Expression of Hoxa-1 and Hoxb-7 is regulated by extracellular matrix-dependent signals in mammary epithelial cells. J Cell Biochem 69:377–391.

Srebrow A, Friedmann Y, Ravanpay A, Daniel CW, Bissell MJ (1998): Expression of Hoxa-1 and Hoxb-7 is regulated by extracellular matrix-dependent signals in mammary epithelial cells. J Cell Biochem 69:377–391. In Figure 3 on pages 384 and Figure 4 on page 385, two labels were misprinted. The top label on the right side of Figure 3B should have been Hoxb-7 instead of Hoxb-1, and the center label of Figure 4B should have been Hoxb-7 instead of Hoxa-7. The corrected figures are reprinted on the following pages. The Publisher apologizes for the error.     

Erratum to Beicheng Sun et al. Cell Cycle Volume 7, Issue 7; pp. 934-939

In the paper, “The level of oncogene H-Ras correlates with tumorigenicity” by Beicheng Sun, Yun Gao, Lei Deng, Guoqiang Li, Feng Cheng and Xuehao Wang (Cell Cycle 2008; 7:934-9), the authors found that Figure 2D is incorrect. The original data found in the report is correct, and the correct figure is included here.     

Retraction: The Escherichia coli ycbQRST operon encodes fimbriae with laminin-binding and epithelial cell adherence properties in Shiga-toxigenic E. coli O157:H7

Samadder, P., Xicohtencatl-Cortes, J., Saldaña, Z., Jordan, D., Tarr, P.I., Kaper, J.B., & Girón, J.A. The Escherichia coli ycbQRST operon encodes fimbriae with laminin-binding and epithelial cell adherence properties in Shiga-toxigenic E.coli O157:H7. Environmental Microbiology, 11, 1815–1826. https://doi.org/10.1111/j.1462-2920.2009.01906.x The above article, published online 1 July 2009 on Wiley Online Library ( wileyonlinelibrary.com ), has been retracted by agreement between the authors, the journal Editor-in-Chief, Applied Microbiology International and John Wiley & Sons Ltd. The retraction has been agreed due to concerns raised by a third party regarding the appearance of Figures 2 and 7. Figure 7D appears to be digitally manipulated while Figure 7F is a duplication of Figure 2, Lane 4. The raw data were not available upon request. As a result, the data and the conclusions are considered unreliable.     

Quantitative genetic analysis of life-history traits of Caenorhabditis elegans in stressful environments

In Figure 1 of [Harvey et al (Evolutionary Biology 2008, 8:15)] the plotted data were inverted. The correct Figure is shown below. The text and statistical analyses in [Harvey et al (Evolutionary Biology 2008, 8:15)] are correct.     

Erratum to Wolfgang Benetka et al., Cell Cycle Volume 7, Issue 23; pp. 3709-3719

In the paper, "Experimental testing of predicted myristoylation targets involved in asymmetric cell division and calcium-dependent signalling" by Wolfgang Benetka, Norbert Mehlmer, Sebastian Maurer-Stroh, Michaela Sammer, Manfred Koranda, Ralph Neumüller, Jörg Betschinger, Jürgen A. Knoblich, Markus Teige and Frank Eisenhaber (Cell Cycle 2008; 7:3709-19), Figure 5 was published two times but Figure 2 was not included. Figure 2 and 5 appear correct below.     

Contribution on the diagnosis ofStaphylococcus aureus rosenbach

Возможность трансформации прогестерона, стероида ?S? (11-дезокси-17-гидроксикортикостерон), дегидроэпиандростерона и

     

Expression of Concern

“MiRNA‐218 regulates osteoclast differentiation and inflammation response in periodontitis rats through MMP9”, Cell. Microbiol. 2019;21:e12979, by Jie Guo, Xuemin Zeng, Jie Miao, Chunpeng Liu, Fulan Wei, Dongxu Liu, Zhong Zheng, Kang Ting, Chunling Wang, and Yi Liu. The Editors of Cellular Microbiology and the publisher John Wiley & Sons agree to publish an Expression of Concern regarding the above article, published online in Cellular Microbiology on November 16, 2018, in Wiley Online Library ( https://onlinelibrary.wiley.com/doi/full/10.1111/cmi.12979 ). In September 2019, the journal was contacted regarding concerns about the data presented in Figures 6 and 7 because of high level of similarities in the graphs presented in these figures. The different bars in the graphs show identical height. The standard deviation bars are also of identical length. Although one graph expresses the number of TRAP‐positive cells (Figure 6b) and the other graphs express the relative mRNA expression of different osteoclast‐related genes (Figure 6c‐g), all graphs are identical. The bars in the graphs in Figure 7 that represent 5 different osteoclast genes show the same height. Figures 6 and 7 show identical mRNA expression for a series of different genes: V‐ATPase, NFATc1, CTSK, DC‐STAMP and TRAP. In December 2019, the journal requested the authors to provide the raw data of the experiments presented in the article and for explanations of the similarities. The authors responded that the similarities were due to unintentional errors and provided Excel spread sheets containing processed data in March 2020. The data provided in the Excel sheets that were sent by the authors were analyzed and it was concluded that the calculations as shown in the Excel sheets are correct. However, the concerns raised regarding similarities in the heights of bars representing different parameters and narrow range of standard deviations presented in Figures 6–7 remained. The authors disagree with the concerns raised. In addition, the editors were concerned by manipulations of western blot images to represent single bands instead of doublets for COL1 in Figures 5 and 8 and for MMP9 in Figures 3A and C, 4C, 5A and D, and 8A. The first issue concerning COL1 bands has been addressed and corrected during the peer‐review process. The latter has been clarified after publication and following a request from the editors for the raw data of all figures in the article. In the published article, western blots of MMP‐9 in Figures 3A and C, 4C, 5A and D, and 8A show active‐MMP‐9 only and do not include pro‐MMP‐9 bands that were present in the original western blot experiments. The authors explained that on the original blots that were provided during the peer‐review process, MMP‐9 show doublets that represent pro‐MMP‐9 and active‐MMP‐9. As no significant difference was found for pro‐MMP‐9, the authors only presented single bands for active‐MMP‐9 in the publication version. The authors’ institution, Shandong University, did not respond to a request from the Publisher and the Editor‐in‐Chief to investigate whether the data arose from the originally reported experiments, are unmodified, and are suitable for publication. As a result, the journal is issuing this expression of concern to readers.     

CircHIPK3 sponges miR‐558 to suppress heparanase expression in bladder cancer cells

Correction to: EMBO Reports (2017) 18(9): 1646–1659. DOI: 10.15252/embr.201643581 ¦ Published online 9 August 2017The authors contacted the journal after being alerted to issues in the figures. The authors state that while preparing the figures, images were mislabelled leading to partial duplications in two figure panels. The authors requested to withdraw the affected panels and to replace them with correct representative images that had been generated at the time of the original experimentation. The panels listed below are therefore withdrawn and replaced. The related source data are published with this note.Figure 4DThe transwell assay image for UMUC3 cells showing invasion behaviour upon miR‐558 mimic treatment (“miR‐558”) had been incorrect. An image showing the invasion behaviour of UMUC3 cells upon depletion of circHIPK3 (“si‐circHIPK3#1”) showing the same cells as depicted in Fig 2H was erroneously used. A representative image of the correct data is now displayed in the paper.Figure 4EThe transwell assay image for UMUC3 cells showing migration behaviour upon treatment with an miR‐588 anti‐miR (“anti‐miR‐558”) had been incorrect. An image showing the migration behaviour of UMUC3 cells upon circHIPK3 overexpression (“circHIPK3”) showing the same cells as those depicted in Fig 2D was erroneously used. A representative image of the correct data is now displayed in the paper.Figure 5CThe Western blot image showing the β‐actin loading control for T24T cells had been incorrect. A representative image of the correct data is now displayed in the paper.Figure 5FThe image for UMUC3 cells showing tube formation upon treatment with a control mimic and overexpression of circHIPK3 “mimicNC+circHIPK3” had been incorrect. A representative image of the correct data is now displayed in the paper.The figure issues described above are herewith corrected. The authors state that the errors do not affect the results or conclusions of the study and apologize for any confusion these errors may have caused. Figure 4D. Original. Figure 4D. Corrected. Figure 4E. Original. Figure 4E. Corrected. Figure 5C. Original. Figure 5C. Corrected. Figure 5F. Original. Figure 5F. Corrected.      

Retracted: A proteomic approach for investigation of photosynthetic apparatus in plants

Retraction: The following article from Proteomics, “A proteomic approach for investigation of photosynthetic apparatus in plants” by C. Ciambella, P. Roepstorff, E.M. Aro and L. Zolla, published online on 28 January 2005 in the Wiley Online Library ( http://onlinelibrary.wiley.com/doi/10.1002/pmic.200401129/full ), has been retracted by agreement between the authors, the Editor‐in‐Chief and Wiley‐VCH GmbH & Co. KGaA. The retraction has been agreed due to the similarity of Figure 4 in this article and an image from an article by B. Granvogl and L.A. Eichacker which was originally submitted to Proteomics on November 1^st, 2002 and which was finally published online on 6 June 2006 in the Wiley Online Library ( http://onlinelibrary.wiley.com/doi/10.1002/pmic.200500924/full ) as Figure 1 in Proteomics, “Mapping the proteome of thylakoid membranes by de novo sequencing of intermembrane peptide domains” by B. Granvogl, V. Reisinger and L.A. Eichacker.     

Exercise‐induced α‐ketoglutaric acid stimulates muscle hypertrophy and fat loss through OXGR1‐dependent adrenal activation

The authors approached the journal to correct a mistake in the data presented in Appendix␣Fig S3D. The authors state that the mouse images in Appendix␣Fig S3D mistakenly displayed images from Fig 2F and Appendix␣Fig S1F. The images in Appendix␣Fig S3D are herewith corrected. The authors state that this change does not affect the conclusions or the statistics. The source data for these panels have been added to the original publication.The authors note that the following sentence needs to be corrected from: Appendix Figure S3D. Original. Appendix Figure S3D. Corrected. “Interestingly, several well‐established accumulation signatures of succinate, malate, hypoxanthine, and xanthine induced by endurance exercise (Lewis et␣al, 2010) were found to be decreased by endurance exercise (Figs 1D and EV1A–D)”.to“Interestingly, several well‐established accumulation signatures of succinate, malate, hypoxanthine, and xanthine induced by endurance exercise (Lewis et␣al, 2010) were found to be decreased by resistance exercise (Figs 1D and EV1A–D)”.Further, the authors requested to amend the legend of Appendix␣Fig S3R to indicate that the same sample for the iWAT group, “WT+2%AKG” treatment, is shown in Fig 3P. The corrected legend reads: “(R‐S). Representative images (R) and quantification (S) of p‐HSL DAB staining from male OXGR1OE^AG mice treated with AKG for 12 weeks (n = 6 per group). The same sample is shown as in Fig 3P ”.The authors regret these errors and any confusion they may have caused. All authors approve of this correction.     

Cover Picture: Proteomics 5/2008

In this issue of Proteomics you will find the following highlighted articles: When is a stain not a stain? When it's dyeing! [Dumb proteomics joke!] This silly riddle is actually relat­ed to a recurrent question in proteomics: when is the best time to apply detection reagents to proteins for quantitative analysis? (a) pre‐electrophoresis labeling with DIGE/Cy‐type of covalent stains, or (b) post‐electrophoresis staining with silver, Sypro Ruby or Deep Purple? Karp et al. explore the question using a bacterial extract as a typical sample, DIGE Cy labels, and Deep Purple. It gets more complex when they have to deal with the “missingness” of spots: just because a spot doesn’t show up doesn’t mean it is not there, there just may not be enough to detect. Progenesis SameSpots software was used to analyze images for missing spots. In the end, DIGE gave better sensitivity as previously reported, and fewer missing spots. Deep Purple was more competitive when analyzed with SameSpots software. Karp, N. A. et al., Proteomics 2008, 8, 948–960. Your own best enemy? If there weren’t one maverick, black sheep, rebel, outlaw, eccentric, or rotten apple in most families, a lot of novels would never have been written. Mammalian immune systems seem to have the same structure – they mostly target enemies of the body but there always seem to be a few maverick antibodies that are targeted at their own body’s antigens. Servettaz et al. take up proteomic tools to identify the targets of the anti‐self antibodies expressed by apparently healthy individuals. Using umbilical cord endothelial cells as a source of antigens, the authors found 884 spots by ­2‐­DE, and 61 ± 25 of those were recognized by serum IgGs. All 12 sera tested recognized 11 antigens derived from 6 proteins. There were 3 cytoskeletal, 2 glycolytic, and 1 disulfide isomerase protein seen. These were confirmed by immunoblotting of 2‐D gels and identification by in‐gel tryptic digestion and MALDI‐TOF MS. Servettaz, A. et al., Proteomics 2008, 8, 1000–1008. Signature in scraps from kidney growth stages You can tell a lot about the quality of a new building, residential or commercial, by what doesn’t go into it. The scraps of lumber, pieces of masonry, lengths and varieties of cables are all revealing. Lee et al. watch the final maturation of the rat urinary tract by proteomic analysis of the debris found in urine over time. Taking special care not to mix adult and neonatal urine, they examined four samples over 2 weeks after birth and one at maturity, >30 d. Using nano‐ESI‐LC‐MS/MS technology, six proteins were found in all samples, 30 were adult specific. Proteins were further characterized by large format 1‐ and 2‐DE, immunoblots, and immunofluorescent analysis of tissue sections. Days 1, 3, and 7 had 37% of proteins in common whereas days 7, 14 and >30 shared only 7.4% of proteins. Levels of fibronectin and location of E‐cadherin expression shifted during maturation. Lee, R. S. et al., Proteomics 2008, 8, 1097–1112.     

In this issue: Proteomics 5/2008

In this issue of Proteomics you will find the following highlighted articles: When is a stain not a stain? When it's dyeing! [Dumb proteomics joke!] This silly riddle is actually relat­ed to a recurrent question in proteomics: when is the best time to apply detection reagents to proteins for quantitative analysis? (a) pre‐electrophoresis labeling with DIGE/Cy‐type of covalent stains, or (b) post‐electrophoresis staining with silver, Sypro Ruby or Deep Purple? Karp et al. explore the question using a bacterial extract as a typical sample, DIGE Cy labels, and Deep Purple. It gets more complex when they have to deal with the “missingness” of spots: just because a spot doesn’t show up doesn’t mean it is not there, there just may not be enough to detect. Progenesis SameSpots software was used to analyze images for missing spots. In the end, DIGE gave better sensitivity as previously reported, and fewer missing spots. Deep Purple was more competitive when analyzed with SameSpots software. Karp, N. A. et al., Proteomics 2008, 8, 948–960. Your own best enemy? If there weren’t one maverick, black sheep, rebel, outlaw, eccentric, or rotten apple in most families, a lot of novels would never have been written. Mammalian immune systems seem to have the same structure – they mostly target enemies of the body but there always seem to be a few maverick antibodies that are targeted at their own body’s antigens. Servettaz et al. take up proteomic tools to identify the targets of the anti‐self antibodies expressed by apparently healthy individuals. Using umbilical cord endothelial cells as a source of antigens, the authors found 884 spots by ­2‐­DE, and 61 ± 25 of those were recognized by serum IgGs. All 12 sera tested recognized 11 antigens derived from 6 proteins. There were 3 cytoskeletal, 2 glycolytic, and 1 disulfide isomerase protein seen. These were confirmed by immunoblotting of 2‐D gels and identification by in‐gel tryptic digestion and MALDI‐TOF MS. Servettaz, A. et al., Proteomics 2008, 8, 1000–1008. Signature in scraps from kidney growth stages You can tell a lot about the quality of a new building, residential or commercial, by what doesn’t go into it. The scraps of lumber, pieces of masonry, lengths and varieties of cables are all revealing. Lee et al. watch the final maturation of the rat urinary tract by proteomic analysis of the debris found in urine over time. Taking special care not to mix adult and neonatal urine, they examined four samples over 2 weeks after birth and one at maturity, >30 d. Using nano‐ESI‐LC‐MS/MS technology, six proteins were found in all samples, 30 were adult specific. Proteins were further characterized by large format 1‐ and 2‐DE, immunoblots, and immunofluorescent analysis of tissue sections. Days 1, 3, and 7 had 37% of proteins in common whereas days 7, 14 and >30 shared only 7.4% of proteins. Levels of fibronectin and location of E‐cadherin expression shifted during maturation. Lee, R. S. et al., Proteomics 2008, 8, 1097–1112.     

Retraction statement: The protective effects of propofol against renal ischemia-reperfusion injury are potentiated by norisoboldine treatment via inhibition of oxidative stress pathways

The following article, published online on 31 October 2021 in Wiley Online Library ( wileyonlinelibrary.com ), has been retracted by agreement between the authors, the journal Editor in Chief, Hari Bhat, and Wiley Periodicals, LLC. Following publication, concerns were raised by authors regarding Figure 2. The retraction has been agreed because of concerns that the figures were duplicated and/or manipulated, affecting the interpretation of the data and results presented.     

In the wake of the double helix: from the green revolution to the gene revolution * Tuberosa R, Phillips RL, Gale M. eds. 2005. * Bologna: Avenue Media. {euro}25 (softback). 722 pp.

This volume isthe proceedings of an international congress held at the Universityof Bologna, Italy, 27–31 May 2003. Major sections aredevoted to the architects of the green revolution: biodiversityand germplasm     

Apparatus for simultaneous spectrophotometric and polarographic measurements

We have recently constructed a 10-mm, light path quartz cuvet which will accept a Clark oxygen electrode; it is temperature controlled and is suitable for use in a Unicam (Cambridge, England) SP 800 recording spectrophotometer. Several enquiries have prompted this publication, although such an apparatus was mentioned much earlier by Chance and Williams,¹ and has been used extensively. Figure 1a, b, c, and d and their legends provide sufficient detail for the construction of the cuvet and provision of the commercially available electrode, quartz faces, stirring motor and disk magnet. Circuit diagrams for temperature control (range 22–38°C., ± 0.2°C.) and stirrer speed control are shown in Figure 2a and b. The cuvet is shown situated in the spectrophotometer cell housing in Figure 3, and the cuvet with its associated equipment is shown in Figure 4.     

A simplified method for extracting androgens from avian egg yolks

Female birds deposit significant amounts of steroid hormones into the yolks of their eggs. Studies have demonstrated that these hormones, particularly androgens, affect nestling growth and development. In order to measure androgen concentrations in avian egg yolks, most authors follow the extraction methods outlined by Schwabl (1993. Proc. Nat. Acad. Sci. USA 90:11446–11450). We describe a simplified method for extracting androgens from avian egg yolks. Our method, which has been validated through recovery and linearity experiments, consists of a single ethanol precipitation that produces substantially higher recoveries than those reported by Schwabl (1993. Proc. Nat. Acad. Sci. USA 90:11446–11450). Zoo Biol 28:137–143, 2009. © 2008 Wiley-Liss, Inc.