Mini-scale bioprocessing systems for highly parallel animal cell cultures

Animal cells have been used extensively in therapeutic protein production. The growth of animal cells and the expression of therapeutic proteins are highly dependent on the culturing environments. A large number of experimental permutations need to be explored to identify the optimal culturing conditions. Miniaturized bioreactors are well suited for such tasks as they offer high-throughput parallel operation and reduce cost of reagents. They can also be automated and be coupled to downstream analytical units for online measurements of culture products. This review summarizes the current status of miniaturized bioreactors for animal cell cultivation based on the design categories: microtiter plates, flasks, stirred tank reactors, novel designs with active mixing, and microfluidic cell culture devices. We compare cell density and product titer, for batch or fed-batch modes for each system. Monitoring/controlling devices for engineering parameters such as pH, dissolved oxygen, and dissolved carbon dioxide, which could be applied to such systems, are summarized. Finally, mini-scale tools for process performance evaluation for animal cell cultures are discussed: total cell density, cell viability, product titer and quality, substrates, and metabolites profiles.     

A generic hierarchical screening method for the analysis of microscale refolds using an automated robotic platform

The refolding of protein derived from inclusion bodies is often characterized by low yields of active protein. The optimization of the refolding step is achieved empirically and consequently is time-consuming slowing process development. An automated robotic platform has been used to develop a dilution refold process-screening platform upon which a hierarchical set of assays rapidly determine optimal refolding conditions at the microscale. This hierarchy allows the simplest, cheapest, and most generic high-throughput assays to first screen for a smaller subset of potentially high-yielding conditions to take forward for analysis by slower, more expensive, or protein specific assays, thus saving resources whilst maximizing information output. An absorbance assay was used to initially screen out aggregating conditions, followed by an intrinsic fluorescence assay of the soluble protein to identify the presence of native-like tertiary structure, which was then confirmed by an activity assay. Results show that fluorescence can be used in conjunction with absorbance to eliminate low-yielding conditions, leaving a significantly reduced set of conditions from which the highest yielding ones can then be identified with slower and often more costly activity or RP-HPLC assays, thus reducing bottlenecks in high-throughput analysis. The microwell-based automated process sequence with generic hierarchical assays was also used to study and minimize the effect on redox potential or misfolding, of oxygenation due to agitation, before demonstrating that the platform can be used to rapidly collect data and evaluate different refolding conditions to speed up the acquisition of process development data in a resource efficient manner.     

Taphonomic windows and molluscan preservation

Recent studies on silicified fossil biotas have suggested that substantial skewing of the molluscan record resulted from early aragonite dissolution in mid-outer carbonate ramp settings. If those rare skeletal lagerstätten are representative, then the quality and completeness of the molluscan record are thrown into doubt. Yet database studies suggest that the bivalve fossil record is actually relatively complete. If so, then biodiversity must be captured by other processes that preserved shells vulnerable to early dissolution, and which operated on a relatively high frequency, i.e., less than the species duration for bivalves.Storm beds, shell plasters and submarine hardgrounds are identified as fossil deposits that can preserve the labile aragonitic component of the fauna and thus represent potential taphonomic windows. Many storm event beds include rich accumulations of shelly benthos. Differences between storm bed faunas and those of the background facies could reflect transportation effects. However, some storm bed assemblages are rich in originally aragonitic infaunal bivalves that are not represented in background facies or more proximal shelf equivalents, and here rapid burial and removal of organic matter by winnowing may be the keys to aragonite shell preservation. Despite Palaeozoic to Cenozoic changes in the thickness and frequency of shell beds that reflect the predominant bioclast producers, shallow infaunas are commonly concentrated together with epifauna in such deposits.Some low energy, organic-rich mud-dominated settings are associated with preservation of aragonitic molluscs. Infaunal bivalves are a prominent component of shell plasters or pavements in such settings, linked to episodic bottom water anoxia. Decaying algal blooms drew the redox boundary up above the sediment–water interface, and brought populations of infaunal bivalves to the surface where they died. Isolated from the oxic taphonomically active zone, the shells were not dissolved and were buried as thin shell layers. In similar settings, aragonitic shells were preserved as moulds through early pyritisation, or even through preservation of original shell aragonite.In oxic environments, bioturbational reworking of surface sediment destroyed moulds of aragonitic shells after early dissolution. In some hardgrounds, these delicate moulds were preserved due to synsedimentary cementation, probably using carbonate released by aragonite dissolution. The examples included here come from both intervals of “calcite” and “aragonite” seas, and it is not possible to assess whether the saturation state (with respect to aragonite) of the ambient sea water played a role in the selective removal of aragonitic shells.While taphonomic windows may have captured the diversity of individual groups, it is clear from quantitative data involving skeletal lagerstätten that the scale of loss from early aragonite dissolution has drastically altered the trophic composition of some fossil assemblages commonly used as the basis for reconstructions of past communities.     

Recursive construction of perfect DNA molecules from imperfect oligonucleotides

Making faultless complex objects from potentially faulty building blocks is a fundamental challenge in computer engineering, nanotechnology and synthetic biology. Here, we show for the first time how recursion can be used to address this challenge and demonstrate a recursive procedure that constructs error‐free DNA molecules and their libraries from error‐prone oligonucleotides. Divide and Conquer (D&C), the quintessential recursive problem‐solving technique, is applied in silico to divide the target DNA sequence into overlapping oligonucleotides short enough to be synthesized directly, albeit with errors; error‐prone oligonucleotides are recursively combined in vitro, forming error‐prone DNA molecules; error‐free fragments of these molecules are then identified, extracted and used as new, typically longer and more accurate, inputs to another iteration of the recursive construction procedure; the entire process repeats until an error‐free target molecule is formed. Our recursive construction procedure surpasses existing methods for de novo DNA synthesis in speed, precision, amenability to automation, ease of combining synthetic and natural DNA fragments, and ability to construct designer DNA libraries. It thus provides a novel and robust foundation for the design and construction of synthetic biological molecules and organisms.     

太湖现生介形虫

分别于1989年和2004年两次共采集了43个太湖表层沉积物样品,检查发现其中的34个样品中含有现生介形虫,共计12属15种,其中Dolerocypria taalensis,Fabae formiscandona cf.fabaeformis,Physocypria kraepelini和Darwinula stevensoni等4个种最为常见和数量最多,构成了太湖现生介形虫群中的优势成分。长期以来,国内有学者将水体矿化度180mg／l作为介形虫生存的低极限值,由此认为矿化度低于此值的太湖等水体中不存在介形虫(杨留法,1986,1992)。本次调查和国外的相关资料证明,淡水介形虫可以在矿化度低于180mg／l的水体中生存。     

Automated Identification of Filaments in Cryoelectron Microscopy Images

Since the foundation for the three-dimensional image reconstruction of helical objects from electron micrographs was laid more than 30 years ago, there have been sustained developments in specimen preparation, data acquisition, image analysis, and interpretation of results. However, the boxing of filaments in large numbers of images--one of the critical steps toward the reconstruction at high resolution--is still constrained by manual processing even though interactive interfaces have been built to aid the tedious and sometimes inaccurate boxing process. This article describes an accurate approach for automated detection of filamentous structures in low-contrast images acquired in defocus pairs using cryoelectron microscopy. The performance of the approach has been evaluated across various magnifications and at a series of defocus values using tobacco mosaic virus (TMV) preserved in vitreous ice as a test specimen. By integrating the proposed approach into our automated data acquisition and reconstruction system, we are now able to generate a three-dimensional map of TMV to approximately 10-A resolution within 24 h of inserting the specimen grid into the microscope.     

Towards automation: Radiata pine shoot hedges in vitro

A novel system for in vitro shoot production has been developed whereby shoot hedges are maintained in one vessel. Monthly crops of shoots are produced for rooting. Radiata pine shoot hedges were maintained on Lepoivre (LP) nutrient agar medium for 18 months using a weekly liquid-nutrient replenishment system. In a separate experiment liquid-LP-nutrient replenishment of shoots twice weekly without transfers (D) resulted in better shoot growth and health than monthly transfers to fresh agar medium (B), monthly transfers to fresh agar medium plus aeration twice weekly (C), or no transfers and no liquid nutrient addition (A). Liquid nutrient replenishment twice weekly was better than 2 weekly or 4 weekly replenishment. The percentage of normal waxy (abundant tubular epicuticular wax) shoots harvested monthly increased significantly over the culture period from 41% at the first harvest to 93% at the eight harvest, and remained high at 97% from the ninth to twelfth harvest. The percentage of wet (no tubular epicuticular wax, small amounts of globular epicuticular wax) shoots harvested showed a corresponding decline—from 59%, to 7% at the eighth harvest. Shoots were harvested at a rate of 672/h (1.19 cents/shoot at a labour cost of NZ$8.00/h) and approximately 1100 shoots were produced per square metre of agar surface per month. Initial problems of contamination and crowding were overcome. These results will greatly facilitate progress towards automation of shoot production and reduction of costs of micropropagated trees. An automated system used in combination with other cost-saving techniques or robotics could potentially result in a substantial reduction in costs. This is the first report of a method of culturing shoots as hedges for a period of up to 18 months without manual subculturing.     

Rapid Analysis of Protein Structure and Dynamics by Hydrogen/Deuterium Exchange Mass Spectrometry

An automated approach for the rapid analysis of protein structure has been developed and used to study acid-induced conformational changes in human growth hormone. The labeling approach involves hydrogen/deuterium exchange (H/D-Ex) of protein backbone amide hydrogens with rapid and sensitive detection by mass spectrometry (MS). Briefly, the protein is incubated for defined intervals in a deuterated environment. After rapid quenching of the exchange reaction, the partially deuterated protein is enzymatically digested and the resulting peptide fragments are analyzed by liquid chromatography mass spectrometry (LC-MS). The deuterium buildup curve measured for each fragment yields an average amide exchange rate that reflects the environment of the peptide in the intact protein. Additional analyses allow mapping of the free energy of folding on localized segments along the protein sequence affording unique dynamic and structural information. While amide H/D-Ex coupled with MS is recognized as a powerful technique for studying protein structure and protein–ligand interactions, it has remained a labor-intensive task. The improvements in the amide H/D-Ex methodology described here include solid phase proteolysis, automated liquid handling and sample preparation, and integrated data reduction software that together improve sequence coverage and resolution, while achieving a sample throughput nearly 10-fold higher than the commonly used manual methods.     

Weathering of Granite from the Damma Glacier Area: The Contribution of Cyanogenic Bacteria

The dissolution potential of five cyanogenic bacteria was studied at 25°C during 32 days using granite material from the Damma glacier (Central Alps, Switzerland) as the sole source of nutrients. The bacterial species Pseudomonas fluorescens and Pseudomonas sp. CCOS 191 were the most effective to exudate various organic acids and consequently mobilized Fe. The molecular mechanisms include both, proton-promoted and ligand-promoted dissolution, preferentially at pH below 5 and in the pH range between 5.0 and 5.8, respectively. In addition, bacterially produced cyanide plays a minor role through the formation of soluble hexacyanoferrate complexes. To our knowledge, this study is the first that reveals the direct measurement of metal-cyanide complexes formed during biotic granite weathering.