. This has opened up new frontiers in genome engineering, including the potential to treat or cure human genetic disorders. Now the potential risks as well as the ethical, social, and legal implications of this powerful new technique move into the limelight.     

Quantitative predictions for DNA two-dimensional display according to size and nucleotide sequence composition

2-D DNA display is a simple separation method that provides a fast and economical way of visualizing polymorphism and comparing genomes. The DNA fragments are separated first according to their size by standard gel electrophoresis and then according to their sequence composition using denaturing gradient gel electrophoresis. First developed by Fischer and Lerman (Cell 1979, 16, 191-200), this method has recently been used to distinguish strains within a bacterial species. The genomic restriction fragments are displayed as spots on a 2-D surface. Although most of the relevant physical mechanisms are understood, this technique is mostly empirical and remains essentially qualitative. In view of optimizing this procedure, we combine our understanding of the different physical mechanisms at play to develop a complete numerical model to predict the relative coordinates of the spots as a function of the corresponding DNA sequence and of the experimental conditions. We experimentally validate our model by predicting the outcome of a 2-D display of the lambda phage genome. It thus becomes possible to optimize in silico the experimental parameters, to predict whether specific mutations as well as yet undescribed genetic polymorphisms can be resolved, and to assist in interpreting the experimental data.     

Alpha‐Helical Fragaceatoxin C Nanopore Engineered for Double‐Stranded and Single‐Stranded Nucleic Acid Analysis

Nanopores are used in single‐molecule DNA analysis and sequencing. Herein, we show that Fragaceatoxin C (FraC), an α‐helical pore‐forming toxin from an actinoporin protein family, can be reconstituted in sphingomyelin‐free standard planar lipid bilayers. We engineered FraC for DNA analysis and show that the funnel‐shaped geometry allows tight wrapping around single‐stranded DNA (ssDNA), resolving between homopolymeric C, T, and A polynucleotide stretches. Remarkably, despite the 1.2 nm internal constriction of FraC, double‐stranded DNA (dsDNA) can translocate through the nanopore at high applied potentials, presumably through the deformation of the α‐helical transmembrane region of the pore. Therefore, FraC nanopores might be used in DNA sequencing and dsDNA analysis.     

Benzofurazane as a New Redox Label for Electrochemical Detection of DNA: Towards Multipotential Redox Coding of DNA Bases

Benzofurazane has been attached to nucleosides and dNTPs, either directly or through an acetylene linker, as a new redox label for electrochemical analysis of nucleotide sequences. Primer extension incorporation of the benzofurazane‐modified dNTPs by polymerases has been developed for the construction of labeled oligonucleotide probes. In combination with nitrophenyl and aminophenyl labels, we have successfully developed a three‐potential coding of DNA bases and have explored the relevant electrochemical potentials. The combination of benzofurazane and nitrophenyl reducible labels has proved to be excellent for ratiometric analysis of nucleotide sequences and is suitable for bioanalytical applications.     

Tuning single nucleotide discrimination in polymerase chain reactions (PCRs): synthesis of primer probes bearing polar 4'-C-modifications and their application in allele-specific PCR

There are many methods available for the detection of nucleotide variations in genetic material. Most of these methods are applied after amplification of the target genome sequence by the polymerase chain reaction (PCR). Many efforts are currently underway to develop techniques that can detect single nucleotide variations in genes either by means of, or without the need for, PCR. Allele-specific PCR (asPCR), which reports nucleotide variations based on either the presence or absence of a PCR-amplified DNA product, has the potential to combine target amplification and analysis in one single step. The principle of asPCR is based on the formation of matched or mismatched primer-target complexes by using allele-specific primer probes. PCR amplification by a DNA polymerase from matched 3'-primer termini proceeds, whereas a mismatch should obviate amplification. Given the recent advancements in real-time PCR, this technique should, in principle, allow single nucleotide variations to be detected online. However, this method is hampered by low selectivity, which necessitates tedious and costly manipulations. Recently, we reported that the selectivity of asPCR can be significantly increased through the employment of chemically modified primer probes. Here we report further significant advances in this area. We describe the synthesis of various primer probes that bear polar 4'-C-modified nucleotide residues at their 3' termini, and their evaluation in real-time asPCR. We found that primer probes bearing a 4'-C-methoxymethylene modification have superior properties in the discrimination of single nucleotide variations by PCR.     

The oxygen reduction reaction at silver electrodes in high chloride media and the implications for silver nanoparticle toxicity

The oxygen reduction reaction (ORR) at neutral pH in various aqueous chloride-containing solutions was investigated voltammetrically. In particular, the ORR was performed in high chloride containing aqueous media including authentic and synthetic seawater under oxygen saturated conditions and compared with that in aqueous nitrate and perchlorate media. The experimental voltammograms revealed a two-electron process forming hydrogen peroxide in low chloride media. In contrast, high concentration chloride solutions, including both synthetic and authentic seawater showed an increase of overpotential, accompanied by a splitting of the voltammetric peak into two one-electron features indicating the formation of superoxide in the first step and its release from the silver-solution interface. The implications for silver nanoparticle toxicology are discussed given the markedly greater toxicity of superoxide over peroxide and the high levels of chloride in biological media as well as in seawater.

Superoxide produced at silver electrode in seawater.     

Occupational and environmental laboratory medicine: A network of EQAS organisers

Most people in any community come into contact with chemicals that are potentially harmful to their health. Some elements are essential to health and inadequate amounts in food may also lead to ill health. Measurement of chemicals in blood, urine or other specimens is a fundamental feature of studies undertaken in the field of Occupational and Environmental Laboratory Medicine (OELM). Results are used to assess the risk for either overexposure or deficiency of essential nutrients. External Quality Assessment Schemes (EQAS) aid laboratories to achieve accurate and consistent data and 11 organisers of EQAS in Europe and North America are working to improve the effectiveness of their activities.The aims of the Network of EQAS Organisers in OELM are to stimulate improvements in analytical results, establish equivalence of assessment among Schemes, collaborate to enhance the practice of EQA including whenever possible to warrant traceability of EQAS to primary standards.Presented at the Eurachem PT Workshop September 2005, Portorož, Slovenia.     

Hyperpolarized 83Kr and 129Xe NMR relaxation measurements of hydrated surfaces: implications for materials science and pulmonary diagnostics

In this proof of principle work, a technique is introduced to study hydrated surfaces using hyperpolarized (hp) 83Kr NMR spectroscopy. The longitudinal (T1) relaxation of hp-83Kr is shown to be extremely sensitive to the presence of adsorbed water on hydrophilic borosilicate and hydrophobic siliconized glass surfaces. The krypton surface relaxation is found to be largely independent of the total gas pressure applied to the studied materials, and the presented technique is therefore fairly robust. However, the relaxational properties of hp-83Kr can be "tuned" by adjusting the composition of the optical pumping gas mixture. This effect may be important for practical applications such as hp-83Kr MR imaging and can be achieved without sacrificing signal intensity. Complementary information to that of hp-83Kr surface relaxation data can be obtained from hp-129Xe relaxation measurements that are sensitive to the presence of paramagnetic surface sites. In contrast to the signal decay of hp-129Xe, the longitudinal relaxation of 83Kr is largely unaffected by paramagnetic impurities, and in some materials, 83Kr and 129Xe show comparable T1 times that are caused by two completely different relaxation mechanisms. Finally, the relaxation times of 83Kr in contact with bovine lung surfactant coated glass pores that are similar in size to mammalian alveoli are presented. The results suggest that in vivo MR studies may be feasible and could provide valuable information about changes in pulmonary surface chemistry.