Biology subjects

Zhang, R.

Publications and source records attributed to Zhang, R..

At least 235 records · Page 13Linked to original sources

bioRxiv2024

Structural basis of phosphate export by human XPR1

Phosphorus is an essential element for all living organisms. While inorganic phosphate (Pi) cellular import is well documented, export is poorly characterized despite the recent discovery of the inositol pyrophosphate (PP-IP)-dependent Pi exporter XPR1. In this study, we determined the cryo-EM structures of XPR1. XPR1 forms a loose dimer, with each protomer containing 10 transmembrane helices (TMs) that can be divided into a peripheral domain (TM1, 3 and 4) and a core domain (TM2 and TM5-10) structurally related to ion-translocating rhodopsins. Bound Pi is observed in a tunnel formed by the helical bundle inside the core domain at a narrowest point that separates the tunnel into an intracellular vestibule (IV) and an extracellular vestibule (EV). This narrowest point contains a cluster of Pi-coordinating basic residues, and their substitution by mutagenesis strongly impaired phosphate export. PP-Ips stimulate XPR1 activity by binding to its SPX domain. Loss of this interaction induces a conformational change of the wide open EV (conducting state) into a collapsed EV (closed state), mainly caused by structural movements of TM9 and the bulky sidechain of Trp573 right above the Pi binding site, which are essential for the Pi export activity of XPR1. Our structural and functional characterization paves the way for further in-depth studies of XPR1.

biochemistry↗

bioRxiv2024

Signal peptidase SpsB coordinates staphylococcal cell cycle, surface protein septal trafficking and LTA synthesis

Many cell wall anchored surface proteins of Gram-positive bacteria harbor a highly conserved YSIRK/G-S signal peptide (SPYSIRK+), which deposits surface protein precursors at the cell division septum where they are subsequently anchored to septal peptidoglycan. Previously we identified that LtaS-mediated lipoteichoic acid (LTA) synthesis regulates septal trafficking of YSIRK+ proteins in S. aureus. Interestingly, both LtaS and SPYSIRK+ are cleaved by the signal peptidase SpsB, but the biological implications remain unclear. Here we show that SpsB is required for cleaving SPSpA(YSIRK+) of staphylococcal surface protein A (SpA). Depletion of spsB not only diminished SPSpA processing but also abolished SpA septal localization. The mis-localization is attributed to the cleavage activity of SpsB, as an A37P mutation of SPSpA that disrupted SpsB cleavage also abrogated SpA septal localization. Strikingly, depletion of spsB led to aberrant cell morphology, cell cycle arrest and daughter cell separation defects. Localization studies showed that SpsB predominantly localized at the septum of dividing staphylococcal cells. Finally, we show that SpsB spatially regulates LtaS as spsB depletion enriched LtaS at the septum. Collectively, the data suggest a new dual-mechanism model mediated by SpsB: the abundant YSIRK+ proteins are efficiently processed by septal localized SpsB; SpsB cleaves LtaS at the septum, which spatially regulates LtaS activity contributing to YSIRK+ proteins septal trafficking. The study identifies SpsB as a novel and key regulator orchestrating protein secretion, cell cycle and cell envelope biogenesis. ImportanceSurface proteins containing a YSIRK/G-S positive signal peptide are widely distributed in Gram-positive bacteria and play essential roles in bacterial pathogenesis. They are highly expressed proteins that are enriched at the septum during cell division. The biogenesis of these proteins is coordinated with cell cycle and LTA synthesis. The current study identified the staphylococcal signal peptidase SpsB as a key determinant in regulating surface protein septal trafficking. Furthermore, this study highlights the novel functions of SpsB in coordinating LtaS-mediated LTA production and regulating staphylococcal cell cycle. As SpsB, YSIRK+ proteins and LTA synthesis are widely distributed and conserved, the mechanisms identified here may be shared across Gram-positive bacteria.

microbiology↗

bioRxiv2024

Abnormal activation of the mineralocorticoid receptor in the aldosterone-sensitive distal nephron contributes to fructose-induced salt-sensitive hypertension

Fructose high-salt (FHS) diets increase blood pressure (BP) in an angiotensin II (Ang II)-dependent manner. Ang II stimulates aldosterone release, which, by acting on the mineralocorticoid receptor (MR), regulates Na+ reabsorption by the aldosterone-sensitive distal nephron (ASDN). The MR can be transactivated by glucocorticoids, including those locally produced by 11{beta}-HSD1. The epithelial sodium channel (ENaC) is a key transporter regulated by MRs. We hypothesized that fructose-induced salt-sensitive hypertension depends in part on abnormal activation of MRs in the ASDN with consequent increases in ENaC expression. We found that aldosterone-upregulated genes in mice ASDN, significantly overlapped with 74 genes upregulated by FHS in the rat kidney cortex (13/74; p[≤]1x10-8), and that these 74 genes are prominently expressed in rat ASDN cells. Additionally, the average z-score expression of mice-aldosterone-upregulated genes is highly correlated with FHS compared to glucose high-salt (GHS) in the rat kidney cortex (Pearson correlation; r=0.66; p[≤]0.005). There were no significant differences in plasma aldosterone concentrations between the FHS and GHS. However, 11{beta}-HSD1 transcripts were upregulated by FHS (log2FC=0.26, p[≤]0.02). FHS increased BP by 23{+/-}6 mmHg compared to GHS, and blocking MRs with eplerenone prevented this increase. Additionally, inhibiting ENaC with amiloride significantly reduced BP in FHS from 148{+/-}6 to 134{+/-}5 mmHg (p[≤]0.019). Compared to GHS, FHS increased total and cleaved ENaC protein by 89{+/-}14 % (p[≤]0.03) and 47{+/-}16 % (p[≤]0.01) respectively. FHS did not change {beta}- or {gamma}-subunit expression. These results suggest that fructose-induced salt-sensitive hypertension depends, in part, on abnormal Na+ retention by ENaC, resulting from the activation of MRs by glucocorticoids.

physiology↗

bioRxiv2024

Centimeter-scale, physiologically relevant intestinal organoids generated entirely from pluripotent stem cells

Over the past decade, intestinal organoids have shown great promise as a platform to study the development of intestine, elucidate the pathogenesis of diseases such as inflammatory bowel disease (IBD), and model physiological features of intestinal tissue for high-throughput drug screening. However, intestinal organoids derived from adult epithelial stem cells lack cellular diversity, especially those resides in the lamina propria. Intestinal organoids derived from embryonic stem (ES) cells or induced-pluripotent stem cells (iPSCs) has greater cellular diversity, but are still limited in size and physiological features such as peristalsis. In this study, we generated centimeter-scale, full-thickness, and physiologically relevant intestinal organoids in suspension culture without usage of Matrigel. Using a series of optimized culture media, multiple lineages of cells were differentiated from iPSCs and spontaneously assembled to achieve the intestinal architecture. These bubble-like organoids have a thickness of 500 microns, exhibit a mature vasculature network, and have smooth muscle-like cells to conduct regular peristalsis. In addition, adipocyte-like cells and granulocyte-like cells are also observed in these organoids, which are important in immune homeostasis. Lastly, these organoids show mature crypt structures, response to lipopolysaccharides (LPS), and increases luminal influx upon forskolin treatment, suggesting the organoids have intact epithelial integrity. Thus, this study provides a highly reproducible approach to produce large and physiologically relevant intestinal organoids that are suitable for different biomedical applications.

cell biology↗

bioRxiv2024

Placental and fetal microbiota in rhesus macaque: a case study using metagenomic sequencing

Recent evidence challenging the notion of a sterile intrauterine environment has sparked research into the origins and effects of fetal microbiota on immunity development during gestation. Rhesus macaques (RMs) serve as valuable non-human primate (NHP) models due to their similarities to humans in development, placental structure, and immune response. In this study, metagenomic analysis was applied to the placenta, umbilical cord, spleen, gastrointestinal (GI) tissues of an unborn RM fetus, and the maternal intestine, revealing the diversity and functionality of microbes in these tissues. We observed substantial microbial sharing between the mother and fetus, with the microbial composition of the placenta and umbilical cord more closely resembling that of the fetal organs than the maternal intestine. Notably, compared with other adult RMs, there was a clear convergence between maternal and fetal microbiota, alongside distinct differences between the microbiota of adults and the fetus, which underscores the unique microbial profiles in fetal environments. Furthermore, the fetal microbiota displayed a less developed carbohydrate metabolism capacity than adult RMs. It also shared antibiotic resistance genes (ARGs) with both maternal and adult RM microbiomes, indicating potential vertical transmission. Comparative analysis of the metagenomes between the RM fetus and a human fetus revealed significant differences in microbial composition and genes, yet also showed similarities in certain abundant microbiota. Collectively, our results contribute to a more comprehensive understanding of the intrauterine microbial environment in macaques.

microbiology↗

bioRxiv2024

Inference technique for the synaptic conductances in rhythmically active networks and application to respiratory central pattern generation circuits

Unraveling synaptic interactions between excitatory and inhibitory interneurons within rhythmic neural circuits, such as central pattern generation (CPG) circuits for rhythmic motor behaviors, is critical for deciphering circuit interactions and functional architecture, which is a major problem for understanding how neural circuits operate. Here we present a general method for extracting and separating patterns of inhibitory and excitatory synaptic conductances at high temporal resolution from single neuronal intracellular recordings in rhythmically active networks. These post-synaptic conductances reflect the combined synaptic inputs from the key interacting neuronal populations and can reveal the functional connectome of the active circuits. To illustrate the applicability of our analytic technique, we employ our method to infer the synaptic conductance profiles in identified rhythmically active interneurons within key microcircuits of the mammalian (mature rat) brainstem respiratory CPG and provide a perspective on how our approach can resolve the functional interactions and circuit organization of these interneuron populations. We demonstrate the versatility of our approach, which can be applied to any other rhythmic circuits where conditions allow for neuronal intracellular recordings.

neuroscience↗

bioRxiv2024

A Tough Biointerface in Human Knee Empowered by Dynamic Phase-transforming Minerals in Collagenous Matrix

Joining heterogeneous materials in engineered structures remains a daunting challenge because of stress concentration, often resulting in unexpected failures1,2. Studying the structures in organisms that evolved for centuries provides valuable insights that can be instrumental in addressing this mechanical challenge3-5. The human meniscus root-bone interface is a remarkable example known for its exceptional fatigue resistance, toughness and interfacial adhesion properties throughout its lifespan6-8. We studied the multiscale graded mineralization structure designs within the 30-micron soft-hard interface at the root-bone junction and examined its toughening mechanisms. This graded interface with interdigitated structures and exponential modulus increase exhibits a phase transition from amorphous calcium phosphate (ACP) to gradually matured hydroxyapatite (HAP) crystals, mediated by location-specific distributed biomolecules. In coordination with collagen fibril deformation and reorientation, ACP particles debond with collagen and slide to new positions which enable frictional energy dissipation, and HAP particles arrest cracks. The mineral in transforming phases work synergistically to provide interfacial toughening. The presented biointerface model exemplifies human musculoskeletal systems adaptations to mechanical requirements, offering a blueprint for developing tough interfaces in broad applications.

bioengineering↗

bioRxiv2024

Metabolic Segregation and Characteristic Genes of the Key Functional Populations in Anaerobic Digestion Consortia

Enrichment experiment integrated with genome-centric meta-omics analysis revealed that metabolic specificity, rather than metabolic flexibility, governs the anaerobic digestion (AD) ecosystem. This study provides new insights into interspecies electron transfer in the AD process, highlighting a segregation in the metabolism of H2 and formate. Our findings indicate that H2 serves as the primary electron sink for recycling redox cofactors, NAD and oxidized ferredoxin (Fdox), during primary fermentation. In contrast, formate predominates in the co- occurring secondary fermentation, particularly under conditions of elevated H2 concentrations. Notably, no evidence of biochemical interconversion between H2 and formate was identified in the primary fermenting bacteria or in syntrophs enriched in this study. This segregation of H2 and formate metabolism likely benefit the anaerobic oxidation of butyrate and propionate with a higher tolerance to H2 accumulation. Furthermore, this study underscores the functional partitioning among microbial populations within key niches of the AD bioprocess: primary fermentation, secondary fermentation (syntrophic acetogenesis), hydrogenotrophic methanogenesis, and acetoclastic methanogenesis. Through genome-centric analysis of the AD microbiome, we identified several key functional gene clusters, highlighting the potential for improving genome-centric genotype-phenotype correlations, which is particularly valuable for strict anaerobes that remain challenging to isolate and characterize in pure culture.

genomics↗

bioRxiv2024

A neurofunctional signature of affective arousal generalizes across valence domains and distinguishes subjective experience from autonomic reactivity

Arousal is fundamental for affective experience and, together with valence, defines the core affective space. Precise brain models of affective arousal are lacking, leading to continuing debates of whether the neural systems generalize across valence domains and are separable from those underlying autonomic arousal or wakefulness. Here, we combined naturalistic fMRI with predictive modeling to develop a brain affective arousal signature (BAAS, discovery-validation design, n=60, 36). We demonstrate its (1) sensitivity and generalizability across mental processes and valence, and (2) neural distinction from autonomic arousal, wakefulness, and stimulation modality (24 studies, n=868). Affective arousal was encoded in distributed cortical-subcortical (e.g., prefrontal, PAG) systems with local similarities in thalamo-amygdala-insula systems between affective and autonomous arousal. We demonstrate application of the BAAS to improve specificity of established valence-specific neuromarkers. Our study provides a biologically plausible model for affective arousal that aligns with the affective space and has a high application potential.

neuroscience↗

bioRxiv2024

A unique mechanism of snRNP core assembly

The assembly of spliceosomal snRNP cores involves seven Sm proteins (D1/D2/F/E/G/D3/B) forming a ring around each snRNA and typically requires several essential assembly chaperones, particularly the SMN-Gemins complex implicated in spinal muscular atrophy (SMA). Strikingly, in budding yeast, snRNP core assembly only involves Brr1, a nonessential homolog of Gemin2. To unravel this enigma, we systematically investigated snRNP core assembly in budding yeast using biochemical and genetic approaches. We discovered two distinct pathways in budding yeast: chaperone-mediated and direct. The chaperone-mediated pathway involves two proteins, Brr1 and a novel protein, Lot5, but is inefficient. Lot5 binds D1/D2/F/E/G to form a heterohexameric ring (6S). Brr1 binds D1/D2/F/E/G and 6S but cannot displace Lot5 to facilitate assembly. Disruption of both BRR1 and LOT5 genes caused mild growth retardation, but LOT5 overexpression substantially impeded growth. The direct pathway uniquely involves F/E/G as a trimer and a stable D1/D2/F/E/G intermediate complex, explaining the non-essentiality of assembly chaperones. These findings unveil a unique assembly mechanism of snRNP cores, illuminate the evolution of assembly chaperones, and suggest avenues for studying SMA pathophysiology.

molecular biology↗

bioRxiv2024

Interspecies interaction reshapes the fitness landscape of evolved genotypes

Microbial interaction and their evolution is vital for shaping the structure and function of microbial communities. However, the mechanisms governing the directionality and stability of the evolution of interactions within microbial communities remain poorly understood. Here, we used a syntrophic two-species biofilm consortium composed of Bacillus velezensis SQR9 and Pseudomonas stutzeri XL272 that promotes plant growth through their metabolic interactions and investigated how the interactions within the consortium change over evolutionary timescale to characterize the phenotypic and genetic diversification. The focal species B. velezensis SQR9 rapidly diversified into diverse colony morphotypes, both in the presence and absence of its interactor, P. stutzeri XL272, with variable frequencies. These morphotypes displayed phenotypic differentiation among biofilm formation, planktonic growth, and spore formation. The evolved P. stutzeri altered the fitness landscape of B. velezensis morphotypes, allowing the weaker rough morphotype to outcompete the biofilm-enhanced slimy morphotype. Whole genome re-sequencing correlated these phenotypic changes with mutations in specific genes encoding regulators of B. velezensis, including ywcC, comA, comP, degS, degQ and spo0F. The coevolutionary partner, P. stutzeri increased its exopolysaccharide production that could be explained by a frame shift mutation in cpsA gene encoding capsular polysaccharide (CPS) biosynthesis protein. Compared with the mono-evolution, co-evolved B. velezensis populations showed greater mutation accumulation in intergenic regions, which led to greater genetic parallelism. Furthermore, the dissimilarity between mono-evolved and co-evolved populations increased over time. Our study reveals intricate genetic diversification and fitness differentiation within a biofilm consortium, shaped by both abiotic conditions and biotic interactions.

microbiology↗

bioRxiv2024

The m6A reader IGF2BP3 promotes gastric cancer progression via increasing the expression of FBXO32 protein

N6-methyladenosine (m6A) represents the most prevalent chemical modification on eukaryotic mRNA, with an accumulating body of literature indicating its pivotal significance in the pathogenesis of human cancers. Nevertheless, the precise molecular interplay between the m6A reader protein IGF2BP3 and gastric cancer remains to be thoroughly delineated. Our study uncovered that the expression of IGF2BP3 in gastric cancer tissues is markedly elevated in comparison to adjacent normal tissues, and this upregulation is tightly correlated with the incidence of lymph node metastasis, more advanced TNM stages, and deeper invasion depth of tumor in patients. In vitro experiments demonstrated that IGF2BP3 potentiates the proliferative, migratory, and invasive capacities of gastric cancer cells, while concurrently inhibiting apoptosis and augmenting the intracellular levels of aerobic glycolysis. In vivo experiments revealed that IGF2BP3 contributes to the growth of gastric cancer. Mechanistically, IGF2BP3 can increase the expression of FBXO32 protein by recognizing and binding to the m6A binding site on FBXO32 mRNA and further activate the downstream cGMP-PKG signaling pathway, thereby modulating various biological functions of gastric cancer cells and ultimately promoting the progression of gastric cancer. In summary, our findings suggest that IGF2BP3 upregulates the expression of FBXO32 protein in an m6A dependent manner and subsequently activates the cGMP-PKG signaling pathway, ultimately leading to the onset and progression of gastric cancer. Consequently, the targeting of the IGF2BP3/FBXO32/cGMP-PKG axis emerges as a promising therapeutic modality for the treatment of gastric cancer.

cancer biology↗

bioRxiv2024

Intraperitoneal activation of myeloid cells clears ascites and reveals IL27-dependent regression of metastatic ovarian cancer

Patients with metastatic ovarian cancer (OvCa) have a 5-year survival rate of less than 30% due to persisting dissemination of chemoresistant cells in the peritoneal fluid and the immunosuppressive microenvironment in the peritoneal cavity. Here, we report that intraperitoneal administration of {beta}-glucan and IFN{gamma} (BI) induced robust tumor regression in clinically relevant models of metastatic OvCa. BI induced tumor regression by controlling fluid tumor burden and activating localized antitumor immunity. {beta}-glucan alone cleared ascites and eliminated fluid tumor cells by inducing intraperitoneal clotting in the fluid and Dectin-1-Syk-dependent NETosis in the omentum. In omentum tumors, BI expanded a novel subset of immunostimulatory IL27+ macrophages and neutralizing IL27 impaired BI efficacy in vivo. Moreover, BI directly induced IL27 secretion in macrophages where single agent treatment did not. Finally, BI extended mouse survival in a chemoresistant model and significantly improved chemotherapy response in a chemo-sensitive model. In summary, we propose a new therapeutic strategy for the treatment of metastatic OvCa.

immunology↗

bioRxiv2024

Mapping individual differences in intermodal coupling in neurodevelopment

Within-individual coupling between measures of brain structure and function evolves in development and may underlie differential risk for neuropsychiatric disorders. Despite increasing interest in the development of structure-function relationships, rigorous methods to quantify and test individual differences in coupling remain nascent. In this article, we explore and address gaps in approaches for testing and spatially localizing individual differences in intermodal coupling, including a new method, called CEIDR. CEIDR controls false positives in individual differences in intermodal correlations that arise from mean and variance heterogeneity and improves statistical power by adopting adaptive cluster enhancement. Through a comparison across different approaches to testing individual differences in intermodal coupling, we delineate subtle differences in the hypotheses they test, which may ultimately lead researchers to arrive at different results. Finally, we illustrate these differences in two applications to brain development using data from the Philadelphia Neurodevelopmental Cohort.

neuroscience↗

bioRxiv2024

Integrated single-cell RNA-seq analysis revealed PTN secreted by fibroblasts acting on itself and macrophages via SDC4 ligand in myocardial hypertrophy

BackgroundHypertrophic cardiomyopathy (HCM) is characterized by massive myocardial hypertrophy, which is the most frequent cause of sudden death and can lead to heart failure (HF) or stroke. The objective of this study was to explore the communication network among various cells in the heart of pathological HCM derived from transverse aortic constriction (TAC) mouse model, and investigate the potential mechanism through data mining, biological informatics analysis, and experimental validation. Methods and ResultsThe integrated analyses including CellChat, Seurat, gene ontology (GO), pseudo-time trajectory analysis, and weighted gene co-expression network analysis (WGCNA) were performed based on the single-cell RNA-seq data (scRNA-seq). In vitro tests were conducted to verify bioinformatic analysis findings through enzyme-linked immunosorbent assay (ELISA), real-time quantitative PCR (RT-qPCR), Edu staining, and transwell assay. In vivo tests were also performed to further verify bioinformatic analysis findings by western blot and immunofluorescence assays based on our established TAC mouse model with myocardial hypertrophy. Our results showed that in the heart of TAC mouse, the interaction between cardiac fibroblasts and macrophages was most common, and the increasing pleiotrophin (PTN) secreted by cardiac fibroblasts could promote themselves proliferation or invasion as well as stimulate macrophage activation to release inflammatory cytokines, such as TNF-, IL-6, Cox-2, Cd83, Egr2, and IL-10 through acting on its ligand recombinant Syndecan 4 (SDC4), which may affect cardiomyocyte normal function and eventually cause HCM. This study first demonstrated that PTN derived from cardiac fibroblasts may act on SDC4 to play crucial role in myocardial hypertrophy, which may be a potential therapeutic targets for patients with pathological HCM. ConclusionsIn this study, the complex interaction network between cardiac fibroblasts and macrophages of TAC mice based on the scRNA-seq data was investigated, and we found that the increasing PTN secreted by cardiac fibroblasts under cardiac pressure overload could promote themselves proliferation or invasion as well as stimulate macrophage activation to release inflammatory cytokines through acting on SDC4 ligand, which may affect cardiomyocyte normal function and eventually cause HCM. In addition, our study suggested that PTN derived from cardiac fibroblasts may act on SDC4 ligand to play crucial role in myocardial hypertrophy, which may be a potential therapeutic targets for patients with pathological HCM.

cell biology↗

bioRxiv2024

Presynaptic GABAA receptors control integration of nicotinic input onto dopaminergic axons in the striatum

Axons of dopaminergic neurons express gamma-aminobutyric acid type-A receptors (GABAARs) and nicotinic acetylcholine receptors (nAChRs) which are both independently positioned to shape striatal dopamine release. Using electrophysiology and calcium imaging, we investigated how interactions between GABAARs and nAChRs influence dopaminergic axon excitability. Direct axonal recordings showed that benzodiazepine application suppresses subthreshold axonal input from cholinergic interneurons (CINs). In imaging experiments, we used the first temporal derivative of presynaptic calcium signals to distinguish between direct- and nAChR-evoked activity in dopaminergic axons. We found that GABAAR antagonism with gabazine selectively enhanced nAChR-evoked axonal signals. Acetylcholine release was unchanged in gabazine suggesting that GABAARs located on dopaminergic axons, but not CINs, mediated this enhancement. Unexpectedly, we found that a widely used GABAAR antagonist, picrotoxin, inhibits axonal nAChRs and should be used cautiously for striatal circuit analysis. Overall, we demonstrate that GABAARs on dopaminergic axons regulate integration of nicotinic input to shape presynaptic excitability.

neuroscience↗

bioRxiv2024

Infralimbic projections to the basal forebrain mediate extinction learning

Fear extinction learning and retrieval are critical for decreasing fear responses to a stimulus that no longer poses a threat. While it is known that the infralimbic region (IL) of the medial prefrontal cortex mediates retrieval of an extinction memory through projections to the basolateral amygdala (BLA), the contribution of the IL to extinction learning is not well-understood. Given the strong projection from the IL to the basal forebrain (BF), a center of attentional processing, we investigated whether this pathway participates in extinction, and compared it to the IL-BLA pathway. Using retrograde tracing, we first demonstrate that projections from the IL to the BF originate from superficial (L2/3) and deep cortical layers (L5), and that they are denser than IL projections to the BLA. Next, combining retrograde tracing with labeling of the immediate early gene cFos, we show increased activity of the L5 IL-BF pathway during extinction learning and increased activity of the L2/3 IL-BLA pathway during extinction retrieval. Our in vitro recordings demonstrate that neurons in the IL-BF pathway become more excitable towards the end of extinction learning, but less excitable during extinction retrieval. Finally, using optogenetics we show that inactivation of the IL-BF pathway impairs extinction learning, leaving retrieval intact. We propose that the IL acts as a switchboard operator during extinction, with increased L5 IL-BF communication during learning and increased L2/3 IL-BLA communication during retrieval. Anxiety and stress-related changes in IL physiology could affect one or multiple lines of communication, impairing different aspects of extinction. Significance StatementExtinction of conditioned fear is a widely used behavioral approach to diminish fear, with projections from infralimbic prefrontal cortex to the amygdala known for mediating extinction memory retrieval. However, less is known about infralimbic pathways involved in extinction learning. We use neuroanatomical tracing, behavior, slice recordings, and circuit manipulation to show that infralimbic output to the basal forebrain, an attention processing center, is denser than to the amygdala, and is active during extinction learning rather than retrieval. Neurons in the infralimbic-basal forebrain pathway become more excitable as extinction learning progresses, and then less excitable during extinction retrieval. Moreover, inhibiting this pathway impairs extinction learning. Our findings identify different lines of communication the infralimbic cortex uses for extinction learning and retrieval.

neuroscience↗

bioRxiv2024

Marseilleviruses biological properties and viral translation-associated proteins based on in silico tertiary structure

Marseilleviruses are a group of double-strand DNA viruses that infect amoeba within the Nucleocytoviricota phylum and are ubiquitous in water and soil globally. Here, we report four novel strains isolated from mangroves in Guangdong province, China, namely, futianmevirus, futianmfvirus, dashavirus str. E, and xiwanvirus. Viral particles presented about 220[~]240 nm icosahedrally shaped capsids and were wrapped by membranes to form giant vesicles. Based on stability assays, viral particles were halotolerant and acid-tolerant, but sensitive to chloroform and high temperature, while giant vesicles conferred thermal and acid/alkaline resistance to particles. Genomics and phylogenetic analyses showed that the four strains formed divergent branches within different lineages of marseillevirus. Notably, to our knowledge, futianmevirus was the first reported marseillevirus lacking translation elongation factor EF-1alpha (EF1A). Our in silico analysis of marseillevirus coded translation-associated homolgs suggested their conserved functions. Additionally, we predicted at least four novel proteins that were structurally similar to components of the protozoan ribosome. Overall, not only our data comprehensively described the diversity of marseillevirus biological properties, but also proposed a new perspective on the giant virus translation system. ImportanceThe family Marseilleviridae was the second reported family of giant viruses and distributed globally. In this work, we reported the four novel marseilleviruses isolated from saltwater samples of mangrove. Difference of biological properties between giant vesicles and viral particles revealed the environment fitness of marseillevirus. On the other hand, sensitivity to chloroform indicated the importance of lipid components for viral infection. Additionally, our comparative genomics, phylogenetic analysis, and protein structure comparison revealed the diverse translation-associated gene sets of marseilleviruses. The prediction of ribosome components expands the knowledge about the giant viral translation-associated proteins, and will be helpful in future to reveal how giant viruses hijack the amoeba translation system.

microbiology↗