Biology subjects

Saxena, N.

Publications and source records attributed to Saxena, N..

10 recordsLinked to original sources

bioRxiv2025

Instrument-free quantitative detection of analytes using a novel combo lateral flow assay

Lateral flow assays (LFA) are widely regarded as the cheapest, fastest, and easiest point-of-care (PoC) tests available.1,2 A key advantage is that results can be visually interpreted without the need for specialized equipment, enabling on-site applications while keeping costs low.3 However, conventional LFAs are typically qualitative, limiting their use to simply detect the presence or absence of analytes.4 Additional limitations include narrow dynamic ranges and false negatives due to the Hook Effect in sandwich LFAs.5 In this work, we present a combo lateral flow assay (CLFA) that integrates both sandwich and competitive assay formats, enabling the quantitative detection of analytes across a broad concentration range without an external instrument. The precision of CLFA measurements can be further enhanced with artificial intelligence (AI)-based image analysis via a smartphone app. Importantly, CLFA is not subject to the Hook Effect. CLFA is easily implemented by adding just one extra test line to the standard LFA design, resulting in minimal additional manufacturing effort and cost. Given these benefits, we anticipate that CLFA will have broad applications in diagnostics and research applications. Several examples are provided to illustrate its potential.

biochemistry↗

bioRxiv2021

Dynamic phase separation of the androgen receptor and its coactivators to regulate gene expression.

Numerous cancers, including prostate cancer (PCa), are addicted to transcription programs driven by superenhancers (SEs). The transcription of genes at SEs is enabled by the formation of phase-separated condensates by transcription factors and co-activators with intrinsically disordered regions. The androgen receptor (AR), main oncogenic driver in PCa, contains large disordered regions and is co-recruited with the co-activator MED1 to SEs to promote oncogenic programs. In this work, we show that dynamic AR-rich, liquid-like foci form in PCa models upon androgen stimulation and correlate with AR transcriptional activity. The co-activator MED1 plays an essential role in the formation of AR foci while AR antagonists hinder their formation. These results suggest that enhanced compartmentalization of AR and co-activators at SEs may play an important role in the activation of oncogenic transcription programs in PCa. A better understanding of the assembly and the regulation of these AR-rich compartments may provide novel therapeutic options.

cancer biology↗

bioRxiv2021

Pre-metastatic niche drives breast cancer invasion by modulating MSC homing and CAF differentiation

The extent to which cancer-associated alterations in extracellular matrix stiffness influences the crosstalk between cancer cells and mesenchymal stem cells (MSCs) remains unclear. By analyzing multiple singlecell RNA sequencing datasets, we establish the existence of a cell sub-population co-expressing MSC and cancer associated fibroblast (CAF) markers in highly aggressive triple-negative breast cancers in primary tumor, secondary sites, and in circulatory tumor cell clusters. Using hydrogels of varying stiffness corresponding to different stages of cancer progression, we show that on pre-metastatic stroma mimetic 2 kPa gels, MDA-MB-231 breast cancer cell secreted conditioned media drives efficient MSC chemotaxis and induces stable CAF differentiation in a TGF{beta}/contractility-dependent manner. In addition to enhancing cancer cell proliferation, 2 kPa CAFs maximally boost local invasion and confer resistance to flow-induced shear stresses. Together, our results suggest that homing of MSCs at the pre-metastatic stage and their differentiation into CAFs actively drives breast cancer invasion and metastasis.

cancer biology↗

bioRxiv2021

-actinin-4 drives invasiveness by regulating myosin IIB expression and myosin IIA localization

The mechanisms by which the mechanoresponsive actin crosslinking protein -actinin-4 (ACTN4) regulates cell motility and invasiveness remains incompletely understood. Here we show that in addition to regulating protrusion dynamics and focal adhesion formation, ACTN4 transcriptionally regulates expression of non-muscle myosin IIB (NMM IIB), which is essential for mediating nuclear translocation during 3D invasion. We further demonstrate association between NMM IIA and ACTN4 at the cell front ensures retention of NMM IIA at the cell periphery. A protrusion-dependent model of confined migration recapitulating experimental observations predicts a dependence of protrusion forces on the degree of confinement and on the ratio of nucleus to matrix stiffness. Together, our results suggest that ACTN4 is a master regulator of cancer invasion that regulates invasiveness by controlling NMM IIB expression and NMM IIA localization.

cell biology↗

bioRxiv2021

Using dual-calibrated functional MRI to map brain oxygen supply and consumption in multiple sclerosis

Evidence suggests that cerebrovascular function and oxygen consumption are altered in multiple sclerosis (MS). Here, we quantified the vascular and oxygen metabolic MRI burden in patients with MS (PwMS) and assessed the relationship between these MRI measures of and metrics of damage and disability. In PwMS and in matched healthy volunteers, we applied a newly developed dual-calibrated fMRI method of acquisition and analysis to map grey matter (GM) cerebral blood flow (CBF), oxygen extraction fraction (OEF), cerebral metabolic rate of oxygen consumption (CMRO2) and effective oxygen diffusivity of the capillary network (DC). We also quantified physical and cognitive function in PwMS and controls. There was no significant difference in GM volume between 22 PwMS and 20 healthy controls (p=0.302). Significant differences in CBF (PwMS vs. controls: 44.91 {+/-} 6.10 vs. 48.90 {+/-} 5.87 ml/100g/min, p=0.010), CMRO2 (117.69 {+/-} 17.31 vs. 136.49 {+/-} 14.48 mol/100g/min p<0.001) and DC (2.70 {+/-} 0.51 vs. 3.18 {+/-} 0.41 mol/100g/mmHg/min, p=0.002) were observed in the PwMS. No significant between-group differences were observed for OEF (PwMS vs. controls: 0.38 {+/-} 0.09 vs. 0.39 {+/-} 0.02, p=0.358). Regional analysis showed widespread reductions in CMRO2 and DC for PwMS compared to healthy volunteers. There was a significant correlation between physiological measures and T2 lesion volume, but no association with current clinical disability. Our findings demonstrate concurrent reductions in oxygen supply and consumption in the absence of an alteration in oxygen extraction that may be indicative of a reduced demand for oxygen (O2), an impaired transfer of O2 from capillaries to mitochondria, and/or a reduced ability to utilise O2 that is available at the mitochondria. With no between-group differences in GM volume, our results suggest that changes in brain physiology may precede MRI-detectable GM loss and thus may be one of the pathological drivers of neurodegeneration and disease progression.

neuroscience↗

bioRxiv2020

A comparison of GABA-ergic (propofol) and non-GABA-ergic (dexmedetomidine) sedation on visual and motor cortical oscillations, using magnetoencephalography.

BackgroundUnderstanding the effects of anaesthetic drugs on cortical oscillations can help to elucidate the mechanistic link between receptor physiology and their clinical effects. Propofol produces divergent effects on visual cortical activity: increasing induced gamma-band responses (GBR) while decreasing stimulus-onset-evoked responses) 1. Dexmedetomidine, an 2-adrenergic agonist, differs from GABA-ergic sedatives both mechanistically and clinically as it allows easy arousability from deeper sedation with less cognitive side-effects. Here we use magnetoencephalography (MEG) to characterize and compare the effects of GABAergic (propofol) and non-GABA-ergic (dexmedetomidine) sedation, on visual and motor cortical oscillations. MethodsSixteen male participants received target-controlled infusions of propofol and dexmedetomidine, producing mild-sedation, in a placebo-controlled, cross-over study. MEG data was collected during a combined visual and motor task. ResultsThe key findings were that propofol significantly enhanced visual stimulus induced GBR (44% increase in amplitude) while dexmedetomidine decreased it (40%). Propofol also decreased the amplitudes of the M100 (27%) and M150 (52%) evoked responses, whilst dexmedetomidine had no effect on these. During the motor task, neither drug had any significant effect on motor GBR or movement related beta de-synchronisation (MRBD). However, dexmedetomidine increased (92%) post-movement beta synchronisation/rebound (PMBR) power while propofol reduced it (70%). ConclusionsDexmedetomidine and propofol, at equi-sedative doses, have contrasting effects on visual stimulus induced GBR, visual evoked responses and PMBR. These findings provide a mechanistic link between the known receptor physiology of these sedative drugs and their known clinical effects and may be used to explore mechanisms of other anaesthetic drugs on human consciousness.

neuroscience↗

bioRxiv2019

In-silico evidence that increased cortico-thalamic connectivity and superficial pyramidal disinhibition underlie broadband task-related spectral changes induced by ketamine

Cortical recordings of task-induced oscillations following subanaesthetic ketamine administration demonstrate alterations in amplitude, including increases at high-frequencies (gamma) and reductions at low frequencies (theta, alpha). To investigate the population-level interactions underlying these changes, we implemented a thalamo-cortical model (TCM) capable of recapitulating broadband spectral responses. Compared with an existing cortex-only 4-population model, Bayesian Model Selection preferred the TCM. The model was able to accurately and significantly recapitulate ketamine-induced reductions in alpha amplitude and increases in gamma amplitude. Parameter analysis revealed no change in receptor time-constants but significant increases in select synaptic connectivity with ketamine. Significantly increased connections included both AMPA and NMDA mediated connections from layer 2/3 superficial pyramidal cells to inhibitory interneurons and both GABAA and NMDA mediated within-population gain control of layer 5 pyramidal cells. These results support the use of extended generative models for explaining oscillatory data and provide in silico support for ketamines ability to alter local coupling mediated by NMDA, AMPA and GABA-A.

neuroscience↗

bioRxiv2018

Fate Before Function: Specification of the Hair Follicle Niche Occurs Prior to its Formation and Is Progenitor Dependent

Cell fate transitions are essential for specialization of stem cells and their niches, but the precise timing and sequence of molecular events during embryonic development are largely unknown. Here, we show that dermal condensates (DC), signaling niches for epithelial progenitors in hair placodes, are specified before niche formation and function. With 3D/4D microscopy we identify unclustered DC precursors. With population-based and single-cell transcriptomics we define a molecular time-lapse of dynamic niche signatures and the developmental trajectory as the DC lineage emerges from fibroblasts. Co-expression of downregulated fibroblast and upregulated DC genes in niche precursors reveals a transitory molecular state following a proliferation shutdown. Waves of transcription factor and signaling molecule expression then consolidate DC niche formation. Finally, ablation of epidermal Wnt signaling and placode-derived FGF20 demonstrates their requirement for DC-precursor specification. These findings uncover a progenitor-dependent niche precursor fate and the transitory molecular events controlling niche formation and function.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC=\"FIGDIR/small/414839_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (78K):\norg.highwire.dtl.DTLVardef@13fa73aorg.highwire.dtl.DTLVardef@1fbd280org.highwire.dtl.DTLVardef@1b8f66borg.highwire.dtl.DTLVardef@3a1ef9_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIPrecursors of the hair follicle niche are specified before niche cluster formation\nC_LIO_LIBulk/single cell RNA-seq defines early niche fate at molecular transitional state\nC_LIO_LISuccessive waves of transcription factor/signaling genes mark niche fate acquisition\nC_LIO_LINiche fate acquisition is not \"pre-programmed\" and requires FGF20 from progenitors\nC_LI

developmental biology↗

bioRxiv2018

Gene Correction for SCID-X1 in Long-Term Hematopoietic Stem Cells

Gene correction in human long-term hematopoietic stem cells (LT-HSCs) could be an effective therapy for monogenic diseases of the blood and immune system. High frequencies of reproducible targeted integration of a wild-type cDNA into the endogenous start codon of a gene in LT-HSCs could provide a robust genome editing approach to cure genetic diseases in which patients have different mutations throughout the gene. We describe a clinically relevant method for correcting X-linked severe combined immunodeficiency (SCID-X1). By using a highly specific and active CRISPR/Cas9-AAV6 based strategy and selection-free approach, we achieve up to 20% genome integration frequencies in LT-HSCs of a full-length IL2RG cDNA at the endogenous start site as demonstrated by serial transplantation and analysis of genome edited human cells eight months following initial transplantation. In addition to high frequencies of functional gene correction in LT-HSCs we observed no evidence of abnormal hematopoiesis following transplantation, a functional measure of the lack of genotoxicity. Deep analysis of potential off-target activity detected two sites with low frequency (<0.3%) of off-target mutations. The level of off-target mutations was reduced to below the limit of detection using a high fidelity Cas9. Moreover, karyotype evaluation identified no genomic instability events. We achieved high levels of genome targeting frequencies (median 45%) in CD34+ HSPCs from six SCID-X1 patients and demonstrate rescue of lymphopoietic defect of patient derived cells both in vitro and in vivo. In sum, our study provides specificity, toxicity and efficacy data supportive of clinical development of genome editing to treat SCID-Xl.

bioengineering↗

bioRxiv2017

Odor source localization in complex visual environments by fruit flies

Flying insects routinely forage in complex and cluttered sensory environments. Their search for a food or a pheromone source typically begins with a whiff of odor, which triggers a flight response, eventually bringing the insect in the vicinity of the odor source. The precise localization of an odor source, however, requires the use of both visual and olfactory modalities, aided by air currents that trap odor molecules into turbulent plumes, which the insects track. Here, we investigated odor tracking behavior in fruit flies (Drosophila melanogaster) presented with low- or high-contrast visual landmarks, which were either paired with or separate from an attractive odor cue. These experiments were conducted either in a gentle air stream which generated odor plumes, or in still air in which odor dissipates uniformly in all directions. The trajectories of the flies revealed several novel features of their odor-tracking behavior in addition to those that have been previously documented (e.g. cast- and-surge maneuvers). First, in both moving and still air, odor-seeking flies rely on the co-occurrence of visual landmarks with olfactory cues to guide them to putative odorant objects in the decisive phase before landing. Second, flies abruptly decelerate when they encounter an odor plume, and thereafter steer towards nearby visual objects that had no inherent salience in the absence of odor. This indicates that the interception of an attractive odor increases their salience to nearby high-contrast visual landmarks. Third, flies adopt distinct odor tracking strategies during flight in moving vs. still air. Whereas they weave in and out of plumes towards an odor source when airflow is present, their approach is more gradual and incremental in still air. Both strategies are robust and flexible, and can ensure that the flies reliably find the odor source under diverse visual and airflow environments. Our experiments also indicate the possibility of an olfactory \" working memory\" that enables flies to continue their search even when the olfactory feedback is reduced or absent. Together, these results provide insights into how flies determine the precise location of an odor source.

animal behavior and cognition↗