The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

In recent years, enzyme immobilization has been presented as a powerful tool for the improvement of enzyme properties such as stability and reusability. However, the type of support material used plays a crucial role in the immobilization process due to the strong effect of these materials on the properties of the produced catalytic system. A large variety of inorganic and organic as well as hybrid and composite materials may be used as stable and efficient supports for biocatalysts. This review provides a general overview of the characteristics and properties of the materials applied for enzyme immobilization. For the purposes of this literature study, support materials are divided into two main groups, called Classic and New materials. The review will be useful in selection of appropriate support materials with tailored properties for the production of highly effective biocatalytic systems for use in various processes.

A general overview of support materials for enzyme immobilization: Characteristics, properties, practical utility

Biocatalysis has found numerous applications in various fields as an alternative to chemical catalysis. The use of enzymes in organic synthesis, especially to make chiral compounds for pharmaceuticals as well for the flavors and fragrance industry, are the most prominent examples. In addition, biocatalysts are used on a large scale to make specialty and even bulk chemicals. This review intends to give illustrative examples in this field with a special focus on scalable chemical production using enzymes. It also discusses the opportunities and limitations of enzymatic syntheses using distinct examples and provides an outlook on emerging enzyme classes.

/pdf/biocatalysis-enzymatic-synthesis-for-industrial-applications-ldqm2uv3af.pdf

Biocatalysis: Enzymatic Synthesis for Industrial Applications

The efficiency, selectivity and sustainability benefits offered by enzymes are enticing chemists to consider biocatalytic transformations to complement or even supplant more traditional synthetic routes. Increasing demands for efficient and versatile synthetic methods, combined with powerful new discovery and engineering tools, has prompted innovations in biocatalysis, especially the development of new enzymes for precise transformations or ‘molecular editing’. As a result, the past decade has witnessed an impressive expansion of the catalytic repertoire of enzymes to include new and useful transformations not known (or relevant) in the biological world. In this Review we illustrate various ways in which researchers have approached using the catalytic machineries of enzymes for new-to-nature transformations. These efforts have identified genetically encoded catalysts that can be tuned and diversified by engineering the protein sequence, particularly by directed evolution. Discovery and improvement of these new enzyme activities is opening a floodgate that connects the chemistry of the biological world to that invented by humans over the past 100 years. Advances in enzyme performance and capabilities are making them increasingly attractive to synthetic chemists. In this Review Chen and Arnold outline the ways that enzymes have been engineered to achieve reactivities well beyond their original functions.

Engineering new catalytic activities in enzymes

Transition-metal catalyzed reactions that are able to construct complex aliphatic amines from simple, readily available feedstocks have become a cornerstone of modern synthetic organic chemistry. I...

New Strategies for the Transition-Metal Catalyzed Synthesis of Aliphatic Amines.

Chiral amines are valuable building blocks for the pharmaceutical industry. ω-TAms have emerged as an exciting option for their synthesis, offering a potential “green alternative” to overcome the drawbacks associated with conventional chemical methods. In this review, we explore the application of ω-TAms for pharmaceutical production. We discuss the diverse array of reactions available involving ω-TAms and process considerations of their use in both kinetic resolution and asymmetric synthesis. With the aid of specific drug intermediates and APIs, we chart the development of ω-TAms using protein engineering and their contribution to elegant one-pot cascades with other enzymes, including carbonyl reductases (CREDs), hydrolases and monoamine oxidases (MAOs), providing a comprehensive overview of their uses, beginning with initial applications through to the present day.

Application of ω-Transaminases in the Pharmaceutical Industry

The identification and use of robust transaminases from a domestic drain metagenome

Efficient magnetic recycling of covalently attached enzymes on carbon-coated metallic nanomagnets.

Oxidation of benzoic acid by a microorganism expressing benzoate dioxygenase leads to the formation of an unusual ipso, ortho arene cis-diol in sufficient quantities to be useful for synthesis. This homochiral diol possesses an array of differentiated functionality which can be exploited to access diverse highly oxygenated structures by concise synthetic sequences.

https://pubs.rsc.org/en/content/articlepdf/2014/QO/C3QO00057E

Benzoate dioxygenase from Ralstonia eutropha B9 – unusual regiochemistry of dihydroxylation permits rapid access to novel chirons

Continuous flow chemistry is becoming an established technology platform that finds frequent application in industrial chemical manufacture with support and endorsements by the FDA for pharmaceuticals. Amongst the various advantages that are commonly cited for flow chemistry over batch processing, sustainability continues to require further advances and joint efforts by chemists and chemical engineers in both academia and industry. This short review highlights developments between 2015 and early 2021 that positively impact on the green credentials associated with flow chemistry, specifically when applied to the preparation of pharmaceuticals. An industrial perspective on current challenges is provided to whet discussion and stimulate further investment towards achieving greener modern synthetic technologies. 1 	Introduction 2 	Subject Areas and Relevant Case Studies 3 	Industrial Outlook on Future Sustainability Driven through 	Continuous Manufacturing Approaches 4 	Conclusions and Outlook

/pdf/evaluating-the-green-credentials-of-flow-chemistry-towards-4zyhi54ch5.pdf

Thomas S. Moody

Papers

Application of ω-Transaminases in the Pharmaceutical Industry

The identification and use of robust transaminases from a domestic drain metagenome

Efficient magnetic recycling of covalently attached enzymes on carbon-coated metallic nanomagnets.

Benzoate dioxygenase from Ralstonia eutropha B9 – unusual regiochemistry of dihydroxylation permits rapid access to novel chirons

Evaluating the Green Credentials of Flow Chemistry towards Industrial Applications