Biology subjects

Xiao, Q.

Publications and source records attributed to Xiao, Q..

69 records · Page 4Linked to original sources

bioRxiv2020

Bursting firing in ventromedial hypothalamic neurons exerts dual control of anxiety-like behavior and energy expenditure

Exposure to chronic stress induces anxiety-like behavior and metabolic changes in animals, resulting in adaptive or maladaptive responses to the stressful environment. Recent studies have indicated the dorsomedial ventromedial hypothalamus (dmVMH) as an important hub that regulates both anxiety and energy homeostasis. However, up to now, how dmVMH neurons exert dual control of chronic stress-induced anxiety and energy expenditure remains poorly understood. Here, we established a chronic-stress mouse model that induced anxiety-like behavior, reduced food consumption, and decreased energy expenditure. We found that c-fos expression increased and theta band power is higher in the dmVMH after chronic stress, and the proportion of burst firing neurons significantly increased, which was mediated by elevated expression of T-type calcium channel Cav 3.1. Optogenetically evoked burst firing of dmVMH neurons induced anxiety-like behavior, shifted the respiratory exchange ratio toward fat oxidation, and decreased food intake, while knockdown of Cav3.1 in the dmVMH had the opposite effects. Collectively, our study first revealed an important role of dmVMH burst firing in the dual regulation of anxiety-like behavior and energy expenditure, and identified Cav 3.1 as a crucial regulator of the activity of the burst firing neurons in dmVMH. These molecular and cellular level findings will advance our understanding of the chronic stress-induced emotional malfunction and energy expenditure disorders.

neuroscience↗

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

Parvalbumin interneurons in the nucleus accumbens regulate impairment of risk avoidance in DISC1 transgenic mice

One strong survival instinct in animals is to approach things that are of benefit and avoid risk. In humans, a large portion of mental disorders are accompanied by cognition-related impairments including the inability to recognize potential risks. One of the most important genes involved in risk behavior is disrupted-in-schizophrenia-1 (DISC1), and animal models where this gene has some dysfunction show cognitive impairments. However, whether DISC1 mice models have an impairment in avoiding potential risks is still not fully understood. In the present study, we used DISC1-N terminal truncation (DISC1-NTM) mice to study cognitive abilities related to potential risks. We found that DISC1-NTM mice were impaired in risk avoidance on the elevated plus maze (EPM) test, and showed impairment in social preference in a three-chamber social interaction test. Staining for c-Fos following the EPM indicated that the nucleus accumbens (NAc) was associated with risk avoidance behavior in DISC1-NTM mice. Meanwhile, in vivo electrophysiological recordings showed that firing rates of fast spiking neurons (FS) in the NAc significantly decreased in DISC1-NTM mice following tamoxifen administration. In addition, theta band power was lower when mice shuttled from the safe (closed) arms to the risky (open) arms, an effect which disappeared after induction of the truncated DISC1 gene. Furthermore, we found through in vitro patch clamp recording that the frequency of action potentials stimulated by current injection was lower in parvalbumin (PV) neurons in the NAc of DISC1-NTM mice than their wild-type littermates. Risk-avoidance impairments in DISC1-NTM mice were rescued using optogenetic tools that activated NAcPV neurons. Finally, we inhibited activitiy of NAcPV neurons in PV-Cre mice, which mimicked the risk-avoidance impairment found in the DISC1-NTM mice during tests on the elevated zero maze. Taken together, our findings confirmed a cognitive impairment in DISC1-NTM mice related to risk recognition and suggests that reduced excitability of NAcPV neurons may be responsible.

neuroscience↗

bioRxiv2020

Genome assembly and transcriptome analysis provide insights into the anti-schistosome mechanism of Microtus fortis

Microtus fortis (M. fortis) so far is the only mammal host that exhibits intrinsic resistance against Schistosoma japonicum infection. However, the underlying molecular mechanisms of this intrinsic resistance are not yet known. Here we performed the first de novo genome assembly of M. fortis, comprehensive gene annotation and evolution analysis. Furthermore, we compared the recovery rate of schistosome, pathological change and liver transcriptome between non-permissive host M. fortis and susceptible host mouse at different time points after Schistosome infection. We reveal that Immune response of M. fortis and mouse is different in time and type. M. fortis activates immune and inflammatory responses on the 10th days post infection, involving in multiple pathways, such as leukocyte extravasation, antibody activation (especially IgG3), Fc-gamma receptor mediated phagocytosis, and interferon signaling cascade. The strong immune responses of M. fortis in early stages of infection play important roles in preventing the development of schistosome. On the contrary, intense immune response occurred in mouse in late stages of infection (28~42 days post infection), and cannot eliminate schistosome. Infected mouse suffers severe pathological injury and continuous decrease of important functions such as cell cycle and lipid metabolism. Our findings offer new insights to the intrinsic resistance mechanism of M. fortis against schistosome infection. The genome sequence also provides bases for future studies of other important traits in M. fortis.

bioinformatics↗

bioRxiv2020

Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism

Steroid hormones are essential in stress response, immune system regulation, and reproduction in mammals. Steroids with 3-oxo-{Delta}4 structure, such as testosterone, androstenedione and progesterone, could be catalyzed by steroid 5-reductases (SRD5As) to generate their corresponding 3-oxo-5 steroids, which are essential for multiple physiological and pathological processes. Abnormal activities of SRD5As will lead to benign prostatic hyperplasia, alopecia, prostatic cancer or infertility due to the poor quality of sperms. However, the detailed reduction mechanisms of SRD5As remain elusive. Here we report the crystal structure of PbSRD5A, which shares 60.6% and 51.5% sequence similarities with human SRD5A1 and -2 respectively, from Proteobacteria bacterium in complex with the cofactor NADPH at 2.0 [A] resolution. PbSRD5A exists as a monomer comprised of seven transmembrane segments (TMs). The TM1-4 enclose a hydrophobic cavity for steroids substrates binding, whereas TM5-7 coordinate with cofactor NADPH through extensive hydrogen bonds network. Homology-based structural models of HsSRD5A1 and -2, together with extensive biochemical characterizations, for the first time unveiled the substrate recognition of SRD5As and provide an important framework for further understanding of the mechanism of NADPH mediated steroids 3-oxo-{Delta}4 reduction. Based on these analyses, the design of therapeutic molecules targeting SRD5As with improved specificity and therapeutic efficacy would be possible. One Sentence SummaryStructural and biochemical characterizations decipher the evolutionarily conserved mechanism in steroid 5-reductases catalyzing NADPH mediated steroids reduction.

biochemistry↗

bioRxiv2020

PCV2 aggravated SS2 infection directly showed from differentially expressed proteome of PK15 cells.

PCV2 and SS2 were clinically two major pathogens in pigs and they were zoonotic pathogens. There was extensive cellular tropism for both PCV2 and SS2, as well as, PK15 cells was PCV2 infection mainly cell model. It was found that when PCV2 infected PK15 cells before at the MOI=0.1, SS2 could cause more damage to PK15 cells. ITRAQ labeling proteomic technology was used to explore the differentially expressed proteome of PCV2 and SS2 single infection and co-infection in PK15 cells. The results showed that there were total 4736 proteins distinct changed in this infection models for PK15 cells. PCV2 aggravated SS2 infection were showed directly in the big amount of differentially expressed proteins like AGO3, OSBPL1A, ALB, RIC8A, UBL4A, INTS5 and so on. For the KEGG pathway analysis, it indicated that PCV2 mainly induced the proteins lessen though a series of disease pathway like metabolic pathways, huntingtons disease, insulin signaling pathways, long-term depression, etc. to make cell at a state of compensation. PCV2 before infection made the cells was on the chopping block. Contemporary, SS2 induced the proteins of PK15 rapidly changing, including pathways like spliceosome, endoplasmic reticulum, tight junction, actin cytoskeleton and some involved in parasitic infections pathways like ECM-receptor interaction, Leishmaniasis, Toxoplasmosis and so on. Simultaneously, PCV2 and SS2 existed common ground that they influence PK15 cell by some virulence factor interacted with cytomembrane, influenced the function of ribosome and tRNA. The role of SS2 in the co-infection like a cook chopper.

microbiology↗

bioRxiv2019

A new GABAergic projection from the BNST onto accumbal parvalbumin neurons controls anxiety

The prevailing view is that parvalbumin (PV) interneurons play modulatory roles in emotional response through local medium spiny projection neurons (MSNs). Here, we show that PV activity within the nucleus accumbens shell (sNAc) is required for producing anxiety-related avoidance when mice are under anxiogenic situations; sNAcPV neurons exhibited high excitability in chronically stressed mice model, which generated excessive maladaptive avoidance behavior in an anxiogenic context. We also discovered a novel GABAergic projections from the anterior dorsal bed nuclei of stria terminalis (adBNST) to sNAcPV neurons; optogenetic activation of these afferent terminals in sNAc produced an anxiolytic effect via GABA transmission. Next, we further demonstrated that chronic stressors attenuated the inhibitory synaptic transmission at adBNSTGABA [Formula] sNAcPV synapses, which in turn explains the hyperexcitability of sNAcPV neurons on stressed models; therefore, activation of these GABAergic afferents in sNAc rescued the excessive avoidance behavior related to anxious state.\n\nOur findings reveal the coordination between BNST and NAc through an inhibitory architecture in controlling of anxiety-related response and provide a neurobiological basis for therapeutic interventions in pathological anxiety.

neuroscience↗

bioRxiv2019

Integrative framework of cross-module deep biomarker for the prognosis of clear cell renal cell carcinoma: A retrospective TCGA project

PurposeWe aimed to integrate cross-module data for predicting the prognosis of clear cell renal cell carcinoma (ccRCC) based on deep learning and to explore the relationship between deep features from images and eigengenes form gene data.\n\nExperimental designA total of 209 patients with ccRCC with computed tomography (CT), histopathological images and RNA sequences were enrolled. A deep biomarker-based integrative framework was proposed to construct a prognostic model. Deep features extracted from CT and histopathological images by using deep learning combined with eigengenes generated from functional genomic data were used to predict ccRCC prognosis. Furthermore, the relationship between deep features and eigengenes was explored, and two survival subgroups identified by integrative cross-module biomarkers were subjected to functional analysis.\n\nResultsThe model based on the integrative framework stratified two subgroups of patients with a significant prognostic difference (P = 6.51e-6, concordance index [C-index] = 0.808, 95% confidence interval [CI] = 0.728-0.888) and outperformed the prediction based on their individual biomarkers in the independent validation cohort (n = 70, gene data: C-index = 0.452, CI = 0.336-0.567; histopathological images: C-index = 0.677, CI = 0.577-0.776; CT images: C-index = 0.774, CI = 0.670-0.879). On the basis of statistical relationship, deep features correlated or complemented with eigengenes both enhanced the predictive performance of eigengenes (P = 0.439, correlated: C-index = 0.785, CI = 0.685-0.886; complemented: C-index = 0.778, CI = 0.683-0.872). The functional analysis of subgroups also exhibited reasonable results.\n\nConclusionThe model based on the integrative framework of cross-module deep biomarkers can efficiently predict ccRCC prognosis, and the framework with a code is shared to act as a reliable and powerful tool for further studies.

bioinformatics↗

bioRxiv2019

Circulating bacterial DNA as a tool towards non-invasive biomarkers for colorectal cancer and adenoma

ObjectiveThe gut microbiota is closely associated with colorectal neoplasia. While most metagenomics studies utilized fecal samples, circulating microbial DNA in colorectal neoplasia patients remained unexplored. This study aimed to characterize microbial DNA in plasma samples and build a machine learning model for colorectal neoplasia early detection.\n\nDesignWe performed whole genome sequencing of plasma samples from 25 colorectal cancer (CRC) patients, 10 colorectal adenoma (CRA) patients and 22 healthy controls (HC). Microbial DNA was obtained by removing the host genome and relative abundance was measured by mapping reads into microbial genomes. Significant biomarker species were identified in the discovery cohort and built into a random forest model, which was tested in the validation cohort.\n\nResultsIn the discovery cohort, there were 127 significant species between CRC patients and HC. Based on the random forest model, 28 species were selected from the discovery cohort (AUC=0.944) and yielded an AUC of 1 in the validation cohort. Interestingly, relative abundance of most biomarker species in CRA patients were between CRC patients and HC with a trend towards CRC patients. Furthermore, pathway enrichment analysis also showed similar pattern where CRA patients had intermediate relative abundance of significant pathways compared to CRC patients and HC. Finally, species network analysis revealed that CRC and HC displayed distinct patterns of species association.\n\nConclusionsWe demonstrated characteristic alteration of circulating bacterial DNA in colorectal neoplasia patients. The predictive model accurately distinguished CRC and CRA from HC, suggesting the utility of circulating bacterial biomarkers as a non-invasive tool for colorectal neoplasia screening and early diagnosis.

cancer biology↗

bioRxiv2019

Toxic Effects of Crude Extracts from Chinese Herbal Toothpastes on Solenopsis invicta (Hymenoptera: Formicidae)

Red imported fire ant is an invasive species with the characteristics of quick dispersion, strong ferocity and aggression. For a long time, chemical control has been used as a main means of prevention and control of this pest, but the long-term use of high toxic pesticides will lead to a serious impact on the environment and non-target organisms. The toxicity of Chinese herbal toothpaste and its crude extracts against red imported fire ant was evaluated in the laboratory bioassay. The results showed that the traditional Chinese medicine toothpaste with watermelon cream has significant toxicity to red imported fire ants. The mortality reached more than 80% after 48h treatment, and the mortality was 100% after 72h treatment. Among the fractions separated from watermelon cream after the extraction of toothpaste, the ethyl acetate fraction has higher activity, and the mortality was more than 80% when the concentration was 1% after 72h. Our results suggest that Chinese herbal toothpaste is toxic to insects and have the potential for bait application in pest control.

animal behavior and cognition↗

bioRxiv2019

Angiocrine FSTL1 insufficiency leads to atrial and vein wall fibrosis via SMAD3 activation

Angiocrine factors, mediating the endothelial-mural cell interaction in vascular wall construction as well as maintenance, are incompletely characterized. Here we show that loss of follistatin-like protein 1 (FSTL1) in endothelial cells (Fstl1ECKO) led to an increase of pulmonary vascular resistance, resulting in the heart regurgitation especially with tricuspid valves. However, this abnormality was not detected in mutant mice with Fstl1 deletion in smooth muscle cells or hematopoietic cells. We further showed that there was excessive alpha-smooth muscle actin (SMA) associated with atrial endocardia, heart valves, veins and microvessels after the endothelial FSTL1 deletion. Consistently, there was an increase of collagen deposition as demonstrated in livers of Fstl1ECKO mutants. The SMAD3 phosphorylation was significantly enhanced and pSMAD3 staining was colocalized with SMA in vein walls, suggesting the activation of TGF{beta} signaling in vascular mural cells of Fstl1ECKO mice. The findings imply that endothelial FSTL1 is critical for the homeostasis of atria and veins and its insufficiency may favor cardiovascular fibrosis leading to heart failure.

developmental biology↗

bioRxiv2018

Stereotyped Terminal Axon Branching of Leg Motor Neurons Mediated by IgSF Proteins DIP-α and Dpr10

The ability of animals to perform coordinated movements depends on the precise organization of neural circuits controlling motor function. Motor neurons (MNs), which are key components of these circuits, must project their axons out of the central nervous system and form precise terminal branching patterns at specific muscles in the periphery. By focusing on the Drosophila adult leg neuromuscular system we show that the stereotyped terminal branching of a subset of leg MNs is mediated by interacting transmembrane Ig superfamily (IgSF) proteins DIP- and Dpr10, present in MNs and target muscles, respectively. Importantly, the DIP-/Dpr10 interaction is needed only after MN axons reach the vicinity of their muscle targets. Live imaging of this process suggests that precise terminal branching patterns are gradually established by DIP-/Dpr10-dependent interactions between fine axon filopodia and developing muscles. Further, different leg MNs depend on the DIP- and Dpr10 interaction to varying degrees that correlate with the morphological complexity of the MNs and their muscle targets, suggesting that some MNs depend upon multiple sets of interacting proteins to establish terminal axon branching.

neuroscience↗

bioRxiv2018

Transsynaptic interactions between IgSF proteins DIP-α and Dpr10 are required for motor neuron targeting specificity in Drosophila

The Drosophila larval neuromuscular system provides an ideal context in which to study synaptic partner choice, because it contains a small number of pre- and postsynaptic cells connected in an invariant pattern. The discovery of interactions between two subfamilies of IgSF cell surface proteins, the Dprs and the DIPs, provided new candidates for cellular labels controlling synaptic specificity. Here we show that DIP- is expressed by two identified motor neurons, while its binding partner Dpr10 is expressed by postsynaptic muscle targets. Removal of either DIP- or Dpr10 results in loss of specific axonal branches and NMJs formed by one motor neuron, MNISN-1s, while other branches of the MNISN-1s axon develop normally. The temporal and spatial expression pattern of dpr10 correlates with muscle innervation by MNISN-1s during embryonic development. We propose a model whereby DIP- and Dpr10 on opposing synaptic partners interact with each other to generate proper motor neuron connectivity.

neuroscience↗

bioRxiv2018

Multiple modulation synthesis with high spatial resolution for noninvasive deep neurostimulation

Noninvasive neurostimulation plays a pivotal role in direct control of neural circuit and modulating neuronal function. However, it is difficult to balance both spatial focality and depth of penetration in stimulating deep neurons. Here, we designed time-division, frequency & polarity modulation synthesis (TMFPMS) for stimulating deep neurons noninvasively with low-frequency envelope. We demonstrated its spatial resolution: mm-level via computational simulation including finite element analysis and Hodgkin-Huxley action potential model. Taken together, the results of this study indicate that TMFPMS neurostimulation with high spatial resolution is steerable and may replace traditional implanted electrode.

neuroscience↗

bioRxiv2018

Genetic variants associated with Alzheimer's disease confer different cerebral cortex cell-type population structure

Alzheimers disease (AD) is characterized by neuronal loss and astrocytosis in the cerebral cortex. However, the effects of brain cellular composition are often ignored in high-throughput molecular studies. We developed and optimized a cell-type specific expression reference panel and employed digital deconvolution methods to determine brain cellular distribution in three independent transcriptomic studies. We found that neuronal and astrocyte proportions differ between healthy and diseased brains and also among AD cases that carry specific genetic risk variants. Brain carriers of pathogenic mutations in APP, PSEN1 or PSEN2 presented lower neurons and higher astrocytes proportions compared to sporadic AD. Similarly, the APOE {varepsilon}4 allele also showed decreased neurons and increased astrocytes compared to AD non-carriers. On the contrary, carriers of variants in TREM2 risk showed a lower degree of neuronal loss than matched AD cases in multiple independent studies. These findings suggest that genetic risk factors associated with AD etiology have a specific imprinting in the cellular composition of AD brains. Our digital deconvolution reference panel provides an enhanced understanding of the fundamental molecular mechanisms underlying neurodegeneration, enabling the analysis of large bulk RNA-seq studies for cell composition, and suggests that correcting for the cellular structure when performing transcriptomic analysis will lead to novel insights of AD.

genetics↗