Synthesis of bioprocesses using physical properties data

The aim of this article is to illustrate and evaluate a synthesis procedure which has been extended to tackle bioprocesses. Physical property information is used to screen candidate units thereby reducing the size of the synthesis problem. In this way, only units which exploit large property differences between components in a stream are selected. This is important for bioprocesses because of the large number of components and wide range of unit operations which are available. The screening technique and bioprocess-unit-design methodologies have been incorporated within an implicit enumeration algorithm which was developed for chemical process synthesis and is implemented in Java programming language. An important advantage is the ability of the bioprocess synthesis software to generate a ranked list of flowsheets which may subsequently be analyzed in more detail. Two case studies are used to evaluate the bioprocess-synthesis technique. The first system involves a product which is secreted from the host organism. The second has significantly different characteristics in that the product is intracellular and forms inclusion bodies. The latter case study, in particular, is a large synthesis problem with 12 unit operations and 20 contaminant compounds. The results show that the synthesis methodology identifies a set of economically optimal flowsheets in a reasonable computational time which demonstrates its ability to deal with large synthesis problems. Using the synthesis methodology we can generate bioprocesses which are optimal in a system-wide, rather than unit-by-unit, sense.     

Biosensors: recent trends

One of the major bottlenecks in automation and process control of industrial bioprocesses is the lack of suitable sensing devices to accurately measure the concentrations of biomolecules. The measurement of ions (e.g., H⁺, NH₄⁺) and gases (e.g., O₂, CO₂, NH₃) using standard ion-selective and gas sensing electrodes respectively, is well established. Chemical analysis of biomolecules off-line is generally unreliable, labour intensive and may lead to contamination of the biological systems. Problems of maintaining sterile conditions are especially important when dealing with slow growing mammalian or plant cells in culture. Active research in the development of biosensors for monitoring fermentation processes, food production and pollution control, and for medical and veterinary applications is currently underway. This paper reviews recent approaches toward the development of biosensors which involve a biochemical interaction to measure the concentrations of biomolecules, primarily for the on-line monitoring and control of fermentation processes.     

An instrument to evaluate the time dependent flow properties of blood at moderate shear rates

The rheology of blood is characterized by shear thinning, viscoelasticity, and thixotropy. Its rheological evaluation is usually accomplished using a torque balance technique during rotational viscometry. Because a stable torque balance does not develop instantly, studies of thixotropy and viscoelasticity of blood have usually been carried out only at low shear rate where their development is slow enough to be monitored accurately. The torque balance technique may be converted from static to dynamic by incorporating the rate of change of sensing system angular momentum. We have modified our Couette viscometer, adding a computer-controlled stepping motor and a second digital voltmeter. The latter is used to determine the angular position of the sensing system every 25 or 50 msec. The new approach allows rapid observation of the development and disappearance of shear stress, enabling us to examine the transient behavior of blood at moderate shear rate (1 to 100 inverse seconds). The transient flow behavior of blood at moderate shear rate is most easily compared directly with the behavior of Newtonian fluids. We present information about the response of our system using a torque balance observation rate of 20 per second. Blood's viscoelasticity is observed to fall substantially as shear rate rises, while its thixotropic transient excess stress rises steadily with increasing shear rate.     

Biocatalysis: applications and potentials for the chemical industry

The chemical industry is exploring the use of renewable feed stocks to improve sustainability, prompting the exploration of bioprocesses for the production of chemicals. Attractive features of biological systems include versatility, substrate selectivity, regioselectivity, chemoselectivity, enantioselectivity and catalysis at ambient temperatures and pressures. However, a challenge facing bioprocesses is cost competitiveness with chemical processes because capital assets associated with the existing commercial processes are high. The chemical industry will probably use biotechnology with existing feed stocks and processes to extract higher values from feed stocks, process by-products and waste streams. In this decade, bioprocesses that offer either a process or a product advantage over traditional chemical routes will become more widely used.     

分子对接技术在研究群体感应抑制剂中的进展

在大多数致病菌中都存在群体感应系统,而群体感应抑制剂就是以此系统作为靶点,在不影响细菌生长的情况下阻断细菌生物被膜形成或抑制毒力基因表达,不易导致耐药性的产生,是一种理想的抗菌增效剂。分子对接作为虚拟筛选技术之一,其目标具体、效率高、成本低,是药物研发的重要手段。本文重点介绍了分子对接的主要模块及其在研究群体感应抑制剂中的进展。     

Real-time dissolved carbon dioxide monitoring I: Application of a novel in situ sensor for CO2 monitoring and control

Dissolved carbon dioxide (dCO₂) is a well-known critical parameter in bioprocesses due to its significant impact on cell metabolism and on product quality attributes. Processes run at small-scale faces many challenges due to limited options for modular sensors for online monitoring and control. Traditional sensors are bulky, costly, and invasive in nature and do not fit in small-scale systems. In this study, we present the implementation of a novel, rate-based technique for real-time monitoring of dCO₂ in bioprocesses. A silicone sampling probe that allows the diffusion of CO₂ through its wall was inserted inside a shake flask/bioreactor and then flushed with air to remove the CO₂ that had diffused into the probe from the culture broth (sensor was calibrated using air as zero-point calibration). The gas inside the probe was then allowed to recirculate through gas-impermeable tubing to a CO₂ monitor. We have shown that by measuring the initial diffusion rate of CO₂ into the sampling probe we were able to determine the partial pressure of the dCO₂ in the culture. This technique can be readily automated, and measurements can be made in minutes. Demonstration experiments conducted with baker's yeast and Yarrowia lipolytica yeast cells in both shake flasks and mini bioreactors showed that it can monitor dCO₂ in real-time. Using the proposed sensor, we successfully implemented a dCO₂-based control scheme, which resulted in significant improvement in process performance.     

Engineering of a green‐light inducible gene expression system in Synechocystis sp. PCC6803

In order to construct a green‐light‐regulated gene expression system for cyanobacteria, we characterized a green‐light sensing system derived from Synechocystis sp. PCC6803, consisting of the green‐light sensing histidine kinase CcaS, the cognate response regulator CcaR, and the promoter of cpcG2 (P_cpcG2). CcaS and CcaR act as a genetic controller and activate gene expression from P_cpcG2 with green‐light illumination. The green‐light induction level of the native P_cpcG2 was investigated using GFPuv as a reporter gene inserted in a broad‐host‐range vector. A clear induction of protein expression from native P_cpcG2 under green‐light illumination was observed; however, the expression level was very low compared with P_trc, which was reported to act as a constitutive promoter in cyanobacteria. Therefore, a Shine‐Dalgarno‐like sequence derived from the cpcB gene was inserted in the 5′ untranslated region of the cpcG2 gene, and the expression level of CcaR was increased. Thus, constructed engineered green‐light sensing system resulted in about 40‐fold higher protein expression than with the wild‐type promoter with a high ON/OFF ratio under green‐light illumination. The engineered green‐light gene expression system would be a useful genetic tool for controlling gene expression in the emergent cyanobacterial bioprocesses.     

Process economics evaluation of cell-free synthesis for the commercial manufacture of antibody drug conjugates

Continuous improvements of cell-free synthesis (CFS) systems have generated interest in adopting the technology for the manufacture of biologics. This paper provides an evaluation of the manufacturing cost-effectiveness of CFS for the commercial production of antibody-drug conjugates (ADCs). The evaluation was performed using an advanced techno-economic engine (TEE) built in Python. The TEE is programmed in an object-oriented environment capable of simulating a plethora of process flowsheets and predicting size and cost metrics for the process and the facility. A case study was formulated to compare the economics of whole bioprocesses based on either a CFS system or a mammalian cell system (CHO) for the manufacture of an ADC at a range of product demands. The analysis demonstrated the potential of CFS for the commercial manufacture of biologics and identified key cost drivers related to the system. The CFS system showed an approximately 80% increase in the cost of goods compared to CHO with a significant cost attributed to the in-house manufacture of the bacterial cell extract, necessary for the CFS reaction step in the process. A sensitivity and target analysis highlighted the need for further process improvements especially in the titer for the CFS process to become more competitive against well-established systems.     

Determination of trace copper ions with ultrahigh sensitivity and selectivity utilizing CdTe quantum dots coupled with enzyme inhibition

Nanomaterial-based enzyme-linked immunosorbent assay (ELISA) with sufficient sensing specificity is a useful analytical tool for the detection of toxicologically important substances in complicated biological systems. Increasing worldwide demand for nanomaterials and increasing concern on their safe development and use, require a simple, stable, and sensitive detection assay for pathogen evaluation and environmental monitoring. However, this goal is not yet achieved. A design for a hybrid MnO(2) nanowire-ELISA using the sandwich assay format, which provides quantitative binding information for both a specific antibody and the pathogen, sulfate-reducing bacteria, and detects pathogen concentration, is presented. 3,3',5,5'-Tetramethylbenzidine was used as the substrate and was allowed to react with the MnO(2) nanowires without H(2)O(2) in the reaction system. The kinetic parameters were measured with the system acting as a catalytic biosensor. The effectiveness of the MnO(2) nanowire-based biosensor was demonstrated by its sensitive detection of the pathogen.     

植物对开放式CO2 浓度增高(FACE)的响应与适应研究进展

开放式CO2浓度增高(FACE)系统是近年研究植物对高CO2浓度响应和适应的新手段,它比以往密闭和半密闭系统对实验植物生长环境的干扰少.利用FACE系统进行研究更有助于正确地预测未来大气CO2浓度增高对植物的影响.该文结合作者的研究工作简要评介了FACE系统与以往密闭和半密闭式CO2浓度增高实验系统的不同之处以及近年来利用FACE系统所作的最新研究进展.     

轻小型无人机低空遥感及其在生态学中的应用进展

无人机低空遥感系统弥补了航天和航空遥感在影像分辨率、重访周期、云层影响以及高成本等方面的不足,为中观尺度的生态学研究提供了新方法.本文介绍了轻小型无人机低空遥感系统的组成,从物种、种群、群落和生态系统尺度综述了其在生态学中的应用现状,并指出目前存在的不足和未来的发展方向,以期为无人机生态学的后续研究提供参考.无人机生态学当前面临的挑战和未来发展的方向主要有物种形态和光谱特征库的建立、物种自动识别、光谱数据与植物生理生态过程之间关系的进一步挖掘、生态系统三维立体监测、多来源多尺度遥感数据融合等.随着无人机平台技术、传感器技术以及数据传输处理技术的成熟,以无人机低空遥感技术为基础的无人机生态学将迎来发展的机遇和曙光.     

Development and evaluation of an online CO(2) evolution test and a multicomponent biodegradation test system

Well-established biodegradation tests use biogenously evolved carbon dioxide (CO(2)) as an analytical parameter to determine the ultimate biodegradability of substances. A newly developed analytical technique based on the continuous online measurement of conductivity showed its suitability over other techniques. It could be demonstrated that the method met all criteria of established biodegradation tests, gave continuous biodegradation curves, and was more reliable than other tests. In parallel experiments, only small variations in the biodegradation pattern occurred. When comparing the new online CO(2) method with existing CO(2) evolution tests, growth rates and lag periods were similar and only the final degree of biodegradation of aniline was slightly lower. A further test development was the unification and parallel measurement of all three important summary parameters for biodegradation--i.e., CO(2) evolution, determination of the biochemical oxygen demand (BOD), and removal of dissolved organic carbon (DOC)--in a multicomponent biodegradation test system (MCBTS). The practicability of this test method was demonstrated with aniline. This test system had advantages for poorly water-soluble and highly volatile compounds and allowed the determination of the carbon fraction integrated into biomass (heterotrophic yield). The integrated online measurements of CO(2) and BOD systems produced continuous degradation curves, which better met the stringent criteria of ready biodegradability (60% biodegradation in a 10-day window). Furthermore the data could be used to calculate maximal growth rates for the modeling of biodegradation processes.     

CO(2) acts as a signalling molecule in populations of the fungal pathogen Candida albicans

When colonising host-niches or non-animated medical devices, individual cells of the fungal pathogen Candida albicans expand into significant biomasses. Here we show that within such biomasses, fungal metabolically generated CO(2) acts as a communication molecule promoting the switch from yeast to filamentous growth essential for C. albicans pathology. We find that CO(2)-mediated intra-colony signalling involves the adenylyl cyclase protein (Cyr1p), a multi-sensor recently found to coordinate fungal responses to serum and bacterial peptidoglycan. We further identify Lys 1373 as essential for CO(2)/bicarbonate regulation of Cyr1p. Disruption of the CO(2)/bicarbonate receptor-site interferes selectively with C. albicans filamentation within fungal biomasses. Comparisons between the Drosophila melanogaster infection model and the mouse model of disseminated candidiasis, suggest that metabolic CO(2) sensing may be important for initial colonisation and epithelial invasion. Our results reveal the existence of a gaseous Candida signalling pathway and its molecular mechanism and provide insights into an evolutionary conserved CO(2)-signalling system.     

A rapid analytical technique for the determination of energy expenditure by the doubly labelled water method

The doubly labelled water method involves the administration of water enriched in 2H and 18O followed by determination of the turnover rates of these isotopes. Since 18O is eliminated from the body as both CO2 and water, while 2H leaves only as water, the difference between the two turnover rates provides a measure of CO2 production and hence energy expenditure. Isotopic analysis by conventional stable isotope ratio analysis (SIRA) is labour intensive and time consuming, as it requires off-line conversion of water samples to gases (H2 and CO2) followed by sequential analysis for each of the two isotopes using the mass spectrometer. Lack of suitable automated instrumentation with the ability to process large numbers of samples has prevented routine application of the method. We describe here an automated technique in which body water samples (urine, saliva, breath water or milk) are analysed simultaneously for 2H and 18O. The single bench system comprises two mass spectrometer analysers, one for measuring 2H from H2 gas, the other for measuring 18O from the water vapour (masses 18, 20). Both analysers share a common heated inlet system into which microlitre quantities of the body fluids are injected from an autosampler (102 samples). The water vapour flows both directly to one analyser for 18O measurement and into a uranium reduction furnace for conversion to H2, prior to 2H measurement by the second analyser. Both analysers also share vacuum and electronic components, enabling savings in both space and cost. In this paper we present results illustrating performance characteristics and procedures for routine application to human subjects.(ABSTRACT TRUNCATED AT 250 WORDS)     

CO2/H(+) sensing: peripheral and central chemoreception

H(+) is maintained constant in the internal environment at a given body temperature independent of external environment according to Bernard's principle of "milieu interieur". But CO2 relates to ventilation and H(+) to kidney. Hence, the title of the chapter. In order to do this, sensors for H(+) in the internal environment are needed. The sensor-receptor is CO2/H(+) sensing. The sensor-receptor is coupled to integrate and to maintain the body's chemical environment at equilibrium. This chapter dwells on this theme of constancy of H(+) of the blood and of the other internal environments. [H(+)] is regulated jointly by respiratory and renal systems. The respiratory response to [H(+)] originates from the activities of two groups of chemoreceptors in two separate body fluid compartments: (A) carotid and aortic bodies which sense arterial P(O2) and H(+); and (B) the medullary H(+) receptors on the ventrolateral medulla of the central nervous system (CNS). The arterial chemoreceptors function to maintain arterial P(O2) and H(+) constant, and medullary H(+) receptors to maintain H(+) of the brain fluid constant. Any acute change of H(+) in these compartments is taken care of almost instantly by pulmonary ventilation, and slowly by the kidney. This general theme is considered in Section 1. The general principles involving cellular CO2 reactions mediated by carbonic anhydrase (CA), transport of CO2 and H(+) are described in Section 2. Since the rest of the chapter is dependent on these key mechanisms, they are given in detail, including the role of Jacobs-Stewart Cycle and its interaction with carbonic anhydrase. Also, this section deals briefly with the mechanisms of membrane depolarization of the chemoreceptor cells because this is one mechanism on which the responses depend. The metabolic impact of endogenous CO2 appears in the section with a historical twist, in the context of acclimatization to high altitude (Section 3). Because low P(O2) at high altitude stimulates the peripheral chemoreceptors (PC) increasing ventilation, the endogenous CO2 is blown off, making the internal milieu alkaline. With acclimatization however ventilation increases. This alkalinity is compensated in the course of time by the kidney and the acidity tends to be restored, but the acidification is not great enough to increase ventilation further. The question is what drives ventilation during acclimatization when the central pH is alkaline? The peripheral chemoreceptor came to the rescue. Its sensitivity to P(O2) is increased which continues to drive ventilation further during acclimatization at high altitude even when pH is alkaline. This link of CO2 through the O2 chemoreceptor is described in Section 4 which led to hypoxia-inducible factor (HIF-1). HIF-1 is stabilized during hypoxia, including the carotid body (CB) and brain cells, the seat of CO2 chemoreception. The cells are always hypoxic even at sea level. But how CO2 can affect the HIF-1 in the brain is considered in this section. CO2 sensing in the central chemoreceptors (CC) is given in Section 5. CO(2)/H(+) is sensed by the various structures in the central nervous system but its respiratory and cardiovascular responses are restricted only to some areas. How the membranes are depolarized by CO2 or how it works through Na(+)/Ca(2+) exchange are discussed in this section. It is obvious, however, that CO2 is not maintained constant, decreasing with altitude as alveolar P(O2) decreases and ventilation increases. Rather, it is the [H(+)] that the organism strives to maintain at the expense of CO2. But then again, [H(+)] where? Perhaps it is in the intracellular environment. Gap junctions in the carotid body and in the brain are ubiquitous. What functions they perform have been considered in Section 6. CO2 changes take place in lung alveoli where inspired air mixes with the CO2 from the returning venous blood. It is the interface between the inspired and expired air in the lungs where CO2 change is most dramatic. As a result, various investigators have looked for CO2 receptors in the lung, but none have been found in the mammals. Instead, CO2/H(+) receptors were found in birds and amphibians. However, they are inhibited by increasing CO2/H(+), instead of stimulated. But the afferent impulses transmitted to the brain produced stimulation in the efferents. This reversal of afferent-efferent inputs is a curious situation in nature, and this is considered in Section 7. The NO and CO effects on CO2 sensing are interesting and have been briefly mentioned in Section 8. A model for CO2/H(+) sensing by cells, neurons and bare nerve endings are also considered. These NO effects, models for CO2/H(+) and O2-sensitive cells in the CNS have been considered in the perspectives. Finally, in conclusion, the general theme of constancy of internal environment for CO2/H(+) is reiterated, and for that CO2/H(+) sensors-receptors systems are essential. Since CO2/H(+) sensing as such has not been reviewed before, the recent findings in addition to defining basic CO2/H(+) reactions in the cells have been briefly summarized.     

Digital Computer Simulation of Respiratory Response to Cerebrospinal Fluid PCO2 in the Cat

The respiratory control system is treated as linear with a transmission delay between ventilation and sensing points (chemoreceptors). To the accepted variables involving body gas stores, ventilatory effects, transmission effects, and steady state pH, P(CO2), P(O2) chemoreceptor response, certain detailed analysis of the central receptors have been added. By construction of a model for medullary CO(2) receptor utilizing expected values of CNS (central nervous system) circulation, CO(2) production, and tissue-buffering effects, results of experimental observation of the effects of alteration of CSF were simulated. The inclusion of CSF effects also allowed simulation of the response to alteration in inspired CO(2), hyperventilation, and the periodic breathing with prolongation of circulation time.     

Use of at-line spectrophotometry for the rapid definition of pilot-scale flocculation processes

Traditionally most downstream bioprocesses have been operated without real-time knowledge of product and key contaminants, yielding little confidence in their operation and the impact on subsequent operations. A rapid UV-vis spectral prediction technique has been successfully demonstrated for the at-line characterization of a large scale continuous flocculation process in terms of RNA, key protein contaminants, and cell debris. A comparison was made between the spectral predictions and retrospective wet chemical assays, and a highly linear correlation was obtained. The spectral analysis technique allowed for real-time system information, which was applied to control the flocculation process to maintain satisfactory process performance, even when subjected to given possible process disturbances.     

High-stability non-invasive autoclavable naked optical CO2 sensor

The fabrication and characterization of a high-stability non-invasive autoclavable naked optical CO(2) sensor is described in this report. The sensor was made by using 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS) as the fluorescence dye and cetyltrimethylammonium hydroxide (CTMAOH) as the phase transfer agent (the base). A highly hydrophobic two-component silicone film was used as the polymer matrix, which overcame some of the limitations of the existing plastic type CO(2) sensors, such as dye leaching and cross-sensitivity to ions. To improve the stability of the sensor, several affecting factors were investigated. Experimental results showed that sufficient base and a small amount of water in the sensing film were critical factors that affected the stability of the sensor. Although the sensor was more stable when kept in water, the function of the sensor could recover when the sensor kept in air was transferred into water. The sensor has a lifetime of several months. The detection limit of the sensing film was about 0.03%. The average response and recovery times were 0.66 and 1.94 min, respectively. It had no cross-sensitivity to salt concentrations in the range of 0-0.2 M and to pH in the range of 5.6-8.0, so it can be used in processes with changing ion concentration and pH. It was sterilizable and could be autoclaved many times without losing its sensitivity. The applicability of the sensor in real application was successfully tested in the fermentation of Escherichia coli.