Project description:Organisms had to evolve mechanisms that regulate the properties of biogenic crystals to support a wide range of functions, from vision and camouflage to communication and thermal regulation. Yet, the mechanism underlying the formation of diverse intracellular crystals remains enigmatic. Here, we have unraveled the bio-chemical control over crystal morphogenesis in zebrafish iridophores. We show that the chemical composition of the crystals determines their shape, specifically by the ratio between the nucleobases guanine and hypoxanthine. Moreover, we reveal that these variations in composition are genetically controlled through tissue-specific expression of specialized paralogues, which exhibits remarkable substrate selectivity. This orchestrated combination grants the organism with the capacity to generate a broad spectrum of crystal morphologies. Overall, our findings suggest a new mechanism for the morphological and functional diversity of biogenic crystals and may thus inspire the development of genetically designed biomaterials and medical therapeutics.
Project description:This study evaluated and compared three sample preparation strategies for proteomic analysis of equine cerebrospinal fluid (CSF): native in-solution digestion, the ProteoMiner™ Small-Capacity Enrichment Kit (Bio-Rad®), and the PreOmics Enrich-iST™ Kit (PreOmics®). CSF is in direct contact with the central nervous system (CNS), and its protein content reflects both physiological and pathological states, making it an ideal fluid for biomarker discovery in neurological diseases. However, its analysis is hindered by the wide dynamic range of protein concentrations and the predominance of highly abundant proteins (HAPs), such as albumin, which can obscure the detection of diagnostically relevant low-abundance proteins (LAPs). To address these limitations, enrichment kits such as ProteoMiner and PreOmics have been employed to reduce HAPs and enhance LAP detection prior to mass spectrometry. While ProteoMiner uses a combinatorial hexapeptide ligand library to compress the dynamic range by saturating binding sites of abundant proteins, PreOmics relies on paramagnetic beads with hydrophobic and charge-based retention to selectively bind peptides and improve sample purity. This is the first study to apply the PreOmics Enrich-iST kit to equine CSF. Label-free LC-MS/MS was used to analyse the samples. A total of 849 unique proteins were identified across all methods, with the PreOmics kit identifying the highest number of proteins and achieving the most consistent depletion of HAPs. emPAI scores were used to quantify protein abundance, revealing that albumin levels decreased by over 60% with PreOmics but slightly increased with ProteoMiner. Pathway enrichment analysis using PANTHER showed that the PreOmics kit enabled detection of a broader and more statistically significant array of biological pathways, while ProteoMiner selectively enriched for HAPs with known roles in neurodegenerative disorders, such as Dickkopf WNT signalling pathway inhibitor 3 (DKK3) and clusterin (CLU). These findings highlight that although both kits are capable of enriching LAPs, they differ in their enrichment patterns and efficiency. PreOmics provides better overall proteome coverage and greater statistical power in pathway analysis, whereas ProteoMiner may be more effective for targeted studies of specific neuropathology-related proteins. This study provides valuable insights into the applicability and complementarity of these enrichment methods for biomarker discovery in equine neurological disease.
Project description:Membrane contact sites are molecular bridges between organelles that are sustained by tethering proteins and enable organelle communication. The endoplasmic reticulum (ER) membrane harbors many distinct families of tether proteins that enable the formation of contacts with all other organelles. One such example is the LAM (Lipid transfer protein At Membrane contact sites) family, composed of six members. All six LAM proteins share the presence of a sterol transfer domain and a transmembrane segment that anchors them to the ER. However, the six proteins are divided into three homologous pairs each unique in their molecular architecture and localization to different ER subdomains. What determines the distinct localization of the different LAMs and which specific roles they carry out in each contact are still open questions. To address these, we utilized a proximity labeling approach to profile the interaction landscape of the entire family. Focusing on unique interactors we could support a role for Lam5 at the ER-mitochondria contact site. Capturing shared interactors of multiple LAMs explains how Lam1/3 and Lam2/4 paralogous pairs could be associated specifically with the plasma membrane. Overall, our work provides new insights into the regulation and function of the pan-ER contact LAM family proteins. More globally it demonstrates how proximity labeling can help identify the shared or unique functions of paralogous proteins.
Project description:We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of the International Headache Genetics consortium and EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls.
Project description:We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of the International Headache Genetics consortium and EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls.