Biology subjects

Xu, Z.

Publications and source records attributed to Xu, Z..

514 records · Page 29Linked to original sources

bioRxiv2018

TP53I11 Suppresses Extracellular Matrix-independent Survival and Mesenchymal Transition in Mammary Epithelial Cells

Extracellular matrix (ECM)-independent survival is an essential prerequisite for tumor metastasis and a hallmark of epithelial cancer stem cells and epithelial-mesenchymal transition (EMT). We found that, in MCF10A and MDA-MB-231 cells, loss of TP53I11 (Tumor Protein P53 Inducible Protein 11) enhanced the ECM-independent survival and suppressed glucose starvation induced cell death by increasing the activation of AMPK that confer cells metabolic flexibility to survive under stress conditions. We show here that, TP53I11 enhanced glycolysis and promoted proliferation of MCF10A and MDA-MB-231 cells in normal culture, but exerted negative effect on EMT, cell migration and invasion, and its overexpression suppressed tumor progression and metastasis of MDA-MB-231 cells in vivo. Considering cancer cells also are confronted with the hostile environment such as nutrient scarcity during tumorigenesis and metastasis, our findings suggested that the disruption of metabolic flexibility by TP53I11 through inhibiting AMPK activation resulted in the suppression of tumorigenesis and metastasis of breast cancer.

molecular biology↗

bioRxiv2018

Visual physiology of the Layer 4 cortical circuit in silico

Despite advances in experimental techniques and accumulation of large datasets concerning the composition and properties of the cortex, quantitative modeling of cortical circuits under in-vivo-like conditions remains challenging. Here we report and publicly release a biophysically detailed circuit model of layer 4 in the mouse primary visual cortex, receiving thalamo-cortical visual inputs. The 45,000-neuron model was subjected to a battery of visual stimuli, and results were compared to published work and new in vivo experiments. Simulations reproduced a variety of observations, including effects of optogenetic perturbations. Critical to the agreement between responses in silico and in vivo were the rules of functional synaptic connectivity between neurons. Interestingly, after extreme simplification the model still performed satisfactorily on many measurements, although quantitative agreement with experiments suffered. These results emphasize the importance of functional rules of cortical wiring and enable a next generation of data-driven models of in vivo neural activity and computations.\n\nAUTHOR SUMMARYHow can we capture the incredible complexity of brain circuits in quantitative models, and what can such models teach us about mechanisms underlying brain activity? To answer these questions, we set out to build extensive, bio-realistic models of brain circuitry employing systematic datasets on brain structure and function. Here we report the first modeling results of this project, focusing on the layer 4 of the primary visual cortex (V1) of the mouse. Our simulations reproduced a variety of experimental observations in a large battery of visual stimuli. The results elucidated circuit mechanisms determining patters of neuronal activity in layer 4 - in particular, the roles of feedforward thalamic inputs and specific patterns of intracortical connectivity in producing tuning of neuronal responses to the orientation of motion. Simplification of neuronal models led to specific deficiencies in reproducing experimental data, giving insights into how biological details contribute to various aspects of brain activity. To enable future development of more sophisticated models, we make the software code, the model, and simulation results publicly available.

neuroscience↗

bioRxiv2018

Coordinated cerebellar climbing fiber activity is gated by behavioral context in a voluntary motor regime

The prevailing model of cerebellar learning states that climbing fibers (CFs) are both driven by, and serve to correct, erroneous motor output. However, this model is grounded largely in studies of behaviors that utilize hardwired neural pathways to link sensory input to motor output. To test whether this model applies to more flexible learning regimes that require arbitrary sensorimotor associations, we have developed a cerebellar-dependent motor learning paradigm compatible with both mesoscale and single dendrite resolution calcium imaging in mice. Here, we find that CFs are preferentially driven by and more time-locked to correctly executed movements and other task parameters that predict reward outcome, exhibiting widespread correlated activity within parasagittal processing zones that is governed by these predictions. Together, such CF activity patterns are well-suited to drive learning by providing predictive instructional input consistent with an unsigned reinforcement learning signal that does not rely exclusively on motor errors.

neuroscience↗

bioRxiv2017

Identification of methylation and hydroxymethylation haplotype blocks as distal regulatory elements aids in deconvolution of heterogeneous brain tissues

5-Hydroxymethylcytosine (5hmC) is an oxidation product of 5-methylcytosine (5mC), and adjacent CpG sites in the mammalian genome can be co-methylated and co-hydroxymethylated due to the processivity of DNMT and TET enzymes. We applied TAB-seq and oxBS-seq to selectively detect 5hmC and 5mC, respectively, at base resolution in the mouse cortex, olfactory bulb and cerebellum tissues. We found that majority of the called 5hmC CpG sites frequently had 5mC modification simultaneously and enriched in gene body regions of neuron development related genes in brain tissues. These results supported a prominent role of oxidizing 5mC to 5hmC as new epigenetic mark. Strikingly, by a systematic search of regions that show highly coordinated methylation and hydroxymethylation (MHBs and hMHBs), we found that MHBs significantly overlapped with hMHBs in gene body regions which further supported that oxidized 5mC to 5hmC co-ordinately in a subset of cells within heterogeneous brain tissues. Consistently, using a metric called methylation haplotype load, we defined a subset of 1,361 tissue-specific MHBs and 3,818 shared MHBs which were predominantly regulatory elements, and aids in deconvolution of heterogeneous brain tissues. Our results provide new insights into the role of co-ordinately oxidized 5mC to 5hmC as distal regulatory elements may involve in regulating tissue identity.

genetics↗

bioRxiv2017

Genetic Single Neuron Anatomy reveals fine granularity of cortical interneuron subtypes

Parsing diverse nerve cells into biological types is necessary for understanding neural circuit organization. Morphology is an intuitive criterion for neuronal classification and a proxy of connectivity, but morphological diversity and variability often preclude resolving the granularity of discrete cell groups from population continuum. Combining genetic labeling with high-resolution, large volume light microscopy, we established a platform of genetic single neuron anatomy that resolves, registers and quantifies complete neuron morphologies in the mouse brain. We discovered that cortical axo-axonic cells (AACs), a cardinal GABAergic interneuron type that controls pyramidal neuron (PyN) spiking at axon initial segment, consist of multiple subtypes distinguished by laminar position, dendritic and axonal arborization patterns. Whereas the laminar arrangements of AAC dendrites reflect differential recruitment by input streams, the laminar distribution and local geometry of AAC axons enable differential innervation of PyN ensembles. Therefore, interneuron types likely consist of fine-grained subtypes with distinct input-output connectivity patterns.

neuroscience↗

bioRxiv2017

Exchange protein directly activated by cAMP plays a critical role in regulation of vascular fibrinolysis

RationaleTo maintain vascular patency, endothelial cells (ECs) actively regulate hemostasis. Among the myriad of pathways by which they control both fibrin formation and fibrinolysis is EC expression of annexin A2 (ANXA2) in a heterotetrameric complex with S100A10 [(ANXA2-S100A10)2]. This complex is a well-recognized endothelial surface platform for the activation of plasminogen by tissue plasminogen activator. A noteworthy advance in this field came about when it was shown that the cAMP pathway is linked to the regulation of (ANXA2-S100A10)2 in ECs.\n\nObjectiveThese findings prompted us to determine whether a druggable target, namely the exchange protein directly activated by cAMP (EPAC) pathway, plays a role in vascular luminal fibrinolysis.\n\nMethods and ResultsTaking advantage of our Epac1-null mouse model, we found that depletion of Epac1 results in fibrin deposition, fibrinolytic dysfunction, and decreased endothelial surface ANXA2 in mice, which are similar to phenomena discovered in ANXA2-null and S100A10-null mice. We observed upregulation of EPAC1 and downregulation of fibrin in endocardial tissues beneath atrial mural thrombi in humans. Of note, our thrombosis model revealed that dysfunction of fibrinolysis in EPAC1-null mice can be ameliorated by recombinant ANXA2. Furthermore, we demonstrated that suppression of EPAC1 using a small-molecule inhibitor (ESI09) reduces the expression of ANXA2 in lipid rafts and impedes ANXA2 association with S100A10. Endothelial apical surface expression of both ANXA2 and S100A10 were markedly decreased in ESI09-treated ECs, which was corroborated by results from a nanoforce spectroscopy study. Moreover, inactivation of EPAC1 decreases tyrosine 23 phosphorylation of ANXA2 in the cell membrane compartment.\n\nConclusionsOur data reveal a novel role for EPAC1 in vascular fibrinolysis, by showing that EPAC1 is responsible for the translocation of ANXA2 to the EC surface. This process promotes conversion of plasminogen to plasmin, thereby enhancing local fibrinolytic activity.

cell biology↗

bioRxiv2017

Maize leaf functional responses to drought episode and rewatering

Effects of crop growth and physiological activity to drought and irrigation regimes have been extensively studied; however, the responses of plant growth, morphological and photosynthetic behaviors to drought episodes and thereafter rewatering receive a less attention. This field experiment was carried out directly in situ at an agricultural ecosystem research station during 2015-2016, in a northeastern China, on the renowned northeastern maize production belt, where is being threatened by severe drought. A field automatic rain-shelter was used, and five irrigation regimes including control, four drought episodes, and rewatering treatments were established. The chlorophyll contents (SPAD values), light-saturated photosynthetic rate (Asat), and photosystem II actual quantum yield ({Phi}PSII), maximum quantum yield (Fv'/Fm') decreased at lower leaf positions and with plant development. Episodic drought effects on plant growth, leaf morphological traits and photosynthetic processes at both vegetative and reproductive stages were severely remarked, particularly at late development stage and with longer drought duration. The recovery of leaf functional traits of the plants experienced historical-drought following re-irrigating was not fully restored to the level of the plants subjected to ample and normal water status; and the strength of recovery was proportional to the persistence of pre-drought episodes. The relationship of Asat with SPAD depends on water status and plant development. A principal component analysis can well denote the change patterns in responses to water status treatments with plant development. The results may give an insight into how to understand the maize traits responses to drought episode and rewatering, and this also might assist the drought-stricken crops to cope with future climatic change.

plant biology↗

bioRxiv2017

Plasmids, Viruses, And Other Circular Elements In Rat Gut

Circular DNA such as plasmids and some viruses is the major source of genetic variation in bacteria and thus has the same important evolutionary function as sexual reproduction in eukaryotic species: It allows dissemination of advantageous traits through bacterial populations. Here, we present the largest collection of novel complete extrachromosomal genetic elements to date, and compare the diversity, distribution, and content of circular sequences from 12 rat cecum samples from the pristine Falkland Islands and Danish hospital sewers, two environments with contrasting anthropogenic impact. Using a validated pipeline, we find 1,869 complete, circular, non-redundant sequences, of which only 114 are previously described. While sequences of similar size from the two environments share general features, the size distribution of the elements between environments differs significantly, with hospital sewer samples hosting larger circular elements than Falkland Island samples, a possible consequence of the massive anthropogenic influence in the hospital sewer environment. Several antibiotic resistance genes have been identified with a notably larger diversity in hospital sewer samples than in Falkland Islands samples in concordance with expectations. Our findings suggest that even though sequences of similar length carry similar traits, the mobilome of rat gut bacteria are affected by human activities in that sewer rats have larger elements and more diverse large elements than pristine island rats. More than 1000 novel and not classified small sequences was identified and hint the existence of a biological unit not previously described on a community level.\n\nList of figures O_LISampling sites and Rat gut anatomy\nC_LIO_LIRarefaction curves of circular elements\nC_LIO_LIElements shared between environments\nC_LIO_LISize distribution plots of rep, mob, stab, capsid carrying elements.\nC_LIO_LIGraphical representation of representative elements\nC_LIO_LIReplication genes content, diversity\nC_LIO_LIRep_2 plasmid replication gene phylogeny\nC_LIO_LITable Resfams findings\nC_LI\n\nList of appendices O_LIbasic statistics table\nC_LIO_LIPhylogeny of plasmid replication genes\nC_LIO_LIList of known plasmids and circular sequences found in 1869 elements\nC_LIO_LIAutomatic identification of identical circular elements with different breaking points\nC_LIO_LITest of separation of plasmids and viruses based on predicted, annotated genes\nC_LIO_LINo false positive circular sequences from MG1655 genomic sequencing.\nC_LI

microbiology↗

bioRxiv2017

HUGIn: Hi-C Unifying Genomic Interrogator

MotivationHigh throughput chromatin conformation capture (3C) technologies, such as Hi-C and ChlA-PET, have the potential to elucidate the functional roles of non-coding variants. However, most of published genome-wide unbiased chromatin organization studies have used cultured cell lines, limiting their generalizability.\n\nResultsWe developed a web browser, HUGIn, to visualize Hi-C data generated from 21 human primary tissues and cell liens. HUGIn enables assessment of chromatin contacts both constitutive across and specific to tissue(s) and/or cell line(s) at any genomic loci, including GWAS SNPs, eQTLs and cis-regulatory elements, facilitating the understanding of both GWAS and eQTLs results and functional genomics data.\n\nAvailabilityHUGIn is available at http://yunliweb.its.unc.edu/HUGIn.\n\nContactyunli@med.unc.edu and hum@ccf.org\n\nSupplementary information:

genetics↗

bioRxiv2017

MmpL3 is the flippase for mycolic acids in mycobacteria

The defining feature of the mycobacterial outer membrane (OM) is the presence of mycolic acids (MAs), which in part render the bilayer extremely hydrophobic and impermeable to external insults, including many antibiotics. While the biosynthetic pathway of MAs is well studied, the mechanism(s) by which these lipids are transported across the cell envelope is(are) much less known. MmpL3, an essential inner membrane (IM) protein, is implicated in MA transport, but its exact function has not been elucidated. It is believed to be the cellular target of several anti-mycobacterial compounds; however, evidence for direct inhibition of MmpL3 activity is also lacking. Here, we establish that MmpL3 is the MA flippase at the IM of mycobacteria, and is the molecular target of BM212, a 1,5-diarylpyrrole compound. We develop assays that selectively access mycolates on the surface of Mycobacterium smegmatis spheroplasts, allowing us to monitor flipping of MAs across the IM. Using these assays, we establish the mechanism-of-action of BM212 as a potent MmpL3 inhibitor, and employ it as a molecular probe to demonstrate the requirement for functional MmpL3 in the transport of MAs across the IM. Finally, we show that BM212 binds MmpL3 directly and inhibits its activity. Our work provides fundamental insights into OM biogenesis and MA transport in mycobacteria. Furthermore, our assays serve as an important platform for accelerating the validation of small molecules that target MmpL3, and their development as future anti-tuberculosis drugs.

biochemistry↗