Advances in ultrahigh-throughput screening technologies for protein evolution

Inspired by natural evolution, directed evolution randomly mutates the gene of interest through artificial evolution conditions with variants being screened for the required properties. Directed evolution is vital to the enhancement of protein properties and comprises the construction of libraries with considerable diversity as well as screening methods with sufficient efficiency as key steps. Owing to the various characteristics of proteins, specific methods are urgently needed for library screening, which is one of the main limiting factors in accelerating evolution. This review initially organizes the principles of ultrahigh-throughput screening from the perspective of protein properties. It then provides a comprehensive introduction to the latest progress and future trends in ultrahigh-throughput screening technologies for directed evolution.     

Alkoxyl lipids--relics of the organic world: their formation, biotransformation and evolution]

The data on discovery, biosynthesis and distribution of alcoxylipids in different kingdoms of the organic world, their physiologic role and biologic action are given. A conception of possible abiotic synthesis of alcoxylipids on the early stages of the Earth evolution and the ways of their biotransformation is considered. The first biologic membranes are suggested to contain primarily alcoxylipids. During the appearing of photosynthetic mechanism and its improving the alcoxylipids of biomembranes oxidized in plasmalogens and then into diacyl lipids. The possibilities to use alcoxylipids as chemical makers of biomembranes for chemotaxonomy are under discussion.     

Bioinformatics technologies for the analysis of antigenic evolution of influenza viruses

Human influenza viruses mutate from time to time, causing annual epidemics worldwide. The strong immune pressure in the human population selects a new variant every year, and the antigenic change is one of the primary reasons why vaccination is not a perfect measure to control seasonal influenza. Thus prediction of antigenic change of influenza A virus has been one of the major public health goals. In this review bioinformatics technologies that have been developed to achieve this goal were summarized.     

The biotransformation of tranylcypromine by Cunninghamella echinulata.

When incubated alone for 7 days with the fungus Cunninghamella echinulata, tranylcypromine was extensively metabolized. As observed in mammalian systems, N-acetyltranylcypromine was the major metabolite recovered along with lesser amounts of 4-hydroxytranylcypromine, as its N,O-diacetyl derivative. The rate and extent of tranylcypromine biotransformation was affected by whether incubation was on either 30 degrees or flat brackets with a gyratory shaker. There is a strong association between the rate of biotransformation and the utilization of glucose, formation of ammonia, and pH. The slowest rates of biotransformation and metabolic response were observed with the large fungal pellets formed during incubation on flat brackets. These findings raise the possibility that, as in mammalian systems, fungal metabolism of xenobiotics can be affected by nutrient and environmental conditions.     

The biotransformation of simple phenolic compounds by Brettanomyces anomalus

Abstract Brettanomyces anomalus is shown here to metabolise p -coumaric, caffeic and ferulic acid to 4-vinyl and 4-ethyl derivatives. We also demonstrate the transformation of vanillin to both vanillyl alcohol and vanillic acid by this yeast. The results presented here show the production of these compounds during the fermentation of this organism and also the effects of these and other simple phenolic compounds on the growth of the organism. The products were analysed and their identities were determined by TLC, HPLC and by mass spectrometry.     

The evolution of concerted evolution

Concerted evolution is a consequence of processes that convert copies of a gene in a multigene family into the same copy. Here we ask whether this homogenization may be adaptive. Analysis of a modifier of homogenization reveals (1) that the trait is most likely to spread if interactions between deleterious mutations are not strongly synergistic; (2) that selection on the modifier is of the order of the mutation rate, hence the modifier is most likely to be favoured by selection when the species has a large effective population size and/or if the modifier affects many genes simultaneously; and (3) that linkage between the genes in the family, and between these genes and the modifier, makes invasion of the modifier easier, suggesting that selection may favour multigene families being in clustered arrays. It follows from the first conclusion that genes for which mutations may often be dominant or semi-dominant should undergo concerted evolution more commonly than others. By analysis of the mouse knockout database, we show that mutations affecting growth-related genes are more commonly associated with dominant lethality than expected by chance. We predict then that selection will favour homogenization of such genes, and possibly others that are significantly dosage dependent, more often than it favours homogenization in other genes. The first condition is almost the opposite of that required for the maintenance of sexual reproduction according to the mutation-deterministic theory. The analysis here therefore suggests that sexual organisms can simultaneously minimize both the effects of deleterious, strongly synergistically, interacting mutations and those that interact either weakly synergistically, multiplicatively, or antagonistically, assuming the latter class belong to a multicopy gene family. Recombination and an absence of homogenization are efficient in purging deleterious mutations in the former class, homogenization and an absence of recombination are efficient at minimizing the costs imposed by the latter classes.     

The evolution of cultural evolution

Humans are unique in their range of environments and in the nature and diversity of their behavioral adaptations. While a variety of local genetic adaptations exist within our species, it seems certain that the same basic genetic endowment produces arctic foraging, tropical horticulture, and desert pastoralism, a constellation that represents a greater range of subsistence behavior than the rest of the Primate Order combined. The behavioral adaptations that explain the immense success of our species are cultural in the sense that they are transmitted among individuals by social learning and have accumulated over generations. Understanding how and when such culturally evolved adaptations arise requires understanding of both the evolution of the psychological mechanisms that underlie human social learning and the evolutionary (population) dynamics of cultural systems.     

The commercialization of genome-editing technologies

The emergence of new gene-editing technologies is profoundly transforming human therapeutics, agriculture, and industrial biotechnology. Advances in clustered regularly interspaced short palindromic repeats (CRISPR) have created a fertile environment for mass-scale manufacturing of cost-effective products ranging from basic research to translational medicine. In our analyses, we evaluated the patent landscape of gene-editing technologies and found that in comparison to earlier gene-editing techniques, CRISPR has gained significant traction and this has established dominance. Although most of the gene-editing technologies originated from the industry, CRISPR has been pioneered by academic research institutions. The spinout of CRISPR biotechnology companies from academic institutions demonstrates a shift in entrepreneurship strategies that were previously led by the industry. These academic institutions, and their subsequent companies, are competing to generate comprehensive intellectual property portfolios to rapidly commercialize CRISPR products. Our analysis shows that the emergence of CRISPR has resulted in a fivefold increase in genome-editing bioenterprise investment over the last year. This entrepreneurial movement has spurred a global biotechnology revolution in the realization of novel gene-editing technologies. This global shift in bioenterprise will continue to grow as the demand for personalized medicine, genetically modified crops and environmentally sustainable biofuels increases. However, the monopolization of intellectual property, negative public perception of genetic engineering and ambiguous regulatory policies may limit the growth of these market segments.     

The use of Aspergillus niger cultures for biotransformation of terpenoids

Aspergillus niger is a well-known fungus that has been used for many different biotransformations of organic compounds. The terpenoids include a large variety of natural hydrocarbons and their derivatives, mostly obtained from plant essential oils, but some obtained from animals or fungi. They may be acyclic or have one or more rings of various sizes, and they show a variety of biological activities that include antibacterial, antifungal, antiparasitic, antiviral, and anticancer activities. Terpenoids are classified as monoterpenoids (C₁₀), sesquiterpenoids (C₁₅), diterpenoids (C₂₀), triterpenoids (C₃₀), and others. This review summarizes experimental processes that use cultures of various A. niger strains to carry out stereoselective biochemical reactions in terpenoids, including related epoxides, lactones, N-phenylcarbamates, and saponins, to produce metabolites that may be useful as flavors and fragrances or as new experimental drug candidates. Cultures of A. niger that add hydroxyl, carbonyl, and other groups at specific positions or reduce double bonds have resulted in the production of valuable new compounds.