In order to contribute to the scientific development to the field and contribute to reproducibility, our lab developed an internal policy of total transparency.
All full scans of all publications are now freely available here in the website. In addition, we are in the process of providing all original raw data for each paper from our lab that was created in 2008 at the University of Chile. In the last years, all has been stored on a server organized by figure panel and is fully available for researchers upon request.
Here we have generated a data repository for full scans of Western blots and agarose gels. We are also currently including for recent papers statistical analysis of independent experiments. This will help our colleagues troubleshooting antibodies and also accessing raw data of cropped gels. In addition, since 2017 as part of this policy all lab books are revised once a moth and all image splicing and statistical analysis and number of replicates are indicated in figure legends.
Importantly, we are aware of the posts of PubPeer pointing out to possible errors in some of our publications. We have considered these comments seriously, and we have uploaded here responses to all queries to the papers of our lab as Principal investigator, an effort lead by each first author of the studies. In addition, we posted many of our responses to PubPeer for transparency. Editorial offices have been informed when errors were confirmed by our group to define further actions. All communication with editorial offices is included in the single files provided here.
We are currently in the process of improving our lab standards to avoid this type of mistakes in the future. These include:
- Revision and sing by the principal investigator of all lab books of all lab members in principle once a month.
- Reduction of lab size.
- A politic of lab books storage and data backup with a lab server.
- The obligation to provide raw data and all individual measurements, images etc, before publications.
- Post in our website full scans of all papers, and excel files with individual N and statistical analysis.
- We review manuscripts and figures by a team of lab members before submission, in addition to an external investigator.
- As director of the Biomedical Neuroscience Institute (BNI) I personally generated and led a “Science Comitee” composed by professors, postdocs and students to generate strategies and common lab standard to improve the quality of our science. These included two workshops about lab book use, talks about animal experimentation ethics, discussions about data storage with all PIs and the obligation to backup all data of papers published by BNI as a server.
ANSWERS TO PUBPEER QUERIES
SUPORTING DATA OF PUBLICATIONS
Vidal RL. et al.(2021). Enforced dimerization between XBP1s and ATF6f enhances the protective effects of the UPR in models of neurodegeneration. Mol Ther. S1525-0016(21)00067-8.#*
Rozas P. et al. (2021). Protein disulfide isomerase ERp57 protects early muscle denervation in experimental ALS. Acta Neuropathol Commun. 9(1):21.#*
Dufey E., et al. (2020). Genotoxic stress triggers the activation of IRE1a-dependent RNA decay to modulate the DNA damage response. Nature Communications. 11(1):2401.#*
Garcia-Huerta P., et al. (2020). Insulin-like growth factor 2 (IGF2) protects against Huntington’s disease through the extracellular disposal of protein aggregates. Acta Neuropathol. 10.1007/s00401-020-02183-1.
Carreras-Sureda A., et al. (2019). Non-canonical role of IRE1 as a functional determinant of mitochondria-associated endoplasmatic reticulum composition to control calcium transfer and bioenergetics. Nature Cell Biology. 21(6):755-767.#*
Urra H., et al. (2018). IRE1 governs cytoskeleton remodeling and cell migration through a direct interaction with Filamin A. Nature Cell Biology. 20:942-953.#*
Medinas D., et al. (2018). Endoplasmatic reticulum stress leads to accumulation of wild-type SOD1 aggreegates associated with sporadic amyotrophic lateral sclerosis. Proc. Natl. Acad. Asci USA. pii: 201801109.#*
Sepulveda D., et al. (2018). Interactome screening identifies a novel function of the collagen chaperon Hsp47 as an adjustor of the unfolded protein response (UPR) transducer IRE1. Mol Cell. 69:238-252. #*
Mercado G., et al. (2018). Targeting PERK signaling with the small molecule GSK2606414 prevents neurodegeneration in a model of Parkinson’s disease. Neurobiol. Dis. 112:136-148.#*
Duran-Aniotz C., et al. 2017 . IRE1 signaling exacerbates Alzheimer’s disease pathogenesis. Acta Neuropathol. 134:489-506.*#
Bargsted L., et al 2017. Disulfide cross-linked multimers of TDP-43 and spinal motor neuron loss in a TDP-43A315T ALS/FTD mouse model. Scientific Reports. 7:14266*#
Martínez G., et al. (2016). Regulation of memory formation by the transcription factor XBP1. Cell Rep. 14:1382-1394. *#
Woehlbier U., et al. (2016). ALS-linked Protein Disulfide Isomerase Variants cause motor dysfunction. EMBO J. 35:845-65. *#
Oñate M., et al. 2016. Activation of the unfolded protein response promotes axonal regeneration after peripheral nerve injury. Scientific Reports. 6:21709. *#
Torres M., et al. (2015). The Protein Disulfide Isomerase ERp57 Regulates the Steady-State Levels of the Prion Protein. J Biol Chem. 290:23631-45*#
Castillo V., et al. (2015). Functional Role of the Disulfide Isomerase ERp57 in Axonal Regenerartion. PLoS One. 10:eo136620.*
Nassif M., et al. (2014). Pathogenic role of BECN1/Beclin 1 in the development of amyotrophic lateral sclerosis. Autophagy. 10: 1256-1271#*.
Matus L., et al. (2013). Functional role of the transcription factor ATF4 in the pathogenesis of amyotrophic lateral sclerosis. PloS One. 8:e66672.
Rodriguez D., et al. (2012). BH3-only proteins are part of a regulatory network that control the sustained signaling of the Unfolded Protein Response sensor IRE1. EMBO J. 31(10):2322-35. #*
Vidal R., et al. (2012). Targeting the UPR transcription factor XBP1 protects against Huntington’s disease through the regulation of FoxO1 and autophagy. Hum. Mol. Gen. 21(10):2245-62. #*
Rojas-Rivera D., et al. (2012). TMBIM3/GRINA is a novel Unfolded Protein Response (UPR) target gene that controls apoptosis through the modulation of ER calcium homeostasis. Cell Death Diff. 9:1013-26. *#
Zamorano S., et al. (2012). A BAX/BAK and Cyclophilin D-independent Intrinsic Apoptosis Pathway. PLoS One :e37782. *#
Valenzuela V, et al. (2012). Activation of the Unfolded Protein Response enhances motor recovery after spinal cord injury. Cell Death Dis. 3, e272 *#
Torres M., et al. (2012). Altered Prion protein expression pattern in CSF as a biomarker for Creutzfeldt-Jakob Disease. PLoS One .7:e36159. *#
Castillo K, et al. (2011). BAX inhibitor-1 regulates autophagy by controlling the IRE1?/JNK branch of the unfolded protein response. EMBO J. 4465-78 *#
Torres M., et al. (2010). Prion Protein Misfolding Affects Calcium Homeostasis and Sensitizes Cells to Endoplasmic Reticulum Stress. PlosOne. 5: e15658- e15658.*#
Hetz C., et al. (2009). XBP-1 deficiency in the nervous system protects against amyotrophic lateral sclerosis by increasing autophagy. Genes & Dev. 23:2294–2306 *#
Lisbona F., et al. (2009). BAX Inhibitor-1 is a negative regulator of the ER stress sensor IRE1. Mol. Cell. 33:679-691.*#