Biology subjects

Li, G.

Publications and source records attributed to Li, G..

At least 379 records · Page 21Linked to original sources

bioRxiv2022

An intergeneric recombinant geminivirus causes soybean stay-green disease

Soybean is one of the most valuable legume crops in the world with high nutritional value. Recently, the outbreak of soybean stay-green syndrome has swept the soybean production in the Huang-Huai-Hai region of China, resulting in huge yield losses, which has become an epidemic and prominent problem in soybean production. However, the cause of the stay-green syndrome remains obscure. Here, we report a novel intergeneric recombinant geminivirus which causes soybean stay-green symptoms. Viral small RNA-based screening identified a new recombinant geminvirus from field soybean stay-green samples. The complete genome sequence of the virus contains 2762 nucleotide (nt) and appears to be an intergeneric recombinant virus in which protein coding for coat protein (V1) is similar to member of genus Mastrevirus, whereas proteins coding for V2, C2, C3 are most similar to those of viruses in the Maldovirus genus, and C1 and C4 are most similar to virus in genus Begomovirus. Inoculation of the infectious clone of the recombinant geminivirus through Agrobacterium rhizogenes causes typical soybean stay-green syndrome which resembles field symptoms including delayed leaf senescence, flat pods and abnormal seeds. The recombinant geminivirus can be detected in seed coat but not in cotyledon and embryo, thus failing to be transmitted by seeds. Moreover, the genome variation and epidemiological dynamic analysis were also carried out to help the continuous epidemiological surveillance of this emerging geminivirus. Collectively, this new geminivirus is tentatively named soybean stay-green associated virus (SoSGV). Our determination of the causal agent of soybean stay-green disease will bolster efforts to develop effective management strategies to control this prevalent disease in the field.

microbiology↗

bioRxiv2022

Hindbrain catecholaminergic inputs to the paraventricular thalamus scale feeding and metabolic efficiency in stress-related contexts

The regulation of food intake and energy balance relies on the dynamic integration of exteroceptive and interoceptive signals monitoring nutritional, metabolic, cognitive and emotional states. The paraventricular thalamus (PVT) is a central hub that, by integrating sensory, metabolic and emotional states, may contribute to the regulation of feeding and homeostatic/allostatic processes. However, the underlying PVT circuits remain still elusive. Here, we aimed at unraveling the role of catecholaminergic (CA) inputs to the PVT in scaling feeding and metabolic efficiency. First, using region-specific retrograde disruption of CA projections, we show that PVT CA inputs mainly arise from the hindbrain, notably the locus coeruleus (LC) and the nucleus tractus solitarius (NTS). Second, taking advantage of integrative calorimetric measurements of metabolic efficiency, we reveal that CA inputs to the PVT scale adaptive feeding and metabolic responses in environmental, behavioral, physiological and metabolic stress-like contexts. Third, we show that hindbrainTH[->]PVT inputs contribute in modulating the activity of PVT as well as lateral (LH) and dorsomedial (DMH) hypothalamic neurons. In conclusion, this study, by assessing the key role of CA inputs to the PVT in scaling homeostatic/allostatic regulations of feeding patterns, reveals the integrative and converging hindbrainTH[->]PVT paths that contribute to whole-body metabolic adaptations in stress-like contexts. Key pointsO_LIThe paraventricular thalamus (PVT) is known to receive projections from the hindbrain. Here, we confirm and further extend current knowledge on the existence of hindbrainTH[->]PVT catecholaminergic (CA) inputs, notably from the locus coeruleus (LC) and the nucleus tractus solitarius (NTS), with the NTS representing the main source. C_LIO_LIDisruption of hindbrainTH[->]PVT inputs contribute to the modulation of PVT-neurons activity. C_LIO_LIHindbrainTH[->]PVT inputs scale feeding strategies in environmental, behavioral, physiological and metabolic stress-like contexts. C_LIO_LIHindbrainTH[->]PVT inputs participate in regulating metabolic efficiency and nutrient partitioning in stress-like contexts. C_LIO_LIHindbrainTH[->]PVT, directly and/or indirectly, contribute in modulating the downstream activity of lateral (LH) and dorsomedial (DMH) hypothalamic neurons. C_LI

neuroscience↗

bioRxiv2022

Single-nuclei transcriptomics of dog hippocampus reveals the distinct cellular mechanism of domestication

The process of dog domestication leads to dramatic differences in behavioral traits compared to grey wolves. A class of putative positively selected genes is related to learning and memory, for instance, long-term potentiation and long-term depression. In this study, we constructed a single-nuclei transcriptomic atlas of the dog hippocampus to illustrate its cell types, cell lineage, and molecular features. Using the transcriptomes of 105,057 single-nuclei from the hippocampus of a Beagle dog, we identified 26 cell clusters and a putative trajectory of oligodendrocyte development. Comparative analysis revealed a significant convergence between dog differentially expressed genes (DEGs) and putative positively selected genes (PSGs). 40 putative PSGs were DEGs in the glutamatergic neurons, especially in the cluster 14, which is related to the regulation of nervous system development. In summary, this study provided a blueprint to understand the cellular mechanism of dog domestication.

evolutionary biology↗

bioRxiv2022

A scalp geometry parameter-space for optimization and implementation of conventional TMS coil placement

Transcranial magnetic stimulation efficacy is largely dependent upon coil position and orientation. A good method for describing coil placement is required for both computational optimization (planning) and actual placement (implementation). In coordinate dependent parameter-spaces (CDPs), three-dimensional coordinates are used to represent coil position and three orthogonal unit vectors are used to represent coil orientation. A CDP can precisely describe arbitrary coil placement; therefore it offers great advantage in computational optimization which checks through all possible placements. However, a neuronavigation system is usually required to accurately implement the optimized CDP parameters on a participants head. Routine clinical practice, on the other hand, often uses the International 10-20 system to describe coil placement. Although the 10-20 system can only perform modeling and placement at limited scalp landmarks, it allows the synthesis of different individuals targeting effects to find group-optimal parameters; it also allows manual placement, which is important for commonly-seen use cases without individual MRI scans and navigation devices. This study proposes a new scalp geometry based parameter-space (SGP), integrating the advantages of CDP and 10-20 methods. Our SGP 1) can quantitatively specify all possible conventional coil positions and orientations on an individuals scalp, which is important for electrical modeling and optimization, 2) maintains inter-individual correspondence, which is important for synthesizing TMS effects from different individuals and studies. 3) enables fast and simple manual implementation. Demonstration experiments were conducted to illustrate the application of an SGP-based framework for both individual and group-based optimization. A measurement experiment was performed to evaluate speed, precision and reliability of SGP-based manual implementation; results show it surpasses previous manual placement methods.

neuroscience↗

bioRxiv2022

Palatal morphology predicts the paleobiology of early salamanders

Ecological preferences and life history strategies have enormous impacts on the evolution and phenotypic diversity of salamanders, but the yet established reliable ecological indicators hinder investigations on the paleobiology of early salamanders. Here we statistically demonstrate using geometric morphometric analysis that both the shape of the palate and many non-shape variables particularly associated with vomerine teeth are ecologically informative in early stem- and basal crown-group salamanders. The morphology of the palate is heavily impacted by convergence constrained by feeding mechanisms and also exhibits clear stepwise evolutionary patterns with alternative phenotypic designs to cope with similar functional demand. Paleoecological disparities in early salamanders had took place before the Middle Jurassic and have achieved all ecological preferences in the Early Cretaceous. Metamorphosis is significant in the expansion of ecomorphospace of the palate in early salamanders. The common ancestor of salamanders is metamorphosed and terrestrial, and share unified lifestyles with other modern amphibians.

evolutionary biology↗

bioRxiv2022

Asymmetric Pendrin Homodimer Reveals its Molecular Mechanism as Anion Exchanger

Pendrin SLC26A4 is an anion exchanger expressed in apical membranes of selected epithelia. Pendrin ablation causes Pendred syndrome, a genetic disorder disease associated with sensorineural hearing loss, hypothyroid goiter, and reduced blood pressure. However, its molecular structure has remained unknown limiting our understanding. Here, we determined the structures of mouse pendrin with symmetric and characteristically asymmetric homodimer conformations by cryo-electron microscopy. The asymmetric homodimer consists of an inward-facing protomer and an intermediate-state protomer, representing the coincident uptake and secretion process, and exhibits the unique state of pendrin as an electroneutral exchanger. This previously unrevealed conformation, together with other conformations we captured, provides an inverted alternate-access mechanism for anion exchange. Furthermore, our structural and functional data disclosed the properties of anion exchange cleft and interpreted the important pathogenetic mutations. These investigations shed light on the pendrin exchange mechanism and extend our structure-guided understanding of pathogenetic mutations. One-Sentence SummaryCryo-EM asymmetric Pendrin homodimer cracks its exchange mechanism and guides our understanding for pathogenetic mutations.

biophysics↗

bioRxiv2022

Probabilistic modeling of ambient noise in single-cell omics data

Droplet-based single-cell omics, including single-cell RNA sequencing (scRNAseq), single-cell CRISPR perturbations (e.g., CROP-seq), and single-cell protein and transcriptomic profiling (CITE-seq) hold great promise for comprehensive cell profiling and genetic screening at the single-cell resolution. However, these technologies suffer from substantial noise, among which ambient signals present in the cell suspension may be the predominant source. Current models to address this issue are highly technology-specific and relatively scRNAseq-centric. while a universal model to describe the noise across these technologies may reveal this common source, improving the denoising accuracy. To this end, we explicitly examined these unexpected signals in multiple datasets across droplet-based technologies, summarised a predictable pattern, and developed single-cell Ambient Remover (scAR) - a hypothesis-driven machine learning model to predict and remove ambient signals (including mRNA counts, protein counts, and sgRNA counts) at the molecular level. We benchmarked scAR on three technologies - single-cell CRISPR screens, CITE-seq, and scRNAseq along with the state-of-the-art single-technology-specific approaches. scAR showed high denoising accuracy for each type of dataset.

bioinformatics↗

bioRxiv2022

Three amphioxus reference genomes reveal gene and chromosome evolution of chordates

The slow-evolving invertebrate amphioxus has an irreplaceable role in advancing our understanding into the vertebrate origin and innovations. Here we resolve the nearly complete chromosomal genomes of three amphioxus species, one of which best recapitulates the 17 chordate ancestor linkage groups. We reconstruct the fusions, retention or rearrangements between descendants of whole genome duplications (WGDs), which gave rise to the extant microchromosomes likely existed in the vertebrate ancestor. Similar to vertebrates, the amphioxus genome gradually establishes its 3D chromatin architecture at the onset of zygotic activation, and forms two topologically associated domains at the Hox gene cluster. We find that all three amphioxus species have ZW sex chromosomes with little sequence differentiation, and their putative sex-determining regions are nonhomologous to each other. Our results illuminate the unappreciated interspecific diversity and developmental dynamics of amphioxus genomes, and provide high-quality references for understanding the mechanisms of chordate functional genome evolution.

evolutionary biology↗

bioRxiv2021

Simultaneous Optimization of Excitation Wavelength and Emission Window for Semiconducting Polymer Nanoparticles to Improve Imaging Quality

Optimized excitation wavelength and emission window are essential for fluorescence imaging with high quality. Semiconducting polymer nanoparticles (SPNs) as fluorescent contrast agents have been extensively studied, but their imaging abilities in the second near-infrared IIb window (NIR-IIb, 1500-1700 nm) with long excitation wavelength have not been reported yet. Herein, as a proof-of-concept, we demonstrate for the first time that an SPN named L1057 nanoparticles (NPs) exhibit intense NIR-IIb signal due to its ultra-high brightness and broad emission spectrum. After screening 915 nm as an optimal excitation wavelength, we applied L1057 NPs to visualize the whole-body vessels, cerebral vessels, gastrointestinal tract, and tumor progression in different stages, achieving superior spatial resolution and signal to background ratio in the NIR-IIb window with respect to NIR-II window (1000-1700 nm). This study reveals that simultaneous optimization of excitation wavelength and emission window is an efficient strategy to enhance imaging quality and that L1057 NPs can serve as a promising NIR-IIb contrast agent for high-resolution and deep-tissue imaging.

bioengineering↗

bioRxiv2021

Contrasting effects of accumulation and tolerance characteristics in Arabidopsis thaliana under Cr(III) and Cr(VI) stress

In this study, for the first time we investigated Cr(III) and Cr(VI) stress-induced physiological and biochemical responses in Arabidopsis thaliana. The capacity of A. thalian to accumulate Cr is closely related to the valence of chromium. Cr(VI) was more toxic than Cr(III) as indicated by chromium accumulation and growth inhibition. When the concentration of chromium is greater than 200M, the root length and biomass of A. thaliana are reduced. But interestingly, Cr(III) at 200M increased the root length and biomass of A. thaliana compared to the control. The transmission electron microscope shows that Cr(VI) can cause the chloroplasts damaged and the chlorophyll reduced more than Cr(III). The chloroplasts were filled the starch grains. An increase of lipid peroxidation in A. thaliana roots caused by Cr was measured, and this effect increases as the increasing Cr. It indicated that A. thaliana suffers from Cr-induced oxidative stress which resulted cell death in roots. To fight against oxidative stress, Ascorbate peroxidase and Glutathione reductase were activated by Cr in antioxidant defense. The inhibition of growth, the accumulation of chromium, the responses of antioxidant systems, and the ultra-morphological changes indicate that Cr(VI) was more toxic than Cr(III).

biochemistry↗

bioRxiv2021

High-fidelity Cas13 variants for targeted RNA degradation with minimal collateral effect

CRISPR-Cas13 systems have recently been employed for targeted RNA degradation in various organisms. However, collateral degradation of bystander RNAs has imposed a major barrier for their in vivo applications. We designed a dual-fluorescent reporter system for detecting collateral effects and screening Cas13 variants in mammalian cells. Among over 200 engineered variants, several Cas13 variants (including Cas13d and Cas13X) exhibit efficient on-target activity but markedly reduced collateral activity. Furthermore, transcriptome-wide off-targets and cell growth arrest induced by Cas13 are absent for these variants. Importantly, high-fidelity Cas13 variants show comparable RNA knockdown activity with wild-type Cas13 but no detectable collateral damage in transgenic mice and adeno-associated virus-mediated somatic cell targeting. Thus, high-fidelity Cas13 variants with minimal collateral effect are now available for targeted degradation of RNAs in basic research and therapeutic applications.

molecular biology↗

bioRxiv2021

Fast Medical Image Auto-segmentation for Bleeding Gastric Tissue Detection based on Deep DuS-KFCM Clustering

BackgroundDetection and classification of gastric bleeding tissues are one of the challenging tasks in endoscopy image analysis. Lesion detection plays an important role in gastric cancer (GC) diagnosis and follow-up. Manual segmentation of endoscopy images is a very time-consuming task and subject to intra- and interrater variability. Accurate GB segmentation in abdominal sequences is an essential and crucial task for surgical planning and navigation in gastric lesion ablation. However, GB segmentation in endoscope is a substantially challenging work because the intensity values of gastric blood are similar to those of adjacent structures. ObjectiveIn this paper the idea is to combine two parts: Neural Network and Fuzzy Logic--Hybrid Neuro-Fuzzy system. The objective of this manuscript is to provide an efficient way to segment the gastric bleeding lesion area. This work focuses on design and development of an automated diagnostic system using gastric bleeding cancer endoscopy images. MethodsIn this paper, a coarse-to-fine method was applied to segment gastric bleeding lesion from endoscopy images, which consists of two stages including rough segmentation and refined segmentation. The rough segmentation is based on a kernel fuzzy C-means algorithm with spatial information (SKFCM) algorithm combined with spatial gray level co-occurrence matrix (GLCM) and the refined segmentation is implemented with deeplabv3+ (backbone with resnet50) algorithm to improve the overall accuracy. ResultsExperimental results for gastric bleeding segmentation show that the method provides an accuracy of 87.9476% with specificity of 96.3343% and performs better than other related methods. onclusionsThe performance of the method was evaluated using two benchmark datasets: The GB Segmentation and the healthy datasets. Then use the gastric red spots (GRS) dataset to do the final test to verify weak bleeding symptoms. Our method achieves high accuracy in gastric bleeding lesion segmentation. The work describes an innovative way of using GLCM based textural features to extract underlying information in gastric bleeding cancer imagery. Modified deep DuS-KFCM endoscopy image segmentation method based on GLCM feature, The experimental results shown to be effective in image segmentation and has good performance of resisting noise, segmentation effect more ideal.

bioinformatics↗

bioRxiv2021

A Deep Learning Approach for NeoAG-Specific Prediction Considering Both HLA-Peptide Binding and Immunogenicity: Finding Neoantigens to Making T-Cell Products More Personal

BackgroundAn emerging type of cancer treatment, known as cell immunotherapy, is gaining popularity over chemotherapy or other radiation therapy that causes mass destruction to our body. One favourable approach in cell immunotherapy is the use of neoantigens as targets that help our body immune system identify the cancer cells from healthy cells. Neoantigens, which are non-autologous proteins with individual specificity, are generated by non-synonymous mutations in the tumor cell genome. Owing to its strong immunogenicity and lack of expression in normal tissues, it is now an important target for tumor immunotherapy. Neoantigens are some form of special protein fragments excreted as a by-product on the surface of cancer cells during the DNA mutation at the tumour. In cancer immunotherapies, certain neoantigens which exist only on cancer cells elicit our white blood cells (bodys defender, anti-cancer T-cell) responses that fight the cancer cells while leaving healthy cells alone. Personalized cancer vaccines therefore can be designed de novo for each individual patient, when the specific neoantigens are found to be relevant to his/her tumour. The vaccine which is usually coded in synthetic long peptides, RNA or DNA representing the neoantigens trigger an immune response in the body to destroy the cancer cells (tumour). The specific neoantigens can be found by a complex process of biopsy and genome sequencing. Alternatively, modern technologies nowadays tap on AI to predict the right neoantigen candidates using algorithms. However, determining the binding and non-binding of neoantigens on T-cell receptors (TCR) is a challenging computational task due to its very large search space. ObjectiveTo enhance the efficiency and accuracy of traditional deep learning tools, for serving the same purpose of finding potential responsiveness to immunotherapy through correctly predicted neoantigens. It is known that deep learning is possible to explore which novel neoantigens bind to T-cell receptors and which ones dont. The exploration may be technically expensive and time-consuming since deep learning is an inherently computational method. one can use putative neoantigen peptide sequences to guide personalized cancer vaccines design. MethodsThese models all proceed through complex feature engineering, including feature extraction, dimension reduction and so on. In this study, we derived 4 features to facilitate prediction and classification of 4 HLA-peptide binding namely AAC and DC from the global sequence, and the LAAC and LDC from the local sequence information. Based on the patterns of sequence formation, a nested structure of bidirectional long-short term memory neural network called local information module is used to extract context-based features around every residue. Another bilstm network layer called global information module is introduced above local information module layer to integrate context-based features of all residues in the same HLA-peptide binding chain, thereby involving inter-residue relationships in the training process. introduced ResultsFinally, a more effective model is obtained by fusing the above two modules and 4 features matric, the method performs significantly better than previous prediction schemes, whose overall r-square increased to 0.0125 and 0.1064 on train and increased to 0.0782 and 0.2926 on test datasets. The RMSE for our proposed models trained decreased to approximately 0.0745 and 1.1034, respectively, and decreased to 0.6712 and 1.6506 on test dataset. ConclusionOur work has been actively refining a machine-learning model to improve neoantigen identification and predictions with the determinants for Neoantigen identification. The final experimental results show that our method is more effective than existing methods for predicting peptide types, which can help laboratory researchers to identify the type of novel HLA-peptide binding.

bioinformatics↗

bioRxiv2021

DNA methylation in transposable elements disrupts the connection between three-dimensional chromatin organization and gene expression upon rice genome duplication.

Polyploidy serves as a major force in plant evolution and domestication of cultivated crops. However, the relationship and underlying mechanism between three-dimensional (3D) chromatin organization and gene expression upon rice genome duplication is largely unknown. Here we compared the 3D chromatin structures between diploid (2C) and autotetraploid (4C) rice by high-throughput chromosome conformation capture analysis, and found that 4C rice presents weakened intra-chromosomal interactions compared to its 2C progenitor. Moreover, we found that changes of 3D chromatin organizations including chromatin compartments, topologically associating domain (TAD) and loops uncouple from gene expression. Moreover, DNA methylations in the regulatory sequences of genes in compartment A/B switched regions and TAD boundaries are not related to their expressions. Importantly, in contrast to that there was no significant difference of methylation levels in TEs in promoters of differentially expressed genes (DEGs) and non-DEGs between 2C and 4C rice, we found that the hypermethylated transposable elements across genes in compartment A/B switched regions and TAD boundaries suppress the expression of these genes. We propose that the rice genome doubling might modulate TE methylation which results in the disconnection between the alteration of 3D chromatin structure and gene expression.

plant biology↗

bioRxiv2021

Generation of Infant-dedicated Fine-grained Functional Parcellation Maps of Cerebral Cortex

Infancy is a dynamic and immensely important period in human brain development. Studies of infant functional development using resting-state fMRI rely on precisely defined cortical parcellation maps. However, available adult-based functional parcellation maps are not applicable for infants due to their substantial differences in functional organizations. Fine-grained infant-dedicated cortical parcellation maps are highly desired but remain scarce, due to difficulties ranging from acquiring to processing of infant brain MRIs. In this study, leveraging 1,064 high-resolution longitudinal rs-fMRIs from 197 infants from birth to 24 months and advanced infant-dedicated processing tools, we create the first set of infant-specific, fine-grained cortical functional parcellation maps. Besides the conventional folding-based cortical registration, we specifically establish the functional correspondences across individuals using functional gradient densities and generate both age-specific and age-common fine-grained parcellation maps. The first set of comprehensive brain functional developmental maps are accordingly derived, and reveals a complex, hitherto unseen multi-peak fluctuation development pattern in temporal variations of gradient density, network sizes, and local efficiency, with more dynamic changes during the first 9 months than other ages. Our proposed method is applicable in generating fine-grained parcellations for the whole lifespan, and our parcellation maps will be available online to advance the neuroimaging field.

neuroscience↗

bioRxiv2021

Ser68 phosphoregulation is essential for CENP-A deposition, centromere function and viability in mice

Centromere identity is defined by nucleosomes containing CENP-A, a histone H3 variant. The deposition of CENP-A at centromeres is tightly regulated in a cell-cycle-dependent manner. We previously reported that the spatiotemporal control of centromeric CENP-A incorporation is mediated by the phosphorylation of CENP-A Ser68. However, a recent report argued that Ser68 phosphoregulation is dispensable for accurate CENP-A loading. Here, we report that the substitution of Ser68 of endogenous CENP-A with either Gln68 or Glu68 severely impairs CENP-A deposition and cell viability. We also find that mice harboring the corresponding mutations are lethal. Together, these results indicate that the dynamic phosphorylation of Ser68 ensures cell-cycle-dependent CENP-A deposition and cell viability.

cell biology↗

bioRxiv2021

Maize root-associated microbes likely under adaptive selection by the host to enhance phenotypic performance

The root-associated microbiome (rhizobiome) plays a non-negligible role in determining plant health, stress tolerance, and nutrient use efficiency. However, it remains unclear to what extent the composition of the rhizobiome is governed by intraspecific variation in host plant genetics in the field and the degree to which host plant selection can reshape the composition of the rhizobiome. Here we quantify the rhizosphere microbial communities associated with a replicated diversity panel of 230 maize (Zea mays L.) genotypes grown in agronomically relevant conditions under high N (+N) and low N (-N) treatments. We show that the abundance of many root-associated microbes within a functional core microbial community of 150 abundant and consistently reproducible microbial groups is explainable by natural genetic variation in the host plant, with a greater proportion of microbial variance attributable to plant genetic variation in low N conditions. Population genetic approaches identify signatures of purifying selection in the maize genome associated with the abundance of several groups of microbes in the maize rhizobiome. Genome-wide association studies conducted using rhizobiome phenotypes identified n = 467 microbe-associated plant loci (MAPLs) in the maize genome linked to variation in the abundance of n = 115 microbial groups in the maize rhizosphere. In 62/115 cases, which is more than expected by chance, the abundance of these same microbial groups was correlated with variation in plant vigor indicators derived from high throughput phenotyping of the same field experiment. This study provides insights into harnessing the full potential of root-associated microbial symbionts in maize production.

plant biology↗

bioRxiv2021

Cholesterol and sphingomyelin are critical for Fcγ receptor-mediated phagocytosis of Cryptococcus neoformans by macrophages

Cryptococcus neoformans is a fungal pathogen that causes life-threatening meningoencephalitis in lymphopenic patients. Pulmonary macrophages comprise the first line of host defense upon inhalation of fungal spores, whereby macrophages either aid in clearance or serve as a niche for its dissemination. Given that macrophages play a key role in the outcome of a cryptococcal infection, it is crucial to understand factors that mediate phagocytosis of C. neoformans. Since lipid rafts (high order plasma membrane domains enriched in cholesterol and sphingomyelin) have been implicated in facilitating phagocytosis, we evaluated whether these ordered domains govern macrophages ability to phagocytose C. neoformans. We found that cholesterol or sphingomyelin depletion resulted in significantly deficient IgG-mediated phagocytosis of the fungus. Moreover, repletion of macrophage cells with a raft-promoting sterol (7-dehydrocholesterol) rescued this phagocytic deficiency while a raft-inhibiting sterol (coprostanol) significantly decreased IgG-mediated phagocytosis of C. neoformans. Using a photoswitchable sphingomyelin (AzoSM), we observed that the raft-promoting conformation (trans-AzoSM) resulted in efficient phagocytosis whereas raft-inhibiting conformation (cis-AzoSM) significantly blunted phagocytosis in a reversible manner. We observed that the effect on phagocytosis may be mediated by facilitating Fc{gamma} receptor (Fc{gamma}R) function, whereby IgG immune complexes cross-link to Fc{gamma}RIII, resulting in tyrosine phosphorylation of FcR {gamma}-subunit (FcR{gamma}), an important accessory protein in the Fc{gamma}R signaling cascade. Correspondingly, cholesterol or sphingomyelin depletion resulted in decreased FcR{gamma} phosphorylation. Repletion with 7-dehydrocholesterol restored phosphorylation, whereas repletion with coprostanol showed FcR{gamma} phosphorylation comparable to unstimulated cells. Together, these data suggest that lipid rafts are critical for facilitating Fc{gamma}RIII-mediated phagocytosis of C. neoformans.

microbiology↗