Biology subjects

Zhang, M.

Publications and source records attributed to Zhang, M..

At least 469 records · Page 26Linked to original sources

bioRxiv2022

Mycobacterium tuberculosis disease associates with higher HIV-1-specific antibody responses

Mycobacterium tuberculosis (Mtb) can enhance immune responses against unrelated pathogens. Although Mtb is the most common co-infection in people living with HIV (PWH), there has been no examination of its impact on HIV-1 immune responses. Plasma neutralization and antibody dependent cellular cytotoxicity (ADCC) was compared among PWH and Mtb disease (PWH/Active Mtb) and PWH/No Mtb both prior to and after antiretroviral treatment (ART) and completion of Mtb therapy. We assessed HIV-1 sequences, total antibody quantities and isotypes, and plasma cytokine levels to ascertain mechanisms that affect humoral responses. HIV-1 neutralizing antibodies (nAbs) were broader and more potent in PWH/Active Mtb as compared to PWH/No Mtb, and nAbs increased among PWH who developed Mtb after ART initiation. ADCC was also higher in the PWH who had Mtb disease after starting ART. PWH/Active Mtb as compared to PWH/No Mtb had unique HIV-1 envelope sequence motifs associated with neutralization resistance further implying differences in humoral selection. The Mtb-linked antibody augmentation associated with elevated plasma cytokine levels important for B cells and antibody production, namely interleukin-6, a proliferation-inducing ligand (APRIL), and B-cell activating factor (BAFF). Increased plasma virus levels, greater HIV-1 envelope diversity, higher levels of all antibodies, and cross-reactive responses did not explain the enhanced HIV-1 humoral responses in those with Mtb. Mtb disease enhances HIV-1 humoral responses likely by perturbing pathways important for antibody production in lymphoid tissue that has both pathogens. These findings have implications for using antibody-based therapies and inducing optimal HIV-1 antibody responses. Author SummaryMycobacterium tuberculosis (Mtb) is the most common infection among people with HIV (PWH) in the world. Mtb infection can enhance immune responses against unrelated pathogens. Previous studies have not examined the impact of Mtb disease on HIV antibodies in PWH. This information has importance for future strategies aimed at enhancing HIV antibody responses in naive individuals or PWH. We show that HIV neutralizing antibodies and antibody-dependent cellular cytotoxicity are broader and more potent in PWH in the presence as compared to the absence of Mtb disease. PWH and Mtb disease as compared to those without Mtb also harbor unique HIV envelope sequences, which further indicates that there is differential antibody selection pressure. The Mtb linked HIV antibody enhancement associated with specific mediators important for B cell and antibody development. Importantly, the Mtb mediated HIV antibody augmentation was not due to cross-reactivity, a generalized increase in all antibodies, or a higher level, more diverse, or longer duration of antigen exposure. We speculate that more potent HIV antibodies arise in lymphatic tissue that harbors both Mtb and HIV. Our findings have implications for both future uses of HIV antibodies as prophylaxis or treatment and strategies aimed inducing better HIV antibody responses.

microbiology↗

bioRxiv2022

Soft and stretchable organic bioelectronics for continuous intra-operative neurophysiological monitoring during microsurgery

Continuous intra-operative neurophysiological monitoring (CINM) that provides precise mapping of neural anatomy through the entire microsurgery process is essential to preserve the structural and functional integrity of the nerve. However, bulky and rigid electrodes used currently in clinics are usually unable to reliably maintain continuous and stable contacts with the vulnerable and complex nerve networks, thus often resulting in detrimental post-operative complications, such as hemiplegia and sensory disturbances. Here, we describe a biomechanically compatible, suture-free, and individually reconfigurable CINM based on soft and stretchable organic electronic materials. Due to both low impedance and modulus of our conducting polymer electrodes, we achieved for the first time continuous recording of near-field action potential with high signal-to-noise ratio and minimal invasiveness during microsurgeries. Utilizing this unprecedented CINM modality, in conjunction with localized neurostimulation, we further demonstrated our approach in enabling optimal post-operative prognosis in preclinical animal models by preserving normal neural functions after a variety of tumor resection surgeries.

bioengineering↗

bioRxiv2022

Transcription factor TFAP2C affects porcine early embryo development via regulating epigenetic modification

Transcription factors (TFs) have the potential function in regulating gene expression. Transcription factor TFAP2C plays important roles in the regulation of post-implantation embryonic development in mice, the reprogramming process, trophectoderm formation and carcinogenesis, but its role in porcine early embryo development remains unclear. This study was conducted to investigate the role of TFAP2C in porcine early embryo development using siRNA cytoplasmic injection. The RNAseq and immunofluorescence staining were performed to detect gene expression, and ChIP and dual luciferase reporter assays were used to elucidate the mechanism. The results showed that the deficiency of TFAP2C could lead to embryonic development disorder. The percentage of the blastocyst in the TFAP2C knockdown (TFAP2C-KD) group (7.76{+/-}1.86%) was significantly decreased compared to the control group (22.92{+/-}1.97%) (P**<0.01). The RNAseq results showed that 1208 genes were downregulated and 792 genes were upregulated after siRNA injection. The expression of epigenetic modification enzymes KDM5B, SETD2 (P**<0.01) etc. were significantly elevated in TFAP2C-KD group. Meanwhile, the modification levels of H3K4me3, H3K4me2 and H3K9me3 (P*<0.05) were significantly decreased, and the modification levels of H3K36me3 (P**<0.01) and DNA methylation (P**<0.01) were significantly increased in TFAP2C-KD group. DNMT1 was mostly expressed in cytoplasm in the control group, while it was mainly expressed in nuclei in the TFAP2C-KD group. In addition, TFAP2C could bind to the promoter region of SETD2, and the mutation of the TFAP2C binding site resulted in increased activity of SETD2 promoter (P**<0.01). The knockdown of TFAP2C affects histone modification and DNA methylation by regulating the expression of SETD2, KDM5B etc. and other genes, thereby inhibiting embryonic development. TFAP2C binds to the promoter region of SETD2 and acts as a hindrance protein. This study fills in the deficiency of TFAP2C in porcine early embryo development and provides theoretical support for animal husbandry production and biomedicine. Author SummaryThe correct activation of embryonic genes is required during early embryonic development, and the activation of these genes is subject to strict epigenetic regulation, such as DNA methylation, histone acetylation and methylation, with abnormalities in either leading to birth defects and developmental defects in individuals. TFs have specific binding motifs that regulate gene expression by binding to them. TFAP2C has been studied in post-implantation embryonic development and trophectoderm generation, however, the effect on early embryo development is unknown. Our findings suggest that TFAP2C deficiency disrupts gene expression patterns and leads to abnormal epigenetic modifications, resulting in abnormal embryo development. Furthermore, we found for the first time that TFAP2C can bind to the promoter region of SETD2, thereby affecting early embryo development in pigs. This indicates the critical role of TFAP2C in early embryo development in pigs on one hand, and also provides theoretical support for livestock production and biomedicine.

developmental biology↗

bioRxiv2022

The Cation/H+ exchanger OsCAX2 is involved in cadmium tolerance and accumulation through vacuolar sequestration in rice

Excessive cadmium (Cd) in rice grains is a serious food safety problem. The development of Cd-safe varieties requires the identification of germplasms and genes with major effect on Cd accumulation but without negative effects on other important traits. Here, we reported that OsCAX2, a member of the rice Cation/H+ exchanger (CAX) family, is an important Cd transporter. OsCAX2 encodes a tonoplast-localized protein and is strongly upregulated by Cd, mainly expresses in root exodermis, parenchyma in cortex, endodermis and stele cells. Depletion of OsCAX2 resulted in enhanced Cd sensitivity and root-to-shoot translocation in rice, while overexpression of OsCAX2 significantly increased Cd tolerance and reduced Cd transport by promoting root Cd influx and vacuolar storage, which ultimately reduced Cd transport via xylem. OsCAX2 also had significant effects on tissues/organs distribution of Cd but had no effects on grain yield and agronomic traits. Importantly, the OsCAX2 overexpressing lines had more than 70% lower grain Cd accumulation, increased iron (Fe), zinc (Zn) and manganese (Mn) and reduced copper (Cu) accumulation. Therefore, OsCAX2 is an ideal gene for developing Cd-safe rice varieties via transgenic approach.

plant biology↗

bioRxiv2022

Distinct structure and gating mechanism in diverse NMDA receptors with GluN2C and GluN2D subunits

N-Methyl-D-Aspartate (NMDA) receptors are essential for many brain functions. These receptors are heterotetramers typically comprising two GluN1 subunits and two GluN2 subunits. The latter could alternate among four subtypes (N2A-N2D) and determine the functional diversity of NMDA receptors1, 2. For example, receptors containing N2C or N2D exhibit 50-fold lower channel open probability (Po) than those containing N2A (ref.3-5). Structures of N2A- and N2B-containing receptors have been extensively characterized, providing molecular basis for understanding NMDA receptor function6-14. Here we report the cryo-EM structures of N1-N2D and N1-N2C di-heterotetramers (di-receptors), and N1-N2A-N2C tri-heterotetramer (tri-receptor) at a resolution up to 3.0 [A]. Structural analysis showed that the bilobate N-terminal domain (NTD) in N2D adopted an intrinsic closed conformation, leading to a compact NTD tetramer in N1-N2D receptor. Functional studies further demonstrated that, in di-receptors containing N2D but not N2A or N2B, crosslinking NTD at the tetrameric interface had no effect on channel activity, while crosslinking ligand-binding domain (LBD) of two N1 protomers significantly elevated Po. Surprisingly, we found that the N1-N2C di-receptors spontaneously oscillated between symmetric and asymmetric conformation. The later one occupied a predominant population, whereby two N2C protomers exhibited distinct conformation. This asymmetry, which was also found to a lesser extent in N1-N2A di-receptor10, was further locked by the binding of an N2C-specific allosteric potentiator PYD-106 to a unique binding pocket between NTD and LBD in only one N2C protomer. Finally, N2A and N2C in the N1-N2A-N2C tri-receptor displayed the conformation close to that found in one protomer of N1-N2A and N1-N2C di-receptors, respectively. These findings provide a comprehensive structural understanding of diverse functional properties of major NMDA receptor subtypes.

neuroscience↗

bioRxiv2022

NSC-derived exosomes enhance therapeutic effects of NSC transplantation on cerebral ischemia in mice

AbstractTransplantation of neural stem cells (NSCs) has been proved to promote functional rehabilitation of brain lesions including ischemic stroke. However, the therapeutic effects of NSC transplantation is limited by the low survival and differentiation rates of NSCs due to the harsh environment in the brain after ischemic stroke. Here, we employed NSCs derived from human induced pluripotent stem cells (iPSCs) together with exosomes extracted from NSCs to treat cerebral ischemia induced by middle cerebral artery occlusion/reperfusion (MCAO/R) in mice. The results showed that NSC-derived exosomes significantly reduced the inflammatory response, alleviated oxidative stress after NSC transplantation, and facilitated NSCs differentiation in vivo. The combination of NSCs with exosomes ameliorated the injury of brain tissue including cerebral infarct, neuronal death and glial scarring, and promoted the motor function recovery. To explore the underlying mechanisms, we analyzed the miRNA profiles of NSC-derived exosomes and the potential downstream genes. Our study provided the rationale for the clinical application of NSC-derived exosomes as a supportive adjuvant for NSC transplantation after stroke.

neuroscience↗

bioRxiv2022

Cryo-EM structures of kalium channelrhodopsins KCRs

H. catenoides kalium channelrhodopsins (HcKCR1 and HcKCR2) are potassium-selective light-gated ion channels with unique properties for optogenetics. Here we report cryo-electron microscopy (cryo-EM) structures of HcKCR1 and HcKCR2 with endogenous retinal. Strikingly, one structure of HcKCR1 represents the conducting state with continuous potassium ion flow in the lumen, while another in non-conducting state with discontinuous potassium ion flow. Further electrophysiological studies identified extracellular side of ion permeation region as the major element for channel potassium selectivity and retinal binding region for channel gating. Our results uncover the unprecedented potassium selectivity and light-gating mechanism, and may facilitate the rational design of new optogenetic tools.

biophysics↗

bioRxiv2022

Exosome-mediated viral nucleic acid presentation in a crustacean reveals innate immunity evolution from a novel perspective

As an enduring hot topic in the field of innate immunity, apoptosis is widely considered as an effective approach to eliminate pathogenic microbes, and possesses crucial role during host-pathogen interactions. Recently, researchers have found that virus-containing host cells could transmit apoptotic signals to surrounding uninfected cells during infection, but the mechanism remains unclear. Here, we found that exosomes secreted by WSSV-infected mud crab hemocytes contain viral nucleic acid wsv277, which could be transported to the recipient cells and further expressed viral protein with phosphokinase activity. Besides, by using transcriptome, proteome, ChIP-seq and coIP techniques, the results revealed that wsv277 could activate the transcription and translation of apoptotic genes via interacting with CBF and EF-1, so as to suppress the spread of virus infection by inducing apoptosis of the surrounding cells. Therefore, for the first time, our study proved that the components of DNA virus could be encapsulated into exosomes, and elucidated the mechanism of apoptotic signal transduction between cells from the perspective of exosome. Moreover, comparing those of invertebrates, we hypothesized that the innate immune system of vertebrate was weakened or degenerated, allowing exosomes to be employed by virus as the vehicle for immune escape. Significance statementOur study revealed that the components of DNA virus could be packaged and transmitted through the exosomes of lower invertebrates, which strongly demonstrated the diversity of exosome-mediated viral immunity and its universality in animals. Furthermore, we elucidated the mechanism of apoptotic signal transduction between cells from the perspective of exosome, and revealed a novel strategy for the host to cope with viral infection. Since exosome is an important innate immune regulation approach, we hypothesize that the innate immune system of vertebrates is weakened or degenerated, allowing exosomes to be employed by virus as the vehicle for immune escape.

immunology↗

bioRxiv2022

Reduced acetylation of TFAM promotes bioenergetic dysfunction in the failing heart

General Control of Amino-Acid Synthesis 5-like 1 (GCN5L1) was previously identified as a key regulator of protein lysine acetylation in mitochondria. Subsequent studies demonstrated that GCN5L1 regulates the acetylation status and activity of mitochondrial fuel substrate metabolism enzymes. However, the role of GCN5L1 in response to chronic hemodynamic stress is largely unknown. Here, we show that cardiomyocyte-specific GCN5L1 knockout mice (cGCN5L1 KO) display exacerbated pressure overload-induced heart failure progression following transaortic constriction (TAC). Mitochondrial DNA and mitochondrial electron transport chain protein levels were decreased in cGCN5L1 KO hearts after TAC, and isolated neonatal cardiomyocytes with reduced GCN5L1 expression had lower bioenergetic output in response to hypertrophic stress. Loss of GCN5L1 expression led to a decrease in the acetylation status of mitochondrial transcription factor A (TFAM) after TAC in vivo, which was linked to a reduction in mtDNA levels in vitro. Together, these data suggest that GCN5L1 may protect from hemodynamic stress by maintaining mitochondrial bioenergetic output. HighlightsO_LIReduced GCN5L1 expression in the failing heart promotes contractile dysfunction C_LIO_LIMitochondrial DNA (mtDNA) levels are reduced in cardiomyocyte-specific GCN5L1 knockout mice following hemodynamic stress C_LIO_LIGCN5L1 knockdown reduces, and GCN5L1 overexpression increases, bioenergetic output in hypertrophic cardiomyocytes C_LIO_LIGCN5L1-mediated acetylation of TFAM promotes increased mtDNA levels C_LI

physiology↗

bioRxiv2022

Cross-attractor modeling of resting-state functional connectivity in psychiatric disorders reveals disturbances in excitation, inhibition, and energy gaps

Resting-state functional connectivity (RSFC) is altered across various psychiatric disorders. Brain network modeling (BNM) has the potential to reveal the neurobiological underpinnings of such abnormalities by dynamically modeling the structure-function relationship and examining biologically relevant parameters after fitting the models with real data. Although innovative BNM approaches have been developed, two main issues need to be further addressed. First, previous BNM approaches are primarily limited to simulating noise-driven dynamics near a chosen attractor (or a stable brain state). An alternative approach is to examine multi(or cross)-attractor dynamics, which can be used to better capture non-stationarity and switching between states in the resting brain. Second, previous BNM work is limited to characterizing one disorder at a time. Given the large degree of co-morbidity across psychiatric disorders, comparing BNMs across disorders might provide a novel avenue to generate insights regarding the dynamical features that are common across (vs. specific to) disorders. Here, we address these issues by (1) examining the layout of the attractor repertoire over the entire multi-attractor landscape using a recently developed cross-attractor BNM approach; and (2) characterizing and comparing multiple disorders (schizophrenia, bipolar, and ADHD) with healthy controls using an openly available and moderately large multimodal dataset from the UCLA Consortium for Neuropsychiatric Phenomics. Both global and local differences were observed across disorders. Specifically, the global coupling between regions was significantly decreased in schizophrenia patients relative to healthy controls. At the same time, the ratio between local excitation and inhibition was significantly higher in the schizophrenia group than the ADHD group. In line with these results, the schizophrenia group had the lowest switching costs (energy gaps) across groups for several networks including the default mode network. Paired comparison also showed that schizophrenia patients had significantly lower energy gaps than healthy controls for the somatomotor and visual networks. Overall, this study provides preliminary evidence supporting transdiagnostic multi-attractor BNM approaches to better understand psychiatric disorders pathophysiology.

neuroscience↗

bioRxiv2022

ASO targeting temperature-controlled RBM3 poison exon splicing prevents neurodegeneration in vivo

Neurodegenerative diseases are increasingly prevalent in the aging population, yet currently no disease-modifying treatments are available. Increasing the expression of the cold-shock protein, RBM3, through therapeutic hypothermia is remarkably neuroprotective, but cooling poses a health risk itself, strongly limiting its clinical application. Selective upregulation of RBM3 at normothermia thus holds immense therapeutic potential. Here we identify a poison exon within the RBM3 gene that is solely responsible for cold-induced RBM3 expression. Genetic removal or ASO-mediated manipulation of this exon yields high RBM3 levels independent of cooling. Notably, a single administration of ASO to exclude the poison exon, using FDA-approved chemistry, results in long-lasting increase of RBM3 expression in mouse brains. In prion-diseased mice, this treatment leads to remarkable neuroprotection, with prevention of neuronal loss and spongiosis despite high levels of prion protein. RBM3-inducing ASOs could thus broadly deliver protection in humans in conditions ranging from acute brain injury to Alzheimers disease. One sentence summaryInducing cold shock protein RBM3 by modulating its alternative splicing at normothermia is neuroprotective in vivo

molecular biology↗

bioRxiv2022

Eliminate false positives in metagenomic profiling based on type IIB restriction sites

Accurate species identification and abundance estimation are critical for the interpretation of whole metagenome shotgun sequencing (WMS) data. Numerous computational methods, broadly referred to as metagenomic profilers, have been developed to identify species in microbiome samples by classification of sequencing reads and quantification of their relative abundances. Yet, existing metagenomic profilers typically suffer from false positive identifications and consequently biased relative abundance estimation (as false positives can be accounted for more than 90% of total identified species). Here, we present a new metagenomic profiler MAP2B (MetAgenomic Profiler based on type IIB restriction site) to resolve those issues. We first illustrate the pitfalls of using relative abundance as the only feature in determining false positives. We then propose a feature set to distinguish false positives from true positives. By benchmarking the performance in metagenomic profiling using data from CAMI2 (Critical Assessment of Metagenome Interpretation: second round of challenge), we illustrate the superior performance of MAP2B (F1 score ~ 0.93) over existing metagenomic profilers (F1 score ranges from 0.18 to 0.58). We further tested the performance of MAP2B using real WMS data from an ATCC mock community, confirming its superior performance and robustness against sequencing depth. In addition, by leveraging WMS data from an IBD cohort, we demonstrate the taxonomic features obtained by MAP2B can better discriminate disease status and predict metabolomic profiles.

bioinformatics↗

bioRxiv2022

Quantitative profiling of pseudouridylation landscape in the human transcriptome

Pseudouridine ({Psi}) is an abundant post-transcriptional RNA modification in ncRNA and mRNA. However, transcriptome-wide measurement of individual {Psi} sites remains unaddressed. Here, we develop "PRAISE", via selective chemical labeling of {Psi} by bisulfite to induce nucleotide deletion signature during reverse transcription, to realize quantitative assessment of the {Psi} landscape in the human transcriptome. Unlike traditional RNA/DNA bisulfite treatment, our approach is based on quaternary base mapping and revealed a ~10% median modification level for 2,714 confident {Psi} sites in HEK293T cells. By perturbing pseudouridine synthases, we obtained differential mRNA targets of PUS1, PUS7 and TRUB1, with TRUB1 mRNA targets showing the highest modification stoichiometry. In addition, we identified and quantified known and novel {Psi} sites in mitochondrial mRNA, catalyzed by a mitochondria-localized isoform of PUS1. Collectively, we provide a sensitive and convenient method to measure transcriptome-wide {Psi}; we envision this quantitative approach would facilitate emerging efforts to elucidate the function and mechanism of mRNA pseudouridylation.

molecular biology↗

bioRxiv2022

Field dependent deep learning enables high-throughput whole-cell 3D super-resolution imaging

Single-molecule localization microscopy (SMLM) in a typical wide-field setup has been widely used for investigating sub-cellular structures with super resolution. However, field-dependent aberrations restrict the field of view (FOV) to only few tens of micrometers. Here, we present a deep learning method for precise localization of spatially variant point emitters (FD-DeepLoc) over a large FOV covering the full chip of a modern sCMOS camera. Using a graphic processing unit (GPU) based vectorial PSF fitter, we can fast and accurately model the spatially variant point spread function (PSF) of a high numerical aperture (NA) objective in the entire FOV. Combined with deformable mirror based optimal PSF engineering, we demonstrate high-accuracy 3D SMLM over a volume of ~180 x 180 x 5 m3, allowing us to image mitochondria and nuclear pore complex in the entire cells in a single imaging cycle without hardware scanning - a 100-fold increase in throughput compared to the state-of-the-art.

biophysics↗

bioRxiv2022

Increased public health threat of avian-origin H3N2 influenza virus during evolution in dogs

Influenza A viruses in animal reservoirs repeatedly cross species barrier to infect humans. Once an animal-borne virus with novel antigenicity acquired the efficient human to human transmissibility, it will become epidemic in the population. Dogs are the closest animal companions to humans and canine respiratory tract expresses both SA2,3-(avian type) and 2,6-Gal (human type) receptors. However, the role of dogs in the ecology of influenza viruses is unclear. H3N2 avian influenza viruses transmitted to dogs around 2006 and have formed stable lineages. The long-term epidemic of avian-origin H3N2 virus in canine offers the best models to investigate the effect of dogs on the evolution of influenza viruses. Here, we carried out a systematic and comparative identification of the biological characteristics of H3N2 canine influenza viruses (CIVs) isolated in the worldwide over 10 years. We found that during the adaptation of H3N2 CIVs to dogs, H3N2 CIVs became to recognize the human-like SA2,6-Gal receptor, gradually increased HA acid stability and replication ability in human airway epithelial cells, and acquired a 100% transmission rate via respiratory droplet in ferret model, which were essential hallmarks of being adapted to humans. We also identified that the frequency of substitutions related to human adaptation has gradually increased in H3N2 CIVs, and determined four cumulative molecular changes responsible for the increased airborne transmission ability in ferrets. Our results suggested that canine may serve as an intermediate for the adaptation of avian influenza virus to human. Continuous surveillance coordinated with risk assessment for CIVs is necessary.

microbiology↗

bioRxiv2022

GESIAP: A Versatile Genetically Encoded Sensor-based Image Analysis Program

Intercellular communication mediated by a large number of neuromodulators diversifies physiological actions, yet neuromodulation remains poorly understood despite the recent upsurge of genetically encoded transmitter sensors. Here, we report the development of a versatile genetically encoded sensor-based image analysis program (GESIAP) that utilizes MATLAB-based algorithms to achieve high-throughput, high-resolution processing of sensor-based functional imaging data. GESIAP enables delineation of fundamental properties (e.g., transmitter spatial diffusion extent, quantal size, quantal content, release probability, pool size, and refilling rate at single release sites) of transmission mediated by various transmitters (i.e., monoamines, acetylcholine, neuropeptides, and glutamate) at various cell types (i.e., neurons, astrocytes, and other non-neuronal cells) of various animal species (i.e., mouse, rat, and human). Our analysis appraises a dozen of newly developed transmitter sensors, validates a conserved model of restricted non-volume neuromodulatory synaptic transmission, and accentuates a broad spectrum of presynaptic release properties that variegate neuromodulation.

neuroscience↗

bioRxiv2022

A comprehensive view of cell-type-specific temporal dynamics in human and mouse brains

Progenitor cells play fundamental roles in preserving optimal organismal functions under normal, aging, and disease conditions. However, progenitor cells are incompletely characterized, especially in the brain, partly because conventional methods are restricted by inadequate throughput and resolution for deciphering cell-type-specific proliferation and differentiation dynamics in vivo. Here, we developed TrackerSci, a new technique that combines in vivo labeling of newborn cells with single-cell combinatorial indexing to profile the single-cell chromatin landscape and transcriptome of rare progenitor cells and track cellular differentiation trajectories in vivo. We applied TrackerSci to analyze the epigenetic and gene expression dynamics of newborn cells across entire mouse brains spanning three age stages and in a mouse model of Alzheimers disease. Leveraging the dataset, we identified diverse progenitor cell types less-characterized in conventional single cell analysis, and recovered their unique epigenetic signatures. We further quantified the cell-type-specific proliferation and differentiation potentials of progenitor cells, and identified the molecular programs underlying their aging-associated changes (e.g., reduced neurogenesis/oligodendrogenesis). Finally, we expanded our analysis to study progenitor cells in the aged human brain through profiling [~]800,000 single-cell transcriptomes across five anatomical regions from six aged human brains. We further explored the transcriptome signatures that are shared or divergent between human and mouse oligodendrogenesis, as well as the region-specific down-regulation of oligodendrogenesis in the human cerebellum. Together, the data provide an in-depth view of rare progenitor cells in mammalian brains. We anticipate TrackerSci will be broadly applicable to characterize cell-type-specific temporal dynamics in diverse systems.

genomics↗

bioRxiv2022

Heterogeneous and Surface-Catalyzed Amyloid Aggregation Monitored by Spatially Resolved Fluorescence and Single Molecule Microscopy

Amyloid aggregation is associated with many diseases and may also occur in therapeutic protein formulations. Addition of co-solutes is a key strategy to modulate the stability of proteins in pharmaceutical formulations and select inhibitors for drug design in the context of diseases. However, the heterogeneous nature of this multi-component system in terms of structures and mechanisms poses a number of challenges for the analysis of the chemical reaction. Combining a spatially resolved fluorescence approach with single molecule microscopy and machine learning approaches, we disentangle the different contributions from multiple species within a single aggregation experiment. Moreover, we link the presence of interfaces to the degree of heterogeneity of the aggregation kinetics and retrieve the rate constants and underlying mechanisms for single aggregation events, providing a general tool for a comprehensive analysis of self-assembly reactions. Table of Contents O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/510935v2_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@c678eaorg.highwire.dtl.DTLVardef@2c6decorg.highwire.dtl.DTLVardef@e4c2e4org.highwire.dtl.DTLVardef@b741aa_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗