Optimized in situ construction of oligomers on an array surface

Oligonucleotide arrays are powerful tools to study changes in gene expression for whole genomes. These arrays can be synthesized by adapting photolithographic techniques used in microelectronics. Using this method, oligonucleotides are built base by base directly on the array surface by numerous cycles of photodeprotection and nucleotide addition. In this paper we examine strategies to reduce the number of synthesis cycles required to construct oligonucleotide arrays. By computer modeling oligonucleotide synthesis, we found that the number of required synthesis cycles could be significantly reduced by focusing upon how oligonucleotides are chosen from within genes and upon the order in which nucleotides are deposited on the array. The methods described here could provide a more efficient strategy to produce oligonucleotide arrays.     

A Dde resin based strategy for inverse solid-phase synthesis of amino terminated peptides, peptide mimetics and protected peptide intermediates.

This report describes a Dde resin based attachment strategy for inverse solid-phase peptide synthesis (ISPPS). This attachment strategy can be used for the synthesis of amino terminated peptides with side chains and the carboxyl terminus either protected or deprotected. Amino acid t-butyl esters were attached through their free amino group to the Dde resin. The t-butyl carboxyl protecting group was removed by 50% TFA, and inverse peptide synthesis cycles performed using an HATU/TMP based coupling method. Protected peptides were cleaved from the resin with dilute hydrazine. Side chain protecting groups could then be removed by treatment with TFMSA/TFA. The potential of this approach was demonstrated by the synthesis of several short protected and unprotected peptides in good yield and with low epimerization. Its potential for peptide mimetic synthesis was demonstrated by the synthesis of two peptide trifluoromethylketones.     

Bio-Inspired Binary Bees Algorithm for a Two-Level Distribution Optimisation Problem

<正> Two uncoupleable distributions, assigning missions to robots and allocating robots to home stations, accompany the use ofmobile service robots in hospitals.In the given problem, two workload-related objectives and five groups of constraints areproposed.A bio-mimicked Binary Bees Algorithm (BBA) is introduced to solve this multiobjective multiconstraint combinatorialoptimisation problem, in which constraint handling technique (Multiobjective Transformation, MOT), multiobjectiveevaluation method (nondominance selection), global search strategy (stochastic search in the variable space), local searchstrategy (Hamming neighbourhood exploitation), and post-processing means (feasibility selection) are the main issues.TheBBA is then demonstrated with a case study, presenting the execution process of the algorithm, and also explaining the change ofelite number in evolutionary process.Its optimisation result provides a group of feasible nondominated two-level distributionschemes.     

LiCl-induced improvement of multilayer nanofibrous lipase for biodiesel synthesis

A unique method that applied a multilayer-immobilization strategy was developed to prepare nanofibrous enzymes for biosynthesis. LiCl co-electrospun with polyurethane nanofibers enabled strong physical adsorption of bovine serum albumin (BSA), forming the first layer of protein on the nanofibers; lipase AK was subsequently crosslinked to BSA as an outer layer of enzyme. The content of LiCl in nanofibers was found to be a sensitive factor affecting the activity and stability of the immobilized lipase. For biodiesel synthesis from soybean oil and methanol in isooctane, the reaction rate catalyzed by nanofibrious lipase carrying 5 wt% LiCl was 6.6-fold higher than fibers without LiCl, with a conversion of 91% was achieved within 2 h. LiCl also induced much improved enzyme stability. The nanofibrous lipase with 5% LiCl could be repeatedly used for 42 cycles without apparent activity loss, while the immobilized lipase without LiCl lost over 90% activity within 13 reuse cycles.     

Rapid solid-phase peptide synthesis using thermal and controlled microwave irradiation.

A rapid and efficient microwave-assisted solid-phase synthesis method is described for the preparation of the nonapeptide WDTVRISFK, using conventional Fmoc/Bu(t) orthogonal protection strategy. The synthesis protocol is based on the use of cycles of pulsed microwave irradiation with intermittent cooling of the reaction during the removal of the Fmoc protecting group and during the coupling. The desired nonapeptide was obtained in highest yield and purity by employing MicroKan technology. The chemical reactions were carried out in a single-mode microwave reactor, equipped with a fiber-optic probe to monitor the reaction temperature continuously.     

基于总体最小二乘方法的基因表达缺失数据估计

在基因芯片实验中,数据缺失客观存在,并在一定程度上影响芯片数据后续分析结果的准确性。在不增加实验次数的情况下,缺失值估计是降低缺失数据对后续分析影响的有效方法。针对基因表达数据含有噪声的特点,提出了基于总体最小二乘估计的基因表达缺失值估计算法。实验结果表明,新的估计算法具有比传统缺失值估计算法更好的稳定性和估计准确度。     

Time to Pregnancy: A Computational Method for Using the Duration of Non-Conception for Predicting Conception

An important problem in reproductive medicine is deciding when people who have failed to become pregnant without medical assistance should begin investigation and treatment. This study describes a computational approach to determining what can be deduced about a couple''s future chances of pregnancy from the number of menstrual cycles over which they have been trying to conceive. The starting point is that a couple''s fertility is inherently uncertain. This uncertainty is modelled as a probability distribution for the chance of conceiving in each menstrual cycle. We have developed a general numerical computational method, which uses Bayes'' theorem to generate a posterior distribution for a couple''s chance of conceiving in each cycle, conditional on the number of previous cycles of attempted conception. When various metrics of a couple''s expected chances of pregnancy were computed as a function of the number of cycles over which they had been trying to conceive, we found good fits to observed data on time to pregnancy for different populations. The commonly-used standard of 12 cycles of non-conception as an indicator of subfertility was found to be reasonably robust, though a larger or smaller number of cycles may be more appropriate depending on the population from which a couple is drawn and the precise subfertility metric which is most relevant, for example the probability of conception in the next cycle or the next 12 cycles. We have also applied our computational method to model the impact of female reproductive ageing. Results indicate that, for women over the age of 35, it may be appropriate to start investigation and treatment more quickly than for younger women. Ignoring reproductive decline during the period of attempted conception added up to two cycles to the computed number of cycles before reaching a metric of subfertility.     

Surface Free Energy‐Induced Assembly to the Synthesis of Grid‐Like Multicavity Carbon Spheres with High Level In‐Cavity Encapsulation for Lithium–Sulfur Cathode

Carbon microcapsules with a large interior cavity and porous shell are ideal hosts for guest species, while to maximize in‐cavity volume has always been a challenge. Herein, a surface free energy‐induced assembly approach is proposed for synthesis of multicavity carbon spheres (MCC). When used as a host for lithium–sulfur cathodes, MCC are fully accessible for sulfur—with high level in‐cavity encapsulation ability of grid‐like cavities. The crucial point for this assembly approach is the employment of small sized nanoemulsions with high homogeneity as primary building blocks. Spontaneous aggregation and assembly of substructural units are processing in following hydrothermal synthesis induced by reduction of surface free energy of system. As a result, multicavity structure is formed, where the size and number of cavities can be modulated by changing size of nanoemulsion and concentration of polymer. Confined pyrolysis enables to further enlarge cavity size compared to regular pyrolysis. The carbon–sulfur cathode exhibits excellent cycling stability and rate performance, i.e., high capacity of 943 and 869 mA h g^?1 after 200 cycles at current density of 0.5 and 2.0 C. The strategy has paved the way for custom‐ordered synthesis of nanostructured carbon with keen demands in high loading capacity of guest species.     

A PCR-mediated gene synthesis strategy involving the assembly of oligonucleotides representing only one of the strands.

A modification of PCR-mediated gene synthesis strategy is introduced. This modification enables the synthesis of a gene from oligonucleotides comprising only one of the two strands. Bridging oligonucleotides (approximately 20-mers in length) complementary to the junctions of template strand oligonucleotides and two outer primers are also needed for PCR. A two-step PCR containing a first step of 10 cycles, followed by a second step of 20 cycles, differing only in the annealing conditions was used. A single-step PCR combining the two different cycle conditions could also be used successfully. Optimal conditions for gene synthesis (and amplification) are described. Human and porcine colipase genes (297 and 309 bp, respectively) have been successfully synthesized, cloned into the Invitrogen TA cloning vector and sequenced. There was absolutely no error in the clones that were sequenced.     

A format for phylogenetic placements

We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g., short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format, which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement.     

Building biological foundries for next-generation synthetic biology

Synthetic biology is an interdisciplinary field that takes top-down approaches to understand and engineer biological systems through design-build-test cycles. A number of advances in this relatively young field have greatly accelerated such engineering cycles. Specifically, various innovative tools were developed for in silico biosystems design, DNA de novo synthesis and assembly, construct verification, as well as metabolite analysis, which have laid a solid foundation for building biological foundries for rapid prototyping of improved or novel biosystems. This review summarizes the state-of-the-art technologies for synthetic biology and discusses the challenges to establish such biological foundries.     

Experimental analysis of gene assembly with TopDown one-step real-time gene synthesis

Herein we present a simple, cost-effective TopDown (TD) gene synthesis method that eliminates the interference between the polymerase chain reactions (PCR) assembly and amplification in one-step gene synthesis. The method involves two key steps: (i) design of outer primers and assembly oligonucleotide set with a melting temperature difference of >10°C and (ii) utilization of annealing temperatures to selectively control the efficiencies of oligonucleotide assembly and full-length template amplification. In addition, we have combined the proposed method with real-time PCR to analyze the step-wise efficiency and the kinetics of the gene synthesis process. Gel electrophoresis results are compared with real-time fluorescence signals to investigate the effects of oligonucleotide concentration, outer primer concentration, stringency of annealing temperature, and number of PCR cycles. Analysis of the experimental results has led to insights into the gene synthesis process. We further discuss the conditions for preventing the formation of spurious DNA products. The TD real-time gene synthesis method provides a simple and efficient method for assembling fairly long DNA sequence, and aids in optimizing gene synthesis conditions. To our knowledge, this is the first report that utilizes real-time PCR for gene synthesis.     

An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis

A systems-level understanding of a small but essential population of cells in development or adulthood (e.g. somatic stem cells) requires accurate quantitative monitoring of genome-wide gene expression, ideally from single cells. We report here a strategy to globally amplify mRNAs from single cells for highly quantitative high-density oligonucleotide microarray analysis that combines a small number of directional PCR cycles with subsequent linear amplification. Using this strategy, both the representation of gene expression profiles and reproducibility between individual experiments are unambiguously improved from the original method, along with high coverage and accuracy. The immediate application of this method to single cells in the undifferentiated inner cell masses of mouse blastocysts at embryonic day (E) 3.5 revealed the presence of two populations of cells, one with primitive endoderm (PE) expression and the other with pluripotent epiblast-like gene expression. The genes expressed differentially between these two populations were well preserved in morphologically differentiated PE and epiblast in the embryos one day later (E4.5), demonstrating that the method successfully detects subtle but essential differences in gene expression at the single-cell level among seemingly homogeneous cell populations. This study provides a strategy to analyze biophysical events in medicine as well as in neural, stem cell and developmental biology, where small numbers of distinctive or diseased cells play critical roles.     

From chromatin to splicing: RNA-processing as a total artwork

RNA plays a central role in the determination of the phenotype of the cell. The molecular mechanisms involved in primary RNA synthesis and subsequent post-processing are not completely understood, but there is increasing evidence that they are more tightly coupled than previously expected. The analyses by a number of groups of recently published genome wide maps of chromatin structure have further uncovered a role for primary chromatin structure in RNA processing. Indeed, these analyses have revealed that nucleosomes show a characteristic occupancy pattern in exonic regions of metazoan genomes. The pattern is strongly indicative of an implication of nucleosome positioning in exon recognition during pre-mRNA splicing. Characteristic exonic patterns have also been observed for a number of histone modifications, suggesting the possibility that chromatin state plays a direct role in the regulation of splicing.     

Combined strategy for preparation of a bioimprinted Geotrichum sp. lipase biocatalyst effective in non-aqueous media

Geotrichum sp. lipase with enhanced activity and operational stability was prepared for use in non-aqueous media. A combined strategy comprising bioimprinting with dual imprint molecules and a co-solvent coupled to pH tuning, KCl salt activation, lecithin coating and immobilization on macroporous resin effectively enhanced the activity and operational stability of Geotrichum sp. lipase. The modified lipase exhibited 18.4-fold enhanced esterification activity towards methyl oleate synthesis, and retained 90% activity following repeated use in 10 cycles. The combined strategy exhibited a significant synergistic effect and was suitable for lipase modification, dramatically enhancing the enzyme activity and operational stability. This approach is applicable to the preparation of other enzyme biocatalysts, since the methods are effective for upgrading crude enzyme to a refined product with high activity and stability for use in non-aqueous media.     

A role for cyclin J in the rapid nuclear division cycles of early Drosophila embryogenesis

The nuclear division cycles of early Drosophila embryogenesis have a number of unique features that distinguish them from later cell cycles. These features include the lack of some checkpoints that operate in later cell cycles, the absence of gap phases, and very rapid DNA synthesis phases. The molecular mechanisms that control these rapid nuclear division cycles are poorly understood. Here we describe analysis of cyclin J, a previously uncharacterized cyclin which has an RNA expression pattern that suggests a possible role in early embryogenesis. We show that the cyclin J protein is present in early embryos where it forms active kinase complexes with cyclin-dependent kinase (Cdk) 2. To determine whether cyclin J plays a role in controlling the early nuclear cycles we isolated peptide aptamers that specifically bind to cyclin J and inhibit its ability to activate Cdks. We injected the inhibitory aptamers into syncytial Drosophila embryos and demonstrated that they caused defects in chromosome segregation and progression through mitosis. We obtained similar results by injecting cyclin J antibodies into embryos. Our results suggest that a cyclin J-associated kinase activity is required for the early embryonic division cycles.     

Rapid prototyping enzyme homologs to improve titer of nicotinamide mononucleotide using a strategy combining cell-free protein synthesis with split GFP

Engineering biological systems to test new pathway variants containing different enzyme homologs is laborious and time-consuming. To tackle this challenge, a strategy was developed for rapidly prototyping enzyme homologs by combining cell-free protein synthesis (CFPS) with split green fluorescent protein (GFP). This strategy featured two main advantages: (1) dozens of enzyme homologs were parallelly produced by CFPS within hours, and (2) the expression level and activity of each homolog was determined simultaneously by using the split GFP assay. As a model, this strategy was applied to optimize a 3-step pathway for nicotinamide mononucleotide (NMN) synthesis. Ten enzyme homologs from different organisms were selected for each step. Here, the most productive homolog of each step was identified within 24 h rather than weeks or months. Finally, the titer of NMN was increased to 1213 mg/L by improving physiochemical conditions, tuning enzyme ratios and cofactor concentrations, and decreasing the feedback inhibition, which was a more than 12-fold improvement over the initial setup. This strategy would provide a promising way to accelerate design-build-test cycles for metabolic engineering to improve the production of desired products.     

Correlation between Thermodynamic Efficiency and Ecological Cyclicity for Thermodynamic Power Cycles

A sustainable global community requires the successful integration of environment and engineering. In the public and private sectors, designing cyclical (“closed loop”) resource networks increasingly appears as a strategy employed to improve resource efficiency and reduce environmental impacts. Patterning industrial networks on ecological ones has been shown to provide significant improvements at multiple levels. Here, we apply the biological metric cyclicity to 28 familiar thermodynamic power cycles of increasing complexity. These cycles, composed of turbines and the like, are scientifically very different from natural ecosystems. Despite this difference, the application results in a positive correlation between the maximum thermal efficiency and the cyclic structure of the cycles. The immediate impact of these findings results in a simple method for comparing cycles to one another, higher cyclicity values pointing to those cycles which have the potential for a higher maximum thermal efficiency. Such a strong correlation has the promise of impacting both natural ecology and engineering thermodynamics and provides a clear motivation to look for more fundamental scientific connections between natural and engineered systems.