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2. Semantic Segmentation for Fully Automated Macrofouling Analysis on Coatings after Field Exposure

Author

Krause, Lutz M. K., Manderfeld, Emily, Gnutt, Patricia, Vogler, Louisa, Wassick, Ann, Richard, Kailey, Rudolph, Marco, Hunsucker, Kelli Z., Swain, Geoffrey W., Rosenhahn, Bodo, and Rosenhahn, Axel

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning
Abstract

Biofouling is a major challenge for sustainable shipping, filter membranes, heat exchangers, and medical devices. The development of fouling-resistant coatings requires the evaluation of their effectiveness. Such an evaluation is usually based on the assessment of fouling progression after different exposure times to the target medium (e.g., salt water). The manual assessment of macrofouling requires expert knowledge about local fouling communities due to high variances in phenotypical appearance, has single-image sampling inaccuracies for certain species, and lacks spatial information. Here we present an approach for automatic image-based macrofouling analysis. We created a dataset with dense labels prepared from field panel images and propose a convolutional network (adapted U-Net) for the semantic segmentation of different macrofouling classes. The establishment of macrofouling localization allows for the generation of a successional model which enables the determination of direct surface attachment and in-depth epibiotic studies., Comment: 33 pages, 10 figures

Published
2022

4. Autism-related dietary preferences mediate autism-gut microbiome associations

Author

Yap, Chloe X., Henders, Anjali K., Alvares, Gail A., Wood, David L.A., Krause, Lutz, Tyson, Gene W., Restuadi, Restuadi, Wallace, Leanne, McLaren, Tiana, Hansell, Narelle K., Cleary, Dominique, Grove, Rachel, Hafekost, Claire, Harun, Alexis, Holdsworth, Helen, Jellett, Rachel, Khan, Feroza, Lawson, Lauren P., Leslie, Jodie, Frenk, Mira Levis, Masi, Anne, Mathew, Nisha E., Muniandy, Melanie, Nothard, Michaela, Miller, Jessica L., Nunn, Lorelle, Holtmann, Gerald, Strike, Lachlan T., de Zubicaray, Greig I., Thompson, Paul M., McMahon, Katie L., Wright, Margaret J., Visscher, Peter M., Dawson, Paul A., Dissanayake, Cheryl, Eapen, Valsamma, Heussler, Helen S., McRae, Allan F., Whitehouse, Andrew J.O., Wray, Naomi R., and Gratten, Jacob

Published
2021
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6. Autism-related dietary preferences mediate autism-gut microbiome associations

Author

Yap, Chloe X., primary, Henders, Anjali K., additional, Alvares, Gail A., additional, Wood, David L.A., additional, Krause, Lutz, additional, Tyson, Gene W., additional, Restuadi, Restuadi, additional, Wallace, Leanne, additional, McLaren, Tiana, additional, Hansell, Narelle K., additional, Cleary, Dominique, additional, Grove, Rachel, additional, Hafekost, Claire, additional, Harun, Alexis, additional, Holdsworth, Helen, additional, Jellett, Rachel, additional, Khan, Feroza, additional, Lawson, Lauren P., additional, Leslie, Jodie, additional, Frenk, Mira Levis, additional, Masi, Anne, additional, Mathew, Nisha E., additional, Muniandy, Melanie, additional, Nothard, Michaela, additional, Miller, Jessica L., additional, Nunn, Lorelle, additional, Holtmann, Gerald, additional, Strike, Lachlan T., additional, de Zubicaray, Greig I., additional, Thompson, Paul M., additional, McMahon, Katie L., additional, Wright, Margaret J., additional, Visscher, Peter M., additional, Dawson, Paul A., additional, Dissanayake, Cheryl, additional, Eapen, Valsamma, additional, Heussler, Helen S., additional, McRae, Allan F., additional, Whitehouse, Andrew J.O., additional, Wray, Naomi R., additional, and Gratten, Jacob, additional

Published
2024
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15. The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes

Author

Overbeek, Ross, Begley, Tadhg, Butler, Ralph M, Choudhuri, Jomuna V, Chuang, Han-Yu, Cohoon, Matthew, de Crécy-Lagard, Valérie, Diaz, Naryttza, Disz, Terry, Edwards, Robert, Fonstein, Michael, Frank, Ed D, Gerdes, Svetlana, Glass, Elizabeth M, Goesmann, Alexander, Hanson, Andrew, Iwata-Reuyl, Dirk, Jensen, Roy, Jamshidi, Neema, Krause, Lutz, Kubal, Michael, Larsen, Niels, Linke, Burkhard, McHardy, Alice C, Meyer, Folker, Neuweger, Heiko, Olsen, Gary, Olson, Robert, Osterman, Andrei, Portnoy, Vasiliy, Pusch, Gordon D, Rodionov, Dmitry A, Rückert, Christian, Steiner, Jason, Stevens, Rick, Thiele, Ines, Vassieva, Olga, Ye, Yuzhen, Zagnitko, Olga, and Vonstein, Veronika

Subjects
Biotechnology, Acyl Coenzyme A, Coenzyme A, Computational Biology, Genome, Archaeal, Genome, Bacterial, Genomics, Internet, Leucine, Ribosomal Proteins, Software, Terminology as Topic, Vocabulary, Controlled, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Developmental Biology
Abstract

The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms.

Published
2005

17. Figure S3 from Identification of a Novel, EBV-Based Antibody Risk Stratification Signature for Early Detection of Nasopharyngeal Carcinoma in Taiwan

Author

Coghill, Anna E., primary, Pfeiffer, Ruth M., primary, Proietti, Carla, primary, Hsu, Wan-Lun, primary, Chien, Yin-Chu, primary, Lekieffre, Lea, primary, Krause, Lutz, primary, Teng, Andy, primary, Pablo, Jocelyn, primary, Yu, Kelly J., primary, Lou, Pei-Jen, primary, Wang, Cheng-Ping, primary, Liu, Zhiwei, primary, Chen, Chien-Jen, primary, Middeldorp, Jaap, primary, Mulvenna, Jason, primary, Bethony, Jeff, primary, Hildesheim, Allan, primary, and Doolan, Denise L., primary

Published
2023
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18. Tables S2-S4 from Identification of a Novel, EBV-Based Antibody Risk Stratification Signature for Early Detection of Nasopharyngeal Carcinoma in Taiwan

Author

Coghill, Anna E., primary, Pfeiffer, Ruth M., primary, Proietti, Carla, primary, Hsu, Wan-Lun, primary, Chien, Yin-Chu, primary, Lekieffre, Lea, primary, Krause, Lutz, primary, Teng, Andy, primary, Pablo, Jocelyn, primary, Yu, Kelly J., primary, Lou, Pei-Jen, primary, Wang, Cheng-Ping, primary, Liu, Zhiwei, primary, Chen, Chien-Jen, primary, Middeldorp, Jaap, primary, Mulvenna, Jason, primary, Bethony, Jeff, primary, Hildesheim, Allan, primary, and Doolan, Denise L., primary

Published
2023
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19. Supplemental Methods from Identification of a Novel, EBV-Based Antibody Risk Stratification Signature for Early Detection of Nasopharyngeal Carcinoma in Taiwan

Author

Coghill, Anna E., primary, Pfeiffer, Ruth M., primary, Proietti, Carla, primary, Hsu, Wan-Lun, primary, Chien, Yin-Chu, primary, Lekieffre, Lea, primary, Krause, Lutz, primary, Teng, Andy, primary, Pablo, Jocelyn, primary, Yu, Kelly J., primary, Lou, Pei-Jen, primary, Wang, Cheng-Ping, primary, Liu, Zhiwei, primary, Chen, Chien-Jen, primary, Middeldorp, Jaap, primary, Mulvenna, Jason, primary, Bethony, Jeff, primary, Hildesheim, Allan, primary, and Doolan, Denise L., primary

Published
2023
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20. Table S1 from Identification of a Novel, EBV-Based Antibody Risk Stratification Signature for Early Detection of Nasopharyngeal Carcinoma in Taiwan

Author

Coghill, Anna E., primary, Pfeiffer, Ruth M., primary, Proietti, Carla, primary, Hsu, Wan-Lun, primary, Chien, Yin-Chu, primary, Lekieffre, Lea, primary, Krause, Lutz, primary, Teng, Andy, primary, Pablo, Jocelyn, primary, Yu, Kelly J., primary, Lou, Pei-Jen, primary, Wang, Cheng-Ping, primary, Liu, Zhiwei, primary, Chen, Chien-Jen, primary, Middeldorp, Jaap, primary, Mulvenna, Jason, primary, Bethony, Jeff, primary, Hildesheim, Allan, primary, and Doolan, Denise L., primary

Published
2023
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24. Complex structural rearrangements are present in high-grade dysplastic Barrett’s oesophagus samples

Author

Newell, Felicity, Patel, Kalpana, Gartside, Michael, Krause, Lutz, Brosda, Sandra, Aoude, Lauren G., Loffler, Kelly A., Bonazzi, Vanessa F., Patch, Ann-Marie, Kazakoff, Stephen H., Holmes, Oliver, Xu, Qinying, Wood, Scott, Leonard, Conrad, Lampe, Guy, Lord, Reginald V., Whiteman, David C., Pearson, John V., Nones, Katia, Waddell, Nicola, and Barbour, Andrew P.

Published
2019
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30. Administration of Hookworm Excretory/Secretory Proteins Improves Glucose Tolerance in a Mouse Model of Type 2 Diabetes

Author

Khudhair, Zainab, Alhallaf, Rafid, Eichenberger, Ramon M, Field, Matt, Krause, Lutz, Sotillo, Javier, Loukas, Alex, Eichenberger, Ramon M., University of Zurich, Loukas, Alex, National Health and Medical Research Council (Australia), Australian Research Council, Australian Institute of Tropical Health and Medicine, and James Cook University (Australia)

Subjects
10078 Institute of Parasitology, Ancylostomatoidea, T helper 2, 1303 Biochemistry, Interleukin-6, Diabetes, 610 Medicine & health, Biochemistry, M2 macrophage, Eosinophils, Nippostrongylus, helminth, diabetes, excretory/secretory products, eosinophils, Disease Models, Animal, Mice, Glucose, Excretory/secretory products, Diabetes Mellitus, Type 2, 600 Technology, Helminth, 1312 Molecular Biology, 570 Life sciences, biology, Animals, Insulin Resistance, Molecular Biology
Abstract

Diabetes is recognised as the world's fastest growing chronic condition globally. Helminth infections have been shown to be associated with a lower prevalence of type 2 diabetes (T2D), in part due to their ability to induce a type 2 immune response. Therefore, to understand the molecular mechanisms that underlie the development of T2D-induced insulin resistance, we treated mice fed on normal or diabetes-promoting diets with excretory/secretory products (ES) from the gastrointestinal helminth Nippostrongylus brasiliensis. We demonstrated that treatment with crude ES products from adult worms (AES) or infective third-stage larvae (L3ES) from N. brasiliensis improved glucose tolerance and attenuated body weight gain in mice fed on a high glycaemic index diet. N. brasiliensis ES administration to mice was associated with a type 2 immune response measured by increased eosinophils and IL-5 in peripheral tissues but not IL-4, and with a decrease in the level of IL-6 in adipose tissue and corresponding increase in IL-6 levels in the liver. Moreover, treatment with AES or L3ES was associated with significant changes in the community composition of the gut microbiota at the phylum and order levels. These data highlight a role for N. brasiliensis ES in modulating the immune response associated with T2D, and suggest that N. brasiliensis ES contain molecules with therapeutic potential for treating metabolic syndrome and T2D. This research was supported by a program grant from the National Health and Medical Research Council (1132975), and a strategic research initiative award from the Australian Research Council to The Australian Institute of Tropical Health and Medicine at James Cook University (SRI40200003). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Sí

Published
2022

31. Administration of Hookworm Excretory/Secretory Proteins Improves Glucose Tolerance in a Mouse Model of Type 2 Diabetes

Author

Khudhair, Zainab; https://orcid.org/0000-0003-0294-5385, Alhallaf, Rafid, Eichenberger, Ramon M; https://orcid.org/0000-0002-9337-9616, Field, Matt; https://orcid.org/0000-0003-0788-6513, Krause, Lutz, Sotillo, Javier; https://orcid.org/0000-0002-1443-7233, Loukas, Alex; https://orcid.org/0000-0002-0896-8441, Khudhair, Zainab; https://orcid.org/0000-0003-0294-5385, Alhallaf, Rafid, Eichenberger, Ramon M; https://orcid.org/0000-0002-9337-9616, Field, Matt; https://orcid.org/0000-0003-0788-6513, Krause, Lutz, Sotillo, Javier; https://orcid.org/0000-0002-1443-7233, and Loukas, Alex; https://orcid.org/0000-0002-0896-8441

Abstract

Diabetes is recognised as the world’s fastest growing chronic condition globally. Helminth infections have been shown to be associated with a lower prevalence of type 2 diabetes (T2D), in part due to their ability to induce a type 2 immune response. Therefore, to understand the molecular mechanisms that underlie the development of T2D-induced insulin resistance, we treated mice fed on normal or diabetes-promoting diets with excretory/secretory products (ES) from the gastrointestinal helminth Nippostrongylus brasiliensis. We demonstrated that treatment with crude ES products from adult worms (AES) or infective third-stage larvae (L3ES) from N. brasiliensis improved glucose tolerance and attenuated body weight gain in mice fed on a high glycaemic index diet. N. brasiliensis ES administration to mice was associated with a type 2 immune response measured by increased eosinophils and IL-5 in peripheral tissues but not IL-4, and with a decrease in the level of IL-6 in adipose tissue and corresponding increase in IL-6 levels in the liver. Moreover, treatment with AES or L3ES was associated with significant changes in the community composition of the gut microbiota at the phylum and order levels. These data highlight a role for N. brasiliensis ES in modulating the immune response associated with T2D, and suggest that N. brasiliensis ES contain molecules with therapeutic potential for treating metabolic syndrome and T2D.

Published
2022

32. Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma

Author

Krause, Lutz, Nones, Katia, Loffler, Kelly A., Nancarrow, Derek, Oey, Harald, Tang, Yue Hang, Wayte, Nicola J., Patch, Ann Marie, Patel, Kalpana, Brosda, Sandra, Manning, Suzanne, Lampe, Guy, Clouston, Andrew, Thomas, Janine, Stoye, Jens, Hussey, Damian J., Watson, David I., Lord, Reginald V., Phillips, Wayne A., Gotley, David, Smithers, B.Mark, Whiteman, David C., Hayward, Nicholas K., Grimmond, Sean M., Waddell, Nicola, and Barbour, Andrew P.

Published
2016
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34. Autism-related dietary preferences mediate autism-gut microbiome associations

Author

Yap, Chloe X, Henders, Anjali K, Alvares, Gail A, Wood, David L A, Krause, Lutz, Tyson, Gene W, Restuadi, Restuadi, Wallace, Leanne, McLaren, Tiana, Hansell, Narelle K, Cleary, Dominique, Grove, Rachel, Hafekost, Claire, Harun, Alexis, Holdsworth, Helen, Jellett, Rachel, Khan, Feroza, Lawson, Lauren P, Leslie, Jodie, Frenk, Mira Levis, Masi, Anne, Mathew, Nisha E, Muniandy, Melanie, Nothard, Michaela, Miller, Jessica L, Nunn, Lorelle, Holtmann, Gerald, Strike, Lachlan T, de Zubicaray, Greig I, Thompson, Paul M, McMahon, Katie L, Wright, Margaret J, Visscher, Peter M, Dawson, Paul A, Dissanayake, Cheryl, Eapen, Valsamma, Heussler, Helen S, McRae, Allan F, Whitehouse, Andrew J O, Wray, Naomi R, Gratten, Jacob, Yap, Chloe X, Henders, Anjali K, Alvares, Gail A, Wood, David L A, Krause, Lutz, Tyson, Gene W, Restuadi, Restuadi, Wallace, Leanne, McLaren, Tiana, Hansell, Narelle K, Cleary, Dominique, Grove, Rachel, Hafekost, Claire, Harun, Alexis, Holdsworth, Helen, Jellett, Rachel, Khan, Feroza, Lawson, Lauren P, Leslie, Jodie, Frenk, Mira Levis, Masi, Anne, Mathew, Nisha E, Muniandy, Melanie, Nothard, Michaela, Miller, Jessica L, Nunn, Lorelle, Holtmann, Gerald, Strike, Lachlan T, de Zubicaray, Greig I, Thompson, Paul M, McMahon, Katie L, Wright, Margaret J, Visscher, Peter M, Dawson, Paul A, Dissanayake, Cheryl, Eapen, Valsamma, Heussler, Helen S, McRae, Allan F, Whitehouse, Andrew J O, Wray, Naomi R, and Gratten, Jacob

Abstract

There is increasing interest in the potential contribution of the gut microbiome to autism spectrum disorder (ASD). However, previous studies have been underpowered and have not been designed to address potential confounding factors in a comprehensive way. We performed a large autism stool metagenomics study (n = 247) based on participants from the Australian Autism Biobank and the Queensland Twin Adolescent Brain project. We found negligible direct associations between ASD diagnosis and the gut microbiome. Instead, our data support a model whereby ASD-related restricted interests are associated with less-diverse diet, and in turn reduced microbial taxonomic diversity and looser stool consistency. In contrast to ASD diagnosis, our dataset was well powered to detect microbiome associations with traits such as age, dietary intake, and stool consistency. Overall, microbiome differences in ASD may reflect dietary preferences that relate to diagnostic features, and we caution against claims that the microbiome has a driving role in ASD.

Published
2021

35. Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome

Author

Parks, Donovan H, Rigato, Fabio, Vera-Wolf, Patricia, Krause, Lutz, Hugenholtz, Philip, Tyson, Gene W, Wood, David L.A., Parks, Donovan H, Rigato, Fabio, Vera-Wolf, Patricia, Krause, Lutz, Hugenholtz, Philip, Tyson, Gene W, and Wood, David L.A.

Abstract

A fundamental goal of microbial ecology is to accurately determine the species composition in a given microbial ecosystem. In the context of the human microbiome, this is important for establishing links between microbial species and disease states. Here we benchmark the Microba Community Profiler (MCP) against other metagenomic classifiers using 140 moderate to complex in silico microbial communities and a standardized reference genome database. MCP generated accurate relative abundance estimates and made substantially fewer false positive predictions than other classifiers while retaining a high recall rate. We further demonstrated that the accuracy of species classification was substantially increased using the Microba Genome Database, which is more comprehensive than reference datasets used by other classifiers and illustrates the importance of including genomes of uncultured taxa in reference databases. Consequently, MCP classifies appreciably more reads than other classifiers when using their recommended reference databases. These results establish MCP as best-in-class with the ability to produce comprehensive and accurate species profiles of human gastrointestinal samples.

Published
2021

36. Gastrointestinal Helminth Infection Improves Insulin Sensitivity, Decreases Systemic Inflammation, and Alters the Composition of Gut Microbiota in Distinct Mouse Models of Type 2 Diabetes

Author

Khudhair, Zainab, Alhallaf, Rafid, Eichenberger, Ramon M, Whan, Jen, Kupz, Andreas, Field, Matthew, Krause, Lutz, Wilson, David T, Daly, Norelle L, Giacomin, Paul, Sotillo, Javier, Loukas, Alex, Khudhair, Zainab, Alhallaf, Rafid, Eichenberger, Ramon M, Whan, Jen, Kupz, Andreas, Field, Matthew, Krause, Lutz, Wilson, David T, Daly, Norelle L, Giacomin, Paul, Sotillo, Javier, and Loukas, Alex

Abstract

Type 2 diabetes (T2D) is a major health problem and is considered one of the top 10 diseases leading to death globally. T2D has been widely associated with systemic and local inflammatory responses and with alterations in the gut microbiota. Microorganisms, including parasitic worms and gut microbes have exquisitely co-evolved with their hosts to establish an immunological interaction that is essential for the formation and maintenance of a balanced immune system, including suppression of excessive inflammation. Herein we show that both prophylactic and therapeutic infection of mice with the parasitic hookworm-like nematode, Nippostrongylus brasiliensis, significantly reduced fasting blood glucose, oral glucose tolerance and body weight gain in two different diet-induced mouse models of T2D. Helminth infection was associated with elevated type 2 immune responses including increased eosinophil numbers in the mesenteric lymph nodes, liver and adipose tissues, as well as increased expression of IL-4 and alternatively activated macrophage marker genes in adipose tissue, liver and gut. N. brasiliensis infection was also associated with significant compositional changes in the gut microbiota at both the phylum and order levels. Our findings show that N. brasiliensis infection drives changes in local and systemic immune cell populations, and that these changes are associated with a reduction in systemic and local inflammation and compositional changes in the gut microbiota which cumulatively might be responsible for the improved insulin sensitivity observed in infected mice. Our findings indicate that carefully controlled therapeutic hookworm infection in humans could be a novel approach for treating metabolic syndrome and thereby preventing T2D.

Published
2021

41. The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology

Author

Schlüter, Andreas, Bekel, Thomas, Diaz, Naryttza N., Dondrup, Michael, Eichenlaub, Rudolf, Gartemann, Karl-Heinz, Krahn, Irene, Krause, Lutz, Krömeke, Holger, Kruse, Olaf, Mussgnug, Jan H., Neuweger, Heiko, Niehaus, Karsten, Pühler, Alfred, Runte, Kai J., Szczepanowski, Rafael, Tauch, Andreas, Tilker, Alexandra, Viehöver, Prisca, and Goesmann, Alexander

Published
2008
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42. The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis

Author

Vorhölter, Frank-Jörg, Schneiker, Susanne, Goesmann, Alexander, Krause, Lutz, Bekel, Thomas, Kaiser, Olaf, Linke, Burkhard, Patschkowski, Thomas, Rückert, Christian, Schmid, Joachim, Sidhu, Vishaldeep Kaur, Sieber, Volker, Tauch, Andreas, Watt, Steven Alexander, Weisshaar, Bernd, Becker, Anke, Niehaus, Karsten, and Pühler, Alfred

Published
2008
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45. The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp, michiganensis NCPPB382 reveals a large island involved in pathogenicity

Author

Gartemann, Karl-Heinz, Abt, Birte, Bekel, Thomas, Burger, Annette, Engemann, Jutta, Flugel, Monika, Gaigalat, Lars, Goesmann, Alexander, Grafen, Ines, Kalinowski, Jorn, Kaup, Olaf, Kirchner, Oliver, Krause, Lutz, Linke, Burkhard, McHardy, Alice, Meyer, Folker, Pohle, Sandra, Ruckert, Christian, Schneiker, Susanne, Zellermann, Eva-Maria, Puhler, Alfred, Eichenlaub, Rudolf, Kaiser, Olaf, and Bartels, Daniela

Subjects
Bacteria, Pathogenic -- Genetic aspects, Tomatoes -- Diseases and pests, Biological sciences
Abstract

Clavibacter michiganensis subsp, michiganensis is a plant-pathogenic actinomycete that causes bacterial wilt and canker of tomato. The nucleotide sequence of the genome of strain NCPPB382 was determined. The chromosome is circular, consists of 3.298 Mb, and has a high G+C content (72.6%). Annotation revealed 3,080 putative protein-encoding sequences; only 26 pseudogenes were detected. Two rrn operons, 45 tRNAs, and three small stable RNA genes were found. The two circular plasmids, pCM1 (27.4 kbp) and pCM2 (70.0 kbp), which carry pathogenicity genes and thus are essential for virulence, have lower G+C contents (66.5 and 67.6%, respectively). In contrast to the genome of the closely related organism Ciavibacter michiganensis subsp. sepedonicus, the genome of C. michiganensis subsp, michiganensis lacks complete insertion elements and transposons. The 129-kb chp/tomA region with a low G+C content near the chromosomal origin of replication was shown to be necessary for pathogenicity. This region contains numerous genes encoding proteins involved in uptake and metabolism of sugars and several serine proteases. There is evidence that single genes located in this region, especially genes encoding serine proteases, are required for efficient colonization of the host. Although C. michiganensis subsp, michiganensis grows mainly in the xylem of tomato plants, no evidence for pronounced genome reduction was found. C. michiganensis subsp, michiganensis seems to have as many transporters and regulators as typical soil-inhabiting bacteria. However, the apparent lack of a sulfate reduction pathway, which makes C. michiganensis subsp, michiganensis dependent on reduced sulfur compounds for growth, is probably the reason for the poor survival of C. michiganensis subsp, michiganensis in soil.

Published
2008

46. Erratum: Identification of a novel, EBV-based antibody risk stratification signature for early detection of nasopharyngeal carcinoma in Taiwan (Clinical Cancer Research (2018) 24 (1305–1314) DOI: 10.1158/1078-0432.CCR-17-1929)

Author

Coghill, Anna E., Pfeiffer, Ruth M., Proietti, Carla, Hsu, Wan Lun, Chien, Yin Chu, Lekieffre, Lea, Krause, Lutz, Teng, Andy, Pablo, Jocelyn, Yu, Kelly J., Lou, Pei Jen, Wang, Cheng Ping, Liu, Zhiwei, Chen, Chien Jen, Middeldorp, Jaap, Mulvenna, Jason, Bethony, Jeff, Hildesheim, Allan, Doolan, Denise L., AII - Infectious diseases, and CCA - Cancer biology and immunology

Abstract

In the original version of this article (1), the left panel of Fig. 2 was incorrectly labeled: the BFRF1 IgG antibody was incorrectly labeled as the BALF2 IgG antibody, and the corresponding sentence in the text was also incorrect. These errors have been corrected in the latest online HTML and PDF versions of the article. The authors regret these errors.

Published
2020

47. Additional file 2 of Infection with the sheep gastrointestinal nematode Teladorsagia circumcincta increases luminal pathobionts

Author

Cortés, Alba, Wills, John, Xiaopei Su, Hewitt, Rachel E., Robertson, Jack, Scotti, Riccardo, Price, Daniel R. G., Bartley, Yvonne, McNeilly, Tom N., Krause, Lutz, Powell, Jonathan J., Nisbet, Alasdair J., and Cantacessi, Cinzia

Abstract

Additional file 2. CellProfiler pipeline. Details of every step of all 40 modules used to perform the image analysis using the CellProfiler software.

Published
2020
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