Biology subjects

Segal, M.

Publications and source records attributed to Segal, M..

10 recordsLinked to original sources

bioRxiv2026

Quicklime-based eradication attempt of Xenopus laevis as a model for controlling pondscape invasions

Aquatic non-native invasive species are notoriously difficult to eradicate, particularly in pondscapes where populations can spread rapidly, persist in unmanaged refugia, and recolonise treated sites. In such contexts, high-intensity management interventions may be justified, balancing short-term collateral impacts against the prevention of permanent establishment and long-term damages. Chemical eradication methods, such as rotenone or herbicide application, can be effective but raise ethical and environmental concerns. Here, we evaluate quicklime (calcium oxide, CaO) application as a more sustainable alternative control tool for pondscape invaders compared to other chemical methods, using the African clawed frog (Xenopus laevis) invasion in Belgium as a case study. When applied to water, quicklime hydrates exothermically to calcium hydroxide (Ca(OH)), which releases OH ions upon dissolution, temporarily and rapidly increasing pH to lethal levels. In winter 2023, three ponds with breeding populations of X. laevis of low ecological value were drained, fenced, and treated with quicklime. Treatment effectiveness was assessed through pH measurements, visual surveys, and environmental DNA (eDNA) quantification. Immediately after treatment, large numbers of deceased post-metamorphic individuals were recovered, indicating treatment-induced mortality. Eight weeks post-treatment, eDNA concentrations were markedly lower in two of the three ponds (reductions of 100% and 80%) compared to those during the same period one year later. Although eDNA concentrations increased again during the following summer suggesting partial population recovery through survival and/or recolonisation, they remained lower than pre-treatment conditions. Water pH returned to near baseline levels within one month. We provide the first field-based preliminary evidence that quicklime can induce large-scale mortality in X. laevis populations in small to medium-sized ponds. We discuss practical considerations, limitations, and broader applicability, proposing quicklime as a high-intensity option within integrated management strategies for pondscape invaders.

ecology↗

bioRxiv2025

Kinase interplay centered on two regulatory elements confines the checkpoint protein Lte1 to the bud cell cortical compartment

In budding yeast, Lte1, a component of the spindle position checkpoint, must be confined to the bud for correctly coupling chromosomal segregation across the bud neck with mitotic exit. Bud compartmentalization involves a phospho-dependent program with Ras-GTP acting as the ultimate cortical anchor. Here we have dissected this program by identifying an Lte1 domain participating in Ras binding and two phospho-regulatory motifs, the N- and C-LREs (Lte1 Regulatory Elements). The C-LRE mediates control of Lte1 cortical recruitment by the p21-activated kinase, Cla4. The N-LRE modulates Lte1 binding to Ras more directly and is phosphorylated by the yeast MARK/PAR-1 protein kinases, Kin1/2. Along with previously described CDK phosphorylation sites, the N- and C-LREs are required for Lte1 localization and timely mitotic exit. These studies uncover the coordinated interplay between multiple protein kinases allowing Lte1 to integrate cell polarity and cell cycle cues for strict compartmentalization at the bud cell cortex.

cell biology↗

bioRxiv2022

Kidney tubular epithelial cell ferroptosis links glomerular injury to tubulointerstitial pathology in lupus nephritis

ObjectiveAn appreciation of factors that lead to tubular injury in lupus nephritis is lacking. Iron accumulates in the kidney tubules of nephritic patients and lupus-prone nephritic mice. Ferroptosis is a druggable, iron-dependent form of cell death that has received little attention in lupus nephritis. This study investigated whether intra-renal ferroptosis is a target for intervention in lupus nephritis. MethodsKidneys of lupus nephritis patients and two spontaneous murine models of lupus nephritis were characterized for ferroptosis using protein, RNA, and lipidomics-based approaches. Susceptibility of heavy chain ferritin (FtH1; an essential iron sequestration protein) deficient proximal tubular epithelial cells (PTECs) was studied using nephrotoxic serum nephritis and FtH1 knockdown human PTECs. The benefit of Liproxstatin-2, a novel second-generation ferroptosis, was evaluated using human PTECs exposed to lupus nephritis patients serum. ResultsHuman and murine nephritic kidneys have the characteristic markers of ferroptosis, such as 4-hydroxynonenal and acyl-CoA synthetase long-chain family member 4, mainly in the tubular segments. Murine kidneys showed impairment in the glutathione synthesis pathway, decreased expression of glutathione peroxidase 4, a glutathione-dependent ferroptosis inhibitor, and characteristic ferroptotic lipid signature. Loss of FtH1 increased PTEC pathology independent of glomerular injury. These findings were recapitulated in human PTECs. Of translational relevance, Liproxstatin-2 demonstrated a prophylactic and therapeutic benefit in mitigating lupus nephritis patient serum-induced PTEC ferroptosis. ConclusionOur findings highlight tubular cell ferroptosis as a pathological feature in human and murine lupus nephritis and identify ferroptosis inhibitors as potential novel adjunct therapeutics to treat lupus nephritis.

immunology↗

bioRxiv2022

Statistical curve models for inferring 3D chromatin architecture

Reconstructing three dimensional (3D) chromatin structure from conformation capture assays (such as Hi-C) is a critical task in computational biology, since chromatin spatial architecture plays a vital role in numerous cellular processes and direct imaging is challenging. We previously introduced Poisson metric scaling (PoisMS), a technique that models chromatin by a smooth curve, which yielded promising results. In this paper, we advance several ways for improving PoisMS. In particular, we address initialization issues by using a smoothing spline basis. The resulting SPoisMS method produces a sequence of reconstructions re-using previous solutions as warm starts. Importantly, this approach permits smoothing degree to be determined via cross-validation which was problematic using our prior B-spline basis. In addition, motivated by the sparsity of Hi-C contact data, especially when obtained from single-cell assays, we appreciably extend the class of distributions used to model contact counts. We build a general distribution-based metric scaling (DBMS) framework, from which we develop zero-inflated and Hurdle Poisson models as well as negative binomial applications. Illustrative applications make recourse to bulk Hi-C data from IMR90 cells and single-cell Hi-C data from mouse embryonic stem cells.

bioinformatics↗

bioRxiv2020

Principal Curve Approaches For Inferring 3D Chromatin Architecture

Three dimensional (3D) genome spatial organization is critical for numerous cellular processes, including transcription, while certain conformation-driven structural alterations are frequently oncogenic. Genome architecture had been notoriously difficult to elucidate, but the advent of the suite of chromatin conformation capture assays, notably Hi-C, has transformed understanding of chromatin structure and provided downstream biological insights. Although many findings have flowed from direct analysis of the pairwise proximity data produced by these assays, there is added value in generating corresponding 3D reconstructions deriving from superposing genomic features on the reconstruction. Accordingly, many methods for inferring 3D architecture from proximity d hyperrefata have been advanced. However, none of these approaches exploit the fact that single chromosome solutions constitute a one dimensional (1D) curve in 3D. Rather, this aspect has either been addressed by imposition of constraints, which is both computationally burdensome and cell type specific, or ignored with contiguity imposed after the fact. Here we target finding a 1D curve by extending principal curve methodology to the metric scaling problem. We illustrate how this approach yields a sequence of candidate solutions, indexed by an underlying smoothness or degrees-of-freedom parameter, and propose methods for selection from this sequence. We apply the methodology to Hi-C data obtained on IMR90 cells and so are positioned to evaluate reconstruction accuracy by referencing orthogonal imaging data. The results indicate the utility and reproducibility of our principal curve approach in the face of underlying structural variation.

bioinformatics↗

bioRxiv2020

Orderly assembly underpinning built-in asymmetry in the yeast centrosome duplication cycle requires cyclin-dependent kinase

Asymmetric astral microtubule organization drives the polarized orientation of the S. cerevisiae mitotic spindle and primes the invariant inheritance of the old spindle pole body (SPB, the yeast centrosome) by the bud. This model has anticipated analogous centrosome asymmetries featuring in self-renewing stem cell divisions. We previously implicated Spc72, the cytoplasmic receptor for the gamma-tubulin nucleation complex, as the most upstream determinant linking SPB age, functional asymmetry and fate. Here we used structured illumination microscopy and biochemical analysis to explore the asymmetric landscape of nucleation sites inherently built into the spindle pathway and under the control of cyclin-dependent kinase (CDK). We show that CDK enforces Spc72 asymmetric docking by phosphorylating Nud1/centriolin. Furthermore, CDK-imposed order in the construction of the new SPB promotes the correct balance of nucleation sites between the nuclear and cytoplasmic faces of the SPB. Together these contributions by CDK inherently link correct SPB morphogenesis, age and fate.

cell biology↗

bioRxiv2020

Motor cortical plasticity in response to skill acquisition in adult monkeys

Cortical maps often undergo plastic changes during learning or in response to injury. In sensory areas, these changes are thought to be triggered by alterations in the pattern of converging inputs and a functional reassignment of the deprived cortical region. In the motor cortex, training on a task that engages distal effectors was shown to increase their cortical representation (as measured by response to intracortical microstimulation). However, this expansion could be a specific outcome of using a demanding dexterous task. We addressed this question by measuring the long-term changes in cortical maps of monkeys that were sequentially trained on two different tasks involving either proximal or distal joints. We found that motor cortical remodeling in adult monkeys was symmetric such that both distal and proximal movements can comparably alter motor maps in a fully reversible manner according to task demands. Further, we found that the change in mapping often included a switch between remote joints (e.g., a finger site switched to a shoulder site) and reflected a usage-consistent reorganization of the map rather than the local expansion of one representation into nearby sites. Finally, although cortical maps were considerably affected by the performed task, motor cortical neurons throughout the motor cortex were equally likely to fire in a task-related manner independent of the task and/or the recording site. These results may imply that in the motor system, enhanced motor efficiency is achieved through a dynamical allocation of larger cortical areas and not by specific recruitment of task-relevant cells.

neuroscience↗

bioRxiv2019

High-throughput smFRET analysis of freely diffusing nucleic acid molecules and associated proteins

Single-molecule Forster resonance energy transfer (smFRET) is a powerful technique for nanometer-scale studies of single molecules. Solution-based smFRET, in particular, can be used to study equilibrium intra- and intermolecular conformations, binding/unbinding events and conformational changes under biologically relevant conditions without ensemble averaging. However, single-spot smFRET measurements in solution are slow. Here, we detail a high-throughput smFRET approach that extends the traditional single-spot confocal geometry to a multispot one. The excitation spots are optically conjugated to two custom silicon single photon avalanche diode (SPAD) arrays. Two-color excitation is implemented using a periodic acceptor excitation (PAX), allowing distinguishing between singly- and doubly-labeled molecules. We demonstrate the ability of this setup to rapidly and accurately determine FRET efficiencies and population stoichiometries by pooling the data collected independently from the multiple spots. We also show how the high throughput of this approach can be used to increase the temporal resolution of single-molecule FRET population characterization from minutes to seconds. Combined with microfluidics, this high-throughput approach will enable simple real-time kinetic studies as well as powerful molecular screening applications.

biophysics↗

bioRxiv2017

Optical crosstalk in SPAD arrays for high-throughput single-molecule fluorescence spectroscopy

Single-molecule fluorescence spectroscopy (SMFS), based on the detection of individual molecules freely diffusing through the excitation spot of a confocal microscope, has allowed unprecedented insights into biological processes at the molecular level, but suffers from limited throughput. We have recently introduced a multispot version of SMFS, which allows achieving high-throughput SMFS by virtue of parallelization, and relies on custom silicon single-photon avalanche diode (SPAD) detector arrays. Here, we examine the premise of this parallelization approach, which is that data acquired from different spots is uncorrelated. In particular, we measure the optical crosstalk characteristics of the two 48-SPAD arrays used in our recent SMFS studies, and demonstrate that it is negligible (crosstalk probability [≤] 1.1 10-3) and is undetectable in cross-correlation analysis of actual single-molecule fluorescence data.

biophysics↗

bioRxiv2017

48-spot single-molecule FRET setup with periodic acceptor excitation

Single-molecule FRET (smFRET) allows measuring distances between donor and acceptor fluorophores on the 3-10 nm range. Solution-based smFRET allows measurement of binding-unbinding events or conformational changes of dye-labeled biomolecules without ensemble averaging and free from surface perturbations. When employing dual (or multi) laser exci-tation, smFRET allows resolving the number of fluorescent labels on each molecule, greatly enhancing the ability to study heterogeneous samples. A major drawback to solution-based smFRET is the low throughput, which renders repetitive measurements expensive and hin-ders the ability to study kinetic phenomena in real-time.\n\nHere we demonstrate a high-throughput smFRET system which multiplexes acquisition by using 48 excitation spots and two 48-pixel SPAD array detectors. The system employs two excitation lasers allowing separation of species with one or two active fluorophores. The performance of the system is demonstrated on a set of doubly-labeled double-stranded DNA oligonucleotides with different distances between donor and acceptor dyes along the DNA duplex. We show that the acquisition time for accurate subpopulation identification is reduced from several minutes to seconds, opening the way to high-throughput screening applications and real-time kinetics studies of enzymatic reactions such as DNA transcription by bacterial RNA polymerase.

biophysics↗