Metabolic Engineering of Escherichia coli for Efficient Conversion of Glycerol into Ethanol

Based on elementary mode analysis, an Escherichia coli strain was designed for efficient conversion of glycerol to ethanol. By using nine gene knockout mutations, the functional space of the central metabolism of E. coli was reduced from over 15,000 possible pathways to a total of 28 glycerol-utilizing pathways that support cell function. Among these pathways are eight aerobic and eight anaerobic pathways that do not support cell growth but convert glycerol into ethanol with a theoretical yield of 0.50 g ethanol/g glycerol. The remaining 12 pathways aerobically coproduce biomass and ethanol from glycerol. The optimal ethanol production depends on the oxygen availability that regulates the two competing pathways for biomass and ethanol production. The coupling between cell growth and ethanol production enabled metabolic evolution of the designed strain through serial dilution that resulted in strains with improved ethanol yields and productivities. In defined medium, the evolved strain can convert 40 g/liter of glycerol to ethanol in 48 h with 90% of the theoretical ethanol yield. The performance of the designed strain is predicted by the property space of remaining elementary modes

Microbial biosynthesis of lactate esters

Background Green organic solvents such as lactate esters have broad industrial applications and favorable environmental profiles. Thus, manufacturing and use of these biodegradable solvents from renewable feedstocks help benefit the environment. However, to date, the direct microbial biosynthesis of lactate esters from fermentable sugars has not yet been demonstrated. Results In this study, we present a microbial conversion platform for direct biosynthesis of lactate esters from fermentable sugars. First, we designed a pyruvate-to-lactate ester module, consisting of a lactate dehydrogenase (ldhA) to convert pyruvate to lactate, a propionate CoA-transferase (pct) to convert lactate to lactyl-CoA, and an alcohol acyltransferase (AAT) to condense lactyl-CoA and alcohol(s) to make lactate ester(s). By generating a library of five pyruvate-to-lactate ester modules with divergent AATs, we screened for the best module(s) capable of producing a wide range of linear, branched, and aromatic lactate esters with an external alcohol supply. By co-introducing a pyruvate-to-lactate ester module and an alcohol (i.e., ethanol, isobutanol) module into a modular Escherichia coli (chassis) cell, we demonstrated for the first time the microbial biosynthesis of ethyl and isobutyl lactate esters directly from glucose. In an attempt to enhance ethyl lactate production as a proof-of-study, we re-modularized the pathway into (1) the upstream module to generate the ethanol and lactate precursors and (2) the downstream module to generate lactyl-CoA and condense it with ethanol to produce the target ethyl lactate. By manipulating the metabolic fluxes of the upstream and downstream modules through plasmid copy numbers, promoters, ribosome binding sites, and environmental perturbation, we were able to probe and alleviate the metabolic bottlenecks by improving ethyl lactate production by 4.96-fold. We found that AAT is the most rate-limiting step in biosynthesis of lactate esters likely due to its low activity and specificity toward the non-natural substrate lactyl-CoA and alcohols. Conclusions We have successfully established the biosynthesis pathway of lactate esters from fermentable sugars and demonstrated for the first time the direct fermentative production of lactate esters from glucose using an E. coli modular cell. This study defines a cornerstone for the microbial production of lactate esters as green solvents from renewable resources with novel industrial applications

Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome

Additional file 1. Model structure and biomass term calculations

Evaluating the impacts of rice-based protection dykes on floodwater dynamics in the vietnamese mekong delta using geographical impact factor (Gif)

This study aims at evaluating the geographical influences of rice-based protection dykes on floodwater regimes along the main rivers, namely the Mekong and the Bassac, in the Vietnamese Mekong Delta (VMD). Specifically, numerous low dykes and high dykes have been constructed particularly in the upper delta’s floodplains to protect the double and triple rice cropping against the annual flooding. For the whole deltaic domain, a 1D-quasi-2D hydrodynamic model setup was used to simulate seventy-two (72) scenarios of dyke construction development in the context of low, medium, and high floods that occurred in the VMD to examine the effects of different flood magnitudes on a certain dyke construction area. Based on the model simulation results, we established an evaluation indicator, the so-called Geographical Impact Factor (GIF), to evaluate the impacts of zone-based dyke compartments on the floodwater regimes along the main rivers for different kinds of floods. Our findings revealed different rates of influences on the floodwater levels along the Mekong and Bassac Rivers under different scenarios of zone-based high-dyke developments. GIF is a useful index for scientists and decision-makers in land use planning, especially in rice intensification, in conjunction with flood management for the VMD and for similar deltas worldwide

Correlated Excitonic Signatures in a Nanoscale van der Waals Antiferromagnet

Composite quasi-particles with emergent functionalities in spintronic and quantum information science can be realized in correlated materials due to entangled charge, spin, orbital, and lattice degrees of freedom. Here we show that by reducing the lateral dimension of correlated antiferromagnet NiPS3 flakes to tens of nanometers, we can switch-off the bulk spin-orbit entangled exciton in the near-infrared (1.47 eV) and activate visible-range (1.8 to 2.2 eV) transitions with charge-transfer character. These ultra-sharp lines (<120 ueV at 4.2 K) share the spin-correlated nature of the bulk exciton by displaying a Neel temperature dependent linear polarization. Furthermore, exciton photoluminescence lineshape analysis reveals a polaronic character via coupling with at-least 3 phonon modes and a comb-like Stark effect through discretization of charges in each layer. These findings augment the knowledge on the many-body nature of excitonic quasi-particles in correlated antiferromagnets and also establish the nanoscale platform as promising for maturing integrated magneto-optic devices

The Scaffolding Function of LSD1 Controls DNA Methylation in Mouse ESCs

Lysine-specific histone demethylase 1 (LSD1), which demethylates mono- or di- methylated histone H3 on lysine 4 (H3K4me1/2), is essential for early embryogenesis and development. Here we show that LSD1 is dispensable for mouse embryonic stem cell (ESC) self-renewal but is required for mouse ESC growth and differentiation. Reintroduction of a catalytically-impaired LSD1 (LSD1MUT) recovers the proliferation capability of mouse ESCs, yet the enzymatic activity of LSD1 is essential to ensure proper differentiation. Indeed, increased H3K4me1 in Lsd1 knockout (KO) mouse ESCs does not lead to major changes in global gene expression programs related to stemness. However, ablation of LSD1 but not LSD1MUT results in decreased DNMT1 and UHRF1 proteins coupled to global hypomethylation. We show that both LSD1 and LSD1MUT control protein stability of UHRF1 and DNMT1 through interaction with HDAC1 and the ubiquitin-specific peptidase 7 (USP7), consequently, facilitating the deacetylation and deubiquitination of DNMT1 and UHRF1. Our studies elucidate a mechanism by which LSD1 controls DNA methylation in mouse ESCs, independently of its lysine demethylase activity

Increased Birth Weight Associated with Regular Pre-Pregnancy Deworming and Weekly Iron-Folic Acid Supplementation for Vietnamese Women

Low birth weight is an important risk factor for neonatal and infant morbidity and mortality and may impact on growth and development. Maternal iron deficiency anaemia contributes to intrauterine growth restriction and low birth weight. Hookworm infections and an iron-depleted diet may lead to iron deficiency anaemia, and both are common in many developing countries. A pilot program of deworming and weekly iron-folic acid supplementation for non-pregnant women aiming to prevent iron deficiency was implemented in northern Vietnam. We compared the birth weight of babies born to women who had had access to the intervention to babies born in districts where the intervention had not been implemented. The mean birth weight of the intervention districts' babies was 124 g more than the control districts' babies; the prevalence of low birth weight was also reduced. These results suggest that providing women with deworming and weekly iron-folic acid supplements before pregnancy is associated with increased birth weight in rural Vietnam. This intervention was provided as a health system integrated program which could be replicated in other at-risk rural areas. If so it could increase the impact of prenatal and antenatal programs, improving the health of both women and newborns

Plant biosystems design research roadmap 1.0

Human life intimately depends on plants for food, biomaterials, health, energy, and a sustainable environment. Various plants have been genetically improved mostly through breeding, along with limited modification via genetic engineering, yet they are still not able to meet the ever-increasing needs, in terms of both quantity and quality, resulting from the rapid increase in world population and expected standards of living. A step change that may address these challenges would be to expand the potential of plants using biosystems design approaches. This represents a shift in plant science research from relatively simple trial-and-error approaches to innovative strategies based on predictive models of biological systems. Plant biosystems design seeks to accelerate plant genetic improvement using genome editing and genetic circuit engineering or create novel plant systems through de novo synthesis of plant genomes. From this perspective, we present a comprehensive roadmap of plant biosystems design covering theories, principles, and technical methods, along with potential applications in basic and applied plant biology research. We highlight current challenges, future opportunities, and research priorities, along with a framework for international collaboration, towards rapid advancement of this emerging interdisciplinary area of research. Finally, we discuss the importance of social responsibility in utilizing plant biosystems design and suggest strategies for improving public perception, trust, and acceptance

Comparison of Multi-Objective Evolutionary Algorithms to Solve the Modular Cell Design Problem for Novel Biocatalysis

A large space of chemicals with broad industrial and consumer applications could be synthesized by engineered microbial biocatalysts. However, the current strain optimization process is prohibitively laborious and costly to produce one target chemical and often requires new engineering efforts to produce new molecules. To tackle this challenge, modular cell design based on a chassis strain that can be combined with different product synthesis pathway modules has recently been proposed. This approach seeks to minimize unexpected failure and avoid task repetition, leading to a more robust and faster strain engineering process. In our previous study, we mathematically formulated the modular cell design problem based on the multi-objective optimization framework. In this study, we evaluated a library of state-of-the-art multi-objective evolutionary algorithms (MOEAs) to identify the most effective method to solve the modular cell design problem. Using the best MOEA, we found better solutions for modular cells compatible with many product synthesis modules. Furthermore, the best performing algorithm could provide better and more diverse design options that might help increase the likelihood of successful experimental implementation. We identified key parameter configurations to overcome the difficulty associated with multi-objective optimization problems with many competing design objectives. Interestingly, we found that MOEA performance with a real application problem, e.g., the modular strain design problem, does not always correlate with artificial benchmarks. Overall, MOEAs provide powerful tools to solve the modular cell design problem for novel biocatalysis