Biology subjects

Zhao, L.

Publications and source records attributed to Zhao, L..

At least 163 records · Page 9Linked to original sources

bioRxiv2023

The Origin and Evolution of Sex Peptide and Sex Peptide Receptor Interactions

Post-mating responses play a vital role in successful reproduction across diverse species. In fruit flies, sex peptide (SP) binds to the sex peptide receptor (SPR), triggering a series of post-mating responses. However, the origin of SPR predates the emergence of SP. The evolutionary origins of the interactions between SP and SPR and the mechanisms by which they interact remain enigmatic. In this study, we used ancestral sequence reconstruction, AlphaFold2 predictions, and molecular dynamics simulations to study SP-SPR interactions and their origination. Using AlphaFold2 and long-time molecular dynamics (MD) simulations, we predicted the structure and dynamics of SP-SPR interactions. We show that SP potentially binds to the ancestral states of Diptera SPR. Notably, we found that only a few amino acid changes in SPR are sufficient for the formation of SP-SPR interactions. Ancestral sequence reconstruction and MD simulations further reveal that SPR interacts with SP through residues that are mostly involved in the interaction interface of an ancestral ligand, myoinhibitory peptides (MIPs). We propose a potential mechanism whereby SP-SPR interactions arise from the pre-existing MIP-SPR interface as well as early chance events both inside and outside the pre-existing interface that created novel SP-specific SP-SPR interactions. Our findings provide new insights into the origin and evolution of SP-SPR interactions and their relationship with MIP-SPR interactions.

evolutionary biology↗

bioRxiv2023

Revisiting the Briggs ancient DNA damage model: a fast regression method to estimate postmortem damage

MotivationOne essential initial step in the analysis of ancient DNA is to authenticate its ancientness to ensure reliable conclusions. That is, meticulously assessing whether next-generation sequencing reads exhibit ancient characteristics, with a particular focus on the postmortem damage (PMD) signal induced by cytosine deamination in the fragments termini. We present a novel statistical method implementation in a fast multithreaded program ngsBriggs that enables the rapid quantification of PMD by calculation of the Briggs ancient damage model parameters (Briggs parameters). ResultsUsing a fast multinomial regression approach, ngsBriggs accurately models the Briggs parameters, quantifying the PMD signal from single and double-stranded DNA regions. We revisit and extend the original Briggs model, with ngsBriggs modeling PMD signals for contemporary sequencing platforms. Furthermore, ngsBriggs asserts itself as a reliable and consistent tool, by accurately estimating the Briggs parameters across a variety of contamination levels. The classification accuracy of ngsBriggs significantly exceeds the current tool available when discerning ancient-from modern sequencing reads to decontaminate samples. Our novel method and implementation ngsBriggs outperforms existing tools regarding computational speed and accuracy, establishing its practicality and usability. Our tool, ngsBriggs offers a practical and accurate toolset for researchers seeking to authenticate ancient DNA and improve the quality of their data. Availabilityhttps://github.com/lz398/metadamage_briggs

bioinformatics↗

bioRxiv2023

Mechanisms of ligand recognition and activation of melanin-concentrating hormone receptors

Melanin-concentrating hormone (MCH) is a cyclic neuropeptide that regulates food intake, energy balance, and other physiological functions by stimulating MCHR1 and MCHR2 receptors, both of which are class A G protein-coupled receptors. MCHR1 can couple with multiple G-proteins, including Gi/o, Gq/11, and Gs, while MCHR2 only couple to Gq/11. Here we present cryo-electron microscopy structures of MCH-activated MCHR1 with Gi and MCH-activated MCHR2 with Gq complexes, at the global resolutions of 3.01 [A] and 2.40 [A], respectively. These structures reveal that MCH adopts a consistent cysteine-mediated hairpin loop configuration in both receptors. A central arginine from the LGRVY core motif between the two cysteines of MCH penetrates deeply into the transmembrane pocket, triggering receptor activation. Integrated with mutational and functional insights, our findings elucidate the molecular underpinnings of ligand recognition and MCH receptor activation, offering a structured foundation for targeted drug design.

molecular biology↗

bioRxiv2023

Dense Sampling of Taxa and Genomes Untangles the Phylogenetic Backbone of a Non-model Plant Lineage Rife with Deep Hybridization and Allopolyploidy

Phylogenetic networks, rather than purely bifurcating trees, more accurately depict the intricate evolutionary dynamics of most lineages, especially those characterized by extensive hybridization and allopolyploidization events. However, the challenges of achieving complete taxon sampling, and limited financial resources for studying non-model plant lineages, have hindered comprehensive and robust estimation of phylogenetic backbones with guidance from networks. The bellflower tribe, Campanuleae, characterized by a reticulate evolutionary history, serves as an ideal model to investigate how to diagnose nested ancient reticulation events. Here, by integrating multiple genomic data sources and a range of phylogenetic inference methods, we produced a robust phylogenetic backbone for the tribe Campanuleae. Our investigation of reticulate evolution indicates that hybridization and allopolyploidization were instrumental in shaping the diversity of the bellflower tribe, particularly during the initial diversification of the subtribe Phytematinae. Additionally, we ascertained that conflicting topologies resulting from distinct genomic datasets and inference methodologies significantly impact downstream estimates of divergence dating, ancestral area construction, and diversification rates. This study offers a universally relevant framework for deciphering how to use network-based phylogenetic structures using various genomic sources and inference methods. [Campanulaceae, Campanuleae, Cytonuclear discordance, paralog, phylogenomics, reticulate evolution]

plant biology↗

bioRxiv2023

Host tracheal and intestinal microbiomes inhibit Coccidioides growth in vitro

Coccidioidomycosis, also known as Valley fever, is a disease caused by the fungal pathogen Coccidioides. Unfortunately, patients are often misdiagnosed with bacterial pneumonia leading to inappropriate antibiotic treatment. Soil bacteria B. subtilis-like species exhibits antagonistic properties against Coccidioides in vitro; however, the antagonistic capabilities of host microbiota against Coccidioides are unexplored. We sought to examine the potential of the tracheal and intestinal microbiomes to inhibit the growth of Coccidioides in vitro. We hypothesized that an uninterrupted lawn of microbiota obtained from antibiotic-free mice would inhibit the growth of Coccidioides while partial in vitro depletion through antibiotic disk diffusion assays would allow a niche for fungal growth. We observed that the microbiota grown on 2xGYE (GYE) and CNA w/ 5% sheeps blood agar (5%SB-CNA) inhibited the growth of Coccidioides, but that grown on chocolate agar does not. Partial depletion of the microbiota through antibiotic disk diffusion revealed that microbiota depletion leads to diminished inhibition and comparable growth of Coccidioides growth to controls. To characterize the bacteria grown and narrow down potential candidates contributing to the inhibition of Coccidioides, 16s rRNA sequencing of tracheal and intestinal agar cultures and murine lung extracts was performed. The identity of host bacteria that may be responsible for this inhibition was revealed. The results of this study demonstrate the potential of the host microbiota to inhibit the growth of Coccidioides in vitro and suggest that an altered microbiome through antibiotic treatment could negatively impact effective fungal clearance and allow a niche for fungal growth in vivo. ImportanceCoccidioidomycosis is caused by a fungal pathogen that invades host lungs, causing respiratory distress. In 2019, 20,003 cases of Valley fever were reported to the CDC. However, this number likely vastly underrepresents the true number of Valley fever cases as many go undetected due to poor testing strategies and lack of diagnostic models. Valley fever is also often misdiagnosed as bacterial pneumonia, resulting in 60-80% of patients being treated with antibiotics prior to accurate diagnosis. Misdiagnosis contributes to a growing problem of antibiotic resistance and antibiotic induced microbiome dysbiosis, and the implications on disease outcome are currently unknown. 5%-10% of symptomatic Valley fever patients develop disseminated and/or chronic disease. Valley fever causes a significant financial burden and reduced quality of life. Little is known regarding what factors contribute to the development of chronic infection and treatments for disease are limited.

microbiology↗

bioRxiv2023

Directional predictions of HIV transmission with optimised genomics in cohorts of serodiscordant couples

Viral genetic information from people living with HIV can deepen our understanding of the infections epidemiology at many scales. To better understand the potentials and limits of tools that utilise such information, we show the performance of two representative tools (HIV-TRACE and phyloscanner) in describing HIV transmission dynamics, with different types of genetic data, and compare with previous findings. The samples were collected from three cohort studies in Sub-Saharan Africa and were deep sequenced to produce both short Illumina reads and long PacBio reads. By comparing phyloscanners performance with short and long reads, we show that long reads provide improved phylogenetic resolution for the classic transmission topology in joint within-host trees. Our pipeline accurately predicted the direction of transmission 88%-92% of the time. We also show that the timing of sample collection plays an important role in the reconstruction of directionality using deep sequencing data. Consensus sequences were also generated and used as HIV-TRACE input to show different patterns of clustering sensitivity and specificity for data from different genomic regions or the entire genome. Finally, we discuss adjusting expectations about sensitivity and specificity of different types of sequence data, considering rapid pathogen evolution, and highlight the potentials of high within-host phylogenetic resolution in HIV. In conclusion, viral genetic data collected and presented differently could greatly influence our ability to describe the underlying dynamics. Methods for source attribution analysis have reached levels of superior accuracy. However, residual uncertainty emphasizes sequence analysis alone cannot conclusively prove linkage at the individual level. ImportanceUnderstanding HIV transmission dynamics is key to designing effective HIV testing and prevention strategies. By using different sequencing techniques on well-characterised cohorts, we were able to evaluate the effect of genetic data resolution on the accuracy of identifying likely transmission pairs and the direction of transmission within pairs. We find that the longer reads generated by PacBio sequencing are more suitable for transmission analyses.

genomics↗

bioRxiv2023

Acute avoidance of hydrogen sulfide is modulated by external and internal states in C. elegans

Hydrogen sulfide (H2S) acts as an energy source, a toxin, and a gasotransmitter across diverse biological contexts. We use the robust locomotory responses of Caenorhabditis elegans to high levels of H2S to elucidate the molecular mechanisms underlying its acute and adaptive responses. We find that the H2S-evoked behavioral response is shaped by multiple environmental factors including oxygen (O2) levels and nutritional state, and is modulated by various pathways such as insulin, TGF-{beta}, and HIF-1 signaling, as well as by input from O2-sensing neurons. Prolonged exposure to H2S activates HIF-1 signaling, leading to the upregulation of stress-responsive genes, including those involved in H2S detoxification. This promotes an adaptive state in which locomotory speed is reduced in H2S, while responsiveness to other stimuli is preserved. In mutants deficient in HIF-1 signaling, iron storage, and detoxification mechanisms, animals display a robust initial response but rapidly enter a sleep-like behavior characterized by reduced mobility and diminished responsiveness to subsequent sensory stimuli. Furthermore, while acute production of mitochondria-derived reactive O2 species (ROS) appears to initiate the avoidance response to H2S, persistently high ROS promotes an adaptive state, likely by activating various stress-response pathways, without substantially compromising cellular H2S detoxification capacity. Taken together, our study provides comprehensive molecular insights into the mechanisms through which C. elegans modulates and adapts its response to H2S exposure.

animal behavior and cognition↗

bioRxiv2023

A resource for probing influences of perinatal factors on neurodevelopment in 3-10-years-old Chinese children

Adverse perinatal factors can disrupt the normal development of the brain, with potential long-term impacts on childrens overall development. Currently, the neuropathological mechanisms by which these factors lead to various neurodevelopmental disorders (NDDs) remain largely unknown. An open resource that integrate perinatal factors with brain and mental health development is essential for investigating NDD-related aetiology. In this Data Descriptor, we introduce a multicentre database containing information on perinatal factors that influence childrens brain-mind development, namely, periCBD, that combines neuroimaging and behavioural phenotypes with perinatal factors associated with a high incidence of NDDs at county/region/central district hospitals. PeriCBD was designed to establish a platform for the investigation of individual differences in brain-mind development among children aged 3-10 years are associated with perinatal factors. Ultimately, our goal was to develop an early prediction and screening model for NDDs that leverages normative data to facilitate NDD aetiology research. Herein, we provide a systematic overview of the data acquisition/cleaning/quality control/sharing, processes of periCBD and present preliminary brain-mind associations.

neuroscience↗

bioRxiv2023

TRIM72 restricts lyssavirus infection by inducing K48-linked ubiquitination and proteasome degradation of the matrix protein

The tripartite motif (TRIM) protein family is the largest subfamily of E3 ubiquitin ligases, playing a crucial role in the antiviral process. In this study, we found that TRIM72, a member of the TRIM protein family, was increased in neuronal cells and mouse brains following rabies lyssavirus (RABV) infection. Over-expression of TRIM72 significantly reduced the viral titer of RABV in neuronal cells and mitigated the pathogenicity of RABV in mice. Furthermore, we found that TRIM72 over-expression effectively prevents the release of RABV. In terms of the mechanism, TRIM72 promotes the K48-linked ubiquitination of RABV Matrix protein (M), leading to the degradation of M through the proteasome pathway. TRIM72 directly interacts with M and the interaction sites were identified and confirmed through TRIM72-M interaction model construction and mutation analysis. Further investigation revealed that the degradation of M induced by TRIM72 was attributed to TRIM72s promotion of ubiquitination at site K195 in M. Importantly, the K195 site was found to be partially conserved among lyssaviruss M proteins, and TRIM72 over-expression induced the degradation of these lyssavirus M proteins. In summary, our study has uncovered a TRIM family protein, TRIM72, that can restrict lyssavirus replication by degrading M, and we have identified a novel ubiquitination site (K195) in lyssavirus M. Author SummaryRabies, caused by lyssaviruses, most often by rabies virus, the most lethal zoonotic disease, is responsible for approximately 59000 human deaths globally each year. Lyssavirus M protein displays an essential role in lyssavirus assembly and budding. Here, we found that TRIM family protein TRIM72 directly interacts with lyssavirus M thereby promoting the K48-linked ubiquitination of M, leading to the degradation of M through the proteasome pathway, restricting lyssavirus release. Moreover, we identified a novel important ubiquitination site (K195) in lyssavirus M. Prior to our study, there had been no reports of a direct interaction between TRIM72 and viral proteins, an antiviral function of TRIM72 was proved in our study. It is possible that TRIM72 interacts and ubiquitinates other viral proteins from various viruses, which warrants further investigation. This research contributes to our understanding of how TRIM72 and other TRIM proteins play a role in defending against viral invasions and may inspire further research in this field.

microbiology↗

bioRxiv2023

Maturation and detoxification of synphilin-1 inclusion bodies regulated by sphingolipids

Due to proteostasis stress induced by aging or disease, misfolded proteins can form toxic intermediate species of aggregates and eventually mature into less toxic inclusion bodies (IBs). Here, using a yeast imaging-based screen, we identified 84 potential synphilin-1 (SY1) IB regulators and isolated the conserved sphingolipid metabolic components in the most enriched groups. Furthermore, we show that, in both yeast cells and mammalian cells, SY1 IBs are associated with mitochondria. Pharmacological inhibition of the sphingolipid metabolism pathway or knockout of its key genes results in a delayed IB maturation and increased SY1 cytotoxicity. We postulate that SY1 IB matures by association with the mitochondrion membrane, and that sphingolipids stimulate the maturation via their membrane-modulating function and thereby protecting cells from SY1 cytotoxicity. Our findings identify a conserved cellular component essential for IB maturation and suggest a mechanism by which cells may detoxify the pathogenic protein aggregates through forming mitochondrion-associated IBs.

cell biology↗

bioRxiv2023

ARF6 as a novel activator of HIF-2alpha in pulmonary arterial hypertension

ADP-ribosylation factor 6 (ARF6), a GTPase associated with cancer metastasis, is activated in the lung endothelium in pulmonary arterial hypertension (PAH). To identify ARF6-regulated pathways relevant to PAH, we performed a state-of-the-art proteomic analysis of human pulmonary artery endothelial cells (HPAECs) overexpressing the wildtype, constitutively active, fast-cycling and dominant negative mutants of ARF6. The analysis revealed a novel link of ARF6 with hypoxia-inducible factor (HIF), in addition to endocytotic vesicle trafficking, cell proliferation, angiogenesis, oxidative stress and lipid metabolism. Active ARF6 markedly increased expression and activity of HIF-2, critical in PAH, with HIF-1 relatively unaffected. Hypoxic ARF6 activation was a prerequisite for HIF-2 activation and HIF-dependent gene expression in HPAECs, PAH blood-derived late outgrowth endothelial colony forming cells (ECFCs) and hypoxic mouse lungs in vivo. A novel ARF6 inhibitor, chlortetracycline (CTC), reduced hypoxia-induced HIF-2 activation, proliferation and angiogenesis in HPAECs and reduced HIF-2 expression in lung and heart tissues of hypoxic mice. PAH ECFCs showed elevated expression and activity of ARF6 and HIF2, which was attenuated by CTC. Oral CTC attenuated development of PH in chronically hypoxic mice. In conclusion, we are first to demonstrate a key role of ARF6 in the regulation of HIF-2 activation in vitro and in vivo and show that HIF-2, a master-regulator of vascular remodelling in PAH, can be targeted by a clinically approved antibiotic chlortetracycline.

cell biology↗

bioRxiv2023

X chromosome encoded histone demethylase UTX regulates mammalian axon regeneration via microRNA-124

Epigenetic regulation of neuronal transcriptomic landscape is emerging to be a key coordinator of mammalian neural regeneration. Here we investigated roles of two histone 3 lysine 27 (H3K27) demethylases Kdm6a/b in controlling neuroprotection and axon regeneration. Deleting either Kdm6a or Kdm6b led to enhanced sensory axon regeneration in the PNS, whereas in the CNS only deleting Kdm6a in retinal ganglion cells (RGCs) significantly enhanced optic nerve regeneration. Moreover, both Kdm6a and Kdm6b functioned to regulate RGC survival but with different mechanisms. Mechanistically, Kdm6a regulates RGC regeneration via distinct pathway from that of Pten and co-deleting Kdm6a and Pten resulted in long distance optic nerve regeneration passing the optic chiasm. In addition, RNA-seq profiling revealed that Kdm6a deletion switched the RGC transcriptomics into a developmental-like state and suppressed several known repressors of neural regeneration. Klf4 was identified as a direct downstream target of Kdm6a-H3K27me3 signaling in both sensory neurons and RGCs to regulate axon regeneration. These findings not only revealed different roles of Kdm6a and Kdm6b in regulation of neural regeneration and their underlying mechanisms, but also identified Kdm6a- mediated histone demethylation signaling as a novel epigenetic target for supporting CNS neural regeneration.

neuroscience↗

bioRxiv2023

Tafazzin Mediates Tamoxifen Resistance by Regulating Cellular Phospholipid Composition in ER-Positive Breast Cancer

Tamoxifen is the frontline therapeutic agent for the estrogen receptor-positive (ER+) subtype of breast cancer patients, which accounts for 70-80% of total breast cancer incidents. However, clinical resistance to tamoxifen has become increasingly common, highlighting the need to identify the underlying cellular mechanisms. In our study, we employed a genome-scale CRISPR-Cas9 loss-of-function screen and validation experiments to discover that Tafazzin (TAZ), a mitochondrial transacylase, is crucial for maintaining the cellular sensitivity of ER+ breast cancer cells to tamoxifen and other chemotherapies. Mechanistically, we found that cardiolipin, whose synthesis and maturation rely on TAZ, is required to maintain cellular resistance to tamoxifen. Loss of metabolic enzymatic activity of TAZ causes ER downregulation and therapy resistance. Interestingly, we observed that TAZ deficiency also led to the upregulation of lysophosphatidylcholine (LPC), which in turn suppressed ER expression and nuclear localization, thereby contributing to tamoxifen resistance. LPC is further metabolized to lysophosphatidic acid (LPA), a bioactive molecule that supports cell survival. Thus, our findings suggest that the depletion of TAZ promotes tamoxifen resistance through an LPC-LPA phospholipid synthesis axis, and targeting this lipid metabolic pathway could restore cell susceptibility to tamoxifen treatment.

cancer biology↗

bioRxiv2023

Lymphotoxin-β Promotes Bone Colonization and Osteolytic Outgrowth of Indolent Bone Metastatic cells of Breast Cancer

Bone metastatic relapse is a lethal consequence of breast cancer, occurring years after initial diagnosis. By analyzing single-cell transcriptomes of bone-seeding tumor cells and in vivo barcoded cDNA library screening, LT{beta} (lymphotoxin-{beta}) is identified as a key factor highly expressed in early-stage bone metastatic cells, associated with poor bone metastasis-free survival, and capable of promoting dormancy reactivation in multiple breast cancer models. Mechanistically, tumor-derived LT{beta} activates NF-{kappa}B2 signaling in osteoblasts to express CCL2/5, facilitating tumor cell seeding and accelerating osteoclastogenesis. Both processes contribute to the reactivation of dormancy and metastatic outgrowth. Blocking LT{beta} signaling with a decoy receptor significantly suppressed bone colonization and metastatic progression, whereas clinical sample analysis revealed significantly higher LT{beta} expression in bone metastases than in primary tumors. Our findings highlight LT{beta} as a bone niche-induced factor that promotes tumor cell seeding and dormancy reactivation, underscoring its potential as a therapeutic target for preventing bone metastatic relapse in patients with breast cancer.

cell biology↗

bioRxiv2023

High-throughput generic single-entity sequencing using droplet microfluidics

Single-cell sequencing has revolutionized our understanding of cellular heterogeneity by providing a micro-level perspective over the past decades. Although heterogeneity is essential for various biological communities, the currently demonstrated platform predominantly focuses on eukaryotic cells without cell walls and their transcriptomics 1,2, leaving significant gaps in the study of omics from other single biological entities such as bacteria and viruses. Due to the difficulty of isolating and acquiring their DNA3, contemporary methodologies for the characterization of generic biological entities remain conspicuously constrained, with low throughput4, compromised lysis efficiency5, and highly fragmented genomes6. Herein, we present the Generic Single Entity Sequencing platform (GSE-Seq), which boasts ample versatility, high throughput, and high coverage, and is enabled by an innovative workflow, addressing the critical challenges in single entities sequencing: (1) one-step manufacturing of massive barcodes, (2) degradable hydrogel-based in situ sample processing and whole genome amplification, (3) integrated in-drop library preparation, (4) compatible long-read sequencing. By GSE-Seq, we have achieved a significant milestone by enabling high-throughput, long-read single-entity profiling of dsDNA and ssDNA from single virus sequencing (SV-seq) and single bacteria sequencing (SB-seq) of the human gut and marine sediment for the first time. Notably, our analysis uncovered previously overlooked viral and bacterial dark matter and phage-host interactions. In summary, the presented conceptually new workflow offers a toolbox based on droplet microfluidics to tackle the persistent challenges in high-throughput profiling to generic applications, which hold immense promise for diverse biological entities, especially hard-to-lyse cells.

bioengineering↗

bioRxiv2023

Phylogenomic analyses support a new infrageneric classification of Pourthiaea (Maleae, Rosaceae) using multiple inference methods and extensive taxon sampling

In this comprehensive study, we conducted extensive taxon sampling and performed phylogenomic analyses based on plastome and nuclear ribosomal DNA (nrDNA) datasets. We employed multiple inference methods, including concatenated and coalescent-based strategies, to generate an accurate phylogeny of the woody Rosaceae genus Pourthiaea. The nrDNA phylogeny of Pourthiaea strongly supported three major clades, which were consistent with morphology. However, the plastid tree provided an alternative phylogenetic topology, indicating cytonuclear discordance. Frequent hybridizations between and among the species of Pourthiaea could explain the cytonuclear discordance. Considering the evidence from morphology and phylogenomic data, we propose a new infrageneric classification for Pourthiaea, consisting of three sections: P. sect. Pourthiaea, P. sect. Amphidoxae B.B.Liu, and P. sect. Impressivenae B.B.Liu.

plant biology↗

bioRxiv2023

Human iPSC-derived Microglia Cells Integrated into Mouse Retina and Recapitulated Features of Endogenous Microglia Cells

Microglia exhibit both maladaptive and adaptive roles in the pathogenesis of neurodegenerative diseases and have emerged as a cellular target for central nervous system (CNS) disorders, including those affecting the retina. Replacing maladaptive microglia, such as those impacted by aging or over-activation, with exogenous microglia that can enable adaptive functions has been proposed as a potential therapeutic strategy for neurodegenerative diseases. To investigate microglia replacement as an approach for retinal diseases, we first employed a protocol to efficiently generate human-induced pluripotent stem cells (hiPSC)-derived microglia in quantities sufficient for in vivo transplantation. These cells demonstrated expression of microglia-enriched genes and showed typical microglial functions such as LPS-induced responses and phagocytosis. We then performed xenotransplantation of these hiPSC-derived microglia into the subretinal space of adult mice whose endogenous retinal microglia have been pharmacologically depleted. Long-term analysis post-transplantation demonstrated that transplanted hiPSC-derived microglia successfully integrated into the neuroretina as ramified cells, occupying positions previously filled by the endogenous microglia and expressed microglia homeostatic markers such as P2ry12 and Tmem119. Further, these cells were found juxtaposed alongside residual endogenous murine microglia for up to eight months in the retina, indicating their ability to establish a stable homeostatic state in vivo. Following retinal pigment epithelial (RPE) cell injury, transplanted microglia demonstrated responses typical of endogenous microglia, including migration, proliferation, and phagocytosis. Our findings indicate the feasibility of microglial transplantation and integration in the retina and suggest that modulating microglia through replacement may be a therapeutic strategy for treating neurodegenerative retinal diseases.

neuroscience↗

bioRxiv2023

Ion selectivity and activation mechanism for kalium channelrhodopsins

Channelrhodopsins harvest the light and convert photons to the cellular ion flow. The ion selectivity and activation mechanism at the atomic level remains unknown. Here we describe cryo-EM structures for H. catenoides kalium channelrhodopsin (HcKCR1), its paralog, sodium selective channelrhodopsin (HcCCR), an open state of HcKCR1 (C110T), the voltage-dependent inwardly rectifier (D116N) and higher potassium selective channelrhodopsin (B1ChR2) from Bilabrum sp, illuminating the ion selectivity and activation mechanism. Briefly, the hourglass shaped lumen is occupied by the stepwise dehydrated potassium in both intracellular and extracellular side. The aromatic amino acids likely function as partial dehydrated potassium filter in the extracellular lumen, and intracellular dehydrated ion occupying layer chooses the right size of dehydrated ion, thus specifying ion selectivity and the higher dehydration capacity, the higher potassium selectivity. Furthermore, structural comparison of HcKCR1 and C110T suggested that the conformational changes of retinal triggers the extracellular side of TM6 extension as well as the retinal interaction residues motion, which then leads to ion flow. Our results not only uncovered the ion selectivity mechanism of potassium or sodium selective channelrhodopsins, but also elucidated their activation mechanism. It may provide a framework for designing next generation optogenetic tools.

biophysics↗