Biology subjects

Goel, M.

Publications and source records attributed to Goel, M..

17 recordsLinked to original sources

bioRxiv2026

Target DNA-Mediated Plasmonic Coupling and Assembly Kinetics of Gold Nanorods for Label-Free Nucleic Acid Detection

DNA-programmed assembly of plasmonic nanostructures provides a powerful route to couple molecular recognition with optical signal generation. Here, we report the sequence-specific assembly of DNA-functionalized gold nanorods using a sesame allergen-derived DNA biomarker as a molecular bridge. Target-induced assembly produces concentration-dependent assembly growth, plasmon coupling, and distinct assembly kinetics that are readily monitored by absorption spectroscopy, enabling label-free detection of the target DNA in the nanomolar concentration range. The assembled nanorods further produce strong surface-enhanced Raman scattering (SERS) signals arising from plasmonic coupling within the assemblies, extending detection to the picomolar regime without the use of Raman reporters. Quantitative analysis reveals that both the extent and rate of assembly formation are governed by target DNA concentration. These results establish a direct relationship between molecular recognition, assembly growth, plasmonic coupling, and spectroscopic response, highlighting DNA-programmed gold nanorod assembly as a versatile platform for investigating hybridization-driven plasmonic self-assembly and nucleic acid detection. Table of Content O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/732610v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@e4fcb9org.highwire.dtl.DTLVardef@18c0d89org.highwire.dtl.DTLVardef@1ccb4bborg.highwire.dtl.DTLVardef@6d84ca_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2026

Occurrence of Biased mTOR Signaling in Hepatocellular Carcinoma

BackgroundmTOR signaling promotes cell growth and anabolic processes in all eukaryotes. Hyperactivation of mTOR signaling is associated with various cancers along with hepatocellular carcinoma (HCC). HCC is a highly lethal malignancy with multiple aetiologies such as viral infection, alcohol abuse, and metabolic dysfunction. Therapeutic options for HCC remain limited due to an incomplete understanding of oncogenic drivers and poorly characterized mechanisms of disease progression. MethodsVarious regimens of DEN and CCl4 carcinogen dosage were investigated on C57BL/6J mice to induce HCC. The histological analysis for fibrosis and serum markers for liver function were performed. Molecular analyses of oncogenic drivers were performed in the HCC tissues obtained from mice and HCC patients. The impact of inhibition of mTOR signaling was assessed on HCC progression. ResultsWe established a rapid DEN+CCl4 induced (DCI) HCC model in C57BL/6 mice to study disease progression longitudinally. The molecular analysis revealed upregulation of MAPK and downregulation of mTORC1-S6K-S6 signaling in HCC. However, other branches of mTOR such as mTORC1-ULK1, mTORC1-4EBP1, and mTORC2-PKC were upregulated due to the increased expression. Similar observations were found in tissues derived from HCC patients. Furthermore, inhibition of mTORC1 alone by Rapamycin did not reduce HCC progression but Torin 1 mediated inhibition of both mTORC1 and mTORC2 significantly reduced HCC progression. ConclusionsWe propose this biased mTOR signaling modulates mTOR activity towards specific downstream processes that are crucial for cancer cell growth and targeting both the mTOR complexes has better therapeutic potential in HCC. Impact and ImplicationsThis study provides a rapid pre-clinical model for understanding HCC progression and to explore various intervention strategies. The study reports a novel phenomenon of biased mTOR signaling where deregulation of downstream substrate levels modulates the mTOR activity towards the specific branches, the master regulator of cell growth and metabolism. Furthermore, the study suggests that the clinical investigations exploring the rapalogs against HCC should be cautiously considered depending on the aetiology and signaling status of HCC. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC="FIGDIR/small/727188v2_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@ef3714org.highwire.dtl.DTLVardef@1091b25org.highwire.dtl.DTLVardef@d52f2forg.highwire.dtl.DTLVardef@cc158_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDEN and CCl4 treatment generated a well-established HCC within 4 months. C_LIO_LILiver fibrosis and serum markers correlated with HCC progression. C_LIO_LIUpregulation of mTOR pathway substrates create biased mTOR signaling. C_LIO_LIDual inhibition of mTORC1 and mTORC2 reduced HCC progression significantly. C_LI

cancer biology↗

bioRxiv2026

Protein Stability, Turnover Kinetics, and Abundance Constrain the Scaling of Protein Interaction Networks

The propensity of proteins to form oligomers is ultimately dictated by their structural configuration(s). Proteins that persist in a discrete conformational state may form a limited number of specific interactions while those that sample a broader structural ensemble may instead associate with a wider array of partners. These intrinsic tendencies potentially constrain the way proteins navigate wider interaction networks. In this work, we aggregated and surveyed a wide variety of biophysical, biochemical, and cellular descriptors of the S. cerevisiae proteome to identify biases in the connectivity of its protein-protein interaction network. Using mass spectrometry-based interactome measurements and various protein stability estimates, we find that a disproportionate number of abundant, yet unstable binding proteins act as network hubs. Moreover, we show that these features alone can be used to discriminate between hubs and non-hub proteins with high accuracy (AUROC = 0.898). Interestingly, we find that half-lives of hub proteins depend on whether or not they reside within static complexes and/ or whether they interact with molecular chaperones. Finally, we note that the observed connectivity biases associated with abundant, unstable proteins only pertain to network hubs, but not to the bottlenecks that connect them. Together, our findings reveal how the conformational stability of a protein may constrain its context within protein-protein interaction networks.

systems biology↗

bioRxiv2026

ANYI: The ANnotated Yeast Interactome

Although several existing protein-protein interaction (PPI) databases provide yeast PPI data, none unify large-scale network topology information with detailed biophysical, proteostasis, and regulatory annotations in a single protein-centric framework. To address this gap, we developed the ANnotated Yeast Interactome (ANYI), an open, integrated resource that combines experimental yeast PPIs with sixteen feature annotation types, including protein abundance, half-life, disorder content, post-translational modifications, conformational stability, chaperone interactions, sequence, and structure. ANYI integrates 3,927 proteins with 155 annotation features, forming a unified matrix that enables systematic cross-layer analyses. Available via GitHub and Docker Hub with an interactive network browser for broad accessibility, ANYI provides both experienced and beginner computational scientists with tools to investigate the yeast interactome. For example, users can directly test whether highly connected hub proteins exhibit distinct stability, disorder, or proteostasis signatures relative to peripheral nodes. AVAILABILITY AND IMPLEMENTATIONThe code used to assemble ANYI is available on GitHub at https://github.com/NCEMS/energetic-origins-of-PPI-connectivity and the database itself and interactive browser tool are available on Docker Hub as dannissleypsu/anyi-browser:v1.0.2.

bioinformatics↗

bioRxiv2025

In silico reconstruction of primary and metastatic tumor architecture using GIS-augmented spatial transcriptomics

The tumor microenvironment (TME) comprises different cell populations that interact, contributing to tumor heterogeneity and therapy response. Spatial transcriptomics offers valuable insights into transcriptional complexity and heterogeneity of the TME. We established Geographic Information System (GIS)-augmented In-Silico Reconstruction of Tumor Architecture (GIS-ROTA), a biologically informed analytic framework that integrates pathway or cell type-based enrichment analysis with local Morans I to uncover functional spatial domains. In our Visium dataset of primary and metastatic estrogen receptor-positive breast tumor samples, GIS-ROTA revealed extensive co-localization of estrogen response with metabolic pathway gene sets and mutual exclusivity with metastasis-related and specific immune-related pathway gene sets. The novelty of our approach lies in considering biological functions prior to identifying any spatial domains, providing direct interpretability and minimizing the subjectivity of interpreting clusters observed from conventional analytic methods. Overall, our GIS-ROTA framework integrates biological knowledge first, yielding spatial patterns with functional relevance and enabling identification of novel targets for development of therapeutic strategies.

cancer biology↗

bioRxiv2025

ACSS2-Mediated Metabolic-Epigenetic Crosstalk Drives Fulvestrant Resistance and Represents a Novel Therapeutic Target

1.Endocrine therapies target hormone-dependent cancer cells, primarily through estrogen receptor alpha (ER), expressed in [~]70% of breast cancers (ER+). Despite treatment advances, 30-40% of ER+ breast cancer patients experience recurrence and metastasis, with 5-year survival rates of only 31.9%. We validated poor outcomes for liver metastasis patients treated with Fulvestrant (Fulv) using the local Carle Foundation Hospital cohort and examined metabolic pathways in liver metastatic patient-derived xenograft (PDX) models, revealing upregulated lipid and acetyl-CoA production. Our previous work demonstrated that combining Fulv with acetyl-CoA synthase inhibitor (ACSI) targeting Acyl-CoA Synthetase Short Chain Family Member 2 (ACSS2), synergistically reduced ER+ metastatic breast cancer (MBC) cell viability in vitro. Using multiple analytical approaches-isotope tracing, CUT&RUN sequencing, immunofluorescence, western blot, and RNA sequencing-we characterized the effects of acetyl-CoA synthesis inhibition on Fulv-induced alterations. Fulv treatment of MBC cells increased ACSS2 expression and acetate utilization. Isotope tracing revealed that Fulv decreased acetate flux to the TCA cycle while promoting fatty acid synthesis. Importantly, ACSS2 was predominantly nuclear and CUT&RUN sequencing showed that Fulv treatment increased ACSS2 chromatin occupancy and ER/ACSS2/H3K27ac overlapping sites near genes associated with tumor progression, which was eliminated by combination of ACSI and Fulv. RNA sequencing revealed reduction of Fulv-induced expression of genes involved in cancer cell metabolism and key signaling pathways in cancer with the Fulv+ACSI combination. In a therapy-resistant xenograft model, combining Fulv and ACSI reduced Fulv-dependent increase in metastatic burden. Our findings indicate ACSS2 contributes to endocrine therapy resistance through nuclear acetyl-CoA provision for epigenetic alterations. Targeting these cancer cell adaptations represents a novel therapeutic approach potentially reducing metastasis-related mortality and improving breast cancer treatment outcomes.

cancer biology↗

bioRxiv2025

Deep Receptor Scanning Reveals General Sequence Constraints on GPCR Biosynthesis

G protein-coupled receptors (GPCRs) mediate a variety of signaling pathways and are the most common pharmacological targets. While advances in structural biochemistry have provided deep functional insights into key receptors, many of the 800+ human GPCRs remain understudied. We introduce a versatile "deep receptor scanning" platform that can be used to experimentally characterize 766 human GPCRs and 174 known GPCR splice variants in parallel. We use this platform to quantitatively characterize the relative abundance of canonical and alternative receptor transcripts, their translational efficiency, and the plasma membrane expression of each receptor in the context of a recombinant pool of HEK293T cells expressing individual GPCRs. We then employ machine learning to identify specific structural features that modulate GPCR expression. This experimental platform and informatic approach are compatible with a variety of assays and can be used to efficiently explore the biochemical and pharmacological properties of the GPCRome.

biochemistry↗

bioRxiv2025

AllerStack: Predicting Allergenic Proteins with a Stacked Ensemble Approach

Accurate prediction of protein allergenicity is essential for ensuring food and drug safety. While machine learning and deep learning models have been explored for this task, limitations remain in dataset scale, feature representation, and model architecture. Here, we introduce AllerStack, a two-stage stacked ensemble model integrating handcrafted and ESM2-based learned features for allergenicity classification. The model was developed using a balanced dataset comprising 11,930 allergenic and 11,930 non-allergenic proteins. We extracted amino acid composition, dipeptide composition, and physicochemical features using the Biopython library, alongside contextual embeddings from the pre-trained ESM2 protein language model. Diverse classifiers (QDA, SVM, KNN, and ANN) were trained separately on these features in the base layer. Their predictions were used as input to a meta-classifier based on XGBoost. AllerStack achieved high predictive performance with 96.87% accuracy, 96.86% F1-score, 93.75% Matthews correlation coefficient (MCC), and an AUC of 0.99. A publicly accessible web server (https://cosylab.iiitd.edu.in/allerstack/) enables real-time allergenicity prediction from protein sequences. AllerStack provides a robust, interpretable, and user-friendly platform for allergen detection in computational biology. HighlightsO_LIAn extensive dataset of 23,860 proteins. C_LIO_LICombines handcrafted and ESM2-derived features. C_LIO_LIStacked ensemble model with an accuracy of 96.87%. C_LIO_LISHAP-based model interpretability at the model and feature level. C_LIO_LIPublic web server, AllerStack (https://cosylab.iiitd.edu.in/allerstack/). C_LI

bioinformatics↗

bioRxiv2024

Branched DNA Processing by a Thermostable CAS-Cas4 from Thermococcus onnurineus: Expanding Biochemical Landscape of Nuclease Activity

The adaptive immune function of CRISPR-Cas systems in bacteria and archaea is mediated through CRISPR-Associated Proteins (Cas). The adaptation module, typically involving Cas1, Cas2, and Cas4, helps integrate viral "spacer" sequences into the host genome. Cas4 proteins are classified into two types based on neighboring genes: CAS-Cas4, flanked by other cas genes, and Solo-Cas4, which exist independently. While CAS-Cas4 proteins are implicated in adaptation, they remain biochemically uncharacterized in archaea, unlike archaeal Solo-Cas4 proteins. This study biochemically characterizes TON_0321, a CAS-Cas4 protein from the Type IV-C CRISPR cassette of Thermococcus onnurineus. TON_0321 exhibits 5' to 3' exonuclease activity and unique structure-dependent endonuclease activity, shedding light on CAS-Cas4 functional diversity. A distinct spatial organization of the catalytic site, angled with the positively charged patch on the protein surface, enables TON_0321 to recognize branching points in DNA substrates. Furthermore, this spatial arrangement facilitates cleavage 2 to 3 nucleotides away from the branch point in the 5' direction, demonstrating structure-specific endonuclease activity.

biochemistry↗

bioRxiv2024

The majority of somatic mutations in fruit trees are layer-specific

BackgroundAll plant tissues and organs develop from meristems. Plant meristems are structured organs consisting of distinct layers of stem cells. Somatic mutations occurring in one of these layers can propagate into large sectors of the plant. However, the frequency and characteristics of meristematic mutations that form the basis of somaclonal phenotypic variation remain unclear. ResultsHere, we analysed the frequency and distribution of somatic mutations in an individual Apricot tree. For this, we sequenced the genomes of fruit samples corresponding to distinct meristematic cell layers selected across the entire tree. Most somatic mutations (>90%) were specific to individual layers. Genotyping the somatic mutations in leaves sampled next to the fruits confirmed their meristematic origin. Interestingly, layer 1 (epidermis) had a higher mutation load than layer 2 (mesocarp), implying differential mutational dynamics between the layers. The somatic mutations followed the branching pattern of the tree. These factors led to the unexpected observation that the layer 1 samples from different branches were more similar to each other than to layer 2 samples of the same branch. Further, using single-cell RNA sequencing, we demonstrated that the layer-specific mutant alleles could only be found in the transcripts of the respective, layer-specific cell clusters and could form the basis for somaclonal phenotypic variation. ConclusionsHere, we analyzed the prevalence and distribution of somatic mutations with meristematic origin. Our insights into the yet unexplored layer-specificity of such somatic mutations outlined how they can be identified and how they impact the breeding of clonally propagated crops.

genomics↗

bioRxiv2022

plotsr: Visualising structural similarities and rearrangements between multiple genomes

SummaryThird-generation genomic technologies have led to a sharp increase in the number of high-quality genome assemblies. This allows the comparison of multiple assembled genomes of individual species and demands for new tools for visualising their structural properties. Here we present plotsr, an efficient tool to visualize structural similarities and rearrangements between multiple genomes. It can be used to compare genomes on chromosome level or to zoom in on any selected region. In addition, plotsr can augment the visualisation with regional identifiers (e.g. genes or genomic markers) or histogram tracks for continuous features (e.g. GC content or polymorphism density). Availability and implementationplotsr is implemented as a python package and uses the standard matplotlib library for plotting. It is freely available under the MIT license at GitHub (https://github.com/schneebergerlab/plotsr) and bioconda (https://anaconda.org/bioconda/plotsr). ContactManish Goel (manish.goel@lmu.de), Korbinian Schneeberger (k.schneeberger@lmu.de)

bioinformatics↗

bioRxiv2021

Molecular studies into Copine-4 function in Retinal Ganglion Cells

The molecular mechanisms underlying morphological diversity in retinal cell types are poorly understood. We have previously reported that several members of the Copine family of Ca-dependent membrane adaptors are expressed in Retinal Ganglion Cells (RGCs) and transcriptionally regulated by Brn3 transcription factors. Several Copines are enriched in the retina and their over-expression leads to morphological changes reminiscent of neurite formation in HEK293 cells. However, the role of Copines in the retina is largely unknown. Here we focus on Cpne4, a Copine whose expression is restricted to RGCs. Over-expression of Cpne4 in RGCs in vivo led to formation of large varicosities on the dendrites but did not otherwise visibly affect dendrite or axon formation. Protein interactions studies using yeast two hybrid analysis from whole retina cDNA revealed two Cpne4 interacting proteins - HCFC1 and Morn2. Mass Spectrometry analysis of retina lysate pulled down using Cpne4 or its vonWillebrand A (vWA) domain identified a further 207 interacting proteins. Gene Ontology (GO) analysis of Cpne4 interactors suggests its involvement in several metabolic and signaling pathways, including processes related to vesicle trafficking, intracellular membrane bound organelles, and plasma membrane associated structures, including neurites. We conclude that, consistent with its domain structure, Cpne4 may be involved in assembly and trafficking of several membrane associated cell compartments.

cell biology↗

bioRxiv2021

Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

Potato is the most important tuber crop in the world. However, separate reconstruction of the four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report the 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly of the potato cultivar Otava using high-quality long reads coupled with single-cell sequencing of 717 pollen genomes and Hi-C data. Unexpectedly, almost 50% of the genome were found to be identical-by-descent due to recent inbreeding, which contrasted by highly abundant structural rearrangements involving around 20% of the genome. Among 38,214 genes, only 54% were present in four haplotypes with an average of 3.2 copies per gene. Analyzing the leaf transcriptome as example, we found that 11% of the genes featured differently expressed alleles in at least one of the haplotypes, of which 25% are likely regulated through allele-specific DNA methylation. Our work sheds light on the recent breeding history of potato, the functional organization of its tetraploid genome and has the potential to strengthen the future of genomics-assisted breeding.

genomics↗

bioRxiv2020

Chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes

Generating chromosome-level, haplotype-resolved assemblies of heterozygous genomes remains challenging. To address this, we developed gamete binning, a method based on single-cell sequencing of haploid gametes enabling separation of the whole-genome sequencing reads into haplotype-specific reads sets. After assembling the reads of each haplotype, the contigs are scaffolded to chromosome-level using a genetic map derived from the gametes. As a proof-of-concept, we assembled the two genomes of a diploid apricot tree based on whole-genome sequencing of 445 individual pollen grains. The two haplotype assemblies (N50: 25.5 and 25.8 Mb) featured a haplotyping precision of >99% and were accurately scaffolded to chromosome-level.

genomics↗

bioRxiv2019

Robust lysosomal rewiring in Mtb infected macrophages mediated by Mtb lipids restricts the intracellular bacterial survival

Intracellular pathogens commonly manipulate the host lysosomal system for their survival, however whether this affects the organization and functioning of the lysosomal system itself is not known. Here, we show using in vitro and in vivo infections that the lysosomal content and activity is globally elevated in M. tuberculosis infected macrophages. The enhanced lysosomal state is sustained over time and defines an adaptive homeostasis of the infected cell. Lysosomal alterations are caused by mycobacterial surface components, notably the cell wall lipid SL-1, which functions through the mTORC1-TFEB axis. Mtb mutant defective for SL-1 levels shows reduced lysosomal content and activity compared to wild type. Importantly, this phenotype is conserved during in vivo infection. The alteration in lysosomal phenotype in mutant Mtb lead to decreased lysosomal delivery of Mtb, and importantly, increased survival of intracellular Mtb. These results define the global alterations in the host lysosomal system as a crucial distinguishing feature of Mtb infected macrophages that is host protective and contribute to the containment of the pathogen.

cell biology↗

bioRxiv2019

DNA replication protein Cdc45 directly interacts with PCNA via its PIP box in Leishmania donovani and the Cdc45 PIP box is essential for cell survival

DNA replication protein Cdc45 is an integral part of the eukaryotic replicative helicase whose other components are the Mcm2-7 core, and GINS. We identified a PIP box motif in Leishmania donovani Cdc45. This motif is typically linked to interaction with the eukaryotic clamp proliferating cell nuclear antigen (PCNA). The homotrimeric PCNA can potentially bind upto three different proteins simultaneously via a loop region present in each monomer. Multiple binding partners have been identified from among the replication machinery in other eukaryotes, and the concerted /sequential binding of these partners are central to the fidelity of the replication process. Though conserved in Cdc45 across Leishmania species and Trypanosoma cruzi, the PIP box is absent in Trypanosoma brucei Cdc45. Here we investigate the possibility of Cdc45-PCNA interaction and the role of such an interaction in the in vivo context. Having confirmed the importance of Cdc45 in Leishmania DNA replication we establish that Cdc45 and PCNA interact stably in whole cell extracts, interacting with each other directly in vitro also. The interaction is mediated via the Cdc45 PIP box. This PIP box is essential for Leishmania survival. The importance of the Cdc45 PIP box is also examined in Schizosaccharomyces pombe, and it is found to be essential for cell survival in this organism also. Our results implicate a role for the Leishmania Cdc45 PIP box in recruiting or stabilizing PCNA on chromatin. The Cdc45-PCNA interaction might help tether PCNA and associated replicative DNA polymerase to the DNA template, thus facilitating replication fork elongation. Though multiple replication proteins have been identified to associate with PCNA in other eukaryotes, this is the first report demonstrating a direct interaction between Cdc45 and PCNA, and while our analysis suggests the interaction may not occur in human cells, it indicates that it is not confined to trypanosomatids.\n\nAuthor SummaryLeishmaniases are manifested in three forms: cutaneous, sub-cutaneous and visceral. The prevalent form in the Indian subcontinent is visceral Leishmaniasis (VL), which is fatal if not treated on time. While there are drugs for treatment, the hunt for additional drugs continues due to emerging drug resistance patterns. The parasite is transmitted by the bite of the sandfly, whereupon it establishes itself within cells of the host immune system (macrophages) and reproduces by binary fission. The replication of its genome is essential for parasite survival. Eukaryotic DNA replication is generally conserved across species. This study targets Cdc45, a protein that helps unwind the DNA double helix to enable copying of the two strands into two daughter strands. The new chains of DNA are synthesized by DNA polymerases, and a trimeric protein, proliferating cell nuclear antigen (PCNA), helps clamp the polymerases onto the template. In this study we find Cdc45 to interact with PCNA, and have identified the motif in Cdc45 via which it does so. Our results suggest this interaction is seen in some other eukaryotes as well. Based on the results of our experiments we propose that Cdc45 may help moor PCNA-polymerase complexes to template DNA.

molecular biology↗

bioRxiv2019

SyRI: identification of syntenic and rearranged regions from whole-genome assemblies

Here, we present SyRI, an efficient tool for genome-wide structural rearrangement identification from genome graphs, which are build up from pair-wise whole-genome alignments. Instead of searching for differences, SyRI starts by finding all co-linear regions between the genomes. As all remaining regions are SRs by definition, they just have to be classified as inversions, translocations, or duplications based on their positions in convoluted networks of repetitive alignments. Finally, SyRI reports local variations like SNPs and indels within syntenic and rearranged regions. We show SyRIs broad applicability to multiple species and genetically validate the presence of ~100 translocations identified in Arabidopsis.

bioinformatics↗