Functional Clusters Research Articles

The PRC2.1 Subcomplex Opposes G1 Progression through Regulation of CCND1 and CCND2.

Progression through the G1 phase of the cell cycle is the most highly regulated step in cellular division. We employed a chemogenetic approach to discover novel cellular networks that regulate cell cycle progression. This approach uncovered functional clusters of genes that altered sensitivity of cells to inhibitors of the G1/S transition. Mutation of components of the Polycomb Repressor Complex 2 rescued proliferation inhibition caused by the CDK4/6 inhibitor palbociclib, but not to inhibitors of S phase or mitosis. In addition to its core catalytic subunits, mutation of the PRC2.1 accessory protein MTF2, but not the PRC2.2 protein JARID2, rendered cells resistant to palbociclib treatment. We found that PRC2.1 (MTF2), but not PRC2.2 (JARID2), was critical for promoting H3K27me3 deposition at CpG islands genome-wide and in promoters. This included the CpG islands in the promoter of the CDK4/6 cyclins CCND1 and CCND2, and loss of MTF2 lead to upregulation of both CCND1 and CCND2. Our results demonstrate a role for PRC2.1, but not PRC2.2, in antagonizing G1 progression in a diversity of cell linages, including CML, breast cancer and immortalized cell lines.

Tracking changes in functionality and morphology of repopulated microglia in young and old mice

BackgroundMicroglia (MG) are myeloid cells of the central nervous system that support homeostasis and instigate neuroinflammation in pathologies. Single-cell RNA sequencing (scRNA-seq) revealed the functional heterogeneity of MG in mouse brains. Microglia are self-renewing cells and inhibition of colony-stimulating factor 1 receptor (CSF1R) signaling depletes microglia which rapidly repopulate. The functions of repopulated microglia are poorly known.MethodsWe combined scRNA-seq, bulk RNA-seq, immunofluorescence, and confocal imaging to study the functionalities and morphology of repopulated microglia.ResultsA CSRF1R inhibitor (BLZ-945) depleted microglia within 21 days and a number of microglia was fully restored within 7 days, as confirmed by TMEM119 staining and flow cytometry. ScRNA-seq and computational analyses demonstrate that repopulated microglia originated from preexisting progenitors and reconstituted functional clusters but upregulated inflammatory genes. Percentages of proliferating, immature microglia displaying inflammatory gene expression increased in aging mice. Morphometric analysis of MG cell body and branching revealed a distinct morphology of repopulated MG, particularly in brains of old mice. We demonstrate that with aging some repopulated MG fail to reach the homeostatic phenotype. These differences may contribute to the deterioration of MG protective functions with age.

Visual Performance of People With Albinism Assessed With Generalizable and Adaptive AIM and FInD Methods.

People with albinism (PwA) are known to have visual impairments; however, little is known about whether these functions are disrupted across earlier and later stages of the visual pathway. We investigated distinct perceptual functions and fixation stability within each observer and compared the data with age- (±5years) and sex-matched controls. Twenty-one self-reported PwA and twenty-one controls were recruited. Angular-indication measurement (AIM) and foraging-interactive-D-prime (FInD) psychophysical methods were deployed to measure OS, OD, and OU near visual acuity, spatial contrast sensitivity function (CSF), temporal contrast sensitivity (tCS; 0.5 c/°; horizontal grating: 0, 1, 2, 4, and 8Hz), OU glare acuity, threshold-versus-contrast (2c/° vertical grating), long, medium, and short wavelength cone-isolated color detection, color discrimination, stereoacuity across spatial frequencies (1c/°, 2c/°, 4c/°, 8c/°), horizontal, circular, radial pattern and motion coherence, and equivalent-noise motion detection. Thresholds were determined by AIM and FInD and compared using N-ANOVAs, t-tests, planned multi-comparisons, correlations, and unsupervised, agglomerative hierarchical cluster analysis for each group. We found significant differences between groups for most visual functions except for simple and complex form-coherence (two way-ANOVAs, P > 0.05) and complex motion coherence. Correlations between outcomes revealed more significant correlations for PwA and differences in the specific correlates between groups. Unsupervised hierarchical clustering revealed different functional clusters between groups. AIM and FInD successfully interrogated visual deficits in PwA. Overall, PwA showed impaired performance in achromatic, chromatic, temporal, and binocular functions, and had higher intrinsic noise levels. Midlevel vision was comparable between groups. Unsupervised cluster analysis and correlation between outcomes revealed a difference in functional outcome clusters between groups. The results may help to increase the efficiency of screening and identify target deficits for rehabilitation.

Abstract C153: Transcriptome-wide study identifies unique pathway functional clusters associated with breast cancer subtypes in population with high indigenous american ancestry

Abstract Purpose: Breast cancer incidence and outcomes differ by US census racial/ethnic category. Since large-scale genetic studies of human disease are predominately focused on populations of European ancestry, little is known about breast cancer molecular biology in Hispanic/Latinos which can widen cancer health disparities due to suboptimal translation of discoveries into clinical practice or public health policy. We aim to identify most relevant pathways in breast cancer subtype differentiation in breast cancer patients from Peru and compared them with those obtained analyzing the Cancer Genome Atlas (TCGA) Breast Cancer (BRCA) dataset and with the published results of the Molecular Profile of Breast Cancer Study (MPBCS), a multi-country Latin American cohort. Patients and Methods: Formalin fixed paraffin embedded tumor tissues samples were whole exome sequenced for a total of 271 patients recruited by the Peruvian Breast Cancer Genomics Study (PEGEN-BC). Quality control was conducted to remove genes with low counts for PEGEN and TCGA-BRCA cohorts, and only female stage II-III breast cancer patients were kept for downstream analysis. Intrinsic tumor subtypes were classified using the estrogen receptor (ER) status-adjusted PAM50 method with genefu package in R. Differential gene expression and pathway analyses between subtypes were performed by the GSEA 4.3.2 software. [LF1] [CX2] Statistical and biological significance was determined using p-values < 0.1 and absolute value of enrichment score > 1.5. Top 20 pathways for each cohort were selected and ranked for comparison. Results: PAM50 classification of the PEGEN-BC cohort defined 20.2% of tumors as Luminal A (LumA), 27.9% as Luminal B (LumB), 27.1% as HER2E, 22.5% as Basal and 2.3% as Normal. Transcriptomic pathway analysis showed that most of the significantly changed pathways were similar to previous findings in the literature, for example, proliferation pathways being upregulated in LumB, HER2E and Basal tumors, compared to the LumA subtype, and a strong dependency on the estrogen pathways for LumA and LumB. Within cohorts, we identified novel clusters of pathways that share related functions. For example, 6 out of the 20 top significant pathways in LumB vs. HER2E comparison for the PEGEN-BC cohort were glycan/glycosylation-related, suggesting the possibility of tumor immune response differences between LumB and HER2E due to glycan related pathway differences among Peruvian patients. Conclusions: We identified novel pathway clusters associated with specific breast cancer subtypes in a population with high Indigenous American ancestry from Peru. Further analyses will be conducted next to explore if the observed patterns were specific to genetic ancestry background or observed independently of genetic ancestry. Citation Format: Chenghuiyun Xu, Valentina A. Zavala, David Rocke, Xiaosong Huang, Sandro Casavilca-Zambrano, Jeannie Navarro-Vásquez, Ruddy Liendo-Picoaga, Monica Calderón, Guillermo Valencia, Patricia Rioja, Carlos A Castañeda, Zaida Morante, Silvia P. Neciosup, Hugo A Fuentes, Julio E. Abugattas, Jose M. Cotrina, Luis A. Salinas, Marco Gálvez-Nino, Jovanny Zabaleta, Andrea S. Llera, Tatiana Vidaurre, Laura Fejerman. Transcriptome-wide study identifies unique pathway functional clusters associated with breast cancer subtypes in population with high indigenous american ancestry [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C153.

Identification of potential biomarkers of cuproptosis in cerebral ischemia.

Cerebral ischemia can cause mild damage to local brain nerves due to hypoxia and even lead to irreversible damage due to neuronal cell death. However, the underlying pathogenesis of this phenomenon remains unclear. This study utilized bioinformatics to explore the role of cuproptosis in cerebral ischemic disease and its associated biomarkers. R software identified the overlap of cerebral ischemia and cuproptosis genes, analyzed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and explored hub genes. Expressions and localizations of hub genes in brain tissue, cells, and immune cells were analyzed, along with predictions of protein structures, miRNAs, and transcription factors. A network was constructed depicting hub gene co-expression with miRNAs and interactions with transcription factors. Ferredoxin 1 (FDX1) expression was determined using qRT-PCR. Ten cuproptosis-related genes in cerebral ischemia were identified, with GO analysis revealing involvement in acetyl-CoA synthesis, metabolism, mitochondrial function, and iron-sulfur cluster binding. KEGG highlighted processes like the tricarboxylic acid cycle, pyruvate metabolism, and glycolysis/gluconeogenesis. Using the Human Protein Atlas, eight hub genes associated with cuproptosis were verified in brain tissues, hippocampus, and AF22 cells. Lipoyl(octanoyl) transferase 1 (LIPT1), was undetected, while others were found in mitochondria or both nucleus and mitochondria. These genes were differentially expressed in immune cells. FDX1, lipoic acid synthetase (LIAS), dihydrolipoamide S-acetyltransferase (DLAT), pyruvate dehydrogenase E1 component subunit alpha 1 (PDHA1), PDHB, and glutaminase (GLS) were predicted to target 111 miRNAs. PDHA1, FDX1, LIPT1, PDHB, LIAS, DLAT, GLS, and dihydrolipoamide dehydrogenase (DLD) were predicted to interact with 11, 10, 10, 9, 8, 7, 5, and 4 transcription factors, respectively. Finally, FDX1 expression was significantly upregulated in the hippocampus of ovariectomized rats with ischemia. This study revealed an association between cerebral ischemic disease and cuproptosis, identifying eight potential target genes. These findings offer new insights into potential biomarkers for the diagnosis, treatment, and prognosis of cerebral ischemia, and provide avenues for the exploration of new medical intervention targets.

The dual lens of diversity: Seasonal variability of avian community structure in urban hills

Urbanization has significantly increased the environmental intricacy of low mountainous and hilly urban landscapes, exacerbating the need for biodiversity conservation in these ecosystems. This study involved comprehensive bird surveys across four seasons from July 2022 to April 2023 along 64 transects in the low mountainous terrain of Jiangsu Province. Adopting a dual lens of taxonomic and functional dimensions, our research explored seasonal fluctuations and assembly mechanisms governing avian community diversity (both α and β) on these urban hills. The results showed that species richness and functional diversity (FD) were higher in spring and lower in autumn, whereas functional mean pairwise distance (MFD) and mean nearest functional distance (FD.MNTD) were higher in summer and winter. Although the standardized effect sizes for MFD were not significantly different from zero in any of the four periods, those for FD.MNTD were significantly less than zero in summer, autumn, and winter, indicating a propensity for functional trait clustering within avian communities during these seasons. Taxonomic variations were found to be chiefly governed by species turnover, whereas functional dynamics were principally shaped by nestedness. A marked disparity emerged, with functional β-diversity and its turnover components consistently registering lower values than their taxonomic counterparts, accompanied by a higher level of functional nestedness versus taxonomic nestedness. This study underscores the intricate seasonal dynamics of avian communities in urbanized low mountainous regions and provides crucial insights to devise conservation strategies aimed at preserving avian biodiversity within these ecologically complex urban landscapes.

THSR wave function and non-localized clustering

The main ideas to construct the THSR wave function are given, and the relation to other approaches such as the Brink-type cluster wave function approach is shown. The effect of the Pauli-forbidden states on the inter-cluster potential is described by the orthogonality condition model. The duality of the cluster structure and shell-model structure for nuclei in the ground state and in excited states is discussed. Future work on nα\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$n \\alpha $$\\end{document} condensate states in more complex nuclei and the formation of cluster structures in excited nuclei is outlined.

Fullerene Derivatives for Tumor Treatment: Mechanisms and Application.

Fullerenes hold tremendous potential as alternatives to conventional chemotherapy or radiotherapy for tumor treatment due to their abilities to photodynamically kill tumor cells, destroy the tumor vasculature, inhibit tumor metastasis and activate anti-tumor immune responses, while protecting normal tissue through antioxidative effects. The symmetrical hollow molecular structures of fullerenes with abundant C=C bonds allow versatile chemical modification with diverse functional groups, metal clusters and biomacromolecules to synthesize a wide range of fullerene derivatives with increased water solubility, improved biocompatibility, enhanced photodynamic properties and stronger targeting abilities. This review introduces the anti-tumor mechanisms of fullerenes and summarizes the most recent works on the functionalization of fullerenes and the application of fullerene derivatives in tumor treatment. This review aims to serve as a valuable reference for further development and clinical application of anti-tumor fullerene derivatives.

Abstract P103: Assessment of Angiotensin II-induced Calcium Signals in Primary Human Adrenocortical Cells

Background: Cytosolic and mitochondrial Ca 2+ concentrations are key signals for triggering the secretion of aldosterone in primary aldosteronism (PA), the most common form of secondary hypertension. Aim: To investigate [Ca 2+ ] i transients and oscillations in human CD56 + cells isolated from aldosterone producing adenoma (APA) and normal surrounding adrenocortical (AAC) cells. Methods: We assessed [Ca 2+ ] i in CD56 + APA and APA-adjacent cells (AAC) in basal conditions and after angiotensin II (Ang II) stimulation using Fura-2 dye, live confocal microscopy, and an ad hoc developed custom-made pipeline to analyze [Ca 2+ ] i signals in terms of frequency and peak parameters as amplitude, full width at half maximum (FWHM) and area under the curve (AUC). As the two-pore domain K + TASK- 2 channels are under expressed in APA, we used quinidine (20 μM), 20’ prior to [Ca 2+ ] i imaging acquisition to examine the effect of the pharmacological inhibition of this channel. Results: Resting [Ca 2+ ] i basal levels were higher in AAC (n=11) (0.75, IQR;0.90-0.56) than in APA (n=11) (0.36 IQR;0.69-0.33), (p < 0.02). We detected spontaneous Ca 2+ activity, during resting conditions, in both cell types without significant difference in peak parameters. Upon 1 nM Ang II simulation, AAC showed elevated FWHM, amplitude, and AUC peak parameters of first Ca 2+ transients. However, APA cells exhibited elevated peak parameters of subsequent Ca 2+ oscillations. Ca 2 oscillations frequency and degree of oscillating cells were significantly higher in APA cells than in AAC. After 24 hours in culture, both AAC and APA cells developed rosette-like cell structure resembling the “glomeruli” of the intact zona glomerulosa clusters. Functional Statistics and clustering analysis showed synchronous behavior of cells belonging to the same cluster without significant differences between AAC and APA. In AAC, Task-2 Inhibition with quinidine tended to increase spontaneous activity and altered peak’s parameters but did not influence frequency of oscillation. Conclusion: Quantitative assessment of [Ca 2+ ] i signals unveiled significant differences in [Ca 2+ ] i dynamics between human AAC and APA cells. These results suggest the concurrent modulation of frequency and amplitude of [Ca 2+ ] I subsequent oscillations as a potential driver of increased rate of aldosterone production.

Phospholipid production and signaling by a plant defense inducer against Podosphaera xanthii is genotype-dependent.

Biotrophic phytopathogenic fungi such as Podosphaera xanthii have evolved sophisticated mechanisms to adapt to various environments causing powdery mildews leading to substantial yield losses. Today, due to known adverse effects of pesticides, development of alternative control means is crucial and can be achieved by combining plant protection products with resistant genotypes. Using plant defense inducers, natural molecules that stimulate plant immune system mimicking pathogen attack is sustainable, but information about their mode of action in different hosts or host genotypes is extremely limited. Reynoutria sachalinensis extract, a known plant defense inducer, especially through the Salicylic acid pathway in Cucurbitaceae crops against P. xanthii, was employed to analyze the signaling cascade of defense activation. Here, we demonstrate that R. sachalinensis extract enhances phospholipid production and signaling in a Susceptible to P. xanthii courgette genotype, while limited response is observed in an Intermediate Resistance genotype due to genetic resistance. Functional enrichment and cluster analysis of the upregulated expressed genes revealed that inducer application promoted mainly lipid- and membrane-related pathways in the Susceptible genotype. On the contrary, the Intermediate Resistance genotype exhibited elevated broad spectrum defense pathways at control conditions, while inducer application did not promote any significant changes. This outcome was obvious and at the metabolite level. Main factor distinguishing the Intermediate Resistance form the Susceptible genotype was the epigenetic regulated increased expression of a G3P acyltransferase catalyzing phospholipid production. Our study provides evidence on phospholipid-based signaling after plant defense inducer treatment, and the selective role of plant's genetic background.

Upregulation of miRNA-450b-5p targets ACTB to affect drug resistance and prognosis of ovarian cancer via the PI3K/Akt signaling pathway.

Ovarian cancer (OC) is the most malignant gynecologic cancer, and chemoresistance is a major cause of treatment failure in patients with OC. The understanding of microRNA (miRNA) in cancer is limited, and the role of miRNA (miR)-450b-5p in cancer drug resistance is unknown. In this study, we aim to evaluate the role of miR-450b-5p in drug-resistant OC and its underlying mechanisms. MiR-450b-5p expression was assessed in drug-sensitive and resistant OC cells via quantitative real-time polymerase chain reaction. Cell viability was evaluated using the Cell Counting Kit-8 assay. Progression-free survival (PFS) and overall survival (OS) curves were generated using the Kaplan-Meier method and the log-rank test. Target genes of miR-450b-5p were identified from the Cancer MIRNome database. Co-expressed genes were obtained from The Cancer Genome Atlas and Cancer Genome cBioportal for pathway enrichment and functional clustering analysis. The miRNA-450b-5p expression was significantly increased in A2780 and SKOV3 OC-resistant cells and significantly increased by 17-fold in the A2780-CBP-Lv-miR-450b-5p cells compared to A2780-CBP and A2780-CBP-Lv-NC cells. The up-regulated expression of miR-450b-5p increased the cell viability and half maximal inhibitory concentration (IC50) of A2780 platinum-resistant cells and was associated with poor OS. We obtained 33 potential target genes of miR-450b-5p and beta-actin (ACTB) might be a potential target of miR-450b-5p. Low expression of ACTB predicted poor OS and PFS. We obtained 362 common genes co-expressed with ACTB, which involved 4 critical pathways. PI3K acted as an upstream pathway of the other three pathways, which ultimately responded to drug resistance regulation in OC. The genes enriched in four pathways were cross-analyzed and 13 overlapping genes were obtained. These 13 genes were also significantly and positively co-expressed with ACTB at both protein and mRNA levels. High expression of miRNA-450b-5p might affect drug resistance and prognosis in OC by targeting 13 co-expressed genes of ACTB directly through the PI3K/Akt signaling pathway. Thus, miR-450b-5p might provide a new therapeutic target for drug resistance in OC.

Effect Analysis of Covid-19 on China’s Capital Market for Property-Rights Exchange Based on Functional Clustering

In August 2015, the State Council of the People’s Republic of China listed China’s capital market for property-rights exchange as the capital market along with the Chinese stock market. Consequently, China’s capital market for property-rights exchange is an integral part of the country’s multilayered capital market. The COVID-19 pandemic has had significant effects on the capital markets. Since China’s capital market for property-rights exchange mainly serves nonlisted companies, it is complicated to obtain its exchange data to perform COVID-19’s effect analysis. This study investigates COVID-19’s effect on China’s capital market for property-rights exchange. In this paper, we collected the online property rights-exchange data from 2017 to 2020 of an electric trading platform. The functional principal component analysis method is innovatively introduced to explore the online property rights-exchange fluctuation to get an insight into COVID-19’s effect on China’s capital market for property-rights exchange. Based on the principal component scores, COVID-19’s effect on different property rights-exchange institutions are divided into two categories using principal component clustering. A time-series model is used to quantify the effects in the two categories. The research results finally show that online property rights-exchange can reduce the negative effect of COVID-19 on China’s capital market for property-rights exchange, which encourages property rights-exchange institutions to accelerate the use of the online platform to overcome the challenges of the pandemic.

Local organization of spatial and shape information in the primate prefrontal cortex.

The current understanding of sensory and motor cortical areas has been defined by the existence of topographical maps across the brain surface, however, higher cortical areas, such as the prefrontal cortex, seem to lack an equivalent organization, and only limited evidence of functional clustering of neurons with similar stimulus properties is evident in them. We thus sought to examine whether neurons that represent similar spatial and object information are clustered in the monkey prefrontal cortex and whether such an organization only emerges as a result of training. To this end, we analyzed neurophysiological recordings from male macaque monkeys before and after training in spatial and shape working memory tasks. Neurons with similar spatial or shape selectivity were more likely than chance to be encountered at short distances from each other. Some aspects of organization were present even in naïve animals, however other changes appeared after cognitive training. Our results reveal that prefrontal microstructure automatically supports orderly representations of spatial and object information.

Distance-based Clustering of Functional Data with Derivative Principal Component Analysis

Functional data analysis (FDA) is an important modern paradigm for handling infinite-dimensional data. An important task in FDA is clustering, which identifies subgroups based on the shapes of measured curves. Considering that derivatives can provide additional useful information about the shapes of functionals, we propose a novel L 2 distance between two random functions by incorporating the functions and their derivative information to determine the dissimilarity of curves under a unified scheme for dense observations. The Karhunen–Loève expansion is used to approximate the curves and their derivatives. Cluster membership prediction for each curve intends to minimize the new distances between the observed and predicted curves through subspace projection among all possible clusters. We provide consistent estimators for the curves, curve derivatives, and the proposed distance. Identifiability issues of the clustering procedure are also discussed. The utility of the proposed method is illustrated via simulation studies and applications to two real datasets. The proposed method can considerably improve cluster performance compared with existing functional clustering methods. Supplementary materials for the article are available online.

Seqrutinator: scrutiny of large protein superfamily sequence datasets for the identification and elimination of non-functional homologues

Seqrutinator is an objective, flexible pipeline that removes sequences with sequencing and/or gene model errors and sequences from pseudogenes from complex, eukaryotic protein superfamilies. Testing Seqrutinator on major superfamilies BAHD, CYP, and UGT removes only 1.94% of SwissProt entries, 14% of entries from the model plant Arabidopsis thaliana, but 80% of entries from Pinus taeda’s recent complete proteome. Application of Seqrutinator on crude BAHDomes, CYPomes, and UGTomes obtained from 16 plant proteomes shows convergence of the numbers of paralogues. MSAs, phylogenies, and particularly functional clustering improve drastically upon Seqrutinator application, indicating good performance.

Elucidating the Functional Roles of Long Non-Coding RNAs in Alzheimer's Disease.

Alzheimer's disease (AD) is a multifaceted neurodegenerative disorder characterized by cognitive decline and neuronal loss, representing a most challenging health issue. We present a computational analysis of transcriptomic data of AD tissues vs. healthy controls, focused on the elucidation of functional roles played by long non-coding RNAs (lncRNAs) throughout the AD progression. We first assembled our own lncRNA transcripts from the raw RNA-Seq data generated from 527 samples of the dorsolateral prefrontal cortex, resulting in the identification of 31,574 novel lncRNA genes. Based on co-expression analyses between mRNAs and lncRNAs, a co-expression network was constructed. Maximal subnetworks with dense connections were identified as functional clusters. Pathway enrichment analyses were conducted over mRNAs and lncRNAs in each cluster, which served as the basis for the inference of functional roles played by lncRNAs involved in each of the key steps in an AD development model that we have previously built based on transcriptomic data of protein-encoding genes. Detailed information is presented about the functional roles of lncRNAs in activities related to stress response, reprogrammed metabolism, cell polarity, and development. Our analyses also revealed that lncRNAs have the discerning power to distinguish between AD samples of each stage and healthy controls. This study represents the first of its kind.

Boosting immunity: synergistic antiviral effects of luteolin, vitamin C, magnesium and zinc against SARS-CoV-2 3CLpro.

SARS-CoV-2 was first discovered in 2019 and has disseminated throughout the globe to pandemic levels, imposing significant health and economic burdens. Although vaccines against SARS-CoV-2 have been developed, their long-term efficacy and specificity have not been determined, and antiviral drugs remain necessary. Flavonoids, which are commonly found in plants, fruits, and vegetables and are part of the human diet, have attracted considerable attention as potential therapeutic agents due to their antiviral and antimicrobial activities and effects on other biological activities, such as inflammation. The present study uses a combination of biochemical, cellular, molecular dynamics, and molecular docking experiments to provide compelling evidence that the flavonoid luteolin (2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one) has antiviral activity against SARS-CoV-2 3-chymotrypsin-like protease (3CLpro) that is synergistically enhanced by magnesium, zinc, and vitamin C. The IC50 of luteolin against 2 µM 3CLpro is 78 µM and decreases 10-fold to 7.6 µM in the presence of zinc, magnesium, and vitamin C. Thermodynamic stability analyses revealed that luteolin has minimal effects on the structure of 3CLpro, whereas metal ions and vitamin C significantly alter the thermodynamic stability of the protease. Interactome analysis uncovered potential host-virus interactions and functional clusters associated with luteolin activity, supporting the relevance of this flavone for combating SARS-CoV-2 infection. This comprehensive investigation sheds light on luteolin's therapeutic potential and provides insights into its mechanisms of action against SARS-CoV-2. The novel formulation of luteolin, magnesium, zinc, and vitamin C may be an effective avenue for treating COVID-19 patients.

Metagenome comparison (MC): A new framework for detecting unique/enriched OMUs (operational metagenomic units) derived from whole-genome sequencing reads

BackgroundCurrent methods for comparing metagenomes, derived from whole-genome sequencing reads, include top-down metrics or parametric models such as metagenome-diversity, and bottom-up, non-parametric, model-free machine learning approaches like Naïve Bayes for k-mer-profiling. However, both types are limited in their ability to effectively and comprehensively identify and catalogue unique or enriched metagenomic genes, a critical task in comparative metagenomics. This challenge is significant and complex due to its NP-hard nature, which means computational time grows exponentially, or even faster, with the problem size, rendering it impractical for even the fastest supercomputers without heuristic approximation algorithms. MethodIn this study, we introduce a new framework, MC (Metagenome-Comparison), designed to exhaustively detect and catalogue unique or enriched metagenomic genes (MGs) and their derivatives, including metagenome functional gene clusters (MFGC), or more generally, the operational metagenomic unit (OMU) that can be considered the counterpart of the OTU (operational taxonomic unit) from amplicon sequencing reads. The MC is essentially a heuristic search algorithm guided by pairs of new metrics (termed MG-specificity or OMU-specificity, MG-specificity diversity or OMU-specificity diversity). It is further constrained by statistical significance (P-value) implemented as a pair of statistical tests. ResultsWe evaluated the MC using large metagenomic datasets related to obesity, diabetes, and IBD, and found that the proportions of unique and enriched metagenomic genes ranged from 0.001% to 0.08 % and 0.08%–0.82 % respectively, and less than 10 % for the MFGC. ConclusionThe MC provides a robust method for comparing metagenomes at various scales, from baseline MGs to various function/pathway clusters of metagenomes, collectively termed OMUs.

Effective knockdown-replace gene therapy in a novel mouse model of DNM1 developmental and epileptic encephalopathy

Effective gene therapy for gain-of-function or dominant-negative disease mutations may require eliminating expression of the mutant copy together with wildtype replacement. We evaluated such a “knockdown-replace” strategy in a mouse model of DNM1 disease, a debilitating and intractable neurodevelopmental epilepsy. To challenge the approach robustly, we expressed a patient-based variant in GABAergic neurons - which resulted in growth delay and lethal seizures evident by postnatal week three - and delivered to newborn pups an AAV9-based vector encoding a ubiquitously-expressed, Dnm1-specific interfering RNA (RNAi) bivalently in tail-to-tail configuration with a neuron-specific, RNAi-resistant, codon-optimized Dnm1 cDNA. Pups receiving RNAi or cDNA alone fared no better than untreated, whereas the vast majority of mutants receiving modest doses survived with almost full growth recovery. Synaptic recordings of cortical neurons derived from treated pups revealed that significant alterations in transmission from inhibitory to excitatory neurons were rectified by bivalent vector application. To examine the mutant transcriptome and impact of treatment, we used RNAseq and functional annotation clustering. Mutants displayed abnormal expression of >1000 genes in highly significant and relevant functional clusters, clusters that were abrogated by treatment. Together these results suggest knockdown-replace as a potentially effective strategy for treating DNM1 and related genetic neurodevelopmental disease.

Revisiting Possibilistic Fuzzy C-Means Clustering Using the Majorization-Minimization Method.

Possibilistic fuzzy c-means (PFCM) clustering is a kind of hybrid clustering method based on fuzzy c-means (FCM) and possibilistic c-means (PCM), which not only has the stability of FCM but also partly inherits the robustness of PCM. However, as an extension of FCM on the objective function, PFCM tends to find a suboptimal local minimum, which affects its performance. In this paper, we rederive PFCM using the majorization-minimization (MM) method, which is a new derivation approach not seen in other studies. In addition, we propose an effective optimization method to solve the above problem, called MMPFCM. Firstly, by eliminating the variable V∈Rp×c, the original optimization problem is transformed into a simplified model with fewer variables but a proportional term. Therefore, we introduce a new intermediate variable s∈Rc to convert the model with the proportional term into an easily solvable equivalent form. Subsequently, we design an iterative sub-problem using the MM method. The complexity analysis indicates that MMPFCM and PFCM share the same computational complexity. However, MMPFCM requires less memory per iteration. Extensive experiments, including objective function value comparison and clustering performance comparison, demonstrate that MMPFCM converges to a better local minimum compared to PFCM.