Research integrity Smut Clyde

The Perennial Northern Blot of Lopez-Otin

Cancer researcher Carlos López-Otín published the same Northern blot no less than 23 times in 23 publications, between 1994 and 2006. Eventually Lopez-Otin et al even stopped caring what order of samples that original loading control had.

On the Iberian peninsula, there seems to be a tradition to give well-connected scientists suspected (or even convinced) of data fudging an award. In Spain, Carlos López-Otín, Professor of Biochemistry and Molecular Biology at the University of Oviedo, was given a Mentoring Award from the elite journal Nature, on recommendation from Spanish academia and despite evidence of data irregularities in his papers. This prompted my readers, in particular the famous pseudonymous data integrity sleuth Clare Francis, to comment on on PubPeer and on my site (as “Zebedee”) with additional evidence, which made Lopez-Otin’s scientific credibility look progressively worse and worse, with each new post.

Eventually, an image of a Northern blot (showing expression of mRNAs which code for proteins) was found to appear recurrently across several papers from that Oviedo lab, where the authors pretended it was a newly produced analysis. In reality, it was a “library” loading control reused so the authors could re-run same RNA gel of human tissue lysates over the years and never check ever again what they have actually loaded on their gels. Eventually Lopez-Otin et al even stopped caring what order of samples that original loading control had.

Clare Francis was soon joined on his quest for the Perennial Northern Blot of Oviedo by Elisabeth Bik, famous microbiology blogger and image duplication detective, and my regular contributor (also pseudonymous) Smut Clyde, who now presents you the findings of no less than 23 appearances of that same northern blot in 23 publications from Lopez-Otin’s lab in the guest post below. It is just as convincing as if the Spanish actor Antonio Banderas appeared in 23 different films still dressed in same costume from his 1995 hit Desperado, carrying same guitar case. Incidentally, also Lopez-Otin’s Perennial Northern Blot made its first appearance at around that year.

screenshot-vimeo.com-2018-05-04-12-18-38
Celebrity friends. Still from a 2017 video by Fundació Princesa de Girona

The cancer researcher Lopez-Otin is an actual real-life celebrity in Spain. On 29 June 2017, he helped the King of Spain open the Princess of Girona Foundation Awards ceremony, together with another Spanish celebrity of the creative art of the pretend, Antonio Banderas. The Princess Foundation wrote about their 2017 gala host:

“Carlos Lopez-Otín is an academician of the European Academy and the Royal Academy of Sciences of Spain, and Doctor Honoris Causa by several Spanish and foreign universities. Throughout his scientific career he has received several awards such as the European FEBS Prize for Biochemistry, the DuPont Award for Life Sciences, the “Carmen and Severo Ochoa” Award, the Mexico Prize for Science and Technology, King Jaime I Prize Research and the National Research Award “Santiago Ramón y Cajal”

That multiple award winning research star is also EMBO member, just like some other of his Spain-based colleagues of questionable research integrity are: Maria Pia Cosma and Pura Munoz-Canoves. These two also regularly receive juicy research grants and recognition: Munoz-Canoves’ most recent was the “Vanguardia de la Ciencia” award, while Cosma was given in 2016 “Ciutat de Barcelona” award. Another Spanish researcher with shady data in his papers is Manel Esteller, he also gets awarded regularly, in 2016 it was the Catalonia International Prize from (now fugitive) President Puigdemont. In Portugal, Esteller’s former PhD student and now zombie scientist Sonia Melo was given a Prémio FAZ Ciência award from Fundação AstraZeneca, only two months ago. There are surely more of such questionable Iberic awardees, readers are welcome to salute these stars of Photoshop in the comment section.

Lopez-Otin’s data integrity issues involve also such obviously manipulated gels like this Northern Blot in Llano et al Cancer Research 1999. What was it the authors didn’t like that they had to duplicative parts of this gel and introduce other digital “modifications”?

I personally have a theory that in this way the system of Iberian academia announces who is untouchable, in order to intimidate critics of research misconduct in their own ranks. Probably a pathetic left-over from the fascist past of Spain and Portugal. The subliminal message is: yes, we all know what these award-winners did to create those big papers and we don’t mind at all. The award-giving farce shows who the role models are and what Spanish and Portuguese scientists are expected to do with their silly notions of research integrity: shove it, start making big papers whatever it takes, or lose your job. In fact, not even the arch-zombie scientist Susana Gonzalez had to suffer unemployment, unlike masses of honest young Spanish scientists.


A Perennial Northern Blot, by Smut Clyde

The title of this post refers to the famously picaresque Western blot belonging to a Brazilian diabetes researcher. sinbt0jIn its protean versatility, Mario Saad‘s pentadecaplicating blot could transform itself into any protein — tubulin, actin, GLUT4, IRS1 — from any combination of source conditions. It thereby appeared in at least 15 versions, spread across 10 papers in “an intricate publishing web“, serving as the loading control in that many different experiments (that is, as a measure of the total level of extracted protein, for normalising the measurements of the protein of interest). In my imagination it spoke with the voice of Robin Williams. This site forwarded a report on the Wandering Western… the ensuing saga included editorial Expressions of Concern, lawsuits, an investigation by Saad’s university that saw no evidence of misconduct, and 13 retractions so far (RetractionWatch are keeping score).

The present case also concerns re-use of a loading control, but this time featuring a Northern blot. The compass-point tradition for naming gel-electrophoresis techniques began with Sir Edwin Southern, pioneer of Southern blotting, for this is how humor works in molecular biology. It has been explained to me that Northern blots do not directly measure the popularity of a protein in the cellular economy; instead, mRNA (encoding for a protein) is the chemical species, extracted from various sources (lanes), and spread out into bands according to molecular weight. Then transferred (blotted) from the electrophoresis gel to a filter for stability, and detected by inducing the mRNA to bind to a matching and radiotracing DNA probe.

So in this case, a team of researchers have a bank of 28 “cell smoothies”: two sets of eight tissue types, one set of eight cancer-cell lines, and four fetal-tissue samples. In a series of papers published over a decade, the team have characterised numerous proteins from within the self-organising complexity of the human cell — sequencing the DNA for each protein and specifying its chromosomal location, describing its role within that complexity, and checking which tissues express it (which depends on which genes remained active in each lineage of cells that differentiated and specialised and became a tissue). That is to say, the Northern Blots were just one aspect of the papers, and they are all outside my comfort grade and above my pay zone.

the future

Each study took a few drops from the stored samples, blotted it (“Filters containing about 2 µg of polyadenylated RNAs from the indicated human tissues”), and probed for the mRNA of choice. But there are limits to the precision that a pipette can provide — even in the hands of a trained gene-modified laboratory monkey — so the final stage is to wash the probe DNA out of the filter and probe it again for Actin (a background “housekeeping” protein, required by cells to maintain their architecture, unless they are dead) to correct for the actual aliquots that were used. Thus papers in this sequence typically include a phrase along these lines:

“Filters were subsequently hybridized with a human actin probe to ascertain differences in RNA loading”.

It is conceivable, however, that this phrase was repeated from the first paper, along with the loading blot itself. Comparing 23 papers, there appears to be one original blot for each bank: four blots, which are variously compressed and clipped according to the exigencies of publication, and varying also in exposure, rather than a separate measurement after each separate exercise in tissue localisation. The sources are ‘Zebedee’, commenting on threads at this site; anonymous contributors to PubPeer threads; Elisabeth Bik; and myself.

northern1-5

This comes to our notice because a 23-fold replication beats the 15-fold record of the Brazilian wanderer. Crucially, though the possible copies are consistently identified as Actin, and the authors have tried to label the sources of the lanes consistently. The reuse of a ‘loading library’ is deprecated, but this does not begin to approach the problematic level of the Brazilian Western: there was no attempt to mislead (other than the claim that the control in each study was specific to it, made subsequently to the data to be controlled). It is a perennial blot, always in the same place, rather than a wanderer or vagrant.

northern6-10

northern11-15

Regrettably, the labelling of lanes was not as consistent as was intended. In a 2003 appearance of the fetal-tissue blot, it was flipped horizontally relative to the lane labels, as marked with a red box in the Figures. Note that in some publications the lanes are listed in reverse order — from Leucocytes to Heart rather than vice versa — and in the Figures I have flipped each band and labels in such cases, to keep a single sequence of tissue types (hence the mirror-image text in places).

Red boxes were also necessary in some cases where the cancer-cell blot was flipped relative to its lane labels, and for the #2 array of tissue cells in the 1999 paper. In addition, that blot was rotated through 180° from 2001 onwards (so that the Actin background for Thymus cells becomes that of Colon cells, and vice versa, while Testes and Ovary change places, and Spleen with Leucocytes). This is marked with orange boxes. One can only hope that these pictorial labelling issues did not extend into the measurements of Actin from the blots, as used in the quantitative results.

northern16-20

Finally, two blue arrows mark the omission of ‘Pancreas’ and ‘Skeletal muscle’ from one study each, with the loading band spliced to remove that lane.

I am going to play ‘good cop’ here, and propose that the corner-cutting absence of study-specific controls probably made little difference to the results. Corrigenda to the paper acknowledging the use of archival controls would be appropriate (along with correction of any flipped and rotated bands). Other issues have been raised about other figures in some of the papers, but I do not address those here.

Details of the 23 publications follow. We are still hopeful of finding a few more examples of the Perennial Northern Blot.

  1. 1994. “Human cathepsin O. Molecular cloning from a breast carcinoma, production of the active enzyme in Escherichia coli, and expression analysis in human tissues“, Velasco et al; J Biol Chem., 269(43):27136-42.
  2. 1995. “Cloning and expression analysis of a novel human serine hydrolase with sequence similarity to prokaryotic enzymes involved in the degradation of aromatic compounds“, Puente & López-Otín; Journal of Biological Chemistry 270, 12926-12932. DOI 10.1074/jbc.270.21.12926 Figure 5.
  3. 1996. “Cloning and Expression Analysis of Human Bleomycin Hydrolase, a Cysteine Proteinase Involved in Chemotherapy Resistance“, Ferrando et al.; Cancer Research 56: 1746-1750. PMID: 8620487
  4. 1996. “Molecular Cloning of a Novel Membrane-type Matrix Metalloproteinase from a Human Breast Carcinoma“, Puente et al; Cancer Research 56:944-949.
  5. 1997. “Identification and characterization of a novel human matrix metalloproteinase with unique structural characteristics, chromosomal location, and tissue distribution“, Pendás et al; J Biol Chem. 272(7):4281-6. doi: 10.1074/jbc.272.7.4281 Figure 7.
  6. 1998. “Cathepsin L2, a Novel Human Cysteine Proteinase Produced by Breast and Colorectal Carcinomas“, Santamaría et al; Cancer Res. 58(8):1624-30.
  7. 1998. “Cathepsin Z, a novel human cysteine proteinase with a short propeptide domain and a unique chromosomal location“, Santamaría et al; J Biol Chem. 273(27):16816-23. doi: 10.1074/jbc.273.27.16816 Figure 5.
  8. 1999. “Cloning and characterization of human MMP-23, a new matrix metalloproteinase predominantly expressed in reproductive tissues and lacking conserved domains in other family members“, Velasco et al; J Biol Chem. 274(8):4570-6. doi: 10.1074/jbc.274.8.4570 Figure 6.
  9. 1999. “Molecular cloning and structural and functional characterization of human cathepsin F, a new cysteine proteinase of the papain family with a long propeptide domain“, Santamaría et al; J Biol Chem. 274(20):13800-9. doi: 10.1074/jbc.274.20.13800 Figure 6.
  10. 1999. “Identification and Chromosomal Location of Two Human Genes Encoding Enzymes Potentially Involved in Proteolytic Maturation of Farnesylated Proteins“, Freije et al; Genomics 58, 270–280. DOI: 10.1006/geno.1999.5834
  11. 2000. “Human MT6-matrix metalloproteinase: identification, progelatinase A activation, and expression in brain tumors“, Velasco et al; Cancer Research 60, 877–882. pubmed: 10706098
  12. 2001. “Identification, Characterization, and Intracellular Processing of ADAM-TS12, a Novel Human Disintegrin with a Complex Structural Organization Involving Multiple Thrombospondin-1 Repeats“, Cal et al; Journal of Biological Chemistry 276, 17932-17940. doi: 10.1074/jbc.M100534200 Figure 5.
  13. 2002. “Matriptase-2, a Membrane-bound Mosaic Serine Proteinase Predominantly Expressed in Human Liver and Showing Degrading Activity against Extracellular Matrix Proteins“, Velasco et al; J Biol Chem. 277(40):37637-46. doi: 10.1074/jbc.M203007200 Figure 8.
  14. 2002Cloning, expression analysis, and structural characterization of seven novel human ADAMTSs, a family of metalloproteinases with disintegrin and thrombospondin-1 domains“, Cal et al; Gene 283 49-62. doi: 10.1016/S0378-1119(01)00861-7
  15. 2003. “Polyserase-I, a human polyprotease with the ability to generate independent serine protease domains from a single translation product“, Cal et al; PNAS 100(16): 9185–9190. doi: 10.1073/pnas.1633392100 Figure 4.
  16. 2003. “Human Autophagins, a Family of Cysteine Proteinases Potentially Implicated in Cell Degradation by Autophagy“, Mariño et al; Journal of Biological Chemistry 278, 3671-3678. doi: 10.1074/jbc.M208247200 Figure 3.
  17. 2003. “Identification and Characterization of ADAMTS-20 Defines a Novel Subfamily of Metalloproteinases-Disintegrins with Multiple Thrombospondin-1 Repeats and a Unique GON Domain“, Llamazares et al; Journal of Biological Chemistry 278(15):13382-13389. doi: 10.1074/jbc.M211900200 Figure 4.
  18. 2004. “Identification and Characterization of Human and Mouse Ovastacin“, Quesada et al; JBC 279 (25) 26627-26634. doi: 10.1074/jbc.M401588200 Figure 3.
  19. 2004. “Cloning and enzymatic analysis of 22 novel human ubiquitin-specific proteases“, Queseda et al; Biochemical and Biophysical Research Communications 314, 54-62. doi: 10.1016/j.bbrc.2003.12.050
  20. 2005. “Identification of Human Aminopeptidase O, a Novel Metalloprotease with Structural Similarity to Aminopeptidase B and Leukotriene A4 Hydrolase“, Díaz-Perales et al; Journal of Biological Chemistry 280, 14310-14317. doi: 10.1074/jbc.M413222200 Figure 4.
  21. 2005. “Human Polyserase-2, a Novel Enzyme with Three Tandem Serine Protease Domains in a Single Polypeptide Chain“, Cal et al; JBC 280, 1953-1961. doi: 10.1074/jbc.M409139200 Figure 3.
  22. 2005. “Identification and Characterization of Human Archaemetzincin-1 and -2, Two Novel Members of a Family of Metalloproteases Widely Distributed in Archaea“, Diaz-Perales et al; JBC 280(34):30367-30375. doi: 10.1074/jbc.M504533200 Figure 4.
  23. 2006. “Identification and characterization of human polyserase-3, a novel protein with tandem serine-protease domains in the same polypeptide chain“, Cal et al; BMC Biochemistry. doi: 10.1186/1471-2091-7-9 Figure 7.

Update 7.05.2018. Based on reader comment:

oviedo

 

 

 

 

Donate!

If you are interested to support my work, you can leave here a small tip of $5. Or several of small tips, just increase the amount as you like (2x=€10; 5x=€25). Your generous patronage of my journalism will be most appreciated!

€5.00

103 comments on “The Perennial Northern Blot of Lopez-Otin

  1. In addition to patchwork of bands, their tradition of perennial blots appear again in Soria-Valles’s Nature Cell Biology paper.
    All the tricks of Lopez-Otin group, both traditional ones and brush-up ones gathered in this paper.
    May see more examples coming…

    Like

  2. The 2015 Nature Cell Biology paper from Soria-Valles is receiving almost 80 commments.

    NF-κB activation impairs somatic cell reprogramming in ageing
    Nature Cell Biology (2015) – 78 Comments
    pubmed: 26214134 doi: 10.1038/ncb3207 issn: 1465-7392 issn: 1476-4679

    Clara Soria-Valles , Fernando G. Osorio , Ana Gutiérrez-Fernández , Alejandro De Los Angeles , Clara Bueno , Pablo Menéndez , José I. Martín-Subero , George Q. Daley , José M. P. Freije , Carlos López-Otín

    https://pubpeer.com/publications/836AB3A8AB4FD562A2D4CBFBF8ED18#79

    “Figure 3c and 6b. The complete lack of molecular size marker makes it difficult to tell if the entire film was submitted for deposition. The size of P-IKK2 and IKBA implies that they were from independent film. Just bands were pasted to represent entire film.”

    “Cell senescence assay in supplementary figure 5. Both samples A and B have very similar number of senescent cells under microscopic images. But the cell count says one is 5% (A) and the other is 60% (B). How did the authors count the cells?
    I could not find the quantification method in the paper. “Cell senescence was assessed by detecting the senescence associated β-galactosidase activity at pH6.0 (SA-β-Gal) using a commercial kit (Cell Signaling).”

    “Figure 6d. Colony number between IKKi and IKK2-KI has no difference according to bar graph. Though I found that actual image of colonies very differ.IKK2-KI has apparently >2-fold more colonies. Despite, error bars are really tiny.”

    Like

  3. Pubpeer comment on Soria-Valles et al. 2015 NCB paper.

    NF-κB activation impairs somatic cell reprogramming in ageing
    Nature Cell Biology (2015) – 82 Comments
    pubmed: 26214134 doi: 10.1038/ncb3207 issn: 1465-7392 issn: 1476-4679

    Clara Soria-Valles , Fernando G. Osorio , Ana Gutiérrez-Fernández , Alejandro De Los Angeles , Clara Bueno , Pablo Menéndez , José I. Martín-Subero , George Q. Daley , José M. P. Freije , Carlos López-Otín

    https://pubpeer.com/publications/836AB3A8AB4FD562A2D4CBFBF8ED18#77

    “Here is the image of figure 6b. NF-kB bands were contrasted a lot. Oct-1 bands were distorted. They came from different membranes, and received very different contrast respectively.”

    https://imgur.com/a/LsicJBw

    Like

  4. Image duplication was found in Soria-Valles et al., 2015 NCB paper.

    NF-κB activation impairs somatic cell reprogramming in ageing
    Nature Cell Biology (2015) – 82 Comments
    pubmed: 26214134 doi: 10.1038/ncb3207 issn: 1465-7392 issn: 1476-4679

    Clara Soria-Valles , Fernando G. Osorio , Ana Gutiérrez-Fernández , Alejandro De Los Angeles , Clara Bueno , Pablo Menéndez , José I. Martín-Subero , George Q. Daley , José M. P. Freije , Carlos López-Otín

    https://pubpeer.com/publications/836AB3A8AB4FD562A2D4CBFBF8ED18#78

    “Duplicated images in figure 3 and figure 4. Beta-actin bands were copied and pasted.”

    https://imgur.com/a/TdoK4Pm

    Like

  5. Carlos Lopez-Otin at uniovi and George Daley, Dean of Harvard Medical School, produced a very fruitful paper. Pubpeer >80 comments and image duplication (actually triplication!). @uniovi_info @harvardmed @G_Q_Daley @NatureCellBio @alexia_zz

    Like

  6. Triplicated images in Soria-Valles Nature Cell Biology 2015.

    NF-κB activation impairs somatic cell reprogramming in ageing
    Nature Cell Biology (2015) – 83 Comments
    pubmed: 26214134 doi: 10.1038/ncb3207 issn: 1465-7392 issn: 1476-4679

    Clara Soria-Valles , Fernando G. Osorio , Ana Gutiérrez-Fernández , Alejandro De Los Angeles , Clara Bueno , Pablo Menéndez , José I. Martín-Subero , George Q. Daley , José M. P. Freije , Carlos López-Otín

    https://pubpeer.com/publications/836AB3A8AB4FD562A2D4CBFBF8ED18#83

    “The beta-actin bands were triplicated in 3 figures. Figs. 3, 4 and supplimentary 6.”

    Like

  7. Fernando

    Image duplication, suspicious bar graphs, missing raw data. Say Bingo! to the editor of Nature Cell Bio.

    Like

  8. Need a version 2.0 thread for this topic. The list of comments keeps growing… Now you guys got a new target in addition to NCB.

    Like

  9. Another paper authored by Lopez-Otin is gaining attentions on pubpeer. Similar claim to Soria-Valles NCB, duplication of WB controls.
    I see common co-authors between these papers including Soria-Valles.

    Nuclear lamina defects cause ATM-dependent NF- B activation and link accelerated aging to a systemic inflammatory response
    Genes & Development (2012) – 4 Comments
    pubmed: 23019125 doi: 10.1101/gad.197954.112 issn: 1549-5477 issn: 0890-9369

    Fernando G Osorio , Clea Bárcena , Clara Soria-Valles , Andrew J Ramsay , Félix De Carlos , Juan Cobo , Antonio Fueyo , José M P Freije , Carlos López-Otín

    https://pubpeer.com/publications/4E89FBEE8E6605B592593CF801E7BD#5

    “Duplicated images. Figures 2 and 5.”

    Like

    • Smut Clyde

      Some of the responses in that PubPeer thread are arguing that the two Figures are probably reporting results from the same experiment (at least the details are the same in both cases), so the repeat of the beta-actin band is legitimate and appropriate.

      Like

  10. The first author of Nature Cell Biology (2015), Soria-Valles, is currently a postdoc of George Daley’s group, a dean of Harvard Medical School and her senior co-author of the paper.
    Daley lab website
    https://daley.med.harvard.edu/people

    PCTC website
    https://translationalcells.org/content/clara-soria-valles

    Like

  11. Interesting to see the association of the first author of NCB paper with senior author George Daley, dean of Harvard Medical School. At Daley lab Soria-Valles got trained for the NCB paper and stays there to continue postdoc traning.

    Like

  12. Pubpeer comment described how the raw data were made by Soria-Valles et al., 2015 Nature Cell Biology.

    NF-κB activation impairs somatic cell reprogramming in ageing
    Nature Cell Biology (2015) – 86 Comments
    pubmed: 26214134 doi: 10.1038/ncb3207 issn: 1465-7392 issn: 1476-4679

    Clara Soria-Valles , Fernando G. Osorio , Ana Gutiérrez-Fernández , Alejandro De Los Angeles , Clara Bueno , Pablo Menéndez , José I. Martín-Subero , George Q. Daley , José M. P. Freije , Carlos López-Otín

    https://pubpeer.com/publications/836AB3A8AB4FD562A2D4CBFBF8ED18#87

    “Comprehensive view of 3 figures with raw films.
    How come one single control serves over 7 blots.
    Some of the samples were apparently coming from different gels.
    Identical bands were detected on different blots. Pasted…?
    Trace of cropping bands were detected.”

    NF-κB activation impairs somatic cell reprogramming in ageingClaraSoria-Valles1,8,FernandoG.Osorio1,8,AnaGutiérrez-Fernández1,AlejandroDeLosAngeles2,ClaraBueno3, PabloMenéndez3,4,JoséI.Martín-Subero5,GeorgeQ.Daley2,6,7,JoséM.P.Freije1,9 andCarlosLópez-Ot

    //s.imgur.com/min/embed.js

    Like

  13. Veo cierto ensañamiento con una persona brillante y honesta.
    Cabe preguntarse:
    -¿Parte todo esto de las personas de la Universidad de Oviedo que no sacaron la plaza de profesores por su curriculum mediocre? Quizás ahí están los vestigios de la España con pasado fascista que dice el autor de este blog, que da la sensación que se está convirtiendo en la correa de transmisión de envidias de gente de baja ralea.
    -¿Son reproducibles los resultados fundamentales de los trabajos que se citan?
    – ¿Se está poniendo en duda la credibilidad de unas revistas científicas de alto prestigio? No creo que estas revistas arriesguen su prestigio para salvar a una persona.

    Escribo en castellano porque creo que es la lengua materna de los que comentan esta entrada del blog.

    Like

  14. Comments on G&D paper continue.

    Nuclear lamina defects cause ATM-dependent NF- B activation and link accelerated aging to a systemic inflammatory response
    Genes & Development (2012) – 5 Comments
    pubmed: 23019125 doi: 10.1101/gad.197954.112 issn: 1549-5477 issn: 0890-9369

    Fernando G Osorio , Clea Bárcena , Clara Soria-Valles , Andrew J Ramsay , Félix De Carlos , Juan Cobo , Antonio Fueyo , José M P Freije , Carlos López-Otín

    https://pubpeer.com/publications/4E89FBEE8E6605B592593CF801E7BD#6

    “They are identical. However, the samples in figure 2 and 5 seems to be the same, and therefore not so critical, although I am always sceptical when I see too many blots with one single loading control, like in this example.”

    “How likely 9 strips come the same blot? If they are done together they should stacked above each other in the same figure.
    Also, in figure 2 the nNEMO and tNEMO panels do not look like they come from the same blot.”

    “Indeed the shapes of nNEMO and tNEMO bands so differ in figure 2. More logical explanation is that they came from independent blots that one missing loading control.”

    Like

  15. Leonid, need a new post on Iberian mess on science. So much things are going on. Carlos Lopez-Otin, Jose Rojas and dead scientists. We now are seeing new generation of Lopez-Otin’s lab churning out papers done with similar tricks as decades ago..

    Like

  16. New issue on 2012 G&D paper.
    Horizontal flip of bands to make up different samples.

    Nuclear lamina defects cause ATM-dependent NF- B activation and link accelerated aging to a systemic inflammatory response
    Genes & Development (2012) – 8 Comments
    pubmed: 23019125 doi: 10.1101/gad.197954.112 issn: 1549-5477 issn: 0890-9369

    Fernando G Osorio , Clea Bárcena , Clara Soria-Valles , Andrew J Ramsay , Félix De Carlos , Juan Cobo , Antonio Fueyo , José M P Freije , Carlos López-Otín

    https://pubpeer.com/publications/4E89FBEE8E6605B592593CF801E7BD#9

    “Figures 2 and 6”

    Like

  17. PubPeer pointed out 2015 NCB paper from Soria-Valles et al. having more issues on loading controls.

    NF-κB activation impairs somatic cell reprogramming in ageing
    Nature Cell Biology (2015) – 90 Comments
    pubmed: 26214134 doi: 10.1038/ncb3207 issn: 1465-7392 issn: 1476-4679

    Clara Soria-Valles , Fernando G. Osorio , Ana Gutiérrez-Fernández , Alejandro De Los Angeles , Clara Bueno , Pablo Menéndez , José I. Martín-Subero , George Q. Daley , José M. P. Freije , Carlos López-Otín

    https://pubpeer.com/publications/836AB3A8AB4FD562A2D4CBFBF8ED18#

    “This paper does not comply with NCB guideline that “Loading controls (e.g. GAPDH, actin) must be run on the same blot. ” All the loading control were run on different blots as revealed in supplimentary figure 9, deposit of all the blots used in the paper.”

    https://imgur.com/a/0A7IHDM

    Like

  18. New PubPeer comments on Soria-Valles 2015 NCB paper.
    Readers pointing out the authors non-compliance to NCB policy on raw data.

    NF-κB activation impairs somatic cell reprogramming in ageing
    Nature Cell Biology (2015) – 90 Comments
    pubmed: 26214134 doi: 10.1038/ncb3207 issn: 1465-7392 issn: 1476-4679

    Clara Soria-Valles , Fernando G. Osorio , Ana Gutiérrez-Fernández , Alejandro De Los Angeles , Clara Bueno , Pablo Menéndez , José I. Martín-Subero , George Q. Daley , José M. P. Freije , Carlos López-Otín

    https://pubpeer.com/publications/836AB3A8AB4FD562A2D4CBFBF8ED18

    “They need to comply with the policy of NCB journal to explain how they had counted cells. “Authors should list all image acquisition tools and image processing software packages used. Authors should document key image-gathering settings and processing manipulations in the Methods.” The current method section has no description on this regard.”

    “This mismatch of bands with original blots is an allegation against NCB polycy; The bands were too much overexposed and contrasted to be in shape, if the bands in original blots actually correpsond to the ones in figures. “High-contrast gels and blots are discouraged, as overexposure may mask additional bands. Authors should strive for exposures with gray backgrounds. ”

    “The quantification in figure 4i depends on irrelevant loading controls from unrelated samples.
    Even if the actin bands were to come from corresponding samples (unlikely though), the guideline of Nature Celll Biology says “Loading controls (e.g. GAPDH, actin) must be run on the same blot.”

    Like

  19. J Biol Chem. 2005 Jan 21;280(3):1953-61. Epub 2004 Nov 9.
    Human polyserase-2, a novel enzyme with three tandem serine protease domains in a single polypeptide chain.
    Cal S1, Quesada V, Llamazares M, Díaz-Perales A, Garabaya C, López-Otín C.
    Author information
    1
    Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, 33006 Oviedo, Spain.

    2018 correction.
    http://www.jbc.org/content/293/30/11784.short

    There was an error in Fig. 3. The actin panel for the Northern blot containing spleen, thymus, prostate, testis, ovary, intestine, colon, and leukocyte samples was inadvertently rotated 180 degrees. Since the amount of RNA in each lane was equivalent, this error does not alter the interpretation of the results shown in the figure. Additionally, the actin panels shown in this figure were reused from previous publications describing the hybridization of other human genes to a different set of the same commercial filters used in this article (Multiple Tissue poly(A) Northern blots, Clontech). This commercial product was guaranteed by the manufacturer to have equal loading (approximately 2 μg of polyadenylated RNA per lane). Therefore, the corrected version of Fig. 3 is provided in which these panels are omitted. The authors apologize for these errors. This correction does not affect the results or conclusions of this work.

    Like

  20. J Biol Chem. 2003 Apr 11;278(15):13382-9. Epub 2003 Jan 31.
    Identification and characterization of ADAMTS-20 defines a novel subfamily of metalloproteinases-disintegrins with multiple thrombospondin-1 repeats and a unique GON domain.
    Llamazares M1, Cal S, Quesada V, López-Otín C.
    Author information
    1
    Departamento de Bioquíimica y Biologíia Molecular, Facultad de Medicina, Instituto Universitario de Oncologíia, Universidad de Oviedo, 33006-Oviedo, Spain.

    2018 correction.
    http://www.jbc.org/content/293/30/11785.short

    In Fig. 4A, the actin panel for the Northern blot containing spleen, thymus, prostate, testis, ovary, intestine, colon, and leukocyte samples was inadvertently rotated 180°. Since the amount of RNA in each lane was equivalent, this change does not affect the results for the Northern blot detecting ADAMTS-20. Additionally, the actin panels shown in this figure were reused from previous publications describing the hybridization of other human genes to a different set of the same commercial filters used in this article (Multiple Tissue polyA Northern blots, Clontech). This commercial product was guaranteed by the manufacturer to have equal loading (approximately 2 μg of polyadenylated RNA per lane). Therefore, the corrected version of Fig. 4A is provided in which these panels are omitted. The authors apologize for any inconvenience these errors may have caused. This correction does not affect the results or conclusions of this work.

    Like

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

%d bloggers like this: