MbT-Tool: An open-access tool based on Thermodynamic Electron Equivalents Model to obtain microbial-metabolic reactions to be used in biotechnological process

Probably not a substantial claim: may not pass S3 (load-bearing).

The MbT-Tool's code contains twenty inorganic reduction-half-reactions.

“The MbT-Tool's code contains eighteen organic and twenty inorganic reduction-half-reactions, four N-sources (NH4+, NO3−, NO2−, N2) to biomass synthesis and twenty-four microbial empirical formulas, one of which can be determined by the user (CnHaObNc).”

Probably not a substantial claim: may not pass S3 (load-bearing).

The MbT-Tool's code contains eighteen organic reduction-half-reactions.

“The MbT-Tool's code contains eighteen organic and twenty inorganic reduction-half-reactions, four N-sources (NH4+, NO3−, NO2−, N2) to biomass synthesis and twenty-four microbial empirical formulas, one of which can be determined by the user (CnHaObNc).”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

The MbT-Tool's code contains twenty-four microbial empirical formulas, one of which can be determined by the user (CnHaObNc).

“The MbT-Tool's code contains eighteen organic and twenty inorganic reduction-half-reactions, four N-sources (NH4+, NO3−, NO2−, N2) to biomass synthesis and twenty-four microbial empirical formulas, one of which can be determined by the user (CnHaObNc).”

Probably not a substantial claim: may not pass S3 (load-bearing).

The MbT-Tool's code contains four N-sources (NH4+, NO3−, NO2−, N2) to biomass synthesis.

“The MbT-Tool's code contains eighteen organic and twenty inorganic reduction-half-reactions, four N-sources (NH4+, NO3−, NO2−, N2) to biomass synthesis and twenty-four microbial empirical formulas, one of which can be determined by the user (CnHaObNc).”

Classified as probably not a substantial claim. May combine two claims.

The MbT-Tool displays the following outputs: the Rd, Ra and Rc half-reactions, the energy reaction (Re), the synthesis reaction (Rs), feo, fso, ε, the MMR (R) and the calculated microbial yield.

“With all this data, the MbT-Tool displays the following outputs: the Rd, Ra and Rc half-reactions, the energy reaction (Re), the synthesis reaction (Rs), feo, fso, ε, the MMR (R) and the calculated microbial yield (Fig. 3).”

Classified as probably not a substantial claim.

The MbT-Tool by itself does not simulate any microbiological, ecological or biotechnological process.

“The MbT-Tool by itself does not simulate any microbiological, ecological or biotechnological process”

Classified as probably not a substantial claim. May combine two claims.

Users without extensive programming experience can modify the code, introducing new chemical species to write new reduction-half-reactions, as well as other options for investigating alternative metabolic pathways or adapting certain processes according to specific studies.

“Users without extensive programming experience can modify the code, introducing new chemical species to write new reduction-half-reactions, as well as other options for investigating alternative metabolic pathways or adapting certain processes according to specific studies.”

May combine two claims.

MbT-Tool considers Battley's hypothesis as valid and allows use of the same microbial biomass formula and writing MMR using different growing substrates.

“Therefore, the MbT-Tool considers Battley's hypothesis as valid and allows use of the same microbial biomass formula and writing MMR using different growing substrates.”

• cites Battley (2013) sourceNot checked — no full text of the source

• AssumptionThe authors state this as an assumption: The empirical composition of the same cells metabolizing any given substrate is expected to be the same.

May combine two claims.

For Escherichia coli diauxic growth on glucose and lactose, using the MbT-Tool with TEEM2, NH4+ as N-source, two electron donors (glucose and lactate) and one electron acceptor (oxygen), and ε=0.37, the predicted bacterial yields are Yg/m = 97.139 g cells/mol donor, Yc/m = 3.917 molCcells/mol donor, and Yc/c = 0.435 molCcell/molCdonor.

“Bacterial yield: Yg/m = 97.139 (gramscells/moldonor); Yc/m = 3.917 (molCcells/moldonor) and Yc/c = 0.435 (molCcell/molCdonor).”

Classified as probably not a substantial claim.

The user does not have to pay for using the MbT-Tool.

“that the user doesn't have to pay for using the MbT-Tool”

Classified as probably not a substantial claim.

The MbT-Tool user interface displays all variables and parameters regarding the composition of the microbial biomass and the substrates that can be selected to describe the metabolic processes, avoiding the complex and tedious calculations of the implemented thermodynamic model by the user.

“The MbT-Tool user interface displays all variables and parameters regarding the composition of the microbial biomass and the substrates that can be selected to describe the metabolic processes, avoiding the complex and tedious calculations of the implemented thermodynamic model by the user.”

Classified as probably not a substantial claim.

The non-expert user achieves an MMR in which one of the products is the chemical composition of the microorganism involved in the process and some values of its bacterial yield.

“The non-expert user achieves an MMR in which one of the products is the chemical composition of the micro-organism involved in the process and some values of its bacterial yield.”

Probably not a substantial claim: may not pass S3 (load-bearing).

An inconsistent value will be obtained when these fractions of electrons are greater than one or below zero.

“An inconsistent value will be obtained when these fractions of electrons are greater than one or below zero.”

Probably not a substantial claim: may not pass S3 (load-bearing).

The user could download these outputs in an archive with a '.txt' extension.

“The user could also download these outputs in an archive with a “.txt” extension.”

Probably not a substantial claim: may not pass S3 (load-bearing).

If this numerical inconsistency occurs, the MbT-Tool stops and shows an alert message to the user.

“If this numerical inconsistency occurs, the MbT-Tool stops and shows an alert message to the user.”

Classified as probably not a substantial claim.

The user is able to modify the source-code to extend the scope of the MbT-Tool into their specific research field and expertise.

“that the user is able to modify the source-code to extend the scope of the MbT-Tool into their specific research field and expertise.”

Classified as probably not a substantial claim.

With the MbT-Tool it is possible to write MMRs conducted by microbes.

“With the MbT-Tool it is possible to write MMRs conducted by microbes.”

Classified as probably not a substantial claim.

It is not possible to compare the MbT-Tool's outputs directly with experimental results.

“However, this tool has a limitation: it is not possible to compare the MbT-Tool's outputs directly with experimental results.”

Probably not a substantial claim: may not pass S3 (load-bearing).

The scope of the MbT-Tool is not limited to the number of pre-programmed half-reactions included in this version.

“Moreover, the scope of the MbT-Tool is not limited to the number of the pre-programmed half-reactions included in this version.”

Classified as probably not a substantial claim.

If eD and eA are the same, the result of the calculations using their standard Gibbs free energy could provoke an inconsistent value on the fraction of electrons destined for cellular synthesis or electrons destined for energy.

“If eD and eA are the same, the result of the calculations using their standard Gibbs free energy could provoke an inconsistent value on the fraction of electrons destined for cellular synthesis or electrons destined for energy.”

May combine two claims.

Using the MbT-Tool, it is possible to represent two metabolic pathways for Saccharomyces cerevisiae: biomass synthesis from glucose, and biomass synthesis from pyruvate to ethanol.

“Considering this information, using the MbT-Tool it is possible to represent two metabolic pathways: the biomass synthesis from glucose, and the biomass synthesis from pyruvate to ethanol.”

Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

The power and scope of the MbT-Tool increases if the molar relationship between the main four elements can be changed to define the empirical chemical formula that represents the microbial biomass.

“Also, the power and scope of the MbT-Tool increases if we take into account the possibility of changing the molar relationship between the main four elements to define the empirical chemical formula that represents the microbial biomass.”

Probably not a substantial claim: may not pass S3 (load-bearing).

MbT-Tool runs on any computer that supports JAVA with an operating system (OS): Windows, Mac OS X and Linux.

“It runs on any computer that supports JAVA with an operating system (OS): Windows, Mac OS X and Linux [22], [39], [40].”

• cites [22] Hellweger F.L. Clegg R.J. Clark J.R. Plugge C.M. Kreft J.-U. Advancing microbial sciences by individual-based modelling Nat Rev Microbiol 14 2016 461 471 27265769Not checked yet

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• cites [39] Wilensky U. NetLogo. Cent Connect Learn Comput Model Northwest Univ Evanston, IL http://ccl.northwestern.edu/netlogo/ 1999 [accessed March 5, 2014]Not checked yet

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• cites [40] Tisue S. Wilensky U. Netlogo: a simple environment for modeling complexity Int Conf … 2004Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Classified as probably not a substantial claim.

MbT-Tool is applicable in a wide range of academic research interested in designing, optimizing and modelling microbial activity without any extensive chemical, microbiological and programing experience.

“MbT-Tool is an open-source program capable of writing MMRs based on thermodynamic concepts, which are applicable in a wide range of academic research interested in designing, optimizing and modelling microbial activity without any extensive chemical, microbiological and programing experience.”

Probably not a substantial claim: may not pass S3 (load-bearing).

TEEM has two versions, TEEM1 and TEEM2.

“TEEM has two versions, the first one, TEEM1 [4], considers a realistic formulation of the anabolic reaction taking into account different N-sources such as ammonium (NH4+), nitrate (NO3−), nitrite (NO2−) and di-nitrogen (N2), and a complete explanation of ε between catabolism and anabolism.”

• cites [4] Rittmann B.E. McCarty P.L. Environmental biotechnology: principles and applications 2001Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

• cites [11] McCarty P.L. Thermodynamic electron equivalents model for bacterial yield prediction: Modifications and comparative evaluations Biotechnol Bioeng 97 2007 377 388 17089390Not checked yet

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Classified as probably not a substantial claim.

Rc is a hypothetical half-reaction, which considers as reactants the N-source (NH4+, NO3−, NO2− or N2), carbon dioxide (CO2) and bicarbonate (HCO3−), and as products water and the microbial biomass represented by an empirical chemical formula of cells (CnHaObNc).

“Rc is a hypothetical half-reaction, which considers as reactants the N-source (NH4+, NO3−, NO2− or N2), carbon dioxide (CO2) and bicarbonate (HCO3−), and as products water and the microbial biomass represented by an empirical chemical formula of cells (CnHaObNc).”

• cites [4] Rittmann B.E. McCarty P.L. Environmental biotechnology: principles and applications 2001Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

TEEM1 considers a realistic formulation of the anabolic reaction taking into account different N-sources such as ammonium (NH4+), nitrate (NO3−), nitrite (NO2−) and di-nitrogen (N2), and a complete explanation of ε between catabolism and anabolism.

“TEEM has two versions, the first one, TEEM1 [4], considers a realistic formulation of the anabolic reaction taking into account different N-sources such as ammonium (NH4+), nitrate (NO3−), nitrite (NO2−) and di-nitrogen (N2), and a complete explanation of ε between catabolism and anabolism.”

• cites [4] Rittmann B.E. McCarty P.L. Environmental biotechnology: principles and applications 2001Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Classified as probably not a substantial claim.

To establish the adequacy of the empirical chemical formula, researchers compared theoretical thermodynamic calculations using the cell's empirical chemical formula with the thermodynamics of growth of the same micro-organism on several substrates using batch cultures growing in the exponential phase at μmax.

“To establish the adequacy of this formula, researchers compared theoretical thermodynamic calculations using the cell's empirical chemical formula with the thermodynamics of growth of the same micro-organism on several substrates using batch cultures growing in the exponential phase at μmax[32], [33], [34], [35].”

• cites [32] Battley E.H. The sources of thermal energy exchange accompanying microbial anabolism J Therm Anal Calorim 87 2007 105 111Not checked yet

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• cites [33] Battley E. Energetics of microbial growth 1987 WileyNot matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

• cites [34] Battley E.H. The thermodynamics of growth of Escherichia coli K-12 on succinic acid Pure Appl Chem 65 1993 1881 1886Not checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing).

In other research fields, e.g. bio-geochemical processes in marine environments, and taking into account different pressure, temperature, pH and N-sources for cell synthesis, the reported ∆Gpc value is 302 J per gram cells.

“In other research fields, e.g. bio-geochemical processes in marine environments, and taking into account different pressure, temperature, pH and N-sources for cell synthesis the reported ∆Gpc value is 302 J per gram cells [3], [37], [38].”

• cites [3] Amend J.P. LaRowe D.E. McCollom T.M. Shock E.L. The energetics of organic synthesis inside and outside the cell Philos Trans R Soc Lond B Biol Sci 368 2013 20120255 23754809 PMC3685458Not checked yet

  Not checked in the free run.

• cites [37] LaRowe D.E. Amend J.P. The energetics of anabolism in natural settings ISME J 10 2016 1285 1295 26859771 PMC5029197Not checked yet

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• cites [38] LaRowe D.E. Amend J.P. Catabolic rates, population sizes and doubling/replacement times of microorganisms in natural settings Am J Sci 315 2015 167 203Not checked yet

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Classified as probably not a substantial claim.

TEEM writes a stoichiometric reaction to describe the overall cellular metabolism from reduction-half-reactions for the electron-donor (Rd), electron-acceptor (Ra) and cell synthesis (Rc).

“TEEM writes a stoichiometric reaction to describe the overall cellular metabolism from reduction-half-reactions for: the electron-donor (Rd), electron-acceptor (Ra) and cell synthesis (Rc).”

• cites [4] Rittmann B.E. McCarty P.L. Environmental biotechnology: principles and applications 2001Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

• cites [7] McCarty P.L. Thermodynamics of biological synthesis and growth Adv Water Pollut Res 2 1965 169 187 5837726Not checked yet

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• cites [8] Stratton F.E. McCarty P.L. Graphical evaluation of the kinetic parameters for bacterial growth Can J Microbiol 15 1969 1201 1205 5371000Not checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing).

In most common cases, the q value ranges from 0 to 4.

“But in the most common cases, the “q” value ranges from 0 to 4.”

• cites [13] Xiao J. VanBriesen J.M. Expanded thermodynamic model for microbial true yield prediction Biotechnol Bioeng 93 2006 110 121 16155947Not checked yet

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• cites [14] Xiao J. VanBriesen J.M. Expanded thermodynamic true yield prediction model: Adjustments and limitations Biodegradation 19 2008 99 127 17562190Not checked yet

  Not checked in the free run.

May combine two claims.

TEEM calculates the relationship between feo and fso using (i) standard Gibbs free energy of Rd, Ra and Rc, (ii) standard Gibbs free energy of the intracellular intermediates compounds, and (iii) an appropriate ε value.

“TEEM calculates the relationship between feo and fso using: (i) standard Gibbs free energy of Rd, Ra and Rc, (ii) standard Gibbs free energy of the intracellular intermediates compounds, and (iii) an appropriate ε value.”

• cites [4] Rittmann B.E. McCarty P.L. Environmental biotechnology: principles and applications 2001Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

NetLogo is licensed under GPL and it was chosen mainly for the way this platform is organized: the source-code is very well documented, open and easy to read, giving the option to share this developed tool with other researchers without difficulty.

“NetLogo is licensed under GPL (GNU General Public Licence) and it was chosen mainly for the way this platform is organized: the source-code is very well documented, open and easy to read, giving the option to share this developed tool with other researchers without difficulty.”

Probably not a substantial claim: may not pass S3 (load-bearing).

The empirical formula C5H7O2N represents a gram-negative bacterium.

“In the MbT-Tool, we selected a gram-negative bacterium with the empirical formula of C5H7O2N [5].”

• cites [5] VanBriesen J.M. Rittmann B.E. Mathematical description of microbiological reactions involving intermediates Biotechnol Bioeng 67 2000 35 52 10581434Not checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing).

Microorganisms use oxygenase reactions to create more biodegradable forms of substrates.

“Basically, micro-organisms utilize the oxygenase reactions to create more biodegradable forms of substrates.”

• cites [41] Schirmer A. Rude M.A. Li X. Popova E. del Cardayre S.B. Microbial biosynthesis of alkanes Science 329 80- 2010 559 562 20671186Not checked yet

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• cites [42] Peters J. Witholt B. Solubilization of the overexpressed integral membrane protein alkane monooxygenase of the recombinant Escherichia coli W3110[pGEc47] Biochim Biophys Acta Biomembr 1196 1994 145 153 7841178Not checked yet

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• cites [43] Timkovich R. Thrasher J.S. Carbon monoxide oxygenase activity of cytochrome cd1 Biochemistry 27 1988 5383 5388 3139034Not checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing).

The MMR (R) is the reaction that McCarty defines as global reaction, which arises from the combination between the catabolic reaction with the anabolic reaction and the value of ε.

“This MMR is the reaction that McCarty defines as global reaction, which arises from the combination between: the catabolic reaction with the anabolic reaction and the value of ε[11].”

• cites [11] McCarty P.L. Thermodynamic electron equivalents model for bacterial yield prediction: Modifications and comparative evaluations Biotechnol Bioeng 97 2007 377 388 17089390Not checked yet

  Not checked in the free run.

Classified as probably not a substantial claim.

The results obtained from the MbT-Tool allow the user to start with calculations or simulations for studying microbiological, ecological or biotechnological processes.

“but the results obtained from the MbT-Tool allow the user to start with the calculations or the simulations for the study of any of these research fields.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

The composition of the microbial biomass, represented by CnHaObNc, seems to be related to the substrates where the micro-organism grows and it can be slightly different depending on the C-sources and N-sources.

“The composition of the microbial biomass, which is represented by CnHaObNc, seems to be related to the substrates where the micro-organism grows and it can be slightly different depending on the C-sources and N-sources [14].”

• cites [14] Xiao J. VanBriesen J.M. Expanded thermodynamic true yield prediction model: Adjustments and limitations Biodegradation 19 2008 99 127 17562190Not checked yet

  Not checked in the free run.

Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing). May combine two claims.

NetLogo's flat learning curve and comprehensive documentation make it a user-friendly tool, easily accessible to chemists, biologists, ecologists, engineers and modellers.

“Additionally, the NetLogo's rather flat learning curve and comprehensive documentation [57] make this a user-friendly tool, easily accessible to chemists, biologists, ecologists, engineers and modellers, among others.”

• cites [57] Railsback S.F. Grimm V. Agent-based and individual-based modeling: a practical introduction 2012 Princeton University PressNot checked yet

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