Active and machine learning-based approaches to rapidly enhance microbial chemical production

In order to make renewable fuels and chemicals from microbes, new methods are required to engineer microbes more intelligently. Computational approaches, to engineer strains for enhanced chemical production typically rely on detailed mechanistic models (e.g., kinetic/stoichiometric models of metabolism)—requiring many experimental datasets for their parameterization—while experimental methods may require screening large mutant libraries to explore the design space for the few mutants with desired behaviors. To address these limitations, we developed an active and machine learning approach (ActiveOpt) to intelligently guide experiments to arrive at an optimal phenotype with minimal measured datasets. ActiveOpt was applied to two separate case studies to evaluate its potential to increase valine yields and neurosporene productivity in Escherichia coli. In both the cases, ActiveOpt identified the best performing strain in fewer experiments than the case studies used. This work demonstrates that machine and active learning approaches have the potential to greatly facilitate metabolic engineering efforts to rapidly achieve its objectives.     

Media optimization studies for glucose isomerase production by arthrobacter species

Media optimization studies are carried out with the objective of maximising glucose isomerase production by Arthrobacter sp. The recommended media consists of 1.0% (w/v) xylose, 1.0% peptone, 0.5% yeast extract, 0.025% MgSO₄·7H₂O, 0.6% (NH₄)₂HPO₄ and 0.2% KH₂PO₄. Activity of the enzyme produced in this media is 11.2 units/ml. Growth cycle for batch cultivation is studied and the lag period is 2 hours, followed by exponential phase extending upto 32 hours.     

A chemical surface modification of chitosan by glycoconjugates to enhance the cell-biomaterial interaction

The use of wheat germ agglutinin (WGA), a lectin molecule, to modify chitosan and enhance the cell-biomaterial interaction was examined. The percentage of living fibroblast cells on the surfaces of tissue culture polystyrene (TCPS) control, WGA-modified chitosan, and unmodified chitosan films increased to 99%, 99%, and 85%, respectively, after seeding for 48 h. DNA staining revealed that a portion of fibroblasts cultivated on chitosan films( )were undergoing apoptosis. In contrast, fibroblasts growing on WGA-modified chitosan film surfaces did not show any indication of apoptosis. The number of fibroblast cells was the highest on the WGA-modified chitosan surfaces, followed by the TCPS and unmodified chitosan surfaces. This WGA-mediated enhancement on the fibroblast cell-biomaterial interaction was cell type dependent. Other types of cells may need different lectin molecules for enhanced interaction with biomaterials. Further, the evaluation of the heat shock protein (HSP) mRNA expression indicated that HSP 90 expression was increased in the fibroblast cells cultivated on chitosan films and decreased to basal levels on the WGA-modified chitosan films. Taken together, our data suggest that the use of WGA and other lectin molecules to enhance the cell-biomaterial interaction via oligosaccharide-mediated cell adhesion is a promising way to improve cell adhesion and proliferation, the two key issues in tissue engineering.     

Formulation of medium constituents by multiresponse analysis of central composite design to enhance chitinase production in Pantoea dispersa

In the present study, a high chitinase producing strain Pantoea dispersa was isolated from the sea dumps at Bhavnagar, India. Chitin, urea, CaCl2 and MgSO4 x 7H2O were variables used in central composite design for chitinase production. Chitinase, biomass and pH were the responses used in different models to evaluate individually fit ones. Quadratic model was found to be fit for chitinase response whereas in the case of biomass and pH, linear model was found to be fit without the effect of others. Chitinase production was optimized with respect to other responses such as biomass and pH in multiresponse analysis of response surface design by using desirability approach. In multiresponse analysis, following medium formulation (g/l), chitin, 15; urea, 0.32; CaCl2, 0.10 and MgSO4 x 7H2O, 0.08 was found to predict optimum chitinase production of 482.77 units/ml with overall highest desirability of 0.854 as compared to other formulations. The selection of model was done on the basis of high Adjusted R-squared value and lowered p-value for each model in individual analysis of each response. In multiresponse experiment, it was found that for response chitinase quadratic model and for responses pH and biomass linear models were well fit. Through desirability analysis, it was found that in the chitinase production, pH was essential as compared to biomass in P. dispersa. Endochitinase and chitobiase actvities were also studied.     

Methods to enhance signal using isotopic in situ hybridization.

Isotopic in situ hybridization (ISH) has been established as a uniquely powerful tool for the study of gene expression in specific cell types. This technique allows the visualization and quantification of gene expression and gene expression changes in cells. In our study of biological and molecular phenomena, we have increasingly encountered the need to detect small changes in gene expression as well as genes of low abundance, such as the oxytocin receptor (OTR) and the tuberoinfundibular peptide of 39 residues (Tip39). To increase the sensitivity of isotopic ISH for detection of rare mRNAs, we performed ISH on cryostat sections of rat hypothalamus and thalamus with 35S-labeled riboprobes and amplified the signal by hybridizing over 2 nights as well as labeling the probe with both [35S]-UTP and [35S]-ATP. These two methods of enhancement independently and in combination demonstrated a dramatic increase in signal, allowing the visualization of low levels of gene expression previously undetectable by conventional methods.     

Simultaneous heat shock and in situ adsorption enhance plumbagin production in Plumbago indica root cultures

Plumbago indica L. is an important source of plumbagin, a commercially valuable bioactive compound. However, the uses of plumbagin are limited due to its low supply as well as low yields and slow growth of the plant sources. This study evaluated the use of a simple, easy, and low‐cost approach using heat shock (HS) and ultrasound (US), and an in situ adsorption using a nonpolar copolymer adsorbent styrene‐divynilbenzene resin (Diaion^® HP‐20) to enhance plumbagin production in Plumbago indica root cultures. Treatment with HS (60°C) for 10 min significantly increased the production of plumbagin (5.51 mg/g DW) by up to five‐fold, compared to the level in untreated root cultures (1.14 mg/g DW). In contrast, treatments with US alone or with HS treatment produced no satisfactory increase of plumbagin production. However, combined treatment of a 20‐day‐old root culture with HS (60°C, for 10 min) in the presence of Diaion^® HP‐20 (10 g/L) markedly increased the production up to 20.28 mg/g DW of plumbagin that was almost 14‐fold higher, compared to the level in an untreated root culture. Such an increase would be sufficient for commercial applications of this method to produce plumbagin.     

Proposals to enhance the quality of observational cohort studies

For herbal medicinal products the methodology of observational cohort studies (observational studies, drug monitoring studies, Anwendungsbeobachtung) represents a useful addition to clinical trials. The key objectives are the documentation of efficacy in particular under conditions of everyday medical practice in authentic patients and the documentation of the safety profile. Supplementary to earlier activities, members of the "Clinical Trials of Herbal Medicinal Products" Working Party of the German Society for Phytotherapy have therefore again addressed the issue of observational cohort studies for to enhance the informative value and importance of this clinical research methodology. Recommendations were developed on quality aspects, methodological approaches of observation parameters, and for the reporting of the study's results. Properly planned and conducted observational cohort studies may contribute to the documentation and proof of well-established medicinal use according the EU Directive 2001/83/EC.     

Combining metabolic flux analysis and adaptive evolution to enhance lipase production in Bacillus subtilis

Journal of Industrial Microbiology & Biotechnology - Metabolic fluxes during lipase production by Bacillus subtilis CICC 20034 in synthetic medium were studied using metabolic flux analysis...     

Metabolic engineering to enhance bacterial hydrogen production

Hydrogen fuel is renewable, efficient and clean, and fermentative bacteria hold great promise for its generation. Here we use the isogenic Escherichia coli K‐12 KEIO library to rapidly construct multiple, precise deletions in the E. coli genome to direct the metabolic flux towards hydrogen production. Escherichia coli has three active hydrogenases, and the genes involved in the regulation of the formate hydrogen lyase (FHL) system for synthesizing hydrogen from formate via hydrogenase 3 were also manipulated to enhance hydrogen production. Specifically, we altered regulation of FHL by controlling the regulators HycA and FhlA, removed hydrogen consumption by hydrogenases 1 and 2 via the hyaB and hybC mutations, and re‐directed formate metabolism using the fdnG, fdoG, narG, focA, fnr and focB mutations. The result was a 141‐fold increase in hydrogen production from formate to create a bacterium (BW25113 hyaB hybC hycA fdoG/pCA24N‐FhlA) that produces the largest amount of hydrogen to date and one that achieves the theoretical yield for hydrogen from formate. In addition, the hydrogen yield from glucose was increased by 50%, and there was threefold higher hydrogen production from glucose with this strain.     

Solid state NMR chemical shift assignment and conformational analysis of a cellulose binding protein facilitated by optimized glycerol enrichment

Magic-angle spinning solid-state NMR has been applied to study CBM3b–Cbh9A (CBM3b), a cellulose binding module protein belonging to family 3b. It is a 146-residue protein having a unique nine-stranded β-sandwich fold, in which 35 % of the structure is in a β-sheet conformation and the remainder of the protein is composed of loops and unstructured regions. Yet, the protein can be crystalized and it forms elongated needles. Close to complete chemical shift assignment of the protein was obtained by combining two- and three-dimensional experiments using a fully labeled sample and a glycerol-labeled sample. The use of an optimized protocol for glycerol-based sparse labeling reduces sample preparation costs and facilitates the assignment of the large number of aromatic signals in this protein. Conformational analysis shows good correlation between the NMR-predicted secondary structure and the reported X-ray crystal structure, in particular in the structured regions. Residues which show high B-factor values are situated mainly in unstructured regions, and are missing in our spectra indicating conformational flexibility rather than heterogeneity. Interestingly, long-range contacts, which could be clearly detected for tyrosine residues, could not be observed for aromatic phenylalanine residues pointing into the hydrophobic core, suggesting possible high ring mobility. These studies will allow us to further investigate the cellulose-bound form of CBM proteins.     

Enzymatic microreactors in chemical analysis and kinetic studies

The fields of application of microreactors are becoming wider every year. A considerable number of papers have been published recently reporting successful application of enzymatic microreactors in chemistry and biochemistry. Most are devices with enzymes immobilized on beads or walls of microfluidic channels, whilst some use dissolved enzymes to run a reaction in the microfluidic system. Apart from model systems, mostly with glucose oxidase, horseradish peroxidase and alkaline phosphatase, the principal fields of application of microreactors are tryptic digestion of proteins and polymerase chain reaction in automated analyses of proteomic and genetic material, respectively. Enzymatic microreactors also facilitate characterization of enzyme activity as a function of substrate concentration, and enable fast screening of new biocatalysts and their substrates. They may constitute key parts of lab-on-a-chip and muTAS, assisting the analysis of biomolecules. This review provides systematic coverage of examples of reports on enzymatic microreactors published recently, as well as relevant older papers.     

Tuber-specific cphA expression to enhance cyanophycin production in potatoes

The production of biodegradable polymers that can be used to substitute petrochemical compounds in commercial products in transgenic plants is an important challenge for plant biotechnology. Nevertheless, it is often accompanied by reduced plant fitness. To decrease the phenotypic abnormalities of the sprout and to increase polymer production, we restricted cyanophycin accumulation to the potato tubers by using the cyanophycin synthetase gene ( cph A_Te) from Thermosynechococcus elongatus BP-1, which is under the control of the tuber-specific class 1 promoter (B33). Tuber-specific cytosolic (pB33- cph A_Te) as well as tuber-specific plastidic (pB33-PsbY- cph A_Te) expression resulted in significant polymer accumulation solely in the tubers. In plants transformed with pB33- cph A_Te, both cyanophycin synthetase and cyanophycin were detected in the cytoplasm leading to an increase up to 2.3% cyanophycin of dry weight and resulting in small and deformed tubers. In B33-PsbY- cph A_Te tubers, cyanophycin synthetase and cyanophycin were exclusively found in amyloplasts leading to a cyanophycin accumulation up to 7.5% of dry weight. These tubers were normal in size, some clones showed reduced tuber yield and sometimes exhibited brown sunken staining starting at tubers navel. During a storage period over of 32 weeks of one selected clone, the cyanophycin content was stable in B33-PsbY- cph A_Te tubers but the stress symptoms increased. However, all tubers were able to germinate. Nitrogen fertilization in the greenhouse led not to an increased cyanophycin yield, slightly reduced protein content, decreased starch content, and changes in the amounts of bound and free arginine and aspartate, as compared with control tubers were observed.     

Co-fermentation of carbon sources by Enterobacter aerogenes ATCC 29007 to enhance the production of bioethanol

We investigated the enhancement of bioethanol production in Enterobacter aerogenes ATCC 29007 by co-fermentation of carbon sources such as glycerol, glucose, galactose, sucrose, fructose, xylose, starch, mannitol and citric acid. Biofuel production increases with increasing growth rate of microorganisms; that is why we investigated the optimal growth rate of E. aerogenes ATCC 29007, using mixtures of different carbon sources with glycerol. E. aerogenes ATCC 29007 was incubated in media containing each carbon source and glycerol; growth rate and bioethanol production improved in all cases compared to those in medium containing glycerol alone. The growth rate and bioethanol production were highest with mannitol. Fermentation was carried out at 37 °C for 18 h, pH 7, using 50 mL defined production medium in 100 mL serum bottles at 200 rpm. Bioethanol production under optimized conditions in medium containing 16 g/L mannitol and 20 g/L glycerol increased sixfold (32.10 g/L) than that containing glycerol alone (5.23 g/L) as the carbon source in anaerobic conditions. Similarly, bioethanol production using free cells in continuous co-fermentation also improved (27.28 g/L) when 90.37 % of 16 g/L mannitol and 67.15 % of 20 g/L glycerol were used. Although naturally existing or engineered microorganisms can ferment mixed sugars sequentially, the preferential utilization of glucose to non-glucose sugars often results in lower overall yield and productivity of ethanol. Here, we present new findings in E. aerogenes ATCC 29007 that can be used to improve bioethanol production by simultaneous co-fermentation of glycerol and mannitol.     

植物细胞培养技术提高次生代谢物产量的方法(综述)

介绍植物细胞培养技术提高次生代谢物产量的方法。     

通过在低细胞浓度下启动甲醇诱导、优化碳/能量代谢模式促进毕赤酵母表达Monellin

重组毕赤酵母生产表达外源蛋白的过程中,一般在细胞达到高密度后开始启动甲醇诱导。也有报道指出,在较低细胞浓度下,启动甲醇诱导可以有效地控制整个发酵过程的溶解氧浓度,缓解毒副产物的积累,促进目标蛋白的表达。但是,该操作策略下,甲醇/能量调控机制不明,相关研究报道很少。文中以生产表达monellin(甜味蛋白)的重组毕赤酵母为模式菌株,通过在线分析计量甲醇消耗速率、CO2释放速率和O2摄取速率,探讨了不同细胞浓度下启动甲醇诱导和外源蛋白表达体系的甲醇/能量代谢模式。结果表明,在较低细胞浓度(50 g DCW/L)启动诱导并将温度控制在30℃,走向合成monellin前体物质途径的碳流最大(65%),且能与用于ATP再生的碳流形成最佳匹配;monellin的比合成速率与细胞比生长速率完全耦联,且耦联系数最大,比生长速率也较高;理论NADH(能量)利用效率η最高,η在甲醇诱导的绝大部分时段(89%)处于高水平(≥0.8),可以为monellin合成提供足够的能量。因此,该操作条件下,monellin浓度达到2.62 g/L的最高水平,是高细胞密度(100 g DCW/L)启动诱导策略下monellin浓度的2.5-4.9倍。     

Statistical optimization of the medium composition by response surface methodology to enhance schizophyllan production by Schizophyllum commune

The response surface methodology (RSM) involving central composite design (CCD) was employed to optimize the fermentation medium for the cell growth and schizophllan production by Schizophyllum commune CGMCC 5.113 in submerged culture at pH 6.5 and 26 degrees C. The four variables involved in this study were glucose, yeast extract, ammonium nitrate, and magnesium sulfate. The statistical analysis of the results showed that, in the range studied, glucose and yeast extract had a highly significant effect on schizophyllan production. The optimal medium for schizophyllan production calculated from the regression model of RSM was as follows: glucose, 18 g/l; yeast extract, 0.5 g/l; NH4NO3, 0.48 g/l; and MgSO4, 0.05 g/l, with a predicted maximum schizophyllan production of 11.74 g/l. These predicted values were experimentally validated. The excellent correlation between predicted and measured values justifies the validity of the response model. The results of bioreactor fermentation also show that the optimized medium enhanced schizophyllan production (12.80 g/l) by S. commune in a 5-1 fermenter.