Linear constraint relations in biochemical reaction systems: II. Diagnosis and estimation of gross errors

Heijden, R. T. J. M. van der; Romein, B.; Heijnen, Joseph J.; Hellinga, C.; Luyben, K. Ch. A. M.

doi:10.1002/bit.260430104

Cited by 148 publications

(98 citation statements)

References 11 publications

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“…The residuals obtained after multiplication of the redundancy matrix by the measured exchange rates could be explained on the basis of random measurement variances with test values that were lower than the 95 % chi-squared critical value of 5.992 (van der Heijden et al, 1994). In addition, the individual carbon and nitrogen balances could be closed for all datasets.…”

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confidence: 99%

Expression of phosphofructokinase in Neisseria meningitidis

et al. 2010

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Neisseria meningitidis serogroup B is a pathogen that can infect diverse sites within the human host. According to the N. meningitidis genomic information and experimental observations, glucose can be completely catabolized through the Entner-Doudoroff pathway and the pentose phosphate pathway. The Embden-Meyerhof-Parnas pathway is not functional, because the gene for phosphofructokinase (PFK) is not present. The phylogenetic distribution of PFK indicates that in most obligate aerobic organisms, PFK is lacking. We conclude that this is because of the limited contribution of PFK to the energy supply in aerobically grown organisms in comparison with the energy generated through oxidative phosphorylation. Under anaerobic or microaerobic conditions, the available energy is limiting, and PFK provides an advantage, which explains the presence of PFK in many (facultatively) anaerobic organisms. In accordance with this, in silico flux balance analysis predicted an increase of biomass yield as a result of PFK expression. However, analysis of a genetically engineered N. meningitidis strain that expressed a heterologous PFK showed that the yield of biomass on substrate decreased in comparison with a pfkA-deficient control strain, which was associated mainly with an increase in CO 2 production, whereas production of by-products was similar in the two strains. This might explain why the pfkA gene has not been obtained by horizontal gene transfer, since it is initially unfavourable for biomass yield. No large effects related to heterologous expression of pfkA were observed in the transcriptome. Although our results suggest that introduction of PFK does not contribute to a more efficient strain in terms of biomass yield, achievement of a robust, optimal metabolic network that enables a higher growth rate or a higher biomass yield might be possible after adaptive evolution of the strain, which remains to be investigated.Abbreviations: dcw, dry cell weight; ED, Entner-Doudoroff; EMP, Embden-Meyerhof-Parnas; F6P, fructose 6-phosphate; FBA, flux balance analysis; FR, fold ratio; HGT, horizontal gene transfer; LP, linear programming; MCS, Monte Carlo simulation; NVI, Netherlands Vaccine Institute; PEP, phosphoenolpyruvate; PP, pentose phosphate, PTS system, phosphotransferase system. The microarray data discussed in this paper are available under GEO accession number GSE18951.Three supplementary tables, showing the relationships in bacterial species between PFK (encoded by pfkA), the glucose-specific PTS transporter EIIB Glc (encoded by ptsG) and glucokinase, GK (encoded by glk), are available with the online version of this paper. Additional data are also available with the online version of this paper in the form of the Excel file Additional data.xls, which includes six worksheets. The first worksheet, named 'model', contains the simplified metabolic model. The second worksheet, named 'abbreviations', contains a list of abbreviations of the metabolites. The third worksheet, named 'flux distributions', contains the calculated flux...

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Expression of phosphofructokinase in Neisseria meningitidis

et al. 2010

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“…The trends for biomass decrease, release of ammonium, and release of SOC were not significant when they were tested independently. However, together they possibly described a physiological response in which some por- d Rates (average Ϯ standard error) were first determined by linear regression and then adjusted by data reconciliation (30). e NA, not applicable.…”

Section: Resultsmentioning

confidence: 99%

“…g Probability of the h-statistics (no difference between the measured and balanced rates) from a 2 distribution with 2 degrees of freedom (30). h Composition (average Ϯ standard error) during the feast phase (n ϭ 6 to 8).…”

Section: Resultsmentioning

confidence: 99%

rRNA and Poly-β-Hydroxybutyrate Dynamics in Bioreactors Subjected to Feast and Famine Cycles

Frigon

Muyzer

Loosdrecht

et al. 2006

Appl Environ Microbiol

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Feast and famine cycles are common in activated sludge wastewater treatment systems, and they select for bacteria that accumulate storage compounds, such as poly-␤-hydroxybutyrate (PHB). Previous studies have shown that variations in influent substrate concentrations force bacteria to accumulate high levels of rRNA compared to the levels in bacteria grown in chemostats. Therefore, it can be hypothesized that bacteria accumulate more rRNA when they are subjected to feast and famine cycles. However, PHB-accumulating bacteria can form biomass (grow) throughout a feast and famine cycle and thus have a lower peak biomass formation rate during the cycle. Consequently, PHB-accumulating bacteria may accumulate less rRNA when they are subjected to feast and famine cycles than bacteria that are not capable of PHB accumulation. These hypotheses were tested with Wautersia eutropha H16 (wild type) and W. eutropha PHB-4 (a mutant not capable of accumulating PHB) grown in chemostat and semibatch reactors. For both strains, the cellular RNA level was higher when the organism was grown in semibatch reactors than when it was grown in chemostats, and the specific biomass formation rates during the feast phase were linearly related to the cellular RNA levels for cultures. Although the two strains exhibited maximum uptake rates when they were grown in semibatch reactors, the wild-type strain responded much more rapidly to the addition of fresh medium than the mutant responded. Furthermore, the chemostat-grown mutant culture was unable to exhibit maximum substrate uptake rates when it was subjected to pulse-wise addition of fresh medium. These data show that the ability to accumulate PHB does not prevent bacteria from accumulating high levels of rRNA when they are subjected to feast and famine cycles. Our results also demonstrate that the ability to accumulate PHB makes the bacteria more responsive to sudden increases in substrate concentrations, which explains their ecological advantage.rRNA-targeted hybridization techniques, such as fluorescence in situ hybridization and oligonucleotide membrane hybridization, are increasingly used to study microbial population diversity and dynamics in wastewater treatment systems (34). Although the temporal trends determined by these two techniques often agree with each other, their evaluations of population abundance may differ considerably. For example, Oerther and coworkers (19) reported that the Acinetobacter spp. population accounted for up to 43% of the total rRNA, while this population accounted for only up to 4.4% of the total number of cells in a municipal activated sludge system, suggesting that the cellular rRNA levels for this population were relatively high. In a related study, an opposite trend was found for the Gordonia spp. population in the same activated sludge treatment system (20). Some of the discrepancies can probably be explained by variation in the regulation of rRNA between species. However, the reactor conditions, specific metabolic functions, and ecological interactions...

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“…If not, there are infinite solutions. Further discussion of these techniques can be found elsewhere in relevant literature (Villadsen et al, 2011;Meijer et al, 2002;van der Heijden et al, 1994).…”

Section: ⋅ + ⋅mentioning

confidence: 99%

Experimental Methods in Wastewater Treatment

Loosdrecht¹,

Nielsen²,

López-Vázquez³

et al. 2016

Water Intelligence Online

143

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PrefaceWastewater treatment is a core technology for water resources protection and reuse, as is clearly demonstrated by the great success of its consequent implementation in many countries worldwide. During the last decennia scientific research has made vast progress in understanding the complex and interdisciplinary aspects of the biological, biochemical, chemical and mechanical processes involved. It can be concluded that the global application of existing knowledge and experience in wastewater treatment technology will represent a cornerstone in future water management, as expressed in the Strategic Development Goals accepted by the UN in September 2015.Only about one fifth of the wastewater produced globally is currently being adequately treated. To achieve the goal for sustainable water management by 2030 would require extra wastewater treatment facilities for about 600,000 people each day. I am convinced that this book will make its own significant contribution to meeting this ambitious goal.In the near future, most of the global population will live in cities and in low and middle-income countries, where most wastewater is not adequately treated. Probably the most limiting factor in achieving the goals for sustainable water management is the lack of qualified, well-trained professionals, able to comprehend the scientific research results and transfer them into practice. It is therefore of prime importance to make currently available scientific advances and proven experiences in wastewater treatment technology applications easily accessible worldwide. This was one of the drivers for the development of this book, which represents an innovative contribution to help overcome such a capacity development challenge. The book is most definitely expected to contribute to bridging the gaps between the science and technology, and their practical applications.The great collection of authors and reviewers represents an interdisciplinary team of globally acknowledged experts. The book will therefore make a major contribution to establishing a common professional language, enhancing global communication between wastewater professionals. In addition, the authors have linked the description of the scientific basis for wastewater treatment processes with a video-based online course for the training of students, researchers, engineers, laboratory technicians and treatment plant operators, demonstrating commonly accepted experimentation procedures and their application for lab-, pilot-, and full-scale treatment plant operation.From the perspective of the IWA this book also has the great potential to enhance the development of a new generation of researchers and enable them to communicate on a global scale and beyond their specific field of expertise. Both aspects are urgently needed to develop adapted solutions for specific local conditions and to make them globally available for implementation.There has been a trend for some time that scientific research and practice have been growing apart from each other. Part of the rea...

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Linear constraint relations in biochemical reaction systems: II. Diagnosis and estimation of gross errors

Cited by 148 publications

References 11 publications

Expression of phosphofructokinase in Neisseria meningitidis

Expression of phosphofructokinase in Neisseria meningitidis

rRNA and Poly-β-Hydroxybutyrate Dynamics in Bioreactors Subjected to Feast and Famine Cycles

Experimental Methods in Wastewater Treatment

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