Biology subjects

Denis, A.

Publications and source records attributed to Denis, A..

5 recordsLinked to original sources

bioRxiv2025

A low-cost immersive Virtual Reality system to study social interactions and collective behavior in fish

1This study introduces a low-cost, open-source, immersive Virtual Reality (VR) system designed to investigate real-time social interactions and collective behaviors in fish. Understanding collective animal behaviors, such as schooling in fish, presents significant observational challenges due to rapid and complex interactions. To address these difficulties, we developed an innovative closed-loop VR environment allowing precise control and measurement of interactions between real and virtual fish. This setup incorporates high-speed 3D tracking, real-time visual feedback, and automated data processing, creating realistic and interactive scenarios. We present experimental results, obtained with rummy-nose tetras (Hemigrammus rhodostomus ), showing that freely moving real fish consistently adjusted their speed, depth, and spatial positioning to follow virtual fish effectively. Fish matched moderate virtual speeds comfortably, struggled slightly at higher speeds, and actively maintained vertical positioning to sustain group cohesion. The implementation of this VR system provides critical insights into sensory and cognitive processes underlying collective movement and decision-making in fish. By revealing both flexibility and constraints in fish behavior, our findings underscore the potential of VR technology to study social interactions in controlled yet realistic settings. Ultimately, this VR system advances our understanding of collective animal behavior, providing a foundation for cross-species studies linking neural processes, behavioral interactions, and group dynamics.

animal behavior and cognition↗

bioRxiv2021

Replication Study: RAF inhibitors prime wild-type RAF to activate the MAPK pathway and enhance growth

As part of the Reproducibility Project: Cancer Biology, we published a Registered Report (Bhargava et al., 2016) that described how we intended to replicate selected experiments from the paper "RAF inhibitors prime wild-type RAF to activate the MAPK pathway and enhance growth" (Hatzivassiliou et al., 2010). Here we report the results. We found two unrelated RAF inhibitors, PLX4720 or GDC-0879, selectively inhibited BRAF(V600E) cell proliferation, while the MEK inhibitor, PD0325901, inhibited BRAF(V600E), wild-type RAF/RAS, and mutant RAS cancer cell proliferation, similar to the original study (Figure 1A; Hatzivassiliou et al., 2010). We found knockdown of CRAF, but not BRAF, in mutant RAS cells attenuated the phospho-MEK induction observed after PLX4720 treatment, similar to the original study (Figure 2B; Hatzivassiliou et al., 2010). The original study reported analogous results with GDC-0879, which was not observed in this replication, although unexpected control results confound the interpretation. We also attempted a replication of an assay with recombinant proteins to test the differential effect of RAF inhibitors on BRAF-CRAF heterodimerization (Figure 4A; Hatzivassiliou et al., 2010). Although we were unable to conduct the experiment as planned, we observed differential binding of BRAF by RAF inhibitors; however, it was between BRAF and beads, independent of CRAF. While these data were unable to address whether, under the conditions of the original study, the same observations could be observed, we discuss key differences between the original study and this replication that are important to consider for further experiments. Finally, where possible, we report meta-analyses for each result. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=62 SRC="FIGDIR/small/470372v2_fig1.gif" ALT="Figure 1"> View larger version (7K): org.highwire.dtl.DTLVardef@1f77d0eorg.highwire.dtl.DTLVardef@1333494org.highwire.dtl.DTLVardef@c10824org.highwire.dtl.DTLVardef@fda30f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Cellular dose response curves for RAF and MEK inhibitors in BRAF(V600E), mutant RAS, and wild-type RAF/RAS cell lines Cell viability assays were performed for RAF inhibitors (PLX4720 and GDC-0879) and MEK inhibitor (PD0325901) against A375, (BRAF(V600E)), HCT116 (mutant RAS), and MeWo (wild-type RAF/RAS) cells. Absolute half-maximum effective concentration (EC50) values ({micro}M) were determined for each biological repeat. EC50 values unable to be accurately estimated are reported as either >20 {micro}M or <0.078 {micro}M, which are the largest and smallest doses tested, respectively. Absolute EC50 values for each biological repeat for A375, HCT116, and MeWo cells treated with (A) PLX4720, (B) GDC-0879, or (C) PD0325901 for this replication attempt are plotted with the EC50 value reported in Hatzivassiliou et al. (2010) displayed as a single point (red triangle) for comparison. Where possible the mean and 95% confidence interval of the replication data are shown. Additional details for this experiment can be found at https://osf.io/52zp9/. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/470372v2_fig2.gif" ALT="Figure 2"> View larger version (34K): org.highwire.dtl.DTLVardef@1dc3058org.highwire.dtl.DTLVardef@e9f5d9org.highwire.dtl.DTLVardef@baf5eorg.highwire.dtl.DTLVardef@126717a_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 2.C_FLOATNO Cellular dose response curves for each biological repeat This is the same experiment as in Figure 1. The dose response curve of each biological repeat [n=4] for A375, HCT116, and MeWo cells treated with (A) PLX4720, (B) GDC-0879, or (C) PD0325901 for this replication attempt are plotted. Additional details for this experiment can be found at https://osf.io/52zp9/. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/470372v2_fig4.gif" ALT="Figure 4"> View larger version (33K): org.highwire.dtl.DTLVardef@e4357eorg.highwire.dtl.DTLVardef@73e9ceorg.highwire.dtl.DTLVardef@1fb01c6org.highwire.dtl.DTLVardef@31a799_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 4.C_FLOATNO Testing of BRAF and CRAF antibodies used in original study The BRAF and CRAF antibodies reported in the original study (Hatzivassiliou et al., 2010) were tested for suitability by Western blot. (A) Representative Western blots and Ponceau-stained membrane (experiment performed independently 3 times) of 0.5 {micro}g of purified recombinant BRAF kinase domain (KD). Membranes were probed with the BRAF antibody used in the original study (RRID:AB_1840330) or with a different BRAF antibody used in this replication attempt (RRID:AB_2721113). (B) Representative Western blots and Ponceau-stained membrane (experiment performed independently 3 times) of 0.5 {micro}g of purified recombinant GST tagged CRAF KD. Membranes were probed with the CRAF antibody used in the original study (RRID:AB_397552) or with a different CRAF antibody used in this replication attempt (RRID:AB_10989977). (C) Representative Western blots (experiment performed once) of 16 {micro}g of whole cell lysates from the indicated human cell lines. Membranes were probed with the BRAF (RRID:AB_1840330) or CRAF (RRID:AB_397552) antibodies used in the original study. (D) Screenshot from the Constraint-based Multiple Alignment Tool (COBALT) (Papadopoulos and Agarwala, 2007) showing the alignment of full-length BRAF (NCBI Reference Sequence: NP_004324.2), the region of BRAF used as the immunogenic peptide used to generate the BRAF antibody used in the original study (RRID:AB_1840330), the BRAF KD used in this replication attempt, and the BRAF KD used in the original study. (E) Screenshot from COBALT showing the alignment of full-length CRAF (NCBI Reference Sequence: NP_002871.1), the region of CRAF used as the immunogenic peptide used to generate the CRAF antibody used in the original study (RRID:AB_397552), and the CRAF KD used in the original study and this replication attempt. Additional details for this experiment can be found at https://osf.io/6f3sk/. C_FIG

cancer biology↗

bioRxiv2020

An hACE2 peptide mimic blocks SARS-CoV-2 Pulmonary Cell Infection

In the light of the recent accumulated knowledge on SARS-CoV-2 and its mode of human cells invasion, the binding of viral spike glycoprotein to human Angiotensin Converting Enzyme 2 (hACE2) receptor plays a central role in cell entry. We designed a series of peptides mimicking the N-terminal helix of hACE2 protein which contains most of the contacting residues at the binding site and have a high helical folding propensity in aqueous solution. Our best peptide mimics bind to the virus spike protein with high affinity and are able to block SARS-CoV-2 human pulmonary cell infection with an inhibitory concentration (IC50) in the nanomolar range. These first in class blocking peptide mimics represent powerful tools that might be used in prophylactic and therapeutic approaches to fight the coronavirus disease 2019 (COVID-19).

pharmacology and toxicology↗

bioRxiv2020

Development of a small molecule that corrects misfolding and increases secretion of Z α1-antitrypsin

Severe 1-antitrypsin deficiency results from the Z allele (Glu342Lys) that causes the accumulation of homopolymers of mutant 1-antitrypsin within the endoplasmic reticulum of hepatocytes in association with liver disease. We have used a DNA-encoded chemical library to undertake a high throughput screen to identify small molecules that bind to, and stabilise Z 1-antitrypsin. The lead compound blocks Z 1-antitrypsin polymerisation in vitro, reduces intracellular polymerisation and increases the secretion of Z 1-antitrypsin three-fold in mammalian cells including an iPSC model of disease. Crystallographic and biophysical analyses demonstrate that GSK716 and related molecules bind to a cryptic binding pocket, negate the local effects of the Z mutation and stabilise the bound state against progression along the polymerization pathway. Oral dosing of transgenic mice at 100 mg/kg three times a day for 20 days increased the secretion of Z 1-antitrypsin into the plasma by 7-fold. There was no observable clearance of hepatic inclusions with respect to controls. This study provides proof-of-principle that mutation ameliorating small molecules are a viable approach to treat protein conformational diseases.

pharmacology and toxicology↗

bioRxiv2018

Genome-Wide Association Studies of malaria susceptibility and resistance: progress, pitfalls and prospects

P. falciparum malaria is still among the leading causes of child mortality in sub-Saharan Africa; killing hundreds of thousands of children each year. Malaria has been recognized as one of the prominent evolutionary selective forces of human genome that led to the emergence of multiple host protective polymorphisms associated with minimizing the risk of developing severe malaria in endemic areas. A comprehensive understanding of the genetic bases of malaria resistance can shed light to the molecular mechanisms of host-parasite interactions that can potentially pave ways to the development of new therapeutics and vaccines. Genome-wide association studies (GWASs) have recently been implemented in malaria endemic areas and identified a number of novel association genetic variants. Despite this success, only few variants did replicate across the studies and the underlying biology is yet to be understood for the majority of the novel variants. Besides, there are several open questions around heritability, polygenic effects, epistatic interactions, genetic correlations and associated molecular pathways among others. In this review, we first assess the progress and pitfalls of malaria susceptibility GWASs. We then, provide an overview of the current progress in post-GWAS approaches and discuss how these approaches can potentially be implemented in malaria susceptibility GWASs to extract further functional information. We conclude by highlighting the importance of multi-step and multidimensional integrative studies for unravelling the genetic basis of malaria susceptibility and resistance at systems biology level.

genomics↗