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Rosenthal, A.

Publications and source records attributed to Rosenthal, A..

At least 19 recordsLinked to original sources

Predicting alcohol consumption from resting-state functional connectivity: Feature relevance and the potential of meta-matching.

Alcohol use disorder (AUD) is among the most prevalent mental disorders. Associations between resting-state fMRI functional connectivity (FC) and AUD have been reported but rarely replicated. In this preregistered study, we investigated the extent to which FC predicts alcohol consumption, as measured by the AUDIT-C score, in a large sample of non-treatment-seeking alcohol consumers (N = 739), including 528 participants with varying degrees of AUD severity. To optimize performance, we compared kernel ridge regression (KRR) trained directly on this sample with transfer-learning models based on multilayer meta-matching embeddings, from which we derived data-driven relevance maps at the connection, region, and network levels. We tested split-half reliability, reproducibility across cohorts, and outcome specificity of the relevance maps. Both models predicted AUDIT-C scores moderately but significantly (r {approx} 0.15). Meta-matching did not outperform KRR in prediction. Relevance maps showed limited split-half reliability, consistent with the modest predictive performance, but reproduced moderately well across two independent cohorts. These maps indicate reduced connectivity among limbic regions, the anterior middle temporal gyrus, the dorsomedial prefrontal cortex, and dorsal attention network regions. In contrast, hypothesized hyperconnectivity patterns involving the striatum, anterior cingulate cortex, and precuneus were less reliable and mostly non-significant. Overall, our findings suggest that resting-state FC contains reproducible but weak signals related to alcohol consumption. Transfer learning improved relevance-map reliability but not prediction performance and reduced outcome specificity. These results support the utility of interpretable machine learning for identifying connectivity patterns related to drinking behavior, while also highlighting current limitations in its predictive power.

neuroscience↗

Temporal dynamics of RNA phage infection reveal bacterial recovery despite ongoing viral replication

Bacterial defenses against DNA phages are well documented, yet responses to RNA phages remain largely unexplored. Here, we characterize the population dynamics and host responses of Escherichia coli infected by the lytic RNA phage MS2 across multiple timescales, using bulk and single-cell transcriptomics, fluorescence microscopy, whole-genome sequencing, and genetic perturbations. Despite rapid viral takeover and extensive cell death, the bacterial population subsequently rebounds, revealing an unusual state in which host proliferation persists under intense phage pressure. Early in infection, heterogeneous subpopulations are evident, including one with low or undetectable viral transcript levels, low expression of the F-plasmid genes encoding the F-pilus (the MS2 receptor), and a distinct metabolic state. Strikingly, the rebounding population carries MS2 RNA in the great majority of cells, with evidence for active viral replication and continued cell division despite high viral loads. This rebound coincides with strong induction of biofilm-associated genes, including the pga operon, which synthesizes the biofilm-matrix exopolysaccharide PNAG. Deletion of pgaA causes earlier population decline and reduced population survival, indicating that pga-dependent matrix production delays viral lysis. Over longer timescales, phage-exposed populations show heterogeneous F-plasmid prevalence and plasmid-wide expression, consistent with dynamic cycling between plasmid-bearing and plasmid-free states: MS2 selects against F-plasmid-bearing cells, whereas conjugation may restore plasmid carriage. We propose that the biofilm-associated matrix delays viral lysis relative to continued cell division, long enough for rare F-plasmid-free daughter cells to arise and expand. Our results suggest that bacterial survival is determined by a dynamic race between viral lysis and host-cell division.

microbiology↗

Impaired Control Symptoms in Alcohol Use Disorder Show Convergent Associations Across Behavioral and Neural Markers of Inhibitory Control and Drinking Behavior

Background: Deficits in inhibitory control are considered a central feature of alcohol use disorder (AUD), yet behavioral and neuroimaging findings have been inconsistent. One potential explanation is the marked heterogeneity of AUD, which encompasses multiple symptom dimensions that may differ in their underlying neurocognitive mechanisms. In this study, we investigated whether behavioral and neural markers of inhibitory control are associated with specific DSM-5 AUD symptom domains. Methods: A total of 589 participants (432 with non-treatment seeking AUD, 157 controls) completed a Stop-Signal Task (SST) during fMRI. Associations between DSM-5 symptom domains (impaired control over alcohol use, risky use, social problems, physical dependence) and SST performance, inhibition-related brain activation, and alcohol consumption were examined. Real-life drinking behavior was additionally assessed over 12 months using ecological momentary assessment (EMA). Results: Greater impaired control symptom severity was associated with poorer performance on go trials and diminished post-error slowing during SST. At the neural level, higher impaired control symptom severity was associated with reduced activation across fronto-insular, parietal, cingulate, supplementary motor, and cerebellar regions. In contrast, other symptom domains showed little to no associations with inhibition-related behavioral or neural measures. Higher impaired control symptom severity was associated with greater alcohol consumption across questionnaire-based and EMA-based assessments. Conclusions: In this large cohort, altered behavioral performance and recruitment of inhibition-related brain regions in the SST was selectively linked to impaired control symptoms. These findings highlight the importance of symptom-based approaches for understanding heterogeneity in addiction and may inform the development of more targeted interventions.

neuroscience↗

Gene conversion is a key driver of diversity hotspots in M. tuberculosis antigens and virulence-associated loci

Despite the long-held view of Mycobacterium tuberculosis (Mtb) as a genetically conserved pathogen, many genomic regions remain poorly resolved due to high sequence homology and repetitive content. Using complete genome assemblies generated from long-read sequencing of 151 globally representative clinical isolates, we comprehensively analyzed genome-wide patterns of genetic diversity and evolution across the Mtb genome. Our analysis uncovers pronounced diversity hotspots within paralogous regions generated by recurrent gene conversion between homologous genes. In many cases, these hotspots exhibit more than an order of magnitude greater genetic diversity than the rest of the Mtb genome, which is otherwise characterized by remarkably low variation. Mutations within these regions display clustered substitution patterns, excess paralog-matching variants, and distinct mutational spectra consistent with ongoing gene conversion. Our analysis identifies over 300 individual gene conversion events distributed throughout the Mtb phylogeny. These gene conversion events occur predominantly within gene families associated with virulence and host-pathogen interactions, including the PE, PPE, and ESX families. Several of the most pronounced diversity hotspots occur in antigens encoded within paralogous regions. Among these, the vaccine candidate PPE18 harbors mutations in validated epitope sequences and predicted alterations in HLA-II binding. Together, these findings demonstrate that gene conversion actively shapes antigenic and virulence-associated diversity in Mtb.

genomics↗

RNA Quality Control Enables Antibiotic Tolerance

The mechanisms underlying adaptation to antibiotic pressure within complex host environments remain incompletely understood. By experimentally evolving Streptococcus pneumoniae subjected to various antibiotics and immune states, we demonstrate populations adopting distinct adaptive strategies depending on specific selective context. General antibiotic stress drives convergent mutations in rny, encoding the RNA degradosome scaffold RNase Y, that exhibit broad-spectrum antibiotic tolerance and accelerated recovery. Single-cell transcriptomics revealed antibiotic-induced death is driven by transcriptional collapse, a catastrophic loss of RNA quantity and integrity. In contrast, rny mutants avert this via a bet-hedging strategy: a resilient minority maintains a baseline transcriptional profile, while a quiescent majority undergoes selective RNA degradation to preserve transcript fidelity. Upon stress removal, these populations execute a prioritized transcriptional ribosomal reboot, facilitating accelerated recovery. These findings identify RNA turnover as a tunable master regulator to survive combined pressures of antibiotics and immunity.

microbiology↗

In Situ Photoactivated Hydrogel Adhesive Dressings for Post Colon Polypectomies (PolypCures)

Colon polypectomy is a widely performed endoscopic procedure that reduces the incidence of colorectal cancer but leaves exposed colonic wounds susceptible to bleeding, perforation, and infection. The current standard of wound care, mechanical clips, is limited by technical complexity, high cost, and poor efficacy for large (> 2 cm in diameter) or difficult-to-access lesions. Here, we present PolypCure, an in situ photoactivated hydrogel adhesive dressing delivered via a single catheter, through either oozing or spraying methods, to achieve rapid, spatiotemporally controlled sealing and hemostasis (within 2 min) of colon lesions using the white light source integrated into standard endoscopic instruments. The hydrogel, composed of norbornene- and thiol-functionalized polyethylene glycol, carboxymethyl cellulose, and Eosin Y, exhibits mechanical properties comparable to colon tissue (G [~] 6 kPa), strong shear strength (> 15 kPa), low swelling (< 200%), and small pore size ([~] 20 {micro}m), ensuring long-term stability (up to 30 days) and protection against bacterial infiltration. The formulation also demonstrates biocompatibility and hemocompatibility. In an in vivo pig colon endoscopic mucosal resection (EMR) model, PolypCure fully adheres to large lesions for at least 3 days and promotes early-stage wound healing. Overall, PolypCure is a promising solution to wound management post-polypectomy.

bioengineering↗

Integrative analysis of pooled CRISPR screens provide functional insights into AD GWAS risk genes

Emerging research has implicated Alzheimers disease (AD) pathology with dysregulation of many key pathways in microglia, including lipid transport and metabolism, phagocytosis of plaques, and lysosomal function. However, the exact mechanisms underlying these pathways remain poorly understood. Leveraging high-throughput CRISPR screens to understand the interplay between these pathways may enable novel therapeutic strategies for AD and other neurological diseases. Here, we constructed activation and interference CRISPRa/i libraries targeting 203 genes, 71 of which were identified through neurodegenerative GWAS, and 132 additional genes linked to microglial functions. We used this library to conduct pooled CRISPRa/i screens across a range of functional assays relating to lipid metabolism and lysosomal function using a monocytic cell line, THP-1. We identified a core set of lipid and lysosome mediators and validated a subset in primary macrophages. To gain insights into transcriptional states modulated by these genes we also applied the CRISPRa/i libraries to Perturb-seq, enabling us to capture transcriptomic changes. Through non-negative matrix factorization, we identified five gene programs altered by our perturbation library. We then used an integrative analysis of functional screen data with Perturb-seq data that enabled us to uncover novel functions and genetic relationships between perturbations. This multidimensional resource links genetic perturbations to phenotypes and transcriptional programs, establishing a scalable framework for systematic gene discovery in neurodegeneration and beyond. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC="FIGDIR/small/660041v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@5b2acborg.highwire.dtl.DTLVardef@156a0b1org.highwire.dtl.DTLVardef@4fdbb8org.highwire.dtl.DTLVardef@e2166c_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

genetics↗

Simultaneous measurements of translation rate and transcriptome in single bacterial cells by scTR-seq uncovers linked regulation within a specialized active cell population.

Cell-to-cell variation within clonal bacterial populations provides bacterial communities important advantages including opportunities for bet-hedging and metabolic division of labor. In recent years the extent of bacterial heterogeneity has been documented both at the transcriptome level and with physiological measurements of cell growth rate and translation rate. However, methods that link physiological parameters to a single cells full transcriptomic state are lacking, making it difficult to identify the regulatory mechanisms that couple physiology and transcriptional output. Here we introduce a method that combines click-chemistry enabled labeling of nascent polypeptides to measure translation rates in single cells alongside microfluidic encapsulation and single cell transcriptomic measurements, providing a tandem measurement of translation rate and transcriptome in thousands of single Bacillus subtilis cells. In a culture experiencing nutrient limitation, we identified a subpopulation of cells with a higher rate of protein translation that uniquely overexpresses genes for several metabolic processes including acetoin production and arginine synthesis. Using a genetic approach informed by the gene expression in this subpopulation, we identified a regulatory mechanism that couples the increase in protein abundance of a transcriptional regulator AlsR with expression of alsR regulated genes in this subpopulation.

microbiology↗

The Alzheimers Disease Risk Genes MS4A4A And MS4A6A Cooperate to Negatively Regulate Trem2 and Microglia states

Genetic variations in MS4A4A and MS4A6A are linked to the regulation of cerebrospinal fluid soluble TREM2 (sTREM2) levels and are associated with Alzheimers disease (AD) risk and progression. Using CRISPR knockout and MS4A4A-degrading antibodies in primary human microglia, non-human primates (NHP), and a xenotransplantation model of amyloid pathology, we provide evidence that MS4A4A and MS4A6A are negative regulators of both the transmembrane and soluble TREM2 proteins. They also negatively regulate microglia proliferation, survival, metabolism, lysosomal function, energetics, phagocytosis, and disease-fighting states. Mechanistically, we find that MS4A4A exerts negative regulation by interacting with MS4A6A and protecting it from degradation. MS4A6A in turn forms a complex with and blocks the co-receptor DAP12, which is required for the stability, cell surface localization, and signaling of TREM2 and other receptors. Taken together, the data indicate that MS4A4A and MS4A6A are cooperating, post-transcriptional negative regulators of TREM2 and microglial function, and potential drug targets for AD.

neuroscience↗

Heartbeat perception is causally linked to frontal delta oscillations

The ability to accurately perceive ones own bodily signals, such as the heartbeat, plays a vital role in physical and mental health. However, the neurophysiological mechanisms underlying this ability, termed interoception, are not fully understood. Converging evidence suggests that cardiac rhythms are linked to frontal brain activity, particularly oscillations in the delta (0.5 - 4 Hz) band, but their causal relationship remained elusive. Using amplitude-modulated transcranial alternating current stimulation (AM-tACS), a method to enhance or suppress brain oscillations in a phase-specific manner, we investigated whether frontal delta oscillations are causally linked to heartbeat perception. We found that enhancement of delta phase synchrony suppressed heartbeat detection accuracy, while suppression of delta phase synchrony enhanced heartbeat detection accuracy. These findings suggest that frontal delta oscillations play a critical role in heartbeat perception, paving the way for causal investigations of interoception and potential clinical applications. SignificanceAlthough bodily signals are known to influence perception and behavior, little is known about the underlying neurophysiological mechanisms. Here, we show that perception of the heartbeat is anticorrelated with phase synchrony of frontal delta oscillations, and that modulating these oscillations with transcranial electric stimulation influences heartbeat perception. Our results suggest that delta oscillations play a key role in processing bodily signals, with potential implications for theories of emotions and clinical neuroscience.

neuroscience↗

Analysis of the limited M. tuberculosis accessory genome reveals potential pitfalls of pan-genome analysis approaches

Pan-genome analysis is a fundamental tool for studying bacterial genome evolution; however, the variety of methods used to define and measure the pan-genome poses challenges to the interpretation and reliability of results. To quantify sources of bias and error related to common pan-genome analysis approaches, we evaluated different approaches applied to curated collection of 151 Mycobacterium tuberculosis (Mtb) isolates. Mtb is characterized by its clonal evolution, absence of horizontal gene transfer, and limited accessory genome, making it an ideal test case for this study. Using a state-of-the-art graph-genome approach, we found that a majority of the structural variation observed in Mtb originates from rearrangement, deletion, and duplication of redundant nucleotide sequences. In contrast, we found that pan-genome analyses that focus on comparison of coding sequences (at the amino acid level) can yield surprisingly variable results, driven by differences in assembly quality and the softwares used. Upon closer inspection, we found that coding sequence annotation discrepancies were a major contributor to inflated Mtb accessory genome estimates. To address this, we developed panqc, a software that detects annotation discrepancies and collapses nucleotide redundancy in pan-genome estimates. When applied to Mtb and E. coli pan-genomes, panqc exposed distinct biases influenced by the genomic diversity of the population studied. Our findings underscore the need for careful methodological selection and quality control to accurately map the evolutionary dynamics of a bacterial species.

bioinformatics↗

Genetic diversity within diagnostic sputum samples is mirrored in the culture of Mycobacterium tuberculosis

Culturing Mycobacterium tuberculosis (MTB) from tuberculosis cases is the basis for many research and clinical applications. Paradoxically, it is assumed to impose a diversity bottleneck, which, if true, would entail unexplored consequences. The alternative, culture-free sequencing from diagnostic samples, is a promising but challenging approach both to obtain and analyse the MTB genome from the complex sample. This study obtains high-quality genomes of sputum-culture pairs from two different settings after developing a workflow for sequencing from sputum and a tailored bioinformatics pipeline. Our approach reveals that 88% of variants called in culture-free sequencing analysis are false positives due to supplementary alignments, mostly in enriched-sputa samples. Overall, contrary to the bottleneck dogma, we identify a 97% variant agreement within sputum-culture pairs, with a high correlation also in the variants frequency (0.98). Our findings extrapolate to all publicly available data, thus demonstrating that in most cases culture accurately mirrors clinical samples.

genomics↗

The multi-Siglec inhibitor AL009 reprograms suppressive macrophages and activates innate and adaptive tumor immunity

Sialic acid-binding immunoglobulin-type lectins (Siglecs) are cell surface receptors that regulate innate and adaptive immunity, with inhibitory Siglecs promoting immune tolerance. In the tumor microenvironment, overexpression of sialic acid glycans exploits inhibitory Siglec signaling, leading to a cancer-permissive phenotype. AL009 is an engineered Siglec-9-Fc fusion molecule that functions as a sialic acid trap and reprograms suppressive macrophages to activate an anti-tumor immune response. AL009 treatment of human myeloid-derived suppressor cells, an in vitro model of tumor-associated macrophages, resulted in an increase in proinflammatory cytokines and chemokines, changes in cell surface markers, and potent relief of T cell inhibition in a co-culture assay. In syngeneic mouse (Mus musculus) tumor models, AL009 engineered with a mouse Fc (AL009m) reduced tumor growth as a monotherapy and in combination with the checkpoint inhibitor anti-PD-L1. In addition, AL009m synergized with the tumor-targeting therapy anti-TRP1 to reduce lung nodules in the B16-F10 intravenous model. Pharmacodynamic marker analysis in syngeneic and humanized mouse tumor models supported an AL009 mechanism of action based on reprogramming tumor-associated macrophages and enhanced T cell activation. Future clinical studies are warranted to further elucidate the safety and efficacy of AL009.

cancer biology↗

Modifying Pavlovian-To-Instrumental Transfer By Approach Avoidance Training In Healthy Subjects - A Proof of Concept Study

The modulation of instrumental action by conditioned Pavlovian cues is hypothesized to play a role in the emergence and maintenance of maladaptive behavior. The Pavlovian-to-instrumental transfer (PIT) task is designed to examine the magnitude of the influence of cues on behavior and we aim to manipulate the motivational value of Pavlovian cues to reduce their effect on instrumental responding. To this end, we utilized a joystick-based modification of approach and avoidance propensities that has shown success in clinical populations. In 35 healthy subjects, we examined changes in PIT after completion of either avoidance training or sham training. We found no effect of training on approach avoidance propensities but higher response rate towards negative stimuli during PIT after systematic avoidance training compared to sham training. On the other hand, we saw an increased PIT effect after sham training. These results imply that training can alter the strength of the influence of cues on instrumental behavior and suggest training to be beneficial in reducing environmental triggers of maladaptive behavior.

neuroscience↗

Comparative analysis of machine learning algorithms on the microbial strain-specific AMP prediction

The evolution of drug-resistant pathogenic microbial species is a major global health concern. Naturally occurring, antimicrobial peptides (AMPs) are considered promising candidates to address antibiotic resistance problems. A variety of computational methods have been developed to accurately predict AMPs. The majority of such methods are not microbial strain-specific (MSS): they can predict whether a given peptide is active against some microbe, but cannot accurately calculate whether such peptide would be active against a particular microbial strain. Due to insufficient data on most microbial strains, only a few MSS predictive models have been developed so far. To overcome this problem, we developed a novel approach that allows to improve MSS predictive models (MSSPM), based on properties, computed for AMP sequences and characteristics of genomes, computed for target microbial strains. New models can perform predictions of AMPs for microbial strains that do not have data on peptides tested on them. We tested various types of feature engineering as well as different machine learning (ML) algorithms to compare the predictive abilities of resulting models. Among the ML algorithms, Random Forest and AdaBoost performed best. By using genome characteristics as additional features, the performance for all models increased significantly--on average by 7%--relative to models relying on AMP sequence-based properties only. Our novel MSS AMP predictor is freely accessible as part of DBAASP database resource at https://dbaasp.org/tools?page=genome-prediction

bioinformatics↗

Genomic sequence characteristics and the empiric accuracy of short-read sequencing

BackgroundShort-read whole genome sequencing (WGS) is a vital tool for clinical applications and basic research. Genetic divergence from the reference genome, repetitive sequences, and sequencing bias, reduce the performance of variant calling using short-read alignment, but the loss in recall and specificity has not been adequately characterized. For the clonal pathogen Mycobacterium tuberculosis (Mtb), researchers frequently exclude 10.7% of the genome believed to be repetitive and prone to erroneous variant calls. To benchmark short-read variant calling, we used 36 diverse clinical Mtb isolates dually sequenced with Illumina short-reads and PacBio long-reads. We systematically study the short-read variant calling accuracy and the influence of sequence uniqueness, reference bias, and GC content. [a] ResultsReference based Illumina variant calling had a recall [&ge;]89.0% and precision [&ge;]98.5% across parameters evaluated. The best balance between precision and recall was achieved by tuning the mapping quality (MQ) threshold, i.e. confidence of the read mapping (recall 85.8%, precision 99.1% at MQ [&ge;] 40). Masking repetitive sequence content is an alternative conservative approach to variant calling that maintains high precision (recall 70.2%, precision 99.6% at MQ[&ge;]40). Of the genomic positions typically excluded for Mtb, 68% are accurately called using Illumina WGS including 52 of the 168 PE/PPE genes (34.5%). We present a refined list of low confidence regions and examine the largest sources of variant calling error. ConclusionsOur improved approach to variant calling has broad implications for the use of WGS in the study of Mtb biology, inference of transmission in public health surveillance systems, and more generally for WGS applications in other organisms.

bioinformatics↗

Metabolic fate of human immunoactive sterols in Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) infection is among top ten causes of death worldwide, and the number of drug-resistant strains is increasing. The direct interception of human immune signaling molecules by Mtb remains elusive, limiting drug discovery. Oxysterols and secosteroids regulate both innate and adaptive immune responses. Here we report a functional, structural, and bioinformatics study of Mtb enzymes initiating cholesterol catabolism and demonstrated their interrelation with human immunity. We show that these enzymes metabolize human immune oxysterol messengers. Rv2266, the most potent among them, can also metabolize vitamin D3 (VD3) derivatives. High-resolution structures show common patterns of sterols binding and reveal a site for oxidative attack during catalysis. Finally, we designed a compound that binds and inhibits three studied proteins. The compound shows activity against Mtb H37Rv residing in macrophages. Our findings contribute to molecular understanding of suppression of immunity and suggest that Mtb has its own transformation system resembling the human phase I drug-metabolizing system.Competing Interest StatementA.Gi. and E.S. are employees of MT-Medicals LLC. The other authors declare no competing interests.View Full Text

biochemistry↗

Prediction of multiple drug resistant pulmonary tuberculosis against drug sensitive pulmonary tuberculosis by CT nodular consolidation sign

Multidrug-resistant tuberculosis (mdrtb) refers to TB infection resistant to at least two most powerful anti-TB drugs, isoniazid and rifampincin. It has been estimated that globally 3.5% (which can be much higher in some regions) of newly diagnosed TB patients, and 20.5% of previously treated patients had mdrtb. Extensively drug-resistant TB (xdrtb) has resistance to rifampin and isoniazid, as well as to any member of the quinolone family and at least one of the second line injectable drugs: kanamycin, amikacin and capreomycin. xdrtb accounts for 4-20% of mdrtb. Early detection and targeted treatment are priorities for mdrtb/xdrtb control. The suspicion of mdr/xdr -pulmonary TB (mdrptb or xdrptb) by chest imaging shall suggest intensive diagnostic testing for mdrptb/xdrptb. We hypothesize that multiple nodular consolidation (NC) may serve one of the differentiators for separating dsptb vs mdrptb/xdrptb cases. For this study, mdrptb cases (n=310) and XDR-PTB cases ([xcap]=I58) were from the NIAID TB Portals Program (TBPP) . Drug sensitive pulmonary TB (dsptb) cases were from the TBPP collection (n=112) as well as the Shenzhen Center for Chronic Disease Control (n=111), Shenzhen, China, and we excluded patients with HIV(+) status. Our study shows NC, particularly multiple NCs, is more common in mdrptb than in dsptb, and more common in xdrptb than in mdrptb. For example, 2.24% of dsptb patients, 13.23% of mdrptb patients, and 20.89% of xdrptb patients, respectively, have NCs with diameter >= 10mm equal or more than 2 in number.

pathology↗