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Sharma, A.

Publications and source records attributed to Sharma, A..

At least 217 records · Page 12Linked to original sources

L-Dopa incorporation into tubulin alters microtubule dynamics and reduces dendritic spine invasion and synapse maintenance

Previous studies have shown that L-Dopa, a tyrosine analog used in Parkinsons disease treatment, can be incorporated into -tubulin C-terminal tail via the tubulin tyrosine ligase (TTL) and polymerize into microtubules. In this work, we demonstrated that mature wild type hippocampal neurons treated with L-Dopa exhibited reduced dendritic spine density, primarily affecting mature dendritic spines. In these neurons, L-Dopa treatment significantly reduced tyrosinated -tubulin levels without altering detyrosinated or {Delta}2 -tubulin levels, suggesting the formation of a new tubulin pool, likely composed of L-Dopa--tubulin. In vitro analysis of the activity of the purified VASH1-SVBP complex, the most abundant tubulin carboxypeptidase in brain, revealed that L-Dopa incorporation into -tubulin modified the binding of the complex to microtubules and reduced its carboxypeptidase activity. These results suggest that L-Dopa incorporation into tubulin alters the properties of microtubules and affects their ability to interact with the enzyme. To confirm the implication of L-Dopa-microtubules in dendritic spine alterations observed in wild type neurons, we analyzed the effect of L-Dopa treatment in neurons lacking the enzymes of the -tubulin detyrosination/tyrosination cycle. In these cells, L-Dopa cannot be incorporated into -tubulin due to the absence of the ligase (in TTL KO neurons) or the reduction of detyrosinated -tubulin levels (in SVBP KO neurons). L-Dopa treatment did not modify dendritic spine density in TLL KO or SVBP KO neurons, clearly demonstrating that the alterations in dendritic spines seen in WT neurons are due to the incorporation of L-Dopa into tubulin. Further analysis revealed that L-Dopa treatment decreased the percentage of spines containing excitatory synapses in wild type neurons, but not in TTL KO or SVBP KO neurons, suggesting a cumulative synaptic defect due to L-Dopa incorporation into microtubules. Additionally, L-Dopa altered microtubule dynamics by increasing catastrophe frequency and reducing comet lifetime, which led to fewer microtubules entering dendritic spines and decreased spine resistance to pruning. Taken together, our results demonstrate that L-Dopa incorporation into -tubulin drastically affects synaptic homeostasis, reaffirming the importance of balanced detyrosination/tyrosination of tubulin within the synaptic compartment. The abnormal dynamics of L-Dopa-microtubules and the reduction of dendritic spines and excitatory synapses highlight a novel mechanism of L-Dopa-induced synaptotoxicity.

neuroscience↗

Deep phenotyping of the prostate tumor microenvironment reveals molecular stratifiers of relapse and links inflammatory chemokine expression to aberrant metabolism

Understanding the molecular characteristics and changes of the tumor microenvironment (TME) associated with aggressive prostate cancer (PCa) is essential for precise diagnosis and treatment. We interrogated spatially resolved integrated transcriptomics and metabolomics data to build molecular strafiers discriminating patients with aggressive, potentially relapsing, and metastasizing PCa. We report a relapse associated (RA) gene expression signature characterized by upregulated immune response related gene expression scoring high in cancer, stroma, and glandular tissue of relapsing patients. Further, we identified a signature specific to a distinct sub-group of morphologically non-cancerous glands in prostate tissue from patients with relapsing cancer. This signature, named chemokine-enriched-gland (CEG) signature, was characterized by upregulated gene expression of pro-inflammatory chemokines. Glands with a high CEG score were enriched for club-like cells and surrounding stroma was infiltrated by immune cells. Tissue regions scoring high for both CEG and RA signatures were associated with reduced levels of citrate and zinc and loss of normal prostate secretory gland functions via reduced expression of genes necessary for citrate secretion. In summary we report that aggressive PCa is associated with an increased inflammatory status linked to chemokine production and club-like cell enrichment in potentially pre-cancerous prostate glands displaying an aberrant metabolism.

cancer biology↗

Fluid flow overcomes antimicrobial resistance by boosting delivery

Antimicrobial resistance is an emerging global threat to humanity. As resistance outpaces development, new perspectives are required. For decades, scientists have prioritized chemical optimization, while largely ignoring the physical process of delivery. Here, we used biophysical simulations and microfluidic experiments to explore how fluid flow delivers antimicrobials into communities of the highly resistant pathogen Pseudomonas aeruginosa. We discover that increasing flow overcomes bacterial resistance towards three chemically distinct antimicrobials: hydrogen peroxide, gentamicin, and carbenicillin. Without flow, resistant P. aeruginosa cells generate local zones of depletion by neutralizing all three antimicrobials through degradation or chemical modification. As flow increases, delivery overwhelms neutralization, allowing antimicrobials to regain effectiveness against resistant bacteria. Additionally, we discover that cells on the edge of a community shield internal cells, and cell-cell shielding is abolished in higher flow regimes. Collectively, our quantitative experiments reveal the unexpected result that physical flow and chemical dosage are equally important to antimicrobial effectiveness. Thus, our results should inspire the incorporation of flow into the discovery, development, and implementation of antimicrobials, and could represent a new strategy to combat antimicrobial resistance.

microbiology↗

Prediction of pathological subthalamic nucleus beta burst occurrence in Parkinson's disease

The cortico-basal ganglia network in Parkinsons disease (PD) is characterized by the emergence of transient episodes of exaggerated beta frequency oscillatory synchrony known as bursts. Although it is well established that bursts of prolonged duration associate closely with motor impairments, the mechanisms leading to burst initiation remain poorly understood. Crucially, it is unclear whether there are features of basal ganglia activity which reliably predict burst onset. Current adaptive Deep Brain Stimulation (aDBS) approaches can only reactively deliver stimulation following burst detection and are unable to stimulate proactively to prevent burst onset. The discovery of predictive biomarkers could allow for such proactive stimulation, thereby offering potential for improvements in therapeutic efficacy. Here, using deep learning, we show that the timing of subthalamic nucleus (STN) beta bursts can be accurately predicted up to 60 ms prior to onset. Furthermore, we highlight that a dip in the beta amplitude - which is likely to be indicative of a phase reset of oscillatory populations occurring between 80-100 ms prior to burst onset - is a predictive biomarker for burst occurrence. These findings demonstrate proof-of-principle for the feasibility of beta burst prediction for DBS and provide insights into the mechanisms of burst initiation.

neuroscience↗

Development and IND-enabling studies of a novel Cas9 genome-edited autologous CD34+ cell therapy to induce fetal hemoglobin for sickle cell disease

Sickle cell disease (SCD) is a common severe blood disorder, caused by one major point mutation in the HBB gene. Current pharmacotherapies are only partially effective and potentially curative allogeneic hematopoietic stem cell transplantation (HSCT) is associated with immune toxicities. Genome editing of autologous patient hematopoietic stem cells (HSCs) to reactivate fetal hemoglobin (HbF) in erythroid progeny offers a potentially curative approach to treat SCD and circumvents some problems associated with allogeneic HSCT. Although the FDA has released guidelines for evaluating genome editing risks, it remains unclear how to best to assess the preclinical safety and efficacy of genome-edited cellular drug products to prepare for a clinical trial. Here we describe rigorous pre-clinical characterization and optimization of a therapeutic {gamma}-globin gene promoter editing strategy that supported an investigational new drug (IND) application cleared by the FDA. We compared targets in the {gamma}-globin promoter and BCL11A erythroid-specific enhancer, identified a lead candidate that potently induces HbF, and tested our approach in mobilized CD34+ HSPCs from normal donors and individuals with SCD. We observed efficient editing, induction of HbF to levels predicted to be therapeutic, and reduction of sickling in red blood cells derived from edited HSPCs. With single-cell western and RNA-seq analyses, we defined the heterogeneity and specificity of HbF induction and HBG1/HBG2 transcription. With CHANGE-seq for sensitive and unbiased genome-wide off-target discovery followed by multiplexed targeted sequencing, we did not detect off-target activity in edited HSPCs. Our study provides a blueprint for translating new discoveries on ex vivo genome editing of HSCs towards clinical trials for treating SCD and other blood disorders.

genomics↗

Impact of Species-Specific Plant Growth-Promoting Rhizobacteria (PGPR) on Maize (Zea mays) Phenotypic and Biochemical Diversity

Maize (Zea mays) is a vital cereal crop used as a staple diet in many countries. In contemporary farming practises, inoculation with plant-growth-promoting rhizobacteria (PGPR) can be promoted as a sustainable alternative to chemical fertilizers and pesticides in cereal crops including maize. For experimental verification of the above-mentioned hypothesis, four PGPR inoculants Pseudomonas fluorescens, P. putida, Azospirillum lipoferum and Bacillus subtilis were applied to three maize genotypes (AXE*, PMH1 and PMH10) and their effects were studied by measurement of various morphological and biochemical paramters. Substantial increase in the amount of chlorophyll a (45%), chlorophyll b (100%), total chlorophyll (95%), nitrate reductase (22%), superoxide dismutase (52%), protein content (16%), methionine content (31.8%), grain protein content (69%) were recorded over the control (non-treated or mock) plants. Morphological parameters also exhibited an increase in leaf number (53%), fresh weight (41%) and dry weight (62%) in test plants. Comparable outcome was observed for whole cob weight showing an increase of 42%, cob weight (60%), hundred-grain weight (25.9%), maize grain yield m-2 (18%) and yield ha-1 (18%) over the control. This study highlights the efficacy of the aforementioned four PGPR species as the most effective for maize crops. Bacillus subtilis and Azospirillum lipoferum may be considered species-specific PGPRs due to their superior performance compared to other strains. The considerable growth-promoting advantages observed in maize plants treated with bacterial inoculation indicated that PGPRs have the potential to be employed as sustainable solutions in maize production.

plant biology↗

Xanthomonas protegens sp. nov., a rice seed-associated probiotic and taxonomic outlier species of Xanthomonas sontii

Rice seed microbiota play a vital role throughout their growth and developmental stages. Xanthomonas sontii is known as an abundant, core-vertically transmitted rice seed endophyte with probiotic properties. Studies reveal a less explored world of non-pathogenic Xanthomonas (NPX) species like X. sontii and X. indica that are associated with healthy rice seeds. The present study reports the isolation, biochemical characterization, and in-depth taxonogenomic evidence for a third NPX species, X. protegens, from rice seeds, a taxonomic outlier of X. sontii. It also highlights the importance of using multiple taxonogenomic indices to identify taxonomic outlier species. Similar to the other two NPX species, the new member species is also non-pathogenic and provides in vivo protection to rice plants from Xanthomonas oryzae pv. oryzae upon leaf clip inoculation. The pangenome investigation suggested a set of unique genes to the novel species that might be important in adaptation to rice plants and differentiate it from other NPX species. The study will allow the design of markers for the identification of these NPX members, targeted culturomics of a particular NPX species and in the discovery of other novel NPX species from healthy rice seed microbiome for further exploitation in rice health.

evolutionary biology↗

Arabidopsis ubiquitin ligase PUB41 is a positive regulator of the ABA response

Seed germination is a highly controlled developmental process. Prevention of early germination is essential to avoid germination at a time that is not likely to allow the completion of the plant life cycle before entering unfavorable seasons. The plant hormone ABA is the key regulator of seed dormancy and inhibition of germination. ABA is also involved in the plant response to drought. Here we report on the involvement of AtPUB41, a U-BOX E3 ubiquitin ligase from Arabidopsis thaliana, in regulating ABA signaling, seed dormancy, germination, and drought resilience. AtPUB41 is expressed in most plant vegetative and reproductive tissues. AtPUB41 protein is localized in the cytosol and nucleus. pub41 T-DNA insertion mutants display reduced seed dormancy, and their germination is less inhibited by exogenous ABA than seeds of wild-type plants. pub41 mutant plants are also hypersensitive to drought. ABA induces AtPUB41 promoter activity and steady-state mRNA levels in the roots. Our data suggest that AtPUB41 is a positive regulator of ABA signaling. Main ConclusionArabidopsis ubiquitin ligase PUB41 is induced by ABA and acts as a positive regulator of ABA signaling by modulating seed dormancy, germination, and drought resilience.

plant biology↗

Remodeling Ca2+ dynamics by targeting a promising E-box containing G-quadruplex at ORAI1 promoter in triple-negative breast cancer.

ORAI1 is an intrinsic component of store-operated calcium entry (SOCE) that strictly regulates Ca2+ influx in most non-excitable cells. ORAI1 has been extensively studied to have been overexpressed in various cancer phenotypes, and its signal transduction has been associated with oncotherapy resistance. There is extensive proteomic interaction of ORAI1 with other channels and effectors, resulting in various altered phenotypes. However, the transcription regulation of this gene is not well understood. We have found a putative G-quadruplex (G4) motif, ORAI1-Pu, in the upstream promoter region of the gene, having regulatory functions. High-resolution 3-D NMR structure elucidation suggests that ORAI1-Pu is a stable parallel-stranded G4, having an unusual 8-nt loop imparting dynamics without affecting the structural stability. The protruded loop further houses an E-box motif that provides a docking site for transcription factors like Zeb1. The G4 structure was also endogenously observed using Chromatin Immunoprecipitation (ChIP) with anti-G4 antibody (BG4) in the MDA-MB-231 cell line overexpressing ORAI1. Ligand-mediated stabilization suggested that the stabilized G4 represses transcription in cancer cell line MDA-MB-231. Downregulation of transcription further cascaded down to a decrease in Ca2+ entry by the SOCE pathway, as observed by Fura-2 confocal Ca2+ imaging.

biochemistry↗

Guava cv. Allahabad Safeda Chromosome scale assembly and comparative genomics decodes breeder choice marker trait association for pink pulp colour

Deciphering chromosomal length genome assemblies has the potential to unravel an organisms evolutionary relationships and genetic mapping of traits of commercial importance. We assembled guava genome using a hybrid sequencing approach with [~]450x depth Illumina short reads, [~]35x PacBio long reads and Bionano maps to [~]594 MB Scaffold length on 11 pseudo chromosomes ([~]479 MB contig length). Maker pipeline predicted 17,395 genes, 23% greater from earlier draft produced in same cultivar Allahabad Safeda. The genome assembly clarified guava evolutionary history, for example revealing predominance of gene expansion by dispersed duplications, in particular contributing to abundance of monoterpene synthases; and supporting evidence of a whole genome duplication event in guava as in other Myrtaceae. Guava breeders have been aiming to reduce screening time for selecting pink pulp colour progenies using marker-trait associations, but a previous comparative transcriptomics and comparative genomics approach with draft genome assembly to identify the effector gene associated with pink pulp was unsuccessful. Here, genome re-sequencing with Illumina short reads at [~]25x depth of 20 pink fleshed and/or non-coloured guava cultivars and comprehensive analysis for genes in the carotenoid biosynthesis pathway identified structural variations in Phytoene Synthase 2. Further, ddRAD based association mapping in core-collection of 82 coloured and non-coloured genotypes from Indian sub-continent found strong association with the same causal gene. Subsequently, we developed PCR based Indel/SSR breeder friendly marker that can readily be scored in routine agarose gels and empowers accurate selection for seedlings that will produce fruits with pink pulp.

plant biology↗

Androgen deprivation therapy-resistant club cells are linked to myeloid cell-driven immunosuppression in the prostate tumor microenvironment

Prostate cancer treatment resistance is a significant challenge facing the field. Genomic and transcriptomic profiling have partially elucidated the mechanisms through which cancer cells escape treatment, but their relation toward the tumor microenvironment (TME) remains elusive. Here we present a comprehensive transcriptomic landscape of the prostate TME at multiple points in the standard treatment timeline employing single-cell RNA-sequencing and spatial transcriptomics data from 110 patients. We identify club-like cells as a key epithelial cell subtype that acts as an interface between the prostate and the immune system. Tissue areas enriched with club-like cells have depleted androgen signaling and upregulated expression of luminal progenitor cell markers. Club-like cells display a senescence-associated secretory phenotype and their presence is linked to increased polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC) activity. Our results indicate that club-like cells partake in inducing myeloid inflammation previously associated with androgen deprivation therapy resistance, providing a rationale for their therapeutic targeting.

cancer biology↗

Intercontinental dissemination and diversification of Xanthomonas perforans in tomato production

Emerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution. Xanthomonas euvesicatoria pv. perforans (Xep), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a model for understanding diversification of recently emerged bacterial plant pathogens. Although Xep has been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinct Xep populations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization of Xop effector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of the Xep pangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.

microbiology↗

Modulation of SARS-CoV-2 spike binding to ACE2 throughconformational selection

The first step of SARS-CoV-2 infection involves the interaction between the trimeric viral spike protein (S) and the host angiotensin-converting enzyme 2 (ACE2). The receptor binding domain (RBD) of S adopts two conformations: open and closed, respectively, accessible and inaccessible to ACE2. Therefore, RBD motions are suspected to affect ACE2 binding; yet a quantitative description of the underlying mechanism has been elusive. Here, using single-molecule approaches, we visualize RBD opening and closing and probe the S/ACE2 interaction. Our results show that RBD dynamics affect ACE2 binding but not unbinding. The resulting modulation is quantitatively predicted by a conformational selection model in which each protomer behaves independently. Our work reveals a general molecular mechanism affecting binding affinity without altering binding strength, helping to understand coronavirus infection and immune evasion.

biophysics↗

Phylogenetically distant enzymes localized in cytosol and plastids drive citral biosynthesis in lemongrass

Except for the genetic basis of citral-forming alcohol dehydrogenases (ADHs) in Litsea cubeba tree, and biochemical studies on citral-forming enzymes from select plants, knowledge regarding in-planta biosynthesis of citral and its metabolic origin remains limited. Here, we have elucidated the functions of an ADH (CfADH1) and an aldoketo-reductase (CfAKR2b) in citral biosynthesis in lemongrass (Cymbopogon flexuosus), one of the most cultivated aromatic crops for its citral-rich essential oil. Expression of both CfADH1 and CfAKR2b showed correlation with citral accumulation in different developmental stages. Recombinant CfADH1 and CfAKR2b, despite their sequence unrelatedness, exhibited similar kinetic properties and formed citral from geraniol with NADP cofactor. Virus-induced gene silencing in lemongrass, and transient expression in lemon balm (Melissa officinalis), demonstrated the in-planta involvement of CfADH1 and CfAKR2b in citral biosynthesis. While CfADH1 exhibited a dual cytosolic/plastidial localization, CfAKR2b was localized to cytosol. Moreover, feeding lemongrass seedlings with mevalonate- and methylerythritol-phosphate-pathway specific inhibitors combined with volatile profiling supported the role of both pathways in citral formation. Our results demonstrate phylogenetically distant enzymes localized in cytosol and plastids drive citral biosynthesis in lemongrass, indicating an evolutionary scenario aimed at maximizing the utilization of precursor pools from both cytosolic and plastidial pathways for high citral production.

plant biology↗

A multi-modal image fusion workflow incorporating MALDI imaging mass spectrometry and microscopy for the study of small pharmaceutical compounds

Multi-modal imaging analyses of dosed tissue samples can provide more comprehensive insight into the effects of a therapeutically active compound on a target tissue compared to single-modal imaging. For example, simultaneous spatial mapping of pharmaceutical compounds and endogenous macromolecule receptors is difficult to achieve in a single imaging experiment. Herein, we present a multi-modal workflow combining imaging mass spectrometry with immunohistochemistry (IHC) fluorescence imaging and brightfield microscopy imaging. Imaging mass spectrometry enables direct mapping of pharmaceutical compounds and metabolites, IHC fluorescence imaging can visualize large proteins, and brightfield microscopy imaging provides tissue morphology information. Single-cell resolution images are generally difficult to acquire using imaging mass spectrometry, but are readily acquired with IHC fluorescence and brightfield microscopy imaging. Spatial sharpening of mass spectrometry images would thus allow for higher fidelity co-registration with higher resolution microscopy images. Imaging mass spectrometry spatial resolution can be predicted to a finer value via a computational image fusion workflow, which models the relationship between the intensity values in the mass spectrometry image and the features of a high spatial resolution microscopy image. As a proof of concept, our multi-modal workflow was applied to brain tissue extracted from a Sprague Dawley rat dosed with a kratom alkaloid, corynantheidine. Four candidate mathematical models including linear regression, partial least squares regression (PLS), random forest regression, and two-dimensional convolutional neural network (2-D CNN), were tested. The random forest and 2-D CNN models most accurately predicted the intensity values at each pixel as well as the overall patterns of the mass spectrometry images, while also providing the best spatial resolution enhancements. Herein, image fusion enabled predicted mass spectrometry images of corynantheidine, GABA, and glutamine to approximately 2.5 m spatial resolutions, a significant improvement compared to the original images acquired at 25 m spatial resolution. The predicted mass spectrometry images were then co-registered with an H&E image and IHC fluorescence image of the - opioid receptor to assess co-localization of corynantheidine with brain cells. Our study also provides insight into the different evaluation parameters to consider when utilizing image fusion for biological applications.

biochemistry↗

The Role of Ebola Virus VP24 Nuclear Trafficking Signals in Infectious Particle Production

Ebola virus (EBOV) protein VP24 carries out at least two critical functions. It promotes condensation of viral nucleocapsids, which is crucial for infectious virus production, and it suppresses interferon (IFN) signaling, which requires interaction with the NPI-1 subfamily of importin- (IMPA) nuclear transport proteins. Interestingly, over-expressed IMPA leads to VP24 nuclear accumulation and a carboxy-terminus nuclear export signal (NES) has been reported, suggesting that VP24 may undergo nuclear trafficking. For the first time, we demonstrate that NPI-1 IMPA overexpression leads to the nuclear accumulation of VP24 during EBOV infection. To assess the functional impact of nuclear trafficking, we generated tetracistronic minigenomes encoding VP24 nuclear import and/or export signal mutants. The minigenomes, which also encode Renilla luciferase and viral proteins VP40 and GP, were used to generate transcription and replication competent virus-like particles (trVLPs) that can be used to assess EBOV RNA synthesis, gene expression, entry and viral particle production. With this system, we confirmed that NES or IMPA binding site mutations altered VP24 nuclear localization, demonstrating functional trafficking signals. While these mutations minimally affected transcription and replication, the trVLPs exhibited impaired infectivity and formation of shortened nucleocapsids for the IMPA binding mutant. For the NES mutants, infectivity was reduced approximately 1000-fold. The NES mutant could still suppress IFN signaling but failed to promote nucleocapsid formation. To determine whether VP24 nuclear export is required for infectivity, the residues surrounding the wildtype NES were mutated to alanine or the VP24 NES was replaced with the Protein Kinase A Inhibitor NES. While nuclear export remained intact for these mutants, infectivity was severely impaired. These data demonstrate that VP24 undergoes nuclear trafficking and illuminates a separate and critical role for the NES and surrounding sequences in infectivity and nucleocapsid assembly. Author StatementEbola virus (EBOV) viral protein 24 (VP24) interacts with importin- (IMPA) nuclear transport proteins to inhibit interferon signaling. VP24 also contains a nuclear export signal (NES). The capacity to bind IMPA and the presence of a NES suggest that VP24 traffics to the nucleus. However, this had not been demonstrated in the context of EBOV replication. In addition, whether these signals influence virus replication beyond effects on interferon responses has been unclear. Here, we demonstrate that VP24 traffics to the nucleus via IMPA during EBOV infection and in the context of an EBOV transcription and replication competent virus-like particle (trVLP) assay. Using the trVLP system, we also confirmed that VP24 possesses a functional nuclear export signal (NES). Mutations disrupting VP24-IMPA interaction or nuclear export reduced or abrogated trVLP infectivity, respectively. VP24 is known to be necessary for viral nucleocapsid maturation. The VP24 IMPA interface mutants yielded shortened nucleocapsids while VP24 NES mutations led to loss of nucleocapsid formation. Interestingly, VP24 mutants with intact NES function but altered sequences near the NES remain incapable of producing nucleocapsids. Together, these data demonstrate VP24 undergoes nuclear trafficking and reveals additional roles for both the IMPA interaction interface and the NES in nucleocapsid assembly.

microbiology↗

DR5 disulfide bonding as a sensor and effector of protein folding stress

New agents are needed that selectively kill cancer cells without harming normal tissues. The TRAIL ligand and its receptors, DR5 and DR4, exhibit cancer-selective toxicity, but TRAIL analogs or agonistic antibodies targeting these receptors have not received FDA approval for cancer therapy. Small molecules for activating DR5 or DR4 independently of protein ligands may bypass some of the pharmacological limitations of these protein drugs. Previously described Disulfide bond Disrupting Agents (DDAs) activate DR5 by altering its disulfide bonding through inhibition of the Protein Disulfide Isomerases (PDIs) ERp44, AGR2, and PDIA1. Work presented here extends these findings by showing that disruption of single DR5 disulfide bonds causes high-level DR5 expression, disulfide-mediated clustering, and activation of Caspase 8-Caspase 3 mediated pro-apoptotic signaling. Recognition of the extracellular domain of DR5 by various antibodies is strongly influenced by the pattern of DR5 disulfide bonding, which has important implications for the use of agonistic DR5 antibodies for cancer therapy. Disulfide-defective DR5 mutants do not activate the ER stress response or stimulate autophagy, indicating that these DDA-mediated responses are separable from DR5 activation and pro-apoptotic signaling. Importantly, other ER stressors, including Thapsigargin and Tunicamycin also alter DR5 disulfide bonding in various cancer cell lines and in some instances, DR5 mis-disulfide bonding is potentiated by overriding the Integrated Stress Response (ISR) with inhibitors of the PERK kinase or the ISR inhibitor ISRIB. These observations indicate that the pattern of DR5 disulfide bonding functions as a sensor of ER stress and serves as an effector of proteotoxic stress by driving extrinsic apoptosis independently of extracellular ligands.

cancer biology↗

Deep learning methods to forecasting human embryo development in time-lapse videos

BackgroundIn assisted reproductive technology, evaluating the quality of the embryo is crucial when selecting the most viable embryo for transferring to a woman. Assessment also plays an important role in determining the optimal transfer time, either in the cleavage stage or in the blastocyst stage. Several AI-based tools exist to automate the assessment process. However, none of the existing tools predicts upcoming video frames to assist embryologists in the early assessment of embryos. In this paper, we propose an AI system to forecast the dynamics of embryo morphology over a time period in the future. MethodsThe AI system is designed to analyze embryo development in the past two hours and predict the morphological changes of the embryo for the next two hours. It utilizes a predictive model incorporating Convolutional LSTM layers, to predict the future video frame by analyzing prior morphological changes within the embryos video sequence. The system uses the predictions recursively and forecasts up to 23 hours of embryo development. ResultsThe results demonstrated that the AI system could accurately forecast embryo development at the cleavage stage on day 2 and the blastocyst stage on day 4. The system provided valuable information on the cell division processes on day 2 and the start of the blastocyst stage on day 4. The system focused on specific developmental features effective across both the categories of embryos. The embryos that were transferred to the female, and the embryos that were discarded. However, in the transfer category, the forecast had a clearer cell membrane and less distortion as compared to the avoid category. ConclusionThis study assists in the embryo evaluation process by providing early insights into the quality of the embryo for both the transfer and avoid categories of videos. The embryologists recognize the ability of the forecast to depict the morphological changes of the embryo. Additionally, enhancement in image quality has the potential to make this approach relevant in clinical settings. Author summaryThe emergence of assisted reproductive technology has significantly improved infertility treatments. It involves fertilization of an egg outside the body, and the resultant embryos are developed in time-lapse incubators. The embryologists manually evaluate embryos using time-lapse videos and rank each embryo on the basis of several criteria including the dynamics of embryo cell stages, such as the start of the blastocyst stage. Traditional manual analysis is subjective and time-consuming, and AI tools are introduced to automate and enhance embryo selection efficiency. However, current AI tools do not generate video frames that forecast changes in embryo morphology. This study fills this gap by introducing an AI system that forecasts upcoming frames of a time-lapse video. In this approach, several hours were predicted ahead of the last video frame. The system was evaluated on crucial days of embryo evaluation. Our approach was effective in both good quality (transfer) and poor quality (avoid) video categories, and the forecast revealed crucial insights about embryo cell division and the start of the blastocyst stage. Despite some image quality issues, the proposed AI system demonstrated the potential for early and accurate assessment of embryo quality.

cell biology↗