Biology subjects

Velasquez, A.

Publications and source records attributed to Velasquez, A..

4 recordsLinked to original sources

bioRxiv2026

Coiled-coil homo-oligomerization and disaggregase Hsp104 act in parallel to stabilize orphan septins

Multiple septin family proteins co-assemble with strict subunit stoichiometry into hetero-oligomers. In the absence of native septin partners, purified septins aggregate in vitro, and "orphan" septins are found in pathological aggregates associated with neurodegenerative diseases. Cytosolic chaperones bind the septin GTPase domain to promote on-pathway septin folding but it was unclear how cells manage orphan septins to maintain septin subunit stoichiometry. Most septins have C-terminal domains (CTDs) that form heteromeric coiled coils within or between septin complexes. Here we present evidence that orphan yeast septins are protected from proteasomal degradation by forming transient coiled-coil homodimers and trimers and, in parallel, by the disaggregase chaperone Hsp104. Septins unable to undergo CTD-mediated homo-oligomerization require Hsp104 to accumulate to super-stoichiometric levels. We show that the number of septin-encoding mRNAs per yeast cell is low and variable, creating opportunities for transient subunit imbalances. These findings reveal a novel role for coiled coils and the cellular proteostasis machinery in the fidelity of higher-order septin assembly.

molecular biology↗

bioRxiv2025

Transcriptomic module fingerprint reveals heterogeneity of whole blood transcriptome in type 1 diabetic patients

BackgroundType 1 diabetes (T1D) is a complex autoimmune disease resulting from {beta}-cell destruction in the pancreas. Yet, no gene signature derived from whole blood samples has been established to differentiate T1D patients from healthy donors, likely because of the high heterogeneity of the underlying pathophysiological mechanisms. MethodsWe analysed whole blood transcriptomic profiles from 39 patients and 43 healthy donors, collected as part of our observational clinical trial, using a multi-step multivariate statistical analysis. This approach combined classical differential analysis, random forest and support vector machine classifications, gene set functional enrichment analysis to construct the most stable and reliable gene signature. ResultsClassical differential analysis did not separate clearly samples into healthy and T1D clusters, but rather spread samples into three clusters. On the contrary, we show that our approach, which combined molecular signatures independently constructed, adds robustness to the analysis without compromising the specificity. This efficiency was demonstrated by the clear separation of the samples according to their diagnosis group. Also, the functional annotation of the gene modules that we obtained was more associated with T1D-related pathways compared to the classical statistical analysis. ImpactsThese results emphasize that single differential analyses are not able to capture immune continuums involved in such a complex pathophysiological process. We hypothesize that T1D patients can have different molecular pathways involved in their pathology or/and can display unsynchronized -omics profiles. These findings call for further investigations to identify the molecular pathways involved in T1D patients, and for revising the nosology of autoimmune diseases.

bioinformatics↗

bioRxiv2019

Host engineering for improved valerolactam production in Pseudomonas putida

Pseudomonas putida is a promising bacterial chassis for metabolic engineering given its ability to metabolize a wide array of carbon sources, especially aromatic compounds derived from lignin. However, this omnivorous metabolism can also be a hindrance when it can naturally metabolize products produced from engineered pathways. Herein we show that P. putida is able to use valerolactam as a sole carbon source, as well as degrade caprolactam. Lactams represent important nylon precursors, and are produced in quantities exceeding one million tons per year[1]. To better understand this metabolism we use a combination of Random Barcode Transposon Sequencing (RB-TnSeq) and shotgun proteomics to identify the oplBA locus as the likely responsible amide hydrolase that initiates valerolactam catabolism. Deletion of the oplBA genes prevented P. putida from growing on valerolactam, prevented the degradation of valerolactam in rich media, and dramatically reduced caprolactam degradation under the same conditions. Deletion of oplBA, as well as pathways that compete for precursors L-lysine or 5-aminovalerate, increased the titer of valerolactam from undetectable after 48 hours of production to ~90 mg/L. This work may serve as a template to rapidly eliminate undesirable metabolism in non-model hosts in future metabolic engineering efforts.

synthetic biology↗

bioRxiv2018

Deep structural brain lesions associated with consciousness impairment early after haemorrhagic stroke

BackgroundThe significance of deep structural lesions on level of consciousness early after intracerebral haemorrhage (ICH) is largely unknown.\n\nMethodsWe studied a consecutive series of patients with spontaneous ICH that underwent MRI within 7 days of the bleed. We assessed consciousness by testing for command following from time of MRI to hospital discharge, and determined 3-months functional outcomes using the Glasgow Outcome Scale-Extended (GOS-E). ICH and oedema volumes, intraventricular haemorrhage (IVH), and midline shift (MLS) were quantified. Presence of blood and oedema in deep brain regions previously implicated in consciousness were assessed. A machine learning approach using logistic regression with elastic net regularization was applied to identify parameters that best predicted consciousness at discharge controlling for confounders.\n\nResultsFrom 158 ICH patients that underwent MRI, 66% (N=105) were conscious and 34% (N=53) unconscious at the time of MRI. Almost half of unconscious patients (49%, N= 26) recovered consciousness by ICU discharge. Focal lesions within subcortical structures predicted persistent impairment of consciousness at discharge together with MLS, IVH, and ICH and oedema volumes (AUC 0.74; 95%-CI 0.73-0.75). Caudate nucleus, midbrain peduncle, and pontine tegmentum were implicated as critical structures. Unconscious patients predicted to recover consciousness had better 3-month functional outcomes than those predicted to remain unconscious (35% vs 0% GOS-E [≥]4; p-value=0.02).\n\nConclusionMRI lesions within key subcortical structures together with measures reflecting the mass effect of the haemorrhage (lesion volumes, IVH, MLS) obtained within one week of ICH can help predict early recovery of consciousness and 3-month functional outcome.

neuroscience↗