Biology subjects

Gupta, P.

Publications and source records attributed to Gupta, P..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

Transcriptional modulation during photomorphogenesis in rice seedlings

Light is one of the most important factors regulating plant gene expression patterns, metabolism, physiology, growth, and development. To explore how light may induce or alter transcript splicing, we conducted RNA-Seq-based transcriptome analyses by comparing the samples harvested as etiolated seedlings grown under continuous dark conditions vs. the light-treated green seedlings. We identified 14,766 differentially expressed genes, of which 4369 genes showed alternative splicing. We observed that genes mapped to the plastid-localized methyl-erythritol-phosphate (MEP) pathway were light-upregulated compared to the cytosolic mevalonate (MVA) pathway genes. Many of these genes also undergo splicing. These pathways provide crucial metabolite precursors for the biosynthesis of secondary metabolic compounds needed for chloroplast biogenesis, the establishment of successful photosynthetic apparatus, and photomorphogenesis. In the chromosome-wide survey of the light-induced transcriptome, we observed intron retention as the most predominant splicing event. In addition, we identified 1709 novel lncRNA transcripts in our transcriptome data.

plant biology↗

bioRxiv2023

Double Imprinted Nanoparticles for Sequential Membrane-to-Nuclear Drug Delivery

Nanoparticles functionalized with specific receptors (e.g., antibodies, peptides) are used for targeted drug delivery of anti-cancer agents but their side effects include hypersensitivity reactions, toxicity, inflammation, and life-threatening allergic reactions (Anaphylaxis) [1,2]. Consequently, double imprinted molecularly imprinted nanoparticles (nanoMIPs) against a linear epitope of breast cancer cell receptor estrogen alpha (ER) and loaded with an anti-cancer agent (doxorubicin, DOX) are synthesized via a solid-phase approach. Surface plasmon resonance (SPR) measurements reveal that the produced nanoMIPs exhibit KD values of 19 nM (against the epitope used for imprinting) and 10 nM (ER receptor), and thus rival the affinity of nanoparticles decorated with natural affinity reagents (e.g., antibodies, peptides), whilst offering the advantages of low-cost and enhanced cellular uptake due to the receptor mediated endocytosis. We present the results of in vitro flow cytometry that DOX loaded nanoMIPs can preferentially bind to MCF-7 (ER positive) breast cancer (BC) cells vs MDA-MB-231 (ER negative) BC cells. Confocal imaging witnessed the above results and showed the sequential movement of the DOX loaded nanoMIPs from membrane to the nucleus of MCF-7 BC cells and achieve delivery of DOX once internalised in the cells (directly to the nucleus). As a result, enhanced cell toxicity in MCF-7 cells ([~]80%) as compared to MDA-MB-231 cells ([~]15%) is observed via MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide) cytotoxicity assay in a time dependent manner. Overall, this study provides a promising approach for the targeted drug delivery of chemotherapeutic drugs to breast cancer cells, which has the potential to significantly improve patient outcome whilst also reducing debilitating side effects of current treatment.

cancer biology↗

bioRxiv2023

Faulty Metabolism: A Potential Instigator of an Aggressive Phenotype in Cdk5-dependent Medullary Thyroid Carcinoma

Mechanistic modeling of cancers such as Medullary Thyroid Carcinoma (MTC) to emulate patient-specific phenotypes is challenging. The discovery of potential diagnostic markers and druggable targets in MTC urgently requires clinically relevant animal models. Here we established orthotopic mouse models of MTC driven by aberrantly active Cdk5 using cell-specific promoters. Each of the two models elicits distinct growth differences that recapitulate the less or more aggressive forms of human tumors. The comparative mutational and transcriptomic landscape of tumors revealed significant alterations in mitotic cell cycle processes coupled with the slow-growing tumor phenotype. Conversely, perturbation in metabolic pathways emerged as critical for aggressive tumor growth. Moreover, an overlapping mutational profile was identified between mouse and human tumors. Gene prioritization revealed putative downstream effectors of Cdk5 which may contribute to the slow and aggressive growth in the mouse MTC models. In addition, Cdk5/p25 phosphorylation sites identified as biomarkers for Cdk5-driven neuroendocrine tumors (NETs) were detected in both slow and rapid onset models and were also histologically present in human MTC. Thus, this study directly relates mouse and human MTC models and uncovers vulnerable pathways potentially responsible for differential tumor growth rates. Functional validation of our findings may lead to better prediction of patient-specific personalized combinational therapies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=159 HEIGHT=200 SRC="FIGDIR/small/544755v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@196ed2dorg.highwire.dtl.DTLVardef@1ad2d59org.highwire.dtl.DTLVardef@7c6e84org.highwire.dtl.DTLVardef@13bd7db_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LICGRP driven aberrant Cdk5 activation develops early onset aggressive MTC C_LIO_LIGenetic alterations in mouse and human tumors disrupt common pathways C_LIO_LIAggressive tumor model characterized by alterations in metabolic pathways C_LIO_LISlow growing tumor model elicits disruption of mitotic spindle assembly C_LI

cancer biology↗

bioRxiv2023

Introgression of a dominant phototropin1 mutant superenhances carotenoids and boosts flavor-related volatiles in genome-edited tomato RIN mutants

The tomato (Solanum lycopersicum) ripening inhibitor (rin) mutation is known to completely repress fruit ripening. The heterozygous (RIN/rin) fruits have extended shelf life, ripen normally, but have poor taste and flavour. Even the CRISPR/Cas9-generated rin alleles have these undesirable attributes associated with the rin mutation. To address this, we used genome editing to generate newer alleles of RIN (rinCR) by targeting the K domain, which is essential for the oligomerization of MADS-box transcription factors. Unlike previously reported CRISPR alleles, the rinCRalleles displayed delayed onset of ripening, suggesting that the mutated K domain represses the onset of ripening. The rinCR fruits had extended shelf life and accumulated carotenoids at an intermediate level between rin and wild-type parent. Besides, the metabolites and hormonal levels in rinCR fruits were more akin to rin. To overcome the negative attributes of rin, we crossed the rinCR alleles with Nps1, which enhances carotenoid levels in tomato fruits. Nps1 harbours a dominant-negative mutation in the plant photoreceptor phototropin1. The resulting Nps1/rinCR hybrids had extended shelf life and 4.4-7.1-fold higher carotenoid levels than the wild-type parent. The Nps1/rinCR fruits had higher auxin and reduced ABA levels, which are reportedly linked with slower ripening. The metabolome of Nps1/rinCRfruits revealed higher sucrose, malate, and volatiles associated with tomato taste and flavour. Notably, the boosted volatile levels in Nps1/rinCR were only observed in fruits bearing the homozygous Nps1 (Nps1/Nps1) mutation. Our findings suggest that the Nps1 introgression into tomato ripening mutants provides a promising strategy for developing tomato cultivars with extended shelf life, improved taste, and flavour.

plant biology↗

bioRxiv2023

Multiplexed fluorescence and scatter detection with single cell resolution using on-chip fiber optics for droplet microfluidic applications

Droplet microfluidics has emerged as a critical component of several high-throughput single cell analysis techniques in biomedical research and diagnostics. However, while there has been significant progress in the individual assays being developed, multi-parametric optical sensing of droplets and their encapsulated contents remains challenging. The current common approach of microscopy based high-speed imaging of droplets is technically complex and requires expensive instrumentation limiting their large-scale adoption. Here we have adapted the principles of the widely established technique of flow cytometry to a novel optofluidic setup - the OptiDrop platform, with on-chip detection of scatter and multiple fluorescence signals from microfluidic droplets and their contents using optical fibers. The highly customizable on-chip optical fiber-based signal detection system enables simplified, miniaturized, low-cost, multi-parametric sensing of optical signals with high sensitivity and single cell resolution within each droplet. Our work on differential expression analysis of the Major Histocompatibility Complex (MHC) protein in response to IFN{gamma} stimulation further demonstrates the OptiDrop platforms capabilities in sensitively detecting cell surface biomarkers using fluorescently labeled antibodies. The OptiDrop platform thus combines the versatility of flow cytometry with the power of droplet microfluidics to provide wide-ranging optical sensing solutions for research and diagnostics.

bioengineering↗

bioRxiv2023

Trilliumosides A-B, two novel steroidal saponins isolated from Rhizomes of Trillium govanianum as potent anticancer agents targeting apoptosis in A-549 cancer cell line.

Two novel steroidal saponins, Trilliumosides A (1) and B (2) were isolated from the rhizomes of Trillium govanianum by bioactivity-guided phytochemical investigation along with seven known compounds protodioscin (3) govanoside B (4), borassoside E (5), 20-hydroxyecdysone (6), 5-20-hydroxyecdysone (7), govanic acid (8), and diosgenin (9). The structure of novel compounds 1-2 were established using spectroscopic methods such as 1D, 2D NMR data and HR-ESI-MS. The isolated compounds were evaluated for in-vitro cytotoxic activity against a panel of human cancer cell lines. Compound 1 showed significant cytotoxic activity against A-549 (Lung) and SW-620 (Colon) cell lines with IC50 values of 1.83 and 1.85 {micro}M, whereas compound (2) IC50 value against A-549 cell line was found to be 1.79 {micro}M. Among previously known compounds (3), (5) and (9) their cytotoxic IC50 value was found to be in the range of 5-10 {micro}M. In detailed anticancer analysis compound (2) was seen inhibiting colony forming potential and in-vitro migration in the A-549 cell line. Furthermore, the mechanistic study of compound (2) on the A-549 cell line revealed characteristic changes including nuclear morphology, increased ROS generation, and reduced levels of MMP. Above mentioned events eventually induce apoptosis, a key hallmark in cancer studies, by upregulating the pro-apoptotic protein BAX and downregulating the anti-apoptotic protein BCL-2 thereby activating Caspase-3. Our study reports the first mechanistic anticancer evaluation of the compounds isolated from the rhizomes of Trillium govanianumwith remarkable activity in the desired micro molar range. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/537170v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@14d9769org.highwire.dtl.DTLVardef@10f7658org.highwire.dtl.DTLVardef@22a38borg.highwire.dtl.DTLVardef@1f0b28_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2023

Triggering receptor expressed on myeloid cells 2 (TREM2) regulates phagocytosis in glioblastoma

Glioblastomas (GBMs) are tumors of the central nervous system that remain recalcitrant to both standard of care chemo-radiation and immunotherapies. Emerging approaches to treat GBMs include depletion or re-education of innate immune cells including microglia (MG) and macrophages (MACs). Here we show myeloid cell restricted expression of triggering receptor expressed on myeloid cells 2 (TREM2) across low- and high-grade human gliomas. TREM2 expression did not correlate with immunosuppressive pathways, but rather showed strong positive association with phagocytosis markers such as lysozyme (LYZ) and CD163 in gliomas. In line with these observations in patient tumors, Trem2-/- mice did not exhibit improved survival compared to wildtype (WT) mice when implanted with mouse glioma cell lines, unlike observations previously seen in peripheral tumor models. Gene expression profiling revealed pathways related to inflammation, adaptive immunity, and autophagy that were significantly downregulated in tumors from Trem2-/- mice compared to WT tumors. Using ZsGreen-expressing CT-2A orthotopic implants, we found higher tumor antigen engulfment in Trem2+ MACs, MG, and dendritic cells. Our data uncover TREM2 as an important immunomodulator in gliomas and inducing TREM2 mediated phagocytosis can be a potential immunotherapeutic strategy for brain tumors. Key pointsO_LITREM2 is not associated with immunosuppressive molecules in GBM C_LIO_LITREM2 is associated with phagocytosis in both human and mouse gliomas C_LIO_LIDeletion of Trem2 in mice does not improve survival in glioma models C_LI Importance of the studyTriggering receptor expressed on myeloid cells 2 (TREM2) has been implicated as a major immunoregulator in both neurodegenerative diseases and systemic cancers, yet its functional role in gliomas remains unclear. This study reveals that unlike in other cancers, TREM2 is not associated with immunosuppression in the glioma microenvironment. In fact, TREM2 expression is associated with phagocytosis in both human and mouse gliomas, similar to its role in Alzheimers disease. These findings indicate that TREM2 blockade will not be a viable treatment strategy for gliomas. Instead, TREM2 induction may boost the potential of myeloid cells in the tumor microenvironment to engulf cancer cells.

cancer biology↗

bioRxiv2023

ZEB1-dependent modulation of fibroblast polarization governs inflammation and immune checkpoint blockade sensitivity in colorectal cancer

The EMT-transcription factor ZEB1 is heterogeneously expressed in tumor cells and in cancer-associated fibroblasts (CAFs) in colorectal cancer (CRC). While ZEB1 in tumor cells regulates metastasis and therapy resistance, its role in CAFs is largely unknown. Combining fibroblast-specific Zeb1 deletion with immunocompetent mouse models of CRC, we observe that inflammation-driven tumorigenesis is accelerated, whereas invasion and metastasis in sporadic cancers is reduced upon fibroblast-specific loss of Zeb1. Single-cell transcriptomics, histological and in vitro characterization reveal a crucial role in CAF polarization, promoting myofibroblastic features whilst restricting inflammatory activation. Zeb1 deficiency impairs collagen deposition and CAF barrier function but increases cytokine production, jointly promoting lymphocyte recruitment and immune checkpoint activation. Strikingly, the Zeb1-deficient CAF repertoire sensitizes to immune checkpoint inhibition, pointing to a therapeutic opportunity of targeting ZEB1 in CAFs and its usage as a prognostic biomarker. Collectively, we demonstrate that ZEB1-dependent plasticity of CAFs suppresses anti-tumor immunity and promotes metastasis.

cancer biology↗

bioRxiv2023

A surprising lack of presaccadic benefits during visual change detection

Even before the eyes move, visual sensitivity improves at the target of the planned eye movement. Yet, it is unknown if such "presaccadic" benefits are merely sensory, or also influence decisional processes. We teased apart these contributions with signal detection theory, and discovered a surprising absence of presaccadic benefits in visual change detection tasks. Participants planned and executed saccades while concurrently detecting and localizing either orientation or contrast changes. Spatial choice bias reliably improved presaccadically but, surprisingly, without a concomitant increase in perceptual sensitivity. Additional investigation with an orientation estimation task, and a Bayesian "variable precision" model, revealed that sensory precision increased at the saccade target, but only for the most recent of two successive stimuli. Moreover, the recent stimulus perceptually biased feature estimates of the prior stimulus, rendering accurate change detection even more challenging. Our results uncover novel perceptual and decisional mechanisms that mediate presaccadic change detection. Lay SummaryPlanning a rapid eye movement (saccade) changes how we perceive our visual world. Even before we move the eyes visual sensitivity improves at the impending target of eye movements, a phenomenon termed "presaccadic attention". We report a surprising lack of such presaccadic attention benefits in a common, everyday setting: change detection. In fact, presaccadic attention renders change detection more challenging by biasing percepts toward the most recent of successive stimuli at the saccade target location. With a Bayesian model, we show how such perceptual and choice biases induced by eye movement planning affect change detection behavior. Our findings may have critical implications for real-world scenarios, like driving, that involve rapid gaze shifts in dynamically changing environments.

neuroscience↗

bioRxiv2022

Ythdf2 regulates cardiac remodeling through its m6A-mRNA target transcripts

m6A mRNA methylation controls cardiomyocyte function and increased overall m6A levels are a stereotyping finding in heart failure independent of the underlying etiology. However, it is largely unknown how the information is read by m6A reader proteins in heart failure. Here we show that the m6A reader protein Ythdf2 controls cardiac function and identified a novel mechanism how reader proteins control gene expression and cardiac function. Deletion of Ythdf2 in cardiomyocytes in vivo leads to cardiac hypertrophy, reduced heart function, and increased fibrosis during pressure overload as well as during aging. Similarly, in vitro the knockdown of Ythdf2 results in cardiomyocyte growth and remodeling. Mechanistically, we identified the eucaryotic elongation factor 2 as a major target of Ythdf2 using cell type specific Ribo-seq data. Our study expands our understanding on the regulatory functions of m6A methylation in cardiomyocytes and how cardiac function is controlled by the m6A reader protein Ythdf2.

molecular biology↗

bioRxiv2022

Novel Peptide Inhibitor of Human Tumor Necrosis Factor-α has Antiarthritic Activity

The inhibition of tumor necrosis factor- (TNF) trimer formation renders it inactive for binding to its receptors thus mitigating the vicious cycle of inflammation. We designed a peptide (PIYLGGVFQ) that simulates a sequence strand of human TNF monomer using a series of in silico methods, such as active site finding (Acsite), protein-protein interaction (PPI), docking studies (GOLD and Modeller) followed by molecular dynamics (MD) simulation studies. The MD studies confirmed the intermolecular interaction of the peptide with the TNF. Fluorescence-activated cell sorting (FACS) and fluorescence microscopy revealed that the peptide effectively inhibited the binding of TNF to the cell surface receptors. The cell culture assays showed that the peptide significantly inhibited the TNF-mediated cell death. In addition, the nuclear translocation of the nuclear factor kappa B (NF{kappa}B) was significantly suppressed in the peptide-treated A549 cells as observed in immunofluorescence and gel mobility-shift assays. Furthermore, peptide protected against joint damage in collagen-induced arthritis (CIA) mouse model as revealed in the microfocal-CT scans. In conclusion, this TNF antagonist would be useful for the prevention and repair of inflammatory bone destruction and subsequent loss in the mouse model of CIA as well as human rheumatoid arthritis (RA) patients. This calls upon further clinical investigation to utilize its potential effect as an anti-arthritic drug.

immunology↗

bioRxiv2022

Immune Contexture of Isocitrate Dehydrogenase stratified Human Gliomas

The brain tumor immune microenvironment (TIME) continuously evolves during glioma progression, but only a limited view of a highly complex glioma associated immune contexture across isocitrate dehydrogenase mutation (IDH) classified gliomas is known. Herein, we present an unprecedentedly comprehensive view of myeloid and lymphoid cell type diversity based on our single cell RNA sequencing and spectral cytometry-based interrogation of tumor-associated leukocytes from fifty-five IDH stratified primary and recurrent human gliomas and three non-glioma brains. Our analyses revealed twenty-two myeloid and lymphoid cell types within and across glioma subtypes. Glioma severity correlated with microglial attrition concomitant with a continuum of invading monocyte-derived microglia-like and macrophages amongst other infiltrating conventional T and NK lymphocytes and unconventional mucosa associated invariant T (MAIT) cells. Specifically, certain microglial and monocyte-derived subpopulations were associated with antigen presentation gene modules, akin to cross-presenting dendritic cells (DCs). Furthermore, we identified phagocytosis and antigen presentation gene modules enriched in Triggering receptor expressed on myeloid (TREM)-2+ cells as a putative anti-glioma axis. Accelerated glioma growth was observed in Trem2 deficient mice implanted with CT2A glioma cells affirming the anti-glioma role of TREM2+ myeloid cells. In addition to providing a comprehensive landscape of glioma-specific immune contexture, our investigations discover TREM2 as a novel immunotherapy target for brain malignancies.

immunology↗

bioRxiv2022

A mechanistic insight into Nigella sativa mediated anticancer effect on breast cancer through regulation of various miRNAs: An in vitro & in vivo study

BackgroundCancer continues to threat the mortal alongside scientific community with its burgeoning grasp. Although efforts have been directed to tame cancer by radiotherapy, photodynamic therapy, chemotherapy it came at a cost of fatal side effects. PurposePlant derived bioactive compounds carries an inevitable advantage of being safer, bioavailable & less toxic compared to contemporary chemotherapeutics. This study analyzed anti-cancerous potential of volatile oil, extracted from Nigella sativa, in-vitro against MDA-MB-231, MCF-7 & in-vivo on tumor growth in mice after successful oral administration. Study DesignOur strategic approach employed solvent extraction of black seed oil (BSO) to highlight orchestrated use of its potent integrants - TQ, Carvacrol & TA which in modest amounts show anti-cancerous properties compared to their individual treatment. We attempted to show this cost effective, safe & bioavailable form of dealing with the atrocities of breast cancer by means of MTT, Apoptotic, Western Blot Assays besides Transwell & Wound healing Assay. Reduction in the solid tumour in-vivo & near normalcy restoration of tissue section architecture from the BSO treated tumour sets are indicative of the better anti-tumorigenic potential of BSO. MethodsBSOs Solvent extraction was performed followed by its characterization. MTT aided cytotoxicity study of BSO alongside major components in PBMC & cancer cells while its efficacy was presented by flow cytometric ROS analysis, cell cycle arrest & apoptosis assessment. Anti-migratory potential evaluated by Wound Healing, Transwell Migration & Western Blot while the expression study of a wide range of proteins, miRNAs & the in-vivo studies undertaken climaxed the confirmation of the anti-cancerous potential of BSO. ResultsComparatively reduced concentrations of TQ, TA & Carvacrol in BSO played a synergistic role to enhance apoptotic potential via Caspase 7 & 9, through enhanced ROS & expression of apoptotic family of proteins, miRNAs besides uplifting the anti-migratory perspective by effectively enhancing E-cad & downregulating lamellipodia, filopodia assembly & MMPs in MCF-7 & MDA-MB-231. Similar observations in-vivo outlined the therapeutic potential of BSO. ConclusionThis study culminates isolation & processing of BSO in a simplified procedure, thereby aiming at a more lucrative paradigm to be accepted in contemporary phytomedicine research.

cancer biology↗

bioRxiv2022

UBA52 attunes VDAC1-mediated mitochondrial dysfunction and dopaminergic neuronal death

Mitochondrial homeostasis regulates energy metabolism, calcium buffering, cell function and apoptosis. The present study has been conducted to investigate the implications of ubiquitin-encoding gene UBA52 in mitochondrial physiology. Transient expression of Myc-UBA52 in neurons significantly inhibited the rotenone-induced increase in reactive oxygen species generation, nitrite level and depleted glutathione level. Mass spectrometric and co-immunoprecipitation data suggested the profound interaction of UBA52 with mitochondrial outer membrane channel protein, VDAC1 in both the wild-type and Myc--synuclein overexpressed neuronal cells and in the Parkinsons disease (PD)-specific substantia nigra and striatal region of the rat brain. In vitro ubiquitylation assay revealed that UBA52 participates in the ubiquitylation of VDAC1 through E3 ligase CHIP. Myc-UBA52 overexpression in neurons further improved the mitochondrial functionality and cell viability by preventing the alteration in mitochondrial membrane potential, mitochondrial complex-I activity, translocation of cytochrome-c and p-Nrf2 along with effect on intracellular calcium uptake, thus collectively inhibiting the opening of mitochondrial permeability transition pore. Additionally, Myc-UBA52 expression in neuronal cells offered protection against apoptotic and autophagic cell death. Altogether, our findings delineate functional association between UBA52 and mitochondrial homeostasis, providing new insights into the deterrence of dopaminergic cell death during acute PD pathogenesis.

neuroscience↗

bioRxiv2022

UBA52 is crucial in HSP90 ubiquitylation and neurodegenerative signaling during early phase of Parkinson disease

Protein aggregation is one of the major pathological events in age-related Parkinsons disease (PD) pathology, predominantly regulated by the ubiquitin-proteasome system (UPS). UPS essentially requires core component ubiquitin however, its role in PD pathology is obscure. This study aimed to investigate the role of ubiquitin encoding genes in the early phase of PD pathology. Wild-type human Myc--synuclein transfected neurons, -synuclein-PFFs treated cells, rotenone-induced sporadic models of PD and SNCA C57BL/6J-Tg (Th-SNCA*A30P*A53T)39 Eric/J transgenic mice showed downregulated level of UBA52 in conjunction with significant downregulation of tyrosine hydroxylase (TH) and neuronal death. In silico predictions, mass spectrometric analysis and co-immunoprecipitation findings suggested strong interaction of UBA52 with -synuclein, HSP90 and E3-ubiquitin ligase CHIP, besides its co-localization with -synuclein in the mitochondrion. Next, in vitro ubiquitylation assay indicated an imperative requirement of the lysine-63 residue of UBA52 in CHIP-mediated HSP90 ubiquitylation. Myc-UBA52 expressed neurons exhibited the downregulated -synuclein protein abundance with increased TH and restored proteasome activity during the diseased condition. Furthermore, Myc-UBA52 expression inhibited the augmented HSP90 protein level along with its various client proteins, HSP75 (homologue of HSP90 in mitochondrion) and ER stress-related markers during early PD. Taken together, data highlights the critical role of UBA52 in HSP90 ubiquitylation in parallel to its potential contribution to the modulation of various disease-related neurodegenerative signaling targets during the early phase of PD pathology.

neuroscience↗

bioRxiv2022

Neuronal Maturation-dependent Nano-Neuro Interaction and Modulation

Nanotechnology-enabled neuromodulation, a rapidly growing technique, is a promising minimally-invasive tool in neuroscience and engineering for both fundamental studies as well as clinical applications. However, the nano-neuro interactions at different stages of maturation of a neural network and its implications on the nano-neuromodulation remain unclear. Here, we report heterogeneous to homogenous transformation of neuromodulation in a progressively maturing neural network. Utilizing plasmonic fluors as ultrabright fluorescent nanolabels, we reveal that negative surface charge of the nanoparticles renders selective nano-neuro interaction with a strong correlation between the maturation stage of the individual neurons in the neural network and the density of the nanoparticles bound on the neurons. In stark contrast to homogeneous neuromodulation in a mature neural network reported so far, the maturation-dependent density of the nanoparticles bound to neurons in a developing neural network resulted in a heterogeneous optical neuromodulation (i.e., simultaneous excitation and inhibition of neural network activity). This study advances our understanding of nano-neuro interactions and nano-neuromodulation with potential applications in minimally-invasive technologies for treating neuronal disorders in parts of mammalian brain where neurogenesis persists throughout aging.

bioengineering↗

bioRxiv2022

Reduced γ-glutamyl hydrolase activity likely contributes to high folate levels in Periyakulam-1 tomato

Tomato cultivars show wide variation in nutraceutical folate in ripe fruits, yet the loci regulating folate levels in fruits remain unexplored. To decipher regulatory points, we compared two contrasting tomato cultivars: Periyakulam-1 (PKM-1) with high folate and Arka Vikas (AV) with low folate. The progression of ripening in PKM-1 was nearly similar to AV but had substantially lower ethylene emission. In parallel, the levels of phytohormones salicylic acid, ABA, and jasmonic acid were substantially lower than AV. The fruits of PKM-1 were also metabolically distinct from AV, with upregulation of several amino acids. Consistent with higher {degrees}Brix levels, the red ripe fruits also showed upregulation of sugars and sugar-derived metabolites. In parallel with higher folate, PKM-1 fruits also had higher carotenoid levels, especially lycopene and {beta}-carotene. Transcript levels of genes encoding folate biosynthesis did not show a perceptible difference in relative expression. The proteome analysis showed upregulation of carotenoid sequestration and folate metabolism-related proteins in PKM-1. The deglutamylation pathway mediated by {gamma}-glutamyl hydrolase (GGH) was substantially reduced in PKM-1 at the red-ripe stage. The red-ripe fruits had reduced transcript levels of GGHs and lower GGH activity than AV. Conversely, the percent polyglutamylation of folate was much higher in PKM-1. Our analysis indicates the regulation of GGH activity as a potential target to elevate folate levels in tomato fruits.

plant biology↗

bioRxiv2022

Shear stress induced KLF4 is a key determinant in AVM pathogenesis

BackgroundVascular networks form, remodel and mature under the influence of both fluid shear stress (FSS) and soluble factors. For example, FSS synergizes with Bone Morphogenic Protein 9 (BMP9) and BMP10 to promote and maintain vascular stability. Mutation of the BMP receptors ALK1, Endoglin or the downstream effector SMAD4 leads to Hereditary Hemorrhagic Telangiectasia (HHT), characterized by fragile and leaky arterial-venous malformations (AVMs). But how endothelial cells (EC) integrate FSS and BMP signals in normal vascular development and homeostasis, and how mutations give rise to malformations is not well understood. ResultsHere we show that loss of Smad4 in murine ECs increases cells sensitivity to flow and the resulting AVMs are characterized by excessive elongation and polarity against the flow. Smad4 deletion also blocks the anti-proliferative response to high FSS, leading to loss of arterial identity. Our data show that loss of cell cycle arrest leads to loss of arterial identity, which is essential in AVM formation upon Smad4 depletion in ECs. Excessive flow-induced activation of KLF4-PI3K/AKT due to Cyclin dependent Kinase (CDK) activation mediates the aberrant morphological responses to flow triggering AVM formation. ConclusionsOur results show that loss of polarization against the flow is not required for AVM formation upon EC Smad4 depletion. Instead, increased EC proliferation-mediated loss of arterial identity due to flow-induced PI3K/Akt/Cdks hyperactivation and Klf4 over-expression are the main events associated with AVM formation.

molecular biology↗