Biology subjects

Singla, R.

Publications and source records attributed to Singla, R..

5 recordsLinked to original sources

bioRxiv2026

Aerobic GenX Defluorination by a Wastewater Cladosporium halotolerans Strain with a Genomically Expanded Haloacid Dehalogenase Repertoire

Per- and polyfluoroalkyl substances (PFAS) such as GenX (HFPO-DA) are aerobically recalcitrant contaminants for which biological treatment options remain scarce; the best-characterized microbial degraders require strictly anaerobic conditions and external cofactors. We isolated Cladosporium halotolerans strain CsHGX-1 from activated sludge at a municipal wastewater treatment plant using GenX as the sole carbon source. Whole-genome sequencing (32.4 Mb; 11,201 genes) revealed a PFAS-degradation gene repertoire substantially expanded relative to congeneric Cladosporium species, including 26 dehalogenases (four type-II haloacid dehalogenases, HADs), 141 cytochrome P450s, and 558 esterases/hydrolases. Under aerobic conditions with GenX (50 mg L-1) as the sole carbon source, strain CsHGX-1 removed 47.6 {+/-} 1.7% of GenX within 48 h, accompanied by fluoride release (0.079 {+/-} 0.018 mM) that was absent in abiotic controls, confirming genuine C-F bond cleavage. Time-resolved RNA sequencing (0, 6, 24, 48 h; n = 6 biological replicates) revealed a phase-structured transcriptional program: oxidative genes, including cytochrome P450s, peaked first (6 h; up to 25.4-fold), hydroxylation and reactive-oxygen-species-management genes peaked next (24 h; up to 33.5-fold), and the three type-II HAD genes peaked last (48 h; up to 50.9-fold), coincident with fluoride accumulation. A parallel resazurin metabolic assay over 5 days confirmed sustained catabolic activity in GenX-exposed cultures relative to controls (1.37-1.52-fold; p [≤] 0.003). These findings identify strain CsHGX-1 as, to our knowledge, the first Ascomycete fungus for which genomic and transcriptomic evidence links oxidative activation to haloacid-dehalogenase-mediated defluorination of an aerobically recalcitrant PFAS, extending the known diversity of fungal PFAS degraders beyond Basidiomycota white-rot taxa. IMPORTANCEGenX is a PFAS "replacement" chemical that the U.S. Environmental Protection Agency added to its list of hazardous constituents in 2024, yet no aerobic biological treatment exists for it: every well-characterized microbial degrader requires oxygen-free conditions and added cofactors. We show that a fungus recovered from ordinary wastewater sludge breaks down GenX while using oxygen, the same conditions already used in conventional treatment plants, with no nutrient or reductant supplementation. Genome sequencing showed why this strain is unusual: it carries far more dehalogenase and cytochrome P450 genes than its close relatives. Time-course RNA sequencing showed these genes switch on in a defined order, oxidation first, then carbon-fluorine bond cleavage, matching the appearance of free fluoride in the culture. This links genome content to a functional outcome in an Ascomycete fungus, suggesting aerobic fungal defluorinators may already be present, unrecognized, in engineered wastewater systems.

microbiology↗

bioRxiv2025

Parallelized Brightfield and Fluorescence Imaging of Organoids Using a Scalable Multi-Camera Platform

Organoid viability, maturation, and growth is commonly assayed through brightfield and fluorescence microscopy using a single objective lens. However, standard microscopic imaging systems pose significant limitations for high-throughput applications, particularly in large-scale experiments where simultaneous imaging of multiple organoids requires increased throughput. There is a strong need for systems that can capture organoid growth rapidly and consistently while minimizing disturbances to culture conditions. Here, we present a novel multi-camera array scanner (MCAS) that parallelizes imaging through the simultaneous use of 48 objective lenses and sensors, resulting in a 95% reduction in acquisition times compared to commercial high-content imagers. We demonstrate and validate this system in multiple well plate formats, in both 2D and 3D neural cell cultures, and in brightfield and fluorescence. The MCAS improves efficiency for measuring organoid growth rates, assessing responses to morphogens and drugs, and measuring viral transduction efficiency. Together, these findings establish the MCAS as a scalable and versatile imaging platform for rapid phenotyping in organoid research.

neuroscience↗

bioRxiv2022

Post-activation depression produces extensor H-reflex suppression following flexor afferent conditioning

Suppression of the extensor H-reflex by flexor afferent conditioning is thought to be produced by a long-lasting inhibition of extensor Ia-afferent terminals via primary afferent depolarization (PAD) activated by GABAA receptors. Considering the recent finding that PAD does not produce presynaptic inhibition of Ia-afferent terminals, we examined if H-reflex suppression is instead mediated by post-activation depression of the test extensor Ia-afferents triggered by PAD-evoked spikes and/or by a long-lasting inhibition of the extensor motoneurons. A brief conditioning vibration of the flexor tendon suppressed both the extensor soleus H-reflex and the tonic discharge of soleus motor units for 300 ms, indicating that part of the H-reflex suppression was mediated by a long-lasting inhibition of the extensor motoneurons. When activating the flexor afferents electrically to produce conditioning, the soleus H-reflex was also suppressed for 300 ms, but only when a short-latency reflex was evoked in the soleus muscle by the conditioning input itself. In mice, a similar short-latency reflex was evoked when optogenetic or afferent activation of GABAergic (GAD2+) neurons produced PAD large enough to evoke orthodromic spikes in the test Ia-afferents, causing post-activation depression of subsequent monosynaptic excitatory-post-synaptic potentials. The time course of this post-activation depression and related H-reflex suppression (lasting 2 s) was like rate-dependent depression that is also due to post-activation depression. We conclude that extensor H-reflex inhibition by brief flexor afferent conditioning is produced by both post-activation depression of extensor Ia-afferents and long-lasting inhibition of extensor motoneurons, rather than from PAD directly inhibiting Ia afferent terminals.

neuroscience↗

bioRxiv2021

Nodal GABA facilitates axon spike transmission in the spinal cord.

Movement and posture depend on sensory feedback that is regulated by specialized GABAergic neurons (GAD2+) that form axo-axonic contacts onto myelinated proprioceptive sensory axons and are thought to be inhibitory. However, we report here that activating GAD2+ neurons, directly with optogenetics or indirectly by cutaneous stimulation, facilitates sensory feedback to motoneurons in awake rodents and humans. GABAA receptors and GAD2+ innervation at or near nodes of Ranvier of sensory axons cause this facilitation, preventing spike propagation failure at the many axon branch points, which is otherwise common without GABA. In contrast, GABAA receptors are generally lacking from axon terminals (unlike GABAB) and do not presynaptically inhibit transmitter release onto motoneurons. GABAergic innervation near nodes and branch points allows individual branches to function autonomously, with GAD2+ neurons regulating which branches conduct, adding a computational layer to the neuronal networks generating movement and likely generalizing to other CNS axons.

neuroscience↗

bioRxiv2020

Shortlisting genes important in seed maturation by principal component analysis of gene expression data

Transcriptome data are widely used for functional analysis of genes. De-novo assembly of transcriptome gives a large number of unigenes. A large proportion of them remain unannotated. Efficient computational methods are required for identifying genes and modeling those for regulatory and functional roles. Principal component analysis (PCA) was used in a novel approach to shortlist genes, independently of annotation in genome expression data, taking seed development in Arabidopsis thaliana as a representative case. PCA was applied to published genome expression data from four lines of Arabidopsis, mutated in seed development. The PC separating all the developmental stages between a mutant and its respective wild type was selected for shortlisting genes as functionally more important. The shortlisted genes identified by PCA belong to a number of biological functions. The genes reported to give sensitivity to desiccation were identified in PCA analysis also in desiccation intolerant lines only. With respect to the network of 98 genes targeted by ABI3, a higher number of genes was identified as important in the mutants abi 3-5, fus 3-3 andlec 1-1 in comparison to abi 3-1. Ontological analysis and comparison with earlier studies suggest that PCA of genome expression data is useful for shortlisting functionally important genes.

bioinformatics↗