Biology subjects

Cramer, N.

Publications and source records attributed to Cramer, N..

12 recordsLinked to original sources

bioRxiv2025

Revisiting the Evolution of Lactase Persistence: Insights from South Asian Genomes

Lactase persistence (LP), the ability to digest lactose from milk into adulthood, is a classic example of natural selection in humans. Multiple mutations upstream of the LCT gene are associated with LP and have been previously shown to be under selection in Europeans and Africans. South Asia is the worlds largest producer of dairy, and milk and dairy products are widely consumed throughout the subcontinent. However, the origin, evolutionary history and selective pressures associated with LP in South Asia remain elusive. We assembled genome-wide data from [~]8,000 present-day and ancient genomes from India, Pakistan, and Bangladesh, spanning diverse timescales ([~]3300 BCE-1650 CE), geographic regions, and ethnolinguistic and subsistence groups. We find that the Eurasian LP-associated variant,-13.910:C>T, is widespread across South Asia, exhibiting clinal variation along north-south and east-west gradients. Ancient DNA analysis reveals that this variant first appeared in South Asia during the historical and medieval periods through Steppe pastoralist-related gene flow. Interestingly, unlike in other worldwide populations, the LP prevalence is almost entirely explained by Steppe ancestry--not selection--in most contemporary South Asians. A notable exception is the only two pastoralist groups, Toda in South India and Gujjar in Pakistan, that have unexpectedly high frequencies of-13.910*T, comparable to estimates in Northern Europeans. By performing local ancestry inference, we find significant enrichment for Steppe pastoralist ancestry around the LCT locus in these two geographically-distant pastoralist groups, indicative of strong selection. Together, these findings highlight the complex role of ancestry and natural selection in shaping the prevalence of lactase persistence on the subcontinent.

evolutionary biology↗

bioRxiv2025

Identification of proteins exhibiting in vitro RNA chaperone activity through gradient profiling in the Lyme disease spirochete, Borrelia burgdorferi

RNA-binding proteins (RBPs) play key roles in regulating gene expression in bacteria. However, relatively few RBPs have been discovered and characterized in Borrelia (Borreliella) burgdorferi, the causative agent of Lyme disease. We utilized gradient profiling to identify putative RBPs that co-sediment with small RNAs (sRNAs) and nascent mRNAs. We employed in vitro and in vivo assays to characterize the RNA chaperone activities of several proteins we identified in the gradient profiling. The previously hypothetical proteins BB0749, BB0713 and BB0796, as well as the chemotaxis-related protein CheY2 and the flagella-associated protein FlgV displayed RNA annealing and/or strand displacement activity. Moreover, in vivo Co-IP assays demonstrated BB0749 binds RNA in B. burgdorferi.

molecular biology↗

bioRxiv2025

Rewilding beyond the wilderness: Beavers can restore stream biodiversity from urban to agricultural to natural landscapes

1 Beavers have been promoted as a cost-effective nature-based solution to restore degraded stream ecosystems and enhance overall biodiversity. However, the extent to which beaver-engineering boosts biodiversity in human-impacted landscapes remains poorly understood. 2 We assessed the responses of aquatic and terrestrial taxa (amphibians, dragonflies, fish, macrophytes, plankton, terrestrial vegetation, bats, aquatic, flying and terrestrial invertebrates) to beaver-engineering along a gradient of human land-use intensity in Switzerland. In 16 streams, we measured species richness, abundance, unique species richness, evenness, beta and gamma diversity in a beaver-engineered site with beaver dams and a control site without beaver activity. 3 Especially aquatic and semi-aquatic species profited from beaver-engineering. In response to beaver-engineering, amphibians, dragonflies, macrophytes, and plankton increased in species richness, abundance and unique species richness, while fish and terrestrial plants increased in species richness and unique species richness. Bats only increased in unique species richness, while for the other terrestrial taxa, we found no difference between beaver-engineered and control sites. Community evenness remained largely unaffected across all groups. 4 Overall, beaver-engineering increased biodiversity across a land-use gradient. For macrophytes and amphibians (species richness, unique species richness and abundance), as well for dragonflies (species richness and unique species richness), increases were smaller under higher land-use intensity. For the remaining taxa and metrics, we found no relationship between land-use intensity and responses to beaver engineering. 5 However, for beta-diversity, we found that sites with a high land-use intensity had a lower component of nestedness and stronger community turnover in comparison to more natural sites, with a significant effect for macrophytes. Gamma species richness was generally unaffected by land- use intensity, except for amphibians, which were often only found in beaver-engineered sites in high- land-use intensity areas. 6 Synthesis and applications. Our findings demonstrate that beaver-engineering significantly enhances local biodiversity across aquatic and terrestrial ecosystems, even at sites with high land-use intensity. Hence, beavers can effectively restore stream biodiversity from urban to agricultural to natural landscapes. Integrating beaver-engineering into river restoration strategies can substantially advance biodiversity goals under frameworks such as the EU Water Framework Directive and national conservation policies.

ecology↗

bioRxiv2025

Lasting Increases in Neuronal Activity and Serotonergic Receptor Expression Following Gestational Chlorpyrifos Exposure

Perinatal exposure to the organophosphorus insecticide chlorpyrifos (CPF) is associated with an increased incidence of neurodevelopmental disorders, such as autism spectrum disorder. While these behavioral detriments have been modeled in rodents, the underlying functional alterations in the developing brain are largely unknown. Previous reports using a rat model have identified alterations to both inhibitory synaptic transmission and serotonergic (5-HT) receptor binding in the cortex following developmental CPF exposure. Here, we use a rat model of gestational CPF exposure to investigate whether this altered inhibitory activity is driven by increased spontaneous firing of inhibitory interneurons and altered 5-HT receptor expression. Using cell-attached ex vivo electrophysiology in young rats of both sexes, we identified a significant increase in the number of spontaneously firing neurons in the somatosensory cortex of CPF-exposed offspring. Analysis of action potential metrics identified a sub-set of these neurons as fast-spiking parvalbumin (PV) interneurons. Immunohistochemical labeling of c-Fos, a marker of neuronal activity, further revealed a pronounced increase in activity of neurons of the somatosensory cortex in both juvenile and adult rats that had been gestationally exposed to CPF. Finally, RNAscope in situ hybridization showed an increase in the expression of the inhibitory receptor 5-HT1B in PV neurons. The data here demonstrate that gestational exposure to CPF results in persistent hyper-excitation of the somatosensory cortex, potentially through increased expression of the receptor 5-HT1B and resulting disinhibition. These neurophysiological effects may contribute to the established behavioral outcomes resulting from gestational exposure to CPF and offer guidance for novel preventative interventions. SIGNIFICANCE STATEMENTWe report persistent increases in spontaneous neuronal firing in the somatosensory cortex following a brief gestational exposure to the organophosphorus insecticide CPF in rats. This occurred in conjunction with increased expression of the 5-HT1B receptor measured specifically in PV interneurons. The hyper-excitability of the somatosensory cortex described here agrees with the established hyper-sensitivity to sensory stimulation seen in neurodevelopmental disorders such as autism spectrum disorder. These results offer a possible mechanistic framework underlying the neurophysiological effects associated with early life exposures to the organophosphorus insecticide CPF.

neuroscience↗

bioRxiv2025

Gestational Chlorpyrifos Exposure Imparts Lasting Alterations to the Rat Somatosensory Cortex

Chlorpyrifos is an organophosphorus pesticide used extensively in agricultural and residential settings for nearly 60 years. Gestational, sub-acute exposure to chlorpyrifos is linked to increased prevalence of neurodevelopmental disorders. Animal studies have modeled these neurobehavioral detriments, however, the functional alterations in the brain induced by this exposure remain largely unknown. To address this, we used a rat model of gestational chlorpyrifos exposure to interrogate the alterations in the developing somatosensory (barrel) cortex. Rat dams were exposed to chlorpyrifos (5 mg/kg) or vehicle on gestational days 18-21 via subcutaneous injection, with no overt acute toxicity. Acetylcholinesterase was modestly inhibited but returned to baseline levels by postnatal day 12. We performed whole-cell patch clamp recordings on postnatal days 12-20 in both male and female progeny of the treated dams. A spike timing dependent plasticity protocol revealed changes to the normal development of use-dependent plasticity, including interference in long-term synaptic depression. Recording inhibitory synaptic activity revealed an increase in the frequency of spontaneous postsynaptic currents and in paired pulse ratios, in conjunction with a significant decrease in miniature postsynaptic currents. These findings suggest a presynaptic mechanism of inhibited GABA release, with potential disinhibition of inhibitory neurons. Evaluation of barrel cortex development displayed disruptions to normal barrel field patterning, with increases in both the septal area and total barrel field. We provide evidence for functional and structural alterations during brain development induced by in utero exposure to the organophosphorus pesticide chlorpyrifos that may account for the well-established behavioral outcomes. SIGNIFICANCE STATEMENTWe demonstrate persistent alterations to synaptic function and plasticity in the somatosensory cortex following a brief, sub-acute exposure to the organophosphorus pesticide chlorpyrifos in a gestational rat model. These occur in conjunction with structural changes to cellular patterning of this brain region. These previously unknown consequences are potential causal mechanisms to the well-established neurodevelopmental detriments associated with early life exposure to chlorpyrifos. Clarifying these mechanisms could aid in ameliorating or preventing their persistent effects.

neuroscience↗

bioRxiv2024

Sex differences in central amygdala glutamate responses to calcitonin gene-related peptide

Women are disproportionately affected by chronic pain compared to men. While societal and environmental factors contribute to this disparity, sex-based biological differences in the processing of pain are also believed to play significant roles. The central lateral nucleus of the amygdala (CeLC) is a key region for the emotional-affective dimension of pain, and a prime target for exploring sex differences in pain processing since a recent study demonstrated sex differences in CGRP actions in this region. Inputs to CeLC from the parabrachial nucleus (PB) play a causal role in aversive processing, and release both glutamate and calcitonin gene-related peptide (CGRP). CGRP is thought to play a crucial role in chronic pain by potentiating glutamatergic signaling in CeLC. However, it is not known if this CGRP-mediated synaptic plasticity occurs similarly in males and females. Here, we tested the hypothesis that female CeLC neurons experience greater potentiation of glutamatergic signaling than males following endogenous CGRP exposure. Using trains of optical stimuli to evoke transient CGRP release from PB terminals in CeLC, we find that subsequent glutamatergic responses are preferentially potentiated in CeLC neurons from female mice. This potentiation was CGRP-dependent and involved a postsynaptic mechanism. This sex difference in CGRP sensitivity may explain sex differences in affective pain processing. Significance statementThe central lateral nucleus of the amygdala (CeLC) receives a dense projection from parabrachial nucleus (PB) neurons that corelease calcitonin gene-related peptide (CGRP) and glutamate following aversive stimuli. This PBCGRP[->]CeLC projection plays a causal role in chronic pain. We show that endogenous CGRP release potentiates glutamate signaling in female, but not male, CeLC neurons. In the context of previous work in male CeLC, this suggests that that females are more sensitive to even transient CGRP release events. Understanding how this sex difference in CGRP sensitivity arises could enhance strategies for treating chronic pain in both women and men.

neuroscience↗

bioRxiv2023

Divergent changes in PBN excitability in a mouse model of neuropathic pain

The transition from acute to chronic pain involves maladaptive plasticity in central nociceptive pathways. Growing evidence suggests that changes within the parabrachial nucleus (PBN), an important component of the spino-parabrachio-amygdaloid pain pathway, are key contributors to the development and maintenance of chronic pain. In animal models of chronic pain, PBN neurons become sensitive to normally innocuous stimuli and responses to noxious stimuli become amplified and more often produce after-discharges that outlast the stimulus. Using ex vivo slice electrophysiology and two mouse models of neuropathic pain, sciatic cuff and chronic constriction of the infraorbital nerve (CCI-ION), we find that changes in the firing properties of PBN neurons and a shift in inhibitory synaptic transmission may underlie this phenomenon. Compared to PBN neurons from shams, a larger proportion of PBN neurons from mice with a sciatic cuff were spontaneously active at rest, and these same neurons showed increased excitability relative to shams. In contrast, quiescent PBN neurons from cuff mice were less excitable than those from shams. Despite an increase in excitability in a subset of PBN neurons, the presence of after-discharges frequently observed in vivo were largely absent ex vivo in both injury models. However, GABAB-mediated presynaptic inhibition of GABAergic terminals is enhanced in PBN neurons after CCI-ION. These data suggest that the amplified activity of PBN neurons observed in rodent models of chronic pain arise through a combination of changes in firing properties and network excitability. Significance StatementHyperactivity of neurons in the parabrachial nucleus (PBN) is causally linked to exaggerated pain behaviors in rodent models of chronic pain but the underlying mechanisms remain unknown. Using two mouse models of neuropathic pain, we show the intrinsic properties of PBN neurons are largely unaltered following injury. However, subsets of PBN neurons become more excitable and GABAB receptor mediated suppression of inhibitory terminals is enhanced after injury. Thus, shifts in network excitability may be a leading factor in injury induced potentiation of PBN activity.

neuroscience↗

bioRxiv2023

Elevated serotonin in mouse spinal dorsal horn is pronociceptive

Serotonergic neurons in the rostral ventral medulla (RVM) contribute to bidirectional control of pain through modulation of spinal and trigeminal nociceptive networks. Deficits in this pathway are believed to contribute to pathological pain states, but whether changes in serotonergic mechanisms are pro or anti-nociceptive are debated. We used a combination of optogenetics and fiber photometry to examine these mechanisms more closely. We find that optogenetic activation of RVM serotonergic afferents in the spinal cord of naive mice produces mechanical hypersensitivity and conditioned place aversion. Neuropathic pain, produced by chronic constriction injury of the infraorbital nerve (CCI-ION), evoked a tonic increase in serotonin concentrations within the spinal trigeminal nucleus caudalis (SpVc), measured with liquid chromatography-tandem mass spectroscopy (LC-MS/MS). By contract, CCI-ION had no effect on the phasic serotonin transients in SpVc, evoked by noxious pinch, and measured with fiber photometry of a serotonin sensor. These findings suggest that serotonin release in the spinal cord is pronociceptive and that an increase is sustained serotonin signaling, rather than phasic or event driven increases, potentiate nociception in models of chronic pain. Significance StatementSerotonergic neurons of the rostral ventral medulla participate in descending pain modulation by regulating spinal and trigeminal nociceptive circuits. Whether changes in serotonergic mechanisms are pro or anti-nociceptive is debated. We show that serotonin release within the spinal trigeminal nucleus is pronociceptive and that enhanced tonic, but not phasic serotonin release may contribute to sensitization in mouse models of chronic pain. These results further clarify the role of serotonin in nociception and suggest that local inhibition of serotonin release or increase of uptake may be a viable therapeutic approach in treating chronic pain.

neuroscience↗

bioRxiv2022

Noradrenergic input from nucleus of the solitary tract regulates parabrachial activity in mice

The parabrachial complex (PB) is critically involved in aversive processes, and chronic pain is associated with amplified activity of PB neurons in rodent models of neuropathic pain. Here we demonstrate that catecholaminergic input from the caudal nucleus of the solitary tract (cNTScat)--a stress responsive region that integrates intero- and exteroceptive signals--causes amplification of PB activity and their sensory afferents. We used a virally mediated expression of a norepinephrine (NE) sensor, NE2h, fiber photometry, and extracellular recordings in anesthetized mice to show that noxious mechanical and thermal stimuli activate cNTS neurons. These stimuli also produce prolonged NE transients in PB that far outlast the noxious stimuli. Similar NE transients can be evoked by focal electrical stimulation of cNTS, a region that contains the noradrenergic A2 cell group that projects densely upon PB. In vitro, optical stimulation of cNTScat terminals depolarized PB neurons and caused a prolonged increase the frequency of excitatory synaptic activity. A dual opsin approach showed that sensory afferents from the caudal spinal trigeminal nucleus are potentiated by cNTScat terminal activation. This potentiation was coupled with a decrease in the paired pulse ratio, consistent with an cNTScat - mediated increase in the probability of release at SpVc synapses. Together, these data suggest that A2 neurons of the cNTS generate long lasting NE transients in PB which increase excitability and potentiate responses of PB neurons to sensory inputs. These reveal a mechanism through which stressors from multiple modalities may potentiate the aversiveness of nociceptive stimuli. Significance StatementIncreased excitability of the parabrachial nucleus (PB), a key integrative hub for aversive stimuli, is linked to amplified pain behaviors. We show that prolonged norepinephrine (NE) transients in PB following noxious stimulation in mice. These NE transients potentiate sensory input to PB and arise, at least in part, from catecholaminergic projections from the caudal nucleus of the solitary tract (cNTScat). We propose that activity this cNTScat to PB pathway may potentiate the aversiveness of pain.

neuroscience↗

bioRxiv2021

Insight into Cross-Amyloid Interactions and Morphologies: Molecular Dynamics Simulations of Model Peptide Fragments of Amyloid-β (Aβ16-22) and Islet Amyloid Polypeptide (IAPP20-29)

Amyloid-beta (A{beta}) and islet amyloid polypeptide (IAPP) are small peptides, classified as amyloids, that have the potential to self-assemble and form cytotoxic species, such as small soluble oligomers and large insoluble fibrils. The formation of A{beta} aggregates facilitates the progression of Alzheimers disease (AD), while IAPP aggregates induce pancreatic {beta}-cell apoptosis, leading to exacerbation of Type 2 diabetes (T2D). Cross-amyloid interactions between A{beta} and IAPP have been described both in vivo and in vitro, implying the role of A{beta} or IAPP as modulators of cytotoxic self-aggregation of each peptide, and suggesting that A{beta}-IAPP interactions are a potential molecular link between AD and T2D. Using molecular dynamics simulations, "hot spot" regions of the two peptides were studied to understand the formation of hexamers in a heterogenous and homogenous peptide-containing environment. Systems of only A{beta}(16-22) peptides formed antiparallel, {beta}-barrel-like structures, while systems of only IAPP(20-29) peptides formed stacked, parallel beta strands and had relatively unstable aggregation structures after 2 s of simulation time. Systems containing both A{beta} and IAPP (1:1 ratio) hexamers showed antiparallel, {beta}-barrel-like structures, with an interdigitated arrangement of A{beta}(16-22) and IAPP(20-29). These {beta}-barrel structures have features of cytotoxic amyloid species identified in previous literature. Ultimately, this work seeks to provide atomistic insight into both the mechanism behind cross-amyloid interactions and structural morphologies of these toxic amyloid species. Statement of SignificanceMolecular knowledge, biophysical characterization, structural morphologies, and formation pathways of amyloid oligomers - specifically low-molecular weight, cross-amyloid oligomers - remain preliminary and undefined. Characterizing interactions between homogenous and heterogenous amyloid oligomers is of great interest given that certain oligomer morphologies contribute to cytotoxicity, eventually resulting in comorbid diseases such as Alzheimers disease (AD) and Type 2 Diabetes Mellitus (T2DM). Utilizing model systems (e.g., fragments of full-length peptides) and molecular dynamics (MD) simulations to probe the biophysical underpinnings of cross-amyloid oligomer structures is the first step in understanding the dynamics, stability, and potential modes of cytotoxicity of these species, providing important insights into targetable biomolecular structures.

biochemistry↗

bioRxiv2020

Perinatal fentanyl exposure leads to long-lasting impairments in somatosensory circuit function and behavior

One consequence of the opioid epidemic are lasting neurodevelopmental sequelae afflicting adolescents exposed to opioids in the womb. A translationally relevant and developmentally accurate preclinical model is needed to understand the behavioral, circuit, network, and molecular abnormalities resulting from this exposure. By employing a novel preclinical model of perinatal fentanyl exposure, our data reveal that fentanyl has several dose-dependent, developmental consequences to somatosensory function and behavior. Newborn male and female mice exhibit signs of withdrawal and sensory-related deficits that extend at least to adolescence. As fentanyl exposure does not affect dams health or maternal behavior, these effects result from the direct actions of perinatal fentanyl on the pups developing brain. At adolescence, exposed mice exhibit reduced adaptation to sensory stimuli, and a corresponding impairment in primary somatosensory (S1) function. In vitro electrophysiology demonstrates a long-lasting reduction in S1 synaptic excitation, evidenced by decreases in release probability, NMDA receptor-mediated postsynaptic currents, and frequency of miniature excitatory postsynaptic currents, as well as increased frequency of miniature inhibitory postsynaptic currents. In contrast, anterior cingulate cortical neurons exhibit an opposite phenotype, with increased synaptic excitation. Consistent with these canghes, electrocorticograms reveal suppressed ketamine-evoked {gamma} oscillations. Morphological analysis of S1 pyramidal neurons indicate reduced dendritic complexity, dendritic length, and soma size. Further, exposed mice exhibited abnormal cortical mRNA expression of key receptors and neuronal growth and development, changes that were consistent with the electrophysiological and morphological changes. These findings demonstrate the lasting sequelae of perinatal fentanyl exposure on sensory processing and function.

neuroscience↗

bioRxiv2020

An amygdalo-parabrachial pathway regulates pain perception and chronic pain

The parabrachial (PB) complex mediates both ascending nociceptive signaling and descending pain modulatory information in the affective/emotional pain pathway. We have recently reported that chronic pain is associated with amplified activity of PB neurons in a rat model of neuropathic pain. Here we demonstrate that similar activity amplification occurs in mice, and that this is related to suppressed inhibition to PB neurons from the central nucleus of the amygdala (CeA). Animals with pain after chronic constriction injury of the infraorbital nerve (CCI-Pain) displayed higher spontaneous and evoked activity in PB neurons, and a dramatic increase in after-discharges--responses that far outlast the stimulus--compared to controls. PB neurons in CCI-Pain animals showed a reduction in inhibitory, GABAergic inputs. We show that--in both rats and mice--PB contains few GABAergic neurons, and that most of its GABAergic inputs arise from CeA. These CeA GABA neurons express dynorphin, somatostatin and/or corticotropin releasing hormone. We find that the efficacy of this CeA-LPB pathway is suppressed in chronic pain. Further, optogenetically stimulating this pathway suppresses acute pain, and inhibiting it, in naive animals, evokes pain behaviors. These findings demonstrate that the CeA-LPB pathway is critically involved in pain regulation, and in the pathogenesis of chronic pain. Significance StatementWe describe a novel pathway, consisting of inhibition by dynorphin, somatostatin and corticotropin-releasing hormone expressing neurons in the central nucleus of the amygdala that project to the parabrachial nucleus (PB). We show that this pathway regulates the activity of pain-related neurons in PB, and that, in chronic pain, this inhibitory pathway is suppressed, and that this suppression is causally related to pain perception. We propose that this amygdalo-parabrachial pathway is a key regulator of both chronic and acute pain, and a novel target for pain relief.

neuroscience↗