On 2017 Jul 07, Wei Wang commented:

Several issues has been raised about this paper on PubPeer below I highlight a few of the comments:

Comment #1: "This review focuses on highlighting two research papers coauthored by Maria Barna. Peers have raised questions about both papers and the questions remain unanswered: 1) https://pubpeer.com/publications/A77C7AE5A8AEF8F5E36C4FC7139B03 2) https://pubpeer.com/publications/25409156

The review omits many of the seminal papers, including:

1) The the ribosome filter hypothesis that introduced the idea of specialized ribosomes in the post-genomic era: Mauro, V.P., and Edelman, G.M. (2002). The ribosome filter hypothesis. PNAS 99, 12031–36

2) Earlier demonstrations of translation initiation dependent on the interaction between IRESs and ribosomal proteins: Landry, D.M., Hertz, M.I., and Thompson, S.R. (2009). RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs. Genes Dev. 23, 2753–64".

Comment #3: "This review offers two line of evidence for heterogeneous ribosomes:

1) Levels of mRNAs encoding ribosomal proteins. -- Inferring protein levels from mRNA levels is generally precarious, especially for ribosomal proteins that correlate very poorly (or even negatively) to their transcript levels. For example see Figure 2c in Zhang et al., 2014: doi:10.1038/nature13438. Why are these data not mentioned ? -- There is wealth of transcript data, and the data included in this review are among the least convincing.

2) Protein separated on 1-D gels and stained with coomassie blue -- How do the authors know that the spots correspond to ribosomal proteins, as apposed to translation factors ? -- How do the authors know that the spots do not correspond mostly to immature ribosomes ? -- How do the authors know that the spots staining is quantitative ? -- I did not find these papers convincing decades ago when they were first published, and they did not convince the community. Are they more convincing now? What am I missing?

Many of the references are incorrect. Examples include asserting a change in the ribosomal composition, while the referenced article actually reported change in the total cytoplasmic levels of ribosomal proteins or change in their rate of protein synthesis."

On 2017 Jul 07, Wei Wang commented:

Several issues has been raised about this paper on PubPeer below I highlight a few of the comments:

Comment #1: "This review focuses on highlighting two research papers coauthored by Maria Barna. Peers have raised questions about both papers and the questions remain unanswered: 1) https://pubpeer.com/publications/A77C7AE5A8AEF8F5E36C4FC7139B03 2) https://pubpeer.com/publications/25409156

The review omits many of the seminal papers, including:

1) The the ribosome filter hypothesis that introduced the idea of specialized ribosomes in the post-genomic era: Mauro, V.P., and Edelman, G.M. (2002). The ribosome filter hypothesis. PNAS 99, 12031–36

2) Earlier demonstrations of translation initiation dependent on the interaction between IRESs and ribosomal proteins: Landry, D.M., Hertz, M.I., and Thompson, S.R. (2009). RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs. Genes Dev. 23, 2753–64".

Comment #3: "This review offers two line of evidence for heterogeneous ribosomes:

1) Levels of mRNAs encoding ribosomal proteins. -- Inferring protein levels from mRNA levels is generally precarious, especially for ribosomal proteins that correlate very poorly (or even negatively) to their transcript levels. For example see Figure 2c in Zhang et al., 2014: doi:10.1038/nature13438. Why are these data not mentioned ? -- There is wealth of transcript data, and the data included in this review are among the least convincing.

2) Protein separated on 1-D gels and stained with coomassie blue -- How do the authors know that the spots correspond to ribosomal proteins, as apposed to translation factors ? -- How do the authors know that the spots do not correspond mostly to immature ribosomes ? -- How do the authors know that the spots staining is quantitative ? -- I did not find these papers convincing decades ago when they were first published, and they did not convince the community. Are they more convincing now? What am I missing?

Many of the references are incorrect. Examples include asserting a change in the ribosomal composition, while the referenced article actually reported change in the total cytoplasmic levels of ribosomal proteins or change in their rate of protein synthesis."