Biology subjects

Chen, Z.

Publications and source records attributed to Chen, Z..

At least 865 records · Page 48Linked to original sources

bioRxiv2020

Structure-based inhibitors reveal roles for the clathrin terminal domain and its W-box binding site in CME

Clathrin-mediated endocytosis (CME) occurs via the formation of clathrin-coated vesicles from clathrin-coated pits (CCPs). Clathrin is recruited to CCPs through interactions between the AP2 complex and its N-terminal domain (TD), which in turn recruits endocytic accessory proteins. Inhibitors of CME that interfere with clathrin function have been described, but their specificity and mechanisms of action are unclear. Here we show that overexpression of the TD with or without the distal leg specifically inhibits CME and CCP dynamics by perturbing clathrin interactions with AP2 and SNX9. We designed small membrane-penetrating peptides that mimic the four known binding sites on the TD. A peptide, Wbox2, designed to mimic to the W-box motif binding surface on TD binds to SNX9 and AP2, and potently and acutely inhibits CME, while not perturbing AP1-dependent lysosomal trafficking from the Golgi or bulk, fluid phase endocytosis. SummaryChen et al define the role the N-terminal domain (TD) of clathrin heavy chain in early and late stages of clathrin-mediated endocytosis, and guided by its structure, design a membrane-penetrating peptide, Wbox2, that acutely and potently inhibits CME.

cell biology↗

bioRxiv2020

From SARS-CoV to Wuhan 2019-nCoV: Will History Repeat Itself?

This manuscript has been withdrawn as it was submitted without the full consent of all the authors. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

microbiology↗

bioRxiv2020

Harmonic-Balance Circuit Analysis for Electro-Neural Interfaces

ObjectiveAvoidance of the adverse electrochemical reactions at the electrode-electrolyte interface defines the voltage safety window and limits the charge injection capacity (CIC) of an electrode material. For an electrode that is not ideally capacitive, the CIC depends on the waveform of the stimulus. We study the modeling of the charge injection dynamics to optimize the waveforms for efficient neural stimulation within the electrochemical safety limits. ApproachThe charge injection dynamics at the electrode-electrolyte interface is typically characterized by the electrochemical impedance spectrum, and is often approximated by discrete-element circuit models. We compare the modeling of the complete circuit, including a non-linear driver such as a photodiode, based on the harmonic-balance (HB) analysis with the analysis based on various discrete element approximations. To validate the modeling results, we performed experiments with iridium-oxide electrodes driven by a current source with diodes in parallel, which mimics a photovoltaic circuit. Main resultsApplication of HB analysis based on a full impedance spectrum in frequency domain eliminates the complication of finding the discrete-element circuit model in traditional approaches. HB-based results agree with the experimental data better than the discrete-element circuit analysis. HB technique can be applied not only to demonstrate the circuit response to periodic stimulation, but also to describe the initial transient behavior when a burst waveform is applied. SignificanceHB-based circuit analysis accurately describes the dynamics of electrode-electrolyte interfaces and driving circuits for all pulsing schemes. This allows optimizing the stimulus waveform to maximize the CIC, based on the impedance spectrum alone.

bioengineering↗

bioRxiv2020

Counteracting Genome Instability by p53-dependent Mintosis

Entosis was proposed to promote aneuploidy and genome instability by cell-in-cell mediated engulfment in tumor cells. We reported here, in epithelial cells, that entosis coupled with mitotic arrest functions to counteract genome instability by targeting aneuploid mitotic progenies for engulfment and elimination. We found that the formation of cell-in-cell structures associated with prolonged mitosis, which was sufficient to induce entosis. This process was controlled by the tumor suppressor p53 (wild type) that upregulates Rnd3 expression in response to DNA damages associated with prolonged metaphase. Rnd3 compartmentalized RhoA activities accumulated during prolonged metaphase to drive cell-in-cell formation. Remarkably, this prolonged mitosis-induced entosis (mintosis) selectively targets non-diploid progenies for internalization, blockade of which increased aneuploidy. Thus, our work uncovered a heretofore unrecognized mechanism of mitotic surveillance for entosis, which eliminates newly-born abnormal daughter cells in a p53-depedent way to maintain genome integrity.

cell biology↗

bioRxiv2020

Factor VIII exhibits chaperone-dependent and glucose-regulated reversible amyloid formation in the endoplasmic reticulum

Factor VIII (FVIII) is the coagulation factor deficient in hemophilia A, which is treated by protein replacement. Unfortunately, this regimen is costly due to the expense of producing recombinant FVIII as a consequence of its low level secretion. FVIII expression activates the endoplasmic reticulum (ER) stress response, causes oxidative stress and induces apoptosis. Importantly, little is known about the factors that cause protein misfolding and aggregation in metazoans. Here we identified intrinsic and extrinsic factors that cause FVIII to form aggregates in the ER. We show that FVIII forms amyloid-like fibrils within the ER upon increased FVIII synthesis or inhibition of glucose metabolism. Significantly, FVIII amyloids can be dissolved upon restoration of glucose metabolism to produce functional secreted FVIII. Two ER chaperones and their co-chaperones, BiP and CANX/CRT, promote FVIII solubility in the ER, where the former is also required for disaggregation. A short aggregation motif in the FVIII A1 domain (termed Aggron) is necessary and sufficient to seed {beta}-sheet polymerization and BiP binding to this Aggron prevents amyloidogenesis. Our findings provide novel insight into mechanisms that limit FVIII secretion and ER protein folding in general and have implication for ongoing hemophilia A gene therapy clinical trials. Key Points- FVIII forms amyloid aggregates in the ER that are dissolved in a chaperone- and glucose-dependent manner to produce secreted active FVIII. - A short amino acid sequence in the A1 domain causes {beta} sheet polymerization and ER chaperone BiP binding to this site prevents aggregation.

molecular biology↗

bioRxiv2020

Chop/Ddit3 depletion in β-cells alleviates ER stress and corrects hepatic steatosis

Type 2 diabetes (T2D) is a metabolic disorder characterized by hyperglycemia, hyperinsulinemia and insulin resistance (IR). During the early phase of T2D, insulin synthesis and secretion by pancreatic {beta} cells is enhanced, which can lead to proinsulin (ProIns) misfolding that aggravates endoplasmic reticulum (ER) homeostasis in {beta} cells. Moreover, increased insulin in the circulation may contribute to fatty liver disease. Medical interventions aimed at alleviating ER stress in {beta} cells while maintaining optimal insulin secretion are therefore an attractive therapeutic strategy for T2D. Previously, we demonstrated that germline Chop gene deletion preserved {beta} cells in high fat diet (HFD) fed mice and in leptin receptor-deficient db/db mice. In the current study, we further investigated whether targeting Chop/Ddit3 specifically in murine {beta} cells confers therapeutic benefits. First, we show that Chop deletion in {beta} cells alleviates {beta} cell ER stress and delays glucose-stimulated insulin secretion (GSIS) in HFD fed mice. Second, importantly, {beta} cell-specific Chop deletion prevented liver steatosis and hepatomegaly in aged HFD fed mice without affecting basal glucose homeostasis. Third, we provide the first mechanistic evidence that ER remodeling secondary to Chop deletion modulates glucose-induced islet Ca2+ oscillations. Finally, using state-of-the-art GLP1-conjugated Chop AntiSense Oligonucleotides (GLP1-Chop ASO), we demonstrated that the Chop deletion induced GSIS change is a long term complex event in {beta} cells. In summary, our results demonstrate that Chop depletion in {beta} cells is a new therapeutic strategy to alleviate dysregulated insulin secretion and the consequently fatty liver disease in T2D.

physiology↗

bioRxiv2020

Epitope-tagging of the endogenous murine BiP/GRP78/Hspa5 locus allows direct analysis of the BiP interactome and protein misfolding in vivo.

BiP/GRP78, encoded by the Hspa5 gene, is the major HSP70 family member in the endoplasmic reticulum (ER) lumen, and controls ER protein folding. The essential functions of BiP in facilitating proper protein folding are mainly mediated through its dynamic interaction with unfolded or misfolded client proteins, and by serving as a negative regulator of the Unfolded Protein Response. A mechanistic understanding of the dynamics of BiP interaction with its protein partners is essential to understand ER biology, and therefore, we have sought to develop a tractable model to study misfolded protein interaction with BiP. For this purpose, we have used homologous recombination to insert a 3xFLAG epitope tag into the endogenous murine Hspa5 gene, just upstream from the essential KDEL signal necessary for ER localization of BiP. Tagging BiP in this way did not alter Hspa5 expression under basal or ER-stress induced conditions in hepatocytes ex vivo or in fibroblasts. Furthermore, the tag did not alter the cellular localization of BiP or its functionality. All of these findings in primary tissue culture were also confirmed in vivo in livers of heterozygous mice harboring one WT and one FLAG-tagged Hspa5 allele. Hepatocyte-specific BiP-FLAG modification did not alter liver function or UPR signaling. Importantly, immunoprecipitation with anti-FLAG antibody completely pulled down FLAG-tagged BiP from lysates of BiP-FLAG expressing livers. Affinity purification-mass spectrometry (AP-MS) of BiP-FLAG protein complexes isolated from the BiP-FLAG-expressing livers of tunicamycin (TM)- and vehicle-treated mice revealed a marked increase in interaction of glycoproteins with BiP-FLAG in response to inhibition of N-glycosylation due to TM-treatment, validating utility of our BiP-Flag mice as a tool to identify ER misfolded proteins in vivo. Significantly, our AP-MS analysis also provided in vivo evidence demonstrating that BiP-FLAG binds to UPR transducers IRE1 and PERK under basal conditions but is released upon TM-treatment to activate UPR. We have also employed this mouse model to demonstrate that proinsulin in pancreatic {beta} cells misfolds and interacts with BiP-FLAG in healthy mice. In summary, we generated a novel model that can be used to investigate the BiP interactome in vivo under physiological and pathophysiological conditions in a cell type-specific manner. This tool provides, for the first time, an unbiased approach to identify unfolded and misfolded BiP-client proteins, and a new approach to study ER protein misfolding in a cell-type and temporal manner to uncover the role of BiP in many essential ER processes.

molecular biology↗

bioRxiv2019

The Feasibility of Predicting Impending Malignant Ventricular Arrhythmias on the basis of Signal Complexity of Heartbeat Intervals

Malignant ventricular arrhythmias (MAs), such as ventricular tachycardia (VT) that presages cardiac arrest, present the highest hurdle for the healthcare community to overcome. Given that MAs occur unpredictably and lead to emergencies, convenient tracking devices, e.g. photoplethysmogram (PPG), that could predict MAs would be irreplaceably valuable. Since the use of heartbeat intervals (HbI) to predict the occurrence of arrhythmias is becoming more feasible, a further attempt to establish a new convenient approach for predicting impending MAs with HbI is worth trying. Assuming that intrinsic characteristics of MAs (VT and ventricular fibrillation: VF) can be revealed by a suitable approach on the basis of signal complexity, we propose an approach that first expresses the physiological status of the heart by HbI; then delineates the patterns of HbI by a new complexity metric (refined composite multi-scale entropy: RCMsEn); and finally trains a nonlinear machine learning model (random forest: RF) to learn the specific patterns of MAs so as to differentiate them from the normal sinus heart rhythm(N) and other prevalent arrhythmias (atrial fibrillation: AF, and premature ventricular contraction: V). For calculating entropy values and predicting MAs as early as possible (which is the aim of this study), two specifications are of interest: the minimal length of HbI needed to delineate the MAs patterns sufficiently (lenmin), and the maximum time length at which our model can predict impending MAs (timemax). We compared the RF model with support vector machine (SVM) models based on linear and Gaussian kernels. Results show that the RF model performs the best, reaching a 99.24% recall and a 99.87% precision for a HbI of 500 heartbeats (the lenmin) 374 seconds (the timemax) preceding the occurrence of MAs. The HbI samples in this study were extracted from an electrocardiograph (ECG). However, given the subtle difference (0.1 ms typically) between the R-R interval of ECG and the P-P interval of PPG, this approach could be extended to HbI acquired by the PPG sensor and thus should be of substantial theoretical and practical significance in cardiac arrest prevention.

bioinformatics↗

bioRxiv2019

Single cell transcriptome of CD8+ T cells in multiple cancers reveals comprehensive exhaustion associated mechanisms

T cell exhaustion is one of the main reasons of tumor immune escape. Using single cell transcriptome data of CD8+ T cells in multiple cancers, we identified different cell types, in which Pre_exhaust and exhausted T cells participated in negative regulation of immune system process. By analyzing the co-expression network patterns and differentially expressed genes of Pre_exhaust, exhausted and effector T cells, we identified 35 genes related to T cell exhaustion, which high GSVA scores were associated with significantly poor prognosis in various cancers. In the differentially expressed genes, RGS1 showed the greatest fold change in Pre_exhaust and exhausted cells of three cancers compared with effector T cells, and high expression of RGS1 was also associated with poor prognosis in various cancers. Additionally, RGS1 protein was upregulated significantly in tumor tissues in the immunohistochemistry verification. Furthermore, RGS1 displayed positive correlation with the 35 genes, especially highly correlated with PDCD1, CTLA4, HAVCR2 and TNFRSF9 in CD8+ T cells and cancer tissues, indicating important roles of RGS1 in CD8+ T cell exhaustion. Considering the GTP-hydrolysis activity of RGS1 and significantly high mRNA and protein expression in cancer tissues, we speculated that RGS1 potentially mediate the T cell retention to lead to the persistent antigen stimulation, resulting in T cell exhaustion. In conclusion, our findings suggest that RGS1 is a new marker and promoting factor for CD8+ T cell exhaustion, and provide theoretical basis for research and immunotherapy of exhausted cells.

cancer biology↗

bioRxiv2019

Cytological abnormalities and pollen abortion in interspecific hybrids of Nicotiana

Interspecific cross breeding introduces superior agronomic traits into cultivated species; however, problematic pollen sterility occurs in the hybrids. Our previous study obtained interspecific hybrids from the cross between a cytoplasmic male sterility line of Nicotiana tabacum and Nicotiana alata, and some of the hybrids were pollen sterile. Here, we conducted an in-depth cellular study to understand the cytological mechanism of pollen abortion in these hybrids (F1-D sterile) compared with pollen development in the fertile hybrids (F1-S sterile) from the same cross. The ultrastructure observation showed that the membrane of microspore in F1-D sterile hybrid was deficient at all represented developmental stages. Chromosome behavior during meiosis was studied by carbol fuchsin staining, which indicated that cytomixis, chromosome leakage and asymmetric callose wall deposition occurred with high frequency in the microsporocyte of F1-D sterile. The results of the ultrastructure and 6-diamidino-2-phenylindole (DAPI) analyses also showed that the cytoplasm and nucleus were unstable and extruded from F1-D sterile microspore during the developmental process, leading to mature pollen grains that were vacuous and collapsed in the aperture region. In addition, delayed tapetum degradation was also detected in the anther of F1-D sterile, and might be associated with irregular sporopollenin deposition in the aperture region of F1-D sterile pollen. Genetic unbalance and cytomembrane deficiency might both be responsible for the instability of the chromosome, nuclear and cytoplasm, and resulted in pollen abortion in F1-D sterile hybrids, and irregular tapetum degradation might also be related with pollen sterility.

developmental biology↗

bioRxiv2019

Serial assessment of iron in the motor cortex in limb-onset Amyotrophic Lateral Sclerosis using Quantitative Susceptibility Mapping

ObjectiveDysregulation of iron in the cerebral motor areas has been hypothesized to occur in individuals with Amyotrophic Lateral Sclerosis (ALS). There is still limited knowledge regarding iron dysregulation in the progression of ALS pathology. Our objectives were to use magnetic resonance based Quantitative Susceptibility Mapping (QSM) to investigate the association between iron dysregulation in the motor cortex and clinical manifestations in patients with limb-onset ALS, and to examine changes in the iron concentration in the motor cortex in these patients over a six-month period. MethodsIron concentration was investigated using magnetic resonance based -QSM in the primary motor cortex and the pre-motor area in thirteen limb-onset ALS patients (including five lumbar onset, six cervical onset and two flail arm patients), and eleven age and sex-matched healthy controls. Nine ALS patients underwent follow-up scans at six months. ResultsSignificantly increased QSM was observed in the left posterior primary motor area (p = 0.02, Cohens d = 0.9) and right anterior primary motor area (p = 0.02, Cohens d = 0.92) in all individuals with limb-onset ALS compared to healthy controls. Increased QSM was observed in the primary motor and pre-motor area at baseline in patients with lumbar onset ALS patients, but not cervical limb-onset ALS patients, compared to healthy controls. No significant change in QSM was observed at the six-month follow-up scans in the ALS patients. ConclusionsThe findings suggest that iron dysregulation can be detected in the motor cortex in limb-onset ALS, which does not appreciably change over a further 6 months. Individuals with lumbar onset ALS appear to be more susceptible to motor cortex iron dysregulation compared to the individuals with cervical onset ALS. Importantly, this study highlights the potential use of QSM as a radiological indicator in disease diagnosis, and in clinical trials in limb-onset ALS and its subtypes. HighlightsO_LISerial measurement of QSM in the motor cortex in limb-onset ALS was performed C_LIO_LIQSM changes in the motor cortex in ALS sub-groups were investigated C_LIO_LIHigher QSM was observed in the motor cortex in Lumbar ALS relative to controls C_LIO_LIQSM is sensitive to iron dysregulation in the motor cortex in limb-onset ALS C_LI

neuroscience↗

bioRxiv2019

Single-cell transcriptomics reveals diverse and complex gene expression alterations in human trisomy 18

Trisomy 18, commonly known as Edwards syndrome, is the second most common autosomal trisomy among live born neonates. Multiple tissues including cardiac, abdominal, and nervous systems are affected by an extra chromosome 18. To delineate the complexity of anomalies of trisomy 18, we analyzed amniotic fluid cells from two normal and three trisomy 18 samples using single-cell transcriptomics. We identified six cell groups, which function in major tissue development such as kidney, vasculature, and smooth muscle, and display significant alterations in gene expression detected by single-cell RNA-sequencing. Moreover, we demonstrated significant gene expression changes in previously proposed trisomy 18 critical regions, and identified three new regions such as 18p11.32, 18q11, 18q21.32, which are likely associated with trisomy 18 phenotypes. Our results indicate complexity of trisomy 18 at the gene expression level and reveal genetic reasoning of diverse phenotypes in trisomy 18 patients.

genetics↗

bioRxiv2019

Ultra-low input single tube linked-read library method enables short-read NGS systems to generate highly accurate and economical long-range sequencing information for de novo genome assembly and haplotype phasing

Long-range sequencing information is required for haplotype phasing, de novo assembly and structural variation detection. Current long-read sequencing technologies can provide valuable long-range information but at a high cost with low accuracy and high DNA input requirement. We have developed a single-tube Transposase Enzyme Linked Long-read Sequencing (TELL-Seq) technology, which enables a low-cost, high-accuracy and high-throughput short-read next generation sequencer to routinely generate over 100 Kb long-range sequencing information with as little as 0.1 ng input material. In a PCR tube, millions of clonally barcoded beads are used to uniquely barcode long DNA molecules in an open bulk reaction without dilution and compartmentation. The barcode linked reads are used to successfully assemble genomes ranging from microbes to human. These linked-reads also generate mega-base-long phased blocks and provide a cost-effective tool for detecting structural variants in a genome, which are important to identify compound heterozygosity in recessive Mendelian diseases and discover genetic drivers and diagnostic biomarkers in cancers.

genomics↗

bioRxiv2019

The Collaborative Cross Graphical Genome

The mouse reference is one of the most widely used and accurately assembled mammalian genomes, and is the foundation for a wide range of bioinformatics and genetics tools. However, it represents the genomic organization of a single inbred mouse strain. Recently, inexpensive and fast genome sequencing has enabled the assembly of other common mouse strains at a quality approaching that of the reference. However, using these alternative assemblies in standard genomics analysis pipelines presents significant challenges. It has been suggested that a pangenome reference assembly, which incorporates multiple genomes into a single representation, are the path forward, but there are few standards for, or instances of practical pangenome representations suitable for large eukaryotic genomes. We present a pragmatic graph-based pangenome representation as a genomic resource for the widely-used recombinant-inbred mouse genetic reference population known as the Collaborative Cross (CC) and its eight founder genomes. Our pangenome representation leverages existing standards for genomic sequence representations with backward-compatible extensions to describe graph topology and genome-specific annotations along paths. It packs 83 mouse genomes (8 founders + 75 CC strains) into a single graph representation that captures important notions relating genomes such as identity-by-descent and highly variable genomic regions. The introduction of special anchor nodes with sequence content provides a valid coordinate framework that divides large eukaryotic genomes into homologous segments and addresses most of the graph-based position reference issues. Parallel edges between anchors place variants within a context that facilitates orthogonal genome comparison and visualization. Furthermore, our graph structure allows annotations to be placed in multiple genomic contexts and simplifies their maintenance as the assembly improves. The CC reference pangenome provides an open framework for new tool chain development and analysis.

bioinformatics↗

bioRxiv2019

Active monomer RTR-1 derived from the root of Rhodomyrtus tomentosa induces apoptosis in gastric carcinoma cells by inducing ER stress and inhibiting the STAT3 signalling pathway

ObjectiveRhodomyrtus tomentosa, a flowering plant belonging to the Myrtaceae family, is considered an antitumour substance with versatile biological and pharmacological activities. And RTR-1 is an active monomer purified from the root of Rhodomyrtus tomentosa. However, the detail of the mechanisms of anti-cancer activity of RTR-1 remains to be elucidated and the effect on gastric cancer cells is unknown. MethodsCell proliferation was determined by MTT and clone formation assay. The effect of RTR-1 on cell cycle and apoptosis was analyzed utilizing flow cytometry, respectively. Moreover, western blotting was used to detect the expression of cell cycle- and apoptosis-related protein. ResultsBased on MTT and clone formation assay, we noticed that RTR-1 inhibited the proliferation of gastric carcinoma (BGC823 and SGC7901) cells in a dose- and time-dependent manner. Furthermore, the results of flow cytometry and western blotting showed that RTR-1 induced cell cycle arrest in the G2/M phase through the ATM-Chk2-p53-p21 signalling pathway and induced cell apoptosis by inhibiting the signal transducers and activators of transcription 3 (STAT3) pathway and activating the endoplasmic reticulum stress (ER stress) pathway. ConclusionTaken together, these results demonstrate that RTR-1 induces cell cycle arrest and promotes apoptosis in gastric carcinoma, indicating its potential application for gastric cancer therapy.

cancer biology↗

bioRxiv2019

A synthetic approach reveals a highly sensitive maize auxin response circuit

Auxin plays a key role across all land plants in growth and developmental processes. Although auxin signaling function has diverged and expanded, differences in the molecular functions of signaling components have largely been characterized in Arabidopsis thaliana. Here, we used the Auxin Response Circuit recapitulated in Saccharomyces cerevisiae (ARCSc) system to functionally annotate maize auxin signaling components, focusing on genes expressed during development of ear and tassel inflorescences. All 16 maize Auxin (Aux)/Indole-3-Acetic Acid (IAA) repressor proteins are degraded in response to auxin, with rates that depended on both receptor and repressor identity. When fused to the maize TOPLESS (TPL) homolog RAMOSA1 ENHANCER LOCUS2 (REL2), maize Aux/IAAs were able to repress AUXIN RESPONSE FACTOR (ARF) transcriptional activity. A complete auxin response circuit comprised of all maize components, including ZmAFB2/3 b1 maize AUXIN SIGNALING F-BOX (AFB) receptor, was found to be fully functional. The ZmAFB2/3 b1 auxin receptor was found to be more sensitive to hormone than AtAFB2 and allowed for rapid circuit activation upon auxin addition. These results validate the conserved role of predicted auxin response genes in maize, as well as provide evidence that a synthetic approach can facilitate broader comparative studies across the wide range of species with sequenced genomes. A synthetic maize auxin response circuit is recapitulated in Saccharomyces cerevisiae, revealing a highly sensitive auxin signaling network with functional homology to the Arabidopsis circuit.

plant biology↗

bioRxiv2019

MACS: Rapid aqueous clearing system for three-dimensional mapping of intact organs

Tissue optical clearing techniques have provided important tools for large-volume imaging. Aqueous-based clearing methods are known for good fluorescence preservation and scalable size maintenance, but are limited by either long incubation time, or insufficient clearing performance, or requirements for specialized devices. Additionally, due to the use of high concentration organic solvents or detergents, few clearing methods are compatible with lipophilic dyes while maintaining high clearing performance. To address these issues, we developed a rapid, highly efficient aqueous clearing method with robust compatibility, termed m-xylylenediamine (MXDA)-based Aqueous Clearing System (MACS). MACS can render intact organs highly transparent in a fairly short time and possesses ideal compatibility with multiple probes, especially for lipophilic dyes. Using MACS, we cleared the adult mouse brains within only 2.5 days for three-dimensional (3D) imaging of the neural structures labelled by various techniques. Combining MACS with DiI labelling, we visualized the vascular structures of various organs. MACS provides a useful tool for 3D mapping of intact tissues and is expected to facilitate morphological, physiological and pathological studies of various organs.

bioengineering↗

bioRxiv2019

Diversity and complexity of the large surface protein family in the compacted genomes of various Pneumocystis species

Pneumocystis, a major opportunistic pathogen in patients with a broad range of immunodeficiencies, contains abundant surface proteins encoded by a multi-copy gene family, termed the major surface glycoprotein (Msg) gene superfamily. This superfamily has been identified in all Pneumocystis species characterized to date, highlighting its important role in Pneumocystis biology. In this report, through a comprehensive and in-depth characterization of 459 msg genes from 7 Pneumocystis species, we demonstrate, for the first time, the phylogeny and evolution of conserved domains in Msg proteins, and provide detailed description of the classification, unique characteristics and phylogenetic relatedness of five Msg families. We further describe the relative expression levels of individual msg families in two rodent Pneumocystis species, the substantial variability of the msg repertoires in P. carinii from laboratory and wild rats, and the distinct features of the expression site for the classic msg genes in Pneumocystis from 8 mammalian host species. Our analysis suggests a wide variety of functions for this superfamily, not only conferring antigenic variation to allow immune evasion but also mediating life-stage development, optimizing cell mobility and adhesion, and adapting to specific host niches or environmental conditions. This study provides a rich source of information that lays the foundation for the continued experimental exploration of the functions of the Msg superfamily in Pneumocystis biology.

molecular biology↗