Biology subjects

Chang, Z.

Publications and source records attributed to Chang, Z..

30 records · Page 2Linked to original sources

bioRxiv2020

SingleChannelNet: A model for Automatic Sleep Stage Classification with Raw Single-Channel EEG

In diagnosing sleep disorders, sleep stage classification is a very essential yet time-consuming process. Most of the existing state-of-the-art approaches rely on hand-crafted features and multi-modality polysomnography (PSG) data, where prior knowledge is compulsory and high computation cost can be expected. Besides, few studies are able to obtain high accuracy sleep staging using raw single-channel electroencephalogram (EEG). To overcome these shortcomings, this paper proposes an end-to-end framework with a deep neural network, namely SingleChannelNet, for automatic sleep stage classification based on raw single-channel EEG. The proposed model utilizes a 90s epoch as the textual input and employs two multi-convolution blocks and several max-average pooling layers to learn different scales of feature representations. To demonstrate the efficiency of the proposed model, we evaluate our model using different raw single-channel EEGs (C4/A1 and Fpz-Cz) on two different datasets (CC-SHS and Sleep-EDF datasets). Experimental results show that the proposed architecture can achieve better over-all accuracy and Cohens kappa (CCSHS: 90.2%-86.5%, Sleep-EDF: 86.1%-80.5%) compared with state-of-the-art approaches. Additionally, the proposed model can learn features automatically for sleep stage classification using different single-channel EEGs with distinct sampling rates from different datasets without using any hand-engineered features.

bioengineering↗

bioRxiv2020

Regeneration of Functional Retinal Ganglion Cells by Neuronal Identity Reprogramming

Degeneration of retinal ganglion cells (RGCs) and their axons underlies vision loss in glaucoma and various optic neuropathies. There are currently no treatments available to restore lost vision in patients affected by these diseases. Regenerating RGCs and reconnecting the retina to the brain represent an ideal therapeutic strategy; however, mammals do not have a reservoir of retinal stem/progenitor cells poised to produce new neurons in adulthood. Here, we regenerated RGCs in adult mice by direct lineage reprogramming of retinal interneurons. We successfully converted amacrine and displaced amacrine interneurons into RGCs, and observed that regenerated RGCs projected axons into brain retinorecipient areas. They convey visual information to the brain in response to visual stimulation, and are able to transmit electrical signals to postsynaptic neurons, in both normal animals and in a diseased model. The generation of functional RGCs in adult mammals points to a therapeutic strategy for vision restoration in patients.

neuroscience↗

bioRxiv2020

Dissecting endothelial to haematopoietic stem cell transition by single-cell transcriptomic and functional analyses

Haematopoietic stem cells (HSCs) in adults are believed to be born from hemogenic endothelial cells (HECs) in mid-gestational mouse embryos. Due to rare and transient nature, the HSC-competent ECs have never been stringently identified and accurately captured, let alone their genuine vasculature precursors. Here, we firstly used high-precision single-cell transcriptomics to unbiasedly examine relevant EC populations at continuous developmental stages and transcriptomically identified putative HSC-primed HECs. Combining computational prediction and in vivo functional validation, we precisely captured HSC-competent HECs by newly constructed Neurl3-EGFP reporter mouse model, and realized enrichment further by surface marker combination. Surprisingly, endothelial-haematopoietic bi-potential was rarely but reliably witnessed in culture of single HECs. Noteworthy, primitive vascular ECs experienced two-step fate choices to become HSC-primed HECs, resolving several previously observed contradictions. Taken together, comprehensive understanding of endothelial evolutions and molecular programs underlying HSC-primed HEC specification in vivo will facilitate future investigations directing HSC production in vitro.

developmental biology↗

bioRxiv2019

Lesions of canine prostate underwent laser ablation, radiofrequency ablation, and microwave ablation: Lesions shapes and clinical significances

ObjectiveTo explore the shapes and clinical significances of the lesions of canine prostate underwent laser ablation (LA), radiofrequency ablation (RFA), and microwave ablation (MWA).\n\nMethodsHere, 6 male Beagle dogs were randomly assigned to LA, RFA, and MWA groups, respectively. The ablations were conducted with the doses commonly applied in clinical practice (LA: 3 W/1200 J; RFA and MWA: 30 W/120 s) for one region in the left and right lobes of the prostate, which totally resulted in 12 lesions. An energy transmitter was inserted via the perineum under the guidance of transrectal ultrasound (TRUS) and the ablation process was observed dynamically. After ablation, the efficacy was assessed by contrast-enhanced ultrasonography (CEUS), and transverse diameter (TRD), anteroposterior diameter (APD), and longitudinal diameter (TRD) were measured. Then, the volume (V) was calculated according to the following formulae, V = 1/6 x {pi} x (MLD x APD x LD), and ratio (R) R =[(MLD + APD)/2 x LD], which was used to show the shape of the lesion (The closer R is to 1, the more spherical it is).\n\nResultsThe shapes and sizes of the lesions underwent the three techniques varied under the clinically commonly used doses. The R values, reflecting the changes in shapes of lesions, were 0.89{+/-}0.02, 0.72{+/-}0.01, and 0.65{+/-}0.03 for RFA, MWA, and LA, respectively, which were significantly different (P =0.027). The volumes of the lesions underwent the three ablation techniques significantly varied as well (P=0.001), which were 2.17{+/-}0.10, 1.51{+/-}0.20, and 0.79{+/-}0.07 ml for MWA, LA, and RFA, respectively. Conclusion: The above-mentioned three techniques could be used for ablation of prostate cancer using the clinically commonly used doses. The shapes of the lesions underwent the three ablation techniques varied evidently, with the lesions received RFA and LA were more spherical and oval, respectively, while the shapes of lesions underwent MWA were between spherical and oval. The lesions received MWA and RFA had the largest and smallest sizes, respectively, while sizes of lesions underwent LA were in the middle. These findings may assist physicians to select an appropriate therapeutic method for treatment of prostate disease.

cancer biology↗

bioRxiv2019

High-throughput living-cell protein crosslinking analysis uncovers the physiological relevance of forming the \"inserted\" state of the ATP synthase ϵ-subunit

ATP synthase, a highly conserved multi-subunit enzyme complex having a common stoichiometry of 3{beta}3{gamma}{delta}{varepsilon}ab2c8-15, functions to supply ATP as the universal energy currency for cells. It comprises of the peripheral F1 sector (3{beta}3{gamma}{delta}{varepsilon}) and the membrane-integrated Fo sector (ab2c8-15). In vitro structural analyses revealed that the C-terminal domain of the {varepsilon}-subunit could adopt either an \"inserted\" or \"non-inserted\" state (with or without interacting with the /{beta}-subunits), with the former being viewed as inhibitory for the ATP hydrolysis activity of ATP synthase. Nevertheless, as common in current protein researches, the physiological relevance of such an \"inserted\" state for ATP synthase functioning is hardly known. To decipher this, designed an unnatural amino acid-mediated living-cell protein photocrosslinking analysis pipeline by developing the scarless genome-targeted site-directed mutagenesis and the high-throughput gel polyacrylamide gel electrophoresis (HT-PAGE) techniques. Employing this powerful approach, we systematically examined the interactions involving the C-terminal helix of the {varepsilon}-subunit in cells living under a variety of experimental conditions. These studies enabled us to uncover that the \"inserted\" and \"non-inserted\" states of the {varepsilon}-subunit exist as an equilibrium in cells cultured under common experimental conditions, shifting to the former upon the appearance of unfavorable conditions, acting as a low-gear state to strengthen the ATP synthesis function. Such a fine-tuning mechanism allows the ATP synthase to reversibly and instantly switch between two functional states. Further, the two powerful techniques that we developed here might be applied to many aspects of protein researches.

biochemistry↗

bioRxiv2019

Drug-resistant epimutants exhibit organ-specific stability and induction during murine infections caused by the human fungal pathogen Mucor circinelloides

The environmentally ubiquitous fungus Mucor circinelloides is a primary cause of the emerging disease mucormycosis. Mucor infection is notable for causing high morbidity and mortality, especially in immunosuppressed patients, while being inherently resistant to the majority of clinically available antifungal drugs. A new, RNAi-dependent, and reversible epigenetic mechanism of antifungal resistance - epimutation - was recently discovered in M. circinelloides. However, the effects of epimutation in a host-pathogen setting were unknown. We employed a systemic, intravenous murine model of Mucor infection to elucidate the potential impact of epimutation in vivo. Infection with an epimutant strain resistant to the antifungal agents FK506 and rapamycin revealed that the epimutant-induced drug resistance was stable in vivo in a variety of different organs and tissues. Reversion of the epimutant-induced drug resistance was observed to be more rapid in isolates from the brain, as compared to those recovered from the liver, spleen, kidney, or lungs. Importantly, infection with a wild-type strain of Mucor led to increased rates of epimutation after strains were recovered from organs and exposed to FK506 stress in vitro. Once again, this effect was more pronounced in strains recovered from the brain than from other organs. In summary, we report the rapid induction and reversion of RNAi-dependent drug resistance after in vivo passage through a murine model, with pronounced impact in strains recovered from brain. Defining the role played by epimutation in drug resistance and infection advances our understanding of Mucor and other fungal pathogens, and may have implications for antifungal therapy.\n\nIMPORTANCEThe emerging fungal pathogen Mucor circinelloides causes a severe infection, mucormycosis, which leads to considerable morbidity and mortality. Treatment of Mucor infection is challenging because Mucor is inherently resistant to nearly all clinical antifungal agents. An RNAi-dependent and reversible mechanism of antifungal resistance, epimutation, was recently described in Mucor. Epimutation has not been studied in vivo and it was unclear whether it would contribute to antifungal resistance observed clinically. We demonstrate that epimutation can be both induced and reverted after in vivo passage through a mouse model; rates of both induction and reversion are higher after brain infection than after infection of other organs (liver, spleen, kidneys, or lungs). Elucidating the roles played by epimutation in drug resistance and infection will improve our understanding of Mucor and other fungal pathogens, and may have implications for antifungal treatment.

microbiology↗

bioRxiv2019

Broad antifungal resistance mediated by RNAi-dependent epimutation in the basal human fungal pathogen Mucor circinelloides

Mucormycosis - an emergent, deadly fungal infection - is difficult to treat, in part because the causative species demonstrate broad clinical antifungal resistance. However, the mechanisms underlying drug resistance in these infections remain poorly understood. Our previous work demonstrated that one major agent of mucormycosis, Mucor circinelloides, can develop resistance to the antifungal agents FK506 and rapamycin through a novel, transient RNA interference-dependent mechanism known as epimutation. Epimutations silence the drug target gene and are selected by drug exposure; the target gene is re-expressed and sensitivity is restored following passage without drug. This silencing process involves generation of small RNA (sRNA) against the target gene via core RNAi pathway proteins. To further elucidate the role of epimutation in the broad antifungal resistance of Mucor, epimutants were isolated that confer resistance to another antifungal agent, 5-fluoroorotic acid (5-FOA). We identified epimutant strains that exhibit resistance to 5-FOA without mutations in PyrF or PyrG, enzymes which convert 5-FOA into the active toxic form. Using sRNA hybridization as well as sRNA library analysis, we demonstrate that these epimutants harbor sRNA against either pyrF or pyrG, and further show that this sRNA is lost after reversion to drug sensitivity. We conclude that epimutation is a mechanism capable of targeting multiple genes, enabling Mucor to develop resistance to a variety of antifungal agents. Elucidation of the role of RNAi in epimutation affords a fuller understanding of mucormycosis. Furthermore, it improves our understanding of fungal pathogenesis and adaptation to stresses, including the evolution of drug resistance.

microbiology↗

bioRxiv2018

The long noncoding RNA Hand2as orchestrates heart development through regulation of precise expression of HAND2

Rigorous exploration and dissection of potential actions and effects of long noncoding RNA (lncRNA) in animals remain challenging. Here using multiple knockout mouse models and single-cell RNA sequencing, we demonstrate that the divergent lncRNA Hand2as has a key, complex modulatory effect on the expression of its neighboring gene HAND2 and subsequently on heart development and function, largely independent of Hand2as transcription and transcripts. Full-length deletion of Hand2as in mouse causes moderate yet prevalent upregulation of HAND2 in hundreds of cardiac cells, resulting in profound biological consequences, including dysregulated cardiac gene programs, congenital heart defects and perinatal lethality. We propose a cis-functional role for the Hand2as locus in dampening HAND2 expression to restrain cardiomyocyte proliferation, thereby orchestrating a balanced development of cardiac cell lineages. This study highlights the need for complementary genetic and single-cell approaches to delineate the function and primary molecular effects of an lncRNA in animals.\n\nImpact statementThe long noncoding RNA Hand2as critically controls the precise expression of its neighboring gene HAND2, thereby balancing cardiac lineages and expression programs that are essential for heart development and function.

developmental biology↗

bioRxiv2018

Regrowth-delay Body as a Bacterial Subcellular Structure marking multidrug tolerant Persisters

Bacteria have long been recognized to be capable of entering a phenotypically non-growing persister state, in which the cells exhibit an extended regrowth lag and a multidrug tolerance, thus posing a great challenge in treating infectious diseases. Owing to their non-inheritability, low abundance of existence, lack of metabolic activities, and high heterogeneity, properties of persisters remain poorly understood. Here, we report our accidental discovery of a hitherto unreported subcellular structure that we term the regrowth-delay body, which is formed only in non-growing bacterial cells and sequesters multiple key proteins. As of now, this structure, that dissolves when the cell resumes growth, is the most distinguishable subcellular structure marking persisters. Our studies also indicate that persisters exhibit different depth of persistence, as determined by the status of their regrowth-delay bodies. Our findings imply that suppressing the formation and/or promoting the dissolution of regrowth-delay bodies could be viable strategies for eradicating persisters.

microbiology↗

bioRxiv2018

Absence of GdX/UBL4A protects against inflammatory bowel diseases by regulating NF-κB signaling in DCs and macrophages

Nuclear factor-kappa B (NF-{kappa}B) activation is critical for innate immune responses. Here we report that the UBL4A (Ubiquitin-like protein 4A, also named GdX) enhances dendritic cells (DCs) and macrophages (M{varphi})-mediated innate immune defenses by positively regulating NF-{kappa}B signaling. GdX-deficient mice were resistant to LPS-induced endotoxin shock and DSS-induced colitis. DC- or M{varphi}-specific GdX-deficient mice displayed alleviated mucosal inflammation, and the production of pro-inflammatory cytokines by GdX-deficient DCs and M{varphi} was reduced. Mechanistically, we found that PTPN2 (TC45) and PP2A form a complex with RelA (p65) to mediate its dephosphorylation whereas GdX interrupts the TC45/PP2A/p65 complex formation and restrict p65 dephosphorylation by trapping TC45. Our study provides a mechanism by which NF-{kappa}B signaling is positively regulated by an adaptor protein GdX in DC or M{varphi} to maintain the innate immune response. Targeting GdX could be a strategy to reduce over-activated immune response in inflammatory diseases.

immunology↗

bioRxiv2017

A Shortened Version Of SecA (SecAN) Functions As The Protein-Conducting Channel For Nascent β-Barrel Outer Membrane Proteins

Many proteins are translocated across biomembranes via protein translocons in targeting to their subcellular destinations. Hitherto, the SecYEG/Sec61 translocon, existing in prokaryotes and eukaryotes, represents the most intensively studied one. According to the current perception, both periplasmic and {beta}-barrel outer membrane proteins ({beta}-barrel OMPs) are translocated via the SecYEG translocon in bacterial cells, although direct living cell evidences remain lacking. Here, mainly via in vivo protein photo-crosslinking analysis, we revealed that the never reported membrane-integrated SecAN protein apparently functions as the translocon for {beta}-barrel OMPs. Additionally, SecAN contains a GXXXG motif known for mediating protein interactions in biomembranes, and processing of {beta}-barrel OMP precursors was severely affected in cells producing an assembly-defective SecAN variant resulted from the GXXXG motif mutations. Furthermore, SecAN was demonstrated to directly interact with the Bam complex, thus likely be a part of the supercomplex that we revealed earlier to be responsible for {beta}-barrel OMP biogenesis.

biochemistry↗

bioRxiv2017

An Organelle-like Structure Correlated with the Quiescent State of Bacterial Cells

Bacterial cells take a variable lag time and maintain a multi-drug tolerant non-growing state before resuming growth when encountering growth-supportive conditions. Some of them exhibit an extraordinarily long lag, as pathogenic persisters do. It remains unknown on what determines lag time duration. Here, we unveiled a subcellular structure, termed quiescent body, that is formed in bacterial cells entering non-growing state and sequesters selected proteins essential for cell growth. Their formation occurs progressively in each cell and heterogeneously among individual cells. They only dissolve in re-growing cells to release proteins for immediate re-functioning when conditions become fit. Quiescent body, whose degree of formation is highly correlated with duration of lag time or level of antibiotic tolerance, apparently functions as a biological timer for bacterial growth resumption. Further, suppressing their formation, which directly relies on cellular respiration complexes, or promoting their dissolution might be a viable strategy to eradicate persisters.

microbiology↗