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153. Studies in protein targeting to the endoplasmic reticulum

Author

McDonald, James Christopher

Subjects
572
Abstract

Soluble proteins can be targeted and inserted into the Endoplasmic Reticulum (ER) co-translationally or post-translationally, Co-translational translocation requires a ribonucleoprotein complex. Signal Recognition Particle (SRP), to target the ribosome-nascent chain complex to the ER-localised translocon. The targeting and insertion of membrane-bound proteins into the ER is more complex. One class of membrane proteins have the transmembrane domain near their C-terminus (tail-anchor proteins), and whilst the other classes of membrane proteins have had their mode of insertion elucidated, the insertion mechanism of these proteins remains unknown. This thesis deals with two areas of protein targeting in Saccharomyces cerevisiae. First the mode of insertion of Ufe1p, a tail-anchor protein, was examined by use of a variety of reporters. This work identified a region N-terminal to the transmembrane domain that is required for correct localisation of the protein. Second, the role of the SRP component, Srp72p was examined, Srp72p is essential for SRP function, but its role has not been determined. A screen was set up to identify conditional mutants of SRP72. In addition, deletions and point mutations were created to analyse the roles of conserved residues within the protein. Mutations affecting a conserved region of the protein towards the C-terminus were found to confer slight defects in SRP-dependent translocation. Intracellular localisation of the mutant proteins was identical to that of the wild-type protein. A mini-screen performed on two mutants identified multicopy suppressors of translocation defects. Finally, preliminary comparison of the binding affinities of SRP containing mutated Srp72p or wild-type SRP with the SRP receptor revealed a subtle difference.

Published
2001

155. Associations between provider and hospital volumes and postoperative mortality following total hip arthroplasty in New Brunswick: results from a provincial-level cohort study

Author

Crouse, Dan L., Leonard, Philip S.J., Boudreau, Jonathan, and McDonald, James T.

Subjects
Mortality -- Analysis -- Risk factors -- New Brunswick, Hospital size -- Influence, Postoperative complications -- Risk factors, Medical research, Hip replacement arthroplasty -- Health aspects -- Analysis -- Patient outcomes, Health services administration -- Research, Health, Health care industry
Abstract

Background: Several international studies have reported negative associations between hospital and/or provider volume and risk of postoperative death following total hip arthroplasty (THA). The only Canadian studies to report on this have been based in Ontario and have found no such association. We describe associations between postoperative deaths following THA and provider caseload volume, also adjusted for hospital volume, in a population-based cohort in New Brunswick. Methods: Our analyses are based on hospital discharge abstract data linked to vital statistics and to patient registry data. We considered all first known admissions for THA in New Brunswick between Jan. 1, 2007, and Dec. 31, 2013. Provider volume was defined as total THAs performed over the preceding 2 years. We fit logistic regression models to identify odds of dying within 30 and 90 days according to provider caseload volume adjusted for selected personal and contextual characteristics. Results: About 7095 patients were admitted for THA in New Brunswick over the 7-year study period and 170 died within 30 days. We found no associations with provider volume and postoperative mortality in any of our models. Adjustment for contextual characteristics or hospital volume had no effects on this association. Conclusion: Our results suggest that patients admitted for hip replacements in New Brunswick can expect to have similar risk of death regardless of whether they are admitted to see a provider with high or low THA volumes and of whether they are admitted to the province's larger or smaller hospitals. Contexte : Plusieurs etudes internationales rapportent un lien negatif entre le volume d'activite de l'hopital ou du fournisseur de soins de sante et le risque de deces postoperatoire lie a une arthroplastie totale de la hanche. Les seules etudes canadiennes qui se sont interessees a cette question ont ete realisees en Ontario et n'ont pas rapporte ce lien. Dans notre etude, nous tentons de decrire des liens entre le deces postoperatoire lie a une arthroplastie totale de la hanche et le volume de la charge de travail du fournisseur de soins de sante, egalement ajustes pour tenir compte du volume d'activite de l'hopital, au sein d'une cohorte basee sur la population au Nouveau-Brunswick Methodes : Nos analyses reposent sur les donnees portant sur les conges des hopitaux, associees aux statistiques de l'etat civil et aux donnees des registres des patients. Nous avons examine toutes les premieres hospitalisations connues en vue d'une arthroplastie totale de la hanche au Nouveau-Brunswick entre le 1 (er) janvier 2007 et le 31 decembre 2013. Le volume d'activite du fournisseur de soins de sante a ete defini comme etant la totalite des arthroplasties totales de la hanche pratiquees au cours des 2 annees precedentes. Nous avons ajuste les modeles de regression logistique de maniere a identifier le risque de deces dans les 30 et 90 jours en fonction du volume de la charge de travail du fournisseur de soins de sante, pour tenir compte de caracteristiques personnelles et contextuelles choisies. Resultats : Environ 7095 patients ont ete admis pour une arthroplastie totale de la hanche au Nouveau-Brunswick au cours de la periode de 7 ans a l'etude, et 170 patients sont decedes dans les 30 jours. Nous n'avons pas observe de liens entre le volume d'activite du fournisseur de soins de sante et la mortalite postoperatoire dans nos modeles. L'ajustement pour tenir compte des caracteristiques contextuelles ou du volume d'activite de l'hopital n'a eu aucune incidence sur ce lien. Conclusion : Nos resultats suggerent que les patients hospitalises afin de subir une arthroplastie de la hanche au Nouveau-Brunswick peuvent s'attendre a un risque similaire de deces, peu importe que leur fournisseur de soins de sante pratique un volume faible ou eleve d'arthroplasties totales de la hanche ou que le patient soit admis dans un petit ou un grand hopital de la province., Extensive research has established that for some surgeries, higher provider caseload volume and/or higher hospital volumes are associated with lower risk of postoperative death. (1-3) This association is based on [...]

Published
2018
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156. Cross platform SCA component using C++ builder and KYLIX

Author

Nishimura, Hiroshi, Timossi, Chris, and McDonald, James L.

Subjects
Particle accelerators, EPICS SCA Component CLX
Abstract

A cross-platform component for EPICS Simple Channel Access (SCA) has been developed. EPICS client programs with GUI become portable at their C++ source-code level both on Windows and Linux by using Borland C++ Builder 6 and Kylix 3 on these platforms respectively.

Published
2003

163. Oncogenic Transformation Drives DNA Methylation Loss and Transcriptional Activation at Transposable Element Loci

Author

Kanholm, Tomas, primary, Rentia, Uzma, additional, Hadley, Melissa, additional, Karlow, Jennifer A., additional, Cox, Olivia L., additional, Diab, Noor, additional, Bendall, Matthew L., additional, Dawson, Tyson, additional, McDonald, James I., additional, Xie, Wenbing, additional, Crandall, Keith A., additional, Burns, Kathleen H., additional, Baylin, Stephen B., additional, Easwaran, Hari, additional, and Chiappinelli, Katherine B., additional

Published
2023
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167. Spatial patterns and environmental constraints on ecosystem services at a catchment scale

Author

Emmett, Bridget A., Cooper, David, Smart, Simon, Jackson, Bethanna, Thomas, Amy, Cosby, Bernard, Evans, Chris, Glanville, Helen, McDonald, James E., Malham, Shelagh K., Marshall, Miles, Jarvis, Susan, Rajko-Nenow, Paulina, Webb, Gearoid P., Ward, Sue, Rowe, Ed, Jones, Laurence, Vanbergen, Adam J., Keith, Aidan, Carter, Heather, Pereira, M. Glória, Hughes, Steve, Lebron, Inma, Wade, Andrew, and Jones, David L.

Published
2016
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175. Establishing an Online HIV Peer Helping Programme: A Review of Process Challenges and Lessons Learned

Author

Harris, Gregory E., Corcoran, Valerie, Myles, Adam, Lundrigan, Philip, White, Robert, Greidanus, Elaine, Savage, Stephanie L., Pope, Leslie, McDonald, James, and Yetman, Gerard

Abstract

Background: Online peer support can be a valuable approach to helping people living with HIV, especially in regions with large rural populations and relatively centralised HIV services. Design: This paper focuses on a community-university partnership aimed at developing an online peer support programme in the Canadian province of Newfoundland and Labrador. Setting: Team members included community representatives and people living with HIV from the AIDS Committee of Newfoundland and Labrador (ACNL) as well as academic researchers. Objectives: Goals and objectives of the programme included reaching disconnected people living with HIV, reducing isolation among people living with HIV and connecting people living with HIV with support, education and professional resources. Method and Results: Through a process orientated and iterative decision-making approach, the team established the website, peer helping training curriculum, a recruitment plan as well as other core considerations. The current paper emphasises several process challenges and lessons learned from the development stage of the online support programme. Conclusion: It is hoped that this information will assist others in avoiding or overcoming similar process challenges arising during such work.

Published
2015
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185. Removal of hydrophilic, hydrophobic, and charged xenobiotic organic compounds from greywater using green wall media

Author

Abd-ur-Rehman, Hafiz Muhammad, Prodanović, Veljko, Deletic, Ana, Khan, Stuart, McDonald, James, zhang, Kefeng, Abd-ur-Rehman, Hafiz Muhammad, Prodanović, Veljko, Deletic, Ana, Khan, Stuart, McDonald, James, and zhang, Kefeng

Abstract

Green walls offer a novel on-site approach for greywater treatment and reuse in densely build urban environments. However, they need to be engineered for effective removal of a wide range of emerging contaminants such as xenobiotic organic compounds (XOCs), which may be present in greywater due to extensive use of personal care products and household chemicals. This study used laboratory column design and batch experiments to investigate the performance of three lightweight green wall media (coco coir, zeolite, and perlite) and their mixture in three different combinations for the removal of twelve XOCs, covering wide range of hydrophilic, hydrophobic, and charged pollutants in greywater. The experiments were designed to assess the removal of targeted XOCs under different operational condition (i.e., hydraulic loading, infiltration rate, drying) and uncover the dominant mechanisms of their removal. Results showed excellent removal (>90%) of all XOCs in coco coir and media mix columns at the start of the experiment (i.e., fresh media and initial 2 pore volume (PV) of greywater dosing). The removal of highly hydrophobic and positively charged XOCs remained high (>90%) under all operational conditions, while hydrophilic and negatively charged XOCs exhibited significant reduction in removal after 25 PV and 50 PV, possibly due to their low adsorption affinity and electrostatic repulsion from negatively charged media. The effect of infiltration rate on the removal of XOCs was not significant; however, higher removal was achieved after 2-weeks of drying in coco coir and media mix columns. The dominant removal mechanism for most XOCs was found to be adsorption, however, a few hydrophilic XOCs (i.e., acetaminophen and atrazine) exhibited both adsorption and biodegradation removal processes. While findings showed promising prospects of unvegetated media for removing XOCs from greywater, long term studies on vegetated green wall systems are needed to understand any synergetic

Published
2023

186. Comparison of socio-economic determinants of COVID-19 testing and positivity in Canada:A multi-provincial analysis

Author

Antonova, Lilia, Somayaji, Chandy, Cameron, Jillian, Sirski, Monica, Sundaram, Maria E., McDonald, James Ted, Mishra, Sharmistha, Kwong, Jeffrey C., Katz, Alan, Baral, Stefan, Caulley, Lisa, Calzavara, Andrew, Corsten, Martin, Johnson-Obaseki, Stephanie, Antonova, Lilia, Somayaji, Chandy, Cameron, Jillian, Sirski, Monica, Sundaram, Maria E., McDonald, James Ted, Mishra, Sharmistha, Kwong, Jeffrey C., Katz, Alan, Baral, Stefan, Caulley, Lisa, Calzavara, Andrew, Corsten, Martin, and Johnson-Obaseki, Stephanie

Abstract

BACKGROUND: The effects of the COVID-19 pandemic have been more pronounced for socially disadvantaged populations. We sought to determine how access to SARS-CoV-2 testing and the likelihood of testing positive for COVID-19 were associated with demographic factors, socioeconomic status (SES) and social determinants of health (SDH) in three Canadian provinces. METHODS: An observational population-based cross-sectional study was conducted for the provinces of Ontario, Manitoba and New Brunswick between March 1, 2020 and April 27, 2021, using provincial health administrative data. After excluding residents of long-term care homes, those without current provincial health insurance and those who were tested for COVID-19 out of province, records from provincial healthcare administrative databases were reviewed for 16,900,661 healthcare users. Data was modelled separately for each province in accordance to a prespecified protocol and follow-up consultations among provincial statisticians and collaborators. We employed univariate and multivariate regression models to examine determinants of testing and test results. RESULTS: After adjustment for other variables, female sex and urban residency were positively associated with testing, while female sex was negatively associated with test positivity. In New Brunswick and Ontario, individuals living in higher income areas were more likely to be tested, whereas in Manitoba higher income was negatively associated with both testing and positivity. High ethnocultural composition was associated with lower testing rates. Both high ethnocultural composition and high situational vulnerability increased the odds of testing positive for SARS-CoV-2. DISCUSSION: We observed that multiple demographic, income and SDH factors were associated with SARS-CoV-2 testing and test positivity. Barriers to healthcare access identified in this study specifically relate to COVID-19 testing but may

Published
2023

187. Supplementary Figure from Epigenetic Therapies in Ovarian Cancer Alter Repetitive Element Expression in a TP53-Dependent Manner

Author

McDonald, James I., primary, Diab, Noor, primary, Arthofer, Elisa, primary, Hadley, Melissa, primary, Kanholm, Tomas, primary, Rentia, Uzma, primary, Gomez, Stephanie, primary, Yu, Angela, primary, Grundy, Erin E., primary, Cox, Olivia, primary, Topper, Michael J., primary, Xing, Xiaoyun, primary, Strissel, Pamela L., primary, Strick, Reiner, primary, Wang, Ting, primary, Baylin, Stephen B., primary, and Chiappinelli, Katherine B., primary

Published
2023
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188. Supplementary Table 1 from Assessment of Total Lesion Glycolysis by 18F FDG PET/CT Significantly Improves Prognostic Value of GEP and ISS in Myeloma

Author

McDonald, James E., primary, Kessler, Marcus M., primary, Gardner, Michael W., primary, Buros, Amy F., primary, Ntambi, James A., primary, Waheed, Sarah, primary, van Rhee, Frits, primary, Zangari, Maurizio, primary, Heuck, Christoph J., primary, Petty, Nathan, primary, Schinke, Carolina, primary, Thanendrarajan, Sharmilan, primary, Mitchell, Alan, primary, Hoering, Antje, primary, Barlogie, Bart, primary, Morgan, Gareth J., primary, and Davies, Faith E., primary

Published
2023
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189. Supplementary Figure/Table Legend from Assessment of Total Lesion Glycolysis by 18F FDG PET/CT Significantly Improves Prognostic Value of GEP and ISS in Myeloma

Author

McDonald, James E., primary, Kessler, Marcus M., primary, Gardner, Michael W., primary, Buros, Amy F., primary, Ntambi, James A., primary, Waheed, Sarah, primary, van Rhee, Frits, primary, Zangari, Maurizio, primary, Heuck, Christoph J., primary, Petty, Nathan, primary, Schinke, Carolina, primary, Thanendrarajan, Sharmilan, primary, Mitchell, Alan, primary, Hoering, Antje, primary, Barlogie, Bart, primary, Morgan, Gareth J., primary, and Davies, Faith E., primary

Published
2023
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190. Supplementary Table from Epigenetic Therapies in Ovarian Cancer Alter Repetitive Element Expression in a TP53-Dependent Manner

Author

McDonald, James I., primary, Diab, Noor, primary, Arthofer, Elisa, primary, Hadley, Melissa, primary, Kanholm, Tomas, primary, Rentia, Uzma, primary, Gomez, Stephanie, primary, Yu, Angela, primary, Grundy, Erin E., primary, Cox, Olivia, primary, Topper, Michael J., primary, Xing, Xiaoyun, primary, Strissel, Pamela L., primary, Strick, Reiner, primary, Wang, Ting, primary, Baylin, Stephen B., primary, and Chiappinelli, Katherine B., primary

Published
2023
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191. Data from Epigenetic Therapies in Ovarian Cancer Alter Repetitive Element Expression in a TP53-Dependent Manner

Author

McDonald, James I., primary, Diab, Noor, primary, Arthofer, Elisa, primary, Hadley, Melissa, primary, Kanholm, Tomas, primary, Rentia, Uzma, primary, Gomez, Stephanie, primary, Yu, Angela, primary, Grundy, Erin E., primary, Cox, Olivia, primary, Topper, Michael J., primary, Xing, Xiaoyun, primary, Strissel, Pamela L., primary, Strick, Reiner, primary, Wang, Ting, primary, Baylin, Stephen B., primary, and Chiappinelli, Katherine B., primary

Published
2023
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192. Supplementary Data from Epigenetic Therapies in Ovarian Cancer Alter Repetitive Element Expression in a TP53-Dependent Manner

Author

McDonald, James I., primary, Diab, Noor, primary, Arthofer, Elisa, primary, Hadley, Melissa, primary, Kanholm, Tomas, primary, Rentia, Uzma, primary, Gomez, Stephanie, primary, Yu, Angela, primary, Grundy, Erin E., primary, Cox, Olivia, primary, Topper, Michael J., primary, Xing, Xiaoyun, primary, Strissel, Pamela L., primary, Strick, Reiner, primary, Wang, Ting, primary, Baylin, Stephen B., primary, and Chiappinelli, Katherine B., primary

Published
2023
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193. Supplementary Figure 1 from Assessment of Total Lesion Glycolysis by 18F FDG PET/CT Significantly Improves Prognostic Value of GEP and ISS in Myeloma

Author

McDonald, James E., primary, Kessler, Marcus M., primary, Gardner, Michael W., primary, Buros, Amy F., primary, Ntambi, James A., primary, Waheed, Sarah, primary, van Rhee, Frits, primary, Zangari, Maurizio, primary, Heuck, Christoph J., primary, Petty, Nathan, primary, Schinke, Carolina, primary, Thanendrarajan, Sharmilan, primary, Mitchell, Alan, primary, Hoering, Antje, primary, Barlogie, Bart, primary, Morgan, Gareth J., primary, and Davies, Faith E., primary

Published
2023
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200. A communal catalogue reveals Earths multiscale microbial diversity

Author

Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vzquez-Baeza, Yoshiki, Gonzlez, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Barta, Jiri, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Monica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frederic, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibanez-Alamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martin-Platero, Antonio M., Martin-Vivaldi, Manuel, Martinez, L. Margarita, Martinez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Monica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, OBrien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sanchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjoling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia

Subjects
Biological diversity -- Observations -- Environmental aspects, Microbial colonies -- Environmental aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Our growing awareness of the microbial worlds importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earths microbial diversity., Author(s): Luke R. Thompson [1, 2, 3]; Jon G. Sanders [1]; Daniel McDonald [1]; Amnon Amir [1]; Joshua Ladau [4]; Kenneth J. Locey [5]; Robert J. Prill [6]; Anupriya Tripathi [...]

Published
2017
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