Cooperative nutrient accumulation sustains growth of mammalian cells
Authors: David Sabatini
Yaochung Weng
Carson Thoreen
Hui Xiao Chao
Matthew G Vander Heiden
Mark M Stevens
Sungmin Son
Lawrence D Schweitzer
Aaron M Hosios
Scott Manalis
Kris Wood
Journal: Scientific Reports (2015)
Discipline: Multidisciplinary
Keywords: metabolic processes; nutrient uptake; macromolecular synthesis; cell growth; mammalian cells
Affiliations: Whitehead Institute for Biomedical Research Nine Cambridge Center, Cambridge, MA., Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, MA., Dana-Farber Cancer Institute, Boston, MA.

Abstract:  The coordination of metabolic processes to allow increased nutrient uptake and utilization for macromolecular synthesis is central for cell growth. Although studies of bulk cell populations have revealed important metabolic and signaling requirements that impact cell growth on long time scales, whether the same regulation influences short-term cell growth remains an open question. Here we investigate cell growth by monitoring mass accumulation of mammalian cells while rapidly depleting particular nutrients. Within minutes following the depletion of glucose or glutamine, we observe a growth reduction that is larger than the mass accumulation rate of the nutrient. This indicates that if one particular nutrient is depleted, the cell rapidly adjusts the amount that other nutrients are accumulated, which is consistent with cooperative nutrient accumulation. Population measurements of nutrient sensing pathways involving mTOR, AKT, ERK, PKA, MST1, or AMPK, or pro-survival pathways involving autophagy suggest that they do not mediate this growth reduction. Furthermore, the protein synthesis rate does not change proportionally to the mass accumulation rate over these time scales, suggesting that intracellular metabolic pools buffer the growth response. Our findings demonstrate that cell growth can be regulated over much shorter time scales than previously appreciated. 

Retracted: No

PubPeer comments:
 Fig. 4,  EDX spectrum of Cu NPs  Unexpectedly similar to  Figure 2. ... EDX of copper nanoparticles synthesized using C. vitiginea leaf extract , from [Wu et al (2020)] .  Could the authors comment on the apparent re-use modification? , 
  Fig. 2. UVu2013vis spectra of Cu nanoparticles.  Such an extremely sharp-edged notch filter is not physically obtainable. , 
 #2 The graph seems to be OK. If you are worried about the sharp peak between 345-360 nm , I would say that the authors have used a very high concentration of the nano-particles and the system is kind of saturated to give any meaningful information. That is why you see such a peak. The authors should have been more careful once they observed this kind of peak. It is advisable to dilute the sample a bit and collect the spectra once again. Now, by  sharp if you are talking about the abnormal spike around 375 nm, I would say that is also perfectly normal. If you are familiar with a UV-Vis Spectrophotometer, you will understand that the spikes in UV-VIS spectrum are due to change in the lamp. They are not due to compound or nano-particle or anything else for that matter. For your reference I am attaching an example where a similar spike (at the same wavelength) has been observed. You can find similar examples all over the internet. Once again, it is due to the automatic change in the lamp while recording the spectra. According to my experience the spectra in question (#2) is perfectly fine.  , 
 #3 Many thanks for the correction! , 
 #1 The elemental analytical data reveals presence of oxygen and carbon, the amount of oxygen is more than that of copper. Does this mean that copper nanoparticles formed got oxidised by oxygen to become CuO? The EDX results appear truly remarkable. Did the authors study copper nanoparticles or copper oxide nanopartticles or carbon doped copper oxide nanoparticles. Authors may like to explain. , 
 #3 The experimental section mentions that a Shimadzu UV-2450 spectrophotometer was used for UV-Vis (Fig. 2). This device was very popular in the 90 and 2000 . It is true that two lamps were used (D2 and W), with a switch at 375 nm. However, the switch never produced a spike over a so huge range of 25 nm, like that you present in your spectrum. Actually, the switch was almost undetectable, and was corrected by the software. A small discontinuity at 375 nm was indeed a symptom of lamp failure. On the other hand, Cu-NPs have their maximum absorption around 575 nm. This is the absorption expected for the green color of NPs you can see in Fig. 1d. The spectrum in Fig. 2 has its maximum around 340 nm and no absorption at all at 575 nm. This is inconsistent with Fig. 1d. For an example of what is expected for Cu-NPs, please see the following spectra:  (Taken at random from: https: doi.org 10.1515 gps-2018-0038. Check with Google Image, if you wish). , 
 #6 Dear Dr. Sylvain Bernu00e8s The spectrum that I shared was not mine, I just googled it and shared it. This phenomenon does exist, you can find 100s of images on google for your consideration. However, I feel that this problem can be corrected by altering the settings of the software which is linked with the instrument used for acquiring the spectra. Both lamps have to be properly aligned mechanically and corrected for the difference in light output intensity. Manufacturers often provide a built -in solution for this . Since the commenter in #2 mentioned  Such an extremely sharp-edged notch filter is not physically obtainable , I posted a simple example to explain that these things do exist. Secondly, the authors have clearly mentioned that  blueu2013green solution gradually turns to brownish black color the changing of color from the bluish green color of the CuSO4 solution to brown color is because of the surface Plasmon resonance. Also, in the Results Section 2.10, the authors explicitly mention that  When the P. americana extract added with copper sulfate does not change nanoparticles shape but it increases the size of the nanoparticles . Now if surface plasmon resonance is actually taking place and if the size of the nano-particles is increasing upon addition of P. americana extract, it should create a red shift in the absoption spectrum of the nano-particles and that is why we do not see a peak around 575 nm. In my opinion, the peak should be around 650-700 nm. This can be easily clarified if the authors wish to share the complete wavelength scan from 200-800 nm of copper sulfate nano-particles alone, P. americana extract alone, and nano-particles prepared in the presence of the P. americana extract. Also, many papers do not show the 575 nm peak of Cu-Nps. I am putting some refs below for your kind consideration. 1. https: doi.org 10.1039 C6RA08571G  2. DOI: 10.1039 b920301j  , 
 The authors reported the following in the experimental: **2. Materials and method** *2.1. Preparation of seed extract Avocado fruits were purchased from Vellore market and the seed was collected and washed thoroughly using distilled water the seed was ground well by mortar and pestle and 1u202fg of seed powder boiled with 100u202fml of deionized water for 5 min and allowed to cool at room temperature. The mixture of the extract was filtered through filter paper (what man No. 1) and stored in the refrigerator for further use. ***2.2. Synthesis of the CuNPs** *The synthesis of copper nanoparticles, 20u202fml of seed extract was added with 80u202fml of CuSO4 kept under constant stirring using magnetic stirrer at 45u201350u00b0C for 6u20137u202fh. At the end of the step brownish black color was obtained after centrifugation process the product was washed twice with de-ionized water and dried in hot air oven at 100u00b0C for 3u202fh. Finally, the dried powder was stored in properly labeled and used for further analysis.* For the above experimental procedure which shows changes in colour is shown in Figure 1. (See below) However the discussion does not explain anywhere as to what chemical that is present in the Avocado seed is responsible for the reduction of Cu(II) or for the colour changes. If this is can be understood then the explanation of spectra makes scientific sense. Really the UV-VIS spectrum (Fig. 2) appears quite remarkable. The authors also have put up a powder pattern (which they call XRD spectrum) which looks even more remarkable. If authors have done an analysis of the chemical composition of the seed extract, they are requested to share this information. so that the formation of copper nano can be understood better. But still the oxygen in the EDX analysis (commenter 5) requires explanation The open access fee is 1800 USD and it looks like the authors have many projects OR are from an institute which can support such amounts of open access fee. Fig. 1. Visual observation of copper nanoparticles synthesis (A) seed extract (B) copper sulfate solution (C) initial color change (D) final color.  For Powder pattern (so-called XRD spectrum) of copper nano pl. see below  , 
 #8 The avocado seed extract (Fig.1) is a colored solution containing some chemical (organic) which is reducing. Have authors recorded the UV-Vis spectrum of the extract? The possibility that a colored substance (seed extract) on oxidation by Cu(II) can become a more colored substance. How did authors rule out that the color is NOT due to the oxidized species but due to formation of copper nano particles. ,