Biology subjects

Jan, A.

Publications and source records attributed to Jan, A..

12 recordsLinked to original sources

bioRxiv2026

Ancient nervous system architecture in a living ctenophore

The evolutionary origin of nervous systems in animals remains elusive and is largely hidden from the fossil record. Ctenophores, one of the earliest-branching animals possessing neurons, are instrumental to our understanding of nervous system origin, and a few rare ctenophore fossils preserve traces of nervous tissue as carbonaceous remains. Cambrian ctenophores appear to exhibit a more diverse neuroanatomy than that of modern species, suggesting secondary loss in extant ctenophores. However, much remains unknown about the origin and ontogeny giving rise to the structural organization of modern ctenophore nervous systems. Here, by investigating the neural anatomy of the ctenophore Mnemiopsis leidyi during development, we identified a ladder-like nerve net (LNN) beneath the comb rows that converges into condensed neurites and connects to the aboral organ. Examination of carbon-rich areas of Ctenorhabdotus capulus, an extinct ctenophore from the Burgess Shale, reveals a pattern similar to that of M. leidyi, consistent with a shared neural organization. Furthermore, M. leidyi exhibits a condensed comb nerve, resembling the longitudinal nerve preserved in the Cambrian ctenophore Fasciculus vesanus and the giant axon of extant Euplokamis dunlapae. Our study reveals conserved evolutionary constraints shaping nervous system architectures linked to locomotory organs and indicates that the different modes of nervous system organization observed in Cambrian ctenophores are variably retained in modern species.

neuroscience↗

bioRxiv2025

Evaluating the Synergetic Effect of Nigella sativa Extract and Metal Oxide Nanoparticles Against Different Microbes

BackgroundThe emergence of antibiotic-resistant bacteria necessitates the exploration of alternative antimicrobial agents. Nigella sativa (black seed) and metal oxide nanoparticles have independently shown antimicrobial properties, but their synergetic effects remain understudied. ObjectiveThis study investigated the individual and combined antimicrobial activities of Nigella sativa extract with zinc oxide (ZnO), manganese-doped zinc oxide (Mn-ZnO), and cobalt-doped zinc oxide (Co-ZnO) nanoparticles against Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa. MethodsNanoparticles were synthesized via co-precipitation method and characterized using UV-Vis spectroscopy, X-ray diffraction (XRD), transmission electron microscopy (TEM), and scanning electron microscopy (SEM). N. sativa extract was prepared through maceration in 70% methanol. Antimicrobial activity was assessed using agar well diffusion assay and minimum inhibitory concentration (MIC) determination. ResultsNanoparticles demonstrated significant antimicrobial activity against E. coli (inhibition zones: 2.5-2.7 cm) but showed no activity against S. aureus and P. aeruginosa. Conversely, N. sativa extract exhibited antimicrobial activity against S. aureus and P. aeruginosa (inhibition zones: 2.0-2.2 cm) but not against E. coli. No synergetic effect was observed when nanoparticles and N. sativa extract were combined. ConclusionThe study revealed complementary but non-synergistic antimicrobial activities between N. sativa extract and metal oxide nanoparticles. Future research should investigate the molecular mechanisms preventing synergy and explore potential antagonistic interactions.

microbiology↗

bioRxiv2025

The 3D architecture of the ctenophore aboral organ and the evolution of complex integrative centers in animals

The ability to sense and respond to environmental cues is fundamental to animal behavior and survival. In ctenophores - early-branching marine animals - a syncytial nerve net underlies complex behaviors such as geotaxis, feeding, and escape. At the center of this system is the aboral organ (AO), a dense sensory hub that detects motion, light, and pressure and coordinates ciliary movement. However, the AOs cellular architecture and its integration with the nerve net remain poorly understood. Here, using volume electron microscopy in Mnemiopsis leidyi, we reveal that the syncytial nerve net converges and condenses around the AO, forming synaptic connections with diverse effector cells. We annotated 17 distinct cell types, including candidate light and pressure sensors, novel ciliated and secretory cells, and non-synaptic vesicle-rich cells likely involved in volume transmission. Our data shows that signal processing within the AO relies on both synaptic and non-synaptic communication. Gene expression profiling of conserved transcription factors indicates that the AO is a functionally convergent, evolutionarily distinct sensory structure that retains minimal homology. Our findings redefine the ctenophore AO as a highly integrated, multilayered sensory system critical for behavioral regulation.

evolutionary biology↗

bioRxiv2025

Pathogenic O-GlcNAc dyshomeostasis associated with cortical malformations and hyperactivity

Missense variants in the O-GlcNAc transferase (OGT) gene have recently been shown to segregate with a syndromic form of intellectual disability (OGT-ID), underscoring the importance of protein O-GlcNAcylation in brain function. However, the underlying pathophysiological mechanisms linking ID to potential OGT malfunction--whether developmental, neurophysiological, or both--remain unclear. Here, we present comprehensive analyses encompassing behaviour and brain architecture of a rodent model carrying the pathogenic C921Y OGT-ID variant. These mice show a range of behavioural deficits, including hyperactivity, impulsivity, and associative learning phenotypes. Structural studies, using micro-computed tomography and magnetic resonance imaging, revealed reduced skull size, microcephaly, reduced cortical thickness and hypoplastic corpus callosum. Detailed histological analyses revealed dysplastic changes in the neocortex, predominantly affecting the superficial layers of cingulate cortex. Mechanistically, quantitative proteomic analyses revealed O-GlcNAc dyshomeostasis associated with distinct perturbed molecular pathways involved in brain development. Taken together, these data reveal neurodevelopmental defects associated with O-GlcNAc dyshomeostasis and provide a platform for dissecting mechanism and treatments of OGT-ID.

neuroscience↗

bioRxiv2025

Label-free Machine Learning Prediction of Chemotherapy on Tumor Spheroids using a Microfluidics Droplet Platform

To rapidly evaluate the effects of anticancer treatments in 3D models, an integrated approach is proposed, combining a droplet-based microfluidic platform for spheroid formation and single-spheroid chemotherapy application, label-free morphological analysis, and machine learning to assess treatment response. Morphological features of spheroids, such as size and color intensity, are extracted and selected using the Multivariate Information-based Inductive Causation (MIIC) algorithm, and used to train a neural network for spheroid classification into viability classes, derived from metabolic assays performed within the same platform as a benchmark. The model was tested on Ewing sarcoma cell line and patient-derived xenograft (PDX) cells, demonstrating robust performance across datasets. It accurately predicts spheroid viability, used to generate dose-response curves and to determine half-maximal inhibitory concentration (IC50) values comparable to traditional biochemical assays. Notably, a model trained on cell line spheroids successfully classifies PDX spheroids, highlighting its adaptability. Compared to convolutional neural network-based approaches, this method works with smaller training datasets and provides greater interpretability by identifying key morphological features. The droplet platform further reduces cell requirements, while single spheroid confinement enhances classification quality. Overall, this label-free experimental and analytical platform is confirmed as a scalable, efficient, and dynamic tool for drug screening.

bioengineering↗

bioRxiv2025

Improved Graph-based Antibody-aware Epitope Prediction with Protein Language Model-based Embeddings

The accurate identification of B-cell epitopes is critical in antibody design, diagnostics, and immunotherapies. Many in silico approaches have recently been proposed to predict epitopes, but these approaches struggle primarily because of the variational and conformational nature of epitopes. However, deep learning-based approaches have recently shown great promise in achieving better performance at the epitope prediction task. In this paper, we employ a graph convolutional network (GCN) coupled with pre-trained protein language model (PLM)-based embeddings for epitope prediction on a benchmark antibody-specific epitope prediction (AsEP) dataset. We explore the use of different PLM-embedding methods on the epitope prediction task and show that the choice of PLM embeddings impacts the performance. Specifically, we find that antibody-specific PLMs such as AntiBERTy and general PLMs such as ProtTrans and ESM-2 for antigens provide improved epitope prediction performance with an AUCROC of 0.65, precision of 0.28, and recall of 0.46. The source code is available at: https://github.com/mansoor181/walle-pp.git.

bioinformatics↗

bioRxiv2024

Molecular signatures of altered energy metabolism and circadian rhythm perturbations in a model of extra-nigral Synucleinopathy.

A pathological role of alpha-Synuclein (aSyn) aggregation in the central nervous system (CNS) is a recognized feature in Parkinson disease (PD) and related neurodegenerative conditions termed synucleinopathies. In order to characterize the cellular response in CNS to incipient and advanced aSyn pathology, we applied spatial transcriptomics on brain sections derived from a transgenic mouse model (M83+/+ line, Prnp-SNCA*A53T) in which aSyn aggregation was induced in a prion-like fashion through hindlimb intramuscular delivery of pre-formed fibrillar (PFF) murine aSyn. Our spatially-resolved transcriptomics (ST) data point to unique perturbations in brain energy metabolism during the progression of aSyn pathology, such that the early stage of aSyn aggregate pathology activates molecular pathways controlling metabolic flux through glycolysis, oxidative phosphorylation and fatty acid metabolism. In contrast, the ST data indicate a profound decline in mitochondrial metabolism in the brains of symptomatic animals with advanced aSyn pathology. The latter stage was also associated with drastic reduction in mRNA translation machinery, along with aberrant expression of molecular drivers involved in RNA splicing and inflammatory response. Intriguingly, our ST data also point to perturbed regulation of circadian rhythm, was corroborated by increased immunodetection of CREB-binding protein (a modulator of core clock machinery) in the brains of symptomatic animals, and transcriptional upregulation of CREBBP in 4 independent PD microarray datasets. Collectively, we anticipate that our findings offer novel opportunities in knowledge translation for mechanism-based drug discovery and biomarkers in neurodegenerative synucleinopathies.

neuroscience↗

bioRxiv2024

Bradykinesia and postural instability in a model of prodromal Synucleinopathy with alpha-Synuclein aggregation in the gigantocellular nuclei.

-Synuclein (aSyn) accumulation within the extra-nigral neuronal populations in brainstem, including the gigantocellular nuclei (GRN/Gi) of reticular formation, is a recognized feature during the prodromal phase of Parkinson disease (PD). Accordingly, there is a burgeoning interest in animal model development for understanding the pathological significance of extra-nigral synucleinopathy, in relation to motor and/or non-motor symptomatology in PD. Here, we report an experimental paradigm for the induction of aSyn aggregation in brainstem, with stereotaxic delivery of pre-formed fibrillar (PFF) aSyn in the pontine GRN of transgenic mice expressing the mutant human Ala53Thr aSyn (M83 line). Our data show that PFF aSyn-induced aggregate pathology in GRN leads to progressive decline in spontaneous locomotion and an early phenotype of postural instability. This early phase of bradykinesia was followed by a moribund stage, characterized by worsening motor performance and impaired survival with substantial aSyn aggregation in several brain regions beyond the GRN. Collectively, our observations suggest an experimental framework for studying the pathological significance of aSyn aggregation in GRN in relation to features of movement disability in PD. With further refinements, we anticipate that this model holds promise as a test-bed for translational research in PD and related disorders.

neuroscience↗

bioRxiv2022

Surface tension drives neuronal sorting in magnetically engineered brain-like tissue

Engineered 3D brain-like models have advanced the understanding of neurological mechanisms and disease, yet their mechanical signature, while fundamental for brain function, remains understudied. The surface tension for instance controls brain development and is a marker of cell-cell interactions. Here, we engineered 3D magnetic brain-like tissue spheroids composed of intermixed primary glial and neuronal cells at different ratios. Remarkably, the two cell types self-assemble into a functional tissue, with the sorting of the neuronal cells towards the periphery of the spheroids, whereas the glial cells constitute the core. The magnetic fingerprint of the spheroids then allows their deformation when placed under a magnetic field gradient, at a force equivalent to a 70 g increased gravity at the spheroid level. The tissue surface tension and elasticity can be directly inferred from the resulting deformation, revealing a transitional dependence on the glia/neuron ratio, with the surface tension of neuronal tissue being much lower. This provides the underlying mechanical explanation for the exclusion of the neurons towards the outer spheroid region, and depicts the glia/neuron organization as a surface tension-driven sophisticated mechanism that should in turn influence brain development and homeostasis.

bioengineering↗

bioRxiv2021

α-Synuclein pathology in Parkinson disease activates homeostatic NRF2 anti-oxidant response

Circumstantial evidence points to a pathological role of alpha-synuclein (aSyn; gene symbol SNCA), conferred by aSyn misfolding and aggregation, in Parkinson disease (PD) and related synucleionpathies. Several findings in experimental models implicate perturbations in the tissue homeostatic mechanisms triggered by pathological aSyn accumulation, including impaired redox homeostasis, as significant contributors in the pathogenesis of PD. The nuclear factor erythroid 2-related factor (NRF2) is recognized as the master regulator of cellular anti-oxidant response, both under physiological as well as in pathological conditions. Using immunohistochemical analyses, we show a robust nuclear NRF2 accumulation in post-mortem PD midbrain, detected by NRF2 phosphorylation on serine residue 40 (nuclear active p-NRF2, S40). Curated gene expression analyses of four independent publicly available microarray datasets revealed considerable alterations in NRF2-responsive genes in the disease affected regions in PD, including substantia nigra, dorsal motor nucleus of vagus, locus coeruleus and globus pallidus. To further examine the putative role of pathological aSyn accumulation on nuclear NRF2 response, we employed a transgenic mouse model of synucleionopathy (M83 line, Prnp-SNCA*Ala53Thr), which manifest widespread aSyn pathology (phosphorylated aSyn; S129) in the nervous system following intramuscular inoculation of exogenous fibrillar aSyn. We observed strong immunodetection of nuclear NRF2 in neuronal populations harboring p-aSyn (S129), and found an aberrant anti-oxidant and inflammatory gene response in the affected neuraxis. Taken together, our data support the notion that pathological aSyn accumulation impairs the redox homeostasis in nervous system, and boosting neuronal anti-oxidant response is potentially a promising approach to mitigate neurodegeneration in PD and related diseases.

neuroscience↗

bioRxiv2020

Parallelized manipulation of adherent living cells by magnetic nanoparticles-mediated forces

The remote actuation of cellular processes such as migration or neuronal outgrowth is a challenge for future therapeutic applications in regenerative medicine. Among the different methods that have been proposed, the use of magnetic nanoparticles appears to be promising since magnetic fields can act at a distance without interactions with the surrounding biological system. To control biological processes at a subcellular spatial resolution, magnetic nanoparticles can be used either to induce biochemical reactions locally or to apply forces on different elements of the cell. Here, we show that cell migration and neurite outgrowth can be directed by the forces produced by a switchable parallelized array of micro-magnetic pillars, following passive uptake of nanoparticles. Using live cell imaging, we first demonstrate that adherent cell migration can be biased toward magnetic pillars and that cells can be reversibly trapped onto these pillars. Second, using differentiated neuronal cells we were able to induce events of neurite outgrowth in the direction of the pillars without impending cell viability. Our results show that the range of forces applied needs to be adapted precisely to the cellular process under consideration. We propose that cellular actuation is the result of the force on the plasma membrane caused by magnetically filled endo-compartments, which exert a pulling force on the cell periphery.

bioengineering↗

bioRxiv2019

An improved whole life cycle culture protocol for the hydrozoan genetic model Clytia hemisphaerica.

The jellyfish species Clytia hemisphaerica (Cnidaria, Hydrozoa) has emerged as a new experimental model animal in the last decade. Favorable characters include a fully transparent body suitable for microscopy, daily gamete production and a relatively short life cycle. Furthermore, whole genome sequence assembly and efficient gene editing techniques using CRISPR/Cas9 have opened new possibilities for genetic studies. The quasi-immortal vegetatively-growing polyp colony stage provides a practical means to maintain mutant strains. In the context of developing Clytia as a genetic model, we report here an improved whole life cycle culture method including an aquarium tank system designed for culture of the tiny jellyfish form. We have compared different feeding regimes using Artemia larvae as the food and demonstrate that the stage-dependent feeding control is the key for rapid and reliable medusa and polyp rearing. Metamorphosis of the planula larvae into a polyp colony can be efficiently induced using a new synthetic peptide. The optimized procedures detailed here make it practical to generate new genetically modified Clytia strains and to safely maintain their whole life cycle in the laboratory.

developmental biology↗