Biology subjects

Santos, A. M.

Publications and source records attributed to Santos, A. M..

5 recordsLinked to original sources

bioRxiv2018

A haplotype-resolved draft genome of the European sardine (Sardina pilchardus)

BackgroundThe European sardine (Sardina pilchardus Walbaum, 1792) has a high cultural and economic importance throughout its distribution. Monitoring studies of sardine populations report an alarming decrease in stocks due to overfishing and environmental change, which has resulted in historically low captures along the Iberian Atlantic coast. Consequently, there is an urgent need to better understand the causal factors of this continuing decrease in the sardine stock. Important biological and ecological features such as levels of population diversity, structure, and migratory patterns can be addressed with the development and use of genomics resources.\n\nFindingsThe sardine genome of a single female individual was sequenced using Illumina HiSeq X Ten 10X Genomics linked-reads generating 113.8 Gb of data. Three draft genomes were assembled: two haploid genomes with a total size of 935 Mbp (N50 103Kb) each, and a consensus genome with a total size of 950 Mbp (N50 97Kb). The genome completeness assessment captured 84% of Actinopterygii Benchmarking Universal Single-Copy Orthologs. To obtain a more complete analysis, the transcriptomes of eleven tissues were sequenced and used to aid the functional annotation of the genome, resulting in 40 777 genes predicted. Variant calling on nearly half of the haplotype genome resulted in the identification of more than 2.3 million phased SNPs with heterozygous loci.\n\nConclusionsA draft genome was obtained with the 10X Genomics linked-reads technology, despite a high level of sequence repeats and heterozygosity that are expected genome characteristics of a wild sardine. The reference sardine genome and respective variant data are a cornerstone resource of ongoing population genomics studies to be integrated into future sardine stock assessment modelling to better manage this valuable resource.

genomics↗

bioRxiv2018

Chikungunya in Colombia: a description of an epidemic within the framework of a COPCORD study

During 2014 and 2015 the chikungunya virus reached Colombia unleashing an epidemic that spread throughout the whole territory. Concurrently, the Colombian Rheumatology Association was conducting a Community Oriented Program for Control of Rheumatic Diseases (COPCORD) to establish rheumatic disease prevalence in the country. Chikungunya infected patients were identified within the COPCORD population. The aim of this study was to describe the demographics, clinical characteristics and disability of patients with clinical suspicion of chikungunya infection. To confirm chikungunya infection, ELISA IgM and IgG serology was performed. From the 6528-surveyed people of the COPCORD study, 548 where included in the study because of clinical suspicion of chikungunya virus infection. Of those, 295 were positive for IgG or IgM chikungunya serology with 151 patients fulfilling WHO clinical criteria for chikungunya infection (true positives). Most patients were > 45 years (57.7%), and females (69.7%). Patients with low income and low socio-economic strata had increased risk of chikungunya infection (p = 0.00; OR: 2.36, CI: 1.47-3.77 and p = 0.00; OR: 2.81, CI: 1.90-4.17 respectively). True positive patients were associated with symmetric arthritis (p = 0.00; OR: 22.49, CI: 12.71-39.80) of ankles (p = 0.00; OR: 16.06, CI: 7.57-34.08), hands (p = 0.00; OR: 16.12, CI: 8.25-39.79), feet (p = 0.00; OR: 16.35, CI: 7.41-36.05) and elbows (p = 0.00; OR: 14.00, CI: 3.03-64.70). Most patients developed mild to moderate disability (95.2 to 100%). Our study showed that poverty and low socioeconomic status are associated with increased risk of chikungunya infection. Also, we found two distinctive phenotypes of chikungunya infection; those with positive chikungunya serology and typical clinical symptoms (true positives) and those with positive serology without clinical symptoms (false negatives). Finally, a distinctive clinical picture presented by chikungunya infected patients was found which should be considered as the hallmark for diagnostic clinical criteria.

epidemiology↗

bioRxiv2018

Hydrodynamic trapping measures the interaction between membrane-associated molecules

How membrane proteins distribute and behave on the surface of cells is determined by the molecules interaction potential. However, measuring this potential, and how it varies with protein-to-protein distance, has been challenging. We here present how a method we call hydrodynamic trapping can achieve this. Our method uses the focused liquid flow from a micropipette to locally accumulate molecules protruding from a lipid membrane. The interaction potential, as well as information about the dimensions of the studied molecule, are obtained by relating the degree of accumulation to the strength of the trap. We have used this to study four representative proteins, with different height-to-width ratios and protein properties; from the globular streptavidin, to the rod-like immune cell proteins CD2, CD4 and CD45. The obtained data illustrates how protein shape, glycosylation and flexibility influence the behaviour of membrane proteins as well as underline the general applicability of the method.

biophysics↗

bioRxiv2018

Reconstitution of immune cell interactions in free-standing membranes

The spatiotemporal regulation of signalling proteins at the contacts formed between immune cells and their targets determines how and when immune responses begin and end. It is important, therefore, to be able to elucidate molecular processes occurring at these interfaces. However, the detailed investigation of each components contribution to the formation and regulation of the contact is hampered by the complexity of cellular composition and architecture. Moreover, the transient nature of these interactions creates additional challenges, especially for using advanced imaging technology. One approach to circumventing these problems is to establish in vitro systems that faithfully mimic immune cell interactions, incorporating complexity that can be dialled-in as needed. Here, we present an in vitro system making use of synthetic vesicles that mimic important aspects of immune cell surfaces. Using this system, we begin to investigate the spatial distribution of signalling molecules (receptors, kinases and phosphatases) and the intracellular rearrangements that accompany the initiation of signalling in T cells. The model system presented here is expected to be widely applicable.\n\nSummary StatementImmune cell-cell interactions are reconstituted in free-standing vesicles wherein spatiotemporal aspects of immune synapse formation can be investigated.

immunology↗

bioRxiv2017

Constraining CD45 exclusion at close-contacts provides a mechanism for discriminatory T-cell receptor signalling

The T-cell receptor (TCR) triggers the elimination of pathogens and tumors by T lymphocytes. In order for this to avoid damage to the host, the receptor has to discriminate between thousands of peptide ligands presented by each host cell. Exactly how the TCR does this is unknown. In resting T-cells, the TCR is largely unphosphorylated due to the dominance of phosphatases over kinases expressed at the cell surface. When agonist peptides are presented to the TCR by major histocompatibility complex (MHC) proteins expressed by antigen-presenting cells (APCs), very fast receptor triggering occurs, leading to TCR phosphorylation. Recent work suggests that this depends on the local exclusion of the phosphatases from regions of contact of the T cells with the APCs. Here, we develop and test a quantitative treatment of receptor triggering reliant only upon TCR dwell-time in phosphatase-depleted cell-cell contacts constrained in area by cell topography. Using the model and experimentally-derived parameters, we find that ligand discrimination is possible but that it depends crucially on individual contacts being 400 nm in diameter or smaller, i.e. the size generated by microvilli. The model not only correctly predicts the relative signaling potencies of known agonists and non-agonists, but achieves this in the absence of conventional, multi-step kinetic proof-reading. Our work provides a simple, quantitative and predictive molecular framework for understanding why TCR triggering is so selective and fast, and reveals that for some receptors, cell topography crucially influences signaling outcomes.\n\nSignificance statementOne approach to testing biological theories is to determine if they are predictive. A simple, theoretical treatment of TCR triggering suggests that ligand discrimination by the receptor relies on just two physical principles: (1) the time TCRs spend in cell-cell contacts depleted of large tyrosine phosphatases; and (2) constraints on contact size imposed by T cells using finger-like protrusions to interrogate their targets. The theory not only allows agonistic and non-agonistic TCR ligands to be distinguished but predicts the relative signalling potencies of agonists with remarkable accuracy. This suggests that the theory captures the essential features of receptor triggering.

immunology↗