Biology subjects

Rosenberg, M.

Publications and source records attributed to Rosenberg, M..

15 recordsLinked to original sources

bioRxiv2026

Incomplete killing by antimicrobial metals generates transient antibiotic tolerance via delayed recovery in Escherichia coli

Incomplete killing is common after application of disinfectants or use of antimicrobial surfaces, leaving behind bacterial survivors with poorly characterized physiology. Here, we investigated the effects of short biocidal exposure to the common antimicrobial metals copper and silver as metal ions in suspension or under semi-dry conditions on solid metallic surfaces used against Escherichia coli. Survivors exhibited delayed regrowth and increased tolerance to bactericidal antibiotics without changes in MIC, consistent with a transient, non-genetic tolerance phenotype. When the magnitude of killing by silver or copper was matched between exposure formats, antibiotic tolerance patterns converged across metals and exposure conditions, indicating that the survivor state is governed more strongly by the severity of the primary lethal stress than by metal identity or exposure format alone. Incremental copper exposure revealed a dose- dependent increase in delayed regrowth and antibiotic tolerance but reduced tolerance to subsequent copper exposure. Post-exposure antibiotic tolerance as well as copper hypersensitivity phenotypes reverted after regrowth. Together, this supports a model of injury-linked delayed recovery rather than generalized stress priming. These findings demonstrate that incomplete disinfection can reshape survivor physiology, transiently increasing antibiotic tolerance through combined effects of selective survival acting on pre-existing phenotypic heterogeneity and acute injury-linked delayed recovery.

microbiology↗

bioRxiv2026

Development of a Fully Non-Viral 1XX-enhanced BCMA CAR-T Cell Therapy for Multiple Myeloma

Multiple myeloma (MM) is a clonal plasma cell malignancy characterized by bone marrow infiltration, monoclonal immunoglobulin production, and microenvironmental dysregulation that leads to systemic organ damage. The advent of B-cell maturation antigen (BCMA)-directed chimeric antigen receptor (CAR) T-cell therapy has induced unprecedented responses and durability for patients with relapsed/refractory MM. These outcomes are rarely observed with prior salvage strategies, although relapse remains the predominant long-term challenge for most patients. The two currently approved BCMA CAR-T cell products use viral vectors to semi-randomly insert the CAR gene, which results in heterogeneous genomic composition and variability in efficacy, safety, and product consistency. To address these challenges, we integrated targeted CRISPR genome engineering with precise CAR transgene insertion at the T-cell receptor alpha constant (TRAC) locus, 1XX CAR signaling architecture to enhance potency and durability, and non-viral manufacturing with a single-stranded DNA repair template to improve efficiency and yield. This approach confers physiological CAR expression, reduces insertional mutagenesis, and improves persistence by mitigating tonic signaling and exhaustion. Our GMP manufacturing process consistently achieved high CAR integration (37.7-72.7%) and yields across all full-scale runs and met predefined release criteria for identity, purity, safety, and quality. In NSG mouse models of MM, the UCCT-BCMA-1 product exhibited exceptionally potent tumor control, CAR-T cell expansion 100-1000-fold greater than that of lentiviral constructs, and durable clearance of myeloma cells after multiple rechallenges. These findings establish a CRISPR-edited, fully non-viral manufacturing platform for next-generation 1XX-BCMA CAR-T therapies with enhanced persistence, safety, and efficacy. One Sentence SummaryCRISPR-engineered, TRAC-targeted 1XX-BCMA CAR-T therapy with improved safety, potency, and persistence in relapsed and refractory multiple myeloma.

cancer biology↗

bioRxiv2026

Loss of hand control expressiveness revealed by task- and individual-specificity in spatiotemporal finger coordination

Stroke impairs dexterous hand use in daily activities, with prior studies of endpoint postures demonstrating reduced coordination complexity and diminished task-appropriate and individually-distinctive (termed expressiveness) coordination required by these daily activities. However, how spatiotemporal coordination reveals individual differences in post-stroke coordination remains unclear. Here, we characterized spatiotemporal coordination in able-bodied and post-stroke hands during finger individuation. We quantified coordination complexity and expressiveness (task-, individual-, and group-specificity) using principal component analysis (PCA) and linear discriminant analysis of 3D isometric forces from all five fingers. Paretic fingers showed reduced complexity and expressiveness, which was associated with greater intrusion of flexor bias in the paretic hand. Higher-variance PCs were characteristic of tasks and groups, while both higher- and lower-variance PCs were characteristic of individual-specific coordination. These findings suggest that stroke reduces spatiotemporal finger coordination complexity and expressiveness, limiting the coordination patterns available for daily hand use.

neuroscience↗

bioRxiv2025

Sub-MIC kill kinetics of copper and silver in Escherichia coli

Copper and silver are well-known and widely used antimicrobial metals that are often considered to employ diverse overlapping biocidal mechanisms of action and induce corresponding bacterial defense responses. Exposure to antimicrobial metals at concentrations below the minimal inhibitory concentration (sub-MIC) are widespread in natural, clinical and built environments and can shape evolutionary trajectories of the affected microbes that could lead to antimicrobial tolerance and/or resistance. By analyzing growth and kill kinetics of Escherichia coli under copper or silver exposure we observed that sub-MIC copper concentrations resulted in a lasting dose-dependent slowing of exponential growth with reduced yield while silver seemed to cause dose-dependent growth delay without substantially affecting exponential growth or yield. Time-kill experiments revealed minimal loss of viability in early copper exposure while in case of silver a rapid dose-dependent transient killing followed by normal exponential regrowth of the survivors was observed, underlying the seemingly dose-dependently extended lag phase durations. Distinguishing conditions that select for antimicrobial resistance (sustained growth) versus tolerance (survival without growth) is essential for antimicrobial stewardship as acquiring tolerance is considered a steppingstone towards developing resistance. Our results suggest that short-term survival of the initial killing by silver is sufficient for selective advantage while maintaining energy-intensive enhanced growth in the presence of copper is needed to gain competitive benefit over the general population. The findings highlight new and known challenges in antimicrobial characterization and risk assessment of metal-based formulations by using wide-spread non-kinetic endpoint assays such as MIC.

microbiology↗

bioRxiv2024

Re-analysis of CLAP data affirms PRC2 as an RNA binding protein

Using CLAP methodology, Guo et al. recently concluded that PRC2 is not an RNA binding protein (RBP). They suggest that prior findings were CLIP artifacts and argue against RNAs direct role in PRC2 regulation. Here, we re-analyze their raw datasets and reach contrary conclusions. Through an independent computational pipeline, we observe significant PRC2 enrichment throughout the transcriptome, including XIST. Applying the authors published computational pipeline also reaffirms PRC2 as an RBP. Detailed investigation of the authors pipeline reveals several unconventional practices. First, Guo et al. retained reads from foreign species and other unmappable reads to obtain a normalization factor. Second, they selectively removed read duplicates from the mappable fraction, while retaining them in the unmappable fraction. Finally, the authors applied an arbitrary cutoff for enrichment values in XIST. Their pipeline thereby inflated PRC2s background reads and suppressed mappable signals, creating the impression that PRC2 is not a robust RBP.

genomics↗

bioRxiv2024

Experimental evolution of Escherichia coli on solid silver, copper, stainless steel, and glass surfaces

To study bacterial adaptation to antimicrobial metal surfaces in application-relevant conditions, Escherichia coli was exposed to copper and silver surfaces for thirty exposure cycles in low-organic dry or high-organic humid conditions. The evolved populations demonstrated increased metal surface tolerance without concurrent increase in MBC and MIC values of respective metal ions or selected antibiotics. Mutation analysis did not detect increased mutation accumulation nor mutations in cop, cus, cue, sil, pco or general efflux genes known to actively maintain copper/silver homeostasis. Instead, during cyclic exposure mutations in genes related to cellular barrier functions and sulfur metabolism were enriched potentially suggesting that reducing bioavailability and passively restricting uptake of the toxic metals rather than active efflux is selected for on copper and silver surfaces. The changes detected in the evolved populations did not indicate an increased risk of antibiotic cross-resistance as a result of copper or silver surface exposure. However, rapid emergence of mutations in silS activated the cryptic sil efflux locus during silver ion challenge in liquid MBC assay with the evolved populations. The silS mutants showed no benefit on copper and silver surfaces but demonstrated decreased sensitivity to ampicillin and ciprofloxacin as well as copper and silver ions in liquid tests indicating that efflux might be specific to granting heavy metal tolerance in liquid but not surface exposure format. Our findings highlight the critical importance of appropriate exposure conditions not only in efficacy assessment but also risk assessment of antimicrobial surface applications. ImportanceThis study examines the evolutionary adaptations of Escherichia coli after semi-dry exposure to copper and silver surfaces, leading to an increase in surface tolerance but no increase in mutation accumulation or substantially enhanced metal ion tolerance in standard tests. Notably, enriched mutations indicate a shift toward more energy-passive mechanisms of metal tolerance. Additionally, while enhanced silver efflux was rapidly selected for in a single round of silver exposure in liquid tests and substantially increased copper and silver ion tolerance in conventional test formats, the causal mutations did not improve viability on silver and copper surfaces, underscoring the different fitness scenarios of tolerance mechanisms dependent on exposure conditions. These findings emphasize the need for appropriate exposure conditions in evaluating of both efficacy and the potential risks of using antimicrobial surfaces, as the results from conventional liquid-based tests may not apply in solid contexts.

microbiology↗

bioRxiv2024

Correspondence of fentanyl brain pharmacokinetics and behavior measured via engineering opioids biosensors and computational ethology

Despite the ongoing epidemic of opioid use disorder and death by fentanyl overdose, opioids remain the gold standard for analgesics. Pharmacokinetics (PK) dictates the individuals experience and utility of drugs; however, PK and behavioral outcomes have been conventionally studied in separate groups, even in preclinical models. To bridge this gap, we developed the first class of sensitive, selective, and genetically encodable fluorescent opioid biosensors, iOpioidSnFRs, including the fentanyl sensor, iFentanylSnFR. We expressed iFentanylSnFR in the ventral tegmental area of mice and recorded [fentanyl] alongside videos of behaviors before and after administration. We developed a machine vision routine to quantify the effects of the behavior on locomotor activity. We found that mice receiving fentanyl exhibited a repetitive locomotor pattern that paralleled the [fentanyl] time course. In a separate experiment, mice navigating a complex maze for water showed a dose-dependent impairment in navigation, in which animals repeated incorrect paths to the exclusion of most of the unexplored maze for the duration of the average fentanyl time course. This approach complements classical operant conditioning experiments and introduces a key feature of human addiction, the ability to carry out an ethologically relevant survival task, only now quantified in rodents. Finally, we demonstrate the utility of iFentanylSnFR in detecting fentanyl spiked into human biofluids and the generalizability of engineering methods to evolve selective biosensors of other opioids, such as tapentadol and levorphanol. These results encourage diagnostic and continuous monitoring approaches to personalizing opioid regimens for humans.

neuroscience↗

bioRxiv2023

Antibacterial activity of solid surfaces is critically dependent on relative humidity, inoculum volume and organic soiling

Antimicrobial surface materials potentially prevent pathogen transfer from contaminated surfaces. Efficacy of such surfaces is assessed by standard methods using wet exposure conditions known to overestimate antimicrobial activity compared to dry exposure. Some dry test formats have been proposed but semi-dry exposure scenarios e.g., oral spray or water droplets exposed to ambient environment, are less studied. We aimed to determine the impact of environmental test conditions on antibacterial activity against the model species Escherichia coli and Staphylococcus aureus. Surfaces based on copper, silver, and quaternary ammonium with known or claimed antimicrobial properties were tested in conditions mimicking microdroplet spray or larger water droplets exposed to variable relative air humidity in the presence or absence of organic soiling. All the environmental parameters critically affected antibacterial activity of the tested surfaces from no effect in high-organic dry conditions to higher effect in low-organic humid conditions but not reaching the effect size demonstrated in the ISO 22169 wet format. Copper was the most efficient antibacterial surface followed by silver and quaternary ammonium based coating. Antimicrobial testing of surfaces using small droplet contamination in application-relevant conditions could therefore be considered as one of the worst-case exposure scenarios relevant to dry use surfaces. Featured image + One Sentence summaryAntibacterial activity of copper and silver surfaces is highly dependent on environmental testing conditions with maximum efficiency in low-organic wet conditions to no antibacterial activity in high-organic dry conditions indicating the need to test antimicrobial surface materials in application-relevant test formats as opposed to current standards. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/534510v3_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@17eb30eorg.highwire.dtl.DTLVardef@11d9a72org.highwire.dtl.DTLVardef@86ea55org.highwire.dtl.DTLVardef@1828c5d_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

Endotaxis: A Universal Algorithm for Mapping, Goal-Learning, and Navigation

An animal entering a new environment typically faces three challenges: explore the space for resources, memorize their locations, and navigate towards those targets as needed. Experimental work on exploration, mapping, and navigation has mostly focused on simple environments - such as an open arena [68], a pond [42], or a desert [44] - and much has been learned about neural signals in diverse brain areas under these conditions [12, 54]. However, many natural environments are highly structured, such as a system of burrows, or of intersecting paths through the underbrush. Similarly, for many cognitive tasks, a sequence of simple actions can give rise to complex solutions. Here we propose an algorithm that learns the structure of a complex environment, discovers useful targets during exploration, and navigates back to those targets by the shortest path. It makes use of a behavioral module common to all motile animals, namely the ability to follow an odor to its source [4]. We show how the brain can learn to generate internal "virtual odors" that guide the animal to any location of interest. This endotaxis algorithm can be implemented with a simple 3-layer neural circuit using only biologically realistic structures and learning rules. Several neural components of this scheme are found in brains from insects to humans. Nature may have evolved a general mechanism for search and navigation on the ancient backbone of chemotaxis.

neuroscience↗

bioRxiv2021

RNA-controlled nucleocytoplasmic shuttling of mRNA decay factors regulates mRNA synthesis and initiates a novel mRNA decay pathway

mRNA level is controlled by factors that mediate both mRNA synthesis and decay, including the exonuclease Xrn1 - a major mRNA synthesis and decay factor. Here we show that nucleocytoplasmic shuttling of Xrn1 and of some of its associated mRNA decay factors plays a key role in determining both mRNA synthesis and decay. Shuttling is regulated by RNA-controlled binding of the karyopherin Kap120 to two nuclear localization sequences (NLSs) in Xrn1. The decaying RNA binds and masks NLS1, establishing a link between mRNA decay and Xrn1 shuttling. Mutations in the two NLSs, which prevent Xrn1 import, compromise transcription and, unexpectedly, also the cytoplasmic decay of [~]50% of the cellular mRNAs - comparably to Xrn1 deletion. These findings uncover a cytoplasmic mRNA decay pathway that begins in the nucleus. Interestingly, Xrn1 shuttling is required for proper adaptation to environmental changes, in particular to ever changing environmental fluctuations.

molecular biology↗

bioRxiv2021

Mice in a labyrinth: Rapid learning, sudden insight, and efficient exploration

Animals learn certain complex tasks remarkably fast, sometimes after a single experience. What behavioral algorithms support this efficiency? Many contemporary studies based on two-alternative-forced-choice (2AFC) tasks observe only slow or incomplete learning. As an alternative, we study the unconstrained behavior of mice in a complex labyrinth and measure the dynamics of learning and the behaviors that enable it. A mouse in the labyrinth makes ~2000 navigation decisions per hour. The animal quickly discovers the location of a reward in the maze and executes correct 10-bit choices after only 10 reward experiences - a learning rate 1000-fold higher than in 2AFC experiments. Many mice improve discontinuously from one minute to the next, suggesting moments of sudden insight about the structure of the labyrinth. The underlying search algorithm does not require a global memory of places visited and is largely explained by purely local turning rules.

neuroscience↗

bioRxiv2020

Selective antibiofilm properties and biocompatibility of nano-ZnO and nano-ZnO/Ag coated surfaces

Spread of pathogenic microbes and antibiotic-resistant bacteria in health-care settings and public spaces is a serious public health challenge. Materials that prevent solid surface colonization or impede touch-transfer of viable microbes could provide means to decrease pathogen transfer from high-touch surfaces in critical applications. ZnO and Ag nanoparticles have shown great potential in antimicrobial applications. Less is known about nano-enabled surfaces. Here we demonstrate that surfaces coated with nano-ZnO or nano-ZnO/Ag composites are not cytotoxic to human keratinocytes and possess species-selective medium-dependent antibiofilm activity against Escherichia coli, Staphylococcus aureus and Candida albicans. Colonization of nano-ZnO and nano-ZnO/Ag surfaces by E. coli and S. aureus was decreased in static oligotrophic conditions (no planktonic growth). Moderate to no effect was observed for bacterial biofilms in growth medium (supporting exponential growth). Inversely, nano-ZnO surfaces enhanced biofilm formation by C. albicans in oligotrophic conditions. However, enhanced C. albicans biofilm formation on nano-ZnO surfaces was effectively counteracted by the addition of Ag. Possible selective enhancement of biofilm formation by the yeast C. albicans on Zn-enabled surfaces should be taken into account in antimicrobial surface development. Our results also indicated the importance of the use of application-appropriate test conditions and exposure medium in antimicrobial surface testing.

microbiology↗

bioRxiv2018

Propidium iodide staining underestimates viability of adherent bacterial cells

Combining membrane impermeable DNA-binding stain propidium iodide (PI) with membrane-permeable DNA-binding counterstains is a widely used approach for bacterial viability staining. In this paper we show that PI staining of adherent cells in biofilms may significantly underestimate bacterial viability due to the presence of extracellular nucleic acids. We demonstrate that gram-positive Staphylococcus epidermidis and gram-negative Escherichia coli 24-hour initial biofilms on glass consist of 76 and 96% PI-positive red cells in situ, respectively, even though 68% the cells of either species in these aggregates are metabolically active. Furthermore, 82% of E. coli and 89% S. epidermidis are cultivable after harvesting. Confocal laser scanning microscopy (CLSM) revealed that this false dead layer of red cells is due to a subpopulation of double-stained cells that have green interiors under red coating layer which hints at extracellular DNA (eDNA) being stained outside intact membranes. Therefore, viability staining results of adherent cells should always be validated by an alternative method for estimating viability, preferably by cultivation.

microbiology↗

bioRxiv2018

A conserved morphogenetic mechanism for epidermal ensheathment of nociceptive sensory neurites

Interactions between epithelial cells and neurons influence a range of sensory modalities including taste, touch, and smell. Vertebrate and invertebrate keratinocytes/keratinocyte-like epidermal cells ensheath peripheral arbors of somatosensory neurons, including nociceptors, yet the developmental origins and functional roles of this ensheathment are largely unknown. Here, we describe an evolutionarily conserved morphogenetic mechanism for epidermal ensheathment of somatosensory neurites. We found that somatosensory neurons in Drosophila and zebrafish induce formation of epidermal sheaths, which wrap neurites of different types of neurons to different extents. Neurites induce formation of plasma membrane phosphatidylinositol 4,5-bisphosphate microdomains at nascent sheaths, followed by a filamentous actin network, and recruitment of junctional proteins that likely form autotypic junctions to seal sheaths. Finally, blocking epidermal sheath formation destabilized dendrite branches and reduced nociceptive sensitivity in Drosophila. Epidermal somatosensory neurite ensheathment is thus a deeply conserved cellular process that contributes to the morphogenesis and function of nociceptive sensory neurons.

neuroscience↗

bioRxiv2017

Framework For Quality Assessment Of Whole Genome, Cancer Sequences

Working with cancer whole genomes sequenced over a period of many years in different sequencing centres requires a validated framework to compare the quality of these sequences. The Pan-Cancer Analysis of Whole Genomes (PCAWG) of the International Cancer Genome Consortium (ICGC), a project a cohort of over 2800 donors provided us with the challenge of assessing the quality of the genome sequences. A non-redundant set of five quality control (QC) measurements were assembled and used to establish a star rating system. These QC measures reflect known differences in sequencing protocol and provide a guide to downstream analyses of these whole genome sequences. The resulting QC measures also allowed for exclusion samples of poor quality, providing researchers within PCAWG, and when the data is released for other researchers, a good idea of the sequencing quality. For a researcher wishing to apply the QC measures for their data we provide a Docker Container of the software used to calculate them. We believe that this is an effective framework of quality measures for whole genome, cancer sequences, which will be a useful addition to analytical pipelines, as it has to the PCAWG project.

genomics↗