PReD-Bench/PRed-Bench huggingface dataset:
SOCS3 inhibits insulin signaling in porcine primary adipocytes
Authors: Shuang-Juan Yang
Cheng-Quan Xu
Gong-She Yang
Jiang-Wei Wu
Journal: Molecular and Cellular Biochemistry (2010)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: Insulin resistance; SOCS3; porcine adipocyte; insulin signaling; obesity
Affiliations: Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi Province, People's Republic of China.

Abstract:  Insulin resistance is a major player in the pathogenesis of type II diabetes, the metabolic syndrome, and obesity. SOCS3 plays an important role in the development of insulin resistance. To investigate the role of SOCS3 in porcine adipocyte insulin signaling, we first detected the effect of insulin on SOCS3 mRNA and protein expression in porcine primary adipocytes by real-time RT-PCR and Western blotting. Then, we constructed a recombinant adenovirus encoding SOCS3 gene (Ad-SOCS3) which was used to infect differentiated porcine primary adipocytes for 3 days. The expression and phosphorylation of main insulin signaling components were detected by Western blotting. The results showed that 100 nM insulin could induce SOCS3 mRNA expression but not protein expression, and overexpression of SOCS3 decreased IRS1 protein level, insulin-stimulated IRS1 tyrosine phosphorylation, PI3K activation, and Akt phosphorylation, but increased IRS1 serine phosphorylation in porcine primary adipocytes. These results indicate that SOCS3 is an important negative regulator of insulin signaling in porcine adipocytes. Thus, SOCS3 may be a novel therapeutic target for the prevention or treatment of insulin resistance and type II diabetes. 

Retracted: No

PubPeer comments:
 Figure 5 and 6. * Red boxes: Two b-actin panels look similar if one of them is in mirror image. Figure 4. * Blue boxes: Two panels appear to show an overlap. Reported to the journal in October 2015, with a friendly reminder in 2017, but no response as of today. ![file] ,
MicroRNA-936 promotes proliferation and invasion of gastric cancer cells by down-regulating FGF2 expression and activating P13K/Akt signaling pathway
Authors: J Wang
Y Yu
W Wei
Z-F Chen
Journal: European review for medical and pharmacological sciences (2020)
Discipline: PHARMACOLOGY & TOXICOLOGY
Keywords: microRNA-936; gastric cancer; FGF2; PI3K/Akt signaling pathway; qPCR
Affiliations: Department of General Surgery, People's Hospital of Rizhao, Rizhao, China. .

Abstract:  Objective: This study was designed to investigate whether microRNA-936 can be involved in the development of gastric cancer (GCa) by down-regulating FGF2 expression and activating the phosphatidylinositol 3-kinase/protein kinase B (P13K/Akt) signaling pathway. Patients and methods: Quantitative polymerase chain reaction (qPCR) was carried out to examine microRNA-936 and FGF2 levels in GCa tissue samples and adjacent normal ones, and further in GCa cell lines. After transfection of microRNA-936 inhibitor in GCa cell lines BGC and SGC, cell invasion, and proliferation abilities were evaluated by transwell and cell counting kit-8 (CCK-8) assays, respectively. In addition, the Dual-Luciferase reporting assay was conducted to verify the binding relationship between microRNA-936 and FGF2. After simultaneous transfection of microRNA-936 inhibitor and si-FGF2 in GCa cells, we detected the expression of FGF2/P13K/Akt by performing qPCR and Western blot experiments to further verify the regulation of microRNA-936 on FGF2 and PI3K/AKT pathway. Results: QPCR detection revealed that microRNA-936 was remarkably up-regulated while FGF2 was conversely down-regulated in GCa tissue samples, indicating a negative correlation between the two. In addition, compared with normal gastric mucosal cells GES, microRNA-936 showed a significant increased expression in GCa cell lines. Meanwhile, down-regulation of microRNA-936 caused a marked reduction in invasive and proliferation ability of GCa cells. Dual-Luciferase reporting assay demonstrated a direct binding of microRNA-936 to FGF2. QPCR and Western blot showed that microRNA-936 can inhibit FGF2 expression and activate the PI3K/AKT pathway at the same time. Further studies found that silencing FGF2 induced an enhancement in cell proliferation and invasiveness, which could be reversed by simultaneous downregulation of microRNA-936. The above observations suggested that microRNA-936 may accelerate the progression of GCa by inhibiting FGF2 expression and activating the PI3K/AKT pathway. Conclusions: Overexpression of microRNA-936 can be conducive to the development of GCa, mainly through the down-regulation of FGF2 and activation of the P13K/Akt signaling pathway. 

Retracted: No

PubPeer comments:
 Figure 3E. This picture seems to be pieced together from several bands. ![file] ,
Intestinal sugar absorption is regulated by phosphorylation and turnover of protein kinase C betaII mediated by phosphatidylinositol 3-kinase- and mammalian target of rapamycin-dependent pathways
Authors: Philip A Helliwell
Martin G Rumsby
George L Kellett
Journal: Journal of Biological Chemistry (2003)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: intestinal fructose absorption; phorbol 12-myristate 13-acetate; PMA; GLUT2; protein kinase C betaII
Affiliations: Department of Biology (Area 3), University of York, York YO10 5YW, United Kingdom.

Abstract:  Stimulation of intestinal fructose absorption by phorbol 12-myristate 13-acetate (PMA) results from rapid insertion of GLUT2 into the brush-border membrane and correlates with protein kinase C (PKC) betaII activation. We have therefore investigated the role of phosphatidylinositol 3 (PI3)-kinase and mammalian target of rapamycin in the regulation of fructose absorption by PKC betaII phosphorylation. In isolated jejunal loops, stimulation of fructose absorption by PMA was inhibited by preperfusion with wortmannin or rapamycin, which blocked GLUT2 activation and insertion into the brush-border membrane. Antibodies to the last 18 and last 10 residues of the C-terminal region of PKC betaII recognized several species differentially in Western blots. Extensive cleavage of native enzyme (80/78 kDa) to a catalytic domain product of 49 kDa occurred. PMA and sugars provoked turnover and degradation of PKC betaII by dephosphorylation to a 42-kDa species, which was converted to polyubiquitylated species detected at 180 and 250+ kDa. PMA increased the level of the PKC betaII 49-kDa species, which correlates with the GLUT2 level; wortmannin and rapamycin blocked these effects of PMA. Rapamycin and wortmannin inhibited PKC betaII turnover. PI3-kinase, PDK-1, and protein kinase B were present in the brush-border membrane, where their levels were increased by PMA and blocked by the inhibitors. We conclude that GLUT2-mediated fructose absorption is regulated through PI3-kinase and mammalian target of rapamycin-dependent pathways, which control phosphorylation of PKC betaII and its substrate-induced turnover and ubiquitin-dependent degradation. These findings suggest possible mechanisms for short term control of intestinal sugar absorption by insulin and amino acids. 

Retracted: No

PubPeer comments:
 Figure 2: In red, bands seem to be the same, however, in blue bands differ. Could authors provide an explanation? ![file] ,
Enteric pathogenic bacteria and resistance gene carriage in the homeless population in Marseille, France
Authors: Tran Duc Anh Ly
Herve Tissot-Dupont
Philippe Gautret
Sekene Badiaga
Linda Hadjadj
Didier Raoult
Philippe Brouqui
Ndiaw Goumbala
Thi Loi Dao
Van Thuan Hoang
Jean-Marc Rolain
Journal: Acta Microbiologica et Immunologica Hungarica (2021)
Discipline: MICROBIOLOGY
Keywords: Escherichia coli pathotypes; Tropheryma whipplei; antibiotic resistance gene; enteric bacteria; homeless
Affiliations: 1Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France., 2IHU-Méditerranée Infection, Marseille, France., 3Aix Marseille University, MEPHI, Marseille, France., 6Pneumology Department, Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam., 5VITROME, Campus International IRD-UCAD de l'IRD, Dakar, Senegal., 4Family Medicine Department, Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam., 7Aix Marseille University, Service des urgences CHU Hôpital Nord, Marseille, France.

Abstract:  We aimed to assess the prevalence of pathogenic bacteria and resistance genes in rectal samples collected among homeless persons in Marseille, France. In February 2014 we enrolled 114 sheltered homeless adults who completed questionnaires and had rectal samples collected. Eight types of enteric bacteria and 15 antibiotic resistance genes (ARGs) were sought by real-time polymerase chain reaction (qPCR) performed directly on rectal samples. ARG-positive samples were further tested by conventional PCR and sequencing. We evidenced a 17.5% prevalence of gastrointestinal symptoms, a 9.6% prevalence of enteric pathogenic bacteria carriage, including Escherichia coli pathotypes (8.7%) and Tropheryma whipplei (0.9%). Only 2 persons carried blaCTX-M-15 resistance genes (1.8%), while other genes, including carbapenemase-encoding genes and colistin-resistance genes, (mcr-1 to mcr-6, mcr-8) were not detected. Our results suggest that sheltered homeless persons in Marseille do not have a high risk of harbouring gastrointestinal antibiotic resistant bacteria. 

Retracted: No

PubPeer comments:
 Figure 8. Much more similar than you would expect. https: imgur.com b0QE1DG ,
Melanoma-derived exosomes induce reprogramming fibroblasts into cancer-associated fibroblasts via Gm26809 delivery
Authors: Jiacai Hu
Tairan Hu
Journal: Cell Cycle (2019)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: Gm26809; Melanoma; cancer-associated fibroblasts; exosome.
Affiliations: Department of Dermatology, Renmin Hospital of Wuhan University, Wuhan, China, Department of Traditional Chinese Medicine, Renmin Hospital of Wuhan University, Wuhan, China

Abstract:  Cancer-associated fibroblasts (CAFs) are activated fibroblasts and can interact with cancer cells to promote tumor progression. The process of how tumor cells reprogram normal fibroblasts (NFs) to tumor-promoting CAFs regulated by long non-coding RNA (lncRNA) remains incompletely understood. The tumor cells-released exosomes can induce reprogramming of NFs into CAFs. This study aimed to explore the role of melanoma-derived exosomes in regulating NF-CAF transition and to clarify whether lncRNA Gm26809 was involved in this process. The results showed that the exosomes secreted by melanoma cell B16F0 induced reprogramming of fibroblast NIH/3T3 cells into CAFs, as evidenced by increased expression of CAFs markers (α-SMA and FAP) and facilitated cell migration. Mechanistically, B16F0-secreted exosome delivered Gm26809 into NIH/3T3 cells where Gm26809 mediated reprogramming of fibroblast NIH/3T3 cells into CAFs. Furthermore, the conditioned medium from the co-culture of NIH/3T3 cells and B16F0-exosomes facilitated cell proliferation and migration in a melanoma cell line (Cloundman S91), and the effect was abrogated by Gm26809 knockdown in B16F0 cells. In summary, melanoma-derived exosomes facilitate melanoma cell proliferation and migration through reprogramming fibroblasts into tumor-promoting CAFs via transferring Gm26809. 

Retracted: No

PubPeer comments:
 I am questioning the initial exosome data in this publication. The electron microscopy images for exosomes (FIgure 1) do not look like exosomes and may well be artefacts. Western blotting of CD63 always show a characteristic smear, not a clear thin band as here (Figure 1). ![file] ,
Evaluation of the role of human β-defensin 3 in modulation of immunity and inflammatory response after knee replacement
Authors: Hao Peng
Jiguang Jia
Sen Chen
Journal: Experimental and Therapeutic Medicine (2017)
Discipline: CLINICAL MEDICINE
Keywords: T lymphocyte; alkaline phosphatase; human β-defensin 3; implant-related infection; interleukin-2
Affiliations: Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China.

Abstract:  The present study investigated the value of human β-defensin 3 (HBD-3) in adjusting the immunity and inflammatory response of T lymphocytes in the body after knee replacement. Sixty-four cases of knee replacement patients were successively selected and randomly divided into the control group and the observation group each with 32 cases. Once a day, for 7 days, patients in the control group were injected with placebo saline solution in the articular cavity. Levels of Th1 and/Th2, interleukin (IL)-2 and IL-10, tumor necrosis factor (TNF)-α, toll-like receptor (TLR)-4, and alkaline phosphatase (ALP) were compared one month later, and implant infection rates were compared within 1-year follow-up. Compared with patients in the control group, the levels of Th1 and Th1/Th2 in the observation group significantly increased, yet their Th2 decreased. The levels of IL-2 and TNF-α were also observed to be significantly elevated, yet IL-10 decreased. Furthermore, their TLR-4 and ALP levels were significantly higher. Three cases of implant-related infection occurred in the control group and 1 case in the observation group. In conclusion, HBD-3 could adjust the immunity and inflammatory response of cells in the body after knee replacement, possibly playing an important role in implant-related infection. 

Retracted: No

PubPeer comments:
 Figure 1. * Green boxes: Panels A and D appear to look very similar, with some differences noted in the bottom left quadrant, and very different gating percentages. ![file] ,
Chick Embryo: A Preclinical Model for Understanding Ischemia-Reperfusion Mechanism
Authors: Avril A B Robertson
Mohsin Ali Khan
Manish Kumar
Eram Fauzia
Syed Shadab Raza
Paarth Garg
Tarun Kumar Barbhuyan
Amit Kumar Shrivastava
Journal: Frontiers in Pharmacology (2018)
Discipline: PHARMACOLOGY & TOXICOLOGY
Keywords: Doppler blood flow imaging; Hook I/R model; MCC950; NLRP3 inflammasome; autophagy
Affiliations: Laboratory for Stem Cell and Restorative Neurology, Department of Biotechnology, Era's Lucknow Medical College and Hospital, Era University, Lucknow, India., Era's Lucknow Medical College and Hospital, Era University, Lucknow, India., School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia., Department of Stem Cell Biology and Regenerative Medicine, Era University, Lucknow, India.

Abstract:  Ischemia-reperfusion (I/R)-related disorders, such as stroke, myocardial infarction, and peripheral vascular disease, are among the most frequent causes of disease and death. Tissue injury or death may result from the initial ischemic insult, primarily determined by the magnitude and duration of the interruption in blood supply and then by the subsequent reperfusion-induced damage. Various in vitro and in vivo models are currently available to study I/R mechanism in the brain and other tissues. However, thus far, no in ovo I/R model has been reported for understanding the I/R mechanisms and for faster drug screening. Here, we developed an in ovo Hook model of I/R by occluding and releasing the right vitelline artery of a chick embryo at 72 h of development. To validate the model and elucidate various underlying survival and death mechanisms, we employed imaging (Doppler blood flow imaging), biochemical, and blotting techniques and evaluated the cell death mechanism: autophagy and inflammation caused by I/R. In conclusion, the present model is useful in parallel with established in vitro and in vivo I/R models to understand the mechanisms of I/R development and its treatment. 

Retracted: No

PubPeer comments:
 It seems duplicated GAPDH blot. Arthur need to show complete picture. ![file] ,
Small molecule-directed immunotherapy against recurrent infection by Mycobacterium tuberculosis
Authors: Luc Van Kaer
Debapriya Bhattacharya
Mariama Maiga
William R Bishai
Mamoudou Maiga
Ved Prakash Dwivedi
Gobardhan Das
Journal: Journal of Biological Chemistry (2014)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Immunology; Immunotherapy; Interleukin; Mycobacterium tuberculosis; T Cell.
Affiliations: From the Laboratory Medicine and Medical Sciences, College of Health Sciences, University of Kwazulu Natal, Durban 4001, South Africa., the Center for Tuberculosis Research, Department of Medicine, The Johns Hopkins University, Baltimore, Maryland 21231-1001, and., the Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232., From the Laboratory Medicine and Medical Sciences, College of Health Sciences, University of Kwazulu Natal, Durban 4001, South Africa, .

Abstract:  Tuberculosis remains the biggest infectious threat to humanity with one-third of the population infected and 1.4 million deaths and 8.7 million new cases annually. Current tuberculosis therapy is lengthy and consists of multiple antimicrobials, which causes poor compliance and high treatment dropout, resulting in the development of drug-resistant variants of tuberculosis. Therefore, alternate methods to treat tuberculosis are urgently needed. Mycobacterium tuberculosis evades host immune responses by inducing T helper (Th)2 and regulatory T (Treg) cell responses, which diminish protective Th1 responses. Here, we show that animals (Stat-6(-/-)CD4-TGFβRIIDN mice) that are unable to generate both Th2 cells and Tregs are highly resistant to M. tuberculosis infection. Furthermore, simultaneous inhibition of these two subsets of Th cells by therapeutic compounds dramatically reduced bacterial burden in different organs. This treatment was associated with the generation of protective Th1 immune responses. As these therapeutic agents are not directed to the harbored organisms, they should avoid the risk of promoting the development of drug-resistant M. tuberculosis variants. 

Retracted: No

PubPeer comments:
 Figure 9 appears to include two images which overlap. *** ![file] ![file] , 
 In addition to the concern within the figure above, there appears to be overlap between images in two different papers. Thread for the other paper https: pubpeer.com publications A29E5F8B79A7E9164A782EA7E433B4 *** ![file] ,
MicroRNA-26a suppresses the malignant biological behaviors of papillary thyroid carcinoma by targeting ROCK1 and regulating PI3K/AKT signaling pathway
Authors: S-Y Li
Y-C Wu
Y-F Jia
Journal: European review for medical and pharmacological sciences (2019)
Discipline: PHARMACOLOGY & TOXICOLOGY
Keywords: Papillary thyroid carcinoma; MicroRNA; miR-26a; Carcinogenesis; ROCK1
Affiliations: Department of Endocrinology, The People's Hospital of Linqing, Liaocheng, P.R. China. .

Abstract:  Objective: Papillary thyroid carcinoma (PTC) is an endocrine malignancy, the morbidity of which has kept rising in recent years. MicroRNA (miRNA/miR) is emerging as a key regulator in carcinogenesis, including PTC. The current study concentrates on the biological roles and mechanisms of miR-26a in the PTC progression. Patients and methods: 51 pairs of PTC tissue samples and matched adjacent thyroid tissues were collected from PTC patients who received surgical excisions at The People's Hospital of Linqing between July 2015 and June 2018 with informed consent. Quantitative Real Time-Polymerase Chain Reaction (qRT-PCR) was performed to detect expressions of miR-26a and rho-associated coiled-coil-containing protein kinase 1 (ROCK1) mRNA in PTC tissues and cells. Functional assays, including (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) MTT assays and transwell assays were performed to determine the roles of miR-26a in the PTC progression. Western blot was used to detect expression levels of the related proteins. Results: Findings demonstrated prominently down-regulated miR-26a in PTC tissues and cells. Down-regulated miR-26a indicated malignant clinicopathologic characteristics and shorter overall survival rate of PTC patients. MTT assay and transwell assay indicated that miR-26a up-regulation significantly repressed PTC cell viability, invasion, and metastasis. Western blot analysis revealed that miR-26a exerted its anti-PTC effects via phosphatidylinositol 3-kinase/protein kinase B pathway (PI3K/AKT) and epithelial-to-mesenchymal transition (EMT). ROCK1 was a target of miR-26a in PTC cells and ROCK1 was mediated by miR-26a, as a regulatory mechanism in PTC. Conclusions: Taken together, these findings demonstrated the anti-tumor functions of miR-26a in PTC, providing novel strategies for PTC diagnosis and therapy. 

Retracted: No

PubPeer comments:
 Two bands in figure 5D appear to be the same. *** ![file] , 
  51 pairs of PTC tissue samples and matched adjacent thyroid tissues were collected from PTC patients who received surgical excisions at The Peopleu2019s Hospital of Linqing between July 2015 and June 2018 with informed consent. The paper was published in October 2019, **four-and-a-bit years** after subject recruitment began. According to Fig 1B, the authors followed their subjects survival for **five years** after recruitment. Was a time machine involved? ![file] ,
Inhibition of adenine nucleotide translocator pore function and protection against apoptosis in vivo by an HIV protease inhibitor
Authors: Gary D Bren
Jessica Lallier
Morgane Lebras
Andre Douen
Barbara N Phenix
Aurelien Deniaud
Steffany A L Bennett
Agathe Tarze
Joel G R Weaver
Mario Y Morin
Guido Kroemer
Romano T Kroemer
Bogdan Zurakowski
Catherine Brenner
Heather Hardin
Tia C Moffat
Andrew D Badley
Sheng T Hou
Li Dong
Valerie L Sim
David H Lynch
Rolf P G van Heeswijk
Susan X Jiang
Peter Wettstein
Journal: Journal of Clinical Investigation (2005)
Discipline: CLINICAL MEDICINE
Keywords: HIV protease inhibitor; nelfinavir; ritonavir; apoptosis; in vivo
Affiliations: Division of General Surgery, University of Ottawa, Ottawa, Ontario, Canada.

Abstract:  Inhibitors of HIV protease have been shown to have antiapoptotic effects in vitro, yet whether these effects are seen in vivo remains controversial. In this study, we have evaluated the impact of the HIV protease inhibitor (PI) nelfinavir, boosted with ritonavir, in models of nonviral disease associated with excessive apoptosis. In mice with Fas-induced fatal hepatitis, Staphylococcal enterotoxin B-induced shock, and middle cerebral artery occlusion-induced stroke, we demonstrate that PIs significantly reduce apoptosis and improve histology, function, and/or behavioral recovery in each of these models. Further, we demonstrate that both in vitro and in vivo, PIs block apoptosis through the preservation of mitochondrial integrity and that in vitro PIs act to prevent pore function of the adenine nucleotide translocator (ANT) subunit of the mitochondrial permeability transition pore complex. 

Retracted: No

PubPeer comments:
 Figure 6c: More similar than expected. Could authors check this issue please? ![file] ,
Transforming growth factor-β2 promotes Snail-mediated endothelial–mesenchymal transition through convergence of Smad-dependent and Smad-independent signalling
Authors: Raghu Kalluri
Scott Potenta
Damian Medici
Journal: Biochemical Journal (2011)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: EndMT; TGF-β2; signalling pathways; Smad; MEK
Affiliations: Division of Matrix Biology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA., Division of Matrix Biology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, U.S.A., Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, U.S.A., Harvard-MIT Division of Health Sciences and Technology, Boston, MA 02115, U.S.A.

Abstract:  EndMT (endothelial-mesenchymal transition) is a critical process of cardiac development and disease progression. However, little is know about the signalling mechanisms that cause endothelial cells to transform into mesenchymal cells. In the present paper we show that TGF-β2 (transforming growth factor-β2) stimulates EndMT through the Smad, MEK [MAPK (mitogen-activated protein kinase)/ERK (extracellular-signal-regulated kinase) kinase], PI3K (phosphinositide 3-kinase) and p38 MAPK signalling pathways. Inhibitors of these pathways prevent TGF-β2-induced EndMT. Furthermore, we show that all of these pathways are essential for increasing expression of the cell-adhesion-suppressing transcription factor Snail. Inhibition of Snail with siRNA (small interfering RNA) prevents TGF-β2-induced EndMT. However, overexpression of Snail is not sufficient to cause EndMT. Chemical inhibition of GSK-3β (glycogen synthase kinase-3β) allows EndMT to be induced by Snail overexpression. Expression of a mutant Snail protein that is resistant to GSK-3β-dependent inactivation also promotes EndMT. These results provide the foundation for understanding the roles of specific signalling pathways in mediating EndMT. 

Retracted: No

PubPeer comments:
 Figure 2A appears to have an overlap. *** ![file] , 
 Figures 1D and 2C appear to contain a recycled band. *** ![file] ,
The CD40L promoter contains nuclear factor of activated T cells-binding motifs which require AP-1 binding for activation of transcription
Authors: A V Tsytsykova
E N Tsitsikov
R S Geha
Journal: Journal of Biological Chemistry (1996)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: NF-AT; CD40 ligand promoter; Electrophoretic mobility shift assays; Cyclosporin A; AP-1 proteins
Affiliations: Division of Immunology, Children's Hospital and Departments of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.

Abstract:  Four nuclear factor of activated T cells (NF-AT) binding motifs were found in the murine CD40 ligand promoter. Electrophoretic mobility shift assays using 18-base pair (bp) long oligonucleotides corresponding to the proximal site and nuclear extracts from activated T cells revealed two complexes which were inhibited by cyclosporin A and contained NF-ATc and NF-ATp. Neither complex contained AP-1 proteins. Multimers of the 18-bp oligonucleotides were not active in transient transfection assays using luciferase reporter gene constructs. In contrast, a 30-bp long oligonucleotide bound AP-1 proteins in addition to NF-AT proteins and its multimers strongly induced luciferase gene expression. These results suggested that NF-AT proteins play an important role in the expression of the CD40L gene and that their transcriptional activity requires AP-1 binding. 

Retracted: No

PubPeer comments:
 Figure 1. Much more similar than expected. ![file] , 
 Figure 1A continued. NM-4* unstimulated and IL2-kappaB lanes much more similar than expected. ![file] ,
Anti-hsp60 antibody responses based on Helicobacter pylori in patients with multiple sclerosis: (ir)Relevance to disease pathogenesis
Authors: Dimitrios P Bogdanos
Efthymios Dardiotis
Christos Liaskos
Wolfgang Meyer
Emmanouela Marou
Georgios Hadjigeorgiou
Georgios Efthymiou
Alexandros Daponte
Vana Tsimourtou
Thomas Scheper
Lazaros I Sakkas
Journal: Journal of Neuroimmunology (2016)
Discipline: NEUROSCIENCE & BEHAVIOR
Keywords: Antibody; Autoimmunity; Heat shock protein; Molecular mimicry.
Affiliations: Cellular Immunotherapy & Molecular Immunodiagnostics, Biomedical Section, Centre for Research and Technology-Hellas (CERTH), Institute for Research and Technology-Thessaly (IRETETH), 41222 Larissa, Greece; Department of Neurology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 40500 Larissa, Greece; Department of Rheumatology, University General Hospital, Faculty of Medicine, School of Health Sciences, University of Thessaly, Viopolis, 41110 Larissa, Greece., Department of Neurology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 40500 Larissa, Greece., Cellular Immunotherapy & Molecular Immunodiagnostics, Biomedical Section, Centre for Research and Technology-Hellas (CERTH), Institute for Research and Technology-Thessaly (IRETETH), 41222 Larissa, Greece; Department of Rheumatology, University General Hospital, Faculty of Medicine, School of Health Sciences, University of Thessaly, Viopolis, 41110 Larissa, Greece., Institute of Immunology, EUROIMMUN, 23560 Lubeck, Germany., Department of Obstetrics and Gyneocology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 40500 Larissa, Greece., Department of Rheumatology, University General Hospital, Faculty of Medicine, School of Health Sciences, University of Thessaly, Viopolis, 41110 Larissa, Greece., Cellular Immunotherapy & Molecular Immunodiagnostics, Biomedical Section, Centre for Research and Technology-Hellas (CERTH), Institute for Research and Technology-Thessaly (IRETETH), 41222 Larissa, Greece; Department of Rheumatology, University General Hospital, Faculty of Medicine, School of Health Sciences, University of Thessaly, Viopolis, 41110 Larissa, Greece. Electronic address: .

Abstract:  In view of published data suggesting that Helicobacter pylori (Hp) is a trigger of multiple sclerosis (MS), we assessed anti-heat shock protein 60 (hsp60)Hp antibody reactivity in 129 MS patients and 48 demograpically-matched healthy controls (HCs). Anti-Hp antibodies by ELISA were more elevated in MS than HCs but did not differ between different MS phenotypes. All anti-Hp-positive MS sera, irrespectively of their clinical phenotype, were anti-anti-hsp60 positive. Anti-hsp60 Hp seropositivity correlated with age at disease onset. In conclusion, anti-hsp60 Hp antibodies are present in all anti-Hp positive MS patients, and their relevance to disease pathogenesis is questionable. 

Retracted: No

PubPeer comments:
 Figure 2. Could the authors please check? Lanes 6 and 7 appear to look very similar. ![file] ,
Structural characterization of a novel Chlamydia pneumoniae type III secretion-associated protein, Cpn0803
Authors: Jerry W Slootstra
Murray S Junop
David C Bulir
Seiji Sugiman-Marangos
Tiffany L Leighton
Rob C Clayden
James B Mahony
Chris B Stone
Journal: PLoS ONE (2012)
Discipline: Multidisciplinary
Keywords: Type III secretion; gram-negative bacteria; Chlamydia; C. trachomatis; C. pneumoniae
Affiliations: M. G. DeGroote Institute for Infectious Disease Research, Faculty of Health Sciences and the Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada.

Abstract:  Type III secretion (T3S) is an essential virulence factor used by gram-negative pathogenic bacteria to deliver effector proteins into the host cell to establish and maintain an intracellular infection. Chlamydia is known to use T3S to facilitate invasion of host cells but many proteins in the system remain uncharacterized. The C. trachomatis protein CT584 has previously been implicated in T3S. Thus, we analyzed the CT584 ortholog in C. pneumoniae (Cpn0803) and found that it associates with known T3S proteins including the needle-filament protein (CdsF), the ATPase (CdsN), and the C-ring protein (CdsQ). Using membrane lipid strips, Cpn0803 interacted with phosphatidic acid and phosphatidylinositol, suggesting that Cpn0803 may associate with host cells. Crystallographic analysis revealed a unique structure of Cpn0803 with a hydrophobic pocket buried within the dimerization interface that may be important for binding small molecules. Also, the binding domains on Cpn0803 for CdsN, CdsQ, and CdsF were identified using Pepscan epitope mapping. Collectively, these data suggest that Cpn0803 plays a role in T3S. 

Retracted: No

PubPeer comments:
 Figure 6 appears to suffer from several repeated images which are labeled differently. A similar concern was previously flagged by Dr. Bik on [another paper] which shares the same first and last author. It seems as if the first author may have left academia. In fact, the figure I have posted here appears to be drawn from Figure 5.6 in the [first authoru2019s PhD thesis] , which makes one wonder if these concerns were identified by others previously. *** False color ![file] *** Original ![file] *** ![file] ![file] , 
 Figure 9. * Red boxes: Two panels, that according to the labels represent different samples and different antibodies, appear to look more similar than expected. Image contrast a bit enhanced to bring out the background details. ![file] , 
 Hi yes, lead author here. The journal contacted me about this several years ago- I sent in all the original gels, which corroborated the results. It seems that some of the blank negative control lanes were mixed up and duplicated at times. I do apologize for this mistake. That being said, the images do represent the true results and the lanes showing positive findings are accurate. Hope this helps and I apologize. ,
Mutation in the glucose-6-phosphate dehydrogenase gene leads to inactivation of Ku DNA end binding during oxidative stress
Authors: Steven W Tuttle
John E Biaglow
Iraimoudi S Ayene
Stanley K Mauldin
Cameron J Koch
Susan F Jenkins
Thomas D Stamato
Journal: Journal of Biological Chemistry (2002)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Glucose-6-phosphate dehydrogenase; G6PD deficiency; NADPH/NADP(+) ratio; oxidative stress; DNA repair

Abstract:  Glucose-6-phosphate dehydrogenase (G6PD), the rate-limiting enzyme of the oxidative pentose phosphate cycle, regulates the NADPH/NADP(+) ratio in eukaryotic cells. G6PD deficiency is one of the most common mutations in humans and is known to cause health problems for hundreds of millions worldwide. Although it is known that decreased G6PD functionality can result in increased susceptibility to oxidative stress, the molecular targets of this stress are not known. Using a Chinese hamster ovary G6PD-null mutant, we previously demonstrated that exposure to a thiol-specific oxidant, hydroxyethyldisulfide, caused enhanced radiation sensitivity and an inability to repair DNA double strand breaks. We now demonstrate a molecular mechanism for these observations: the direct inhibition of DNA end binding activity of the Ku heterodimer, a DNA repair protein, by oxidation of its cysteine residues. Inhibition of Ku DNA end binding was found to be reversible by treatment of the nuclear extract with dithiothreitol, suggesting that the homeostatic regulation of reduced cysteine residues in Ku is a critical function of G6PD and the oxidative pentose cycle. In summary, we have discovered a new layer of DNA damage repair, that of the functional maintenance of repair proteins themselves. In view of the rapidly escalating number of roles ascribed to Ku, these results may have widespread ramifications. 

Retracted: No

PubPeer comments:
 Figure 6. much more similar than you would expect. https: imgur.com D8a1ynu ,
Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter
Authors: Graziella Penot
Michael R Hübner
Martin Kos
Frank Gannon
Heike Brand
George Reid
Raphaël Métivier
Journal: Cell (2003)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: Transcriptional activation; Basal transcription machinery; Chromatin structure; Posttranslational modifications; Histone tails
Affiliations: European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany. 

Abstract:  Transcriptional activation of a gene involves an orchestrated recruitment of components of the basal transcription machinery and intermediate factors, concomitant with an alteration in local chromatin structure generated by posttranslational modifications of histone tails and nucleosome remodeling. We provide here a comprehensive picture of events resulting in transcriptional activation of a gene, through evaluating the estrogen receptor-alpha (NR3A1) target pS2 gene promoter in MCF-7 cells. This description integrates chromatin remodeling with a kinetic evaluation of cyclical networks of association of 46 transcription factors with the promoter, as determined by chromatin immunoprecipitation assays. We define the concept of a "transcriptional clock" that directs and achieves the sequential and combinatorial assembly of a transcriptionally productive complex on a promoter. Furthermore, the unanticipated findings of key roles for histone deacetylases and nucleosome-remodeling complexes in limiting transcription implies that transcriptional activation is a cyclical process that requires both activating and repressive epigenetic processes. 

Retracted: No

PubPeer comments:
 Multiple possible gel image duplications throughout the manuscript. Non-uniform background of Figure 2A revealed upon adjusting brightness contrast settings (unclear what this means). ![file] ![file] ![file] ,
A common biosynthetic pathway governs the dimerization and secretion of inhibin and related transforming growth factor beta (TGFbeta) ligands
Authors: Craig A Harrison
Kelly L Walton
Yogeshwar Makanji
Karen L Chan
David M Robertson
Matthew C Wilce
Journal: Journal of Biological Chemistry (2009)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: transforming growth factor beta superfamily; ligands; non-covalent interactions; prodomain; mature domain
Affiliations: Prince Henry's Institute of Medical Research, 246 Clayton Road, Clayton, Victoria 3168, Australia.

Abstract:  The assembly and secretion of transforming growth factor beta superfamily ligands is dependent upon non-covalent interactions between their pro- and mature domains. Despite the importance of this interaction, little is known regarding the underlying regulatory mechanisms. In this study, the binding interface between the pro- and mature domains of the inhibin alpha-subunit was characterized using in vitro mutagenesis. Three hydrophobic residues near the N terminus of the prodomain (Leu(30), Phe(37), Leu(41)) were identified that, when mutated to alanine, disrupted heterodimer assembly and secretion. It is postulated that these residues mediate dimerization by interacting non-covalently with hydrophobic residues (Phe(271), Ile(280), Pro(283), Leu(338), and Val(340)) on the outer convex surface of the mature alpha-subunit. Homology modeling indicated that these mature residues are located at the interface between two beta-sheets of the alpha-subunit and that their side chains form a hydrophobic packing core. Mutation of these residues likely disturbs the conformation of this region, thereby disrupting non-covalent interactions with the prodomain. A similar hydrophobic interface was identified spanning the pro- and mature domains of the inhibin beta(A)-subunit. Mutation of key residues, including Ile(62), Leu(66), Phe(329), and Pro(341), across this interface was disruptive for the production of both inhibin A and activin A. In addition, mutation of Ile(62) and Leu(66) in the beta(A)-propeptide reduced its ability to bind, or inhibit the activity of, activin A. Conservation of the identified hydrophobic motifs in the pro- and mature domains of other transforming growth factor beta superfamily ligands suggests that we have identified a common biosynthetic pathway governing dimer assembly. 

Retracted: No

PubPeer comments:
 ![file] ,
Surface modified liposomes for nasal delivery of DNA vaccine
Authors: Amit K Goyal
Suresh P Vyas
Prem N Gupta
Kapil Khatri
Abhinav Mehta
Neeraj Mishra
Journal: Vaccine (2008)
Discipline: IMMUNOLOGY
Keywords: glycol chitosan; liposomes; nasal vaccine delivery; humoral mucosal immune response; cellular immune response
Affiliations: Drug Delivery Research Laboratory, Department of Pharmaceutical Sciences, Dr. Harisingh Gour Vishwavidyalaya, Sagar 470003, M.P., India.

Abstract:  The aim of the present work was to investigate the potential utility of glycol chitosan coated liposomes as nasal vaccine delivery vehicle for eliciting viral specific humoral mucosal and cellular immune responses. Plasmid pRc/CMV-HBs(S) encapsulated liposomes were prepared by dehydration-rehydration method and subsequently coated with glycol chitosan by simple incubation method. Liposomes were then characterized for their size, surface charge, entrapment efficiency, and ability to protect encapsulated DNA against nuclease digestion and for their mucoadhesiveness. The liposomes were then administered to mice in order to study their feasibility as nasal vaccine carriers. The developed liposomes possessed +9.8 mV zeta potential and an average vesicle size less than 1 microm and entrapment efficiency of approximately 53%. Following intranasal administration, glycol chitosan coated liposomes elicited humoral mucosal and cellular immune responses that were significant as compared to naked DNA justifying the potential advantage of mucosal vaccination in the production of local antibodies at the sites where pathogens enters the body. 

Retracted: No

PubPeer comments:
 Fig 4(C):  Fluorescence micrographs of the nasal tissue of rats excised following administration of ... (C) FITC-BSA encapsulated in **glycol chitosan coated liposomes**. ![file] Later to reappear Fig 5(C D) of [Tiwari et al (2009)] :  Fluorescent microscopy images showing the uptake of FITC-BSA loaded different liposomal formulations by nasal mucosal surface after intranasal administration. (A) soluble FITC-BSA (control); (B) CL **(C) [gel core] (D) LIGS**.  ![] ,
A deacetylase-deficient SIRT1 variant opposes full-length SIRT1 in regulating tumor suppressor p53 and governs expression of cancer-related genes
Authors: John R P Knight
Shafiq U Ahmed
Simon J Allison
Jo Milner
Jack R Ford
Zahid H Shah
Journal: Molecular and Cellular Biology (2012)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: SIRT1; splice variant; deacetylase; CUGBP2; p53
Affiliations: P53 Research Unit, Department of Biology, University of York, York, United Kingdom.

Abstract:  SIRT1 is an NAD-dependent deacetylase and epigenetic regulator essential for normal mammalian development and homeostasis. Here we describe a human SIRT1 splice variant, designated SIRT1-Δ2/9, in which the deacetylase coding sequence is lost due to splicing between exons 2 and 9. This work aimed to determine if SIRT1-Δ2/9 is a novel functional product of the SIRT1 gene. Endogenous SIRT1-Δ2/9 protein was identified in human cell lysate by immunoblotting and splice variant-specific RNA interference (RNAi). SIRT1-Δ2/9 mRNA is bound by CUGBP2, which downregulates its translation. Using pulldown assays, we demonstrate that SIRT1-Δ2/9 binds p53 protein. SIRT1-Δ2/9 maintains basal p53 protein levels and supports p53 function in response to DNA damage, as evidenced by RNAi-mediated depletion of SIRT1-Δ2/9 prior to damage. In turn, basal p53 downregulates SIRT1-Δ2/9 RNA levels, while stress-activated p53 eliminates SIRT1-Δ2/9. Loss of wild-type (wt) p53 has been correlated with overexpression of SIRT1-Δ2/9 in a range of human cancers. Exogenous SIRT1-Δ2/9 protein associates with specific promoters in chromatin and can regulate cancer-related gene expression, as evidenced by chromatin immunoprecipitation analysis and RNAi/genomic array data. SIRT1 is of major therapeutic importance, and potential therapeutic drugs are screened against SIRT1 deacetylase activity. Our discovery of SIRT1-Δ2/9 identifies a new, deacetylase-independent therapeutic target for SIRT1-related diseases, including cancer. 

Retracted: No

PubPeer comments:
 July 2017 Correction: https: mcb.asm.org content 37 16 e00238-17 It reads:  *Fig. 2C: The GAPDH loading control in the right panel was an inadvertent duplication of the middle panel. The corrected image appears below. This change does not affect any of the results or conclusions of our study.* Here is the original Figure 2C, with red boxes marking the duplication: ![file] This paper was part of a structured search for image duplications in Molecular and Cellular Biology paper, which was published here: https: mcb.asm.org content 38 20 e00309-18.long ,
RNAi-mediated silencing of Atp6i and Atp6i haploinsufficiency prevents both bone loss and inflammation in a mouse model of periodontal disease
Authors: Byron Tucker
Liang Hao
Wei Chen
Guochun Zhu
Philip Stashenko
Lijie Zhang
Hongliang Ci
Junqing Ma
Shengmei Feng
Lin Wang
Yi-Ping Li
Hongbing Jiang
Journal: PloS one (2013)
Discipline: Multidisciplinary
Keywords: Periodontal disease; oral bacterial infection; bone resorption; tooth loss; rheumatoid arthritis
Affiliations: Department of Pathology, University of Alabama at Birmingham, Alabama, USA.

Abstract:  Periodontal disease affects about 80% of adults in America, and is characterized by oral bacterial infection-induced gingival inflammation, oral bone resorption, and tooth loss. Periodontitis is also associated with other diseases such as rheumatoid arthritis, diabetes, and heart disease. Although many efforts have been made to develop effective therapies for this disease, none have been very effective and there is still an urgent need for better treatments and preventative strategies. Herein we explored for the first time the possibility that adeno-associated virus (AAV)-mediated RNAi knockdown could be used to treat periodontal disease with improved efficacy. For this purpose, we used AAV-mediated RNAi knockdown of Atp6i/TIRC7 gene expression to target bone resorption and gingival inflammation simultaneously. Mice were infected with the oral pathogen Porphyromonas gingivalis W50 (P. gingivalis) in the maxillary periodontium to induce periodontitis. We found that Atp6i depletion impaired extracellular acidification and osteoclast-mediated bone resorption. Furthermore, local injection of AAV-shRNA-Atp6i/TIRC7 into the periodontal tissues in vivo protected mice from P. gingivalis infection-stimulated bone resorption by &gt;85% and decreased the T-cell number in periodontal tissues. Notably, AAV-mediated Atp6i/TIRC7 knockdown also reduced the expression of osteoclast marker genes and inflammation-induced cytokine genes. Atp6i(+/-) mice with haploinsufficiency were similarly protected from P. gingivalis infection-stimulated bone loss and gingival inflammation. This suggests that AAV-shRNA-Atp6i/TIRC7 therapeutic treatment may significantly improve the health of millions who suffer from P. gingivalis-mediated periodontal disease. 

Retracted: No

PubPeer comments:
 Figure 1C. * Red ellipses: Two panels appear to show an overlap. ![file] ,