Biology subjects

Das, S.

Publications and source records attributed to Das, S..

At least 145 records · Page 8Linked to original sources

bioRxiv2024

Threshold-dependent negative autoregulation of PIF4 gene expression optimizes growth and fitness in Arabidopsis

PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is a vital transcription factor that controls plant growth by integrating environmental signals like light and temperature. Though upstream regulators of PIF4 are known, transcriptional regulation of PIF4 is poorly understood. Here, we demonstrate that the PIF4 undergoes negative autoregulation. We show that PIF4 promoter activity is more in the pif4 mutant but significantly reduced in PIF4 overexpression transgenic lines. Moreover, CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), which enhances PIF4 protein stability, promotes PIF4 autoinhibition. However, Phytochrome B (phyB), a photoreceptor that decreases PIF4 stability, inhibits autoinhibition. We further develop a network-based mathematical model incorporating the PIF4 autoinhibition and other key interactions. Our modeling and data analysis reveals that PIF4 autoregulation depends on a threshold of cellular PIF4 concentration. Our model also successfully predicts the hypocotyl growth and PIF4 promoter activity in various light and temperature conditions. Moreover, we show that the transgenic lines with enhanced PIF4 function negatively influence biomass and yield, irrespective of photoperiod and temperature. Together, the negative feedback of PIF4 dampens its own function and restraints unregulated growth. Our study thus elucidates the mechanisms of how the phyB-COP1/DET1-PIF4 module controls PIF4 transcription in tune with the endogenous PIF4 level.

plant biology↗

bioRxiv2024

Auditory brainstem responses to speech-in-noise reflect selective attention, comprehension, and subjective listening effort

The auditory brainstem plays a crucial role in speech-in-noise listening, refining numerous acoustic features such as pitch and spatial location under continual descending influence from cortex. However, the difficulty of characterizing brainstem activity during continuous speech listening has obscured its functional role in ecologically valid contexts--not only the effects of selective attention on neural responses, but also their impact on comprehension and listening effort. Here, we evaluate the role of the brainstem on speech-in-noise perception and selective attention using a continuous, speech-based stimulus with embedded chirps (Cheech) that rapidly and effectively evokes auditory brainstem responses (ABRs) while participants listen to short story narratives. The Cheech-modified stories were presented alone or in the presence of another spatially separated talker, and neural responses were measured throughout by EEG. Both word-level detection performance and narrative-level comprehension were evaluated, as well as subjective reports of listening effort. ABR wave V was modulated by the presence of a competing talker, selective attention for the target versus masker, and the talker sex. Additionally, faster wave V peak latencies and larger amplitudes were associated with identification of the target words embedded within the stories, while faster latencies additionally related to better comprehension question accuracy and lower subjective listening effort. Collectively, our results provide evidence for the influence of brainstem encoding processes on individual speech-listening behaviors, including the ability to selectively attend to and comprehend target speech in the presence of a competing talker. Significance statementThis study highlights the crucial role of the brainstem in speech-in-noise perception and higher-level language abilities like comprehension and subjective listening effort. Through the use of a novel speech stimulus blended with embedded chirps (Cheech) to evoke brainstem responses while listening to short story narratives, we show how selective attention influences subcortical processes. Faster and more robust subcortical processes, in turn, were associated with more successful speech-listening performance across multiple behavioral metrics. These findings advance our understanding of how the brainstem supports selective attention and speech perception in challenging listening environments.

neuroscience↗

bioRxiv2024

Enhanced identification of small molecules binding to hnRNPA1 via cryptic pockets mapping coupled with X-Ray fragment screening

The human heterogeneous nuclear ribonucleoprotein (hnRNP) A1 is a prototypical RNA-binding protein essential in regulating a wide range of post-transcriptional events in cells. As a multifunctional protein with a key role in RNA metabolism, deregulation of its functions has been linked to neurodegenerative diseases, tumour aggressiveness and chemoresistance, which has fuelled efforts to develop novel therapeutics that modulates its RNA binding activities. Here, using a combination of Molecular Dynamics (MD) simulations and graph neural network pockets predictions, we showed that hnRNPA1 N-terminal RNA binding domain (UP1) contains several cryptic pockets capable of binding small molecules. To identify chemical entities for development of potent drug candidates and experimentally validate identified druggable hotspots, we carried out a large fragment screening on UP1 protein crystals. Our screen identified 36 hits which extensively samples UP1 functional regions involved in RNA recognition and binding, as well as mapping hotspots onto novel protein interaction surfaces. We observed a wide range of ligand-induced conformational variation, by stabilisation of dynamic protein regions. Our high-resolution structures, the first of an hnRNP in complex with a fragment or small molecule, provides rapid routes for the rational development of a range of different inhibitors and chemical tools for studying molecular mechanisms of hnRNPA1 mediated splicing regulation.

biochemistry↗

bioRxiv2024

Decoding the effect of temperatures on conformational stability and order of the ligand unbound thermo-sensing adenine riboswitch using molecular dynamics simulation

The structure-function relationship of the riboswitch is governed mainly by two factors, ligand binding and temperature. Most of the experimental studies shed light on structural dynamics and gene regulation function of Adenine riboswitch from the aspect of ligand instead of temperature. Two unliganded Adenine riboswitch conformations (apoA and apoB) from the thermophile Vibrio vulnificus draw particular attention to the Biophysics research community due to their diverse and polymorphic structures. Ligand-free apoB Adenine riboswitch conformation is not able to interact with the ligand whereas ligand-free apoA Adenine riboswitch conformation adopts ligand-receptive form. The interconversion between apoA and apoB conformation is temperature-dependent and thermodynamically controlled. Therefore Adenine riboswitch is called a temperature sensing RNA. The molecular mechanism underlying the thermosensitivity of ligand free Adenine riboswitch is not well known. Hence it is essential to explore temperature-induced conformational dynamics of unliganded Adenine riboswitch. In this research work I make an attempt to examine conformational stability and order of apoA with respect to apoB Adenine riboswitch aptamer using conformational thermodynamics derived from all-atom molecular dynamics trajectories in the temperature range 283K-400K. The changes in conformational free energy and entropy of conformational degrees of freedom like pseudo-torsion angle and {theta} are computed. RMSD, RMSF, RG, principal component analysis, hydrogen bonding interaction, and conformational thermodynamics data demonstrate that conformational stability and order of apoA with respect to apoB adenine riboswitch conformation is significant at 293K and 303K. The temperatures corresponding to the conformational order and stability of apoA adenine riboswitch with respect to apoB adenine riboswitch whole aptamer are shown in descending order 293K[~]303K> 313K[~]283K>373K>323K. The topological and conformational changes related to hydrogen bonding reorganization occur mostly at temperature 323K and 400K. Ligand unbound adenine riboswitch is sensitive to heat and may be inactivated at temperatures 323K and 400K. HighlightsO_LIMolecular Dynamics Simulation of ligand unbound two different conformations of adenine riboswitch with the same sequence at different temperatures are performed. C_LIO_LIAt low temperatures (293K and 303K) the conformational stability of apoA is more pronounced compared to apoB adenine riboswitch. C_LIO_LIThermal stability of apoA compared to apoB adenine riboswitch is the least at 323K temperature. C_LIO_LIAt higher temperature (373K) and lower temperature (283K) apoA adenine riboswitch exerts moderate conformational stability. C_LIO_LIThe nucleotides from stem2 and junction (J1/2, J2/3) regions of adenine riboswitch contribute the most to the conformational stability and order. C_LI

biophysics↗

bioRxiv2024

Mechanistic Insights into FNBP4-Mediated Regulation of non-diaphanous Formin FMN1 in Actin Cytoskeleton Dynamics

Formin1 (FMN1), a member of the non-diaphanous formin family, is essential for development and neuronal function. Unlike diaphanous-related formins, FMN1 is not subject to canonical autoinhibition through the DID and DAD domains, nor is it activated by Rho GTPase binding. Recent studies suggest that formins also play roles in the nucleus, influencing DNA damage response and transcriptional regulation. However, the mechanisms regulating nuclear formins particularly non-diaphanous ones like FMN1 remain poorly understood. Our previous research identified the interaction between FMN1 and FNBP4, prompting further investigation into its functional role in regulating actin dynamics. Results reveal that FNBP4 inhibits FMN1-mediated actin assembly in vitro. It is shown that FNBP4 prevents FMN1 from displacing the capping protein CapZ at the growing barbed end of actin filaments. Additionally, FNBP4 inhibits FMN1s bundling activity in a concentration-dependent manner. Further analysis indicates that FNBP4 interacts with the FH1 domain and the interdomain connector between the FH1 and FH2 domains, creating spatial constraints on the FH2 domain. We propose that FNBP4 acts as a stationary inhibitor of FMN1. In addition, we identify a monopartite nuclear localization signal (NLS) in FNBP4, and subcellular localization studies show that FNBP4 colocalizes with FMN1. This study provides new insights into the regulatory role of FNBP4 in modulating FMN1-mediated actin dynamics, suggesting that FNBP4 may function as a nuclear inhibitor of actin polymerization and shedding light on regulatory mechanisms specific to non-diaphanous formins.

cell biology↗

bioRxiv2024

Hypocretin Receptor 1 Blockade Early in Abstinence Prevents Incubation of Cocaine Seeking and Normalizes Dopamine Transmission

Abstinence from cocaine use has been shown to elicit a progressive intensification or incubation of cocaine craving/seeking that is posited to contribute to propensity for relapse. While the mechanisms underlying incubation of cocaine seeking remain elusive, considerable evidence suggests that abstinence from cocaine promotes mesolimbic dopamine adaptations that contribute to exaggerated cocaine seeking. Consequently, preventing these dopamine adaptations may reduce incubation of cocaine seeking and thereby reduce the likelihood of relapse. In the present studies, we first examined if incubation of cocaine seeking was associated with aberrant dopamine transmission in the nucleus accumbens after seven days of abstinence from intermittent access to cocaine. Given the extensive evidence that hypocretins/orexins regulate motivation for cocaine, we then examined to what extent hypocretin receptor 1 antagonism on the first day of abstinence prevented incubation of cocaine seeking and dopamine adaptations later in abstinence. Results indicated that abstinence from intermittent access to cocaine engendered robust incubation of cocaine seeking in both female and male rats. We also observed aberrant dopamine transmission, but only in rats that displayed incubation of cocaine seeking. Further, we showed that a single injection of the hypocretin receptor 1 antagonist, RTIOX-276, on the first day of abstinence prevented incubation of cocaine seeking and aberrant dopamine transmission. These findings suggest that hypocretin receptor 1 antagonism may serve as a viable therapeutic for reducing cocaine craving/seeking, thus reducing the likelihood of relapse.

neuroscience↗

bioRxiv2024

Functional insights on chemical communication of fishing cats: a strategic mechanism for adaptation in semi-aquatic habitat

Chemical communication system of fishing cats, focusing on volatile organic compounds present in their urine (UR) and marking fluid (MF) has been explored. Using solid-phase microextraction guided gas chromatography mass spectrometry analysis, a diverse range of functional groups from UR and MF were detected, including ketones, aldehydes, sulfur- and nitrogen-containing compounds, among which 3-Mercapto-3-methylbutanol (3MMB) and its related sulfur compounds were found to be sex-specific, predominantly present in males. The unique behavior of fishing cats to urinate frequently in water when experimentally tested with synthetic 3MMB, was aligned for its retention in aqueous medium upto 21 days. This suggests that fishing cats may employ an energy-efficient scent-marking strategy by leveraging aquatic environments for prolonging chemical signalling process. The analysis of less-volatile compounds, such as triglycerides and fatty acids, suggests that these compounds could be acted as fixatives, helping to stabilize and prolong the intensity of chemical messages coded to highly volatile molecules. The combination of highly volatile, less volatile compounds and lipids may create complex synergy to facilitate interindividual communication, potentially serving as pheromones. This research enhances our understanding of the fishing cats adaptation to semi-aquatic environments and its unique behavioural pattern in marshy landforms, thus concentrated with high population density in deltaic South Bengal.

zoology↗

bioRxiv2024

In vivo Treatment of a Severe Vascular Disease via a Bespoke CRISPR-Cas9 Base Editor

Genetic vascular disorders are prevalent diseases that have diverse etiologies and few treatment options. Pathogenic missense mutations in the alpha actin isotype 2 gene (ACTA2) primarily affect smooth muscle cell (SMC) function and cause multisystemic smooth muscle dysfunction syndrome (MSMDS), a genetic vasculopathy that is associated with stroke, aortic dissection, and death in childhood. Here, we explored genome editing to correct the most common MSMDS-causative mutation ACTA2 R179H. In a first-in-kind approach, we performed mutation-specific protein engineering to develop a bespoke CRISPR-Cas9 enzyme with enhanced on-target activity against the R179H sequence. To directly correct the R179H mutation, we screened dozens of configurations of base editors (comprised of Cas9 enzymes, deaminases, and gRNAs) to develop a highly precise corrective A-to-G edit with minimal deleterious bystander editing that is otherwise prevalent when using wild-type SpCas9 base editors. We then created a murine model of MSMDS that exhibits phenotypes consistent with human patients, including vasculopathy and premature death, to explore the in vivo therapeutic potential of this base editing strategy. Delivery of the customized base editor via an engineered SMC-tropic adeno-associated virus (AAV-PR) vector substantially prolonged survival and rescued systemic phenotypes across the lifespan of MSMDS mice, including in the vasculature, aorta, and brain. Together, our optimization of a customized base editor highlights how bespoke CRISPR-Cas enzymes can enhance on-target correction while minimizing bystander edits, culminating in a precise editing approach that may enable a long-lasting treatment for patients with MSMDS.

bioengineering↗

bioRxiv2024

Identification of novel thiazole derivatives as flaviviral protease inhibitors against DENV and JEV

Flaviviruses are the causative agents of viral hemorrhagic fever (VHF) globally and have demonstrated the capacity to result in fatal outcomes if not managed effectively. Among different types of flaviviruses, dengue (DENV) and Japanese encephalitis (JEV) are the most common in tropical and subtropical countries. Given the scarcity of effective vaccines against flaviviral infections, small molecule agents that target crucial viral proteins emerge as the sole feasible option. This study outlines the synthesis of novel thiazole compounds as flavivirus NS2B-NS3 protease inhibitor and characterization of their antiviral activity against DENV and JEV. We synthesized a heterocyclic template derived from a substrate-based retrotripeptide dengue protease inhibitor, leading to forty-eight thiazole derivatives. Two compounds demonstrated significant inhibition of dengue virus protease activity in vitro. Comprehensive characterization of these two compounds was conducted through biochemical assay which revealed an uncompetitive mode of inhibition. Subsequent cell-based assays using Dengue and Japanese encephalitis viruses as representatives Flaviviruses imparted the potential of these compounds to block viral RNA synthesis, and viral replication. Finally time-course experiments unveiled that the two compounds impeded the accumulation of viral genomic RNA primarily at later stages of infection, aligning with their capacity to hinder NS2B-NS3 protease activity, polyprotein processing and viral genomic RNA replication. Together our work presents the development and validation of flavivirus protease inhibitors with therapeutic potential against Dengue and Japanese encephalitis virus.

microbiology↗

bioRxiv2024

Scrutinized lipid utilization disrupts Amphotericin-B responsiveness in clinical isolates of Leishmania donovani

The management of Leishmania donovani (LD), responsible for fatal visceral leishmaniasis (VL), faces increasing challenges due to rising drug-unresponsiveness, leading to increasing treatment failures. While hypolipidemia characterizes VL, LD, a cholesterol auxotroph, relies on host lipid scavenging for its intracellular survival. The aggressive pathology, in terms of increased organ parasite load, observed in hosts infected with antimony-unresponsive-LD (LD-R) as compared to their sensitive counterparts (LD-S), highlights LD-Rs heightened reliance on host lipids. Here we report that LD-R-infection promotes fluid-phase endocytosis in the host, selectively accumulating neutral lipids while excluding oxidized-LDL. LD-R enhances the fusion of endocytosed LDL-vesicles with its phagolysosomal membrane and inhibits cholesterol mobilization from these vesicles by suppressing NPC-1. This provides LD-R amastigotes with excess lipids, supporting their rapid proliferation and membrane synthesis. This excess LDL-influx leads to an eventual accumulation of neutral lipid droplets around LD-R amastigotes, thereby increasing their unresponsiveness towards Amphotericin-B, a second-line amphiphilic antileishmanial. Notably, VL patients showing relapse with Amphotericin-B treatment exhibited significantly lower serum LDL and cholesterol than cured cases. Treatment with Aspirin, a lipid droplet blocker, reduced lipid droplets around LD-R amastigotes, restoring Amphotericin-B responsiveness.

microbiology↗

bioRxiv2024

Unlocking the role of SH3PXD2B in epithelial-to-mesenchymal transition driving Breast Cancer Lung Metastasis

Despite advancements in breast cancer treatment, metastasis remains a significant challenge, contributing to high mortality rates. This study investigates the mechanisms underlying breast cancer lung metastasis, with a particular emphasis on the role of SH3PXD2B in driving epithelial-to-mesenchymal transition. Here, we analyzed RNA sequencing data from CCLE and TCGA databases and characterized that SH3PXD2B expression is elevated in breast cancer (BC) and lung cancer (LC) tissues compared to non-transformed tissues. Bioinformatics analysis revealed that SH3PXD2B regulates several cellular processes and is associated with poor prognosis in breast cancer (BRCA) and lung adenocarcinoma (LUAD) patients. Functional experiments underscore that the upregulation of SH3PXD2B promoted BC and LC cell migration in vitro; however, its knockdown inhibited the effect. Mechanistically, the mass spectrometry analysis was utilized to pull down interacting partners of SH3PXD2B, and the findings were substantiated by immunoblotting. Additionally, our findings on immunofluorescence and gene expression analysis demonstrated the additive role of SH3PXD2B and migratory proteins in promoting breast cancer progression. Further, we performed bioluminescent IVIS imaging analysis to trace the metastatic spread of MDA-MB-468 cells and observed strong signals and a high degree of dissemination to distant organs. Collectively, our results highlight the importance of SH3 domains in aggravating breast transformation, which can therefore serve as a promising therapeutic strategy in counteracting breast-related malignancy. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/618596v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@1fe7792org.highwire.dtl.DTLVardef@15c4481org.highwire.dtl.DTLVardef@9575f4org.highwire.dtl.DTLVardef@72ea93_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2024

Perceptual Expertise and Attention: An Exploration using Deep Neural Networks

Perceptual expertise and attention are two important factors that enable superior object recognition and task performance. While expertise enhances knowledge and provides a holistic understanding of the environment, attention allows us to selectively focus on task-related information and suppress distraction. It has been suggested that attention operates differently in experts and in novices, but much remains unknown. This study investigates the relationship between perceptual expertise and attention using convolutional neural networks (CNNs), which are shown to be good models of primate visual pathways. Two CNN models were trained to become experts in either face or scene recognition, and the effect of attention on performance was evaluated in tasks involving complex stimuli, such as superimposed images containing superimposed faces and scenes. The goal was to explore how feature-based attention (FBA) influences recognition within and outside the domain of expertise of the models. We found that each model performed better in its area of expertise--and that FBA further enhanced task performance, but only within the domain of expertise, increasing performance by up to 35% in scene recognition, and 15% in face recognition. However, attention had reduced or negative effects when applied outside the models expertise domain. Neural unit-level analysis revealed that expertise led to stronger tuning towards category-specific features and sharper tuning curves, as reflected in greater representational dissimilarity between targets and distractors, which, in line with the biased competition model of attention, leads to enhanced performance by reducing competition. These findings highlight the critical role of neural tuning at single as well as network level neural in distinguishing the effects of attention in experts and in novices and demonstrate that CNNs can be used fruitfully as computational models for addressing neuroscience questions not practical with the empirical methods.

neuroscience↗

bioRxiv2024

Molecular and cell phenotype programs in oral epithelial cells directed by co-exposure to arsenic and smokeless tobacco

Chronic arsenic exposure can lead to various health issues, including cancer. Concerns have been mounting about the enhancement of arsenic toxicity through co-exposure to various prevalent lifestyle habits. Smokeless tobacco products are commonly consumed in South Asian countries, where their use frequently co-occurs with exposure to arsenic from contaminated groundwater. To decipher the in vitro molecular and cellular responses to arsenic and/or smokeless tobacco, we performed temporal multi-omics analysis of the transcriptome and DNA methylome remodelling in exposed hTERT-immortalized human normal oral keratinocytes (NOK), as well as arsenic and/or smokeless tobacco genotoxicity and mutagenicity investigations in NOK cells and in human p53 knock-in murine embryonic fibroblasts (Hupki MEF). RNAseq results from acute exposures to arsenic alone and in combination with smokeless tobacco extract revealed upregulation of genes with roles in cell cycle changes, apoptosis and inflammation responses. This was in keeping with global DNA hypomethylation affecting genes involved in the same processes in response to chronic treatment in NOK cells. At the phenotypic level, we observed a dose-dependent decrease in NOK cell viability, induction of DNA damage, cell cycle changes and increased apoptosis, with the most pronounced effects observed under arsenic and SLT co-exposure conditions. Live-cell imaging experiments indicated that the DNA damage likely resulted from induction of apoptosis, an observation validated by a lack of exome-wide mutagenesis in response to chronic exposure to arsenic and/or smokeless tobacco. In sum, our integrative omics study provides novel insights into the acute and chronic responses to arsenic and smokeless tobacco (co-)exposure, with both types of responses converging on several key mechanisms associated with cancer hallmark processes. The generated rich catalogue of molecular programs in oral cells regulated by arsenic and smokeless tobacco (co-)exposure may provide bases for future development of biomarkers for use in molecular epidemiology studies of exposed populations at risk of developing oral cancer.

cancer biology↗

bioRxiv2024

Constitutive expression of Cas9 and rapamycin-inducible Cre recombinase facilitates conditional genome editing in Plasmodium berghei

Malaria is caused by protozoan parasites of the genus Plasmodium and remains a global health concern. The parasite has a highly adaptable life cycle comprising successive rounds of asexual replication in a vertebrate host and sexual maturation in the mosquito vector Anopheles. Genetic manipulation of the parasite has been instrumental for deciphering the function of Plasmodium genes. Conventional reverse genetic tools cannot be used to study essential genes of the asexual blood stages, thereby necessitating the development of conditional strategies. Among various such strategies, the rapamycin-inducible dimerisable Cre (DiCre) recombinase system emerged as a powerful approach for conditional editing of essential genes in human-infecting P. falciparum and in the rodent malaria model parasite P. berghei. We previously generated a DiCre-expressing P. berghei line and validated it by conditionally deleting several essential asexual stage genes, revealing their important role also in sporozoites. The advent of CRISPR enabled targeted genome editing with higher accuracy and specificity and greatly advanced genome engineering in Plasmodium spp. Here, we developed new P. berghei parasite lines by integrating the DiCre cassette and a fluorescent marker in parasites constitutively expressing Cas9. Owing to the dual integration of CRISPR-Cas9 and DiCre, these new lines allow unparalleled levels of gene modification and conditional regulation simultaneously. To illustrate the versatility of this new tool, we conditionally knocked-out the essential gene encoding the claudin-like apicomplexan micronemal protein (CLAMP) in P. berghei and confirm the role of CLAMP during invasion of erythrocytes.

microbiology↗

bioRxiv2024

Deep Learning enabled discovery of kinase drug targets in Pharos

AO_SCPLOWBSTRACTC_SCPLOWWe use machine learning with standardized molecular structure and gene ontology data to predict ligand interactions for a set of human kinases. We realize this by leveraging information from the TCRD / Pharos database, developed and maintained within the Illuminating the Druggable Genome (IDG) project. Pharos collects relevant biochemical and clinically relevant information of a large set of biologically important (human) proteins from publicly available sources, including scientific publications as well as specialized databases. The 635 kinases listed in Pharos are classified into levels reflecting the relative amount and type of accumulated information. Importantly, molecular structure and Gene Ontology annotations are available for the entire set, but only 455 of the kinases have recorded ligand affinity data. We developed a deep neural network-based framework to predict the ligand affinity profile for kinases using generally available information (molecular structure and Gene Ontology annotations) as input. The input data is organized into a 2,770 - dimensional vector with binary entries. The output data are predicted affinity values for interactions between the respective kinase and possible ligands. To address the very large number of possible ligands (58,800) and the sparsity of available binding data, we organized the ligands into 5,275 clusters based on structural similarity measures. Our model framework is trained to predict likely interactions between kinases and these ligand clusters. We aim to identify sets of likely ligand partners associated with high predicted relative affinities for a given kinase. We measure performance by evaluating the efficiency in identifying known ligand partners for documented kinases that were not included in the training data. Our results indicate that our model framework can identify sets of ligands that will contain a significant fraction of the correct (known) ligand partners.

bioinformatics↗

bioRxiv2024

Unveiling the chemical and behavioural ecology of Tribolium castaneum (Herbst, 1797) in wheat flour: Alterations in flour metabolic content and the role of chemical cues in modulating beetles' behaviour and regulating population growth.

Tribolium castaneum (Herbst, 1797) (Coleoptera: Tenebrionidae) is a notorious secondary pest of stored grains and flours, accounting for 10-15% of global annual losses in stored products. This study first evaluated the impact of T. castaneum infestation on the nutritional parameters of stored wheat flour. Infested flour exhibited reductions in total soluble sugars, triacylglycerol levels, and unsaturated fatty acids, particularly Oleic and Linoleic acid, while secondary metabolites such as phenolics, flavonoids, and tannins were increased. Behavioural assays revealed that adult beetles were significantly more attracted towards infested flour odour due to the presence of 4,8-Dimethyldecanal (4,8-DMD), an aggregation pheromone of T. castaneum. Another key compound in infested flour, 1-Pentadecene, derived from the beetles cuticular wax, was found to influence adult beetle behaviour. At higher concentrations, 1-Pentadecene acted as a repellent for the species. Molecular docking studies suggested that 1-Pentadecene competes with 4,8-DMD for binding to the odorant receptor TcOR1, which could potentially inhibit aggregation behaviour and reduce population growth. The docking analysis revealed that 1-Pentadecene interacts with the same binding pocket on TcOR1, sharing key amino acids (MET49, PHE69, THR72, GLN73, THR134, VAL135, TYR138, LEU154, ILE177, GLY180, ALA181, TYR286) and forming similar intermolecular bonds, such as a pi-alkyl bond, with a binding affinity ({Delta}G = -5.7) comparable to 4,8-DMD ({Delta}G = -5.8). Additionally, beetles reared in wheat flour containing higher concentrations of 1-Pentadecene exhibited lower population growth compared to those reared in flour with lower concentrations of this compound.

zoology↗

bioRxiv2024

Loss of PARP7 increases type I interferon signalling and prevents pancreatic tumour growth by enhancing immune cell infiltration

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal forms of cancer, and despite low incidence rates, it remains the sixth leading cause of cancer related deaths worldwide. Immunotherapy, which aims to enhance the immune systems ability to recognize and eliminate cancer cells, has emerged as a promising approach in the battle against PDAC. PARP7, a mono-ADP-ribosyltransferase, is a negative regulator of the type I interferon (IFN-I) pathway and has been reported to reduce anti-tumour immunity. Using murine pancreatic cancer cells, we found that loss of Parp7 elevated the levels of interferon stimulated gene factor 3 (ISGF3) and its downstream target genes, even in the absence of STING. Cancer cells deficient in Parp7 produced smaller tumours when injected into immunocompetent mice. Transcriptomic analyses revealed that tumours knocked out for Parp7 (Parp7KO) had increased expression of genes involved in immunoregulatory interactions and interferon signalling pathways. Characterization of tumour infiltrating leukocyte (TIL) populations showed that Parp7KO tumours had higher proportions of natural killer cells, CD8 T cells and a lower proportion of anti-inflammatory macrophages (M2). The overall TIL profile of Parp7KO tumours was suggestive of a less suppressive microenvironment. Our data show that loss of Parp7 reduces PDAC tumour growth by increasing the infiltration of immune cells and enhancing anti-tumour immunity. These findings provide support to pursue PARP7 as a therapeutic target for PDAC.

cancer biology↗

bioRxiv2024

ARF degradation defines a deeply conserved step in auxin response

Auxin response critically depends on the concentrations and stoichiometry of competing A- and B-class AUXIN RESPONSE FACTOR (ARF) proteins. In Marchantia polymorpha, both A- and B-ARFs are unstable, and here we identify a minimal necessary and sufficient region for ARF degradation that is critical for development, and auxin response. Through comparative analysis, we find that ARF instability likely preceded the emergence of the auxin response system.

plant biology↗