Advances in Strain Engineering for Improved Bio-fuel Production- a Perspective

2020 ◽  
Vol 7 (1) ◽  
pp. 1-5
Author(s):  
Supriya Ratnaparkhe ◽  
Milind B. Ratnaparkhe
Keyword(s):  
Metabolic Engineering ◽  
Genetic Engineering ◽  
Fossil Fuel ◽  
Strain Engineering ◽  
Research Community ◽  
The Novel ◽  
Fuel Production ◽  
Genetic Manipulations ◽  
Ecologically Sustainable ◽  
Complex Genome

Bio-fuels are ecologically sustainable alternates of fossil fuel and have attracted interest of research community in the last few decades. Microorganisms such as bacteria, fungi and microalgae have important roles to play at various steps of bio-fuel production. And therefore several efforts such as genetic engineering have been made to improve the performance of these microbes to achieve the desired results. Metabolic engineering of organisms has benefitted immensely from the novel tools and technologies that have recently been developed. Microorganisms have the advantage of smaller and less complex genome and hence are best suitable for genetic manipulations. In this perspective, we briefly review a few interesting studies which represent some recent advances in the field of metabolic engineering of microbes.

scholarly journals Momo – Multi-Objective Metabolic mixed integer Optimization: application to yeast strain engineering

2018 ◽  
Author(s):  
Ricardo Andrade ◽  
Mahdi Doostmohammadi ◽  
João L. Santos ◽  
Marie-France Sagot ◽  
Nuno P. Mira ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
Strain Engineering ◽  
Mixed Integer ◽  
Cell Factory ◽  
Integer Optimization ◽  
Multi Objective ◽  
Genetic Manipulations ◽  
Multi Objective Programming ◽  
Decision Variables

AbstractIn this paper, we explore the concept of multi-objective optimization in the field of metabolic engineering when both continuous and integer decision variables are involved in the model. In particular, we propose a multi-objective model that may be used to suggest reaction deletions that maximize and/or minimize several functions simultaneously. The applications may include, among others, the concurrent maximization of a bioproduct and of biomass, or maximization of a bioproduct while minimizing the formation of a given by-product, two common requirements in microbial metabolic engineering.Production of ethanol by the widely used cell factorySaccharomyces cerevisiaewas adopted as a case study to demonstrate the usefulness of the proposed approach in identifying genetic manipulations that improve productivity and yield of this economically highly relevant bioproduct. We did anin vivovalidation and we could show that some of the predicted deletions exhibit increased ethanol levels in comparison with the wild-type strain. The multi-objective programming framework we developed, called Momo, is open-source and uses PolySCIP‡as underlying multi-objective solver. Momo is available athttp://momo-sysbio.gforge.inria.fr

scholarly journals A toolset of constitutive promoters for metabolic engineering ofRhodosporidium toruloides

2019 ◽  
Author(s):  
Luísa Czamanski Nora ◽  
Maren Wehrs ◽  
Joonhoon Kim ◽  
Jan-Fang Cheng ◽  
Angela Tarver ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
Genetic Engineering ◽  
Strain Engineering ◽  
Pathway Engineering ◽  
Transcriptional Analysis ◽  
Reporter System ◽  
Fluorescent Reporter ◽  
Promoter Sequences ◽  
Engineering Studies ◽  
Over Time

ABSTRACTBackgroundRhodosporidium toruloidesis a promising host for the production of bioproducts from lignocellulosic biomass. A key prerequisite for efficient pathway engineering is the availability of robust genetic tools and resources. However, there is a lack of characterized promoters to drive expression of heterologous genes for strain engineering inR. toruloides.ResultsOur data describes a set of nativeR. toruloidespromoters, characterized over time in four different media commonly used for cultivation of this yeast. The promoter sequences were selected using transcriptional analysis and several of them were found to drive expression bidirectionally. We measured promoter expression strength by flow cytometry using a dual fluorescent reporter system. From these analyses, we found a total of 20 constitutive promoters (12 monodirectional and 8 bidirectional) of potential value for genetic engineering ofR. toruloides.ConclusionsWe present a list of robust and constitutive, native promoters to facilitate genetic engineering ofR. toruloides.This set of thoroughly characterized promoters significantly expands the range of engineering tools available for this yeast and can be applied in future metabolic engineering studies.

Portico

2017 ◽  
Author(s):  
Paula Pryce
Keyword(s):  
Religious Pluralism ◽  
Intimate Relationship ◽  
Research Community ◽  
The Novel ◽  
Centering Prayer ◽  
Ritual Studies ◽  
Meditation Technique ◽  
Ethnographic Methodology ◽  
Contemplative Traditions

Using evocative language, the book opens with a historical and contemporary exploration of the desire that motivates contemplative practitioners to seek an intimate relationship with the divine. It describes the effect of globalization and religious pluralism by noting a trend of Americans’ abandonment of mainline Christian institutions, their exploration of other contemplative traditions, and their subsequent return to Christianity when they discover its mystical history and current-day contemplative practices. The chapter describes core terms, concepts, research parameters, and basic sociological and historical information about the research community, a network of American monastic and non-monastic contemplative Christians who practice a meditation technique called Centering Prayer. Chapter 1 also introduces the terms apophatic and cataphatic to the ritual studies lexicon and offers a basic description of the novel ethnographic methodology that the author developed for research in silent communities.

scholarly journals Constraint-based metabolic control analysis for rational strain engineering

2020 ◽  
Author(s):  
Sophia Tsouka ◽  
Meric Ataman ◽  
Tuure Hameri ◽  
Ljubisa Miskovic ◽  
Vassily Hatzimanikatis
Keyword(s):  
Metabolic Engineering ◽  
Genome Editing ◽  
Metabolic Control ◽  
Metabolic Flux ◽  
Strain Engineering ◽  
Metabolic Control Analysis ◽  
Physiological Data ◽  
Response Analysis ◽  
Control Analysis ◽  
Wide Range

AbstractThe advancements in genome editing techniques over the past years have rekindled interest in rational metabolic engineering strategies. While Metabolic Control Analysis (MCA) is a well-established method for quantifying the effects of metabolic engineering interventions on flows in metabolic networks and metabolic concentrations, it fails to account for the physiological limitations of the cellular environment and metabolic engineering design constraints. We report here a constraint-based framework based on MCA, Network Response Analysis (NRA), for the rational genetic strain design that incorporates biologically relevant constraints, as well as genome editing restrictions. The NRA core constraints being similar to the ones of Flux Balance Analysis, allow it to be used for a wide range of optimization criteria and with various physiological constraints. We show how the parametrization and introduction of biological constraints enhance the NRA formulation compared to the classical MCA approach, and we demonstrate its features and its ability to generate multiple alternative optimal strategies given several user-defined boundaries and objectives. In summary, NRA is a sophisticated alternative to classical MCA for rational metabolic engineering that accommodates the incorporation of physiological data at metabolic flux, metabolite concentration, and enzyme expression levels.

scholarly journals A successful use of a new shuttle cloning vector pA13 for the cloning of the bacteriocins BacSJ and acidocin 8912

2010 ◽  
Vol 62 (2) ◽  
pp. 231-243 ◽  
Author(s):  
Milan Kojic ◽  
Jelena Lozo ◽  
B. Jovcic ◽  
Ivana Strahinic ◽  
D. Fira ◽  
...  
Keyword(s):  
In Silico Analysis ◽  
Functional Expression ◽  
Open Reading Frames ◽  
Cloning Vector ◽  
The Novel ◽  
Genetic Manipulations ◽  
Genes Encoding ◽  
Editorial Decision ◽  
Terminal Amino

The aim of this paper was to research the molecular cloning of genes encoding the novel bacteriocin BacSJ from Lactobacillus paracasei subsp. paracasei BGSJ2-8 by using a newly constructed shuttle cloning vector pA13. A new shuttle-cloning vector, pA13, was constructed and successfully introduced into Escherichia coli, Lactobacillus and Lactococcus strains, showing a high segregational and structural stability in all three hosts. The natural plasmid pSJ2-8 from L. paracasei subsp. paracasei BGSJ2-8 was cloned in the pA13 using BamHI, obtaining the construct pB5. Sequencing and in silico analysis of the pB5 revealed 15 open reading frames (ORF). Plasmid pSJ2-8 harbors the genes encoding the production of two bacteriocins, BacSJ and acidocin 8912. The combined N-terminal amino acid sequencing of BacSJ in combination with DNA sequencing of the bacSJ2-8 gene enabled the determination of the primary structure of a bacteriocin BacSJ. The production and functional expression of BacSJ in homologous and heterologous hosts suggest that bacSJ2-8 and bacSJ2-8i together with the genes encoding the ABC transporter and accessory protein are the minimal requirement for the production of BacSJ. Biochemical and genetic analyses showed that BacSJ belongs to the class II bacteriocins. The shuttle cloning vector pA13 could be used as a tool for genetic manipulations in lactobacilli and lactococci. <br><br><b><font color="red">withdrawn; due to a printing error. Link to the Editorial Decision <u><a href="http://dx.doi.org/10.2298/ABS1004251U">10.2298/ABS1004251U</a></u></font></b><br>

scholarly journals A knowledge network for a dynamic taxonomy of psychiatric disease

2015 ◽  
Vol 17 (1) ◽  
pp. 79-87 ◽  
Keyword(s):  
Mental Disorders ◽  
Strategic Plan ◽  
Research Community ◽  
Mental Illnesses ◽  
Knowledge Network ◽  
Psychiatric Disease ◽  
The Novel ◽  
Research Domain Criteria ◽  
Novel Approach ◽  
Research Domain

The Research Domain Criteria (RDoC) project was initiated by the National Institute of Mental Health (NIMH) in early 2009 as the implementation of Goal 1.4 of its just-issued strategic plan. In keeping with the NIMH mission, to "transform the understanding and treatment of mental illnesses through basic and clinical research," RDoC was explicitly conceived as a research-related initiative. The statement of the relevant goal in the strategic plan reads: "Develop, for research purposes, new ways of classifying mental disorders based on dimensions of observable behavior and neurobiological measures." Due to the novel approach that RDoC takes to conceptualizing and studying mental disorders, it has received widespread attention, well beyond the borders of the immediate research community. This review discusses the rationale for the experimental framework that RDoC has adopted, and its implications for the nosology of mental disorders in the future.

Profitability of fossil-fuel production under different instruments in international climate policies

2007 ◽  
Vol 7 (1) ◽  
pp. 60-72
Author(s):  
Finn Roar Aune ◽  
Snorre Kverndokk ◽  
Lars Lindholt ◽  
Knut Einar Rosendahl
Keyword(s):  
Fossil Fuel ◽  
Fuel Production ◽  
Climate Policies ◽  
International Climate

The Economics of Just Transition: A Framework for Supporting Fossil Fuel–Dependent Workers and Communities in the United States

2018 ◽  
Vol 44 (2) ◽  
pp. 93-138 ◽  
Author(s):  
Robert Pollin ◽  
Brian Callaci
Keyword(s):  
United States ◽  
Fossil Fuel ◽  
Transition Programs ◽  
The United States ◽  
Fuel Production

We develop a Just Transition framework for U.S. workers and communities that are currently dependent on domestic fossil fuel production. Our rough high-end estimate for such a program is a relatively modest $600 million per year. This level of funding would pay for (1) income, retraining, and relocation support for workers facing retrenchments; (2) guaranteeing the pensions for workers in the affected industries; and (3) mounting effective transition programs for what are now fossil fuel–dependent communities.

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