Biology subjects

Wang, M.

Publications and source records attributed to Wang, M..

At least 253 records · Page 14Linked to original sources

bioRxiv2025

GABAergic network from AVP neurons to VIP neurons in the suprachiasmatic nucleus sets the activity/rest time of the circadian behavior rhythm

The central circadian clock of the suprachiasmatic nucleus (SCN) is a network composed of multiple types of {gamma}-aminobutyric acid (GABA)-ergic neurons and glial cells. However, the precise role of GABAergic transmission in the SCN remains unclear. In this study, we investigated the GABAergic regulation from arginine vasopressin (AVP)-producing neurons in the SCN shell to vasoactive intestinal polypeptide (VIP)-producing neurons in the SCN core. Blocking GABA release from AVP neurons by a vesicular GABA transporter (Vgat) gene deletion lengthened the activity time (the interval between the onset and offset of locomotor activity) and shortened the duration of high Ca2+ activity in VIP neurons to match the behavioral rest time. Conversely, eliminating functional GABAA receptors (GABAAR) in VIP neurons by in vivo genome editing reduced locomotor activity level and the activity time, and lengthened the high Ca2+ duration in VIP neurons. Optogenetic activation of AVP neurons in vivo increased Ca2+ in VIP neurons during the night. A similar Ca2+ response of VIP neurons to AVP neuronal activation was also observed in SCN slices and was inhibited by a GABAAR antagonist, gabazine. Importantly, gabazine application alone raised the baseline Ca2+ in VIP neurons, suggesting a tonic depression of these neurons by GABA. Moreover, AVP neuronal activation decreased Ca2+ in non-AVP neurons located between AVP- and VIP-rich regions in the SCN. These results suggest that GABA from AVP neurons disinhibits VIP neurons indirectly by suppressing other intermediate GABA neurons to set the behavior activity/rest time precisely.

neuroscience↗

bioRxiv2025

A Multi-Organ Murine Metabolomics Atlas Reveals Molecular Dysregulations in Alzheimer's Disease

The etiology of Alzheimers Disease (AD) remains largely unclear but is likely driven by gene-environment interactions. Here, we present a multi-organ untargeted metabolomics dataset (2,271 samples) generated from five tissue types in two genetic AD mouse models under colonized or germ-free conditions, complemented by shotgun metagenomics sequencing data (666 samples). Systems-level analyses of 3xTg and 5xFAD mice reveal clusters of dysregulated molecular classes across tissues including carnitines, bile acids, B vitamins, and neurotransmitters. This signature, coupled with microbiome profiles, suggests increased oxidative stress via mitochondrial dysfunction. Molecular feature tracking via tissueMASST, a mass spectrometry search tool we developed to bridge animal model findings with human data, identifies microbially-modulated phenylacetyl-carnitine as positively associated with aging and cognitive impairment across human AD studies. With hundreds of yet-to-be-characterized metabolites, this public resource and its associated tools will aid future research in the pathophysiology of AD.

microbiology↗

bioRxiv2025

Unique Gluing Effect of ASXL1 K351 Monoubiquitination Stimulates PR-DUB-Mediated Nucleosomal H2AK119Ub Deubiquitination

Protein ubiquitination plays a critical role in regulating fundamental biological processes through both proteolytic and nonproteolytic mechanisms. While classically known for its role in targeting proteins for degradation, ubiquitination can also modulate enzymatic activity. However, all of the known mechanisms of such modulation involve spatially constrained mechanisms that take place near the enzyme-substrate interfaces. Here, we report an unprecedented regulatory paradigm mediated by ubiquitination that is located distal to the enzyme-substrate interface but can still activate the polycomb repressive deubiquitinase (PR-DUB) complex. Using cryo-electron microscopy, molecular dynamics (MD) simulations, hydrogen-deuterium exchange mass spectrometry (HDX-MS), and kinetics assays, we determined that the ASXL1 K351 monoubiquitination promotes PR-DUB-mediated nucleosomal H2AK119Ub deubiquitination by stabilizing the catalytic pocket of PR-DUB, causing significant increase in maximal catalytic velocity (Vmax) but almost no change in the substrate binding affinity (Km). Structural analysis revealed that the ubiquitin moiety at ASXL1 K351 bridges the BAP1 and ASXL1 subunits, acting as an intramolecular "glue" that constrains the conformational dynamics of these subunits without altering the nucleosome binding interface. Further MD and HDX-MS results demonstrated the monoubiquitination of ASXL1 K351 enables PR-DUB to effectively maintain a spatial arrangement of the catalytic conformation that closely aligns with substrate cleavage. This study expands our understanding of the mechanisms of ubiquitin function to include intramolecular fastening with a molecular gluing effect and provides a deeper mechanistic understanding of PR-DUB activation in nucleosomal H2AK119Ub removal.

biochemistry↗

bioRxiv2025

Single-Cell eQTL Mapping Reveals Cell Type-Specific Genetic Regulation in Lung Cancer

Genome-wide association studies (GWAS) have identified over 50 lung cancer risk loci; however, the precise cellular context of these genetic mechanisms remains unclear due to limitations in bulk tissue eQTL analyses. Here, we present the largest single-cell eQTL atlas of human lung tissue to date, profiling 222 donors using multiplexed scRNA-seq. We identified 16,785 eQTLs across 17 cell types, with over 90% of sc-eQTLs and 59% eGene being cell-type-specific, and fewer than 23% were detectable in paired bulk datasets. Integration with GWAS for non-small cell lung cancer highlighted epithelial and immune cells as key contributors to genetic susceptibility, identifying 28 candidate genes within known risk loci and 24 in novel regions. Notably, 47% of established NSCLC susceptibility loci exhibited cell-type-specific pleiotropic genetic regulation. This study provides a valuable resource of lung sc-eQTLs and illuminates how genetic variation modulates gene expression in a cell-type-specific fashion, contributing to lung cancer susceptibility.

genetics↗

bioRxiv2025

Mechanistic basis for protection against fatty liver disease by CIDEB loss-of-function mutations

Background & AimsSomatic and germline CIDEB mutations are associated with protection from chronic liver diseases. The mechanistic basis and whether CIDEB suppression would be an effective therapy against fatty liver disease remain unclear. Methods21 CIDEB somatic mutations were introduced into cells to assess functionality. In vivo screening was used to trace Cideb mutant clones in mice fed normal chow, western (WD), and choline-deficient, L-amino acid-defined, high-fat (CDA-HFD) diets. Constitutive and conditional Cideb knockout mice were generated to study Cideb in liver disease. Isotope tracing was used to evaluate fatty acid oxidation and de novo lipogenesis. Transcriptomics, lipidomics, and metabolic analyses were utilized to explore molecular mechanisms. Double knockout models (Cideb/Atgl and Cideb/Ppara) tested mechanisms underlying Cideb loss. ResultsMost CIDEB mutations showed that they impair function, and lineage-tracing showed that loss-of-function clones were positively selected with some, but not all fatty liver inducing diets. Cideb KO mice were protected from WD, CDA-HFD, and alcohol diets, but had the greatest impact on CDA-HFD induced liver disease. Hepatocyte-specific Cideb deletion could ameliorate disease after MASLD establishment, modeling the impact of therapeutic siRNAs. Cideb loss protected livers via increased {beta}-oxidation, specifically through ATGL and PPARa activation. ConclusionsCideb deletion is more protective in some types of fatty liver disease. {beta}-oxidation is an important component of the Cideb protective mechanism. CIDEB inhibition represents a promising approach, and somatic mutations in CIDEB might predict the patient populations that might benefit the most.

physiology↗

bioRxiv2025

Two CENH3 paralogs in the green alga Chlamydomonas reinhardtii have a redundantly essential function and associate with ZeppL-LINE1 elements

Centromeres in eukaryotes are defined by the presence of histone H3 variant CENP-A/CENH3. Chlamydomonas encodes two predicted CENH3 paralogs, CENH3.1 and CENH3.2, that have not been previously characterized. We generated peptide antibodies to unique N-terminal epitopes for each of the two predicted Chlamydomonas CENH3 paralogs as well as an antibody against a shared CENH3 epitope. All three CENH3 antibodies recognized proteins of the expected size on immunoblots and had punctuated nuclear immunofluorescence staining patterns. These results are consistent with both paralogs being expressed and localized to centromeres. CRISPR-Cas9 mediated insertional mutagenesis was used to generate predicted null mutations in either CENH3.1 or CENH3.2. Single mutants were viable but cenh3.1 cenh3.2 double mutants were not recovered, confirming that the function of CENH3 is essential. We sequenced and assembled two chromosome-scale Chlamydomonas genomes from strains CC-400 and UL-1690 (a derivative of CC-1690) with complete centromere sequences for 17/17 and 14/17 chromosomes respectively, enabling us to compare centromere evolution across four isolates with near complete assemblies. These data revealed significant changes across isolates between homologous centromeres including mobility and degeneration of ZeppL-LINE1 (ZeppL) transposons that comprise the major centromere repeat sequence in Chlamydomonas. We used Cleavage Under Targets and Tagmentation (CUT&Tag) to purify and map CENH3-bound genomic sequences and found enrichment of CENH3-binding almost exclusively at predicted centromere regions. An interesting exception was chromosome 2 in UL-1690, which had enrichment at its genetically mapped centromere repeat region as well as a second, distal location, centered around a single recently acquired ZeppL insertion. The CENH3-bound regions of the 17 Chlamydomonas centromeres ranged from 63.5kb (average lower estimate) to 175kb (average upper estimate). The relatively small size of its centromeres suggest that Chlamydomonas may be a useful organism for testing and deploying artificial chromosome technologies. Significance statementHistone H3 variant CENP-A/CENH3 is a conserved centromere protein in eukaryotes but has not been well-characterized in green algae. Our data establish the function of CENH3 at Chlamydomonas centromeres and identify an unexpected strain-specific neocentromere candidate region in chromosome 2 likely caused by a single ZeppL-LINE1 insertion into a genic region that is distal to the native chromosome 2 centromere.

genetics↗

bioRxiv2025

AT1R and Integrin β3 Synergize to Drive Aortic Dissection via Non-Canonical Wnt/β-Catenin Signaling

Aortic dissection (AD), a life-threatening cardiovascular emergency, continues to impose high mortality due to insufficient therapeutic options, as monotherapy targeting angiotensin II type 1 receptor (AT1R) demonstrates limited clinical efficacy. Utilizing single-cell RNA sequencing, we identified integrin {beta}3 as a critical driver of AD progression, with expression levels positively correlated with disease severity. Histopathological validation in human AD specimens and a murine angiotensin II (AngII)-infusion model confirmed marked upregulation of integrin {beta}3 activation. Pharmacological blockade of integrin {beta}3 with Cyclo(-RGDfK) significantly attenuated aortic pathogenesis in vivo, reducing dissection incidence and aortic degeneration. Mechanistically, AngII-mediated AT1R activation induced formation of a receptor complex with integrin {beta}3, triggering its conformational activation. Transcriptomic profiling revealed that activated integrin {beta}3 potentiates vascular endothelial dysfunction by binding glycogen synthase kinase 3{beta} (GSK3{beta}), which stabilizes {beta}-catenin via a non-canonical Wnt signaling axis. This pathway drives endothelial barrier disruption, hallmarks of aortic wall destabilization in AD. Our findings unveil a previously unrecognized synergy between AT1R and integrin {beta}3, implicating aberrant Wnt/{beta}-catenin signaling as a nexus of endothelial injury in AD pathogenesis. These results advocate for a paradigm-shifting dual-therapeutic strategy concurrently targeting AT1R and integrin {beta}3 to restore vascular homeostasis, offering a mechanistically grounded approach to mitigate this lethal disease. This work bridges critical gaps in understanding AD pathophysiology and provides a transformative framework for precision therapeutics.

pharmacology and toxicology↗

bioRxiv2025

SIRT2 Mediates Integrated Stress Response by Deacetylating and Stabilizing 4EBP1 to Suppress Translation

The ability to alleviate nutrient stress, such as amino acid limitation, is crucial for cell survival. The mTORC1 complex and integrated stress response (ISR) are mechanisms that sense the availability of amino acids and regulate ribosomal protein synthesis. Here we have discovered a new SIRT2-mediated pathway, downstream of ISR, that senses the limitation of amino acids to regulate translation. Under amino acid deprivation, SIRT2 protein level is upregulated translationally by its upstream open reading frame (uORF). SIRT2 in turn suppresses global protein translation, which helps cells to survive amino acid limitation. Mechanistically, we identified eukaryotic translation initiation factor 4E (eIF4E) binding protein 1 (4EBP1), which negatively regulates translation, as a substrate of SIRT2. SIRT2 deacetylates 4EBP1 at Lys69 and stabilizes 4EBP1 by protecting it from proteasomal degradation. Our study reveals a novel role for SIRT2 in regulating protein translation and a new regulatory mechanism of 4EBP1 in cells. Our study provides a better understanding of the intricate regulation of translation and may explain the known non-oncogene addiction role of SIRT2 in cancer cells.

cell biology↗

bioRxiv2025

Termites became the dominant decomposers of the tropics after two diversification pulses

Insects have the highest species richness among animals, but the extent of their diversity and the timing of their diversification remain unclear. Insect diversification is difficult to infer due to the incompleteness of the fossil record. Phylogenetic trees of extant species reconstructed from an exhaustive sampling can be useful to address major evolutionary questions. Here, we investigated the diversification of termites, which comprise 2,995 described species, using estimates of speciation, extinction, and net diversification rates inferred from molecular phylogenies including 2,800 samples representing 1,377 putative species. Termites originated in the Early Cretaceous [~]132 million years ago. Estimated extinction rates were close to zero despite fossil evidence of extinction; therefore, we focused our interpretations on the net diversification rates. Our analyses detected two significant rate shifts. The first shift occurred at the end of the Cretaceous, initially in the Kalotermitidae, then in the Neoisoptera as they started outcompeting Kalotermitidae. The second shift involved multiple lineages of Neoisoptera, especially Termitidae, which diversified as they colonized the world after the global cooling initiated at the Eocene-Oligocene transition. Our results indicate that termites became the dominant insect decomposers of tropical ecosystems as global climate change impacted ecosystems.

evolutionary biology↗

bioRxiv2025

Construction of Complete Telomere-to-Telomere Genome Assembly of the Rabbit Using Haploid Embryonic Stem Cells

The rabbit owns commercial importance in meat and fur production, and also has long served as a valuable animal model in biomedical research. Yet, the complete assembly of a high-quality rabbit reference genome has not been established. Here, we present a telomere-to-telomere (T2T) genome assembly of the New Zealand White (NZW) rabbit, the most complete and accurate rabbit genome to date. Using a haploid embryonic stem cells (haESCs) to overcame the challenges of homologous sequence interference and structural variation, we generate a genome with a contig N50 of 137.71 Mb, anchoring all chromosomes with only three gaps, through integrating long-read sequencing (PacBio HiFi, Oxford Nanopore), Hi-C, and Illumina data. Quality assessments reveal near-complete coverage of the BUSCO mammalian gene set, with 99.61% completeness. Notably, this complete assembly allowed for the first comprehensive annotation of the rabbit immunoglobulin loci and major histocompatibility complex region, which were previously unresolved in earlier genome versions. The NZW-T2T assembly based on haESCs not only provides a critical resource for advancing rabbit-based research, but also set a new benchmark for de novo genome assembly for other animals with complex genome.

genomics↗

bioRxiv2025

TMEM41B Contributes to Atherosclerosis by Promoting Lipid Synthesis in Vascular Smooth Muscle Cells via Fatty Acid Synthase Stabilization

Foam cell formation has traditionally been attributed to macrophages; however, emerging evidence highlights vascular smooth muscle cells (VSMCs) as another significant contributor. Here, we found TMEM41B is significantly upregulated in VSMCs of both human atherosclerotic (AS) lesions and murine models. VSMCs specific silencing TMEM41B expression in apolipoprotein E-deficient (ApoE-/-) mice markedly reduced plaque size and macrophage infiltration. Overexpressing TMEM41B in cultured VSMCs alters intracellular lipid profiles through stabilizing fatty acid synthase (FASN), a crucial enzyme in fatty acids synthesis, via inhibiting its ubiquitination and degradation. The TMEM41B/FASN axis drives lipid synthesis, promotes intracellular lipid storage, and facilitates the release of pro-inflammatory cytokines. Further, herpes simplex virus (HSV) infection amplified TMEM41B expression via OCT-1-mediated transcriptional activation, linking viral infection to lipid metabolic reprogramming in AS. These findings redefine the paradigm of VSMC-derived foam cell formation and suggest that targeting the TMEM41B/FASN axis could offer a transformative therapeutic strategy for AS, particularly in patients with HSV infection.

molecular biology↗

bioRxiv2025

Spermatogonia derived RpS13 non-autonomously regulates the cyst cell differentiation via Rho1-mediated adhesion junctions in Drosophila testis

ObjectiveIn the testis of Drosophila, spermatogonia transit-amplification (TA) divisions are necessary for germline proliferation and differentiation. Both the germline and the surrounding somatic cyst cells (SCCs) have a significant influence on these processes. However, the underlying mechanism is largely unknown. MethodsFlies were used to generate tissue-specific gene knockdown. Immunofluorescence was used to determine protein localization and expression pattern. Small interfering RNAs were used to knockdown genes in S2 cells. qRT-PCR was used to examine the relative mRNA expression level. ResultsOur findings indicate that spermatogonial RpS13 regulates cyst cell growth through a non-autonomous manner. In terms of mechanism, RpS13 may regulate the adhesion junctions of the soma-germline via the DE-cad and Arm proteins in addition to dpERK, which is found in SCCs. Interestingly, Rho1 and RpS13 mutually inhibit each other in Drosophila S2 cells. Additionally, Rho1 controlled cell adhesions that rely on DE-cad, Arm, and dpERK and imitated the actions of RpS13 in Drosophila testis. ConclusionAll of these findings implied that during spermatogonia TA-divisions in the testis of Drosophila, RpS13 regulates the development of cyst cells via Rho1-mediated adhesion junctions.

developmental biology↗

bioRxiv2025

AMULETY: A Python package to embed adaptive immune receptor sequences

Large language models have been developed to capture relevant features of adaptive immune receptors, each with unique potential applications. However, the diversity in available models presents challenges in accessibility and usability for downstream applications. Here we present AMULETY (Adaptive imMUne receptor Language model Embedding Tool), a Python-based software package to generate language model embeddings for adaptive immune receptor sequences, enabling users to leverage the strengths of different models without the need for complex configuration. AMULETY offers functions for embedding adaptive immune receptor amino acid sequences using pre-trained protein or antibody language models for paired heavy and light chain or single chain sequences. We showcase the variability on the embedding space for several embeddings on a dataset of antibody binders to several SARS-CoV-2 epitopes and showed that different models may be effective at capturing different aspects of the distinctions between epitope groups. AMULETY is available under GPL v3 license from https://github.com/immcantation/amulety or via pip from the Python Package Index (PyPI) from https://pypi.org/project/amulety/. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=164 SRC="FIGDIR/small/644583v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1c0bafaorg.highwire.dtl.DTLVardef@337816org.highwire.dtl.DTLVardef@111136forg.highwire.dtl.DTLVardef@1300dc_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Biphasic bactericidal activity of nitroxoline against Acinetobacter baumannii isolates from urinary tract infections

Acinetobacter baumannii is a critical pathogen which can cause hospital-acquired infections, particularly urinary tract infections (UTIs). The antimicrobial resistance (AMR) of A. baumannii is rising which poses a significant challenge to clinical management. Nitroxoline, an old antibiotic for treating uncomplicated UTIs, has gained renewed interest as a potential therapeutic option. Here, we investigates the bactericidal activity of nitroxoline against 34 A. baumannii (17 carbapenem-resistant and 17 carbapenem-sensitive isolates) collected from UTI patients. Nitroxoline exhibited a biphasic bactericidal effect, characterized by enhanced efficacy up to an optimal bactericidal concentration (OBC), followed by declined activity at higher nitroxoline concentrations. The OBCs, minimum bactericidal concentration (MBC), minimum inhibitory concentration (MIC), and time-killing curves were evaluated to elucidate bactericidal activity. Raman deuterium stable isotope probing (Raman-DIP) was employed to validate nitroxolines bactericidal effect and its impact on bacterial metabolic activity and survival rates. These results demonstrate that nitroxoline exhibits excellent inhibitory and bactericidal activity against A. baumannii. While nitroxoline exhibits biphasic bactericidal activity with OBC50/90 values of 4/8 mg/L. Raman spectroscopy identified a decreased C-D ratio as nitroxoline concentration increased, indicating reduced metabolic activity. Notably, an inverse correlation (r = -0.7594, p <0.0001) was observed between bacterial survival and the ccratio at concentrations above the OBC. These findings underscore the necessity of optimizing dosing regimens to enhance nitroxolines therapeutic efficacy and alleviate AMR development. Raman-DIP emerges as a robust tool for assessing nitroxolines effects on bacterial metabolism and determining MIC, offering valuable insights for future clinical applications.

microbiology↗

bioRxiv2025

Manganese suppresses tumor growth through hyper-activating IRE1α

IRE1 and its downstream XBP1 signal is the most conserved unfolded protein response pathway that cells utilize to combat endoplasmic reticulum stress, also known to be utilized by tumor cells to adapt to harsh environment, leading to tumor progression. Several inhibitors against IRE1 have been developed, some of which show promising effect in clinical trial for cancer therapy, but none of them have been used in practice. Considering that hyper-activation of IRE1 induces cell death, we hypothesize that activation of IRE1 could be an alternative way for tumor suppression. Here, we identified divalent manganese ion as a potent activator to IRE1, which interacts with the cytosolic part of IRE1 directly, augmenting the downstream pro-apoptotic pathway but not the pro-survival outcome. Mn2+ limits tumor growth in xenograft model in an IRE1-dependent way. Our finding suggests pharmacological activation of IRE1 as an underestimated but promising way in cancer therapy. HighlightsO_LIMn2+ binds to cytosolic segment of IRE1 and promotes its oligomerization C_LIO_LIMn2+ hyper-activates IRE1 and induces downstream terminal UPR under ER stress C_LIO_LIMn2+ does not elevate XBP1s expression C_LIO_LIMn2+ as an IRE1 activator impairs tumor growth in xenograft model C_LI

cancer biology↗

bioRxiv2025

Interstitial fluid transport dynamics predict glioblastoma invasion and progression

Glioblastoma is characterized by aggressive infiltration into surrounding brain tissue, hindering complete surgical resection and contributing to poor patient outcomes. Identifying tumor-specific invasion patterns is essential for advancing our understanding of glioblastoma progression and improving surgical and radiotherapeutic strategies. Here, we leverage in vivo dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) to noninvasively quantify interstitial fluid velocity, direction, and diffusion within and around glioblastomas. We introduce a novel vector-based pathline analysis to trace downstream accumulation of fluid flow originating from the tumor core, providing a spatially explicit perspective on local flow patterns. We find that localized fluid transport metrics predict glioblastoma invasion and progression, offering a new framework to non-invasively identify high-risk regions and guide targeted treatment approaches. One sentence summaryInvasion and progression of glioblastoma can be predicted with interstitial fluid flow patterns via magnetic resonance imaging.

bioengineering↗

bioRxiv2025

RamEx: An R package for high-throughput microbial ramanome analyses with accurate quality assessment

Microbial single-cell Raman spectroscopy (SCRS) has emerged as a powerful tool for label-free phenotyping, enabling rapid characterization of microbial diversity, metabolic states, and functional interactions within complex communities. However, high-throughput SCRS datasets often contain spectral anomalies from noise and fluorescence interference, which obscure microbial signatures and hinder accurate classification. Robust algorithms for outlier detection and microbial ramanome analysis remain underdeveloped. Here, we introduce RamEx, an R package specifically designed for high-throughput microbial ramanome analyses with robust quality control and phenotypic classification. At the core of RamEx is the Iterative Convolutional Outlier Detection (ICOD) algorithm, which dynamically detects spectral anomalies without requiring predefined thresholds. Benchmarking on both simulated and real microbial datasets--including pathogenic bacteria, probiotic strains, and yeast fermentation populations--demonstrated that ICOD achieves an F1 score of 0.97 on simulated datasets and 0.74 on real datasets, outperforming existing approaches by at least 19.8%. Beyond anomaly detection, RamEx provides a modular and scalable workflow for microbial phenotype differentiation, taxonomic marker identification, metabolic fingerprinting, and intra-population heterogeneity analysis. It integrates Raman-based species-specific biomarkers, enabling precise classification of microbial communities and facilitating functional trait mapping at the single-cell level. To support large-scale studies, RamEx incorporates C++ acceleration, GPU parallelization, and optimized memory management, enabling the rapid processing of over one million microbial spectra within an hour. By bridging the gap between high-throughput Raman-based microbial phenotyping and computational analysis, RamEx provides a comprehensive toolkit for exploring microbial ecology, metabolic interactions, and antibiotic susceptibility at the single-cell resolution. RamEx is freely available under the MIT license at https://github.com/qibebt-bioinfo/RamEx.

bioinformatics↗

bioRxiv2025

Targeting dCas9-SunTag to a susceptibility gene promoter is sufficient for CRISPR interference

Cassava production in sub-Saharan Africa is severely impacted by diseases. Most pathogens require interaction with host susceptibility factors to complete their life cycles and cause disease. Targeted DNA methylation is an epigenetic strategy to alter gene expression in plants and we previously reported that a zinc-finger fused to DMS3 could establish methylation at the promoter of MeSWEET10a, a bacterial susceptibility gene, and this resulted in decreased disease. Here, we attempt a similar strategy for cassava brown streak disease. This disease is caused by the ipomoviruses CBSV and UCBSV. These viruses belong to the family Potyviridae, which has been shown extensively to require host eIF4E-family proteins to infect plants and cause disease. We previously found that cassava plants with simultaneous knockout mutations in two eIF4E genes, nCBP-1 and nCBP-2, resulted in decreased susceptibility to CBSD. Here, we report successful simultaneous targeting of both promoters with methylation using a dCas9-DMRcd-SunTag system. However, in contrast to our previous work with MeSWEET10a, controls indicate that CRISPR interference is occurring in these lines and is sufficient for reduction of gene expression. Future research will use genetic crosses to segregate away the DNA methylation reagents and, if DNA methylation proves heritable, assess whether methylation alone is sufficient increase resistance to CBSD.

plant biology↗