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2. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.

Author

Yooseph, S, Sutton, G, Rusch, DB, Halpern, AL, Williamson, SJ, Remington, K, Eisen, JA, Heidelberg, KB, Manning, G, Li, W, Jaroszewski, L, Cieplak, P, Miller, CS, Li, H, Mashiyama, ST, Joachimiak, MP, van Belle, C, Chandonia, JM, Soergel, DA, Zhai, Y, Natarajan, K, Lee, S, Raphael, BJ, Bafna, V, Friedman, R, Brenner, SE, Godzik, A, Eisenberg, D, Dixon, JE, Taylor, SS, Strausberg, RL, Frazier, M, and Venter, JC

Subjects
Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a comprehensive dataset consisting of sequences from available databases together with 6.12 million proteins predicted from an assembly of 7.7 million Global Ocean Sampling (GOS) sequences. The GOS dataset covers nearly all known prokaryotic protein families. A total of 3,995 medium- and large-sized clusters consisting of only GOS sequences are identified, out of which 1,700 have no detectable homology to known families. The GOS-only clusters contain a higher than expected proportion of sequences of viral origin, thus reflecting a poor sampling of viral diversity until now. Protein domain distributions in the GOS dataset and current protein databases show distinct biases. Several protein domains that were previously categorized as kingdom specific are shown to have GOS examples in other kingdoms. About 6,000 sequences (ORFans) from the literature that heretofore lacked similarity to known proteins have matches in the GOS data. The GOS dataset is also used to improve remote homology detection. Overall, besides nearly doubling the number of current proteins, the predicted GOS proteins also add a great deal of diversity to known protein families and shed light on their evolution. These observations are illustrated using several protein families, including phosphatases, proteases, ultraviolet-irradiation DNA damage repair enzymes, glutamine synthetase, and RuBisCO. The diversity added by GOS data has implications for choosing targets for experimental structure characterization as part of structural genomics efforts. Our analysis indicates that new families are being discovered at a rate that is linear or almost linear with the addition of new sequences, implying that we are still far from discovering all protein families in nature.

Published
2007

4. Ca2+-dependent liquid-liquid phase separation underlies intracellular Ca2+ stores

Author

Joshua E. Mayfield, Dixon Je, Alexandra C. Newton, Worby Ca, Junqian Xu, Tandon, and Pollak Aj

Subjects
chemistry.chemical_classification, medicine.anatomical_structure, chemistry, Kinase, Endoplasmic reticulum, Binding protein, medicine, Biophysics, Phosphorylation, Skeletal muscle, Intracellular, Secretory pathway, Divalent
Abstract

Endoplasmic/sarcoplasmic reticulum Ca2+ stores are essential to myriad cellular processes, however, the structure of these stores is largely unknown and existing models neither explain observations made in vivo nor sufficiently account for physiological data. We investigate CASQ1 - the major Ca2+ binding protein of skeletal muscle – and discover Ca2+-dependent liquid-liquid phase separation activity. The intrinsic disorder of CASQ1 underlies this activity and is regulated via phosphorylation by the secretory pathway kinase FAM20C. This novel divalent cation driven condensation demonstrates liquid-liquid phase separation occurs within the endoplasmic/sarcoplasmic reticulum, mechanistically explains efficient Ca2+ buffering and storage, and represents a largely unexplored mechanism of divalent-cation driven protein association.

Published
2021

5. SARS-CoV-2 spike RBD and nucleocapsid encoding DNA vaccine elicits T cell and neutralising antibody responses that cross react with variants

Author

Brentville, VA, primary, Vankemmelbeke, M, additional, Metheringham, RL, additional, Symonds, P, additional, Cook, KW, additional, Urbanowicz, RA, additional, Tsoleridis, T, additional, Coleman, CM, additional, Chang, K-C, additional, Skinner, A, additional, Dubinina, E, additional, Daniels, I, additional, Shah, S, additional, Argonza, M, additional, Delgado, J, additional, Dwivedi, V, additional, Kulkarni, V, additional, Dixon, JE, additional, Pockley, AG, additional, Adams, SE, additional, Paston, SJ, additional, Daly, JM, additional, Ball, JK, additional, and Durrant, LG, additional

Published
2021
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6. References

Author

Dixon, Jeremy

Published
2023

7. Conclusion

Author

Dixon, Jeremy

Published
2023

9. Index

Author

Dixon, Jeremy

Published
2023

10. Notes

Author

Dixon, Jeremy

Published
2023

20. Widespread dynamic DNA methylation in response to biotic stress

Author

Dowen, R, Pelizzola, M, Schmitz, R, Lister, R, Dowen, J, Nery, J, Dixon, J, Ecker, J, Dowen, RH, Schmitz, RJ, Dowen, JM, Nery, JR, Dixon, JE, Ecker, JR, Dowen, R, Pelizzola, M, Schmitz, R, Lister, R, Dowen, J, Nery, J, Dixon, J, Ecker, J, Dowen, RH, Schmitz, RJ, Dowen, JM, Nery, JR, Dixon, JE, and Ecker, JR

Abstract

Regulation of gene expression by DNA methylation is crucial for defining cellular identities and coordinating organism-wide developmental programs in many organisms. In plants, modulation of DNA methylation in response to environmental conditions represents a potentially robust mechanism to regulate gene expression networks; however, examples of dynamic DNA methylation are largely limited to gene imprinting. Here we report an unexpected role for DNA methylation in regulation of the Arabidopsis thaliana immune system. Profiling the DNA methylomes of plants exposed to bacterial pathogen, avirulent bacteria, or salicylic acid (SA) hormone revealed numerous stress-induced differentially methylated regions, many of which were intimately associated with differentially expressed genes. In response to SA, transposon-associated differentially methylated regions, which were accompanied by upregulation of 21-nt siRNAs, were often coupled to transcriptional changes of the transposon and/or the proximal gene. Thus, dynamic DNA methylation changes within repetitive sequences or transposons can regulate neighboring genes in response to SA stress.

Published
2012

22. A Mutation in Adenylosuccinate Lyase Associated With Mental-retardation and Autistic Features

Author

UCL - MD/BICL - Département de biochimie et de biologie cellulaire, Stone, RL., Aimi, J., Barshop, BA., Jaeken, J., Van den Berghe, Georges, Zalkin, H., Dixon, JE., UCL - MD/BICL - Département de biochimie et de biologie cellulaire, Stone, RL., Aimi, J., Barshop, BA., Jaeken, J., Van den Berghe, Georges, Zalkin, H., and Dixon, JE.

Abstract

We have examined the molecular basis of three cases of severe mental retardation with autistic features in one family. A point mutation in a purine nucleotide biosynthetic enzyme, adenylosuccinate lyase (ASL), segregates with the disorder. The affected children are homozygous for the point mutation while the parents and all four unaffected children are heterozygous. The point mutation is absent in control subjects. The point mutation results in a Ser413Pro substitution which leads to structural instability of the recombinant mutant enzyme, and this instability lowers ASL levels in lymphocytes. These observations suggest that the instability of ASL underlies the severe developmental disorder in the affected children, and that mutations in the ASL gene may result in other cases of mental retardation and autistic features.

Published
1992

24. Chapter 5 Doing adult safeguarding with service users and carers

Author

Dixon, Jeremy

Subjects
Adult protection, Care act 2014, Risk and uncertainty, Safeguarding, Social work, bic Book Industry Communication::J Society & social sciences::JH Sociology & anthropology::JHB Sociology, bic Book Industry Communication::J Society & social sciences::JK Social services & welfare, criminology::JKS Social welfare & social services::JKSN Social work
Abstract

Chapters 1, 3 and 5 are available Open Access under CC-BY licence. Safeguarding adults at risk of abuse or neglect is a core area of social work practice but knowledge of how social workers make adult safeguarding decisions is limited. Applying recent sociological and ethnographic research to this area for the first time, this book considers how adult safeguarding practice is developing, with a focus on risk management. The author explores how social workers conduct safeguarding adults assessments, work with multiple agencies and involve service users in risk decisions. The book is essential reading for those wishing to understand how risk and uncertainty are managed within frontline adult social work and how current practice can be improved.

Published
2023
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25. Chapter 3 Referrals and Assessments

Author

Dixon, Jeremy

Subjects
Adult protection, Care act 2014, Risk and uncertainty, Safeguarding, Social work, bic Book Industry Communication::J Society & social sciences::JH Sociology & anthropology::JHB Sociology, bic Book Industry Communication::J Society & social sciences::JK Social services & welfare, criminology::JKS Social welfare & social services::JKSN Social work
Abstract

Chapters 1, 3 and 5 are available Open Access under CC-BY licence. Safeguarding adults at risk of abuse or neglect is a core area of social work practice but knowledge of how social workers make adult safeguarding decisions is limited. Applying recent sociological and ethnographic research to this area for the first time, this book considers how adult safeguarding practice is developing, with a focus on risk management. The author explores how social workers conduct safeguarding adults assessments, work with multiple agencies and involve service users in risk decisions. The book is essential reading for those wishing to understand how risk and uncertainty are managed within frontline adult social work and how current practice can be improved.

Published
2023
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26. Chapter 1 The Problem of Adult Safeguarding

Author

Dixon, Jeremy

Subjects
Adult protection, Care act 2014, Risk and uncertainty, Safeguarding, Social work, bic Book Industry Communication::J Society & social sciences::JH Sociology & anthropology::JHB Sociology, bic Book Industry Communication::J Society & social sciences::JK Social services & welfare, criminology::JKS Social welfare & social services::JKSN Social work
Abstract

Chapters 1, 3 and 5 are available Open Access under CC-BY licence. Safeguarding adults at risk of abuse or neglect is a core area of social work practice but knowledge of how social workers make adult safeguarding decisions is limited. Applying recent sociological and ethnographic research to this area for the first time, this book considers how adult safeguarding practice is developing, with a focus on risk management. The author explores how social workers conduct safeguarding adults assessments, work with multiple agencies and involve service users in risk decisions. The book is essential reading for those wishing to understand how risk and uncertainty are managed within frontline adult social work and how current practice can be improved.

Published
2023
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36. Adult Safeguarding Observed

Author

Dixon, Jeremy

Subjects
Adult protection, Care act 2014, Risk and uncertainty, Safeguarding, Social work, bic Book Industry Communication::J Society & social sciences::JH Sociology & anthropology::JHB Sociology, bic Book Industry Communication::J Society & social sciences::JK Social services & welfare, criminology::JKS Social welfare & social services::JKSN Social work
Abstract

Chapters 1, 3 and 5 are available Open Access under CC-BY licence. Safeguarding adults at risk of abuse or neglect is a core area of social work practice but knowledge of how social workers make adult safeguarding decisions is limited. Applying recent sociological and ethnographic research to this area for the first time, this book considers how adult safeguarding practice is developing, with a focus on risk management. The author explores how social workers conduct safeguarding adults assessments, work with multiple agencies and involve service users in risk decisions. The book is essential reading for those wishing to understand how risk and uncertainty are managed within frontline adult social work and how current practice can be improved.

Published
2023
Full Text
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48. Reviews

Author

Dixon, Jennifer

Published
1999

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