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Latest publications of CIBIO affiliates (last updated on March 1st, 2019)

Polsinelli I, Borruso L, Caliandro R, Triboli L, Esposito A, Benini S (2019) A genome-wide analysis of desferrioxamine mediated iron uptake in Erwinia spp. reveals genes exclusive of the Rosaceae infecting strains. Sci Rep, 9(1):2818, doi:10.1038/s41598-019-39787-x.

De Filippis F, Pasolli E, Tett A, Tarallo S, Naccarati A, De Angelis M, Neviani E, Cocolin L, Gobbetti M, Segata N, Ercolini D (2019) Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets. Cell Host Microbe, doi:10.1016/j.chom.2019.01.004.

Uluşeker C, Torres-Bacete J, García JL, Hanczyc MM, Nogales J, Kahramanoğulları O (2019) Quantifying dynamic mechanisms of auto-regulation in Escherichia coli with synthetic promoter in response to varying external phosphate levels. Sci Rep, 9(1):2076, doi:10.1038/s41598-018-38223-w.

Guida M, Zanon A, Montibeller L, Lavdas AA, Ladurner J, Pischedda F, Rakovic A, Domingues FS, Piccoli G, Klein C, Pramstaller PP, Hicks AA, Pichler I (2019) Parkin Interacts with Apoptosis-Inducing Factor and Interferes with Its Translocation to the Nucleus in Neuronal Cells. Int J Mol Sci, 20(3), doi:10.3390/ijms20030748.

Avogaro L, Oss Pegorar C, Bettin N, Cusanelli E (2019) Generation of Cancer Cell Clones to Visualize Telomeric Repeat-containing RNA TERRA Expressed from a Single Telomere in Living Cells. J Vis Exp, (143), doi:10.3791/58790.

Bianconi I, D'Arcangelo S, Esposito A, Benedet M, Piffer E, Dinnella G, Gualdi P, Schinella M, Baldo E, Donati C, Jousson O (2018) Persistence and Microevolution of  Front Microbiol, 9:3242, doi:10.3389/fmicb.2018.03242.

Salama M, Benitez-Riquelme D, Elabd S, Munoz L, Zhang P, Glanemann M, Mione MC, Goldin R, Soussi T, Davidson G, Blattner C (2019) Fam83F induces p53 stabilisation and promotes its activity. Cell Death Differ., doi:10.1038/s41418-019-0281-1.

Cayuela ML, Claes KBM, Ferreira MG, Henriques CM, van Eeden F, Varga M, Vierstraete J, Mione MC (2018) The Zebrafish as an Emerging Model to Study DNA Damage in Aging, Cancer and Other Diseases. Front Cell Dev Biol, 6:178, doi:10.3389/fcell.2018.00178.

Grassi E, Santoro R, Umbach A, Grosso A, Oliviero S, Neri F, Conti L, Ala U, Provero P, DiCunto F, Merlo GR (2018) Choice of Alternative Polyadenylation Sites, Mediated by the RNA-Binding Protein Elavl3, Plays a Role in Differentiation of Inhibitory Neuronal Progenitors. Front Cell Neurosci, 12:518, doi:10.3389/fncel.2018.00518.

Pedron R, Esposito A, Bianconi I, Pasolli E, Tett A, Asnicar F, Cristofolini M, Segata N, Jousson O (2019) Genomic and metagenomic insights into the microbial community of a thermal spring. Microbiome, 7(1):8, doi:10.1186/s40168-019-0625-6.

Song Y, Rongvaux A, Taylor A, Jiang T, Tebaldi T, Balasubramanian K, Bagale A, Terzi YK, Gbyli R, Wang X, Fu X, Gao Y, Zhao J, Podoltsev N, Xu M, Neparidze N, Wong E, Torres R, Bruscia EM, Kluger Y, Manz MG, Flavell RA, Halene S (2019) A highly efficient and faithful MDS patient-derived xenotransplantation model for pre-clinical studies. Nat Commun, 10(1):366, doi:10.1038/s41467-018-08166-x.

Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, Beghini F, Manghi P, Tett A, Ghensi P, Collado MC, Rice BL, DuLong C, Morgan XC, Golden CD, Quince C, Huttenhower C, Segata N (2019) Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. Cell, 176(3):649-662.e20, doi:10.1016/j.cell.2019.01.001.

Profumo V, Forte B, Percio S, Rotundo F, Doldi V, Ferrari E, Fenderico N, Dugo M, Romagnoli D, Benelli M, Valdagni R, Dolfini D, Zaffaroni N, Gandellini P (2019) LEADeR role of miR-205 host gene as long noncoding RNA in prostate basal cell differentiation. Nat Commun, 10(1):307, doi:10.1038/s41467-018-08153-2.

Zielonka M, Probst J, Carl M, Hoffmann GF, Kölker S, Okun JG (2019) Bioenergetic dysfunction in a zebrafish model of acute hyperammonemic decompensation. Exp. Neurol., 314:91-99, doi:10.1016/j.expneurol.2019.01.008.

Cleverley RM, Rutter ZJ, Rismondo J, Corona F, Tsui HT, Alatawi FA, Daniel RA, Halbedel S, Massidda O, Winkler ME, Lewis RJ (2019) The cell cycle regulator GpsB functions as cytosolic adaptor for multiple cell wall enzymes. Nat Commun, 10(1):261, doi:10.1038/s41467-018-08056-2.

Zellweger F, De Frenne P, Lenoir J, Rocchini D, Coomes D (2019) Advances in Microclimate Ecology Arising from Remote Sensing. Trends Ecol. Evol. (Amst.), doi:10.1016/j.tree.2018.12.012.

Schiffer L, Azhar R, Shepherd L, Ramos M, Geistlinger L, Huttenhower C, Dowd JB, Segata N, Waldron L (2019) HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor. Am. J. Epidemiol., doi:10.1093/aje/kwz006.

Ciribilli Y, Borlak J (2018) Correction: Oncogenomics of c-Myc transgenic mice reveal novel regulators of extracellular signaling, angiogenesis and invasion with clinical significance for human lung adenocarcinoma. Oncotarget, 9(98):37269, doi:10.18632/oncotarget.26489.

Matsushita-Ishiodori Y, Hanczyc MM, Wang A, Szostak JW, Yomo T (2019) Using Imaging Flow Cytometry to Quantify and Optimize Giant Vesicle Production by Water-in-oil Emulsion Transfer Methods. Langmuir, 35(6):2375-2382, doi:10.1021/acs.langmuir.8b03635.

Smurova K, De Wulf P (2018) Centromere and Pericentromere Transcription: Roles and Regulation … in Sickness and in Health. Front Genet, 9:674, doi:10.3389/fgene.2018.00674.

Anelli V, Ordas A, Kneitz S, Sagredo LM, Gourain V, Schartl M, Meijer AH, Mione M (2018) Ras-Induced miR-146a and 193a Target Jmjd6 to Regulate Melanoma Progression. Front Genet, 9:675, doi:10.3389/fgene.2018.00675.

D'Agostino VG, Sighel D, Zucal C, Bonomo I, Micaelli M, Lolli G, Provenzani A, Quattrone A, Adami V (2019) Screening Approaches for Targeting Ribonucleoprotein Complexes: A New Dimension for Drug Discovery. SLAS Discov, 24(3):314-331, doi:10.1177/2472555218818065.

Sznarkowska A, Kostecka A, Kawiak A, Acedo P, Lion M, Inga A, Zawacka-Pankau J (2018) Reactivation of TAp73 tumor suppressor by protoporphyrin IX, a metabolite of aminolevulinic acid, induces apoptosis in  Cell Div, 13:10, doi:10.1186/s13008-018-0043-3.

Pasternak G, Yang Y, Santos BB, Brunello F, Hanczyc MM, Motta A (2019) Regenerated silk fibroin membranes as separators for transparent microbial fuel cells. Bioelectrochemistry, 126:146-155, doi:10.1016/j.bioelechem.2018.12.004.

Zizioli D, Mione M, Varinelli M, Malagola M, Bernardi S, Alghisi E, Borsani G, Finazzi D, Monti E, Presta M, Russo D (2019) Zebrafish disease models in hematology: Highlights on biological and translational impact. Biochim Biophys Acta Mol Basis Dis, 1865(3):620-633, doi:10.1016/j.bbadis.2018.12.015.

Chelini G, Zerbi V, Cimino L, Grigoli A, Markicevic M, Libera F, Robbiati S, Gadler M, Bronzoni S, Miorelli S, Galbusera A, Gozzi A, Casarosa S, Provenzano G, Bozzi Y (2019) Aberrant Somatosensory Processing and Connectivity in Mice Lacking  J. Neurosci., 39(8):1525-1538, doi:10.1523/JNEUROSCI.0612-18.2018.

Romagnoli D, Boccalini G, Bonechi M, Biagioni C, Fassan P, Bertorelli R, De Sanctis V, Di Leo A, Migliaccio I, Malorni L, Benelli M (2018) ddSeeker: a tool for processing Bio-Rad ddSEQ single cell RNA-seq data. BMC Genomics, 19(1):960, doi:10.1186/s12864-018-5249-x.

Poggi L, Casarosa S, Carl M (2018) An Eye on the Wnt Inhibitory Factor Wif1. Front Cell Dev Biol, 6:167, doi:10.3389/fcell.2018.00167.

de Sousa-Pereira P, Abrantes J, Bauernfried S, Pierini V, Esteves PJ, Keppler OT, Pizzato M, Hornung V, Fackler OT, Baldauf HM (2019) The antiviral activity of rodent and lagomorph SERINC3 and SERINC5 is counteracted by known viral antagonists. J. Gen. Virol., 100(2):278-288, doi:10.1099/jgv.0.001201.

Jurman G, Filosi M, Visintainer R, Riccadonna S, Furlanello C (2019) Stability in GRN Inference. Methods Mol. Biol., 1883:323-346, doi:10.1007/978-1-4939-8882-2_14.

Berto G, Ferreira-Cerca S, De Wulf P (2018) The Rio1 protein kinases/ATPases: conserved regulators of growth, division, and genomic stability. Curr. Genet., doi:10.1007/s00294-018-0912-y.

Toparlak OD, Mansy SS (2018) Progress in synthesizing protocells. Exp. Biol. Med. (Maywood), doi:10.1177/1535370218816657.

Berti A, Caporali R, Montecucco C, Paolazzi G, Monti S (2019) Aging in Primary Systemic Vasculitis: Implications for Diagnosis, Clinical Manifestations, and Management. Drugs Aging, 36(1):53-63, doi:10.1007/s40266-018-0617-4.

Muglia P, Filosi M, Da Ros L, Kam-Thong T, Nardocci F, Trabetti E, Ratti E, Rizzini P, Zuddas A, Bernardina BD, Domenici EItalian Autism Network,  (2018) The Italian autism network (ITAN): a resource for molecular genetics and biomarker investigations. BMC Psychiatry, 18(1):369, doi:10.1186/s12888-018-1937-y.

Borrenberghs D, Zurnic I, De Wit F, Acke A, Dirix L, Cereseto A, Debyser Z, Hendrix J (2018) Post-mitotic BET-induced reshaping of integrase quaternary structure supports wild-type MLV integration. Nucleic Acids Res., doi:10.1093/nar/gky1157.

Raneri M, Pinatel E, Peano C, Rampioni G, Leoni L, Bianconi I, Jousson O, Dalmasio C, Ferrante P, Briani F (2018) Pseudomonas aeruginosa mutants defective in glucose uptake have pleiotropic phenotype and altered virulence in non-mammal infection models. Sci Rep, 8(1):16912, doi:10.1038/s41598-018-35087-y.

Manara S, Pasolli E, Dolce D, Ravenni N, Campana S, Armanini F, Asnicar F, Mengoni A, Galli L, Montagnani C, Venturini E, Rota-Stabelli O, Grandi G, Taccetti G, Segata N (2018) Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital. Genome Med, 10(1):82, doi:10.1186/s13073-018-0593-7.

Maurer SE, Tølbøl Sørensen K, Iqbal Z, Nicholas J, Quirion K, Gioia M, Monnard PA, Hanczyc MM (2018) Vesicle Self-Assembly of Monoalkyl Amphiphiles under the Effects of High Ionic Strength, Extreme pH, and High Temperature Environments. Langmuir, 34(50):15560-15568, doi:10.1021/acs.langmuir.8b02830.

Ghensi P, Tonetto G, Soldini C, Bettio E, Mortellaro C, Soldini C (2018) Dental Implants With a Platform-Switched Morse Taper Connection and an Osteo Growth Induction Surface. J Craniofac Surg, doi:10.1097/SCS.0000000000004795.

Romanel A (2019) Allele-Specific Expression Analysis in Cancer Using Next-Generation Sequencing Data. Methods Mol. Biol., 1878:125-137, doi:10.1007/978-1-4939-8868-6_7.

Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Lipson KS, Knight R, Caporaso JG, Segata N, Huttenhower C (2018) Species-level functional profiling of metagenomes and metatranscriptomes. Nat. Methods, 15(11):962-968, doi:10.1038/s41592-018-0176-y.

Cesaratto F, Sasset L, Myers MP, Re A, Petris G, Burrone OR (2019) BiP/GRP78 Mediates ERAD Targeting of Proteins Produced by Membrane-Bound Ribosomes Stalled at the STOP-Codon. J. Mol. Biol., 431(2):123-141, doi:10.1016/j.jmb.2018.10.009.

Pollini D, Loffredo R, Cardano M, Conti L, Lattante S, Notarangelo A, Sabatelli M, Provenzani A (2018) Generation and characterization of a human iPSC line from an ALS patient carrying the Q66K-MATR3 mutation. Stem Cell Res, 33:146-150, doi:10.1016/j.scr.2018.10.011.

O'Sullivan A, Salcedo J, Rubert J (2018) Correction to: Advanced analytical strategies for measuring free bioactive milk sugars: from composition and concentrations to human metabolic response. Anal Bioanal Chem, 410(30):7997, doi:10.1007/s00216-018-1389-8.

Nava Rodrigues D, Casiraghi N, Romanel A, Crespo M, Miranda S, Rescigno P, Figueiredo I, Riisnaes R, Carreira S, Sumanasuriya S, Gasperini P, Sharp A, Mateo J, Makay A, McNair C, Schiewer M, Knudsen K, Boysen G, Demichelis F, de Bono JS (2019) RB1 Heterogeneity in Advanced Metastatic Castration-Resistant Prostate Cancer. Clin. Cancer Res., 25(2):687-697, doi:10.1158/1078-0432.CCR-18-2068.

Beltran H, Oromendia C, Danila DC, Montgomery B, Hoimes C, Szmulewitz RZ, Vaishampayan U, Armstrong AJ, Stein M, Pinski J, Mosquera JM, Sailer V, Bareja R, Romanel A, Gumpeni N, Sboner A, Dardenne E, Puca L, Prandi D, Rubin MA, Scher HI, Rickman DS, Demichelis F, Nanus DM, Ballman KV, Tagawa ST (2019) A Phase II Trial of the Aurora Kinase A Inhibitor Alisertib for Patients with Castration-resistant and Neuroendocrine Prostate Cancer: Efficacy and Biomarkers. Clin. Cancer Res., 25(1):43-51, doi:10.1158/1078-0432.CCR-18-1912.

Liang Y, Tebaldi T, Rejeski K, Joshi P, Stefani G, Taylor A, Song Y, Vasic R, Maziarz J, Balasubramanian K, Ardasheva A, Ding A, Quattrone A, Halene S (2018) SRSF2 mutations drive oncogenesis by activating a global program of aberrant alternative splicing in hematopoietic cells. Leukemia, 32(12):2659-2671, doi:10.1038/s41375-018-0152-7.