|Word Cloud from the Acknowledgements
So I always end up on Thanksgiving thinking about all the people I should thank for contributing to my career. Today I decided to go through all of my publications (well, not all of them, I did not include Data Report types papers for which I have > 100) and compile all the Acknowledgement sections from these papers. A few did not have such sections but many did.
And, well, here they are all put together into one page (below the line). I have separately also compiled all the funding sections from all these papers and will also post that at some point.
But anyway - my point is - I feel greatly in debt to a huge number of people and entities and just want to thank them. Note - for some of these papers where I was not a key author, other people wrote the Acknowledgement sections and I do not actually know what all of these people or organizations did in every case. But still I feel in debt.
Note - these are in reverse chronological order.
We thank the Gordon and Betty Moore Foundation and the Smithsonian Tropical Research Institute in Panamá for facilitating the #istmobiome workshop (https://istmobiome.net) where we initiated this article. We are especially thankful to Urania Gonzales, Plinio Gondola, and Fabiola Jenkins for organizing and facilitating this workshop. We also thank other workshop participants including Rachel Collin (ORCID: 0000-0001-5103-4460), Ross Robertson (ORCID: 0000-0003-3972-149X), Jarrod Scott, Jennifer McMillan, and Jon Kaye (ORCID: 0000-0002-3653-4253) for seminal discussions.
We would like to thank Katherine Dynarski (ORCID: 0000-0001-5101-9666) and Sonia Ghose (ORCID: 0000-0001-5667-6876) for their help with sample collection. We would also like to thank John J. Stachowicz for use of his scientific sampling permit, California Department of Fish and Wildlife Scientific Collecting Permit # SC 4874. We are grateful to Marina LaForgia (ORCID: 0000-0003-4377-0841) for her helpful comments on the R code used.
We thank the members of the Flint Water Study Team at Virginia Polytechnic Institute and State University who volunteered their time to collect samples and the Flint citizens and businesses that supported this study. We thank Joan Rose for providing access to the laboratory at Michigan State University to support the fieldwork.
We thank Leah K. Isaacson, DVM for expressing the anal sacs and providing these samples to us. The authors would also like to thank Petra Dahms, Dana De Vries, and Alex Martin who worked on the initial stages of this project. We thank Alexandria Falcon for contributing her technical expertise.
The authors would like to acknowledge the laboratory staff at WALTHAM Centre for Pet Nutrition for growing the bacterial isolates, extracting genomic DNA, and for initial species identification, and Zoe Lonsdale for figure creation and bioinformatics support. The authors would also like to acknowledge John Zhang from UC Davis for the sequencing library preparation of isolates. The sequencing was carried by the DNA Technologies and Expression Analysis Cores at the UC Davis Genome Center, supported by NIH Shared Instrumentation Grant 1S10OD010786-01.
The authors would like to thank the many program grantees who assisted us in refining the list of publications. Also thanks to Julia Maritz for compiling the initial list of publications.
We especially thank Thein Mai and Matt Wein for access to and assistance with the aquaria used in this study. We also thank the staff in the DNA Technologies Core facility at the UC Davis Genome Center for generating all sequence data.
We would like to thank Russell Neches (ORCID: 0000-0002-2055-8381) for the use of photographs taken on a trip to Kamchatka, Russia in 2012. We also would like to thank Elizabeth A. Burgess and Juergen Wiegel for providing JAE with the DNA used here. We are also grateful to Christopher Brown (ORCID: 0000-0002-7758-6447) and Laura Hug (ORCID: 0000-0001-5974-9428) for their help getting access to the genomes used in Figure 2. A special thank you goes to Alexandros Stamatakis (ORCID: 0000-0003-0353-0691), Wayne Pfeiffer and Mark Miller for offering their help with getting the CIPRES Science Gateway server to run RAxML-HPC2 v.8 on XSEDE. We also thank two anonymous reviewers for comments on earlier versions of this manuscript. A. Murat Eren (ORCID: 0000-0001-9013-4827) provided constructive feedback on the publicly available preprint version of this article.
We thank Madhi Moradi, Cassia Jonck, Cátia Barbosa, and Alexandre Rosado for logistical support during the mesocosm experiment and helpful suggestions and discussion. We also thank Fabiano Thompson for providing Vibrio coralliilyticus cells for previous pilot experiments, and Leonardo Carvalho, Igor Albergaria, Marcelo Cunha and Robson Aragão for providing coral colonies.
We acknowledge Magdalena Plancarte, Winston Vickers, Matt Rolston and Guillaume Jospin for their contributions to this project. We also thank the United States Geological Survey, the California Waterfowl Association, and the California Department of Fish and Wildlife for their cooperation and assistance in sample collection.
This paper is dedicated to the life and memory of Cristobal Heitmann. Cristobal’s energy and enthusiasm was a major catalyst in completing this research. He died tragically while the manuscript was under review. We thank Vicente Vasquez and Maria del Refugio Vasquez for assistance in developing the program in Mexico; Carmen Ortega and Saulon Zamora for sample collection and field trial assistance; Shawn Kaeppler, Natalia de Leon, and Jillian Foerster for field assistance; Nguyet Dao for microbial 15N-fixation assays; Harry Read for processing 15N2-enrichment samples; John Zhang for assistance with library construction; and Armando Garcia-Llanos for assistance in sample processing. We thank the Comisiriado of the Sierra Mixe, Mexico, for their support and access to community genetic resources.
The authors would like to acknowledge Dr. Jan S. Suchodolski, Gastrointestinal Laboratory, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, for his critical review of our manuscript. We thank members of the Eisen lab for technical assistance at various time points in the study, and Clarissa Santos Rocha for providing training and expertise on QIIME and R software.
We thank first all the citizen science volunteers around the world. We also thank Katherine Amato, Margaret K. Butler, Gabriela Surdulescu, Luke Ursell, Jeff DeReus, Evguenia Kopylova, John Graham, Victoria Vazquez, Jai Ram Rideout, Merete Eggesbo, Steve Green, Kathy Holt, Jim Huntley, Zehra Esra Ilhan, Daniel Mayer, Catherine Nicholas, Laura Parfrey, Juanma Peralta, Dorota Porazinska, Jennifer Smilowitz, Matt Gebert, Se Jin Song, Kumar Thurimella, Sam Way, Tony Walters, Sophie Weiss, Ulla Westermann, Shawnelle White, Doug Woodhams, Jerry Kennedy, Scott Handley, Chandni Desai, Carolina Carpenter, Gabriella Fanelli, Deborah L. Bright, and Xochitl C. Morgan for their contributions to the American Gut Project. Some sequencing was conducted by Mahdieh Khosroheidari and Clifford L. Green at the IGM Genomics Center, University of California, San Diego, La Jolla, CA. We thank the BioFrontiers Institute for their administrative support for the project while it was based at the University of Colorado Boulder.
We would also like to thank Cheyne Flanagan (Port Macquarie Koala Hospital), Rosie Booth and Amber Gillet (Australia Zoo Wildlife Hospital) for coordinating and help with sampling the koalas in the study. Special thanks to Alyce Taylor-Brown, Cassie Ettinger (ORCID 0000-0001-7334-403X) and David Coil (ORCID 0000-0001-6049-8240) for their guidance and expertise throughout different stages of this project. Thank you to Guillaume Jospin (ORCID 0000-0002-8746-2632) for providing his bioinformatics skills. And lastly, thank you to the Bosward family for their help with logistics.
The authors would like to thank Summer Williams for the inception of the idea to get Science Cheerleader involved in space research. In addition we give thanks to Carl Carruthers at Nanoracks LLC for managing our space payload. We are also grateful to Holly Menninger and Rob Dunn for sharing data from the Wildlife of Our Homes pilot project, and Steven Kembel (ORCID ID: 0000-0001-5224-0952) for publishing the original version of Fig. 7 in an open access journal, as well as sharing the underlying data.
We thank the staff of the Bigelow Laboratory Single-Cell Genomics Center and the Joint Genome Institute for the generation of single-cell and metagenomic data. We are grateful to Olukayode Kuloyo, Borja Linage, Sarah Hendrickson, Cara Magnabosco, Melody Lindsay, Petra Diamonds and the management and staff for Finsch diamond mine, South Africa for their help obtaining the samples. We are also grateful to Laura Vann for her help obtaining Nevada field samples. Thanks also to Darrell Lacy, Levi Kryder, and John Klenke of the Nevada Nuclear Waste Repository Program Office (NWRPO) and the Nature Conservancy for access to and sampling assistance with well OV-2. We are grateful to Refuge Manager, Annji Bagozzi, and the U.S. Fish and Wildlife service for permitting and guidance related to the sampling of Crystal Spring at Ash Meadows National Wildlife Refuge. We are also grateful to Jaret Heise, Tom Regan, Kathy Hart, and many others at the Sanford Underground Research Facility for safe underground access and sampling assistance. Special thanks to Brittany Kruger, Joshua Sackett, and Scott Hamilton-Brehm of the Moser Lab for sample and metadata collection.
We would like to acknowledge the excellent work of many students, teaching fellows, and instructors who have investigated these aggregates in the Microbial Diversity course at the Marine Biological Laboratory. In particular, we thank Margret Gentile for her pioneering studies, James R. Henriksen for microscopy, and Nanelle R. Barash and Douglas C. Nelson for insightful discussions.
Illumina sequencing was performed at the DNA Technologies Core facility in the UC Davis Genome Center in Davis, California. We thank Qingyi ‘‘John’’ Zhang for his help with the DNA extractions and Illumina library preparation.
We thank H. Maughan for constructive feedback and editing of the manuscript and Z. Rostomian for support with illustrations.
We thank H. Maughan for critical reading and feedback on the paper. We would also like to thank B.J. Tindall, S. Spring, R. Pukall, E. Lang, S. Gronow and S. Verbarg from Leibniz Institute DSMZ for contributing the cell pastes for the GEBA-I strains, E. Brambilla and B. Trümper, DSMZ, for preparing genomic DNA, B. Beck and T. Lilburn from ATCC, as well as all the JGI staff that contributed to this project including T.B.K. Reddy, I. Pagani, E. Lobos, J. Mallajosyula, M. Isbandi, A. Thomas, D. Stamatis and J. Bertsch for metadata curation, C.-L. Wei for sequencing, J. Han, A. Clum, B. Bushnell and A. Copeland for assembly, K. Mavromatis, M. Huntemann, G. Ovchinnikova and N. Mikhailova for annotation and submission to IMG, A. Chen, K. Chu, K. Palaniappan, M. Pillay, J. Huang, E. Szeto and V. Markowitz for additional annotation and integration into IMG, A. Schaumberg, E. Andersen, S. Hua, H. Nordberg, I. Dubchak, S. Wilson, A. Shahab for NCBI registrations and submission to INSDC, L. Goodwin, N. Shapiro and T. Tatum for project management and J. Bristow and E. Rubin for supporting the project. The use of the bwGRiD cluster for the GBDP analysis is gratefully acknowledged. We also thank J.M. Tiedje at Michigan State University for generously providing metadata specifics for his metagenomic samples.
Illumina sequencing was performed at the DNA Technologies Core facility in the Genome Center at UC Davis, Davis, California. We thank Qingyi ‘‘John’’ Zhang for his help with the Illumina library preparation and Hannah Holland-Moritz for her help with DNA extractions. We thank Ted Grosholz and Susan Williams for hosting Sofie Voerman during her visit and for help with the sampling design. We thank Daniel Bradley for his help with sample collection.
The authors would like to thank the many people who helped to playtest Gut Check: The Microbiome Game, especially the members of the Eisen lab, Phil Seitzer, and the Friday Night Game Group. Special thanks to MO BIO Laboratories, a QIAGEN company, for editing and producing the commercial version. The art and design for the print-at-home version was cre- ated by Erin Johnson and for the commercial version by Wendy Ochoa.
We thank the ZEN partners, Guillaume Jospin, and Pamela Reynolds for their assistance with data collection. We also thank Roxana Hickey, Steve Kembel, James Meadow, James O’Dwyer, and three reviewers for helpful discussions and comments.
The authors are grateful to the other participants of the AgMicrobiomes Consortium (Asilomar, March 2016) for contributing to the development of research priorities discussed in this paper: Andrea Ottesen, Angela Kent, Ann Lichens-Park, Ben Wolfe, Carolyn Young, Cassie Wattenberger, Dale Pelletier, Dan Tomso, Diane Wu, Doug Cook, George Newcombe, Joyce Loper, Julia Vorholt, Larry Halverson, Laurie Drinkwater, Maria J. Pozo, Matt Ashby, Michael Mishkind, Patrick Bradley, Paul Schulze-Lefert, Penny Hirsch, Poornima Parameswaran, Ricardo Oliva, Sarah Grant, Sarah Lebeis, Sue Turner, Susannah Tringe, Tom Mitchell-Olds, Ulrich Mueller, Varghese Thomas, and Venkat Sundaresan.
We thank Magdalena Plancarte and Winston Vickers for their contributions to the influenza study and Matt Rolston for sample preparation for the bacterial microbiome characterization. We also thank the United States Geological Survey, the California Waterfowl Association, and the California Department of Fish and Wildlife, Grizzly Island Wildlife Area, for their cooperation and assistance in sample collection from mallards.
We thank Navneet Madhar (University of Guelph) for technical help with the mutant screen. We thank Eric Lyons (University of Guelph) for the gift of creeping bentgrass seed. We thank Walaa Mousa and Bob Harris (University of Guelph) for assistance with the electron microscopy experiments.
The authors thank M. Struder-Kypke (Department of Molecular and Cellular Biology, University of Guelph) for assistance with confocal microscopy and for her comments. The authors thank A. Schaafsma and L. Tamburic-Ilincic (Ridgetown College, University of Guelph) for providing hybrid maize and wheat seeds, respectively. The authors also thank M. Atalla for assistance with disease scoring. W.K.M. was supported by generous scholarships from the Government of Egypt and the University of Guelph (International Graduate Student Scholarships, 2012, 2014). The authors thank L. Smith (University of Guelph) for graphics.
The authors would like to thank the many people who contributed to Project MERCCURI and to the processing of these cultures including Pop Warner, Science Cheerleaders, Nanoracks LLC, Space Florida, SciStarter, Jennifer Flanagan, Ruth Lee, Hannah Holland-Moritz, Alex Alexiev, Madison Dunitz, and Holly Bik. In particular, thanks to Carl Carruthers at Nanoracks LLC who shepherded the payload through all challenges. This article was written using the Authorea scientific writing platform.
The authors would like to thank the Coronado Pop Warner Islanders for initial collection of the sample and participation in Project MERCCURI, as well as Kris Tracy who assisted in the etymology of the proposed species name.
The 16S rRNA sequence analysis was performed under the MiSeq Com- petition MkIIm by New Zealand Genome Limited and with the assistance of Patrick Biggs (NZGL) for MiSeq sequence processing. We thank Alex- ander Forrest for the loan of the Brancker CTD. We are grateful to three anonymous reviewers for their comments and suggestions. We thank the Antarctica New Zealand and U.S. Antarctic Program for logistics support and facilities, and we also thank Anthea Fisher (Antarctica New Zealand) for her assistance with the field work.
We are grateful to Aaron Darling, Guillaume Jospin, Morgan Langille, and Dongying Wu for their helpful discussions.
The authors would like to thank the many people who contributed to this workflow by field-testing various sections; Makayla Betts, Camilla Dayrit, Andrew Stump, Muntaha Samad, Henna Hundal, Cassie Ettinger, and Hannah Holland-Moritz. Additionally the authors would like to thank Authorea for technical assistance with their article platform.
We thank Dr. A. L. Reyesenbach and Dr. Krista Longnecker for advice and assistance in collecting isolates and 16S RNA analysis.
We thank Dr. Jacques Mokhbat, Mrs. Sanaa Zoghbi and the bacteriology team at the LAUMCRH for all their help and support.
We thank Lance Benson and Jessica Lundberg of Lundberg Family Farms; George Tibbetts and Michael Lear for generously providing samples and access to their field facilities; Derek Lundberg and Jeffery Dangl (The University of North Carolina) for sharing their protocol for root sonication prior to publication; Kelsey Galimba, John Jaeger, Cassandra Ramos, and Paul Tisher for technical assistance at the early stages of the project; Gurdev Khush and Kate Scow for valuable advice; and members of the J.A.E. and V.S. laboratories for helpful discussions.
The authors would like to thank members of the Facciotti and Eisen labs for helpful discussions and for critically reviewing the manuscript. Special thanks to Guillaume Jospin in the Eisen lab for providing BLAST filtering scripts and for assistance in selecting appropriate filtering parameters.
We would like to express special thanks to Grace Pai for creating Sanger sequencing libraries and Shannon Smith and Terry Utterback for coordinating sequencing at TIGR.
We wish to acknowledge the substantial efforts of Michael Lewis, administrator of the UC Davis Genome Center Cluster Computing Resource, to provide and maintain the computing resources on which these analyses were performed. We would also like to acknowledge Matthew DeMaere (UTS) for his contribution to Fig. 3.
We would like to acknowledge the excellent work of many students, teaching fellows, and instructors who contributed to this research over the many years of the Microbial Diver- sity course at the Marine Biological Laboratory; in particular we thank Cristina Moraru and Rebekah J. Ward for assis- tance in developing embedding and CARD-FISH protocols, Jarrod J. Scott for providing 16S rRNA gene sequence data from 2007 and Alexander P. Petroff for helpful discussions. Many thanks to Douglas C. Nelson and Susan E. Alford for their work with the radiocarbon fixation assay, Abigail Green- Saxena and Yunbin Guan for assistance with nanoSIMS data acquisition, Fotios C. Kafantaris for microvoltammetry work, Jennifer Houghton Julie Huber for use of her lab and Claire Beaudoin for sulfide microsensors measurements, and to Nanelle R. Barash and Annette R. Rowe for their critical reading of the manuscript.
We also thank the members of the BE community and the GSC for their comments on this minimal standard, especially Jessica Green, Jordan Peccia, Ju-Hyeong Park, Janet Macher and Renzo Kottmann.
Report prepared by George Garrity (chair) and Lynne Goodwin (acting recording secretary) for comment and approval by all attending members of the Advisory Committee on June 20, 2013.
We thank Blythe Durbin-Johnson for her guidance on the statistical analyses. Frederick Bushman and David Relman generously provided sequences from published rhesus macaque gut and human gastric libraries.
We thank the DOE JGI production sequencing, IMG and GOLD teams for their support; J. Lee and E. Ng for experimental assistance; H.-P. Klenk and D. Gleim for providing a DSMZ inventory database dump and I. Letunic ́ for his knowledge and support to make iTOL work for this project. We are very grateful to B. Schink for invaluable etymological advice.
We thank the Galapagos National Parks Service and Charles Darwin Research Station for permission to obtain and export material and for logistical support. We would like to thank Greg Wray from the Duke Institute for Genome Sciences and Policy for helpful suggestions during the initial planning of the project and for providing significant funds to help cover the sequencing. We express our gratitude to Luis Sánchez-Pulido for helping with the protein sequence analysis, and we thank Wilfried Haerty and Yang Li for helpful discussions.
We thank the following people for assistance in aspects of the project including data management, analyses not included here, and discussions: J. Bristow, K. Mavramotis, N. C. Kyrpides, J. Cameron, M. Sutter, D. Stanley, O. Erbilgin, J. Zarzycki, J. Kinney, P. Schwientek, S. Prochnik, and K. K. Niyogi.
We thank the members of the iSEEM project (‘‘Integrating Statistical, Evolutionary, and Ecological Approaches to Metagenomics’’) and three anonymous reviewers for feedback that improved the quality of the manuscript.
We thank Martin Wu for help with phylogenetic profiling and Rick Gourse for bringing to our attention the similarity of yteA and ylyA to dksA. We thank members of the Losick laboratory for helpful discussion.
We would like to thank: the Department of Energy Joint Genome Institute for providing access to sequence annotations, the developers of the various open source software packages we used in our study and the other members of the Eisen and Pollard labs for helpful discussions. We also appreciate the recommendations of two anonymous reviewers, which served to strengthen the manuscript.
The authors thank Miguel Fortuna for helpful conversations that contributed to project development. The authors thank several anonymous reviewers for feedback on the manuscript.
We thank Vadim Mozhayskiy for beta testing a version of the A5 software.
This work would not have been possible without the help of many colleagues around the world. Wild Drosophila samples were collected for us by Olga Barmina, Marie-Louise Cariou, Bill Etges, Jenna Morgan Lang, Delphine Legrand, Shane McEvey, Chen-Siang Ng, and John True. We thank Jenna Morgan Lang and David Plachetzki for advice on phyloge- netic and bioinformatic methods and Olga Barmina and Matt Rolston for technical help. Kyria Boundy-Mills and Marc-André Lachance provided helpful suggestions for improving the manuscript.
The authors would like to thank members of the Facciotti and Eisen labs for helpful discussions and for critically reviewing the manuscript.
We would like to thank Aaron Darling for useful discussions.
Thanks to GigaScience editors and the authors of the McDonald et al. article referred to here for inspiring this essay. Thanks to all the people who have sent me badomics words via various electronic communication systems.
This work would not be possible without the help of many colleagues around the world. Wild Drosophila samples were collected for us by Olga Barmina, Marie-Louise Cariou, Bill Etges, Delphine Legrand, Nina Ly, Shane McEvey, Chen-Siang Ng, and John True. We thank Deborah Kimbrell for providing lab Drosophila strains; Gideon Bradburd and Greg Pauly for advice on phylogenetic and bioinformatic methods; and Holly Huse, Pamela James, and Olga Barmina for technical help.
We thank the captain and crews of the R/V Seward Johnson and R/V Western Flyer as well as J Zehr and J Montoya for cruise space on SJ0609. We are deeply grateful to A Engman, E Demir-Hilton, ML Cuvelier and MP Simmons for providing invaluable assistance with cruise sampling, H Wilcox for performing traditional metagenomic extractions as well as T Ishoey, T Woyke and SG Tringe for help with the population metagenome. C Suttle and MB Sullivan provided helpful discussions. H Moreau and E Derelle kindly confirmed Bathycoccus genome characteristics reported herein by com- parison with a genome project for Bathycoccus.
Thanks to Srijak Bhatnagar, Jessica Bryant, Alexandros Stamatakis, Dongying Wu, and Martin Wu for assistance and advice on bioinformatics and phylogenetic analyses.
We thank Alex Horner-Devine, Pedro Flombaum, Adam Martiny, Francois Primeau, and Jim Randerson for assistance with data analysis; Brendan Bohannan, Lauren Buckley, Adam Martiny, and two anonymous reviewers for useful suggestions on the manuscript; Melissa Lage, Helen Bekris, Michael Boyce, Stephanie Chen, Edgar Leighton, and Juna Konomi for providing crucial laboratory and analysis help; and Mark Bertness, Dixie Birch, Keryn Bromberg, Jane Casey, Caitlin Crain, Jeffrey Dukes, Jose Farina, Roger Fuller, Melissa Lage, Adam Martiny, Devon Bradley Mohamed, Brian Silliman, and Kathleen Treseder, who aided in sampling.
We acknowledge Jonathan Badger for help with informatics, Merry Youle for help with manuscript editing, past and present members of the Eisen Lab, TIGR, and JCVI for helpful discussions, and the reviewers and editors for helpful comments.
We would like to thank the RDP for providing access to their curated SSU- rRNA multiple sequence alignments and CAMERA for enabling access to the Global Ocean Survey Data. We would also like to thank the authors and developers of the various software packages we’ve leveraged, especially the BioPerl and R developer communities. Finally, we thank Dr. Aaron Darling, Dr. Dongying Wu and Dr. Rebecca Lamb for their insight and the reviewers of this manuscript for their critical and informative suggestions.
We are grateful to Srijak Bhatnagar and Jenna Morgan for assistance with pre- liminary testing of WATERS.
We thank David Mills, Mitchell Singer, and Alison Berry for supplying cultures for the lactic acid bacteria, Myxococcus xanthus, and Acidothermus cellulolyticus, respectively. We thank Morgan G. I. Langille for comments on a draft of this manuscript. Sequencing was performed at the DOE Joint Genome Institute in Walnut Creek, CA.
The authors would like to thank Cheryl Zidel and Deborah Stevens for their diligent efforts in organizing the meeting.
The authors would like to thank Elizabeth Wilbanks and Aaron Darling for reading and editing of the manuscript, and Mike Chelen and reviewer Andrew Perry for suggesting several improvements for the BioTorrents website.
We thank Shannon Smith, (for constructing the genomic libraries for shotgun sequencing), Kevin Penn (for laboratory assistance), Merry Youle (for assistance with manuscript editing), the informatics and IT groups at TIGR/JCVI (for general support), Nikos Kyrpides (for help with MIGS), members of the Eisen lab and UC Davis Genome Center (for helpful discussions) and members of the community (for their patience and assistance).
We thank the following people for assistance in aspects of the project including planning and discussions (R. Stevens, G. Olsen, R. Edwards, J. Bristow, N. Ward, S. Baker, T. Lowe, J. Tiedje, G. Garrity, A. Darling, S. Giovannoni), analysis of genomes whose work could not be included in this report (B. Henrissat, G. Xie, J. Kinney, I. Paulsen, N. Rawlings, M. Huntemann), project management (M. Miller, M. Fenner, M. McGowen, A. Greiner), sequencing and finishing (K. Ikeda, M. Chovatia, P. Richardson, T. Glavinadelrio, C. Detter), culture growth, DNA extraction, and metadata (D. Gleim, E. Brambilla, S. Schneider, M. Schro ̈der, M. Jando, G. Gehrich-Schro ̈ter, C. Wahrenburg, K. Steenblock, S. Welnitz, M. Kopitz, R. Fa ̈hnrich, H. Pomrenke, A. Schu ̈tze, M. Rohde, M. Go ̈ker), and manuscript editing (M. Youle).
We thank the 17 individuals that made this study possi-ble; Charles Bevins and Scott Dawson for critical reading of the manuscript; Joseph Abdo, Cyril Chemali, and Gennadiy Novitsky at GUMC for technical assistance with sample and clinical data collection; Bertrand Perroud for assistance with the self-organizing-map software; Merry Youle for editing assistance; and Erin Esp, Senke Chen, Changjie Mathe, and Hans Mueller as part of the statistical consulting class (STA 401) at UC Davis for valuable feedback on the statistical methodology used here.
We are grateful for the financial support of New England Biolabs, the National Science Foundation (grant no. 0523862 to D.L.D.) and Oregon Opportunity Funds from the State of Oregon, NIH (to M.G.H.). Contributions by A. E. Trindade-Silva and C. A. G. Soares were supported in part by the Brazilian agency CNPq (Grant MCT/CNPq 02/2006 No.: 470967/2006-4) and by the Brazilian fellowship programs of CNPq and PDEE/CAPES.
I thank Merry Youle for assistance in the editing of this manuscript and Martin Wu and Dongying Wu for help in many of the genome analyses reported here. In addition, I thank the many people at TIGR and UC Davis who provided help in generating and analyzing the genome and metagenomes under discussion.
We thank Lynne Goodwin for her efforts in coordinating the sequencing project at JGI, Hank Tu for input on the chimer detection analysis, Natalia Ivanova for annotation advice, Nicole Poulton for flow cytometry, and Wendy Bellows for PCR analyses.
The authors would like to thank the Captain and Crew of the R/V l’Atalante and especially the Nautile pilots for help with sample collection.
We thank James Sakwa for helping coordinate initial analysis, Grace Pai and Shannon Smith for making libraries, Tamara Feldblyum and Terry Utterback for coordinating sequencing, Julia Enticknap for growing the biomass for the carotenoid analysis and the CO consumption experiments, and Elizabeth O’Connor for her contribution in the early stages of the genome project. We also thank the IT and bioinformatics staff at TIGR for creating computational tools for aiding in the sequencing and annotation of the genome.
We thank Joel Malek, the laboratory, IT and Bioinformatics staff at The Institute for Genomic Research (now incorporated within the JC Venter Institute) for assistance with sequencing and analysis
The authors wish to thank Hean Koo, Paolo Amedeo, Seth Schobel, Kevin Galinsky, and Jessica Chen for their assistance in submission of ESTs and updated gene models, contigs, and scaffolds to sequence databases. We thank Steven Salzberg, Art Delcher, Mihai Pop and Martin Wu for help with analysis of assemblies for closure.
We thank Aaron Halpern, Doug Rusch, and Phil Hugenholtz for helpful discussions; Kevin Penn, Jen Hughes Martiny, Jonathan Badger and Qi Zhao for help with pipeline testing; Elies Bik for providing ARB alignments, taxonomy files and useful comments; RDP II, Greengenes, and the European database for making resources publicly available.
We thank Ambuj Tewari, Martin Wu, Lior Pachter, Jonathan Dushoff, Joshua Weitz, Dongying Wu, Amber Hartman, and Jenna Morgan for their helpful suggestions and comments.
I would like to thank Philip C. Hanawalt for his support during and after my Ph.D research in his lab. Everyone in the field knows he is a great scientist. What they may not all know is that he is an even better human being.
We thank Mary Barnstead, Susan van Aken, Grace Pai, and M. Brook Craven for coordinating the library construction and sequencing of the plasmids. Also, we thank Ryan Mills and Heath Mills for the initial annotation work performed on the plasmids and Forest Rohwer for valuable suggestions for the sequence analysis and manuscript preparation.
Mass spectrometric analyses were performed by Dr. A. Daniel Jones (Michigan State University, East Lansing, MI). The plasmid pAC-LYC was the gift of Dr. Francis X. Cunningham, Jr. (University of Maryland, College Park, MD). We thank an anonymous reviewer for helpful suggestions that improved the manuscript.
We thank Moshe Mevarech for H. volcanii strains WR340 and WR480; Sam Haldenby for help with shuttle vector construction; Jonathan Badger for help in analysis of the H. volcanii genome; Ste ́phane Delmas for advice; Steve Bell for communicating results prior to publication; and Shiladitya DasSarma for constructive discussions.
I thank Simon Levin, Joshua Weitz, Jonathan Dushoff, Maria-Inés Benito, Doug Rusch, Aaron Halpern, and Shibu Yooseph for helpful discussions, and Melinda Simmons, Merry Youle, and three anonymous reviewers for helpful comments on the manuscript.
We are also indebted to a large group of individuals and groups for facilitating our sampling and analysis. We thank the governments of Canada, Mexico, Honduras, Costa Rica, Panama, Ecuador, French Polynesia, and France for facilitating sampling activities. All sequencing data collected from waters of the above-named countries remain part of the genetic patrimony of the country from which they were obtained. Canada’s Bedford Institute of Oceanography provided a vessel and logistical support for sampling in Bedford Basin. The Universidad Nacional Autonoma de Mexico (UNAM) facilitated permitting and logistical arrangements and identified a team of scientists for collaboration. The scientists and staff of the Smithsonian Tropical Research Institute (STRI) hosted our visit in Panama. Representatives from Costa Rica’s Organization for Tropical Studies (Jorge Arturo Jimenez and Francisco Campos Rivera), the University of Costa Rica (Jorge Corte ́s), and the National Biodiversity Institute (INBio) provided assistance with planning, logistical arrangements, and scientific analysis. Our visit to the Galapagos Islands was facilitated by assistance from the Galapagos National Park Service Director, Washington Tapia, and the Charles Darwin Research Institute, especially Howard Snell and Eva Danulat. We especially thank Greg Estes (guide), Hector Chauz Campo (Institute of Oceanography of the Ecuador Navy), and a National Park Representative, Simon Ricardo Villemar Tigrero, for field assistance while in the Galapagos Islands. Martin Wilkalski (Princeton University) and Rod Mackie (University of Illinois) provided planning advice for the Galapagos sampling plan. We thank Matthew Charette (Woods Hole Oceanographic Institute) for nutrient data analysis. We also acknowledge the help of Michael Ferrari and Jennifer Clark for remote sensing data. The U.S. Department of State facilitated Governmental communications on multiple occasions. John Glass (J. Craig Venter Institute [JCVI]) provided valuable assistance in methods development. The dedicated efforts of the quality systems, library construction, template, and sequencing teams at the JCVI Joint Technology Center produced the high quality sequence data that was the basis of this paper. We thank Matthew LaPointe, Creative Director of JCVI, for assistance with figure design, and the JCVI information technology support team who facilitated many of the vessel related technical needs. Special thanks are due for Charles H. Howard, captain of the Sorcerer II, and fellow crew members Cyrus Foote and Brooke A. Dill for their time and effort in support of this research. We gratefully acknowledge Dr. Michael Sauri, who oversaw medical related issues for the crew of the Sorcerer II.
We are indebted to a large group of individuals and groups for facilitating our sampling and analysis. We thank the governments of Canada, Mexico, Honduras, Costa Rica, Panama, and Ecuador and French Polynesia/France for facilitating sampling activities. All sequencing data collected from waters of the above-named countries remain part of the genetic patrimony of the country from which they were obtained. We also acknowledge TimeLogic (Active Motif, Inc.) and in particular Chris Hoover and Joe Salvatore for helping make the DeCypher system available to us; the Department of Energy for use of their NERSC Seaborg compute cluster; Marty Stout, Randy Doering, Tyler Osgood, Scott Collins, and Marshall Peterson (J. Craig Venter Institute) for help with the compute resources; Peter Davies and Saul Kravitz (J. Craig Venter Institute) for help with data accessibility issues; Kelvin Li and Nelson Axelrod (J. Craig Venter Institute) for discussions on data formats; K. Eric Wommack (University of Delaware, Newark) and the captain and crew of the R/V Cape Henlopen for their assistance in field collection of Chesapeake Bay virioplankton samples; John Glass (J. Craig Venter Institute) for assistance with the collection and processing of the virioplankton samples; Beth Hoyle and Laura Sheahan (J. Craig Venter Institute) for help with paper editing; and Matthew LaPointe and Jasmine Pollard (J. Craig Venter Institute) for help with figure formatting. STM, MPJ, CvB, DAS, and SEB acknowledge Kasper Hansen for statistical advice. We also acknowledge the reviewers for their valuable comments.
Sequencing was carried out at the JGI, and we thank D. Bruce and E. Rubin for project management, D. Fraenkel for review of metabolic pathways in Ruthia, and P. Girguis and K. Scott for their helpful comments on the manuscript. The Candidatus R. magnifica genome can be found in GenBank (CP000488).
We thank Carol Berthiaume for artistic rendering of the Myxococcus lifecycle; D. E. Whitworth for verifying the list of two-component systems before his publication; and the following members of the Myxococcus community who helped annotate the genome: J. S. Jakob- sen, L. J. Shimkets, R. Welch, M. S. Avadhani, W. P. Black, H. B. Bode, P. J. Bonner, J. M. Buchner, V. Bustamante, A. Castan ̃eda-Garc ́ıa, M. Chavira, P. J. A. Cock, P. Curtis, M. E. Diodati, X. Y. Duan, A. Garza, R. E. Gill, J. C. Haller, P. Hartzell, P. I. Higgs, D. A. Hodgson, S. Inouye, L. Jelsbak, B. Julien, A. C. Karls, J. Kirby, L. Kroos, Y. Li, A. Lu, R. Lux, X. Ma, R. Mu ̈ller, J. Mun ̃oz-Dorado, H. Nariya, J. P ́erez, V. D. Pham, R. Reid, J. J. Rivera, W. Shi, M. Singer, L. Søgaard-Andersen, D. Srinivasan, A. Treuner-Lange, L. Tzeng, P. Viswanathan, Z. Yang, D. R. Yoder, R. Yu, and D. R. Zusman.
We would like to acknowledge the Tetrahymena research community and the members of our Tetrahymena Scientific Advisory Board for advice, support, encouragement, and assistance. In addition, we would like to specifically acknowledge many people for assistance: John Gill (sample tracking); Hean Koo (contaminant identification and trace archive and EST submission); Shannon Smith, Susan van Aken, and William Nierman (library construction); Sam Angiuoli (Web and BLAST page maintenance); Jeff Shao (database construction); Jessica Vamathevan (initial work on genome closure); Tamara Feldblyum, Terry Utterback, and the staff at the J. Craig Venter Institute’s Joint Technology Center (sequencing); Lauren Smith and Jyoti Shetty (fosmid construction); Malcolm Gardner (advice); Martin Shumway (general software engineering support); Owen White (general informatics support); Leslie Bisignano and Lynn McKenna (grants support); Aimee Turner (financial operations); Tinu Akinyemi (administrative support); and Claire Fraser (for supporting the scientific research within TIGR).
We thank Dawn Field and Peter Sterk for organizing the “Cataloguing our Current Genome Collection” workshop at EBI, where some of these ideas were first proposed. We also thank Dawn Field, Susanna San- sone, and Eugene Kolker for their roles in putting together this special issue.
We thank Steven Salzberg and Art Delcher (TIGR) for making public and calling our attention to Tetrahymena weak link files at the TIGR Web site, and to Martin Wu (TIGR) for providing a repeat-masked version of the genome.
We are grateful to Heather Costa for assistance with sharpshooter collecting in Riverside and to Colin Dale and Wendy Smith for help with collections in 2001. Howard Ochman gave advice on the DNA isolation. We would like to acknowledge the TIGR Bioinformatics and IT departments for general support, Claire Fraser-Liggett and Eric Eisenstadt for encouragement, and members of the Eisen research group, especially Martin Wu and Jonathan Badger, for providing bioinformatics tools.
We acknowledge Jessie Goodman, University of Minnesota, for providing the stock culture of A. phagocytophilum MN; Robert F. Massung at the Centers for Disease Control and Prevention, Atlanta for providing the stock culture of A. phagocytophilum MRK; Derrick Fouts for examination of the genomes for prophage elements; Robert DeBoy for examination of the genome for transposons; Leka Papazisi for assistance with statistical analysis; Karen Nelson, Ian Paulsen, and Emmanuel Mongodin for helpful discussions; Chun-Ha Wan for assistance depositing data in ArrayExpress; Robert Munson at Child- ren’s Hospital, Ohio State University for assistance with the grant proposal; David Dyer at University of Oklahoma for initial sequencing efforts; and our reviewers for their helpful comments and suggestions.
We thank R/V Atlantis and DSV Alvin personnel, NOAA’s Ocean Exploration Program, and Brad Stevens, Randy Keller, Tom Shirley, and Tom Guilderson for help with data acquisition.
We would like to thank The Institute for Genomic Research’s (TIGR) Bioinformatics Department for supporting the infrastructure asso- ciated with genome annotation and analysis; the TIGR IT Depart- ment for general IT support; Dan Haft for discussions regarding selenoproteins; Anne Ciecko, Kristi Berry, and Chris Larkin for initial work on genome closure; Patrick Eichenberger, Richard Losick, and Jim Brannigan for discussions about sporulation; Vitali Svetlichnyi for general discussions about the organism; Terry Utterback and Tamara Feldblyum for coordinating the shotgun sequencing; William C. Nierman for making the genomic libraries; and Claire M. Fraser for supporting the selection of this genome as part of the DOE project referenced below.
We thank the Republic of Palau and the Coral Reef Research Foun- dation for providing the opportunity to collect samples and perform field research, B. O. Bachmann for helpful discussions, and E. M. Rachlin for mass-spectrometry training and help with selective reaction monitoring.
Samples from Yellowstone National Park were taken under permit number 4056. We gratefully acknowledge the help of Steven Miller, who accompanied us with GPS survey equipment on sampling surveys to Norris Basin, Potts Area and the Glen Africa Basin.
We thank Gary Olsen for valuable discussion, and Herve ́ Tettelin for the use of prepublication data from Anaplasma phagocytophilum, Ehrlichia chaffeensis and Neorickettsia sennetsu. We also thank the US Department of Energy Joint Genome Institute for the use of their sequence data from Novosphingobium aromaticivorans and Rhodo spirillum rubrum prior to publication and Integrated Genomics for the use of their Rhodobacter capsulatus genome data.
We thank G. S. A. Myers, S. Salzberg, M. Pop, O. White, M. Heaney, S. Lo, M. Holmes, M. Covarrubias, J. Sitz, A. Resnick, J. Zhao, M. Zhurkin, S. Sengamalay, P. Sellers, R. Deal, R. Karamchedu, and V. Sapiro for informatics, database, and software support. Sequence data for Silicibacter pomeroyi were obtained from The Institute for Genomic Research Web site (www.tigr.org).
We acknowledge TIGR seqcore, informatics, and IT groups for support. We thank A. Cook for analysis of the taurine pathway and T. M. Davidsen, N. Zafar, L. Zhou, M. Gwinn and T. Creasy for bioinformatics support
The authors gratefully acknowledge Michael M. Cox for helpful discussions and for critically reading the manuscript and we appreciate the technical assistance of L. Alice Simmons.
We thank the TIGR sequencing facility, informatics group, and IT group, as well as sponsored projects, legal, and other administrative staff, for their support. Ivar Lossius is thanked for his invaluable support throughout this project. Tanja Davidsen is thanked for her help with the Comprehensive Microbial Resource.
We thank J.K. Voordouw for DNA isolation, S. Salzberg, O. White, M. Heaney, S. Lo, M. Holmes, M. Covarrubias, J. Sitz, A. Resnick, Y. Zhao, M. Zhurkin, R. Deal, R. Karamchedu and V. Sapiro for informatics, database and software support, and the TIGR faculty and sequencing core for expert advice and assistance.
The authors would like to acknowledge P. Lethaby, M. Roadman, D. Clougherty, N. Buck, J. Selengut, A. Delcher, M. Pop, H. Koo, R. Doering, M. Wu, J. Badger, K. Moffat, S. Yooseph, E. Kirkness, D. Karl, K. Heidelberg, B. Friedman, H. Kowalski, and the staff of the J. Craig Venter Science Foundation Joint Technology Center. We also acknowledge the help of N. Nelson at UCSB- ICESS for assistance in acquiring the satellite image in Fig. 1.
We thank S. Salzberg, O. White, M. Heaney, S. Lo, M. Holmes, M. Covarrubias, J. Sitz, A. Resnick, J. Zhao, M. Zhurkin, R. Deal, R. Karamchedu, and V. Sapiro for informatics, database, and software support. This work was supported by the National Institute of Dental and Craniofacial Research Grant RO1-DE12488.
We acknowledge Barton Slatko, Jeremy Foster, New England Biolabs, and Mark Blaxter for helping inspire this project; Rehka Seshadri for help in examining pathogenicity factors and reading the manuscript; Derek Fouts for examination of group II introns; Susan Lo, Michael Heaney, Vadim Sapiro, and Billy Lee for IT support; Maria-Ines Benito, Naomi Ward, Michael Eisen, Howard Ochman, and Vincent Daubin for helpful discussions; Steven Salzberg and Mihai Pop for help in comparing wMel with the D. melanogaster genome; Elodie Ghedin for access to the B. malayi Wolbachia sequence data; Maria Ermolaeva for assistance with analysis of operons; Dan Haft for designing protein family hidden Markov models for annotation; Owen White for general bioinformatics support; four anonymous reviewers for very helpful comments and suggestions; and Claire M. Fraser for continuing support of TIGR’s scientific research.
The authors would like to ac- knowledge John Donelson and Joanna DaSilva for editing the manuscript, Jinming Song and Samir Kaul for useful discussions, and John Swindle for donating the T. cruzi BAC 12A5.
We thank M. Heaney, S. Lo, M. Holmes, B. Lee, C. Irwin, R. Karamchedu, and V. Sapiro for database and information technology support at TIGR; the TIGR faculty and sequencing core for expert advice and assistance; and A. Kwamena-Poh for assistance in the preparation of this manuscript.
We thank Toni Pollin for a critical reading of the manuscript, and Bob Stephens and Toni Harbaugh-Blackford for bioinformatics sup- port at Advanced Biomedical Computing Center, NCI-FCRDC.
We thank Michael Heaney, Michael Holmes, Vadim Sapiro, and Emmanuel Mongodin for informatics support at TIGR. We thank J. F. Tomb for assistance in the early stages of the project.
H. Ackermann and M. Matsuzaki provided bacterial and bacterio- phage strains to initiate this work. We are grateful to Gisela Mosig for comments on the manuscript and to many other individuals in the phage research community who provided thoughtful insights. We thank M. Heany, S. Lo, V. Sapiro, B. Lee, R. Karamchedu, and M. Holmes for database and software support and J. Peterson, L. Umayam, I. Holt, and D. Haft for informatics support. M. Bessman, J. Grose, and J. Roth provided stimulating discussion on NAD metabolism.
We thank the officers and crew of R/V Atlantis, Alvin, and the ABE Operations Group, and the shore-based personnel of the National Deep Submergence Facility at the Woods Hole Oceanographic Institution (WHOI) for their expertise and dedication in helping us acquire these data.
We would like to thank Chris Town and Brian Haas for useful discussions and comments.
We acknowledge the contributions of P. Turnbull, E. Saile, Y. Chen, J. Hunter-Cevera, N. McKinney, S. Cendrowski, M. Weiner, A. Fouet, A. Harrison, S. Leppla, M. Mock, C. Moran, G. Myers, G. Patra, J. Ravel, E. Reilly and T. Torok.
We thank O. White, S. Salzberg, M. Heaney, M. Covarrubias, S. Hodge, R. Karamchedu, B. Lee, S. Lo, M. Holmes, and V. Sapiro for informatics, database, and software support, and The Institute for Genomic Research faculty and sequencing core for advice and assistance.
We thank M. Heaney, S. Lo, M. Holmes, B. Lee, R. Karamchedu, and V. Sapiro for database and information technology support at TIGR, and we thank the TIGR faculty and sequencing core for expert advice and assistance. We thank M. Gilmore for generously providing E. faecalis V583. We thank D. Clewell for providing the complete sequence of pAD1 for comparative analysis.
The authors would like to thank Michael Holmes, Michael Heaney, Herve Tettelin, John Heidelberg, Michael Kertesz, Prabhakar Salunkhe, Michael Brown and Ed Moore for assistance at various stages of the project
We thank our colleagues at The Wellcome Trust Sanger Institute, The Institute for Genomic Research, the Stanford Genome Technology Center, and the Naval Medical Research Center for their support. We thank J. Foster for providing markers for chromosome 14; R. Huestis and K. Fischer for providing RT–PCR data for chromosomes 2 and 3 before publication; A. Waters for assistance with ribosomal RNAs; S. Cawley for assistance with phat; and M. Crawford and R. Wang for discussions.
We thank S. Salzberg, M. Heany, M. Covarrubias, S. Hodge, R. Karamchedu, B. Lee, S. Lo, M. Holmes, and V. Sapiro for informatics, database and software support, and the TIGR faculty and sequencing core for expert advice and assistance.
We thank M. Heaney, S. Lo, M. Holmes, B. Lee, R. Karamchedu, and V. Sapiro for database and IT support at The Institute for Genomic Research (TIGR), and the TIGR faculty and sequencing core for expert advice and assistance.
We thank J. Parkhill, The Sanger Center, for review of the H37Rv electropherograms; A. Duesterhoeft and K. Dix, Qiagen Genomic, Inc., for Masscode verification of SNPS; and The Sanger Center for the availability of the M. bovis sequence data.
We thank O. White, S. Angiuoli, L. Umayam, J. Peterson, M. Wu, M. Heaney, S. Lo, M. Holmes, B. Lee, R. Karamchedu, and V. Sapiro for informatics support at The Institute for Genomic Research (TIGR) and the TIGR faculty and sequencing core for expert advice and assistance. We also thank G. Orefici and M. Oggioni for isolation and characterization of the sequenced strain.
We acknowledge J. Buchoff, M. Heaney, M. Holmes, D. Kosack, B. Lee, V. Sapiro, and J. Shao for IT support; T. Dickinson, S. Angiuoli, M. Ermoleva, S. Salzberg, M. Eisen, M-I. Benito, R. Roberts, J. Posfai, C. Dunn, C. Friedrich, C. Dahl, and anonymous reviewers for comments and assistance with genome analysis; and the TIGR seqcore, informatics, and IT groups for support.
We wish to thank Fiona Stewart for all of her help and suggestions for optimising the GPS conditions.
We thank S. Haddock for computational advice; J. Zehr and D. Karl for the HOT samples; the captains and crew of the RV Point Lobos and Western Flyer for assistance at sea; and M. Heaney, V. Sapiro, S. Lo, and M. Holmes for database and software support. Preliminary sequence data for R. palustris was obtained from the DOE Joint Genome Institute (JGI) at http://www.jgi.doe.gov/JGI_microbial/html/index.html.
We thank P. Green for useful discussions, R. Gibson for providing the genome_plot program, and J. Staley for critical review of the manuscript.
We thank M. Heaney, J. Scott, M. Holmes, V. Sapiro, B. Lee, and B. Vincent for software and database support at TIGR; M. Ermolaeva and M. Pertea for specific computer analyses; the TIGR faculty and sequencing core for ex- pert advice and assistance; I. Aaberge (National Institute of Public Health, Oslo, Norway) for providing the initial clinical isolate labeled JNR.7/87; and G. Zysk and A. Polissi for sharing specific sequence data not deposited in GenBank.
The authors wish to thank E. Magnien, D. Nasser and J. D. Watson for their continual support and encouragement.
We thank S. Eddy, M.A. Riley, T. Read, A. Stoltzfus, M-I Benito and I. Paulsen for helpful comments, suggestions and discussions.
Natural history museums at Louisiana State University and the University of New Mexico contributed invaluable cooperation in making available the details of their frozen tissue collections for our analyses. C.-B. Stewart and D. Mindell both contributed expert consultation in mtDNA analysis, and we thank S. Easteal and an anonymous reviewer for helpful and insightful comments on the manuscript.
I thank all the people at TIGR for support, assistance, and helpful discussions.
I thank all the people at The Institute for Genomic Research for support, assistance, and helpful discussions.
We thank M. Heaney, V. Sapiro, B. Lee, M. Holmes and B. Vincent for database and software support.
We thank the IMAGE Consortium, Aaron Adamson, and Drs. Irene Jones, Mark Shannon, James George, Ian McConnell, and David Wilson III for technical help as well as for preparation of the manuscript. We also thank the Joint Genome Institute and Jane Lamerdin for assistance and helpful advice in the sequencing of BAC clones.
We thank M. Heaney, J. Scott, M. Holmes, D. Richardson, B. Loftus, B. Lee, and B. Vincent for software and database support; the TIGR faculty and sequencing core for advice and assistance; the Oxford Super Computing Centre for access to its resources; and D. Kingsbury for initial handling of sequences for Chiron.
We thank S. Jackson, J. Jiang, K. Meyer, E. Richards and S. Tabata for helpful contributions in completing the chromosome. In addition, we would like to thank the TIGR faculty, system administrators, sequencing facility, bioinformatics department and administrative staff.
We would like to thank M.B. Eisen, M.-I. Benito, J.H. Miller, A.J. Clark, J. Laval, B. van Houten, I. Mellon, P. Warren, R. Woodgate, W.F. Doolittle, J. Hays, S. Henikoff, P. Forterre, D. Botstein, R. My-ers, A. Ganesan, J. DiRuggiero, H. Ochman, F. Robb, M. Riley, S. Suzen, M. White, V. Mizrahi, A. Villeneuve, M. Galperin, C.M. Fraser, and J.C. Venter for helpful comments and encouragement. In addition, we would like to thank the two anonymous reviewers for helpful comments and criticisms.
We thank E. V. Koonin for thoughtful contributions to this manuscript.
We thank M. Heaney, J. Scott, D. Maas and B. Vincent for software and database support; R. Roberts, F. Kunst, and M. Simon for useful discussions; and R. Huber for providing T. maritima MSB8 cells.
My thesis has represented a relatively long and twisting road. In acknowledging the people who have helped make this possible I think it is useful to provide some of the history of each of the projects and my scientific development along the way. I have tried to make these brief and have put them in somewhat chronological order. I owe my general interest in science and science research to my parents, Howard and Laura Eisen and to my grandfather Benjamin Post. They did not force me to become a scientist, but they did help me learn how to think critically and to appreciate some of the wonders of science. As an undergraduate at Harvard, I was very fortunate to interact with many great biology researchers and teachers. During that time, I become interested in evolutionary biology and in particular in molecular evolution. The people I am particularly grateful to include: Stephen J. Gould (for his excellent class on evolution which was my first introduction to evolutionary biology as a science); Wayne and David Maddison (who, as Teaching Assistants for Gould's class, introduced me to computational evolutionary biology); Stephen Austad (for getting me interested in field biology research through the field "laboratories" for his Ecology class); Eric Fajer and Scott Melvin (for giving me my first experience designing a semi-independent research project for their Conservation Biology); Alan Launer (for lending me the equipment to collect fish from the pond, which, according to him, I never returned); William A. Calder III (for giving me my first experience as doing real science research at the Rocky Mountain Biological Laboratory); Fakhri A. Bazzaz (for being an excellent advisor throughout my time at Harvard and afterward, and for giving me a chance to do my first truly independent research project); Peter Wayne, David Ackerly, and Susan Morse for helping me with the jet-lag experiment; P. Wayne, again, for hiring me as a research assistant and teaching me about science research and culture; Jennifer Doudna (for introducing me to molecular evolution and for teaching me how to critically read a scientific paper); Dennis Powers (for introducing me to molecular ecology), Colleen M. Cavanaugh (for too many things to list here including teaching me to keep a good notebook and to do controls for every experiment, for introducing me to microbiology, and introducing me to the powers of a phylogenetic perspective in biological research); Rob Dorit and Hiroshi Akashi who helped me learn how to do some molecular biology experiments; and all my other teachers and colleagues at Harvard including Woody Hastings, Karl Liem, Peter Ashton, and Otto Solbrig. And so, with a great debt to all of these people, I moved on to Stanford. Although I have officially worked on DNA repair in Phil Hanawalt's lab, I have benefited a great deal from many people at Stanford including: Ward Watt (for teaching me about biochemical evolution), Sharon Long (who somehow taught me many valuable lessons in a short rotation project but in particular, for infusing in me the benefits of working on an organism that has good genetic tools available); Shi-Kau Liu (for help in initial projects and for initiating all of my work on RecA); Charlie Yanofsky (for many things but in particular for helping me realize just how powerful it is to have a crystal structure of the protein one is interested in); Kurt Gish, for help with sequencing and cloning; Allan Campbell and Richard Lenski (for helping me discover some of the flaws of adaptive mutation experiments and thus leading me to look for a new project); Patrick Keeling and W. Ford Doolittle for getting me started working on Haloferax volcanii; Mitch Sogin and the Woods Hole Molecular Evolution course (for teaching me how molecular evolutionary methods worked and how to think about evolutionary questions at the molecular level); David Botstein (for convincing me that teaching and research are not incompatible, despite what many Stanford professors try to claim); all the people involved in the SME core, in particular D. Botstein, Rick Myers, David Cox, Bob Simoni, and Brad Osgood; Rick Myers (for encouraging me to develop methods and ideas behind phylogenomics); my brother Mike Eisen for help with virtually everything; Sam Karlin and Volker Brendel for teaching me about mathematical methods in molecular biology, and for making me be more critical of some of the methods used in molecular evolutionary studies; David Ackerly for teaching me about the uses of evolutionary approaches in comparative biology; Russ Fernald for general advice on life and science as well as for valuable discussions on the uses of evolutionary analysis in molecular biology; Marc Feldman, for many helpful discussions about evolution; Steve Smith, David Swofford, and Joe Felsenstein for making the GDE, PAUP, and PHYLIP computer programs freely available; Steve Henikoff and Amos Bairoch for inspiring me to put information about the gene families I work on onto the World Wide Web; and many of the people I have collaborated with over the years including Bob Shafer and Michael Lerman. I am particularly grateful to my advisor Philip C. Hanawalt for allowing me the freedom to explore the areas of science that interested me and for being not only a great advisor, but a great human being too, showing me that one can do good scientific research without losing touch with ones humanity. I am also grateful to many of the members of the Hanawalt Lab including David Crowley, Justin Courcelle, and Jennifer Halliday. Many people provided basic resources that helped me get my work done and get through my time at Stanford more easily including the library staff, in particular Jill Otto; Steve and Pat at the copy center; all the people in the Biostores especially Darnell, Joe and Manual; and all the people in the Biology Department main office. On a personal level, I want to thank all of my many friends who have helped me get through graduate school whether it was by playing hockey and softball, going for bike rides, going hiking and camping doing many other things. These people include Bob Fisher, Chester Washington, Jochen Kumm, David Pollock, David Goldstein, Joanna Mountain, Mo Badi, Grant Hoyt, Becky Taylor, James Keddie, Healy Hamilton, Sinan Suzen, and Aviv Bergman. Many of these people are both good friends and colleagues. I am also grateful to my family, especially my brother Mike Eisen, my sister Lisa Eisen, and my mother Laura Eisen, my mother’s parents Annie and Ben Post, and my little brother Matthew Glenn, my uncle David Post, and my pseudo-brother Saul Jacobson for support and encouragement. And in particular, I want to thank Maria-Ines Benito for being there through all the good and bad times and for listening to me read sections of papers she had no interest in, and for proofreading various papers and for just about everything. I dedicate this thesis to the memory of my father, Howard J. Eisen.
We wish to thank Jerrold Ward for helping to interpret the rat brain in situ hybridization patterns in development and Alex Bateman and Evan (sic) Birney for helping with Pfam analysis of the domain structure of CALL.
I would like to thank P. Hanawalt for his continued support; J. Halliday, R. Myers and M.-I. Benito for helpful discussions; F. Taddei, D. Berg, K. Culligan and G. Meyer-Gauen for suggestions on earlier versions of this work; D. Swofford for making PAUP* available prior to release and The Institute for Genomic Research and Oklahoma University for making sequences available prior to publication. The comments of two anonymous reviewers were particularly helpful.
We would also like to thank Alberto I. Roca for help in tracking down unpublished RecA sequences and Rob Wheeler for sharing the Caulobacter crescentus RecA sequence prior to publication.
We thank D. Anderson, E. Gestrin, H. Hofmann, K. Hoke, R. Robison, and S. White for comments on the manuscript, L. Clark and K. Wilhelmsen for use of the PAC library, U. Demarco and M. Benson for technical assistance, E. Rissman for musk shrew tissue, J. Adelman for GnRH-I cDNA, and J. Felsenstein for providing PHYLIP free of charge.
We thank Lynn Zejenah (University of Zimbabwe) and Tina Chiu (Stanford University) for initial virus isolation. We thank Dereck Moore and Haynes Shepherd (California State Health Department Virology Laboratory, Berkeley) for providing heteroduplex mobility assay results. We thank Darcy Levee (Stanford University) for assistance with DNA sequencing and Muoi Loi (Stanford University) for assistance with drug susceptibility testing. We thank Jan Albert (Karolinska Institute, Stockholm, Sweden) for critical review of the manuscript.
I would like to thank Steven Smith for making the GDE software package freely available and continuing to improve it. I would also like to thank all of the researchers who have made their sequence analysis programs into shareware and allowed people like myself to perform highly powerful sequence analysis without much expense.
I would like to thank P.C. Hanawait for support and encouragement; M.B. Eisen for help with computer analysis; S. Smith and J. Felsenstein for making their computer programs freely available; M. Huang, J. Coleman, A.J. Clark, S. Sandler, W. Finch, and S. Mongkolsuk for making sequences available prior to publication; M. Feldman for the use of computer equipment; and D. Pollock, M.B. Eisen, M.-I. Benito, H. Hamilton, D. Distel, and J.D. Palmer for helpful discussion. Finally, I want to thank A.I. Roca for help in all aspects of this project including and especially the identification of errors in recA sequences in databases and aid in getting access to unpublished sequences.
We would like to thank J.H.J. Hoeijmakers for helpful comments on earlier versions of this work and Marc Feldman for the use of computer equipment.
We would like to thank M.Feldman for the use of computer equipment, S.Smith for the GDE program ,the NCBI and EMBL for free use of sequence analysis email servers, and two anonymous reviewers for very helpful suggestions
We are grateful to several people for their kind assistance: Michael Eisen for help with downloading the structural information and converting it to a useful format, Christopher Lee for help with details of the Midas program and for discussions on the interpretations of structural changes, Matthew A. Kennedy for measuring the repair sector of some of the suppressor mutants, Ann Ganesan for critical reading of the manuscript, and Michael Levitt and Marc Feldman for use of computer equipment. The reviewers were particularly helpful in their criticisms.
We thank Dave Lane and Will Weisburg for providing PCR primers and advice; Sabrina Drill and Michael Eisen for skilled technical assistance; Rob Dorit, Barbara Bowen, and Adam Mars for helpful advice and discussion; and Wally Gilbert for the use of equipment