Biology subjects

Qin, Y.

Publications and source records attributed to Qin, Y..

At least 145 records · Page 8Linked to original sources

bioRxiv2020

Reference-free and de novo Identification of Circular RNAs

BackgroundEarly studies have unveiled multiple regulatory functions of circular RNAs (circRNAs); however, accurate detection and quantification of circRNAs, especially in understudied organisms, is unsolved yet. ResultsIn this study, we developed a new reference-free method, namely Cirit, to de novo detect circRNAs with sequence support from the next generation sequencing (NGS) transcriptome. The Cirit showed remarkable performance in accurate detection and quantification of circRNAs via comparing with current methods from different aspects. Using Cirit, we detected 28,813 nonredundant human circRNAs from 91 transcriptome datasets, as well as 2,385 circRNAs from four understudied organisms. Subsequent analyses found that the majority of human circRNAs expressed spatiotemporally; only a very small portion of circRNAs were back-splice junction (BSJ)-consistent (maximally 5.17%) or sequence-consistent (under 2%). Furthermore, circRNA genesis were relatively flexible that only about 60% of human circRNAs used the canonical GT-AG pattern for back-splice. The inconsistent expression of circRNAs challenges their roles as precise transcriptional regulators. ConclusionsIn summary, the reference-free method provides a straightforward and universal way for reliable circRNA research. It will largely boost the successful rate in designing highly specific probes to monitor circRNA behavior in cell. In particular, it brings circRNA research to the organisms that have no genome or draft genome.

bioinformatics↗

bioRxiv2020

Insulin/IGF signaling and TOR promote vitellogenesis via inducing juvenile hormone biosynthesis

Vitellogenesis, including vitellogenin (Vg) production in the fat body and Vg uptake by maturing oocytes, is of great importance for the successful reproduction of adult females. The endocrinal and nutritional regulation of vitellogenesis differs distinctly in insects. Here, the complex crosstalk between juvenile hormone (JH) and the two nutrient sensors, insulin/IGF signaling (IIS) and target of rapamycin (TOR), was investigated to elucidate the molecular mechanisms regulating vitellogenesis in the American cockroach, Periplaneta americana. Our data showed that a block of JH biosynthesis or JH action arrested vitellogenesis, partially by inhibiting the expression of doublesex (Dsx), a key transcription factor gene involved in the sex determination cascade. Depletion of IIS and TOR blocked both JH biosynthesis and vitellogenesis. Importantly, the JH analog methoprene, but not bovine insulin (to restore IIS) and amino acids (to restore TOR activity), restored vitellogenesis in the neck-ligated (both nutrient- and JH-deficient) cockroaches. Combining classic physiology with modern molecular techniques, we have demonstrated that JH signaling alone is able to induce vitellogenesis and thus ovarian maturation. By contrast, IIS and TOR do not induce vitellogenesis independent of JH, the nutrient sensors promote vitellogenesis in an indirect manner via activating JH biosynthesis.

developmental biology↗

bioRxiv2020

Somatic cell-derived BMPs induce male germ cell meiosis initiation during embryonic stage via regulating Dazl expression

Germ cell fate is believed to be determined by the signaling from sexually differentiated somatic cell. However, the molecular mechanism remains elusive. In this study, ectopic initiation of meiosis in male germ cells was observed during embryonic stage by over-activating CTNNB1 in Sertoli cells. Somatic cell transcriptome and single germ cell RNA-seq analysis indicated that TGF-{beta} signaling was activated after CTNNB1 over-activation. In vitro and in vivo experiments confirmed somatic cell-derived BMPs played crucial roles in germ cell meiosis initiation. Further studies revealed that Dazl was significantly increased in germ cells of CTNNB1 over-activated testes and induced by BMP signaling. DNMT3a and DNA methylation was also reduced in germ cells of CTNNB1 over-activated testes and increased by BMP signaling inhibitor treatment. Taken together, this study demonstrates that germ cell fate could be reprogrammed after sex determination. BMP signaling pathway is involved in germ cell meiosis initiation via up-regulating Dazl expression.

developmental biology↗

bioRxiv2019

SIRT2-knockdown Rescues GARS-induced Charcot-Marie-Tooth Neuropathy

Charcot-Marie-Tooth disease is the most common inherited peripheral neuropathy. Dominant mutations in glycyl-tRNA synthetase (GARS) gene cause peripheral nerve degeneration and lead to CMT disease type 2D. Mutations in GARS (GARSCMT2D) show partial loss-of-function features, suggesting that tRNA-charging deficits play a role in disease pathogenesis, but the underlying mechanisms are not fully understood. In this study we report that wild-type GARS tightly binds the NAD+-dependent deacetylase SIRT2 and inhibits its deacetylation activity, resulting in the hyperacetylated -tubulin, the major substrate of SIRT2. Previous studies showed that acetylation of -tubulin protects microtubules from mechanical breakage and keep axonal transportation. However, CMT2D mutations in GARS can not inhibit SIRT2 deacetylation, which leads to decrease acetylated -tubulin and severe axonal transport deficits. Genetic reduction of SIRT2 in the Drosophila model rescues the GARS-induced axonal CMT neuropathy and extends the life span. Our findings demonstrate the pathogenic role of SIRT2-dependent -tubulin deacetylation in mutant GARS-induced neuropathies and provide new perspectives for targeting SIRT2 as a potential therapy against hereditary axonopathies.

cell biology↗

bioRxiv2019

Sleep-related thalamocortical spindles and delta oscillations are reduced during a ketamine-induced psychosis-relevant transition state.

BackgroundIn schizophrenia, sleep spindles are reduced, supporting the hypothesis that the thalamus and glutamate receptors play a crucial etio-pathophysiological role, whose underlying mechanisms remain unknown. We hypothesized that a reduced function of NMDA receptors is involved in the psychosis-related spindle deficit.\n\nMethodsAn electrophysiological multisite cell-to-network exploration was used to investigate, in sleeping rats, the effects of a ketamine-induced psychosis-relevant transition state in the sensorimotor and associative/cognitive thalamocortical (TC) systems.\n\nResultsUnder the control condition, spontaneously-occurring spindles (intra-frequency: 10-16 waves/s) and delta-frequency (1-4Hz) oscillations were recorded in the EEG of the frontoparietal cortex, in thalamic extracellular recordings (n=16), in dual juxtacellularly recorded GABAergic thalamic reticular nucleus (TRN) and glutamatergic TC neurons (n=8), and in intracellularly recorded TC neurons (n=8). The TRN cells rhythmically exhibited robust high-frequency bursts of action potentials (7 to 15 APs at 200-700 Hz). A single administration of low-dose ketamine fleetingly reduced TC spindles and delta oscillations, amplified ongoing gamma-(30-80Hz) and higher-frequency oscillations, and switched the firing pattern of both TC and TRN neurons from a burst mode to a single AP mode. Furthermore, ketamine strengthened the gamma-frequency band TRN-TC connectivity (n=11). The antipsychotic clozapine consistently prevented the ketamine effects on spindles, delta- and gamma-/higher-frequency TC oscillations (n=7).\n\nConclusionThe present findings support the hypothesis that NMDA receptor hypofunction is involved in the psychosis-related reduction in sleep spindles and delta oscillations. The ketamine-induced swift conversion (from burst to single APs) of ongoing TC-TRN activities may have involved both the ascending reticular activating system and the corticothalamic pathway.\n\nLAY ABSTRACTSchizophrenia is a chronic debilitating disease. Sleep disturbances associated with a reduction in spindles are observed as warning signs prior to the first psychotic episode. Every spindle is a short-lasting (~0.5 s) set of bioelectric sinusoidal waves at the frequency of 10-16 Hz generated within the thalamus. Sleep spindles, easily identifiable in a scalp electroencephalogram, occur hundreds of times during sleep and are implicated in cognition like memory processes. For this reason, spindles are seen as an electro-biomarker of the quality of sleep and cognitive performance. In patients at high risk of psychotic transition, the density (number/time unit) of spindles is reduced. The underlying mechanisms of this change are unknown. Glutamate-mediated neurotransmission in the thalamus plays a key role in the generation of spindles and the etiology of schizophrenia. Therefore, we tested the hypothesis that a reduced function of glutamate receptors at the thalamic level is involved in the psychosis-related reduction in spindles. Using cell-to-network neurophysiological methods in sleeping rats, we demonstrate that systemic administration of the NMDA glutamate receptor antagonist, ketamine, significantly decreases spindle density. This effect is consistently prevented by the widely used antipsychotic drug, clozapine. These original findings support the hypothesis of the involvement of a reduced function of NMDA glutamate receptors in the sleep spindle deficit observed in psychosis-related disorders. The present findings lay the foundation for the development of innovative therapies aimed at preventing psychotic, bipolar, and depressive disorders.\n\nHIGHLIGHTSO_LILow-dose ketamine has a fast onset arousal promoting effect.\nC_LIO_LIKetamine fleetingly reduces, in the first-/higher-order thalamocortical systems, sleep spindles and slow-waves, and amplifies gamma- and higher-frequency oscillations.\nC_LIO_LIKetamine switches the firing pattern from a burst mode to a single action potential mode in both the glutamatergic thalamocortical neurons and the GABAergic thalamic reticular nucleus neurons.\nC_LIO_LIKetamine strengthens the gamma-frequency band connectivity between thalamocortical and thalamic reticular nucleus neurons.\nC_LIO_LIThe reference antipsychotic clozapine consistently prevents the ketamine effects.\nC_LI

neuroscience↗

bioRxiv2019

Generation of non-integrated iPSCs from achondroplasia patient skin and urine and gene correction in them using CRISPR-Cas9

BackgroundAchondroplasia (ACH) is the most common genetic form of dwarfism and belongs to dominant monogenic disorder caused by a gain-of-function point mutation in the transmembrane region of FGFR3. There are no effective treatments for ACH. Stem cells and gene-editing technology provide us with effective methods and ideas for ACH research and treatment. MethodsWe generated non-integrated iPSCs from an ACH girls skin and an ACH boys urine by Sendai virus. The mutation of ACH iPSCs was precisely corrected by CRISPR-Cas9. ResultsChondrogenic differentiation ability of ACH iPSCs was confined compared with that of healthy iPSCs. Chondrogenic differentiation ability of corrected ACH iPSCs could be restored. These corrected iPSCs displayed pluripotency, maintained normal karyotype, and demonstrated none of off-target indels. ConclusionsThis study may provide an important theoretical and experimental basis for the ACH research and treatment.

genetics↗

bioRxiv2019

Essential role of Bone morphogenetic protein 15 in porcine ovarian and follicular development and ovulation

Bone morphogenetic protein 15 (BMP15) is a multifunctional oocyte-specific secreted factor. It controls female fertility and follicular development in both species-specific and dosage-sensitive manners. Previous studies found that BMP15 played a critical role on follicular development and ovulation rate of mono-ovulatory mammalian species, but has minimal impact on poly-ovulatory mice. However, whether this is true in non-rodent poly-ovulatory species need to be validated. To investigate this question, we generated a BMP15 knockdown pig model. We found that BMP15 knockdown gilts showed markedly reduced fertility accompanied with phenotype of dysplastic ovaries containing significantly declined number of follicles, increased number of abnormal follicles, and abnormally enlarged antral follicles resulting in disordered ovulation. Molecular and transcriptome analysis revealed that knockdown of BMP15 significantly suppressed cell proliferation, differentiation, Fshr expression, leading to premature luteinization and reduced estradiol production in GCs, and simultaneously decreased the quality and meiotic maturation of oocyte. Our results provide in vivo evidences for the essential role of BMP15 in porcine ovarian and follicular development, and new insight into the complicated regulatory function of BMP15 in female fertility of poly-ovulatory species.

developmental biology↗

bioRxiv2019

Functional analysis of KIT gene structural mutations causing porcine dominant white phenotype by using genome edited mouse models

Dominant white phenotype in pigs is considered to be caused by two structural mutations in KIT gene, including a 450-kb duplication encompassing the entire KIT gene, and a splice mutation (G > A) at the first base in intron 17, which leads to the deletion of exon 17 in mature KIT mRNA, and the production of KIT protein lacking a critical catalytic domain of kinase. However, this speculation has not yet been validated by functional studies. Here, by using CRISPR/Cas9 technology, we created two mouse models mimicing the structural mutations of KIT gene in dominant white pigs, including the splice mutation mouse model KIT D17/+ with exon 17 of one allele of KIT gene deleted, and duplication mutation mouse model KIT Dup/+ with one allele of KIT gene coding sequence (CDS) duplicated. We found that each mutation individually can not cause dominant white phenotype. Splice mutation homozygote is lethal and heterozygous mice present piebald coat. Inconsistent with previous speculation, we found KIT gene duplication mutation did not confer the patched phenotype, and had no obvious impact on coat color. Interestingly, combination of these two mutations lead to dominant white phenotype. Further molecular analysis revealed that combination of these two structural mutations could inhibit the kinase activity of the KIT protein, thus reduce the phosphorylation level of PI3K and MAPK pathway associated proteins, which may be related to the observed impaired migration of melanoblasts during embryonic development, and eventually lead to dominant white phenotype. Our study provides a further insight into the underlying genetic mechanisms of porcine dominant white coat colour.\n\nAuthor summaryKIT plays a critical role in control of coat colour in mammals. Two mutation coexistence in KIT are considered to be the cause of the Dominant white phenotype in pigs. One mutation is a 450-kb large duplication encompassing the entire KIT gene, another mutation is a splice mutation causing the skipping of KIT exon 17. The mechanism of these two mutations of KIT on coat color formation has not yet been validated. In this study, by using genome edited mouse models, we found each structural mutation individual does not lead dominant white phenotype, but combination of these two mutations could lead to a nearly complete white coat colour similar to pig dominant white phenotype, possibly due to the inhibition of the kinase activity of the KIT protein, thus its signalling function on PI3K and MAPK pathways, leading to impaired migration of melanoblasts during embryonic development, and eventually lead to dominant white phenotype. Our study provides a further insight into the underlying genetic mechanisms of porcine dominant white coat colour.

molecular biology↗

bioRxiv2019

iRhom2 serves as a facilitator in obesity by enhancing adipose inflammation and insulin resistance

Chronic inflammation of adipose tissues contributes to obesity-triggered insulin resistance. Unfortunately, the potential molecular mechanisms regarding obesity associated systemic inflammation and metabolic disorder remain complicated. Here we display that inactive rhomboid-like protein 2 (iRhom2) is increased in mice fat with adipose inflammation. After 16 weeks on a high fat diet (HFD), obesity, chronic inflammation in adipose tissues and insulin resistance are markedly mitigated in iRhom2-knockout (iRhom2 KO) mice, but exaggerated in iRhom2-overactivated mice. The adverse impressions of iRhom2 on adipose inflammation and associated pathologies are determined in db/db mice. Also, we further exhibit that in response to HFD, iRhom2 KO mice and mice with deletion only in myeloid cells showed less severe adipose inflammation and insulin resistance than the control groups. Conversely, transplantation of bone marrow cells from normal mice to iRhom2 KO mice unleashed the severity of systemic inflammation and metabolic dysfunction after HFD ingestion. In conclusion, we identify iRhom2 as a key regulator that promotes obesity-associated metabolic disorder. Loss of iRhom2 from macrophages in adipose tissues inhibited the inflammation and insulin resistance. iRhom2 might be a therapeutic target for obesity-induced metabolic dysfunction.\n\nSignificanceIncreased inactive rhomboid-like protein 2 signaling has recently been shown to trigger inflammation-associated activation of innate immune responses. Herein we investigate that this signal also plays a crucial role in obesity-triggered adipose tissue inflammation infiltration and metabolic disorder, beyond the well-known assignment in innate immune supervision. Also, we have reported the iRhom2 as a key promoter in regulating metabolic function, which enhances obesity-stimulated inflammation and systemic insulin resistance by up regulation of macrophages pro-inflammatory activation. Our current study indicates that targeting the iRhom2 signaling in adipose tissues could possibly be an efficient strategy to mitigating obesity-associated systemic inflammation and metabolic dysfunction.

pathology↗

bioRxiv2019

DNA damage-specific effects of Tel1/ATM and γH2A/γH2AX on checkpoint signaling in Saccharomyces cerevisiae

DNA lesions trigger the activation of DNA damage checkpoints (DDCs) that stop cell cycle progression and promote DNA damage repair. Saccharomyces cerevisiae Tel1 is a homolog of mammalian ATM kinase that plays an auxiliary role in DDC signaling. {gamma}H2A, equivalent to {gamma}H2AX in mammals, is an early chromatin mark induced by DNA damage that is recognized by a group of DDC and DNA repair factors. We find that both Tel1 and {gamma}H2A negatively impact G2/M checkpoint in response to DNA topoisomerase I poison camptothecin independently of each other. {gamma}H2A also negatively regulates DDC induced by DNA alkylating agent methyl methanesulfonate. These results, together with prior findings demonstrating positive or no roles of Tel1 and {gamma}H2A in DDC in response to other DNA damaging agents such as phleomycin and ionizing radiation, suggest that Tel1 and {gamma}H2A have DNA damage-specific effects on DDC. We present data indicating that Tel1 acts in the same pathway as Mre11-Rad50-Xrs2 complex to suppress CPT induced DDC possibly by repairing topoisomerase I-DNA crosslink. On the other hand, we find evidence consistent with the notion that {gamma}H2A regulates DDC by mediating the competitive recruitment of DDC mediator Rad9 and DNA repair factor Rtt107 to sites of DNA damage. We propose that {gamma}H2A serves to create a dynamic balance between DDC and DNA repair that is influenced by the nature of DNA damage.

molecular biology↗

bioRxiv2019

LRRC33 is a novel binding and regulating protein of TGF-β1 function in human acute myeloid leukemia cells

Transforming growth factor - {beta}1 (TGF-{beta}1) is a versatile cytokine. It has context-dependent pro- and anti-cell proliferation functions. Activation of latent TGF-{beta}1 requires release of the growth factor from pro-complexes and is regulated through TGF-{beta} binding proteins. Two types of TGF-{beta} binding partners, latent TGF-{beta}-binding proteins (LTBPs) and leucine-rich-repeat-containing protein 32 (LRRC32), have been identified and their expression are cell specific. TGF-{beta}1 also plays important roles in acute myeloid leukemia (AML) cells. However, the expression of LTBPs and LRRC32 are lacking in myeloid lineage cells and the binding protein of TGF-{beta}1 in these cells are unknown. Here we show that a novel leucine-rich-repeat-containing protein family member, LRRC33, with high mRNA level in AML cells, to be the binding and regulating protein of TGF-{beta}1 in AML cells. Using two representative cell lines MV4-11 and AML193, we demonstrate that the protein expression of LRRC33 and TGF-{beta}1 are correlated. LRRC33 co-localizes and forms complex with latent TGF-{beta}1 protein on the cell surface and intracellularly in these cells. Similar as in other cell types, the activation of TGF-{beta}1 in MV4-11 and AML193 cells are also integrin dependent. We anticipate our study to be a starting point of more comprehensive research on LRRC33 as novel TGF-{beta} regulating protein and potential non-genomic based drug target for AML and other myeloid malignancy.

biochemistry↗

bioRxiv2019

The fitness cost of a congenital heart defect shapes its genetic architecture

BackgroundIn newborns, severe congenital heart defects are rarer than mild ones. The reason why is unknown, but presumably related to a liability threshold that rises with the severity of a defect. Because the same genetic mutation can cause different defects, other variables may contribute to pushing an individual past a defect-specific liability threshold. We consider here how variables in the genetic architecture of a heart defect depend upon its fitness cost, as defined by the likelihood of survival to reproductive age in natural history studies. MethodsWe phenotyped ~10,000 Nkx2-5+/- newborn mice, a model of human congenital heart disease, from two inbred strain crosses. Genome-wide association analyses detected loci that modify the risk of an atrial septal defect, membranous or muscular ventricular septal defect, or atrioventricular septal defect. The number of loci, heritability and quantitative effects on risk of pairwise (GxGNkx) and higher-order (GxGxGNkx) epistasis between the loci and Nkx2-5 mutation were examined as a function of the fitness cost of a defect. ResultsNkx2-5+/- mice have pleiotropic heart defects; about 70% have normal hearts. The model recapitulates the epidemiological relationship between the severity and incidence of a heart defect. Neither the number of modifier loci nor heritability depends upon the severity of a defect, but GxGNkx and GxGxGNkx effects on risk do. Interestingly, GxGxGNkx effects are three times more likely to suppress risk when the genotypes at the first two loci are homozygous and from the same, rather than opposite strains in a cross. Syn- and anti-homozygous genotypes at GxGxGNkx interactions can have an especially large impact on the risk of an atrioventricular septal defect. ConclusionsGiven a modestly penetrant mutation, epistasis contributes more to the risk of severe than mild congenital heart defect. Conversely, genetic compatibility between interacting genes, as indicated by the protective effects of syn-homozygosity at GxGxGNkx interactions, plays a newfound role in the robustness of cardiac development. The experimental model offers practical insights into the nature of genetic risk in congenital heart disease. The results more fundamentally address a longstanding question regarding how mutational robustness could arise from natural selection.

genetics↗

bioRxiv2019

A chromosome-level genome of black rockfish, Sebastes schlegelii, provides insights into the evolution of live birth

Black rockfish (Sebastes schlegelii) is a teleost species where eggs are fertilized internally and retained in the maternal reproductive system, where they undergo development until live birth (termed viviparity). In the present study, we report a chromosome-level black rockfish genome assembly. High-throughput transcriptome analysis (RNA-seq and ATAC-seq), coupled with in situ hybridization (ISH) and immunofluorescence, identify several candidate genes for maternal preparation, sperm storage and release, and hatching. We propose that zona pellucida (ZP) genes retain sperm at the oocyte envelope, while genes in two distinct astacin metalloproteinase subfamilies serve to release sperm from the ZP and free the embryo from chorion at pre-hatching stage. Finally, we present a model of black rockfish reproduction, and propose that the rockfish ovarian wall has a similar function to uterus of mammals. Taken together, these genomic data reveal unprecedented insights into the evolution of an unusual teleost life history strategy, and provide a sound foundation for studying viviparity in non-mammalian vertebrates and an invaluable resource for rockfish ecology and evolution research.

genomics↗

bioRxiv2019

Recent origin of an XX/XY sex-determination system in the ancient plant lineage Ginkgo biloba

Sexual dimorphism like dioecy (separate male and female individuals) have evolved in diverse multicellular eukaryotes while the molecular mechanisms underlying the development of such a key biological trait remains elusive (1). The living fossil Ginkgo biloba represents an early diverged lineage of land plants with dioecy. However, its sex-determination system and molecular basis have long been controversial or unknown. In the present research, we assembled the first and largest to date chromosome-level genome of a non-model tree species using Hi-C data. With this reference genome, we addressed both questions using genome resequencing data gathered from 97 male and 265 female trees of ginkgo, as well as transcriptome data from three developmental stages for both sexes. Our results support vertebrate-like XY chromosomes for ginkgo and five potential sex-determination genes, which may originate ~14 million years ago. This is the earliest diverged sex determination region in all reported plants as yet. The present research resolved a long-term controversy, lay a foundation for future studies on the origin and evolution of plant sexes, and provide genetic markers for sex identification of ginkgo which will be valuable for both nurseries and field ecology of ginkgo.

evolutionary biology↗

bioRxiv2018

TURBULENCE IN THE HIPPOCAMPUS: AN ANSATZ FOR THE ENERGY CASCADEHYPOTHESIS

Mesoscopic neural activity may play an important role in the cross-scale integration of brain activity and in the emergence of cognitive behavior. Mesoscale activity in the cortex can be defined as the organization of activity of large populations of neurons into collective actions, such as traveling waves in the hippocampus. A comprehensive description of collective activity is still lacking, in part because it cannot be built directly with methods and models developed for the microscale (individual neurons): the laws governing mesoscale dynamics are different from those governing a few neurons. To identify the characteristic features of mesoscopic dynamics, and to lay the foundations for a theoretical description of mesoscopic activity in the hippocampus, we conduct a comprehensive examination of observational data of hippocampal local field potential (LFP) recordings. We use the strong correlation between rat running-speed and the LFP power to parameterize the energy input into the hippocampus, and show that both the power, and the nonlinearity of mesoscopic scales of collective action (e.g., theta and gamma rhythms) increase as with energy input. Our results point to a few fundamental characteristics: collective-action dynamics are stochastic (the precise state of a single neuron is irrelevant), weakly nonlinear, and weakly dissipative. These are the principles of the theory of weak turbulence. Therefore, we propose weak turbulence as an ansatz for the development of a theoretical description of mesoscopic activity. The perspective of weak turbulence provides simple and meaningful explanations for the major features observed in the evolution of LFP spectra and bispectra with energy input, such as spectral slopes and their evolution, the increased nonlinear coupling observed between theta and gamma, as well as specific phase lags associated with their interaction. The weak turbulence ansatz is consistent with the theory of self organized criticality, which provides a simple explanation for the existence of the power-law background spectrum, and could provide a unifying approach to modeling the dynamics of mesoscopic activity.

neuroscience↗

bioRxiv2018

Theta-Gamma Cascades and Running Speed

The local field potentials (LFPs) of the hippocampus are primarily generated by the spatiotemporal accretion of electrical currents via activated synapses. Oscillations in the hippocampal LFP at theta and gamma frequencies are prominent during awake-behavior and have demonstrated several behavioral correlates. In particular, both oscillations have been observed to increase in amplitude and frequency as a function of running velocity. Previous investigations, however, have examined the relationship between velocity and each of these oscillation bands separately. Based on energy cascade models where \"...perturbations of slow frequencies cause a cascade of energy dissipation at all frequency scales\" (Buzsaki 2006), we hypothesized that the cross-frequency interactions between theta and gamma should increase as a function of velocity. We examined these relationships across multiple layers of the CA1 subregion and found a reliable correlation between the power of theta and the power of gamma, indicative of an amplitude-amplitude relationship. Moreover, there was an increase in the coherence between the power of gamma and the phase of theta, demonstrating increased phase-amplitude coupling with velocity. Finally, at higher velocities, phase entrainment between theta and gamma becomes stronger. These results have important implications and provide new insights regarding how theta and gamma are integrated for neuronal circuit dynamics, with coupling strength determined by the excitatory drive within the hippocampus.

neuroscience↗

bioRxiv2018

TP promotes malignant progression in hepatocellular carcinoma through pentose Warburg effect

Tumor progression is dependent on metabolic reprogramming. Metastasis and vasculogenic mimicry (VM) are typical tumor progression. The relationship of metastasis, VM and metabolic reprogramming is not clear. In this study, we identified the novel role of Twist1, a VM regulator, in the transcriptional regulation of the expression of thymidine phosphorylase (TP). We demonstrated that TP promoted extracellular thymidine metabolization into ATP and amino acids through pentose Warburg effect by coupling the pentose phosphate pathway and glycolysis. Moreover, Twist1 relied on TP-induced metabolic reprogramming to promote hepatocellular carcinoma (HCC) metastasis and VM formation mediated by VE-Cad, VEGFR1, and VEGFR2 in vitro and in vivo. TP inhibitor tipiracil reduced promotion effect of TP enzyme activity on HCC VM formation and metastasis. Our findings demonstrate that TP, transcriptionally activated by Twist1, promotes HCC VM formation and metastasis through pentose Warburg effect, contributing to tumor progression.

cell biology↗

bioRxiv2018

Theta-gamma coupling: a nonlinear dynamical model

Cross-frequency coupling in the hippocampus has been hypothesized to support higher-cognition functions. While gamma modulation by theta is widely accepted, evidence of phase-coupling between the two frequency components is so far unconvincing. Our observations show that theta and gamma energy increases with rat speed, while the overall nonlinearity of the LFP trace also increases, suggesting that energy flow is fundamental for hippocampal dynamics. This contradicts current representations based on the Kuramoto phase model. Therefore, we propose a new approach, based on the three-wave equation, a universally-valid nonlinear-physics paradigm that synthesizes the effects of leading order, quadratic nonlinearity. The paradigm identifies bispectral analysis as the natural tool for investigating LFP cross-frequency coupling. Our results confirm the effectiveness of the approach by showing unambiguous coupling between theta and gamma. Bispectra features agree with predictions of the three-wave model, supporting the conclusion that cross-frequency coupling is a manifestation of nonlinear energy transfers.

neuroscience↗