Biology subjects

Joshi, N.

Publications and source records attributed to Joshi, N..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Mechanically Tunable, Compostable, Healable and Scalable Engineered Living Materials

Novel design strategies are essential to realize the full potential of Engineered Living Materials (ELMs), including their biodegradability, manufacturability, sustainability, and ability to tailor functional properties. Toward these goals, we present Mechanically Engineered Living Material with Compostability, Healability, and Scalability (MECHS) - a material that integrates these features in the form of a stretchable plastic that is simultaneously flushable, compostable, and exhibits the characteristics of paper. This plastic/paper-like material is produced directly from cultured bacterial biomass (40%) producing engineered curli protein nanofibers in scalable quantities (0.5-1 g L-1). The elongation at break (1-160%) and Youngs modulus (6-450 MPa) of MECHS was tuned to more than two orders of magnitude. By genetically encoded covalent crosslinking of curli nanofibers, we increase the Youngs modulus by two times. MECHS biodegrades completely in 15-75 days, while its mechanical properties are comparable to petrochemical plastics and thus may find use as compostable materials for primary packaging.

bioengineering↗

bioRxiv2023

An injectable in situ crosslinkable platform for ultra-long-acting delivery of hydrophilic therapeutics

Achieving ultra-long-term release of hydrophilic drugs over several months remains a significant challenge for existing long-acting injectables (LAIs). Existing platforms, such as in situ forming implants (ISFI), exhibit high burst release due to solvent efflux and microsphere-based approaches lead to rapid drug diffusion due to significant water exchange and large pores. Addressing these challenges, we have developed an injectable platform that, for the first time, achieves ultra-long-term release of hydrophilic drugs for over six months. This system employs a methacrylated ultra-low molecular weight pre-polymer (polycaprolactone) to create in situ cross-linked depots (ISCD). The ISCDs solvent-free design and dense mesh network, both attributed to the ultra-low molecular weight of the pre-polymer, effectively minimizes burst release and water influx/efflux. In vivo studies in rats demonstrate that ISCD outperforms ISFI by achieving lower burst release and prolonged drug release. We demonstrated the versatility of ISCD by showcasing ultra-long-term delivery of several hydrophilic drugs, including antiretrovirals (tenofovir alafenamide, emtricitabine, abacavir, and lamivudine), antibiotics (vancomycin and amoxicillin) and an opioid antagonist naltrexone. Additionally, ISCD achieved ultra-long-term release of the hydrophobic drug tacrolimus and enabled co-delivery of hydrophilic drug combinations encapsulated in a single depot. We also identified design parameters to tailor the polymer network, tuning drug release kinetics and ISCD degradation. Pharmacokinetic modeling predicted over six months of drug release in humans, significantly surpassing the one-month standard achievable for hydrophilic drugs with existing LAIs. The platforms biodegradability, retrievability, and biocompatibility further underscore its potential for improving treatment adherence in chronic conditions.

bioengineering↗

bioRxiv2023

A Drug-Free Pathogen Capture and Neutralizing Nasal Spray to Prevent Emerging Respiratory Infections

Respiratory infections pose a global health crisis. Vaccines are pathogen specific, and new vaccines are needed for mutants and emerging pathogens. Here, we report a "drug free" prophylactic platform - a "Pathogen Capture and Neutralizing Spray" (PCANS) that acts via a multi-pronged approach to prevent a broad spectrum of respiratory infections. PCANS forms a protective coating in the nasal cavity that enhances the capture of large respiratory droplets. The coating acts as a physical barrier against a broad spectrum of viruses and bacteria, and rapidly neutralizes them, reducing the pathogen load by >99.99%. In mice, PCANS showed nasal retention for at least 8 h and was safe for daily administration. A single prophylactic dose of PCANS protected mice against supra-lethal dosages of a mouse-adapted H1N1 Influenza virus (PR8), reduced lung viral titer by >99.99%, improved survival, and suppressed pathological manifestations. Together, our data suggest PCANS as a promising daily-use prophylactic approach against current and emerging respiratory infections.

bioengineering↗

bioRxiv2023

Split-intein Gal4 provides intersectional genetic labeling that is fully repressible by Gal80

The split-Gal4 system allows for intersectional genetic labeling of highly specific cell-types and tissues in Drosophila. However, the existing split-Gal4 system, unlike the standard Gal4 system, cannot be repressed by Gal80, and therefore cannot be controlled temporally. This lack of temporal control precludes split-Gal4 experiments in which a genetic manipulation must be restricted to specific timepoints. Here, we describe a new split-Gal4 system based on a self-excising split-intein, which drives transgene expression as strongly as the current split-Gal4 system and Gal4 reagents, yet which is fully repressible by Gal80. We demonstrate the potent inducibility of "split-intein Gal4" in vivo using both fluorescent reporters and via reversible tumor induction in the gut. Further, we show that our split-intein Gal4 can be extended to the drug-inducible GeneSwitch system, providing an independent method for intersectional labeling with inducible control. We also show that the split-intein Gal4 system can be used to generate highly cell-type specific genetic drivers based on in silico predictions generated by single cell RNAseq (scRNAseq) datasets, and we describe a new algorithm ("Two Against Background" or TAB) to predict cluster-specific gene pairs across multiple tissue-specific scRNA datasets. We provide a plasmid toolkit to efficiently create split-intein Gal4 drivers based on either CRISPR knock-ins to target genes or using enhancer fragments. Altogether, the split-intein Gal4 system allows for the creation of highly specific intersectional genetic drivers that are inducible/repressible. Significance statementThe split-Gal4 system allows Drosophila researchers to drive transgene expression with extraordinary cell type specificity. However, the existing split-Gal4 system cannot be controlled temporally, and therefore cannot be applied to many important areas of research. Here, we present a new split-Gal4 system based on a self-excising split-intein, which is fully controllable by Gal80, as well as a related drug-inducible split GeneSwitch system. This approach can both leverage and inform single-cell RNAseq datasets, and we introduce an algorithm to identify pairs of genes that precisely and narrowly mark a desired cell cluster. Our split-intein Gal4 system will be of value to the Drosophila research community, and allow for the creation of highly specific genetic drivers that are also inducible/repressible.

genetics↗

bioRxiv2022

Effect of Organic and Chemical Fertilizers on the Nutritional Composition of Amaranthus spinosus

Organic and chemical fertilizers are used in agriculture as they improve the fertility of soil and the growth of plants. So, the present investigation was designed to determine the effect of different fertilizers on the nutritional value of Amaranthus spinosus plant. The quantity of different fertilizers was used as 500 kg h-1. Some selected parameters of soil such as temperature (29.50 C), moisture (3.5 %), Water holding capacity (74%), pH (8.17), organic carbon % (1.90) and organic matter % (3.28) were measured and analysed. There was no significant variation in these parameters under different fertilizers treatment. The phytochemicals of Organic fertilizers treated plant sample had higher concentration of Alkaloid (1.06), flavonoid (0.89), tannin (1.48) and saponin (1.67), ash (7.75), moisture (87.6) and protein (9.1), Fe (0.054), Zn (0.008), Cu (0.001), Na (0.0080), Ca (113) and Mg (93) when compared to the other fertilizer treatments. Inorganic fertilizer did not show any significant effect on plant growth, while the combination of organic and chemical fertilizers was found to have a significant effect. The results reveal that organic fertilizers or their combination with chemical fertilizer are better for the crops than chemical fertilizers.

biochemistry↗

bioRxiv2022

TDP 2 modulates the expression of estrogen-responsive oncogenes

With its ligand estrogen, the estrogen receptor (ER) stimulates tumor cell growth by activating a global transcriptional program. This activation involves topoisomerase 2 (TOP2), which resolves topological problems by transiently creating and re-ligating DNA double-strand breaks (DSBs). Recent studies have uncovered the involvement of DNA repair proteins in the repair of TOP2-induced DSBs. These noncanonical repair pathways may serve as backup processes when TOP2 is halted and fails to re-ligate DSBs, but their impact on transcription remains elusive. In this study, we investigated the role of tyrosyl-DNA phosphodiesterase 2 (TDP2), an enzyme that acts for the removal of halted TOP2 from the 5-end of the DNA, in the estrogen-induced transcriptome. Using TDP2-deficient ER-positive cells and mice, we showed that TDP2 regulates the expression of oncogene MYC. MYC induction by estrogen was a very early event (1 hour) and TOP2-dependent. In TDP2-deficient cells, the induction of MYC by estrogen became prolonged and volatile. Bulk and single-cell RNA-seq identified the oncogenes MYC and CCND1 as genes whose estrogen response was regulated by TDP2. These results suggest that TDP2 may play a role in the repair of TOP2-induced DSBs in specific genomic loci and tightly regulates the expression of oncogenes.

molecular biology↗

bioRxiv2021

Generation of transducible version of a recombinant human HAND2 transcription factor from Escherichia coli

Transcription factor HAND2 has a significant role in vascularization, angiogenesis, and cardiac neural crest development. Also, it is one of the key cardiac factors crucial for the enhanced derivation of functional and mature myocytes from non-myocyte cells. Here, we report the generation of the recombinant human HAND2 fusion protein from the heterologous system. First, we cloned the full-length human HAND2 gene (only protein-coding sequence) after codon optimization along with the fusion tags (for cell penetration, nuclear translocation, and affinity purification) into the expression vector. We then transformed and expressed it in Escherichia coli (E. coli) strain, BL21(DE3). Next, the effect (in terms of expression) of tagging of fusion tags with this recombinant protein at two different terminals was also investigated. Notably, using affinity chromatography, we established the one-step homogeneous purification of human recombinant HAND2 protein; and through circular dichroism spectroscopy, we established that this purified protein had retained its secondary structure. Furthermore, we show that this purified human protein could transduce the human cells and translocate to its nucleus. Prospectively, the purified recombinant HAND2 protein can potentially be a safe and effective molecular tool in the direct cardiac reprogramming process and other biological applications.

bioengineering↗

bioRxiv2021

Wilson disease: intersecting DNA methylation and histone acetylation regulation of gene expression in a mouse model of hepatic copper accumulation

The pathogenesis of Wilson disease (WD) is multi-factorial, involving hepatic and brain copper accumulation due to pathogenic variants affecting the ATP7B gene and downstream epigenetic and metabolic mechanisms. Prior DNA methylation investigations in human WD liver and blood and in a WD mouse model revealed an epigenetic signature of WD, including alterations in the histone deacetylase HDAC5. To test the hypothesis that histone acetylation is altered with respect to copper overload and aberrant DNA methylation in WD, we investigated class IIa histone deacetylases (HDAC4 and HDAC5) and H3K9/H3K27 histone acetylation in the Jackson Laboratory toxic milk (tx-j) mouse model of WD compared to C3HeB/FeJ (C3H) control in response to 3 treatments: 60% kcal fat diet (HFD), D-penicillamine (PCA, copper chelator), and choline (methyl group donor). HDAC5 levels significantly increased in 9-week tx-j livers after 8 days of HFD compared to chow. In 24-week tx-j livers, HDAC4/5 levels were reduced 5- to 10-fold compared to C3H likely through mechanisms involving HDAC phosphorylation. HDAC4/5 levels were also affected by disease progression and accompanied by increased acetylation. PCA and choline partially restored HDAC4, HDAC5, H3K9ac, and H3K27ac levels to that of CH3 liver. Integrated RNA and chromatin immunoprecipitation sequencing analyses revealed genes regulating energy metabolism and cellular stress/development were, in turn, regulated by histone acetylation in tx-j mice compared to C3H, with Ppar and Ppar{gamma} among the most relevant targets. These results suggest dietary modulation of class IIa HDAC4/5, and subsequent H3K9/H3K27 acetylation/deacetylation, can regulate gene expression in key metabolic pathways in the pathogenesis of WD. Significance StatementWilson disease is considered a monogenic disease caused by pathogenic variants in the ATP7B copper transporter, resulting in hepatic and brain copper accumulation. Given the lack of genotype-phenotype correlation, evidence of epigenetic and metabolic mechanisms regulating phenotype in patients and in animal models could explain the high phenotype variability observed in WD. In this study, we identify class IIa histone deacetylases as players involved in the epigenetic regulation of key metabolic pathways that can affect WD severity as well as targets sensitive to dietary modulations, which is an important characteristic for designing effective and feasible therapies. Understanding the epigenetic mechanisms in WD pathogenesis contributes to a better understanding of the phenotypic variability in WD and other common liver conditions.

molecular biology↗

bioRxiv2021

Targeting the artemisinin resistant malaria by repositioning of the anti-Hepatitis C Virus drug Alisporivir

The rapid emergence of P. falciparum-resistant strains raises an urgent need to find new antimalarial drug candidates. This study reports the rational repositioning of the anti-Hepatitis C Virus drug, Alisporivir, a non-immunosuppressive analog of cyclosporin A (CsA) against multiple, drug-resistant strains of P. falciparum. Alisporivir being non-hemolytic has been proven to be a better drug than CsA. Indeed, our study also demonstrated the same. Alisporivir inhibited chloroquine-sensitive parasite growth with an IC50 of 196.6nM. Alisporivir also inhibited the growth of chloroquine-resistant parasites with an IC50 of 422.1nM. Alisporivir exhibited, anti-malarial activity in in vivo. Further, we exploited the Cyclophilins targeting potential of Alisporivir against artemisinin-resistant malaria parasite owing to the fact that PfCyP-19B is one of the genes that is overexpressed in artemisinin-resistant parasite revealed by a population transcriptomic study. Our semiquantitative real-time transcript and immunofluorescence analysis confirmed the overexpression of PfCyP-19B in Artemisinin-resistant P. falciparum (PfKelch13R539T). Artemisinin resistance is attributed to slow clearance of ring stage parasites. Ring survival assay (RSA) is designed to access the potency of compounds on these dormant slow clearing parasites leading to drug resistance. Thus, the potency of Alisporivir against PfKelch13R539T was evaluated by RSA. A 2.5-fold decrease in parasite survival was detected with Alisporivir. Further, combination of Alisporivir with DHA found to potentiate the efficacy of DHA by 4.55-fold. These results support the hypothesis that targeting of resistance mechanism is a potential approach to deal with resistant parasite. Overall, this study demonstrates the rational reposition of Alisporivir against resistant malaria resistance.

microbiology↗

bioRxiv2020

Antimalarial and Plasmodium falciparum serpentine receptor 12 targeting effect of a purinergic receptor antagonist FDA approved drug

Intraerythrocytic stages of Plasmodium falciparum responsible for all clinical manifestations of malaria are regulated by array of signaling cascades and effector molecules that represents attractive targets for antimalarial therapy. G-protein coupled receptors (GPCRs) are druggable targets in treatment of various pathological conditions however there is limited understanding about the role of GPCRs in malaria pathogenesis. In Plasmodium, serpentine receptors (PfSR1, PfSR10, PfSR12 and PfSR25) with GPCR like membrane topology have been reported with the finite knowledge about their potential as antimalarial targets. Herein we evaluated the druggability of PfSR12 using FDA approved P2Y type of purinergic signaling antagonist, Prasugrel. Blocking of purinergic receptor signaling resulted in inhibition of growth and development of P. falciparum. Progression studies indicated the inhibitory effect of purinergic signalling inhibitor begins in late erythrocyte stages predominantly in the schizonts. Furthermore, purinoreceptor inhibitor blocked in vivo growth of malaria parasite in mouse experimental model. The localization of PfSR1, PfSR10, PfSR12 and PfSR25 was analyzed by immunofluorescence assays. The putative purinergic receptor PfSR12 is found to be expressed in late intraerythrocytic stages. Prasugrel, a generic purinoreceptor inhibitor and agonist ATP showed specific binding to recombinant PfSR12 confirming it as purinergic receptor. This study indicates the presence of P2Y type of purinergic signaling in growth and development of malaria parasite and suggests PfSR12 as putative purinergic receptor.

microbiology↗

bioRxiv2020

Metalloprotease Gp63 targeting novel glycoside exhibits potential antileishmanial activity

Visceral Leishmaniasis (VL) and its aggressive cutaneous exacerbation known as Post Kala-azar Dermal Leishmaniasis (PKDL) cause a huge disease burden in tropics and sub-tropic endemic zones worldwide. Contemporary treatment modalities have been associated with various complications. Encouraged from the recent marked antimalarial effects from plant derived glycosides; here we have chemically synthesized a library of diverse Glycoside derivatives (Gly 1-12) and evaluated their inhibitory efficacy against Ag83 strain of Leishmania donovani. In vitro activity of Glycoside-2 (Gly 2) on promastigote form of Ag83 strain, unravelled its prominent anti-leishmanial property with IC50 value of 1.13M. In-silico studies also unveiled the efficacy of Gly 2 to bind to the membrane surface of parasite. The toxic effect of Gly 2 causes necrosis like death in promastigote by abrogating its proliferation leading to imbalanced redox homeostasis by disruption of mitochondrial membrane potential. Additionally, Gly 2 treatment demonstrated increased susceptibility of parasites towards complement mediated lysis and displayed strong lethal effect on amastigote-macrophage infection model mimicking pathophysiological condition of body. This lead molecule was quite effective against the clinical on promastigotes form of PKDL strain BS12 with IC50 value of 1.97 M making it the most suitable drug so far which can target both VL and PKDL simultaneously. Based on the above experimental validations we narrowed our thoughts regarding the potent role of Gly 2 targeting surface protein of L. donovani such as Gp63, a zinc metalloprotease. Further analysis of structure activity relationship (SAR) of these glycoside derivatives, demonstrated exceptional binding affinity of Gly 2 towards Gp63, a zinc metalloprotease of L. donovani; with strong H-bond interactions of Gly 2 with catalytic domain in the -helix B region of Gp63. The strong confined interactions between Gly 2 and the target protein Gp63 in a physiologically relevant cellular environment was further assessed by Cellular Thermal Shift Assay (CETSA) which corroborated with our previous results. Taken together, this study reports the serendipitous discovery of glycoside derivative Gly 2 with enhanced leishmanicidal activity and proves to be novel chemotherapeutic prototype against VL and PKDL. HighlightsO_LIA novel glycoside derivative (Gly 2) targets Gp63 functioning in L. donovani promastigotes, resulting in its abrogated proliferation and severely detabilized redox homeostasis, leading to parasitic death. C_LIO_LIStructure activity relationship (SAR) analysis revealed exceptional ligandability of Gly 2 towards Gp63 catalytic domain both in silico and in Cellular Thermal Shift Assay (CETSA) based in vitro analysis. C_LIO_LIGly 2 treatment exhibited increased parasite susceptibility towards complement mediated lysis and reduced macrophage infection in vitro mimicking the pathophysiological conditions. C_LIO_LIGly 2 showed profound antileishmanial activity against the clinical isolates of Post Kala-azar Dermal Leishmaniasis (PKDL). C_LI

pharmacology and toxicology↗

bioRxiv2020

Analysis and Visualization of Sleep Stages based on Deep Neural Networks

Automatic sleep stage scoring based on deep neural networks has come into focus of sleep researchers and physicians, as a reliable method able to objectively classify sleep stages, would save human resources and thus would simplify clinical routines. Due to novel open-source software libraries for Machine Learning in combination with enormous progress in hardware development in recent years a paradigm shift in the field of sleep research towards automatic diagnostics could be observed. We argue that modern Machine Learning techniques are not just a tool to perform automatic sleep stage classification but are also a creative approach to find hidden properties of sleep physiology. We have already developed and established algorithms to visualize and cluster EEG data, in a way so that we can already make first assessments on sleep health in terms of sleep-apnea and consequently daytime vigilance. In the following study, we further developed our method by the innovative approach to analyze cortical activity during sleep by computing vectorial cross-correlations of different EEG channels represented by hypnodensity graphs. We can show that this measure serves to estimate the period length of sleep cycles and thus can help to find disturbances due to pathological conditions.

neuroscience↗

bioRxiv2020

BBB pathophysiology independent delivery of siRNA in traumatic brain injury

Small interfering RNA (siRNA) represents a powerful strategy to mitigate the long-term sequelae of traumatic brain injury (TBI). However, poor permeability of siRNA across the blood brain barrier (BBB) poses a major hurdle. One approach to overcome this challenge involves treatment administration while the BBB is physically breached post-injury. However, this approach is only applicable to a subset of injuries with substantial BBB breach and can lead to variable therapeutic response due to the heterogeneity of physical breaching of BBB in TBI. Moreover, since physical breaching of BBB is transient, this approach offers a limited window for therapeutic intervention, which is not ideal as repeated dosing beyond the transient window of physically breached BBB might be required. Herein, we report a nanoparticle platform for BBB pathophysiology-independent delivery of siRNA in TBI. We achieved this by combined modulation of surface chemistry and coating density, which maximized the active transport of nanoparticles across BBB. Intravenous injection of engineered nanoparticles, within or outside the window of physically breached BBB in TBI mice resulted in 3-fold higher brain accumulation compared to conventional PEGylated nanoparticles and demonstrated up to 50% gene silencing. To our knowledge, this is the first reported example of BBB pathophysiology-independent drug delivery in TBI, and the first time combined modulation of surface chemistry and coating density has been shown to tune BBB penetration of nanoparticles. Taken together, our approach offers a clinically relevant approach to develop siRNA therapeutics for preventing long-term effects of TBI and deserves further exploration.Competing Interest StatementJMK has been a paid consultant and or equity holder for multiple biotechnology companies (listed here https://www.karplab.net/team/jeff-karp). The interests of JMK were reviewed and are subject to a management plan overseen by his institutions in accordance with its conflict of interest policies. N.J., J.MK., W.L., R.M., J.Q. and R.L. have one unpublished patent based on the nanoparticle work presented in this manuscript. For a list of entities with which R.L. is involved, compensated or uncompensated, see www.dropbox.com/s/yc3xqb5s8s94v7x/Rev%20Langer%20COI.pdf?dl=0.View Full Text

bioengineering↗

bioRxiv2020

Resetting proteostasis with ISRIB prevents pulmonary fibrosis

Aging is among the most important risk factors for the development of pulmonary fibrosis. We found that a small molecule that specifically inhibits translational inhibition induced by activation of the integrated stress response (ISRIB) attenuated the severity of pulmonary fibrosis in young and old mice. The more severe fibrosis in old compared to young mice was associated with increased recruitment of pathogenic monocyte-derived alveolar macrophages. Using genetic lineage tracing and transcriptomic profiling we found that ISRIB modulates stress response signaling in alveolar epithelial cells resulting in decreased apoptosis and decreased recruitment of pathogenic monocyte-derived alveolar macrophages. These data support multicellular model of fibrosis involving epithelial cells, pathogenic monocyte-derived alveolar macrophages and fibroblasts. Inhibition of the integrated stress response in the aging lung epithelium ameliorates pulmonary fibrosis by preventing the prolonged recruitment of monocyte-derived alveolar macrophages.

immunology↗

bioRxiv2020

Alterations in the intrinsic properties of striatal cholinergic interneurons after dopamine lesion and chronic L-DOPA

SO_SCPLOWUMMARYC_SCPLOWChanges in striatal cholinergic interneuron (ChI) activity are thought to contribute to Parkinsons disease pathophysiology and dyskinesia from chronic L-3,4-dihydroxyphenylalanine (L-DOPA) treatment, but the physiological basis of these changes are unknown. We find that dopamine lesion decreases the spontaneous firing rate of ChIs, whereas chronic treatment with L-DOPA of lesioned mice increases baseline ChI firing rates to levels beyond normal activity. The effect of dopamine loss on ChIs was due to decreased currents of both hyperpolarization-activated cyclic nucleotide-gated (HCN) and small conductance calcium-activated potassium (SK) channels. L-DOPA reinstatement of dopamine normalized HCN activity, but SK current remained depressed. Pharmacological blockade of HCN and SK activities mimicked changes in firing, confirming that these channels are responsible for the molecular adaptation of ChIs to dopamine loss and chronic L-DOPA treatment. These findings suggest that targeting ChIs with channel-specific modulators may provide therapeutic approaches for alleviating L-DOPA-induced dyskinesia in PD patients.

neuroscience↗

bioRxiv2020

Sleep-like behavior is a fundamental property of the tripartite synapse

The tripartite synapse, consisting of the presynaptic neuron, post-synaptic neuron, and an astrocyte, is considered to be the main locus of signaling between neurons in the brain.1,2 Neurotransmission is energetically very expensive3,4, and the primary neurotransmitter utilized for signaling is glutamate. It has been found that glutamate is also used as a substrate for energy generation.5,6 However, it is unclear what the relationship is between energy generation and availability of neurotransmitter during glutamatergic neurotransmission. Here we show that availability of energy, represented by adenosine triphosphate (ATP), and glutamate for neurotransmission are intimately related, and in fact determine the ability to signal at the tripartite synapse. Using a novel neurochemical mathematical model of the tripartite synapse, we found that glutamate concentrations for neurotransmission and ATP concentrations were interdependent, and their interplay controlled the firing pattern of the presynaptic terminal, as defined by synaptic vesicle release. Furthermore, we found that depending on the parameters chosen in the model, the tripartite synapse demonstrated behavior with limit cycles, alternating between high- and low-frequency firing rates. Our results show that complex behavior with high- and low-activity states, qualitatively meeting the characteristics of sleep7 emerges directly from the nature of the tripartite synapse, with glutamate and ATP concentrations serving as the signals for state changes. We anticipate that our model will serve as a starting point to further elucidate the energetics of neuronal and brain functioning, and eventually shed light on the fundamental question of the nature and necessity of sleep.

neuroscience↗

bioRxiv2019

Impaired phagocytic function in CX3CR1+ tissue-resident skeletal muscle macrophages prevents muscle recovery after influenza A virus-induced pneumonia in aged mice

Skeletal muscle dysfunction in survivors of pneumonia is a major cause of lasting morbidity that disproportionately affects older individuals. We found that skeletal muscle recovery was impaired in aged compared with young mice after influenza A virus-induced pneumonia. In young mice, recovery of muscle loss was associated with expansion of tissue-resident skeletal muscle macrophages and downregulation of MHC II expression, followed by a proliferation of muscle satellite cells. These findings were absent in aged mice and in mice deficient in Cx3cr1. Transcriptomic profiling of tissue-resident skeletal muscle macrophages from aged compared with young mice showed downregulation of pathways associated with phagocytosis and proteostasis, and persistent upregulation of inflammatory pathways. Consistently, skeletal muscle macrophages from aged mice failed to downregulate MHCII expression during recovery from influenza A virus induced pneumonia and showed impaired phagocytic function in vitro. Like aged animals, mice deficient in the phagocytic receptor Mertk showed no macrophage expansion, MHCII downregulation or satellite cell proliferation and failed to recover skeletal muscle function after influenza A pneumonia. Our data suggest that a loss of phagocytic function in a CX3CR1+ tissue-resident skeletal muscle macrophage population in aged mice precludes satellite cell proliferation and recovery of skeletal muscle function after influenza A pneumonia.

immunology↗

bioRxiv2019

A Human Accelerated Region participates in early human forebrain patterning and expansion

The expansion of the mammalian brain is associated with specific developmental processes; however, not much is known about how evolutionary changes participated in the acquisition of human brain traits during early developmental stages. Here we investigated whether enhancers active during the phylotypic stage show human-specific genomic divergence which could contribute to the evolutionary expansion of the forebrain. Notably, we identified an active enhancer containing a human accelerated region (HAR) located in the Chromosome 14q12, a region enriched with neurodevelopmental genes, such as Foxg1, Nkx2.1 and Nova1. Reporter analysis revealed that the human variant is active in the forebrain in transgenic mice and that it has stronger enhancer activity than the mouse or chimpanzee versions. Humanization of the mouse enhancer variant in transgenic mice and in mouse organoids resulted in an expansion of Foxg1 expressing domains in the forebrain early neural progenitors with a bias towards dorsal identities. Overall, our results suggest that human-specific mutations in critical regulatory elements controlling early brain development impact the expansion and patterning of the forebrain.

developmental biology↗