Biology subjects

del Valle, J.

Publications and source records attributed to del Valle, J..

4 recordsLinked to original sources

bioRxiv2025

Biomarkers in cerebrospinal fluid sediments

Cerebrospinal fluid (CSF) biomarkers for neurodegenerative diseases have been extensively studied over the years. However, CSF samples are routinely centrifuged, and the resulting sediment or pellet is typically discarded to remove cellular debris and high-density particles. This standard practice raises a critical question: could these discarded sediments harbour potential biomarkers relevant to the diagnosis and prognosis of certain brain diseases? In this study, we analysed CSF pellets from various cases and identified, entrapped among undetermined remnants, brain-derived structures such as wasteosomes and psammoma bodies. Furthermore, we observed that disease-relevant proteins can become deposited in the sediment, as is the case for both tau and A{beta}42 in Alzheimers disease or tau in progressive supranuclear palsy disease. These findings suggest that some potential biomarkers might accumulate or be hidden in the sediment and, taken as a whole, the results underscore the need to broaden the scope of biomarker research. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/657984v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1d5b55corg.highwire.dtl.DTLVardef@175ae02org.highwire.dtl.DTLVardef@f30e42org.highwire.dtl.DTLVardef@12d326b_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG

neuroscience↗

bioRxiv2022

Graphene-based thin film microelectrode technology for in vivo high resolution neural recording and stimulation

Neuroprosthetic technology aims to restore nervous system functionality in cases of severe damage or degeneration by recording and stimulating the electrical activity of the neural tissue. One of the key factors determining the quality of the neuroprostheses is the electrode material used to establish electrical communication with the neural tissue, which is subject to strict electrical, electrochemical, and mechanical specifications as well as biological and microfabrication compatibility requirements. This work presents a nanoporous graphene-based thin film technology and its engineering to form flexible neural implants. Bench measurements show that the developed microelectrodes offer low impedance and high charge injection capacity throughout millions of pulses. In vivo electrode performance was assessed in rodents both from brain surface and intracortically showing high-fidelity recording performance, while stimulation performance was assessed with an intrafascicular implant that demonstrated low current thresholds and high selectivity for activating subsets of axons within the sciatic nerve. Furthermore, the tissue biocompatibility of the devices was validated by chronic epicortical and intraneural implantation. Overall, this works describes a novel graphene-based thin film microelectrode technology and demonstrates its potential for high-precision neural interfacing in both recording and stimulation applications.

bioengineering↗

bioRxiv2019

Benchmark of tools for CNV detection from NGS panel data in a genetic diagnostics context

MotivationAlthough germline copy number variants (CNVs) are the genetic cause of multiple hereditary diseases, detecting them from targeted next-generation sequencing data (NGS) remains a challenge. Existing tools perform well for large CNVs but struggle with single and multi-exon alterations. The aim of this work is to evaluate CNV calling tools working on gene panel NGS data with CNVs up to single-exon resolution and their suitability as a screening step before orthogonal confirmation in genetic diagnostics strategies. ResultsFive tools (DECoN, CoNVaDING, panelcn.MOPS, ExomeDepth and CODEX2) were tested against four genetic diagnostics datasets (495 samples, 231 CNVs), using the default and sensitivity-optimized parameters. Most tools were highly sensitive and specific, but the performance was dataset-dependant. In our in-house datasets, DECoN and panelcn.MOPS with optimized parameters showed enough sensitivity to be used as screening methods in genetic diagnostics. AvailabilityBenchmarking-optimization code is freely available at https://github.com/TranslationalBioinformaticsIGTP/CNVbenchmarkeR.

bioinformatics↗

bioRxiv2018

A universal set of primers to study animal associated microeukaryotic communities

BackgroundUnlike the study of bacterial microbiomes, the study of the microeukaryotes associated with animals has largely been restricted to visual identification or molecular targeting of particular groups. The application of high-throughput sequencing (HTS) approaches, such as those used to look at bacteria, has been restricted because the barcoding gene traditionally used to study microeukaryotic ecology and distribution in the environment, the Small Subunit of the Ribosomal RNA gene (18S rRNA), is also present in the animal host. As a result, when host-associated microbial eukaryotes are analyzed by HTS, the obtained reads tend to be dominated by host sequences.\n\nResultsWe have done an in-silico validation against the SILVA 18S rRNA reference database of contrametazoan primers that cover the V4 region of the 18S rRNA, and compared these with universal V4 18S rRNA primers that are widely used by the microbial ecology community. We observe that the contrametazoan primers recover only 2.6% of all the metazoan sequences present in SILVA, while the universal primers recover up to 20%. Among metazoans, the contrametazoan primers are predicted to amplify 74% of Porifera sequences and 4% and 15% of ctenophore and Cnidaria, respectively, while amplifying almost no sequences within Bilateria.\n\nWe tested these predictions in-vivo, and observed that contrametazoan primers amplify the 18SrRNA from two ctenophore species, but reduce significantly the metazoan signal from material derived from coral and from human samples. When compared in-vivo against universal primers, contrametazoan primers worked in 8 out of 9 samples, providing at worst a 2-fold decrease in the number of metazoan reads, and at best a 2800-fold decrease.\n\nConclusionsWe have validated an easy, inexpensive, and near-universal method for the study of microeukaryotes associated with animal hosts using 18S rRNA Illumina metabarcoding. This method will contribute to a better understanding of microbial communities, as they related to the wellbeing of animals and humans.

microbiology↗