Author: "Institute of Biotechnology (-2009)" - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Institute of Biotechnology (-2009)"' showing total 42 results

Start Over Author "Institute of Biotechnology (-2009)"

42 results on '"Institute of Biotechnology (-2009)"'

1. Functional reconstitution of human equilibrative nucleoside transporter-1 into styrene maleic acid co-polymer lipid particles

Author: University of Helsinki, Institute of Biotechnology, University of Helsinki, Institute of Biotechnology (-2009), Rehan, Shahid, Paavilainen, Ville O., Jaakola, Veli-Pekka, University of Helsinki, Institute of Biotechnology, University of Helsinki, Institute of Biotechnology (-2009), Rehan, Shahid, Paavilainen, Ville O., and Jaakola, Veli-Pekka
Abstract: The human equilibrative nucleoside transporter-1 (hENT1) is important for the entry of anti-cancer and antiviral nucleoside analog therapeutics into the cell, and thus for their efficacy. Understanding of hENT1 structure -function relationship could assist with development of nucleoside analogs with better cellular uptake properties. However, structural and biophysical studies of hENT1 remain challenging as the hydrophobic nature of the protein leads to complete aggregation upon detergent-based membrane isolation. Here we report detergent-free reconstitution of the hENT1 transporter into styrene maleic acid co-polymer lipid particles (SMALPs) that form a native lipid disc. SMALP-purified hENT1, expressed in Sf9 insect cells binds a variety of ligands with a similar affinity as the protein in native membrane, and exhibits increased thermal stability compared to detergent-solubilized hENT1. hENT1-SMALPs purified using FLAG affinity M2 resin yielded similar to 0.4 mg of active and homogenous protein per liter of culture as demonstrated by ligand binding, size-exclusion chromatography and SDS-PAGE analyses. Electrospray ionization mass spectrometry (ESI-MS) analysis showed that each hENT1 lipid disc contains 16 phosphatidylcholine (PC) and 2 phosphatidylethanolamine (PE) lipid molecules. Polyunsaturated lipids are specifically excluded from the hENT1 lipid discs, possibly reflecting a functional requirement for a dynamic lipid environment. Our work demonstrates that human nucleoside transporters can be extracted and purified without removal from their native lipid environment, opening up a wide range of possibilities for their biophysical and structural studies. (C) 2017 Elsevier B.V. All rights reserved.
Published: 2017

2. Exploring the Conserved Role of MANF in the Unfolded Protein Response in Drosophila melanogaster

Author: University of Helsinki, Institute of Biotechnology, University of Helsinki, Institute of Biotechnology (-2009), University of Helsinki, Department of Biosciences, Lindström, Riitta, Lindholm, Päivi, Kallijärvi, Jukka, Palgi, Mari, Saarma, Mart, Heino, Tapio I., University of Helsinki, Institute of Biotechnology, University of Helsinki, Institute of Biotechnology (-2009), University of Helsinki, Department of Biosciences, Lindström, Riitta, Lindholm, Päivi, Kallijärvi, Jukka, Palgi, Mari, Saarma, Mart, and Heino, Tapio I.
Abstract: Disturbances in the homeostasis of endoplasmic reticulum (ER) referred to as ER stress is involved in a variety of human diseases. ER stress activates unfolded protein response (UPR), a cellular mechanism the purpose of which is to restore ER homeostasis. Previous studies show that Mesencephalic Astrocyte-derived Neurotrophic Factor (MANF) is an important novel component in the regulation of UPR. In vertebrates, MANF is upregulated by ER stress and protects cells against ER stress-induced cell death. Biochemical studies have revealed an interaction between mammalian MANF and GRP78, the major ER chaperone promoting protein folding. In this study we discovered that the upregulation of MANF expression in response to drug-induced ER stress is conserved between Drosophila and mammals. Additionally, by using a genetic in vivo approach we found genetic interactions between Drosophila Manf and genes encoding for Drosophila homologues of GRP78, PERK and XBP1, the key components of UPR. Our data suggest a role for Manf in the regulation of Drosophila UPR.
Published: 2016

3. Protist predation can select for bacteria with lowered susceptibility to infection by lytic phages

Author: University of Helsinki, Department of Biosciences, University of Helsinki, Department of Food and Environmental Sciences, University of Helsinki, Faculty of Veterinary Medicine, University of Helsinki, Institute of Biotechnology (-2009), Örmälä-Odegrip, Anni-Maria, Ojala, Ville, Hiltunen, Teppo, Zhang, Ji, Bamford, Jaana K. H., Laakso, Jouni, University of Helsinki, Department of Biosciences, University of Helsinki, Department of Food and Environmental Sciences, University of Helsinki, Faculty of Veterinary Medicine, University of Helsinki, Institute of Biotechnology (-2009), Örmälä-Odegrip, Anni-Maria, Ojala, Ville, Hiltunen, Teppo, Zhang, Ji, Bamford, Jaana K. H., and Laakso, Jouni
Abstract: Background: Consumer-resource interactions constitute one of the most common types of interspecific antagonistic interaction. In natural communities, complex species interactions are likely to affect the outcomes of reciprocal co-evolution between consumers and their resource species. Individuals face multiple enemies simultaneously, and consequently they need to adapt to several different types of enemy pressures. In this study, we assessed how protist predation affects the susceptibility of bacterial populations to infection by viral parasites, and whether there is an associated cost of defence on the competitive ability of the bacteria. As a study system we used Serratia marcescens and its lytic bacteriophage, along with two bacteriovorous protists with distinct feeding modes: Tetrahymena thermophila (particle feeder) and Acanthamoeba castellanii (surface feeder). The results were further confirmed with another study system with Pseudomonas and Tetrahymena thermophila. Results: We found that selection by protist predators lowered the susceptibility to infections by lytic phages in Serratia and Pseudomonas. In Serratia, concurrent selection by phages and protists led to lowered susceptibility to phage infections and this effect was independent from whether the bacteria shared a co-evolutionary history with the phage population or not. Bacteria that had evolved with phages were overall more susceptible to phage infection (compared to bacteria with history with multiple enemies) but they were less vulnerable to the phages they had co-evolved with than ancestral phages. Selection by bacterial enemies was costly in general and was seen as a lowered fitness in absence of phages, measured as a biomass yield. Conclusions: Our results show the significance of multiple species interactions on pairwise consumer-resource interaction, and suggest potential overlap in defending against predatory and parasitic enemies in microbial consumer-resource communities. Ultimately, our
Published: 2015

4. Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses

Author: University of Helsinki, Institute of Biotechnology (-2009), University of Helsinki, Department of Biosciences, Krupovic, Mart, Bamford, Dennis H., Koonin, Eugene V., University of Helsinki, Institute of Biotechnology (-2009), University of Helsinki, Department of Biosciences, Krupovic, Mart, Bamford, Dennis H., and Koonin, Eugene V.
Published: 2014

5. Short-term Preoperative Dietary Restriction Is Neuroprotective in a Rat Focal Stroke Model

Author: University of Helsinki, Institute of Biotechnology, University of Helsinki, Institute of Biotechnology (-2009), Varendi, Kärt, Airavaara, Mikko, Anttila, Jenni, Vose, Sarah, Planken, Anu, Saarma, Mart, Mitchell, James R., Andressoo, Jaan-Olle, University of Helsinki, Institute of Biotechnology, University of Helsinki, Institute of Biotechnology (-2009), Varendi, Kärt, Airavaara, Mikko, Anttila, Jenni, Vose, Sarah, Planken, Anu, Saarma, Mart, Mitchell, James R., and Andressoo, Jaan-Olle
Published: 2014

6. The role of Tal2 and Tal1 in the differentiation of midbrain GABAergic neuron precursors.

Author: University of Helsinki, Institute of Biotechnology, University of Helsinki, Institute of Biotechnology (-2009), University of Helsinki, Department of Biosciences, University of Helsinki, Faculty of Veterinary Medicine, Achim, Kaia, Peltopuro, Paula Piritta, Lahti, Laura Susanna, Tsai, Hui-Hsin, Zachariah, Alyssa, Åstrand, Mia, Salminen, Marjo, Rowitch, David, Partanen, Juha, University of Helsinki, Institute of Biotechnology, University of Helsinki, Institute of Biotechnology (-2009), University of Helsinki, Department of Biosciences, University of Helsinki, Faculty of Veterinary Medicine, Achim, Kaia, Peltopuro, Paula Piritta, Lahti, Laura Susanna, Tsai, Hui-Hsin, Zachariah, Alyssa, Åstrand, Mia, Salminen, Marjo, Rowitch, David, and Partanen, Juha
Published: 2013

7. Gene expression analysis of Drosophilaa Manf mutants reveals perturbations in membrane traffic and major metabolic changes

Author: University of Helsinki, Institute of Biotechnology (-2009), University of Helsinki, Institute of Biotechnology, University of Helsinki, Department of Biosciences, Palgi, Mari, Greco, Dario, Lindström, Riitta, Auvinen, Petri, Heino, Tapio I., University of Helsinki, Institute of Biotechnology (-2009), University of Helsinki, Institute of Biotechnology, University of Helsinki, Department of Biosciences, Palgi, Mari, Greco, Dario, Lindström, Riitta, Auvinen, Petri, and Heino, Tapio I.
Published: 2012

8. Analysis of the Potential Role of GluA4 Carboxyl-Terminus in PDZ Interactions

Author: University of Helsinki, Department of Biosciences, University of Helsinki, Institute of Biotechnology (-2009), University of Helsinki, Institute of Biotechnology, University of Helsinki, Medicum, Coleman, Sarah Kate, Cai, Chunlin, Kalkkinen, Nisse, Korpi, Esa R., Keinanen, Kari, University of Helsinki, Department of Biosciences, University of Helsinki, Institute of Biotechnology (-2009), University of Helsinki, Institute of Biotechnology, University of Helsinki, Medicum, Coleman, Sarah Kate, Cai, Chunlin, Kalkkinen, Nisse, Korpi, Esa R., and Keinanen, Kari
Published: 2010

9. The dynamic interest in topics within the biomedical scientific community

Author: University of Helsinki, Institute of Biotechnology (-2009), Michon, Frederic, Tummers, Mark, University of Helsinki, Institute of Biotechnology (-2009), Michon, Frederic, and Tummers, Mark
Published: 2009

10. Design, synthesis, and biological activity of isophthalic acid derivatives targeted to the C1 domain of protein kinase C

Author: University of Helsinki, Farmaseuttisen kemian osasto (-2009), University of Helsinki, Farmakologian ja toksikologian osasto (-2009), University of Helsinki, Institute of Biotechnology (-2009), University of Helsinki, Lääkkeen keksintä- ja kehitysteknologian keskus (DDTC) (-2009), Boije af Gennäs, Gustav, Talman, Virpi, Aitio, Olli, Ekokoski, Elina, Finel, Moshe, Tuominen, Raimo K, Yli-Kauhaluoma, Jari, University of Helsinki, Farmaseuttisen kemian osasto (-2009), University of Helsinki, Farmakologian ja toksikologian osasto (-2009), University of Helsinki, Institute of Biotechnology (-2009), University of Helsinki, Lääkkeen keksintä- ja kehitysteknologian keskus (DDTC) (-2009), Boije af Gennäs, Gustav, Talman, Virpi, Aitio, Olli, Ekokoski, Elina, Finel, Moshe, Tuominen, Raimo K, and Yli-Kauhaluoma, Jari
Abstract: Protein kinase C (PKC) is a widely studied molecular target for the treatment of cancer and other diseases. We have approached the issue of modifying PKC function by targeting the C1 domain in the regulatory region of the enzyme. Using the X-ray crystal structure of the PKC delta C1b domain, we have discovered conveniently synthesizable derivatives of dialkyl 5-(hydroxymethyl)isophthalate that can act as potential C1 domain ligands. Structure-activity studies confirmed that the important functional groups predicted by modeling were indispensable for binding to the C1 domain and that the modifications of these groups diminished binding. The most promising compounds were able to displace radiolabeled phorbol ester ([H-3]PDBu) from PKC alpha and delta at K-i values in the range of 200-900 nM. Furthermore, the active isophthalate derivatives could modify PKC activation in living cells either by inducing PKC-dependent ERK phosphorylation or by inhibiting phorbol-induced ERK phosphorylation. In conclusion, we report here, for the first time. that derivatives of isophthalic acid represent an attractive novel group of C1 domain ligands that can be used as research tools or further modified for potential drug development.
Published: 2009

11. Physiology, pathology and relatedness of human tissues from gene expression meta-analysis

Author: University of Helsinki, Institute of Biotechnology (-2009), University of Helsinki, Department of Biosciences, University of Helsinki, Neuroscience center (-2009), Greco, Dario, Somervuo, Panu, Di Lieto, Antonio, Raitila, Tuomas, Nitsch, Lucio, Castren, Eero, Auvinen, Petri, University of Helsinki, Institute of Biotechnology (-2009), University of Helsinki, Department of Biosciences, University of Helsinki, Neuroscience center (-2009), Greco, Dario, Somervuo, Panu, Di Lieto, Antonio, Raitila, Tuomas, Nitsch, Lucio, Castren, Eero, and Auvinen, Petri
Published: 2008

12. Bacteria, phages and septicemia

Author: University of Helsinki, Institute of Biotechnology (-2009), University of Helsinki, Dep. of Bacteriology and Immunology (Haartman Institute) (-2009), University of Helsinki, Department of Biological and Environmental Sciences (-2009), Gaidelyte, Ausra, Vaara, Martti, Bamford, Dennis H, University of Helsinki, Institute of Biotechnology (-2009), University of Helsinki, Dep. of Bacteriology and Immunology (Haartman Institute) (-2009), University of Helsinki, Department of Biological and Environmental Sciences (-2009), Gaidelyte, Ausra, Vaara, Martti, and Bamford, Dennis H
Abstract: The use of phages is an attractive option to battle antibiotic resistant bacteria in certain bacterial infections, but the role of phage ecology in bacterial infections is obscure. Here we surveyed the phage ecology in septicemia, the most severe type of bacterial infection. We observed that the majority of the bacterial isolates from septicemia patients spontaneously secreted phages active against other isolates of the same bacterial strain, but not to the strain causing the disease. Such phages were also detected in the initial blood cultures, indicating that phages are circulating in the blood at the onset of sepsis. The fact that most of the septicemic bacterial isolates carry functional prophages suggests an active role of phages in bacterial infections. Apparently, prophages present in sepsis-causing bacterial clones play a role in clonal selection during bacterial invasion.
Published: 2007

13. Cryo-EM structure of ssDNA bacteriophage ΦCjT23 provides insight into early virus evolution

Author: Nejc Kejzar, Elina Laanto, Ilona Rissanen, Vahid Abrishami, Muniyandi Selvaraj, Sylvain Moineau, Janne Ravantti, Lotta-Riina Sundberg, Juha T. Huiskonen, Institute of Biotechnology (-2009), Helsinki Institute of Life Science HiLIFE, Joint Activities, Molecular and Integrative Biosciences Research Programme, Molecular Principles of Viruses, Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, Biosciences, Laanto, Elina [0000-0003-4172-3128], Rissanen, Ilona [0000-0003-4937-1825], Abrishami, Vahid [0000-0002-3772-7663], Selvaraj, Muniyandi [0000-0001-7793-6323], Moineau, Sylvain [0000-0002-2832-5101], Sundberg, Lotta-Riina [0000-0003-3510-4398], Huiskonen, Juha T [0000-0002-0348-7323], and Apollo - University of Cambridge Repository
Subjects: 631/326/1321, bacteriophages, virukset, cryoelectron microscopy, evoluutio, General Physics and Astronomy, elektronimikroskopia, DNA, Single-Stranded, 45/23, Flavobacterium, General Biochemistry, Genetics and Molecular Biology, bakteriofagit, 631/45/535/1258/1259, viral evolution, 631/326/596/2554, Bacteriophages, Multidisciplinary, fylogenia, 45, fylogenetiikka, Cryoelectron Microscopy, 101/28, article, General Chemistry, perimä, 1182 Biochemistry, cell and molecular biology, Capsid Proteins
Abstract: The origin of viruses remains an open question. While lack of detectable sequence similarity hampers the analysis of distantly related viruses, structural biology investigations of conserved capsid protein structures facilitate the study of distant evolutionary relationships. Here we characterize the lipid-containing ssDNA temperate bacteriophage ΦCjT23, which infects Flavobacterium sp. (Bacteroidetes). We report ΦCjT23-like sequences in the genome of strains belonging to several Flavobacterium species. The virion structure determined by cryogenic electron microscopy reveals similarities to members of the viral kingdom Bamfordvirae that currently consists solely of dsDNA viruses with a major capsid protein composed of two upright β-sandwiches. The minimalistic structure of ΦCjT23 suggests that this phage serves as a model for the last common ancestor between ssDNA and dsDNA viruses in the Bamfordvirae. Both ΦCjT23 and the related phage FLiP infect Flavobacterium species found in several environments, suggesting that these types of viruses have a global distribution and a shared evolutionary origin. Detailed comparisons to related, more complex viruses not only expand our knowledge about this group of viruses but also provide a rare glimpse into early virus evolution.
Published: 2022
Full Text: View/download PDF

14. Climate mediates continental scale patterns of stream microbial functional diversity

Author: Jizhong Zhou, Emilio O. Casamayor, Félix Picazo, Lijuan Ren, Jianjun Wang, Qinglong L. Wu, Annika Vilmi, Yongqin Liu, Janne Soininen, Juha Aalto, Ji Shen, National Natural Science Foundation of China, Chinese Academy of Sciences, Institute of Biotechnology (-2009), Department of Geosciences and Geography, Biosciences, and Helsinki Institute of Sustainability Science (HELSUS)
Subjects: DECOMPOSITION, 0106 biological sciences, Microbiology (medical), China, Microbial functional genes, Climate, Biodiversity, Beta diversity, Climate change, Elevational gradients, Biology, 010603 evolutionary biology, 01 natural sciences, Microbiology, Freshwater ecosystem, lcsh:Microbial ecology, 03 medical and health sciences, Rivers, REGRESSION, WATER, Ecosystem, 14. Life underwater, BETA-DIVERSITY, Macroecology, TEMPERATURE, 1172 Environmental sciences, 030304 developmental biology, 0303 health sciences, Norway, Ecology, Research, SPECIES RICHNESS, 15. Life on land, COMMUNITY, Stream biofilm, Spain, 13. Climate action, lcsh:QR100-130, BIODIVERSITY, Alpha diversity, Species richness, SOIL CARBON, human activities
Abstract: [Background]: Understanding the large-scale patterns of microbial functional diversity is essential for anticipating climate change impacts on ecosystems worldwide. However, studies of functional biogeography remain scarce for microorganisms, especially in freshwater ecosystems. Here we study 15,289 functional genes of stream biofilm microbes along three elevational gradients in Norway, Spain and China., [Results]: We find that alpha diversity declines towards high elevations and assemblage composition shows increasing turnover with greater elevational distances. These elevational patterns are highly consistent across mountains, kingdoms and functional categories and exhibit the strongest trends in China due to its largest environmental gradients. Across mountains, functional gene assemblages differ in alpha diversity and composition between the mountains in Europe and Asia. Climate, such as mean temperature of the warmest quarter or mean precipitation of the coldest quarter, is the best predictor of alpha diversity and assemblage composition at both mountain and continental scales, with local non-climatic predictors gaining more importance at mountain scale. Under future climate, we project substantial variations in alpha diversity and assemblage composition across the Eurasian river network, primarily occurring in northern and central regions, respectively., [Conclusions]: We conclude that climate controls microbial functional gene diversity in streams at large spatial scales; therefore, the underlying ecosystem processes are highly sensitive to climate variations, especially at high latitudes. This biogeographical framework for microbial functional diversity serves as a baseline to anticipate ecosystem responses and biogeochemical feedback to ongoing climate change., The study was supported by National Natural Science Foundation of China (91851117), the Program of Global Change and Mitigation (2017YFA0605200), CAS Key Research Program of Frontier Sciences (QYZDB-SSW-DQC043), CAS Strategic Pilot Science and Technology (XDA20050101), and National Natural Science Foundation of China (41571058, 41871048). AV was supported by the Chinese Academy of Sciences President’s International Fellowship Initiative (2018PS0007). EOC was supported by grant BRIDGES CGL2015-69043-P (Spanish Office for Science-MINECO-ERDF).
Published: 2020
Full Text: View/download PDF

15. Activated I-BAR IRSp53 clustering controls the formation of VASP-actin-based membrane protrusions

Author: Feng-Ching Tsai, J. Michael Henderson, Zack Jarin, Elena Kremneva, Yosuke Senju, Julien Pernier, Oleg Mikhajlov, John Manzi, Konstantin Kogan, Christophe Le Clainche, Gregory A. Voth, Pekka Lappalainen, Patricia Bassereau, TRIMM - Translational Immunology Research Program, Institute of Biotechnology, Institute of Biotechnology (-2009), Biosciences, and Pekka Lappalainen / Principal Investigator
Subjects: Multidisciplinary, 1182 Biochemistry, cell and molecular biology, macromolecular substances
Abstract: Funding Information: Acknowledgments: The computations were supported by the University of Chicago Research Funding Information: The computations were supported by the University of Chicago Research Computing Center (RCC). We thank E. Coudrier and C. Simon for insightful discussions. We also thank F. Di Federico for handling plasmids, F. Tabarin-Cayrac for cell sorting, and A.-S. Mace for ImageJ programming assistance. F.-C.T., C.L.C., and P.B. are members of the CNRS consortium AQV. F.-C.T. and P.B. are members of the Labex Cell(n)Scale (ANR-11-LABX0038) and Paris Sciences et Lettres (ANR-10-IDEX-0001-02). We acknowledge the Cell and Tissue Imaging Core facility (PICT IBiSA), Institut Curie, member of the French National Research Infrastructure France-BioImaging (ANR10-INBS-04). This work was supported by Human Frontier Science Program (HFSP) grant RGP0005/2016 (to F.-C.T., J.M.H., G.A.V., P.L., and P.B.), Institut Curie and the Centre National de la Recherche Scientifique (CNRS) (to F.-C.T., J.M.H., and P.B.), Marie Curie actions H2020-MSCA-IF-2014 (to F.-C.T.), EMBO Long-Term fellowship ALTF 1527-2014 (to F.-C.T.), Pasteur Foundation Fellowship (to J.M.H.), Agence Nationale pour la Recherche ANR-20-CE13-0032 (to J.M.H. and P.B.) and ANR-20-CE11-0010-01 (to F.-C.T), Université Paris Sciences et Lettres-QLife Institute ANR-17-CONV-0005 Q-LIFE (to P.B.), FY 2015 Researcher Exchange Program between the Japan Society for the Promotion of Science and Academy of Finland (to Y.S.), the Takeda Science Foundation (to Y.S.), the Wesco Scientific Promotion Foundation (to Y.S.), Agence Nationale pour la Recherche ANR-18-CE13-0026-01 and ANR-21-CE13-0010-03 (to C.L.C.), Cancer Society Finland 4705949 (to P.L.), and U.S. National Institutes of Health (NIH) Institute of General Medical Sciences (NIGMS) grant R01-GM063796 (to G.A.V. and Z.J.) Publisher Copyright: Copyright © 2022 The Authors, some rights reserved. Filopodia are actin-rich membrane protrusions essential for cell morphogenesis, motility, and cancer invasion. How cells control filopodium initiation on the plasma membrane remains elusive. We performed experiments in cellulo, in vitro, and in silico to unravel the mechanism of filopodium initiation driven by the membrane curvature sensor IRSp53 (insulin receptor substrate protein of 53 kDa). We showed that full-length IRSp53 self-assembles into clusters on membranes depending on PIP2. Using well-controlled in vitro reconstitution systems, we demonstrated that IRSp53 clusters recruit the actin polymerase VASP (vasodilator-stimulated phosphoprotein) to assemble actin filaments locally on membranes, leading to the generation of actin-filled membrane protrusions reminiscent of filopodia. By pulling membrane nanotubes from live cells, we observed that IRSp53 can only be enriched and trigger actin assembly in nanotubes at highly dynamic membrane regions. Our work supports a regulation mechanism of IRSp53 in its attributes of curvature sensation and partner recruitment to ensure a precise spatial-temporal control of filopodium initiation.
Published: 2022
Full Text: View/download PDF

16. A kinder approach to science

Author: Almeida-Souza, Leonardo, O'Brien, Lilian, Faculty of Biological and Environmental Sciences, Institute of Biotechnology (-2009), Helsinki Institute of Life Science HiLIFE, Faculty Common Matters (Faculty of Social Sciences), Practical Philosophy, and Helsinki Collegium for Advanced Studies
Subjects: 611 Philosophy, Abusive supervision
Abstract: Publisher Copyright: © 2021 Elsevier Ltd To be kind is to protect and promote the well-being of others. We borrow this definition from the philosophical literature to formulate a simple and powerful principle to make scientific communities and institutions healthier, fairer, and more inclusive. Non
Published: 2022

17. Characterizing the initial conditions of heavy-ion collisions at the LHC with mean transverse momentum and anisotropic flow correlations

Author: Acharya, Shreyasi, Adamova, Dagmar, Adler, Alexander, Adolfsson, Jonatan, Aglieri Rinella, Gianluca, Agnello, Michelangelo, Agrawal, Neelima, Ahammed, Zubayer, Ahmad, Shakeel, Ahn, Sang Un, Ahuja, Ishaan, Akbar, Zaenal, Akindinov, Alexander, Al-Turany, Mohammad, Alam, Sk Noor, Aleksandrov, Dmitry, Alessandro, Bruno, Alfanda, Haidar Mas'ud, Alfaro Molina, Jose Ruben, Ali, Bushra, Ali, Yasir, Alici, Andrea, Alizadehvandchali, Negin, Alkin, Anton, Alme, Johan, Alocco, Giacomo, Alt, Torsten, Altsybeev, Igor, Anaam, Mustafa, Andrei, Cristian, Andreou, Dimitra, Andronic, Anton, Angeletti, Massimo, Anguelov, Venelin, Antinori, Federico, Antonioli, Pietro, Chandra, Anuj, Apadula, Nicole, Aphecetche, Laurent Bernard, Appelshaeuser, Harald, Arcelli, Silvia, Arnaldi, Roberta, Arsene, Ionut Cristian, Arslandok, Mesut, Augustinus, Andre, Averbeck, Ralf Peter, Aziz, Sizar, Azmi, Mohd Danish, Badala, Angela, Baek, Yongwook, Bai, Xiaozhi, Bailhache, Raphaelle Marie, Bailung, Yoshini, Bala, Renu, Balbino, Alessandro, Baldisseri, Alberto, Balis, Bartosz, Banerjee, Debjani, Banoo, Zarina, Barbera, Roberto, Barioglio, Luca, Barlou, Maria, Barnafoldi, Gergely Gabor, Barnby, Lee Stuart, Ramillien Barret, Valerie, Bartels, Clara, Barth, Klaus, Bartsch, Esther, Baruffaldi, Filippo, Bastid, Nicole, Basu, Sumit, Batigne, Guillaume, Batyunya, Boris, Bauri, Dibakar, Bazo Alba, Jose Luis, Bearden, Ian Gardner, Beattie, Caitlin, Becht, Pascal, Belikov, Iouri, Bell Hechavarria, Ailec, Bellini, Francesca, Bellwied, Rene, Belokurova, Svetlana, Belyaev, Vladimir, Bencedi, Gyula, Beole, Stefania Maria, Bercuci, Alexandru, Berdnikov, Yaroslav, Berdnikova, Anastasia, Bergmann, Luisa, Besoiu, Mihaela Gabriela, Betev, Latchezar, Bhaduri, Partha Pratim, Bhasin, Anju, Bhat, Inayat Rasool, Bhat, Mohammad Asif, Bhattacharjee, Buddhadeb, Bhattacharya, Purba, Bianchi, Livio, Bianchi, Nicola, Bielcik, Jaroslav, Bielcikova, Jana, Biernat, Jacek Bogumil, Bilandzic, Ante, Biro, Gabor, Biswas, Saikat, Blair, Justin Thomas, Blau, Dmitry, Blidaru, Bogdan Mihail, Blume, Christoph, Boca, Gianluigi, Bock, Friederike, Bogdanov, Alexey, Boi, Stefano, Bok, Jeongsu, Boldizsar, Laszlo, Bolozdynya, Alexander, Bombara, Marek, Bond, Peter Matthew, Bonomi, Germano, Borel, Herve, Borissov, Alexander, Bossi, Hannah, Botta, Elena, Bratrud, Lars, Braun-munzinger, Peter, Bregant, Marco, Broz, Michal, Bruno, Giuseppe Eugenio, Buckland, Matthew Daniel, Budnikov, Dmitry, Buesching, Henner, Bufalino, Stefania, Bugnon, Ophelie, Buhler, Paul Alois, Buthelezi, Edith Zinhle, Bashir Butt, Jamila, Bylinkin, Aleksandr, Bysiak, Sebastian Adam, Cai, Mengke, Caines, Helen Louise, Caliva, Alberto, Calvo Villar, Ernesto, Mejia Camacho, Juan Manuel, Soto Camacho, Rabi, Camerini, Paolo, De Moraes Canedo, Fabio, Carnesecchi, Francesca, Caron, Robin Albert Andre, Castillo Castellanos, Javier Ernesto, Casula, Ester Anna Rita, Catalano, Fabio, Ceballos Sanchez, Cesar, Chakraborty, Pritam, Chandra, Sinjini, Chapeland, Sylvain, Chartier, Marielle, Chattopadhyay, Subhasis, Chattopadhyay, Sukalyan, Garcia Chavez, Tonatiuh, Cheng, Tiantian, Cheshkov, Cvetan Valeriev, Cheynis, Brigitte, Chibante Barroso, Vasco Miguel, Dobrigkeit Chinellato, David, Cho, Soyeon, Chochula, Peter, Christakoglou, Panagiotis, Christensen, Christian Holm, Christiansen, Peter, Chujo, Tatsuya, Cicalo, Corrado, Cifarelli, Luisa, Cindolo, Federico, Ciupek, Michael, Clai, Giulia, Cleymans, Jean Willy Andre, Colamaria, Fabio Filippo, Colburn, Jonathan Samuel, Colella, Domenico, Collu, Alberto, Colocci, Manuel, Concas, Matteo, Conesa Balbastre, Gustavo, Conesa Del Valle, Zaida, Contin, Giacomo, Contreras Nuno, Jesus Guillermo, Coquet, Maurice Louis, Cormier, Thomas Michael, Cortese, Pietro, Cosentino, Mauro Rogerio, Costa, Filippo, Costanza, Susanna, Crochet, Philippe, Cruz Torres, Reynier, Cuautle Flores, Eleazar, Cui, Pengyao, Cunqueiro Mendez, Leticia, Dainese, Andrea, Danisch, Meike Charlotte, Danu, Andrea, Das, Prottay, Das, Prottoy, Das, Supriya, Dash, Sadhana, De Caro, Annalisa, De Cataldo, Giacinto, De Cilladi, Lorenzo, De Cuveland, Jan, De Falco, Alessandro, De Gruttola, Daniele, De Marco, Nora, De Martin, Chiara, De Pasquale, Salvatore, Deb, Suman, Franz Degenhardt, Hermann, Deja, Kamil Rafal, Del Grande, Raffaele, Dello Stritto, Luigi, Deng, Wenjing, Dhankher, Preeti, Di Bari, Domenico, Di Mauro, Antonio, Arteche Diaz, Raul, Dietel, Thomas, Ding, Yanchun, Divia, Roberto, Dixit, Dhruv Utpalkumar, Djuvsland, Oeystein, Dmitrieva, Uliana, Do, Jaehyeon, Dobrin, Alexandru Florin, Donigus, Benjamin, Dubey, Anand Kumar, Dubla, Andrea, Dudi, Sandeep, Dupieux, Pascal, Dzalaiova, Natalia, Eder, Tabea Maria, Ehlers, Raymond James, Eikeland, Viljar Nilsen, Eisenhut, Florian, Elia, Domenico, Erazmus, Barbara Ewa, Ercolessi, Francesca, Erhardt, Filip, Erokhin, Andrey, Ersdal, Magnus Rentsch, Espagnon, Bruno, Eulisse, Giulio, Evans, David, Evdokimov, Sergey, Fabbietti, Laura, Faggin, Mattia, Faivre, Julien, Fan, Feng, Fantoni, Alessandra, Fasel, Markus, Fecchio, Pietro, Feliciello, Alessandro, Feofilov, Grigorii, Fernandez Tellez, Arturo, Ferrero, Andrea, Ferretti, Alessandro, Feuillard, Victor Jose Gaston, Figiel, Jan, Filova, Vendulka, Finogeev, Dmitry, Fionda, Fiorella, Fiorenza, Gabriele, Flor, Fernando Antonio, Flores, Amanda Nicole, Foertsch, Siegfried Valentin, Fokin, Sergey, Fragiacomo, Enrico, Frajna, Eszter, Francisco, Audrey, Fuchs, Ulrich, Funicello, Nicola, Furget, Christophe, Furs, Artur, Gaardhoeje, Jens Joergen, Gagliardi, Martino, Gago Medina, Alberto Martin, Gal, Arthur Willem Jean, Duarte Galvan, Carlos, Gangadharan, Dhevan Raja, Ganoti, Paraskevi, Garabatos Cuadrado, Jose Maria, Alvarado Garcia, Jesus Ricardo, Garcia-solis, Edmundo Javier, Garg, Kunal, Gargiulo, Corrado, Garibli, Aydan, Demmich, Katharina, Gasik, Piotr, Gauger, Erin Frances, Gautam, Amrit, De Leone Gay, Maria Beatriz, Germain, Marie, Ghosh, Premomoy, Ghosh, Sanjay Kumar, Giacalone, Marco, Gianotti, Paola, Giubellino, Paolo, Giubilato, Piero, Glaenzer, Aude Marie Camille, Glassel, Peter, Glimos, Ewa, Goh, Daniel Jia Qin, Gonzalez, Victor, Gonzalez Trueba, Laura Helena, Gorbunov, Sergey, Gorgon, Marek Boguslaw, Gorlich, Lidia Maria, Gotovac, Sven, Grabski, Varlen, Graczykowski, Lukasz Kamil, Greiner, Leo Clifford, Grelli, Alessandro, Grigoras, Costin, Grigoryev, Vladislav, Grigoryan, Smbat, Grosa, Fabrizio, Grosse-oetringhaus, Jan Fiete, Grosso, Raffaele, Grund, David, Garcia Guardiano, Gabriel, Guernane, Rachid, Guilbaud, Maxime Rene Joseph, Gulbrandsen, Kristjan Herlache, Gunji, Taku, Guo, Wenda, Gupta, Anik, Gupta, Ramni, Paisano Guzman, Sergio, Gyulai, Laszlo, Habib, Michael Karim, Hadjidakis, Cynthia Marie, Hamagaki, Hideki, Hamid, Mohammed, Hannigan, Ryan Patrick, Haque, Md Rihan, Gromada, Alena, Harris, John William, Harton, Austin Vincent, Hasenbichler, Jan Anton, Hassan, Hadi, Hatzifotiadou, Despina, Hauer, Philip, Havener, Laura Brittany, Heckel, Stefan Thomas, Hellbär, Ernst, Helstrup, Haavard, Herman, Tomas, Gonzalez Hernandez, Emma, Herrera Corral, Gerardo Antonio, Herrmann, Florian, Hetland, Kristin Fanebust, Hillemanns, Hartmut, Hills, Christopher, Hippolyte, Boris, Hofman, Bas, Hohlweger, Bernhard, Honermann, Jan, Hong, Geun Hee, Horak, David, Hornung, Sebastian, Horzyk, Adrian, Hosokawa, Ritsuya, Hou, Yongzhen, Hristov, Peter Zahariev, Hughes, Charles, Huhn, Patrick, Huhta, Laura Maria, Van Hulse, Charlotte, Humanic, Thomas, Hushnud, Hushnud, Tarasovicova, Lucia Anna, Hutson, Alek, Iddon, James Philip, Ilkaev, Radiy, Ilyas, Hira, Inaba, Motoi, Innocenti, Gian Michele, Ippolitov, Mikhail, Isakov, Artem, Isidori, Tommaso, Islam, Md Samsul, Ivanov, Marian, Ivanov, Vladimir, Izucheev, Vladimir, Jablonski, Miroslaw, Jacak, Barbara, Jacazio, Nicolo, Jacobs, Peter Martin, Jadlovska, Slavka, Jadlovsky, Jan, Jaelani, Syaefudin, Jahnke, Cristiane, Jakubowska, Monika Joanna, Jalotra, Ashish, Janik, Malgorzata Anna, Janson, Thomas, Jercic, Marko, Jevons, Oliver Thomas, Paz Jimenez, Alom Antonio, Jonas, Florian, Jones, Peter Graham, Jowett, John, Jung, Jerome, Jung, Michael, Junique, Antoine Jean-simon, Jusko, Anton, Kabus, Maja Jadwiga, Kaewjai, Jetnipit, Kalinak, Peter, Kalteyer, Annalena, Kalweit, Alexander Philipp, Kaplin, Vladimir, Karasu Uysal, Ayben, Karatovic, David, Karavichev, Oleg, Karavicheva, Tatiana, Karczmarczyk, Przemyslaw, Karpechev, Evgeny, Kashyap, Varchaswi, Kazantsev, Andrey, Kebschull, Udo Wolfgang, Keidel, Ralf, Keijdener, Darius, Keil, Markus, Ketzer, Bernhard Franz, Khabanova, Zhanna, Khan, Ahsan Mehmood, Khan, Shaista, Khanzadeev, Alexei, Kharlov, Yury, Khatun, Anisa, Khuntia, Arvind, Kileng, Bjarte, Kim, Beomkyu, Kim, Chong, Kim, Dong Jo, Kim, Eun Joo, Kim, Jaehyun, Kim, Jinsook, Kim, Jiyoung, Kim, Junlee, Kim, Minjung, Kim, Se Yong, Kim, Taejun, Kirsch, Stefan, Kisel, Ivan, Kiselev, Sergey, Kisiel, Adam Ryszard, Kitowski, Jacek Pawel, Klay, Jennifer Lynn, Klein, Jochen, Klein, Spencer Robert, Klein-boesing, Christian, Kleiner, Matthias, Klemenz, Thomas, Kluge, Alexander, Knospe, Anders Garritt, Kobdaj, Chinorat, Kollegger, Thorsten, Kondratyev, Andrey, Kondratyeva, Natalia, Kondratyuk, Evgeny, Konig, Joshua Leon, Konigstorfer, Stephan Alexander, Konopka, Piotr Jan, Kornakov, Georgui, Koryciak, Sebastian Dominik, Kotliarov, Artem, Kovalenko, Oleksandr, Kovalenko, Vladimir, Kowalski, Marek, Kralik, Ivan, Kravcakova, Adela, Kreis, Lukas, Krivda, Marian, Krizek, Filip, Krizkova Gajdosova, Katarina, Kroesen, Martin, Kruger, Mario, Krupova, Diana Maria, Kryshen, Evgeny, Krzewicki, Mikolaj, Kucera, Vit, Kuhn, Christian Claude, Kuijer, Paulus Gerardus, Kumaoka, Takuya, Kumar, Deekshit, Kumar, Lokesh, Kumar, Navneet, Kundu, Sourav, Kurashvili, Podist, Kurepin, Alexander, Kurepin, Alexey, Kuryakin, Alexey, Kushpil, Svetlana, Kvapil, Jakub, Kweon, Min Jung, Kwon, Jiyeon, Kwon, Youngil, La Pointe, Sarah Louise, La Rocca, Paola, Lai, Yue Shi, Lakrathok, Anantachai, Lamanna, Massimo, Langoy, Rune, Lapidus, Kirill, Larionov, Pavel, Laudi, Elisa, Lautner, Lukas, Lavicka, Roman, Lazareva, Tatiana, Lea, Ramona, Lehrbach, Johannes, Lemmon, Roy Crawford, Leon Monzon, Ildefonso, Lesser, Ezra Douglas, Lettrich, Michael, Levai, Peter, Li, Xiaomei, Li, Xing Long, Lien, Jorgen Andre, Lietava, Roman, Lim, Bong-hwi, Lim, Sanghoon, Lindenstruth, Volker, Lindner, Amelia, Lippmann, Christian, Liu, Alwina Ruixin, Liu, Dong Hai, Liu, Jian, Lofnes, Ingrid Mckibben, Loginov, Vitaly, Loizides, Constantinos, Loncar, Petra, Lopez Lopez, Jorge Andres, Lopez, Xavier Bernard, Lopez Torres, Ernesto, Luhder, Jens Robert, Lunardon, Marcello, Luparello, Grazia, Ma, Yugang, Maevskaya, Alla, Mager, Magnus, Mahmoud, Tariq, Maire, Antonin, Malaev, Mikhail, Malik, Nasir Mehdi, Malik, Qasim Waheed, Malik, Salman Khurshid, Malinina, Liudmila, Mal Kevich, Dmitry, Mallick, Dukhishyam, Mallick, Neelkamal, Mandaglio, Giuseppe, Manko, Vladislav, Manso, Franck, Manzari, Vito, Mao, Yaxian, Margagliotti, Giacomo Vito, Margotti, Anselmo, Marin, Ana Maria, Markert, Christina, Marquard, Marco, Martin, Nicole Alice, Martinengo, Paolo, Martinez, Jacobb Lee, Martinez Hernandez, Mario Ivan, Martinez-garcia, Gines, Masciocchi, Silvia, Masera, Massimo, Masoni, Alberto, Massacrier, Laure Marie, Mastroserio, Annalisa, Mathis, Andreas Michael, Matonoha, Oliver, Toledo Matuoka, Paula Fernanda, Matyja, Adam Tomasz, Mayer, Christoph, Lafuente Mazuecos, Antonio, Mazzaschi, Francesco, Mazzilli, Marianna, Mazzoni, Alessandra Maria, Mdhluli, Joyful Elma, Mechler, Adrian Florin, Melikyan, Yury, Menchaca-rocha, Arturo Alejandro, Meninno, Elisa, Sasikumar Menon, Anjaly, Meres, Michal, Mhlanga, Sibaliso, Miake, Yasuo, Micheletti, Luca, Migliorin, Lucrezia Camilla, Mihaylov, Dimitar Lubomirov, Mikhaylov, Konstantin, Mishra, Aditya Nath, Miskowiec, Dariusz Czeslaw, Modak, Abhi, Mohanty, Auro Prasad, Mohanty, Bedangadas, Khan, Mohammed Mohisin, Molander, Mikael Andreas, Moravcova, Zuzana, Mordasini, Cindy, Moreira De Godoy, Denise Aparecida, Morozov, Igor, Morsch, Andreas, Mrnjavac, Teo, Muccifora, Valeria, Mudnic, Eugen, Muhlheim, Daniel Michael, Muhuri, Sanjib, Mulligan, James Declan, Mulliri, Alice, Gameiro Munhoz, Marcelo, Munzer, Robert Helmut, Murakami, Hikari, Murray, Sean, Musa, Luciano, Musinsky, Jan, Myrcha, Julian Wojciech, Naik, Bharati, Nair, Rahul Ramachandran, Nandi, Basanta Kumar, Nania, Rosario, Nappi, Eugenio, Nassirpour, Adrian Fereydon, Nath, Abhishek, Nattrass, Christine, Neagu, Alexandra, Negru, Adrian-eduard, Nellen, Lukas, Nesbo, Simon Voigt, Neskovic, Gvozden, Nesterov, Dmitrii, Nielsen, Borge Svane, Nielsen, Emil Gorm, Nikolaev, Sergey, Nikulin, Sergey, Nikulin, Vladimir, Noferini, Francesco, Noh, Seoyoung, Nomokonov, Petr, Norman, Jaime, Novitzky, Norbert, Nowakowski, Piotr, Nyanin, Alexander, Nystrand, Joakim Ingemar, Ogino, Masanori, Ohlson, Alice Elisabeth, Okorokov, Vitaly, Oleniacz, Janusz, Oliveira Da Silva, Antonio Carlos, Oliver, Michael Henry, Onnerstad, Anna, Oppedisano, Chiara, Ortiz Velasquez, Antonio, Osako, Takumi, Oskarsson, Anders Nils Erik, Otwinowski, Jacek Tomasz, Oya, Motomi, Oyama, Ken, Pachmayer, Yvonne Chiara, Padhan, Sonali, Pagano, Davide, Paic, Guy, Palasciano, Antonio, Pan, Jinjin, Panebianco, Stefano, Park, Jonghan, Parkkila, Jasper Elias, Pathak, Surya Prakash, Patra, Rajendra Nath, Paul, Biswarup, Pei, Hua, Peitzmann, Thomas, Peng, Xinye, Pereira, Luis Gustavo, Pereira Da Costa, Hugo Denis Antonio, Peresunko, Dmitry Yurevich, Mesa Perez, Guillermo, Perrin, Sebastien, Pestov, Yury, Petracek, Vojtech, Petrovici, Mihai, Peretti Pezzi, Rafael, Piano, Stefano, Pikna, Miroslav, Pillot, Philippe, Pinazza, Ombretta, Pinsky, Lawrence, Pinto, Chiara, Pisano, Silvia, Ploskon, Mateusz Andrzej, Planinic, Mirko, Pliquett, Fabian, Poghosyan, Martin, Polishchuk, Boris, Politano, Stefano, Poljak, Nikola, Pop, Amalia, Porteboeuf, Sarah Julie, Porter, R. Jefferson, Pozdniakov, Valeriy, Prasad, Sidharth Kumar, Preghenella, Roberto, Prino, Francesco, Pruneau, Claude Andre, Pshenichnov, Igor, Puccio, Maximiliano, Qiu, Shi, Quaglia, Luca, Quishpe Quishpe, Raquel Estefania, Ragoni, Simone, Rakotozafindrabe, Andry Malala, Ramello, Luciano, Rami, Fouad, Rodriguez Ramirez, Saul Anibal, Torres Ramos, Arianna Grisel, Rancien, Thibaut Albert, Raniwala, Rashmi, Raniwala, Sudhir, Rasanen, Sami Sakari, Rath, Rutuparna, Ravasenga, Ivan, Read, Kenneth Francis, Redelbach, Andreas Ralph, Redlich, Krzysztof, Rehman, Attiq Ur, Reichelt, Patrick Simon, Reidt, Felix, Reme-ness, Haakon Andre, Jakubcinova, Zuzana, Reygers, Klaus Johannes, Riabov, Andrei, Riabov, Viktor, Richert, Tuva Ora Herenui, Richter, Matthias Rudolph, Riegler, Werner, Riggi, Francesco, Ristea, Catalin-lucian, Rodriguez Cahuantzi, Mario, Roeed, Ketil, Rogalev, Roman, Rogochaya, Elena, Rogoschinski, Tim Sebastian, Rohr, David Michael, Roehrich, Dieter, Fierro Rojas, Pablo, Rojas Torres, Solangel, Rokita, Przemyslaw Stefan, Ronchetti, Federico, Rosano, Antonina, Dominguez Rosas, Edgar, Rossi, Andrea, Roy, Ankhi, Roy, Pradip Kumar, Roy, Subhadeep, Rubini, Nicola, Vazquez Rueda, Omar, Ruggiano, Daniela, Rui, Rinaldo, Rumyantsev, Boris, Russek, Pawel Grzegorz, Russo, Roberto, Rustamov, Anar, Ryabinkin, Evgeny, Ryabov, Yury, Rybicki, Andrzej, Rytkonen, Heidi Maria, Rzesa, Wioleta, Saarimaki, Oskari Antti Matti, Sadek, Rita, Sadovskiy, Sergey, Saetre, Jon-are, Safarik, Karel, Saha, Sumit Kumar, Saha, Swati, Sahoo, Baidyanath, Sahoo, Pragati, Sahoo, Raghunath, Sahoo, Sarita, Sahu, Dushmanta, Sahu, Pradip Kumar, Saini, Jogender, Sakai, Shingo, Panikkassery Salvan, Malavika, Sambyal, Sanjeev Singh, Samsonov, Vladimir, Badaro Saramela, Thiago, Sarkar, Debojit, Sarkar, Nachiketa, Sarma, Pranjal, Mantovani Sarti, Valentina, Sas, Mike Henry Petrus, Schambach, Johann Joachim, Scheid, Horst Sebastian, Schiaua, Claudiu Cornel, Schicker, Rainer Martin, Schmah, Alexander, Schmidt, Christian Joachim, Schmidt, Hans Rudolf, Schmidt, Marten Ole, Schmidt, Martin, Schmidt, Nicolas, Schmier, Austin Robert, Schotter, Romain, Schukraft, Jurgen, Schwarz, Kilian, Schweda, Kai Oliver, Scioli, Gilda, Scomparin, Enrico, Seger, Janet Elizabeth, Sekiguchi, Yuko, Sekihata, Daiki, Selyuzhenkov, Ilya, Senyukov, Serhiy, Seo, Jin Joo, Serebryakov, Dmitry, Serksnyte, Laura, Sevcenco, Adrian, Shaba, Tebogo Joyce, Shabanov, Arseniy, Shabetai, Alexandre, Shahoyan, Ruben, Shaikh, Wadut, Shangaraev, Artem, Sharma, Anjali, Sharma, Himanshu, Sharma, Meenakshi, Sharma, Natasha, Sharma, Sheetal, Sharma, Upasana, Shatat, Afnan, Sheibani, Oveis, Shigaki, Kenta, Hachiya Shimomura, Maya, Shirinkin, Sergey, Shou, Qiye, Sibiryak, Yury, Siddhanta, Sabyasachi, Siemiarczuk, Teodor, Fiorini Da Silva, Tiago, Silvermyr, David Olle Rickard, Simantathammakul, Tawanchat, Simonetti, Giuseppe, Singh, Bhawani, Singh, Ranbir, Singh, Randhir, Singh, Ravindra, Singh, Vivek, Singhal, Vikas, Sarkar - Sinha, Tinku, Sitar, Branislav, Sitta, Mario, Skaali, Bernhard, Skorodumovs, Georgijs, Slupecki, Maciej, Smirnov, Nikolai, Snellings, Raimond, Soncco Meza, Carlos, Song, Jihye, Songmoolnak, Arnon, Soramel, Francesca, Sorensen, Soren Pontoppidan, Sputowska, Iwona Anna, Stachel, Johanna, Stan, Ionel, Steffanic, Patrick John, Stiefelmaier, Stephan Friedrich, Stocco, Diego, Storehaug, Ida, Storetvedt, Maksim Melnik, Stratmann, Peter, Pliatskas Stylianidis, Christos, Alarcon Do Passo Suaide, Alexandre, Suire, Christophe Pierre, Sukhanov, Mikhail, Suljic, Miljenko, Sultanov, Rishat, Sumberia, Vikash, Sumowidagdo, Suharyo, Swain, Sagarika, Szabo, Alexander, Szarka, Imrich, Tabassam, Uzma, Taghavi, Seyed Farid, Taillepied, Guillaume, Takahashi, Jun, Tambave, Ganesh Jagannath, Tang, Siyu, Tang, Zebo, Tapia Takaki, Daniel Jesus, Tarhini, Mohamad, Tarzila, Madalina-gabriela, Tauro, Arturo, Tejeda Munoz, Guillermo, Telesca, Adriana, Terlizzi, Livia, Terrevoli, Cristina, Tersimonov, Georgy, Thakur, Sanchari, Thomas, Deepa, Tieulent, Raphael Noel, Tikhonov, Anatoly, Timmins, Anthony Robert, Tkacik, Milan, Toia, Alberica, Topilskaya, Nataliya, Toppi, Marco, Torales Acosta, Fernando, Tork, Theraa, Trifiro, Antonio, Tripathy, Sushanta, Tripathy, Tulika, Trogolo, Stefano, Trubnikov, Victor, Trzaska, Wladyslaw Henryk, Trzcinski, Tomasz Piotr, Tumkin, Alexandr, Turrisi, Rosario, Tveter, Trine Spedstad, Ullaland, Kjetil, Uras, Antonio, Urioni, Marta, Usai, Gianluca, Vala, Martin, Valle, Nicolo', Vallero, Sara, Van Doremalen, Lennart, Van Leeuwen, Marco, Vande Vyvre, Pierre, Varga, Dezso, Varga, Zoltan, Varga-kofarago, Monika, Vasileiou, Maria, Vasiliev, Andrey, Vazquez Doce, Oton, Vechernin, Vladimir, Velure, Arild, Vercellin, Ermanno, Vergara Limon, Sergio, Vermunt, Lucas Anne, Vertesi, Robert, Verweij, Marta, Vickovic, Linda, Vilakazi, Zabulon, Villalobos Baillie, Orlando, Vino, Gioacchino, Vinogradov, Alexander, Virgili, Tiziano, Vislavicius, Vytautas, Vodopyanov, Alexander, Voelkel, Benedikt, Volkl, Martin Andreas, Voloshin, Kirill, Voloshin, Sergey, Volpe, Giacomo, Von Haller, Barthelemy, Vorobyev, Ivan, Vozniuk, Nikita, Vrlakova, Janka, Wagner, Boris, Wang, Chunzheng, Wang, Dongfang, Weber, Michael, Van Weelden, Roelof Jan Gijs, Wegrzynek, Adam Tadeusz, Wenzel, Sandro Christian, Wessels, Johannes Peter, Wiechula, Jens, Wikne, Jon, Wilk, Grzegorz Andrzej, Wilkinson, Jeremy John, Willems, Guido Alexander, Windelband, Bernd Stefan, Winn, Michael Andreas, Witt, William Edward, Wright, Josephina Rae, Wu, Wenya, Wu, Yitao, Xu, Ran, Yadav, Arun Kumar, Yalcin Kuzu, Serpil, Yamaguchi, Yorito, Yamakawa, Kosei, Yang, Shiming, Yano, Satoshi, Yin, Zhongbao, Yoo, In Kwon, Yoon, Jin Hee, Yuan, Shiming, Yuncu, Alperen, Zaccolo, Valentina, Zampolli, Chiara, Correia Zanoli, Henrique Jose, Zardoshti, Nima, Zarochentsev, Andrey, Zavada, Petr, Zavyalov, Nikolay, Zhalov, Mikhail, Zhang, Biao, Zhang, Song, Zhang, Xiaoming, Zhang, Yifei, Zherebchevskii, Vladimir, Yu, Zhi, Zhigareva, Natalia, Zhou, Daicui, Zhou, You, Zhu, Jianhui, Zhu, Ya, Zinovjev, Gennady, Zurlo, Nicola, ALICE Collaboration, Laboratoire de physique subatomique et des technologies associées (SUBATECH), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ), Laboratoire de Physique des 2 Infinis Irène Joliot-Curie (IJCLab), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Recherches sur les lois Fondamentales de l'Univers (IRFU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Laboratoire de Physique de Clermont (LPC), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Institut de Physique des 2 Infinis de Lyon (IP2I Lyon), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Subatomique et de Cosmologie (LPSC), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), ALICE, Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), S. Acharya, D. Adamov??, A. Adler, J. Adolfsson, G. Aglieri Rinella, M. Agnello, N. Agrawal, Z. Ahammed, S. Ahmad, S.U. Ahn, I. Ahuja, Z. Akbar, A. Akindinov, M. Al-Turany, S.N. Alam, D. Aleksandrov, B. Alessandro, H.M. Alfanda, R. Alfaro Molina, B. Ali, Y. Ali, A. Alici, N. Alizadehvandchali, A. Alkin, J. Alme, G. Alocco, T. Alt, I. Altsybeev, M.N. Anaam, C. Andrei, D. Andreou, A. Andronic, M. Angeletti, V. Anguelov, F. Antinori, P. Antonioli, C. Anuj, N. Apadula, L. Aphecetche, H. Appelsh??user, S. Arcelli, R. Arnaldi, I.C. Arsene, M. Arslandok, A. Augustinu, R. Averbeck, S. Aziz, M.D. Azmi, A. Badal??, Y.W. Baek, X. Bai, R. Bailhache, Y. Bailung, R. Bala, A. Balbino, A. Baldisseri, B. Bali, D. Banerjee, Z. Banoo, R. Barbera, L. Barioglio, M. Barlou, G.G. Barnaf??ldi, L.S. Barnby, V. Barret, C. Bartel, K. Barth, E. Bartsch, F. Baruffaldi, N. Bastid, S. Basu, G. Batigne, B. Batyunya, D. Bauri, J.L. Bazo Alba, I.G. Bearden, C. Beattie, P. Becht, I. Belikov, A.D.C. Bell Hechavarria, F. Bellini, R. Bellwied, S. Belokurova, V. Belyaev, G. Bencedi, S. Beole, A. Bercuci, Y. Berdnikov, A. Berdnikova, L. Bergmann, M.G. Besoiu, L. Betev, P.P. Bhaduri, A. Bhasin, I.R. Bhat, M.A. Bhat, B. Bhattacharjee, P. Bhattacharya, L. Bianchi, N. Bianchi, J. Biel????k, J. Biel????kov??, J. Biernat, A. Bilandzic, G. Biro, S. Biswa, J.T. Blair, D. Blau, M.B. Blidaru, C. Blume, G. Boca, F. Bock, A. Bogdanov, S. Boi, J. Bok, L. Boldizs??r, A. Bolozdynya, M. Bombara, P.M. Bond, G. Bonomi, H. Borel, A. Borissov, H. Bossi, E. Botta, L. Bratrud, P. Braun-Munzinger, M. Bregant, M. Broz, G.E. Bruno, M.D. Buckland, D. Budnikov, H. Buesching, S. Bufalino, O. Bugnon, P. Buhler, Z. Buthelezi, J.B. Butt, A. Bylinkin, S.A. Bysiak, M. Cai, H. Caine, A. Caliva, E. Calvo Villar, J.M.M. Camacho, R.S. Camacho, P. Camerini, F.D.M. Canedo, F. Carnesecchi, R. Caron, J. Castillo Castellano, E.A.R. Casula, F. Catalano, C. Ceballos Sanchez, P. Chakraborty, S. Chandra, S. Chapeland, M. Chartier, S. Chattopadhyay, T.G. Chavez, T. Cheng, C. Cheshkov, B. Cheyni, V. Chibante Barroso, D.D. Chinellato, S. Cho, P. Chochula, P. Christakoglou, C.H. Christensen, P. Christiansen, T. Chujo, C. Cicalo, L. Cifarelli, F. Cindolo, M.R. Ciupek, G. Clai, J. Cleyman, F. Colamaria, J.S. Colburn, D. Colella, A. Collu, M. Colocci, M. Conca, G. Conesa Balbastre, Z. Conesa del Valle, G. Contin, J.G. Contrera, M.L. Coquet, T.M. Cormier, P. Cortese, M.R. Cosentino, F. Costa, S. Costanza, P. Crochet, R. Cruz-Torre, E. Cuautle, P. Cui, L. Cunqueiro, A. Dainese, M.C. Danisch, A. Danu, P. Da, S. Da, S. Dash, A. De Caro, G. de Cataldo, L. De Cilladi, J. de Cuveland, A. De Falco, D. De Gruttola, N. De Marco, C. De Martin, S. De Pasquale, S. Deb, H.F. Degenhardt, K.R. Deja, R. Del Grande, L. Dello Stritto, W. Deng, P. Dhankher, D. Di Bari, A. Di Mauro, R.A. Diaz, T. Dietel, Y. Ding, R. Divi??, D.U. Dixit, Djuvsland, U. Dmitrieva, J. Do, A. Dobrin, B. D??nigu, A.K. Dubey, A. Dubla, S. Dudi, P. Dupieux, N. Dzalaiova, T.M. Eder, R.J. Ehler, V.N. Eikeland, F. Eisenhut, D. Elia, B. Erazmu, F. Ercolessi, F. Erhardt, A. Erokhin, M.R. Ersdal, B. Espagnon, G. Eulisse, D. Evan, S. Evdokimov, L. Fabbietti, M. Faggin, J. Faivre, F. Fan, A. Fantoni, M. Fasel, P. Fecchio, A. Feliciello, G. Feofilov, A. Fern??ndez T??llez, A. Ferrero, A. Ferretti, V.J.G. Feuillard, J. Figiel, V. Filova, D. Finogeev, F.M. Fionda, G. Fiorenza, F. Flor, A.N. Flore, S. Foertsch, S. Fokin, E. Fragiacomo, E. Frajna, A. Francisco, U. Fuch, N. Funicello, C. Furget, A. Fur, J.J. Gaardh??je, M. Gagliardi, A.M. Gago, A. Gal, C.D. Galvan, D.R. Gangadharan, P. Ganoti, C. Garabato, J.R.A. Garcia, E. Garcia-Soli, K. Garg, C. Gargiulo, A. Garibli, K. Garner, P. Gasik, E.F. Gauger, A. Gautam, M.B. Gay Ducati, M. Germain, P. Ghosh, S.K. Ghosh, M. Giacalone, P. Gianotti, P. Giubellino, P. Giubilato, A.M.C. Glaenzer, P. Gl??ssel, E. Glimo, D.J.Q. Goh, V. Gonzalez, L.H. Gonz??lez-Trueba, S. Gorbunov, M. Gorgon, L. G??rlich, S. Gotovac, V. Grabski, L.K. Graczykowski, L. Greiner, A. Grelli, C. Grigora, V. Grigoriev, S. Grigoryan, F. Grosa, J.F. Grosse-Oetringhau, R. Grosso, D. Grund, G.G. Guardiano, R. Guernane, M. Guilbaud, K. Gulbrandsen, T. Gunji, W. Guo, A. Gupta, R. Gupta, S.P. Guzman, L. Gyulai, M.K. Habib, C. Hadjidaki, H. Hamagaki, M. Hamid, R. Hannigan, M.R. Haque, A. Harlenderova, J.W. Harri, A. Harton, J.A. Hasenbichler, H. Hassan, D. Hatzifotiadou, P. Hauer, L.B. Havener, S.T. Heckel, E. Hellb??r, H. Helstrup, T. Herman, E.G. Hernandez, G. Herrera Corral, F. Herrmann, K.F. Hetland, H. Hillemann, C. Hill, B. Hippolyte, B. Hofman, B. Hohlweger, J. Honermann, G.H. Hong, D. Horak, S. Hornung, A. Horzyk, R. Hosokawa, Y. Hou, P. Hristov, C. Hughe, P. Huhn, L.M. Huhta, C.V. Hulse, T.J. Humanic, H. Hushnud, L.A. Husova, A. Hutson, J.P. Iddon, R. Ilkaev, H. Ilya, M. Inaba, G.M. Innocenti, M. Ippolitov, A. Isakov, T. Isidori, M.S. Islam, M. Ivanov, V. Ivanov, V. Izucheev, M. Jablonski, B. Jacak, N. Jacazio, P.M. Jacob, S. Jadlovska, J. Jadlovsky, S. Jaelani, C. Jahnke, M.J. Jakubowska, A. Jalotra, M.A. Janik, T. Janson, M. Jercic, O. Jevon, A.A.P. Jimenez, F. Jona, P.G. Jone, J.M. Jowett, J. Jung, M. Jung, A. Junique, A. Jusko, M.J. Kabu, J. Kaewjai, P. Kalinak, A.S. Kalteyer, A. Kalweit, V. Kaplin, A. Karasu Uysal, D. Karatovic, O. Karavichev, T. Karavicheva, P. Karczmarczyk, E. Karpechev, V. Kashyap, A. Kazantsev, U. Kebschull, R. Keidel, D.L.D. Keijdener, M. Keil, B. Ketzer, Z. Khabanova, A.M. Khan, S. Khan, A. Khanzadeev, Y. Kharlov, A. Khatun, A. Khuntia, B. Kileng, B. Kim, C. Kim, D.J. Kim, E.J. Kim, J. Kim, J.S. Kim, M. Kim, S. Kim, T. Kim, S. Kirsch, I. Kisel, S. Kiselev, A. Kisiel, J.P. Kitowski, J.L. Klay, J. Klein, S. Klein, C. Klein-B??sing, M. Kleiner, T. Klemenz, A. Kluge, A.G. Knospe, C. Kobdaj, T. Kollegger, A. Kondratyev, N. Kondratyeva, E. Kondratyuk, J. Konig, S.A. Konigstorfer, P.J. Konopka, G. Kornakov, S.D. Koryciak, A. Kotliarov, O. Kovalenko, V. Kovalenko, M. Kowalski, I. Kr??lik, A. Krav????kov??, L. Krei, M. Krivda, F. Krizek, K. Krizkova Gajdosova, M. Kroesen, M. Kr??ger, D.M. Krupova, E. Kryshen, M. Krzewicki, V. Ku??era, C. Kuhn, P.G. Kuijer, T. Kumaoka, D. Kumar, L. Kumar, N. Kumar, S. Kundu, P. Kurashvili, A. Kurepin, A.B. Kurepin, A. Kuryakin, S. Kushpil, J. Kvapil, M.J. Kweon, J.Y. Kwon, Y. Kwon, S.L. La Pointe, P. La Rocca, Y.S. Lai, A. Lakrathok, M. Lamanna, R. Langoy, K. Lapidu, P. Larionov, E. Laudi, L. Lautner, R. Lavicka, T. Lazareva, R. Lea, J. Lehrbach, R.C. Lemmon, I. Le??n Monz??n, E.D. Lesser, M. Lettrich, P. L??vai, X. Li, X.L. Li, J. Lien, R. Lietava, B. Lim, S.H. Lim, V. Lindenstruth, A. Lindner, C. Lippmann, A. Liu, D.H. Liu, J. Liu, I.M. Lofne, V. Loginov, C. Loizide, P. Loncar, J.A. Lopez, X. Lopez, E. L??pez Torre, J.R. Luhder, M. Lunardon, G. Luparello, Y.G. Ma, A. Maevskaya, M. Mager, T. Mahmoud, A. Maire, M. Malaev, N.M. Malik, Q.W. Malik, S.K. Malik, L. Malinina, D. Mal'Kevich, D. Mallick, N. Mallick, G. Mandaglio, V. Manko, F. Manso, V. Manzari, Y. Mao, G.V. Margagliotti, A. Margotti, A. Mar??n, C. Markert, M. Marquard, N.A. Martin, P. Martinengo, J.L. Martinez, M.I. Mart??nez, G. Mart??nez Garc??a, S. Masciocchi, M. Masera, A. Masoni, L. Massacrier, A. Mastroserio, A.M. Mathi, O. Matonoha, P.F.T. Matuoka, A. Matyja, C. Mayer, A.L. Mazueco, F. Mazzaschi, M. Mazzilli, M.A. Mazzoni, J.E. Mdhluli, A.F. Mechler, Y. Melikyan, A. Menchaca-Rocha, E. Meninno, A.S. Menon, M. Mere, S. Mhlanga, Y. Miake, L. Micheletti, L.C. Migliorin, D.L. Mihaylov, K. Mikhaylov, A.N. Mishra, D. Mi??kowiec, A. Modak, A.P. Mohanty, B. Mohanty, M. Mohisin Khan, M.A. Molander, Z. Moravcova, C. Mordasini, D.A. Moreira De Godoy, I. Morozov, A. Morsch, T. Mrnjavac, V. Muccifora, E. Mudnic, D. M??hlheim, S. Muhuri, J.D. Mulligan, A. Mulliri, M.G. Munhoz, R.H. Munzer, H. Murakami, S. Murray, L. Musa, J. Musinsky, J.W. Myrcha, B. Naik, R. Nair, B.K. Nandi, R. Nania, E. Nappi, A.F. Nassirpour, A. Nath, C. Nattra, A. Neagu, A. Negru, L. Nellen, S.V. Nesbo, G. Neskovic, D. Nesterov, B.S. Nielsen, E.G. Nielsen, S. Nikolaev, S. Nikulin, V. Nikulin, F. Noferini, S. Noh, P. Nomokonov, J. Norman, N. Novitzky, P. Nowakowski, A. Nyanin, J. Nystrand, M. Ogino, A. Ohlson, V.A. Okorokov, J. Oleniacz, A.C. Oliveira Da Silva, M.H. Oliver, A. Onnerstad, C. Oppedisano, A. Ortiz Velasquez, T. Osako, A. Oskarsson, J. Otwinowski, M. Oya, K. Oyama, Y. Pachmayer, S. Padhan, D. Pagano, G. Pai??, A. Palasciano, J. Pan, S. Panebianco, J. Park, J.E. Parkkila, S.P. Pathak, R.N. Patra, B. Paul, H. Pei, T. Peitzmann, X. Peng, L.G. Pereira, H. Pereira Da Costa, D. Peresunko, G.M. Perez, S. Perrin, Y. Pestov, V. Petr????ek, M. Petrovici, R.P. Pezzi, S. Piano, M. Pikna, P. Pillot, O. Pinazza, L. Pinsky, C. Pinto, S. Pisano, M. P??osko??, M. Planinic, F. Pliquett, M.G. Poghosyan, B. Polichtchouk, S. Politano, N. Poljak, A. Pop, S. Porteboeuf-Houssai, J. Porter, V. Pozdniakov, S.K. Prasad, R. Preghenella, F. Prino, C.A. Pruneau, I. Pshenichnov, M. Puccio, S. Qiu, L. Quaglia, R.E. Quishpe, S. Ragoni, A. Rakotozafindrabe, L. Ramello, F. Rami, S.A.R. Ramirez, A.G.T. Ramo, T.A. Rancien, R. Raniwala, S. Raniwala, S.S. R??s??nen, R. Rath, I. Ravasenga, K.F. Read, A.R. Redelbach, K. Redlich, A. Rehman, P. Reichelt, F. Reidt, H.A. Reme-ne, Z. Rescakova, K. Reyger, A. Riabov, V. Riabov, T. Richert, M. Richter, W. Riegler, F. Riggi, C. Ristea, M. Rodr??guez Cahuantzi, K. R??ed, R. Rogalev, E. Rogochaya, T.S. Rogoschinski, D. Rohr, D. R??hrich, P.F. Roja, S. Rojas Torre, P.S. Rokita, F. Ronchetti, A. Rosano, E.D. Rosa, A. Rossi, A. Roy, P. Roy, S. Roy, N. Rubini, O.V. Rueda, D. Ruggiano, R. Rui, B. Rumyantsev, P.G. Russek, R. Russo, A. Rustamov, E. Ryabinkin, Y. Ryabov, A. Rybicki, H. Rytkonen, W. Rzesa, O.A.M. Saarimaki, R. Sadek, S. Sadovsky, J. Saetre, K. ??afa????k, S.K. Saha, S. Saha, B. Sahoo, P. Sahoo, R. Sahoo, S. Sahoo, D. Sahu, P.K. Sahu, J. Saini, S. Sakai, M.P. Salvan, S. Sambyal, V. Samsonov, T.B. Saramela, D. Sarkar, N. Sarkar, P. Sarma, V.M. Sarti, M.H.P. Sa, J. Schambach, H.S. Scheid, C. Schiaua, R. Schicker, A. Schmah, C. Schmidt, H.R. Schmidt, M.O. Schmidt, M. Schmidt, N.V. Schmidt, A.R. Schmier, R. Schotter, J. Schukraft, K. Schwarz, K. Schweda, G. Scioli, E. Scomparin, J.E. Seger, Y. Sekiguchi, D. Sekihata, I. Selyuzhenkov, S. Senyukov, J.J. Seo, D. Serebryakov, L. ??erk??nyt??, A. Sevcenco, T.J. Shaba, A. Shabanov, A. Shabetai, R. Shahoyan, W. Shaikh, A. Shangaraev, A. Sharma, H. Sharma, M. Sharma, N. Sharma, S. Sharma, U. Sharma, A. Shatat, O. Sheibani, K. Shigaki, M. Shimomura, S. Shirinkin, Q. Shou, Y. Sibiriak, S. Siddhanta, T. Siemiarczuk, T.F. Silva, D. Silvermyr, T. Simantathammakul, G. Simonetti, B. Singh, R. Singh, V.K. Singh, V. Singhal, T. Sinha, B. Sitar, M. Sitta, T.B. Skaali, G. Skorodumov, M. Slupecki, N. Smirnov, R.J.M. Snelling, C. Soncco, J. Song, A. Songmoolnak, F. Soramel, S. Sorensen, I. Sputowska, J. Stachel, I. Stan, P.J. Steffanic, S.F. Stiefelmaier, D. Stocco, I. Storehaug, M.M. Storetvedt, P. Stratmann, C.P. Stylianidi, A.A.P. Suaide, C. Suire, M. Sukhanov, M. Suljic, R. Sultanov, V. Sumberia, S. Sumowidagdo, S. Swain, A. Szabo, I. Szarka, U. Tabassam, S.F. Taghavi, G. Taillepied, J. Takahashi, G.J. Tambave, S. Tang, Z. Tang, J.D. Tapia Takaki, M. Tarhini, M.G. Tarzila, A. Tauro, G. Tejeda Mu??oz, A. Telesca, L. Terlizzi, C. Terrevoli, G. Tersimonov, S. Thakur, D. Thoma, R. Tieulent, A. Tikhonov, A.R. Timmin, M. Tkacik, A. Toia, N. Topilskaya, M. Toppi, F. Torales-Acosta, T. Tork, A. Trifir??, S. Tripathy, T. Tripathy, S. Trogolo, V. Trubnikov, W.H. Trzaska, T.P. Trzcinski, A. Tumkin, R. Turrisi, T.S. Tveter, K. Ullaland, A. Ura, M. Urioni, G.L. Usai, M. Vala, N. Valle, S. Vallero, L.V.R. van Doremalen, M. van Leeuwen, P. Vande Vyvre, D. Varga, Z. Varga, M. Varga-Kofarago, M. Vasileiou, A. Vasiliev, O. V??zquez Doce, V. Vechernin, A. Velure, E. Vercellin, S. Vergara Lim??n, L. Vermunt, R. V??rtesi, M. Verweij, L. Vickovic, Z. Vilakazi, O. Villalobos Baillie, G. Vino, A. Vinogradov, T. Virgili, V. Vislaviciu, A. Vodopyanov, B. Volkel, M.A. V??lkl, K. Voloshin, S.A. Voloshin, G. Volpe, B. von Haller, I. Vorobyev, N. Vozniuk, J. Vrl??kov??, B. Wagner, C. Wang, D. Wang, M. Weber, R.J.G.V. Weelden, A. Wegrzynek, S.C. Wenzel, J.P. Wessel, J. Wiechula, J. Wikne, G. Wilk, J. Wilkinson, G.A. Willem, B. Windelband, M. Winn, W.E. Witt, J.R. Wright, W. Wu, Y. Wu, R. Xu, A.K. Yadav, S. Yalcin, Y. Yamaguchi, K. Yamakawa, S. Yang, S. Yano, Z. Yin, I.-K. Yoo, J.H. Yoon, S. Yuan, A. Yuncu, V. Zaccolo, C. Zampolli, H.J.C. Zanoli, N. Zardoshti, A. Zarochentsev, P. Z??vada, N. Zaviyalov, M. Zhalov, B. Zhang, S. Zhang, X. Zhang, Y. Zhang, V. Zherebchevskii, Y. Zhi, N. Zhigareva, D. Zhou, Y. Zhou, J. Zhu, Y. Zhu, G. Zinovjev, N. Zurlo, Afd Subatomic Physics (SAP), Sub GRASP, Sub Algemeen Physics Education, Sub Subatomic Physics (SAP), Gravitational and Subatomic Physics (GRASP), Helsinki Institute of Physics, Acharya, S., Adamov??, D., Adler, A., Adolfsson, J., Aglieri Rinella, G., Agnello, M., Agrawal, N., Ahammed, Z., Ahmad, S., Ahn, S. U., Ahuja, I., Akbar, Z., Akindinov, A., Al-Turany, M., Alam, S. N., Aleksandrov, D., Alessandro, B., Alfanda, H. M., Alfaro Molina, R., Ali, B., Ali, Y., Alici, A., Alizadehvandchali, N., Alkin, A., Alme, J., Alocco, G., Alt, T., Altsybeev, I., Anaam, M. N., Andrei, C., Andreou, D., Andronic, A., Angeletti, M., Anguelov, V., Antinori, F., Antonioli, P., Anuj, C., Apadula, N., Aphecetche, L., Appelsh??user, H., Arcelli, S., Arnaldi, R., Arsene, I. C., Arslandok, M., Augustinus, A., Averbeck, R., Aziz, S., Azmi, M. D., Badal??, A., Baek, Y. W., Bai, X., Bailhache, R., Bailung, Y., Bala, R., Balbino, A., Baldisseri, A., Balis, B., Banerjee, D., Banoo, Z., Barbera, R., Barioglio, L., Barlou, M., Barnaf??ldi, G. G., Barnby, L. S., Barret, V., Bartels, C., Barth, K., Bartsch, E., Baruffaldi, F., Bastid, N., Basu, S., Batigne, G., Batyunya, B., Bauri, D., Bazo Alba, J. L., Bearden, I. G., Beattie, C., Becht, P., Belikov, I., Bell Hechavarria, A. D. C., Bellini, F., Bellwied, R., Belokurova, S., Belyaev, V., Bencedi, G., Beole, S., Bercuci, A., Berdnikov, Y., Berdnikova, A., Bergmann, L., Besoiu, M. G., Betev, L., Bhaduri, P. P., Bhasin, A., Bhat, I. R., Bhat, M. A., Bhattacharjee, B., Bhattacharya, P., Bianchi, L., Bianchi, N., Biel????k, J., Biel????kov??, J., Biernat, J., Bilandzic, A., Biro, G., Biswas, S., Blair, J. T., Blau, D., Blidaru, M. B., Blume, C., Boca, G., Bock, F., Bogdanov, A., Boi, S., Bok, J., Boldizs??r, L., Bolozdynya, A., Bombara, M., Bond, P. M., Bonomi, G., Borel, H., Borissov, A., Bossi, H., Botta, E., Bratrud, L., Braun-Munzinger, P., Bregant, M., Broz, M., Bruno, G. E., Buckland, M. D., Budnikov, D., Buesching, H., Bufalino, S., Bugnon, O., Buhler, P., Buthelezi, Z., Butt, J. B., Bylinkin, A., Bysiak, S. A., Cai, M., Caines, H., Caliva, A., Calvo Villar, E., Camacho, J. M. M., Camacho, R. S., Camerini, P., Canedo, F. D. M., Carnesecchi, F., Caron, R., Castillo Castellanos, J., Casula, E. A. R., Catalano, F., Ceballos Sanchez, C., Chakraborty, P., Chandra, S., Chapeland, S., Chartier, M., Chattopadhyay, S., Chavez, T. G., Cheng, T., Cheshkov, C., Cheynis, B., Chibante Barroso, V., Chinellato, D. D., Cho, S., Chochula, P., Christakoglou, P., Christensen, C. H., Christiansen, P., Chujo, T., Cicalo, C., Cifarelli, L., Cindolo, F., Ciupek, M. R., Clai, G., Cleymans, J., Colamaria, F., Colburn, J. S., Colella, D., Collu, A., Colocci, M., Concas, M., Conesa Balbastre, G., Conesa del Valle, Z., Contin, G., Contreras, J. G., Coquet, M. L., Cormier, T. M., Cortese, P., Cosentino, M. R., Costa, F., Costanza, S., Crochet, P., Cruz-Torres, R., Cuautle, E., Cui, P., Cunqueiro, L., Dainese, A., Danisch, M. C., Danu, A., Das, P., Das, S., Dash, S., De Caro, A., de Cataldo, G., De Cilladi, L., de Cuveland, J., De Falco, A., De Gruttola, D., De Marco, N., De Martin, C., De Pasquale, S., Deb, S., Degenhardt, H. F., Deja, K. R., Del Grande, R., Dello Stritto, L., Deng, W., Dhankher, P., Di Bari, D., Di Mauro, A., Diaz, R. A., Dietel, T., Ding, Y., Divi??, R., Dixit, D. U., Djuvsland, ??., Dmitrieva, U., Do, J., Dobrin, A., D??nigus, B., Dubey, A. K., Dubla, A., Dudi, S., Dupieux, P., Dzalaiova, N., Eder, T. M., Ehlers, R. J., Eikeland, V. N., Eisenhut, F., Elia, D., Erazmus, B., Ercolessi, F., Erhardt, F., Erokhin, A., Ersdal, M. R., Espagnon, B., Eulisse, G., Evans, D., Evdokimov, S., Fabbietti, L., Faggin, M., Faivre, J., Fan, F., Fantoni, A., Fasel, M., Fecchio, P., Feliciello, A., Feofilov, G., Fern??ndez T??llez, A., Ferrero, A., Ferretti, A., Feuillard, V. J. G., Figiel, J., Filova, V., Finogeev, D., Fionda, F. M., Fiorenza, G., Flor, F., Flores, A. N., Foertsch, S., Fokin, S., Fragiacomo, E., Frajna, E., Francisco, A., Fuchs, U., Funicello, N., Furget, C., Furs, A., Gaardh??je, J. J., Gagliardi, M., Gago, A. M., Gal, A., Galvan, C. D., Gangadharan, D. R., Ganoti, P., Garabatos, C., Garcia, J. R. A., Garcia-Solis, E., Garg, K., Gargiulo, C., Garibli, A., Garner, K., Gasik, P., Gauger, E. F., Gautam, A., Gay Ducati, M. B., Germain, M., Ghosh, P., Ghosh, S. K., Giacalone, M., Gianotti, P., Giubellino, P., Giubilato, P., Glaenzer, A. M. C., Gl??ssel, P., Glimos, E., Goh, D. J. Q., Gonzalez, V., Gonz??lez-Trueba, L. H., Gorbunov, S., Gorgon, M., G??rlich, L., Gotovac, S., Grabski, V., Graczykowski, L. K., Greiner, L., Grelli, A., Grigoras, C., Grigoriev, V., Grigoryan, S., Grosa, F., Grosse-Oetringhaus, J. F., Grosso, R., Grund, D., Guardiano, G. G., Guernane, R., Guilbaud, M., Gulbrandsen, K., Gunji, T., Guo, W., Gupta, A., Gupta, R., Guzman, S. P., Gyulai, L., Habib, M. K., Hadjidakis, C., Hamagaki, H., Hamid, M., Hannigan, R., Haque, M. R., Harlenderova, A., Harris, J. W., Harton, A., Hasenbichler, J. A., Hassan, H., Hatzifotiadou, D., Hauer, P., Havener, L. B., Heckel, S. T., Hellb??r, E., Helstrup, H., Herman, T., Hernandez, E. G., Herrera Corral, G., Herrmann, F., Hetland, K. F., Hillemanns, H., Hills, C., Hippolyte, B., Hofman, B., Hohlweger, B., Honermann, J., Hong, G. H., Horak, D., Hornung, S., Horzyk, A., Hosokawa, R., Hou, Y., Hristov, P., Hughes, C., Huhn, P., Huhta, L. M., Hulse, C. V., Humanic, T. J., Hushnud, H., Husova, L. A., Hutson, A., Iddon, J. P., Ilkaev, R., Ilyas, H., Inaba, M., Innocenti, G. M., Ippolitov, M., Isakov, A., Isidori, T., Islam, M. S., Ivanov, M., Ivanov, V., Izucheev, V., Jablonski, M., Jacak, B., Jacazio, N., Jacobs, P. M., Jadlovska, S., Jadlovsky, J., Jaelani, S., Jahnke, C., Jakubowska, M. J., Jalotra, A., Janik, M. A., Janson, T., Jercic, M., Jevons, O., Jimenez, A. A. P., Jonas, F., Jones, P. G., Jowett, J. M., Jung, J., Jung, M., Junique, A., Jusko, A., Kabus, M. J., Kaewjai, J., Kalinak, P., Kalteyer, A. S., Kalweit, A., Kaplin, V., Karasu Uysal, A., Karatovic, D., Karavichev, O., Karavicheva, T., Karczmarczyk, P., Karpechev, E., Kashyap, V., Kazantsev, A., Kebschull, U., Keidel, R., Keijdener, D. L. D., Keil, M., Ketzer, B., Khabanova, Z., Khan, A. M., Khan, S., Khanzadeev, A., Kharlov, Y., Khatun, A., Khuntia, A., Kileng, B., Kim, B., Kim, C., Kim, D. J., Kim, E. J., Kim, J., Kim, J. S., Kim, M., Kim, S., Kim, T., Kirsch, S., Kisel, I., Kiselev, S., Kisiel, A., Kitowski, J. P., Klay, J. L., Klein, J., Klein, S., Klein-B??sing, C., Kleiner, M., Klemenz, T., Kluge, A., Knospe, A. G., Kobdaj, C., Kollegger, T., Kondratyev, A., Kondratyeva, N., Kondratyuk, E., Konig, J., Konigstorfer, S. A., Konopka, P. J., Kornakov, G., Koryciak, S. D., Kotliarov, A., Kovalenko, O., Kovalenko, V., Kowalski, M., Kr??lik, I., Krav????kov??, A., Kreis, L., Krivda, M., Krizek, F., Krizkova Gajdosova, K., Kroesen, M., Kr??ger, M., Krupova, D. M., Kryshen, E., Krzewicki, M., Ku??era, V., Kuhn, C., Kuijer, P. G., Kumaoka, T., Kumar, D., Kumar, L., Kumar, N., Kundu, S., Kurashvili, P., Kurepin, A., Kurepin, A. B., Kuryakin, A., Kushpil, S., Kvapil, J., Kweon, M. J., Kwon, J. Y., Kwon, Y., La Pointe, S. L., La Rocca, P., Lai, Y. S., Lakrathok, A., Lamanna, M., Langoy, R., Lapidus, K., Larionov, P., Laudi, E., Lautner, L., Lavicka, R., Lazareva, T., Lea, R., Lehrbach, J., Lemmon, R. C., Monz??n, I. Le??n., Lesser, E. D., Lettrich, M., L??vai, P., Li, X., Li, X. L., Lien, J., Lietava, R., Lim, B., Lim, S. H., Lindenstruth, V., Lindner, A., Lippmann, C., Liu, A., Liu, D. H., Liu, J., Lofnes, I. M., Loginov, V., Loizides, C., Loncar, P., Lopez, J. A., Lopez, X., L??pez Torres, E., Luhder, J. R., Lunardon, M., Luparello, G., Ma, Y. G., Maevskaya, A., Mager, M., Mahmoud, T., Maire, A., Malaev, M., Malik, N. M., Malik, Q. W., Malik, S. K., Malinina, L., Mal'Kevich, D., Mallick, D., Mallick, N., Mandaglio, G., Manko, V., Manso, F., Manzari, V., Mao, Y., Margagliotti, G. V., Margotti, A., Mar??n, A., Markert, C., Marquard, M., Martin, N. A., Martinengo, P., Martinez, J. L., Mart??nez, M. I., Mart??nez Garc??a, G., Masciocchi, S., Masera, M., Masoni, A., Massacrier, L., Mastroserio, A., Mathis, A. M., Matonoha, O., Matuoka, P. F. T., Matyja, A., Mayer, C., Mazuecos, A. L., Mazzaschi, F., Mazzilli, M., Mazzoni, M. A., Mdhluli, J. E., Mechler, A. F., Melikyan, Y., Menchaca-Rocha, A., Meninno, E., Menon, A. S., Meres, M., Mhlanga, S., Miake, Y., Micheletti, L., Migliorin, L. C., Mihaylov, D. L., Mikhaylov, K., Mishra, A. N., Mi??kowiec, D., Modak, A., Mohanty, A. P., Mohanty, B., Mohisin Khan, M., Molander, M. A., Moravcova, Z., Mordasini, C., Moreira De Godoy, D. A., Morozov, I., Morsch, A., Mrnjavac, T., Muccifora, V., Mudnic, E., M??hlheim, D., Muhuri, S., Mulligan, J. D., Mulliri, A., Munhoz, M. G., Munzer, R. H., Murakami, H., Murray, S., Musa, L., Musinsky, J., Myrcha, J. W., Naik, B., Nair, R., Nandi, B. K., Nania, R., Nappi, E., Nassirpour, A. F., Nath, A., Nattrass, C., Neagu, A., Negru, A., Nellen, L., Nesbo, S. V., Neskovic, G., Nesterov, D., Nielsen, B. S., Nielsen, E. G., Nikolaev, S., Nikulin, S., Nikulin, V., Noferini, F., Noh, S., Nomokonov, P., Norman, J., Novitzky, N., Nowakowski, P., Nyanin, A., Nystrand, J., Ogino, M., Ohlson, A., Okorokov, V. A., Oleniacz, J., Oliveira Da Silva, A. C., Oliver, M. H., Onnerstad, A., Oppedisano, C., Ortiz Velasquez, A., Osako, T., Oskarsson, A., Otwinowski, J., Oya, M., Oyama, K., Pachmayer, Y., Padhan, S., Pagano, D., Pai??, G., Palasciano, A., Pan, J., Panebianco, S., Park, J., Parkkila, J. E., Pathak, S. P., Patra, R. N., Paul, B., Pei, H., Peitzmann, T., Peng, X., Pereira, L. G., Pereira Da Costa, H., Peresunko, D., Perez, G. M., Perrin, S., Pestov, Y., Petr????ek, V., Petrovici, M., Pezzi, R. P., Piano, S., Pikna, M., Pillot, P., Pinazza, O., Pinsky, L., Pinto, C., Pisano, S., P??osko??, M., Planinic, M., Pliquett, F., Poghosyan, M. G., Polichtchouk, B., Politano, S., Poljak, N., Pop, A., Porteboeuf-Houssais, S., Porter, J., Pozdniakov, V., Prasad, S. K., Preghenella, R., Prino, F., Pruneau, C. A., Pshenichnov, I., Puccio, M., Qiu, S., Quaglia, L., Quishpe, R. E., Ragoni, S., Rakotozafindrabe, A., Ramello, L., Rami, F., Ramirez, S. A. R., Ramos, A. G. T., Rancien, T. A., Raniwala, R., Raniwala, S., R??s??nen, S. S., Rath, R., Ravasenga, I., Read, K. F., Redelbach, A. R., Redlich, K., Rehman, A., Reichelt, P., Reidt, F., Reme-ness, H. A., Rescakova, Z., Reygers, K., Riabov, A., Riabov, V., Richert, T., Richter, M., Riegler, W., Riggi, F., Ristea, C., Rodr??guez Cahuantzi, M., R??ed, K., Rogalev, R., Rogochaya, E., Rogoschinski, T. S., Rohr, D., R??hrich, D., Rojas, P. F., Rojas Torres, S., Rokita, P. S., Ronchetti, F., Rosano, A., Rosas, E. D., Rossi, A., Roy, A., Roy, P., Roy, S., Rubini, N., Rueda, O. V., Ruggiano, D., Rui, R., Rumyantsev, B., Russek, P. G., Russo, R., Rustamov, A., Ryabinkin, E., Ryabov, Y., Rybicki, A., Rytkonen, H., Rzesa, W., Saarimaki, O. A. M., Sadek, R., Sadovsky, S., Saetre, J., afa????k, K., Saha, S. K., Saha, S., Sahoo, B., Sahoo, P., Sahoo, R., Sahoo, S., Sahu, D., Sahu, P. K., Saini, J., Sakai, S., Salvan, M. P., Sambyal, S., Samsonov, V., Saramela, T. B., Sarkar, D., Sarkar, N., Sarma, P., Sarti, V. M., Sas, M. H. P., Schambach, J., Scheid, H. S., Schiaua, C., Schicker, R., Schmah, A., Schmidt, C., Schmidt, H. R., Schmidt, M. O., Schmidt, M., Schmidt, N. V., Schmier, A. R., Schotter, R., Schukraft, J., Schwarz, K., Schweda, K., Scioli, G., Scomparin, E., Seger, J. E., Sekiguchi, Y., Sekihata, D., Selyuzhenkov, I., Senyukov, S., Seo, J. J., Serebryakov, D., erk??nyt??, L., Sevcenco, A., Shaba, T. J., Shabanov, A., Shabetai, A., Shahoyan, R., Shaikh, W., Shangaraev, A., Sharma, A., Sharma, H., Sharma, M., Sharma, N., Sharma, S., Sharma, U., Shatat, A., Sheibani, O., Shigaki, K., Shimomura, M., Shirinkin, S., Shou, Q., Sibiriak, Y., Siddhanta, S., Siemiarczuk, T., Silva, T. F., Silvermyr, D., Simantathammakul, T., Simonetti, G., Singh, B., Singh, R., Singh, V. K., Singhal, V., Sinha, T., Sitar, B., Sitta, M., Skaali, T. B., Skorodumovs, G., Slupecki, M., Smirnov, N., Snellings, R. J. M., Soncco, C., Song, J., Songmoolnak, A., Soramel, F., Sorensen, S., Sputowska, I., Stachel, J., Stan, I., Steffanic, P. J., Stiefelmaier, S. F., Stocco, D., Storehaug, I., Storetvedt, M. M., Stratmann, P., Stylianidis, C. P., Suaide, A. A. P., Suire, C., Sukhanov, M., Suljic, M., Sultanov, R., Sumberia, V., Sumowidagdo, S., Swain, S., Szabo, A., Szarka, I., Tabassam, U., Taghavi, S. F., Taillepied, G., Takahashi, J., Tambave, G. J., Tang, S., Tang, Z., Tapia Takaki, J. D., Tarhini, M., Tarzila, M. G., Tauro, A., Tejeda Mu??oz, G., Telesca, A., Terlizzi, L., Terrevoli, C., Tersimonov, G., Thakur, S., Thomas, D., Tieulent, R., Tikhonov, A., Timmins, A. R., Tkacik, M., Toia, A., Topilskaya, N., Toppi, M., Torales-Acosta, F., Tork, T., Trifir??, A., Tripathy, S., Tripathy, T., Trogolo, S., Trubnikov, V., Trzaska, W. H., Trzcinski, T. P., Tumkin, A., Turrisi, R., Tveter, T. S., Ullaland, K., Uras, A., Urioni, M., Usai, G. L., Vala, M., Valle, N., Vallero, S., van Doremalen, L. V. R., van Leeuwen, M., Vande Vyvre, P., Varga, D., Varga, Z., Varga-Kofarago, M., Vasileiou, M., Vasiliev, A., V??zquez Doce, O., Vechernin, V., Velure, A., Vercellin, E., Vergara Lim??n, S., Vermunt, L., V??rtesi, R., Verweij, M., Vickovic, L., Vilakazi, Z., Villalobos Baillie, O., Vino, G., Vinogradov, A., Virgili, T., Vislavicius, V., Vodopyanov, A., Volkel, B., V??lkl, M. A., Voloshin, K., Voloshin, S. A., Volpe, G., von Haller, B., Vorobyev, I., Vozniuk, N., Vrl??kov??, J., Wagner, B., Wang, C., Wang, D., Weber, M., Weelden, R. J. G. V., Wegrzynek, A., Wenzel, S. C., Wessels, J. P., Wiechula, J., Wikne, J., Wilk, G., Wilkinson, J., Willems, G. A., Windelband, B., Winn, M., Witt, W. E., Wright, J. R., Wu, W., Wu, Y., Xu, R., Yadav, A. K., Yalcin, S., Yamaguchi, Y., Yamakawa, K., Yang, S., Yano, S., Yin, Z., Yoo, I. -K., Yoon, J. H., Yuan, S., Yuncu, A., Zaccolo, V., Zampolli, C., Zanoli, H. J. C., Zardoshti, N., Zarochentsev, A., Z??vada, P., Zaviyalov, N., Zhalov, M., Zhang, B., Zhang, S., Zhang, X., Zhang, Y., Zherebchevskii, V., Zhi, Y., Zhigareva, N., Zhou, D., Zhou, Y., Zhu, J., Zhu, Y., Zinovjev, G., Zurlo, N., Medicum, General Division (Department of Physics) (-2009), Department of Forest Sciences, Faculty of Social Sciences, Department of Mathematics and Statistics, Department of Computer Science, Department of Chemistry, Mitochondrial Morphogenesis, Department of Geosciences and Geography, Particle Physics and Astrophysics, Department of Digital Humanities, Department of Agricultural Sciences, Algorithmic Bioinformatics, Department of Languages, Asian Languages, Teacher Education, Ecology and Evolutionary Biology, Institute of Biotechnology, Department of Education, Doctoral Programme in Particle Physics and Universe Sciences, Institute for Molecular Medicine Finland, Data Science Genetic Epidemiology Lab, Division of Pharmaceutical Chemistry and Technology, Nanomedicines and Biomedical Engineering, Doctoral Programme in Drug Research, Department of Food and Nutrition, Environmental Sciences, Department of Physics, Doctoral Programme in Plant Sciences, Department of Medicine, Department of Social Research (2010-2017), Life Science Education, Production Animal Medicine, Department of Cultures, Global Development Studies, Institute of Biotechnology (-2009), Teaching and Learning Services, Institute for Atmospheric and Earth System Research (INAR), Doctoral Programme in Atmospheric Sciences, Neuroscience Center, Doctoral Programme in Computer Science, Faculty of Medicine, and Departments of Faculty of Veterinary Medicine
Subjects: Kjerne- og elementærpartikkelfysikk: 431 [VDP], heavy ion: scattering, Nuclear Experiment, High Energy Physics - Experiment, hiukkasfysiikka, nucl-ex, Elliptic-flow, High Energy Physics - Experiment (hep-ex), ALICE, 5020: 5440 GeV-cms/nucleon, [PHYS.HEXP]Physics [physics]/High Energy Physics - Experiment [hep-ex], Quark-gluon plasma, elliptic flow, Pb collisions, Nuclear Experiment (nucl-ex), Viscosity, elliptic flow, Quark-gluon plasma, flow: anisotropy, gluon: saturation, correlation: higher-order, initial state, transverse momentum, boundary condition, CERN LHC Coll, hydrodynamics, color glass condensate, numerical calculations, experimental results, High Energy Heavy Ion Collisions, Nuclear and elementary particle physics: 431 [VDP], Perspective, ydinfysiikka, higher-order [correlation], Particle Physics - Experiment, anisotropy [flow], Nuclear and High Energy Physics, Evolution, FOS: Physical sciences, Pb collisions, [PHYS.NEXP]Physics [physics]/Nuclear Experiment [nucl-ex], 114 Physical sciences, scattering [heavy ion], Nuclear Physics - Experiment, ddc:530, saturation [gluon], hep-ex, kvarkki-gluoniplasma, heavy-ion collisions, nuclear physics, correlations, LHC, 5440 GeV-cms/nucleon [5020]
Abstract: Physics letters / B 834, 137393 (2022). doi:10.1016/j.physletb.2022.137393, Correlations between mean transverse momentum p$_T$ and anisotropic flow coefficients v$_2$ or v$_3$ are measured as a function of centrality in Pb–Pb and Xe–Xe collisions at $\sqrt{s_{\rm NN}}$ = 5.02 TeV and 5.44 TeV, respectively, with ALICE. In addition, the recently proposed higher-order correlation between p$_T$, v$_2$, and v$_3$ is measured for the first time, which shows an anticorrelation for the presented centrality ranges. These measurements are compared with hydrodynamic calculations using IP-Glasma and TRENTo initial-state shapes, the former based on the Color Glass Condensate effective theory with gluon saturation, and the latter a parameterized model with nucleons as the relevant degrees of freedom. The data are better described by the IP-Glasma rather than the TRENTo based calculations. In particular, Trajectum and JETSCAPE predictions, both based on the TRENTo initial state model but with different parameter settings, fail to describe the measurements. As the correlations between p$_T$ and v$_n$ are mainly driven by the correlations of the size and the shape of the system in the initial state, these new studies pave a novel way to characterize the initial state and help pin down the uncertainty of the extracted properties of the quark–gluon plasma recreated in relativistic heavy-ion collisions., Published by North-Holland Publ., Amsterdam
Published: 2022
Full Text: View/download PDF

18. Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization

Author: Pawel Roszak, Jung-ok Heo, Bernhard Blob, Koichi Toyokura, Yuki Sugiyama, Maria Angels de Luis Balaguer, Winnie W. Y. Lau, Fiona Hamey, Jacopo Cirrone, Ewelina Madej, Alida M. Bouatta, Xin Wang, Marjorie Guichard, Robertas Ursache, Hugo Tavares, Kevin Verstaen, Jos Wendrich, Charles W. Melnyk, Yoshihisa Oda, Dennis Shasha, Sebastian E. Ahnert, Yvan Saeys, Bert De Rybel, Renze Heidstra, Ben Scheres, Guido Grossmann, Ari Pekka Mähönen, Philipp Denninger, Berthold Göttgens, Rosangela Sozzani, Kenneth D. Birnbaum, Yrjö Helariutta, Institute of Biotechnology (-2009), University of Helsinki, Helsinki Institute of Life Science HiLIFE, Institute of Biotechnology, Organismal and Evolutionary Biology Research Programme, Plant Biology, Viikki Plant Science Centre (ViPS), Yrjö Helariutta / Principal Investigator, Roszak, Pawel [0000-0002-7822-494X], Heo, Jung-Ok [0000-0002-5088-6044], Blob, Bernhard [0000-0003-4269-7742], Toyokura, Koichi [0000-0001-7775-7886], Sugiyama, Yuki [0000-0002-5235-2943], Lau, Winnie WY [0000-0003-1209-1854], Hamey, Fiona [0000-0001-7299-2860], Madej, Ewelina [0000-0002-0729-0245], Bouatta, Alida M [0000-0001-9326-7561], Guichard, Marjorie [0000-0003-4417-3504], Tavares, Hugo [0000-0001-9373-2726], Verstaen, Kevin [0000-0003-3582-0298], Wendrich, Jos [0000-0002-6198-3763], Melnyk, Charles W [0000-0003-3251-800X], Oda, Yoshihisa [0000-0001-6934-4424], Shasha, Dennis [0000-0002-7036-3312], Ahnert, Sebastian E [0000-0003-2613-0041], Saeys, Yvan [0000-0002-0415-1506], De Rybel, Bert [0000-0002-9551-042X], Heidstra, Renze [0000-0001-9032-5770], Scheres, Ben [0000-0001-5400-9578], Grossmann, Guido [0000-0001-7529-9244], Mähönen, Ari Pekka [0000-0001-6051-866X], Denninger, Philipp [0000-0003-3794-2360], Göttgens, Berthold [0000-0001-6302-5705], Sozzani, Rosangela [0000-0003-3316-2367], Birnbaum, Kenneth D [0000-0002-8423-6859], Helariutta, Yrjö [0000-0002-7287-8459], and Apollo - University of Cambridge Repository
Subjects: EXPRESSION, Meristem, Arabidopsis, Phloem, Plant Roots, Article, ROOT, RHO, GTP-Binding Proteins, REVEALS, Life Science, Laboratorium voor Moleculaire Biologie, RNA-SEQ, RNA-Seq, Multidisciplinary, Arabidopsis Proteins, REGULATORY NETWORK, fungi, 1184 Genetics, developmental biology, physiology, Biology and Life Sciences, food and beverages, Cell Differentiation, GENE, GTPASES, MORPHOGENESIS, GROWTH, Laboratory of Molecular Biology, EPS, Single-Cell Analysis, Transcriptome, Signal Transduction, Transcription Factors
Abstract: Publisher Copyright: Copyright © 2021 The Authors, some rights reserved; In the plant meristem, tissue-wide maturation gradients are coordinated with specialized cell networks to establish various developmental phases required for indeterminate growth. Here, we used single-cell transcriptomics to reconstruct the protophloem developmental trajectory from the birth of cell progenitors to terminal differentiation in the Arabidopsis thaliana root. PHLOEM EARLY DNA-BINDING-WITH-ONE-FINGER (PEAR) transcription factors mediate lineage bifurcation by activating guanosine triphosphatase signaling and prime a transcriptional differentiation program. This program is initially repressed by a meristem-wide gradient of PLETHORA transcription factors. Only the dissipation of PLETHORA gradient permits activation of the differentiation program that involves mutual inhibition of early versus late meristem regulators. Thus, for phloem development, broad maturation gradients interface with cell-type-specific transcriptional regulators to stage cellular differentiation.
Published: 2021
Full Text: View/download PDF

19. Cryogenic land surface processes shape vegetation biomass patterns in northern European tundra

Author: Pekka Niittynen, Miska Luoto, Henri Riihimäki, Juha Aalto, Institute of Biotechnology (-2009), Department of Geosciences and Geography, Helsinki Institute of Sustainability Science (HELSUS), and BioGeoClimate Modelling Lab
Subjects: DYNAMICS, IMPACTS, 0106 biological sciences, 010504 meteorology & atmospheric sciences, Climate change, 010603 evolutionary biology, 01 natural sciences, PERMAFROST, ARCTIC VEGETATION, GE1-350, Ecosystem, Arctic vegetation, DISTURBANCE, EQUATIONS, 1172 Environmental sciences, 0105 earth and related environmental sciences, General Environmental Science, QE1-996.5, Biomass (ecology), CLIMATE-CHANGE, ICE-WEDGE DEGRADATION, Global warming, Biosphere, Geology, Vegetation, PERFORMANCE, 15. Life on land, Tundra, Environmental sciences, 13. Climate action, FEEDBACKS, General Earth and Planetary Sciences, Environmental science, Physical geography
Abstract: Tundra ecosystems have experienced changes in vegetation composition, distribution, and productivity over the past century due to climate warming. However, the increase in above-ground biomass may be constrained by cryogenic land surface processes that cause topsoil disturbance and variable microsite conditions. These effects have remained unaccounted for in tundra biomass models, although they can impact multiple opposing feedbacks between the biosphere and atmosphere, ecosystem functioning and biodiversity. Here, by using field-quantified data from northern Europe, remote sensing, and machine learning, we show that cryogenic land surface processes substantially constrain above-ground biomass in tundra. The three surveyed processes (cryoturbation, solifluction, and nivation) collectively reduced biomass by an average of 123.0 g m(-2) (-30.0%). This effect was significant over landscape positions and was especially pronounced in snowbed environments, where the mean reduction in biomass was 57.3%. Our results imply that cryogenic land surface processes are pivotal in shaping future patterns of tundra biomass, as long as cryogenic ground activity is retained by climate warming. Vegetation in tundra ecosystems is constrained by cryogenic land surface processes, despite the fact that models of future biomass changes rarely take these into account, according to field and remote sensing data from northern Europe.
Published: 2021
Full Text: View/download PDF

20. Reviews and syntheses: Arctic fire regimes and emissions in the 21st century

Author: Nikolaos Evangeliou, Simon Wilson, Lin Huang, Jessica L. McCarty, Elena I. Parfenova, Ville-Veikko Paunu, Kaarle Kupiainen, Zbigniew Klimont, Ari Venäläinen, Justin J. Fain, Steve R. Arnold, Amber J. Soja, Juha Aalto, Sabine Eckhardt, N. M. Tchebakova, and Institute of Biotechnology (-2009)
Subjects: 1171 Geosciences, QE1-996.5, 010504 meteorology & atmospheric sciences, Fire regime, Ecology, Prescribed burn, Taiga, Climate change, Geology, 15. Life on land, 010501 environmental sciences, Permafrost, 01 natural sciences, Tundra, Boreal, Arctic, Life, 13. Climate action, QH501-531, Environmental science, Physical geography, Ecology, Evolution, Behavior and Systematics, QH540-549.5, 0105 earth and related environmental sciences, Earth-Surface Processes
Abstract: In recent years, the pan-Arctic region has experienced increasingly extreme fire seasons. Fires in the northern high latitudes are driven by current and future climate change, lightning, fuel conditions, and human activity. In this context, conceptualizing and parameterizing current and future Arctic fire regimes will be important for fire and land management as well as understanding current and predicting future fire emissions. The objectives of this review were driven by policy questions identified by the Arctic Monitoring and Assessment Programme (AMAP) Working Group and posed to its Expert Group on Short-Lived Climate Forcers. This review synthesizes current understanding of the changing Arctic and boreal fire regimes, particularly as fire activity and its response to future climate change in the pan-Arctic have consequences for Arctic Council states aiming to mitigate and adapt to climate change in the north. The conclusions from our synthesis are the following. (1) Current and future Arctic fires, and the adjacent boreal region, are driven by natural (i.e. lightning) and human-caused ignition sources, including fires caused by timber and energy extraction, prescribed burning for landscape management, and tourism activities. Little is published in the scientific literature about cultural burning by Indigenous populations across the pan-Arctic, and questions remain on the source of ignitions above 70∘ N in Arctic Russia. (2) Climate change is expected to make Arctic fires more likely by increasing the likelihood of extreme fire weather, increased lightning activity, and drier vegetative and ground fuel conditions. (3) To some extent, shifting agricultural land use and forest transitions from forest–steppe to steppe, tundra to taiga, and coniferous to deciduous in a warmer climate may increase and decrease open biomass burning, depending on land use in addition to climate-driven biome shifts. However, at the country and landscape scales, these relationships are not well established. (4) Current black carbon and PM2.5 emissions from wildfires above 50 and 65∘ N are larger than emissions from the anthropogenic sectors of residential combustion, transportation, and flaring. Wildfire emissions have increased from 2010 to 2020, particularly above 60∘ N, with 56 % of black carbon emissions above 65∘ N in 2020 attributed to open biomass burning – indicating how extreme the 2020 wildfire season was and how severe future Arctic wildfire seasons can potentially be. (5) What works in the boreal zones to prevent and fight wildfires may not work in the Arctic. Fire management will need to adapt to a changing climate, economic development, the Indigenous and local communities, and fragile northern ecosystems, including permafrost and peatlands. (6) Factors contributing to the uncertainty of predicting and quantifying future Arctic fire regimes include underestimation of Arctic fires by satellite systems, lack of agreement between Earth observations and official statistics, and still needed refinements of location, conditions, and previous fire return intervals on peat and permafrost landscapes. This review highlights that much research is needed in order to understand the local and regional impacts of the changing Arctic fire regime on emissions and the global climate, ecosystems, and pan-Arctic communities.
Published: 2021

21. NOTUM from Apc-mutant cells biases clonal competition to initiate cancer

Author: Pirjo Nummela, Colin Nixon, William C. Clark, Ella Gilchrist, Simon J. Leedham, Michael C. Hodder, Nalle Pentinmikko, Arafath Kaja Najumudeen, Nathalie Sphyris, E. Yvonne Jones, Jean-Paul Vincent, Hans Clevers, Nicky J. Willis, Alexander Raven, Kristina Kirschner, Dustin J. Flanagan, Paul V. Fish, Emma Minnee, Pekka Katajisto, Ville Hietakangas, Owen J. Sansom, Christine Perret, Lynn McGarry, Nadia Nasreddin, Rachel A. Ridgway, Ann C. Williams, Kathryn Gilroy, Kalle Luopajärvi, Sandra Scharaw, Béatrice Romagnolo, Marianne Lähde, Ari Ristimäki, Johanna Englund, Anna Taylor Webb, Kari Alitalo, Ann Hedley, Hubrecht Institute for Developmental Biology and Stem Cell Research, Institute of Biotechnology (-2009), University of Helsinki, CAN-PRO - Translational Cancer Medicine Program, Centre of Excellence in Stem Cell Metabolism, Helsinki Institute of Life Science HiLIFE, Institute of Biotechnology, Juha Klefström / Principal Investigator, Research Programs Unit, Department of Pathology, Doctoral Programme in Biomedicine, ATG - Applied Tumor Genomics, Doctoral Programme in Integrative Life Science, HUSLAB, Kari Alitalo / Principal Investigator, Molecular and Integrative Biosciences Research Programme, Biosciences, and Nutrient sensing laboratory
Subjects: 0301 basic medicine, Male, HOMEOSTASIS, Cell, medicine.disease_cause, Cell Transformation, Inbred C57BL, Ligands, BETA-CATENIN, ACTIVATION, PATHWAY, Mice, 0302 clinical medicine, Conditioned, INTESTINE, Stem Cells/cytology, Wnt Signaling Pathway, Cell Competition/genetics, Esterases/antagonists & inhibitors, Mutation, Multidisciplinary, biology, Stem Cells, Cell Transformation, Neoplastic/genetics, Wnt signaling pathway, Esterases, Cell Differentiation, Neoplastic/genetics, Cell biology, Organoids, POLYPOSIS, medicine.anatomical_structure, Cell Transformation, Neoplastic, 030220 oncology & carcinogenesis, Disease Progression, Organoids/cytology, Female, Stem cell, Colorectal Neoplasms, STEM-CELLS, BONE-FORMATION, Adenoma, Beta-catenin, Genes, APC, 3122 Cancers, Crypt, Adenomatous Polyposis Coli Protein, WNT, 03 medical and health sciences, Cancer stem cell, Wnt Proteins/metabolism, medicine, Animals, Humans, Adenomatous Polyposis Coli Protein/genetics, Cell Proliferation, Adenoma/genetics, Colorectal Neoplasms/genetics, Notum, Culture Media, APC, Wnt Proteins, Mice, Inbred C57BL, 030104 developmental biology, Genes, Cell Competition, Culture Media, Conditioned, biology.protein, 1182 Biochemistry, cell and molecular biology
Abstract: Funding Information: Acknowledgements We thank the Core Services and Advanced Technologies at the Cancer Research UK Beatson Institute (C596/A17196 and A31287), and particularly the Biological Services Unit, Histology Service and Molecular Technologies; members of the Sansom and Katajisto laboratories for discussions of the data and manuscript; and BRC Oxford for supplying patient material. O.J.S. and his laboratory members were supported by Cancer Research UK (A28223, A21139, A12481 and A17196). D.J.F. and M.C.H. were supported by the UK Medical Research Council (MR/R017247/1 and MR/J50032X/1, respectively). SpecifiCancer CRUK Grand Challenge (C7932/A29055) is funded by Cancer Research UK and the Mark Foundation for Cancer Research. P.K. and his laboratory members were supported by the Academy of Finland Centre of Excellence MetaStem (266869, 304591 and 320185), the ERC Starting Grant 677809, the Swedish Research Council 2018-03078, the Cancerfonden 190634, the Jane and Aatos Erkko Foundation and the Cancer Foundation Finland. N.P. was supported by the Finnish Cultural Foundation, the Biomedicum Helsinki Foundation, the Orion Research Foundation sr and The Paulo Foundation. P.V.F. was supported by Alzheimer’s Research UK and The Francis Crick Institute. The ARUK UCL Drug Discovery Institute receives its core funding from Alzheimer’s Research UK (520909). The Francis Crick Institute receives its core funding from Cancer Research UK (FC001002), the UK Medical Research Council (FC001002) and the Wellcome Trust (FC001002). Publisher Copyright: © 2021, The Author(s), under exclusive licence to Springer Nature Limited. The tumour suppressor APC is the most commonly mutated gene in colorectal cancer. Loss of Apc in intestinal stem cells drives the formation of adenomas in mice via increased WNT signalling(1), but reduced secretion of WNT ligands increases the ability of Apc-mutant intestinal stem cells to colonize a crypt (known as fixation)(2). Here we investigated how Apc-mutant cells gain a clonal advantage over wild-type counterparts to achieve fixation. We found that Apc-mutant cells are enriched for transcripts that encode several secreted WNT antagonists, with Notum being the most highly expressed. Conditioned medium from Apc-mutant cells suppressed the growth of wild-type organoids in a NOTUM-dependent manner. Furthermore, NOTUM-secreting Apc-mutant clones actively inhibited the proliferation of surrounding wild-type crypt cells and drove their differentiation, thereby outcompeting crypt cells from the niche. Genetic or pharmacological inhibition of NOTUM abrogated the ability of Apc-mutant cells to expand and form intestinal adenomas. We identify NOTUM as a key mediator during the early stages of mutation fixation that can be targeted to restore wild-type cell competitiveness and provide preventative strategies for people at a high risk of developing colorectal cancer.
Published: 2021
Full Text: View/download PDF

22. Environmental Controls of InSAR-based Periglacial Ground Dynamics in a Sub-Arctic Landscape

Author: Miska Luoto, Juha Aalto, Pekka Niittynen, Jan Hjort, Line Rouyet, Tom Rune Lauknes, Olli Karjalainen, Yngvar Larsen, Department of Geosciences and Geography, Helsinki Institute of Sustainability Science (HELSUS), BioGeoClimate Modelling Lab, Institute of Biotechnology (-2009), and Division of Urban Geography and Regional Studies
Subjects: ACTIVE-LAYER, 010504 meteorology & atmospheric sciences, 0211 other engineering and technologies, Climate change, PERMAFROST DISTRIBUTION, SURFACE DEFORMATION, 02 engineering and technology, Solifluction, DISTRIBUTION MODELS, 01 natural sciences, InSAR, Sub arctic, SNOW COVER, Interferometric synthetic aperture radar, VDP::Matematikk og Naturvitenskap: 400::Geofag: 450, SPATIAL AUTOCORRELATION, periglacial, 1172 Environmental sciences, 021101 geological & geomatics engineering, 0105 earth and related environmental sciences, Earth-Surface Processes, Ground movement, ground dynamics, CLIMATE-CHANGE, VDP::Mathematics and natural science: 400::Geosciences: 450, Cryoturbation, cryoturbation, Lead (sea ice), modeling, 15. Life on land, NORTHERN-HEMISPHERE, ABISKO MOUNTAINS, Geophysics, 13. Climate action, solifluction, Physical geography, SOLIFLUCTION PROCESSES, Snow cover, Geology
Abstract: Periglacial environments are characterized by highly dynamic landscapes. Freezing and thawing lead to ground movement, associated with cryoturbation and solifluction. These processes are sensitive to climate change and variably distributed depending on multiple environmental factors. In this study, we used multi-geometry Sentinel-1 Synthetic Aperture Radar Interferometry (InSAR) to investigate the spatial distribution of the mean annual ground velocity in a mountainous landscape in Northern Norway. Statistical modeling was employed to examine how periglacial ground velocity is related to environmental variables characterizing the diverse climatic, geomorphic, hydrological and biological conditions within a 148 km(2) study area. Two-dimensional (2D) InSAR results document mean annual ground velocity up to 15 mm/yr. Vertical and horizontal velocity components in the East-West plane show variable spatial distribution, which can be explained by the characteristics of cryoturbation and solifluction operating differently over flat and sloping terrain. Statistical modeling shows that slope angle and mean annual air temperature variables are the most important environmental factors explaining the distribution of the horizontal and vertical components, respectively. Vegetation and snow cover also have a local influence, interpreted as indicators of the ground material and moisture conditions. The results show contrasted model performance depending on the velocity component used as a response variable. In general, our study highlights the potential of integrating radar remote sensing and statistical modeling to investigate mountainous regions and better understand the relations between environmental factors, periglacial processes and ground dynamics.
Published: 2021
Full Text: View/download PDF

23. High potential for loss of permafrost landforms in a changing climate

Author: Juha Aalto, Jan Hjort, Miska Luoto, Bernd Etzelmüller, Guido Grosse, Benjamin M. Jones, Olli Karjalainen, Karianne Staalesen Lilleøren, Helsinki Institute of Sustainability Science (HELSUS), BioGeoClimate Modelling Lab, Department of Geosciences and Geography, Institute of Biotechnology (-2009), and Division of Urban Geography and Regional Studies
Subjects: 010504 meteorology & atmospheric sciences, Environmental change, Climate change, Rock glacier, 010501 environmental sciences, Permafrost, 01 natural sciences, TEMPERATURES, ground ice, Precipitation, geodiversity, COLLAPSE, 1172 Environmental sciences, 0105 earth and related environmental sciences, General Environmental Science, geography, environmental space, geography.geographical_feature_category, Renewable Energy, Sustainability and the Environment, Landform, ICE-WEDGE DEGRADATION, Public Health, Environmental and Occupational Health, PATHWAYS, statistical ensemble modelling, ROCK GLACIERS, environmental change, 15. Life on land, NORTHERN-HEMISPHERE, Tundra, TUNDRA, climate change, Arctic, 13. Climate action, THERMAL REGIME, Physical geography, PENINSULA, Geology, permafrost, RESPONSES
Abstract: The presence of ground ice in Arctic soils exerts a major effect on permafrost hydrology and ecology, and factors prominently into geomorphic landform development. As most ground ice has accumulated in near-surface permafrost, it is sensitive to variations in atmospheric conditions. Typical and regionally widespread permafrost landforms such as pingos, ice-wedge polygons, and rock glaciers are closely tied to ground ice. However, under ongoing climate change, suitable environmental spaces for preserving landforms associated with ice-rich permafrost may be rapidly disappearing. We deploy a statistical ensemble approach to model, for the first time, the current and potential future environmental conditions of three typical permafrost landforms, pingos, ice-wedge polygons and rock glaciers across the Northern Hemisphere. We show that by midcentury, the landforms are projected to lose more than one-fifth of their suitable environments under a moderate climate scenario (RCP4.5) and on average around one-third under a very high baseline emission scenario (RCP8.5), even when projected new suitable areas for occurrence are considered. By 2061–2080, on average more than 50% of the recent suitable conditions can be lost (RCP8.5). In the case of pingos and ice-wedge polygons, geographical changes are mainly attributed to alterations in thawing-season precipitation and air temperatures. Rock glaciers show air temperature-induced regional changes in suitable conditions strongly constrained by topography and soil properties. The predicted losses could have important implications for Arctic hydrology, geo- and biodiversity, and to the global climate system through changes in biogeochemical cycles governed by the geomorphology of permafrost landscapes. Moreover, our projections provide insights into the circumpolar distribution of various ground ice types and help inventory permafrost landforms in unmapped regions.
Published: 2020

24. Mso1p Regulates Membrane Fusion through Interactions with the Putative N-Peptide–binding Area in Sec1p Domain 1

Author: Marion Weber, Konstantin G. Chernov, Maria Pajunen, Harri Savilahti, Jussi Jäntti, Gerd Wohlfahrt, Hilkka Turakainen, Weber, Marion, Chernov, Konstantin, Pajunen, Maria, Jantti, Jussi, University of Helsinki, Institute of Biotechnology (-2009), and University of Helsinki, Institute of Biotechnology
Subjects: Models, Molecular, Munc18 Proteins, Peptide binding, Membrane Fusion, Protein Structure, Secondary, SACCHAROMYCES-CEREVISIAE, 0302 clinical medicine, Protein Interaction Mapping, Syntaxin, 0303 health sciences, VAMP2, Protein Stability, Qa-SNARE Proteins, TERMINAL PEPTIDE, Articles, Spores, Fungal, 3. Good health, Cell biology, MOLECULAR-INTERACTIONS, Biochemistry, NEURONAL SNARE COMPLEX, SECRETION, Protein Binding, Binding domain, Vesicle-associated membrane protein 8, Saccharomyces cerevisiae Proteins, education, Saccharomyces cerevisiae, Biology, 03 medical and health sciences, YEAST, Molecular Biology, SEC1/MUNC18 PROTEINS, 030304 developmental biology, Binding Sites, BIMOLECULAR FLUORESCENCE COMPLEMENTATION, Membrane Proteins, IN-VITRO, Cell Biology, SM-PROTEIN, Protein Structure, Tertiary, Amino Acid Substitution, Membrane protein, Membrane Trafficking, Mutation, Rab, 118 Biological sciences, Peptides, 030217 neurology & neurosurgery
Abstract: We show that the putative N-peptide binding area in Sec1p domain 1 is important for Mso1p binding and that Mso1p can interact with Sso1p and Sso2p. Our results suggest that Mso1p mimics N-peptide binding to facilitate membrane fusion., Sec1p/Munc18 (SM) family proteins regulate SNARE complex function in membrane fusion through their interactions with syntaxins. In addition to syntaxins, only a few SM protein interacting proteins are known and typically, their binding modes with SM proteins are poorly characterized. We previously identified Mso1p as a Sec1p-binding protein and showed that it is involved in membrane fusion regulation. Here we demonstrate that Mso1p and Sec1p interact at sites of exocytosis and that the Mso1p–Sec1p interaction site depends on a functional Rab GTPase Sec4p and its GEF Sec2p. Random and targeted mutagenesis of Sec1p, followed by analysis of protein interactions, indicates that Mso1p interacts with Sec1p domain 1 and that this interaction is important for membrane fusion. In many SM family proteins, domain 1 binds to a N-terminal peptide of a syntaxin family protein. The Sec1p-interacting syntaxins Sso1p and Sso2p lack the N-terminal peptide. We show that the putative N-peptide binding area in Sec1p domain 1 is important for Mso1p binding, and that Mso1p can interact with Sso1p and Sso2p. Our results suggest that Mso1p mimics N-peptide binding to facilitate membrane fusion.
Published: 2010
Full Text: View/download PDF

25. Insights into the pre-initiation events of bacteriophage φ6 RNA-dependent RNA polymerase: towards the assembly of a productive binary complex

Author: David I. Stuart, Antti P. Aalto, Minni R. L. Koivunen, L. Peter Sarin, Janne J. Ravantti, Dennis H. Bamford, Minna M. Poranen, N. Marika Lehti, Jonathan M. Grimes, Alberdina A. van Dijk, Institute of Biotechnology (-2009), Biosciences, Molecular and Translational Virology, and Structure of the Viral Universe
Subjects: viruses, Molecular Sequence Data, RNA-dependent RNA polymerase, Biology, 03 medical and health sciences, chemistry.chemical_compound, Viral Proteins, Transcription (biology), RNA polymerase, Genetics, Amino Acid Sequence, Polymerase, 1183 Plant biology, microbiology, virology, 030304 developmental biology, 0303 health sciences, Nucleic Acid Enzymes, 030302 biochemistry & molecular biology, Bacteriophage phi 6, Helicase, RNA, Templates, Genetic, RNA-Dependent RNA Polymerase, Cell biology, RNA silencing, chemistry, biology.protein, Mutagenesis, Site-Directed, 1182 Biochemistry, cell and molecular biology
Abstract: The RNA-dependent RNA polymerase (RdRP) of double-stranded RNA (dsRNA) viruses performs both RNA replication and transcription. In order to initiate RNA polymerization, viral RdRPs must be able to interact with the incoming 3 terminus of the template and position it, so that a productive binary complex is formed. Structural studies have revealed that RdRPs of dsRNA viruses that lack helicases have electrostatically charged areas on the polymerase surface, which might facilitate such interactions. In this study, structure-based mutagenesis, enzymatic assays and molecular mapping of bacteriophage 6 RdRP and its RNA were used to elucidate the roles of the negatively charged plough area on the polymerase surface, of the rim of the template tunnel and of the template specificity pocket that is key in the formation of the productive RNA-polymerase binary complex. The positively charged rim of the template tunnel has a significant role in the engagement of highly structured ssRNA molecules, whereas specific interactions further down in the template tunnel promote ssRNA entry to the catalytic site. Hence, we show that by aiding the formation of a stable binary complex with optimized RNA templates, the overall polymerization activity of the 6 RdRP can be greatly enhanced. The RNA-dependent RNA polymerase (RdRP) of double-stranded RNA (dsRNA) viruses performs both RNA replication and transcription. In order to initiate RNA polymerization, viral RdRPs must be able to interact with the incoming 3 terminus of the template and position it, so that a productive binary complex is formed. Structural studies have revealed that RdRPs of dsRNA viruses that lack helicases have electrostatically charged areas on the polymerase surface, which might facilitate such interactions. In this study, structure-based mutagenesis, enzymatic assays and molecular mapping of bacteriophage 6 RdRP and its RNA were used to elucidate the roles of the negatively charged plough area on the polymerase surface, of the rim of the template tunnel and of the template specificity pocket that is key in the formation of the productive RNA-polymerase binary complex. The positively charged rim of the template tunnel has a significant role in the engagement of highly structured ssRNA molecules, whereas specific interactions further down in the template tunnel promote ssRNA entry to the catalytic site. Hence, we show that by aiding the formation of a stable binary complex with optimized RNA templates, the overall polymerization activity of the 6 RdRP can be greatly enhanced. The RNA-dependent RNA polymerase (RdRP) of double-stranded RNA (dsRNA) viruses performs both RNA replication and transcription. In order to initiate RNA polymerization, viral RdRPs must be able to interact with the incoming 3 terminus of the template and position it, so that a productive binary complex is formed. Structural studies have revealed that RdRPs of dsRNA viruses that lack helicases have electrostatically charged areas on the polymerase surface, which might facilitate such interactions. In this study, structure-based mutagenesis, enzymatic assays and molecular mapping of bacteriophage 6 RdRP and its RNA were used to elucidate the roles of the negatively charged plough area on the polymerase surface, of the rim of the template tunnel and of the template specificity pocket that is key in the formation of the productive RNA-polymerase binary complex. The positively charged rim of the template tunnel has a significant role in the engagement of highly structured ssRNA molecules, whereas specific interactions further down in the template tunnel promote ssRNA entry to the catalytic site. Hence, we show that by aiding the formation of a stable binary complex with optimized RNA templates, the overall polymerization activity of the 6 RdRP can be greatly enhanced.
Published: 2009

26. Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function

Author: Pekka Marttinen, Liisa Holm, Petri Törönen, Pauli J. Ojala, Institute of Biotechnology (-2009), Biosciences, Bioinformatics, and Computational genomics
Subjects: Class (set theory), Computer science, education, lcsh:Computer applications to medicine. Medical informatics, computer.software_genre, Biochemistry, Set (abstract data type), 03 medical and health sciences, 0302 clinical medicine, Structural Biology, Databases, Genetic, Research article, Gene expression, Gene set analysis, Differential (infinitesimal), lcsh:QH301-705.5, Molecular Biology, Gene, 030304 developmental biology, 0303 health sciences, Gene Expression Profiling, Applied Mathematics, Computational Biology, Function (mathematics), Computer Science Applications, Identification (information), lcsh:Biology (General), 030220 oncology & carcinogenesis, lcsh:R858-859.7, Data mining, DNA microarray, computer, Software
Abstract: Background A central task in contemporary biosciences is the identification of biological processes showing response in genome-wide differential gene expression experiments. Two types of analysis are common. Either, one generates an ordered list based on the differential expression values of the probed genes and examines the tail areas of the list for over-representation of various functional classes. Alternatively, one monitors the average differential expression level of genes belonging to a given functional class. So far these two types of method have not been combined. Results We introduce a scoring function, Gene Set Z-score (GSZ), for the analysis of functional class over-representation that combines two previous analysis methods. GSZ encompasses popular functions such as correlation, hypergeometric test, Max-Mean and Random Sets as limiting cases. GSZ is stable against changes in class size as well as across different positions of the analysed gene list in tests with randomized data. GSZ shows the best overall performance in a detailed comparison to popular functions using artificial data. Likewise, GSZ stands out in a cross-validation of methods using split real data. A comparison of empirical p-values further shows a strong difference in favour of GSZ, which clearly reports better p-values for top classes than the other methods. Furthermore, GSZ detects relevant biological themes that are missed by the other methods. These observations also hold when comparing GSZ with popular program packages. Conclusion GSZ and improved versions of earlier methods are a useful contribution to the analysis of differential gene expression. The methods and supplementary material are available from the website http://ekhidna.biocenter.helsinki.fi/users/petri/public/GSZ/GSZscore.html.
Published: 2009
Full Text: View/download PDF

27. Design, synthesis, and biological activity of isophthalic acid derivatives targeted to the C1 domain of protein kinase C

Author: Olli Aitio, Gustav Boije af Gennäs, Virpi Talman, Raimo K. Tuominen, Elina Ekokoski, Jari Yli-Kauhaluoma, Moshe Finel, Farmaseuttisen kemian osasto (-2009), Farmakologian ja toksikologian osasto (-2013), Institute of Biotechnology (-2009), and Lääkkeen keksintä- ja kehitysteknologian keskus (DDTC) (-2009)
Subjects: Insecta, Protein Kinase C-alpha, Stereochemistry, Phthalic Acids, PKC alpha, 01 natural sciences, Binding, Competitive, Cell Line, 03 medical and health sciences, Enzyme activator, Structure-Activity Relationship, Drug Discovery, Structure–activity relationship, Animals, Humans, Binding site, Phosphorylation, Protein Kinase Inhibitors, Protein kinase C, Protein Kinase C, 030304 developmental biology, C1 domain, 0303 health sciences, Binding Sites, 010405 organic chemistry, Chemistry, Biological activity, 3. Good health, 0104 chemical sciences, Enzyme Activation, Protein Kinase C-delta, Biochemistry, 317 Pharmacy, Drug Design, Molecular Medicine, HeLa Cells
Abstract: Protein kinase C (PKC) is a widely studied molecular target for the treatment of cancer and other diseases. We have approached the issue of modifying PKC function by targeting the C1 domain in the regulatory region of the enzyme. Using the X-ray crystal structure of the PKC delta C1b domain, we have discovered conveniently synthesizable derivatives of dialkyl 5-(hydroxymethyl)isophthalate that can act as potential C1 domain ligands. Structure-activity studies confirmed that the important functional groups predicted by modeling were indispensable for binding to the C1 domain and that the modifications of these groups diminished binding. The most promising compounds were able to displace radiolabeled phorbol ester ([H-3]PDBu) from PKC alpha and delta at K-i values in the range of 200-900 nM. Furthermore, the active isophthalate derivatives could modify PKC activation in living cells either by inducing PKC-dependent ERK phosphorylation or by inhibiting phorbol-induced ERK phosphorylation. In conclusion, we report here, for the first time. that derivatives of isophthalic acid represent an attractive novel group of C1 domain ligands that can be used as research tools or further modified for potential drug development. Protein kinase C (PKC) is a widely studied molecular target for the treatment of cancer and other diseases. We have approached the issue of modifying PKC function by targeting the C1 domain in the regulatory region of the enzyme. Using the X-ray crystal structure of the PKC delta C1b domain, we have discovered conveniently synthesizable derivatives of dialkyl 5-(hydroxymethyl)isophthalate that can act as potential C1 domain ligands. Structure-activity studies confirmed that the important functional groups predicted by modeling were indispensable for binding to the C1 domain and that the modifications of these groups diminished binding. The most promising compounds were able to displace radiolabeled phorbol ester ([H-3]PDBu) from PKC alpha and delta at K-i values in the range of 200-900 nM. Furthermore, the active isophthalate derivatives could modify PKC activation in living cells either by inducing PKC-dependent ERK phosphorylation or by inhibiting phorbol-induced ERK phosphorylation. In conclusion, we report here, for the first time. that derivatives of isophthalic acid represent an attractive novel group of C1 domain ligands that can be used as research tools or further modified for potential drug development. Protein kinase C (PKC) is a widely studied molecular target for the treatment of cancer and other diseases. We have approached the issue of modifying PKC function by targeting the C1 domain in the regulatory region of the enzyme. Using the X-ray crystal structure of the PKC delta C1b domain, we have discovered conveniently synthesizable derivatives of dialkyl 5-(hydroxymethyl)isophthalate that can act as potential C1 domain ligands. Structure-activity studies confirmed that the important functional groups predicted by modeling were indispensable for binding to the C1 domain and that the modifications of these groups diminished binding. The most promising compounds were able to displace radiolabeled phorbol ester ([H-3]PDBu) from PKC alpha and delta at K-i values in the range of 200-900 nM. Furthermore, the active isophthalate derivatives could modify PKC activation in living cells either by inducing PKC-dependent ERK phosphorylation or by inhibiting phorbol-induced ERK phosphorylation. In conclusion, we report here, for the first time. that derivatives of isophthalic acid represent an attractive novel group of C1 domain ligands that can be used as research tools or further modified for potential drug development.
Published: 2009

28. In Vivo and In Vitro Protein Ligation by Naturally Occurring and Engineered Split DnaE Inteins

Author: Hideo Iwaï, Edith Buchinger, Sara Züger, A. Sesilja Aranko, and Institute of Biotechnology (-2009)
Subjects: dnaE, DNA polymerase, Protein Conformation, education, Molecular Sequence Data, lcsh:Medicine, Peptide, Biochemistry/Biocatalysis, Protein Engineering, 01 natural sciences, Biochemistry, Inteins, src Homology Domains, 03 medical and health sciences, Protein structure, Bacterial Proteins, Protein splicing, Biochemistry/Protein Chemistry, Protein Splicing, Chemistry/Biochemistry, Amino Acid Sequence, Biochemistry/Macromolecular Chemistry, Biophysics/Biocatalysis, lcsh:Science, Nostoc, Peptide sequence, 030304 developmental biology, DNA Polymerase III, chemistry.chemical_classification, 0303 health sciences, Multidisciplinary, biology, 010405 organic chemistry, lcsh:R, Synechocystis, Protein engineering, 0104 chemical sciences, chemistry, biology.protein, lcsh:Q, Biotechnology/Protein Chemistry and Proteomics, Ligation, Research Article
Abstract: BACKGROUND: Protein trans-splicing by naturally occurring split DnaE inteins is used for protein ligation of foreign peptide fragments. In order to widen biotechnological applications of protein trans-splicing, it is highly desirable to have split inteins with shorter C-terminal fragments, which can be chemically synthesized. PRINCIPAL FINDINGS: We report the identification of new functional split sites in DnaE inteins from Synechocystis sp. PCC6803 and from Nostoc punctiforme. One of the newly engineered split intein bearing C-terminal 15 residues showed more robust protein trans-splicing activity than naturally occurring split DnaE inteins in a foreign context. During the course of our experiments, we found that protein ligation by protein trans-splicing depended not only on the splicing junction sequences, but also on the foreign extein sequences. Furthermore, we could classify the protein trans-splicing reactions in foreign contexts with a simple kinetic model into three groups according to their kinetic parameters in the presence of various reducing agents. CONCLUSION: The shorter C-intein of the newly engineered split intein could be a useful tool for biotechnological applications including protein modification, incorporation of chemical probes, and segmental isotopic labelling. Based on kinetic analysis of the protein splicing reactions, we propose a general strategy to improve ligation yields by protein trans-splicing, which could significantly enhance the applications of protein ligation by protein trans-splicing.
Published: 2009

29. Molecular basis of filamin a-filGAP interaction and its impairment in congenital disorders associated with filamin a mutations

Author: Olga Kupiainen, Outi Heikkinen, John H. Hartwig, Teresia Osborn, Karen E. Kasza, Olli T. Pentikäinen, Ilkka Kilpeläinen, Fumihiko Nakamura, Perttu Permi, Jari Ylänne, David A. Weitz, Thomas P. Stossel, Department of Chemistry, and Institute of Biotechnology (-2009)
Subjects: Immunoprecipitation, Filamins, Molecular Sequence Data, education, lcsh:Medicine, Computational Biology/Protein Structure Prediction, Biology, Filamin, Cell Biology/Cell Signaling, Congenital Abnormalities, Biochemistry/Protein Folding, 03 medical and health sciences, 0302 clinical medicine, Protein structure, Contractile Proteins, Cell Biology/Cytoskeleton, FLNA, Humans, FLNB, FLNC, Amino Acid Sequence, lcsh:Science, 030304 developmental biology, Genetics, 0303 health sciences, Multidisciplinary, Binding Sites, Molecular Structure, Sequence Homology, Amino Acid, Point mutation, lcsh:R, GTPase-Activating Proteins, Microfilament Proteins, 3. Good health, Biochemistry/Bioinformatics, Mutation, Protein folding, lcsh:Q, 118 Biological sciences, 030217 neurology & neurosurgery, Research Article
Abstract: Background Mutations in filamin A (FLNa), an essential cytoskeletal protein with multiple binding partners, cause developmental anomalies in humans. Methodology/Principal Findings We determined the structure of the 23rd Ig repeat of FLNa (IgFLNa23) that interacts with FilGAP, a Rac-specific GTPase-activating protein and regulator of cell polarity and movement, and the effect of the three disease-related mutations on this interaction. A combination of NMR structural analysis and in silico modeling revealed the structural interface details between the C and D β-strands of the IgFLNa23 and the C-terminal 32 residues of FilGAP. Mutagenesis of the predicted key interface residues confirmed the binding constraints between the two proteins. Specific loss-of-function FLNa constructs were generated and used to analyze the importance of the FLNa-FilGAP interaction in vivo. Point mutagenesis revealed that disruption of the FLNa-FilGAP interface perturbs cell spreading. FilGAP does not bind FLNa homologs FLNb or FLNc establishing the importance of this interaction to the human FLNa mutations. Tight complex formation requires dimerization of both partners and the correct alignment of the binding surfaces, which is promoted by a flexible hinge domain between repeats 23 and 24 of FLNa. FLNa mutations associated with human developmental anomalies disrupt the binding interaction and weaken the elasticity of FLNa/F-actin network under high mechanical stress. Conclusions/Significance Mutational analysis informed by structure can generate reagents for probing specific cellular interactions of FLNa. Disease-related FLNa mutations have demonstrable effects on FLNa function.
Published: 2009

30. Generation of Gene Ontology benchmark datasets with various types of positive signal

Author: Petri Pehkonen, Petri Törönen, Liisa Holm, Institute of Biotechnology (-2009), Biosciences, Bioinformatics, and Computational genomics
Subjects: Computer science, education, Information Storage and Retrieval, Binary number, lcsh:Computer applications to medicine. Medical informatics, computer.software_genre, 01 natural sciences, Biochemistry, Correlation, User-Computer Interface, 010104 statistics & probability, 03 medical and health sciences, Structural Biology, Databases, Genetic, 0101 mathematics, MATLAB, Cluster analysis, lcsh:QH301-705.5, Molecular Biology, 030304 developmental biology, computer.programming_language, 0303 health sciences, Class (computer programming), Methodology Article, Applied Mathematics, SIGNAL (programming language), Computational Biology, Computer Science Applications, lcsh:Biology (General), Benchmark (computing), lcsh:R858-859.7, Embedding, Data mining, computer, Algorithms
Abstract: Background The analysis of over-represented functional classes in a list of genes is one of the most essential bioinformatics research topics. Typical examples of such lists are the differentially expressed genes from transcriptional analysis which need to be linked to functional information represented in the Gene Ontology (GO). Despite the importance of this procedure, there is a little work on consistent evaluation of various GO analysis methods. Especially, there is no literature on creating benchmark datasets for GO analysis tools. Results We propose a methodology for the evaluation of GO analysis tools, which consists of creating gene lists with a selected signal level and a selected number of independent over-represented classes. The methodology starts with a real life GO data matrix, and therefore the generated datasets have similar features to real positive datasets. The user can select the signal level for over-representation, the number of independent positive classes in the dataset, and the size of the final gene list. We present the use of the effective number and various normalizations while embedding the signal to a selected class or classes and the use of binary correlation to ensure that the selected signal classes are independent with each other. The usefulness of generated datasets is demonstrated by comparing different GO class ranking and GO clustering methods. Conclusion The presented methods aid the development and evaluation of GO analysis methods as they enable thorough testing with different signal types and different signal levels. As an example, our comparisons reveal clear differences between compared GO clustering and GO de-correlation methods. The implementation is coded in Matlab and is freely available at the dedicated website http://ekhidna.biocenter.helsinki.fi/users/petri/public/POSGODA/POSGODA.html.
Published: 2009

31. Identification of flowering genes in strawberry, a perennial SD plant

Author: Katriina Mouhu, Lars Paulin, Petri Auvinen, Timo Hytönen, Paula Elomaa, Marja Rantanen, Kevin M. Folta, Kasvipatologia, Valkonen Jari (-2009), Institute of Biotechnology (-2009), Asteraceae developmental biology and secondary metabolism, Plant Production Sciences, Strawberry research group, and DNA Sequencing and Genomics
Subjects: 0106 biological sciences, DNA, Plant, Genotype, Photoperiod, 411 Agriculture and forestry, Molecular Sequence Data, education, Locus (genetics), Flowers, Plant Science, Genes, Plant, Fragaria, 01 natural sciences, Genetic analysis, 03 medical and health sciences, Gene Expression Regulation, Plant, Arabidopsis, Flower induction, lcsh:Botany, Botany, Amino Acid Sequence, Gene, Gene Library, 030304 developmental biology, Expressed Sequence Tags, 2. Zero hunger, photoperiodism, Genetics, 0303 health sciences, biology, Gene Expression Profiling, fungi, Temperature, Computational Biology, Gene Expression Regulation, Developmental, food and beverages, Sequence Analysis, DNA, 414 Agricultural biotechnology, 15. Life on land, biology.organism_classification, lcsh:QK1-989, Shoot, Sequence Alignment, Research Article, 010606 plant biology & botany
Abstract: BackgroundWe are studying the regulation of flowering in perennial plants by using diploid wild strawberry (Fragaria vescaL.) as a model. Wild strawberry is a facultative short-day plant with an obligatory short-day requirement at temperatures above 15°C. At lower temperatures, however, flowering induction occurs irrespective of photoperiod. In addition to short-day genotypes, everbearing forms of wild strawberry are known. In 'Baron Solemacher' recessive alleles of an unknown repressor,SEASONAL FLOWERING LOCUS(SFL), are responsible for continuous flowering habit. Although flower induction has a central effect on the cropping potential, the molecular control of flowering in strawberries has not been studied and the genetic flowering pathways are still poorly understood. The comparison of everbearing and short-day genotypes of wild strawberry could facilitate our understanding of fundamental molecular mechanisms regulating perennial growth cycle in plants.ResultsWe have searched homologs for 118Arabidopsisflowering time genes fromFragariaby EST sequencing and bioinformatics analysis and identified 66 gene homologs that by sequence similarity, putatively correspond to genes of all known genetic flowering pathways. The expression analysis of 25 selected genes representing various flowering pathways did not reveal large differences between the everbearing and the short-day genotypes. However, putative floral identity and floral integrator genesAP1andLFYwere co-regulated during early floral development.AP1mRNA was specifically accumulating in the shoot apices of the everbearing genotype, indicating its usability as a marker for floral initiation. Moreover, we showed that flowering induction in everbearing 'Baron Solemacher' and 'Hawaii-4' was inhibited by short-day and low temperature, in contrast to short-day genotypes.ConclusionWe have shown that many central genetic components of the flowering pathways inArabidopsiscan be identified from strawberry. However, novel regulatory mechanisms exist, likeSFLthat functions as a switch between short-day/low temperature and long-day/high temperature flowering responses between the short-day genotype and the everbearing 'Baron Solemacher'. The identification of putative flowering gene homologs andAP1as potential marker gene for floral initiation will strongly facilitate the exploration of strawberry flowering pathways.
Published: 2009

32. Gata2 is a tissue-specific post-mitotic selector gene for midbrain GABAergic neurons

Author: Kaia Kala, Juha Partanen, Marjo Salminen, Kersti Lilleväli, Maarja Haugas, Wolfgang Wurst, Jordi Guimera, Institute of Biotechnology (-2009), Veterinary Biosciences, and Developmental neurogenetics
Subjects: Male, medicine.medical_specialty, Neurogenesis, Models, Neurological, Mitosis, Mice, Transgenic, GATA3 Transcription Factor, Biology, Serotonergic, Midbrain, Mice, 03 medical and health sciences, Glutamatergic, 0302 clinical medicine, Mesencephalon, Pregnancy, Internal medicine, Basic Helix-Loop-Helix Transcription Factors, medicine, Animals, Tissue Distribution, RNA, Messenger, Molecular Biology, Embryonic Stem Cells, gamma-Aminobutyric Acid, Body Patterning, 030304 developmental biology, Mice, Knockout, Neurons, Regulation of gene expression, 0303 health sciences, Dopaminergic, 1184 Genetics, developmental biology, physiology, Gene Expression Regulation, Developmental, Cell Differentiation, Mice, Mutant Strains, GATA2 Transcription Factor, Repressor Proteins, Endocrinology, Animals, Newborn, nervous system, GABAergic, 1182 Biochemistry, cell and molecular biology, Female, Ectopic expression, Neuroscience, 030217 neurology & neurosurgery, Developmental Biology
Abstract: Midbrain GABAergic neurons control several aspects of behavior, but regulation of their development and diversity is poorly understood. Here, we further refine the midbrain regions active in GABAergic neurogenesis and show their correlation with the expression of the transcription factor Gata2. Using tissue-specific inactivation and ectopic expression, we show that Gata2 regulates GABAergic neuron development in the mouse midbrain, but not in rhombomere 1, where it is needed in the serotonergic lineage. Without Gata2, all the precursors in the embryonic midbrain fail to activate GABAergic neuron-specific gene expression and instead switch to a glutamatergic phenotype. Surprisingly, this fate switch is also observed throughout the neonatal midbrain, except for the GABAergic neurons located in the ventral dopaminergic nuclei, suggesting a distinct developmental pathway for these neurons. These studies identify Gata2 as an essential post-mitotic selector gene of the GABAergic neurotransmitter identity and demonstrate developmental heterogeneity of GABAergic neurons in the midbrain. Midbrain GABAergic neurons control several aspects of behavior, but regulation of their development and diversity is poorly understood. Here, we further refine the midbrain regions active in GABAergic neurogenesis and show their correlation with the expression of the transcription factor Gata2. Using tissue-specific inactivation and ectopic expression, we show that Gata2 regulates GABAergic neuron development in the mouse midbrain, but not in rhombomere 1, where it is needed in the serotonergic lineage. Without Gata2, all the precursors in the embryonic midbrain fail to activate GABAergic neuron-specific gene expression and instead switch to a glutamatergic phenotype. Surprisingly, this fate switch is also observed throughout the neonatal midbrain, except for the GABAergic neurons located in the ventral dopaminergic nuclei, suggesting a distinct developmental pathway for these neurons. These studies identify Gata2 as an essential post-mitotic selector gene of the GABAergic neurotransmitter identity and demonstrate developmental heterogeneity of GABAergic neurons in the midbrain. Midbrain GABAergic neurons control several aspects of behavior, but regulation of their development and diversity is poorly understood. Here, we further refine the midbrain regions active in GABAergic neurogenesis and show their correlation with the expression of the transcription factor Gata2. Using tissue-specific inactivation and ectopic expression, we show that Gata2 regulates GABAergic neuron development in the mouse midbrain, but not in rhombomere 1, where it is needed in the serotonergic lineage. Without Gata2, all the precursors in the embryonic midbrain fail to activate GABAergic neuron-specific gene expression and instead switch to a glutamatergic phenotype. Surprisingly, this fate switch is also observed throughout the neonatal midbrain, except for the GABAergic neurons located in the ventral dopaminergic nuclei, suggesting a distinct developmental pathway for these neurons. These studies identify Gata2 as an essential post-mitotic selector gene of the GABAergic neurotransmitter identity and demonstrate developmental heterogeneity of GABAergic neurons in the midbrain.
Published: 2009

33. Clathrin-independent entry of baculovirus triggers uptake of E. coli in non-phagocytic human cells

Author: Paula Turkki, Elina Kakkonen, Johan Peränen, Anna R. Mäkelä, Johanna P. Laakkonen, Sari P. Kukkonen, Varpu Marjomäki, Seppo Ylä-Herttuala, Maija Vihinen-Ranta, Christian Oker-Blom, Kari J. Airenne, and Institute of Biotechnology (-2009)
Subjects: RHOA, Science, viruses, media_common.quotation_subject, education, Gene delivery, Clathrin, Cell Line, Membrane Lipids, 03 medical and health sciences, Phagocytosis, Cell Biology/Membranes and Sorting, Viral entry, Virology, Escherichia coli, Biochemistry/Cell Signaling and Trafficking Structures, Humans, Internalization, 030304 developmental biology, media_common, Adenosine Triphosphatases, 0303 health sciences, Multidisciplinary, Base Sequence, biology, ADP-Ribosylation Factors, 030302 biochemistry & molecular biology, HEK 293 cells, Transfection, Molecular biology, Endocytosis, Nucleopolyhedroviruses, 3. Good health, Cell biology, virologia, ADP-Ribosylation Factor 6, Cell culture, biology.protein, Medicine, RNA Interference, Research Article
Abstract: The prototype baculovirus, Autographa californica multiple nucleopolyhedrovirus, an insect pathogen, holds great potential as a gene therapy vector. To develop transductional targeting and gene delivery by baculovirus, we focused on characterizing the nature and regulation of its uptake in human cancer cells. Baculovirus entered the cells along fluid-phase markers from the raft areas into smooth-surfaced vesicles devoid of clathrin. Notably, regulators associated with macropinocytosis, namely EIPA, Pak1, Rab34, and Rac1, had no significant effect on viral transduction, and the virus did not induce fluid-phase uptake. The internalization and nuclear uptake was, however, affected by mutants of RhoA, and of Arf6, a regulator of clathrin-independent entry. Furthermore, the entry of baculovirus induced ruffle formation and triggered the uptake of fluorescent E. coli bioparticles. To conclude, baculovirus enters human cells via a clathrin-independent pathway, which is able to trigger bacterial uptake. This study increases our understanding of virus entry strategies and gives new insight into baculovirus-mediated gene delivery in human cells. peerReviewed
Published: 2009

34. Comparison of gene expression profile in embryonic mesencephalon and neuronal primary cultures

Author: Antonio Di Lieto, Dario Greco, Umberto di Porzio, Floriana Volpicelli, Carla Perrone-Capano, Petri Auvinen, Damiana Leo, Dario, Greco, Volpicelli, Floriana, Antonio Di, Lieto, Damiana, Leo, PERRONE CAPANO, Carla, Petri, Auvinen, Umberto di, Porzio, Institute of Biotechnology (-2009), and DNA Sequencing and Genomics
Subjects: Dopamine, Science, education, Molecular Sequence Data, Gene regulatory network, Substantia nigra, Biology, Bioinformatics, Midbrain, Rats, Sprague-Dawley, 03 medical and health sciences, 0302 clinical medicine, Mesencephalon, Pregnancy, medicine, Animals, Gene Regulatory Networks, Cells, Cultured, 030304 developmental biology, Regulation of gene expression, Neurons, 0303 health sciences, Multidisciplinary, Microarray analysis techniques, Gene Expression Profiling, Genetics and Genomics/Functional Genomics, Computational Biology, Gene Expression Regulation, Developmental, Genetics and Genomics/Gene Expression, Genetics and Genomics/Bioinformatics, Microarray Analysis, Rats, Gene expression profiling, Ventral tegmental area, Developmental Biology/Neurodevelopment, medicine.anatomical_structure, nervous system, Developmental Biology/Cell Differentiation, Medicine, Female, Functional genomics, Neuroscience, 030217 neurology & neurosurgery, Research Article
Abstract: In the mammalian central nervous system (CNS) an important contingent of dopaminergic neurons are localized in the substantia nigra and in the ventral tegmental area of the ventral midbrain. They constitute an anatomically and functionally heterogeneous group of cells involved in a variety of regulatory mechanisms, from locomotion to emotional/motivational behavior. Midbrain dopaminergic neuron (mDA) primary cultures represent a useful tool to study molecular mechanisms involved in their development and maintenance. Considerable information has been gathered on the mDA neurons development and maturation in vivo, as well as on the molecular features of mDA primary cultures. Here we investigated in detail the gene expression differences between the tissue of origin and ventral midbrain primary cultures enriched in mDA neurons, using microarray technique. We integrated the results based on different re-annotations of the microarray probes. By using knowledge-based gene network techniques and promoter sequence analysis, we also uncovered mechanisms that might regulate the expression of CNS genes involved in the definition of the identity of specific cell types in the ventral midbrain. We integrate bioinformatics and functional genomics, together with developmental neurobiology. Moreover, we propose guidelines for the computational analysis of microarray gene expression data. Our findings help to clarify some molecular aspects of the development and differentiation of DA neurons within the midbrain.
Published: 2009

35. Transposition-based method for the rapid generation of gene-targeting vectors to produce Cre/Flp-modifiable conditional knock-out mice

Author: Hilkka Turakainen, Jonna Saarimäki-Vire, Juha Partanen, Natalia Sinjushina, Harri Savilahti, Institute of Biotechnology (-2009), Timo Pyry Juhani Otonkoski / Principal Investigator, and Developmental neurogenetics
Subjects: Transposable element, Genetics and Genomics/Animal Genetics, education, Genetic Vectors, Cloning vector, lcsh:Medicine, Biology, Polymerase Chain Reaction, Transposition (music), 03 medical and health sciences, Mice, 0302 clinical medicine, Recombinase, Animals, Vector (molecular biology), lcsh:Science, Gene, Molecular Biology, Alleles, Embryonic Stem Cells, 030304 developmental biology, Genetics, Mice, Knockout, 0303 health sciences, Multidisciplinary, Integrases, lcsh:R, Intracellular Signaling Peptides and Proteins, Gene targeting, Membrane Proteins, Reproducibility of Results, Cadherins, Attachment Sites, Microbiological, DNA Nucleotidyltransferases, Gene Targeting, DNA Transposable Elements, lcsh:Q, 030217 neurology & neurosurgery, Research Article, Biotechnology
Abstract: Conditional gene targeting strategies are progressively used to study gene function tissue-specifically and/or at a defined time period. Instrumental to all of these strategies is the generation of targeting vectors, and any methodology that would streamline the procedure would be highly beneficial. We describe a comprehensive transposition-based strategy to produce gene-targeting vectors for the generation of mouse conditional alleles. The system employs a universal cloning vector and two custom-designed mini-Mu transposons. It produces targeting constructions directly from BAC clones, and the alleles generated are modifiable by Cre and Flp recombinases. We demonstrate the applicability of the methodology by modifying two mouse genes, Chd22 and Drapc1. This straightforward strategy should be readily suitable for high-throughput targeting vector production.
Published: 2008

36. Automated 3D phenotype analysis using data mining

Author: Alistair R. Evans, Aleksis Karme, Ilya Plyusnin, Aristides Gionis, Jukka Jernvall, Institute of Biotechnology (-2009), Geology (-2014), and Evolutionary Palaeontology group
Subjects: Evolutionary Biology/Paleontology, 0106 biological sciences, Geographic information system, 117 Geography, Environmental sciences, education, Evolutionary Biology/Bioinformatics, lcsh:Medicine, Evolutionary Biology/Evolutionary Ecology, Feature selection, Biology, computer.software_genre, 010603 evolutionary biology, 01 natural sciences, Pattern Recognition, Automated, 03 medical and health sciences, Phenomics, Feature (machine learning), Computer Simulation, lcsh:Science, 030304 developmental biology, Electronic Data Processing, 0303 health sciences, Biological data, Probabilistic classification, Multidisciplinary, business.industry, lcsh:R, Computational Biology, Class (biology), Diet, Variable (computer science), Phenotype, Database Management Systems, lcsh:Q, Mathematics/Statistics, Data mining, business, Tooth, computer, Algorithms, Research Article
Abstract: The ability to analyze and classify three-dimensional (3D) biological morphology has lagged behind the analysis of other biological data types such as gene sequences. Here, we introduce the techniques of data mining to the study of 3D biological shapes to bring the analyses of phenomes closer to the efficiency of studying genomes. We compiled five training sets of highly variable morphologies of mammalian teeth from the MorphoBrowser database. Samples were labeled either by dietary class or by conventional dental types (e.g. carnassial, selenodont). We automatically extracted a multitude of topological attributes using Geographic Information Systems (GIS)-like procedures that were then used in several combinations of feature selection schemes and probabilistic classification models to build and optimize classifiers for predicting the labels of the training sets. In terms of classification accuracy, computational time and size of the feature sets used, non-repeated best-first search combined with 1-nearest neighbor classifier was the best approach. However, several other classification models combined with the same searching scheme proved practical. The current study represents a first step in the automatic analysis of 3D phenotypes, which will be increasingly valuable with the future increase in 3D morphology and phenomics databases.
Published: 2008

37. Physiology, pathology and relatedness of human tissues from gene expression meta-analysis

Author: Tuomas Raitila, Eero Castrén, Panu Somervuo, Petri Auvinen, Lucio Nitsch, Dario Greco, Antonio Di Lieto, Institute of Biotechnology (-2009), Neuroscience center (-2009), DNA Sequencing and Genomics, Greco, D., Somervuo, P., DI LIETO, A., Raitila, T., Nitsch, Lucio, Castren, E., and Auvinen, P.
Subjects: Quality Control, 515 Psychology, Science, education, Physiology, Gene Expression, Biology, Hippocampus, 03 medical and health sciences, 0302 clinical medicine, tissue-specific, Gene expression, Databases, Genetic, Cluster Analysis, Humans, 311 Basic medicine, Tissue Distribution, Promoter Regions, Genetic, Gene, Genetics and Genomics/Genetics of Disease, 030304 developmental biology, Oligonucleotide Array Sequence Analysis, Regulation of gene expression, Genetics, Neurons, 0303 health sciences, Multidisciplinary, Models, Genetic, Gene Expression Profiling, NF-kappa B, Genetics and Genomics/Gene Expression, Genetics and Genomics/Physiogenomics, Genetics and Genomics/Bioinformatics, Housekeeping gene, E2F Transcription Factors, Gene expression profiling, Genetics and Genomics/Gene Function, Multicellular organism, Gene Expression Regulation, Medicine, DNA microarray, 118 Biological sciences, transcriptome, microarray, 030217 neurology & neurosurgery, Whole Organism, Research Article
Abstract: BackgroundDevelopment and maintenance of the identity of tissues is of central importance for multicellular organisms. Based on gene expression profiles, it is possible to divide genes in housekeeping genes and those whose expression is preferential in one or a few tissues and which provide specialized functions that have a strong effect on the physiology of the whole organism.ResultsWe have surveyed the gene expression in 78 normal human tissues integrating publicly available microarray gene expression data. A total amount of 1601 genes were identified as selectively expressed in one or more tissues. The tissue-selective genes covered a wide range of cellular and molecular functions, and could be linked to 361 human diseases with Mendelian inheritance. Based on the gene expression profiles, we were able to form a network of tissues reflecting their functional relatedness and, to certain extent, their development. Using co-citation driven gene network technique and promoter analysis, we predicted a transcriptional module where the co-operation of the transcription factors E2F and NF-kappaB can possibly regulate a number of genes involved in the neurogenesis that takes place in the adult hippocampus.ConclusionsHere we propose that integration of gene expression data from Affymetrix GeneChip experiments is possible through re-annotation and commonly used pre-processing methods. We suggest that some functional aspects of the tissues can be explained by the co-operation of multiple transcription factors that regulate the expression of selected groups of genes.
Published: 2008

38. Bacteria, phages and septicemia

Author: Aušra Gaidelytė, Dennis H. Bamford, Martti Vaara, Institute of Biotechnology (-2009), Biosciences, Haartman Institute (-2014), and Structure of the Viral Universe
Subjects: medicine.drug_class, viruses, Antibiotics, lcsh:Medicine, medicine.disease_cause, Bacterial Physiological Phenomena, Microbiology, Sepsis, Infectious Diseases/Bacterial Infections, 03 medical and health sciences, Antibiotic resistance, medicine, Humans, Phage ecology, Bacteriophages, lcsh:Science, Prophage, 030304 developmental biology, 0303 health sciences, Multidisciplinary, biology, Infectious Diseases/Antimicrobials and Drug Resistance, 030306 microbiology, lcsh:R, Microbiology/Medical Microbiology, biology.organism_classification, medicine.disease, Virology, Microscopy, Electron, Staphylococcus aureus, lcsh:Q, 118 Biological sciences, Bacteria, Research Article
Abstract: The use of phages is an attractive option to battle antibiotic resistant bacteria in certain bacterial infections, but the role of phage ecology in bacterial infections is obscure. Here we surveyed the phage ecology in septicemia, the most severe type of bacterial infection. We observed that the majority of the bacterial isolates from septicemia patients spontaneously secreted phages active against other isolates of the same bacterial strain, but not to the strain causing the disease. Such phages were also detected in the initial blood cultures, indicating that phages are circulating in the blood at the onset of sepsis. The fact that most of the septicemic bacterial isolates carry functional prophages suggests an active role of phages in bacterial infections. Apparently, prophages present in sepsis-causing bacterial clones play a role in clonal selection during bacterial invasion. The use of phages is an attractive option to battle antibiotic resistant bacteria in certain bacterial infections, but the role of phage ecology in bacterial infections is obscure. Here we surveyed the phage ecology in septicemia, the most severe type of bacterial infection. We observed that the majority of the bacterial isolates from septicemia patients spontaneously secreted phages active against other isolates of the same bacterial strain, but not to the strain causing the disease. Such phages were also detected in the initial blood cultures, indicating that phages are circulating in the blood at the onset of sepsis. The fact that most of the septicemic bacterial isolates carry functional prophages suggests an active role of phages in bacterial infections. Apparently, prophages present in sepsis-causing bacterial clones play a role in clonal selection during bacterial invasion. The use of phages is an attractive option to battle antibiotic resistant bacteria in certain bacterial infections, but the role of phage ecology in bacterial infections is obscure. Here we surveyed the phage ecology in septicemia, the most severe type of bacterial infection. We observed that the majority of the bacterial isolates from septicemia patients spontaneously secreted phages active against other isolates of the same bacterial strain, but not to the strain causing the disease. Such phages were also detected in the initial blood cultures, indicating that phages are circulating in the blood at the onset of sepsis. The fact that most of the septicemic bacterial isolates carry functional prophages suggests an active role of phages in bacterial infections. Apparently, prophages present in sepsis-causing bacterial clones play a role in clonal selection during bacterial invasion.
Published: 2007

39. Dual-trap optical tweezers with real-time force clamp control

Author: Gabija Ziedaite, Heikki Ojala, Edward Hæggström, Anders Wallin, University of Helsinki, Department of Physics (-2009), University of Helsinki, Institute of Biotechnology (-2009), University of Helsinki, Biosciences, and University of Helsinki, Department of Physics
Subjects: Physics, 0303 health sciences, Magnetic tweezers, Tension (physics), Work (physics), Molecular biophysics, Dynamics (mechanics), 114 Physical sciences, 01 natural sciences, Molecular physics, 3. Good health, 03 medical and health sciences, Clamp, Optical tweezers, 0103 physical sciences, Molecular motor, Biophysics, 010306 general physics, Instrumentation, 030304 developmental biology
Abstract: Single molecule force clamp experiments are widely used to investigate how enzymes, molecular motors, and other molecular mechanisms work. We developed a dual-trap optical tweezers instrument with real-time (200 kHz update rate) force clamp control that can exert 0–100 pN forces on trapped beads. A model for force clamp experiments in the dumbbell-geometry is presented. We observe good agreement between predicted and observed power spectra of bead position and force fluctuations. The model can be used to predict and optimize the dynamics of real-time force clamp optical tweezers instruments. The results from a proof-of-principle experiment in which lambda exonuclease converts a double-stranded DNA tether, held at constant tension, into its single-stranded form, show that the developed instrument is suitable for experiments in single molecule biology. Peer reviewed
Published: 2011
Full Text: View/download PDF

40. Vitamin C and the common cold

Author: Harri Hemilä and Institute of Biotechnology (-2009)
Subjects: Antioxidant, Time Factors, Neutrophils, medicine.medical_treatment, Medicine (miscellaneous), Common Cold, Ascorbic Acid, DEFICIENT GUINEA-PIGS, Antioxidants, chemistry.chemical_compound, 0302 clinical medicine, HYPOCHLORITE, INFECTION, Medicine, 030212 general & internal medicine, 0303 health sciences, Clinical Trials as Topic, Nutrition and Dietetics, Common cold, EPITHELIAL-CELLS, RHINOVIRUS COLDS, Vitamin C and the common cold, 3. Good health, Dose–response relationship, Chemotaxis, Leukocyte, OXYGEN RADICALS, Vitamin, medicine.medical_specialty, Histamine Antagonists, SUPEROXIDE, 03 medical and health sciences, TUBULIN TYROSINOLATION, Phagocytosis, Internal medicine, Humans, HYPOCHLOROUS ACID, 030304 developmental biology, Vitamin C, Dose-Response Relationship, Drug, business.industry, POLYMORPHONUCLEAR LEUKOCYTES, Scurvy, medicine.disease, Ascorbic acid, HUMAN-BLOOD PLASMA, Endocrinology, chemistry, 416 Food Science, ASCORBIC-ACID, Immunology, HUMAN-NEUTROPHILS, business
Abstract: The effect of vitamin C on the common cold has been the subject of several studies. These studies do not support a considerable decrease in the incidence of the common cold with supplemental vitamin C. However, vitamin C has consistently decreased the duration of cold episodes and the severity of symptoms. The benefits that have been observed in different studies show a large variation and, therefore, the clinical significance may not be clearly inferred from them. The biochemical explanation for the benefits may be based on the antioxidant property of vitamin C. In an infection, phagocytic leucocytes become activated and they produce oxidizing compounds which are released from the cell. By reacting with these oxidants, vitamin C may decrease the inflammatory effects caused by them. Scurvy, which is caused by a deficiency in vitamin C, is mostly attributed to the decreased synthesis of collagen. However, vitamin C also participates in several other reactions, such as the destruction of oxidizing substances. The common cold studies indicate that the amounts of vitamin C which safely protect from scurvy may still be too low to provide an efficient rate for other reactions, possibly antioxidant in nature, in infected people.
Published: 1992

41. The Dynamic Interest in Topics within the Biomedical Scientific Community

Author: Frederic Michon, Mark Tummers, and Institute of Biotechnology (-2009)
Subjects: PubMed, Biomedical Research, Bibliometric analysis, Science Policy, Science, education, Human immunodeficiency virus (HIV), Distribution (economics), Biology, medicine.disease_cause, Bioinformatics, Citation impact, 03 medical and health sciences, 0302 clinical medicine, medicine, 030304 developmental biology, 0303 health sciences, Multidisciplinary, business.industry, Scientific production, Novelty, Data science, Variable (computer science), Non-Clinical Medicine/History of Medicine, 030220 oncology & carcinogenesis, Medicine, Journal Impact Factor, 118 Biological sciences, business, Research Article, Developmental Biology
Abstract: The increase in the size of the scientific community created an explosion in scientific production. We have analyzed the dynamics of biomedical scientific output during 1957-2007 by applying a bibliometric analysis of the PubMed database using different keywords representing specific biomedical topics. With the assumption that increased scientific interest will result in increased scientific output, we compared the output of specific topics to that of all scientific output. This analysis resulted in three broad categories of topics; those that follow the general trend of all scientific output, those that show highly variable output, and attractive topics which are new and grow explosively. The analysis of the citation impact of the scientific output resulted in a typical longtail distribution: the majority of journals and articles are of very low impact. This distribution has remained unchanged since 1957, although the interests of scientists must have shifted in this period. We therefore analyzed the distribution of articles in top journals and lower impact journals over time for the attractive topics. Novelty is rewarded by publication in top journals. Over time more articles are published in low impact journals progressively creating the longtail distribution, signifying acceptance of the topic by the community. There can be a gap of years between novelty and acceptance. Within topics temporary novelty is created with new subtopics. In conclusion, the longtail distribution is the foundation of the scientific output of the scientific community and can be used to examine different aspects of science practice.
Published: 2009
Full Text: View/download PDF

42. Secretory S complex of Bacillus subtilis: sequence analysis and identity to pyruvate dehydrogenase

Author: Ilkka Palva, Airi Palva, Harri Hemilä, Lars Paulin, S. Arvidson, and Institute of Biotechnology (-2009)
Subjects: Operon, Sequence analysis, Protein subunit, Blotting, Western, Molecular Sequence Data, education, Pyruvate Dehydrogenase Complex, Bacillus subtilis, Microbiology, Ribosome, Homology (biology), 03 medical and health sciences, Sequence Homology, Nucleic Acid, Escherichia coli, Amino Acid Sequence, Cloning, Molecular, Molecular Biology, Peptide sequence, 030304 developmental biology, Gene Library, 0303 health sciences, biology, Base Sequence, 030306 microbiology, Nucleic acid sequence, Chromosome Mapping, biology.organism_classification, Blotting, Northern, Molecular biology, RNA, Bacterial, Biochemistry, Research Article
Abstract: We have cloned the operon coding for the Bacillus subtilis S complex, which has been proposed to be a component in protein secretion machinery. A lambda gt10 library of B. subtilis was screened with antiserum directed against the Staphylococcus aureus membrane-bound ribosome protein complex, which is homologous to the B. subtilis S complex. Two positive overlapping lambda clones were sequenced. The S-complex operon, 5 kilobases in size, was shown to contain four open reading frames and three putative promoters, which are located upstream of the first, the third, and the last gene. The four proteins encoded by the operon are 42, 36, 48, and 50 kilodaltons in size. All of these proteins were recognized by antisera separately raised against each protein of the S. aureus membrane-bound ribosome protein and B. subtilis S complexes, thus verifying the S-complex identity of the lambda clones. Sequence analysis revealed that all four proteins of the B. subtilis S complex are homologous to the four subunits of the human pyruvate dehydrogenase (PDH). Also, the N terminus of the 48-kilodalton protein was found to have 70% amino acid identity with the N-terminal 211 amino acids, determined so far, from the E2 subunit of B. stearothermophilus PDH. Furthermore, chromosomal mapping of the S-complex operon gave a linkage to a marker gene located close to the previously mapped B. subtilis PDH genes. Thus, the S complex is evidently identical to the B. subtilis PDH, which has been shown to contain four subunits with molecular weights very similar to those of the S complex. Therefore, we propose that the S complex is not a primary component of protein secretion.
Published: 1990

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Publication Type

Journal

Database

Publisher

42 results on '"Institute of Biotechnology (-2009)"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources