Biology subjects

Khan, A. M.

Publications and source records attributed to Khan, A. M..

At least 19 recordsLinked to original sources

bioRxiv2025

Mechanism of ERK-mediated Rho Activation and Stress Fiber Assembly for Cell Migration

The growth factor-activated RAS/Extracellular Regulated Kinase (ERK) pathway is a fundamental regulatory pathway that induces cell migration. ERK supports protrusion of a leading edge and also activates the small GTPase Rho, which induces actin assembly into contractile stress fibers that pull the cell body forward. Yet, the mechanism behind ERKs induction of Rho in the cell body has remained elusive. We discover here that ERK controls Rho activity and contractile stress fibers by inhibiting Ezrin, a protein that physically links proximal actin filaments to the plasma membrane, but which also inhibits Rho by recruiting and activating ARHGAP18. ERK specifically reduces Ezrin activity in the cell body by phosphorylating the C-terminal tail of the Ezrin-activating kinase lymphocyte-oriented kinase (LOK). This phosphorylation inhibits LOKs activation of Ezrin, thereby releases Ezrins inhibition of Rho and stress fibers. The ERK-LOK-Ezrin-ARHGAP18-Rho signal provides key mechanistic insight into how ERK, activated during development, wound healing, and cancer, induces Rho activity and stress fibers for cell migration.

cell biology↗

bioRxiv2025

Elaborating the connections of a closed-loop forebrain circuit in the rat: Circumscribed evidence for novel topography within a cortico-striato-pallidal triple descending projection, with thalamic feedback, to the anterior lateral hypothalamic area

Motivated behaviors are regulated by distributed forebrain networks. Traditional approaches have often focused on individual brain regions and connections that do not capture the topographic organization of forebrain connectivity. We performed co-injections of anterograde and retrograde tract tracers in rats to provide novel high-spatial resolution evidence of topographic connections that elaborate a previously identified closed-loop forebrain circuit implicated in affective and motivational processes. The nodes of this circuit include select regions of the medial prefrontal cortex (defined here more specifically as the cingulate region, CNG), a dorsomedial portion of the nucleus accumbens (ACBdm), a portion of the medial substantia innominata (SIm), and the anterior lateral hypothalamic area (LHAa). The circuit also reportedly receives a feedback loop from the anterior region of the paraventricular thalamic nucleus (PVTa). In this draft report, we provide detailed circumscribed evidence supporting these regions as interconnected nodes, and provide several novel findings concerning the topographic organization of their projections. First, we identified the ACBdm based on its unique connectivity. Anterograde labeling from anterior paraventricular thalamic nucleus (PVTa) and retrograde labeling from medial substantia innominata (SIm) and lateral hypothalamic area (LHA) were restricted to the dorsomedial ACB (ACBdm). Strikingly, this labeling formed a longitudinal column extending along virtually the entire anteroposterior axis of ACBdm. Subsequent analysis revealed a convergence of ACBdm axon terminals and retrogradely labeled neurons from LHA within the anterior SIm. Furthermore, we identified cortical CNG regions related to this circuit. These regions contained retrograde labeling from both ACBdm and LHA, and anterograde labeling from PVTa. These cortical subdomains included regions previously implicated in the circuit but for which detailed organization has been unknown: (1) a region between the posterior prelimbic and infralimbic areas; (2) posterior part of basolateral and basomedial amygdalar nuclei, and (3) anterior pole of ventral subiculum. Our circumscribed findings, which await additional samples and analysis, support the existence of a topographically organized closed-loop circuit and identify two additional novel features: (1) direct evidence for an elaborate core rostrocaudal topography for a cortico-striato-pallidal motif comprising a triple descending projection to the LHA via direct, indirect, and "hyperdirect" pathways, and (2) a thalamic feedback system with specific projections to each cortical and striatal node of the circuit. We discuss the implications of this newly elaborated circuit for understanding the neural basis of motivational processes. Significance StatementWe used a bottom-up approach to identify a distinct longitudinal column of dorsomedial nucleus accumbens (ACBdm) that spans its anteroposterior axis. This region projects to medial substantia innominata (SIm) and lateral hypothalamic area (LHA), resembling the "direct" and "indirect" pathways of the classical basal ganglia circuit. We also identified topographically distinct regions in medial prefrontal cortex (strictly delineated here as the cingulate region, CNG), ventral subiculum (SUBv), and basolateral amygdala (BLA) that project to both ACBdm and LHA, further defining the circuit. Finally, we identified an LHA-to-anterior paraventricular thalamic nucleus (PVTa) feedback projection that selectively targets cortical and striatal nodes within the circuit. Our work provides novel detailed maps that bolster the proposal that this "triple descending projection" (cortico-striato-pallidal) and associated thalamic feedback loop play a role in affective and motivational processes.

neuroscience↗

bioRxiv2024

Chemoarchitectural studies of the rat hypothalamus and zona incerta.Chemopleth 1.0, a downloadable interactive Brain Maps spatial database of five co-visualizable neurochemical systems, with novel feature- and grid-based mapping tools

The hypothalamus and zona incerta of the brown rat (Rattus norvegicus), a model organism important for translational neuroscience research, contain diverse neuronal populations essential for survival, but how these populations are structurally organized as systems remains elusive. With the advent of novel gene-editing technologies and artificial intelligence, there is an apparent research need for high-spatial-resolution maps of rat hypothalamic neurochemical cell types to aid in their gene-directed targeting, to validate their expression in transgenic lines, or to supply precious ground-truth training data for machine learning algorithms. Here, we present Chemopleth 1.0 [available at: https://doi.org/10.5281/zenodo.15788189], a chemoarchitecture database for the rat hypothalamus (HY) and zona incerta (ZI), which features downloadable interactive maps featuring the census distributions of five immunoreactive neurochemical systems: (1) vasopressin (as detected from its gene co-product, copeptin); (2) neuronal nitric oxide synthase (EC 1.14.13.39); (3) hypocretin 1/orexin A; (4) melanin-concentrating hormone; and (5) alpha-melanocyte-stimulating hormone. These maps are formatted for the widely used Brain Maps 4.0 (BM4.0) open-access rat brain atlas (RRID:SCR_017314). Importantly, this dataset retains atlas stereotaxic coordinates that facilitate the precise targeting of the cell bodies and/or axonal fibers of these neurochemical systems, thereby potentially serving to streamline delivery of viral vectors for gene-directed manipulations. The maps are presented together with novel open-access tools to visualize the data, including a new workflow to quantify cell positions and fiber densities for BM4.0. The workflow produces "heat maps" of neurochemical distributions from multiple subjects: 1) isopleth maps that represent consensus distributions independent of underlying atlas boundary conditions, and 2) choropleth maps that provide distribution differences based on cytoarchitectonic boundaries. The database files, generated using the Adobe(R) Illustrator(R) vector graphics environment, can also be opened using the free vector graphics editor, Inkscape. We also introduce a refined grid-based coordinate system for this dataset, register it with previously published spatial data for the HY and ZI, and introduce novel grid-based annotation of experimental observations. This database provides critical spatial targeting information for these neurochemical systems unavailable from mRNA-based maps and allows readers to place their own datasets in register with them. It also provides a space for the continued buildout of a community-driven atlas-based spatial model of rat hypothalamic chemoarchitecture, allowing experimental observations from multiple laboratories to be registered to a common spatial framework.

neuroscience↗

bioRxiv2024

Topographic organization of bidirectional connections between the cingulate region (infralimbic area and anterior cingulate area, dorsal part) and the interbrain (diencephalon) of the adult male rat

The medial prefrontal cortex [cingulate region (Brodmann, 1909) (CNG)] in the rat is a connectionally and functionally diverse structure. It harbors cerebral nuclei that use long-range connections to promote adaptive changes to ongoing behaviors. The CNG is often described across functional and anatomical gradients, a dorsal-ventral gradient being the most prominent. Topographic organization is a general feature of the nervous system, and it is becoming clear that such spatial arrangements can reflect connectional, functional, and cellular differences. Portions of the CNG are known to form reciprocal connections with cortical areas and thalamus; however, these connectional features have not been described in detail or mapped to standardized rat brain atlases. Here, we used co-injected anterograde (Phaseolus vulgaris leucoagglutinin) and retrograde (cholera toxin B subunit) tracers throughout the CNG to identify zones of reciprocal connectivity in the diencephalon [or interbrain (Baer, 1837) (IB)]. Tracer distributions were observed using a Nissl-based atlas-mapping approach that facilitates description of topographic organization. This draft report describes CNG connections of the infralimbic area (Rose & Woolsey, 1948) (ILA) and the anterior cingulate area, dorsal part (Krettek & Price, 1977) (ACAd) throughout the IB. We found that corticothalamic connections are predominantly reciprocal, and that ILA and ACAd connections tended to be spatially segregated with minimal overlap. In the hypothalamus (Kuhlenbeck, 1927), we found dense and specific ILA-originating terminals in the following Brain Maps 4.0 atlas territories: dorsal region (Swanson, 2004) (LHAd) and suprafornical region (Swanson, 2004) (LHAs) of the lateral hypothalamic area (Nissl, 1913), parasubthalamic nucleus (Wang & Zhang, 1995) (PSTN), tuberal nucleus, terete part (Petrovich et al., 2001) (TUte), and an ill-defined dorsal cap of the medial mammillary nucleus (Gudden, 1881) (MM). We discuss these findings in the context of feeding behaviors.

neuroscience↗

bioRxiv2024

Sympathetic innervation of interscapular brown adipose tissue is not a predominant mediator of OT-elicited reductions of body weight gain and adiposity in male diet-induced obese rats

Recent studies indicate that central administration of oxytocin (OT) reduces body weight (BW) in high fat diet-induced obese (DIO) rodents by reducing energy intake and increasing energy expenditure (EE). Previous studies in our lab have shown that administration of OT into the fourth ventricle (4V; hindbrain) elicits weight loss and stimulates interscapular brown adipose tissue temperature (TIBAT) in DIO rats. We hypothesized that OT-elicited stimulation of sympathetic nervous system (SNS) activation of IBAT contributes to its ability to activate BAT and reduce BW in DIO rats. To test this, we determined the effect of disrupting SNS activation of IBAT on OT-elicited stimulation of TIBAT and reduction of BW in DIO rats. We first confirmed that bilateral surgical SNS denervation to IBAT was successful based on having achieved [≥] 60% reduction in IBAT norepinephrine (NE) content from DIO rats. NE content was selectively reduced in IBAT by 94.7 {+/-} 2.7, 96.8 {+/-} 1.8 and 85.9 {+/-} 6.1% (P<0.05) at 1, 6 and 7-weeks post-denervation, respectively, and was unchanged in liver or inguinal white adipose tissue. We then measured the impact of bilateral surgical SNS denervation to IBAT on the ability of acute 4V OT (1, 5 {micro}g) to stimulate TIBAT in DIO rats. We found that the high dose of 4V OT (5 {micro}g) stimulated TIBAT similarly between sham and denervated rats (P=NS) and that the effects of 4V OT to stimulate TIBAT did not require beta-3 adrenergic receptor signaling. We subsequently measured the effect of bilateral surgical denervation of IBAT on the effect of chronic 4V OT (16 nmol/day) or vehicle infusion to reduce BW, adiposity, and energy intake in DIO rats. Chronic 4V OT reduced BW gain by -7.2 {+/-} 9.6 g and -14.1 {+/-} 8.8 g in sham and denervated rats (P<0.05 vs vehicle treatment), respectively, and this effect was similar between groups (P=NS). These effects were associated with reductions in adiposity and energy intake (P<0.05). Collectively, these findings support the hypothesis that sympathetic innervation of IBAT is not required for central OT to increase BAT thermogenesis and reduce BW gain and adiposity in male DIO rats.

neuroscience↗

bioRxiv2024

Brain-wide projections of mouse dopaminergic zona incerta neurons

The zona incerta (ZI) supports diverse behaviors including binge feeding, sleep/wake cycles, nociception, and hunting. This diversity of functions can be attributed to the heterogenous neurochemicals, cytoarchitecture, and efferent connections that characterize the ZI. The ZI is predominantly GABAergic, but we recently identified a subset of medial ZI GABA cells that co-express dopamine (DA), as marked by the enzyme tyrosine hydroxylase (TH). While the role of GABA within the ZI is well studied, little is understood about the function of ZI DA cells. To identify potential roles of ZI DA cells we mapped the efferent fiber projections from Th-cre ZI cells. We first validated a Th-cre;L10-Egfp mouse line and found that medial Egfp ZI cells were more likely to co-express TH-immunoreactivity (TH-ir). We thus delivered a cre-dependent virus into the medial ZI of Th-cre or Th-cre;L10-Egfp mice and selected two injection cases for full brain mapping. We selected the cases with the lowest (17%) and highest (53%) percentage of colocalization between TH-ir and virus transfected cells labelled with DsRed. Overall, DsRed-labelled fibers were observed throughout the brain and were most prominent within motor-related regions of the midbrain (MBmot), notably the periaqueductal grey area and superior colliculus. We also observed considerable DsRed-labelled fibers within the polymodal cortex associated regions of the thalamus (DORpm), including the paraventricular thalamic nucleus and nucleus of reunions. Overall, ZI DA cells displayed a similar connectivity profile to ZI GABA cells, suggesting that ZI DA cells may perform synergistic or opposing functions at the same target sites. List of RRIDsAB_2201528, AB_10013483, AB_11177031, AB_2340593, AB_2315778, SCR_016477 Three key points- Tyrosine hydroxylase immunoreactivity was more prominent in the medial zona incerta - Intersection points from two Th-cre injection cases revealed common target regions - Dopaminergic zona incerta cells project predominantly to motor-related brain regions

neuroscience↗

bioRxiv2024

MDRepo - an open environment for data warehousing and knowledge discovery from molecular dynamics simulations

BackgroundMolecular Dynamics (MD) simulation of biomolecules provides important insights into conformational changes and dynamic behavior, revealing critical information about folding and interactions with other molecules. This enables advances in drug discovery and the design of therapeutic interventions. The collection of simulations stored in computers across the world holds immense potential to serve as training data for future Machine Learning models that will transform the prediction of structure, dynamics, drug interactions, and more. A needIdeally, there should exist an open access repository that enables scientists to submit and store their MD simulations of proteins and protein-drug interactions, and to find, retrieve, analyze, and visualize simulations produced by others. However, despite the ubiquity of MD simulation in structural biology, no such repository exists; as a result, simulations are instead stored in scattered locations without uniform metadata or access protocols. A solutionHere, we introduce MDRepo, a robust infrastructure that supports a relatively simple process for standardized community contribution of simulations, activates common downstream analyses on stored data, and enables search, retrieval, and visualization of contributed data. MDRepo is built on top of the open-source CyVerse research cyberinfrastructure, and is capable of storing petabytes of simulations, while providing high bandwidth upload and download capabilities and laying a foundation for cloud-based access to its stored data.

biochemistry↗

bioRxiv2023

Dextromethorphan inhibits collagen transport in the endoplasmic reticulum eliciting an anti-fibrotic response in ex-vivo and in vitro models of pulmonary fibrosis

Excessive deposition of fibrillar collagen in the interstitial extracellular matrix (ECM) of human lung tissue causes fibrosis, which can ultimately lead to organ failure. Despite our understanding of the molecular mechanisms underlying the disease, a cure for pulmonary fibrosis has not yet been found. In this study, we screened an FDA-approved drug library containing 712 drugs and found that Dextromethorphan (DXM), a cough expectorant, significantly reduces the amount of excess fibrillar collagen deposited in the ECM in in-vitro cultured primary human lung fibroblasts (NHLF) and ex-vivo cultured human precision-cut lung slice (hPCLS) models of lung fibrosis. Reduced extracellular fibrillar collagen levels in the ECM upon DXM treatment are due to a reversible trafficking inhibition of collagen type I (COL1) in the endoplasmic reticulum (ER) in TANGO1 and HSP47 positive structures. Mass spectrometric analysis shows that DXM causes hyper-hydroxylation of proline and lysine residues on Collagen (COL1, COL3, COL4, COL5, COL7, COL12) and Latent-transforming growth factor beta-binding protein (LTBP1 and LTBP2) peptides coinciding with their secretion block. In addition, thermal proteome profiling of cells treated with DXM shows increased thermal stability of prolyl-hydroxylases such as P3H2, P3H3, P3H4, P4HA1 and P4HA2, suggesting a change in activity. Transcriptome analysis of pro-fibrotic stimulated NHLFs and hPCLS upon DXM treatment showed activation of an anti-fibrotic program via regulation of pathways such as those involved in the MMP-ADAMTS axis, WNT, and fibroblast-to-myofibroblast differentiation. Taken together, the data obtained from both in-vitro and ex-vivo models of fibrogenesis show that Dextromethorphan has potent anti-fibrotic activity by efficient inhibition of COL1 membrane trafficking in the ER.

cell biology↗

bioRxiv2022

Age-associated downregulation of glutamate and GABA neurotransmission-related gene expression in the rostral ventrolateral medulla of male Fischer 344 rats

The rostral ventrolateral medulla (RVLM), a part of the medullary reticular formation, plays a major role in several physiological responses, including cardiovascular and sympathetic nervous system functions. Although aging causes disturbances in the responses of these physiological systems, RVLM involvement in these age-related changes is not clear. Previous work using high-throughput gene expression analysis of the RVLM in aged animals suggested that chemical neurotransmission-related genes might be downregulated with advancing age. Since RVLM function involves a balance of signals from inhibitory and excitatory inputs, which is largely mediated by gamma-aminobutyric acid (GABA) and excitatory amino acid (EAA) neurotransmission, we hypothesized that aging is associated with altered excitatory and/or inhibitory neurotransmission-related gene expression in the RVLM. To test this hypothesis, we micropunched an RVLM-containing area from young (3-5 months), middle-aged (12-14 months), and aged (22- 26 months) Fischer 344 male rats. RNA purified from these micropunches was analyzed using GABA and Glutamate RT2 Profiler PCR arrays (n= 8-10). Each profiler array has primers for 84 GABA and glutamate neurotransmission related genes. In addition, the expression of selected genes was validated at the RNA level using TaqMan(R) based-qPCR and at the protein level using western blotting. All the genes that displayed significant differential expression (1.5-fold, p < .05, FDR < .05) were identified to be downregulated in the RVLM of aged and middle-aged rats compared to young rats. This downregulation did not appear to be a result of RVLM tissue sampling differences among the age groups, since a separate validation of our sampling method, which involved careful mapping of micropunched regions to a standardized brain atlas, revealed no spatial differences in sampled sites among age groups. Among the downregulated genes, the percentage of glutamate neurotransmission-related genes was higher than GABA neurotransmission-related genes. The Solute carrier family 1 member 6 (Slc1a6) gene showed the highest fold downregulation at the RNA level in the RVLM of aged compared to young rats, and its protein product, Excitatory amino acid transporter 4 (EAAT4), showed a downregulatory trend in the RVLM of aged and middle-aged rats. These results suggest that molecular constituents of both GABA and glutamate neurotransmission might be altered in the RVLM of aged and middle-aged rats, and the changes in glutamate neurotransmission might be more prominent. Investigating age-associated anatomical and functional changes in RVLM GABA and glutamate neurotransmission might provide a foundation for understanding the effects of aging on physiological function.

neuroscience↗

bioRxiv2022

Negligible peptidome diversity of SARS-CoV-2 and its higher taxonomic ranks

The unprecedented increase in SARS-CoV-2 sequence data limits the application of alignment-dependent approaches to study viral diversity. Herein, we applied our recently published UNIQmin, an alignment-free tool to study the protein sequence diversity of SARS-CoV-2 (sub-species) and its higher taxonomic lineage ranks (species, genus, and family). Only less than 0.5% of the reported SARS-CoV-2 protein sequences are required to represent the inherent viral peptidome diversity, which only increases to a mere [~]2% at the family rank. This is expected to remain relatively the same even with further increases in the sequence data. The findings have important implications in the design of vaccines, drugs, and diagnostics, whereby the number of sequences required for consideration of such studies is drastically reduced, short-circuiting the discovery process, while still providing for a systematic evaluation and coverage of the pathogen diversity.

bioinformatics↗

bioRxiv2022

Glycemic challenge is associated with the rapid cellular activation of the locus ceruleus and nucleus of solitary tract: Circumscribed spatial analysis of phosphorylated MAP kinase immunoreactivity in relation to catecholaminergic and cholinergic chemoarchitecture

Rodent studies indicate that impaired glucose utilization or hypoglycemia is associated with cellular activation of neurons in the medulla (Winslow, 1733) (MY) believed to control feeding behavior and glucose counterregulation. However, such activation has been tracked primarily within hours of the challenge, rather than sooner, and has been poorly mapped within standardized brain atlases. Here, we report that within 15 min of receiving 2-deoxy-D-glucose (2-DG; 250 mg/kg, i.v.), which can trigger glucoprivic feeding behavior, marked elevations were observed in the numbers of rhombic brain (His, 1893) (RB) neuronal cell profiles immunoreactive for the cellular activation marker(s), phosphorylated p44/42 MAP kinases (phospho-ERK1/2), some of which were also catecholaminergic. We mapped their distributions within an open-access rat brain atlas and found that 2-DG-treated rats (compared to their saline-treated controls) displayed greater numbers of phospho-ERK1/2+ neurons in the locus ceruleus (Wenzel & Wenzel, 1812) (LC) and the nucleus of solitary tract (>1840) (NTS). Thus, 2-DG-activation of certain RB neurons is more rapid than perhaps previously realized, engaging neurons that serve multiple functional systems and are of varying cellular phenotypes. Mapping these populations within standardized brain atlas maps streamlines their targeting and/or comparable mapping in preclinical rodent models of disease.

neuroscience↗

bioRxiv2022

UNIQmin, an alignment-free tool to study viral sequence diversity across taxonomic lineages: a case study of monkeypox virus

Sequence changes in viral genomes generate protein sequence diversity that enable viruses to evade the host immune system, hindering the development of effective preventive and therapeutic interventions. Massive proliferation of sequence data provides unprecedented opportunities to study viral adaptation and evolution. Alignment-free approach removes various restrictions, otherwise posed by an alignment-dependent approach for the study of sequence diversity. The publicly available tool, UNIQmin offers an alignment-free approach for the study of viral sequence diversity at any given rank of taxonomy lineage and is big data ready. The tool performs an exhaustive search to determine the minimal set of sequences required to capture the peptidome diversity within a given dataset. This compression is possible through the removal of identical sequences and unique sequences that do not contribute effectively to the peptidome diversity pool. Herein, we describe a detailed three-part protocol utilizing UNIQmin to generate the minimal set for the purpose of viral diversity analyses, alignment-free at any rank of the taxonomy lineage, using the latest global public health threat monkeypox virus (MPX) as a case study. This protocol enables systematic diversity study across the taxonomic lineage, which are much needed for our future preparedness of a viral epidemic, in particular when data is in abundance, freely available, and alignment is not an option.

bioinformatics↗

bioRxiv2022

Ecosystem gross primary productivity after autumn snowfall and melt events in a mountain meadow

Vegetation productivity is increasing across much of the U.S. Northern Great Plains but is decreasing in some nearby Northern Rocky Mountain grasslands due to increases in aridity. Mountain grasslands support critical ecosystem services that are under threat from ongoing land use and climate changes, and it is important to understand their function across all changing seasons. Observing the full range of montane ecosystem productivity is challenging because site access is often difficult during the "shoulder seasons" in spring and autumn if the snowpack is not fully developed or degrading. It is unclear if decreases to montane grassland productivity from drying autumns can be offset in part by late-season green-ups after precipitation events. These include the snowfall/snowmelt periods that often characterize the summer-to-winter transition in the Northern Rockies. Here, we quantify the ecosystem carbon uptake that occurs after snowfall and melt in climatological autumn (September, October, and November) in a montane grassland in Montana, USA using a combination of eddy covariance, phenological camera, and remote sensing analyses. Carbon dioxide flux follows a diurnal pattern after autumn snowmelt events despite overall ecosystem losses of C, suggesting that post-snowmelt photosynthesis helps dampen C loss during autumn and provides fresh photosynthate to support ecosystem functioning. Light-saturated photosynthesis after two snow events was not different than before snowfall ([~]6 {micro}mol CO2 m-2 s-1 in 2016 and [~]2.5 {micro}mol CO2 m-2 s-1 in 2017); observations are consistent with the notion that canopy photosynthesis is resistant, rather than resilient, to the first snow disturbances. MODIS observations also suggest that post-snowfall increases in NDVI can occur but do not happen every year, such that late-season photosynthesis is not a reliable source of fresh photosynthate. These late-season carbon uptake events likely play a small role in the annual ecosystem carbon balance but may be disproportionately important for organisms faced with dwindling late-season forage and regrowth in spring. Future efforts should seek to understand the community and ecosystem consequences of vegetation functioning during autumn as part of an expanded effort to understand phenological changes during this under-studied and changing time of year.

ecology↗

bioRxiv2022

Withdrawal from repeated nicotine vapor exposure increases somatic signs of physical dependence, anxiety-like behavior, and brain reward thresholds in adult male rats.

In recent years, there has been a dramatic increase in nicotine vapor consumption via electronic nicotine delivery systems (i.e., e-cigarettes), particularly in adolescents. While recent work has focused on the health effects of nicotine vapor exposure, its effects on the brain and behavior remain unclear. In this study, we assessed the effects that cessation from repeated nicotine vapor exposure had on behavioral and neuronal measures of withdrawal. For Experiment 1, fifty-six adult male rats were tested for plasma cotinine levels, somatic withdrawal signs, and anxiety-like behavior in the elevated plus maze, immediately following precipitated withdrawal from repeated exposure to 12 or 24 mg/mL nicotine vapor. In Experiment 2, twelve adult male rats were tested for intracranial self-stimulation (ICSS) across 14 days of exposure to 24 mg/mL nicotine vapor and across the 14 days immediately following nicotine exposure. Results revealed that plasma cotinine, somatic signs, anxiety-like behavior, and ICSS stimulation thresholds were all observed to be elevated during withdrawal in the 24 mg/mL nicotine group, when compared to vehicle controls (50/50 vegetable glycerin/propylene glycol). The data suggest that cessation from repeated nicotine vapor exposure using our preclinical model leads to nicotine dependence and withdrawal, and demonstrates that the vapor system described in these experiments is a viable pre-clinical model of e-cigarette use in humans. Further characterization of the mechanisms driving nicotine vapor abuse and dependence is needed to improve policies and educational campaigns related to e-cigarette use. HighlightsO_LIA rodent model of nicotine e-cigarette vapor use was utilized to assess effects of cessation from repeated nicotine vapor exposure on behavioral and neuronal measures of drug withdrawal. C_LIO_LICessation of repeated nicotine vapor exposure resulted in increased plasma cotinine levels, somatic withdrawal signs, and anxiety-like behavior. C_LIO_LICessation of repeated nicotine vapor exposure resulted in elevations of ICSS reward threshold. C_LIO_LIElectrode implantations for ICSS were mapped by location and threshold to a standardized reference atlas of the rat brain to facilitate comparisons with the published literature. C_LI

neuroscience↗

bioRxiv2021

Nascent adhesions differentially regulate lamellipodium velocity and persistence

Cell migration is essential to physiological and pathological biology. Migration is driven by the motion of a leading edge, in which actin polymerization pushes against the edge and adhesions transmit traction to the substrate while membrane tension increases. How the actin and adhesions synergistically control edge protrusion remains elusive. We addressed this question by developing a computational model in which the Brownian ratchet mechanism governs actin filament polymerization against the membrane and the molecular clutch mechanism governs adhesion to the substrate (BR-MC model). Our model predicted that actin polymerization is the most significant driver of protrusion, as actin had a greater effect on protrusion than adhesion assembly. Increasing the lifetime of nascent adhesions also enhanced velocity, but decreased the protrusions motional persistence, because filaments maintained against the cell edge ceased polymerizing as membrane tension increased. We confirmed the model predictions with measurement of adhesion lifetime and edge motion in migrating cells. Adhesions with longer lifetime were associated with faster protrusion velocity and shorter persistence. Experimentally increasing adhesion lifetime increased velocity but decreased persistence. We propose a mechanism for actin polymerization-driven, adhesion-dependent protrusion in which balanced nascent adhesion assembly and lifetime generates protrusions with the power and persistence to drive migration.

cell biology↗

bioRxiv2019

Cognitive and non-cognitive outcomes associated with student engagement in a novel brain mapping and connectomics course-based undergraduate research experience

Course-based undergraduate research experiences (CUREs) engage emerging scholars in the authentic process of scientific discovery, and foster their development of content knowledge, motivation, and persistence in the science, technology, engineering, and mathematics (STEM) disciplines. Importantly, authentic research courses simultaneously offer investigators unique access to an extended population of students who receive education and mentoring in conducting scientifically relevant investigations and who are thus able to contribute effort toward big-data projects. While this paradigm benefits fields in neuroscience, such as atlas-based brain mapping of nerve cells at the tissue level, there are few documented cases of such laboratory courses offered in the domain.\n\nHere, we describe a curriculum designed to address this deficit, evaluate the scientific merit of novel student-produced brainatlasmapsofimmunohistochemically-identifiednervecellpopulations for the rat brain, and assess shifts in science identity, attitudes, and science communication skills of students engaged in the introductory-level Brain Mapping and Connectomics (BM&C) CURE. BM&C students reported gains in research and science process skills following participation in the course. Furthermore, BM&C students experienced a greater sense of science identity, including a greater likelihood to discuss course activities with non-class members compared to their non-CURE counterparts. Importantly, evaluation of student-generated brain atlas maps indicated that the course enabled students to produce scientifically valid products and make new discoveries to advance the field of neuroanatomy. Together, these findings support the efficacy of the BM&C course in addressing the relatively esoteric demands of chemoarchitectural brain mapping.

scientific communication and education↗

bioRxiv2019

Distributions of hypothalamic neuron populations co-expressing tyrosine hydroxylase and the vesicular GABA transporter in the mouse

The hypothalamus contains catecholaminergic neurons marked by the expression of tyrosine hydroxylase (TH). As multiple chemical messengers coexist in each neuron, we determined if hypothalamic TH-immunoreactive (ir) neurons express glutamate or GABA. We used Cre/loxP recombination to express enhanced GFP fluorescence (EGFP) in neurons that express the vesicular glutamate (vGLUT2) or GABA transporter (vGAT), then determined TH immunoreactivity in glutamatergic or GABAergic neurons, respectively. EGFP-positive vGLUT2 neurons were not TH-ir. However, discrete TH-ir signals colocalized with EGFP-positive vGAT neurons, which we validated by in situ hybridization for Vgat mRNA. In order to contextualize the observed pattern of TH+EGFP colocalization in vGAT neurons, we first performed Nissl-based parcellation and plane-of-section analysis, and then mapped the distribution of TH-ir vGAT neurons onto atlas templates from the Allen Reference Atlas (ARA) of the mouse brain. TH-ir vGAT neurons were distributed throughout the rostrocaudal extent of the hypothalamus. Within the ARA ontology of gray matter regions, TH-ir neurons localized primarily to the periventricular hypothalamic zone, periventricular hypothalamic region, and lateral hypothalamic zone. There was a very strong presence of EGFP fluorescence in TH-ir neurons across all brain regions, but the most striking colocalization was found in the zona incerta (ZI) - a region assigned to the hypothalamus in the ARA - where every TH-ir neuron was EGFP-positive. Neurochemical characterization of these ZI neurons revealed that they display immunoreactivity for dopamine but not dopamine {beta}-hydroxylase. In aggregate, these findings indicate the existence of a novel hypothalamic population in the mouse that may signal through the release of GABA and/or dopamine.

neuroscience↗

bioRxiv2019

BIN overlap confirms transcontinental distribution of pest aphids (Hemiptera: Aphididae)

DNA barcoding is highly effective for identifying specimens once a reference sequence library is available for the species assemblage targeted for analysis. Despite the great need for an improved capacity to identify the insect pests of crops, the use of DNA barcoding is constrained by the lack of a well-parameterized reference library. The current study begins to address this limitation by developing a DNA barcode reference library for the pest aphids of Pakistan. It also examines the affinities of these taxa with conspecific taxa from other geographic regions based on both conventional taxonomy and Barcode Index Numbers (BINs). A total of 809 aphids were collected from 123 plant species at 87 sites across Pakistan. Morphological study and DNA barcoding allowed 774 specimens to be identified to one of 42 species while the others were placed to a genus or subfamily. The 801 sequences obtained from these specimens were assigned to 52 BINs whose monophyly were supported by neighbor-joining (NJ) clustering and Bayesian inference. The 42 species were assigned to 41 BINs with 38 showing BIN concordance; one species (Rhopalosiphum padi) was assigned to two BINs, while two others (Aphis affinis, Aphis gossypii) were assigned to the same BIN, while one species (Aphis astragalina) lacked a qualifying sequence. The 42 Linnaean species were represented on BOLD by 7,870 records from 69 countries. Combining these records with those from Pakistan produced to 60 BINs with 12 species showing a BIN split and three a BIN merger. Geo-distance correlations showed that intraspecific divergence values for 18 of 37 species were not affected by the distance between populations. Forty four of the 52 BINs from Pakistan had counterparts in 73 countries across six continents, documenting the broad distributions of pest aphids.

ecology↗