Toward Best Practices for Controlling Mammalian Cell Culture Environments
Open accessAbstract
The characterization, control, and reporting of environmental conditions in mammalian cell cultures is fundamental to ensure physiological relevance and reproducibility in basic and preclinical biomedical research. The potential issue of environment instability in routine cell cultures in affecting biomedical experiments was identified many decades ago. Despite existing evidence showing variable environmental conditions can affect a suite of cellular responses and key experimental readouts, the underreporting of critical parameters affecting cell culture environments in published experiments remains a serious problem. Here, we outline the main sources of potential problems, improved guidelines for reporting, and deliver recommendations to facilitate improved culture-system based research. Addressing the lack of attention paid to culture environments is critical to improve the reproducibility and translation of preclinical research, but constitutes only an initial step towards enhancing the relevance of in vitro cell cultures towards in vivo physiology.
AI snapshot
Written from the paper’s full text.
TL;DR
This perspective/guideline paper argues that mammalian cell culture environments are routinely uncontrolled and underreported, producing environmental drift that threatens reproducibility and translational relevance. It proposes the PRINCE reporting checklist and practical steps to measure, control, and report temperature, O₂, CO₂, pH, osmolarity, and humidity.
Key findings
- Standard batch cultures show substantial environmental drift: median pH shift of 0.425 units and median O₂ shift of 10.6% from nominal values; pH declines reaching 0.9 units, O₂ down to 0.95%, and CO₂ up to 10.45%. Another synthesis reported median dissolved O₂ declines to 7.3%, CO₂ increases to 7.5%–9.5% versus nominal 21% O₂ and 5% CO₂, and a median pH decline of 0.43 units.
- Reporting is poor: among 688 papers from 2014–2019, most reported the medium manufacturer, only one third reported the culture system type, and 42% reported temperature and CO₂ incubator settings; less than 0.05% monitored pH, CO₂, or O₂. In *Cancer Research* and *Nature* in Q3 2017, less than half described the medium brand and only one-tenth declared the buffering regime.
- Environmental instability affects cell behavior: pH deviations >0.3 units from 7.4 reduced proliferation in three colorectal cell lines; pH 6.7 altered 2,068 of 12,565 genes by more than two-fold in human fibroblasts after 24 h; HepG2 cultures at confluence depleted O₂ to <1%. Non-physiological buffers such as HEPES can introduce artifacts, and osmolarity changes >10% can alter responses, with hybridoma growth declining by 30% at 415 mOsm kg⁻¹ versus 361 mOsm kg⁻¹ under elevated CO₂.
- The authors recommend measuring and reporting temperature, O₂, CO₂, pH, osmolarity, and humidity; for batch cultures, initial and final values are the minimum requirement. They propose the PRINCE checklist and note that chemostat/perfusion and bioreactor systems improve control but have cost, maintenance, and replication constraints.
Methods
- Design: perspective/guideline article; no new experimental data are reported.
- Data or sample: synthesizes published literature and prior syntheses, including a sub-sample of 688 papers published 2014–2019 and a survey of journal reporting requirements; no primary sample is described.
- Main analysis: narrative synthesis and proposal of the PRINCE reporting checklist and recommendations; no formal meta-analysis is described.
Limitations
- The paper acknowledges limited evidence linking variable culture environments to reproducibility, noting that only three papers collectively measured and reported O₂ or CO₂ regimes in mammalian in vitro cultures; reliable reports of environmental parameters within selected human tissues are presently limited, and affordable advanced monitoring/control systems are limited.
- Evident from the text: the recommendations are expert/guideline-based and are not empirically validated in this paper, and no new data are presented to test the PRINCE checklist or quantify the impact of the proposed standards.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
42 of 96 cited sources checked · 18 supported · 2 flagged · accuracy not yet measured
- Premisecitation
Medium acidification during in vitro cell culture can initiate pro-inflammatory signaling responses in human aortic smooth muscle cells and cells of the human nucleus pulposus.
“Medium acidification during in vitro cell culture can also initiate pro-inflammatory signaling responses in human aortic smooth muscle cells (Tomura et al., 2005) and cells of the human nucleus pulposus (Gilbert et al., 2016).”
Quote in the paperSubstantial claim2 of 2 sources checked- cites Tomura et al., 2005 source
The Results show that acidic medium triggers OGR1-mediated PGI2 production and cAMP accumulation in human aortic smooth muscle cells. But the Discussion characterizes this response as a possible mechanism that counteracts inflammation, not a pro-inflammatory response. The separate nucleus pulposus claim is attributed to Gilbert et al., not to this source. (LLM, conf=0.86)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measured - cites Gilbert et al., 2016 source
- Premisecitation
A number of studies used different culture temperatures.
“However, a number of studies used different culture temperatures (Brinkhof et al., 2015; Xu et al., 2017), which highlights the need to declare and monitor the incubation temperature.”
Quote in the paperSubstantial claim1 of 2 sources checked- cites Brinkhof et al., 2015 source
- cites Xu et al., 2017
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisecitation
The initial stability of medium pH is typically achieved by mimicking the physiologically relevant CO2/HCO3− buffering system.
“The initial stability of medium pH is typically achieved by mimicking the physiologically relevant CO2/HCO3 − buffering system (Michl et al., 2019).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Michl et al., 2019 source
- Premisecitation
Medium deoxygenation in cell cultures of human cancer cell lines induced the expression and activity of carbonic anhydrases, which resulted in enhanced acidification of the culture medium.
“Švastová and others showed that medium deoxygenation in cell cultures of human cancer cell lines induced the expression and activity of carbonic anhydrases, which resulted in enhanced acidification of the culture medium (Švastová et al., 2004).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Švastová et al., 2004 source
Section 3.3 (page unavailable) reports that hypoxic HeLa and SiHa cancer-cell cultures had lower medium pH, elevated CA IX expression, and catalytically active CA IX; a CA IX-selective inhibitor partially reduced the acidosis. Section 3.5 (page unavailable) further supports CA IX's role in acidification. The claim overgeneralizes this finding to carbonic anhydrases in the plural and presents them as the sole cause, whereas the paper studies CA IX and describes its contribution as partial. (LLM, conf=0.83)
Experimental — accuracy not yet measured
- Premisecitation
O2 first dissolves at the air-medium interface and then diffuses through the liquid (at least several millimeters) to reach and oxygenate cell microenvironments even as cells undergo exponential growth.
“Specifically, O2 first dissolves at the air-medium interface and then diffuses through the liquid (at least several millimeters) to reach and oxygenate cell microenvironments (Place et al., 2017) even as cells undergo exponential growth.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Place et al., 2017 source
- Premisecitation
These processes interact to create a changing environmental gradient from the surface of the medium down to the microenvironment of the cells.
“In concert, these processes interact to create a changing environmental gradient from the surface of the medium down to the microenvironment of the cells (Place et al., 2017).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Place et al., 2017 source
- Premisecitation
Cells are capable of buffering against extracellular reductions in pH to maintain alkaline pH of the cytoplasm.
“Cells are capable of buffering against extracellular reductions in pH to maintain alkaline pH of the cytoplasm (Johnson et al., 1976; L’allemain et al., 1984; Lindström and Sehlin, 1984; Pouyssegur et al., 1985; McBrian et al., 2013).”
Quote in the paperSubstantial claim1 of 3 sources checked- cites Johnson et al., 1976 source
- cites L’allemain et al., 1984 source
- cites McBrian et al., 2013 source
The Discussion says cells regulate intracellular pH in response to extracellular pH changes, and the Introduction describes proton export that resists further intracellular acidification. But the Results report that intracellular pH fell as extracellular pH fell, reaching 6.3; the paper does not establish that cells generally maintain an alkaline cytoplasm under those conditions. The Discussion presents alkaline intracellular pH in acidic cancer environments as a possibility. (LLM, conf=0.83)
Experimental — accuracy not yet measured
- Premisecitation
In the case of O2, medium deoxygenation is caused by the disparity between rates of O2 consumption via cellular metabolism and the replenishment of O2 at the air-medium interface.
“In the case of O2, medium deoxygenation is caused by the disparity between rates of O2 consumption via cellular metabolism and the replenishment of O2 at the air-medium interface (Place et al., 2017; Al-Ani et al., 2018).”
Quote in the paperSubstantial claim2 of 2 sources checked - Premisecitation
The lack of monitoring and reporting of environmental conditions in cell culture systems is a pervasive but under-recognized problem.
“The lack of monitoring and reporting of environmental conditions in cell culture-systems is a pervasive, but under-recognized problem (Hunter, 2017; Al-Ani et al., 2018; Michl et al., 2019; Klein et al., 2021a; Klein et al., 2021b).”
Quote in the paperSubstantial claim1 of 3 sources checked- cites Hunter, 2017 source
- cites Al-Ani et al., 2018 source
The Results and discussion report that 94% of the 200 articles examined omitted at least one critical oxygenation variable, and none attempted to calculate oxygen levels around the cells. The Introduction and Conclusion describe inadequate attention to oxygenation conditions as an under-recognized, prevalent problem. The paper establishes this for oxygenation, not for environmental conditions in cell culture generally. (LLM, conf=0.84)
Experimental — accuracy not yet measured - cites Klein et al., 2021b
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisecitation
Barcoding experiments showed that cancer cell-line evolution occurred from positive clonal selection that was highly sensitive to culture conditions.
“Indeed, barcoding experiments showed that cancer cell-line evolution occurred from positive clonal selection that was highly sensitive to culture conditions (Ben-David et al., 2018).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Ben-David et al., 2018 source
- Premisecitation
Existing evidence, although limited, indicates that NVBs could induce toxicity and anomalous cellular responses in particular cell types.
“However, it is vital to consider how NVBs introduce active molecules and acid-base reactions absent from mammalian fluids and existing evidence, although limited, indicates that NVBs could induce toxicity and anomalous cellular responses in particular cell types (Good et al., 1966; Lepe-Zuniga et al., 1987; Hanrahan and Tabcharani, 1990; Stea and Nurse, 1991).”
Quote in the paperSubstantial claim1 of 3 sources checked- cites Good et al., 1966 source
- cites Lepe-Zuniga et al., 1987 source
- cites Stea and Nurse, 1991 source
- Rests on an assumption: NVBs introduce active molecules and acid-base reactions absent from mammalian fluids.
- Premisecitation
Chemostat and perfusion systems can maintain environmental conditions and cell growth rates via a continuous dilution of the culture with fresh medium.
“Such systems can maintain environmental conditions and cell growth rates via a continuous dilution of the culture with fresh medium (Cohen and Eagle, 1961).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Cohen and Eagle, 1961 source
The introduction (p. 467) says continuous fresh-medium input and removal sustain growth in a constant environment. The Results (pp. 469–472) show that dilution rate affects stabilized cell counts and generation time in the mammalian-cell chemostat. The paper does not establish the same claim for perfusion systems, so the citation supports the chemostat portion only. (LLM, conf=0.82)
Experimental — accuracy not yet measured
- Premisecitation
The physical structure of cell microenvironments can alter cell morphology and function.
“as well as the physical structure of cell microenvironments, which can alter cell morphology and function (Darnell et al., 2018).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Darnell et al., 2018 source
- Premisecitation
Non-physiological concentrations of growth factors and antibiotics are commonly used in cell culture.
“Such factors include, but are not limited to, the common usage non-physiological concentrations of growth factors (Rubin, 2007; Holohan et al., 2013; Langhans, 2018), and antibiotics (Ryu et al., 2017)”
Quote in the paperSubstantial claim1 of 2 sources checked- cites Rubin, 2007 source
- cites Ryu et al., 2017 source
The Introduction and Discussion say that antibiotics are routinely used in cell culture, and the Methods specify a standard antibiotic concentration. The paper does not characterize that concentration as non-physiological. The growth-factor portion of the sentence is attributed to other citations, not Ryu et al.; our copy provides no page numbers for these passages. (LLM, conf=0.84)
Experimental — accuracy not yet measured
- Premisecitation
There is currently an absence of a culture of enhancing standards for environmental control, monitoring, and reporting in biomedical research.
“The task of enhancing standards for environmental control, monitoring, and reporting in biomedical research may initially seem overwhelming provided the current absence of a culture to this end (Collins and Tabak, 2014; Baker, 2016; Hunter, 2017).”
Quote in the paperNot a substantial claim1 of 3 sources checked- cites Collins and Tabak, 2014 source
The Abstract says basic experimental-design details often go unreported, and PRECLINICAL PROBLEMS identifies different lab environments as a cause of irreproducible results. The paper calls for changes across the research community, but it does not specifically describe an absence of a culture of environmental control, monitoring, and reporting. Page numbers are unavailable in our copy. (LLM, conf=0.84)
Experimental — accuracy not yet measured - cites Baker, 2016 source
- cites Hunter, 2017 source
- Premisecitation
The solubility of dissolved gases, and thus the influence of CO2 on acid-base chemistry, is strongly dependent on temperature, osmolarity, humidity, and pressure.
“For instance, the solubility of dissolved gases, and thus the influence of CO2 on acid-base chemistry, is strongly dependent on temperature, osmolarity, humidity, and pressure (Christmas and Bassingthwaighte, 2017).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Christmas and Bassingthwaighte, 2017 source
The introductory passage says O₂ and CO₂ solubilities decrease as temperature and solute concentration increase, and the Discussion links solubility to gas concentrations relevant to reactions and CO₂ buffering. The paper does not identify humidity as a determinant of solubility. It says dissolved gas concentration is proportional to partial pressure under Henry’s law, not that the solubility itself depends strongly on pressure; the Methods standardize solubility measurements at 1 atm. (LLM, conf=0.88)
Experimental — accuracy not yet measured
- Premisecitation
Existing recommendations that aim to increase the relevance of in vitro cultures to in vivo physiology are available for many of these factors.
“For many of these factors, existing recommendations that aim to increase the relevance of in vitro cultures to in vivo physiology are available (Baker, 2016; Muelas et al., 2018; Hirsch and Schildknecht, 2019).”
Quote in the paperNot a substantial claim2 of 3 sources checked- cites Baker, 2016 source
- cites Muelas et al., 2018 source
The Discussion (page unavailable) describes existing reporting standards and recommends documenting culture factors including cell density, medium, nutrients, and pH. It presents these measures as ways to improve reproducibility and assay evaluation, not specifically as recommendations to make in vitro cultures more representative of in vivo physiology. (LLM, conf=0.82)
Experimental — accuracy not yet measured - cites Hirsch and Schildknecht, 2019 source
The Recommendations section discusses several culture factors, including media composition, and notes that common media are not ideal physiological environments. The section on Insufficient Reproducibility in Cell Models also says 3D cultures were introduced to recapitulate the in vivo environment. However, the paper presents its practical recommendations primarily as ways to improve reproducibility, not as recommendations aimed at increasing physiological relevance across many factors. (LLM, conf=0.83)
Experimental — accuracy not yet measured
- Premisecitation
Reliable reports of environmental parameters within selected human tissues are presently limited.
“although reliable reports of environmental parameters within selected human tissues are presently limited (Al-Ani et al., 2018; Ast and Mootha, 2019)”
Quote in the paperSubstantial claim1 of 2 sources checked- cites Al-Ani et al., 2018 source
The Results and discussion section (page not provided) finds that oxygenation-related parameters are often missing from reports of mammalian cell cultures. The Introduction discusses oxygen levels in vivo, but does not say that reliable reports of environmental parameters within human tissues are limited. Searches for human-tissue measurements and available in vivo data did not establish that claim. (LLM, conf=0.74)
Experimental — accuracy not yet measured - cites Ast and Mootha, 2019 source
- Findingown data
None of the information required in the standardized reporting declaration forms of Nature Research, Science, Cell, and EMBO press journals addresses the monitoring and control of critical environmental conditions for research using mammalian cell cultures.
“However, none of the information required in this form addresses the monitoring and control of critical environmental conditions for research conducted using mammalian cell cultures (hereafter referred to as “cell-based experiments”).”
Quote in the paperSubstantial claim - Findingown data
The majority of scientific journals have not sufficiently emphasized or enforced reporting of the procedures used to monitor and control environmental conditions for mammalian cell cultures.
“Precise control and monitoring of environmental conditions for mammalian cell cultures need be accompanied by reporting of the procedures used—a requirement, that is, not yet sufficiently emphasized nor enforced by the majority of scientific journals.”
Quote in the paperSubstantial claim - Premisecitation
Published bioreactor experiments report only the target levels of environmental parameters.
“The apparent under appreciation of reporting measured environmental parameters is exemplified by published bioreactor experiments that report only the target levels of environmental parameters (e.g., Karst et al., 2016; Abecasis et al., 2017).”
Quote in the paperSubstantial claim0 of 2 sources checked - Premisecitation
Perturbed O2 levels correlated with anomalous cellular responses in human hepatocytes and rat renal mesangial cells.
“including human hepatocytes (Ng et al., 2014) and rat renal mesangial cells (Metzen et al., 1995), where perturbed O2 levels correlated with anomalous cellular responses (Keeley and Mann, 2019).”
Quote in the paperSubstantial claim0 of 3 sources checked - Premisecitation
Cellular uptake of HEPES in human cell lines (MCF-7, U2OS, HeLa) persisted for 48 h after cells were returned to HEPES-free media.
“Another study showed cellular uptake of HEPES in human cell lines (MCF-7, U2OS, HeLa) that persisted for 48 h after cells were returned to HEPES-free media (Depping and Seeger, 2019).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Depping and Seeger, 2019 source
- Premisenone given
Variable environmental conditions can affect a suite of cellular responses and key experimental readouts.
“Despite existing evidence showing variable environmental conditions can affect a suite of cellular responses and key experimental readouts, the underreporting of critical parameters affecting cell culture environments in published experiments remains a serious problem.”
Quote in the paperNot a substantial claim - Premisecitation
Mammalian body systems regulate changes in dissolved gases, waste products such as lactic acid, and H+ ions involved in cellular metabolism, thereby achieving conditions that maintain homeostasis.
“Such systems regulate for the changes in dissolved gases, waste products (e.g., lactic acid), and H+ ions involved in cellular metabolism, thereby achieving conditions that maintain homeostasis (Supplementary Box S1).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Supplementary Box S1
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Interpretationcitation
Changes in the culture environment may initiate complex feedback mechanisms, where cellular responses to variations in the culture environment could, in turn, inflict greater intrusions of environmental stability and promote unpredictable outcomes.
“Changes in the culture environment may also initiate complex feedback mechanisms, where cellular responses to variations in the culture environment could, in turn, inflict greater intrusions of environmental stability and promote unpredictable outcomes.”
Quote in the paperSubstantial claim - Premisenone given
In cases where environmental parameters are measured, these are often not reported.
“In cases where environmental parameters are measured, these are often not reported.”
Quote in the paperSubstantial claim - Premisecitation
HepG2 cultures at confluence rapidly depleted O2 levels to <1% to self-inflict a switch from oxidative phosphorylation to glycolysis, despite being cultured in incubator conditions providing ambient atmospheric O2 levels (18.6%-20.9%).
“HepG2 cultures at confluence rapidly depleted O2 levels to <1% to self-inflict a switch from oxidative phosphorylation to glycolysis, despite being cultured in incubator conditions providing ambient atmospheric O2 levels (18.6%–20.9%) (Wolff et al., 1993).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Wolff et al., 1993 source
- Premisecitation
NVBs (e.g., HEPES, PIPES, or MES) are used to enhance acid-base stability of medium because the physiological HCO3−/CO2 buffering system can exhibit high volatility and a weak buffering capacity.
“For instance, NVBs (e.g., HEPES, PIPES, or MES) are used to enhance acid-base stability of medium because the physiological HCO3 −/CO2 buffering system can exhibit high volatility and a weak buffering capacity (Supplementary Box S1).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Supplementary Box S1
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Interpretationreasoning
Some approaches to control culture conditions misrepresent in vivo physiology and inadvertently introduce artefacts and biases that could compromise reproducibility and relevance of the study to cellular function in the living organism.
“However, some approaches misrepresent in vivo physiology and in doing so, inadvertently introduce artefacts and biases that could compromise reproducibility and relevance of the study to cellular function in the living organism.”
Quote in the paperSubstantial claim- Rests on an assumption: NVBs introduce active molecules and acid-base reactions absent from mammalian fluids.
- Premisecitation
Some evidence suggests that variable culture environments can also affect the reproducibility of cell culture experiments.
“Although limited, some evidence suggests that variable culture environments can also affect the reproducibility of cell culture experiments.”
Quote in the paperSubstantial claim - Premisecitation
A recent synthesis revealed that despite differences in cell type, medium formulation, and buffering components, all investigated standard batch cultures exhibited environmental drift after only a few days of culture.
“A recent synthesis revealed that despite differences in cell type, medium formulation, and buffering components, all investigated standard batch cultures exhibited environmental drift after only a few days of culture (Klein et al., 2021b).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Klein et al., 2021b
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisecitation
Reductions in medium pH (to pH 6.7) modulated the expression of 2,068 genes (out of 12,565) by more than two-fold after only 24 h of culture in human fibroblasts.
“A transcriptomic study, focusing on human fibroblasts, revealed that reductions in medium pH (to pH 6.7) modulated the expression of 2,068 genes (out of 12,565) by more than two-fold after only 24 h of culture (Bumke et al., 2003).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Bumke et al., 2003 source
- Premisecitation
Most media formulations contain a known concentration of HCO3−, which upon exposure to an incubator that nominally maintains a CO2-rich atmosphere (typically 5% CO2 in air), equilibrates to spontaneously produce H+ ions and stabilize pH.
“Most media formulations contain a known concentration of HCO3 −, which upon exposure to an incubator that nominally maintains a CO2-rich atmosphere (typically 5% CO2 in air), equilibrates to spontaneously produce H+ ions and stabilize pH (Supplementary Box S1).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Supplementary Box S1
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisecitation
Klein et al. (2021a) reported median declines in dissolved O2 down to 7.3%, and increases in dissolved CO2 to values ranging from 7.5% to 9.5%, compared to the nominal O2 and CO2 targets of 21% and 5%, respectively.
“Klein et al. (2021a) reported median declines in dissolved O2 down to 7.3%, and increases in dissolved CO2 to values ranging from 7.5% to 9.5%, compared to the nominal O2 and CO2 targets of 21% and 5%, respectively.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Klein et al., 2021a
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisenone given
Less than 0.05% of studies monitored pH, CO2, or O2 levels in cell cultures.
“Despite this, less than 0.05% of studies monitored pH, CO2, or O2 levels in cell cultures.”
Quote in the paperSubstantial claim - Premisecitation
Consistent observations of pH instability in standard cell cultures prompted the use of additional exogenous buffers in media formulations to enhance medium buffering capacity.
“Although consistent observations of pH instability in standard cell cultures prompted the use of additional exogenous buffers in media formulations to enhance medium buffering capacity (Eagle, 1971)”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Eagle, 1971 source
- Premisecitation
Documented reports of deoxygenation and disruptions to acid-base stability in culture media caused by cellular metabolism equate to a median pH shift of 0.425 units and a median O2 shift of 10.6% from target (nominal) values.
“Documented reports of deoxygenation and disruptions to acid-base stability in culture media caused by cellular metabolism equate to a median pH shift of 0.425 units and a median O2 shift of 10.6% from target (nominal) values (see, Klein et al., 2021b).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Klein et al., 2021b
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisecitation
Low-cost sensors are available to monitor relative humidity levels inside incubators.
“Low-cost sensors are available to monitor relative humidity levels inside incubators (Supplementary Table S1, Rajan et al., 2017) and should also be reported alongside key environmental variables.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Rajan et al., 2017 source
- Premisecitation
Cellular metabolism directly affects dissolved O2, CO2, and pH in culture medium.
“Although thermal regimes of cell cultures may be reliably inferred from calibrated incubators, levels of dissolved O2 and CO2, as well as pH must be measured directly in the culture medium because cellular metabolism directly affects these parameters (Supplementary Table S1).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Supplementary Table S1
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Interpretationreasoning
Environmental artifacts can affect the reproducibility of findings and comparisons among studies.
“Monitoring and controlling environmental conditions for cell-based experiments must be accompanied by reporting the data obtained as an essential step to identify possible environmental artifacts affecting the reproducibility of the findings and their comparisons among studies.”
Quote in the paperSubstantial claim - Premisecitation
Variations in relative humidity even in sophisticated incubators are common.
“Unfortunately, variations in relative humidity even in sophisticated incubators are common (Triaud et al., 2003), but they should be recognized and remedied.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Triaud et al., 2003 source
- May combine two claims. 36
- Classified as probably not a substantial claim. 16
May combine two claims.
PremisecitationLevels of CO2/HCO3− readily diffuse across cell membranes to moderate intracellular pH, act as metabolic inhibitors, may induce complex transcriptional responses, and signal other critical reactions.
“Besides the role of CO2 in affecting medium acid-base chemistry, levels of CO2/HCO3 − readily diffuse across cell membranes to moderate intracellular pH (Gutknecht et al., 1977), act as metabolic inhibitors, and may induce complex transcriptional responses (Cottier et al., 2012; Follonier et al., 2013), and signal other critical reactions (see, Blombach and Takors, 2015).”
Quote in the paperSubstantial claim3 of 3 sources checked- cites Gutknecht et al., 1977 source
The Gutknecht citation applies to the clause about CO2/HCO3− crossing membranes and moderating intracellular pH, not the later claims about metabolic inhibition or transcription. The Introduction (p. 780) says CO2 gas diffuses across membranes but HCO3− cannot easily do so across most cell membranes; the Results (p. 786) likewise say HCO3− cannot readily cross the membrane. The paper does not establish moderation of intracellular pH. (LLM, conf=0.88)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measured - cites Cottier et al., 2012 source
The Discussion (page not provided) reports that CO2 changes carbonic anhydrase expression through a transcription-factor-mediated pathway in yeast, supporting the cited claim about transcriptional responses. The Introduction describes CO2/HCO3− as important to fungal metabolism, but the passages do not support the adjacent claim that they act as metabolic inhibitors. The membrane-diffusion and other-signalling clauses have separate citations in the citing sentence. (LLM, conf=0.82)
Experimental — accuracy not yet measured - cites Blombach and Takors, 2015 source
May combine two claims.
PremisecitationCellular growth of three colorectal cell-lines (NCI-H747, DLD1, Caco2) was optimal at pH 7.4, but when medium pH deviated from 7.4 by >0.3 units all three cell lines exhibited reduced rates of proliferation.
“Michl and others (2019) showed that cellular growth of three colorectal cell-lines (NCI-H747, DLD1, Caco2) was optimal at pH 7.4, but when medium pH deviated from 7.4 by > 0.3 units all three cell lines exhibited reduced rates of proliferation.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Michl et al., 2019 source
The Results (Stability of CO2/HCO3− buffering, Fig. 2e; page unavailable) report that growth of NCI-H747, DLD1 and Caco2 was optimal near pH 7.4. They say the effect at pH 7.7 varied, with the strongest growth inhibition in NCI-H747; they do not establish a >0.3-unit threshold or explicitly state that all three lines had reduced proliferation beyond it. (LLM, conf=0.86)
Experimental — accuracy not yet measured
May combine two claims.
PremisecitationpH-buffering mechanisms such as Na+/H+ antiporters or histone deacetylation consume cellular energy and can alter gene transcription and reduce cellular growth through changes in the acetylation state of chromatin.
“However, such mechanisms (e.g., Na+/H+ antiporters or histone deacetylation) consume cellular energy and can alter gene transcription and reduce cellular growth through changes in the acetylation state of chromatin (Boron and Russell, 1983; Bowen and Levinson, 1984; Boron, 2004).”
Quote in the paperSubstantial claim1 of 3 sources checked- cites Boron and Russell, 1983 source
The opening summary (p. 373) reports that the squid axon's pH-regulating transport system requires ATP, supporting an energy requirement for the mechanism studied. The discussion (p. 397) identifies Na+/H+ exchange as a distinct pH-regulating system, but does not establish its energy requirement. The paper does not address histone deacetylation, chromatin acetylation, gene transcription, or cellular growth. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites Bowen and Levinson, 1984 source
- cites Boron, 2004 source
May combine two claims.
PremisecitationThe effect of unstirred medium layers presumably determines the delivery of nutrients/growth factors and the removal of other metabolic waste products such as lactic acid, which can also act to directly and indirectly moderate environmental variation.
“The effect of unstirred medium layers also presumably determines the delivery of nutrients/growth factors and the removal of other metabolic waste products (e.g., lactic acid), which can also act to directly and indirectly moderate environmental variation (Michl et al., 2019).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Michl et al., 2019 source
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measured
May combine two claims.
PremisecitationHEPES activated lysosomal transcription factors in macrophages, inhibited the prion protein conversion in neural stem cells and affected their viability and differentiation.
“Briefly, HEPES activated lysosomal transcription factors in macrophages (Tol et al., 2018), inhibited the prion protein conversion in neural stem cells and affected their viability and differentiation (Delmouly et al., 2011).”
Quote in the paperSubstantial claim1 of 2 sources checkedMay combine two claims.
PremisecitationExperiments testing cell-line strains against anti-cancer compounds uncovered disparate drug responses, although the exact sources of instabilities in culture environments that promoted cell-line heterogeneity were not resolved.
“Further experiments testing the cell-line strains against anti-cancer compounds uncovered disparate drug responses, although the exact sources of instabilities in culture environments that promoted cell-line heterogeneity were not resolved (Ben-David et al., 2018).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Ben-David et al., 2018 source
The Functional consequences of genomic variation section reports markedly different responses to anti-cancer compounds across 27 MCF7 strains. The Discussion and Sources of variation sections identify clonal selection under different culture conditions and ongoing genomic instability as contributors to heterogeneity. They do not establish the citing sentence’s additional claim that the exact sources of culture-related instability remained unresolved. No page numbers are available in our copy. (LLM, conf=0.82)
Experimental — accuracy not yet measured
May combine two claims.
PremisecitationExogenous buffer approaches can, in some cases, promote unpredictable changes in pH and introduce confounding artifacts.
“such approaches can, in some cases, promote unpredictable changes in pH and introduce confounding artifacts (Michl et al., 2019, see below).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Michl et al., 2019 source
May combine two claims.
PremisecitationThe majority of research papers rely on nominal set points and fail to directly verify and report environmental parameters.
“recent assessments show that the majority of research papers rely on nominal set points and fail to directly verify and report environmental parameters (Al-Ani et al., 2018; Michl et al., 2019; Klein et al., 2021b).”
Quote in the paperSubstantial claim2 of 3 sources checked- cites Al-Ani et al., 2018 source
The Results and discussion report that 94% of 200 mammalian-cell-culture papers omitted at least one critical oxygenation variable, and none attempted to calculate oxygen levels around the cells. The Introduction also says incubator settings are often assumed to represent oxygen delivered to cells. This supports the claim for oxygenation in the papers studied, but not its broader wording about research papers and environmental parameters generally; the assessment did not establish how many directly measured oxygen levels. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites Michl et al., 2019 source
The Discussion reports that only a small percentage of surveyed cell-culture articles provided necessary information about medium pH and buffering; only a third reported incubator CO2. The Results (“Monitoring culture medium pH under incubation”) also says that medium pH is not routinely monitored. This supports the claim for cell-culture pH, but the paper does not establish it for environmental parameters generally. (LLM, conf=0.86)
Experimental — accuracy not yet measured - cites Klein et al., 2021b
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Classified as probably not a substantial claim.
PremisecitationThe CO2/HCO3− buffer system is the primary physiological buffering system in mammalian fluids.
“Although the CO2/HCO3 − buffer system is indeed the primary physiological buffering system in mammalian fluids (Boron, 2004; Michl et al., 2019)”
Quote in the paperSubstantial claim1 of 2 sources checkedMay combine two claims.
PremisecitationPerturbations to dissolved O2 levels in culture medium can induce cells to switch away from oxidative phosphorylation towards anaerobic glycolysis, leading to large accumulations of lactic acid that force medium acidification.
“For instance, perturbations to dissolved O2 levels in culture medium can induce cells to switch away from oxidative phosphorylation towards anaerobic glycolysis (Wolff et al., 1993), leading to large accumulations of lactic acid that force medium acidification (Michl et al., 2019).”
Quote in the paperSubstantial claim1 of 2 sources checkedMay combine two claims.
PremisecitationAnother post-publication analysis reported that less than half of studies published in Cancer Research and Nature in the third quarter of 2017 described the brand of medium, and only one-tenth declared the medium-buffering regime.
“Another post-publication analysis reported that less than half of studies published in Cancer Research and Nature in the third quarter of 2017 described the brand of medium, and only one-tenth declared the medium-buffering regime (Michl et al., 2019).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Michl et al., 2019 source
May combine two claims.
PremisecitationDeoxygenation can activate the hypoxia-inducible factor (HIF) transcription system, which triggers the expression of most genes responsible for cellular adaptation to varying O2 levels.
“deoxygenation can also activate the hypoxia-inducible factor (HIF) transcription system, which triggers the expression of most genes responsible for cellular adaptation to varying O2 levels (Semenza et al., 1991; Wang et al., 1995; Semenza, 2012).”
Quote in the paperSubstantial claim2 of 3 sources checked- cites Semenza et al., 1991 source
- cites Wang et al., 1995 source
The paper reports that reduced O2 induces HIF-1 and that HIF-1 participates in hypoxia-responsive transcription (opening section; Results and Discussion, page not specified in our copy). It identifies EPO and several glycolytic genes as examples, but does not establish that HIF triggers expression of most genes responsible for cellular adaptation to changing O2 levels; it says HIF-1 may play a general role. (LLM, conf=0.87)
Experimental — accuracy not yet measured - cites Semenza, 2012 source
The Hypoxia-Inducible Factors section (page not specified) reports that HIF-1 levels rise as oxygen falls and that hundreds of genes show HIF-1-dependent responses to hypoxia. The Introduction calls HIFs master regulators of oxygen homeostasis, but the copy does not establish that they trigger expression of most genes responsible for cellular adaptation. (LLM, conf=0.86)
Experimental — accuracy not yet measured
May combine two claims.
PremisecitationSupra-physiological osmolarity can directly affect cell membrane tension and volume, but can also moderate how cells respond to other environmental parameters.
“Supra-physiological osmolarity can directly affect cell membrane tension and volume (Pedersen et al., 2013), but can also moderate how cells respond to other environmental parameters (Dezengotita et al., 1998).”
Quote in the paperSubstantial claim1 of 2 sources checked- cites Pedersen et al., 2013 source
The 'Physiology of epithelial transport and role of cell volume' section says that altered extracellular osmolarity creates osmotic gradients and discusses associated changes in cell volume. It does not specifically address supra-physiological osmolarity or state that osmolarity directly changes cell membrane tension. The later clause about responses to other environmental parameters is attributed to Dezengotita et al., not to this source. (LLM, conf=0.82)
Experimental — accuracy not yet measured - cites Dezengotita et al., 1998 source
May combine two claims.
PremisecitationIn batch culture set-ups, researchers often select culture medium that contains a pH indicator dye such as Phenol Red to guide the renewal of cell medium, but medium color changes assessed "by eye" can lead to undetected pH declines.
“In batch culture set-ups, researchers often select culture medium that contains a pH indicator dye [e.g., Phenol Red (PhR)] to guide the renewal of cell medium, but medium color changes assessed “by eye” can lead to undetected pH declines (Michl et al., 2019).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Michl et al., 2019 source
The Results section, “Monitoring culture medium pH under incubation” (page unavailable), says Phenol Red is routinely included to assess medium acidity and that assessment can be done ‘by eye,’ while absorbance provides a more quantitative reading. It also warns that medium pH is not routinely monitored despite possible acid production. It does not say that visual assessment guides medium renewal in batch cultures or establish that it leads to undetected pH declines. (LLM, conf=0.85)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationChemostat and perfusion systems were first described in 1950 for use in bacterial cultures and later adopted for mammalian cells in 1961.
“Chemostat and perfusion systems were first described in 1950 for use in bacterial cultures (Novick and Szilard, 1950a; b) and later adopted for mammalian cells in 1961 (Cohen and Eagle, 1961).”
Quote in the paperNot a substantial claim1 of 2 sources checked- cites Novick and Szilard, 1950a
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites Cohen and Eagle, 1961 source
May combine two claims.
PremisecitationTitration of acids and bases (including HCl, NaOH, and NVBs) introduces osmolytes (Na+, Cl−) to cell medium and can result in substantial changes to medium osmolarity by >10%.
“The titration of acids and bases (including HCl, NaOH, and NVBs) introduces osmolytes (Na+, Cl−) to cell medium and can result in substantial changes to medium osmolarity by > 10% (Michl et al., 2019).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Michl et al., 2019 source
The Results section (‘Effect of NVBs on the stability of medium pH’) says that titrating non-volatile buffers with HCl or NaOH introduces Na+ and Cl− and can substantially increase osmolality. Its example estimates an increase of approximately 10%, not greater than 10%, so the stated threshold is not established by that passage. (LLM, conf=0.86)
Experimental — accuracy not yet measured
May combine two claims.
PremisecitationNVB addition may not fully prevent pH declines in standard batch cultures and may lead to unexpected pH changes when interacting with the HCO3−/CO2 buffering system, although predictable pH levels can be obtained when appropriate protocols are used.
“Recent assessments also shows that NVB addition may not fully prevent pH declines in standard batch cultures and may lead to unexpected pH changes when interacting with the HCO3 −/CO2 buffering system, although predictable pH levels can be obtained when appropriate protocols are used (see, Michl et al., 2019).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Michl et al., 2019 source
Probably not a substantial claim: may not pass S3 (load-bearing).
Findingnone givenAcquiring a bioreactor is high in cost.
“E.g., acquirement of a bioreactor is high in cost”
Quote in the paperNot a substantial claimMay combine two claims.
PremisecitationThe reported median decline in pH was 0.43 units, but in some particularly extreme cases, cell metabolic activity promoted pH reductions that approached one pH unit and dissolved O2 decreased down to 0.95%.
“The reported median decline in pH was 0.43 units, but in some particularly extreme cases, cell metabolic activity promoted pH reductions that approached one pH unit (Eagle, 1971) and dissolved O2 decreased down to 0.95% (Vallejos et al., 2010).”
Quote in the paperNot a substantial claim0 of 2 sources checkedProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based).
Premisenone givenBioreactor systems, by design, typically require consistent monitoring of the controlled parameters via a feedback loop to achieve the desired control.
“Indeed, these systems, by design, typically require consistent monitoring of the controlled parameters via a feedback loop to achieve the desired control.”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationcitationIn extreme cases, variations in culture conditions may resemble levels consistent with hypercapnia and hypoxia rather than conditions typical of in vivo extracellular fluids, although in vivo environments vary considerably among selected tissues.
“In such extreme cases, variations in culture conditions may resemble levels consistent with hypercapnia and hypoxia rather than conditions typical of in vivo extracellular fluids, although in vivo environments vary considerably among selected tissues (Ast and Mootha, 2019).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Ast and Mootha, 2019 source
May combine two claims.
PremisecitationEven when protocols are declared, there is an unfortunate prevalence of papers stating "as previously described by ref. (x)," which often leads to a chain of citations that generate confusion as to the specific procedures, reagents, and materials involved.
“Even when protocols are declared, there is an unfortunate prevalence of papers stating, “as previously described by ref. (x),” which often leads to a chain of citations that generate confusion as to the specific procedures, reagents, and materials involved (Freedman et al., 2015).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Freedman et al., 2015 source
May combine two claims.
PremisecitationA recent synthesis examining the lack of monitoring and reporting sub-sampled 688 papers published between 2014 and 2019 and found that most papers reported the medium manufacturer, but only one third reported the type of culture system utilized and 42% reported temperature and CO2 incubator settings.
“A recent synthesis examining this problem sub-sampled 688 papers published between 2014 and 2019 and found that most papers reported the medium manufacturer, but only one third reported the type of culture system utilized and 42% reported temperature and CO2 incubator settings (Klein et al., 2021b).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Klein et al., 2021b
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
May combine two claims.
Premisenone givenMost commercial media contain buffering systems that act only to regulate pH, whereas levels of dissolved O2 and CO2 are regulated by atmosphere re-equilibration.
“Most commercial media contain buffering systems that act only to regulate pH, whereas levels of dissolved O2 and CO2 are regulated by atmosphere re-equilibration.”
Quote in the paperSubstantial claimMay combine two claims.
PremisecitationStandard batch culture systems undergo substantial environmental changes owing to cell metabolic activity, with pH declines reaching 0.9 units, O2 levels declining down to 0.95%, and CO2 values reaching up to 10.45%.
“Standard batch culture systems undergo substantial environmental changes owing to cell metabolic activity (Balin et al., 1976; Naciri et al., 2008; Vallejos et al., 2010; Pradhan et al., 2012; Al-Ani et al., 2018; Michl et al., 2019), with pH declines reaching 0.9 units, O2 levels declining down to 0.95%, and CO2 values reaching up to 10.45% (Klein et al., 2021b).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Klein et al., 2021b
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
May combine two claims.
InterpretationreasoningBioreactors provide the best capacity to control environmental conditions, but are most costly in the context of capital investment, maintenance, and operations.
“Bioreactors provide the best capacity to control environmental conditions, but are most costly in the context of capital investment, maintenance, and operations.”
Quote in the paperNot a substantial claimMay combine two claims.
Premisenone givenVariations in relative humidity and media evaporation result in changes to osmolarity as well as solute and gas concentrations, that in turn, affect diffusion.
“Since variations in both factors result in changes to osmolarity as well as solute and gas concentrations, that in turn, affect diffusion.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S4 (based). May combine two claims.
Premisenone givenTraditional bioreactor systems are ideal for cells culture in suspension, while attached cell monolayers require different solutions.
“While traditional bioreactor systems are ideal for cells culture in suspension, attached cell monolayers require different solutions.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S2 (checkable), S4 (based). May combine two claims.
InterpretationreasoningImproved characterization and control over environmental conditions in cell cultures will enhance the reliability of experimental findings and the confidence in their translation to clinical applications.
“Ultimately, improved characterization and control over environmental conditions in cell cultures will enhance the reliability of experimental findings and the confidence in their translation to clinical applications”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationreasoningStrengthening reporting requirements and standards will likely place greater emphasis on cell culturing environments and, in turn, likely enhance the reproducibility of cell-based experiments and their relevance to the in vivo environment.
“Strengthening reporting requirements and standards will likely place greater emphasis on cell culturing environments and, in turn, likely enhance the reproducibility of cell-based experiments as well as their relevance to the in vivo environment.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S2 (checkable).
InterpretationcitationConsidering how niche in vivo environments affect experimental outcomes could increase the robustness of experiments and the likelihood that findings have relevance to focal in vivo compartments.
“By considering how niche in vivo environments affect experimental outcomes, researchers could further increase the robustness of their experiments and increase the likelihood that findings have relevance to focal in vivo compartments (Ast and Mootha, 2019).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Ast and Mootha, 2019 source
Probably not a substantial claim: may not pass S4 (based). May combine two claims.
Premisenone givenMany bioreactor systems lack flexibility in the number of biological replicates and the volume of culture media (often larger than that of batch culture) that can be manipulated, which translates into greater time and monetary costs.
“Importantly, many bioreactor systems lack flexibility in the number of biological replicates and the volume of culture media (often larger than that of batch culture) that can be manipulated, which translates into greater time and monetary costs.”
Quote in the paperNot a substantial claimMay combine two claims.
PremisecitationO2 levels vary across human tissues and range from 13% O2 in the lung-pulmonary vein to 1-3% O2 in the uterus.
“For instance, O2 levels vary across human tissues and range from 13% O2 in the lung-pulmonary vein to 1–3% O2 in the uterus (Ast and Mootha, 2019).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Ast and Mootha, 2019 source
Probably not a substantial claim: may not pass S2 (checkable), S4 (based).
InterpretationreasoningReporting initial and final values of key parameters in batch cultures will capture existing environmental variation affecting published findings, ensuring accurate interpretation of the reported results and improved reproducibility.
“This requirement should capture existing environmental variation affecting published findings, ensuring accurate interpretation of the reported results and improved reproducibility.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S4 (based).
Premisenone givenMeasuring systems capable of delivering the required precision and accuracy are available for all key environmental parameters.
“Measuring systems capable of delivering the required precision and accuracy are available for all key environmental parameters.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S2 (checkable).
Interpretationnone givenTransitioning towards advanced culture systems capable of mimicking in vivo conditions requires attention to other chemical and physical factors known to program cell fate, in addition to environmental parameters.
“Transitioning towards advanced culture systems capable of mimicking in vivo conditions not only requires consideration of environmental parameters, but also necessitates attention to other chemical and physical factors known to program cell fate.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S2 (checkable), S4 (based).
InterpretationreasoningThe PRINCE reporting checklist will ensure standardized reporting of cell culture conditions.
“This will ensure much needed standardized reporting of cell culture conditions.”
Quote in the paperNot a substantial claimMay combine two claims.
PremisecitationBatch cell cultures are the most popular, inexpensive and scalable culture system, in terms of the possible number of replicates and treatments, with <1% of the published literature utilizing cybernetic bioreactor or chemostat culture systems (2014-2019).
“Indeed, batch cell cultures are the most popular, inexpensive and scalable culture system, in terms of the possible number of replicates and treatments, with <1% of the published literature utilizing cybernetic bioreactor or chemostat culture systems (2014–2019, Klein et al., 2021b).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Klein et al., 2021b
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
May combine two claims.
PremisecitationHybridoma cells exposed to elevated CO2 conditions exhibited reduced growth rates when osmolarity was held constant at 361 mOsm kg−1, but cell growth rates further declined by 30% when medium osmolality was 415 mOsm kg−1.
“For instance, hybridoma cells exposed to elevated CO2 conditions exhibited reduced growth rates when osmolarity was held constant at 361 mOsm kg−1, but cell growth rates further declined by 30% when medium osmolality was 415 mOsm kg−1 (Dezengotita et al., 1998).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Dezengotita et al., 1998 source
Probably not a substantial claim: may not pass S4 (based). May combine two claims.
Interpretationnone givenIn bioreactor cultures, often only setpoints are reported without actually measuring environmental conditions in the medium, leading to unknown physiological relevance and low reproducibility.
“but often only setpoints are reported without actually measuring environmental conditions in the medium (mean ± SE) leading to unknown physiological relevance and low reproducibility.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationMore sophisticated bioreactor culture systems were first introduced in the 1970s to culture mammalian cells and typically involve the automated control of temperature, gas addition (O2, CO2), and/or acids and bases to maintain set targets for temperature, dissolved gases and pH.
“More sophisticated bioreactor culture systems were first introduced in the 1970s to culture mammalian cells (Knazek et al., 1972; Fouron, 1987) and typically involve the automated control of temperature, gas addition (O2, CO2), and/or acids and bases to maintain set targets for temperature, dissolved gases and pH.”
Quote in the paperNot a substantial claim0 of 2 sources checkedProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based).
Premisenone givenBatch cultures are typically maintained in incubators that maintain temperature (typically 37°C) and guarantee a CO2 level (typically 5%) in the atmosphere.
“Batch cultures are typically maintained in incubators that maintain temperature (typically 37°C) and guarantee a CO2 level (typically 5%) in the atmosphere.”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationreasoningA reasonable degree of control over environmental conditions is achievable in routine culture systems, but requires consideration of workflow factors that can, directly and indirectly, promote environmental drift.
“A reasonable degree of control over environmental conditions is achievable in routine culture systems, but requires consideration of workflow factors that can, directly and indirectly, promote environmental drift (Figure 2).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Figure 2
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Rests on an assumption: The most common approach to in vitro cell culture is standard batch culture, in which cells are grown either in suspension or as adherent monolayers in standard media within tissue culture flasks.
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationSuch systems range in cost, from moderately priced sensors for temperature, pH, O2, and salinity to the more expensive sensing equipment required for monitoring dissolved CO2, which often require complex calibration protocols.
“Such systems range in cost, from moderately priced sensors for temperature, pH, O2, and salinity to the more expensive sensing equipment required for monitoring dissolved CO2, which often require complex calibration protocols (Supplementary Table S1).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Supplementary Table S1
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
May combine two claims.
Interpretationnone givenEnvironmental stability is most easily achieved in advanced bioreactor culture systems, whereas achieving stability in routine batch culture systems is most challenging, with perfusion systems (and chemostats) providing intermediate solutions.
“Environmental stability is most easily achieved in advanced bioreactor culture systems, whereas achieving stability in routine batch culture systems is most challenging, with perfusion systems (and chemostats) providing intermediate solutions (Table 1).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Table 1
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Rests on an assumption: The most common approach to in vitro cell culture is standard batch culture, in which cells are grown either in suspension or as adherent monolayers in standard media within tissue culture flasks.
The paper relies on this without support.
Best-practice guidelines have not yet included comprehensive standards for the reporting or control of environmental conditions in cell-culture systems.
“Best-practice guidelines are used to ensure standards in biomedical research, encompassing multiple aspects of the research practice (Baust et al., 2017), but have not yet included comprehensive standards for the reporting or control of environmental conditions in cell-culture systems.”
The paper relies on this without support.
Standard cell cultures lack the regulatory systems present in the mammalian body that regulate dissolved gases, waste products, and H+ ions.
“standard cell cultures lack the regulatory systems (e.g., changes in respiratory rate, vascular remodeling, renal control of HCO3 − and H+) present in the mammalian body.”
The paper relies on this without support.
Most cells in vivo exist within 100 µm of the nearest capillaries that replenish O2 and remove excess CO2.
“This is contrary to in vivo physiology, where most cells exist within 100 µm to the nearest capillaries that replenish O2 and act to remove excess CO2.”
The paper relies on this without support.
The characterization, control, and reporting of environmental conditions in mammalian cell cultures is fundamental to ensure physiological relevance and reproducibility in basic and preclinical biomedical research.
“The characterization, control, and reporting of environmental conditions in mammalian cell cultures is fundamental to ensure physiological relevance and reproducibility in basic and preclinical biomedical research.”
The paper relies on this without support.
The most common approach to in vitro cell culture is standard batch culture, in which cells are grown either in suspension or as adherent monolayers in standard media within tissue culture flasks.
“The most common approach to in vitro cell culture is when cells are grown either in suspension or as adherent monolayers in standard media within tissue culture flasks (defined here as “standard batch culture”).”
The paper relies on this without support.
NVBs introduce active molecules and acid-base reactions absent from mammalian fluids.
“However, it is vital to consider how NVBs introduce active molecules and acid-base reactions absent from mammalian fluids and existing evidence, although limited, indicates that NVBs could induce toxicity and anomalous cellular responses in particular cell types (Good et al., 1966; Lepe-Zuniga et al., 1987; Hanrahan and Tabcharani, 1990; Stea and Nurse, 1991).”
The paper relies on this without support.
Enhancing standards for environmental control, monitoring, and reporting is hindered by the limited availability of affordable culture systems capable of advanced environmental monitoring and control for a broad range of cell types.
“Enhancing standards is also hindered by the limited availability of affordable culture systems capable of advanced environmental monitoring and conrtol for a broad range of cell types.”
The paper relies on this without support.
The lack of appropriate tools contributes to the lack of awareness of the true extent of environmental instability.
“The lack of appropriate tools in turn contributes to the lack of awareness of the true extent of environmental instability.”
The paper relies on this without support.
Most journals encourage providing all relevant details in extended materials, thereby extending the space available to accurately describe procedures and report additional data.
“However, while many journals, dictate strict restrictions on the main body of the published text, most journals encourage providing all relevant details in extended materials, thereby extending the space available to accurately describe the procedures used and report additional data helping interpret the results presented.”
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
PRINCE acronym has two different expansions
MinorThe figure caption and the reporting section give different full names for the same PRINCE guidelines.
“PRINCE (Preferred Reporting Items for describing the Nature of Culturing Environments) guidelines.”
“PRINCE (Preferred Reporting Information on the Nature of Cell-culturing Environments) guidelines”
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Flagged first, then by citations
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Klein, S. G., Alsolami, S. M., Arossa, S., Ramos‐Mandujano, G., Parry, A. J., Steckbauer, A., Duarte, C. M., & Li, M. (2022) · Communications Biology · doi:10.1038/s42003-022-03065-w · Cited by 36 · see citing works
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Continuous muscle, glial, epithelial, neuronal, and hemocyte cell lines for Drosophila research
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Applying the Cytocentric Principles to Regenerative Medicine for Reproducibility
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Fluorescence-Enhanced Assessments for Human Breast Cancer Cell Characterizations
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Bioactivity Assessment of Pulp Capping Biomaterials: In vitro Approaches
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Self-citation
- Authors
- Klein, S. G., Steckbauer, A., Alsolami, S. M., Arossa, S., Parry, A. J., Li, M., & Duarte, C. M.
- Affiliations
- King Abdullah University of Science and Technology (SA)
- Corresponding author
- Li, Mo
- Duarte, Carlos M.
- ORCID
- Venue
- Frontiers in Cell and Developmental Biology
- Publisher
- Frontiers Media SA
- Published
- 2022-02-21
- Volume
- 10
- Pages
- 788808-788808
- ISSN
- 2296-634X (ISSN-L)
- PMC
- PMC8900666
- OpenAlex
- W4213198383
- Semantic Scholar
- 3c781fe1714829a9a0d7fd202c458d61d3d14adb
- Cited by
- 23
- References
- 82
- Citations by year
- 2026: 5 · 2025: 6 · 2024: 5 · 2023: 5 · 2022: 2
- FWCI
- 0.92
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Cell and Developmental Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- UWA Profiles and Research Repository (UWA) (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology) (submittedVersion, cc-by)
- Funders
- King Abdullah University of Science and Technology
- Topics
- Health Sciences › Veterinary › Small Animals › Animal testing and alternatives
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Viral Infectious Diseases and Gene Expression in Insects
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular Mechanics and Interactions
- Keywords
- mammalian cell culture, environmental instability, reproducibility, reporting guidelines
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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