Large scale, liquid phase oligonucleotide synthesis by alkyl H-phosphonate approach

A new approach to the liquid phase synthesis of oligonucleotide is described, it is based on oxidative coupling using alkyl H-phosphonate synthon and polyethylene glycol (PEG5000) as a soluble support. Nucleoside alkyl H-phosphonate undergoes oxidative coupling in presence of NBS. The use of polyethylene glycol as a soluble polymeric support preserves some convenient features of the solid phase synthesis with new interesting advantages. This liquid phase method appears effective in terms of speed and coupling yield and can be evaluated for the production of large amount of oligonucleotide (100 microM).     

Liquid chromatography of recombinant proteins and protein drugs

Many recombinant proteins (rPRTs) have a high bioactivity and some of them may eventually be classified as drugs beneficial to human health, recombinant human protein drugs (rPDs). rPDs are a high-technology product with all the associated economic benefits, therefore the liquid chromatography (LC) of rPRT is different from that of proteins isolated in laboratory scale for purely research purposes. The design of a purification scheme for an rPRT depends on the intended function of the purified rPRT, as a pure sample for research in small scale, or as a product for industrial production. This review paper mainly deals with the latter instance, producing rPD at a large scale. Pharmaceutical economics is considered not only for each step of purification, but also the whole production process. This strategy restricts the content of this review paper to the factors affecting the optimization source, the character of rPRT in up-stream technology and the purification of the rPRT in down-stream production. In the latter instance, the purification step is required to be as efficient as possible and LC is the core of the refined purification method, which is either a single LC method or combination of LC methods, sometimes, it may be a combination of LC and other non-LC separation methods comprising an optimized purification technology. Here some typical examples of rPRT purification at the large scale, recent developments, such as protein folding liquid chromatography, short column chromatography, and new packing material and column techniques are introduced.     

Changes in numbers of large ovarian follicles, plasma luteinizing hormone and estradiol-17beta concentrations and egg production figures in farmed ostriches throughout the year

In this study we described and analysed changes in the numbers of large ovarian follicles (diameter 6.1-9.0 cm) and in the plasma concentrations of luteinizing hormone (LH) and estradiol-17beta (E(2)beta) in relation to individual egg production figures of farmed ostriches (Struthio camelus spp.) throughout one year. Ultrasound scanning and blood sampling for plasma hormone analysis were performed in 9 hens on a monthly basis during the breeding season and in two periods of the non-breeding season. Our data demonstrated that: (1) large follicles were detected and LH concentrations were elevated already 1 month before first ovipositions of the egg production season took place; (2) E(2)beta concentrations increased as soon as the egg production season started; (3) numbers of large follicles, LH and E(2)beta concentrations were elevated during the entire egg production season; and that (4) numbers of large follicles, LH and E(2)beta concentrations decreased simultaneous with or following the last ovipositions of the egg production season. By comparing these parameters during the egg production season with their pre-and post-seasonal values, significant differences were found in the numbers of large follicles and E(2)beta concentrations between the pre-seasonal, seasonal and post-seasonal period; while LH concentrations were significantly different between the seasonal and post-seasonal period. In conclusion, our data demonstrate that changes in numbers of large follicles and in concentrations of LH and E(2)beta closely parallel individual egg production figures and provide some new cues that egg production in ostriches is confined to a marked reproductive season. Moreover, our data provide indications that mechanism, initiating, maintaining and terminating the egg production season in farmed breeding ostriches are quite similar to those already known for other seasonal breeding bird species.     

我国半乳甘露聚糖胶资源利用前景初探

半乳甘露聚糖植物胶加工是我国70年代中期兴起的新兴产业。本文从我国植物资源发展的角度。重点论证了瓜尔豆（Cyanopsis tetragonoloba（L.）Taubert.）、田菁（Sesbania cannabina(Retz.)Pers.)、胡芦巴（Trigonella foenum-graecum L.）的生产情况,认为胡芦巴适应性强、产量高、易于机械化大面积种植与轮作,并具有改良土壤以及经济效益好等优势。因此,发展半乳甘露聚糖胶资源,大量种植胡芦巴是最好的选择。     

Nitrate uptake by size-fractionated phytoplankton on the Scotian Shelf (Northwest Atlantic): spatial and temporal variability

New (nitrate) phytoplankton production was estimated monthlyduring 1 year (March 1991–March 1992) at three stationson the Scotian Shelf, Northwest Atlantic. Samples were sizefractionated to assess the uptake of nitrate by small (<5µm) and large (>5 µm) phytoplankton. The biomassof small phytoplankton remained relatively constant over theyear, whereas that of the large size fraction was high in earlyspring and low during the remainder of the year. Monthly variationsin nitrate uptake were similar for the two size fractions, suggestingthat both small and large phytoplankton used nitrate when available.It follows that, outside the spring bloom, new production waslargely due to the small fraction. Our results do not supportthe notion that new production is associated with large phytoplanktonand regenerated production with small phytoplankton.     

Computational design and analysis of modular cells for large libraries of exchangeable product synthesis modules

Microbial metabolism can be harnessed to produce a large library of useful chemicals from renewable resources such as plant biomass. However, it is laborious and expensive to create microbial biocatalysts to produce each new product. To tackle this challenge, we have recently developed modular cell (ModCell) design principles that enable rapid generation of production strains by assembling a modular (chassis) cell with exchangeable production modules to achieve overproduction of target molecules. Previous computational ModCell design methods are limited to analyze small libraries of around 20 products. In this study, we developed a new computational method, named ModCell-HPC, that can design modular cells for large libraries with hundreds of products with a highly-parallel and multi-objective evolutionary algorithm and enable us to elucidate modular design properties. We demonstrated ModCell-HPC to design Escherichia coli modular cells towards a library of 161 endogenous production modules. From these simulations, we identified E. coli modular cells with few genetic manipulations that can produce dozens of molecules in a growth-coupled manner with different types of fermentable sugars. These designs revealed key genetic manipulations at the chassis and module levels to accomplish versatile modular cells, involving not only in the removal of major by-products but also modification of branch points in the central metabolism. We further found that the effect of various sugar degradation on redox metabolism results in lower compatibility between a modular cell and production modules for growth on pentoses than hexoses. To better characterize the degree of compatibility, we developed a method to calculate the minimal set cover, identifying that only three modular cells are all needed to couple with all compatible production modules. By determining the unknown compatibility contribution metric, we further elucidated the design features that allow an existing modular cell to be re-purposed towards production of new molecules. Overall, ModCell-HPC is a useful tool for understanding modularity of biological systems and guiding more efficient and generalizable design of modular cells that help reduce research and development cost in biocatalysis.     

A microtechnique for neutrophil respiratory burst oxidase in a cell-free system--characterization of oxidase activation system

1. A microtechnique for quantitating human neutrophil NADPH oxidase in a cell-free system is described. 2. This spectrophotometric discontinuous (fixed time) method is less material-consuming than existing methods and is more useful for experiments in which superoxide production by neutrophils must be measured in a large number of samples. 3. Measurement of NADPH oxidase using the new method can be accomplished in a final vol of 0.15 ml. 4. In the assay, neutrophil membranes solubilized with deoxycholate were incubated for 3 min with cytosolic fractions, magnesium, sodium dodecyl sulfate, and cytochrome c in the absence of NADPH to preincubate the oxidase before the addition of the reducing agent. 5. The reaction was started by adding NADPH and 2 min later terminated by adding superoxide dismutase. 6. The apparent Km for NADPH obtained by the new method was almost the same as that by the authorized method (39.2 +/- 3.1 SD vs 36.8 +/- 1.6). Activation of neutrophil NADPH oxidase was characterized using the new assay method.     

Considerations for the process development of insect‐derived antimicrobial peptide production

Antimicrobial peptides (AMPs) could evolve into new therapeutic lead molecules against multi‐resistant bacteria. As insects are a rich source of AMP, the identification and characterization of insect‐derived AMPs is particularly emphasized. One challenge of bringing these molecules into market, e.g., as a drug, is to develop a cost‐efficient large‐scale production process. Due to the fact that a direct AMP isolation from insects is not economical and that chemical synthesis is recommended for peptide sizes below 40 amino acids, a viable option is heterologous AMP production. Therefore, previous knowledge concerning the expression of larger proteins can be adapted, but due to the AMP nature (e.g., small size, bactericide) additional challenges have to be faced during up and downstream processing. Nonetheless the bottleneck for large‐scale AMP production is the same as for proteins; mainly the downstream process. This review introduces opportunities for insect‐derived AMP production, like the choice of the expression system (based on previously derived data), depending on the AMP nature, as well as new purification strategies like elastin‐like peptide/intein based purification strategies. All of these aspects are discussed with regard to large‐scale processes and costs. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 31:1–11, 2015     

An engineered hyaluronan synthase: characterization for recombinant human hyaluronan synthase 2 Escherichia coli

The Class I hyaluronan synthase (HAS) is a unique glycosyltransferase synthesizing hyaluronan (HA), a polysaccharide composed of GlcUA and GlcNAc, by using one catalytic domain that elongates two different monosaccharides. As for the synthetic mechanism, there are two alternative manners for the sugar elongation process. Some bacterial HASs add new sugars to the non-reducing end of the acceptor to grow polymers. On the other hand, some vertebrate enzymes seem to transfer sugars to the reducing end. Expression of vertebrate HASs as active and soluble proteins will accelerate further precise insight into mechanisms of sugar elongation reactions by natural HASs. Since large scale production of HA polymers and oligomers would become powerful tools both for basic studies and new biotechnology to create functional carbohydrates in medicinal purposes, advent of an efficient method for the expression of HASs in Escherichia coli is strongly expected. Here we communicate the first success of the production of recombinant human HAS2 proteins composed of only the catalytic region in E. coli as the active form. It was demonstrated that an engineered HAS2 expressed in E. coli exhibited significant activity to synthesize a mixture of HAS oligomers from 8-mer (HA8) to 16-mer (HA16). Engineered HAS2 prepared herein elongated sugars from exogenous tetrasaccharide to form polymers with a direction to the non-reducing end. According to the present results, large scale production of engineered recombinant HASs is to be performed using E. coli that will provide practical and economic advantages in manufacturing enzymes for use in the synthesis of various oligomeric HA molecules and their industrial applications.     

Solving group technology problems via clique partitioning

This paper presents a new clique partitioning (CP) model for the Group Technology (GT) problem. The new model, based on a novel 0/1 quadratic programming formulation, addresses multiple objectives in GT problems by drawing on production relationships to assign differing weights to machine/part pairs. The use of this model, which is readily solved by a basic tabu search heuristic, is illustrated by solving 36 standard test problems from the literature. The efficiency of our new CP model is further illustrated by solving three large scale problems whose linear programming relaxations are much too large to be solved by CPLEX. An analysis of the quality of the solutions produced along with comparisons made with other models and methods highlight both the attractiveness and robustness of the proposed method.     

Efficient Production of Lumichrome by Microbacterium sp. Strain TPU 3598

Lumichrome is a photodegradation product of riboflavin and is available as a photosensitizer and fluorescent dye. To develop new efficient methods of lumichrome production, we isolated bacterial strains with high lumichrome productivity from soil. The strain with highest productivity was identified as Microbacterium sp. strain TPU 3598. Since this strain inductively produced lumichrome when cultivated with riboflavin, we developed two different methods, a cultivation method and a resting cell method, for the production of large amounts of lumichrome using the strain. In the cultivation method, 2.4 g (9.9 mmol) of lumichrome was produced from 3.8 g (10.1 mmol) of riboflavin at the 500-ml scale (98% yield). The strain also produced 4.7 g (19.4 mmol) of lumichrome from 7.6 g (20.2 mmol) of riboflavin (96% yield) by addition of riboflavin during cultivation at the 500-ml scale. In the resting cell method, 20 g of cells (wet weight) in 100 ml of potassium phosphate buffer, pH 7.0, produced 2.4 g of lumichrome from 3.8 g of riboflavin (98% yield). Since the lumichrome production by these methods was carried out in suspension, the resulting lumichrome was easily purified from the cultivation medium or reaction mixture by centrifugation and crystallization. Thus, the biochemical methods we describe here are a significant improvement in terms of simplicity and yield over the existing chemical, photolytic, and other biochemical methods of lumichrome production.     

两步培养法测定真菌产孢营养需求

生防真菌产孢条件的测定一般都是通过连续培养方法,即在同一种限定培养基上完成其生长和产孢过程。文中我们提出分离真菌的生长和产孢阶段,测定产孢营养需求的两步培养新方法。6种生防真菌首先在平板上进行营养生长,然后转移至营养成分和浓度确定的新鲜培养基中继续产孢过程来测定菌株产孢阶段实际营养需求。通过与连续培养方法比较,发现只有淡紫拟青霉Paecilomyces lilacinus、金龟子绿僵菌Metarhizium anisopliae二者产孢条件一致,而厚孢轮枝菌Pochonia chlamydosporia、球孢白僵菌Beauveria bassiana、蜡蚧轮枝菌Lecanicillium lecanii、绿色木霉Trichoderma viride菌株产孢的营养条件存在显著的差异。基于这一方法,确定了绿色木霉最佳产孢条件,即起始碳浓度2g C/L,碳氮比10:1,最佳碳氮源组合纤维二糖和酵母浸膏,为真菌生防制剂生产调控提供了依据。     

Optimal defense strategy: storage vs. new production

If hosts produce defense proteins after they are infected by pathogens, it may take hours to days before defense becomes fully active. By producing defense proteins beforehand, and storing them until infection, the host can cope with pathogens with a short time delay. However, producing and storing defense proteins require energy, and the activated defense proteins often cause harm to the host's body as well as to pathogens. Here, we study the optimal strategy for a host who chooses the amount of stored defense proteins, the activation of the stored proteins upon infection, and the new production of the proteins. The optimal strategy is the one that minimizes the sum of the harm by pathogens and the cost of defense. The host chooses the storage size of defense proteins based on the probability distribution of the magnitude of pathogen infection. When the infection size is predictable, all the stored proteins are to be activated upon infection. The optimal strategy is to have no storage and to rely entirely on new production if the expected infection size n(0) is small, but to have a big storage without new production if n(0) is large. The transition from the "new production" phase to "storage" phase occurs at a smaller n(0) when storage cost is small, activation cost is large, pathogen toxicity is large, pathogen growth is fast, the defense is effective, the delay is long, and the infection is more likely. On the other hand, the storage size to produce for a large n(0) decreases with three cost parameters and the defense effectiveness, increases with the likelihood of infection, the toxicity and the growth rate of pathogens, and it is independent of the time delay. When infection size is much smaller than the expected size, some of the stored proteins may stay unused.     

An Enzymatic Assay for High-Throughput Screening of Cytidine-Producing Microbial Strains

Cytidine is an industrially useful precursor for the production of antiviral compounds and a variety of industrial compounds. Interest in the microbial production of cytidine has grown recently and high-throughput screening of cytidine over-producers is an important approach in large-scale industrial production using microorganisms. An enzymatic assay for cytidine was developed combining cytidine deaminase (CDA) and indophenol method. CDA catalyzes the cleavage of cytidine to uridine and NH₃, the latter of which can be accurately determined using the indophenol method. The assay was performed in 96-well plates and had a linear detection range of cytidine of 0.058 - 10 mM. This assay was used to determine the amount of cytidine in fermentation flasks and the results were compared with that of High Perfomance Liquid Chromatography (HPLC) method. The detection range of the CDA method is not as wide as that of the HPLC, furthermore the correlation factor of CDA method is not as high as that of HPLC. However, it was suitable for the detection of large numbers of crude samples and was applied to high-throughput screening for high cytidine-producing strains using 96-well deep-hole culture plates. This assay was proved to be simple, accurate, specific and suitable for cytidine detection and high-throughput screening of cytidine-producing strains in large numbers of samples (96 well or more).     

Plastoglobules: a new address for targeting recombinant proteins in the chloroplast

Background  

The potential of transgenic plants for cost-effective production of pharmaceutical molecules is now becoming apparent. Plants have the advantage over established fermentation systems (bacterial, yeast or animal cell cultures) to circumvent the risk of pathogen contamination, to be amenable to large scaling up and to necessitate only established farming procedures. Chloroplasts have proven a useful cellular compartment for protein accumulation owing to their large size and number, as well as the possibility for organellar transformation. They therefore represent the targeting destination of choice for recombinant proteins in leaf crops such as tobacco. Extraction and purification of recombinant proteins from leaf material contribute to a large extent to the production costs. Developing new strategies facilitating these processes is therefore necessary.     

A rapid simple procedure for direct measurement of excreted thiamine from yeast

A new rapid method for the detection of extracellular thiamine production in yeast is described. This method is based on a modified thiochrome assay where fluorescent zones surrounding thiamine excretor colonies can be directly visualized under UV light on agar plates. This new procedure is simple to perform on a large number of colonies simultaneously and results can be obtained within minutes.     

Quantitative characterization of metabolism and metabolic shifts during growth of the new human cell line AGE1.HN using time resolved metabolic flux analysis

For the improved production of vaccines and therapeutic proteins, a detailed understanding of the metabolic dynamics during batch or fed-batch production is requested. To study the new human cell line AGE1.HN, a flexible metabolic flux analysis method was developed that is considering dynamic changes in growth and metabolism during cultivation. This method comprises analysis of formation of cellular components as well as conversion of major substrates and products, spline fitting of dynamic data and flux estimation using metabolite balancing. During batch cultivation of AGE1.HN three distinct phases were observed, an initial one with consumption of pyruvate and high glycolytic activity, a second characterized by a highly efficient metabolism with very little energy spilling waste production and a third with glutamine limitation and decreasing viability. Main events triggering changes in cellular metabolism were depletion of pyruvate and glutamine. Potential targets for the improvement identified from the analysis are (i) reduction of overflow metabolism in the beginning of cultivation, e.g. accomplished by reduction of pyruvate content in the medium and (ii) prolongation of phase 2 with its highly efficient energy metabolism applying e.g. specific feeding strategies. The method presented allows fast and reliable metabolic flux analysis during the development of producer cells and production processes from microtiter plate to large scale reactors with moderate analytical and computational effort. It seems well suited to guide media optimization and genetic engineering of producing cell lines.     

Penicillin: the medicine with the greatest impact on therapeutic outcomes

The principal point of this paper is that the discovery of penicillin and the development of the supporting technologies in microbiology and chemical engineering leading to its commercial scale production represent it as the medicine with the greatest impact on therapeutic outcomes. Our nomination of penicillin for the top therapeutic molecule rests on two lines of evidence concerning the impact of this event: (1) the magnitude of the therapeutic outcomes resulting from the clinical application of penicillin and the subsequent widespread use of antibiotics and (2) the technologies developed for production of penicillin, including both microbial strain selection and improvement plus chemical engineering methods responsible for successful submerged fermentation production. These became the basis for production of all subsequent antibiotics in use today. These same technologies became the model for the development and production of new types of bioproducts (i.e., anticancer agents, monoclonal antibodies, and industrial enzymes). The clinical impact of penicillin was large and immediate. By ushering in the widespread clinical use of antibiotics, penicillin was responsible for enabling the control of many infectious diseases that had previously burdened mankind, with subsequent impact on global population demographics. Moreover, the large cumulative public effect of the many new antibiotics and new bioproducts that were developed and commercialized on the basis of the science and technology after penicillin demonstrates that penicillin had the greatest therapeutic impact event of all times.     

Synthesis by high-efficiency liquid-phase (HELP) method of oligonucleotides conjugated with high-molecular weight polyethylene glycols (PEGs)

The chemical modification of synthetic oligonucleotides has recently been investigated to improve their pharmacological utilization. In addition to chemical alterations of the backbone and of the heterocyclic bases, their conjugation with amphiphylic moieties, such as the polyethylene glycol has been proposed. The large scale production of these molecules as demanded for commercial purposes is hampered by the heterogeneity of the solid-phase processes and by the low reactivity of high-molecular weight PEGs in solution. A new synthetic procedure based on the recently developed liquid-phase method (HELP), has been set up to overcome these limitations.     

重组土拉弗朗西斯菌外膜蛋白FopA的融合表达及抗原性分析

目的:探索一种大量表达功能性土拉弗朗西斯菌外膜蛋白FopA的方法。方法:采用SignalP 3.0 Server进行信号肽预测,将土拉弗朗西斯菌外膜蛋白FopA信号肽的基因序列(75bp)去除,将1107bp的核心序列克隆至原核表达载体pET32a,并在大肠杆菌BL21(DE3)中诱导表达。结果:构建了pET32a-fopA载体,重组蛋白FopA表达量约占菌体总蛋白量60%,Western blot分析显示重组FopA蛋白有较好的抗原性。结论:获得了高效表达FopA的pET32a-fopA表达载体,为下一步土拉弗朗西斯菌外膜蛋白FopA应用研究奠定了基础。