Biology subjects

Aryal, S.

Publications and source records attributed to Aryal, S..

33 records · Page 2Linked to original sources

bioRxiv2024

Muti-omics characterization reveals brain-wide disruption of synapses and region- and age-specific changes in neurons and glia in Sp4 mutant mice, a genetic model of schizophrenia and bipolar disorder

Schizophrenia and bipolar disorder are highly heritable mental illnesses with unclear pathophysiology. Heterozygous loss-of-function mutations of Sp4, a zinc-finger transcription factor, greatly increase risk of schizophrenia and bipolar disorder. To investigate the molecular functions of Sp4 in an unbiased manner in vivo, we performed multi-omics analyses of Sp4 mutant mice. Bulk and single nucleus RNA-seq data showed prominent gene expression changes in all brain regions and most cell types, including neuronal and non-neuronal cells. Gene set enrichment analysis of transcriptomic changes revealed alterations in many molecular pathways, including synapse, oxidative phosphorylation, and ribosome. Synapse proteomics of Sp4 mutants pointed to impaired glutamatergic signaling and altered presynaptic function. In Sp4 heterozygous mutant mice, prefrontal cortex and striatum exhibited downregulation of synapse pathways and neuronal hypoactivity at 1 month, associated with reduced sterol biosynthesis in astrocytes, whereas at 3 months, there was a shift to neuronal hyperactivity, concurrent with suppressed immune pathways in the striatal microglia. Furthermore, our study found that much of the transcriptomic changes might be accounted for by a set of transcription regulators (Nr3c1, Creb1, and Kdm5b) under the control of Sp4. Overall, this study provides cellular and molecular features resulting from Sp4 LoF that may explain the pathophysiology of SCZ-BD psychotic disorder spectrum.

neuroscience↗

bioRxiv2024

Elevated synaptic PKA activity and abnormal striatal dopamine signaling in Akap11 mutant mice, a genetic model of schizophrenia and bipolar disorder

AbstractLoss-of-function mutations in AKAP11 (a protein kinase A (PKA)-binding protein) greatly increase the risk of bipolar disorder and schizophrenia. To determine the neurobiological functions of AKAP11, we conduct multi-omic and neurobiological analyses of Akap11 mutant mouse brains. We find that AKAP11 is a key regulator of PKA proteostasis in the brain whose loss leads to dramatically increased levels of PKA subunits and phosphorylated PKA substrates, especially in synapses. Akap11 mutant mice show extensive transcriptomic changes throughout the brain, including prominent decreases in synapse-related genes sets. Gene expression is highly impacted in spiny projection neurons of the striatum, a brain region implicated in motivation, cognition and psychotic disorders. Real-time measurements of PKA activity reveal elevated basal PKA activity in the striatum of Akap11-/- mice, with exaggerated additional response to dopamine receptor antagonists. Behaviorally, Akap11 mutant mice show abnormally prolonged locomotor response to amphetamine, deficits in associative learning and contextual discrimination, as well as depression-like behaviors. Our study connects molecular changes to circuit dysfunction and behavioral disturbance in a genetically valid animal model of psychotic disorder.

neuroscience↗

bioRxiv2023

CREID- A ChemoReceptor-Effector Interaction Database

The ChemoReceptor-Effector Interaction Database (CREID) is a collection of bacterial chemoreceptor and effector protein and interaction data to understand the process that chemoreceptors and effectors play in various environments. Our website includes terms associated with chemosensory pathways to educate users and those involved in collaborative research to help them understand this complex biological network. It includes 2,440 proteins involved in chemoreceptor and effector systems from 7 different bacterial families with 1,996 chemoeffector interactions. It is available at https://react-creid.bicbioeng.org. Key HighlightsO_LICREID links bacterial chemoreceptors with their associated effectors. C_LIO_LIResearchers interested in what attracts or repels bacteria can use CREID as a comprehensive source for information. C_LIO_LIBiosensor developers can leverage CREID to discover better interactions for their applications. C_LIO_LICREID reveals knowledge gaps in chemoreceptor-effector interactions for both model and non-model organisms. C_LI

bioengineering↗

bioRxiv2022

Cell type-specific disruption of cortico-striatal circuitry drive repetitive patterns of behaviour in fragile X syndrome model mice

Individuals with fragile X syndrome (FXS) are frequently diagnosed with autism spectrum disorder (ASD), including increased risk for restricted and repetitive behaviours (RRBs). Consistent with observations in humans, FXS model mice display distinct RRBs and hyperactivity that are consistent with dysfunctional cortico-striatal circuits, an area relatively unexplored in FXS. Using a multidisciplinary approach, we dissected the contribution of two populations of striatal medium spiny neurons (SPNs) in the expression of RRBs in FXS model mice. We found that dysregulated protein synthesis at cortico-striatal synapses is a molecular culprit of the synaptic and ASD-associated motor phenotypes displayed by FXS model mice. Cell-type-specific translational profiling of the FXS mouse striatum revealed differentially translated mRNAs, providing critical information concerning potential therapeutic targets. Our findings represent the first evidence of a cell-type specific impact of the loss of FMRP on translation and the sequence of neuronal events in the striatum that drive RRBs in FXS. HighlightsDysregulated striatal protein synthesis underlies altered synaptic plasticity and RRBs displayed by FXS model mice FXS model mice exhibit cell type-specific molecular, morphological, and synaptic changes in the dorsolateral striatum Selective deletion of Fmr1 from dSNPs in mice alters translation and causes repetitive behavior TRAP-Seq indicates that there is altered binding of >120 mRNAs to ribosomes in dSNPs of Fmr1 KO mice G-protein signaling (RGS) 4 translation is significantly reduced in dSPNs in FXS model mice Treatment of FXS model mice with VU0152100, a positive allosteric modulator of the M4 muscarinic receptor that is upstream of RGS4, can reverse RRBs

neuroscience↗

bioRxiv2022

Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice

Schizophrenia disease mechanisms remain poorly understood, in large part due to a lack of valid animal models. Rare heterozygous loss-of-function mutations in GRIN2A, encoding a subunit of the NMDA (N-methyl-d-aspartate) receptor, greatly increase the risk of schizophrenia. By transcriptomic, proteomic, electroencephalogram (EEG) recording and behavioral analysis, we report that heterozygous Grin2a mutant mice show: (i) large-scale gene expression changes across multiple brain regions and in neuronal (excitatory and inhibitory) and non-neuronal cells (astrocytes, oligodendrocytes); (ii) evidence of reduced activity in prefrontal cortex and increased activity in hippocampus and striatum; (iii) elevated dopamine signaling in striatum; (iv) altered cholesterol biosynthesis in astrocytes; (v) reduction of glutamatergic receptor signalin g proteins in the synapse; (iv) heightened gamma oscillation power in EEG; (vi) aberrant locomotor behavioral pattern opposite of that induced by antipsychotic drugs. These findings reveal potential pathophysiologic mechanisms, provide support for both the "hypo-glutamate" and "hyper-dopamine" hypotheses of schizophrenia, and underscore the utility of Grin2a-deficient mice as a new genetic model of schizophrenia.

neuroscience↗

bioRxiv2022

Deep proteomics identifies shared molecular pathway alterations in synapses of schizophrenia and bipolar disorder patients and mouse model

Synaptic dysfunction is implicated in the pathophysiology of schizophrenia (SCZ) and bipolar disorder (BP). We used quantitative mass-spectrometry to carry out deep and unbiased profiling of the proteome of synapses purified from the dorsolateral prefrontal cortex of 35 cases of SCZ, 35 cases of BP, and 35 controls. Compared to controls, SCZ and BP synapses showed substantial and similar proteomic alterations. Network and gene set enrichment analyses revealed upregulation of proteins associated with autophagy and certain vesicle transport pathways, and downregulation of proteins related to synaptic, mitochondrial, and ribosomal function in the synapses of individuals with SCZ or BP. Some of the same pathways (e.g., upregulation of vesicle transport, downregulation of mitochondrial and ribosomal proteins) were similarly dysregulated in the synaptic proteome of mutant mice deficient in Akap11, a recently discovered shared risk gene for SCZ and BP. Our work provides novel biological insights into molecular dysfunction at the synapse in SCZ and BP and serves as a resource for understanding the pathophysiology of these debilitating neuropsychiatric disorders.

neuroscience↗

bioRxiv2021

The spliced leader RNA silencing (SLS) pathway in Trypanosoma brucei is induced by perturbations of endoplasmic reticulum, Golgi, or mitochondrial proteins factors and functional analysis of SLS inducing kinase, PK3

In the parasite Trypanosoma brucei, the causative agent of human African sleeping sickness, all mRNAs are trans-spliced to generate a common 5 exon derived from the spliced leader RNA (SL RNA). Perturbations of protein translocation across the endoplasmic reticulum (ER) induce the spliced leader RNA silencing (SLS) pathway. SLS activation is mediated by a serine-threonine kinase, PK3, which translocates from the cytosolic face of the ER to the nucleus, where it phosphorylates the TATA binding protein TRF4, leading to the shut-off of SL RNA transcription, followed by induction of programmed cell death. Here, we demonstrate that SLS is also induced by depletion of the essential ER resident chaperones BiP and calreticulin, ER oxidoreductin 1 (ERO1), and the Golgi-localized quiescin sulfhydryl oxidase (QSOX1). Most strikingly, silencing of Rhomboid-like 1(TIMRHOM1) involved in mitochondrial protein import, also induces SLS. The PK3 kinase, which integrates SLS signals, is modified by phosphorylation on multiple sites. To determine which of the phosphorylation events activate PK3, several individual mutations or their combination were generated. These mutations failed to completely eliminate the phosphorylation or translocation of the kinase to the nucleus. The structure of PK3 kinase and its ATP binding domain were therefore modeled. A conserved phenylalanine at position 771 was proposed to interact with ATP, and the PK3F771L mutation completely eliminated phosphorylation under SLS, suggesting that the activation involves most if not all the phosphorylation sites. The study suggests that the SLS occurs broadly in response to failures in protein sorting, folding, or modification across multiple compartments.

molecular biology↗

bioRxiv2021

Purinoreceptors and ectonucleotidases control ATP-induced calcium waveforms and calcium-dependent responses in microglia

1Adenosine triphosphate (ATP) drives microglia motility and cytokine production by activating P2X- and P2Y- class purinergic receptors with extracellular ATP and its metabolites. Purinergic receptor activation gives rise to diverse intracellular Ca2+ signals, or waveforms, that differ in amplitude, duration, and frequency. Whether and how these diverse waveforms influence microglia function is not well established. We developed a computational model trained with published primary murine microglia studies. We simulate how purinoreceptors influence Ca2+ signaling and migration and how purinoreceptor expression modifies these processes. Our simulation confirmed that P2 receptors encode the amplitude and duration of the ATP-induced calcium waveforms. Our simulations also implicate CD39, an ectonucleotidase that rapidly degrades ATP, as a regulator of purinergic receptor-induced Ca2+ responses. We, therefore, next evaluated how purinoreceptors and ectonucleotidase work in tandem. Our modeling results indicate that small transients are sufficient to promote motility, while large and sustained transients are needed for cytokine responses. Lastly, we predict how these phenotypical responses vary in a BV2 microglia cell line using published P2 receptor mRNA data to illustrate how our computer model can be extrapolated to diverse microglia subtypes. These findings provide important insights into how differences in purinergic receptor expression influence the microglias responses to ATP.

physiology↗

bioRxiv2021

Microstructural determinants of lens stiffness in rat versus guinea pig lenses

Proper ocular lens function requires lens biomechanical flexibility which is lost in presbyopia during aging. As increasing lens size has been shown previously to correlate with lens biomechanical stiffness in aging, we tested the hypothesis that whole lens size determines gross biomechanical stiffness. We used an allometric approach to evaluate this hypothesis by comparing lenses from three rodent species (mouse, rats and guinea pigs) of varying size. While rat lenses are larger and stiffer than mouse lenses, guinea pig lenses are even larger than rat lenses but are softer than the rat lens. This indicates that lens size is not a sole determinant of lens stiffness and disproves our hypothesis. Therefore, we investigated the scaling of lens microstructural features that could potentially explain the differences in biomechanical stiffness between rat and guinea pig lenses, including lens capsule thickness, epithelial cell area, fiber cell widths, suture organization, and nuclear size. Capsule thickness, epithelial cell area, and fiber cell widths scaled with lens size (i.e., greater in guinea pig lenses than rats), indicating that sizes of these features do not correlate with the stiffness of rat lenses, while suture organization was similar between rats and guinea pigs. However, we found that the hard rat lens nucleus occupies a greater fraction of the lens than the guinea pig lens nucleus, suggesting a role for nuclear size in determining whole lens stiffness. Therefore, while many features contribute to lens biomechanical properties, the size of the lens nucleus with respect to the size of the lens could be a major determinant of lens stiffness in rats versus guinea pigs.

cell biology↗

bioRxiv2020

EVALUATION OF ANTI-BACTERIAL AND ANTHELMINTIC ACTIVITIES OF BARK OF PLANT CASSIA FISTULA Linn.

This study deals with phytochemical screening and evaluation of anti-bacterial and anthelmintic activities of the bark extracts of Cassia fistula L. The extraction with different solvents - methanol, acetone, distilled water - had been carried out. The anti-bacterial assay was done against two gram +ve and two gram -ve bacteria by agar cup diffusion method. The anthelmintic activity was done on Pheretima posthuma (earthworm) by recording the paralyzing and death time under different concentrations. Methanolic extract showed the maximum activity on both fronts be it anti-bacterial or anthelmintic. The extract was effective only against gram +ve bacteria. Among Staphylococcus aureus and Streptococci faecalis, the former was more susceptible. The activity against gram -ve bacteria was not found. In case of anthelmintic activity, the concentration of 50 mg/ml was effective and near to the paralyzing and death time as recorded for the 10 mg/ml concentration of the standard Albendazole. However, aqueous extract was more effective than the acetone extract.

pharmacology and toxicology↗

bioRxiv2020

Characterization, and Anti-microbial Properties of Zinc Oxide Nanoparticles Synthesized Using Citrus sinensis (L.) Osbeck Peel Extract

BackgroundCitrus sinensis (L.) Osbeck peels are usually discarded as wastes; however, they are rich sources of Vitamin C, fibre, and many nutrients including phenolics and flavonoids which are also good antioxidant agents. This study aimed to examine phytochemical composition, antioxidant capabilities, cytotoxicity of C. sinensis (L.) Osbeck peel extract and and to compare the antibacterial activity with zinc nanoparticles of Citrus sinensis (L.) Osbeck peels with its extract. GC-MS analysis of the compounds present in the peels extract of Citrus sinensis (L.) Osbeck was also done. MethodsC. sinensis (L.) Osbeck fruits were collected from Sindhuli district and were taken to National Herbarium and Plant Laboratory, Godawari, Lalitpur for its identification. Extraction was done by maceration in aqueous solvent. Extract was subjected to Phytochemical screening done by color reactions with different reagents, Antioxidant activities of the peel extracts were examined via the 2,2-diphenylpicrylhydrazyl (DPPH) free radical scavenging activity. Total phenolic content and total flavonoid content of the extracts were measured via the Folin-Ciocalteau method and the aluminium chloride colorimetric method, respectively. Cytotoxic activities of the peel extracts were determined by Brine Shrimp Lethality Bioassay. Comparison of antibacterial activity of extract and zinc oxide nanoparticles prepared via green synthesis using C. sinensis (L.) Osbeck peel extracts as reducing agents. Antibacterial activity was tested by Bore well diffusion method. ResultThe extractive value of C. sinensis (L.) Osbeck was found to be 8.64% in aqueous solvent. GC-MS analysis of peel extract of C. sinensis (L.) Osbeck showed the presence of 2-Methoxy-4-vinylphenol, 4H-Pyran-4-one, 2,3-dihydro-3,5-dihydroxy-6-methyl, Benzoic acid, 3-Deoxy-d-mannoic lactone and 5-Hydroxymethyl-furfuralas major compounds. The qualitative phytochemical test showed the presence of tannin, alkaloid, carbohydrate, flavonoid, cardiac glycoside, terpinoid. The DPPH radical scavenging activity of C. sinensis (L.) Osbeck peel extract was 35.56 g/ml. TPC of C. sinensis (L.) Osbeck peel extracts was 46.07 mg GAE/g. TFC was 1.29 mg QE/g. The LD50 value of Brine Shrimp Lethality assay of the extract showed 312.5g/ml which is indicative. The antibacterial activity of zinc oxide nanoparticles was found to be greater than that of the extract, but the antibacterial activity of Zn-NPs was less than that of the standard. ConclusionHence, the GC-MS analysis of aqueous extracts of leaves of C. sinensis (L.) Osbeck showed the presence of 20 different compounds. Phytochemicals including phenolics and flavonoids in C. sinensis (L.) Osbeck peel extracts exhibited good antioxidant properties. The extract also exhibited antibacterial activity which was 4 times less than that of the standard. The antibacterial activity of standard was 2 times greater than that of Zn-NPs. The extract also exhibited cytotoxic activity. This study indicated that C. sinensis (L.) Osbeck peels contained potential antioxidant, cytotoxic and antibacterial compounds which could be exploited as value added products.

pharmacology and toxicology↗

bioRxiv2020

Origin of Novel Coronavirus (COVID-19): A Computational Biology Study using Artificial Intelligence

Origin of the COVID-19 virus (SARS-CoV-2) has been intensely debated in the scientific community since the first infected cases were detected in December 2019. The disease has caused a global pandemic, leading to deaths of thousands of people across the world and thus finding origin of this novel coronavirus is important in responding and controlling the pandemic. Recent research results suggest that bats or pangolins might be the hosts for SARS-CoV-2 based on comparative studies using its genomic sequences. This paper investigates the SARS-CoV-2 origin by using artificial intelligence (AI) and raw genomic sequences of the virus. More than 300 genome sequences of COVID-19 infected cases collected from different countries are explored and analysed using unsupervised clustering methods. The results obtained from various AI-enabled experiments using clustering algorithms demonstrate that all examined SARS-CoV-2 genomes belong to a cluster that also contains bat and pangolin coronavirus genomes. This provides evidence strongly supporting scientific hypotheses that bats and pangolins are probable hosts for SARS-CoV-2. At the whole genome analysis level, our findings also indicate that bats are more likely the hosts for the COVID-19 virus than pangolins.

bioinformatics↗

bioRxiv2020

Genetic removal of p70 S6K1 corrects coding sequence length-dependent alterations in mRNA translation in fragile X syndrome mice

Loss of the fragile X mental retardation protein (FMRP) causes fragile X syndrome (FXS). FMRP is widely thought to repress protein synthesis, but its translational targets and modes of control remain in dispute. We previously showed that genetic removal of p70 S6 kinase 1 (S6K1) corrects altered protein synthesis as well as synaptic and behavioral phenotypes in FXS mice. In this study, we examined the gene-specificity of altered mRNA translation in FXS and the mechanism of rescue with genetic reduction of S6K1 by carrying out ribosome profiling and RNA-Seq on cortical lysates from wild-type, FXS, S6K1 knockout, and double knockout mice. We observed reduced ribosome footprint abundance in the majority of differentially translated genes in the cortices of FXS mice. We used molecular assays to discover evidence that the reduction in ribosome footprint abundance reflects an increased rate of ribosome translocation, which is captured as a decrease in the number of translating ribosomes at steady state, and is normalized by inhibition of S6K1. We also found that genetic removal of S6K1 prevented a positive-to-negative gradation of alterations in translation efficiencies (RF/mRNA) with coding sequence length across mRNAs in FXS mouse cortices. Our findings reveal the identities of dysregulated mRNAs and a molecular mechanism by which reduction of S6K1 prevents altered translation in FXS.

neuroscience↗

bioRxiv2020

Genetic reduction of PERK-eIF2α signaling in dopaminergic neurons drives cognitive and age-dependent motor dysfunction

An array of phenotypes in animal models of neurodegenerative disease have been shown to be reversed by neuronal inhibition of PERK, an eIF2 kinase that modulates the unfolded protein response (UPR). This suggests that targeting PERK therapeutically could be beneficial for treatment of human disease. Herein, using multiple genetic approaches we show that selective deletion of the PERK in mouse midbrain dopaminergic (DA) neurons results in multiple cognitive and age-dependent motor phenotypes. Conditional expression of phospho-mutant eIF2 in DA neurons recapitulated the phenotypes caused by deletion of PERK, consistent with a causal role of decreased eIF2 phosphorylation. In addition, deletion of PERK in DA neurons resulted in altered de novo translation, as well as age-dependent changes in axonal DA release and uptake in the striatum that mirror the pattern of motor changes observed. Taken together, our findings show that proper regulation of PERK-eIF2 signaling in DA neurons is required for normal cognitive and motor function across lifespan, and also highlight the need for caution in the proposed use of sustained PERK inhibition in neurons as a therapeutic strategy in the treatment of neurodegenerative disorders.

neuroscience↗

bioRxiv2018

Moving beyond P values: Everyday data analysis with estimation plots

Introduction Introduction The two-groups design is... Significance testing obscures... Even when fully visualized,... Five key advantages of... Estimation graphics are... Conclusion Author Contributions Funding sources Code Availability Guide to using DABEST Web application Google Colaboratory Python Matlab DABEST-Python in R References Over the past 75 years, a number of statisticians have advised that the data-analysis method known as null- hypothesis significance testing (NHST) should be deprecated (Berkson, 1942; Halsey et al., 2015). The l ...

bioinformatics↗