Biology subjects

Zhu, X.

Publications and source records attributed to Zhu, X..

At least 127 records · Page 7Linked to original sources

bioRxiv2024

Cytosolic Carboxypeptidase 5 maintains mammalian ependymal multicilia to ensure proper homeostasis and functions of the brain

Ependymal multicilia position at one-side on the cell surface and beat synchronously across tissue to propel the flow of cerebrospinal fluid. Loss of ependymal cilia often causes hydrocephalus. However, molecules contributing to their maintenance remain yet fully revealed. Cytosolic carboxypeptidase (CCP) family are erasers of polyglutamylation, a conserved posttranslational modification of ciliary-axoneme microtubules. CCPs possess a unique domain (N-domain) N-terminal to their carboxypeptidase (CP) domain with unclear function. Here, we show that a novel mutant mouse of Agbl5, the gene encoding CCP5, with deletion of its N-terminus and partial CP domain (designated Agbl5M1/M1), developed lethal hydrocephalus due to degeneration of ependymal multicilia. Interestingly, multiciliogenesis was not impaired in Agbl5M1/M1 ependyma, but the initially formed multicilia beat in intercellularly diverse directions, indicative of aberrant tissue-level coordination. Moreover, actin networks are severely disrupted and basal body patches are improperly displaced in mutant cells, suggesting impaired cell level polarity. In contrast, Agbl5 mutants with disruption solely in the CP domain of CCP5 (Agbl5M2/M2) do not develop hydrocephalus despite increased glutamylation levels in ependymal cilia as similarly seen in Agbl5M1/M1. This study revealed an unappreciated role of CCP5, particularly its N-domain, in ependymal multicilia stability associated with their polarization and coordination.

cell biology↗

bioRxiv2024

TCPGdb: A comprehensive T cell perturbation genomics database for identification of critical T cell regulators

CAR-T therapies utilizing T cells engineered with chimeric antigen receptors (CARs) have revolutionized the treatment of hematologic and immune-related malignancies. However, the anti-tumor capability of engineered CAR-T cells are often not persistent, which greatly dampen its clinical efficacy. To address this limitation, massive parallel genetic screens were widely used to identified novel targets and regulators that enhance T cell anti-tumor capability and persistence in tumor microenvironment. We hypothesized that by combining the pooled screen data from multiple independent genetic screens we could provide a systematic, comprehensive, and robust analysis of the effect of gene perturbation on T-cell based immunotherapies. After collecting data from previously published T cell screens, including CRISPR-based and ORF-based screens, through Gene Expression Omnibus (GEO), we reprocessed the gene hits summary and conducting a pathway enrichment analysis. A T cell screen perturbation score (TPS) was employed to quantifies the impact of the gene on T cell function. Additionally, gene expression data (both bulk RNA level and single-cell RNA level) from autoimmune disease and T cell-derived cancers were analyzed to pick up gene perturbations that potentially augment T cell proliferation. We integrated all data and analysis on 27 T-cells screens into our state-of-the-art T cell perturbation genomics database (TCPGdb), which is made easily accessible through our webserver and allows users to interactively explore the impact of query genes on T cell function based on prior screen data and our TPS scoring module. TCPGdb is publicly accessible at http://tcpgdb.sidichenlab.org/.

bioinformatics↗

bioRxiv2024

The farnesyl transferase inhibitor KO-2806 re-sensitizes relapsing tumors to RAS inhibition

Resistance remains a key issue limiting the clinical benefit from RAS-targeting therapeutic agents and necessitates combination approaches. We identify persistent mTORC1 activity in preclinical KRAS-mutant NSCLC and CRC models as a frequent, nongenetic driver of inherent and adaptive resistance to RAS inhibition. This vulnerability is targetable with the farnesyl transferase inhibitor KO-2806, which blocks mTORC1 activation via RHEB while sparing mTORC2 and its associated toxicities. The addition of KO-2806 to NSCLC or CRC tumors progressing on mutant-selective RAS inhibitors led to rapid and durable tumor regression. In contrast, switching from mutant-selective to pan-RAS inhibitor monotherapy resulted in only stasis of NSCLC tumors and had no effect on CRC tumor progression. Further, the addition of KO-2806 rescued sensitivity of progressing tumors to the pan-RAS inhibitor RMC-6236. Our results establish mTORC1 as an important mediator of escape from RAS inhibition and highlight KO-2806 as a promising RAS companion inhibitor in patients with prior RAS inhibitor exposure. SignificanceUtilizing in vivo models of tumor relapse, we define a subset of RAS inhibitor-resistant tumors in which vertical inhibition of MAPK is insufficient to restore sensitivity. By controlling parallel mTORC1 activity, KO-2806 may expand utility of RAS inhibitors in patients that have progressed on RAS-targeted therapy, regardless of inhibitor class.

cancer biology↗

bioRxiv2024

Modulating Cellular Deformability via 3D Dextran Hydrogel Cultivation to Regulate the Microcirculation of Mesenchymal Stem Cells in Murine Spleen and Liver

For mesenchymal stem cell (MSC) therapy to be effective, the vascular system may be used to deliver and steer the cells to the target tissue. However, the expanded MSCs in petri dishes are usually have a limited deformability and commonly excluded by the capillary networks when homing to the downstream organs via microcirculation. Here, we propose to utilize specially designed 3D dextran hydrogels and tuning the microscopic heterogeneity of hydrogel composition to make the administrated cells mechanically comply with the structure and mechanics of the capillary. The cell deformability in petri dishes, microcosmically homogeneous (HOM) and heterogeneous (HET) dextran hydrogels were investigated in vitro by measuring cell moduli through atomic force microscope (AFM), analyzing the expression of cytoskeletal protein via flow cytometry and fluorescent imaging. The in vitro experimental results demonstrate a progressive increase in cell deformability from 2D dishes, to HOM-hydrogel derived cells, and then to HET-hydrogel derived cells. The in vivo mouse experiment indicates the cells could deform accordingly and pass through easily with reduced resistance inside the mouse organs. It is suggested that the main destination of hMSC microcirculation could be selected between the spleen and liver of mice, by tuning cell mechanics that depends on the stimulus from microcosmically HOM or HET hydrogel, which lays a potential foundation for the mechanically modified MSC therapy for lesions in the organs.

biophysics↗

bioRxiv2024

Identification of Differentially Expressed Genes and Proteins Related to Diapause in Lymantria Dispar: Insights for the Mechanism of Diapause from Transcriptome and Proteome Analyses

Spongy moth (Lymantria dispar Linnaeus) is a globally recognized quarantine leaf-eating pest. Spongy moths typically enter diapause after completing embryonic development and overwinter in the egg stage. They spend three-quarters of their life cycle (approximately nine months) in the egg stage, which requires a period of low-temperature stimulation to break diapause and continue growth and development. In this study, we explored the molecular mechanism underlying the diapause process in spongy moth. We performed bioinformatics analysis on four Asian populations of spongy moth and one Asian-European hybrid population through a transcriptome analysis combined with proteomics. The results revealed that 1,842 genes were differentially expressed upon diapause initiation, while 264 genes were identified upon diapause termination. Eight diapause-related genes were screened out from the three-level pathways that were significantly enriched by differentially expressed genes at the time of diapause and diapause termination, and the phylogenetic tree and protein three-dimensional structure model were constructed. This study elucidates the diapause mechanism of spongy moth at the gene and protein levels, providing theoretical insights into the early and precise prevention and control of spongy moth. This study can facilitate the development of an efficient, environmentally friendly control system for managing spongy moth populations in the field.

genomics↗

bioRxiv2024

Structural and functional interrelationship of histone H2A and its variants H2A.Z and H2A.W in Arabidopsis

Multiple histone H2A variants are known in eukaryotes. However, the functional relationship between H2A and its variants in plants remains largely obscure. Using CRISPR/Cas9 editing, we generated a mutant lacking four H2A isoforms in Arabidopsis and analyzed the functional and structural relationship between H2A and its variants H2A.Z and H2A.W. RNA-sequencing and phenotype analyses revealed mild changes in gene transcription and plant development in the mutants lacking H2A, H2A.Z, or H2A.W compared with the wild-type plants. Chromatin immunoprecipitation sequencing analysis showed that H2A is able to substitute for both H2A.Z and H2A.W across the genome, including in euchromatin and heterochromatin regions. However, H2A.Z replaced both H2A and H2A.W primarily within the euchromatin regions. By using DNA and histones derived from Arabidopsis, we constructed nucleosomes containing H2A, H2A.Z, or H2A.W and resolved their cryogenic electron microscopy structures at near-atomic resolution. Collectively, the results reveal the structural similarity and functional redundancy of H2A and H2A variants in Arabidopsis.

plant biology↗

bioRxiv2024

The dual ubiquitin binding mode of SPRTN secures rapid spatiotemporal proteolysis of DNA-protein crosslinks

DNA-protein crosslinks (DPCs) are endogenous and chemotherapy-induced genotoxic DNA lesions and, if not repaired, lead to embryonic lethality, neurodegeneration, premature ageing, and cancer. DPCs are heavily polyubiquitinated, and the SPRTN protease and 26S proteasome emerged as two central enzymes for DPC proteolysis. The proteasome recognises its substrates by their ubiquitination status. How SPRTN protease, an essential enzyme for DPC proteolysis, achieves specificity for DPCs still needs to be discovered. We found that the N-terminal SPRTN catalytic region (SprT) possesses a ubiquitin-binding domain named the Ubiquitin interface of SprT Domain (USD). Using multiple biochemical, biophysical, and structural approaches, we reveal that USD binds ubiquitin chains. SPRTN binding to ubiquitin chains via USD leads to [~] 67-fold higher activation of SPRTN proteolysis towards polyubiquitinated DPCs than the unmodified DPCs. This study reveals the ubiquitination of DPCs is the key signal for SPRTNs substrate specificity and rapid proteolysis.

biochemistry↗

bioRxiv2024

In-silico modeling and interpretation of RBP binding disentangle m6A-RBP interaction

RNA binding protein (RBP) binding and N6-methyladenosine (m6A) are both essential post-transcriptional regulatory layers for RNA fate decisions. However, the intricate mechanism underlying the interaction between m6A and RBP binding remains underexplored. Here, we develop TransRBP, an interpretable deep learning framework, to model the base-resolution binding of RBPs from RNA sequences and to subsequently investigate the interaction between m6A and RBPs. TransRBP achieves a median accuracy of 0.59 across 32 m6A-related RBPs, representing a 28% increase over the state-of-the-art model. Using gradient-based interpretation, we demonstrate that the binding motifs of the m6A-related RBPs strongly enrich for splicing consensus, laying a foundation for studying the RBP-dependent crosstalk between m6A and splicing. Moreover, we develop an in-silico mutagenesis assay to assess the impact of m6A on RBPs, and utilize the self-attention mechanism to elucidate the interplay between RBP binding and m6A. We further uncover 1,806 variant-RBP combinations with the in-silico mutagenesis, revealing variants that strongly alter RBP binding for genetic diseases including Parkinsons disease, autism, and cardiomyopathy. In particular, we identify m6A cis-acting variants that alter RBP binding in an m6A-proximal manner, including the binding of UPF1 that contributes to Alzheimers disease, and the DDX3X binding to cardiomyopathy and muscular dystrophy. Together, TransRBP accurately models the binding of RBP and its interaction with m6A, shedding light on the m6A-RBP dynamics and providing multi-layer mechanistic insights for genetic diseases.

bioinformatics↗

bioRxiv2024

Chaperonin TRiC bridges radial spokes for folding proteins locally translated in mammalian sperm flagella

As animals evolved from external to internal fertilization, sperm flagella, which once transiently propelled sperm in water to reach nearby eggs, developed to beat for days or even longer within the female reproductive tract. How flagella were remodeled accordingly remains unclear. Unlike externally fertilizing zebrafish and sea urchin, mammalian sperm flagella feature a unique barrel-shaped bridge between axonemal radial spokes RS1 and RS2, though its components and function remain unknown. Here, using cryo-EM and cryo-ET combined with mass spectrometry and immunofluorescence staining, we reveal that this RS1-RS2 barrel (RRB) in mammalian sperm flagella is a group II chaperonin TRiC/CCT. We purified and resolved the unforeseen cryo-EM structure of TRiC from bovine sperm flagella, discovering that flagella TRiC contains the testis-specific CCT6B subunit. Additionally, we resolved the cryo-ET map of mouse sperm flagella RSs, containing the RRB, achieving unprecedented local resolution of 10-14 [A]. The in-situ RRB map displays two extra densities within its chambers in a polarized manner, suggesting the presence of folding substrates and a co-chaperone (likely phosducin-like 2). Notably, mammalian flagella also contain components of translation machineries and actively synthesize proteins. Our results suggest that the RRB TRiC folds locally translated proteins to sustain mammalian flagella, providing new insights into flagellar remodeling in internally fertilizing species. Our findings also shed lights on male fertility and potential treatments for infertility.

biophysics↗

bioRxiv2024

Regulation of Fentanyl Reward in Male and Female Mice by the Circadian Transcription Factor NPAS2

Synthetic opioids like fentanyl are highly potent and prevalent in the illicit drug market, leading to tolerance, dependence, and opioid use disorder (OUD). Chronic opioid use disrupts sleep and circadian rhythms, which persist even during treatment and abstinence, increasing the risk of relapse. The bodys molecular clock, regulated by transcriptional and translational feedback loops, controls various physiological processes, including the expression of endogenous opioids and their receptors. The circadian transcription factor NPAS2, highly expressed in the nucleus accumbens, may have a crucial function in opioid-related behaviors. Our study found sex-specific roles for NPAS2-mediated reward behaviors in male and female mice, including in fentanyl seeking and craving. We also identified specific cell types and transcriptional targets in the nucleus accumbens of both mice and humans by which NPAS2 may mediate the impact of fentanyl on brain physiology and in opioid reward-related behaviors. Ultimately, our findings begin to uncover the mechanisms underlying circadian rhythm dysfunction and opioid addiction.

neuroscience↗

bioRxiv2024

Image-based DNA Sequencing Encoding for Detecting Low-Mosaicism Somatic Mobile Element Insertions

Active LINE-1 (L1), Alu, and SVA mobile elements in the human genome are capable of retrotransposition, resulting in novel mobile element insertions (MEIs) in both germline and somatic tissues. Detecting MEIs through DNA sequencing relies on supporting reads overlapping MEI junctions; however, artifacts from DNA amplification, sequencing, and alignment errors produce numerous false positives. Systematic detection of somatic MEIs, particularly those with low mosaicism, remains a significant challenge. Previous methods had required a high number of supporting reads which limits the detection sensitivity, or human inspections that are susceptible to biases. Here, we developed RetroNet, an algorithm that encodes MEI-supporting sequencing reads into images, and employs a deep neural network to identify somatic MEIs with as few as two reads. Trained on extensive and diverse datasets and benchmarked across various conditions, RetroNet surpasses previous methods and eliminates the need for extensive manual examinations. The RetroNet analysis on the Illumina sequencing of 161x or 195x of a cancer cell line achieved an average precision of 0.885 and recall of 0.579 for detecting somatic L1 insertions that are present in as few as 1.79% of the cells. Additionally, we demonstrated that RetroNet is effective for analyzing highly degraded DNA, such as circulating tumor DNA. RetroNet is applicable to the rapidly generated short-read sequencing data and has the potential to provide further insights into the functional and pathological implications of somatic retrotranspositions.

genomics↗

bioRxiv2024

Activating p53Y220C with a Mutant-Specific Small Molecule

TP53 is the most commonly mutated gene in cancer, but it remains recalcitrant to clinically meaningful therapeutic reactivation. We present here the discovery and characterization of a small molecule chemical inducer of proximity that activates mutant p53. We named this compound TRanscriptional Activator of p53 (TRAP-1) due to its ability to engage mutant p53 and BRD4 in a ternary complex, which potently activates mutant p53 and triggers robust p53 target gene transcription. Treatment of p53Y220C expressing pancreatic cell lines with TRAP-1 results in rapid upregulation of p21 and other p53 target genes and inhibits the growth of p53Y220C-expressing cell lines. Negative control compounds that are unable to form a ternary complex do not have these effects, demonstrating the necessity of chemically induced proximity for the observed pharmacology. This approach to activating mutant p53 highlights how chemically induced proximity can be used to restore the functions of tumor suppressor proteins that have been inactivated by mutation in cancer.

cancer biology↗

bioRxiv2024

Analyzing the Molecular Mechanism of Eucalyptol, Limonene and Pinene Enteric Capsules (QIENUO) in the Treatment of Pulmonary cystic fibrosis with Network Pharmacology and Verifying Molecular Docking

ObjectiveTo explore the mechanism of Eucalyptol, Limonene and Pinene Enteric Capsules (QIENUO) in the treatment of pulmonary cystic fibrosis (CPF), analyze the common targets of QIENUO and CPF, and verify the molecular docking of core proteins and small molecules. MethodsThe main active compounds and their corresponding targets were obtained from PubChem, SwissTargetprediction, GeneCards, PharmMapper and TCMSP databases. Targets related to CPF were screened from GeneCards, OMIM, DisGeNET and TTD databases. The common "QIENUO-CPF" targets were analyzed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) through the website of Weishengxin. Protein-protein interaction (PPI) network and compound-target-pathway network were constructed by Cytoscape, and the network parameters were systematically analyzed. The interaction between core protein and monomer components was evaluated and verified by molecular docking method. Results228 active compounds target and 1354 CPF-related targets were screened out, and 92 common targets were analyzed by GO and KEGG. The results showed that the therapeutic effect of QIENUO on CPF was mainly through AMPK signaling pathway, cGMP-PKG signaling pathway and TGF-{beta} signaling pathway. The results of molecular docking show that the binding energy of 9 of 15 pairs of ligand-receptor pairs is lower than-6 kjmol-1. ConclusionQIENUO exhibits huge potential as a therapeutic agent for the treatment of pulmonary cystic fibrosis. The specific molecular mechanism and effective active components of QIENUO treat CPF were studied and demonstrated, which provided theoretical basis for better clinical application of QIENUO.

bioinformatics↗

bioRxiv2024

Exploring the Correlation Between UVB Sensitivity and SLE Activity: Insights into UVB-Driven Pathogenesis in Lupus Erythematosus

Lupus erythematosus (LE) comprises various autoimmune inflammatory diseases, with significant overlap between cutaneous LE (CLE) and systemic LE (SLE). A key feature of both CLE and SLE is UV photosensitivity, particularly in UV-exposure-related skin inflammation. Despite this, reliable and objective UVB photosensitivity indicators closely correlating with LE activity have yet to be identified, and the underlying cellular and molecular mechanisms linking UVB sensitivity with LE onset and progression remain unclear. We discovered that ultraviolet B minimal erythema dose (UVB-MED), a quantitative photosensitivity measure, is a significant and independent risk factor for SLE activity, demonstrating a negative correlation with SLEDAI (r = -0.58, P < 0.0001). Comprehensive transcriptomic analyses of large-scale CLE and SLE samples revealed more pronounced and extensive UVB-response gene dysregulation in skin tissues compared to blood. Additionally, 14 lupus activity-correlated, UVB-response genes (UVBACGs) were identified, including eight interferon-stimulated genes (IRF7, ISG20, ISG15, IFI44, IFITM1, MX1, LY6E, OASL) and others (JUN, PTTG1, HLA-F, CAV1, HOPX, RPL3), with dysregulation evident in both skin and blood cells, particularly immunocytes. Conventional LE therapies were found to be associated with these genes and may potentially regulate them, thereby contributing to therapeutic effects. These findings highlight the role of UVB in triggering autoimmune inflammation in the skin, which may subsequently spread to systemic inflammation via immune cells and factors. UVBACGs play a critical role in this process and may serve as targets for precise LE therapies, providing insight into the link between UVB photosensitivity and LE progression.

immunology↗

bioRxiv2024

Pancreatic cancer cells overexpressing interleukin 6 induce T-cell-mediated tumor clearance and durable anti-tumor immune response

Background & AimsTumor immune resistance is recognized as a contributor to low survivorship in pancreatic ductal adenocarcinoma (PDAC). The inflammatory cytokine interleukin-6 (IL-6) promotes polarization of CD4 T cell populations away from immune tolerance, and induces differentiation of cytotoxic CD8 T cells. This work aims to test whether IL-6 could stimulate an anti-tumor response in PDAC MethodsWe overexpressed IL-6 in multiple KrasG12D/+, Tp53R172H/+, Pdx1-Cre (KPC) cell lines, which were orthotopically implanted in mice (OT-PDACIL6). We followed mouse survival and measured tumor growth, tumor histology, and plasma IL-6 at 5 and 10 days after tumor implantation. We measured tumor immune cell infiltration via flow cytometry and histology. We used antibody-based T cell depletion and secondary tumor implantation rechallenge to test the dependency of the durable immune reaction on T cells. We use lipid nanoparticle (LNP)-based delivery of IL-6 mRNA to the pancreas as an orthogonal approach for testing the effect of elevated IL-6 in the tumor microenvironment on anti-tumor T cell invasion. ResultsImproved survival occurred in all instances of OT-PDACIL6, with one cell line (KxPxCx) reproducibly resulting in long-term recurrence-free survival. With KxPxCx cells, circulating IL-6 was 100-fold higher in OT-KxPxCxIL6 than in OT-KxPxCxparental mice. Flow cytometry revealed increased T cells and NK cells, and decreased T regulatory cells, and we observed significantly increased lymphoid aggregates in OT-KXPXCXIL6 as compared to OT--KxPxCxparental tumors. Antibody-based CD4+ and CD8+ T cell depletion prevented tumor clearance and completely abolished the survival advantage in OT-KxPxCxIL6 mice. The anti-tumor immune response to OT-KxPxCxIL6 rendered mice immune to re-challenge with OT-KxPxCxparental tumors. LNP delivery of IL-6 to the pancreas elevated systemic IL-6 levels [~]50 fold, lowered tumor burden, and increased anti-tumor T cell phenotypes. ConclusionsLocally high IL-6 concentrations potently enhance the T cell-mediated anti-tumor response to PDAC. SYNOPSISInterleukin-6 induces rapid and durable T cell-driven immune clearance of pancreatic ductal adenocarcinoma. The anti-tumor immune microenvironment is hallmarked by increased lymphoid aggregate formation, increased CD4 T cell abundance, and decreased Treg abundance.

cancer biology↗

bioRxiv2024

Melanocortin-4 receptor antagonist TCMCB07 alleviates chemotherapy-induced anorexia and weight loss

Cancer patients undergoing chemotherapy often experience anorexia and weight loss that significantly deteriorates overall health, reduces treatment tolerance and quality of life, and worsens oncologic outcomes. There are currently few effective therapeutic options to mitigate these side effects. The central melanocortin system, which plays a pivotal role in regulating appetite and energy homeostasis, presents a logical target for treating anorexia and weight loss. In this preclinical study, we evaluated the efficacy of TCMCB07, a synthetic antagonist of the melanocortin-4 receptor, in mitigating anorexia and weight loss in several rat models of chemotherapy: cisplatin, 5-fluorouracil, cyclophosphamide, vincristine, doxorubicin, and a combination of irinotecan and 5-fluorouracil. Our results indicate that peripheral administration of TCMCB07 improved appetite, stabilized body weight, preserved fat and heart mass, and slightly protected lean mass after multiple cycles of chemotherapy. Furthermore, combining TCMCB07 with a growth differentiation factor 15 antibody enhanced treatment effectiveness. Similar effects from TCMCB07 treatment were observed in a rat tumor model following combination chemotherapy. No significant adverse effects nor increased chemotherapy-related toxicities were observed with TCMCB07 treatment. These findings suggest that peripheral administration of TCMCB07 holds promise as a therapeutic approach for alleviating chemotherapy-induced anorexia and weight loss, potentially benefiting numerous patients undergoing chemotherapy. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/613069v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@cbe32borg.highwire.dtl.DTLVardef@1af55e7org.highwire.dtl.DTLVardef@30deb1org.highwire.dtl.DTLVardef@6c39a3_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Neural Circuit Underlying Individual differences in Visual Escape Habituation

Emotions, like fear, are internal states enabling organisms to effectively confront environmental threats. When repeatedly exposed to predators, individuals show divergent adaptive responses. However, the neural circuit mechanisms underlying individual differences in to repeated threats remain largely unknown. Here, we identify two distinct types of visual escape--consistent escape (T1) and rapid habituation (T2) -- with unambiguous arousal states to repetitive threat stimuli. We systematically investigate distinct pathways originating from the superior colliculus (SC) and insula that project to the basolateral amygdala (BLA), with relay stations in the mediodorsal thalamus (MD) and ventral tegmental area (VTA), mediating T1 and T2 behavioral types. Additionally, we identify the MD as a critical hub integrating SC and insula inputs, projecting to the BLA and contributing to reduced arousal and attenuated defensive behaviors against looming stimuli. Our findings offer significant insights into the mechanisms of internal states, arousal modulation, and behavioral adaptability. O_FIG O_LINKSMALLFIG WIDTH=178 HEIGHT=200 SRC="FIGDIR/small/611366v1_ufig1.gif" ALT="Figure 1"> View larger version (77K): org.highwire.dtl.DTLVardef@164df34org.highwire.dtl.DTLVardef@17a01e6org.highwire.dtl.DTLVardef@112de44org.highwire.dtl.DTLVardef@1be6aea_HPS_FORMAT_FIGEXP M_FIG Graph Abstract C_FIG In briefWe identify two distinct visual escape behaviors--consistent escape (T1) and rapid habituation (T2)--linked to unique SC and insula pathways projecting to the BLA via MD and VTA. The MD acts as a hub integrating sensory inputs to modulate arousal and defensive responses. These findings advance our understanding of the neural mechanisms driving internal states, arousal modulation, and behavioral adaptability. Highlights[bullet] We identify two distinct visual escape behaviors with unambiguous arousal states--consistent escape (T1) and rapid habituation (T2) --to repeated looming stimuli. [bullet]The SC-VTA-BLA pathway mediated T1 behavioral type, while the SC-MD-BLA pathway mediated T2 type. [bullet]MD as a central hub integrating SC and insula inputs to modulate arousal and defensive behavioral adaptation.

neuroscience↗

bioRxiv2024

Enhanced Salt Tolerance in Synechocystis sp. PCC 6803 Through Adaptive Evolution: Mechanisms and Applications for Environmental Bioremediation

Salt stress is common in natural environments, where elevated salt levels in brackish water and saline soil can hinder the growth of organisms, thereby exacerbating environmental challenges. Developing salt-tolerant organisms not only uncovers novel mechanisms of salt tolerance but also lays the groundwork for managing and utilizing saline environments. Cyanobacteria, which are widely distributed in hydrosphere and soil, serve as ideal models for studying salt stress. In this study, the model cyanobacterium Synechocystis sp. PCC 6803 was selected, whose salt (NaCl) tolerance improved from 4.0% to 6.5% (m/v) through adaptive laboratory evolution. Genome re-sequencing and mutant analysis identified six key genes associated with salt tolerance. Notably, the deletion of slr1670, which encodes glycerol glucoside hydrolase, improved the strains salt tolerance. In addition, slr1753 encodes a membrane protein that may enhance salt tolerance by facilitating ion transport to the extracellular space. Further analysis revealed that overexpression of slr1753 significantly accumulates Na+ on the cell surface, enabling effective seawater treatment using the engineered strain, resulting in a 6.35% reduction of Na+ in the seawater. Moreover, the adapted bacteria can be used for the remediation of saline soil samples, leading to a 184.2% and 43.8% increase in the germination rate and average height of Brassica rapa chinensis, respectively, along with a 25.3% rise in total organic carbon content and reductions in both total salt content by 1.82% and pH by 1.91% in soil. This study provides novel insights into salt tolerance mechanisms and the bioremediation of high-salinity environments. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/610226v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@cde16aorg.highwire.dtl.DTLVardef@8a27ccorg.highwire.dtl.DTLVardef@3af9bforg.highwire.dtl.DTLVardef@1e29cfb_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗