scholarly journals The metabolic response ofPseudomonas taiwanensisto NADH dehydrogenase deficiency

2019 ◽  
Author(s):  
Salome C. Nies ◽  
Robert Dinger ◽  
Yan Chen ◽  
Gossa G. Wordofa ◽  
Mette Kristensen ◽  
...  
Keyword(s):  
Respiratory Chain ◽  
Large Scale ◽  
Nadh Dehydrogenase ◽  
Metabolic Response ◽  
Metabolic Flexibility ◽  
Second Phase ◽  
Type I ◽  
Depth Analysis ◽  
Nadh Dehydrogenases ◽  
The Impact

AbstractObligate aerobic organisms rely on a functional electron transport chain for energy generation and NADH oxidation. Because of this essential requirement, the genes of this pathway are likely constitutively and highly expressed to avoid a cofactor imbalance and energy shortage under fluctuating environmental conditions.We here investigated the essentiality of the three NADH dehydrogenases of the respiratory chain of the obligate aerobePseudomonas taiwanensisVLB120 and the impact of the knockouts of corresponding genes on its physiology and metabolism. While a mutant lacking all three NADH dehydrogenases seemed to be nonviable, the generated single or double knockout strains displayed none or only a marginal phenotype. Only the mutant deficient in both type 2 dehydrogenases showed a clear phenotype with biphasic growth behavior and strongly reduced growth rate in the second phase. In-depth analyses of the metabolism of the generated mutants including quantitative physiological experiments, transcript analysis, proteomics and enzyme activity assays revealed distinct responses to type II and type I dehydrogenase deletions. An overall high metabolic flexibility enablesP. taiwanensisto cope with the introduced genetic perturbations and maintain stable phenotypes by rerouting of metabolic fluxes.This metabolic adaptability has implications for biotechnological applications. While the phenotypic robustness is favorable in large-scale applications with inhomogeneous conditions, versatile redirecting of carbon fluxes upon genetic interventions can frustrate metabolic engineering efforts.ImportanceWhilePseudomonashas the capability for high metabolic activity and the provision of reduced redox cofactors important for biocatalytic applications, exploitation of this characteristic might be hindered by high, constitutive activity of and consequently competition with the NADH dehydrogenases of the respiratory chain. The in-depth analysis of NADH dehydrogenase mutants ofPseudomonas taiwanensisVLB120 presented here, provides insight into the phenotypic and metabolic response of this strain to these redox metabolism perturbations. The observed great metabolic flexibility needs to be taken into account for rational engineering of this promising biotechnological workhorse towards a host with controlled and efficient supply of redox cofactors for product synthesis.

scholarly journals Systems Analysis of NADH Dehydrogenase Mutants Reveals Flexibility and Limits of Pseudomonas taiwanensis VLB120’s Metabolism

2020 ◽  
Vol 86 (11) ◽  
Author(s):  
Salome C. Nies ◽  
Robert Dinger ◽  
Yan Chen ◽  
Gossa G. Wordofa ◽  
Mette Kristensen ◽  
...  
Keyword(s):  
Respiratory Chain ◽  
Large Scale ◽  
Nadh Dehydrogenase ◽  
Metabolic Flexibility ◽  
Second Phase ◽  
Content Type ◽  
Depth Analysis ◽  
Nadh Dehydrogenases ◽  
The Impact

ABSTRACT Obligate aerobic organisms rely on a functional electron transport chain for energy conservation and NADH oxidation. Because of this essential requirement, the genes of this pathway are likely constitutively and highly expressed to avoid a cofactor imbalance and energy shortage under fluctuating environmental conditions. We here investigated the essentiality of the three NADH dehydrogenases of the respiratory chain of the obligate aerobe Pseudomonas taiwanensis VLB120 and the impact of the knockouts of corresponding genes on its physiology and metabolism. While a mutant lacking all three NADH dehydrogenases seemed to be nonviable, the single or double knockout mutant strains displayed no, or only a weak, phenotype. Only the mutant deficient in both type 2 dehydrogenases showed a clear phenotype with biphasic growth behavior and a strongly reduced growth rate in the second phase. In-depth analyses of the metabolism of the generated mutants, including quantitative physiological experiments, transcript analysis, proteomics, and enzyme activity assays revealed distinct responses to type 2 and type 1 dehydrogenase deletions. An overall high metabolic flexibility enables P. taiwanensis to cope with the introduced genetic perturbations and maintain stable phenotypes, likely by rerouting of metabolic fluxes. This metabolic adaptability has implications for biotechnological applications. While the phenotypic robustness is favorable in large-scale applications with inhomogeneous conditions, the possible versatile redirecting of carbon fluxes upon genetic interventions can thwart metabolic engineering efforts. IMPORTANCE While Pseudomonas has the capability for high metabolic activity and the provision of reduced redox cofactors important for biocatalytic applications, exploitation of this characteristic might be hindered by high, constitutive activity of and, consequently, competition with the NADH dehydrogenases of the respiratory chain. The in-depth analysis of NADH dehydrogenase mutants of Pseudomonas taiwanensis VLB120 presented here provides insight into the phenotypic and metabolic response of this strain to these redox metabolism perturbations. This high degree of metabolic flexibility needs to be taken into account for rational engineering of this promising biotechnological workhorse toward a host with a controlled and efficient supply of redox cofactors for product synthesis.

scholarly journals Synchronization in 5G networks: a hybrid Bayesian approach toward clock offset/skew estimation and its impact on localization

2021 ◽  
Vol 2021 (1) ◽  
Author(s):  
Meysam Goodarzi ◽  
Darko Cvetkovski ◽  
Nebojsa Maletic ◽  
Jesús Gutiérrez ◽  
Eckhard Grass
Keyword(s):  
Bayesian Approach ◽  
Large Scale ◽  
Hybrid Approach ◽  
Position Estimation ◽  
5G Networks ◽  
Clock Skew ◽  
Depth Analysis ◽  
The Impact ◽  
Mean Square Errors ◽  
Clock Offset

AbstractClock synchronization has always been a major challenge when designing wireless networks. This work focuses on tackling the time synchronization problem in 5G networks by adopting a hybrid Bayesian approach for clock offset and skew estimation. Furthermore, we provide an in-depth analysis of the impact of the proposed approach on a synchronization-sensitive service, i.e., localization. Specifically, we expose the substantial benefit of belief propagation (BP) running on factor graphs (FGs) in achieving precise network-wide synchronization. Moreover, we take advantage of Bayesian recursive filtering (BRF) to mitigate the time-stamping error in pairwise synchronization. Finally, we reveal the merit of hybrid synchronization by dividing a large-scale network into local synchronization domains and applying the most suitable synchronization algorithm (BP- or BRF-based) on each domain. The performance of the hybrid approach is then evaluated in terms of the root mean square errors (RMSEs) of the clock offset, clock skew, and the position estimation. According to the simulations, in spite of the simplifications in the hybrid approach, RMSEs of clock offset, clock skew, and position estimation remain below 10 ns, 1 ppm, and 1.5 m, respectively.

scholarly journals Physiological relevance, localization and substrate specificity of the alternative (type II) mitochondrial NADH dehydrogenases of Ogataea parapolymorpha

2021 ◽  
Author(s):  
Hannes Juergens ◽  
Álvaro Mielgo-Gómez ◽  
Albert Godoy-Hernández ◽  
Jolanda ter Horst ◽  
Janine M. Nijenhuis ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Respiratory Chain ◽  
Complex I ◽  
Nadh Dehydrogenase ◽  
Physiological Role ◽  
Proton Pumping ◽  
Type Ii ◽  
Respiratory Chains ◽  
Alternative Type ◽  
Nadh Dehydrogenases

AbstractMitochondria from Ogataea parapolymorpha harbor a branched electron-transport chain containing a proton-pumping Complex I NADH dehydrogenase and three alternative (type II) NADH dehydrogenases (NDH2s). To investigate the physiological role, localization and substrate specificity of these enzymes, growth of various NADH dehydrogenase mutants was quantitatively characterized in shake-flask and chemostat cultures, followed by oxygen-uptake experiments with isolated mitochondria. Furthermore, NAD(P)H:quinone oxidoreduction of the three NDH2s were individually assessed. Our findings show that the O. parapolymorpha respiratory chain contains an internal NADH-accepting NDH2 (Ndh2-1/OpNdi1), at least one external NAD(P)H-accepting enzyme and likely additional mechanisms for respiration-linked oxidation of cytosolic NADH. Metabolic regulation appears to prevent competition between OpNdi1 and Complex I for mitochondrial NADH. With the exception of OpNdi1, the respiratory chain of O. parapolymorpha exhibits metabolic redundancy and tolerates deletion of multiple NADH-dehydrogenase genes without compromising fully respiratory metabolism.ImportanceTo achieve high productivity and yields in microbial bioprocesses, efficient use of the energy substrate is essential. Organisms with branched respiratory chains can respire via the energy-efficient proton-pumping Complex I, or make use of alternative NADH dehydrogenases (NDH2s). The yeast Ogataea parapolymorpha contains three uncharacterized, putative NDH2s which were investigated in this work. We show that O. parapolymorpha contains at least one ‘internal’ NDH2, which provides an alternative to Complex I for mitochondrial NADH oxidation, albeit at a lower efficiency. The use of this NDH2 appeared to be limited to carbon excess conditions and the O. parapolymorpha respiratory chain tolerated multiple deletions without compromising respiratory metabolism, highlighting opportunities for metabolic (redox) engineering. By providing a more comprehensive understanding of the physiological role of NDH2s, including insights into their metabolic capacity, orientation and substrate specificity this study also extends our fundamental understanding of respiration in organisms with branched respiratory chains.

scholarly journals A Large-Scale Pseudoword-Based Evaluation Framework for State-of-the-Art Word Sense Disambiguation

2014 ◽  
Vol 40 (4) ◽  
pp. 837-881 ◽  
Author(s):  
Mohammad Taher Pilehvar ◽  
Roberto Navigli
Keyword(s):  
Large Scale ◽  
State Of The Art ◽  
Word Sense Disambiguation ◽  
Evaluation Framework ◽  
Small Scale ◽  
Word Sense ◽  
Knowledge Based ◽  
Depth Analysis ◽  
Sense Disambiguation ◽  
The Impact

The evaluation of several tasks in lexical semantics is often limited by the lack of large amounts of manual annotations, not only for training purposes, but also for testing purposes. Word Sense Disambiguation (WSD) is a case in point, as hand-labeled datasets are particularly hard and time-consuming to create. Consequently, evaluations tend to be performed on a small scale, which does not allow for in-depth analysis of the factors that determine a systems' performance. In this paper we address this issue by means of a realistic simulation of large-scale evaluation for the WSD task. We do this by providing two main contributions: First, we put forward two novel approaches to the wide-coverage generation of semantically aware pseudowords (i.e., artificial words capable of modeling real polysemous words); second, we leverage the most suitable type of pseudoword to create large pseudosense-annotated corpora, which enable a large-scale experimental framework for the comparison of state-of-the-art supervised and knowledge-based algorithms. Using this framework, we study the impact of supervision and knowledge on the two major disambiguation paradigms and perform an in-depth analysis of the factors which affect their performance.

scholarly journals INTERPRETING LARGE SCALE NATIONAL LEVEL ASSESSMENT DATA IN MATHEMATICS BY USING RASCH ANALYSIS

2020 ◽  
Vol 3 ◽  
pp. 457
Author(s):  
Pāvels Pestovs ◽  
Dace Namsone
Keyword(s):  
Student Achievement ◽  
General Education ◽  
Large Scale ◽  
National Level ◽  
School Level ◽  
Minimum Level ◽  
Assessment Data ◽  
Depth Analysis ◽  
Improve Student Achievement ◽  
The Impact

Latvia is undergoing a nation-wide curriculum reform in general education, with an aim to help students to develop 21st century skills. In order to successfully implement reform, not only teacher performance in the classroom is important, but also the transformation of the school culture is of high priority. One of the key dimensions that is characteristic for a school as learning organization culture is whether it has data-driven culture and is using data on continuous basis to improve student achievement. Large scale national level assessment data is used for many different purposes, however, this data only rarely is recognised as useful data source for planning actions to improve student achievement at school level. Authors argue that in different grades average performance of students cannot be compared in a meaningful way to develop action plan and evaluate the impact of the initiatives at the school level. It is based on the issues rising from varying difficulty level of the tests and different skills, which are being assessed. The study design is based on in-depth analysis of items of large-scale national level assessment in mathematics, defining minimum level of competency of mathematics and calculating percentage of students in school with minimum level of competence in a cohort. This analysis is conveyed for the students of 3rd, 6th and 9th grade by using Rasch model, thus allowing to effectively monitor the student performance during the general education and use of data to make informed decisions.  

scholarly journals V2Karst V1.1: a parsimonious large-scale integrated vegetation–recharge model to simulate the impact of climate and land cover change in karst regions

2018 ◽  
Vol 11 (12) ◽  
pp. 4933-4964 ◽  
Author(s):  
Fanny Sarrazin ◽  
Andreas Hartmann ◽  
Francesca Pianosi ◽  
Rafael Rosolem ◽  
Thorsten Wagener
Keyword(s):  
Land Cover ◽  
Groundwater Recharge ◽  
Large Scale ◽  
Temporal Distribution ◽  
Land Cover Changes ◽  
Depth Analysis ◽  
Karst Areas ◽  
Large Scale Land ◽  
Evapotranspiration Estimation ◽  
The Impact

Abstract. Karst aquifers are an important source of drinking water in many regions of the world. Karst areas are highly permeable and produce large amounts of groundwater recharge, while surface runoff is often negligible. As a result, recharge in these systems may have a different sensitivity to climate and land cover changes than in other less permeable systems. However, little is known about the combined impact of climate and land cover changes in karst areas at large scales. In particular, the representation of land cover, and its controls on evapotranspiration, has been very limited in previous karst hydrological models. In this study, we address this gap (1) by introducing the first large-scale hydrological model including an explicit representation of both karst and land cover properties, and (2) by providing an in-depth analysis of the model's recharge production behaviour. To achieve these aims, we replace the empirical approach to evapotranspiration estimation of a previous large-scale karst recharge model (VarKarst) with an explicit, mechanistic and parsimonious approach in the new model (V2Karst V1.1). We demonstrate the plausibility of V2Karst simulations at four carbonate rock FLUXNET sites by assessing the model's ability to reproduce observed evapotranspiration and soil moisture patterns and by showing that the controlling modelled processes are in line with expectations. Additional virtual experiments with synthetic input data systematically explore the sensitivities of recharge to precipitation characteristics (overall amount and temporal distribution) and land cover properties. This approach confirms that these sensitivities agree with expectations and provides first insights into the potential impacts of future change. V2Karst is the first model that enables the study of the joint impacts of large-scale land cover and climate changes on groundwater recharge in karst regions.

scholarly journals Quantile regression for challenging cases of eQTL mapping

2019 ◽  
Vol 21 (5) ◽  
pp. 1756-1765
Author(s):  
Bo Sun ◽  
Liang Chen
Keyword(s):  
Quantile Regression ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Linear Models ◽  
Real Data ◽  
Type I ◽  
Eqtl Mapping ◽  
Size Estimation ◽  
Rna Seq ◽  
The Impact

Abstract Mapping of expression quantitative trait loci (eQTLs) facilitates interpretation of the regulatory path from genetic variants to their associated disease or traits. High-throughput sequencing of RNA (RNA-seq) has expedited the exploration of these regulatory variants. However, eQTL mapping is usually confronted with the analysis challenges caused by overdispersion and excessive dropouts in RNA-seq. The heavy-tailed distribution of gene expression violates the assumption of Gaussian distributed errors in linear regression for eQTL detection, which results in increased Type I or Type II errors. Applying rank-based inverse normal transformation (INT) can make the expression values more normally distributed. However, INT causes information loss and leads to uninterpretable effect size estimation. After comprehensive examination of the impact from overdispersion and excessive dropouts, we propose to apply a robust model, quantile regression, to map eQTLs for genes with high degree of overdispersion or large number of dropouts. Simulation studies show that quantile regression has the desired robustness to outliers and dropouts, and it significantly improves eQTL mapping. From a real data analysis, the most significant eQTL discoveries differ between quantile regression and the conventional linear model. Such discrepancy becomes more prominent when the dropout effect or the overdispersion effect is large. All the results suggest that quantile regression provides more reliable and accurate eQTL mapping than conventional linear models. It deserves more attention for the large-scale eQTL mapping.

scholarly journals TDD Dynamics: Understanding the Impact of Test-Driven Development on Software Quality and Productivity

2021 ◽  
Author(s):  
Yahha Rafique
Keyword(s):  
Empirical Research ◽  
Large Scale ◽  
Meta Analysis ◽  
Empirical Studies ◽  
Extreme Programming ◽  
Second Phase ◽  
Moderator Variables ◽  
Empirical Measures ◽  
Test Driven Development ◽  
The Impact

Test-Driven Development (TDD) is one of the cornerstone practices of the Extreme Programming agile methodology. Today, despite the large scale adoption of TDD in industry, including large software firms such as Microsoft and IBM, its usefulness with regard to the quality and productivity constructs it still under question. Empirical Research has failed to produce conclusive results; all possible results have been reported for both constructs. This research adopts non-empirical measures to gain a deeper understanding of TDD. A two-phased approach has been undertaken towards the goal. The first phase involves conducting a meta-analysis of past empirical research. The meta-analysis quantitatively combines the results of individual empirical studies and identifies moderator variables that could potentially govern the performance of TDD. The second phase of the approach involves the construction of a simulation model of a TDD-based development process. The presented model further analyzes the impact of changes in moderator variables.

scholarly journals TDD Dynamics: Understanding the Impact of Test-Driven Development on Software Quality and Productivity

2021 ◽  
Author(s):  
Yahha Rafique
Keyword(s):  
Empirical Research ◽  
Large Scale ◽  
Meta Analysis ◽  
Empirical Studies ◽  
Extreme Programming ◽  
Second Phase ◽  
Moderator Variables ◽  
Empirical Measures ◽  
Test Driven Development ◽  
The Impact

Test-Driven Development (TDD) is one of the cornerstone practices of the Extreme Programming agile methodology. Today, despite the large scale adoption of TDD in industry, including large software firms such as Microsoft and IBM, its usefulness with regard to the quality and productivity constructs it still under question. Empirical Research has failed to produce conclusive results; all possible results have been reported for both constructs. This research adopts non-empirical measures to gain a deeper understanding of TDD. A two-phased approach has been undertaken towards the goal. The first phase involves conducting a meta-analysis of past empirical research. The meta-analysis quantitatively combines the results of individual empirical studies and identifies moderator variables that could potentially govern the performance of TDD. The second phase of the approach involves the construction of a simulation model of a TDD-based development process. The presented model further analyzes the impact of changes in moderator variables.

scholarly journals Linking Business Environment Reform with Gender and Inclusion: A Study of Business Licensing Reform in Indonesia

2021 ◽  
Author(s):  
Amrita Saha ◽  
Jodie Thorpe ◽  
Keir Macdonald ◽  
Kelbesa Megersa
Keyword(s):  
Firm Performance ◽  
Business Performance ◽  
Large Scale ◽  
Business Environment ◽  
Performance Outcomes ◽  
Sociocultural Factors ◽  
Detailed Knowledge ◽  
Depth Analysis ◽  
Business Regulations ◽  
The Impact

Business environment reform (BER) targets inadequate business regulations. It is intended to remove constraints to business investment, enabling growth and job creation, and create opportunities for international business to contribute to and benefit from this growth. However, there is a lack of detailed knowledge of the impact of BER on gender and inclusion (G&I). While a review of existing literature suggests that in general, there is no direct link between BER and G&I, indirect links are likely through the influence of BER on firm performance. Outcomes will be influenced by the differential ways in which women-led firms experience the business environment when compared to their male counterparts, with disparities based on how they are treated under the law, as well as structural and sociocultural factors. The fact that in many countries, female-led firms are fewer and smaller than those of their male counterparts, and may operate in different sectors, also affects these dynamics. This research offers new insights through an in-depth analysis of the impact of the Pelayanan Terpadu Satu Pintu (PTSP) or one-stop shop business licensing reform in 2009 on firm performance in Indonesia, and how these impacts vary based on the gender of firm leadership. The results find that on average, firms benefited from improved business performance (sales), as a direct or indirect effect of this reform, as well as an increase in the number of medium and large-scale firms. Outside Jakarta (Bali, Banten, Lampung), women-led firms experienced a small but significant benefit relative to male-led firms, related to both sales and the number of medium and large-scale firms they run. In Jakarta, women-led firms continued to lag behind men and there were no significant effects on employment, and this held across province and gender. These findings are based on an analysis of the PTSP reform using data from the World Bank Enterprise Survey (WBES), a survey of small, medium and large firms (i.e. with more than four employees) which took place in Indonesia between 2009 and 2015.

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