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Biology subjects

Mishra, P.

Publications and source records attributed to Mishra, P..

At least 37 records · Page 2Linked to original sources

Crowding does not suppress the opening of a cryptic pocket

Cryptic pockets are transient structural features that could provide new opportunities for drug design. However, their utility would be greatly diminished if the probability of pocket opening were universally suppressed in cells due to the excluded volume effects of crowding. As a first step to addressing this concern, we study the effect of the synthetic crowder Ficoll 70, which has been shown to mimic the excluded volume effects of biomolecular crowding well, on the opening of a cryptic pocket in the interferon inhibitory domain (IID) of Ebola viral protein 35 (VP35). We find that this synthetic crowder has a negligible effect on the probability of cryptic pocket opening, as measured by both thiol labeling and hydrogen-deuterium exchange mass spectrometry (HDX-MS). The probability that a specific pocket opens may still be altered by the soft, enthalpic interactions of crowding, which will vary between different cellular environments. However, our results demonstrate that excluded volume effects that are at play in all crowded environments do not pose a universal barrier to targeting cryptic pockets.

biophysics↗

AKNA drives neural stem cell fate transition through differential localization and coordinating the modulation of chromatin from H3K27me3 to H3K27ac

Neuronal stem cells (NSCs) play pivotal role in adult neurogenesis, however, detail mechanisms of obtaining pluripotency or undergoing differentiation remain unknown. Herein, how AT-hook protein AKNA regulates pluripotency and stemness in neuroblastoma cells is demonstrated by gene knockdown, immunofluorescence, chromatin immunoprecipitation (ChIP), localization of AKNA, signaling interactions and transcriptional activity. AKNA was abundant and mostly nuclear during induction of pluripotency and its knockdown reduced stemness, even in presence of other pluripotency factors, including OCT4 and SOX2. During the course of induction of differentiation, AKNA remain localized in the cytosol, essential for regulated differentiation. Cytosolic retention of AKNA is possibly driven by FAK signaling. In the nucleus, AKNA promotes KDM6B demethylase for H3K27me3 demethylation to H3K27, and subsequently promotes CBP/p300 to acetylate H3K27 to H3K27ac deposition on promoter region of respective genes to trigger their transcription. Data obtained from knockdown and overexpression of AKNA and KDM6B further reinforce its importance that, they physically interact to drive pluripotency and stemness. These findings establish AKNA as a critical regulator for NSCs fate determination in association with epigenetic modifiers and signaling pathway, offering potential targets for neuroblastoma therapies and regenerative medicines for neurodegenerative diseases.

molecular biology↗

Scaffolded hiPSC liver organoids recapitulating bile duct tubulogenesis and periportal architecture.

Recapitulating the liver periportal area in vitro remains a major challenge due to its complex cellular composition and the coordinated development of both ductal and endothelial networks. Most existing bile duct organoid models fail to reproduce tubular extension and multicellular organization. We present a 3D ECM micro-rods system biofunctionalized with grafted growth factors mimicking fetal liver paracrine signaling to initiate and to coordinate the development of bile ducts, parenchymal cells, and vascular structures. Our system recapitulates key developmental stages, from the formation of the ductal plate to the emergence of elongated tubular ducts. The ECM rod alone provides the biophysical cues initiating the elongation of the bile ducts and the spatial structuration of the cellular organization, while the biofunctionalization with growth factors enhance the organization and maturation of the biliary and vascular systems. We further demonstrate that this approach is scalable and amenable to quantitative analysis through label-free Optical Coherence Tomography combined with AI-driven 3D segmentation.

cell biology↗

Mutant IDH silences GSX2 to reprogram neural progenitor cell fate and promote gliomagenesis

Isocitrate dehydrogenase (IDH) mutations arise early in gliomas and are associated with a defined neurodevelopmental cancer cell hierarchy. However, how mutant IDH contributes to this hierarchy and whether this interaction promotes gliomagenesis remain unclear. We captured the dynamics of IDH-mutant glioma initiation in genetically engineered mice through time-resolved, single-cell genomics. Mutant IDH activates and induces lineage switching of neural progenitor cells (NPCs). These actions expand oligodendrocyte precursor cells, the predominant cell-of-origin for these tumors, at the expense of interneurons. Lineage switching is mediated by promoter hypermethylation and silencing of Gsx2, a homeobox gene required for neurogenesis. Critically, Gsx2 ablation recapitulates NPC fate reprogramming by mutant IDH. We provide a new model of neural cell fate control by IDH oncogenes and insights into the developmental origins of glioma.

cancer biology↗

An ARF2-GRF5 module, operating early and upstream of GLK factors, reveals genetic hierarchy during chloroplast biogenesis

O_LIOur current understanding of the regulation of chloroplast development lags behind that of the process itself. The GOLDEN2-LIKE (GLK) factors drive the expression of photosynthesis-associated nuclear (PhAN) genes. Simultaneous loss of GLK1 and GLK2 in Arabidopsis plants leads to pale-green, incompletely-developed chloroplasts. This highlights the GLKs role but also the involvement of other components. C_LIO_LIWe hypothesised that further regulators could be found by searching for suppressor mutations of a severe glk1 knock-down (KD) glk2 knock-out (KO) mutant. We identified suppressor of glks (sgl) 2, sgl2. C_LIO_LIThe sgl2 glk1 glk2 triple mutant showed significant increases in chlorophyll, expression of PhAN genes, chloroplast thylakoid stacking, and cellular volume of chloroplasts. sgl2 was caused by loss of function of AUXIN RESPONSE FACTOR2, ARF2. arf2sgl2 boosted chloroplast content as a single mutant, and dramatically suppressed the chloroplast delay of the phytochrome-deficient long hypocotyl 1 (hy1) mutant. Overexpression of Growth Regulating Factor 5 (GRF5), which is negatively regulated by ARF2, also rescued chlorophyll levels in glk1 glk2, confirming a role for ARF2 and GRF5 as a transcription module. We observed in glk1 glk2 low but detectable expression of GLK1, which was elevated in arf2sgl2 glk1 glk2, and saw reduced suppression by arf2sgl2 of the phenotype of a separate glk1-2 glk2-2 mutant carrying two KO alleles, revealing partial epistasis. Presumed orthologs of ARF2 and GRF5 are expressed very early in developing cereal leaves, well ahead of the bulk of GLK expression during the greening stage. C_LIO_LIOur results place ARF2 as a negative switch modulating GRF5 early and upstream, whether directly or indirectly, of GLK factors, but also acting independently from them. This reveals a hierarchy of transcription factor action and feed-forward regulation in chloroplast biogenesis during leaf development. C_LI

plant biology↗

Mechanistic basis for protection against fatty liver disease by CIDEB loss-of-function mutations

Background & AimsSomatic and germline CIDEB mutations are associated with protection from chronic liver diseases. The mechanistic basis and whether CIDEB suppression would be an effective therapy against fatty liver disease remain unclear. Methods21 CIDEB somatic mutations were introduced into cells to assess functionality. In vivo screening was used to trace Cideb mutant clones in mice fed normal chow, western (WD), and choline-deficient, L-amino acid-defined, high-fat (CDA-HFD) diets. Constitutive and conditional Cideb knockout mice were generated to study Cideb in liver disease. Isotope tracing was used to evaluate fatty acid oxidation and de novo lipogenesis. Transcriptomics, lipidomics, and metabolic analyses were utilized to explore molecular mechanisms. Double knockout models (Cideb/Atgl and Cideb/Ppara) tested mechanisms underlying Cideb loss. ResultsMost CIDEB mutations showed that they impair function, and lineage-tracing showed that loss-of-function clones were positively selected with some, but not all fatty liver inducing diets. Cideb KO mice were protected from WD, CDA-HFD, and alcohol diets, but had the greatest impact on CDA-HFD induced liver disease. Hepatocyte-specific Cideb deletion could ameliorate disease after MASLD establishment, modeling the impact of therapeutic siRNAs. Cideb loss protected livers via increased {beta}-oxidation, specifically through ATGL and PPARa activation. ConclusionsCideb deletion is more protective in some types of fatty liver disease. {beta}-oxidation is an important component of the Cideb protective mechanism. CIDEB inhibition represents a promising approach, and somatic mutations in CIDEB might predict the patient populations that might benefit the most.

physiology↗

Human Stress Response Specificity through Bioresonance Selectivity

Bold First ParagraphIn eukaryotes, the mitogen activated protein kinase (MAPK) cascade, a multilayered interconnected network of enzymes, connects external stimuli to gene regulation, determining cellular fate 1. Environmental stress sensed by a cell starts a complex chain of reactions between MAPK enzymes that ultimately activates the master stress response regulator protein p38 MAPK 2,3. Thus activated, p38 must then selectively activate targets from a pool of hundreds to initiate appropriate cellular responses 3. Mechanisms for how p38 performs this selection remain unclear 4,5. Here we show that human p38 target selectivity is based on the same principles as modern electronic telecommunications systems, except using waves of chemicals rather than electromagnetic fields or electric currents. p38 encodes information about stimuli as different frequency oscillations of its activation state, and targets are selected through frequency-dependent resonance of oscillating biochemical reactions between p38 and its targets. We demonstrate this mechanism by activating various genetic responses in human cells by applying only sugar at different frequencies. These results unify observations of oscillating signaling components and altered responses 6-19 into a coherent framework to understand and control human gene expression. As failures of this mechanism may contribute to some p38-associated diseases 2,20-28, these findings may have implications for pharmaceutical development and therapeutic strategies.

biophysics↗

Neuronal cell adhesion molecule (NRCAM) variant defined by microexon skipping is an essential, antigenically distinct, and targetable surface proteoform in high-grade glioma

To overcome the paucity of known tumor-specific surface antigens in pediatric high-grade glioma (pHGG), we contrasted splicing patterns in pHGGs and normal brain samples. Among alternative splicing events affecting extracellular protein domains, the most pervasive alteration was the skipping of [≤]30 nucleotide-long exons. Several of these skipped microexons mapped to L1-IgCAM family members, such as NRCAM. Bulk and single-nuclei short- and long-read RNA-seq revealed uniform skipping of NRCAM microexons 5 and 19 in virtually every pHGG sample. Importantly, the {Delta}ex5{Delta}ex19 (but not the full-length) NRCAM proteoform was essential for pHGG cell migration and invasion in vitro and tumor growth in vivo. We developed a monoclonal antibody selective for {Delta}ex5{Delta}ex19 NRCAM and demonstrated that "painting" of pHGG cells with this antibody enables killing by T cells armed with an FcRI-based universal immune receptor. Thus, pHGG-specific NRCAM and possibly other L1-IgCAM proteoforms are promising and highly selective targets for adoptive immunotherapies.

cancer biology↗

Cell-specific oxidative metabolism of the renal cortex

The metabolic health of the kidney is a primary determinant of the risk of progressive kidney disease. Our understanding of the metabolic processes that fuel kidney functions is limited by the kidneys structural and functional heterogeneity. As the kidney contains many different cell types, we sought to determine the intra-renal mitochondrial heterogeneity that contributes to cell-specific metabolism. To interrogate this, we utilized a recently developed mitochondrial tagging technique to isolate kidney cell-type specific mitochondria. Here, we investigate mitochondrial functional capacities and the metabolomes of the early and late proximal tubule (PT) and the distal convoluted tubule (DCT). The conditional MITO-Tag transgene was combined with Slc34a1-CreERT2, Ggt1-Cre, or Pvalb-Cre transgenes to generate mouse models capable of cell-specific isolation of hemagglutinin (HA)-tagged mitochondria from the early PT, late PT, or the DCT, respectively. Functional assays measuring mitochondrial respiratory and fatty acid oxidation (FAO) capacities and metabolomics were performed on anti-HA immunoprecipitated mitochondria from kidneys of ad libitum fed and 24-hour fasted male mice. The renal MITO-Tag models targeting the early PT, late PT, and DCT revealed differential mitochondrial respiratory and FAO capacities which dynamically changed during fasting conditions. The renal MITO-Tag model captured differential mitochondrial metabolism and functional capacities across the early PT, late PT, and DCT at baseline and in response to fasting. New & NoteworthyThis study described the generation and utilization of mouse models capable of interrogating kidney tubular epithelial cell-specific mitochondrial metabolism. Applying the MITO-Tag system in the kidney, we have for the first time defined the mitochondrial metabolic heterogeneity of renal cortical tubular epithelium and discovered differential mitochondrial functional capacities in response to an acute metabolic stress such as fasting.

molecular biology↗

The first assembled chromosome-level genome of an individual from Karnataka, India

We present the first chromosome-level assembled genome of an individual from Karnataka, India (KIn1), using de novo assembly of 12x coverage of PacBio HiFi reads generated in-house and 30x Hi-C data from the most ethnically related individual to KIn1 from Andhra Pradesh (HG04712), publicly available under International Genome Sample Resource (IGSR). We achieved an N50 of 137 Mb and an L50 of 9--very close to the maximum achievable N50 of 147 Mb and minimum achievable L50 of 8 respectively for human genomes. A comparison of the KIn1 assembly with assemblies of four other individual genomes from a Puerto Rican (PR1), Ashkenazi (Ash1), Hans Chinese (Hans1), and Northern European (T2T) reported to date from resources like IGSR and/or Genome-in-a-Bottle (GIBR) collections shows that the longest scaffolds from KIn1 cover 80-90% of the reference chromosomes and exhibit near collinearity. We find a unique inversion in the chromosome 7 euchromatic region and other major translocations in chromosomes 17 and 20 in KIn1. We also produced a chromosome-level assembly for another individual from Punjab, Lahore (HG03492), for use in our comparison. The analysis of variants among select IGSR individuals using the KIn1 assembly as a reference reveals that the Indian Telugu from the UK (ITU) population in IGSR is ethnically closest to KIn1, followed by the Sri Lankan Tamil from the UK (STU) as representatives of South Asian ancestry.

genomics↗

A PthXo2B ortholog in Xanthomonas oryzae pv oryzae strain IX-221 acts as a major virulence factor on indica rice without activating a Clade III SWEET gene.

To infect rice, Xanthomonas oryzae pv. oryzae (Xoo) deploys transcription activator-like effectors (TALEs) that specifically bind and upregulate host "susceptibility" (S) genes. 34-amino acid (aa) repeats in TALEs interact one-to-one with DNA bases. Variation at positions 12 and 13 in each repeat, the repeat-variable diresidue (RVD), determine specificity. Some repeat variants shorter or longer than 34 aa can disengage to accommodate a single base deletion in the target sequence. OsSWEET11, 13, and 14 are key S genes, targeted by different TALEs from diverse Xoo strains. xa13 is a SWEET11 allele lacking the TALE binding site and thus conferring resistance. xa13 is overcome by TALEs that activate SWEET13 or SWEET14. We report here that an xa13-compatible Xoo strain, IX-221, from India, harbours an ortholog of the SWEET14-targeting TALE PthXo3 and two orthologs of the SWEET13-cognate PthXo2, each with one or two 36-aa repeats capable of disengaging. One of the PthXo2 orthologs, PthXo2BIX-221, has a repeat region identical to the previously characterized PthXo2BPXO61, except for a two amino acid difference near the end of the 19th repeat. Like PthXo2BPXO61, PthXo2BIX-221 upregulates SWEET13 in japonica rice and no SWEET in indica rice, but unlike PthXo2BPXO61 it nonetheless renders indica rice susceptible, pointing to an alternative S gene. Further, a designer TALE (dTALE) constructed using a standard, consensus sequence for each repeat and RVDs identical to those of PthXo2BIX-221 failed to render indica rice susceptible. Alignment of the PthXo2BIX-221 repeats shows a departure from the consensus in each of two repeats carrying the RVD NN: the sequence MAIAN in place of VAIAS beginning at position 7. Together, the PthXo2BIX-221 results thus suggest that non-RVD sequence variation affects TALE targeting profiles. More broadly, the presence of the three aberrant repeat-harbouring TALEs in IX-221 suggests that widespread deployment of xa13 in India resulted in strains super-equipped to overcome it, capable of activating multiple SWEET genes and alleles as well as an apparent alternate S gene.

plant biology↗

Diabetic liver-enriched secretory dipeptidyl peptidase 4 (DPP4) fuels gut inflammation via attenuation of autophagy

The recurrent pathological inflammation of the gut is a major concern in diabetic patients. With the failure of anti-inflammatory or diabetic drugs to limit relapse of colon inflammation demands the unearthing of mechanistic details underlying higher incidences of colitis in diabetic patients. Here we report the enrichment of DPP4 in the livers and blood samples of diabetic humans and mice models of diabesity that is in parallel to the development of colitis. Overexpression of DPP4 exacerbates or hepatic silencing of DPP4 impairs experimental colitis induced by DSS and STM. Mechanistically, we identified liver DPP4 attenuates gut-autophagic response to trigger enteric cell apoptosis, reduced mucin secretion, and compromised gut barrier leading to high infiltration of immune cells secreting inflammatory cytokines establishing pathological gut inflammation. Thus, liver-DPP4-mediated gut autophagy inhibition is a key pathway in diabesitic colitis.

physiology↗

Insulin-like Growth Factor 2 mRNA-binding protein 2 (IGF2BP2) Promotes Castration-Resistant Prostate Cancer Progression by Regulating AR-V7 mRNA Stability

The emergence of constitutively active androgen receptor (AR) splice variant AR-V7 poses a formidable challenge in treating prostate cancer, as it lacks the ligand binding region targeted by androgen deprivation therapies such as enzalutamide and abiraterone. AR-V7 is critical for castration-resistant prostate cancer (CRPC) development and progression, however the molecular mechanisms regulating its expression and biological function remain poorly understood. Here, we investigate the role of IGF2BP2 in regulating AR-V7 expression and CRPC progression. We demonstrate that IGF2BP2 silencing leads to downregulation of AR-V7 and its downstream target genes without affecting AR levels. Additionally, IGF2BP2 knockdown also enhances the sensitivity of CRPC cells to enzalutamide while overexpression increases AR-V7 expression and confers increased resistance to enzalutamide. Mechanistically, our experiments demonstrate that IGF2BP2 binds to the intronic splicing enhancer (ISE) region of AR-V7, thereby enhancing its mRNA stability Furthermore, our domain-deletion analysis pinpoints the role of KH3 and KH4 domains of IGF2BP2 in regulating AR-V7 stability and enzalutamide resistance. Taken together, our findings suggest that IGF2BP2 plays a critical role in regulating AR-V7 expression and stability, offering a novel target for developing therapeutic interventions for CRPC.

cancer biology↗

Preferred left-handed conformations of glycyls with pathogenic variants protect against aggregation

Due to the lack of C{beta} atom, the glycyl residues can exhibit left-handed Ramachandran conformations that are mostly disallowed for L-amino acids. The structural and functional significance of distinct glycyl conformations remains under-appreciated. Through systematic analyses of various datasets, we show that: i) the left-handed glycyl residues are over-represented at disease-associated sites and are evolutionarily conserved. ii) The mutations of L-disallowed Gly tend to destabilize the native folding as assessed through the change in free energies. An independent analysis of folding nuclei further corroborates the findings. iii) L-disallowed Gly are enriched at the aggregation gatekeepers, more significantly so in thermophiles, and the mutations thereof reduce the protein solubility. (iv) The positive{Phi} dihedral angle of L-disallowed Gly disorients its C atom out of the phase of alternating pleats of {beta}-strand, conforming a crescent that is incompatible to further pair with other {beta}-strands, and thus discourages the inter-molecular aggregation of {beta}-strands during protein folding. v) L-disallowed conformation of Gly holds predictive power to identify sites having pathogenic variants. Altogether, our observations highlight that the L-disallowed conformations of glycyls are evolutionarily selected to endow protein stability and protection against aggregation. Apart from enhancing the existing knowledge, the findings have implications in prioritizing the genetic lesions implicated in diseases, and in designing proteins with greater stability and solubility.

biochemistry↗

Synthesis, Insertion and Characterization of SARS-CoV-2 Membrane Protein Within Lipid Bilayers

SUMMARY/ABSTRACTThe membrane protein (M) is the most abundant structural protein in the SARS-CoV-2 virus and functions exclusively as a membrane-embedded homodimer. M protein is required for the formation of the SARS-CoV-2 virus particle and has been shown to interact with the Spike and Envelope proteins, as well as the RNA-packaging Nucleocapsid protein. Our knowledge of M protein is very limited due to its small size and challenges in expressing enough protein for use in structural and biophysical experiments. We report the successful development of a SUMO tag-based expression system to produce and purify significant quantities of M protein, and a method to insert the synthesized dimers into a suspended lipid membrane in a homogeneous orientation. We used AFM and Cryo-EM to image individual membrane-bound M protein dimers and characterize the configurations that they can assume. Our experimental results are in agreement with our molecular dynamics simulations which predict thinning of the membrane around the M protein and a propensity to induce local membrane curvature. Taken together, our results shed new light on M protein properties within the lipid bilayer and suggest mechanisms that could contribute to viral assembly and budding.

biophysics↗

A Low-Cost Stage-Top Incubation Device For Human Cell Imaging Using Rapid Prototyping Methods

Live imaging of human or other mammalian cells at multi-hour time scales with minimal perturbation to their growth state requires that the specimens optimal growth conditions are met while fixed to a microscope stage. In general, ideal conditions include culturing in complete growth media, an ambient temperature of 36-37 C, and a humidity-controlled atmosphere comprising typically 5-7% CO2. Commercially available devices that achieve these conditions are not a financially viable option for many labs, with the price ranging anywhere from $12000 to $40000. The advent of 3D printing technology has allowed for low-cost rapid prototyping with precision comparable to traditional fabrication methods, opening the possibility for in-lab design and production of otherwise prohibitively expensive equipment such as stage-top incubation devices. The continued usefulness and widespread availability of single-board computers (SBC) such as Arduino and Raspberry Pi also simplify the process by which these devices can be controlled. Here we report the production of a do-it-yourself (DIY) device for stage-top incubation with temperature and atmospheric control with a cost reduction of approximately 100x.

cell biology↗

Pathogenic mitochondrial DNA mutations inhibit melanoma metastasis

Mitochondrial DNA (mtDNA) mutations are frequently observed in cancer, but their contribution to tumor progression is controversial. To evaluate the impact of mtDNA variants on tumor growth and metastasis, we created human melanoma cytoplasmic hybrid (cybrid) cell lines transplanted with wildtype mtDNA or pathogenic mtDNA encoding variants that partially or completely inhibit oxidative phosphorylation. Homoplasmic pathogenic mtDNA cybrids reliably established tumors despite dysfunctional oxidative phosphorylation. However, pathogenic mtDNA variants disrupted spontaneous metastasis of subcutaneous tumors and decreased the abundance of circulating melanoma cells in the blood. Pathogenic mtDNA did not induce anoikis or inhibit organ colonization of melanoma cells following intravenous injections. Instead, migration and invasion were reduced, indicating that limited circulation entry functions as a metastatic bottleneck amidst mtDNA dysfunction. Furthermore, analysis of selective pressure exerted on the mitochondrial genomes of heteroplasmic cybrid lines revealed a suppression of pathogenic mtDNA allelic frequency during melanoma growth. Collectively, these findings demonstrate that functional mtDNA is favored during melanoma growth and enables metastatic entry into the blood.

cancer biology↗

Adaptive Artificial Intelligence to Teach Interactive Molecular Dynamics in the Context of Human-Computer Interaction

Artificial Intelligence (AI) can be easily integrated into virtual education to drive adaptive instruction and real-time constructive feedback to students, offering a possible conduit for fostering discovery curiosity in learners. This study examines and characterizes Human-AI-Teaming (HAT) coordination dynamics to monitor the inception of discovery curiosity in online laboratories of interactive molecular dynamics (IMD). We used molecular physics measures (kinetic/ potential energy and action) obtained from simple and complex examples of simulated mouse tracking datasets in IMD log files as a proxy for understanding the context of molecular sciences and developing novel interactions for inquiry. These measures are good features of our HAT context because kinetic energy reflects the systems atoms overall motion regarding the individual atoms speed. While kinetic energy represents if a learner applies artificial forces to the task, potential energy can be AIs response to these forces. The action is a systems-level reaction to the changes during the task. By applying nonlinear dynamical systems methods to the physics measures, we extracted the Largest Lyapunov Exponent and Determinism metrics as HATs coordination stability and predictability, respectively. The findings underline that while the more complex IMD task required less stable and predictable HAT coordination dynamics, the simple task is more. One explanation is that AI needs to anticipate the learner by providing feedback at the right time and place during the more complex IMD task to initiate and sustain the learners discovery curiosity. In IMD, future HAT design should consider coordination dynamics for fostering discovery curiosity and practical learning.

bioengineering↗