Efstratios Nikolaivits

Bio: Efstratios Nikolaivits is an academic researcher from National Technical University of Athens. The author has contributed to research in topics: Cutinase & Medicine. The author has an hindex of 9, co-authored 24 publications receiving 269 citations.

A Middle-Aged Enzyme Still in Its Prime: Recent Advances in the Field of Cutinases

Abstract: Cutinases are α/β hydrolases, and their role in nature is the degradation of cutin. Such enzymes are usually produced by phytopathogenic microorganisms in order to penetrate their hosts. The first focused studies on cutinases started around 50 years ago. Since then, numerous cutinases have been isolated and characterized, aiming at the elucidation of their structure–function relations. Our deeper understanding of cutinases determines the applications by which they could be utilized; from food processing and detergents, to ester synthesis and polymerizations. However, cutinases are mainly efficient in the degradation of polyesters, a natural function. Therefore, these enzymes have been successfully applied for the biodegradation of plastics, as well as for the delicate superficial hydrolysis of polymeric materials prior to their functionalization. Even though research on this family of enzymes essentially began five decades ago, they are still involved in many reports; novel enzymes are being discovered, and new fields of applications arise, leading to numerous related publications per year. Perhaps the future of cutinases lies in their evolved descendants, such as polyesterases, and particularly PETases. The present article reviews the biochemical and structural characteristics of cutinases and cutinase-like hydrolases, and their applications in the field of bioremediation and biocatalysis.

Progressing Plastics Circularity: A Review of Mechano-Biocatalytic Approaches for Waste Plastic (Re)valorization.

Abstract: Inspirational concepts, and the transfer of analogs from natural biology to science and engineering, has produced many excellent technologies to date, spanning vaccines to modern architectural feats. This review highlights that answers to the pressing global petroleum-based plastic waste challenges, can be found within the mechanics and mechanisms natural ecosystems. Here, a suite of technological and engineering approaches, which can be implemented to operate in tandem with nature's prescription for regenerative material circularity, is presented as a route to plastics sustainability. A number of mechanical/green chemical (pre)treatment methodologies, which simulate natural weathering and arthropodal dismantling activities are reviewed, including: mechanical milling, reactive extrusion, ultrasonic-, UV- and degradation using supercritical CO2. Akin to natural mechanical degradation, the purpose of the pretreatments is to render the plastic materials more amenable to microbial and biocatalytic activities, to yield effective depolymerization and (re)valorization. While biotechnological based degradation and depolymerization of both recalcitrant and bioplastics are at a relatively early stage of development, the potential for acceleration and expedition of valuable output monomers and oligomers yields is considerable. To date a limited number of independent mechano-green chemical approaches and a considerable and growing number of standalone enzymatic and microbial degradation studies have been reported. A convergent strategy, one which forges mechano-green chemical treatments together with the enzymatic and microbial actions, is largely lacking at this time. An overview of the reported microbial and enzymatic degradations of petroleum-based synthetic polymer plastics, specifically: low-density polyethylene (LDPE), high-density polyethylene (HDPE), polystyrene (PS), polyethylene terephthalate (PET), polyurethanes (PU) and polycaprolactone (PCL) and selected prevalent bio-based or bio-polymers [polylactic acid (PLA), polyhydroxyalkanoates (PHAs) and polybutylene succinate (PBS)], is detailed. The harvesting of depolymerization products to produce new materials and higher-value products is also a key endeavor in effectively completing the circle for plastics. Our challenge is now to effectively combine and conjugate the requisite cross disciplinary approaches and progress the essential science and engineering technologies to categorically complete the life-cycle for plastics.

Identification and Characterization of New Laccase Biocatalysts from Pseudomonas Species Suitable for Degradation of Synthetic Textile Dyes

Abstract: Laccases are multicopper-oxidases with variety of biotechnological applications. While predominantly used, fungal laccases have limitations such as narrow pH and temperature range and their production via heterologous protein expression is more complex due to posttranslational modifications. In comparison, bacterial enzymes, including laccases, usually possess higher thermal and pH stability, and are more suitable for expression and genetic manipulations in bacterial expression hosts. Therefore, the aim of this study was to identify, recombinantly express, and characterize novel laccases from Pseudomonas spp. A combination of approaches including DNA sequence analysis, N-terminal protein sequencing, and genome sequencing data analysis for laccase amplification, cloning, and overexpression have been used. Four active recombinant laccases were obtained, one each from P. putida KT2440 and P. putida CA-3, and two from P. putida F6. The new laccases exhibited broad temperature and pH range and high thermal stability, as well as the potential to degrade selection of synthetic textile dyes. The best performing laccase was CopA from P. putida F6 which degraded five out of seven tested dyes, including Amido Black 10B, Brom Cresol Purple, Evans Blue, Reactive Black 5, and Remazol Brilliant Blue. This work highlighted species of Pseudomonas genus as still being good sources of biocatalytically relevant enzymes.

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

Abstract: 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.

Biodegradation of PET: Current Status and Application Aspects

Abstract: Most petroleum-derived plastics, as exemplified by poly(ethylene terephthalate) (PET), are chemically inactive and highly resistant to microbial attack. The accumulation of plastic waste results in environmental pollution and threatens ecosystems, referred to as the “microplastic issue”. Recently, PET hydrolytic enzymes (PHEs) have been identified and we reported PET degradation by a microbial consortium and its bacterial resident, Ideonella sakaiensis. Bioremediation may thus provide an alternative solution to recycling plastic waste. The mechanism of PET degradation into benign monomers by PET hydrolase and mono(2-hydroxyethyl) terephthalic acid (MHET) hydrolase from I. sakaiensis has been elucidated; nevertheless, biodegradation may require additional development for commercialization owing to the low catalytic activity of these enzymes. Here, we introduce PET degrading microorganisms and the enzymes involved, along with the evolution of PHEs to address the issues that hamper microbial and enzymatic PE...

Bioremediation through microbes: systems biology and metabolic engineering approach

Abstract: Today, environmental pollution is a serious problem, and bioremediation can play an important role in cleaning contaminated sites Remediation strategies, such as chemical and physical approaches, are not enough to mitigate pollution problems because of the continuous generation of novel recalcitrant pollutants due to anthropogenic activities Bioremediation using microbes is an eco-friendly and socially acceptable alternative to conventional remediation approaches Many microbes with a bioremediation potential have been isolated and characterized but, in many cases, cannot completely degrade the targeted pollutant or are ineffective in situations with mixed wastes This review envisages advances in systems biology (SB), which enables the analysis of microbial behavior at a community level under different environmental stresses By applying a SB approach, crucial preliminary information can be obtained for metabolic engineering (ME) of microbes for their enhanced bioremediation capabilities This review also highlights the integrated SB and ME tools and techniques for bioremediation purposes

Impacts of Plastic Pollution on Ecosystem Services, Sustainable Development Goals, and Need to Focus on Circular Economy and Policy Interventions

Abstract: Plastic pollution is ubiquitous in terrestrial and aquatic ecosystems. Plastic waste exposed to the environment creates problems and is of significant concern for all life forms. Plastic production and accumulation in the natural environment are occurring at an unprecedented rate due to indiscriminate use, inadequate recycling, and deposits in landfills. In 2019, the global production of plastic was at 370 million tons, with only 9% of it being recycled, 12% being incinerated, and the remaining left in the environment or landfills. The leakage of plastic wastes into terrestrial and aquatic ecosystems is occurring at an unprecedented rate. The management of plastic waste is a challenging problem for researchers, policymakers, citizens, and other stakeholders. Therefore, here, we summarize the current understanding and concerns of plastics pollution (microplastics or nanoplastics) on natural ecosystems. The overall goal of this review is to provide background assessment on the adverse effects of plastic pollution on natural ecosystems; interlink the management of plastic pollution with sustainable development goals; address the policy initiatives under transdisciplinary approaches through life cycle assessment, circular economy, and sustainability; identify the knowledge gaps; and provide current policy recommendations. Plastic waste management through community involvement and socio-economic inputs in different countries are presented and discussed. Plastic ban policies and public awareness are likely the major mitigation interventions. The need for life cycle assessment and circularity to assess the potential environmental impacts and resources used throughout a plastic product’s life span is emphasized. Innovations are needed to reduce, reuse, recycle, and recover plastics and find eco-friendly replacements for plastics. Empowering and educating communities and citizens to act collectively to minimize plastic pollution and use alternative options for plastics must be promoted and enforced. Plastic pollution is a global concern that must be addressed collectively with the utmost priority.