Biology subjects

Sharma, A.

Publications and source records attributed to Sharma, A..

At least 271 records · Page 15Linked to original sources

bioRxiv2023

ShinyMultiome.UiO: An interactive open-source framework utilizing Seurat Objects for visualizing single-cell Multiomes

MotivationSingle-cell genomics has been revolutionized by the advent of single-cell Multiome sequencing which allows for simultaneous profiling of chromatin accessibility and gene expression in individual nuclei. The analysis and interpretation of large and often complex scMultiome datasets requires in-depth knowledge of computational programming. ResultsWe present ShinyMultiome.UiO, a user-friendly, integrative, and opensource web-based tool that supports Seurat objects for visualization of single-cell Multiome. The ShinyMultiome.UiO facilitates interactive reporting and comprehensive characterization of cellular heterogeneity and regulatory landscapes. With ShinyMultiome.UiO, users can facilitate collaborative efforts for interpre-tation of single-cell Multiome data and make it available to the public. Availability and implementationhttps://github.com/EskelandLab/ShinyMultiomeUiO and demo server, https://cancell.medisin.uio.no/ShinyMultiome.UiO/ set up with a PBMC reference dataset. ContactAnkush.Sharma@medisin.uio.no & Ragnhild.Eskeland@medisin.uio.no

bioinformatics↗

bioRxiv2023

Single-cell transcriptome and TCR analysis of human Cytomegalovirus (hCMV)-specific T cell memory reveals effector and pre-effectors of CD8+ and CD4+ cytotoxic T cells

BackgroundLatent human Cytomegalovirus (hCMV) infection can pose a serious threat of reactivation and disease occurrence in immune-compromised individuals. Though, T cells are at the core of the protective immune response to hCMV infection, a detailed characterization of different T cell subsets involved in hCMV immunity is lacking. ResultsHere, in an unbiased manner, we characterized over 8000 hCMV-reactive peripheral memory T cells isolated from seropositive human donors, at a single-cell resolution by analyzing their single-cell transcriptomes paired with the T cell antigen receptor (TCR) repertoires. The hCMV-reactive T cells were highly heterogeneous and consisted of different developmental and functional memory T cell subsets such as, long-term memory precursors and effectors, T helper-17, T regulatory cells (TREGs) and cytotoxic T lymphocytes (CTLs) of both CD4 and CD8 origin. The hCMV-specific TREGs, in addition to being enriched for molecules known for their suppressive functions, showed enrichment for the interferon response signature gene sets. The hCMV-specific CTLs were of two types, the pre-effector and effector-like. The co-clustering of hCMV-specific CD4-CTLs and CD8-CTLs in both pre-effector as well as effector clusters suggest shared transcriptomic signatures between them. The huge TCR clonal expansion of cytotoxic clusters suggest a dominant role in protective immune response to CMV. ConclusionsThe study uncovers the heterogeneity in the hCMV-specific memory T cells reveling many functional subsets with potential implications in better understanding of hCMV-specific T cell immunity. The data presented can serve as a knowledge base for designing vaccines and therapeutics.

immunology↗

bioRxiv2023

De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity

Relating the macroscopic properties of protein-based materials to their underlying component microstructure is an outstanding challenge. Here, we exploit computational design to specify the size, flexibility, and valency of de novo protein building blocks, as well as the interaction dynamics between them, to investigate how molecular parameters govern the macroscopic viscoelasticity of the resultant protein hydrogels. We construct gel systems from pairs of symmetric protein homo-oligomers, each comprising 2, 5, 24, or 120 individual protein components, that are crosslinked either physically or covalently into idealized step-growth biopolymer networks. Through rheological assessment and molecular dynamics (MD) simulation, we find that the covalent linkage of multifunctional precursors yields hydrogels whose viscoelasticity depends on the crosslink length between the constituent building blocks. In contrast, reversibly crosslinking the homo-oligomeric components with a computationally designed heterodimer results in non-Newtonian biomaterials exhibiting fluid-like properties under rest and low shear, but shear-stiffening solid-like behavior at higher frequencies. Exploiting the unique genetic encodability of these materials, we demonstrate the assembly of protein networks within living mammalian cells and show via fluorescence recovery after photobleaching (FRAP) that mechanical properties can be tuned intracellularly, in correlation with matching formulations formed extracellularly. We anticipate that the ability to modularly construct and systematically program the viscoelastic properties of designer protein-based materials could have broad utility in biomedicine, with applications in tissue engineering, therapeutic delivery, and synthetic biology. SignificanceProtein-based hydrogels have many applications in cellular engineering and medicine. Most genetically encodable protein hydrogels are made from naturally harvested proteins or protein-polymer hybrid constructs. Here we describe de novo protein hydrogels and systematically investigate the impact of microscopic properties of the building blocks (e.g., supramolecular interaction, valencies, geometries, flexibility) on the resultant macroscopic gel mechanics, both intra-and extracellularly. These de novo supramolecular protein assemblies, whose properties can be tuned from solid gels to non-Newtonian fluids, provide expanded opportunities for applications in synthetic biology and medicine.

bioengineering↗

bioRxiv2023

Mitochondrial calcium signaling mediated transcriptional regulation of keratin filaments is a critical determinant of melanogenesis

Mitochondria are versatile organelles that regulate several physiological functions. Many mitochondria-controlled processes are driven by mitochondrial Ca2+ signaling. However, role of mitochondrial Ca2+ signaling in melanosome biology remains unknown. Here, we show that pigmentation requires mitochondrial Ca2+ uptake. In vitro gain and loss of function studies demonstrated that Mitochondrial Ca2+ Uniporter (MCU) is crucial for melanogenesis while the MCU rheostats, MCUb and MICU1 negatively control melanogenesis. Zebrafish and mouse models showed that MCU plays a vital role in pigmentation in vivo. Mechanistically, MCU controls activation of transcription factor NFAT2 to induce expression of three keratins (keratin 5, 7 and 8), which we report as positive regulators of melanogenesis. Interestingly, keratin 5 in turn modulates mitochondrial Ca2+ uptake thereby this signaling module acts as a negative feedback loop that fine-tunes both mitochondrial Ca2+ signaling and melanogenesis. Mitoxantrone, an FDA approved drug that inhibits MCU, decreases physiological melanogenesis. Collectively, our data demonstrates a critical role for mitochondrial Ca2+ signaling in vertebrate pigmentation and reveal the therapeutic potential of targeting MCU for clinical management of pigmentary disorders. Given the centrality of mitochondrial Ca2+ signaling and keratin filaments in cellular physiology, this feedback loop may be functional in a variety of other pathophysiological conditions. HighlightsO_LIMCU complex mediated mitochondrial Ca2+ uptake is a novel regulator of vertebrate pigmentation C_LIO_LIKeratin filaments bridge mitochondrial Ca2+ signaling to melanosome biogenesis and maturation C_LIO_LITranscription factor NFAT2 connects mitochondrial Ca2+ dynamics to keratins expression C_LIO_LIMCU-NFAT2-Keratin 5 signaling module generates a negative feedback loop to maintain mitochondrial Ca2+ homeostasis and to ensure optimal melanogenesis C_LIO_LIInhibiting MCU with mitoxantrone, an FDA approved drug, leads to reduction in physiological pigmentation C_LI

cell biology↗

bioRxiv2023

Live tracking of a plant pathogen outbreak reveals rapid and successive, multidecade episome reduction

Quickly understanding the genomic changes that lead to pathogen emergence is necessary to launch mitigation efforts and reduce harm. Often the evolutionary events that result in an epidemic typically remain elusive long after an outbreak, which is particularly true for plant pathogens. To rapidly define the consequential evolutionary events result in pathogen emergence, we tracked in real-time a 2022 bacterial plant disease outbreak in US geranium (Pelargonium x hortorum) caused by Xhp2022, a novel lineage of Xanthomonas hortorum. Genomes from 31 Xhp2022 isolates from seven states showed limited chromosomal variation, and all contained a single plasmid (p93). Time tree and SNP whole genome analysis estimated that Xhp2022 emerged in the early 2020s. Phylogenomic analysis determined that p93 resulted from cointegration of three plasmids (p31, p45, and p66) present in a 2012 outbreak. p31, p45 and p66 were individually found in varying abundance across X. hortorum isolates from historical outbreaks dating to 1974 suggesting these plasmids were maintained in the broader metapopulation. p93 specifically arose from two co-integration events from homologous and Tn3 and XerC-mediated site-specific recombination. Although p93 suffered a 49kb nucleotide reduction, it maintained critical fitness gene functions encoding, for example, metal resistance and virulence factors, which were likely selected by the ornamental production system. Overall we demonstrate how rapid sequencing of current and historical isolates track the evolutionary history of an emerging, ongoing threat. We show a recent, tractable event of genome reduction for niche adaptation typically observed over millenia in obligate and fastidious pathogens. SignificanceGenome-resolved epidemiology is rapidly changing how we track pathogens in real-time to support stakeholders and health. This research highlights how we responded to a current disease outbreak of geranium. Our work revealed that a new group of the bacterial plant pathogen Xanthomonas horotrum emerged in 2022 as a result of a recent genome reduction. We determined that three distinct plasmids were present in the broader X. hortorum metapopulation since 1974. In 2012, the three plasmids were altogether present in individual isolates; then in 2022, all three plasmids co-integrated while maintaining critical fitness genes but losing extraneous genomic material. This parallels genome efficiency and reduction that we see across millenia or even millions of years with obligate parasites with increased niche-specificity.

microbiology↗

bioRxiv2023

Multi-omics data analysis supporting inheritance of acquired traits in humans

Experimental evidence supports presence of germline mediated nongenetic inheritance in animals including mammalian models. Observational and molecular epidemiological studies also suggest existence of environmental exposure induced germline inheritance in humans. Considering the obvious difficulties in conducting prospective cross-generational human studies, integrative analysis of available multi-omics data may seem to offer a valuable approach for assessing biological plausibility of inheritance of acquired traits in the species. To that end, the concept has mainly been tested here that, under the assumption of inheritance, human exposure to an environmental factor, if known to induce paternal inheritance in mammalian models and to act through molecular pathways conserved across species, would induce correlated changes in sperm epigenome and somatic transcriptome in the exposed subjects. The test is based on physical exercise, a physiologically relevant factor for which multiple datasets of human sperm DNA methylome and somatic transcriptome from interventional pre-post cohort studies, that minimizes inter-individual variability, were available. Existing somatic transcriptome datasets from animal model studies on exercise have been used for comparison. To control the analysis, bariatric surgery, for which exercise matched human datasets existed, have been used. The hypothesis testing involves gene set overrepresentation, comparison between directionality of epigenome and coding transcriptome changes, gene ontology enrichment, and epigenome and non-coding transcriptome interaction. Remarkably, the results show that, in humans, exercise induced DNA methylation changes in sperm specifically represent transcriptional response to exercise in soma. This germline epigenomic encoding of acquired transcriptome changes in soma clearly supports biological plausibility of epigenetic inheritance in humans.

genomics↗

bioRxiv2023

InVitro Biocompatibility Evaluation of Acellular Porcine Dura mater Grafts and Native Dura

Damage to the dura mater may occur during intracranial or spinal surgeries, which can result in cerebrospinal fluid leakage as well as other potentially fatal physiological changes. As a result, biological scaffolds derived from xenogeneic materials are typically used to repair and regenerate dura mater post intracranial or spinal surgeries. The extracellular matrix of xenogeneic dura scaffolds has been shown to exhibit better cell infiltration and regeneration than synthetic material. In this study, we investigated the biocompatibility of native and decellularized porcine dura. Cell proliferation, cell viability, and mechanical properties of dural grafts were evaluated post re-seeding on days 3,7, and 14. Live-dead staining and resazurin salts were used to quantify cell viability and cell proliferation, respectively. Micro indentation was conducted to quantify the mechanical integrity of the native and acellular dura graft. The results show that the acellular porcine dural graft provides a favorable environment for rat fibroblast cell infiltration. Cell viability, proliferation, and micro indentation results on the acellular grafts are comparable with the native control porcine dura tissue. In conclusion, the porcine scaffold material showed increasing viable cells at each time point. The mechanics and biocompatibility results provide promising insight into the potential use of porcine dura in future cranial dura mater graft applications.

bioengineering↗

bioRxiv2023

Acute myeloid leukemia stratifies as two clinically relevant sphingolipidomic subtypes

Acute myeloid leukemia (AML) is an aggressive disease with complex and heterogeneous biology. Although several genomic classifications have been proposed, there is a growing interest in going beyond genomics to stratify AML. In this study, we profile the sphingolipid family of bioactive molecules in 213 primary AML samples and 30 common human AML cell lines. Using an integrative approach, we identify two distinct sphingolipid subtypes in AML characterized by a reciprocal abundance of hexosylceramide (Hex) and sphingomyelin (SM) species. The two Hex-SM clusters organize diverse samples more robustly than known AML driver mutations and are coupled to latent transcriptional states. Using transcriptomic data, we develop a machine-learning classifier to infer the Hex-SM status of AML cases in TCGA and BeatAML clinical repositories. The analyses show that the sphingolipid subtype with deficient Hex and abundant SM is enriched for leukemic stemness transcriptional programs and comprises an unappreciated high-risk subgroup with poor clinical outcomes. Our sphingolipid-focused examination of AML identifies patients least likely to benefit from standard of care and raises the possibility that sphingolipidomic interventions could switch the subtype of AML patients who otherwise lack targetable alternatives. Key Points1.Sphingolipidomics separates acute myeloid leukemia (AML) patients and cell lines into two subtypes. 2.The subtype with low hexosylceramide and high sphingomyelin defines a new high-risk subtype with poor clinical outcomes.

systems biology↗

bioRxiv2023

Charting spatial ligand-target activity using Renoir

The advancement of single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics has enabled the inference of cellular interactions in a tissue microenvironment. Despite the development of cell-cell interaction inference methods, there is a lack of methods capable of mapping the influence of ligands on downstream target genes across a spatial topology with specific cell type composition, with the potential to shed light on niche-specific relationship between ligands and their downstream targets. Here we present Renoir for charting the ligand-target activities across a spatial topology and delineating spatial communication niches harboring specific ligand-target activities. Renoir also spatially maps pathway-level activity of ligand-target genesets and identifies domain-specific ligand-target activities. Across spatial datasets with varying resolution (spot to single-cell) ranging from development to disease, Renoir inferred cellular niches with distinct ligand-target interactions, spatially mapped pathway activities, and identified context-specific novel cell-cell interactions. Renoir uncovers biological insights and therapeutically-relevant cellular crosstalk from spatial transcriptomics data.

bioinformatics↗

bioRxiv2023

Effect of hexanal treatment on fruit qualities and antioxidant activities on 'Umran' Indian jujube fruit during cold storage

Umran Indian jujube is a widely grown cultivar due to its marketable quality and productivity, resulting in excellent market value. Despite its high quality, the products short shelf life poses a challenge for transportation, even within the domestic market. Hexanal with three concentrations (0.15%, 0.20%, and 0.25%) was applied to the fruit of Umran Indian jujube at both pit hardening and color break stages. Harvested fruits were stored for 28 days in a cold chamber of 7.5{+/-}1{degrees}C and 90-95% RH. The changes in fruit qualities were assessed with physicochemical characteristics, bioactive compounds, and enzymatic antioxidant activities every seven days. Fruits treated with hexanal of 0.20% reduced fruit weight loss and spoilage and maintained fruit firmness, soluble solids content, carotenoid content, and antioxidant activity. The activities of cell wall degrading enzymes investigated were suppressed. Of the antioxidant activities, superoxide dismutase and peroxidase were positively activated. Therefore, these results indicated that pre-harvest application of hexanal 0.20% improved physiochemical characteristics, maintained bioactive compounds, antioxidant enzyme activities, and extended the shelf life of Indian jujube fruits up to 21 days during cold storage.

plant biology↗

bioRxiv2023

A local ATR-dependent checkpoint pathway is activated by a site-specific replication fork block in human cells

When replication forks encounter DNA lesions that cause polymerase stalling a checkpoint pathway is activated. The ATR-dependent intra-S checkpoint pathway mediates detection and processing of sites of replication fork stalling to maintain genomic integrity. Several factors involved in the global checkpoint pathway have been identified, but the response to a single replication fork barrier (RFB) is poorly understood. We utilized the E.coli-based Tus-Ter system in human MCF7 cells and showed that the Tus protein binding to TerB sequences creates an efficient site-specific RFB. The single fork RFB was sufficient to activate a local, but not global, ATR-dependent checkpoint response that leads to phosphorylation and accumulation of DNA damage sensor protein {gamma}H2AX, confined locally to within a kilobase of the site of stalling. These data support a model of local management of fork stalling, which allows global replication at sites other than the RFB to continue to progress without delay.

molecular biology↗

bioRxiv2023

DRPBind: prediction of DNA, RNA and protein binding residues in intrinsically disordered protein sequences

DRPbind predicts three components: deoxyribonucleic acid (DNA) binding, ribonucleic acid (RNA) binding and protein-binding residues of query protein sequences. DRPbind utilizes independent sources of information encoded for each component predictor and relies on the information-rich profiles of protein evolutionary-based features, protein physicochemical-based features, and protein structural-based features. DRPbind employs protein profile-based features extracted from the bigrams of PSSM and HMM profiles. It also extracts features from physicochemical and structural attributes. DRPbind takes primary protein sequences as input, and through the Support Vector Machine (SVM) classifier, it provides the binding prediction. DRPbind is optimized based on a specific binding type and shown superior performance in terms of simultaneously predicting the DNA-binding, RNA-binding and protein-binding residues. The source code is available at https://github.com/roneshsharma/DNA-RNA-Protein-Binding/wiki

bioinformatics↗

bioRxiv2023

scDeepInsight: a supervised cell-type identification method for scRNA-seq data with deep learning

Annotation of cell-types is a critical step in the analysis of single-cell RNA sequencing (scRNA-seq) data that allows the study of heterogeneity across multiple cell populations. Currently this is most commonly done using unsupervised clustering algorithms, which project single-cell expression data into a lower dimensional space and then cluster cells based on their distances from each other. However, as these methods do not use reference datasets, they can only achieve a rough classification of cell-types, and it is difficult to improve the recognition accuracy further. To effectively solve this issue we propose a novel supervised annotation method, scDeepInsight. The scDeepInsight method is capable of performing manifold assignments. It is competent in executing data integration through batch normalization, performing supervised training on the reference dataset, doing outlier detection and annotating cell-types on query datasets. Moreover, it can help identify active genes or marker genes related to cell-types. The training of the scDeepInsight model is performed in a unique way. Tabular scRNA-seq data are first converted to corresponding images through the DeepInsight methodology. DeepInsight can create a trainable image transformer to convert non-image RNA data to images by comprehensively comparing interrelationships among multiple genes. Subsequently, the converted images are fed into convolutional neural networks (CNNs) such as EfficientNet-b3. This enables automatic feature extraction to identify the cell-types of scRNA-seq samples. We benchmarked scDeepInsight with six other mainstream cell annotation methods. The average accuracy rate of scDeepInsight reached 87.5%, which is more than 7% higher compared with the state-of-the-art methods.

bioinformatics↗

bioRxiv2023

SMCHD1 loss triggers DUX4 expression by disrupting splicing in FSHD2

Structural Maintenance of Chromosomes Flexible Hinge Domain Containing 1 (SMCHD1) is a non-canonical member of the structural maintenance of chromosomes (SMC) protein family involved in the regulation of chromatin structure, epigenetic regulation, and transcription. Mutations in SMCHD1 cause facioscapulohumeral muscular dystrophy type 2 (FSHD2), a rare genetic disorder characterized by progressive muscle weakness and wasting, believed to be caused by aberrant expression of DUX4 in muscle cells. Here we suggest a new role for SMCHD1 as a regulator of alternative splicing in various cell types. We demonstrate how SMCHD1 mutations cause splicing alterations of DNA Methyltransferase 3 Beta DNMT3B which can lead to hypomethylation, DUX4 expression, and FSHD pathogenesis. Analyzing RNA-seq data from muscle biopsies of FSHD2 patients and Smchd1 knocked out cells, we found that hundreds of genes were mis-spliced upon loss of SMCHD1. At least 20% of mis-spliced genes were associated with abnormalities of the musculature. Moreover, we show that mis-spliced exons tend to be bound by SMCHD1, and these exons demonstrate a slower elongation rate, suggesting SMCHD1 binding promotes exon exclusion by slowing RNA polymerase II (RNAPII). Specifically, we discovered that SMCHD1 mutations promote the splicing of the DNMT3B1 isoform of DNMT3B by perturbing RNAPII elongation rate and recruitment of the splicing factor RBM5. The mis-splicing of DNMT3B leads to hypomethylation of the D4Z4 region and DUX4 overexpression. These results suggest that mis-splicing by SMCHD1 may play a major role in FSHD2 pathogenesis by promoting the mis-splicing of different targets including DNMT3B, and highlight the potential for targeting splicing as a therapeutic strategy for this disorder. Significance statementOur study sheds light on how the loss of SMCHD1 drives the pathogenesis of facioscapulohumeral muscular dystrophy (FSHD), a rare genetic disorder characterized by muscle weakness and wasting. We found that SMCHD1 mutations led to changes in splicing of hundreds of genes, 20% of which were related to muscle abnormalities. We found that SMCHD1 tends to bind mis-spliced exons and that its binding slows down the elongation rate of RNA polymerase II often leading to the exclusion of the exon. One of these targets is DNA Methyltransferase 3 Beta (DNMT3B), and we show that the isoform promoted by SMCHD1 mutations leads to hypomethylation of a repeat region near DUX4 and to DUX4 overexpression, a known cause for FSHD. Our results provide insight into the molecular mechanisms underlying this disorder, and suggest splicing modulation as a therapeutic strategy for FSHD.

genomics↗

bioRxiv2023

Tight hydrophobic core and flexible helices yield MscL with a high tension gating threshold and a membrane area mechanical strain buffer

The mechanosensitive (MS) channel of large conductance, MscL, is the high-tension threshold osmolyte release valve that limits turgor pressure in bacterial cells in the event of drastic hypoosmotic shock. Despite MscL from M. tuberculosis (TbMscL) being the first structurally characterized MS channel, its protective mechanism of activation at nearly-lytic tensions has not been fully understood. Here, we describe atomistic simulations of expansion and opening of wild-type (WT) TbMscL in comparison with five of its gain-of-function (GOF) mutants. We show that under far-field membrane tension applied to the edge of the periodic simulation cell, WT TbMscL expands into a funnel-like structure with trans-membrane helices bent by nearly 70 degrees, but does not break its hydrophobic seal within extended 20 s simulations. GOF mutants carrying hydrophilic substitutions in the hydrophobic gate of increasing severity (A20N, V21A, V21N, V21T and V21D) also quickly transition into funnel-shaped conformations but subsequently fully open within 1-8 us. This shows that solvation of the de-wetted (vapor-locked) constriction is the rate-limiting step in the gating of TbMscL preceded by area-buffering silent expansion. Pre-solvated gates in severe V21N and V21D mutants eliminate this barrier. We predict that the asymmetric shape-change of the periplasmic side of the channel during the silent expansion provides strain-buffering to the outer leaflet thus re-distributing the tension to the inner leaflet, where the gate resides.

biophysics↗

bioRxiv2023

Regional assessment of male murine bone exposes spatial heterogeneity in osteocyte lacunar volume associated with intracortical canals and regulation by VEGF

The porous bone cortex comprises an interconnected network of intracortical vascular canals and osteocyte lacunae, embedded within the bone mineral. Increases in cortical porosity reduce bone strength and increase fracture risk. To date, our understanding of mechanisms coupling the arrangements of the vascular: lacunar network in the bone cortex is poorly understood yet it could be key in establishing regulation of cortical porosity evident with age. Using synchrotron radiation-based computed tomography we develop automated tools to characterise the 3D spatial organisation and morphology of osteocyte lacunae, and the bone vasculature at the tibiofibular junction (TFJ), defining posterior, medial, lateral, and anterior regions in male C57BL/6 mice (n = 3). We also investigate the role of osteoblast-derived VEGF in regulating the 3D spatial arrangement by conditional disruption of VEGF in osteocalcin-expressing cells (OcnVEGFKO versus WT, n = 3). Regional lacunar phenotypes were assessed by 3D distance mapping of lacunar organisation surrounding the vascular compartments, including endosteal and periosteal surfaces, or intracortical canals. Surface-associated lacunae were indistinct in size across posterior, medial, lateral and anterior regions. However, lacunae associated with intracortical canals were significantly larger exclusively within the posterior region. In the absence of VEGF, the increased lacunar volume associated with posterior intracortical canals was lost. Our results suggest that the influence of intracortical canals on lacunar volumes is spatially regulated and sensitive to locally produced growth factors such as osteoblast-derived VEGF.

bioengineering↗

bioRxiv2023

RTCpredictor: Identification of Read-Through Chimeric RNAs from RNA Sequencing Data

Read-through chimeric RNAs are gaining attention in cancer and other research fields, yet current tools often fail in predicting them. We have thus developed the first read-through chimeric RNA specific prediction method, RTCpredictor, utilizing a fast ripgrep algorithm to search for all possible exon-exon combinations of parental gene pairs. Compared with other ten popular tools, RTCpredictor achieved top performance on both simulated and real datasets. We randomly selected up to 30 candidate read-through chimeras predicted from each software method and experimentally validated a total of 109 read-throughs and on this set, RTCpredictor outperformed all the other methods. In addition, RTCpredictor (https://github.com/sandybioteck/RTCpredictor) has less memory requirements and faster execution time.

genomics↗

bioRxiv2023

{Theta}-Net: Achieving Enhanced Phase-Modulated Optical Nanoscopy in silico through a computational 'string of beads' architecture

We present herein a triplet string of concatenated O-Net ( bead) architectures (formulated as discussed in our previous study) which we term {Theta}-Net as a means of improving the viability of generated super-resolved (SR) images in silico. In the present study, we assess the quality of the afore-mentioned SR images with that obtained via other popular frameworks (such as ANNA-PALM, BSRGAN and 3D RCAN). Models developed from our proposed framework result in images which more closely approach the gold standard of the SEM-verified test sample as a means of resolution enhancement for optical microscopical imaging, unlike previous DNNs. In addition, cross-domain (transfer) learning was also utilized to enhance the capabilities of models trained on DIC datasets, where phasic variations are not as prominently manifested as amplitude/intensity differences in the individual pixels [unlike phase contrast microscopy (PCM)]. The present study thus demonstrates the viability of our current multi-paradigm architecture in attaining ultra-resolved images under poor signal-to-noise ratios, while eliminating the need for a priori PSF & OTF information. Due to the wide-scale use of optical microscopy for inspection & quality analysis in various industry sectors, the findings of this study would be anticipated to exhibit a far-ranging impact on several engineering fronts.

bioinformatics↗