Next‐Generation Industrial Biotechnology‐Transforming the Current Industrial Biotechnology into Competitive Processes

The chemical industry has made a contribution to modern society by providing cost‐competitive products for our daily use. However, it now faces a serious challenge regarding environmental pollutions and greenhouse gas emission. With the rapid development of molecular biology, biochemistry, and synthetic biology, industrial biotechnology has evolved to become more efficient for production of chemicals and materials. However, in contrast to chemical industries, current industrial biotechnology (CIB) is still not competitive for production of chemicals, materials, and biofuels due to their low efficiency and complicated sterilization processes as well as high‐energy consumption. It must be further developed into “next‐generation industrial biotechnology” (NGIB), which is low‐cost mixed substrates based on less freshwater consumption, energy‐saving, and long‐lasting open continuous intelligent processing, overcoming the shortcomings of CIB and transforming the CIB into competitive processes. Contamination‐resistant microorganism as chassis is the key to a successful NGIB, which requires resistance to microbial or phage contaminations, and available tools and methods for metabolic or synthetic biology engineering. This review proposes a list of contamination‐resistant bacteria and takes Halomonas spp. as an example for the production of a variety of products, including polyhydroxyalkanoates under open‐ and continuous‐processing conditions proposed for NGIB.     

Biocatalysts: Beautiful creatures

The chemical industry has come under increasing pressure to make chemical production more eco-friendly and independent to fossil resources. The development of industrial processes based on micro-organisms can especially help to eliminate the use or the generation of hazardous substances and can support the transition from dependence on fossil resources towards real sustainable and eco-safety industrial processes. The biocatalysts are the best solution given by nature that can be used to improve some biotechnological applications. In this research review, we report some peculiar properties of biocatalysts, implicated in a range of metabolic pathways and biotechnological tools.     

What should and what can biotechnology contribute to chemical bulk production?

Abstract: In terms of the chemical industry most biotech products have a fine chemical or even speciality character. Nevertheless there is at least one striking example of a fermentation-derived bulk chemical, bio-ethanol, which provides an excellent case study of the economic and technological prerequisites which biotechnology has to attain as a supplier to the chemical marketplace. The competitive position of existing and new products produced from renewable resources through biotechnological conversion methods will depend on its market acceptance - overall environmental compatibility and cost performance. In order to provide significant contributions to chemical bulk production beyond 2000, biotechnologists and chemical engineers are requested to search for new products, new processes to existing products and new technologies to overcome present cost constraints in fermentation, bioconversion and downstream processing.     

Indian Biotech Bazaar: a swot analysis

Biotechnology is a life science-based technique especially used in agriculture, medicine and food sciences. It is generally defined as the manipulation in organisms to generate products for the welfare of the world. Biotechnology combines disciplines such as genetics, biochemistry, microbiology, and cell biology along with information technology, chemical engineering, robotics etc. It includes basic industries such as food processing, tissue culture, plant development and other sophisticated ones such as recombinant therapeutics and diagnostics. Biotechnology, globally recognized as a rapidly emerging and far-reaching technology, is aptly described as the "technology of hope" for its promise of food, health and environmental sustainability. In India, biotechnology employs more than 10 000 people and generates roughly US$ 500 million in revenue annually. The biotechnology market has increased its sales from Rs. 50 billion in 1997 to Rs.70 billion in 2000, and is expected to cross Rs. 240 billion by the year 2010. In India, the human health biotech products account for 60% of the total market; agribiotech and veterinary 25%, medical devices, contract research and development (R&D), reagents and supplies constitute the remaining 15% Moreover, to facilitate foreign investment, capital and government policies are being revised. Other important industries include industrial enzyme manufacture, bioinformatics, and medical devices. Biotechnology has had limited appeal so far on our capital markets, and we have less then a dozen biotech companies listed on the public markets.     

Molecular simulations as a tool for selection of kinetic hydrate inhibitors

Natural gas hydrates are ice-like structures in which water molecules form a cage around gas molecules. They have been a problem in the petroleum industry. The heavy cost of alcohol and glycol injections needed to suppress the formation of hydrates has spurred an interest in so-called “kinetic inhibitors”, able to slow down the hydrate formation rather than prevent it. An earlier work (Kvamme, B. et al. 1997, Mol. Phys., 90, p. 979) proposed a simulation-based scheme to assess the comparative performance of prospective inhibitors and select the best candidates for experimental testing. In this work, we employed molecular dynamics simulations to test several kinetic inhibitors in a multiphase water–hydrate system with rigid hydrate interface. In addition, a long-scale run was implemented for a system where the hydrate was free to melt and reform. Our conclusion that PVCap inhibitor will outperform PVP as a kinetic hydrate inhibitor is supported by experimental data. We demonstrate that numerical experiments can be a valuable tool for selecting kinetic inhibitors as well as provide insight into mechanisms of kinetic inhibition and hydrate melting and reformation.     

Industrial biotechnology: Tools and applications

Industrial biotechnology involves the use of enzymes and microorganisms to produce value-added chemicals from renewable sources. Because of its association with reduced energy consumption, greenhouse gas emissions, and waste generation, industrial biotechnology is a rapidly growing field. Here we highlight a variety of important tools for industrial biotechnology, including protein engineering, metabolic engineering, synthetic biology, systems biology, and downstream processing. In addition, we show how these tools have been successfully applied in several case studies, including the production of 1, 3-propanediol, lactic acid, and biofuels. It is expected that industrial biotechnology will be increasingly adopted by chemical, pharmaceutical, food, and agricultural industries.     

核开关结构、机制及应用新进展

核开关(riboswitch)是Breaker等在2002年发现的一种全新的转录后调节机制．它可以通过小分子与mRNA结合来直接调控基因的表达,不需要任何蛋白质的参与．与常见的经由蛋白质的调控方式相比,riboswitch响应更迅速,对细胞内代谢物的变化更敏感．它的发现为RNA研究展示了新的领域． 目前在这个领域,既有基础研究,如riboswitch晶体结构解析、作用机制和动力学研究,又有前沿应用研究,如基于riboswitch的生物传感器和药物设计．Topp等通过设计riboswitch成功地改变了大肠杆菌的趋化性,这为合成生物学和人工生物网络的设计提供了新思路．目前对于riboswitch结构、机制及动力学的研究为基于riboswitch的合理药物设计奠定了基础,有望针对这一新的机制开发新一代抗菌药物．     

What can we Learn from Oxygen and Hydrogen Isotope Compositions of Tree-ring Cellulose in Higher Plants (英文)

Stable isotope ratios in tree-ring cellulose have been shown to be reliable recorders of changes in the ambient climate (Leuenberger et al., 1998). Thus, isotopic fractionations associated with both physical and biochemical processes during cellulose synthesis in higher plants (Epstein & Krishnaumurthy, 1990; Roden et al., 2000; Saurer et al., 1997a; 1997b; 2000) can be used as archives for past climatic indicators. Superimposed on the climatic induced isotopic signal are the long-term responses of plant physiological processes to past changes in environmental conditions including CO2 enrichment.     

Mutasynthesis - uniting chemistry and genetics for drug discovery

Mutasynthesis couples the power of chemical synthesis with molecular biology to generate derivatives of medicinally valuable, natural products. Recently, this technique has been exploited by Cambridge-based biotech company Biotica Technology Ltd, and their collaborators, to generate promising new variants of the polyketide anti-cancer compounds rapamycin and borrelidin.     

Detecting compensatory dynamics in competitive communities under environmental forcing

Competition is assumed to generate compensatory dynamics where an increase in one species is compensated by a decrease in others. Recently, using a community covariance technique, Houlahan et al. found that compensatory dynamics are only visible in 25–30% of natural communities studied. The study was based on scoring the sum of covariances of population densities. In contrast to the theory, and as a cautionary reminder to the interpretation of natural time series data, we show that negative community covariance can be absent even in strongly competitive communities and can be found present in communities without competitive interactions. Precise knowledge of various features of the underlying species’ biology and characteristics of the environmental variation is required before community covariance can be correctly interpreted as a proxy for the importance of competition or environmental forcing in driving community fluctuations. Other tools may therefore be more appropriate, e.g. explicit modelling of competition using modern time series analytical tools.     

Maßgeschneiderte Mikroorganismen

Tailor‐made microorganisms Microbial diversity provides unlimited resources for the development of novel industrial processes and products. Since the beginning of the 20th century microorganisms have been successfully applied for the large scale production of bio‐based products. In recent years, modern methods of strain development and Synthetic Biology have enabled biotech engineers to design even more sophisticated and tailor‐made microorganisms. These microbes serve industrial processes for the production of bulk chemicals, enzymes, polymers, biofuels as well as plant‐derived ingredients such as Artemisinin in an ecologically and economically sustainable and attractive fashion. In the future, production of advanced biofuels, microbial fuel cells, CO₂ as feedstock and microbial cellulose are research topics as well as challenges of global importance. Continuous efforts in microbiology and biotechnology research will be pivotal for white biotechnology to gain more momentum in transforming the chemical industry towards a knowledge based bio‐economy.     

Fermentative butanol production by Clostridia

Butanol is an aliphatic saturated alcohol having the molecular formula of C(4)H(9)OH. Butanol can be used as an intermediate in chemical synthesis and as a solvent for a wide variety of chemical and textile industry applications. Moreover, butanol has been considered as a potential fuel or fuel additive. Biological production of butanol (with acetone and ethanol) was one of the largest industrial fermentation processes early in the 20th century. However, fermentative production of butanol had lost its competitiveness by 1960s due to increasing substrate costs and the advent of more efficient petrochemical processes. Recently, increasing demand for the use of renewable resources as feedstock for the production of chemicals combined with advances in biotechnology through omics, systems biology, metabolic engineering and innovative process developments is generating a renewed interest in fermentative butanol production. This article reviews biotechnological production of butanol by clostridia and some relevant fermentation and downstream processes. The strategies for strain improvement by metabolic engineering and further requirements to make fermentative butanol production a successful industrial process are also discussed.     

187 Plucking the high hanging fruit: a systematic approach for targeting protein interfaces

Development of specific ligands for protein targets that help decode the complexities of protein–protein interaction networks is a key goal for the field of chemical biology. Despite the emergence of powerful in silico and experimental high-throughput screening strategies, the discovery of synthetic ligands that selectively modulate protein–protein interactions remains a challenge for the chemical biologists. Proteins often utilize small folded domains for recognition of other biomolecules. The basic hypothesis guiding our research is that by mimicking these domains, we can modulate the function of a particular protein with metabolically-stable synthetic molecules (Raj et al., 2013). This presentation will discuss computational approaches (Bullock et al., 2011; Jochim & Arora, 2010) to identify targetable interfaces along with synthetic methods (Patgiri et al., 2008; Tosovska & Arora, 2010) to develop protein domain mimics (PDMs) as modulators of intracellular protein–protein interactions (Henchey et al., 2010; Patgiri et al., 2011).     

Microbial carboxylic ester hydrolases (EC 3.1.1) in food biotechnology

Ester linkages between carboxylic acid groups and hydroxyl groups are basic to the structure of carboxyesters and lipids, and occur commonly as modifications of polysaccharide molecules. Microorganisms produce enzymes which hydrolyse the carboxylic ester linkages in substrates which are being utilized for growth. Such esterase reactions are frequently easily reversible, depending on the concentration of reactants or availability of water. The importance of esters as flavour compounds has resulted in the selection of yeast strains which produce esters in beverage fermentation. The synthetic potential of triacylglycerol lipases (EC 3.1.1.3) has been exploited by use of the purified enzymes in environments of low water activity. The techniques of molecular biology facilitate analysis of the homology between carboxylesterase enzymes and a detailed knowledge of structure and specificity provides the opportunity to modify enzymes to suit particular applications in biotechnology.
Esterase activity can be assayed conveniently by using synthetic chromogenic esters of naphthol or nitrophenol. Naphthyl and nitrophenyl acetates are readily hydrolysed by a wide range of enzymes including lipases (Hofelmann et al. 1985; Brahimi-Horn et al. 1990; Gilbert et al. 1991), serine protease (Klapper et al. 1973) and acetylxylan esterase (Lee et al. 1987). Electrophoretic separation followed by detection using chromogenic esters has demonstrated polymorphism of esterase enzymes and has been used to type strains of bacteria (Goullet & Picard 1990, 1991; Picard & Goullet 1990) but was less discriminating with yeasts (Campbell et al. 1972) and edible mushrooms (Itavaara 1988).     

Roles of Tet2 in meiosis,fertility and reproductive aging

Dear Editor, Ten-eleven translocation(Tet)enzymes play important roles in DNA demethylation involved in various biological pro-cesses including stem cell pluripotency and differentiation,and tumorigenesis(Dawlaty et al.,2013;Wu and Zhang,2017).Tet2 deficiency or mutation leads to severe hematopoietic defects or myeloid malignancies in mice(Delhommeau et al.,2009;Ko et al.,2010;Moran-Crusio et al.,2011).Restoration of TET2 blocks aberrant self-re-newal and leukemia progression in patients possessing TET2 mutations(Cimmino et al.,2017).DNA methylation-based biomarkers,or"epigenetic clocks",link developmental and maintenance processes to biological aging(Horvath and Raj,2018).Interestingly,age-associated TET2 mutations have been found to drive myeloid dysfunction,cancer and cardiovascular disease(review(Ferrone et al.,2020)).Nevertheless,there has been lack of direct evidence demonstrating that Tet2 mutations or deficiency can actually accelerate aging.     

Linear regression and two-class classification with gene expression data

MOTIVATION: Using gene expression data to classify (or predict) tumor types has received much research attention recently. Due to some special features of gene expression data, several new methods have been proposed, including the weighted voting scheme of Golub et al., the compound covariate method of Hedenfalk et al. (originally proposed by Tukey), and the shrunken centroids method of Tibshirani et al. These methods look different and are more or less ad hoc. RESULTS: We point out a close connection of the three methods with a linear regression model. Casting the classification problem in the general framework of linear regression naturally leads to new alternatives, such as partial least squares (PLS) methods and penalized PLS (PPLS) methods. Using two real data sets, we show the competitive performance of our new methods when compared with the other three methods.     

Light-energy conversion in engineered microorganisms

Increasing interest in renewable resources by the energy and chemical industries has spurred new technologies both to capture solar energy and to develop biologically derived chemical feedstocks and fuels. Advances in molecular biology and metabolic engineering have provided new insights and techniques for increasing biomass and biohydrogen production, and recent efforts in synthetic biology have demonstrated that complex regulatory and metabolic networks can be designed and engineered in microorganisms. Here, we explore how light-driven processes may be incorporated into nonphotosynthetic microbes to boost metabolic capacity for the production of industrial and fine chemicals. Progress towards the introduction of light-driven proton pumping or anoxygenic photosynthesis into Escherichia coli to increase the efficiency of metabolically-engineered biosynthetic pathways is highlighted.     

Cross- species communication in bacterial world

Biofilms are the compact association of micro organisms and the communication processes in these biofilms are always a wonder. Electrical and chemical signaling mechanism are the key to understand the bacterial communication network. Quorum sensing so far has been able to explain the coordinated motion of bacteria through its chemical signaling mechanism. Bacteria residing within biofilm communities are trivial to communicate. But the recent observation in 2017 by Humphries et al. has revealed that the ion channels enabled electrical signaling mechanism can be as powerful as to attract the distant cells i.e., this signaling mechanism are capable of holding a long range behavior. As a result long range cross species communication in the bacterial world have been possible. This substantial outcome has brought this field into a new paradigm to investigate the complex co-existence of biofilm communities and distant cells with a possible scope of application in synthetic biology. In this present article, we briefly describe this new signaling mechanism and how it gives rise to a long range communication ability in bacterial communities.     

Immune plexins and semaphorins: old proteins,new immune functions

Plexins and semaphorins are a large family of proteins that are involved in cell movement and response. The importance of plexins and semaphorins has been emphasized by their discovery in many organ systems including the nervous (Nkyimbeng-Takwi and Chapoval, 2011; McCormick and Leipzig, 2012; Yaron and Sprinzak, 2012), epithelial (Miao et al., 1999; Fujii et al., 2002), and immune systems (Takamatsu and Kumanogoh, 2012) as well as diverse cell processes including angiogenesis (Serini et al., 2009; Sakurai et al., 2012), embryogenesis (Perala et al., 2012), and cancer (Potiron et al., 2009; Micucci et al., 2010). Plexins and semaphorins are transmembrane proteins that share a conserved extracellular semaphorin domain (Hota and Buck, 2012). The plexins and semaphorins are divided into four and eight subfamilies respectively based on their structural homology. Semaphorins are relatively small proteins containing the extracellular semaphorin domain and short intracellular tails. Plexins contain the semaphorin domain and long intracellular tails (Hota and Buck, 2012). The majority of plexin and semaphorin research has focused on the nervous system, particularly the developing nervous system, where these proteins are found to mediate many common neuronal cell processes including cell movement, cytoskeletal rearrangement, and signal transduction (Choi et al., 2008; Takamatsu et al., 2010). Their roles in the immune system are the focus of this review.