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Yue, Y.

Publications and source records attributed to Yue, Y..

72 records · Page 4Linked to original sources
bioRxiv2021

Mycobacteria tuberculosis PPE36 modulates host inflammation by promoting E3 ligase Smurf1-mediated MyD88 degradation

Mycobacterium tuberculosis (Mtb) PPE36, a cell-wall associated protein is highly specific and conserved for the Mtb complex group. Although it has been proven essential for iron utilization, little is known about the role of PPE36 in regulating host immune responses. Here we exhibited that PPE36 preferentially enriched in Mtb virulent strains, and could efficiently inhibit host inflammatory responses and increase bacterial loads both in mycobacterium-infected macrophages and mice. In exploring the underlying mechanisms, we found that PPE36 could robustly inhibit the activation of inflammatory NF-{kappa}B and MAPK (ERK, p38 and JNK) pathways by promoting E3 ligase Smurf1-mediated ubiquitination and proteasomal degradation of MyD88 protein. Our research revealed a previously unknown function of PPE36 on modulating host immune responses, and provided some clues to the development of novel tuberculosis treatment strategies based on immune regulation. Author SummaryMycobacterium tuberculosis (Mtb) has developed diverse immune evasion strategies to successfully establish infection in host. Identifying the important Mtb immune regulatory proteins and elucidating the underlying mechanisms are critical for tuberculosis control. Here we demonstrated that PPE36, a Mtb cell-wall associated protein, was predominantly enriched in virulent mycobacterial strains, and obviously inhibited inflammatory responses and facilitated bacterial survival in infected macrophages. Compared with the wild-type BCG, BCG lacking PPE36 (BCG{Delta}PPE36) induced more inflammation, lower bacterial loads as well as the improved histopathological changes in the lungs of infected mice. We further found that PPE36 significantly reduced host MyD88 abundance, and inhibited the activation of subsequunt inflammatory NF-{kappa}B and MAPK pathways. In addition, this direct inhibition effect of PPE36 on MyD88 was mediated by the promoted E3 ligase Smurf1 ubiquitin -protesome pathway. This study identified PPE36 as a immune regulatory protein of Mtb, and showed it played an important role in the Mtb immune evasion.

immunology↗
bioRxiv2021

A simple Agrobacterium-mediated stable transformation technique for the hornwort model Anthoceros agrestis

We have developed a simple Agrobacterium-mediated method for the stable transformation of the hornwort Anthoceros agrestis, the fifth bryophyte species for which a genetic manipulation technique becomes available. High transformation efficiency was achieved by using thallus tissue grown under low-light conditions. We generated a total of 216 transgenic A. agrestis lines expressing the {beta}-Glucuronidase (GUS), cyan, green, and yellow fluorescent proteins under the control of the CaMV 35S promoter and several endogenous promoters. Nuclear and plasma membrane localization with multiple color fluorescent proteins was also confirmed. The transformation technique described here should pave the way for detailed molecular and genetic studies of hornwort biology, providing much needed insight into the molecular mechanisms underlying symbiosis, carbon-concentrating mechanism, RNA editing, and land plant evolution in general.

plant biology↗
bioRxiv2020

Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence

Extensive sequence similarity between duplicated gene pairs produced by paleo-polyploidization may result from illegitimate recombination between homologous chromosomes. The genomes of Asian cultivated rice Xian/indica (XI) and Geng/japonica (GJ) have recently been updated, providing new opportunities for investigating on-going gene conversion events. Using comparative genomics and phylogenetic analyses, we evaluated gene conversion rates between duplicated genes produced by polyploidization 100 million years ago (mya) in GJ and XI. At least 5.19%-5.77% of genes duplicated across three genomes were affected by whole-gene conversion after the divergence of GJ and XI at ~0.4 mya, with more (7.77%-9.53%) showing conversion of only gene portions. Independently converted duplicates surviving in genomes of different subspecies often used the same donor genes. On-going gene conversion frequency was higher near chromosome termini, with a single pair of homoeologous chromosomes 11 and 12 in each genome most affected. Notably, on-going gene conversion has maintained similarity between very ancient duplicates, provided opportunities for further gene conversion, and accelerated rice divergence. Chromosome rearrangement after polyploidization may result in gene loss, providing a basis for on-going gene conversion, and may have contributed directly to restricted recombination/conversion between homoeologous regions. Gene conversion affected biological functions associated with multiple genes, such as catalytic activity, implying opportunities for interaction among members of large gene families, such as NBS-LRR disease-resistance genes, resulting in gene conversion. Duplicated genes in rice subspecies generated by grass polyploidization ~100 mya remain affected by gene conversion at high frequency, with important implications for the divergence of rice subspecies. One-sentence summaryOn-going gene conversion between duplicated genes produced by 100 mya polyploidization contributes to rice subspecies divergence, often involving the same donor genes at chromosome termini.

bioinformatics↗
bioRxiv2020

Machine Learning-Assisted Directed Evolution Navigates a Combinatorial Epistatic Fitness Landscape with Minimal Screening Burden

Due to screening limitations, in directed evolution (DE) of proteins it is rarely feasible to fully evaluate combinatorial mutant libraries made by mutagenesis at multiple sites. Instead, DE often involves a single-step greedy optimization in which the mutation in the highest-fitness variant identified in each round of single-site mutagenesis is fixed. However, because the effects of a mutation can depend on the presence or absence of other mutations, the efficiency and effectiveness of a single-step greedy walk is influenced by both the starting variant and the order in which beneficial mutations are identified--the process is path-dependent. We recently demonstrated a path-independent machine learning-assisted approach to directed evolution (MLDE) that allows in silico screening of full combinatorial libraries made by simultaneous saturation mutagenesis, thus explicitly capturing the effects of cooperative mutations and bypassing the path-dependence that can limit greedy optimization. Here, we thoroughly investigate and optimize an MLDE workflow by testing a number of design considerations of the MLDE pipeline. Specifically, we (1) test the effects of different encoding strategies on MLDE efficiency, (2) integrate new models and a training procedure more amenable to protein engineering tasks, and (3) incorporate training set design strategies to avoid information-poor low-fitness protein variants ("holes") in the training data. When applied to an epistatic, hole-filled, four-site combinatorial fitness landscape of protein G domain B1 (GB1), the resulting focused training MLDE (ftMLDE) protocol achieved the global fitness maximum up to 92% of the time at a total screening burden of 470 variants. In contrast, minimal-screening-burden single-step greedy optimization over the GB1 fitness landscape reached the global maximum just 1.2% of the time; ftMLDE matching this minimal screening burden (80 total variants) achieved the global optimum up to 9.6% of the time with a 49% higher expected maximum fitness achieved. To facilitate further development of MLDE, we present the MLDE software package (https://github.com/fhalab/MLDE), which is designed for use by protein engineers without computational or machine learning expertise.

bioinformatics↗
bioRxiv2020

Reduction of neuronal activity mediated by blood-vessel regression in the brain

The brain vasculature supplies neurons with glucose and oxygen, but little is known about how vascular plasticity contributes to brain function. Using longitudinal in vivo imaging, we reported that a substantial proportion of blood vessels in the adult brain sporadically occluded and regressed. Their regression proceeded through sequential stages of blood-flow occlusion, endothelial cell collapse, relocation or loss of pericytes, and retraction of glial endfeet. Regressing vessels were found to be widespread in mouse, monkey and human brains. Both brief occlusions of the middle cerebral artery and lipopolysaccharide-mediated inflammation induced an increase of vessel regression. Blockage of leukocyte adhesion to endothelial cells alleviated LPS-induced vessel regression. We further revealed that blood vessel regression caused a reduction of neuronal activity due to a dysfunction in mitochondrial metabolism and glutamate production. Our results elucidate the mechanism of vessel regression and its role in neuronal function in the adult brain.

neuroscience↗
bioRxiv2020

In vitro and in vivo characterization of a recombinant rhesus cytomegalovirus containing a complete genome

Cytomegaloviruses (CMVs) are highly adapted to their host species resulting in strict species specificity. Hence, in vivo examination of all aspects of CMV biology employs animal models using host-specific CMVs. Infection of rhesus macaques (RM) with rhesus CMV (RhCMV) has been established as a representative model for infection of humans with HCMV due to the close evolutionary relationships of both host and virus. However, the commonly used 68-1 strain of RhCMV has been passaged in fibroblasts for decades resulting in multiple genomic changes due to tissue culture adaptation that cause reduced viremia in RhCMV-naive animals and limited shedding compared to low passage isolates. Using sequence information from primary RhCMV isolates we constructed a full-length (FL) RhCMV by repairing all presumed mutations in the 68-1 bacterial artificial chromosome (BAC). Inoculation of adult, immunocompetent, RhCMV-naive RM with the reconstituted virus resulted in significant replication in the blood similar to primary isolates of RhCMV and furthermore led to extensive viremia in many tissues at day 14 post infection. In contrast, viral dissemination and viremia was greatly reduced upon deletion of genes also lacking in 68-1. Transcriptome analysis of infected tissues further revealed that chemokine-like genes deleted in 68-1 are among the most highly expressed viral transcripts both in vitro and in vivo consistent with an important immunomodulatory function of the respective proteins. We conclude that FL-RhCMV displays in vitro and in vivo characteristics of a wildtype virus while being amenable to genetic modifications through BAC recombineering techniques. Author SummaryHuman cytomegalovirus (HCMV) infections are generally asymptomatic in healthy immunocompetent individuals, but HCMV can cause serious disease after congenital infection and in individuals with immunocompromised immune systems. Since HCMV is highly species specific and cannot productively infect immunocompetent laboratory animals, experimental infection of rhesus macaques (RM) with rhesus CMV (RhCMV) has been established as a closely related animal model for HCMV. By employing the unique ability of CMV to elicit robust and lasting cellular immunity, this model has also been instrumental in developing novel CMV-based vaccines against chronic and recurring infections with pathogens such as the human immunodeficiency virus (HIV) and Mycobacterium tuberculosis (Mtb). However, most of this work was conducted with derivatives of the 68-1 strain of RhCMV which has acquired multiple genomic alterations in tissue culture. To model pathogenesis and immunology of clinical HCMV isolates we generated a full-length (FL) RhCMV clone representative of low passage isolates. Infection of RhCMV-naive RM with FL-RhCMV demonstrated viremia and tissue dissemination that was comparable to that of non-clonal low passage isolates. We further demonstrate that FL-RhCMV is strongly attenuated upon deletion of gene regions absent in 68-1 thus demonstrating the usefulness of FL-RhCMV to study RhCMV pathogenesis.

microbiology↗
bioRxiv2020

Sonogenetics for noninvasive and cellular-level neuromodulation in rodent brain

Sonogenetics, which uses ultrasound to noninvasively control cells genetically modified with ultrasound-sensitive ion channels, can be a powerful tool for investigating intact brain circuits. Here we show that TRPV1 is an ultrasound-sensitive ion channel that can modify the activity of TRPV1-expressing cells in vitro when exposing to focused ultrasound. We also show that focused ultrasound exposure at the mouse brain in vivo can selectively activate neurons that are genetically modified to express TRPV1. We demonstrate that precise manipulation of neural activity via TRPV1-based sonogenetics can be achieved by spatiotemporal control of ultrasound-induced heating. The focused ultrasound exposure is safe based on our inspection of neuronal integrity, apoptosis, and inflammation markers. This sonogenetic tool enables noninvasive, cell-type specific, spatiotemporally controlled modulation of mammalian brain activity.

neuroscience↗
bioRxiv2020

Late-life restoration of mitochondrial function reverses cardiac dysfunction in old mice

Diastolic dysfunction is a prominent feature of cardiac aging in both mice and humans. We show here that 8-week treatment of old mice with the mitochondrial targeted peptide SS-31 (elamipretide) can substantially reverse this deficit. SS-31 normalized the increase in proton leak and reduced mitochondrial ROS in cardiomyocytes from old mice, accompanied by reduced protein oxidation and a shift towards a more reduced protein thiol redox state in old hearts. Improved diastolic function was concordant with increased phosphorylation of cMyBP-C Ser282 but was independent of titin isoform shift. Late-life viral expression of mitochondrial-targeted catalase (mCAT) produced similar functional benefits in old mice and SS-31 did not improve cardiac function of old mCAT mice, implicating normalizing mitochondrial oxidative stress as an overlapping mechanism. These results demonstrate that pre-existing cardiac aging phenotypes can be reversed by targeting mitochondrial dysfunction and implicate mitochondrial energetics and redox signaling as therapeutic targets for cardiac aging.

physiology↗
bioRxiv2019

Extensive Mammalian Germline Genome Engineering

Xenotransplantation, specifically the use of porcine organs for human transplantation, has long been sought after as an alternative for patients suffering from organ failure. However, clinical application of this approach has been impeded by two main hurdles: 1) risk of transmission of porcine endogenous retroviruses (PERVs) and 2) molecular incompatibilities between donor pigs and humans which culminate in rejection of the graft. We previously demonstrated that all 25 copies of the PERV elements in the pig genome could be inactivated and live pigs successfully generated. In this study, we improved the scale of porcine germline editing from targeting a single repetitive locus with CRISPR to engineering 13 different genes using multiple genome engineering methods. we engineered the pig genome at 42 alleles using CRISPR-Cas9 and transposon and produced PERVKO{middle dot}3KO{middle dot}9TG pigs which carry PERV inactivation, xeno-antigen KO and 9 effective human transgenes. The engineered pigs exhibit normal physiology, fertility, and germline transmission of the edited alleles. In vitro assays demonstrated that these pigs gain significant resistance to human humoral and cell mediated damage, and coagulation dysregulations, similar to that of allotransplantation. Successful creation of PERVKO{middle dot}3KO{middle dot}9TG pigs represents a significant step forward towards safe and effective porcine xenotransplantation, which also represents a synthetic biology accomplishment of engineering novel functions in a living organism. One Sentence SummaryExtensive genome engineering is applied to modify pigs for safe and immune compatible organs for human transplantation

synthetic biology↗
bioRxiv2019

MeCP2 deletion impaired layer 2/3-dominant dynamic reorganization of cortical circuit during motor skill learning

Rett Syndrome (RTT) is a severe neurodevelopmental disorder caused by loss of function of the X-linked Methyl-CpG-binding protein 2 (MECP2). Several case studies report that gross motor function can be improved in children with RTT through treadmill walking, but whether the MeCP2-deficient motor circuit can support actual motor learning remains unclear. We used two-photon calcium imaging to simultaneously observe layer (L) 2/3 and L5a excitatory neuronal activity in the motor cortex (M1) while mice adapted to changing speeds on a computerized running wheel. Despite circuit hypoactivity and weakened functional connectivity across L2/3 and L5a, the Mecp2-null circuits firing pattern evolved with improved performance over two weeks. Moreover, trained mice became less anxious and lived 20% longer than untrained mice. Since motor deficits and anxiety are core symptoms of Rett, which is not diagnosed until well after symptom onset, these results underscore the benefit of motor learning.

neuroscience↗
bioRxiv2019

Microtubule binding of the kinesin-4 KIF7 and its regulation by autoinhibition

KIF7 is a member of the kinesin-4 family and plays critical roles in Hedgehog signaling in vertebrate cells. KIF7 is an atypical kinesin as it binds to microtubules but is immotile. We demonstrate that, like conventional kinesins, KIF7 is regulated by autoinhibition as the full-length motor cannot bind to microtubules whereas truncated versions bind statically to microtubules in cells. Previous work suggested that truncated KIF7 motors bind preferentially to the plus ends of microtubules in vitro, however, we find that truncated KIF7 does not bind preferentially to or track the plus ends of growing microtubules in mammalian cells or in cell extracts. Although the truncated KIF7 did alter microtubule dynamics in cells, this property is not specific to KIF7 as expression of an active kinesin-1 motor also altered microtubule growth rates. The immotile behavior of KIF7 is not due to the extended neck linker domain as its deletion does not activate KIF7 for motility and its presence in a KIF5C/KIF7 chimeric motor does not prevent processive motility. Together this work indicates that the atypical kinesin KIF7 is regulated by autoinhibition to prevent binding to microtubules and alteration of microtubule dynamics in cells.

cell biology↗
bioRxiv2019

The YdiU Domain Modulates Bacterial Stress Signaling through UMPylation

Sensing stressful conditions and adjusting cellular metabolism to adapt to the environment is essential for bacteria to survive in variable situations. Here, we describe a new stress-related protein YdiU, and characterize YdiU as an enzyme that catalyzes the covalent attachment of uridine 5-monophosphate to a protein tyrosine/histidine residue--a novel modification defined as UMPylation. Mn2+ serves as an essential co-factor for YdiU-mediated UMPylation. UTP and Mn2+-binding converts YdiU to an aggregate-prone state facilitating the recruitment of chaperones. The UMPylation of chaperones prevents them from binding co-factors or clients, thereby impairing their function. Consistent with the recent finding that YdiU acts as an AMPylator, we further demonstrate that the self-AMPylation of YdiU padlocks its chaperone-UMPylation activity. The detailed mechanism is proposed based on Apo-YdiU, YdiU-ATP, YdiU-AMP crystal structures and molecular dynamics simulation models of YdiU-UTP and YdiU-UTP-peptide. In vivo data demonstrate that YdiU effectively protects Salmonella from stress-induced ATP depletion through UMPylation. HighlightsO_LIYdiU involves in stress-resistance of Salmonella. C_LIO_LIYdiU mediates protein UMPylation in a Mn2+-dependent manner. C_LIO_LIStructural insights into YdiU-mediated UMPylation. C_LIO_LIUMPylation of chaperones by YdiU modulates their function. C_LI

biochemistry↗
bioRxiv2019

Selection of appropriate reference genes for quantitative real-time PCR in Clerodendrum trichotomum

AbstrsctClerodendrum trichotomum, an important medicinal plant, has excellent salt tolerance and beautiful ornamental character. However, reliable reference genes for quantitative real-time PCR data (qRT-PCR) in C. trichotomum have not been investigated. Using our previous transcriptome data, 17 reference genes were selected in different tissues (leaves, flowers, fruits, stems, and roots) and under various abiotic stresses (salt, drought, flood, and heat) for C. trichotomum, using four different reference gene analysis software types: GeNorm, NormFinder, BestKeeper and ReFinder. The results identified RPL, ACT and HSP70 as the three most suitable reference genes for tissues. Genes ACT and AP-2 were most stably expressed under drought stress; MDH and UBCE2 were stable under flooding stress; RPL and UBCE2 were most stable under salt stress; and MDH and EF-1A were most appropriate under heat stress. For abiotic treatments, RPL, MDH and AP-2 were the most stable reference genes; and AP-2, RPL and ACT were stably expressed in all examined samples. The expression profile of the genes for Na+/H+ Exchanger1 (ClNHX1) and laccase (ClLAC) were selected to validate the stability of the determined reference genes. Our study provided reliable normalization for gene expression analysis and ensured more accurate data for further molecular mechanism research in C. trichotomum.

molecular biology↗
bioRxiv2019

Identification of 12 cancer types through genome deep learning

MotivationCancer is a major cause of death worldwide, and an early diagnosis is required for a favorable prognosis. Histological examination is the gold standard for cancer identification; however, there is a large amount of inter-observer variability in histological diagnosis. Numerous studies have shown that cancer genesis is accompanied by an accumulation of harmful mutations within patients genome, potentiating the identification of cancer based on genomic information. We have proposed a method, GDL (genome deep learning), to study the relationship between genomic variations and traits based on deep neural networks with multiple hidden layers and nonlinear transformations. ResultWe analyzed 6,083 samples from 12 cancer types obtained from the TCGA (The Cancer Genome Atlas) and 1,991 healthy samples from the 1000 Genomes project(Genomes Project, et al., 2010). We constructed 12 specific models to distinguish between certain types of cancers and healthy tissues, a specific model that can identify healthy vs diseased tissues, and a mixture model to distinguish between all 12 types of cancer based on GDL. We present the success obtained with GDL when applied to the challenging problem of cancer based on genomic variations and demonstrate state-of-the-art results (97%, 70.08% and 94.70%) for cancer identification. The mixture model achieved a comparable performance. With the development of new molecular and sequencing technologies, we can now collect circulating tumor DNA (ctDNA) from blood and monitor the cancer risk in real time, and using our model, we can also target cancerous tissue that may develop in the future. We developed a new and efficient method for the identification of cancer based on genomic information that offers a new direction for disease diagnosis while providing a new method to predict traits based on that information. Contactchenwenbin@genomics.cn

bioinformatics↗
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

CSTDB: A Crop Stress-tolerance Gene and Protein Database Integrated by Convolutional Neural Networks

Numerous studies have shown that many genes and proteins in plants are involved in the regulation of plant resistance to abiotic and biotic stresses. The researches on the stress tolerance of crops are also the focus of many researchers. To provides a reliable platform for collecting and retrieving genetic and protein information related to stress tolerance found in crops, we constructed CSTDB(Crops Stress-tolerance Database), an integrated database that includes stress-tolerance genes and proteins for many crop species. The database was developed based on convolutional neural network technology. It is a web-accessible database that contains detailed information on the stress-tolerance genes and proteins of major crop species. Currently, the database records four major crops containing 1,371 abiotic stress-tolerance genes or proteins, and 207 genes or proteins associated with biotic stress. Each gene and protein has detailed functional information and sequence information, such as stress types, Genbank ID, Pubmed ID, Protein ID, 3D model picture and FASTA files. As a user-friendly browsing tool, this database provides search functions, BALST functions and file download functions. CSTDB can be a valuable resource, which is designed to meet the broad needs of researchers working on crops stress-tolerance experiments. Database URL: http://pcsb.ahau.edu.cn:8080/CSTDB

bioinformatics↗
bioRxiv2018

Autoinhibition of kinesin-1 is essential to the dendrite-specific localization of Golgi outposts

Neuronal polarity relies on the selective localization of cargo to axons or dendrites. The molecular motor kinesin-1 moves cargo into axons but is also active in dendrites. This raises the question of how kinesin-1 activity is regulated to maintain the compartment-specific localization of cargo. Our in vivo structure-function analysis of endogenous Drosophila kinesin-1 reveals a novel role for autoinhibition in enabling the dendrite-specific localization of Golgi outposts. Mutations that disrupt kinesin-1 autoinhibition result in the axonal mislocalization of Golgi outposts. Autoinhibition also regulates kinesin-1 localization. Uninhibited kinesin-1 accumulates in axons and is depleted from dendrites, correlating with the change in outpost distribution and dendrite growth defects. Genetic interaction tests show that a balance of kinesin-1 inhibition and dynein activity is necessary to localize Golgi outposts to dendrites and keep them from entering axons. Our data indicate that kinesin-1 activity is precisely regulated by autoinhibition to achieve the selective localization of dendritic cargo.\n\nSummaryNeuronal polarity relies on the axon-or dendrite-specific localization of cargo by molecular motors such as kinesin-1. These studies show autoinhibition regulates both kinesin-1 activity and localization to keep dendritic cargo from entering axons.

cell biology↗