scholarly journals Novel two-stage processes for optimal chemical production in microbes

2019 ◽  
Author(s):  
Kaushik Raj ◽  
Naveen Venayak ◽  
Radhakrishnan Mahadevan
Keyword(s):  
Microbial Metabolism ◽  
Substrate Uptake ◽  
Chemical Production ◽  
Two Stage ◽  
Diverse Range ◽  
E Coli ◽  
Intermediate Growth ◽  
Wide Range ◽  
Production Stages ◽  
The Impact

AbstractMicrobial metabolism can be harnessed to produce a broad range of industrially important chemicals. Often, three key process variables: Titer, Rate and Yield (TRY) are the target of metabolic engineering efforts to improve microbial hosts toward industrial production. Previous research into improving the TRY metrics have examined the efficacy of having distinct growth and production stages to achieve enhanced productivity. However, these studies assumed a switch from a maximum growth to a maximum production phenotype. Hence, phenotypes with intermediate growth and chemical production for the growth and production stages of two-stage processes are yet to be explored. The impact of reduced growth rates on substrate uptake adds to the need for intelligent choice of operating points while designing two-stage processes. In this work, we develop a computational framework that scans the phenotypic space of microbial metabolism to identify ideal growth and production phenotypic targets, to achieve optimal TRY targets. Using this framework, with Escherichia coli as a model organism, we compare two-stage processes that use dynamic pathway regulation, with one-stage processes that use static intervention strategies, for different bioprocess objectives. Our results indicate that two-stage processes with intermediate growth during the production stage always result in optimal TRY values even in cases where substrate uptake is limited due to reduced growth during chemical production. By analyzing the flux distributions for the production enhancing strategies, we identify key reactions and reaction subsystems that require perturbation to achieve a production phenotype for a wide range of metabolites in E. coli. Interestingly, flux perturbations that increase phosphoenolpyruvate and NADPH availability are enriched among these production phenotypes. Furthermore, reactions in the pentose phosphate pathway emerge as key control nodes that function together to increase the availability of precursors to most products in E. coli. The inherently modular nature of microbial metabolism results in common reactions and reaction subsystems that need to be regulated to modify microbes from their target of growth to the production of a diverse range of metabolites. Due to the presence of these common patterns in the flux perturbations, we propose the possibility of a universal production strain.

scholarly journals Impact of Heterologous Expression of Escherichia coli UDP-Glucose Pyrophosphorylase on Trehalose and Glycogen Synthesis in Corynebacterium glutamicum

2004 ◽  
Vol 70 (7) ◽  
pp. 3845-3854 ◽  
Author(s):  
Leandro Padilla ◽  
Susanne Morbach ◽  
Reinhard Krämer ◽  
Eduardo Agosin
Keyword(s):  
Escherichia Coli ◽  
Heterologous Expression ◽  
Corynebacterium Glutamicum ◽  
Glycogen Synthesis ◽  
Glycogen Accumulation ◽  
E Coli ◽  
Wide Range ◽  
The Impact ◽  
Synthetic Operon ◽  
Trehalose Synthesis

ABSTRACT Trehalose is a disaccharide with a wide range of applications in the food industry. We recently proposed a strategy for trehalose production based on improved strains of the gram-positive bacterium Corynebacterium glutamicum. This microorganism synthesizes trehalose through two major pathways, OtsBA and TreYZ, by using UDP-glucose and ADP-glucose, respectively, as the glucosyl donors. In this paper we describe improvement of the UDP-glucose supply through heterologous expression in C. glutamicum of the UDP-glucose pyrophosphorylase gene from Escherichia coli, either expressed alone or coexpressed with the E. coli ots genes (galU otsBA synthetic operon). The impact of such expression on trehalose accumulation and excretion, glycogen accumulation, and the growth pattern of new recombinant strains is described. Expression of the galU otsBA synthetic operon resulted in a sixfold increase in the accumulated and excreted trehalose relative to that in a wild-type strain. Surprisingly, single expression of galU also resulted in an increase in the accumulated trehalose. This increase in trehalose synthesis was abolished upon deletion of the TreYZ pathway. These results proved that UDP-glucose has an important role not only in the OtsBA pathway but also in the TreYZ pathway.

scholarly journals Robustness testing and scalability of phosphate regulated promoters useful for two-stage autoinduction in E. coli

2020 ◽  
Author(s):  
Eirik A Moreb ◽  
Zhixia Ye ◽  
John P Efromson ◽  
Jennifer N Hennigan ◽  
Romel Menacho-Melgar ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Heterologous Protein ◽  
Scale Up ◽  
Mineral Salts ◽  
Two Stage ◽  
Robustness Testing ◽  
E Coli ◽  
Media Formulation ◽  
The Impact ◽  
Regulated Promoters

A key challenge in synthetic biology is the successful utilization of characterized parts, such as promoters, in different biological contexts. We report the robustness testing of a small library of E. coli PhoB regulated promoters that enable heterologous protein production in two-stage cultures. Expression levels were measured both in a rich Autoinduction Broth as well as a minimal mineral salts media. Media dependent differences were promoter dependent. 4 out of 16 promoters tested were identified to have tightly controlled expression which was also robust to media formulation. Improved promoter robustness led to more predictable scale up and consistent expression in instrumented bioreactors. This subset of PhoB activated promoters, useful for two-stage autoinduction, highlight the impact of the environment on the performance of biological parts, and the importance of robustness testing in synthetic biology.

Advances in Therapy and the Management of Antithrombotic Drugs for Venous Thromboembolism

Hematology ◽  
2000 ◽  
Vol 2000 (1) ◽  
pp. 266-284
Author(s):  
Jack E. Ansell ◽  
Jeffrey I. Weitz ◽  
Anthony J. Comerota
Keyword(s):  
Venous Thromboembolism ◽  
Adverse Events ◽  
Venous Thrombosis ◽  
Tissue Factor ◽  
Oral Anticoagulants ◽  
Diverse Range ◽  
Anticoagulant Drugs ◽  
Wide Range ◽  
The Impact ◽  
Block Factor

This review focuses on antithrombotic therapy for venous thromboembolism and covers a diverse range of topics including a discussion of emerging anticoagulant drugs, a renewed focus on thrombolytic agents for selected patients, and an analysis of the factors leading to adverse events in patients on warfarin, and how to optimize therapy. In Section I Dr. Weitz discusses new anticoagulant drugs focusing on those that are in the advanced stages of development. These will include drugs that (a) target factor VIIa/tissue factor, including tissue factor pathway inhibitor and NAPc2; (b) block factor Xa, including the synthetic pentasaccharide and DX9065a; (c) inhibit factors Va and VIIIa, i.e., activated protein C; and (d) block thrombin, including hirudin, argatroban, bivalirudin and H376/95. Oral formulations of heparin will also be reviewed.In Section II, Dr. Comerota will discuss the use of thrombolysis for selected patients with venous thromboembolism. Fibrinolytic therapy, which has suffered from a high risk/benefit ratio for routine deep venous thrombosis, may have an important role to play in patients with iliofemoral venous thrombosis. Dr. Comerota presents his own results with catheter-directed thrombolytic therapy and the results from a large national registry showing long-term outcomes and the impact on quality of life.In Section III, Dr. Ansell presents a critical analysis of the factors responsible for adverse events with oral anticoagulants and the optimum means of improving outcomes. The poor status of present day anticoagulant management is reviewed and the importance of achieving a high rate of “time in therapeutic range,” is emphasized. Models of care to optimize outcomes are described, with an emphasis on models that utilize patient self-testing and patient self-management of oral anticoagulation which are considered to be the ultimate in anticoagulation care. The treatment of venous and arterial thromboembolism is undergoing rapid change with respect to the development of new antithrombotic agents, an expanding list of new indications, and new methods of drug delivery and management. In spite of these changes, many of the traditional therapeutics are still with us and continue to play a vital role in the treatment of thromboembolic disease. The following discussion touches on a wide range of therapeutic interventions, from old to new, exploring the status of anticoagulant drug development, describing a new intervention for iliofemoral venous thrombosis, and analyzing the critical factors for safe and effective therapy with oral anticoagulants.

Approaches to Macrofinancial Surveillance in Article IV Reports

Policy Papers ◽  
2017 ◽  
Vol 17 (13) ◽  
Author(s):  
Keyword(s):  
Low Income ◽  
Global Financial Crisis ◽  
Financial Sector ◽  
Policy Advice ◽  
Low Income Countries ◽  
Financial Shocks ◽  
Diverse Range ◽  
The Past ◽  
Wide Range ◽  
The Impact

The Fund has made good progress over the past two years in integrating macrofinancial analysis into Article IV surveillance for a wide range of members. Building on past work to enhance financial sector analysis, Fund staff has sought to develop a consistent and forward-looking view on how the financial sector affects each member’s economic outlook with the aim of strengthening staff’s capacity to provide advice on macro-critical questions. The focus has been on developing a fuller understanding of macrofinancial linkages, and applying this analysis to inform policy advice. Staff has sought to articulate the role of the financial sector in the macroeconomic baseline, and to integrate the financial sector into the risk assessment, taking into account both the impact of macro shocks on the financial sector as well as the effect of financial shocks on macroeconomic stability. Strengthening the analytical foundations of this work has helped staff provide advice in all policy areas, including financial sector policies. Staff has tailored macrofinancial analysis to the circumstances of a diverse set of economies. Area departments have taken the lead in selecting 66 economies for enhanced macrofinancial coverage and in identifying topics, drawing on targeted support from functional departments. The choice of coverage has included legacies from the global financial crisis—such as deleveraging and stretched balance sheets in advanced economies and some emerging markets—and more recent challenges such as commodity price shocks, especially in low income countries, and the risks of housing booms. The financial sector’s contribution to growth and inclusion has become an important question in countries across all income groups. Staff sees benefits in mainstreaming this approach across the membership, while continuing to address analytical gaps and adapting to new challenges. The work of the past two years has underscored the criticality of macrofinancial analysis for a diverse range of members, and laid the basis for progressively mainstreaming macrofinancial surveillance across the membership. Building on this progress, staff sees scope for the Fund to deepen its understanding of the macroeconomic effects of financial shocks, to better adapt microprudential and macroprudential policy advice with an assessment of macro-critical risks including systemic risk, and to deepen the analysis of outward spillovers. Staff will also need to continue to adapt the focus of analysis and tools, and seek relevant data, as economic challenges evolve.

scholarly journals Virulence factors of Escherichia coli: an overview of animal and human infections with emphasis in bovine mastitis

2019 ◽  
Vol 40 (5) ◽  
pp. 2087
Author(s):  
Simony Trevizan Guerra ◽  
Carolina Lechinski de Paula ◽  
Carmen Alicia Daza Bolaños ◽  
Rodrigo Tavanelli Hernandes ◽  
Márcio Garcia Ribeiro
Keyword(s):  
Escherichia Coli ◽  
Virulence Factors ◽  
Bovine Mastitis ◽  
Clinical Mastitis ◽  
Clinical Severity ◽  
E Coli ◽  
Intestinal Infections ◽  
Wide Range ◽  
Environmental Agents ◽  
The Impact

Escherichia coli is a normal inhabitant of the enteric microflora of human and animal. Intestinal and extra-intestinal infections caused by E. coli in mammals are characterized by the presence of diversity of virulence factors. In addition it can be isolated from environment surrounding human and animal farms. E. coli is the main environmental pathogen causing clinical mastitis in dairy cattle. It causes a wide range of disease severity, from changes seen exclusively in milk to severe systemic signs. The severity of clinical mastitis has been conventionally classified into three levels: mild (grade 1), moderate (score 2), and severe (score 3). Recently, reports of cases of bovine mastitis caused by environmental agents have been on the rise, in particular in countries that have succeeded in controlling contagious microorganisms. Unlike enteric and certain extra-enteric conditions in domestic animals and humans, the impact of virulence factors on the occurrence of bovine mastitis due to E. coli, as well as the clinical severity of the cases, is not fully understood. In this regard, the present study reviewed the most relevant virulence factors of E. coli in human and animals, with emphasis in bovine mastitis.

Viral Architecture, Viral Landscapes: The Impact of Modern Science on Helen Chadwick's Art

Leonardo ◽  
2010 ◽  
Vol 43 (5) ◽  
pp. 458-463 ◽  
Author(s):  
Stephen Walker
Keyword(s):  
Modern Science ◽  
Modern Biology ◽  
Diverse Range ◽  
Research And Practice ◽  
Wide Range ◽  
The Impact ◽  
Theoretical Considerations

This article addresses certain enduring interests that the British artist Helen Chadwick (1953–1996) pursued over the course of her career. While she produced a diverse range of work using a wide range of media, the article will focus on her theoretical considerations of the conjunction of self and world, emphasizing her interest in, and the importance she attached to, the understanding of nature and our place “within” it. She was dissatisfied with received explanations of this relationship, which in her view remained more or less within a Newtonian, mechanical framework. Her research and practice signaled an alternate approach, a “viral technique,” informed by and accommodating her interest in modern biology and physics.

scholarly journals Automation assisted anaerobic phenotyping for metabolic engineering

2021 ◽  
Author(s):  
Kaushik Raj ◽  
Naveen Venayak ◽  
Patrick Diep ◽  
Sai Akhil Golla ◽  
Alexander F. Yakunin ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
High Throughput ◽  
Large Scale ◽  
Small Scale ◽  
Chemical Production ◽  
E Coli ◽  
Strain Design ◽  
Phenotypic Screen ◽  
Wide Range ◽  
Scale Down

Microorganisms can be metabolically engineered to produce a wide range of commercially important chemicals. Advancements in computational strategies for strain design and synthetic biological techniques to construct the designed strains have facilitated the generation of large libraries of potential candidates for chemical production. Consequently, there is a need for a high-throughput, laboratory scale methods to characterize and screen these candidates to select strains for further investigation in large scale fermentation processes. Several small-scale fermentation techniques, in conjunction with laboratory automation have enhanced the throughput of enzyme and strain phenotyping experiments. However, such high throughput experimentation typically entails large operational costs and generate massive amounts of laboratory plastic waste. In this work, we develop an eco-friendly automation workflow that effectively calibrates and decontaminates fixed-tip liquid handling systems to reduce tip waste. We also investigate inexpensive methods to establish anaerobic conditions in microplates for high-throughput anaerobic phenotyping. To validate our phenotyping platform, we assess its performance in two case studies - an anaerobic enzyme screen, and a microbial phenotypic screen. We used our automation platform to investigate conditions under which several strains of E. coli exhibit the same phenotypes in 0.5 L bioreactors and in our scaled-down fermentation platform. Further, we propose the use of dimensionality reduction through t-distributed stochastic neighbours embedding, in conjunction with our phenotyping platform to serve as an effective scale-down model for bioreactor phenotypes. By integrating an in-house data-analysis pipeline, we were able to accelerate the 'test' phase of the design-build-test-learn cycle of metabolic engineering.

Advances in Therapy and the Management of Antithrombotic Drugs for Venous Thromboembolism

Hematology ◽  
2000 ◽  
Vol 2000 (1) ◽  
pp. 266-284
Author(s):  
Jack E. Ansell ◽  
Jeffrey I. Weitz ◽  
Anthony J. Comerota
Keyword(s):  
Venous Thromboembolism ◽  
Adverse Events ◽  
Venous Thrombosis ◽  
Tissue Factor ◽  
Oral Anticoagulants ◽  
Diverse Range ◽  
Anticoagulant Drugs ◽  
Wide Range ◽  
The Impact ◽  
Block Factor

Abstract This review focuses on antithrombotic therapy for venous thromboembolism and covers a diverse range of topics including a discussion of emerging anticoagulant drugs, a renewed focus on thrombolytic agents for selected patients, and an analysis of the factors leading to adverse events in patients on warfarin, and how to optimize therapy. In Section I Dr. Weitz discusses new anticoagulant drugs focusing on those that are in the advanced stages of development. These will include drugs that (a) target factor VIIa/tissue factor, including tissue factor pathway inhibitor and NAPc2; (b) block factor Xa, including the synthetic pentasaccharide and DX9065a; (c) inhibit factors Va and VIIIa, i.e., activated protein C; and (d) block thrombin, including hirudin, argatroban, bivalirudin and H376/95. Oral formulations of heparin will also be reviewed. In Section II, Dr. Comerota will discuss the use of thrombolysis for selected patients with venous thromboembolism. Fibrinolytic therapy, which has suffered from a high risk/benefit ratio for routine deep venous thrombosis, may have an important role to play in patients with iliofemoral venous thrombosis. Dr. Comerota presents his own results with catheter-directed thrombolytic therapy and the results from a large national registry showing long-term outcomes and the impact on quality of life. In Section III, Dr. Ansell presents a critical analysis of the factors responsible for adverse events with oral anticoagulants and the optimum means of improving outcomes. The poor status of present day anticoagulant management is reviewed and the importance of achieving a high rate of “time in therapeutic range,” is emphasized. Models of care to optimize outcomes are described, with an emphasis on models that utilize patient self-testing and patient self-management of oral anticoagulation which are considered to be the ultimate in anticoagulation care. The treatment of venous and arterial thromboembolism is undergoing rapid change with respect to the development of new antithrombotic agents, an expanding list of new indications, and new methods of drug delivery and management. In spite of these changes, many of the traditional therapeutics are still with us and continue to play a vital role in the treatment of thromboembolic disease. The following discussion touches on a wide range of therapeutic interventions, from old to new, exploring the status of anticoagulant drug development, describing a new intervention for iliofemoral venous thrombosis, and analyzing the critical factors for safe and effective therapy with oral anticoagulants.

scholarly journals An ecosystem services perspective of Lake Wairarapa: Insights from the past, present, and toward the future

2021 ◽  
Author(s):  
◽  
Sky Halford
Keyword(s):  
Ecosystem Services ◽  
Service Delivery ◽  
Ecosystem Service ◽  
Collaborative Management ◽  
Coastal Lake ◽  
E Coli ◽  
The Past ◽  
Wide Range ◽  
The Future ◽  
The Impact

<p>Ecosystem services encompass the wide range of intrinsic and extrinsic benefits that humans derive from ecosystems and how such services contribute to community wellbeing. The delivery of effective and efficient provisioning, regulating, and cultural ecosystem services at Lake Wairarapa (a shallow, super-trophic, coastal lake in the lower North Island) has been heavily impacted through current land use. Using a pragmatic epistemology and mixed methods approach, this research sought to understand the past, present, and future delivery of ecosystem services at Lake Wairarapa through three distinct, yet complementary, studies.  Firstly, a palaeo-environmental reconstruction using five proxies was completed to build an understanding of past environmental conditions at Lake Wairarapa. Prior to human arrival, the lake was stable and resilient in response to environmental perturbations. However, alteration of the landscape following human arrival has reduced ecosystem service effectiveness, prompting a transition into an entirely new environmental state at Lake Wairarapa. This chapter highlighted the abrupt removal of mānuka and centennial shift from a forest catchment into one dominated by agriculture so a field trial was conducted to assess the ability of mānuka to reduce nitrogen leaching and E. coli contamination. Mānuka can significantly reduce the conversion of ammonium to nitrate compared to pasture, thus regulating nitrate leaching; however, the impact on E. coli counts was less conclusive. Finally, cultural services present at Lake Wairarapa and future community aspirations were assessed through seven semi-structured interviews of Wairarapa community members. Place attachment was recognised as the underlying factor that facilitated strong cultural service delivery. Social and environmental restoration was identified as the key vision for the future, underpinned by collaboration within resource management.  From this research, four recommendations were made to enhance ecosystem service delivery at Lake Wairarapa: establishment of ecologically appropriate restoration plans, facilitated collaborative management, further investigation of environmental and economic properties of mānuka, and development of community engagement programmes. This multi-disciplinary and holistic approach outlines a pathway towards a positive and inclusive future for Lake Wairarapa and its communities.</p>

scholarly journals The impact of the chemical production of methyl nitrate from the NO + CH<sub>3</sub>O<sub>2</sub> reaction on the global distributions of alkyl nitrates, nitrogen oxides and tropospheric ozone: a global modelling study

2014 ◽  
Vol 14 (5) ◽  
pp. 2363-2382 ◽  
Author(s):  
J. E. Williams ◽  
G. Le Bras ◽  
A. Kukui ◽  
H. Ziereis ◽  
C. A. M. Brenninkmeijer
Keyword(s):  
Branching Ratio ◽  
Global Scale ◽  
Chemical Production ◽  
Alkyl Nitrates ◽  
Mixing Ratios ◽  
Wide Range ◽  
Oceanic Emissions ◽  
Methyl Nitrate ◽  
The Tropics ◽  
The Impact

Abstract. The formation, abundance and distribution of organic nitrates are relevant for determining the production efficiency and resident mixing ratios of tropospheric ozone (O3) on both regional and global scales. Here we investigate the effect of applying the recently measured direct chemical production of methyl nitrate (CH3ONO2) during NOx recycling involving the methyl-peroxy radical on the global tropospheric distribution of CH3ONO2 and the perturbations introduced towards tropospheric NOx and O3 using the TM5 global chemistry transport model. By comparisons against numerous observations, we show that the global surface distribution of CH3ONO2 can be largely explained by introducing the chemical production mechanism using a branching ratio of 0.3%, when assuming a direct oceanic emission source of ~0.15 Tg N yr−1. On a global scale, the chemical production of CH3ONO2 converts 1 Tg N yr−1 from nitrogen oxide for this branching ratio. The resident mixing ratios of CH3ONO2 are found to be highly sensitive to the dry deposition velocity that is prescribed, where more than 50% of the direct oceanic emission is lost near the source regions, thereby mitigating the subsequent effects due to long-range and convective transport out of the source region. For the higher alkyl nitrates (RONO2) we find improvements in the simulated distribution near the surface in the tropics (10° S–10° N) when introducing direct oceanic emissions equal to ~0.17 Tg N yr−1 . In terms of the vertical profile of CH3ONO2, there are persistent overestimations in the free troposphere and underestimations in the upper troposphere across a wide range of latitudes and longitudes when compared against data from measurement campaigns. This suggests either a missing transport pathway or source/sink term, although measurements show significant variability in resident mixing ratios at high altitudes at global scale. For the vertical profile of RONO2, TM5 performs better at tropical latitudes than at mid-latitudes, with similar features in the comparisons to those for CH3ONO2. Comparisons of CH3ONO2 with a wide range of surface measurements shows that further constraints are necessary regarding the variability in the deposition terms for different land surfaces in order to improve on the comparisons presented here. For total reactive nitrogen (NOy) ~20% originates from alkyl nitrates in the tropics and subtropics, where the introduction of both direct oceanic emissions and the chemical formation mechanism of CH3ONO2 only makes a ~5% contribution to the total alkyl nitrate content in the upper troposphere when compared with aircraft observations. We find that the increases in tropospheric O3 that occur due oxidation of CH3ONO2 originating from direct oceanic emission is negated when accounting for the chemical formation of CH3ONO2, meaning that the impact of such oceanic emissions on atmospheric lifetimes becomes marginal when a branching ratio of 0.3% is adopted.

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