Gene Markers of Fracture Healing in Early Stage and the Regulatory Mechanism During the Process Using Microarray Analysis
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Supplementary Materials: Evaluation of Cytotoxicity and Α-Glucosidase Inhibitory Activity of Amide and Polyamino-Derivatives of Lupane Triterpenoids
Supplementary Materials: Evaluation of cytotoxicity and α-glucosidase inhibitory activity of amide and polyamino-derivatives of lupane triterpenoids Oxana B. Kazakova1*, Gul'nara V. Giniyatullina1, Akhat G. Mustafin1, Denis A. Babkov2, Elena V. Sokolova2, Alexander A. Spasov2* 1Ufa Institute of Chemistry of the Ufa Federal Research Centre of the Russian Academy of Sciences, 71, pr. Oktyabrya, 450054 Ufa, Russian Federation 2Scientific Center for Innovative Drugs, Volgograd State Medical University, Novorossiyskaya st. 39, Volgograd 400087, Russian Federation Correspondence Prof. Dr. Oxana B. Kazakova Ufa Institute of Chemistry of the Ufa Federal Research Centre of the Russian Academy of Sciences 71 Prospeсt Oktyabrya Ufa, 450054 Russian Federation E-mail: [email protected] Prof. Dr. Alexander A. Spasov Scientific Center for Innovative Drugs of the Volgograd State Medical University 39 Novorossiyskaya st. Volgograd, 400087 Russian Federation E-mail: [email protected] Figure S1. 1H and 13C of compound 2. H NH N H O H O H 2 2 Figure S2. 1H and 13C of compound 4. NH2 O H O H CH3 O O H H3C O H 4 3 Figure S3. Anticancer screening data of compound 2 at single dose assay 4 Figure S4. Anticancer screening data of compound 7 at single dose assay 5 Figure S5. Anticancer screening data of compound 8 at single dose assay 6 Figure S6. Anticancer screening data of compound 9 at single dose assay 7 Figure S7. Anticancer screening data of compound 12 at single dose assay 8 Figure S8. Anticancer screening data of compound 13 at single dose assay 9 Figure S9. Anticancer screening data of compound 14 at single dose assay 10 Figure S10. -
Analysis of Gene Expression Data for Gene Ontology
ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION A Thesis Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Robert Daniel Macholan May 2011 ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION Robert Daniel Macholan Thesis Approved: Accepted: _______________________________ _______________________________ Advisor Department Chair Dr. Zhong-Hui Duan Dr. Chien-Chung Chan _______________________________ _______________________________ Committee Member Dean of the College Dr. Chien-Chung Chan Dr. Chand K. Midha _______________________________ _______________________________ Committee Member Dean of the Graduate School Dr. Yingcai Xiao Dr. George R. Newkome _______________________________ Date ii ABSTRACT A tremendous increase in genomic data has encouraged biologists to turn to bioinformatics in order to assist in its interpretation and processing. One of the present challenges that need to be overcome in order to understand this data more completely is the development of a reliable method to accurately predict the function of a protein from its genomic information. This study focuses on developing an effective algorithm for protein function prediction. The algorithm is based on proteins that have similar expression patterns. The similarity of the expression data is determined using a novel measure, the slope matrix. The slope matrix introduces a normalized method for the comparison of expression levels throughout a proteome. The algorithm is tested using real microarray gene expression data. Their functions are characterized using gene ontology annotations. The results of the case study indicate the protein function prediction algorithm developed is comparable to the prediction algorithms that are based on the annotations of homologous proteins. -
Nanoparticles to Upregulate Notch Signaling Victor
Notch Intracellular Domain Plasmid Delivery via Poly(lactic-co-glycolic acid) Nanoparticles to Upregulate Notch Signaling Victoria L. Messerschmidt1,2†, Aneetta E. Kuriakose1,2†, Uday Chintapula1, Samantha Laboy1, Thuy Thi Dang Truong1, LeNaiya A. Kydd1, Justyn Jaworski1, Kytai T. Nguyen1,2*, Juhyun Lee1,2* 1Department of Bioengineering, University of Texas at Arlington, Arlington TX 76010 USA 2University of Texas Southwestern Medical Center, Dallas TX 75390 USA † These authors have contributed equally to this work Corresponding Author: Juhyun Lee, Ph.D. Joint Department of Bioengineering UT Arlington / UT Southwestern Arlington, TX 75022 Email: [email protected] Telephone: 817-272-6534 Fax: 817-272-2251 Abstract Notch signaling is a highly conserved signaling system that is required for embryonic development and regeneration of organs. When the signal is lost, maldevelopment occurs and leads to a lethal state. Liposomes and retroviruses are most commonly used to deliver genetic material to cells. However, there are many drawbacks to these systems such as increased toxicity, nonspecific delivery, short half-life, and stability after formulation. We utilized the negatively charged and FDA approved polymer poly(lactic-co-glycolic acid) to encapsulate Notch Intracellular Domain- containing plasmid in nanoparticles. In this study, we show that primary human umbilical vein endothelial cells readily uptake the nanoparticles with and without specific antibody targets. We demonstrated that our nanoparticles also are nontoxic, stable over time, and compatible with blood. We also determined that we can successfully transfect primary human umbilical vein endothelial cells (HUVECs) with our nanoparticles in static and dynamic environments. Lastly, we elucidated that our transfection upregulates the downstream genes of Notch signaling, indicating that the payload was viable and successfully altered the genetic downstream effects. -
Lncegfl7os Regulates Human Angiogenesis by Interacting
RESEARCH ARTICLE LncEGFL7OS regulates human angiogenesis by interacting with MAX at the EGFL7/miR-126 locus Qinbo Zhou1†, Bo Yu1†*, Chastain Anderson1, Zhan-Peng Huang2, Jakub Hanus1, Wensheng Zhang3, Yu Han4, Partha S Bhattacharjee5, Sathish Srinivasan6, Kun Zhang3, Da-zhi Wang2, Shusheng Wang1,7* 1Department of Cell and Molecular Biology, Tulane University, New Orleans, United States; 2Department of Cardiology, Boston Children’s Hospital, Harvard Medical School, Boston, United States; 3Department of Computer Science, Xavier University, New Orleans, United States; 4Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, United States; 5Department of Biology, Xavier University, New Orleans, United States; 6Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma, United States; 7Department of Ophthalmology, Tulane University, New Orleans, United States Abstract In an effort to identify human endothelial cell (EC)-enriched lncRNAs,~500 lncRNAs were shown to be highly restricted in primary human ECs. Among them, lncEGFL7OS, located in the opposite strand of the EGFL7/miR-126 gene, is regulated by ETS factors through a bidirectional promoter in ECs. It is enriched in highly vascularized human tissues, and upregulated in the hearts of dilated cardiomyopathy patients. LncEGFL7OS silencing impairs angiogenesis as shown by EC/fibroblast co-culture, in vitro/in vivo and ex vivo human choroid sprouting angiogenesis assays, while lncEGFL7OS overexpression has the opposite function. Mechanistically, *For correspondence: lncEGFL7OS is required for MAPK and AKT pathway activation by regulating EGFL7/miR-126 [email protected] (BY); expression. MAX protein was identified as a lncEGFL7OS-interacting protein that functions to [email protected] (SW) regulate histone acetylation in the EGFL7/miR-126 promoter/enhancer. -
Targetome Analysis Revealed Involvement of Mir-126 in Neurotrophin Signaling Pathway: a Possible Role in Prevention of Glioma Development
Original Article Targetome Analysis Revealed Involvement of MiR-126 in Neurotrophin Signaling Pathway: A Possible Role in Prevention of Glioma Development 1# 1, 2# 3 4, 5 Maedeh Rouigari, M.Sc. , Moein Dehbashi, Ph.D. , Kamran Ghaedi, Ph.D. , Meraj Pourhossein, Ph.D. * 1. Isfahan Neuroscience Research Center (INRC), Alzahra Hospital, Isfahan University of Medical Sciences, Isfahan, Iran 2. Genetics Division, Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran 3. Cell and Molecular Biology Division, Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran 4. Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences Isfahan, Iran 5. Department of Food Science and Technology, Food Security Research Center, School of Nutrition and Food Science, Isfahan, Iran #The first two authors equally contributed to this article. *Corresponding Address: P.O.Box: 81746-73461, Hezar Jarib Street, Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran Email: [email protected] Received: 21/Nov/2016, Accepted: 14/Mar/2017 Abstract Objective: For the first time, we used molecular signaling pathway enrichment analysis to determine possible involvement of miR-126 and IRS-1 in neurotrophin pathway. Materials and Methods: In this prospective study, validated and predicted targets (targetome) of miR-126 were collected following searching miRtarbase (http://mirtarbase.mbc.nctu.edu.tw/) and miRWalk 2.0 databases, respectively. Then, approximate expression of miR-126 targeting in Glioma tissue was examined using UniGene database (http://www.ncbi. nlm.nih.gov/unigene). In silico molecular pathway enrichment analysis was carried out by DAVID 6.7 database (http://david. -
Micrornas Mediated Regulation of the Ribosomal Proteins and Its Consequences on the Global Translation of Proteins
cells Review microRNAs Mediated Regulation of the Ribosomal Proteins and Its Consequences on the Global Translation of Proteins Abu Musa Md Talimur Reza 1,2 and Yu-Guo Yuan 1,3,* 1 Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; [email protected] 2 Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawi´nskiego5a, 02-106 Warsaw, Poland 3 Jiangsu Key Laboratory of Zoonosis/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China * Correspondence: [email protected]; Tel.: +86-514-8797-9228 Abstract: Ribosomal proteins (RPs) are mostly derived from the energy-consuming enzyme families such as ATP-dependent RNA helicases, AAA-ATPases, GTPases and kinases, and are important structural components of the ribosome, which is a supramolecular ribonucleoprotein complex, composed of Ribosomal RNA (rRNA) and RPs, coordinates the translation and synthesis of proteins with the help of transfer RNA (tRNA) and other factors. Not all RPs are indispensable; in other words, the ribosome could be functional and could continue the translation of proteins instead of lacking in some of the RPs. However, the lack of many RPs could result in severe defects in the biogenesis of ribosomes, which could directly influence the overall translation processes and global expression of the proteins leading to the emergence of different diseases including cancer. While microRNAs (miRNAs) are small non-coding RNAs and one of the potent regulators of the post-transcriptional 0 gene expression, miRNAs regulate gene expression by targeting the 3 untranslated region and/or coding region of the messenger RNAs (mRNAs), and by interacting with the 50 untranslated region, Citation: Reza, A.M.M.T.; Yuan, Y.-G. -
Anti-RPS27A Polyclonal Antibody Cat: K108030P Summary
Anti-RPS27A Polyclonal Antibody Cat: K108030P Summary: 【Product name】: Anti-RPS27A antibody 【Source】: Rabbit 【Isotype】: IgG 【Species reactivity】: Human Mouse Rat 【Swiss Prot】: P62979 【Gene ID】: 6233 【Calculated】: MW:18kDa 【Observed】: MW:12kDa 【Purification】: Affinity purification 【Tested applications】: WB 【Recommended dilution】: WB 1:1000-3000. 【WB Positive sample】: MCF7,Hela,293T,Jurkat,NIH3T3,Mouse kidney,Rat liver 【Subcellular location】: Nucleus Cytoplasm Cell membrane 【Immunogen】: Recombinant protein of human RPS27A 【Storage】: Shipped at 4°C. Upon delivery aliquot and store at -20°C Background: Ubiquitin, a highly conserved protein that has a major role in targeting cellular proteins for degradation by the 26S proteosome, is synthesized as a precursor protein consisting of either polyubiquitin chains or a single ubiquitin fused to an unrelated protein. This gene encodes a fusion protein consisting of ubiquitin at the N terminus and ribosomal protein S27a at the C terminus. When expressed in yeast, the protein is post-translationally processed, generating free ubiquitin monomer and ribosomal protein S27a. Ribosomal protein S27a is a component of the 40S subunit of the ribosome and belongs to the S27AE family of ribosomal proteins. It contains C4-type zinc finger domains and is located in the cytoplasm. Pseudogenes derived from this gene are present in the genome. As with ribosomal protein S27a, ribosomal protein L40 is also synthesized as a fusion protein with ubiquitin; similarly, ribosomal protein S30 is synthesized as a fusion protein with the ubiquitin-like protein fubi. Multiple alternatively spliced transcript variants that encode the same proteins have been identified. Sales:[email protected] For research purposes only. -
EGFL7 Meets Mirna-126: an Angiogenesis Alliance
- http://vascularcell.com/ REVIEW | OPEN ACCESS EGFL7 meets miRNA-126: an angiogenesis alliance Journal of Angiogenesis Research 2:9 | DOI: 10.1186/2040-2384-2-9 | © Li et al.; licensee Publiverse Online S.R.L. 2010 Received: 21 Apr 2010 | Accepted: 8 Apr 2010 | Published: 8 Apr 2010 Nikolic Iva, Plate Karl-Heinz, Schmidt Mirko HH@ + Contributed equally@ Corresponding author Abstract Blood vessels form de novo through the tightly regulated programs of vasculogenesis and angiogenesis. Both processes are distinct but one of the steps they share is the formation of a central lumen, when groups of cells organized as vascular cords undergo complex changes to achieve a tube-like morphology. Recently, a protein termed epidermal growth factor-like domain 7 (EGFL7) was described as a novel endothelial cell-derived factor involved in the regulation of the spatial arrangement of cells during vascular tube assembly. With its impact on tubulogenesis and vessel shape EGFL7 joined the large family of molecules governing blood vessel formation. Only recently, the molecular mechanisms underlying EGFL7's effects have been started to be elucidated and shaping of the extracellular matrix (ECM) as well as Notch signaling might very well play a role in mediating its biological effects. Further, findings in knock-out animal models suggest miR-126, a miRNA located within the egfl7 gene, has a major role in vessel development by promoting VEGF signaling, angiogenesis and vascular integrity. This review summarizes our current knowledge on EGFL7 and miR-126 and we will discuss the implications of both bioactive molecules for the formation of blood vessels. -
Lncrna SNHG8 Is Identified As a Key Regulator of Acute Myocardial
Zhuo et al. Lipids in Health and Disease (2019) 18:201 https://doi.org/10.1186/s12944-019-1142-0 RESEARCH Open Access LncRNA SNHG8 is identified as a key regulator of acute myocardial infarction by RNA-seq analysis Liu-An Zhuo, Yi-Tao Wen, Yong Wang, Zhi-Fang Liang, Gang Wu, Mei-Dan Nong and Liu Miao* Abstract Background: Long noncoding RNAs (lncRNAs) are involved in numerous physiological functions. However, their mechanisms in acute myocardial infarction (AMI) are not well understood. Methods: We performed an RNA-seq analysis to explore the molecular mechanism of AMI by constructing a lncRNA-miRNA-mRNA axis based on the ceRNA hypothesis. The target microRNA data were used to design a global AMI triple network. Thereafter, a functional enrichment analysis and clustering topological analyses were conducted by using the triple network. The expression of lncRNA SNHG8, SOCS3 and ICAM1 was measured by qRT-PCR. The prognostic values of lncRNA SNHG8, SOCS3 and ICAM1 were evaluated using a receiver operating characteristic (ROC) curve. Results: An AMI lncRNA-miRNA-mRNA network was constructed that included two mRNAs, one miRNA and one lncRNA. After RT-PCR validation of lncRNA SNHG8, SOCS3 and ICAM1 between the AMI and normal samples, only lncRNA SNHG8 had significant diagnostic value for further analysis. The ROC curve showed that SNHG8 presented an AUC of 0.850, while the AUC of SOCS3 was 0.633 and that of ICAM1 was 0.594. After a pairwise comparison, we found that SNHG8 was statistically significant (P SNHG8-ICAM1 = 0.002; P SNHG8-SOCS3 = 0.031). -
High Expression Levels of Egfl7 Correlate with Low Endothelial Cell Activation in Peritumoral Vessels of Human Breast Cancer
1422 ONCOLOGY LETTERS 12: 1422-1428, 2016 High expression levels of egfl7 correlate with low endothelial cell activation in peritumoral vessels of human breast cancer DIANE PANNIER1,2*, GÉRALDINE PHILIPPIN‑LAURIDANT1,2*, MARIE‑CHRISTINE BARANZELLI1, DELPHINE BERTIN1, EMILIE BOGART1, VICTOR DELPRAT2, GAËLLE VILLAIN2, VIRGINIE MATTOT2, JACQUES BONNETERRE1 and FABRICE SONCIN2 1Senology Department, Oscar Lambret Center, Université de Lille, 59020 Lille; 2Institut Pasteur de Lille, Centre National de la Recherche Scientifique UMR8161, Université de Lille, 59000 Lille, France Received October 5, 2015; Accepted May 24, 2016 DOI: 10.3892/ol.2016.4791 Abstract. Tumor blood vessels participate in the immune Altogether, these results provide further results that egfl7 response against cancer cells and we previously used pre-clin- serves a regulatory role in endothelial cell activation in rela- ical models to demonstrate that egfl7 (VE‑statin) promotes tion to immune infiltration and that it is a potentialtherapeutic tumor cell evasion from the immune system by repressing target to consider for improving anticancer immunotherapies. endothelial cell activation, preventing immune cells from entering the tumor mass. In the present study, the expression Introduction levels of egfl7 and that of ICAM‑1 as a marker of endothelium activation, were evaluated in peritumoral vessels of human The main therapeutic achievements in treating cancer have breast cancer samples. Breast cancer samples (174 invasive been historically obtained by limiting cancer cell proliferation and 30 in situ) from 204 patients treated in 2005 were immu- or division using non‑specific, thereafter, targeted therapies nostained for CD31, ICAM‑1 and stained for egfl7 usingin situ against these cells. More recently, an increasing interest hybridization. -
Diagnostic and Prognostic Implications of Ribosomal Protein Transcript Coordination in Human Cancers
bioRxiv preprint doi: https://doi.org/10.1101/167940; this version posted July 24, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Diagnostic and Prognostic Implications of Ribosomal Protein Transcript Coordination in Human Cancers James M. Dolezal1, 2, Arie P. Dash1, Edward V. Prochownik1 Running title: Implications of RPT Coordination in Human Cancers Keywords: machine learning, t-SNE, ribosomopathy, transcriptional profiling, TCGA 1Division of Hematology/Oncology, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh PA, 15224 2Correspondence: James M. Dolezal Tel: (765) 513-5561 Email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/167940; this version posted July 24, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract Ribosomes, the organelles responsible for the translation of mRNA, are comprised of rRNA and ~80 ribosomal proteins (RPs). Although canonically assumed to be maintained in equivalent proportions, some RPs have been shown to possess differential expression across tissue types. Dysregulation of RP expression occurs in a variety of human diseases, notably in many cancers, and altered expression of some RPs correlates with different tumor phenotypes and patient survival. To investigate the impact of global RP transcript (RPT) expression patterns on tumor phenotypes, we analyzed RPT expression of ~10,000 human tumors and 700 normal tissues with t-distributed stochastic neighbor embedding (t-SNE). -
RNA-Seq Reveals More Consistent Reference Genes for Gene Expression Studies in Human Non-Melanoma Skin Cancers
RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Hoang, V. L., L. N. Tom, X. Quek, J. Tan, E. J. Payne, L. L. Lin, S. Sinnya, et al. 2017. “RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers.” PeerJ 5 (1): e3631. doi:10.7717/peerj.3631. http:// dx.doi.org/10.7717/peerj.3631. Published Version doi:10.7717/peerj.3631 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:34375065 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers Van L.T. Hoang1,*, Lisa N. Tom1,*, Xiu-Cheng Quek2,3,*, Jean-Marie Tan1, Elizabeth J. Payne1, Lynlee L. Lin1, Sudipta Sinnya1, Anthony P. Raphael1,4, Duncan Lambie5, Ian H. Frazer6, Marcel E. Dinger2,3, H. Peter Soyer1 and Tarl W. Prow1,7 1 Dermatology Research Centre, Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, The University of Queensland, Brisbane, Queensland, Australia 2 Garvan Institute of Medical Research, Sydney, New South Wales, Australia 3 St Vincent's Clinical School, University of New South