Biology subjects

Friedman, A.

Publications and source records attributed to Friedman, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Kingdom-wide Discovery of Type VI Secretion Effectors via AI Uncovers Three New Bacterial Toxins

The type VI secretion system (T6SS) is a molecular harpoon used by 19% of bacteria to inject toxic proteins into microbial or host cells. Despite its widespread distribution, many T6SS effector (T6Es) genes remain unidentified. Here, we developed an XGBoost classifier integrating 42 genetic and biochemical features to identify novel T6Es. Applying our model to 2,559 T6SS-encoding bacterial genomes revealed 19,958 T6E candidates. We validated our computational predictions and confirmed that three effector candidates, having new 3D structures, demonstrated cytotoxicity to bacteria and yeast, mostly in the bacterial periplasm. For two of these, cognate immunity proteins neutralizing toxicity have been validated. T6EC11, a new peptidoglycan degrading effector, quickly leads to spherical E. coli, with inner membrane separation, and gradual peptidoglycan degradation in a unipolar manner, demonstrating an intriguing moon-like structural phenotype. T6EC12, an effector toxic to bacteria and yeast, carries a conserved zinc-binding motif. Mutations the motif markedly reduced toxicity, suggesting that T6EC12 represents a novel metalloprotease. Our study expands the known T6E repertoire, and provides thousands of T6E predictions in all T6SS-encoding bacteria.

microbiology↗

bioRxiv2026

Pain-regulation circuitry as a predictor of chronic pain phenotypes

Chronic pain involves sensory, emotional, and functional disruption, yet diagnostic labels rarely capture this variability, limiting individualized care. Multidimensional models, such as fear-avoidance and predictive coding, suggest that high emotional burden may disrupt expectation-based pain modulation and midbrain pain regulatory pathways, particularly within the periaqueductal gray (PAG). We tested whether chronic pain phenotypes defined by pain intensity, disability, and affective distress (PDA) differ in expectation-induced pain modulation, PAG connectivity, and behavioral markers including catastrophizing, hypervigilance, and medication use, and whether these features aid phenotype classification. We studied 159 patients with fibromyalgia or chronic low back pain and 72 controls. Our data-driven clustering approach identified high and low PDA groups. High PDA patients showed impaired modulation when positive expectations were violated and reported greater cognitive and behavioral burden (P<0.05). They also exhibited more negative connectivity between the dorsolateral/lateral PAG (dl/lPAG) and the dorsomedial prefrontal cortex (dmPFC) (corrected). Machine learning models classified PDA subtypes above chance, with accuracy improving when PAG connectivity was included. Findings highlight disrupted expectation-driven regulation and altered PAG pathways as markers for chronic pain stratification.

neuroscience↗

bioRxiv2025

Elucidating an anterior cingulate circuit for self-initiated actions and rescue of Parkinsonian akinesia

Dopamine (DA) depletion is known to result in Parkinsonian symptoms such as the inability to initiate movements (akinesia). While Parkinsonian akinesia is traditionally associated with reduced DA signaling in the striatum, the contribution of cortical regions that also receive DA projections and project to the striatum remains unclear. Here, we identify a previously unexplored cortical circuit involving D1-like dopamine receptor-expressing neurons in the anterior cingulate cortex (ACC) that is critical for initiating goal-directed movements. We find that a selective activation of ACC-D1+ neurons can flexibly drive targeted movement and locomotion even in akinetic mice after dopamine depletion or receptor antagonism. These findings uncover a cortical mechanism for movement initiation and offer promising new therapeutic targets for treating Parkinsonian akinesia.

neuroscience↗

bioRxiv2025

Lipid Nanoparticles with Aptamers Enable Targeted mRNA Delivery to CD4⁺ T Cells

In vivo genetic engineering of T cells could overcome the logistical, biological, and safety challenges of ex vivo modification, but effective and safe delivery systems remain limited by a lack of cellular specificity. Here, we developed aptamer-functionalized lipid nanoparticles (LNPs) for targeted mRNA delivery to CD4+ T cells, employing both a validated CD4-binding aptamer (Apt62) and novel aptamers generated using our proprietary transformer-based AI language model, AptaBLE. LNPs formulated with ionizable lipid SM102 or MC3 and conjugated with aptamers at controlled densities were physiochemically characterized and assessed for binding, in vitro transfection, in vivo biodistribution, and safety evaluation. Aptamer-functionalized LNPs demonstrated selective nanomolar binding to recombinant CD4, achieved enhanced transfection of CD4+ versus CD4- T cells in vitro, and significantly enriched mRNA delivery to immune-rich tissues in vivo, achieving up to 70-fold spleen signal enhancement with SM102 formulations compared to non-targeted controls, while maintaining suitable safety profiles. Overall, these findings demonstrate aptamer-functionalized LNPs, augmented by AI-guided aptamer design, as a tunable, non-immunogenic platform for in vivo T cell engineering. HighlightsO_LIAptamer-functionalized LNPs enable selective mRNA delivery to CD4+ immune cells rich organs. C_LIO_LIAptamer-functionalized LNPs maintain a favorable systemic safety profile in vivo. C_LIO_LIAI-guided AptaBLE platform generated functional aptamers validated in nanoparticle delivery. C_LI

molecular biology↗

bioRxiv2025

Shared latent representations of speech production for cross-patient speech decoding

Speech brain-computer interfaces (BCIs) can restore communication in individuals with neuromotor disorders who are unable to speak. However, current speech BCIs limit patient usability and successful deployment by requiring large volumes of patient-specific data collected over long periods of time. A promising solution to facilitate usability and accelerate their successful deployment is to combine data from multiple patients. This has proven difficult, however, due to differences in user neuroanatomy, varied placement of electrode arrays, and sparse sampling of targeted anatomy. Here, by aligning patient-specific neural data to a shared latent space, we show that speech BCIs can be trained on data combined across patients. Using canonical correlation analysis and high-density micro-electrocorticography (ECoG), we uncovered shared neural latent dynamics with preserved micro-scale speech information. This approach enabled cross-patient decoding models to achieve improved performance relative to patient-specific models facilitated by the high resolution and broad coverage of ECoG. Our findings support future speech BCIs that are more accurate and rapidly deployable, ultimately improving the quality of life for people with impaired communication from neuromotor disorders.

neuroscience↗

bioRxiv2025

A modular, adaptable, and accessible implant kit for chronic electrophysiological recordings in rats

Electrophysiological implants enable exploration of the relationship between neuronal activity and behavior. These technologies evolve rapidly, with multiple iterations of recording systems developed and utilized. Chronic implants must address a litany of complications, including retention of high signal-to-noise ratio in probes and the ability to withstand excess force over the experimental period. To overcome these issues, we designed a chronic implant for rats. Our comprehensive protocol optimizes the entire implant process, from assembling and testing the probes (Neuropixels) to implantation. In addition to addressing the complications previously mentioned, our implant can vertically adjust probes with micron precision and is constructed using modular components, allowing it to be easily modified for various research contexts, electrophysiological recording systems, headstages, and probe types.

neuroscience↗

bioRxiv2024

A2A-positive neurons in the nucleus accumbens core regulate effort exertion

Previous work has implicated the nucleus accumbens (NAc) in the regulation of effort, defined as the amount of work an animal is willing to perform for a given reward, but little is known about the specific contributions of neuronal populations within the NAc to effort regulation. In this study, we examined the contributions of direct pathway and indirect pathway neurons in the NAc core using an operant effort regulation task, in which the effort requirement is the number of lever presses needed for earning a food reward. Using optogenetics, we manipulated the activity of direct pathway spiny projection neurons (dSPNs, D1+) and indirect pathway SPNs (iSPNs, A2A+). Activating dSPNs reduced lever pressing regardless of the effort requirement, as it elicited gnawing, a competing consummatory behavior. On the other hand, activating iSPNs in the NAc core (but not in the shell) reduced lever pressing in an effort-dependent manner: stimulation-inducted reduction in performance was greater at higher press-to-reward ratio requirements. In contrast, optogenetically inhibiting NAc core iSPN output resulted in increased levels of effort exertion. Our results show that the indirect pathway output from the NAc core can bidirectionally regulate effort exertion.

neuroscience↗

bioRxiv2024

Computational Primitives for Cost-Benefit Decision-Making

Cost-benefit decision-making is a critical process performed by all organisms, including humans. Various factors, including risk1,2, uncertainty3, age4, sex5, and neuropsychiatric disorders6, can alter decision-making. To explore cost-benefit decision-making in humans, we developed a comprehensive task and analysis framework that presents participants with a series of approach-avoid trade-offs across a variety of contexts. With this system, we found that cost-benefit decisions in humans are made using a set of computational strategies that may be used for integrating costs and rewards, which we term decision-making primitives. We further show that these decision-making primitives are used by rodents performing a similar decision-making task7. We find that utilization of these primitives in both rodents and humans shifts based on factors like hunger and sex, and that individuals use primitives differently. We additionally demonstrate that using a naturally-inspired neural network architecture generates output that overlaps with human and rodent performance over a non-constrained neural network. This novel conceptual framework, by isolating discrete decision-making primitives, has potential to help us identify how different brain regions give rise to decision-making behavior, as well as to facilitate better diagnosis of neuropsychiatric disorders and development of naturally-inspired artificial intelligence systems of decision-making.

neuroscience↗

bioRxiv2024

Paroxysmal Slow Wave Events as a diagnostic and predictive biomarker for post-traumatic epilepsy

Traumatic brain injury (TBI) is a major global health concern, affecting more than 40 million people annually. While most cases are mild and present with light symptoms, repeated mild injuries can result in delayed brain pathologies, including cognitive decline, neuropsychiatric complications, and post-traumatic epilepsy (PTE). PTE refers to recurring, unprovoked seizures occurring at least one week after TBI. While the link between moderate to severe TBI and PTE is well established, the epileptogenesis after repetitive mild TBI (rmTBI) is seldom studied. Currently, there are no biomarkers to identify those at risk of developing PTE, and its diagnosis is challenging. Here, we used a rat model to study PTE following rmTBI and assessed human EEG data to identify potential biomarkers for PTE. We employed a closed head TBI model to induce rmTBI, and recorded brain activity using electrocorticography (ECoG) between 2- and 6-months post-injury. Behavioral assessments and post-mortem analysis were also conducted. In humans, we analyzed EEG recordings from the Temple University database to investigate the potential of EEG-derived features for diagnosing PTE. At 6 months post injury, 70% of rmTBI animals developed PTE, compared to 22% in the control group (P=0.01). While neurological assessments following injury did not predict PTE, paroxysmal slow wave events (PSWEs) were found to be a reliable biomarker for PTE prediction. In humans, the percentage time in PSWEs was significantly elevated in PTE patients with epileptiform activity. In conclusion, we suggest PSWEs as a non-invasive, cost-effective biomarker for PTE in rodents and human patients.

neuroscience↗

bioRxiv2024

Neural mechanisms of the transition from planning to execution in speech production

Speaking is the primary way that humans communicate. This communication is enabled by a production system that can plan and execute unique combinations of speech sounds. Although a distributed network of brain regions has been implicated in speaking, it is unclear how planning and execution of speech are coordinated to produce meaningful sounds. Leveraging the high spatio-temporal resolution of intracranial recordings at different spatial scales, we show distinct neural mechanisms that facilitate speech planning and execution. During planning, different levels of speech units are coded discretely at distinct prefrontal sites. These planned units are then dynamically integrated at various cortical levels to guide subsequent execution. During speech execution, speech motor regions generate continuous sequences that reflect both discrete speech sound units and their transitional properties between units. This rapid neural transition from discrete speech units to motor sequences links speech planning with execution and enables our effortless ability to speak.

neuroscience↗

bioRxiv2024

Effect of Acute Alcohol Consumption in a Novel Rodent Model of Decision Making

BackgroundAlcohol use, especially at high consumption levels, can lead to irrational decision-making. In humans, this can lead to harmful outcomes often seen in the context of driving under the influence and or aggressive behavior. To date, the field is lacking comprehensive animal models to examine the impact of alcohol use on decision making in rodents, particularly to examine sex differences in choice behavior. To address this issue, the present study examined the effects of acute alcohol consumption during a behavioral approach-avoidance task that captures momentary changes in decision-making behavior and choice selection in female and male rats. MethodsOur team has developed a novel behavioral protocol involving a concurrent choice to consume four different concentrations of alcohol and sucrose combinations. During the task, female or male rats can approach or avoid drinking solutions in four distinct corners of our test apparatus. The solutions were prepared in inverse concentrations (higher sucrose was paired with lower alcohol and vice versa) so that the rodents pursue minimal alcohol use by consuming the higher sucrose concentrations or higher concentrations of alcohol by drinking the lower sucrose concentrations. The animals also have the option to avoid drinking alcohol by not approaching any of the drinking cups. Behavior and choice were tracked during task performance involving different solution concentrations of alcohol and sucrose. ResultsThe choice of consuming different concentrations of alcohol or sucrose resulted in sex-dependent differences in an approach-avoid trade-off pattern of behavior that was sensitive to different concentrations of alcohol/sucrose combinations. Notably, males were greatly affected by the introduction of alcohol into the task environment, approaching higher alcohol concentrations significantly more often than the non-alcohol containing options. In contrast, females choice patterns and task performance were largely unchanged during alcohol and non-alcohol containing tasks. Regardless of sex, we identify a novel method for identifying individual subject decision-making abnormalities during and after alcohol consumption. ConclusionsThis research reveals a novel approach for examining the effects of acute alcohol exposure during a trade-off task, with decision patterns being more impacted by alcohol use in males as compared to females. We also offer the field a novel approach for identifying individual abnormalities in decision making behavior with the presentation of alcohol. Future research can explore these abnormal patterns in both acute and chronic alcohol conditions to develop methods for identifying subjects at-risk for developing an alcohol use disorder and the deleterious impact of alcohol on rational decision making.

neuroscience↗

bioRxiv2024

Model of a striatal circuit exploring biological mechanisms underlying decision-making during normal and disordered states

Decision-making requires continuous adaptation to internal and external contexts. Changes in decision-making are reliable transdiagnostic symptoms of neuropsychiatric disorders. We created a computational model demonstrating how the striosome compartment of the striatum constructs a mathematical space for decision-making computations depending on context, and how the matrix compartment defines action value depending on the space. The model explains multiple experimental results and unifies other theories like reward prediction error, roles of the direct versus indirect pathways, and roles of the striosome versus matrix, under one framework. We also found, through new analyses, that striosome and matrix neurons increase their synchrony during difficult tasks, caused by a necessary increase in dimensionality of the space. The model makes testable predictions about individual differences in disorder susceptibility, decision-making symptoms shared among neuropsychiatric disorders, and differences in neuropsychiatric disorder symptom presentation. The model reframes the role of the striosomal circuit in neuroeconomic and disorder-affected decision-making. HighlightsO_LIStriosomes prioritize decision-related data used by matrix to set action values. C_LIO_LIStriosomes and matrix have different roles in the direct and indirect pathways. C_LIO_LIAbnormal information organization/valuation alters disorder presentation. C_LIO_LIVariance in data prioritization may explain individual differences in disorders. C_LI eTOCBeck et al. developed a computational model of how a striatal circuit functions during decision-making. The model unifies and extends theories about the direct versus indirect pathways. It further suggests how aberrant circuit function underlies decision-making phenomena observed in neuropsychiatric disorders.

neuroscience↗

bioRxiv2024

Amygdala Self-Neuromodulation Capacity as a Window for Process-Related Network Recruitment

Neurofeedback (NF) has emerged as a promising avenue for demonstrating process-related neuroplasticity, enabling self-regulation of brain function. NF targeting the amygdala has drawn attention for therapeutic potential in psychiatry, by potentially harnessing emotion-regulation processes. However, not all individuals respond equally to NF training, possibly due to varying self-regulation abilities. This underscores the importance of understanding the mechanisms behind successful neuromodulation (i.e. capacity). This study aimed to investigate the establishment and neural correlates of neuromodulation capacity by using data from repeated sessions of Amygdala Electrical Finger Print (EFP)-NF and post-training fMRI-NF session. Results from 97 psychiatric patients and healthy participants revealed increased amygdala-EFP neuromodulation capacity over training, associated with post-training amygdala fMRI modulation-capacity and improvements in alexithymia. Individual differences in this capacity were associated with pre-training amygdala reactivity and initial neuromodulation success. Additionally, amygdala down-regulation during fMRI-NF co-modulated with other regions such as the posterior-insula and parahippocampal gyrus. This combined modulation better explained EFP-modulation capacity and improvement in alexithymia than the amygdala modulation alone, suggesting the relevance of this broader network to the gained capacity. These findings support a network-based approach for NF and highlight the need to consider individual differences in brain function and modulation capacity to optimize NF interventions.

neuroscience↗

bioRxiv2024

Uterus and cervix anatomical changes and cervix stiffness evolution throughout pregnancy

The coordinated biomechanical performance, such as uterine stretch and cervical barrier function, within maternal reproductive tissues facilitates healthy human pregnancy and birth. Quantifying normal biomechanical function and detecting potentially detrimental biomechanical dysfunction (e.g., cervical insufficiency, uterine overdistention, premature rupture of membranes) is difficult, largely due to minimal data on the shape and size of maternal anatomy and material properties of tissue across gestation. This study quantitates key structural features of human pregnancy to fill this knowledge gap and facilitate three-dimensional modeling for biomechanical pregnancy simulations to deeply explore pregnancy and childbirth. These measurements include the longitudinal assessment of uterine and cervical dimensions, fetal weight, and cervical stiffness in 47 low-risk pregnancies at four time points during gestation (late first, middle second, late second, and middle third trimesters). The uterine and cervical size were measured via 2-dimensional ultrasound, and cervical stiffness was measured via cervical aspiration. Trends in uterine and cervical measurements were assessed as time-course slopes across pregnancy and between gestational time points, accounting for specific participants. Patient-specific computational solid models of the uterus and cervix, generated from the ultrasonic measurements, were used to estimate deformed uterocervical volume. Results show that for this low-risk cohort, the uterus grows fastest in the inferior-superior direction from the late first to middle second trimester and fastest in the anterior-posterior and left-right direction between the middle and late second trimester. Contemporaneously, the cervix softens and shortens. It softens fastest from the late first to the middle second trimester and shortens fastest between the late second and middle third trimester. Alongside the fetal weight estimated from ultrasonic measurements, this work presents holistic maternal and fetal patient-specific biomechanical measurements across gestation.

bioengineering↗

bioRxiv2024

The Role of Cilia in the Development, Survival, and Regeneration of Hair Cells

Mutations impacting cilia genes lead to a class of human diseases known as ciliopathies. This is due to the role of cilia in the development, survival, and regeneration of many cell types. We investigated the extent to which disrupting cilia impacted these processes in hair cells. We found that mutations in two intraflagellar transport (IFT) genes, ift88 and dync2h1, which lead to the loss of kinocilia, caused increased hair cell apoptosis in the zebrafish lateral line. IFT gene mutants also have a decreased mitochondrial membrane potential, and blocking the mitochondrial uniporter causes a loss of hair cells in wild-type zebrafish but not mutants, suggesting mitochondria dysfunction may contribute to the apoptosis seen in these mutants. These mutants also showed decreased proliferation during hair cell regeneration, but did not show consistent changes in support cell number or proliferation during hair cell development. These results show that disruption of the cilia through either mutations in anterograde or retrograde IFT genes appear to impact hair cell survival but not necessarily development in the lateral line.

neuroscience↗

bioRxiv2023

Mitochondrial dysfunction underlies impaired neurovascular coupling following traumatic brain injury

Traumatic brain injury (TBI) involves an acute injury (primary damage), which may evolve in the hours to days after impact (secondary damage). Seizures and cortical spreading depolarization (CSD) are metabolically demanding processes that may worsen secondary brain injury. Metabolic stress has been associated with mitochondrial dysfunction, including impaired calcium homeostasis, reduced ATP production, and elevated ROS production. However, the association between mitochondrial impairment and vascular function after TBI is poorly understood. Here, we explored this association using a rodent closed head injury model. CSD resulted in neurobehavioral decline after TBI. Craniotomy was performed to elicit CSD via electrical stimulation or to induce seizures via 4-aminopyridine application. We measured vascular dysfunction following CSDs and seizures in TBI animals using laser doppler flowmetry. We observed a more profound reduction in local cortical blood flow in TBI animals compared to healthy controls. Following TBI, CSD resulted in mitochondrial dysfunction and pathological signs of increased oxidative stress adjacent to the vasculature. We explored these findings further using electron microscopy and found that TBI and CSDs resulted in vascular morphological changes and mitochondrial cristae damage in astrocytes, pericytes and endothelial cells. Overall, we provide evidence that CSDs induce mitochondrial dysfunction, impaired cortical blood flow, and neurobehavioral deficits in the setting of TBI. HighlightsCortical spreading depolarization after TBI causes behavioral decline in rats. Vasoconstriction and oligemia after cortical spreading depolarization is worse in TBI brains. Spreading depolarization causes impaired mitochondrial function. TBI and spreading depolarization result in constricted vessels and increased pericyte size. TBI and spreading depolarization result in mitochondrial damage in vascular cells. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/549872v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@176a9a6org.highwire.dtl.DTLVardef@17bfc19org.highwire.dtl.DTLVardef@e3d74dorg.highwire.dtl.DTLVardef@4c194e_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

Cortical Plasticity is associated with Blood-Brain-Barrier Modulation

Brain microvessels possess the unique properties of a blood-brain barrier (BBB), tightly regulating the passage of molecules from the blood to the brain neuropil and vice versa. In models of brain injury, BBB dysfunction and the associated leakage of serum albumin to the neuropil have been shown to induce pathological plasticity, neuronal hyper-excitability, and seizures. The effect of neuronal activity on BBB function and whether it plays a role in plasticity in the healthy brain remain unclear. Here we show that neuronal activity induces modulation of microvascular permeability in the healthy brain and that it has a role in local network reorganization. Combining simultaneous electrophysiological recording and vascular imaging with transcriptomic analysis in rats, and functional and BBB-mapping MRI in human subjects we show that prolonged stimulation of the limb induces a focal increase in BBB permeability in the corresponding somatosensory cortex that is associated with long-term synaptic plasticity. We further show that the increased microvascular permeability depends on neuronal activity and involves caveolae-mediated transcytosis and transforming growth factor beta signaling. Our results reveal a role of BBB modulation in cortical plasticity in the healthy brain, highlighting the importance of neurovascular interactions for sensory experience and learning.

neuroscience↗

bioRxiv2022

Intramuscular mRNA BNT162b2 vaccine against SARS-CoV-2 induces robust neutralizing salivary IgA

Intramuscularly administered vaccines stimulate robust serum neutralizing antibodies, yet they are often less competent in eliciting sustainable sterilizing immunity at the mucosal level. Our study uncovers, strong neutralizing mucosal component (NT50 [≤] 50pM), emanating from intramuscular administration of an mRNA vaccine. We show that saliva of BNT162b2 vaccinees contains temporary IgA targeting the Receptor-Binding-Domain (RBD) of SARS-CoV-2 spike protein and demonstrate that these IgAs are key mediators of potent neutralization. RBD-targeting IgAs were found to associate with the Secretory Component, indicating their bona-fide transcytotic origin and their dimeric tetravalent nature. The mechanistic understanding of the exceptionally high neutralizing activity provided by mucosal IgA, acting at the first line of defence, will advance vaccination design and surveillance principles, pointing to novel treatment approaches, and to new routes of vaccine administration and boosting. Significance statementWe unveiled powerful mucosal neutralization upon BNT162b2 vaccination, mediated by temporary polymeric IgA and explored its longitudinal properties. We present a model, whereby the molecular architecture of polymeric mucosal IgA and its spatial properties are responsible for the outstanding SARS-CoV-2 neutralization potential. We established a methodology for quantitative comparison of immunoreactivity and neutralization for IgG and IgAs in serum and saliva in molar equivalents for standardization in diagnostics, surveillance of protection and for vaccine evaluations.

microbiology↗