Caspase‐12 and endoplasmic reticulum stress mediate neurotoxicity of pathological prion protein

Correction to: The EMBO Journal (2003) 22: 5435–5445. DOI 10.1093/emboj/cdg537 ¦ Published online 15 October 2003 Figure 7A. Original.Source data are available online for this figure. Figure 7A. Corrected. Source data are available online for this figure. The journal was informed of potential image aberrations in Fig 7A. The authors claim that the loading control in the originally published figure corresponded to a replicate experiment as many Western blots were run in parallel with the same samples to measure levels of ER stress markers. The control panel in Fig 7A is herewith retracted and replaced with the author‐supplied loading control of the experiment shown in Fig 7A.The journal noted that Fig 3 and Appendix Figure 3 were duplicated and that the legend to Appendix Figure 3 did not match the displayed figure. The authors recovered the quantification data for Appendix Figure 3, but not the scanned blots. The authors state that they no longer have access to the laboratory books or primary data and that they cannot definitively say which image was analysed. The authors withdraw Appendix Figure 3.The authors also acknowledge that there are undeclared splice sites in Fig 3, but that they could not locate the source data.The source data for Fig 7A are available with this corrigendum notice.The authors apologize for these errors and agree with this corrigendum; no response could be obtained from MR‐C.     

LncRNA‐PAGBC acts as a microRNA sponge and promotes gallbladder tumorigenesis

Correction to: EMBO Reports (2017) 18: 1837–1853. DOI: 10.15252/embr.201744147 ¦ Published online 8 September 2017The authors contacted the journal after becoming aware of duplications between Figs 3 and 6 and identified additional errors in the process of reanalysing their data. Figure 3B: The authors state that the representative images of the migration and invasion assays of EH‐GB1 cells in the Lv‐Control groups had been incorrectly selected from images belonging to the control groups. The figure is herewith corrected. Figure 6B: The authors state that they had incorrectly displayed representative images for the vector group of SGC‐996, and the vector and PAGBC‐mut (miR‐133b) groups of EH‐GB1. The figure is herewith corrected.In addition, the authors are adding a demarcating line to the PCR product of the 5′‐RACE in Fig EV2B, separating the marker lane, which had been inadvertently omitted. Source data for Fig EV2 were published in the original paper.The source data and replicate data for Figs 3B and 6B are published with this corrigendum.The authors apologize for this oversight and any confusion it may have caused and declare that the conclusions of the study are not affected by these changes.     

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.      

Inactive variants of death receptor p75NTR reduce Alzheimer’s neuropathology by interfering with APP internalization

Correction to: The EMBO Journal (2021) 40: e104450. DOI 10.15252/embj.2020104450 | Published online 1 December 2020The authors correct Figure 6A of this paper. During the revision process, images from p75^NTR‐expressing mice were inadvertently used in place of p75^NTR knock‐out neurons. The corrected figure, showing lack of p75^NTR labeling in knock‐out neurons, along with their corresponding internalized APP, is shown here. This error only concerns the images used to illustrate the quantitative data. It does not affect the analysis itself nor the conclusions derived from it. The authors apologize for this oversight and agree with this corrigendum; no response could be obtained from KT. Figure 6A. Original Figure 6A. Corrected     

Posttranscriptional regulation of colonic epithelial repair by RNA binding protein IMP1/IGF2BP1

Correction to: EMBO Reports (2019) 20: e47074. DOI 10.15252/embr.201847074 | Published online 6 May 2019The authors noticed that the control and disease labels had been inverted in their data analysis resulting in publication of incorrect data in Figure 1C. The corrected figure is displayed below. This change affects the conclusions as detailed below. The authors apologize for this error and any confusion it may have caused.In the legend of 1C, change from, “Differential gene expression analysis of pediatric ileal CD patient samples (n = 180) shows increased (> 4‐fold) IMP1 expression as compared to non‐inflammatory bowel disease (IBD) pediatric samples (n = 43)”.Open in a separate windowFigure 1CCorrected Open in a separate windowFigure 1COriginal To, "Differential gene expression analysis of pediatric ileal CD patient samples (n = 180) shows decreased (> 4‐fold) IMP1 expression as compared to non‐inflammatory bowel disease (IBD) pediatric samples (n = 43)”.In abstract, change from, “Here, we report increased IMP1 expression in patients with Crohn''s disease and ulcerative colitis”.To, “Here, we report increased IMP1 expression in adult patients with Crohn''s disease and ulcerative colitis”.In results, change from, “Consistent with these findings, analysis of published the Pediatric RISK Stratification Study (RISK) cohort of RNA‐sequencing data 38 from pediatric patients with Crohn''s disease (CD) patients revealed that IMP1 is upregulated significantly compared to control patients and that this effect is specific to IMP1 (i.e., other distinct isoforms, IMP2 and IMP3, are not changed; Fig 1C)”.To, “Contrary to our findings in colon tissue from adults, analysis of published RNA‐sequencing data from the Pediatric RISK Stratification Study (RISK) cohort of ileal tissue from children with Crohn’s disease (CD) 38 revealed that IMP1 is downregulated significantly compared to control patients in the RISK cohort and that this effect is specific to IMP1 (i.e., other distinct isoforms, IMP2 and IMP3, are not changed; Fig 1C)”.In discussion, change from, “Indeed, we report that IMP1 is upregulated in patients with Crohn''s disease and ulcerative colitis and that mice with Imp1 loss exhibit enhanced repair following DSS‐mediated damage”.To “Indeed, we report that IMP1 is upregulated in adult patients with Crohn''s disease and ulcerative colitis and that mice with Imp1 loss exhibit enhanced repair following DSS‐mediated damage”.     

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.     

Molecular basis of cross‐species ACE2 interactions with SARS‐CoV‐2‐like viruses of pangolin origin

Correction to: The EMBO Journal (2021) 40: e107786. DOI 10.15252/embj.2021107786 | Published online 8 June 2021The authors would like to add three references to the paper: Starr et al and Zahradník et al also reported that the Q498H or Q498R mutation has enhanced binding affinity to ACE2; and Liu et al reported on the binding of bat coronavirus to ACE2.Starr et al and Zahradník et al have now been cited in the Discussion section, and the following sentence has been corrected from:“According to our data, the SARS‐CoV‐2 RBD with Q498H increases the binding strength to hACE2 by 5‐fold, suggesting the Q498H mutant is more ready to interact with human receptor than the wildtype and highlighting the necessity for more strict control of virus and virus‐infected animals”.to“Here, according to our data and two recently published papers, the SARS‐CoV‐2 RBD with Q498H or Q498R increases the binding strength to hACE2 (Starr et al, 2020; Zahradník et al, 2021), suggesting the mutant with Q498H or Q498R is more ready to interact with human receptor than the wild type and highlighting the necessity for more strict control of virus and virus‐infected animals”.The Liu et al citation has been added to the following sentence:“In another paper published by our group recently, RaTG13 RBD was found to bind to hACE2 with much lower binding affinity than SARS‐CoV‐2 though RaTG13 displays the highest whole‐genome sequence identity (96.2%) with the SARS‐CoV‐2 (Liu et al, 2021)”.Additionally, the authors have added the GISAID accession IDs to the sequence names of the SARS‐CoV‐2 in two human samples (Discussion section). To make identification unambiguous, the sequence names have been updated from “SA‐lsf‐27 and SA‐lsf‐37” to “GISAID accession ID: EPI_ISL_672581 and EPI_ISL_672589”.Lastly, the authors declare in the Materials and Methods section that all experiments employed SARS‐CoV‐2 pseudovirus in cultured cells. These experiments were performed in a BSL‐2‐level laboratory and approved by Science and Technology Conditions Platform Office, Institute of Microbiology, Chinese Academy of Sciences.These changes are herewith incorporated into the paper.     

Deconstructing PML‐induced premature senescence

The authors contacted the journal after being alerted to errors in Fig 6C. The authors provided the source data, which show that the panel had been assembled and presented incorrectly. Fig 6C is herewith corrected. The authors note that the corrected panel shows similar results, although less pronounced for the induction of p53 acetylation by PMLIV, consistent with what had been reported previously in PML+/+ MEFs (Fig 3C in Pearson et al, 2000). PMLIV‐induced increase in p53 acetylation is also shown in human fibroblasts (Fig 5B). The authors state that this correction does not affect the message of Fig 6, nor does it impact the overall conclusions of the article.The authors apologize for this oversight and any confusion it may have caused. The source data are available with this notice together with the corrected figure. Figure 6C. Original. Figure 6C. Corrected.. Source data are available online for this figure      

A New Extracellular β-Galactosidase Producing Kluyveromyces sp. PCH397 from Yak Milk and Its Applications for Lactose Hydrolysis and Prebiotics Synthesis

β-Galactosidase is a crucial glycoside hydrolase enzyme with potential applications in the dairy, food, and pharmaceutical industries. The enzyme is produced in the intracellular environment by bacteria and yeast. The present study reports yeast Kluyveromyces sp. PCH397 isolated from yak milk, which has displayed extracellular β-galactosidase activity in cell-free supernatant through the growth phase. To investigate further, cell counting and methylene blue staining of culture collected at different growth stages were performed and suggested for possible autolysis or cell lysis, thereby releasing enzymes into the extracellular medium. The maximum enzyme production (9.94 ± 2.53U/ml) was achieved at 37 °C in a modified deMan, Rogosa, and Sharpe (MRS) medium supplemented with lactose (1.5%) as a carbon source. The enzyme showed activity at a wide temperature range (4–50 °C), maximum at 50 °C in neutral pH (7.0). In addition to the hydrolysis of lactose (5.0%), crude β-galactosidase also synthesized vital prebiotics (i.e., lactulose and galacto-oligosaccharides (GOS)). Additionally, β-fructofuranosidase (FFase) activity in the culture supernatant ensued the synthesis of a significant prebiotic, fructo-oligosaccharides (FOS). Hence, the unique features such as extracellular enzymes production, efficient lactose hydrolysis, and broad temperature functionality by yeast isolate PCH397 are of industrial relevance. In conclusion, the present study unrevealed for the first time, extracellular production of β-galactosidase from a new yeast source and its applications in milk lactose hydrolysis and synthesis of valuable prebiotics of industrial importance.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12088-021-00955-1.Keyword: β-Galactosidase, Lactulose, Galacto-oligosaccharides, Fructo-oligosaccharides, Milk-microbes

β-Galactosidase (EC 3.2.1.23) hydrolyzes the glycosidic bond in β-galactosides and finds applications in the food industry [1, 2]. The trans-glycosylation property of β-galactosidase (β-gal) is widely used to produce various galactosylated products and prebiotics such as GOS and lactulose [3–7]. The β-gal enzyme is produced intracellularly by many bacteria and yeast, a major constraint for industrial production [1, 8]. Therefore, extracellular β-gal producing bacteria/yeast are of huge relevance. Hence, the present work revealed an efficient extracellular β-gal producing microbe from dairy products of the Indian Himalaya and evaluated its applications in lactose hydrolysis and prebiotics’ synthesis.In this study, twenty milk and four curd samples were collected from the Lahaul and Pangi valleys of Himachal Pradesh, India. The samples were plated on MRS and Elliker agar medium (Himedia, India) for 2–7 days at 28 °C and 37 °C until visible microbial growth. Morphologically distinct isolates were screened for β-gal activity using X-Gal and IPTG plate assay [6, 9]. The positive isolates were screened for β-gal production in liquid MRS medium. The β-gal activity was expressed as U/mg dcw (dry cell weight) for whole cells and U/ml for cell-free supernatant [10, 11]. Yeast isolate PCH397 showing the highest and extracellular enzymatic activity was selected. The culture and reaction conditions for maximum β-gal activity were optimized. FFase activity of whole cells and cell-free supernatant was estimated as described by Lincoln and More [12].The cell-free supernatant (β-gal) was employed for applications in lactose hydrolysis and prebiotic synthesis. The enzyme was incubated with lactose solution (5%, w/v) at 37 °C for lactose hydrolysis followed by thin layer chromatography (TLC) [13] analysis and quantification using the ImageJ program (http://rsbweb.nih.gov/ij/). Further, the cell-free supernatant was incubated with milk at 4 °C for milk lactose hydrolysis. Samples were withdrawn at different time intervals and analyzed for residual lactose concentration using ultra-high performance liquid chromatography-quadrupole-time of flight-ion mobility mass spectrometry (UHPLC-Q-TOF-IMS) [14]. Prebiotic production was carried out by mixing an equal volume of the enzyme with a sugar solution i.e., lactose (40%, w/v) for GOS, and lactose (20%, w/v) + fructose (20%, w/v) for lactulose and FOS production, respectively at 50 °C for 24 h [6]. Samples were analyzed by TLC for GOS, UHPLC-Q-TOF-IMS for FOS and lactulose synthesis.The study resulted in the isolation of 203 morphologically distinct microbes, 62 of which were tested positive for β-gal. Based on quantitative screening, eight isolates showing maximum β-gal activity were selected and examined for the intracellular and extracellular enzymatic activities (Table S1). Yeast isolate PCH397 exhibited maximum extracellular β-gal activity (9.94 ± 2.53 U/ml) along with FFase activity (0.59 ± 0.155) after 48 h of incubation. Isolate PCH397 was identified as Kluyveromyces marxianus by its morphological and molecular characterization (Fig. S1). Phylogenetic tree based on ITS DNA sequence showed similarity (99.63%) with Kluyveromyces marxianus CBS712. To the best of our knowledge, the genus Kluyveromyces has not been reported earlier for extracellular β-gal production. In the past, efforts were made to produce β-gal extracellularly through permeabilization or incorporation of signal peptide to β-gal gene in a fusion construct [15, 16]. The isolate PCH397 was selected due to its generally regarded as safe (GRAS) status and the novel feature of extracellular enzyme production.Highest β-gal activity in the extracellular environment was observed when PCH397 was grown in MRS medium supplemented with 1.5% (w/v) lactose as a substrate and incubated at 37 °C for 48 h (Fig. S2). PCH397 produced extracellular β-gal at lower lactose concentration (1.5%) as compared to various Kluyveromyces spp. [15] where 3% lactose has been used in the growth medium for intracellular β-gal production. Further, whether the extracellular enzyme activity is due to the secretion or cell lysis, the CFU count and cell viability were checked by the methylene blue test. The decreased cell count in the late stationary phase for live cells (Fig. S3) and increased number of methylene blue stained cells indicated cell death (Fig S4). These results suggested that cell lysis in the late stationary phase leads to the secretion of enzymes in extracellular medium. The extracellular production of enzyme would lead to a lower production costs of the enzyme.Cell-free supernatant showed the highest β-gal activity at pH 7.0 in 10 mM sodium phosphate buffer at 50 °C in 5 min (Fig S2). The β-gal enzyme from the current finding holds promise in the sweet whey and milk lactose hydrolysis [1] due to its neutral pH optima. Also, β-gal, which is functional at high temperatures, is used in the synthesis of oligosaccharides [1, 3]. High temperature increases the reaction rate as well as lactose solubility, thus, facilitating transgalactosylation reactions [17]. The β-gal activity (9 U/ml) in cell-free supernatant of PCH397 completely hydrolyzed 5.0% of lactose within 8 h at 37 °C (Fig. 1a, S5a). In a recent study, 5.0% lactose was also hydrolyzed by purified β-gal (5 U/ml) of Paenibacillus barengoltzii CAU904 within 8 h at 40 °C [13]. Under refrigerated conditions (4 °C), the cell free supernatant hydrolyzed ~ 50% milk lactose within 36 h and ~ 80% in 72 h (Fig. 1b, S5b). Since β-gal of PCH397 is active at 4 °C, the enzyme could be utilized to hydrolyze lactose in dairy products under refrigerated conditions. Lactose-free milk products or low-lactose milk products are important dietary constituents for lactose intolerant individuals and deliver essential nutrients to combat nutritional deficiencies [18]. Even with commercially purified enzymes, 100% milk-lactose hydrolysis could not be achieved at a low temperature [19]. However, the crude enzyme from the present investigation can efficiently hydrolyze milk lactose at ambient and refrigerated conditions, reducing the cost associated with enzyme purification. Additionally, the source of enzyme is Kluyveromyces sp. which has GRAS status, therefore, can be used in food applications.Open in a separate windowFig. 1Lactose hydrolysis by crude β-gal of PCH397. a Relative quantification of the hydrolysed products from lactose (5%, w/v) at 37 °C for 24 h. b Relative decrease in lactose concentration (%) at refrigerated conditions obtained by UHPLC-QTOF-IMSFurther, the enzyme was evaluated for its ability to catalyze transgalactosylation reactions at 50 °C. The crude enzyme was incubated with different substrate mixture viz. lactose and fructose. After 8 h of incubation, 50% of lactose was hydrolyzed into glucose, galactose, and GOS (Fig. S6a). Maximum GOS production was achieved after 12 h (Fig. 2a). The purified β-gal from Paenibacillus barengoltzii synthesized GOS from 350 g/L of lactose within 4 h [13]. Though GOS synthesis was faster in comparison to the current study, it is to be noted that we used a crude enzyme mixture instead of a purified enzyme. The crude enzyme has also shown FFase activity (Table S1), and was used for the synthesis of FOS from lactose and fructose mixture. UHPLC-Q-TOF-IMS analysis confirmed the formation of FOS (Fig. 2b). Multiple peaks were observed in the sample containing lactulose, one of which was identical with the peak of lactulose standard (Fig. 2c) as confirmed by HPAEC-PAD (Fig. S6b). The lactulose formation was maximum at 20 h of incubation (Fig. S6c).Open in a separate windowFig. 2Hydrolysis and transgalactosylation of lactose by crude enzyme from PCH397 having β-gal and FFase activity. a Relative quantification of the hydrolyzed and transgalactosylated products. UHPLC-QTOF-IMS detection of prebiotics b FOS and c lactulose with their respective standardIt is the first report of simultaneous co-synthesis of multiple prebiotics i.e., GOS, FOS, and lactulose using a yeast strain. Similar reports for GOS and FOS synthesis have been attempted by enzymatic means from fungal sources in the past [6]. The synthesis of multiple prebiotics is very advantageous. Numerous studies have shown that blended consumption of multiple prebiotics including GOS and FOS has many health benefits [20–24]. The combination of GOS, FOS, and lactulose can be of considerable importance for their prebiotic applications. In conclusion, our findings revealed a yeast source for the cost-effective production of β-galactosidase and a strategy for co-synthesis of valuable prebiotics, which is not reported in the past. The utilization of a yeast source with GRAS status for lactose hydrolysis and co-synthesis of prebiotics promises various health benefits and commercial relevance.     

Structural basis of transport and inhibition of the Plasmodium falciparum transporter PfFNT

In “Structural basis of transport and inhibition of the Plasmodium falciparum transporter PfFNT” by Lyu et al (2021), the authors depict the inhibitor MMV007839 in its hemiketal form in Fig 3A and F, Fig 4C, and Appendix Figs S10A, B and S13. We note that Golldack et al (2017) reported that the linear vinylogous acid tautomer of MMV007839 constitutes the binding and inhibitory entity of PfFNT. The authors are currently obtaining higher resolution cryo‐EM structural data of MMV007839‐bound PfFNT to ascertain which of the interconvertible isoforms is bound and the paper will be updated accordingly.     

Xanthomonas hortorum – beyond gardens: Current taxonomy,genomics, and virulence repertoires

TaxonomyBacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Lysobacterales (earlier synonym of Xanthomonadales); Family Lysobacteraceae (earlier synonym of Xanthomonadaceae); Genus Xanthomonas; Species X. hortorum; Pathovars: pv. carotae, pv. vitians, pv. hederae, pv. pelargonii, pv. taraxaci, pv. cynarae, and pv. gardneri.Host range Xanthomonas hortorum affects agricultural crops, and horticultural and wild plants. Tomato, carrot, artichoke, lettuce, pelargonium, ivy, and dandelion were originally described as the main natural hosts of the seven separate pathovars. Artificial inoculation experiments also revealed other hosts. The natural and experimental host ranges are expected to be broader than initially assumed. Additionally, several strains, yet to be assigned to a pathovar within X. hortorum, cause diseases on several other plant species such as peony, sweet wormwood, lavender, and oak‐leaf hydrangea.Epidemiology and control X. hortorum pathovars are mainly disseminated by infected seeds (e.g., X. hortorum pvs carotae and vitians) or cuttings (e.g., X. hortorum pv. pelargonii) and can be further dispersed by wind and rain, or mechanically transferred during planting and cultivation. Global trade of plants, seeds, and other propagating material constitutes a major pathway for their introduction and spread into new geographical areas. The propagules of some pathovars (e.g., X. horturum pv. pelargonii) are spread by insect vectors, while those of others can survive in crop residues and soils, and overwinter until the following growing season (e.g., X. hortorum pvs vitians and carotae). Control measures against X. hortorum pathovars are varied and include exclusion strategies (i.e., by using certification programmes and quarantine regulations) to multiple agricultural practices such as the application of phytosanitary products. Copper‐based compounds against X. hortorum are used, but the emergence of copper‐tolerant strains represents a major threat for their effective management. With the current lack of efficient chemical or biological disease management strategies, host resistance appears promising, but is not without challenges. The intrastrain genetic variability within the same pathovar poses a challenge for breeding cultivars with durable resistance.Useful websites https://gd.eppo.int/taxon/XANTGA, https://gd.eppo.int/taxon/XANTCR, https://gd.eppo.int/taxon/XANTPE, https://www.euroxanth.eu, http://www.xanthomonas.org, http://www.xanthomonas.org/dokuwiki     

PDBsum1 : A standalone program for generating PDBsum analyses

PDBsum1 is a standalone set of programs to perform the same structural analyses as provided by the PDBsum web server (https://www.ebi.ac.uk/pdbsum). The server has pages for every entry in the Protein Data Bank (PDB) and can also process user‐uploaded PDB files, returning a password‐protected set of pages that are retained for around 3 months. The standalone version described here allows for in‐house processing and indefinite retention of the results. All data files and images are pre‐generated, rather than on‐the‐fly as in the web version, so can be easily accessed. The program runs on Linux, Windows, and mac operating systems and is freely available for academic use at https://www.ebi.ac.uk/thornton-srv/software/PDBsum1.     

Cytosolic GDH1 degradation restricts protein synthesis to sustain tumor cell survival following amino acid deprivation

Correction to: The EMBO Journal (2021) 40: e107480. DOI 10.15252/embj.2020107480 ¦ Published online 6 July 2021The authorship of this research paper is herewith corrected to indicate that Jialiang Shao, Tiezhu Shi, Hua Yu, and Yufeng Ding are all equal co‐first authors.     

An alternative miRISC targets a cancer‐associated coding sequence mutation in FOXL2

The authors note that P values presented in the original Fig 1A and Appendix Fig S1A were not assessed using a proper statistical analysis method. In contrast to the initially employed two‐group t‐test, a one‐sample one‐tailed t‐test is appropriate here, as the basic null hypothesis is that the proportion of MT FOXL2 mRNA in each AGCT patient is lower than WT {H ₀: WT(%) > MT(%) }. New p values are presented in the corrected Fig 1A and Appendix Fig S1A, which are P < 0.00001 and P < 0.05, respectively. These revised P values did not affect the conclusion drawn.     

Experts in science communication: A shift from neutral encyclopedia to equal participant in dialogue

Even if the predominant model of science communication with the public is now based on dialogue, many experts still adhere to the outdated deficit model of informing the public. Subject Categories: Genetics, Gene Therapy & Genetic Disease, S&S: History & Philosophy of Science, S&S: Ethics

During the past decades, public communication of science has undergone profound changes: from policy‐driven to policy‐informing, from promoting science to interpreting science, and from dissemination to interaction (Burgess, 2014). These shifts in communication paradigms have an impact on what is expected from scientists who engage in public communication: they should be seen as fellow citizens rather than experts whose task is to increase scientific literacy of the lay public. Many scientists engage in science communication, because they see this as their responsibility toward society (Loroño‐Leturiondo & Davies, 2018). Yet, a significant proportion of researchers still “view public engagement as an activity of talking to rather than with the public” (Hamlyn et al, 2015). The highly criticized “deficit model” that sees the role of experts as educating the public to mitigate skepticism still persists (Simis et al, 2016; Suldovsky, 2016).Indeed, a survey we conducted among experts in training seems to corroborate the persistence of the deficit model even among younger scientists. Based on these results and our own experience with organizing public dialogues about human germline gene editing (Box 1), we discuss the implications of this outdated science communication model and an alternative model of public engagement, that aims to align science with the needs and values of the public.Box 1

The DNA‐dialogue project

The Dutch DNA‐dialogue project invited citizens to discuss and form opinions about human germline gene editing. During 2019 and 2020, this project organized twenty‐seven dialogues with professionals, such as embryologists and midwives, and various lay audiences. Different scenarios of a world in 2039 (https://www.rathenau.nl/en/making‐perfect‐lives/discussing‐modification‐heritable‐dna‐embryos) served as the starting point. Participants expressed their initial reactions to these scenarios with emotion‐cards and thereby explored the values they themselves and other participants deemed important as they elaborated further. Starting each dialogue in this way provides a context that enables everyone to participate in dialogue about complex topics such as human germline gene editing and demonstrates that scientific knowledge should not be a prerequisite to participate.An important example of “different” relevant knowledge surfaced during a dialogue with children between 8 and 12 years in the Sophia Children’s Hospital in Rotterdam (Fig 1). Most adults in the DNA‐dialogues accepted human germline gene modification for severe genetic diseases, as they wished the best possible care and outcome for their children. The children at Sophia, however, stated that they would find it terrible if their parents had altered something about them before they had been born; their parents would not even have known them. Some children went so far to say they would no longer be themselves without their genetic condition, and that their condition had also given them experiences they would rather not have missed.Open in a separate windowFigure 1 Children participating in a DNA‐dialogue meeting. Photographed by Levien Willemse.