Statistical Population Genomics

This open access volume presents state-of-the-art inference methods in population genomics, focusing on data analysis based on rigorous statistical techniques. After introducing general concepts related to the biology of genomes and their evolution, the book covers state-of-the-art methods for the analysis of genomes in populations, including demography inference, population structure analysis and detection of selection, using both model-based inference and simulation procedures. Last but not least, it offers an overview of the current knowledge acquired by applying such methods to a large variety of eukaryotic organisms. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, pointers to the relevant literature, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Statistical Population Genomics aims to promote and ensure successful applications of population genomic methods to an increasing number of model systems and biological questions

26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3 - Meeting Abstracts - Antwerp, Belgium. 15–20 July 2017

This work was produced as part of the activities of FAPESP Research,\ud Disseminations and Innovation Center for Neuromathematics (grant\ud 2013/07699-0, S. Paulo Research Foundation). NLK is supported by a\ud FAPESP postdoctoral fellowship (grant 2016/03855-5). ACR is partially\ud supported by a CNPq fellowship (grant 306251/2014-0)

Protein Interactions of Epithelial Neutral Amino Acid Transporters

Neutral amino acids are essential for protein synthesis, energy homeostasis, and many vital biochemical pathways. As several neutral amino acids are essential and cannot be synthesised by humans in vivo, their uptake and reuptake by the body’s absorbing epithelial layers is of major importance for systemic amino acid homeostasis and human health. Two of the major pathways for the absorption of neutral amino acids in the small intestine and kidney are the Broad Neutral Amino acid Transporters 1 and 3 (B0AT1 and B0AT3). B0AT1 is of medical interest as an indirect regulator of blood glycemia via cellular amino acid starvation response pathways. Absence of B0AT1 results in improved glycemic control and other metabolic effects, revealing it as a potential pharmacological target to treat type II diabetes. Essential to understanding the role of B0AT1 as a global metabolic regulator is its requirement for plasma membrane expression with heteromeric protein partners: collectrin in the kidney and Angiotensin Converting Enzyme 2 (ACE2) in the small intestine. Both proteins are membrane-anchored by a single trans-membrane domain and are homologous. B0AT3 also requires collectrin or ACE2 for membrane expression. Beyond this requirement for plasma membrane expression, however, little is known about the underlying mechanisms of the interaction. This thesis demonstrates additional protein partners of B0AT1, namely Aminopeptidase N (APN), syntaxin 1A, and syntaxin 3. These proteins facilitate changes in the kinetic parameters of neutral amino acid transport, in addition to regulating membrane expression. Moreover, I demonstrate that collectrin is required for catalytic activation of both B0AT1 and B0AT3, while both APN and ACE2 increase B0AT1 and B0AT3 substrate affinity, respectively. ACE2 and APN also form large complexes with B0AT1 at the small intestine brush border membrane. A binding site in both transporters for collectrin is identified as lying in the hydrophobic pocket between TM 5 and 7 of the transporters. Using a mixture of experimental and bioinformatics tools, I was able to map the interacting domains of collectrin, which involve multiple regions of the protein, including the TM domain and large regions of the N-terminus. The ability of collectrin and B0AT1 orthologs to cross-react with each other and the homologous region of ACE2, suggests a highly conserved structure-function relationship between them. In conclusion, B0AT1 and B0AT3 form large, stable protein complexes with collectrin, ACE2 and other proteins, the binding site and function of which are highly conserved. The necessity of these interactions mean these complexes should be thought of as heteromultimeric transporter metabolons – multimeric protein units facilitating efficient neutral amino acid transport in epithelial cells. There is increasing evidence that the formation of stable heteromeric membrane transport complexes is a common theme underlying the function of many transporters initially studied in isolation. Understanding the physiology and structure-function relationships of transporters in their native multimeric states is fundamental to understanding relevant biological roles. Especially as membrane transporters are heavily over-represented as causative agents of human disease and as therapeutic drug targets. Targeting stable, intrinsic protein-protein interactions presents a still unexplored field of drug treatment in biomedical science