PReD-Bench/PRed-Bench huggingface dataset:
Elicitation of efficient, protective immune responses by using DNA vaccines against tuberculosis
Authors: V D Ramanathan
Anil K Tyagi
Ramandeep Singh
Aparna Khera
H Shakila
Neeraj Dhar
C N Parmasivan
Vivek Rao
P R Narayanan
Journal: Vaccine (2005)
Discipline: IMMUNOLOGY
Keywords: DNA vaccination; humoral immune response; cellular immune response; mycobacterial antigens; ESAT-6
Affiliations: Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.

Abstract:  DNA vaccination is an effective method for elicitation of strong humoral as well as cellular immune responses. DNA vaccines expressing mycobacterial antigens ESAT-6 (Rv3875), alpha-crystallin (Rv2031c) and superoxide dismutase A (Rv3846) were evaluated for their immune responses in Balb/c mice and protective efficacy in guinea pigs. Immunization of mice with the DNA vaccines expressing superoxide dismutase A and alpha-crystallin resulted in markedly higher levels of IFN-gamma as compared to the levels of IL-10. The DNA vaccine expressing ESAT-6 elicited a mixed Th1/Th2 response. Immunization of guinea pigs with these DNA vaccines and subsequent challenge of animals with Mycobacterium tuberculosis H(37)Rv, showed that DNA vaccine expressing superoxide dismutase imparted the maximum protection as observed by a 50 and 10 folds reduction in bacillary load in spleens and lungs, respectively, in comparison to immunization with vector control. 

Retracted: No

PubPeer comments:
 ![file] Figure 5 : The normal section, which is supposed to be lung, was reused from a previous study by the authors (Singh et al., 2003, Mol. Microbiol) where the section is labeled as liver tissue (and looks like so). , 
 Thank you for bringing this to our attention. In this figure, instead of the panel of lung tissue to show normal tissue histology, inadvertently, the panel of liver tissue was added (marked normal in the figure) during the final assembly of the figure. The focus of this study was to evaluate DNA vaccines expressing mycobacterial antigens ESAT-6 (Rv3875) or alpha-crystallin (Rv2031c) or superoxide dismutase A (Rv3846) for their immune responses in Balb c mice and their ability to impart protection in guinea pigs. The sections of lungs from guinea pigs immunized with various DNA vaccines followed by challenge with M. tuberculosis were subjected to histopathological analysis to determine the extent of tissue damage and cellular infiltration in granulomas. The comparisons were made between tissues from guinea pigs immunized with either DNA vaccines or control vector. The lung tissues from guinea pigs immunized with BCG was also used for comparison. The lung tissue from uninfected and unvaccinated animal was supposed to be included as a reference for normal tissue histology. Its inclusion exclusion, however, does not change the scientific conclusions of the study in any way. We are looking for the complete data to get in touch with the Journal and do the needful to address this matter. ,
Artemether combined with shRNA interference of vascular cell adhesion molecule-1 significantly inhibited the malignant biological behavior of human glioma cells
Authors: Yi-Long Yao
Yi-Xue Xue
Yun-Hui Liu
Ying-Bin Wang
Ping Wang
Bo Yu
Zhen Li
Yi Hu
Journal: PLoS ONE (2013)
Discipline: Multidisciplinary
Keywords: Artemether; VCAM-1; Glioma; Migration; Invasion
Affiliations: Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, People's Republic of China.

Abstract:  Artemether is the derivative extracted from Chinese traditional herb and originally used for malaria. Artemether also has potential therapeutic effects against tumors. Vascular cell adhesion molecule-1 (VCAM-1) is an important cell surface adhesion molecule associated with malignancy of gliomas. In this work, we investigated the role and mechanism of artemether combined with shRNA interference of VCAM-1 (shRNA-VCAM-1) on the migration, invasion and apoptosis of glioma cells. U87 human glioma cells were treated with artemether at various concentrations and shRNA interfering technology was employed to silence the expression of VCAM-1. Cell viability, migration, invasiveness and apoptosis were assessed with MTT, wound healing, Transwell and Annexin V-FITC/PI staining. The expression of matrix metalloproteinase-2 (MMP-2), matrix metalloproteinase-9 (MMP-9) and phosphorylated Akt (p-Akt) was checked by Western blot assay. Results showed that artemether and shRNA-VCAM-1 not only significantly inhibited the migration, invasiveness and expression of MMP-2/9 and p-Akt, but also promoted the apoptosis of U87 cells. Combined treatment of both displayed the maximum inhibitory effects on the malignant biological behavior of glioma cells. Our work revealed the potential therapeutic effects of artemether and antiVCAM-1 in the treatments of gliomas. 

Retracted: No

PubPeer comments:
 Figure 9A. * Orange boxes: the MMP-2 and b-Actin panel appear to look very similar. This was reported to the journal in October 2015. ![file] ,
C4b-binding protein and factor H compensate for the loss of membrane-bound complement inhibitors to protect apoptotic cells against excessive complement attack
Authors: Kyra A Gelderman
Anders A Bengtsson
Leendert A Trouw
Gunnar Sturfelt
Björn Dahlbäck
Anna M Blom
Journal: Journal of Biological Chemistry (2007)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Apoptotic cells; complement regulation; fluid phase inhibitors; C4b-binding protein; factor H
Affiliations: Department of Laboratory Medicine, University Hospital Malmö, 5-20502 Malmö, Sweden.

Abstract:  Apoptotic cells have been reported to down-regulate membrane-bound complement regulatory proteins (m-C-Reg) and to activate complement. Nonetheless, most apoptotic cells do not undergo complement-mediated lysis. Therefore, we hypothesized that fluid phase complement inhibitors would bind to apoptotic cells and compensate functionally for the loss of m-C-Reg. We observed that m-C-Reg are down-regulated rapidly upon apoptosis but that complement activation follows only after a gap of several hours. Coinciding with, but independent from, complement activation, fluid phase complement inhibitors C4b-binding protein (C4BP) and factor H (fH) bind to the cells. C4BP and fH do not entirely prevent complement activation but strongly limit C3 and C9 deposition. Late apoptotic cells, present in blood of healthy controls and systemic lupus erythematosus patients, are also positive for C4BP and fH. Upon culture, the percentage of late apoptotic cells increases, paralleled by increased C4BP binding. C4BP binds to dead cells mainly via phosphatidylserine, whereas fH binds via multiple interactions with CRP playing no major role for binding of C4BP or fH. In conclusion, during late apoptosis, cells acquire fluid phase complement inhibitors that compensate for the down-regulation of m-C-Reg and protect against excessive complement activation and lysis. 

Retracted: No

PubPeer comments:
 ![file] , 
 Thank you for alerting us about the mistake. When preparing the figure 1A in the Illustrator software, the dot plot for apoptotic cells 2 hours was copied in twice while the dot plot for apoptotic cells 4 hours was missing. Since the differences between these panels were minute we have unfortunately not noticed the mistake. We have now reached out to JBC to inform them about the mistake and provided the journal with the correct figure. JBC has now accepted the correction and I will post here the link to it when it appears on-line. , 
 2020 correction. https: www.jbc.org content 295 27 9263.short There was an error in Fig. 1A. The forward and side scatter plot for 2-h apoptotic cells was inadvertently duplicated for 4-h apoptotic cells. This error has now been corrected and does not affect the results or conclusions of this work. ,
Male brain processing of the body odor of ovulating women compared to that of pregnant women
Authors: Christina Regenbogen
Catharina Kammann
Natalia Chechko
Ute Habel
Susanne Stickel
Journal: NeuroImage (2021)
Discipline: NEUROSCIENCE & BEHAVIOR
Keywords: Body odor; Fertility cues; Olfaction; Ovulation; Pregnancy
Affiliations: Department of Psychiatry, Psychotherapy and Psychosomatics, Medical Faculty, Uniklinik RWTH Aachen, Pauwelsstrasse 30, 52074 Aachen, Germany; Institute of Neuroscience and Medicine: JARA-Institute Brain Structure Function Relationship (INM 10), Research Center Jülich, Wilhelm-Johne Strasse, 52425 Jülich, Germany. Electronic address: ., Department of Psychiatry, Psychotherapy and Psychosomatics, Medical Faculty, Uniklinik RWTH Aachen, Pauwelsstrasse 30, 52074 Aachen, Germany; Institute of Neuroscience and Medicine: JARA-Institute Brain Structure Function Relationship (INM 10), Research Center Jülich, Wilhelm-Johne Strasse, 52425 Jülich, Germany; Department of Clinical Neuroscience, Karolinska Institutet, Tomtebodavägen 18A, 171 77 Stockholm, Sweden., Department of Psychiatry, Psychotherapy and Psychosomatics, Medical Faculty, Uniklinik RWTH Aachen, Pauwelsstrasse 30, 52074 Aachen, Germany; Faculty of Psychology and Neuroscience, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, the Netherlands.

Abstract:  Female chemical signals underlie the advertising of sexual receptivity and fertility. Whether the body odor of a pregnant woman also has a signaling function with respect to male behavior is yet to be conclusively established. This study examines how the body odors of ovulating and pregnant women differentially affect the behavior of heterosexual men. Body odor samples were collected from 5 pregnant women and 5 matched controls during ovulation. In a double-blind functional magnetic resonance imaging design, 18 heterosexual men were exposed to female body odors during ovulation (OV) and pregnancy (PRG) while being required to indicate the attractiveness of concurrently presented female portrait images. The participants were also required to indicate whether they assumed a depicted woman was pregnant. While neither OV nor PRG altered the perceived attractiveness of a presented face, the men tended to identify the women as pregnant while exposed to a PRG body odor. On the neural level, OV activated a network of the frontotemporal and limbic regions, while PRG activated the superior medial frontal gyrus. The results suggest that the detection of sexual availability activates the male brain regions associated with face processing and reward/motivation, whereas sensing pregnancy activates a region responsible for empathy and prosocial behavior. Thus, the female body odor during pregnancy likely helps foster circumstances conducive to the future care of offspring while the body odor advertising sexual availability promotes mating behavior. The brains of heterosexual men may be capable of unconsciously discriminating between these two types of olfactory stimuli. 

Retracted: No

PubPeer comments:
 undeclared gel slice sites in Fig.4 ![file] ,
Oleanolic acid suppresses the proliferation of lung carcinoma cells by miR-122/Cyclin G1/MEF2D axis
Authors: Daotang Li
Ming Liu
Xiaoming Zhao
Journal: Molecular and Cellular Biochemistry (2015)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: Oleanolic acid; cell cycle progression; lung carcinoma; miR-122; proliferation
Affiliations: Department of Thoracic Surgery, Shandong Cancer Hospital and Institute, 440 Jiyan Road, Jinan, 250117, Shandong, People's Republic of China.

Abstract:  Oleanolic acid (OA) is a natural compound from plants with anti-tumor activities. However, the mechanism of the inhibitory effect of OA on cell cycle progression has not been completely explored. We employed several lung carcinoma cell lines to investigate the cell cycle-related molecular pathway affected by OA. The data revealed that OA suppressed the proliferation of lung cancer cells in both dose- and time-dependent manners, along with an increase in miR-122 abundance. The suppression of miR-122 abolished the effect of OA on lung cancer cells. CCNG1 and MEF2D, two putative miR-122 targets, were found to be downregulated by OA treatment. Restoring their expression counteracted the effect of OA on lung carcinoma cells. OA was further shown to induce the expression of miR-122-regulating transcriptional factors in lung cancer cells. Collectively, OA induced cell cycle arrest in lung cancer cells through miR-122/Cyclin G1/MEF2D pathway. This finding may contribute to the understanding of the molecular mechanism of OA's anti-tumor activity. 

Retracted: No

PubPeer comments:
 Fig 6 A,B.  A549 cells were treated with OA at 15, 30, or 60 lg ml-1 for 48 h (a), or at 30 lg ml-1 for 24, 48, or 72 h . ![file] Other manifestations of the loading control from 6A (here beta-tubulin) include Fig 6b from [Hong et al (2015)] : ![] *[left]* Fig 5a of [Peng et al (2016)] . *[right]* Fig 2a from [Song et al (2016)] . ![] Other manifestations of the loading control from 6B include *[left]* Fig 5E. from [Zhang, Zhang Li (2016)] .  MEF2D protein was examined by immunoblotting in A549 and H460 cells under such treatments . *[right]* Fig 4B from Hong et al (2015).  Western blot assay was conducted to confirm the above results . ![] UPDATE: Another sighting. Fig 2C from [Cao et al (2015)] .  Cardiac myxoma cells were transfected with MEF2D siRNA or control (50 nM). Twenty-four hours later, MEF2A, MEF2C and MEF2D proteins were determined by immunoblot analysis. ![file] ,
Optimization and standardization of the culturomics technique for human microbiome exploration
Authors: Niokhor Dione
Issa Isaac Ngom
Mamadou Lamine Tall
Sara Bellali
Ami Diakite
Grégory Dubourg
Jean-Christophe Lagier
Didier Raoult
Camille Valles
Pamela Afouda
Journal: Scientific Reports (2020)
Discipline: Multidisciplinary
Keywords: Culturomics; high-throughput culture approach; metagenomics; microbiota; bacterial gut repertoire
Affiliations: Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France., IHU Méditerranée Infection, Marseille, France., Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France. ., IHU Méditerranée Infection, Marseille, France. .

Abstract:  Culturomics is a high-throughput culture approach that has dramatically contributed to the recent renewal of culture. While metagenomics enabled substantial advances in exploring the microbiota, culturomics significantly expanded our knowledge regarding the bacterial gut repertoire through the discovery and the description of hundreds of new taxa. While this approach relies on the variation of culture conditions and media, we have tested so far more than 300 conditions since the beginning of culturomics studies. In this context, we aimed herein to identify the most profitable conditions for optimizing culturomics approach. For this purpose, we have analysed a set of 58 culturomics conditions that were previously applied to 8 faecal specimens, enabling the isolation of 497 bacterial species. As a result, we were able to reduce the number of conditions used to isolate these 497 of more than a half (i.e. to 25 culture conditions). We have also established a list of the 16 conditions that allowed to capture 98% of the total number of species previously isolated. These data constitute a methodological starting point for culture-based microbiota studies by improving the culturomics workflow without any loss of captured bacterial diversity. 

Retracted: No

PubPeer comments:
 Retracted 26 August 2020: https: doi.org 10.1098 rsbl.2020.0588 Following publication of the article by Costa-Pereira Pruitt [1], the journal was made aware of potential problems with the associated raw data collected by Pruitt J. An investigation into the data detected duplicated values and as such, results drawn from these data cannot be considered reliable and the journal has decided to retract the article accordingly. , 
 Retracted: https: royalsocietypublishing.org doi full 10.1098 rsbl.2020.0588?af=R ,
Repression of the long noncoding RNA-LET by histone deacetylase 3 contributes to hypoxia-mediated metastasis
Authors: Fu Yang
Xi-song Huo
Wei-ping Zhou
Shu-han Sun
Fang Wang
Ling Zhang
Sheng-xian Yuan
Journal: Molecular Cell (2013)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: lncRNAs; dysregulated; tumors; molecular mechanisms; lncRNA-LET
Affiliations: Department of Medical Genetics, Second Military Medical University, Shanghai, 200433, China.

Abstract:  Recently, long noncoding RNAs (lncRNAs) were found to be dysregulated in a variety of tumors. However, it remains unknown how and through what molecular mechanisms the expression of lncRNAs is controlled. In this study, we found that the lncRNA Low Expression in Tumor (lncRNA-LET) was generally downregulated in hepatocellular carcinomas, colorectal cancers, and squamous-cell lung carcinomas. We demonstrated that hypoxia-induced histone deacetylase 3 repressed lncRNA-LET by reducing the histone acetylation-mediated modulation of the lncRNA-LET promoter region. Interestingly, the downregulation of lncRNA-LET was found to be a key step in the stabilization of nuclear factor 90 protein, which leads to hypoxia-induced cancer cell invasion. Moreover, the relationship among hypoxia, histone acetylation disorder, low lncRNA-LET expression level, and metastasis was found in clinical hepatocellular carcinoma samples. These results advance our understanding of the role of lncRNA-LET as a regulator of hypoxia signaling and offer new avenues for therapeutic intervention against cancer progression. 

Retracted: No

PubPeer comments:
 ![file] NOS2: Lanes 3, 5, 6, 7 look unexpectedly similar. Also NOS2 lanes 2 and 8 appear similar. Plus the NOS1 and NOS3 bands look similar after adjusting brightness contrast. Could authors check this issue, please? , 
 Dear Scopula Virgulata, Thank you for bringing this critical issue to my attention. This experiment and figure were generated by collaborators and I have no access to the original (raw) data. Therefore, I cannot properly answer your inquire. I m not involved with this research group anymore, but I trust Dr Fernandes will contact the coauthors responsible for the western-blot result. Sincerely, Tatiana Domitrovic , 
 The Editors of FEMS Yeast Research are retracting this article due to significant irregularities with Figure 2. Following claims of image manipulation by a reader in December 2021, the journal investigated the matter with the authors in accordance with guidelines from the Committee on Publication Ethics. The editors have ultimately determined retraction is warranted because the figure is invalid and the results and conclusions drawn from it are no longer reliable. The authors agreed with the decision to retract the paper. https: academic.oup.com femsyr article 22 1 foac011 6548907 ,
Effect of miR-196a inhibition on esophageal cancer growth in vitro
Authors: Minghua Bai
Xiao Sun
Yiping Dong
Congya Zhou
Jinlu Ma
Suxia Han
Journal: Anti-Cancer Drugs (2020)
Discipline: PHARMACOLOGY & TOXICOLOGY
Keywords: Esophageal cancer; miR-196a; nuclear factor-κB; PKC; sotrastaurin
Affiliations: Department of Oncology, the 1st Affiliated Hospital, Xi'an Jiaotong University., Department of Oncology, the 2nd Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China.

Abstract:  Esophageal cancer has recent shown a higher incidence but lower 5-year survival rate after normal clinical treatment in China. The aim of this study was to observe whether the inhibition of miR-196a affects esophageal cancer cell growth by modulating the nuclear factor-κB target gene and to detect the possible cooperative therapeutic effects on esophageal cancer by knocking down miR-196a expression combined with the specific inhibitor of nuclear factor-κB target genes. Thus, anti-miR-196a or sotrastaurin, a protein kinase C (PKC) inhibitor, were used to alter PKC expression. We found that miR-196a knockdown or PKC inhibition by sotrastaurin changed PKC expression which then reduced esophageal cancer cell proliferation and downregulated proliferating cell nuclear antigen expression via the classical B-cell receptor-PKC nuclear factor-κB pathway but not the alternative pathway; in addition, miR-196a inhibition can increase the caspase level and induce esophageal cancer cell apoptosis. Our current results provided the evidence that miR-196a was related to the classical nuclear factor-κB pathway, and these new findings proved the potential therapeutic effect of miR-196a in targeted therapy for clinical esophageal cancer patients. 

Retracted: No

PubPeer comments:
 Fig. 2g and Fig. 4d contain two WB bands which look much more similar than expected. ![file] , 
 Thanks for your comments. After rechecking the original data carefully, we found that the wrong u00df-actin image was used in the manuscript preparation. We apologized for this mistake although the u00df-actin level would not change our current experimental results and conclusions, and the following correction step will be started to contact the journal editor immediately. Best wish ,
Facile synthesis and characterizations of antibacterial and antioxidant of chitosan monoterpene nanoparticles and their applications in preserving minced meat
Authors: Mohamed E I Badawy
Samar M S Shawir
Tesby M R Lotfy
Journal: International Journal of Biological Macromolecules (2020)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Chitosan nanoparticles; Meat preservative; Monoterpene.
Affiliations: Department of Pesticide Chemistry and Technology, Faculty of Agriculture, El-Shatby, Alexandria University, 21545 Alexandria, Egypt. Electronic address: ., Home Economics Department, Faculty of Specific Education, Alexandria University, Alexandria, Egypt.

Abstract:  Chitosan nanoparticles loaded monoterpenes (ChMNPs) were prepared for preservation of minced meat from oxidative changes and growth of microorganisms. Four monoterpenes (limonene, linalool, menthol and thymol) were used to synthesis of four different types of ChMNPs. The physicochemical characteristics of nanoparticles were analyzed using Scanning electron microscopy (SEM) and Zeta potential. SEM showed that the nanoparticles were nearly uniformly shape and size and the zeta potential values ranged between 0.0346 and -0.1690 mV. In vitro antimicrobial activity of Ch, monoterpenes (M) and ChMNPs against Gram (-) bacteria Escherichia coli (ATCC 8739) and Salmonella typhimurium (ATCC 1402) was analyzed using serial dilution test. E. coli was more susceptible than S. typhimurium to these products. ChMNPs exhibited good in vivo antimicrobial and antioxidant property for the minced meat samples during refrigerated storage. Verification of testing hypothesis was performed by assessing a DPPH radical scavenging activity, peroxide value and E. coli reduction of experimental nanoparticles. Significant effects of ChMNPs were observed at 1000 and 2500 mg/kg on the total number of E. coli in meat samples during storage time. The results indicate that ChMNPs can be used to preserve food as antimicrobial agents and to extend shelf life. 

Retracted: No

PubPeer comments:
 In Table 3, the SD values 1.44 and 2.78 are repeated surprisingly many times. I am also wondering what is presented in the scanning electron microscopy picture presented in Scheme 1. ![file] ,
LncRNA TTN-AS1 promotes migration, invasion, and epithelial mesenchymal transition of lung adenocarcinoma via sponging miR-142-5p to regulate CDK5
Authors: Jiali Wang
Lihua Liu
Yunlong Jia
Xuexiao Wang
Wei Lv
Tianxu Liu
Yuqing Duan
Mengjie Wang
Journal: Cell death & disease (2019)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: lncRNA; TTN-AS1; lung adenocarcinoma; TNM stage; lymph node metastasis
Affiliations: Department of Tumor Immunotherapy, Fourth Hospital of Hebei Medical University and Hebei Cancer Institute, Shijiazhuang, 050035, Hebei, China., Department of Tumor Immunotherapy, Fourth Hospital of Hebei Medical University and Hebei Cancer Institute, Shijiazhuang, 050035, Hebei, China. .

Abstract:  Emerging evidence suggests that long noncoding RNA (lncRNA) plays pivotal roles in regulating various biological process in human cancers. Titin-antisense RNA1 (TTN-AS1) has been regarded as a tumor promoting lncRNA in numerous cancers. However, the clinical significance and biological function of TTN-AS1 in lung adenocarcinoma (LUAD) remain unclear. In the present study, we revealed that the expression of TTN-AS1 was upregulated in LUAD tissues and cell lines. High TTN-AS1 expression was associated with TNM stage and lymph node metastasis of LUAD patients. In addition, high expression of TTN-AS1 was correlated with poor postoperative prognosis of LUAD patients. Knockdown of TTN-AS1 significantly inhibited the growth, proliferation, migration, and invasion ability of LUAD cells in vitro. Then, by using bioinformation analysis and luciferase reporter experiment, we identified that TTN-AS1 could function as a competing endogenous RNA (ceRNA) by sponging miR-142-5p to regulate the expression of cyclin-dependent kinase 5 (CDK5) in LUAD. Since CDK5 is a key regulator in the process of epithelial mesenchymal transition (EMT), we detected the expression of EMT-related proteins, consequently, EMT was suppressed by knockdown of TTN-AS1 while this phenomenon was rescued by miR-142-5p inhibitor. Taken above, our study revealed that TTN-AS1 played an important role in LUAD progression. TTN-AS1/miR-142-5p/CDK5 regulatory axis may serve as a novel therapeutic target in the treatment of LUAD. 

Retracted: No

PubPeer comments:
 In Figure 2 and 5, four cases of data duplication were detected. Microsgraphs have been duplicated and presented as something else, within Figure 2 and 5 and across the figures. ![file] ,
A plant proton-pumping inorganic pyrophosphatase functionally complements the vacuolar ATPase transport activity and confers bafilomycin resistance in yeast
Authors: Agustín Hernández
José R Pérez-Castiñeira
Aurelio Serrano
Rocío Drake
Journal: Biochemical Journal (2011)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: V-ATPases; H+-PPase; acidification; intracellular compartments; Arabidopsis thaliana
Affiliations: Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Avda. Americo Vespucio, 49, 41092 Sevilla, Spain

Abstract:  V-ATPases (vacuolar H+-ATPases) are a specific class of multi-subunit pumps that play an essential role in the generation of proton gradients across eukaryotic endomembranes. Another simpler proton pump that co-localizes with the V-ATPase occurs in plants and many protists: the single-subunit H+-PPase [H+-translocating PPase (inorganic pyrophosphatase)]. Little is known about the relative contribution of these two proteins to the acidification of intracellular compartments. In the present study, we show that the expression of a chimaeric derivative of the Arabidopsis thaliana H+-PPase AVP1, which is preferentially targeted to internal membranes of yeast, alleviates the phenotypes associated with V-ATPase deficiency. Phenotypic complementation was achieved both with a yeast strain with its V-ATPase specifically inhibited by bafilomycin A1 and with a vma1-null mutant lacking a catalytic V-ATPase subunit. Cell staining with vital fluorescent dyes showed that AVP1 recovered vacuole acidification and normalized the endocytic pathway of the vma mutant. Biochemical and immunochemical studies further demonstrated that a significant fraction of heterologous H+-PPase is located at the vacuolar membrane. These results raise the question of the occurrence of distinct proton pumps in certain single-membrane organelles, such as plant vacuoles, by proving yeast V-ATPase activity dispensability and the capability of H+-PPase to generate, by itself, physiologically suitable internal pH gradients. Also, they suggest new ways of engineering macrolide drug tolerance and outline an experimental system for testing alternative roles for fungal and animal V-ATPases, other than the mere acidification of subcellular organelles. 

Retracted: No

PubPeer comments:
 Duplication of microscopy data between Figure 3E and Figure 5B. ![file] , 
 Supplementary Figure 4A appears to have some images which overlap. *** ![file] ,
Vascular regression precedes motor neuron loss in the FUS (1-359) ALS mouse model
Authors: Karen S Coughlan
Luise Halang
Sebastian A Lewandowski
Marion C Hogg
Martin Crivello
Elisabeth Jirström
Megan Rayner
Ina Woods
Jochen H M Prehn
Journal: Disease models & mechanisms (2019)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Amyotrophic lateral sclerosis; Angiogenin; FUS; Motoneuron; Vascular defects.
Affiliations: Department of Physiology and Medical Physics, Centre for the Study of Neurological Disorders, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2, Ireland., FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin 2, Ireland., Tissue Biology Laboratory, Department of Medical Biochemistry and Biophysics, Center for Molecular Medicine, Karolinska Institute, Scheeles v. 2, 17177 Stockholm, Sweden., Department of Physiology and Medical Physics, Centre for the Study of Neurological Disorders, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2, Ireland .

Abstract:  Amyotrophic lateral sclerosis (ALS) presents a poorly understood pathogenesis. Evidence from patients and mutant SOD1 mouse models suggests vascular damage may precede or aggravate motor dysfunction in ALS. We have previously shown angiogenin (ANG) treatment enhances motor neuron survival, delays motor dysfunction and prevents vascular regression in the SOD1G93A ALS model. However, the existence of vascular defects at different stages of disease progression remains to be established in other ALS models. Here, we assessed vascular integrity in vivo throughout different disease stages, and investigated whether ANG treatment reverses vascular regression and prolongs motor neuron survival in the FUS (1-359) mouse model of ALS. Lumbar spinal cord tissue was collected from FUS (1-359) and non-transgenic control mice at postnatal day (P)50, P90 and P120. We found a significant decrease in vascular network density in lumbar spinal cords from FUS (1-359) mice by day 90, at which point motor neuron numbers were unaffected. ANG treatment did not affect survival or counter vascular regression. Endogenous Ang1 and Vegf expression were unchanged at P50 and P90; however, we found a significant decrease in miRNA 126 at P50, indicating vascular integrity in FUS mice may be compromised via an alternative pathway. Our study demonstrates that vascular regression occurs before motor neuron degeneration in FUS (1-359) mice, and highlights that heterogeneity in responses to novel ALS therapeutics can already be detected in preclinical mouse models of ALS.This article has an associated First Person interview with the joint first authors of the paper. 

Retracted: No

PubPeer comments:
 Figure 6A. Much more similar than you would expect. https: imgur.com HnZRbBe ,
Arsonoliposomes for the potential treatment of medulloblastoma
Authors: Showan Marouf
Marco E Favretto
Paraskevi Kallinteri
Panagiotis Ioannou
Sophia G Antimisiaris
Terence L Parker
Journal: Pharmaceutical Research (2009)
Discipline: PHARMACOLOGY & TOXICOLOGY
Keywords: Arsonoliposome; Medulloblastoma cells; Uptake; Endocytotic mechanism; Cell viability
Affiliations: Medway School of Pharmacy, University of Kent, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK.

Abstract:  Purpose: To investigate the arsonoliposome effect on medulloblastoma cells (VC312Rs) related to uptake, endocytotic mechanism and cell viability. Methods: VC312R viability in presence of either arsonoliposomes or stealth liposomes was studied using MTT assay for 1-4 days. Fibroblasts (3T3) were used as control. Apoptosis was studied for 2 h, 5 h and 24 h. Bodipy-labelled arsonoliposome uptake (time- and dose-dependent) was estimated using FACS analysis. The endocytotic mechanism was investigated using inhibitors of clathrin- (chlorpromazine) and caveolae-mediated endocytosis (filipin). Results: Arsonoliposomes affected significantly the VC312R viability compared to 3T3 cells and induced apoptosis to VC312Rs after 2 h of incubation. Apoptosis was not observed for 3T3 cells. Liposome uptake versus time showed a bimodal pattern. Clathrin-mediated endocytosis was the main endocytotic mechanism at low lipid concentrations and caveolae at higher ones; thus, dose-dependent uptake did not show a plateau at increased lipid concentrations. Conclusions: Arsonoliposomes showed "selective" toxicity towards medulloblastoma cells inducing apoptosis after 2 hs of incubation. Therefore, arsonoliposomes are promising anticancer vehicles for brain tumour treatment. 

Retracted: No

PubPeer comments:
 This paper makes use of the VC312R cell line which was originally thought to originate from a human medulloblastoma. Unfortunatly it was shown in [PMID: 20951163] that VC312R is a rat cell line. At the time this paper was published this was not yet known so the authors of this paper are not to be blamed for using this cell line, nevertheless the conclusions of this paper as to their relevance to medulloblastoma are unfortunately invalidated. See the relevant [Cellosaurus entry] ,
Adjuvanticity and protective immunity of Plasmodium yoelii nigeriensis blood-stage soluble antigens encapsulated in fusogenic liposome
Authors: Khan Arif
Mohammad Owais
Shailja Mishra Bhattacharya
Satish Vedi
Varun Dwivedi
Anil Dangi
Azevedo Vasco
Journal: Vaccine (2009)
Discipline: IMMUNOLOGY
Keywords: lipids; saccharosome; antigen; immune responses; Plasmodium yoelii nigeriensis
Affiliations: Department of Biochemistry, J.N. Medical College, Aligarh Muslim University, Aligarh, India.

Abstract:  In our previous studies we established fusogenic properties of lipids isolated from edible yeast Saccharomyces cerevisiae (S. cerevisiae). We demonstrated that liposomes prepared from S. cerevisiae membrane lipid (saccharosome) can deliver encapsulated antigen into cytosol of the antigen presenting cells and elicit antigen specific cell mediated as well as humoral immune responses. In this study, we evaluated immunological behavior of saccharosome encapsulated cytosolic proteins (sAg) of Plasmodium yoelii nigeriensis in BALB/c mice. Immunization with antigen (sAg) encapsulated in saccharosome resulted in enhancement of CD4+ and CD8+ T cell populations and also up-regulated the expression of CD80 and CD86 molecules on the surface of antigen presenting cells. Further, immunization with saccharosome-encapsulated sAg-induced elevated levels of both IFN-gamma and IL-4 cytokines in the immunized mice when compared to egg PC liposome encapsulated sAg or its IFA emulsified form. Saccharosome-mediated immunization resulted in induction of high level of total antibody response with preponderance of IgG2a isotype as well. The data of this study suggest that saccharosome-based vehicle can emerge as an effective vaccine in imparting protection against various intracellular pathogens including Plasmodium yoelii nigeriensis. 

Retracted: No

PubPeer comments:
 Figure 7. * Blue boxes: Panels A (immunized with PC-sAg) and D (immunized with YL-sAg) appear to show the same graph. Could the authors please check? ![file] , 
 Figure 8. * Red boxes: Panels C (PC) and D (IFA) appear to be identical to each other. * Yellow boxes: the Blank in this Figure 8 appears identical to the Blank in Figure 2 of Dwivedi V et al., Pharmaceut Res (2008) DOI: 10.1007 s11095-008-9631-2. Are these panels both showing the same experiment? ![file] ![file] ,
MicroRNA-373 Inhibits Cell Proliferation and Invasion via Targeting BRF2 in Human Non-small Cell Lung Cancer A549 Cell Line
Authors: Fei Liao
Lei Wang
Li Zhou
Junfeng Qu
Ju Wang
Journal: Cancer Research and Treatment (2018)
Discipline: CLINICAL MEDICINE
Keywords: BRF2; Cell migration inhibition; Cell proliferation; Epithelial-mesenchymal transition; Non-small cell lung carcinoma
Affiliations: Department of Thoracic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China., The Central Operating Room, The First Affiliated Hospital of Harbin Medical University, Harbin, China.

Abstract:  Purpose: The purpose of this study was to investigate the biological role and mechanism of miR-373 targeting of TFIIB-related factor 2 (BRF2) in the regulation of non-small cell lung cancer (NSCLC) cells. Materials and methods: miRNA microarray chip analysis of four paired NSCLC and adjacent non-tumor tissues was performed. Quantitative real-time polymerase chain reaction (qRT-PCR) andwestern blotting were used to detect the expression levels of miR-373 and BRF2 in NSCLC tissues and cell lines. The dual-luciferase reporter method was performed to determine if BRF2 is a target of miR-373. MTT, wound-healing, Transwell, and flow cytometric assays were conducted to examine the proliferation, migration, invasion, and cell cycle progression of NSCLC A549 cells, respectively; western blotting was used to detect the expression of epithelial-mesenchymal transition (EMT)-related proteins. Results: The miRNA microarray chip analysis demonstrated that miR-373 was down-regulated in NSCLC tissues, and this result was confirmed by qRT-PCR. Additionally, miR-373 was confirmed to target BRF2. Moreover, miR-373 expression was inversely correlated with BRF2 expression in NSCLC tissues and cell lines; both miR-373 down-regulation and BRF2 up-regulation were strongly associated with the clinicopathological features and prognosis of NSCLC patients. In vitro, overexpression of miR-373 markedly inhibited cell proliferation, migration, and invasion; up-regulated the expression of E-cadherin; and down-regulated the expression of N-cadherin and Snail in A549 cell. Knockdown BRF2 by siRNA resulted in effects similar to those caused by overexpression of miR-373. Conclusion: MiR-373 is decreased in NSCLC, and overexpression of miR-373 can suppress cell EMT, and inhibit the proliferation, migration, and invasion of NSCLC A549 cells by targeting BRF2. 

Retracted: No

PubPeer comments:
 Fig 6B.  The effect of miR-373 on the cell invasion ability of A549 cells was verified by Transwell experiments . ![file] At left: Figs 5 and 6 from [Zhao et al (2016)] . Figure 5A of [Guo et al (2018)] at bottom left. At right, Figs 7 and 12 from [Li et al (2015)] . ![file] , 
 *[right]* Fig 2C,  Western blotting was performed to measure the relative protein expression level of BRF2 in 92 paired NSCLC tissues and adjacent non-tumor tissues . Sourced from *[left]* Fig 5B of  MicroRNA-500 sustains nuclear factor-u03baB activation and induces gastric cancer cell proliferation and resistance to apoptosis ([Zhang et al 2015] ). ![file] ,
Immunomodulatory Effects of Calcium and Strontium Co-Doped Titanium Oxides on Osteogenesis
Authors: Kaiwei Tang
Mengqi Cheng
Jiaxing Wang
Hui Qin
Huiliang Cao
Xianlong Zhang
Yaochao Zhao
Xuanyong Liu
Bin Li
Xiangwei Yuan
Journal: Frontiers in Immunology (2017)
Discipline: IMMUNOLOGY
Keywords: calcium; immunity; macrophage polarization; osteogenesis; strontium.
Affiliations: Department of Orthopedics, Shanghai Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, China., State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, China.

Abstract:  The effects of calcium (Ca) or strontium (Sr) on host osteogenesis and immune responses have been investigated separately. In clinical practice, these two elements may both be present around an orthopedic device, but their potential synergistic effects on osteogenesis and the immune response have not been explored to date. In this work, we investigated the immunomodulatory effects of Ca and Sr co-doped titanium oxides on osteogenesis in vitro using the mouse macrophage cell line RAW 264.7 alone and in co-culture with mouse bone mesenchymal stem cells (BMSCs), and in vivo using a mouse air-pouch model. Coatings containing Ca and Sr at different concentration ratios were fabricated on titanium substrates using micro-arc oxidation and electrochemical treatment. The in vitro and in vivo results demonstrated that the Ca and Sr concentration ratio has a marked influence on macrophage polarization. The coating with a Ca/Sr ratio of 2:1 was superior to those with other Ca and/or Sr concentrations in terms of modulating M2 polarization, which enhanced osteogenic differentiation of mouse BMSCs in co-culture. These findings suggest that the osteoimmunomodulatory effect of a titanium-oxide coating can be enhanced by modulating the concentration ratio of its components. 

Retracted: No

PubPeer comments:
 Figure 2A: * Cyan, yellow, red boxes: Four panels appear to all overlap with each other. ![file] ,
The glutamate receptors AtGLR1.2 and AtGLR1.3 increase cold tolerance by regulating jasmonate signaling in Arabidopsis thaliana
Authors: Yongping Yang
Xiangxiang Kong
Qian Chen
Yan Zheng
Xiangyang Hu
Jingjing Wei
Landi Luo
Journal: Biochemical and Biophysical Research Communications (2018)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: AtGLR1.2 and 1.3; CBF/DREB1 pathway; Cold; Jasmonate signaling.
Affiliations: Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China; University of Chinese Academy of Sciences, Beijing, 100049, China., School of Ecology and Environmental Science, Yunnan University, Kunming, 650504, China., Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China., Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China. Electronic address: ., Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China. Electronic address: .

Abstract:  Plant glutamate-like receptors (GLRs), which are homologs of mammalian ionotropic glutamate receptors (iGluRs), are thought to be involved in plant growth, development, and environmental stress responses. In this study, we demonstrated that two members of Arabidopsis glutamate-like receptors, AtGLR1.2 and AtGLR1.3, play positive roles in the plant response to cold stress. Genetic and biochemical experiments revealed that exogenous jasmonate could attenuate the cold sensitivity of glr1.2 and glr1.3 mutants, and the overexpression of GLR1.2 or GLR1.3 enhanced cold tolerance by increasing endogenous jasmonate levels under cold stress. In addition, the expression of genes in the CBF/DREB1 signaling pathway was decreased in the glr1.2 and glr1.3 mutants, but was promoted in GLR1.2-OE and GLR1.3-OE transgenic plants compared with the wild-type during cold treatment. Further investigation revealed that AtGLR1.2 and AtGLR1.3 independently drove similar functions without directly interacting. Together, our findings suggest that AtGLR1.2 and 1.3 positively enhance cold tolerance in Arabidopsis by activating endogenous jasmonate accumulation and subsequently promoting the downstream CBF/DREB1 cold response pathway during cold stress. 

Retracted: No

PubPeer comments:
 Figure 3D appears to have a repeated image, after rotation, but they are described differently. *** ![file] ,
Targeted therapy with trastuzumab in dysplasia and adenocarcinoma arising in Barrett's esophagus: a translational approach
Authors: S Grisanti
P Cengia
L Minelli
G Missale
V D Ferrari
R Cestari
G Marini
E Rossi
G Bassotti
V Villanacci
Journal: Minerva Gastroenterologica e Dietologica (2008)
Discipline: CLINICAL MEDICINE
Keywords: HER2; trastuzumab; esophageal dysplasia; adenocarcinoma; Barrett's esophagus
Affiliations: Department of Pathology, University of Brescia, Spedali Civili, Brescia, Italy. 

Abstract:  Aim: Human epidermal growth factor receptor (HER2) protooncogene, overexpressed/ amplified in preneoplastic lesions and in adenocarcinoma (ADC) of the esophagus, can be considered a target for treatment of esophageal dysplasia/ADC. The aim of this study was to evaluate the therapeutic role of the anti-HER2 monoclonal antibody, trastuzumab, in the management of ADC originating from HER2-positive Barrett's esophagus (BE). Methods: Two patients with high-grade dysplasia and ADC of the esophagus after esophageal mucosectomy and no metastatic disease were studied. Patients were not eligible for radical surgery or chemo-radiotherapy because of age and comorbidities. HER2 status was assessed by immunohistochemistry and fluorescence in situ hybridization. Additional immunohistochemical analyses were performed. The whole panel was analysed at baseline, after treatment and at follow-up. Results: At baseline, the two patients showed HER-2 overexpression/amplification in all areas of dysplasia and ADC but not in BE. Six months after treatment no significant differences in terms of endoscopical and histological patterns of the disease were found. HER-2, EGFR, TOPOII-alpha and anti-ssDNA analysis demonstrated a down-regulation of these markers and increased apoptosis. Conclusion: This study demonstrates that this treatment is feasible. No clear evidence of dysplasia regression was observed. However, HER2 and TopoII-alpha downregulation and induction of apoptosis occurring 6 months after treatment encourages further investigation. 

Retracted: No

PubPeer comments:
 ![file] , 
 ![file] ,
Capturing the Geoherbalism Differentiation in Wild Paris polyphylla var. yunnanensis Raw Materials through the Application of Multispectral Information Fusion Combined with Chemometrics
Authors: Yan Li
Jinyu Zhang
Yuanzhong Wang
Journal: ACS Omega (2019)
Discipline: CHEMISTRY
Keywords: Paris polyphylla var. yunnanensis; medicinal plant; geoherbalism; multispectral information fusion; ultraviolet spectroscopy
Affiliations: Institute of Medicinal Plants, Yunnan Academy of Agricultural Sciences, Kunming 650200, China

Abstract:  Paris polyphylla var. yunnanensis is a famous medicinal plant distributed in some Asian countries. This species has attracted a great deal of attention and is often used as raw materials in traditional medicine practices. With the purpose of gaining insight into the geoherbalism of wild P. polyphylla var. yunnanensis, a total of 183 dried rhizome samples from eight different regions including 16 typical or nontypical natural habitats have been analyzed by multispectral information fusion based on ultraviolet and Fourier transform infrared spectroscopies combined with partial least squares discriminant analysis (PLS-DA) and hierarchical cluster analysis. From the results, the use of multispectral information fusion strategy could improve the correct classification of samples, and good classification performances have been shown according to PLS-DA models. The discrimination of samples was obtained successfully with respect to the typical and nontypical natural habitats, different collection areas of typical natural habitats, and various sampling sites in nontypical natural habitats. Additionally, the similarities among samples were presented as well. Overall, the rhizome of wild P. polyphylla var. yunnanensis exhibited various regional dependence and individual differences according to the geographical origins, and the relatively appropriate growth region with better quality consistency of samples was preliminarily selected. This study also revealed that the developed multispectral information fusion method has the potential to be a reliable analytical methodology for capturing the geoherbalism differentiation in wild P. polyphylla var. yunnanensis. Furthermore, it could provide more chemical evidence for the critical supplement of quality evaluation on P. polyphylla var. yunnanensis. 

Retracted: No

PubPeer comments:
 The result of the paper can be useful in the industry. ,